[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/15076851/COAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/COAD-TP/15716527/transformed.cor.cli.txt"

nPatients in clinical file=453, in cluster file=367, common to both=367
[1] "Reduce the number of clustering variables from 1839 to 1834."
[1] 1834  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 
           230            137 
  TP53 MUTATED TP53 WILD-TYPE 
           230            137 
[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] "MUC4 MUTATION ANALYSIS"
[1] 3
  MUC4 MUTATED MUC4 WILD-TYPE 
            93            274 
  MUC4 MUTATED MUC4 WILD-TYPE 
            93            274 
[1] "RBM38 MUTATION ANALYSIS"
[1] 3
  RBM38 MUTATED RBM38 WILD-TYPE 
             35             332 
  RBM38 MUTATED RBM38 WILD-TYPE 
             35             332 
[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 
           16           351 
  B2M MUTATED B2M WILD-TYPE 
           16           351 
[1] "TXNDC2 MUTATION ANALYSIS"
[1] 3
  TXNDC2 MUTATED TXNDC2 WILD-TYPE 
              22              345 
  TXNDC2 MUTATED TXNDC2 WILD-TYPE 
              22              345 
[1] "SELPLG MUTATION ANALYSIS"
[1] 3
  SELPLG MUTATED SELPLG WILD-TYPE 
              16              351 
  SELPLG MUTATED SELPLG WILD-TYPE 
              16              351 
[1] "FAM123B MUTATION ANALYSIS"
[1] 3
  FAM123B MUTATED FAM123B WILD-TYPE 
               49               318 
  FAM123B MUTATED FAM123B WILD-TYPE 
               49               318 
[1] "RBMX MUTATION ANALYSIS"
[1] 3
  RBMX MUTATED RBMX WILD-TYPE 
            21            346 
  RBMX MUTATED RBMX WILD-TYPE 
            21            346 
[1] "ZFP36L2 MUTATION ANALYSIS"
[1] 3
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
               14               353 
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
               14               353 
[1] "BCOR MUTATION ANALYSIS"
[1] 3
  BCOR MUTATED BCOR WILD-TYPE 
            27            340 
  BCOR MUTATED BCOR WILD-TYPE 
            27            340 
[1] "WNT1 MUTATION ANALYSIS"
[1] 3
  WNT1 MUTATED WNT1 WILD-TYPE 
             7            360 
  WNT1 MUTATED WNT1 WILD-TYPE 
             7            360 
[1] "CDH1 MUTATION ANALYSIS"
[1] 3
  CDH1 MUTATED CDH1 WILD-TYPE 
            74            293 
  CDH1 MUTATED CDH1 WILD-TYPE 
            74            293 
[1] "NTAN1 MUTATION ANALYSIS"
[1] 3
  NTAN1 MUTATED NTAN1 WILD-TYPE 
             10             357 
  NTAN1 MUTATED NTAN1 WILD-TYPE 
             10             357 
[1] "RHOA MUTATION ANALYSIS"
[1] 3
  RHOA MUTATED RHOA WILD-TYPE 
            12            355 
  RHOA MUTATED RHOA WILD-TYPE 
            12            355 
[1] "BMPR2 MUTATION ANALYSIS"
[1] 3
  BMPR2 MUTATED BMPR2 WILD-TYPE 
             35             332 
  BMPR2 MUTATED BMPR2 WILD-TYPE 
             35             332 
[1] "CRIPAK MUTATION ANALYSIS"
[1] 3
  CRIPAK MUTATED CRIPAK WILD-TYPE 
              18              349 
  CRIPAK MUTATED CRIPAK WILD-TYPE 
              18              349 
[1] "MVK MUTATION ANALYSIS"
[1] 3
  MVK MUTATED MVK WILD-TYPE 
           15           352 
  MVK MUTATED MVK WILD-TYPE 
           15           352 
[1] "NF2 MUTATION ANALYSIS"
[1] 3
  NF2 MUTATED NF2 WILD-TYPE 
           62           305 
  NF2 MUTATED NF2 WILD-TYPE 
           62           305 
[1] "C15ORF40 MUTATION ANALYSIS"
[1] 3
  C15ORF40 MUTATED C15ORF40 WILD-TYPE 
                10                357 
  C15ORF40 MUTATED C15ORF40 WILD-TYPE 
                10                357 
[1] "STARD3NL MUTATION ANALYSIS"
[1] 3
  STARD3NL MUTATED STARD3NL WILD-TYPE 
                13                354 
  STARD3NL MUTATED STARD3NL WILD-TYPE 
                13                354 
[1] "OR4D10 MUTATION ANALYSIS"
[1] 3
  OR4D10 MUTATED OR4D10 WILD-TYPE 
              14              353 
  OR4D10 MUTATED OR4D10 WILD-TYPE 
              14              353 
[1] "FMN2 MUTATION ANALYSIS"
[1] 3
  FMN2 MUTATED FMN2 WILD-TYPE 
            49            318 
  FMN2 MUTATED FMN2 WILD-TYPE 
            49            318 
[1] "MAPK6 MUTATION ANALYSIS"
[1] 3
  MAPK6 MUTATED MAPK6 WILD-TYPE 
             18             349 
  MAPK6 MUTATED MAPK6 WILD-TYPE 
             18             349 
[1] "NR1H3 MUTATION ANALYSIS"
[1] 3
  NR1H3 MUTATED NR1H3 WILD-TYPE 
             15             352 
  NR1H3 MUTATED NR1H3 WILD-TYPE 
             15             352 
[1] "DIP2B MUTATION ANALYSIS"
[1] 3
  DIP2B MUTATED DIP2B WILD-TYPE 
             27             340 
  DIP2B MUTATED DIP2B WILD-TYPE 
             27             340 
[1] "ATXN3L MUTATION ANALYSIS"
[1] 3
  ATXN3L MUTATED ATXN3L WILD-TYPE 
              17              350 
  ATXN3L MUTATED ATXN3L WILD-TYPE 
              17              350 
[1] "ALPK2 MUTATION ANALYSIS"
[1] 3
  ALPK2 MUTATED ALPK2 WILD-TYPE 
             42             325 
  ALPK2 MUTATED ALPK2 WILD-TYPE 
             42             325 
[1] "P2RY13 MUTATION ANALYSIS"
[1] 3
  P2RY13 MUTATED P2RY13 WILD-TYPE 
              15              352 
  P2RY13 MUTATED P2RY13 WILD-TYPE 
              15              352 
[1] "ALG12 MUTATION ANALYSIS"
[1] 3
  ALG12 MUTATED ALG12 WILD-TYPE 
              7             360 
  ALG12 MUTATED ALG12 WILD-TYPE 
              7             360 
[1] "UBQLN2 MUTATION ANALYSIS"
[1] 3
  UBQLN2 MUTATED UBQLN2 WILD-TYPE 
              10              357 
  UBQLN2 MUTATED UBQLN2 WILD-TYPE 
              10              357 
[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] "MGA MUTATION ANALYSIS"
[1] 3
  MGA MUTATED MGA WILD-TYPE 
           36           331 
  MGA MUTATED MGA WILD-TYPE 
           36           331 
[1] "C14ORF184 MUTATION ANALYSIS"
[1] 3
  C14ORF184 MUTATED C14ORF184 WILD-TYPE 
                  6                 361 
  C14ORF184 MUTATED C14ORF184 WILD-TYPE 
                  6                 361 
[1] "FBXW7 MUTATION ANALYSIS"
[1] 3
  FBXW7 MUTATED FBXW7 WILD-TYPE 
            103             264 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
            103             264 
[1] "RPTN MUTATION ANALYSIS"
[1] 3
  RPTN MUTATED RPTN WILD-TYPE 
            13            354 
  RPTN MUTATED RPTN WILD-TYPE 
            13            354 
[1] "ZBTB20 MUTATION ANALYSIS"
[1] 3
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
              20              347 
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
              20              347 
[1] "TOP2B MUTATION ANALYSIS"
[1] 3
  TOP2B MUTATED TOP2B WILD-TYPE 
             22             345 
  TOP2B MUTATED TOP2B WILD-TYPE 
             22             345 
[1] "SMAD2 MUTATION ANALYSIS"
[1] 3
  SMAD2 MUTATED SMAD2 WILD-TYPE 
             16             351 
  SMAD2 MUTATED SMAD2 WILD-TYPE 
             16             351 
[1] "GMPS MUTATION ANALYSIS"
[1] 3
  GMPS MUTATED GMPS WILD-TYPE 
            17            350 
  GMPS MUTATED GMPS WILD-TYPE 
            17            350 
[1] "SETD2 MUTATION ANALYSIS"
[1] 3
  SETD2 MUTATED SETD2 WILD-TYPE 
             41             326 
  SETD2 MUTATED SETD2 WILD-TYPE 
             41             326 
[1] "PTGDR MUTATION ANALYSIS"
[1] 3
  PTGDR MUTATED PTGDR WILD-TYPE 
              7             360 
  PTGDR MUTATED PTGDR WILD-TYPE 
              7             360 
[1] "PLEKHF2 MUTATION ANALYSIS"
[1] 3
  PLEKHF2 MUTATED PLEKHF2 WILD-TYPE 
               10               357 
  PLEKHF2 MUTATED PLEKHF2 WILD-TYPE 
               10               357 
[1] "ASXL1 MUTATION ANALYSIS"
[1] 3
  ASXL1 MUTATED ASXL1 WILD-TYPE 
             39             328 
  ASXL1 MUTATED ASXL1 WILD-TYPE 
             39             328 
[1] "HPS3 MUTATION ANALYSIS"
[1] 3
  HPS3 MUTATED HPS3 WILD-TYPE 
            20            347 
  HPS3 MUTATED HPS3 WILD-TYPE 
            20            347 
[1] "IDH1 MUTATION ANALYSIS"
[1] 3
  IDH1 MUTATED IDH1 WILD-TYPE 
            18            349 
  IDH1 MUTATED IDH1 WILD-TYPE 
            18            349 
[1] "PIK3R1 MUTATION ANALYSIS"
[1] 3
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
              44              323 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
              44              323 
[1] "TCF7L2 MUTATION ANALYSIS"
[1] 3
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
              31              336 
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
              31              336 
[1] "NLRC4 MUTATION ANALYSIS"
[1] 3
  NLRC4 MUTATED NLRC4 WILD-TYPE 
             24             343 
  NLRC4 MUTATED NLRC4 WILD-TYPE 
             24             343 
[1] "DDX26B MUTATION ANALYSIS"
[1] 3
  DDX26B MUTATED DDX26B WILD-TYPE 
              15              352 
  DDX26B MUTATED DDX26B WILD-TYPE 
              15              352 
[1] "FYN MUTATION ANALYSIS"
[1] 3
  FYN MUTATED FYN WILD-TYPE 
           15           352 
  FYN MUTATED FYN WILD-TYPE 
           15           352 
[1] "ATP6V1B1 MUTATION ANALYSIS"
[1] 3
  ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE 
                14                353 
  ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE 
                14                353 
[1] "NF1 MUTATION ANALYSIS"
[1] 3
  NF1 MUTATED NF1 WILD-TYPE 
           88           279 
  NF1 MUTATED NF1 WILD-TYPE 
           88           279 
[1] "ROS1 MUTATION ANALYSIS"
[1] 3
  ROS1 MUTATED ROS1 WILD-TYPE 
            47            320 
  ROS1 MUTATED ROS1 WILD-TYPE 
            47            320 
[1] "KCNK1 MUTATION ANALYSIS"
[1] 3
  KCNK1 MUTATED KCNK1 WILD-TYPE 
             10             357 
  KCNK1 MUTATED KCNK1 WILD-TYPE 
             10             357 
[1] "MPHOSPH10 MUTATION ANALYSIS"
[1] 3
  MPHOSPH10 MUTATED MPHOSPH10 WILD-TYPE 
                 18                 349 
  MPHOSPH10 MUTATED MPHOSPH10 WILD-TYPE 
                 18                 349 
[1] "CDK12 MUTATION ANALYSIS"
[1] 3
  CDK12 MUTATED CDK12 WILD-TYPE 
             28             339 
  CDK12 MUTATED CDK12 WILD-TYPE 
             28             339 
[1] "CLSPN MUTATION ANALYSIS"
[1] 3
  CLSPN MUTATED CLSPN WILD-TYPE 
             30             337 
  CLSPN MUTATED CLSPN WILD-TYPE 
             30             337 
[1] "EGR1 MUTATION ANALYSIS"
[1] 3
  EGR1 MUTATED EGR1 WILD-TYPE 
             9            358 
  EGR1 MUTATED EGR1 WILD-TYPE 
             9            358 
[1] "CHD3 MUTATION ANALYSIS"
[1] 3
  CHD3 MUTATED CHD3 WILD-TYPE 
            24            343 
  CHD3 MUTATED CHD3 WILD-TYPE 
            24            343 
[1] "ALDH1A3 MUTATION ANALYSIS"
[1] 3
  ALDH1A3 MUTATED ALDH1A3 WILD-TYPE 
               18               349 
  ALDH1A3 MUTATED ALDH1A3 WILD-TYPE 
               18               349 
[1] "CYSLTR2 MUTATION ANALYSIS"
[1] 3
  CYSLTR2 MUTATED CYSLTR2 WILD-TYPE 
               15               352 
  CYSLTR2 MUTATED CYSLTR2 WILD-TYPE 
               15               352 
[1] "GGTLC2 MUTATION ANALYSIS"
[1] 3
  GGTLC2 MUTATED GGTLC2 WILD-TYPE 
               7              360 
  GGTLC2 MUTATED GGTLC2 WILD-TYPE 
               7              360 
[1] "IQCD MUTATION ANALYSIS"
[1] 3
  IQCD MUTATED IQCD WILD-TYPE 
            10            357 
  IQCD MUTATED IQCD WILD-TYPE 
            10            357 
[1] "PRPS1 MUTATION ANALYSIS"
[1] 3
  PRPS1 MUTATED PRPS1 WILD-TYPE 
              8             359 
  PRPS1 MUTATED PRPS1 WILD-TYPE 
              8             359 
[1] "CAB39L MUTATION ANALYSIS"
[1] 3
  CAB39L MUTATED CAB39L WILD-TYPE 
               9              358 
  CAB39L MUTATED CAB39L WILD-TYPE 
               9              358 
[1] "MLH1 MUTATION ANALYSIS"
[1] 3
  MLH1 MUTATED MLH1 WILD-TYPE 
            48            319 
  MLH1 MUTATED MLH1 WILD-TYPE 
            48            319 
[1] "CD58 MUTATION ANALYSIS"
[1] 3
  CD58 MUTATED CD58 WILD-TYPE 
            14            353 
  CD58 MUTATED CD58 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] "NEFH MUTATION ANALYSIS"
[1] 3
  NEFH MUTATED NEFH WILD-TYPE 
            13            354 
  NEFH MUTATED NEFH WILD-TYPE 
            13            354 
[1] "XYLT2 MUTATION ANALYSIS"
[1] 3
  XYLT2 MUTATED XYLT2 WILD-TYPE 
             14             353 
  XYLT2 MUTATED XYLT2 WILD-TYPE 
             14             353 
[1] "GRB2 MUTATION ANALYSIS"
[1] 3
  GRB2 MUTATED GRB2 WILD-TYPE 
             9            358 
  GRB2 MUTATED GRB2 WILD-TYPE 
             9            358 
[1] "L1TD1 MUTATION ANALYSIS"
[1] 3
  L1TD1 MUTATED L1TD1 WILD-TYPE 
             17             350 
  L1TD1 MUTATED L1TD1 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] "KCTD3 MUTATION ANALYSIS"
[1] 3
  KCTD3 MUTATED KCTD3 WILD-TYPE 
             17             350 
  KCTD3 MUTATED KCTD3 WILD-TYPE 
             17             350 
[1] "PRKDC MUTATION ANALYSIS"
[1] 3
  PRKDC MUTATED PRKDC WILD-TYPE 
             60             307 
  PRKDC MUTATED PRKDC WILD-TYPE 
             60             307 
[1] "PCBP1 MUTATION ANALYSIS"
[1] 3
  PCBP1 MUTATED PCBP1 WILD-TYPE 
             10             357 
  PCBP1 MUTATED PCBP1 WILD-TYPE 
             10             357 
[1] "ECT2 MUTATION ANALYSIS"
[1] 3
  ECT2 MUTATED ECT2 WILD-TYPE 
            18            349 
  ECT2 MUTATED ECT2 WILD-TYPE 
            18            349 
[1] "RLIM MUTATION ANALYSIS"
[1] 3
  RLIM MUTATED RLIM WILD-TYPE 
            14            353 
  RLIM MUTATED RLIM WILD-TYPE 
            14            353 
[1] "BIRC3 MUTATION ANALYSIS"
[1] 3
  BIRC3 MUTATED BIRC3 WILD-TYPE 
             11             356 
  BIRC3 MUTATED BIRC3 WILD-TYPE 
             11             356 
[1] "BCORL1 MUTATION ANALYSIS"
[1] 3
  BCORL1 MUTATED BCORL1 WILD-TYPE 
              25              342 
  BCORL1 MUTATED BCORL1 WILD-TYPE 
              25              342 
[1] "SLK MUTATION ANALYSIS"
[1] 3
  SLK MUTATED SLK WILD-TYPE 
           23           344 
  SLK MUTATED SLK WILD-TYPE 
           23           344 
[1] "C15ORF52 MUTATION ANALYSIS"
[1] 3
  C15ORF52 MUTATED C15ORF52 WILD-TYPE 
                12                355 
  C15ORF52 MUTATED C15ORF52 WILD-TYPE 
                12                355 
[1] "TAF7L MUTATION ANALYSIS"
[1] 3
  TAF7L MUTATED TAF7L WILD-TYPE 
             11             356 
  TAF7L MUTATED TAF7L WILD-TYPE 
             11             356 
[1] "TPM4 MUTATION ANALYSIS"
[1] 3
  TPM4 MUTATED TPM4 WILD-TYPE 
             8            359 
  TPM4 MUTATED TPM4 WILD-TYPE 
             8            359 
[1] "OR5V1 MUTATION ANALYSIS"
[1] 3
  OR5V1 MUTATED OR5V1 WILD-TYPE 
             14             353 
  OR5V1 MUTATED OR5V1 WILD-TYPE 
             14             353 
[1] "KDM6A MUTATION ANALYSIS"
[1] 3
  KDM6A MUTATED KDM6A WILD-TYPE 
             26             341 
  KDM6A MUTATED KDM6A WILD-TYPE 
             26             341 
[1] "C2ORF29 MUTATION ANALYSIS"
[1] 3
  C2ORF29 MUTATED C2ORF29 WILD-TYPE 
               16               351 
  C2ORF29 MUTATED C2ORF29 WILD-TYPE 
               16               351 
[1] "GGT1 MUTATION ANALYSIS"
[1] 3
  GGT1 MUTATED GGT1 WILD-TYPE 
             8            359 
  GGT1 MUTATED GGT1 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] "PRDM1 MUTATION ANALYSIS"
[1] 3
  PRDM1 MUTATED PRDM1 WILD-TYPE 
             20             347 
  PRDM1 MUTATED PRDM1 WILD-TYPE 
             20             347 
[1] "ZDHHC7 MUTATION ANALYSIS"
[1] 3
  ZDHHC7 MUTATED ZDHHC7 WILD-TYPE 
              12              355 
  ZDHHC7 MUTATED ZDHHC7 WILD-TYPE 
              12              355 
[1] "ZFYVE26 MUTATION ANALYSIS"
[1] 3
  ZFYVE26 MUTATED ZFYVE26 WILD-TYPE 
               28               339 
  ZFYVE26 MUTATED ZFYVE26 WILD-TYPE 
               28               339 
[1] "ST3GAL6 MUTATION ANALYSIS"
[1] 3
  ST3GAL6 MUTATED ST3GAL6 WILD-TYPE 
               12               355 
  ST3GAL6 MUTATED ST3GAL6 WILD-TYPE 
               12               355 
[1] "CDX2 MUTATION ANALYSIS"
[1] 3
  CDX2 MUTATED CDX2 WILD-TYPE 
             6            361 
  CDX2 MUTATED CDX2 WILD-TYPE 
             6            361 
[1] "PTK2 MUTATION ANALYSIS"
[1] 3
  PTK2 MUTATED PTK2 WILD-TYPE 
            22            345 
  PTK2 MUTATED PTK2 WILD-TYPE 
            22            345 
[1] "KLK10 MUTATION ANALYSIS"
[1] 3
  KLK10 MUTATED KLK10 WILD-TYPE 
              7             360 
  KLK10 MUTATED KLK10 WILD-TYPE 
              7             360 
[1] "SVIL MUTATION ANALYSIS"
[1] 3
  SVIL MUTATED SVIL WILD-TYPE 
            32            335 
  SVIL MUTATED SVIL WILD-TYPE 
            32            335 
[1] "CEP135 MUTATION ANALYSIS"
[1] 3
  CEP135 MUTATED CEP135 WILD-TYPE 
              21              346 
  CEP135 MUTATED CEP135 WILD-TYPE 
              21              346 
[1] "RNF128 MUTATION ANALYSIS"
[1] 3
  RNF128 MUTATED RNF128 WILD-TYPE 
              14              353 
  RNF128 MUTATED RNF128 WILD-TYPE 
              14              353 
[1] "PTCH1 MUTATION ANALYSIS"
[1] 3
  PTCH1 MUTATED PTCH1 WILD-TYPE 
             89             278 
  PTCH1 MUTATED PTCH1 WILD-TYPE 
             89             278 
[1] "ADAM28 MUTATION ANALYSIS"
[1] 3
  ADAM28 MUTATED ADAM28 WILD-TYPE 
              17              350 
  ADAM28 MUTATED ADAM28 WILD-TYPE 
              17              350 
[1] "WEE1 MUTATION ANALYSIS"
[1] 3
  WEE1 MUTATED WEE1 WILD-TYPE 
            12            355 
  WEE1 MUTATED WEE1 WILD-TYPE 
            12            355 
[1] "TNFRSF9 MUTATION ANALYSIS"
[1] 3
  TNFRSF9 MUTATED TNFRSF9 WILD-TYPE 
                9               358 
  TNFRSF9 MUTATED TNFRSF9 WILD-TYPE 
                9               358 
[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] "UQCRC2 MUTATION ANALYSIS"
[1] 3
  UQCRC2 MUTATED UQCRC2 WILD-TYPE 
               8              359 
  UQCRC2 MUTATED UQCRC2 WILD-TYPE 
               8              359 
[1] "LINGO4 MUTATION ANALYSIS"
[1] 3
  LINGO4 MUTATED LINGO4 WILD-TYPE 
              10              357 
  LINGO4 MUTATED LINGO4 WILD-TYPE 
              10              357 
[1] "DCLK2 MUTATION ANALYSIS"
[1] 3
  DCLK2 MUTATED DCLK2 WILD-TYPE 
             14             353 
  DCLK2 MUTATED DCLK2 WILD-TYPE 
             14             353 
[1] "NCAPD2 MUTATION ANALYSIS"
[1] 3
  NCAPD2 MUTATED NCAPD2 WILD-TYPE 
              20              347 
  NCAPD2 MUTATED NCAPD2 WILD-TYPE 
              20              347 
[1] "RSPH3 MUTATION ANALYSIS"
[1] 3
  RSPH3 MUTATED RSPH3 WILD-TYPE 
             10             357 
  RSPH3 MUTATED RSPH3 WILD-TYPE 
             10             357 
[1] "OXSM MUTATION ANALYSIS"
[1] 3
  OXSM MUTATED OXSM WILD-TYPE 
            10            357 
  OXSM MUTATED OXSM WILD-TYPE 
            10            357 
[1] "SENP6 MUTATION ANALYSIS"
[1] 3
  SENP6 MUTATED SENP6 WILD-TYPE 
             15             352 
  SENP6 MUTATED SENP6 WILD-TYPE 
             15             352 
[1] "GNPAT MUTATION ANALYSIS"
[1] 3
  GNPAT MUTATED GNPAT WILD-TYPE 
             17             350 
  GNPAT MUTATED GNPAT WILD-TYPE 
             17             350 
[1] "GPR174 MUTATION ANALYSIS"
[1] 3
  GPR174 MUTATED GPR174 WILD-TYPE 
               8              359 
  GPR174 MUTATED GPR174 WILD-TYPE 
               8              359 
[1] "NOTCH2NL MUTATION ANALYSIS"
[1] 3
  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE 
                 6                361 
  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE 
                 6                361 
[1] "PLXNA3 MUTATION ANALYSIS"
[1] 3
  PLXNA3 MUTATED PLXNA3 WILD-TYPE 
              17              350 
  PLXNA3 MUTATED PLXNA3 WILD-TYPE 
              17              350 
[1] "GPATCH8 MUTATION ANALYSIS"
[1] 3
  GPATCH8 MUTATED GPATCH8 WILD-TYPE 
               14               353 
  GPATCH8 MUTATED GPATCH8 WILD-TYPE 
               14               353 
[1] "FHOD3 MUTATION ANALYSIS"
[1] 3
  FHOD3 MUTATED FHOD3 WILD-TYPE 
             27             340 
  FHOD3 MUTATED FHOD3 WILD-TYPE 
             27             340 
[1] "OR7C2 MUTATION ANALYSIS"
[1] 3
  OR7C2 MUTATED OR7C2 WILD-TYPE 
             10             357 
  OR7C2 MUTATED OR7C2 WILD-TYPE 
             10             357 
[1] "NUP188 MUTATION ANALYSIS"
[1] 3
  NUP188 MUTATED NUP188 WILD-TYPE 
              19              348 
  NUP188 MUTATED NUP188 WILD-TYPE 
              19              348 
[1] "ZNF486 MUTATION ANALYSIS"
[1] 3
  ZNF486 MUTATED ZNF486 WILD-TYPE 
              12              355 
  ZNF486 MUTATED ZNF486 WILD-TYPE 
              12              355 
[1] "SLAMF7 MUTATION ANALYSIS"
[1] 3
  SLAMF7 MUTATED SLAMF7 WILD-TYPE 
              11              356 
  SLAMF7 MUTATED SLAMF7 WILD-TYPE 
              11              356 
[1] "FNDC7 MUTATION ANALYSIS"
[1] 3
  FNDC7 MUTATED FNDC7 WILD-TYPE 
              9             358 
  FNDC7 MUTATED FNDC7 WILD-TYPE 
              9             358 
[1] "B4GALNT4 MUTATION ANALYSIS"
[1] 3
  B4GALNT4 MUTATED B4GALNT4 WILD-TYPE 
                11                356 
  B4GALNT4 MUTATED B4GALNT4 WILD-TYPE 
                11                356 
[1] "MIER3 MUTATION ANALYSIS"
[1] 3
  MIER3 MUTATED MIER3 WILD-TYPE 
             13             354 
  MIER3 MUTATED MIER3 WILD-TYPE 
             13             354 
[1] "ATM MUTATION ANALYSIS"
[1] 3
  ATM MUTATED ATM WILD-TYPE 
          132           235 
  ATM MUTATED ATM WILD-TYPE 
          132           235 
[1] "CHRM2 MUTATION ANALYSIS"
[1] 3
  CHRM2 MUTATED CHRM2 WILD-TYPE 
             23             344 
  CHRM2 MUTATED CHRM2 WILD-TYPE 
             23             344 
[1] "CASP8 MUTATION ANALYSIS"
[1] 3
  CASP8 MUTATED CASP8 WILD-TYPE 
             17             350 
  CASP8 MUTATED CASP8 WILD-TYPE 
             17             350 
[1] "INTS4 MUTATION ANALYSIS"
[1] 3
  INTS4 MUTATED INTS4 WILD-TYPE 
             18             349 
  INTS4 MUTATED INTS4 WILD-TYPE 
             18             349 
[1] "MMP8 MUTATION ANALYSIS"
[1] 3
  MMP8 MUTATED MMP8 WILD-TYPE 
            12            355 
  MMP8 MUTATED MMP8 WILD-TYPE 
            12            355 
[1] "LDHA MUTATION ANALYSIS"
[1] 3
  LDHA MUTATED LDHA WILD-TYPE 
            10            357 
  LDHA MUTATED LDHA WILD-TYPE 
            10            357 
[1] "NAA25 MUTATION ANALYSIS"
[1] 3
  NAA25 MUTATED NAA25 WILD-TYPE 
             13             354 
  NAA25 MUTATED NAA25 WILD-TYPE 
             13             354 
[1] "C11ORF30 MUTATION ANALYSIS"
[1] 3
  C11ORF30 MUTATED C11ORF30 WILD-TYPE 
                21                346 
  C11ORF30 MUTATED C11ORF30 WILD-TYPE 
                21                346 
[1] "ASNSD1 MUTATION ANALYSIS"
[1] 3
  ASNSD1 MUTATED ASNSD1 WILD-TYPE 
               9              358 
  ASNSD1 MUTATED ASNSD1 WILD-TYPE 
               9              358 
[1] "ALG9 MUTATION ANALYSIS"
[1] 3
  ALG9 MUTATED ALG9 WILD-TYPE 
             7            360 
  ALG9 MUTATED ALG9 WILD-TYPE 
             7            360 
[1] "TUBE1 MUTATION ANALYSIS"
[1] 3
  TUBE1 MUTATED TUBE1 WILD-TYPE 
             11             356 
  TUBE1 MUTATED TUBE1 WILD-TYPE 
             11             356 
[1] "MEN1 MUTATION ANALYSIS"
[1] 3
  MEN1 MUTATED MEN1 WILD-TYPE 
            24            343 
  MEN1 MUTATED MEN1 WILD-TYPE 
            24            343 
[1] "GIGYF2 MUTATION ANALYSIS"
[1] 3
  GIGYF2 MUTATED GIGYF2 WILD-TYPE 
              26              341 
  GIGYF2 MUTATED GIGYF2 WILD-TYPE 
              26              341 
[1] "SMAD4 MUTATION ANALYSIS"
[1] 3
  SMAD4 MUTATED SMAD4 WILD-TYPE 
            119             248 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
            119             248 
[1] "TNMD MUTATION ANALYSIS"
[1] 3
  TNMD MUTATED TNMD WILD-TYPE 
            11            356 
  TNMD MUTATED TNMD 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] "ATG5 MUTATION ANALYSIS"
[1] 3
  ATG5 MUTATED ATG5 WILD-TYPE 
             8            359 
  ATG5 MUTATED ATG5 WILD-TYPE 
             8            359 
[1] "CLEC4F MUTATION ANALYSIS"
[1] 3
  CLEC4F MUTATED CLEC4F WILD-TYPE 
              19              348 
  CLEC4F MUTATED CLEC4F WILD-TYPE 
              19              348 
[1] "MKL2 MUTATION ANALYSIS"
[1] 3
  MKL2 MUTATED MKL2 WILD-TYPE 
            10            357 
  MKL2 MUTATED MKL2 WILD-TYPE 
            10            357 
[1] "RAF1 MUTATION ANALYSIS"
[1] 3
  RAF1 MUTATED RAF1 WILD-TYPE 
            13            354 
  RAF1 MUTATED RAF1 WILD-TYPE 
            13            354 
[1] "KLHL10 MUTATION ANALYSIS"
[1] 3
  KLHL10 MUTATED KLHL10 WILD-TYPE 
              19              348 
  KLHL10 MUTATED KLHL10 WILD-TYPE 
              19              348 
[1] "SLC12A6 MUTATION ANALYSIS"
[1] 3
  SLC12A6 MUTATED SLC12A6 WILD-TYPE 
               20               347 
  SLC12A6 MUTATED SLC12A6 WILD-TYPE 
               20               347 
[1] "GNAS MUTATION ANALYSIS"
[1] 3
  GNAS MUTATED GNAS WILD-TYPE 
            33            334 
  GNAS MUTATED GNAS WILD-TYPE 
            33            334 
[1] "USP24 MUTATION ANALYSIS"
[1] 3
  USP24 MUTATED USP24 WILD-TYPE 
             28             339 
  USP24 MUTATED USP24 WILD-TYPE 
             28             339 
[1] "FAM179A MUTATION ANALYSIS"
[1] 3
  FAM179A MUTATED FAM179A WILD-TYPE 
               27               340 
  FAM179A MUTATED FAM179A WILD-TYPE 
               27               340 
[1] "FAM9A MUTATION ANALYSIS"
[1] 3
  FAM9A MUTATED FAM9A WILD-TYPE 
             11             356 
  FAM9A MUTATED FAM9A WILD-TYPE 
             11             356 
[1] "RBM44 MUTATION ANALYSIS"
[1] 3
  RBM44 MUTATED RBM44 WILD-TYPE 
             13             354 
  RBM44 MUTATED RBM44 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] "TNRC6C MUTATION ANALYSIS"
[1] 3
  TNRC6C MUTATED TNRC6C WILD-TYPE 
              18              349 
  TNRC6C MUTATED TNRC6C WILD-TYPE 
              18              349 
[1] "ZNF583 MUTATION ANALYSIS"
[1] 3
  ZNF583 MUTATED ZNF583 WILD-TYPE 
              15              352 
  ZNF583 MUTATED ZNF583 WILD-TYPE 
              15              352 
[1] "PRRG1 MUTATION ANALYSIS"
[1] 3
  PRRG1 MUTATED PRRG1 WILD-TYPE 
             11             356 
  PRRG1 MUTATED PRRG1 WILD-TYPE 
             11             356 
[1] "RGS22 MUTATION ANALYSIS"
[1] 3
  RGS22 MUTATED RGS22 WILD-TYPE 
             24             343 
  RGS22 MUTATED RGS22 WILD-TYPE 
             24             343 
[1] "RB1 MUTATION ANALYSIS"
[1] 3
  RB1 MUTATED RB1 WILD-TYPE 
           87           280 
  RB1 MUTATED RB1 WILD-TYPE 
           87           280 
[1] "TFE3 MUTATION ANALYSIS"
[1] 3
  TFE3 MUTATED TFE3 WILD-TYPE 
            11            356 
  TFE3 MUTATED TFE3 WILD-TYPE 
            11            356 
[1] "AKR1C4 MUTATION ANALYSIS"
[1] 3
  AKR1C4 MUTATED AKR1C4 WILD-TYPE 
               9              358 
  AKR1C4 MUTATED AKR1C4 WILD-TYPE 
               9              358 
[1] "OR52A4 MUTATION ANALYSIS"
[1] 3
  OR52A4 MUTATED OR52A4 WILD-TYPE 
               9              358 
  OR52A4 MUTATED OR52A4 WILD-TYPE 
               9              358 
[1] "TIAL1 MUTATION ANALYSIS"
[1] 3
  TIAL1 MUTATED TIAL1 WILD-TYPE 
             12             355 
  TIAL1 MUTATED TIAL1 WILD-TYPE 
             12             355 
[1] "HNF1B MUTATION ANALYSIS"
[1] 3
  HNF1B MUTATED HNF1B WILD-TYPE 
              9             358 
  HNF1B MUTATED HNF1B 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] "MBD6 MUTATION ANALYSIS"
[1] 3
  MBD6 MUTATED MBD6 WILD-TYPE 
            16            351 
  MBD6 MUTATED MBD6 WILD-TYPE 
            16            351 
[1] "PARG MUTATION ANALYSIS"
[1] 3
  PARG MUTATED PARG WILD-TYPE 
            12            355 
  PARG MUTATED PARG WILD-TYPE 
            12            355 
[1] "FAM134A MUTATION ANALYSIS"
[1] 3
  FAM134A MUTATED FAM134A WILD-TYPE 
                8               359 
  FAM134A MUTATED FAM134A WILD-TYPE 
                8               359 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
           154            213 
  PTEN MUTATED PTEN WILD-TYPE 
           154            213 
[1] "HIPK2 MUTATION ANALYSIS"
[1] 3
  HIPK2 MUTATED HIPK2 WILD-TYPE 
             24             343 
  HIPK2 MUTATED HIPK2 WILD-TYPE 
             24             343 
[1] "TUBA4A MUTATION ANALYSIS"
[1] 3
  TUBA4A MUTATED TUBA4A WILD-TYPE 
               9              358 
  TUBA4A MUTATED TUBA4A WILD-TYPE 
               9              358 
[1] "OR2M3 MUTATION ANALYSIS"
[1] 3
  OR2M3 MUTATED OR2M3 WILD-TYPE 
             15             352 
  OR2M3 MUTATED OR2M3 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] "TRIM13 MUTATION ANALYSIS"
[1] 3
  TRIM13 MUTATED TRIM13 WILD-TYPE 
               7              360 
  TRIM13 MUTATED TRIM13 WILD-TYPE 
               7              360 
[1] "THOC5 MUTATION ANALYSIS"
[1] 3
  THOC5 MUTATED THOC5 WILD-TYPE 
             14             353 
  THOC5 MUTATED THOC5 WILD-TYPE 
             14             353 
[1] "GTF2B MUTATION ANALYSIS"
[1] 3
  GTF2B MUTATED GTF2B WILD-TYPE 
             11             356 
  GTF2B MUTATED GTF2B 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] "C1ORF59 MUTATION ANALYSIS"
[1] 3
  C1ORF59 MUTATED C1ORF59 WILD-TYPE 
               10               357 
  C1ORF59 MUTATED C1ORF59 WILD-TYPE 
               10               357 
[1] "PDCD5 MUTATION ANALYSIS"
[1] 3
  PDCD5 MUTATED PDCD5 WILD-TYPE 
              8             359 
  PDCD5 MUTATED PDCD5 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] "SNTN MUTATION ANALYSIS"
[1] 3
  SNTN MUTATED SNTN WILD-TYPE 
             6            361 
  SNTN MUTATED SNTN WILD-TYPE 
             6            361 
[1] "FGFR2 MUTATION ANALYSIS"
[1] 3
  FGFR2 MUTATED FGFR2 WILD-TYPE 
             45             322 
  FGFR2 MUTATED FGFR2 WILD-TYPE 
             45             322 
[1] "NBPF7 MUTATION ANALYSIS"
[1] 3
  NBPF7 MUTATED NBPF7 WILD-TYPE 
             11             356 
  NBPF7 MUTATED NBPF7 WILD-TYPE 
             11             356 
[1] "LATS1 MUTATION ANALYSIS"
[1] 3
  LATS1 MUTATED LATS1 WILD-TYPE 
             18             349 
  LATS1 MUTATED LATS1 WILD-TYPE 
             18             349 
[1] "KIAA1586 MUTATION ANALYSIS"
[1] 3
  KIAA1586 MUTATED KIAA1586 WILD-TYPE 
                11                356 
  KIAA1586 MUTATED KIAA1586 WILD-TYPE 
                11                356 
[1] "FKBP9 MUTATION ANALYSIS"
[1] 3
  FKBP9 MUTATED FKBP9 WILD-TYPE 
             17             350 
  FKBP9 MUTATED FKBP9 WILD-TYPE 
             17             350 
[1] "SCD5 MUTATION ANALYSIS"
[1] 3
  SCD5 MUTATED SCD5 WILD-TYPE 
             9            358 
  SCD5 MUTATED SCD5 WILD-TYPE 
             9            358 
[1] "SHROOM4 MUTATION ANALYSIS"
[1] 3
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
               21               346 
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
               21               346 
[1] "SNAI2 MUTATION ANALYSIS"
[1] 3
  SNAI2 MUTATED SNAI2 WILD-TYPE 
              8             359 
  SNAI2 MUTATED SNAI2 WILD-TYPE 
              8             359 
[1] "C14ORF43 MUTATION ANALYSIS"
[1] 3
  C14ORF43 MUTATED C14ORF43 WILD-TYPE 
                18                349 
  C14ORF43 MUTATED C14ORF43 WILD-TYPE 
                18                349 
[1] "SMARCA4 MUTATION ANALYSIS"
[1] 3
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
               30               337 
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
               30               337 
[1] "DNAH12 MUTATION ANALYSIS"
[1] 3
  DNAH12 MUTATED DNAH12 WILD-TYPE 
              23              344 
  DNAH12 MUTATED DNAH12 WILD-TYPE 
              23              344 
[1] "OSBPL2 MUTATION ANALYSIS"
[1] 3
  OSBPL2 MUTATED OSBPL2 WILD-TYPE 
              11              356 
  OSBPL2 MUTATED OSBPL2 WILD-TYPE 
              11              356 
[1] "MAGEA1 MUTATION ANALYSIS"
[1] 3
  MAGEA1 MUTATED MAGEA1 WILD-TYPE 
              13              354 
  MAGEA1 MUTATED MAGEA1 WILD-TYPE 
              13              354 
[1] "C9ORF84 MUTATION ANALYSIS"
[1] 3
  C9ORF84 MUTATED C9ORF84 WILD-TYPE 
               20               347 
  C9ORF84 MUTATED C9ORF84 WILD-TYPE 
               20               347 
[1] "NT5DC3 MUTATION ANALYSIS"
[1] 3
  NT5DC3 MUTATED NT5DC3 WILD-TYPE 
              12              355 
  NT5DC3 MUTATED NT5DC3 WILD-TYPE 
              12              355 
[1] "GLI1 MUTATION ANALYSIS"
[1] 3
  GLI1 MUTATED GLI1 WILD-TYPE 
            18            349 
  GLI1 MUTATED GLI1 WILD-TYPE 
            18            349 
[1] "ZFX MUTATION ANALYSIS"
[1] 3
  ZFX MUTATED ZFX WILD-TYPE 
           13           354 
  ZFX MUTATED ZFX WILD-TYPE 
           13           354 
[1] "F2RL1 MUTATION ANALYSIS"
[1] 3
  F2RL1 MUTATED F2RL1 WILD-TYPE 
              7             360 
  F2RL1 MUTATED F2RL1 WILD-TYPE 
              7             360 
[1] "KCNH7 MUTATION ANALYSIS"
[1] 3
  KCNH7 MUTATED KCNH7 WILD-TYPE 
             33             334 
  KCNH7 MUTATED KCNH7 WILD-TYPE 
             33             334 
[1] "COLEC10 MUTATION ANALYSIS"
[1] 3
  COLEC10 MUTATED COLEC10 WILD-TYPE 
                8               359 
  COLEC10 MUTATED COLEC10 WILD-TYPE 
                8               359 
[1] "IVL MUTATION ANALYSIS"
[1] 3
  IVL MUTATED IVL WILD-TYPE 
           17           350 
  IVL MUTATED IVL WILD-TYPE 
           17           350 
[1] "FAHD2B MUTATION ANALYSIS"
[1] 3
  FAHD2B MUTATED FAHD2B WILD-TYPE 
               6              361 
  FAHD2B MUTATED FAHD2B WILD-TYPE 
               6              361 
[1] "TRIP11 MUTATION ANALYSIS"
[1] 3
  TRIP11 MUTATED TRIP11 WILD-TYPE 
              19              348 
  TRIP11 MUTATED TRIP11 WILD-TYPE 
              19              348 
[1] "MLL3 MUTATION ANALYSIS"
[1] 3
  MLL3 MUTATED MLL3 WILD-TYPE 
            58            309 
  MLL3 MUTATED MLL3 WILD-TYPE 
            58            309 
[1] "CBL MUTATION ANALYSIS"
[1] 3
  CBL MUTATED CBL WILD-TYPE 
           34           333 
  CBL MUTATED CBL WILD-TYPE 
           34           333 
[1] "MAGEC1 MUTATION ANALYSIS"
[1] 3
  MAGEC1 MUTATED MAGEC1 WILD-TYPE 
              28              339 
  MAGEC1 MUTATED MAGEC1 WILD-TYPE 
              28              339 
[1] "PCSK1 MUTATION ANALYSIS"
[1] 3
  PCSK1 MUTATED PCSK1 WILD-TYPE 
             16             351 
  PCSK1 MUTATED PCSK1 WILD-TYPE 
             16             351 
[1] "RASA2 MUTATION ANALYSIS"
[1] 3
  RASA2 MUTATED RASA2 WILD-TYPE 
             15             352 
  RASA2 MUTATED RASA2 WILD-TYPE 
             15             352 
[1] "LARP4B MUTATION ANALYSIS"
[1] 3
  LARP4B MUTATED LARP4B WILD-TYPE 
              29              338 
  LARP4B MUTATED LARP4B WILD-TYPE 
              29              338 
[1] "TWISTNB MUTATION ANALYSIS"
[1] 3
  TWISTNB MUTATED TWISTNB WILD-TYPE 
                8               359 
  TWISTNB MUTATED TWISTNB WILD-TYPE 
                8               359 
[1] "BRCA2 MUTATION ANALYSIS"
[1] 3
  BRCA2 MUTATED BRCA2 WILD-TYPE 
             49             318 
  BRCA2 MUTATED BRCA2 WILD-TYPE 
             49             318 
[1] "IFT57 MUTATION ANALYSIS"
[1] 3
  IFT57 MUTATED IFT57 WILD-TYPE 
             10             357 
  IFT57 MUTATED IFT57 WILD-TYPE 
             10             357 
[1] "SPR MUTATION ANALYSIS"
[1] 3
  SPR MUTATED SPR WILD-TYPE 
            7           360 
  SPR MUTATED SPR WILD-TYPE 
            7           360 
[1] "ARFGEF1 MUTATION ANALYSIS"
[1] 3
  ARFGEF1 MUTATED ARFGEF1 WILD-TYPE 
               33               334 
  ARFGEF1 MUTATED ARFGEF1 WILD-TYPE 
               33               334 
[1] "DOCK10 MUTATION ANALYSIS"
[1] 3
  DOCK10 MUTATED DOCK10 WILD-TYPE 
              25              342 
  DOCK10 MUTATED DOCK10 WILD-TYPE 
              25              342 
[1] "EP400 MUTATION ANALYSIS"
[1] 3
  EP400 MUTATED EP400 WILD-TYPE 
             36             331 
  EP400 MUTATED EP400 WILD-TYPE 
             36             331 
[1] "C12ORF5 MUTATION ANALYSIS"
[1] 3
  C12ORF5 MUTATED C12ORF5 WILD-TYPE 
                6               361 
  C12ORF5 MUTATED C12ORF5 WILD-TYPE 
                6               361 
[1] "ERCC5 MUTATION ANALYSIS"
[1] 3
  ERCC5 MUTATED ERCC5 WILD-TYPE 
             24             343 
  ERCC5 MUTATED ERCC5 WILD-TYPE 
             24             343 
[1] "C12ORF40 MUTATION ANALYSIS"
[1] 3
  C12ORF40 MUTATED C12ORF40 WILD-TYPE 
                21                346 
  C12ORF40 MUTATED C12ORF40 WILD-TYPE 
                21                346 
[1] "MYL1 MUTATION ANALYSIS"
[1] 3
  MYL1 MUTATED MYL1 WILD-TYPE 
             8            359 
  MYL1 MUTATED MYL1 WILD-TYPE 
             8            359 
[1] "GPR141 MUTATION ANALYSIS"
[1] 3
  GPR141 MUTATED GPR141 WILD-TYPE 
              11              356 
  GPR141 MUTATED GPR141 WILD-TYPE 
              11              356 
[1] "AKAP3 MUTATION ANALYSIS"
[1] 3
  AKAP3 MUTATED AKAP3 WILD-TYPE 
             21             346 
  AKAP3 MUTATED AKAP3 WILD-TYPE 
             21             346 
[1] "HELQ MUTATION ANALYSIS"
[1] 3
  HELQ MUTATED HELQ WILD-TYPE 
            18            349 
  HELQ MUTATED HELQ WILD-TYPE 
            18            349 
[1] "GLI2 MUTATION ANALYSIS"
[1] 3
  GLI2 MUTATED GLI2 WILD-TYPE 
            20            347 
  GLI2 MUTATED GLI2 WILD-TYPE 
            20            347 
[1] "SULT6B1 MUTATION ANALYSIS"
[1] 3
  SULT6B1 MUTATED SULT6B1 WILD-TYPE 
                9               358 
  SULT6B1 MUTATED SULT6B1 WILD-TYPE 
                9               358 
[1] "LNPEP MUTATION ANALYSIS"
[1] 3
  LNPEP MUTATED LNPEP WILD-TYPE 
             18             349 
  LNPEP MUTATED LNPEP WILD-TYPE 
             18             349 
[1] "OR1J2 MUTATION ANALYSIS"
[1] 3
  OR1J2 MUTATED OR1J2 WILD-TYPE 
             10             357 
  OR1J2 MUTATED OR1J2 WILD-TYPE 
             10             357 
[1] "PRKCH MUTATION ANALYSIS"
[1] 3
  PRKCH MUTATED PRKCH WILD-TYPE 
             13             354 
  PRKCH MUTATED PRKCH WILD-TYPE 
             13             354 
[1] "PPARGC1A MUTATION ANALYSIS"
[1] 3
  PPARGC1A MUTATED PPARGC1A WILD-TYPE 
                23                344 
  PPARGC1A MUTATED PPARGC1A WILD-TYPE 
                23                344 
[1] "DHRS7 MUTATION ANALYSIS"
[1] 3
  DHRS7 MUTATED DHRS7 WILD-TYPE 
             10             357 
  DHRS7 MUTATED DHRS7 WILD-TYPE 
             10             357 
[1] "HAS2 MUTATION ANALYSIS"
[1] 3
  HAS2 MUTATED HAS2 WILD-TYPE 
             9            358 
  HAS2 MUTATED HAS2 WILD-TYPE 
             9            358 
[1] "ANKRD36B MUTATION ANALYSIS"
[1] 3
  ANKRD36B MUTATED ANKRD36B WILD-TYPE 
                 8                359 
  ANKRD36B MUTATED ANKRD36B WILD-TYPE 
                 8                359 
[1] "ZNF280B MUTATION ANALYSIS"
[1] 3
  ZNF280B MUTATED ZNF280B WILD-TYPE 
               12               355 
  ZNF280B MUTATED ZNF280B WILD-TYPE 
               12               355 
[1] "MPO MUTATION ANALYSIS"
[1] 3
  MPO MUTATED MPO WILD-TYPE 
           12           355 
  MPO MUTATED MPO WILD-TYPE 
           12           355 
[1] "EIF5B MUTATION ANALYSIS"
[1] 3
  EIF5B MUTATED EIF5B WILD-TYPE 
             16             351 
  EIF5B MUTATED EIF5B WILD-TYPE 
             16             351 
[1] "PALB2 MUTATION ANALYSIS"
[1] 3
  PALB2 MUTATED PALB2 WILD-TYPE 
             19             348 
  PALB2 MUTATED PALB2 WILD-TYPE 
             19             348 
[1] "NBEA MUTATION ANALYSIS"
[1] 3
  NBEA MUTATED NBEA WILD-TYPE 
            45            322 
  NBEA MUTATED NBEA WILD-TYPE 
            45            322 
[1] "RASAL2 MUTATION ANALYSIS"
[1] 3
  RASAL2 MUTATED RASAL2 WILD-TYPE 
              15              352 
  RASAL2 MUTATED RASAL2 WILD-TYPE 
              15              352 
[1] "C12ORF10 MUTATION ANALYSIS"
[1] 3
  C12ORF10 MUTATED C12ORF10 WILD-TYPE 
                 4                363 
  C12ORF10 MUTATED C12ORF10 WILD-TYPE 
                 4                363 
[1] "ANAPC4 MUTATION ANALYSIS"
[1] 3
  ANAPC4 MUTATED ANAPC4 WILD-TYPE 
              10              357 
  ANAPC4 MUTATED ANAPC4 WILD-TYPE 
              10              357 
[1] "ARNT2 MUTATION ANALYSIS"
[1] 3
  ARNT2 MUTATED ARNT2 WILD-TYPE 
             12             355 
  ARNT2 MUTATED ARNT2 WILD-TYPE 
             12             355 
[1] "AURKA MUTATION ANALYSIS"
[1] 3
  AURKA MUTATED AURKA WILD-TYPE 
              8             359 
  AURKA MUTATED AURKA WILD-TYPE 
              8             359 
[1] "WNT16 MUTATION ANALYSIS"
[1] 3
  WNT16 MUTATED WNT16 WILD-TYPE 
              8             359 
  WNT16 MUTATED WNT16 WILD-TYPE 
              8             359 
[1] "VAV2 MUTATION ANALYSIS"
[1] 3
  VAV2 MUTATED VAV2 WILD-TYPE 
            17            350 
  VAV2 MUTATED VAV2 WILD-TYPE 
            17            350 
[1] "CENPF MUTATION ANALYSIS"
[1] 3
  CENPF MUTATED CENPF WILD-TYPE 
             41             326 
  CENPF MUTATED CENPF WILD-TYPE 
             41             326 
[1] "TOB1 MUTATION ANALYSIS"
[1] 3
  TOB1 MUTATED TOB1 WILD-TYPE 
             6            361 
  TOB1 MUTATED TOB1 WILD-TYPE 
             6            361 
[1] "SLC4A10 MUTATION ANALYSIS"
[1] 3
  SLC4A10 MUTATED SLC4A10 WILD-TYPE 
               27               340 
  SLC4A10 MUTATED SLC4A10 WILD-TYPE 
               27               340 
[1] "KIR2DL3 MUTATION ANALYSIS"
[1] 3
  KIR2DL3 MUTATED KIR2DL3 WILD-TYPE 
               18               349 
  KIR2DL3 MUTATED KIR2DL3 WILD-TYPE 
               18               349 
[1] "ZNF789 MUTATION ANALYSIS"
[1] 3
  ZNF789 MUTATED ZNF789 WILD-TYPE 
               7              360 
  ZNF789 MUTATED ZNF789 WILD-TYPE 
               7              360 
[1] "SYNRG MUTATION ANALYSIS"
[1] 3
  SYNRG MUTATED SYNRG WILD-TYPE 
             14             353 
  SYNRG MUTATED SYNRG WILD-TYPE 
             14             353 
[1] "MLL2 MUTATION ANALYSIS"
[1] 3
  MLL2 MUTATED MLL2 WILD-TYPE 
            52            315 
  MLL2 MUTATED MLL2 WILD-TYPE 
            52            315 
[1] "ANKHD1 MUTATION ANALYSIS"
[1] 3
  ANKHD1 MUTATED ANKHD1 WILD-TYPE 
              23              344 
  ANKHD1 MUTATED ANKHD1 WILD-TYPE 
              23              344 
[1] "CXORF38 MUTATION ANALYSIS"
[1] 3
  CXORF38 MUTATED CXORF38 WILD-TYPE 
                5               362 
  CXORF38 MUTATED CXORF38 WILD-TYPE 
                5               362 
[1] "CLCNKA MUTATION ANALYSIS"
[1] 3
  CLCNKA MUTATED CLCNKA WILD-TYPE 
              10              357 
  CLCNKA MUTATED CLCNKA WILD-TYPE 
              10              357 
[1] "ETAA1 MUTATION ANALYSIS"
[1] 3
  ETAA1 MUTATED ETAA1 WILD-TYPE 
             16             351 
  ETAA1 MUTATED ETAA1 WILD-TYPE 
             16             351 
[1] "TTF1 MUTATION ANALYSIS"
[1] 3
  TTF1 MUTATED TTF1 WILD-TYPE 
             9            358 
  TTF1 MUTATED TTF1 WILD-TYPE 
             9            358 
[1] "USP26 MUTATION ANALYSIS"
[1] 3
  USP26 MUTATED USP26 WILD-TYPE 
             22             345 
  USP26 MUTATED USP26 WILD-TYPE 
             22             345 
[1] "RAB28 MUTATION ANALYSIS"
[1] 3
  RAB28 MUTATED RAB28 WILD-TYPE 
              6             361 
  RAB28 MUTATED RAB28 WILD-TYPE 
              6             361 
[1] "MST4 MUTATION ANALYSIS"
[1] 3
  MST4 MUTATED MST4 WILD-TYPE 
             7            360 
  MST4 MUTATED MST4 WILD-TYPE 
             7            360 
[1] "FAM133B MUTATION ANALYSIS"
[1] 3
  FAM133B MUTATED FAM133B WILD-TYPE 
                5               362 
  FAM133B MUTATED FAM133B WILD-TYPE 
                5               362 
[1] "TRIM32 MUTATION ANALYSIS"
[1] 3
  TRIM32 MUTATED TRIM32 WILD-TYPE 
              11              356 
  TRIM32 MUTATED TRIM32 WILD-TYPE 
              11              356 
[1] "GOLPH3L MUTATION ANALYSIS"
[1] 3
  GOLPH3L MUTATED GOLPH3L WILD-TYPE 
                5               362 
  GOLPH3L MUTATED GOLPH3L WILD-TYPE 
                5               362 
[1] "ACP6 MUTATION ANALYSIS"
[1] 3
  ACP6 MUTATED ACP6 WILD-TYPE 
             6            361 
  ACP6 MUTATED ACP6 WILD-TYPE 
             6            361 
[1] "PPP2R1A MUTATION ANALYSIS"
[1] 3
  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
               14               353 
  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
               14               353 
[1] "INSM2 MUTATION ANALYSIS"
[1] 3
  INSM2 MUTATED INSM2 WILD-TYPE 
             10             357 
  INSM2 MUTATED INSM2 WILD-TYPE 
             10             357 
[1] "TSHR MUTATION ANALYSIS"
[1] 3
  TSHR MUTATED TSHR WILD-TYPE 
            44            323 
  TSHR MUTATED TSHR WILD-TYPE 
            44            323 
[1] "USP34 MUTATION ANALYSIS"
[1] 3
  USP34 MUTATED USP34 WILD-TYPE 
             41             326 
  USP34 MUTATED USP34 WILD-TYPE 
             41             326 
[1] "C14ORF159 MUTATION ANALYSIS"
[1] 3
  C14ORF159 MUTATED C14ORF159 WILD-TYPE 
                  9                 358 
  C14ORF159 MUTATED C14ORF159 WILD-TYPE 
                  9                 358 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
           169            198 
  KRAS MUTATED KRAS WILD-TYPE 
           169            198 
[1] "WASH1 MUTATION ANALYSIS"
[1] 3
  WASH1 MUTATED WASH1 WILD-TYPE 
              7             360 
  WASH1 MUTATED WASH1 WILD-TYPE 
              7             360 
[1] "ZNF189 MUTATION ANALYSIS"
[1] 3
  ZNF189 MUTATED ZNF189 WILD-TYPE 
              17              350 
  ZNF189 MUTATED ZNF189 WILD-TYPE 
              17              350 
[1] "ZNF438 MUTATION ANALYSIS"
[1] 3
  ZNF438 MUTATED ZNF438 WILD-TYPE 
              12              355 
  ZNF438 MUTATED ZNF438 WILD-TYPE 
              12              355 
[1] "WNK1 MUTATION ANALYSIS"
[1] 3
  WNK1 MUTATED WNK1 WILD-TYPE 
            23            344 
  WNK1 MUTATED WNK1 WILD-TYPE 
            23            344 
[1] "GATA3 MUTATION ANALYSIS"
[1] 3
  GATA3 MUTATED GATA3 WILD-TYPE 
             16             351 
  GATA3 MUTATED GATA3 WILD-TYPE 
             16             351 
[1] "CATSPER1 MUTATION ANALYSIS"
[1] 3
  CATSPER1 MUTATED CATSPER1 WILD-TYPE 
                16                351 
  CATSPER1 MUTATED CATSPER1 WILD-TYPE 
                16                351 
[1] "C14ORF102 MUTATION ANALYSIS"
[1] 3
  C14ORF102 MUTATED C14ORF102 WILD-TYPE 
                 17                 350 
  C14ORF102 MUTATED C14ORF102 WILD-TYPE 
                 17                 350 
[1] "RBM7 MUTATION ANALYSIS"
[1] 3
  RBM7 MUTATED RBM7 WILD-TYPE 
            10            357 
  RBM7 MUTATED RBM7 WILD-TYPE 
            10            357 
[1] "GMCL1 MUTATION ANALYSIS"
[1] 3
  GMCL1 MUTATED GMCL1 WILD-TYPE 
             10             357 
  GMCL1 MUTATED GMCL1 WILD-TYPE 
             10             357 
[1] "IKZF4 MUTATION ANALYSIS"
[1] 3
  IKZF4 MUTATED IKZF4 WILD-TYPE 
             13             354 
  IKZF4 MUTATED IKZF4 WILD-TYPE 
             13             354 
[1] "ANKRD50 MUTATION ANALYSIS"
[1] 3
  ANKRD50 MUTATED ANKRD50 WILD-TYPE 
               15               352 
  ANKRD50 MUTATED ANKRD50 WILD-TYPE 
               15               352 
[1] "LHCGR MUTATION ANALYSIS"
[1] 3
  LHCGR MUTATED LHCGR WILD-TYPE 
             24             343 
  LHCGR MUTATED LHCGR WILD-TYPE 
             24             343 
[1] "RUNX1 MUTATION ANALYSIS"
[1] 3
  RUNX1 MUTATED RUNX1 WILD-TYPE 
             37             330 
  RUNX1 MUTATED RUNX1 WILD-TYPE 
             37             330 
[1] "OR51E1 MUTATION ANALYSIS"
[1] 3
  OR51E1 MUTATED OR51E1 WILD-TYPE 
              13              354 
  OR51E1 MUTATED OR51E1 WILD-TYPE 
              13              354 
[1] "NEXN MUTATION ANALYSIS"
[1] 3
  NEXN MUTATED NEXN WILD-TYPE 
            17            350 
  NEXN MUTATED NEXN WILD-TYPE 
            17            350 
[1] "EIF4A2 MUTATION ANALYSIS"
[1] 3
  EIF4A2 MUTATED EIF4A2 WILD-TYPE 
              10              357 
  EIF4A2 MUTATED EIF4A2 WILD-TYPE 
              10              357 
[1] "MYEOV MUTATION ANALYSIS"
[1] 3
  MYEOV MUTATED MYEOV WILD-TYPE 
              6             361 
  MYEOV MUTATED MYEOV WILD-TYPE 
              6             361 
[1] "IGFBP7 MUTATION ANALYSIS"
[1] 3
  IGFBP7 MUTATED IGFBP7 WILD-TYPE 
               4              363 
  IGFBP7 MUTATED IGFBP7 WILD-TYPE 
               4              363 
[1] "RNF182 MUTATION ANALYSIS"
[1] 3
  RNF182 MUTATED RNF182 WILD-TYPE 
              13              354 
  RNF182 MUTATED RNF182 WILD-TYPE 
              13              354 
[1] "SYNCRIP MUTATION ANALYSIS"
[1] 3
  SYNCRIP MUTATED SYNCRIP WILD-TYPE 
               10               357 
  SYNCRIP MUTATED SYNCRIP WILD-TYPE 
               10               357 
[1] "SLC9A10 MUTATION ANALYSIS"
[1] 3
  SLC9A10 MUTATED SLC9A10 WILD-TYPE 
               18               349 
  SLC9A10 MUTATED SLC9A10 WILD-TYPE 
               18               349 
[1] "PDGFRA MUTATION ANALYSIS"
[1] 3
  PDGFRA MUTATED PDGFRA WILD-TYPE 
              47              320 
  PDGFRA MUTATED PDGFRA WILD-TYPE 
              47              320 
[1] "ECM2 MUTATION ANALYSIS"
[1] 3
  ECM2 MUTATED ECM2 WILD-TYPE 
            17            350 
  ECM2 MUTATED ECM2 WILD-TYPE 
            17            350 
[1] "MYST4 MUTATION ANALYSIS"
[1] 3
  MYST4 MUTATED MYST4 WILD-TYPE 
             23             344 
  MYST4 MUTATED MYST4 WILD-TYPE 
             23             344 
[1] "CARD11 MUTATION ANALYSIS"
[1] 3
  CARD11 MUTATED CARD11 WILD-TYPE 
              41              326 
  CARD11 MUTATED CARD11 WILD-TYPE 
              41              326 
[1] "PLCH2 MUTATION ANALYSIS"
[1] 3
  PLCH2 MUTATED PLCH2 WILD-TYPE 
             19             348 
  PLCH2 MUTATED PLCH2 WILD-TYPE 
             19             348 
[1] "C2ORF77 MUTATION ANALYSIS"
[1] 3
  C2ORF77 MUTATED C2ORF77 WILD-TYPE 
                8               359 
  C2ORF77 MUTATED C2ORF77 WILD-TYPE 
                8               359 
[1] "TIFA MUTATION ANALYSIS"
[1] 3
  TIFA MUTATED TIFA WILD-TYPE 
             6            361 
  TIFA MUTATED TIFA WILD-TYPE 
             6            361 
[1] "PIK3C2A MUTATION ANALYSIS"
[1] 3
  PIK3C2A MUTATED PIK3C2A WILD-TYPE 
               14               353 
  PIK3C2A MUTATED PIK3C2A WILD-TYPE 
               14               353 
[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] "IL1RAPL1 MUTATION ANALYSIS"
[1] 3
  IL1RAPL1 MUTATED IL1RAPL1 WILD-TYPE 
                23                344 
  IL1RAPL1 MUTATED IL1RAPL1 WILD-TYPE 
                23                344 
[1] "GPR87 MUTATION ANALYSIS"
[1] 3
  GPR87 MUTATED GPR87 WILD-TYPE 
             10             357 
  GPR87 MUTATED GPR87 WILD-TYPE 
             10             357 
[1] "KPNA5 MUTATION ANALYSIS"
[1] 3
  KPNA5 MUTATED KPNA5 WILD-TYPE 
             11             356 
  KPNA5 MUTATED KPNA5 WILD-TYPE 
             11             356 
[1] "GPNMB MUTATION ANALYSIS"
[1] 3
  GPNMB MUTATED GPNMB WILD-TYPE 
             13             354 
  GPNMB MUTATED GPNMB WILD-TYPE 
             13             354 
[1] "BAG4 MUTATION ANALYSIS"
[1] 3
  BAG4 MUTATED BAG4 WILD-TYPE 
             8            359 
  BAG4 MUTATED BAG4 WILD-TYPE 
             8            359 
[1] "NRAS MUTATION ANALYSIS"
[1] 3
  NRAS MUTATED NRAS WILD-TYPE 
            33            334 
  NRAS MUTATED NRAS WILD-TYPE 
            33            334 
[1] "DDX43 MUTATION ANALYSIS"
[1] 3
  DDX43 MUTATED DDX43 WILD-TYPE 
             11             356 
  DDX43 MUTATED DDX43 WILD-TYPE 
             11             356 
[1] "LIG1 MUTATION ANALYSIS"
[1] 3
  LIG1 MUTATED LIG1 WILD-TYPE 
            16            351 
  LIG1 MUTATED LIG1 WILD-TYPE 
            16            351 
[1] "PRB4 MUTATION ANALYSIS"
[1] 3
  PRB4 MUTATED PRB4 WILD-TYPE 
            10            357 
  PRB4 MUTATED PRB4 WILD-TYPE 
            10            357 
[1] "WDR78 MUTATION ANALYSIS"
[1] 3
  WDR78 MUTATED WDR78 WILD-TYPE 
             12             355 
  WDR78 MUTATED WDR78 WILD-TYPE 
             12             355 
[1] "CYLD MUTATION ANALYSIS"
[1] 3
  CYLD MUTATED CYLD WILD-TYPE 
            19            348 
  CYLD MUTATED CYLD WILD-TYPE 
            19            348 
[1] "ZNF182 MUTATION ANALYSIS"
[1] 3
  ZNF182 MUTATED ZNF182 WILD-TYPE 
              13              354 
  ZNF182 MUTATED ZNF182 WILD-TYPE 
              13              354 
[1] "MAP4K3 MUTATION ANALYSIS"
[1] 3
  MAP4K3 MUTATED MAP4K3 WILD-TYPE 
              16              351 
  MAP4K3 MUTATED MAP4K3 WILD-TYPE 
              16              351 
[1] "DDB1 MUTATION ANALYSIS"
[1] 3
  DDB1 MUTATED DDB1 WILD-TYPE 
            13            354 
  DDB1 MUTATED DDB1 WILD-TYPE 
            13            354 
[1] "ITGAV MUTATION ANALYSIS"
[1] 3
  ITGAV MUTATED ITGAV WILD-TYPE 
             15             352 
  ITGAV MUTATED ITGAV WILD-TYPE 
             15             352 
[1] "F8 MUTATION ANALYSIS"
[1] 3
  F8 MUTATED F8 WILD-TYPE 
          33          334 
  F8 MUTATED F8 WILD-TYPE 
          33          334 
[1] "MBTD1 MUTATION ANALYSIS"
[1] 3
  MBTD1 MUTATED MBTD1 WILD-TYPE 
              9             358 
  MBTD1 MUTATED MBTD1 WILD-TYPE 
              9             358 
[1] "OR1I1 MUTATION ANALYSIS"
[1] 3
  OR1I1 MUTATED OR1I1 WILD-TYPE 
             10             357 
  OR1I1 MUTATED OR1I1 WILD-TYPE 
             10             357 
[1] "IFIT2 MUTATION ANALYSIS"
[1] 3
  IFIT2 MUTATED IFIT2 WILD-TYPE 
              7             360 
  IFIT2 MUTATED IFIT2 WILD-TYPE 
              7             360 
[1] "NUP54 MUTATION ANALYSIS"
[1] 3
  NUP54 MUTATED NUP54 WILD-TYPE 
              8             359 
  NUP54 MUTATED NUP54 WILD-TYPE 
              8             359 
[1] "DMRTB1 MUTATION ANALYSIS"
[1] 3
  DMRTB1 MUTATED DMRTB1 WILD-TYPE 
               6              361 
  DMRTB1 MUTATED DMRTB1 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] "MSH2 MUTATION ANALYSIS"
[1] 3
  MSH2 MUTATED MSH2 WILD-TYPE 
            33            334 
  MSH2 MUTATED MSH2 WILD-TYPE 
            33            334 
[1] "ATP8B1 MUTATION ANALYSIS"
[1] 3
  ATP8B1 MUTATED ATP8B1 WILD-TYPE 
              23              344 
  ATP8B1 MUTATED ATP8B1 WILD-TYPE 
              23              344 
[1] "DAXX MUTATION ANALYSIS"
[1] 3
  DAXX MUTATED DAXX WILD-TYPE 
            12            355 
  DAXX MUTATED DAXX WILD-TYPE 
            12            355 
[1] "CSNK1D MUTATION ANALYSIS"
[1] 3
  CSNK1D MUTATED CSNK1D WILD-TYPE 
              14              353 
  CSNK1D MUTATED CSNK1D WILD-TYPE 
              14              353 
[1] "UBR4 MUTATION ANALYSIS"
[1] 3
  UBR4 MUTATED UBR4 WILD-TYPE 
            39            328 
  UBR4 MUTATED UBR4 WILD-TYPE 
            39            328 
[1] "PRAMEF12 MUTATION ANALYSIS"
[1] 3
  PRAMEF12 MUTATED PRAMEF12 WILD-TYPE 
                 6                361 
  PRAMEF12 MUTATED PRAMEF12 WILD-TYPE 
                 6                361 
[1] "ARHGAP5 MUTATION ANALYSIS"
[1] 3
  ARHGAP5 MUTATED ARHGAP5 WILD-TYPE 
               19               348 
  ARHGAP5 MUTATED ARHGAP5 WILD-TYPE 
               19               348 
[1] "PCDHGA11 MUTATION ANALYSIS"
[1] 3
  PCDHGA11 MUTATED PCDHGA11 WILD-TYPE 
                19                348 
  PCDHGA11 MUTATED PCDHGA11 WILD-TYPE 
                19                348 
[1] "HIST1H1T MUTATION ANALYSIS"
[1] 3
  HIST1H1T MUTATED HIST1H1T WILD-TYPE 
                 9                358 
  HIST1H1T MUTATED HIST1H1T WILD-TYPE 
                 9                358 
[1] "DOCK1 MUTATION ANALYSIS"
[1] 3
  DOCK1 MUTATED DOCK1 WILD-TYPE 
             24             343 
  DOCK1 MUTATED DOCK1 WILD-TYPE 
             24             343 
[1] "ABCC4 MUTATION ANALYSIS"
[1] 3
  ABCC4 MUTATED ABCC4 WILD-TYPE 
             20             347 
  ABCC4 MUTATED ABCC4 WILD-TYPE 
             20             347 
[1] "MOBKL2B MUTATION ANALYSIS"
[1] 3
  MOBKL2B MUTATED MOBKL2B WILD-TYPE 
                7               360 
  MOBKL2B MUTATED MOBKL2B WILD-TYPE 
                7               360 
[1] "TXNDC15 MUTATION ANALYSIS"
[1] 3
  TXNDC15 MUTATED TXNDC15 WILD-TYPE 
                6               361 
  TXNDC15 MUTATED TXNDC15 WILD-TYPE 
                6               361 
[1] "GTF2IRD2 MUTATION ANALYSIS"
[1] 3
  GTF2IRD2 MUTATED GTF2IRD2 WILD-TYPE 
                 6                361 
  GTF2IRD2 MUTATED GTF2IRD2 WILD-TYPE 
                 6                361 
[1] "KDM5B MUTATION ANALYSIS"
[1] 3
  KDM5B MUTATED KDM5B WILD-TYPE 
             23             344 
  KDM5B MUTATED KDM5B WILD-TYPE 
             23             344 
[1] "CRY1 MUTATION ANALYSIS"
[1] 3
  CRY1 MUTATED CRY1 WILD-TYPE 
            12            355 
  CRY1 MUTATED CRY1 WILD-TYPE 
            12            355 
[1] "FBLN5 MUTATION ANALYSIS"
[1] 3
  FBLN5 MUTATED FBLN5 WILD-TYPE 
              8             359 
  FBLN5 MUTATED FBLN5 WILD-TYPE 
              8             359 
[1] "EFHC2 MUTATION ANALYSIS"
[1] 3
  EFHC2 MUTATED EFHC2 WILD-TYPE 
             15             352 
  EFHC2 MUTATED EFHC2 WILD-TYPE 
             15             352 
[1] "E2F7 MUTATION ANALYSIS"
[1] 3
  E2F7 MUTATED E2F7 WILD-TYPE 
            21            346 
  E2F7 MUTATED E2F7 WILD-TYPE 
            21            346 
[1] "MSH6 MUTATION ANALYSIS"
[1] 3
  MSH6 MUTATED MSH6 WILD-TYPE 
            39            328 
  MSH6 MUTATED MSH6 WILD-TYPE 
            39            328 
[1] "CTNNB1 MUTATION ANALYSIS"
[1] 3
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              73              294 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              73              294 
[1] "GPR112 MUTATION ANALYSIS"
[1] 3
  GPR112 MUTATED GPR112 WILD-TYPE 
              30              337 
  GPR112 MUTATED GPR112 WILD-TYPE 
              30              337 
[1] "SLC11A2 MUTATION ANALYSIS"
[1] 3
  SLC11A2 MUTATED SLC11A2 WILD-TYPE 
                8               359 
  SLC11A2 MUTATED SLC11A2 WILD-TYPE 
                8               359 
[1] "CYP4X1 MUTATION ANALYSIS"
[1] 3
  CYP4X1 MUTATED CYP4X1 WILD-TYPE 
               5              362 
  CYP4X1 MUTATED CYP4X1 WILD-TYPE 
               5              362 
[1] "NUP160 MUTATION ANALYSIS"
[1] 3
  NUP160 MUTATED NUP160 WILD-TYPE 
              11              356 
  NUP160 MUTATED NUP160 WILD-TYPE 
              11              356 
[1] "TRPM7 MUTATION ANALYSIS"
[1] 3
  TRPM7 MUTATED TRPM7 WILD-TYPE 
             28             339 
  TRPM7 MUTATED TRPM7 WILD-TYPE 
             28             339 
[1] "MFN1 MUTATION ANALYSIS"
[1] 3
  MFN1 MUTATED MFN1 WILD-TYPE 
            13            354 
  MFN1 MUTATED MFN1 WILD-TYPE 
            13            354 
[1] "RPS6KA3 MUTATION ANALYSIS"
[1] 3
  RPS6KA3 MUTATED RPS6KA3 WILD-TYPE 
               13               354 
  RPS6KA3 MUTATED RPS6KA3 WILD-TYPE 
               13               354 
[1] "FUT10 MUTATION ANALYSIS"
[1] 3
  FUT10 MUTATED FUT10 WILD-TYPE 
              6             361 
  FUT10 MUTATED FUT10 WILD-TYPE 
              6             361 
[1] "ARHGAP32 MUTATION ANALYSIS"
[1] 3
  ARHGAP32 MUTATED ARHGAP32 WILD-TYPE 
                22                345 
  ARHGAP32 MUTATED ARHGAP32 WILD-TYPE 
                22                345 
[1] "CNIH4 MUTATION ANALYSIS"
[1] 3
  CNIH4 MUTATED CNIH4 WILD-TYPE 
              6             361 
  CNIH4 MUTATED CNIH4 WILD-TYPE 
              6             361 
[1] "MET MUTATION ANALYSIS"
[1] 3
  MET MUTATED MET WILD-TYPE 
           42           325 
  MET MUTATED MET WILD-TYPE 
           42           325 
[1] "ERBB3 MUTATION ANALYSIS"
[1] 3
  ERBB3 MUTATED ERBB3 WILD-TYPE 
             26             341 
  ERBB3 MUTATED ERBB3 WILD-TYPE 
             26             341 
[1] "GOLGB1 MUTATION ANALYSIS"
[1] 3
  GOLGB1 MUTATED GOLGB1 WILD-TYPE 
              38              329 
  GOLGB1 MUTATED GOLGB1 WILD-TYPE 
              38              329 
[1] "BRAF MUTATION ANALYSIS"
[1] 3
  BRAF MUTATED BRAF WILD-TYPE 
            96            271 
  BRAF MUTATED BRAF WILD-TYPE 
            96            271 
[1] "HLA-A MUTATION ANALYSIS"
[1] 3
  HLA-A MUTATED HLA-A WILD-TYPE 
             16             351 
  HLA-A MUTATED HLA-A WILD-TYPE 
             16             351 
[1] "C6ORF89 MUTATION ANALYSIS"
[1] 3
  C6ORF89 MUTATED C6ORF89 WILD-TYPE 
                6               361 
  C6ORF89 MUTATED C6ORF89 WILD-TYPE 
                6               361 
[1] "VPS13B MUTATION ANALYSIS"
[1] 3
  VPS13B MUTATED VPS13B WILD-TYPE 
              52              315 
  VPS13B MUTATED VPS13B WILD-TYPE 
              52              315 
[1] "C6ORF170 MUTATION ANALYSIS"
[1] 3
  C6ORF170 MUTATED C6ORF170 WILD-TYPE 
                19                348 
  C6ORF170 MUTATED C6ORF170 WILD-TYPE 
                19                348 
[1] "RAB6C MUTATION ANALYSIS"
[1] 3
  RAB6C MUTATED RAB6C WILD-TYPE 
              5             362 
  RAB6C MUTATED RAB6C WILD-TYPE 
              5             362 
[1] "ZNF708 MUTATION ANALYSIS"
[1] 3
  ZNF708 MUTATED ZNF708 WILD-TYPE 
              10              357 
  ZNF708 MUTATED ZNF708 WILD-TYPE 
              10              357 
[1] "CHML MUTATION ANALYSIS"
[1] 3
  CHML MUTATED CHML WILD-TYPE 
            20            347 
  CHML MUTATED CHML WILD-TYPE 
            20            347 
[1] "PHF3 MUTATION ANALYSIS"
[1] 3
  PHF3 MUTATED PHF3 WILD-TYPE 
            23            344 
  PHF3 MUTATED PHF3 WILD-TYPE 
            23            344 
[1] "STAB2 MUTATION ANALYSIS"
[1] 3
  STAB2 MUTATED STAB2 WILD-TYPE 
             32             335 
  STAB2 MUTATED STAB2 WILD-TYPE 
             32             335 
[1] "TRRAP MUTATION ANALYSIS"
[1] 3
  TRRAP MUTATED TRRAP WILD-TYPE 
             48             319 
  TRRAP MUTATED TRRAP WILD-TYPE 
             48             319 
[1] "PRKAA2 MUTATION ANALYSIS"
[1] 3
  PRKAA2 MUTATED PRKAA2 WILD-TYPE 
              12              355 
  PRKAA2 MUTATED PRKAA2 WILD-TYPE 
              12              355 
[1] "KLRC3 MUTATION ANALYSIS"
[1] 3
  KLRC3 MUTATED KLRC3 WILD-TYPE 
              7             360 
  KLRC3 MUTATED KLRC3 WILD-TYPE 
              7             360 
[1] "FLG2 MUTATION ANALYSIS"
[1] 3
  FLG2 MUTATED FLG2 WILD-TYPE 
            28            339 
  FLG2 MUTATED FLG2 WILD-TYPE 
            28            339 
[1] "PPP1R3A MUTATION ANALYSIS"
[1] 3
  PPP1R3A MUTATED PPP1R3A WILD-TYPE 
               32               335 
  PPP1R3A MUTATED PPP1R3A WILD-TYPE 
               32               335 
[1] "GTF3C3 MUTATION ANALYSIS"
[1] 3
  GTF3C3 MUTATED GTF3C3 WILD-TYPE 
              15              352 
  GTF3C3 MUTATED GTF3C3 WILD-TYPE 
              15              352 
[1] "DDX5 MUTATION ANALYSIS"
[1] 3
  DDX5 MUTATED DDX5 WILD-TYPE 
             9            358 
  DDX5 MUTATED DDX5 WILD-TYPE 
             9            358 
[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] "CLVS2 MUTATION ANALYSIS"
[1] 3
  CLVS2 MUTATED CLVS2 WILD-TYPE 
              8             359 
  CLVS2 MUTATED CLVS2 WILD-TYPE 
              8             359 
[1] "MYO3B MUTATION ANALYSIS"
[1] 3
  MYO3B MUTATED MYO3B WILD-TYPE 
             31             336 
  MYO3B MUTATED MYO3B WILD-TYPE 
             31             336 
[1] "CNTNAP5 MUTATION ANALYSIS"
[1] 3
  CNTNAP5 MUTATED CNTNAP5 WILD-TYPE 
               40               327 
  CNTNAP5 MUTATED CNTNAP5 WILD-TYPE 
               40               327 
[1] "TAT MUTATION ANALYSIS"
[1] 3
  TAT MUTATED TAT WILD-TYPE 
           14           353 
  TAT MUTATED TAT WILD-TYPE 
           14           353 
[1] "MUC17 MUTATION ANALYSIS"
[1] 3
  MUC17 MUTATED MUC17 WILD-TYPE 
             46             321 
  MUC17 MUTATED MUC17 WILD-TYPE 
             46             321 
[1] "ATG2B MUTATION ANALYSIS"
[1] 3
  ATG2B MUTATED ATG2B WILD-TYPE 
             15             352 
  ATG2B MUTATED ATG2B WILD-TYPE 
             15             352 
[1] "NTRK3 MUTATION ANALYSIS"
[1] 3
  NTRK3 MUTATED NTRK3 WILD-TYPE 
             25             342 
  NTRK3 MUTATED NTRK3 WILD-TYPE 
             25             342 
[1] "KRT14 MUTATION ANALYSIS"
[1] 3
  KRT14 MUTATED KRT14 WILD-TYPE 
              8             359 
  KRT14 MUTATED KRT14 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] "ODZ1 MUTATION ANALYSIS"
[1] 3
  ODZ1 MUTATED ODZ1 WILD-TYPE 
            61            306 
  ODZ1 MUTATED ODZ1 WILD-TYPE 
            61            306 
[1] "JAK2 MUTATION ANALYSIS"
[1] 3
  JAK2 MUTATED JAK2 WILD-TYPE 
            40            327 
  JAK2 MUTATED JAK2 WILD-TYPE 
            40            327 
[1] "ADAM18 MUTATION ANALYSIS"
[1] 3
  ADAM18 MUTATED ADAM18 WILD-TYPE 
              18              349 
  ADAM18 MUTATED ADAM18 WILD-TYPE 
              18              349 
[1] "PTPN11 MUTATION ANALYSIS"
[1] 3
  PTPN11 MUTATED PTPN11 WILD-TYPE 
              30              337 
  PTPN11 MUTATED PTPN11 WILD-TYPE 
              30              337 
[1] "EGFR MUTATION ANALYSIS"
[1] 3
  EGFR MUTATED EGFR WILD-TYPE 
            74            293 
  EGFR MUTATED EGFR WILD-TYPE 
            74            293 
[1] "EZH2 MUTATION ANALYSIS"
[1] 3
  EZH2 MUTATED EZH2 WILD-TYPE 
            44            323 
  EZH2 MUTATED EZH2 WILD-TYPE 
            44            323 
[1] "EP300 MUTATION ANALYSIS"
[1] 3
  EP300 MUTATED EP300 WILD-TYPE 
             36             331 
  EP300 MUTATED EP300 WILD-TYPE 
             36             331 
[1] "OSBPL11 MUTATION ANALYSIS"
[1] 3
  OSBPL11 MUTATED OSBPL11 WILD-TYPE 
               16               351 
  OSBPL11 MUTATED OSBPL11 WILD-TYPE 
               16               351 
[1] "FBN2 MUTATION ANALYSIS"
[1] 3
  FBN2 MUTATED FBN2 WILD-TYPE 
            42            325 
  FBN2 MUTATED FBN2 WILD-TYPE 
            42            325 
[1] "DKK2 MUTATION ANALYSIS"
[1] 3
  DKK2 MUTATED DKK2 WILD-TYPE 
            23            344 
  DKK2 MUTATED DKK2 WILD-TYPE 
            23            344 
[1] "KIAA1409 MUTATION ANALYSIS"
[1] 3
  KIAA1409 MUTATED KIAA1409 WILD-TYPE 
                39                328 
  KIAA1409 MUTATED KIAA1409 WILD-TYPE 
                39                328 
[1] "SPANXN2 MUTATION ANALYSIS"
[1] 3
  SPANXN2 MUTATED SPANXN2 WILD-TYPE 
                8               359 
  SPANXN2 MUTATED SPANXN2 WILD-TYPE 
                8               359 
[1] "GRM7 MUTATION ANALYSIS"
[1] 3
  GRM7 MUTATED GRM7 WILD-TYPE 
            25            342 
  GRM7 MUTATED GRM7 WILD-TYPE 
            25            342 
[1] "EPHA3 MUTATION ANALYSIS"
[1] 3
  EPHA3 MUTATED EPHA3 WILD-TYPE 
             56             311 
  EPHA3 MUTATED EPHA3 WILD-TYPE 
             56             311 
[1] "KIT MUTATION ANALYSIS"
[1] 3
  KIT MUTATED KIT WILD-TYPE 
           96           271 
  KIT MUTATED KIT WILD-TYPE 
           96           271 
[1] "GRM8 MUTATION ANALYSIS"
[1] 3
  GRM8 MUTATED GRM8 WILD-TYPE 
            21            346 
  GRM8 MUTATED GRM8 WILD-TYPE 
            21            346 
[1] "APOB MUTATION ANALYSIS"
[1] 3
  APOB MUTATED APOB WILD-TYPE 
            54            313 
  APOB MUTATED APOB WILD-TYPE 
            54            313 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
             175              192 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
             175              192 
[1] "MYH1 MUTATION ANALYSIS"
[1] 3
  MYH1 MUTATED MYH1 WILD-TYPE 
            31            336 
  MYH1 MUTATED MYH1 WILD-TYPE 
            31            336 
[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] "AIFM1 MUTATION ANALYSIS"
[1] 3
  AIFM1 MUTATED AIFM1 WILD-TYPE 
             11             356 
  AIFM1 MUTATED AIFM1 WILD-TYPE 
             11             356 
[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] "USH2A MUTATION ANALYSIS"
[1] 3
  USH2A MUTATED USH2A WILD-TYPE 
             74             293 
  USH2A MUTATED USH2A WILD-TYPE 
             74             293 
[1] "SP4 MUTATION ANALYSIS"
[1] 3
  SP4 MUTATED SP4 WILD-TYPE 
           12           355 
  SP4 MUTATED SP4 WILD-TYPE 
           12           355 
[1] "PLEKHA6 MUTATION ANALYSIS"
[1] 3
  PLEKHA6 MUTATED PLEKHA6 WILD-TYPE 
               18               349 
  PLEKHA6 MUTATED PLEKHA6 WILD-TYPE 
               18               349 
[1] "ZBTB7C MUTATION ANALYSIS"
[1] 3
  ZBTB7C MUTATED ZBTB7C WILD-TYPE 
              14              353 
  ZBTB7C MUTATED ZBTB7C WILD-TYPE 
              14              353 
[1] "VCX2 MUTATION ANALYSIS"
[1] 3
  VCX2 MUTATED VCX2 WILD-TYPE 
             7            360 
  VCX2 MUTATED VCX2 WILD-TYPE 
             7            360 
[1] "PAXIP1 MUTATION ANALYSIS"
[1] 3
  PAXIP1 MUTATED PAXIP1 WILD-TYPE 
              16              351 
  PAXIP1 MUTATED PAXIP1 WILD-TYPE 
              16              351 
[1] "AGBL2 MUTATION ANALYSIS"
[1] 3
  AGBL2 MUTATED AGBL2 WILD-TYPE 
             14             353 
  AGBL2 MUTATED AGBL2 WILD-TYPE 
             14             353 
[1] "KAT2B MUTATION ANALYSIS"
[1] 3
  KAT2B MUTATED KAT2B WILD-TYPE 
             15             352 
  KAT2B MUTATED KAT2B WILD-TYPE 
             15             352 
[1] "RIF1 MUTATION ANALYSIS"
[1] 3
  RIF1 MUTATED RIF1 WILD-TYPE 
            35            332 
  RIF1 MUTATED RIF1 WILD-TYPE 
            35            332 
[1] "KDM5C MUTATION ANALYSIS"
[1] 3
  KDM5C MUTATED KDM5C WILD-TYPE 
             21             346 
  KDM5C MUTATED KDM5C WILD-TYPE 
             21             346 
[1] "IL12RB2 MUTATION ANALYSIS"
[1] 3
  IL12RB2 MUTATED IL12RB2 WILD-TYPE 
               14               353 
  IL12RB2 MUTATED IL12RB2 WILD-TYPE 
               14               353 
[1] "SFRS18 MUTATION ANALYSIS"
[1] 3
  SFRS18 MUTATED SFRS18 WILD-TYPE 
              12              355 
  SFRS18 MUTATED SFRS18 WILD-TYPE 
              12              355 
[1] "ALDH2 MUTATION ANALYSIS"
[1] 3
  ALDH2 MUTATED ALDH2 WILD-TYPE 
             11             356 
  ALDH2 MUTATED ALDH2 WILD-TYPE 
             11             356 
[1] "MDH1 MUTATION ANALYSIS"
[1] 3
  MDH1 MUTATED MDH1 WILD-TYPE 
             8            359 
  MDH1 MUTATED MDH1 WILD-TYPE 
             8            359 
[1] "CYLC1 MUTATION ANALYSIS"
[1] 3
  CYLC1 MUTATED CYLC1 WILD-TYPE 
             28             339 
  CYLC1 MUTATED CYLC1 WILD-TYPE 
             28             339 
[1] "KCNS3 MUTATION ANALYSIS"
[1] 3
  KCNS3 MUTATED KCNS3 WILD-TYPE 
             19             348 
  KCNS3 MUTATED KCNS3 WILD-TYPE 
             19             348 
[1] "SOX7 MUTATION ANALYSIS"
[1] 3
  SOX7 MUTATED SOX7 WILD-TYPE 
            11            356 
  SOX7 MUTATED SOX7 WILD-TYPE 
            11            356 
[1] "OVCH1 MUTATION ANALYSIS"
[1] 3
  OVCH1 MUTATED OVCH1 WILD-TYPE 
             22             345 
  OVCH1 MUTATED OVCH1 WILD-TYPE 
             22             345 
[1] "SLC7A10 MUTATION ANALYSIS"
[1] 3
  SLC7A10 MUTATED SLC7A10 WILD-TYPE 
                9               358 
  SLC7A10 MUTATED SLC7A10 WILD-TYPE 
                9               358 
[1] "TMEM37 MUTATION ANALYSIS"
[1] 3
  TMEM37 MUTATED TMEM37 WILD-TYPE 
               8              359 
  TMEM37 MUTATED TMEM37 WILD-TYPE 
               8              359 
[1] "TMEM169 MUTATION ANALYSIS"
[1] 3
  TMEM169 MUTATED TMEM169 WILD-TYPE 
               13               354 
  TMEM169 MUTATED TMEM169 WILD-TYPE 
               13               354 
[1] "RBL2 MUTATION ANALYSIS"
[1] 3
  RBL2 MUTATED RBL2 WILD-TYPE 
            21            346 
  RBL2 MUTATED RBL2 WILD-TYPE 
            21            346 
[1] "DDX17 MUTATION ANALYSIS"
[1] 3
  DDX17 MUTATED DDX17 WILD-TYPE 
             12             355 
  DDX17 MUTATED DDX17 WILD-TYPE 
             12             355 
[1] "DDX3X MUTATION ANALYSIS"
[1] 3
  DDX3X MUTATED DDX3X WILD-TYPE 
             10             357 
  DDX3X MUTATED DDX3X WILD-TYPE 
             10             357 
[1] "HSD17B11 MUTATION ANALYSIS"
[1] 3
  HSD17B11 MUTATED HSD17B11 WILD-TYPE 
                 4                363 
  HSD17B11 MUTATED HSD17B11 WILD-TYPE 
                 4                363 
[1] "HDAC1 MUTATION ANALYSIS"
[1] 3
  HDAC1 MUTATED HDAC1 WILD-TYPE 
              5             362 
  HDAC1 MUTATED HDAC1 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] "TNPO1 MUTATION ANALYSIS"
[1] 3
  TNPO1 MUTATED TNPO1 WILD-TYPE 
             16             351 
  TNPO1 MUTATED TNPO1 WILD-TYPE 
             16             351 
[1] "KIAA1804 MUTATION ANALYSIS"
[1] 3
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                16                351 
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                16                351 
[1] "PARP12 MUTATION ANALYSIS"
[1] 3
  PARP12 MUTATED PARP12 WILD-TYPE 
              10              357 
  PARP12 MUTATED PARP12 WILD-TYPE 
              10              357 
[1] "SCLT1 MUTATION ANALYSIS"
[1] 3
  SCLT1 MUTATED SCLT1 WILD-TYPE 
             18             349 
  SCLT1 MUTATED SCLT1 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] "CCDC160 MUTATION ANALYSIS"
[1] 3
  CCDC160 MUTATED CCDC160 WILD-TYPE 
               10               357 
  CCDC160 MUTATED CCDC160 WILD-TYPE 
               10               357 
[1] "ATAD5 MUTATION ANALYSIS"
[1] 3
  ATAD5 MUTATED ATAD5 WILD-TYPE 
             21             346 
  ATAD5 MUTATED ATAD5 WILD-TYPE 
             21             346 
[1] "PI4K2B MUTATION ANALYSIS"
[1] 3
  PI4K2B MUTATED PI4K2B WILD-TYPE 
              10              357 
  PI4K2B MUTATED PI4K2B WILD-TYPE 
              10              357 
[1] "FGFR3 MUTATION ANALYSIS"
[1] 3
  FGFR3 MUTATED FGFR3 WILD-TYPE 
             22             345 
  FGFR3 MUTATED FGFR3 WILD-TYPE 
             22             345 
[1] "EEA1 MUTATION ANALYSIS"
[1] 3
  EEA1 MUTATED EEA1 WILD-TYPE 
            13            354 
  EEA1 MUTATED EEA1 WILD-TYPE 
            13            354 
[1] "NCOA7 MUTATION ANALYSIS"
[1] 3
  NCOA7 MUTATED NCOA7 WILD-TYPE 
             15             352 
  NCOA7 MUTATED NCOA7 WILD-TYPE 
             15             352 
[1] "EML4 MUTATION ANALYSIS"
[1] 3
  EML4 MUTATED EML4 WILD-TYPE 
            10            357 
  EML4 MUTATED EML4 WILD-TYPE 
            10            357 
[1] "RBPJ MUTATION ANALYSIS"
[1] 3
  RBPJ MUTATED RBPJ WILD-TYPE 
            14            353 
  RBPJ MUTATED RBPJ WILD-TYPE 
            14            353 
[1] "KDM2B MUTATION ANALYSIS"
[1] 3
  KDM2B MUTATED KDM2B WILD-TYPE 
             20             347 
  KDM2B MUTATED KDM2B WILD-TYPE 
             20             347 
[1] "RTP3 MUTATION ANALYSIS"
[1] 3
  RTP3 MUTATED RTP3 WILD-TYPE 
             5            362 
  RTP3 MUTATED RTP3 WILD-TYPE 
             5            362 
[1] "DDX23 MUTATION ANALYSIS"
[1] 3
  DDX23 MUTATED DDX23 WILD-TYPE 
             18             349 
  DDX23 MUTATED DDX23 WILD-TYPE 
             18             349 
[1] "LNX2 MUTATION ANALYSIS"
[1] 3
  LNX2 MUTATED LNX2 WILD-TYPE 
            16            351 
  LNX2 MUTATED LNX2 WILD-TYPE 
            16            351 
[1] "MARK1 MUTATION ANALYSIS"
[1] 3
  MARK1 MUTATED MARK1 WILD-TYPE 
             24             343 
  MARK1 MUTATED MARK1 WILD-TYPE 
             24             343 
[1] "OVGP1 MUTATION ANALYSIS"
[1] 3
  OVGP1 MUTATED OVGP1 WILD-TYPE 
             14             353 
  OVGP1 MUTATED OVGP1 WILD-TYPE 
             14             353 
[1] "ARMC9 MUTATION ANALYSIS"
[1] 3
  ARMC9 MUTATED ARMC9 WILD-TYPE 
              8             359 
  ARMC9 MUTATED ARMC9 WILD-TYPE 
              8             359 
[1] "NUDCD1 MUTATION ANALYSIS"
[1] 3
  NUDCD1 MUTATED NUDCD1 WILD-TYPE 
               9              358 
  NUDCD1 MUTATED NUDCD1 WILD-TYPE 
               9              358 
[1] "ALG2 MUTATION ANALYSIS"
[1] 3
  ALG2 MUTATED ALG2 WILD-TYPE 
             8            359 
  ALG2 MUTATED ALG2 WILD-TYPE 
             8            359 
[1] "ZNF449 MUTATION ANALYSIS"
[1] 3
  ZNF449 MUTATED ZNF449 WILD-TYPE 
              10              357 
  ZNF449 MUTATED ZNF449 WILD-TYPE 
              10              357 
[1] "MAP9 MUTATION ANALYSIS"
[1] 3
  MAP9 MUTATED MAP9 WILD-TYPE 
            16            351 
  MAP9 MUTATED MAP9 WILD-TYPE 
            16            351 
[1] "IRAK3 MUTATION ANALYSIS"
[1] 3
  IRAK3 MUTATED IRAK3 WILD-TYPE 
              9             358 
  IRAK3 MUTATED IRAK3 WILD-TYPE 
              9             358 
[1] "PTPRK MUTATION ANALYSIS"
[1] 3
  PTPRK MUTATED PTPRK WILD-TYPE 
             33             334 
  PTPRK MUTATED PTPRK WILD-TYPE 
             33             334 
[1] "SCLY MUTATION ANALYSIS"
[1] 3
  SCLY MUTATED SCLY WILD-TYPE 
            10            357 
  SCLY MUTATED SCLY WILD-TYPE 
            10            357 
[1] "RBAK MUTATION ANALYSIS"
[1] 3
  RBAK MUTATED RBAK WILD-TYPE 
            17            350 
  RBAK MUTATED RBAK WILD-TYPE 
            17            350 
[1] "ERBB2 MUTATION ANALYSIS"
[1] 3
  ERBB2 MUTATED ERBB2 WILD-TYPE 
             27             340 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
             27             340 
[1] "ALX4 MUTATION ANALYSIS"
[1] 3
  ALX4 MUTATED ALX4 WILD-TYPE 
            11            356 
  ALX4 MUTATED ALX4 WILD-TYPE 
            11            356 
[1] "MEPE MUTATION ANALYSIS"
[1] 3
  MEPE MUTATED MEPE WILD-TYPE 
            15            352 
  MEPE MUTATED MEPE WILD-TYPE 
            15            352 
[1] "ADNP2 MUTATION ANALYSIS"
[1] 3
  ADNP2 MUTATED ADNP2 WILD-TYPE 
             15             352 
  ADNP2 MUTATED ADNP2 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] "KLC4 MUTATION ANALYSIS"
[1] 3
  KLC4 MUTATED KLC4 WILD-TYPE 
            16            351 
  KLC4 MUTATED KLC4 WILD-TYPE 
            16            351 
[1] "RPA3 MUTATION ANALYSIS"
[1] 3
  RPA3 MUTATED RPA3 WILD-TYPE 
             4            363 
  RPA3 MUTATED RPA3 WILD-TYPE 
             4            363 
[1] "RBBP7 MUTATION ANALYSIS"
[1] 3
  RBBP7 MUTATED RBBP7 WILD-TYPE 
             15             352 
  RBBP7 MUTATED RBBP7 WILD-TYPE 
             15             352 
[1] "SYT1 MUTATION ANALYSIS"
[1] 3
  SYT1 MUTATED SYT1 WILD-TYPE 
            13            354 
  SYT1 MUTATED SYT1 WILD-TYPE 
            13            354 
[1] "STRADB MUTATION ANALYSIS"
[1] 3
  STRADB MUTATED STRADB WILD-TYPE 
               5              362 
  STRADB MUTATED STRADB 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] "ENPP1 MUTATION ANALYSIS"
[1] 3
  ENPP1 MUTATED ENPP1 WILD-TYPE 
             14             353 
  ENPP1 MUTATED ENPP1 WILD-TYPE 
             14             353 
[1] "NRK MUTATION ANALYSIS"
[1] 3
  NRK MUTATED NRK WILD-TYPE 
           23           344 
  NRK MUTATED NRK WILD-TYPE 
           23           344 
[1] "ERCC3 MUTATION ANALYSIS"
[1] 3
  ERCC3 MUTATED ERCC3 WILD-TYPE 
             18             349 
  ERCC3 MUTATED ERCC3 WILD-TYPE 
             18             349 
[1] "GABPA MUTATION ANALYSIS"
[1] 3
  GABPA MUTATED GABPA WILD-TYPE 
             11             356 
  GABPA MUTATED GABPA WILD-TYPE 
             11             356 
[1] "CLIP4 MUTATION ANALYSIS"
[1] 3
  CLIP4 MUTATED CLIP4 WILD-TYPE 
             14             353 
  CLIP4 MUTATED CLIP4 WILD-TYPE 
             14             353 
[1] "PLA2G4E MUTATION ANALYSIS"
[1] 3
  PLA2G4E MUTATED PLA2G4E WILD-TYPE 
               10               357 
  PLA2G4E MUTATED PLA2G4E WILD-TYPE 
               10               357 
[1] "CHUK MUTATION ANALYSIS"
[1] 3
  CHUK MUTATED CHUK WILD-TYPE 
            21            346 
  CHUK MUTATED CHUK WILD-TYPE 
            21            346 
[1] "IDH2 MUTATION ANALYSIS"
[1] 3
  IDH2 MUTATED IDH2 WILD-TYPE 
            16            351 
  IDH2 MUTATED IDH2 WILD-TYPE 
            16            351 
[1] "TET3 MUTATION ANALYSIS"
[1] 3
  TET3 MUTATED TET3 WILD-TYPE 
            20            347 
  TET3 MUTATED TET3 WILD-TYPE 
            20            347 
[1] "SCAI MUTATION ANALYSIS"
[1] 3
  SCAI MUTATED SCAI WILD-TYPE 
            15            352 
  SCAI MUTATED SCAI WILD-TYPE 
            15            352 
[1] "EIF2AK4 MUTATION ANALYSIS"
[1] 3
  EIF2AK4 MUTATED EIF2AK4 WILD-TYPE 
               18               349 
  EIF2AK4 MUTATED EIF2AK4 WILD-TYPE 
               18               349 
[1] "UGT3A2 MUTATION ANALYSIS"
[1] 3
  UGT3A2 MUTATED UGT3A2 WILD-TYPE 
              18              349 
  UGT3A2 MUTATED UGT3A2 WILD-TYPE 
              18              349 
[1] "UGT1A7 MUTATION ANALYSIS"
[1] 3
  UGT1A7 MUTATED UGT1A7 WILD-TYPE 
               8              359 
  UGT1A7 MUTATED UGT1A7 WILD-TYPE 
               8              359 
[1] "NOS3 MUTATION ANALYSIS"
[1] 3
  NOS3 MUTATED NOS3 WILD-TYPE 
            19            348 
  NOS3 MUTATED NOS3 WILD-TYPE 
            19            348 
[1] "GPR75 MUTATION ANALYSIS"
[1] 3
  GPR75 MUTATED GPR75 WILD-TYPE 
              8             359 
  GPR75 MUTATED GPR75 WILD-TYPE 
              8             359 
[1] "FRS3 MUTATION ANALYSIS"
[1] 3
  FRS3 MUTATED FRS3 WILD-TYPE 
            10            357 
  FRS3 MUTATED FRS3 WILD-TYPE 
            10            357 
[1] "CDC42BPA MUTATION ANALYSIS"
[1] 3
  CDC42BPA MUTATED CDC42BPA WILD-TYPE 
                29                338 
  CDC42BPA MUTATED CDC42BPA WILD-TYPE 
                29                338 
[1] "KIAA0195 MUTATION ANALYSIS"
[1] 3
  KIAA0195 MUTATED KIAA0195 WILD-TYPE 
                17                350 
  KIAA0195 MUTATED KIAA0195 WILD-TYPE 
                17                350 
[1] "INPP1 MUTATION ANALYSIS"
[1] 3
  INPP1 MUTATED INPP1 WILD-TYPE 
              7             360 
  INPP1 MUTATED INPP1 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] "CDKL2 MUTATION ANALYSIS"
[1] 3
  CDKL2 MUTATED CDKL2 WILD-TYPE 
             11             356 
  CDKL2 MUTATED CDKL2 WILD-TYPE 
             11             356 
[1] "EXOC4 MUTATION ANALYSIS"
[1] 3
  EXOC4 MUTATED EXOC4 WILD-TYPE 
             18             349 
  EXOC4 MUTATED EXOC4 WILD-TYPE 
             18             349 
[1] "C5ORF22 MUTATION ANALYSIS"
[1] 3
  C5ORF22 MUTATED C5ORF22 WILD-TYPE 
               11               356 
  C5ORF22 MUTATED C5ORF22 WILD-TYPE 
               11               356 
[1] "MMP12 MUTATION ANALYSIS"
[1] 3
  MMP12 MUTATED MMP12 WILD-TYPE 
              8             359 
  MMP12 MUTATED MMP12 WILD-TYPE 
              8             359 
[1] "PAK3 MUTATION ANALYSIS"
[1] 3
  PAK3 MUTATED PAK3 WILD-TYPE 
            17            350 
  PAK3 MUTATED PAK3 WILD-TYPE 
            17            350 
[1] "ZFC3H1 MUTATION ANALYSIS"
[1] 3
  ZFC3H1 MUTATED ZFC3H1 WILD-TYPE 
              19              348 
  ZFC3H1 MUTATED ZFC3H1 WILD-TYPE 
              19              348 
[1] "ZNF547 MUTATION ANALYSIS"
[1] 3
  ZNF547 MUTATED ZNF547 WILD-TYPE 
               8              359 
  ZNF547 MUTATED ZNF547 WILD-TYPE 
               8              359 
[1] "RUFY1 MUTATION ANALYSIS"
[1] 3
  RUFY1 MUTATED RUFY1 WILD-TYPE 
             13             354 
  RUFY1 MUTATED RUFY1 WILD-TYPE 
             13             354 
[1] "THRAP3 MUTATION ANALYSIS"
[1] 3
  THRAP3 MUTATED THRAP3 WILD-TYPE 
              11              356 
  THRAP3 MUTATED THRAP3 WILD-TYPE 
              11              356 
[1] "FAHD2A MUTATION ANALYSIS"
[1] 3
  FAHD2A MUTATED FAHD2A WILD-TYPE 
               6              361 
  FAHD2A MUTATED FAHD2A WILD-TYPE 
               6              361 
[1] "ARFIP1 MUTATION ANALYSIS"
[1] 3
  ARFIP1 MUTATED ARFIP1 WILD-TYPE 
              12              355 
  ARFIP1 MUTATED ARFIP1 WILD-TYPE 
              12              355 
[1] "HM13 MUTATION ANALYSIS"
[1] 3
  HM13 MUTATED HM13 WILD-TYPE 
             5            362 
  HM13 MUTATED HM13 WILD-TYPE 
             5            362 
[1] "WBP11 MUTATION ANALYSIS"
[1] 3
  WBP11 MUTATED WBP11 WILD-TYPE 
              8             359 
  WBP11 MUTATED WBP11 WILD-TYPE 
              8             359 
[1] "RCSD1 MUTATION ANALYSIS"
[1] 3
  RCSD1 MUTATED RCSD1 WILD-TYPE 
             14             353 
  RCSD1 MUTATED RCSD1 WILD-TYPE 
             14             353 
[1] "EAPP MUTATION ANALYSIS"
[1] 3
  EAPP MUTATED EAPP WILD-TYPE 
             4            363 
  EAPP MUTATED EAPP WILD-TYPE 
             4            363 
[1] "NLK MUTATION ANALYSIS"
[1] 3
  NLK MUTATED NLK WILD-TYPE 
           11           356 
  NLK MUTATED NLK WILD-TYPE 
           11           356 
[1] "HERC5 MUTATION ANALYSIS"
[1] 3
  HERC5 MUTATED HERC5 WILD-TYPE 
             18             349 
  HERC5 MUTATED HERC5 WILD-TYPE 
             18             349 
[1] "POLM MUTATION ANALYSIS"
[1] 3
  POLM MUTATED POLM WILD-TYPE 
            11            356 
  POLM MUTATED POLM WILD-TYPE 
            11            356 
[1] "CYP1B1 MUTATION ANALYSIS"
[1] 3
  CYP1B1 MUTATED CYP1B1 WILD-TYPE 
              11              356 
  CYP1B1 MUTATED CYP1B1 WILD-TYPE 
              11              356 
[1] "PNPLA8 MUTATION ANALYSIS"
[1] 3
  PNPLA8 MUTATED PNPLA8 WILD-TYPE 
              18              349 
  PNPLA8 MUTATED PNPLA8 WILD-TYPE 
              18              349 
[1] "DOCK5 MUTATION ANALYSIS"
[1] 3
  DOCK5 MUTATED DOCK5 WILD-TYPE 
             26             341 
  DOCK5 MUTATED DOCK5 WILD-TYPE 
             26             341 
[1] "CUL2 MUTATION ANALYSIS"
[1] 3
  CUL2 MUTATED CUL2 WILD-TYPE 
            14            353 
  CUL2 MUTATED CUL2 WILD-TYPE 
            14            353 
[1] "MTMR8 MUTATION ANALYSIS"
[1] 3
  MTMR8 MUTATED MTMR8 WILD-TYPE 
             11             356 
  MTMR8 MUTATED MTMR8 WILD-TYPE 
             11             356 
[1] "CREBBP MUTATION ANALYSIS"
[1] 3
  CREBBP MUTATED CREBBP WILD-TYPE 
              60              307 
  CREBBP MUTATED CREBBP WILD-TYPE 
              60              307 
[1] "ETF1 MUTATION ANALYSIS"
[1] 3
  ETF1 MUTATED ETF1 WILD-TYPE 
            10            357 
  ETF1 MUTATED ETF1 WILD-TYPE 
            10            357 
[1] "RBM12 MUTATION ANALYSIS"
[1] 3
  RBM12 MUTATED RBM12 WILD-TYPE 
             12             355 
  RBM12 MUTATED RBM12 WILD-TYPE 
             12             355 
[1] "HORMAD1 MUTATION ANALYSIS"
[1] 3
  HORMAD1 MUTATED HORMAD1 WILD-TYPE 
               14               353 
  HORMAD1 MUTATED HORMAD1 WILD-TYPE 
               14               353 
[1] "LRRC39 MUTATION ANALYSIS"
[1] 3
  LRRC39 MUTATED LRRC39 WILD-TYPE 
               8              359 
  LRRC39 MUTATED LRRC39 WILD-TYPE 
               8              359 
[1] "PLK2 MUTATION ANALYSIS"
[1] 3
  PLK2 MUTATED PLK2 WILD-TYPE 
             6            361 
  PLK2 MUTATED PLK2 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] "OLR1 MUTATION ANALYSIS"
[1] 3
  OLR1 MUTATED OLR1 WILD-TYPE 
             9            358 
  OLR1 MUTATED OLR1 WILD-TYPE 
             9            358 
[1] "OR5B2 MUTATION ANALYSIS"
[1] 3
  OR5B2 MUTATED OR5B2 WILD-TYPE 
             12             355 
  OR5B2 MUTATED OR5B2 WILD-TYPE 
             12             355 
[1] "GCNT2 MUTATION ANALYSIS"
[1] 3
  GCNT2 MUTATED GCNT2 WILD-TYPE 
             22             345 
  GCNT2 MUTATED GCNT2 WILD-TYPE 
             22             345 
[1] "SKIV2L MUTATION ANALYSIS"
[1] 3
  SKIV2L MUTATED SKIV2L WILD-TYPE 
              12              355 
  SKIV2L MUTATED SKIV2L WILD-TYPE 
              12              355 
[1] "LAMC1 MUTATION ANALYSIS"
[1] 3
  LAMC1 MUTATED LAMC1 WILD-TYPE 
             21             346 
  LAMC1 MUTATED LAMC1 WILD-TYPE 
             21             346 
[1] "THAP9 MUTATION ANALYSIS"
[1] 3
  THAP9 MUTATED THAP9 WILD-TYPE 
             12             355 
  THAP9 MUTATED THAP9 WILD-TYPE 
             12             355 
[1] "LPCAT3 MUTATION ANALYSIS"
[1] 3
  LPCAT3 MUTATED LPCAT3 WILD-TYPE 
               5              362 
  LPCAT3 MUTATED LPCAT3 WILD-TYPE 
               5              362 
[1] "SLC22A9 MUTATION ANALYSIS"
[1] 3
  SLC22A9 MUTATED SLC22A9 WILD-TYPE 
                9               358 
  SLC22A9 MUTATED SLC22A9 WILD-TYPE 
                9               358 
[1] "RAB38 MUTATION ANALYSIS"
[1] 3
  RAB38 MUTATED RAB38 WILD-TYPE 
              5             362 
  RAB38 MUTATED RAB38 WILD-TYPE 
              5             362 
[1] "ENPEP MUTATION ANALYSIS"
[1] 3
  ENPEP MUTATED ENPEP WILD-TYPE 
             21             346 
  ENPEP MUTATED ENPEP WILD-TYPE 
             21             346 
[1] "AGFG1 MUTATION ANALYSIS"
[1] 3
  AGFG1 MUTATED AGFG1 WILD-TYPE 
             15             352 
  AGFG1 MUTATED AGFG1 WILD-TYPE 
             15             352 
[1] "KDM3B MUTATION ANALYSIS"
[1] 3
  KDM3B MUTATED KDM3B WILD-TYPE 
             32             335 
  KDM3B MUTATED KDM3B WILD-TYPE 
             32             335 
[1] "GAB1 MUTATION ANALYSIS"
[1] 3
  GAB1 MUTATED GAB1 WILD-TYPE 
            15            352 
  GAB1 MUTATED GAB1 WILD-TYPE 
            15            352 
[1] "ADK MUTATION ANALYSIS"
[1] 3
  ADK MUTATED ADK WILD-TYPE 
            7           360 
  ADK MUTATED ADK 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] "BRE MUTATION ANALYSIS"
[1] 3
  BRE MUTATED BRE WILD-TYPE 
           11           356 
  BRE MUTATED BRE WILD-TYPE 
           11           356 
[1] "AMOT MUTATION ANALYSIS"
[1] 3
  AMOT MUTATED AMOT WILD-TYPE 
            13            354 
  AMOT MUTATED AMOT WILD-TYPE 
            13            354 
[1] "HFE2 MUTATION ANALYSIS"
[1] 3
  HFE2 MUTATED HFE2 WILD-TYPE 
             8            359 
  HFE2 MUTATED HFE2 WILD-TYPE 
             8            359 
[1] "SPCS2 MUTATION ANALYSIS"
[1] 3
  SPCS2 MUTATED SPCS2 WILD-TYPE 
              5             362 
  SPCS2 MUTATED SPCS2 WILD-TYPE 
              5             362 
[1] "GPR22 MUTATION ANALYSIS"
[1] 3
  GPR22 MUTATED GPR22 WILD-TYPE 
              9             358 
  GPR22 MUTATED GPR22 WILD-TYPE 
              9             358 
[1] "GPR115 MUTATION ANALYSIS"
[1] 3
  GPR115 MUTATED GPR115 WILD-TYPE 
              18              349 
  GPR115 MUTATED GPR115 WILD-TYPE 
              18              349 
[1] "KIAA0319L MUTATION ANALYSIS"
[1] 3
  KIAA0319L MUTATED KIAA0319L WILD-TYPE 
                 19                 348 
  KIAA0319L MUTATED KIAA0319L WILD-TYPE 
                 19                 348 
[1] "ZKSCAN2 MUTATION ANALYSIS"
[1] 3
  ZKSCAN2 MUTATED ZKSCAN2 WILD-TYPE 
               13               354 
  ZKSCAN2 MUTATED ZKSCAN2 WILD-TYPE 
               13               354 
[1] "PNP MUTATION ANALYSIS"
[1] 3
  PNP MUTATED PNP WILD-TYPE 
            4           363 
  PNP MUTATED PNP WILD-TYPE 
            4           363 
[1] "DSG1 MUTATION ANALYSIS"
[1] 3
  DSG1 MUTATED DSG1 WILD-TYPE 
            18            349 
  DSG1 MUTATED DSG1 WILD-TYPE 
            18            349 
[1] "ENTPD4 MUTATION ANALYSIS"
[1] 3
  ENTPD4 MUTATED ENTPD4 WILD-TYPE 
              17              350 
  ENTPD4 MUTATED ENTPD4 WILD-TYPE 
              17              350 
[1] "ATP6V1D MUTATION ANALYSIS"
[1] 3
  ATP6V1D MUTATED ATP6V1D WILD-TYPE 
                5               362 
  ATP6V1D MUTATED ATP6V1D WILD-TYPE 
                5               362 
[1] "ACTL8 MUTATION ANALYSIS"
[1] 3
  ACTL8 MUTATED ACTL8 WILD-TYPE 
              9             358 
  ACTL8 MUTATED ACTL8 WILD-TYPE 
              9             358 
[1] "MMP13 MUTATION ANALYSIS"
[1] 3
  MMP13 MUTATED MMP13 WILD-TYPE 
             13             354 
  MMP13 MUTATED MMP13 WILD-TYPE 
             13             354 
[1] "SPAST MUTATION ANALYSIS"
[1] 3
  SPAST MUTATED SPAST WILD-TYPE 
              8             359 
  SPAST MUTATED SPAST WILD-TYPE 
              8             359 
[1] "ZNF518B MUTATION ANALYSIS"
[1] 3
  ZNF518B MUTATED ZNF518B WILD-TYPE 
               10               357 
  ZNF518B MUTATED ZNF518B WILD-TYPE 
               10               357 
[1] "DSG4 MUTATION ANALYSIS"
[1] 3
  DSG4 MUTATED DSG4 WILD-TYPE 
            21            346 
  DSG4 MUTATED DSG4 WILD-TYPE 
            21            346 
[1] "NOVA1 MUTATION ANALYSIS"
[1] 3
  NOVA1 MUTATED NOVA1 WILD-TYPE 
             14             353 
  NOVA1 MUTATED NOVA1 WILD-TYPE 
             14             353 
[1] "OR6C75 MUTATION ANALYSIS"
[1] 3
  OR6C75 MUTATED OR6C75 WILD-TYPE 
               7              360 
  OR6C75 MUTATED OR6C75 WILD-TYPE 
               7              360 
[1] "CYP2C18 MUTATION ANALYSIS"
[1] 3
  CYP2C18 MUTATED CYP2C18 WILD-TYPE 
                5               362 
  CYP2C18 MUTATED CYP2C18 WILD-TYPE 
                5               362 
[1] "NCR3 MUTATION ANALYSIS"
[1] 3
  NCR3 MUTATED NCR3 WILD-TYPE 
             6            361 
  NCR3 MUTATED NCR3 WILD-TYPE 
             6            361 
[1] "IQSEC2 MUTATION ANALYSIS"
[1] 3
  IQSEC2 MUTATED IQSEC2 WILD-TYPE 
              16              351 
  IQSEC2 MUTATED IQSEC2 WILD-TYPE 
              16              351 
[1] "DBN1 MUTATION ANALYSIS"
[1] 3
  DBN1 MUTATED DBN1 WILD-TYPE 
            10            357 
  DBN1 MUTATED DBN1 WILD-TYPE 
            10            357 
[1] "TJP1 MUTATION ANALYSIS"
[1] 3
  TJP1 MUTATED TJP1 WILD-TYPE 
            18            349 
  TJP1 MUTATED TJP1 WILD-TYPE 
            18            349 
[1] "ACTL6A MUTATION ANALYSIS"
[1] 3
  ACTL6A MUTATED ACTL6A WILD-TYPE 
               6              361 
  ACTL6A MUTATED ACTL6A WILD-TYPE 
               6              361 
[1] "WT1 MUTATION ANALYSIS"
[1] 3
  WT1 MUTATED WT1 WILD-TYPE 
           26           341 
  WT1 MUTATED WT1 WILD-TYPE 
           26           341 
[1] "ADAMTS4 MUTATION ANALYSIS"
[1] 3
  ADAMTS4 MUTATED ADAMTS4 WILD-TYPE 
               14               353 
  ADAMTS4 MUTATED ADAMTS4 WILD-TYPE 
               14               353 
[1] "JMJD1C MUTATION ANALYSIS"
[1] 3
  JMJD1C MUTATED JMJD1C WILD-TYPE 
              24              343 
  JMJD1C MUTATED JMJD1C WILD-TYPE 
              24              343 
[1] "ERBB2IP MUTATION ANALYSIS"
[1] 3
  ERBB2IP MUTATED ERBB2IP WILD-TYPE 
               15               352 
  ERBB2IP MUTATED ERBB2IP WILD-TYPE 
               15               352 
[1] "ING2 MUTATION ANALYSIS"
[1] 3
  ING2 MUTATED ING2 WILD-TYPE 
             6            361 
  ING2 MUTATED ING2 WILD-TYPE 
             6            361 
[1] "OR4M2 MUTATION ANALYSIS"
[1] 3
  OR4M2 MUTATED OR4M2 WILD-TYPE 
             14             353 
  OR4M2 MUTATED OR4M2 WILD-TYPE 
             14             353 
[1] "ARHGEF10 MUTATION ANALYSIS"
[1] 3
  ARHGEF10 MUTATED ARHGEF10 WILD-TYPE 
                23                344 
  ARHGEF10 MUTATED ARHGEF10 WILD-TYPE 
                23                344 
[1] "MUC7 MUTATION ANALYSIS"
[1] 3
  MUC7 MUTATED MUC7 WILD-TYPE 
             9            358 
  MUC7 MUTATED MUC7 WILD-TYPE 
             9            358 
[1] "EIF2B5 MUTATION ANALYSIS"
[1] 3
  EIF2B5 MUTATED EIF2B5 WILD-TYPE 
              14              353 
  EIF2B5 MUTATED EIF2B5 WILD-TYPE 
              14              353 
[1] "LMTK3 MUTATION ANALYSIS"
[1] 3
  LMTK3 MUTATED LMTK3 WILD-TYPE 
             15             352 
  LMTK3 MUTATED LMTK3 WILD-TYPE 
             15             352 
[1] "MAPK9 MUTATION ANALYSIS"
[1] 3
  MAPK9 MUTATED MAPK9 WILD-TYPE 
             10             357 
  MAPK9 MUTATED MAPK9 WILD-TYPE 
             10             357 
[1] "LBP MUTATION ANALYSIS"
[1] 3
  LBP MUTATED LBP WILD-TYPE 
            7           360 
  LBP MUTATED LBP 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] "FAM160B1 MUTATION ANALYSIS"
[1] 3
  FAM160B1 MUTATED FAM160B1 WILD-TYPE 
                 7                360 
  FAM160B1 MUTATED FAM160B1 WILD-TYPE 
                 7                360 
[1] "NCOA6 MUTATION ANALYSIS"
[1] 3
  NCOA6 MUTATED NCOA6 WILD-TYPE 
             24             343 
  NCOA6 MUTATED NCOA6 WILD-TYPE 
             24             343 
[1] "FUBP3 MUTATION ANALYSIS"
[1] 3
  FUBP3 MUTATED FUBP3 WILD-TYPE 
              9             358 
  FUBP3 MUTATED FUBP3 WILD-TYPE 
              9             358 
[1] "YSK4 MUTATION ANALYSIS"
[1] 3
  YSK4 MUTATED YSK4 WILD-TYPE 
            26            341 
  YSK4 MUTATED YSK4 WILD-TYPE 
            26            341 
[1] "CCAR1 MUTATION ANALYSIS"
[1] 3
  CCAR1 MUTATED CCAR1 WILD-TYPE 
             18             349 
  CCAR1 MUTATED CCAR1 WILD-TYPE 
             18             349 
[1] "HRSP12 MUTATION ANALYSIS"
[1] 3
  HRSP12 MUTATED HRSP12 WILD-TYPE 
               6              361 
  HRSP12 MUTATED HRSP12 WILD-TYPE 
               6              361 
[1] "MCCC1 MUTATION ANALYSIS"
[1] 3
  MCCC1 MUTATED MCCC1 WILD-TYPE 
             17             350 
  MCCC1 MUTATED MCCC1 WILD-TYPE 
             17             350 
[1] "PCDH12 MUTATION ANALYSIS"
[1] 3
  PCDH12 MUTATED PCDH12 WILD-TYPE 
              17              350 
  PCDH12 MUTATED PCDH12 WILD-TYPE 
              17              350 
[1] "CCR2 MUTATION ANALYSIS"
[1] 3
  CCR2 MUTATED CCR2 WILD-TYPE 
             7            360 
  CCR2 MUTATED CCR2 WILD-TYPE 
             7            360 
[1] "G3BP2 MUTATION ANALYSIS"
[1] 3
  G3BP2 MUTATED G3BP2 WILD-TYPE 
              9             358 
  G3BP2 MUTATED G3BP2 WILD-TYPE 
              9             358 
[1] "MOV10L1 MUTATION ANALYSIS"
[1] 3
  MOV10L1 MUTATED MOV10L1 WILD-TYPE 
               15               352 
  MOV10L1 MUTATED MOV10L1 WILD-TYPE 
               15               352 
[1] "MRAS MUTATION ANALYSIS"
[1] 3
  MRAS MUTATED MRAS WILD-TYPE 
             4            363 
  MRAS MUTATED MRAS WILD-TYPE 
             4            363 
[1] "KIFAP3 MUTATION ANALYSIS"
[1] 3
  KIFAP3 MUTATED KIFAP3 WILD-TYPE 
               9              358 
  KIFAP3 MUTATED KIFAP3 WILD-TYPE 
               9              358 
[1] "BCL9L MUTATION ANALYSIS"
[1] 3
  BCL9L MUTATED BCL9L WILD-TYPE 
             19             348 
  BCL9L MUTATED BCL9L WILD-TYPE 
             19             348 
[1] "EFHC1 MUTATION ANALYSIS"
[1] 3
  EFHC1 MUTATED EFHC1 WILD-TYPE 
             11             356 
  EFHC1 MUTATED EFHC1 WILD-TYPE 
             11             356 
[1] "RAB40C MUTATION ANALYSIS"
[1] 3
  RAB40C MUTATED RAB40C WILD-TYPE 
               8              359 
  RAB40C MUTATED RAB40C WILD-TYPE 
               8              359 
[1] "CIC MUTATION ANALYSIS"
[1] 3
  CIC MUTATED CIC WILD-TYPE 
           23           344 
  CIC MUTATED CIC WILD-TYPE 
           23           344 
[1] "TNFAIP3 MUTATION ANALYSIS"
[1] 3
  TNFAIP3 MUTATED TNFAIP3 WILD-TYPE 
               34               333 
  TNFAIP3 MUTATED TNFAIP3 WILD-TYPE 
               34               333 
[1] "MCART1 MUTATION ANALYSIS"
[1] 3
  MCART1 MUTATED MCART1 WILD-TYPE 
              12              355 
  MCART1 MUTATED MCART1 WILD-TYPE 
              12              355 
[1] "MYH3 MUTATION ANALYSIS"
[1] 3
  MYH3 MUTATED MYH3 WILD-TYPE 
            32            335 
  MYH3 MUTATED MYH3 WILD-TYPE 
            32            335 
[1] "DENND4A MUTATION ANALYSIS"
[1] 3
  DENND4A MUTATED DENND4A WILD-TYPE 
               23               344 
  DENND4A MUTATED DENND4A WILD-TYPE 
               23               344 
[1] "SERPINA9 MUTATION ANALYSIS"
[1] 3
  SERPINA9 MUTATED SERPINA9 WILD-TYPE 
                10                357 
  SERPINA9 MUTATED SERPINA9 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] "SP110 MUTATION ANALYSIS"
[1] 3
  SP110 MUTATED SP110 WILD-TYPE 
             10             357 
  SP110 MUTATED SP110 WILD-TYPE 
             10             357 
[1] "FIGNL1 MUTATION ANALYSIS"
[1] 3
  FIGNL1 MUTATED FIGNL1 WILD-TYPE 
              16              351 
  FIGNL1 MUTATED FIGNL1 WILD-TYPE 
              16              351 
[1] "WDR66 MUTATION ANALYSIS"
[1] 3
  WDR66 MUTATED WDR66 WILD-TYPE 
             19             348 
  WDR66 MUTATED WDR66 WILD-TYPE 
             19             348 
[1] "POLD3 MUTATION ANALYSIS"
[1] 3
  POLD3 MUTATED POLD3 WILD-TYPE 
             11             356 
  POLD3 MUTATED POLD3 WILD-TYPE 
             11             356 
[1] "LEF1 MUTATION ANALYSIS"
[1] 3
  LEF1 MUTATED LEF1 WILD-TYPE 
             9            358 
  LEF1 MUTATED LEF1 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] "MRE11A MUTATION ANALYSIS"
[1] 3
  MRE11A MUTATED MRE11A WILD-TYPE 
              12              355 
  MRE11A MUTATED MRE11A 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] "NOX5 MUTATION ANALYSIS"
[1] 3
  NOX5 MUTATED NOX5 WILD-TYPE 
             5            362 
  NOX5 MUTATED NOX5 WILD-TYPE 
             5            362 
[1] "FAS MUTATION ANALYSIS"
[1] 3
  FAS MUTATED FAS WILD-TYPE 
            7           360 
  FAS MUTATED FAS WILD-TYPE 
            7           360 
[1] "OR2V2 MUTATION ANALYSIS"
[1] 3
  OR2V2 MUTATED OR2V2 WILD-TYPE 
              6             361 
  OR2V2 MUTATED OR2V2 WILD-TYPE 
              6             361 
[1] "IGF2R MUTATION ANALYSIS"
[1] 3
  IGF2R MUTATED IGF2R WILD-TYPE 
             35             332 
  IGF2R MUTATED IGF2R WILD-TYPE 
             35             332 
[1] "ZNF180 MUTATION ANALYSIS"
[1] 3
  ZNF180 MUTATED ZNF180 WILD-TYPE 
              14              353 
  ZNF180 MUTATED ZNF180 WILD-TYPE 
              14              353 
[1] "ULK1 MUTATION ANALYSIS"
[1] 3
  ULK1 MUTATED ULK1 WILD-TYPE 
            10            357 
  ULK1 MUTATED ULK1 WILD-TYPE 
            10            357 
[1] "FAM163B MUTATION ANALYSIS"
[1] 3
  FAM163B MUTATED FAM163B WILD-TYPE 
                4               363 
  FAM163B MUTATED FAM163B WILD-TYPE 
                4               363 
[1] "PHF21A MUTATION ANALYSIS"
[1] 3
  PHF21A MUTATED PHF21A WILD-TYPE 
              11              356 
  PHF21A MUTATED PHF21A WILD-TYPE 
              11              356 
[1] "NFASC MUTATION ANALYSIS"
[1] 3
  NFASC MUTATED NFASC WILD-TYPE 
             32             335 
  NFASC MUTATED NFASC WILD-TYPE 
             32             335 
[1] "DDX59 MUTATION ANALYSIS"
[1] 3
  DDX59 MUTATED DDX59 WILD-TYPE 
             11             356 
  DDX59 MUTATED DDX59 WILD-TYPE 
             11             356 
[1] "PTPRC MUTATION ANALYSIS"
[1] 3
  PTPRC MUTATED PTPRC WILD-TYPE 
             25             342 
  PTPRC MUTATED PTPRC WILD-TYPE 
             25             342 
[1] "EFEMP1 MUTATION ANALYSIS"
[1] 3
  EFEMP1 MUTATED EFEMP1 WILD-TYPE 
              20              347 
  EFEMP1 MUTATED EFEMP1 WILD-TYPE 
              20              347 
[1] "KCTD16 MUTATION ANALYSIS"
[1] 3
  KCTD16 MUTATED KCTD16 WILD-TYPE 
              12              355 
  KCTD16 MUTATED KCTD16 WILD-TYPE 
              12              355 
[1] "HNRNPH3 MUTATION ANALYSIS"
[1] 3
  HNRNPH3 MUTATED HNRNPH3 WILD-TYPE 
                9               358 
  HNRNPH3 MUTATED HNRNPH3 WILD-TYPE 
                9               358 
[1] "OAS1 MUTATION ANALYSIS"
[1] 3
  OAS1 MUTATED OAS1 WILD-TYPE 
             8            359 
  OAS1 MUTATED OAS1 WILD-TYPE 
             8            359 
[1] "OTX2 MUTATION ANALYSIS"
[1] 3
  OTX2 MUTATED OTX2 WILD-TYPE 
             6            361 
  OTX2 MUTATED OTX2 WILD-TYPE 
             6            361 
[1] "PAAF1 MUTATION ANALYSIS"
[1] 3
  PAAF1 MUTATED PAAF1 WILD-TYPE 
              5             362 
  PAAF1 MUTATED PAAF1 WILD-TYPE 
              5             362 
[1] "AGTR2 MUTATION ANALYSIS"
[1] 3
  AGTR2 MUTATED AGTR2 WILD-TYPE 
             15             352 
  AGTR2 MUTATED AGTR2 WILD-TYPE 
             15             352 
[1] "GAB2 MUTATION ANALYSIS"
[1] 3
  GAB2 MUTATED GAB2 WILD-TYPE 
             9            358 
  GAB2 MUTATED GAB2 WILD-TYPE 
             9            358 
[1] "SMTN MUTATION ANALYSIS"
[1] 3
  SMTN MUTATED SMTN WILD-TYPE 
            14            353 
  SMTN MUTATED SMTN WILD-TYPE 
            14            353 
[1] "ERBB4 MUTATION ANALYSIS"
[1] 3
  ERBB4 MUTATED ERBB4 WILD-TYPE 
             47             320 
  ERBB4 MUTATED ERBB4 WILD-TYPE 
             47             320 
[1] "POMGNT1 MUTATION ANALYSIS"
[1] 3
  POMGNT1 MUTATED POMGNT1 WILD-TYPE 
                8               359 
  POMGNT1 MUTATED POMGNT1 WILD-TYPE 
                8               359 
[1] "DHX35 MUTATION ANALYSIS"
[1] 3
  DHX35 MUTATED DHX35 WILD-TYPE 
             11             356 
  DHX35 MUTATED DHX35 WILD-TYPE 
             11             356 
[1] "PLEK MUTATION ANALYSIS"
[1] 3
  PLEK MUTATED PLEK WILD-TYPE 
            12            355 
  PLEK MUTATED PLEK WILD-TYPE 
            12            355 
[1] "BMPR1A MUTATION ANALYSIS"
[1] 3
  BMPR1A MUTATED BMPR1A WILD-TYPE 
              18              349 
  BMPR1A MUTATED BMPR1A WILD-TYPE 
              18              349 
[1] "RING1 MUTATION ANALYSIS"
[1] 3
  RING1 MUTATED RING1 WILD-TYPE 
             10             357 
  RING1 MUTATED RING1 WILD-TYPE 
             10             357 
[1] "C17ORF47 MUTATION ANALYSIS"
[1] 3
  C17ORF47 MUTATED C17ORF47 WILD-TYPE 
                 5                362 
  C17ORF47 MUTATED C17ORF47 WILD-TYPE 
                 5                362 
[1] "PALLD MUTATION ANALYSIS"
[1] 3
  PALLD MUTATED PALLD WILD-TYPE 
              9             358 
  PALLD MUTATED PALLD WILD-TYPE 
              9             358 
[1] "AFM MUTATION ANALYSIS"
[1] 3
  AFM MUTATED AFM WILD-TYPE 
           13           354 
  AFM MUTATED AFM WILD-TYPE 
           13           354 
[1] "C1ORF168 MUTATION ANALYSIS"
[1] 3
  C1ORF168 MUTATED C1ORF168 WILD-TYPE 
                14                353 
  C1ORF168 MUTATED C1ORF168 WILD-TYPE 
                14                353 
[1] "ZC3H13 MUTATION ANALYSIS"
[1] 3
  ZC3H13 MUTATED ZC3H13 WILD-TYPE 
              34              333 
  ZC3H13 MUTATED ZC3H13 WILD-TYPE 
              34              333 
[1] "HUWE1 MUTATION ANALYSIS"
[1] 3
  HUWE1 MUTATED HUWE1 WILD-TYPE 
             42             325 
  HUWE1 MUTATED HUWE1 WILD-TYPE 
             42             325 
[1] "SLC26A8 MUTATION ANALYSIS"
[1] 3
  SLC26A8 MUTATED SLC26A8 WILD-TYPE 
               15               352 
  SLC26A8 MUTATED SLC26A8 WILD-TYPE 
               15               352 
[1] "OR4E2 MUTATION ANALYSIS"
[1] 3
  OR4E2 MUTATED OR4E2 WILD-TYPE 
              5             362 
  OR4E2 MUTATED OR4E2 WILD-TYPE 
              5             362 
[1] "ARHGAP25 MUTATION ANALYSIS"
[1] 3
  ARHGAP25 MUTATED ARHGAP25 WILD-TYPE 
                10                357 
  ARHGAP25 MUTATED ARHGAP25 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] "CPZ MUTATION ANALYSIS"
[1] 3
  CPZ MUTATED CPZ WILD-TYPE 
           15           352 
  CPZ MUTATED CPZ WILD-TYPE 
           15           352 
[1] "CD3D MUTATION ANALYSIS"
[1] 3
  CD3D MUTATED CD3D WILD-TYPE 
             4            363 
  CD3D MUTATED CD3D WILD-TYPE 
             4            363 
[1] "OR2T33 MUTATION ANALYSIS"
[1] 3
  OR2T33 MUTATED OR2T33 WILD-TYPE 
              16              351 
  OR2T33 MUTATED OR2T33 WILD-TYPE 
              16              351 
[1] "PTPN3 MUTATION ANALYSIS"
[1] 3
  PTPN3 MUTATED PTPN3 WILD-TYPE 
             15             352 
  PTPN3 MUTATED PTPN3 WILD-TYPE 
             15             352 
[1] "ACVR2A MUTATION ANALYSIS"
[1] 3
  ACVR2A MUTATED ACVR2A WILD-TYPE 
              17              350 
  ACVR2A MUTATED ACVR2A WILD-TYPE 
              17              350 
[1] "MAP7D1 MUTATION ANALYSIS"
[1] 3
  MAP7D1 MUTATED MAP7D1 WILD-TYPE 
              15              352 
  MAP7D1 MUTATED MAP7D1 WILD-TYPE 
              15              352 
[1] "KRT19 MUTATION ANALYSIS"
[1] 3
  KRT19 MUTATED KRT19 WILD-TYPE 
              4             363 
  KRT19 MUTATED KRT19 WILD-TYPE 
              4             363 
[1] "HIST1H1E MUTATION ANALYSIS"
[1] 3
  HIST1H1E MUTATED HIST1H1E WILD-TYPE 
                 6                361 
  HIST1H1E MUTATED HIST1H1E WILD-TYPE 
                 6                361 
[1] "CETN3 MUTATION ANALYSIS"
[1] 3
  CETN3 MUTATED CETN3 WILD-TYPE 
              6             361 
  CETN3 MUTATED CETN3 WILD-TYPE 
              6             361 
[1] "FGFR1 MUTATION ANALYSIS"
[1] 3
  FGFR1 MUTATED FGFR1 WILD-TYPE 
             17             350 
  FGFR1 MUTATED FGFR1 WILD-TYPE 
             17             350 
[1] "PCSK5 MUTATION ANALYSIS"
[1] 3
  PCSK5 MUTATED PCSK5 WILD-TYPE 
             17             350 
  PCSK5 MUTATED PCSK5 WILD-TYPE 
             17             350 
[1] "GRB14 MUTATION ANALYSIS"
[1] 3
  GRB14 MUTATED GRB14 WILD-TYPE 
              9             358 
  GRB14 MUTATED GRB14 WILD-TYPE 
              9             358 
[1] "RANBP1 MUTATION ANALYSIS"
[1] 3
  RANBP1 MUTATED RANBP1 WILD-TYPE 
               6              361 
  RANBP1 MUTATED RANBP1 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] "SLC22A3 MUTATION ANALYSIS"
[1] 3
  SLC22A3 MUTATED SLC22A3 WILD-TYPE 
               12               355 
  SLC22A3 MUTATED SLC22A3 WILD-TYPE 
               12               355 
[1] "OR7C1 MUTATION ANALYSIS"
[1] 3
  OR7C1 MUTATED OR7C1 WILD-TYPE 
              9             358 
  OR7C1 MUTATED OR7C1 WILD-TYPE 
              9             358 
[1] "ZNF473 MUTATION ANALYSIS"
[1] 3
  ZNF473 MUTATED ZNF473 WILD-TYPE 
              14              353 
  ZNF473 MUTATED ZNF473 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] "CTCF MUTATION ANALYSIS"
[1] 3
  CTCF MUTATED CTCF WILD-TYPE 
            17            350 
  CTCF MUTATED CTCF 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] "DNAJC16 MUTATION ANALYSIS"
[1] 3
  DNAJC16 MUTATED DNAJC16 WILD-TYPE 
                9               358 
  DNAJC16 MUTATED DNAJC16 WILD-TYPE 
                9               358 
[1] "ARMCX5 MUTATION ANALYSIS"
[1] 3
  ARMCX5 MUTATED ARMCX5 WILD-TYPE 
               8              359 
  ARMCX5 MUTATED ARMCX5 WILD-TYPE 
               8              359 
[1] "GGT5 MUTATION ANALYSIS"
[1] 3
  GGT5 MUTATED GGT5 WILD-TYPE 
            14            353 
  GGT5 MUTATED GGT5 WILD-TYPE 
            14            353 
[1] "MTDH MUTATION ANALYSIS"
[1] 3
  MTDH MUTATED MTDH WILD-TYPE 
            12            355 
  MTDH MUTATED MTDH WILD-TYPE 
            12            355 
[1] "CAMSAP1L1 MUTATION ANALYSIS"
[1] 3
  CAMSAP1L1 MUTATED CAMSAP1L1 WILD-TYPE 
                 21                 346 
  CAMSAP1L1 MUTATED CAMSAP1L1 WILD-TYPE 
                 21                 346 
[1] "LRRC37B MUTATION ANALYSIS"
[1] 3
  LRRC37B MUTATED LRRC37B WILD-TYPE 
                6               361 
  LRRC37B MUTATED LRRC37B WILD-TYPE 
                6               361 
[1] "MARVELD2 MUTATION ANALYSIS"
[1] 3
  MARVELD2 MUTATED MARVELD2 WILD-TYPE 
                10                357 
  MARVELD2 MUTATED MARVELD2 WILD-TYPE 
                10                357 
[1] "PRKCD MUTATION ANALYSIS"
[1] 3
  PRKCD MUTATED PRKCD WILD-TYPE 
             13             354 
  PRKCD MUTATED PRKCD WILD-TYPE 
             13             354 
[1] "ZNF658 MUTATION ANALYSIS"
[1] 3
  ZNF658 MUTATED ZNF658 WILD-TYPE 
              10              357 
  ZNF658 MUTATED ZNF658 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] "CAPRIN1 MUTATION ANALYSIS"
[1] 3
  CAPRIN1 MUTATED CAPRIN1 WILD-TYPE 
               11               356 
  CAPRIN1 MUTATED CAPRIN1 WILD-TYPE 
               11               356 
[1] "MFAP1 MUTATION ANALYSIS"
[1] 3
  MFAP1 MUTATED MFAP1 WILD-TYPE 
              4             363 
  MFAP1 MUTATED MFAP1 WILD-TYPE 
              4             363 
[1] "ZCCHC6 MUTATION ANALYSIS"
[1] 3
  ZCCHC6 MUTATED ZCCHC6 WILD-TYPE 
              18              349 
  ZCCHC6 MUTATED ZCCHC6 WILD-TYPE 
              18              349 
[1] "HIVEP2 MUTATION ANALYSIS"
[1] 3
  HIVEP2 MUTATED HIVEP2 WILD-TYPE 
              19              348 
  HIVEP2 MUTATED HIVEP2 WILD-TYPE 
              19              348 
[1] "FER MUTATION ANALYSIS"
[1] 3
  FER MUTATED FER WILD-TYPE 
           15           352 
  FER MUTATED FER WILD-TYPE 
           15           352 
[1] "PHF1 MUTATION ANALYSIS"
[1] 3
  PHF1 MUTATED PHF1 WILD-TYPE 
             6            361 
  PHF1 MUTATED PHF1 WILD-TYPE 
             6            361 
[1] "ZNF799 MUTATION ANALYSIS"
[1] 3
  ZNF799 MUTATED ZNF799 WILD-TYPE 
               6              361 
  ZNF799 MUTATED ZNF799 WILD-TYPE 
               6              361 
[1] "CDK17 MUTATION ANALYSIS"
[1] 3
  CDK17 MUTATED CDK17 WILD-TYPE 
             10             357 
  CDK17 MUTATED CDK17 WILD-TYPE 
             10             357 
[1] "FAM98B MUTATION ANALYSIS"
[1] 3
  FAM98B MUTATED FAM98B WILD-TYPE 
               4              363 
  FAM98B MUTATED FAM98B WILD-TYPE 
               4              363 
[1] "NCAPD3 MUTATION ANALYSIS"
[1] 3
  NCAPD3 MUTATED NCAPD3 WILD-TYPE 
              25              342 
  NCAPD3 MUTATED NCAPD3 WILD-TYPE 
              25              342 
[1] "EYS MUTATION ANALYSIS"
[1] 3
  EYS MUTATED EYS WILD-TYPE 
           47           320 
  EYS MUTATED EYS WILD-TYPE 
           47           320 
[1] "NFATC3 MUTATION ANALYSIS"
[1] 3
  NFATC3 MUTATED NFATC3 WILD-TYPE 
              12              355 
  NFATC3 MUTATED NFATC3 WILD-TYPE 
              12              355 
[1] "ADAMTS19 MUTATION ANALYSIS"
[1] 3
  ADAMTS19 MUTATED ADAMTS19 WILD-TYPE 
                19                348 
  ADAMTS19 MUTATED ADAMTS19 WILD-TYPE 
                19                348 
[1] "OR6A2 MUTATION ANALYSIS"
[1] 3
  OR6A2 MUTATED OR6A2 WILD-TYPE 
              8             359 
  OR6A2 MUTATED OR6A2 WILD-TYPE 
              8             359 
[1] "FAM26E MUTATION ANALYSIS"
[1] 3
  FAM26E MUTATED FAM26E WILD-TYPE 
               5              362 
  FAM26E MUTATED FAM26E WILD-TYPE 
               5              362 
[1] "AKAP9 MUTATION ANALYSIS"
[1] 3
  AKAP9 MUTATED AKAP9 WILD-TYPE 
             43             324 
  AKAP9 MUTATED AKAP9 WILD-TYPE 
             43             324 
[1] "VAV3 MUTATION ANALYSIS"
[1] 3
  VAV3 MUTATED VAV3 WILD-TYPE 
            24            343 
  VAV3 MUTATED VAV3 WILD-TYPE 
            24            343 
[1] "C6ORF222 MUTATION ANALYSIS"
[1] 3
  C6ORF222 MUTATED C6ORF222 WILD-TYPE 
                 6                361 
  C6ORF222 MUTATED C6ORF222 WILD-TYPE 
                 6                361 
[1] "LASS3 MUTATION ANALYSIS"
[1] 3
  LASS3 MUTATED LASS3 WILD-TYPE 
             14             353 
  LASS3 MUTATED LASS3 WILD-TYPE 
             14             353 
[1] "PANK1 MUTATION ANALYSIS"
[1] 3
  PANK1 MUTATED PANK1 WILD-TYPE 
              7             360 
  PANK1 MUTATED PANK1 WILD-TYPE 
              7             360 
[1] "TMTC4 MUTATION ANALYSIS"
[1] 3
  TMTC4 MUTATED TMTC4 WILD-TYPE 
             13             354 
  TMTC4 MUTATED TMTC4 WILD-TYPE 
             13             354 
[1] "ZNF721 MUTATION ANALYSIS"
[1] 3
  ZNF721 MUTATED ZNF721 WILD-TYPE 
              15              352 
  ZNF721 MUTATED ZNF721 WILD-TYPE 
              15              352 
[1] "MIA3 MUTATION ANALYSIS"
[1] 3
  MIA3 MUTATED MIA3 WILD-TYPE 
            19            348 
  MIA3 MUTATED MIA3 WILD-TYPE 
            19            348 
[1] "OR8A1 MUTATION ANALYSIS"
[1] 3
  OR8A1 MUTATED OR8A1 WILD-TYPE 
              4             363 
  OR8A1 MUTATED OR8A1 WILD-TYPE 
              4             363 
[1] "METTL9 MUTATION ANALYSIS"
[1] 3
  METTL9 MUTATED METTL9 WILD-TYPE 
               4              363 
  METTL9 MUTATED METTL9 WILD-TYPE 
               4              363 
[1] "ZNF585A MUTATION ANALYSIS"
[1] 3
  ZNF585A MUTATED ZNF585A WILD-TYPE 
               16               351 
  ZNF585A MUTATED ZNF585A WILD-TYPE 
               16               351 
[1] "RAD51AP2 MUTATION ANALYSIS"
[1] 3
  RAD51AP2 MUTATED RAD51AP2 WILD-TYPE 
                16                351 
  RAD51AP2 MUTATED RAD51AP2 WILD-TYPE 
                16                351 
[1] "DNAH8 MUTATION ANALYSIS"
[1] 3
  DNAH8 MUTATED DNAH8 WILD-TYPE 
             59             308 
  DNAH8 MUTATED DNAH8 WILD-TYPE 
             59             308 
[1] "CHM MUTATION ANALYSIS"
[1] 3
  CHM MUTATED CHM WILD-TYPE 
            4           363 
  CHM MUTATED CHM WILD-TYPE 
            4           363 
[1] "POLDIP3 MUTATION ANALYSIS"
[1] 3
  POLDIP3 MUTATED POLDIP3 WILD-TYPE 
                5               362 
  POLDIP3 MUTATED POLDIP3 WILD-TYPE 
                5               362 
[1] "ZNF384 MUTATION ANALYSIS"
[1] 3
  ZNF384 MUTATED ZNF384 WILD-TYPE 
               9              358 
  ZNF384 MUTATED ZNF384 WILD-TYPE 
               9              358 
[1] "C20ORF177 MUTATION ANALYSIS"
[1] 3
  C20ORF177 MUTATED C20ORF177 WILD-TYPE 
                  9                 358 
  C20ORF177 MUTATED C20ORF177 WILD-TYPE 
                  9                 358 
[1] "IFITM3 MUTATION ANALYSIS"
[1] 3
  IFITM3 MUTATED IFITM3 WILD-TYPE 
               6              361 
  IFITM3 MUTATED IFITM3 WILD-TYPE 
               6              361 
[1] "NIPA2 MUTATION ANALYSIS"
[1] 3
  NIPA2 MUTATED NIPA2 WILD-TYPE 
              7             360 
  NIPA2 MUTATED NIPA2 WILD-TYPE 
              7             360 
[1] "C14ORF39 MUTATION ANALYSIS"
[1] 3
  C14ORF39 MUTATED C14ORF39 WILD-TYPE 
                13                354 
  C14ORF39 MUTATED C14ORF39 WILD-TYPE 
                13                354 
[1] "HNMT MUTATION ANALYSIS"
[1] 3
  HNMT MUTATED HNMT WILD-TYPE 
            11            356 
  HNMT MUTATED HNMT WILD-TYPE 
            11            356 
[1] "GMNN MUTATION ANALYSIS"
[1] 3
  GMNN MUTATED GMNN WILD-TYPE 
             3            364 
  GMNN MUTATED GMNN WILD-TYPE 
             3            364 
[1] "MACF1 MUTATION ANALYSIS"
[1] 3
  MACF1 MUTATED MACF1 WILD-TYPE 
             58             309 
  MACF1 MUTATED MACF1 WILD-TYPE 
             58             309 
[1] "UPF3A MUTATION ANALYSIS"
[1] 3
  UPF3A MUTATED UPF3A WILD-TYPE 
              9             358 
  UPF3A MUTATED UPF3A WILD-TYPE 
              9             358 
[1] "MAP7D3 MUTATION ANALYSIS"
[1] 3
  MAP7D3 MUTATED MAP7D3 WILD-TYPE 
              17              350 
  MAP7D3 MUTATED MAP7D3 WILD-TYPE 
              17              350 
[1] "MIER1 MUTATION ANALYSIS"
[1] 3
  MIER1 MUTATED MIER1 WILD-TYPE 
              8             359 
  MIER1 MUTATED MIER1 WILD-TYPE 
              8             359 
[1] "CNTFR MUTATION ANALYSIS"
[1] 3
  CNTFR MUTATED CNTFR WILD-TYPE 
             10             357 
  CNTFR MUTATED CNTFR WILD-TYPE 
             10             357 
[1] "AHCTF1 MUTATION ANALYSIS"
[1] 3
  AHCTF1 MUTATED AHCTF1 WILD-TYPE 
              21              346 
  AHCTF1 MUTATED AHCTF1 WILD-TYPE 
              21              346 
[1] "CWF19L2 MUTATION ANALYSIS"
[1] 3
  CWF19L2 MUTATED CWF19L2 WILD-TYPE 
               15               352 
  CWF19L2 MUTATED CWF19L2 WILD-TYPE 
               15               352 
[1] "ZP3 MUTATION ANALYSIS"
[1] 3
  ZP3 MUTATED ZP3 WILD-TYPE 
            6           361 
  ZP3 MUTATED ZP3 WILD-TYPE 
            6           361 
[1] "ACOT9 MUTATION ANALYSIS"
[1] 3
  ACOT9 MUTATED ACOT9 WILD-TYPE 
              4             363 
  ACOT9 MUTATED ACOT9 WILD-TYPE 
              4             363 
[1] "PPIG MUTATION ANALYSIS"
[1] 3
  PPIG MUTATED PPIG WILD-TYPE 
            12            355 
  PPIG MUTATED PPIG WILD-TYPE 
            12            355 
[1] "LEPRE1 MUTATION ANALYSIS"
[1] 3
  LEPRE1 MUTATED LEPRE1 WILD-TYPE 
               9              358 
  LEPRE1 MUTATED LEPRE1 WILD-TYPE 
               9              358 
[1] "OR4D2 MUTATION ANALYSIS"
[1] 3
  OR4D2 MUTATED OR4D2 WILD-TYPE 
              4             363 
  OR4D2 MUTATED OR4D2 WILD-TYPE 
              4             363 
[1] "MRI1 MUTATION ANALYSIS"
[1] 3
  MRI1 MUTATED MRI1 WILD-TYPE 
             6            361 
  MRI1 MUTATED MRI1 WILD-TYPE 
             6            361 
[1] "STK35 MUTATION ANALYSIS"
[1] 3
  STK35 MUTATED STK35 WILD-TYPE 
              6             361 
  STK35 MUTATED STK35 WILD-TYPE 
              6             361 
[1] "KDELR2 MUTATION ANALYSIS"
[1] 3
  KDELR2 MUTATED KDELR2 WILD-TYPE 
               8              359 
  KDELR2 MUTATED KDELR2 WILD-TYPE 
               8              359 
[1] "HAUS6 MUTATION ANALYSIS"
[1] 3
  HAUS6 MUTATED HAUS6 WILD-TYPE 
             12             355 
  HAUS6 MUTATED HAUS6 WILD-TYPE 
             12             355 
[1] "HCRTR2 MUTATION ANALYSIS"
[1] 3
  HCRTR2 MUTATED HCRTR2 WILD-TYPE 
               7              360 
  HCRTR2 MUTATED HCRTR2 WILD-TYPE 
               7              360 
[1] "CACNG3 MUTATION ANALYSIS"
[1] 3
  CACNG3 MUTATED CACNG3 WILD-TYPE 
               8              359 
  CACNG3 MUTATED CACNG3 WILD-TYPE 
               8              359 
[1] "BST2 MUTATION ANALYSIS"
[1] 3
  BST2 MUTATED BST2 WILD-TYPE 
             6            361 
  BST2 MUTATED BST2 WILD-TYPE 
             6            361 
[1] "OSTM1 MUTATION ANALYSIS"
[1] 3
  OSTM1 MUTATED OSTM1 WILD-TYPE 
              5             362 
  OSTM1 MUTATED OSTM1 WILD-TYPE 
              5             362 
[1] "NGEF MUTATION ANALYSIS"
[1] 3
  NGEF MUTATED NGEF WILD-TYPE 
            16            351 
  NGEF MUTATED NGEF WILD-TYPE 
            16            351 
[1] "ZHX1 MUTATION ANALYSIS"
[1] 3
  ZHX1 MUTATED ZHX1 WILD-TYPE 
             9            358 
  ZHX1 MUTATED ZHX1 WILD-TYPE 
             9            358 
[1] "DUSP1 MUTATION ANALYSIS"
[1] 3
  DUSP1 MUTATED DUSP1 WILD-TYPE 
              6             361 
  DUSP1 MUTATED DUSP1 WILD-TYPE 
              6             361 
[1] "TGFBR1 MUTATION ANALYSIS"
[1] 3
  TGFBR1 MUTATED TGFBR1 WILD-TYPE 
              14              353 
  TGFBR1 MUTATED TGFBR1 WILD-TYPE 
              14              353 
[1] "C1QL3 MUTATION ANALYSIS"
[1] 3
  C1QL3 MUTATED C1QL3 WILD-TYPE 
              4             363 
  C1QL3 MUTATED C1QL3 WILD-TYPE 
              4             363 
[1] "MTTP MUTATION ANALYSIS"
[1] 3
  MTTP MUTATED MTTP WILD-TYPE 
            23            344 
  MTTP MUTATED MTTP WILD-TYPE 
            23            344 
[1] "PTTG1IP MUTATION ANALYSIS"
[1] 3
  PTTG1IP MUTATED PTTG1IP WILD-TYPE 
                7               360 
  PTTG1IP MUTATED PTTG1IP WILD-TYPE 
                7               360 
[1] "ADH1B MUTATION ANALYSIS"
[1] 3
  ADH1B MUTATED ADH1B WILD-TYPE 
              7             360 
  ADH1B MUTATED ADH1B WILD-TYPE 
              7             360 
[1] "LAS1L MUTATION ANALYSIS"
[1] 3
  LAS1L MUTATED LAS1L WILD-TYPE 
              9             358 
  LAS1L MUTATED LAS1L WILD-TYPE 
              9             358 
[1] "SNX2 MUTATION ANALYSIS"
[1] 3
  SNX2 MUTATED SNX2 WILD-TYPE 
            11            356 
  SNX2 MUTATED SNX2 WILD-TYPE 
            11            356 
[1] "SCN4A MUTATION ANALYSIS"
[1] 3
  SCN4A MUTATED SCN4A WILD-TYPE 
             23             344 
  SCN4A MUTATED SCN4A WILD-TYPE 
             23             344 
[1] "B4GALT6 MUTATION ANALYSIS"
[1] 3
  B4GALT6 MUTATED B4GALT6 WILD-TYPE 
               10               357 
  B4GALT6 MUTATED B4GALT6 WILD-TYPE 
               10               357 
[1] "OR10J1 MUTATION ANALYSIS"
[1] 3
  OR10J1 MUTATED OR10J1 WILD-TYPE 
              13              354 
  OR10J1 MUTATED OR10J1 WILD-TYPE 
              13              354 
[1] "PDP2 MUTATION ANALYSIS"
[1] 3
  PDP2 MUTATED PDP2 WILD-TYPE 
             5            362 
  PDP2 MUTATED PDP2 WILD-TYPE 
             5            362 
[1] "EXD2 MUTATION ANALYSIS"
[1] 3
  EXD2 MUTATED EXD2 WILD-TYPE 
            11            356 
  EXD2 MUTATED EXD2 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] "CHEK2 MUTATION ANALYSIS"
[1] 3
  CHEK2 MUTATED CHEK2 WILD-TYPE 
             10             357 
  CHEK2 MUTATED CHEK2 WILD-TYPE 
             10             357 
[1] "DCTN5 MUTATION ANALYSIS"
[1] 3
  DCTN5 MUTATED DCTN5 WILD-TYPE 
              6             361 
  DCTN5 MUTATED DCTN5 WILD-TYPE 
              6             361 
[1] "GABRA6 MUTATION ANALYSIS"
[1] 3
  GABRA6 MUTATED GABRA6 WILD-TYPE 
              19              348 
  GABRA6 MUTATED GABRA6 WILD-TYPE 
              19              348 
[1] "BAP1 MUTATION ANALYSIS"
[1] 3
  BAP1 MUTATED BAP1 WILD-TYPE 
            17            350 
  BAP1 MUTATED BAP1 WILD-TYPE 
            17            350 
[1] "ANKRD17 MUTATION ANALYSIS"
[1] 3
  ANKRD17 MUTATED ANKRD17 WILD-TYPE 
               26               341 
  ANKRD17 MUTATED ANKRD17 WILD-TYPE 
               26               341 
[1] "STAU2 MUTATION ANALYSIS"
[1] 3
  STAU2 MUTATED STAU2 WILD-TYPE 
             10             357 
  STAU2 MUTATED STAU2 WILD-TYPE 
             10             357 
[1] "ELFN2 MUTATION ANALYSIS"
[1] 3
  ELFN2 MUTATED ELFN2 WILD-TYPE 
              9             358 
  ELFN2 MUTATED ELFN2 WILD-TYPE 
              9             358 
[1] "TMEM45A MUTATION ANALYSIS"
[1] 3
  TMEM45A MUTATED TMEM45A WILD-TYPE 
                4               363 
  TMEM45A MUTATED TMEM45A WILD-TYPE 
                4               363 
[1] "ASB11 MUTATION ANALYSIS"
[1] 3
  ASB11 MUTATED ASB11 WILD-TYPE 
              7             360 
  ASB11 MUTATED ASB11 WILD-TYPE 
              7             360 
[1] "NEB MUTATION ANALYSIS"
[1] 3
  NEB MUTATED NEB WILD-TYPE 
           57           310 
  NEB MUTATED NEB WILD-TYPE 
           57           310 
[1] "ZNF691 MUTATION ANALYSIS"
[1] 3
  ZNF691 MUTATED ZNF691 WILD-TYPE 
               7              360 
  ZNF691 MUTATED ZNF691 WILD-TYPE 
               7              360 
[1] "ODAM MUTATION ANALYSIS"
[1] 3
  ODAM MUTATED ODAM WILD-TYPE 
             5            362 
  ODAM MUTATED ODAM WILD-TYPE 
             5            362 
[1] "C12ORF49 MUTATION ANALYSIS"
[1] 3
  C12ORF49 MUTATED C12ORF49 WILD-TYPE 
                 4                363 
  C12ORF49 MUTATED C12ORF49 WILD-TYPE 
                 4                363 
[1] "MAP3K4 MUTATION ANALYSIS"
[1] 3
  MAP3K4 MUTATED MAP3K4 WILD-TYPE 
              36              331 
  MAP3K4 MUTATED MAP3K4 WILD-TYPE 
              36              331 
[1] "OSMR MUTATION ANALYSIS"
[1] 3
  OSMR MUTATED OSMR WILD-TYPE 
            20            347 
  OSMR MUTATED OSMR WILD-TYPE 
            20            347 
[1] "HIST1H1C MUTATION ANALYSIS"
[1] 3
  HIST1H1C MUTATED HIST1H1C WILD-TYPE 
                 7                360 
  HIST1H1C MUTATED HIST1H1C WILD-TYPE 
                 7                360 
[1] "KIAA1797 MUTATION ANALYSIS"
[1] 3
  KIAA1797 MUTATED KIAA1797 WILD-TYPE 
                20                347 
  KIAA1797 MUTATED KIAA1797 WILD-TYPE 
                20                347 
[1] "ZNF83 MUTATION ANALYSIS"
[1] 3
  ZNF83 MUTATED ZNF83 WILD-TYPE 
             17             350 
  ZNF83 MUTATED ZNF83 WILD-TYPE 
             17             350 
[1] "EIF4G2 MUTATION ANALYSIS"
[1] 3
  EIF4G2 MUTATED EIF4G2 WILD-TYPE 
              15              352 
  EIF4G2 MUTATED EIF4G2 WILD-TYPE 
              15              352 
[1] "ALK MUTATION ANALYSIS"
[1] 3
  ALK MUTATED ALK WILD-TYPE 
           33           334 
  ALK MUTATED ALK WILD-TYPE 
           33           334 
[1] "FMO5 MUTATION ANALYSIS"
[1] 3
  FMO5 MUTATED FMO5 WILD-TYPE 
            12            355 
  FMO5 MUTATED FMO5 WILD-TYPE 
            12            355 
[1] "HGS MUTATION ANALYSIS"
[1] 3
  HGS MUTATED HGS WILD-TYPE 
           10           357 
  HGS MUTATED HGS WILD-TYPE 
           10           357 
[1] "SLC41A2 MUTATION ANALYSIS"
[1] 3
  SLC41A2 MUTATED SLC41A2 WILD-TYPE 
                8               359 
  SLC41A2 MUTATED SLC41A2 WILD-TYPE 
                8               359 
[1] "UGT2A1 MUTATION ANALYSIS"
[1] 3
  UGT2A1 MUTATED UGT2A1 WILD-TYPE 
              10              357 
  UGT2A1 MUTATED UGT2A1 WILD-TYPE 
              10              357 
[1] "STK36 MUTATION ANALYSIS"
[1] 3
  STK36 MUTATED STK36 WILD-TYPE 
             15             352 
  STK36 MUTATED STK36 WILD-TYPE 
             15             352 
[1] "MACC1 MUTATION ANALYSIS"
[1] 3
  MACC1 MUTATED MACC1 WILD-TYPE 
             18             349 
  MACC1 MUTATED MACC1 WILD-TYPE 
             18             349 
[1] "BAI3 MUTATION ANALYSIS"
[1] 3
  BAI3 MUTATED BAI3 WILD-TYPE 
            42            325 
  BAI3 MUTATED BAI3 WILD-TYPE 
            42            325 
[1] "POLE MUTATION ANALYSIS"
[1] 3
  POLE MUTATED POLE WILD-TYPE 
            31            336 
  POLE MUTATED POLE WILD-TYPE 
            31            336 
[1] "ABI3BP MUTATION ANALYSIS"
[1] 3
  ABI3BP MUTATED ABI3BP WILD-TYPE 
              21              346 
  ABI3BP MUTATED ABI3BP WILD-TYPE 
              21              346 
[1] "INSRR MUTATION ANALYSIS"
[1] 3
  INSRR MUTATED INSRR WILD-TYPE 
             26             341 
  INSRR MUTATED INSRR WILD-TYPE 
             26             341 
[1] "IQGAP2 MUTATION ANALYSIS"
[1] 3
  IQGAP2 MUTATED IQGAP2 WILD-TYPE 
              21              346 
  IQGAP2 MUTATED IQGAP2 WILD-TYPE 
              21              346 
[1] "SCN2A MUTATION ANALYSIS"
[1] 3
  SCN2A MUTATED SCN2A WILD-TYPE 
             46             321 
  SCN2A MUTATED SCN2A WILD-TYPE 
             46             321 
[1] "KCNG4 MUTATION ANALYSIS"
[1] 3
  KCNG4 MUTATED KCNG4 WILD-TYPE 
             10             357 
  KCNG4 MUTATED KCNG4 WILD-TYPE 
             10             357 
[1] "MANBA MUTATION ANALYSIS"
[1] 3
  MANBA MUTATED MANBA WILD-TYPE 
             12             355 
  MANBA MUTATED MANBA WILD-TYPE 
             12             355 
[1] "SLC22A16 MUTATION ANALYSIS"
[1] 3
  SLC22A16 MUTATED SLC22A16 WILD-TYPE 
                13                354 
  SLC22A16 MUTATED SLC22A16 WILD-TYPE 
                13                354 
[1] "TAOK3 MUTATION ANALYSIS"
[1] 3
  TAOK3 MUTATED TAOK3 WILD-TYPE 
             20             347 
  TAOK3 MUTATED TAOK3 WILD-TYPE 
             20             347 
[1] "RPGRIP1L MUTATION ANALYSIS"
[1] 3
  RPGRIP1L MUTATED RPGRIP1L WILD-TYPE 
                16                351 
  RPGRIP1L MUTATED RPGRIP1L WILD-TYPE 
                16                351 
[1] "GRINA MUTATION ANALYSIS"
[1] 3
  GRINA MUTATED GRINA WILD-TYPE 
              4             363 
  GRINA MUTATED GRINA WILD-TYPE 
              4             363 
[1] "SLC25A44 MUTATION ANALYSIS"
[1] 3
  SLC25A44 MUTATED SLC25A44 WILD-TYPE 
                 5                362 
  SLC25A44 MUTATED SLC25A44 WILD-TYPE 
                 5                362 
[1] "SGK3 MUTATION ANALYSIS"
[1] 3
  SGK3 MUTATED SGK3 WILD-TYPE 
             8            359 
  SGK3 MUTATED SGK3 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] "TXNDC6 MUTATION ANALYSIS"
[1] 3
  TXNDC6 MUTATED TXNDC6 WILD-TYPE 
               8              359 
  TXNDC6 MUTATED TXNDC6 WILD-TYPE 
               8              359 
[1] "UIMC1 MUTATION ANALYSIS"
[1] 3
  UIMC1 MUTATED UIMC1 WILD-TYPE 
              6             361 
  UIMC1 MUTATED UIMC1 WILD-TYPE 
              6             361 
[1] "TGFBR2 MUTATION ANALYSIS"
[1] 3
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
              22              345 
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
              22              345 
[1] "DLL3 MUTATION ANALYSIS"
[1] 3
  DLL3 MUTATED DLL3 WILD-TYPE 
             6            361 
  DLL3 MUTATED DLL3 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] "GPR126 MUTATION ANALYSIS"
[1] 3
  GPR126 MUTATED GPR126 WILD-TYPE 
              16              351 
  GPR126 MUTATED GPR126 WILD-TYPE 
              16              351 
[1] "LYG1 MUTATION ANALYSIS"
[1] 3
  LYG1 MUTATED LYG1 WILD-TYPE 
             6            361 
  LYG1 MUTATED LYG1 WILD-TYPE 
             6            361 
[1] "REXO4 MUTATION ANALYSIS"
[1] 3
  REXO4 MUTATED REXO4 WILD-TYPE 
              5             362 
  REXO4 MUTATED REXO4 WILD-TYPE 
              5             362 
[1] "MSRB3 MUTATION ANALYSIS"
[1] 3
  MSRB3 MUTATED MSRB3 WILD-TYPE 
             11             356 
  MSRB3 MUTATED MSRB3 WILD-TYPE 
             11             356 
[1] "GRIA4 MUTATION ANALYSIS"
[1] 3
  GRIA4 MUTATED GRIA4 WILD-TYPE 
             30             337 
  GRIA4 MUTATED GRIA4 WILD-TYPE 
             30             337 
[1] "TP53RK MUTATION ANALYSIS"
[1] 3
  TP53RK MUTATED TP53RK WILD-TYPE 
               4              363 
  TP53RK MUTATED TP53RK WILD-TYPE 
               4              363 
[1] "TMEM50B MUTATION ANALYSIS"
[1] 3
  TMEM50B MUTATED TMEM50B WILD-TYPE 
                6               361 
  TMEM50B MUTATED TMEM50B WILD-TYPE 
                6               361 
[1] "CRYGA MUTATION ANALYSIS"
[1] 3
  CRYGA MUTATED CRYGA WILD-TYPE 
              5             362 
  CRYGA MUTATED CRYGA WILD-TYPE 
              5             362 
[1] "IL2RG MUTATION ANALYSIS"
[1] 3
  IL2RG MUTATED IL2RG WILD-TYPE 
              7             360 
  IL2RG MUTATED IL2RG WILD-TYPE 
              7             360 
[1] "BAIAP2L1 MUTATION ANALYSIS"
[1] 3
  BAIAP2L1 MUTATED BAIAP2L1 WILD-TYPE 
                12                355 
  BAIAP2L1 MUTATED BAIAP2L1 WILD-TYPE 
                12                355 
[1] "C7ORF58 MUTATION ANALYSIS"
[1] 3
  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
               21               346 
  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
               21               346 
[1] "ATP13A5 MUTATION ANALYSIS"
[1] 3
  ATP13A5 MUTATED ATP13A5 WILD-TYPE 
               22               345 
  ATP13A5 MUTATED ATP13A5 WILD-TYPE 
               22               345 
[1] "AMBRA1 MUTATION ANALYSIS"
[1] 3
  AMBRA1 MUTATED AMBRA1 WILD-TYPE 
              18              349 
  AMBRA1 MUTATED AMBRA1 WILD-TYPE 
              18              349 
[1] "SKIL MUTATION ANALYSIS"
[1] 3
  SKIL MUTATED SKIL WILD-TYPE 
             7            360 
  SKIL MUTATED SKIL WILD-TYPE 
             7            360 
[1] "ZNF570 MUTATION ANALYSIS"
[1] 3
  ZNF570 MUTATED ZNF570 WILD-TYPE 
               9              358 
  ZNF570 MUTATED ZNF570 WILD-TYPE 
               9              358 
[1] "UCHL5 MUTATION ANALYSIS"
[1] 3
  UCHL5 MUTATED UCHL5 WILD-TYPE 
              4             363 
  UCHL5 MUTATED UCHL5 WILD-TYPE 
              4             363 
[1] "CASC1 MUTATION ANALYSIS"
[1] 3
  CASC1 MUTATED CASC1 WILD-TYPE 
             12             355 
  CASC1 MUTATED CASC1 WILD-TYPE 
             12             355 
[1] "CBLL1 MUTATION ANALYSIS"
[1] 3
  CBLL1 MUTATED CBLL1 WILD-TYPE 
              5             362 
  CBLL1 MUTATED CBLL1 WILD-TYPE 
              5             362 
[1] "FOXN3 MUTATION ANALYSIS"
[1] 3
  FOXN3 MUTATED FOXN3 WILD-TYPE 
             11             356 
  FOXN3 MUTATED FOXN3 WILD-TYPE 
             11             356 
[1] "AP1M1 MUTATION ANALYSIS"
[1] 3
  AP1M1 MUTATED AP1M1 WILD-TYPE 
              9             358 
  AP1M1 MUTATED AP1M1 WILD-TYPE 
              9             358 
[1] "ARHGEF3 MUTATION ANALYSIS"
[1] 3
  ARHGEF3 MUTATED ARHGEF3 WILD-TYPE 
               12               355 
  ARHGEF3 MUTATED ARHGEF3 WILD-TYPE 
               12               355 
[1] "KLKB1 MUTATION ANALYSIS"
[1] 3
  KLKB1 MUTATED KLKB1 WILD-TYPE 
             13             354 
  KLKB1 MUTATED KLKB1 WILD-TYPE 
             13             354 
[1] "ZBTB33 MUTATION ANALYSIS"
[1] 3
  ZBTB33 MUTATED ZBTB33 WILD-TYPE 
              16              351 
  ZBTB33 MUTATED ZBTB33 WILD-TYPE 
              16              351 
[1] "H2AFJ MUTATION ANALYSIS"
[1] 3
  H2AFJ MUTATED H2AFJ WILD-TYPE 
              3             364 
  H2AFJ MUTATED H2AFJ WILD-TYPE 
              3             364 
[1] "CBLN3 MUTATION ANALYSIS"
[1] 3
  CBLN3 MUTATED CBLN3 WILD-TYPE 
              6             361 
  CBLN3 MUTATED CBLN3 WILD-TYPE 
              6             361 
[1] "TRIM46 MUTATION ANALYSIS"
[1] 3
  TRIM46 MUTATED TRIM46 WILD-TYPE 
              15              352 
  TRIM46 MUTATED TRIM46 WILD-TYPE 
              15              352 
[1] "CCDC88A MUTATION ANALYSIS"
[1] 3
  CCDC88A MUTATED CCDC88A WILD-TYPE 
               30               337 
  CCDC88A MUTATED CCDC88A WILD-TYPE 
               30               337 
[1] "PRKCI MUTATION ANALYSIS"
[1] 3
  PRKCI MUTATED PRKCI WILD-TYPE 
             18             349 
  PRKCI MUTATED PRKCI WILD-TYPE 
             18             349 
[1] "C10ORF79 MUTATION ANALYSIS"
[1] 3
  C10ORF79 MUTATED C10ORF79 WILD-TYPE 
                27                340 
  C10ORF79 MUTATED C10ORF79 WILD-TYPE 
                27                340 
[1] "WWTR1 MUTATION ANALYSIS"
[1] 3
  WWTR1 MUTATED WWTR1 WILD-TYPE 
              6             361 
  WWTR1 MUTATED WWTR1 WILD-TYPE 
              6             361 
[1] "SLC25A17 MUTATION ANALYSIS"
[1] 3
  SLC25A17 MUTATED SLC25A17 WILD-TYPE 
                 7                360 
  SLC25A17 MUTATED SLC25A17 WILD-TYPE 
                 7                360 
[1] "ZNF334 MUTATION ANALYSIS"
[1] 3
  ZNF334 MUTATED ZNF334 WILD-TYPE 
              19              348 
  ZNF334 MUTATED ZNF334 WILD-TYPE 
              19              348 
[1] "C9ORF71 MUTATION ANALYSIS"
[1] 3
  C9ORF71 MUTATED C9ORF71 WILD-TYPE 
                4               363 
  C9ORF71 MUTATED C9ORF71 WILD-TYPE 
                4               363 
[1] "CD55 MUTATION ANALYSIS"
[1] 3
  CD55 MUTATED CD55 WILD-TYPE 
             7            360 
  CD55 MUTATED CD55 WILD-TYPE 
             7            360 
[1] "EXPH5 MUTATION ANALYSIS"
[1] 3
  EXPH5 MUTATED EXPH5 WILD-TYPE 
             21             346 
  EXPH5 MUTATED EXPH5 WILD-TYPE 
             21             346 
[1] "TMEM41B MUTATION ANALYSIS"
[1] 3
  TMEM41B MUTATED TMEM41B WILD-TYPE 
                4               363 
  TMEM41B MUTATED TMEM41B WILD-TYPE 
                4               363 
[1] "PLEKHB2 MUTATION ANALYSIS"
[1] 3
  PLEKHB2 MUTATED PLEKHB2 WILD-TYPE 
                6               361 
  PLEKHB2 MUTATED PLEKHB2 WILD-TYPE 
                6               361 
[1] "SLC7A6 MUTATION ANALYSIS"
[1] 3
  SLC7A6 MUTATED SLC7A6 WILD-TYPE 
               6              361 
  SLC7A6 MUTATED SLC7A6 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] "CDH10 MUTATION ANALYSIS"
[1] 3
  CDH10 MUTATED CDH10 WILD-TYPE 
             39             328 
  CDH10 MUTATED CDH10 WILD-TYPE 
             39             328 
[1] "PAX6 MUTATION ANALYSIS"
[1] 3
  PAX6 MUTATED PAX6 WILD-TYPE 
            14            353 
  PAX6 MUTATED PAX6 WILD-TYPE 
            14            353 
[1] "SFRP2 MUTATION ANALYSIS"
[1] 3
  SFRP2 MUTATED SFRP2 WILD-TYPE 
              8             359 
  SFRP2 MUTATED SFRP2 WILD-TYPE 
              8             359 
[1] "THOC6 MUTATION ANALYSIS"
[1] 3
  THOC6 MUTATED THOC6 WILD-TYPE 
              8             359 
  THOC6 MUTATED THOC6 WILD-TYPE 
              8             359 
[1] "ZNF620 MUTATION ANALYSIS"
[1] 3
  ZNF620 MUTATED ZNF620 WILD-TYPE 
               8              359 
  ZNF620 MUTATED ZNF620 WILD-TYPE 
               8              359 
[1] "NDUFAF1 MUTATION ANALYSIS"
[1] 3
  NDUFAF1 MUTATED NDUFAF1 WILD-TYPE 
                7               360 
  NDUFAF1 MUTATED NDUFAF1 WILD-TYPE 
                7               360 
[1] "CEL MUTATION ANALYSIS"
[1] 3
  CEL MUTATED CEL WILD-TYPE 
            9           358 
  CEL MUTATED CEL WILD-TYPE 
            9           358 
[1] "PTPN12 MUTATION ANALYSIS"
[1] 3
  PTPN12 MUTATED PTPN12 WILD-TYPE 
              17              350 
  PTPN12 MUTATED PTPN12 WILD-TYPE 
              17              350 
[1] "DHX32 MUTATION ANALYSIS"
[1] 3
  DHX32 MUTATED DHX32 WILD-TYPE 
             10             357 
  DHX32 MUTATED DHX32 WILD-TYPE 
             10             357 
[1] "RIMBP3 MUTATION ANALYSIS"
[1] 3
  RIMBP3 MUTATED RIMBP3 WILD-TYPE 
               6              361 
  RIMBP3 MUTATED RIMBP3 WILD-TYPE 
               6              361 
[1] "CTTN MUTATION ANALYSIS"
[1] 3
  CTTN MUTATED CTTN WILD-TYPE 
             4            363 
  CTTN MUTATED CTTN WILD-TYPE 
             4            363 
[1] "SLC25A13 MUTATION ANALYSIS"
[1] 3
  SLC25A13 MUTATED SLC25A13 WILD-TYPE 
                14                353 
  SLC25A13 MUTATED SLC25A13 WILD-TYPE 
                14                353 
[1] "RBMX2 MUTATION ANALYSIS"
[1] 3
  RBMX2 MUTATED RBMX2 WILD-TYPE 
             11             356 
  RBMX2 MUTATED RBMX2 WILD-TYPE 
             11             356 
[1] "LEO1 MUTATION ANALYSIS"
[1] 3
  LEO1 MUTATED LEO1 WILD-TYPE 
            10            357 
  LEO1 MUTATED LEO1 WILD-TYPE 
            10            357 
[1] "SR140 MUTATION ANALYSIS"
[1] 3
  SR140 MUTATED SR140 WILD-TYPE 
             11             356 
  SR140 MUTATED SR140 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] "HAUS1 MUTATION ANALYSIS"
[1] 3
  HAUS1 MUTATED HAUS1 WILD-TYPE 
              6             361 
  HAUS1 MUTATED HAUS1 WILD-TYPE 
              6             361 
[1] "RNF145 MUTATION ANALYSIS"
[1] 3
  RNF145 MUTATED RNF145 WILD-TYPE 
              15              352 
  RNF145 MUTATED RNF145 WILD-TYPE 
              15              352 
[1] "WNK3 MUTATION ANALYSIS"
[1] 3
  WNK3 MUTATED WNK3 WILD-TYPE 
            24            343 
  WNK3 MUTATED WNK3 WILD-TYPE 
            24            343 
[1] "TDRD7 MUTATION ANALYSIS"
[1] 3
  TDRD7 MUTATED TDRD7 WILD-TYPE 
             15             352 
  TDRD7 MUTATED TDRD7 WILD-TYPE 
             15             352 
[1] "BACE2 MUTATION ANALYSIS"
[1] 3
  BACE2 MUTATED BACE2 WILD-TYPE 
             10             357 
  BACE2 MUTATED BACE2 WILD-TYPE 
             10             357 
[1] "DNMT1 MUTATION ANALYSIS"
[1] 3
  DNMT1 MUTATED DNMT1 WILD-TYPE 
             18             349 
  DNMT1 MUTATED DNMT1 WILD-TYPE 
             18             349 
[1] "WDR65 MUTATION ANALYSIS"
[1] 3
  WDR65 MUTATED WDR65 WILD-TYPE 
             13             354 
  WDR65 MUTATED WDR65 WILD-TYPE 
             13             354 
[1] "ARAP3 MUTATION ANALYSIS"
[1] 3
  ARAP3 MUTATED ARAP3 WILD-TYPE 
             21             346 
  ARAP3 MUTATED ARAP3 WILD-TYPE 
             21             346 
[1] "ZFYVE16 MUTATION ANALYSIS"
[1] 3
  ZFYVE16 MUTATED ZFYVE16 WILD-TYPE 
               17               350 
  ZFYVE16 MUTATED ZFYVE16 WILD-TYPE 
               17               350 
[1] "LGALS9C MUTATION ANALYSIS"
[1] 3
  LGALS9C MUTATED LGALS9C WILD-TYPE 
                5               362 
  LGALS9C MUTATED LGALS9C WILD-TYPE 
                5               362 
[1] "DGKH MUTATION ANALYSIS"
[1] 3
  DGKH MUTATED DGKH WILD-TYPE 
            16            351 
  DGKH MUTATED DGKH WILD-TYPE 
            16            351 
[1] "RTN4 MUTATION ANALYSIS"
[1] 3
  RTN4 MUTATED RTN4 WILD-TYPE 
            19            348 
  RTN4 MUTATED RTN4 WILD-TYPE 
            19            348 
[1] "TRMT5 MUTATION ANALYSIS"
[1] 3
  TRMT5 MUTATED TRMT5 WILD-TYPE 
              8             359 
  TRMT5 MUTATED TRMT5 WILD-TYPE 
              8             359 
[1] "RYR2 MUTATION ANALYSIS"
[1] 3
  RYR2 MUTATED RYR2 WILD-TYPE 
            84            283 
  RYR2 MUTATED RYR2 WILD-TYPE 
            84            283 
[1] "INADL MUTATION ANALYSIS"
[1] 3
  INADL MUTATED INADL WILD-TYPE 
             13             354 
  INADL MUTATED INADL WILD-TYPE 
             13             354 
[1] "JMJD6 MUTATION ANALYSIS"
[1] 3
  JMJD6 MUTATED JMJD6 WILD-TYPE 
              8             359 
  JMJD6 MUTATED JMJD6 WILD-TYPE 
              8             359 
[1] "MAOA MUTATION ANALYSIS"
[1] 3
  MAOA MUTATED MAOA WILD-TYPE 
             5            362 
  MAOA MUTATED MAOA 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] "SAMD9L MUTATION ANALYSIS"
[1] 3
  SAMD9L MUTATED SAMD9L WILD-TYPE 
              22              345 
  SAMD9L MUTATED SAMD9L WILD-TYPE 
              22              345 
[1] "GDE1 MUTATION ANALYSIS"
[1] 3
  GDE1 MUTATED GDE1 WILD-TYPE 
             5            362 
  GDE1 MUTATED GDE1 WILD-TYPE 
             5            362 
[1] "TCEAL5 MUTATION ANALYSIS"
[1] 3
  TCEAL5 MUTATED TCEAL5 WILD-TYPE 
               5              362 
  TCEAL5 MUTATED TCEAL5 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] "DNASE1L3 MUTATION ANALYSIS"
[1] 3
  DNASE1L3 MUTATED DNASE1L3 WILD-TYPE 
                 8                359 
  DNASE1L3 MUTATED DNASE1L3 WILD-TYPE 
                 8                359 
[1] "ZSWIM3 MUTATION ANALYSIS"
[1] 3
  ZSWIM3 MUTATED ZSWIM3 WILD-TYPE 
              12              355 
  ZSWIM3 MUTATED ZSWIM3 WILD-TYPE 
              12              355 
[1] "CDH8 MUTATION ANALYSIS"
[1] 3
  CDH8 MUTATED CDH8 WILD-TYPE 
            32            335 
  CDH8 MUTATED CDH8 WILD-TYPE 
            32            335 
[1] "ADM MUTATION ANALYSIS"
[1] 3
  ADM MUTATED ADM WILD-TYPE 
            6           361 
  ADM MUTATED ADM WILD-TYPE 
            6           361 
[1] "NIPBL MUTATION ANALYSIS"
[1] 3
  NIPBL MUTATED NIPBL WILD-TYPE 
             33             334 
  NIPBL MUTATED NIPBL WILD-TYPE 
             33             334 
[1] "FRMD6 MUTATION ANALYSIS"
[1] 3
  FRMD6 MUTATED FRMD6 WILD-TYPE 
             10             357 
  FRMD6 MUTATED FRMD6 WILD-TYPE 
             10             357 
[1] "CYP4A22 MUTATION ANALYSIS"
[1] 3
  CYP4A22 MUTATED CYP4A22 WILD-TYPE 
               13               354 
  CYP4A22 MUTATED CYP4A22 WILD-TYPE 
               13               354 
[1] "KIF21A MUTATION ANALYSIS"
[1] 3
  KIF21A MUTATED KIF21A WILD-TYPE 
              24              343 
  KIF21A MUTATED KIF21A WILD-TYPE 
              24              343 
[1] "PSD3 MUTATION ANALYSIS"
[1] 3
  PSD3 MUTATED PSD3 WILD-TYPE 
            10            357 
  PSD3 MUTATED PSD3 WILD-TYPE 
            10            357 
[1] "NCF2 MUTATION ANALYSIS"
[1] 3
  NCF2 MUTATED NCF2 WILD-TYPE 
             8            359 
  NCF2 MUTATED NCF2 WILD-TYPE 
             8            359 
[1] "ZNF619 MUTATION ANALYSIS"
[1] 3
  ZNF619 MUTATED ZNF619 WILD-TYPE 
              12              355 
  ZNF619 MUTATED ZNF619 WILD-TYPE 
              12              355 
[1] "NOL9 MUTATION ANALYSIS"
[1] 3
  NOL9 MUTATED NOL9 WILD-TYPE 
             7            360 
  NOL9 MUTATED NOL9 WILD-TYPE 
             7            360 
[1] "PVRL4 MUTATION ANALYSIS"
[1] 3
  PVRL4 MUTATED PVRL4 WILD-TYPE 
              9             358 
  PVRL4 MUTATED PVRL4 WILD-TYPE 
              9             358 
[1] "FAM20B MUTATION ANALYSIS"
[1] 3
  FAM20B MUTATED FAM20B WILD-TYPE 
              10              357 
  FAM20B MUTATED FAM20B WILD-TYPE 
              10              357 
[1] "TM9SF2 MUTATION ANALYSIS"
[1] 3
  TM9SF2 MUTATED TM9SF2 WILD-TYPE 
              10              357 
  TM9SF2 MUTATED TM9SF2 WILD-TYPE 
              10              357 
[1] "PAGE2 MUTATION ANALYSIS"
[1] 3
  PAGE2 MUTATED PAGE2 WILD-TYPE 
              8             359 
  PAGE2 MUTATED PAGE2 WILD-TYPE 
              8             359 
[1] "E2F5 MUTATION ANALYSIS"
[1] 3
  E2F5 MUTATED E2F5 WILD-TYPE 
             7            360 
  E2F5 MUTATED E2F5 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] "SLC2A3 MUTATION ANALYSIS"
[1] 3
  SLC2A3 MUTATED SLC2A3 WILD-TYPE 
              11              356 
  SLC2A3 MUTATED SLC2A3 WILD-TYPE 
              11              356 
[1] "UBA3 MUTATION ANALYSIS"
[1] 3
  UBA3 MUTATED UBA3 WILD-TYPE 
             6            361 
  UBA3 MUTATED UBA3 WILD-TYPE 
             6            361 
[1] "KTN1 MUTATION ANALYSIS"
[1] 3
  KTN1 MUTATED KTN1 WILD-TYPE 
            17            350 
  KTN1 MUTATED KTN1 WILD-TYPE 
            17            350 
[1] "MAGEB2 MUTATION ANALYSIS"
[1] 3
  MAGEB2 MUTATED MAGEB2 WILD-TYPE 
              11              356 
  MAGEB2 MUTATED MAGEB2 WILD-TYPE 
              11              356 
[1] "AXIN2 MUTATION ANALYSIS"
[1] 3
  AXIN2 MUTATED AXIN2 WILD-TYPE 
             21             346 
  AXIN2 MUTATED AXIN2 WILD-TYPE 
             21             346 
[1] "MTA2 MUTATION ANALYSIS"
[1] 3
  MTA2 MUTATED MTA2 WILD-TYPE 
            12            355 
  MTA2 MUTATED MTA2 WILD-TYPE 
            12            355 
[1] "CPS1 MUTATION ANALYSIS"
[1] 3
  CPS1 MUTATED CPS1 WILD-TYPE 
            30            337 
  CPS1 MUTATED CPS1 WILD-TYPE 
            30            337 
[1] "SLC27A2 MUTATION ANALYSIS"
[1] 3
  SLC27A2 MUTATED SLC27A2 WILD-TYPE 
                6               361 
  SLC27A2 MUTATED SLC27A2 WILD-TYPE 
                6               361 
[1] "MOV10 MUTATION ANALYSIS"
[1] 3
  MOV10 MUTATED MOV10 WILD-TYPE 
             13             354 
  MOV10 MUTATED MOV10 WILD-TYPE 
             13             354 
[1] "IFNAR1 MUTATION ANALYSIS"
[1] 3
  IFNAR1 MUTATED IFNAR1 WILD-TYPE 
               7              360 
  IFNAR1 MUTATED IFNAR1 WILD-TYPE 
               7              360 
[1] "DCBLD1 MUTATION ANALYSIS"
[1] 3
  DCBLD1 MUTATED DCBLD1 WILD-TYPE 
               5              362 
  DCBLD1 MUTATED DCBLD1 WILD-TYPE 
               5              362 
[1] "SYNE1 MUTATION ANALYSIS"
[1] 3
  SYNE1 MUTATED SYNE1 WILD-TYPE 
            118             249 
  SYNE1 MUTATED SYNE1 WILD-TYPE 
            118             249 
[1] "PTPDC1 MUTATION ANALYSIS"
[1] 3
  PTPDC1 MUTATED PTPDC1 WILD-TYPE 
               9              358 
  PTPDC1 MUTATED PTPDC1 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] "ZNF605 MUTATION ANALYSIS"
[1] 3
  ZNF605 MUTATED ZNF605 WILD-TYPE 
               8              359 
  ZNF605 MUTATED ZNF605 WILD-TYPE 
               8              359 
[1] "WDR75 MUTATION ANALYSIS"
[1] 3
  WDR75 MUTATED WDR75 WILD-TYPE 
              8             359 
  WDR75 MUTATED WDR75 WILD-TYPE 
              8             359 
[1] "SLITRK2 MUTATION ANALYSIS"
[1] 3
  SLITRK2 MUTATED SLITRK2 WILD-TYPE 
               21               346 
  SLITRK2 MUTATED SLITRK2 WILD-TYPE 
               21               346 
[1] "OR51A4 MUTATION ANALYSIS"
[1] 3
  OR51A4 MUTATED OR51A4 WILD-TYPE 
               8              359 
  OR51A4 MUTATED OR51A4 WILD-TYPE 
               8              359 
[1] "UBR2 MUTATION ANALYSIS"
[1] 3
  UBR2 MUTATED UBR2 WILD-TYPE 
            15            352 
  UBR2 MUTATED UBR2 WILD-TYPE 
            15            352 
[1] "ZKSCAN1 MUTATION ANALYSIS"
[1] 3
  ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE 
                7               360 
  ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE 
                7               360 
[1] "HCLS1 MUTATION ANALYSIS"
[1] 3
  HCLS1 MUTATED HCLS1 WILD-TYPE 
             15             352 
  HCLS1 MUTATED HCLS1 WILD-TYPE 
             15             352 
[1] "PLA2G15 MUTATION ANALYSIS"
[1] 3
  PLA2G15 MUTATED PLA2G15 WILD-TYPE 
                5               362 
  PLA2G15 MUTATED PLA2G15 WILD-TYPE 
                5               362 
[1] "LRRC23 MUTATION ANALYSIS"
[1] 3
  LRRC23 MUTATED LRRC23 WILD-TYPE 
              10              357 
  LRRC23 MUTATED LRRC23 WILD-TYPE 
              10              357 
[1] "CLDN10 MUTATION ANALYSIS"
[1] 3
  CLDN10 MUTATED CLDN10 WILD-TYPE 
              11              356 
  CLDN10 MUTATED CLDN10 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] "CBX3 MUTATION ANALYSIS"
[1] 3
  CBX3 MUTATED CBX3 WILD-TYPE 
             6            361 
  CBX3 MUTATED CBX3 WILD-TYPE 
             6            361 
[1] "TBC1D10C MUTATION ANALYSIS"
[1] 3
  TBC1D10C MUTATED TBC1D10C WILD-TYPE 
                 8                359 
  TBC1D10C MUTATED TBC1D10C WILD-TYPE 
                 8                359 
[1] "BRD8 MUTATION ANALYSIS"
[1] 3
  BRD8 MUTATED BRD8 WILD-TYPE 
            15            352 
  BRD8 MUTATED BRD8 WILD-TYPE 
            15            352 
[1] "MYH15 MUTATION ANALYSIS"
[1] 3
  MYH15 MUTATED MYH15 WILD-TYPE 
             23             344 
  MYH15 MUTATED MYH15 WILD-TYPE 
             23             344 
[1] "PFN4 MUTATION ANALYSIS"
[1] 3
  PFN4 MUTATED PFN4 WILD-TYPE 
             6            361 
  PFN4 MUTATED PFN4 WILD-TYPE 
             6            361 
[1] "MRPS5 MUTATION ANALYSIS"
[1] 3
  MRPS5 MUTATED MRPS5 WILD-TYPE 
             11             356 
  MRPS5 MUTATED MRPS5 WILD-TYPE 
             11             356 
[1] "ATP10B MUTATION ANALYSIS"
[1] 3
  ATP10B MUTATED ATP10B WILD-TYPE 
              15              352 
  ATP10B MUTATED ATP10B WILD-TYPE 
              15              352 
[1] "EPC1 MUTATION ANALYSIS"
[1] 3
  EPC1 MUTATED EPC1 WILD-TYPE 
            13            354 
  EPC1 MUTATED EPC1 WILD-TYPE 
            13            354 
[1] "TBL1XR1 MUTATION ANALYSIS"
[1] 3
  TBL1XR1 MUTATED TBL1XR1 WILD-TYPE 
               13               354 
  TBL1XR1 MUTATED TBL1XR1 WILD-TYPE 
               13               354 
[1] "DNAJC7 MUTATION ANALYSIS"
[1] 3
  DNAJC7 MUTATED DNAJC7 WILD-TYPE 
               7              360 
  DNAJC7 MUTATED DNAJC7 WILD-TYPE 
               7              360 
[1] "AWAT1 MUTATION ANALYSIS"
[1] 3
  AWAT1 MUTATED AWAT1 WILD-TYPE 
              8             359 
  AWAT1 MUTATED AWAT1 WILD-TYPE 
              8             359 
[1] "NEK1 MUTATION ANALYSIS"
[1] 3
  NEK1 MUTATED NEK1 WILD-TYPE 
            12            355 
  NEK1 MUTATED NEK1 WILD-TYPE 
            12            355 
[1] "SLC24A2 MUTATION ANALYSIS"
[1] 3
  SLC24A2 MUTATED SLC24A2 WILD-TYPE 
               17               350 
  SLC24A2 MUTATED SLC24A2 WILD-TYPE 
               17               350 
[1] "RRM2B MUTATION ANALYSIS"
[1] 3
  RRM2B MUTATED RRM2B WILD-TYPE 
              5             362 
  RRM2B MUTATED RRM2B WILD-TYPE 
              5             362 
[1] "SCN3A MUTATION ANALYSIS"
[1] 3
  SCN3A MUTATED SCN3A WILD-TYPE 
             43             324 
  SCN3A MUTATED SCN3A WILD-TYPE 
             43             324 
[1] "KIAA0240 MUTATION ANALYSIS"
[1] 3
  KIAA0240 MUTATED KIAA0240 WILD-TYPE 
                 9                358 
  KIAA0240 MUTATED KIAA0240 WILD-TYPE 
                 9                358 
[1] "IVD MUTATION ANALYSIS"
[1] 3
  IVD MUTATED IVD WILD-TYPE 
            5           362 
  IVD MUTATED IVD WILD-TYPE 
            5           362 
[1] "ZFP57 MUTATION ANALYSIS"
[1] 3
  ZFP57 MUTATED ZFP57 WILD-TYPE 
             12             355 
  ZFP57 MUTATED ZFP57 WILD-TYPE 
             12             355 
[1] "RC3H2 MUTATION ANALYSIS"
[1] 3
  RC3H2 MUTATED RC3H2 WILD-TYPE 
             10             357 
  RC3H2 MUTATED RC3H2 WILD-TYPE 
             10             357 
[1] "CCDC141 MUTATION ANALYSIS"
[1] 3
  CCDC141 MUTATED CCDC141 WILD-TYPE 
               24               343 
  CCDC141 MUTATED CCDC141 WILD-TYPE 
               24               343 
[1] "HEATR4 MUTATION ANALYSIS"
[1] 3
  HEATR4 MUTATED HEATR4 WILD-TYPE 
              14              353 
  HEATR4 MUTATED HEATR4 WILD-TYPE 
              14              353 
[1] "ASPM MUTATION ANALYSIS"
[1] 3
  ASPM MUTATED ASPM WILD-TYPE 
            41            326 
  ASPM MUTATED ASPM WILD-TYPE 
            41            326 
[1] "COL6A5 MUTATION ANALYSIS"
[1] 3
  COL6A5 MUTATED COL6A5 WILD-TYPE 
              33              334 
  COL6A5 MUTATED COL6A5 WILD-TYPE 
              33              334 
[1] "PREX2 MUTATION ANALYSIS"
[1] 3
  PREX2 MUTATED PREX2 WILD-TYPE 
             31             336 
  PREX2 MUTATED PREX2 WILD-TYPE 
             31             336 
[1] "ZNF280C MUTATION ANALYSIS"
[1] 3
  ZNF280C MUTATED ZNF280C WILD-TYPE 
                9               358 
  ZNF280C MUTATED ZNF280C WILD-TYPE 
                9               358 
[1] "TSHZ1 MUTATION ANALYSIS"
[1] 3
  TSHZ1 MUTATED TSHZ1 WILD-TYPE 
             12             355 
  TSHZ1 MUTATED TSHZ1 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] "DNAH17 MUTATION ANALYSIS"
[1] 3
  DNAH17 MUTATED DNAH17 WILD-TYPE 
              34              333 
  DNAH17 MUTATED DNAH17 WILD-TYPE 
              34              333 
[1] "SLC9A9 MUTATION ANALYSIS"
[1] 3
  SLC9A9 MUTATED SLC9A9 WILD-TYPE 
              21              346 
  SLC9A9 MUTATED SLC9A9 WILD-TYPE 
              21              346 
[1] "PCDH19 MUTATION ANALYSIS"
[1] 3
  PCDH19 MUTATED PCDH19 WILD-TYPE 
              14              353 
  PCDH19 MUTATED PCDH19 WILD-TYPE 
              14              353 
[1] "TMCO6 MUTATION ANALYSIS"
[1] 3
  TMCO6 MUTATED TMCO6 WILD-TYPE 
              7             360 
  TMCO6 MUTATED TMCO6 WILD-TYPE 
              7             360 
[1] "FBXL21 MUTATION ANALYSIS"
[1] 3
  FBXL21 MUTATED FBXL21 WILD-TYPE 
               8              359 
  FBXL21 MUTATED FBXL21 WILD-TYPE 
               8              359 
[1] "CCDC55 MUTATION ANALYSIS"
[1] 3
  CCDC55 MUTATED CCDC55 WILD-TYPE 
              13              354 
  CCDC55 MUTATED CCDC55 WILD-TYPE 
              13              354 
[1] "ZNF462 MUTATION ANALYSIS"
[1] 3
  ZNF462 MUTATED ZNF462 WILD-TYPE 
              26              341 
  ZNF462 MUTATED ZNF462 WILD-TYPE 
              26              341 
[1] "SMC2 MUTATION ANALYSIS"
[1] 3
  SMC2 MUTATED SMC2 WILD-TYPE 
            25            342 
  SMC2 MUTATED SMC2 WILD-TYPE 
            25            342 
[1] "SBNO1 MUTATION ANALYSIS"
[1] 3
  SBNO1 MUTATED SBNO1 WILD-TYPE 
             15             352 
  SBNO1 MUTATED SBNO1 WILD-TYPE 
             15             352 
[1] "ALDOB MUTATION ANALYSIS"
[1] 3
  ALDOB MUTATED ALDOB WILD-TYPE 
             15             352 
  ALDOB MUTATED ALDOB WILD-TYPE 
             15             352 
[1] "TAF6 MUTATION ANALYSIS"
[1] 3
  TAF6 MUTATED TAF6 WILD-TYPE 
             8            359 
  TAF6 MUTATED TAF6 WILD-TYPE 
             8            359 
[1] "MKI67 MUTATION ANALYSIS"
[1] 3
  MKI67 MUTATED MKI67 WILD-TYPE 
             36             331 
  MKI67 MUTATED MKI67 WILD-TYPE 
             36             331 
[1] "KCNN4 MUTATION ANALYSIS"
[1] 3
  KCNN4 MUTATED KCNN4 WILD-TYPE 
              6             361 
  KCNN4 MUTATED KCNN4 WILD-TYPE 
              6             361 
[1] "STX16 MUTATION ANALYSIS"
[1] 3
  STX16 MUTATED STX16 WILD-TYPE 
              7             360 
  STX16 MUTATED STX16 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] "CSNK2A2 MUTATION ANALYSIS"
[1] 3
  CSNK2A2 MUTATED CSNK2A2 WILD-TYPE 
                7               360 
  CSNK2A2 MUTATED CSNK2A2 WILD-TYPE 
                7               360 
[1] "CASP4 MUTATION ANALYSIS"
[1] 3
  CASP4 MUTATED CASP4 WILD-TYPE 
              8             359 
  CASP4 MUTATED CASP4 WILD-TYPE 
              8             359 
[1] "WDR5 MUTATION ANALYSIS"
[1] 3
  WDR5 MUTATED WDR5 WILD-TYPE 
             6            361 
  WDR5 MUTATED WDR5 WILD-TYPE 
             6            361 
[1] "ADORA3 MUTATION ANALYSIS"
[1] 3
  ADORA3 MUTATED ADORA3 WILD-TYPE 
              14              353 
  ADORA3 MUTATED ADORA3 WILD-TYPE 
              14              353 
[1] "USP29 MUTATION ANALYSIS"
[1] 3
  USP29 MUTATED USP29 WILD-TYPE 
             18             349 
  USP29 MUTATED USP29 WILD-TYPE 
             18             349 
[1] "IL13RA2 MUTATION ANALYSIS"
[1] 3
  IL13RA2 MUTATED IL13RA2 WILD-TYPE 
               15               352 
  IL13RA2 MUTATED IL13RA2 WILD-TYPE 
               15               352 
[1] "RARRES3 MUTATION ANALYSIS"
[1] 3
  RARRES3 MUTATED RARRES3 WILD-TYPE 
                5               362 
  RARRES3 MUTATED RARRES3 WILD-TYPE 
                5               362 
[1] "EFTUD2 MUTATION ANALYSIS"
[1] 3
  EFTUD2 MUTATED EFTUD2 WILD-TYPE 
              14              353 
  EFTUD2 MUTATED EFTUD2 WILD-TYPE 
              14              353 
[1] "GGNBP2 MUTATION ANALYSIS"
[1] 3
  GGNBP2 MUTATED GGNBP2 WILD-TYPE 
              11              356 
  GGNBP2 MUTATED GGNBP2 WILD-TYPE 
              11              356 
[1] "RAB42 MUTATION ANALYSIS"
[1] 3
  RAB42 MUTATED RAB42 WILD-TYPE 
              4             363 
  RAB42 MUTATED RAB42 WILD-TYPE 
              4             363 
[1] "PER3 MUTATION ANALYSIS"
[1] 3
  PER3 MUTATED PER3 WILD-TYPE 
            17            350 
  PER3 MUTATED PER3 WILD-TYPE 
            17            350 
[1] "KCTD9 MUTATION ANALYSIS"
[1] 3
  KCTD9 MUTATED KCTD9 WILD-TYPE 
              5             362 
  KCTD9 MUTATED KCTD9 WILD-TYPE 
              5             362 
[1] "CCT5 MUTATION ANALYSIS"
[1] 3
  CCT5 MUTATED CCT5 WILD-TYPE 
             8            359 
  CCT5 MUTATED CCT5 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] "NONO MUTATION ANALYSIS"
[1] 3
  NONO MUTATED NONO WILD-TYPE 
            11            356 
  NONO MUTATED NONO WILD-TYPE 
            11            356 
[1] "ZC3H12C MUTATION ANALYSIS"
[1] 3
  ZC3H12C MUTATED ZC3H12C WILD-TYPE 
               12               355 
  ZC3H12C MUTATED ZC3H12C WILD-TYPE 
               12               355 
[1] "PIK3R4 MUTATION ANALYSIS"
[1] 3
  PIK3R4 MUTATED PIK3R4 WILD-TYPE 
              16              351 
  PIK3R4 MUTATED PIK3R4 WILD-TYPE 
              16              351 
[1] "CHRNA3 MUTATION ANALYSIS"
[1] 3
  CHRNA3 MUTATED CHRNA3 WILD-TYPE 
              10              357 
  CHRNA3 MUTATED CHRNA3 WILD-TYPE 
              10              357 
[1] "PRRT2 MUTATION ANALYSIS"
[1] 3
  PRRT2 MUTATED PRRT2 WILD-TYPE 
              6             361 
  PRRT2 MUTATED PRRT2 WILD-TYPE 
              6             361 
[1] "C4ORF49 MUTATION ANALYSIS"
[1] 3
  C4ORF49 MUTATED C4ORF49 WILD-TYPE 
                5               362 
  C4ORF49 MUTATED C4ORF49 WILD-TYPE 
                5               362 
[1] "ANKRD23 MUTATION ANALYSIS"
[1] 3
  ANKRD23 MUTATED ANKRD23 WILD-TYPE 
                4               363 
  ANKRD23 MUTATED ANKRD23 WILD-TYPE 
                4               363 
[1] "AP1G2 MUTATION ANALYSIS"
[1] 3
  AP1G2 MUTATED AP1G2 WILD-TYPE 
             13             354 
  AP1G2 MUTATED AP1G2 WILD-TYPE 
             13             354 
[1] "SATB1 MUTATION ANALYSIS"
[1] 3
  SATB1 MUTATED SATB1 WILD-TYPE 
             16             351 
  SATB1 MUTATED SATB1 WILD-TYPE 
             16             351 
[1] "PPP1R12A MUTATION ANALYSIS"
[1] 3
  PPP1R12A MUTATED PPP1R12A WILD-TYPE 
                13                354 
  PPP1R12A MUTATED PPP1R12A WILD-TYPE 
                13                354 
[1] "GIMAP5 MUTATION ANALYSIS"
[1] 3
  GIMAP5 MUTATED GIMAP5 WILD-TYPE 
               4              363 
  GIMAP5 MUTATED GIMAP5 WILD-TYPE 
               4              363 
[1] "ALCAM MUTATION ANALYSIS"
[1] 3
  ALCAM MUTATED ALCAM WILD-TYPE 
             11             356 
  ALCAM MUTATED ALCAM WILD-TYPE 
             11             356 
[1] "THUMPD3 MUTATION ANALYSIS"
[1] 3
  THUMPD3 MUTATED THUMPD3 WILD-TYPE 
               11               356 
  THUMPD3 MUTATED THUMPD3 WILD-TYPE 
               11               356 
[1] "SMARCA1 MUTATION ANALYSIS"
[1] 3
  SMARCA1 MUTATED SMARCA1 WILD-TYPE 
               19               348 
  SMARCA1 MUTATED SMARCA1 WILD-TYPE 
               19               348 
[1] "SPANXC MUTATION ANALYSIS"
[1] 3
  SPANXC MUTATED SPANXC WILD-TYPE 
               4              363 
  SPANXC MUTATED SPANXC WILD-TYPE 
               4              363 
[1] "RRAGD MUTATION ANALYSIS"
[1] 3
  RRAGD MUTATED RRAGD WILD-TYPE 
              7             360 
  RRAGD MUTATED RRAGD WILD-TYPE 
              7             360 
[1] "MYB MUTATION ANALYSIS"
[1] 3
  MYB MUTATED MYB WILD-TYPE 
            8           359 
  MYB MUTATED MYB WILD-TYPE 
            8           359 
[1] "CHD1 MUTATION ANALYSIS"
[1] 3
  CHD1 MUTATED CHD1 WILD-TYPE 
            23            344 
  CHD1 MUTATED CHD1 WILD-TYPE 
            23            344 
[1] "OR10G4 MUTATION ANALYSIS"
[1] 3
  OR10G4 MUTATED OR10G4 WILD-TYPE 
               5              362 
  OR10G4 MUTATED OR10G4 WILD-TYPE 
               5              362 
[1] "ACAT2 MUTATION ANALYSIS"
[1] 3
  ACAT2 MUTATED ACAT2 WILD-TYPE 
              8             359 
  ACAT2 MUTATED ACAT2 WILD-TYPE 
              8             359 
[1] "MTF1 MUTATION ANALYSIS"
[1] 3
  MTF1 MUTATED MTF1 WILD-TYPE 
             9            358 
  MTF1 MUTATED MTF1 WILD-TYPE 
             9            358 
[1] "HDAC5 MUTATION ANALYSIS"
[1] 3
  HDAC5 MUTATED HDAC5 WILD-TYPE 
             11             356 
  HDAC5 MUTATED HDAC5 WILD-TYPE 
             11             356 
[1] "ZNF443 MUTATION ANALYSIS"
[1] 3
  ZNF443 MUTATED ZNF443 WILD-TYPE 
               8              359 
  ZNF443 MUTATED ZNF443 WILD-TYPE 
               8              359 
[1] "DCAF12L2 MUTATION ANALYSIS"
[1] 3
  DCAF12L2 MUTATED DCAF12L2 WILD-TYPE 
                17                350 
  DCAF12L2 MUTATED DCAF12L2 WILD-TYPE 
                17                350 
[1] "CD244 MUTATION ANALYSIS"
[1] 3
  CD244 MUTATED CD244 WILD-TYPE 
              7             360 
  CD244 MUTATED CD244 WILD-TYPE 
              7             360 
[1] "LIMCH1 MUTATION ANALYSIS"
[1] 3
  LIMCH1 MUTATED LIMCH1 WILD-TYPE 
              13              354 
  LIMCH1 MUTATED LIMCH1 WILD-TYPE 
              13              354 
[1] "ESCO2 MUTATION ANALYSIS"
[1] 3
  ESCO2 MUTATED ESCO2 WILD-TYPE 
             10             357 
  ESCO2 MUTATED ESCO2 WILD-TYPE 
             10             357 
[1] "ABCD4 MUTATION ANALYSIS"
[1] 3
  ABCD4 MUTATED ABCD4 WILD-TYPE 
              9             358 
  ABCD4 MUTATED ABCD4 WILD-TYPE 
              9             358 
[1] "EPHA7 MUTATION ANALYSIS"
[1] 3
  EPHA7 MUTATED EPHA7 WILD-TYPE 
             35             332 
  EPHA7 MUTATED EPHA7 WILD-TYPE 
             35             332 
[1] "CCDC3 MUTATION ANALYSIS"
[1] 3
  CCDC3 MUTATED CCDC3 WILD-TYPE 
              4             363 
  CCDC3 MUTATED CCDC3 WILD-TYPE 
              4             363 
[1] "TMEM131 MUTATION ANALYSIS"
[1] 3
  TMEM131 MUTATED TMEM131 WILD-TYPE 
               21               346 
  TMEM131 MUTATED TMEM131 WILD-TYPE 
               21               346 
[1] "TRIM54 MUTATION ANALYSIS"
[1] 3
  TRIM54 MUTATED TRIM54 WILD-TYPE 
               9              358 
  TRIM54 MUTATED TRIM54 WILD-TYPE 
               9              358 
[1] "NAP1L1 MUTATION ANALYSIS"
[1] 3
  NAP1L1 MUTATED NAP1L1 WILD-TYPE 
               7              360 
  NAP1L1 MUTATED NAP1L1 WILD-TYPE 
               7              360 
[1] "PARP1 MUTATION ANALYSIS"
[1] 3
  PARP1 MUTATED PARP1 WILD-TYPE 
             14             353 
  PARP1 MUTATED PARP1 WILD-TYPE 
             14             353 
[1] "TUT1 MUTATION ANALYSIS"
[1] 3
  TUT1 MUTATED TUT1 WILD-TYPE 
             9            358 
  TUT1 MUTATED TUT1 WILD-TYPE 
             9            358 
[1] "OR4C15 MUTATION ANALYSIS"
[1] 3
  OR4C15 MUTATED OR4C15 WILD-TYPE 
              13              354 
  OR4C15 MUTATED OR4C15 WILD-TYPE 
              13              354 
[1] "ATIC MUTATION ANALYSIS"
[1] 3
  ATIC MUTATED ATIC WILD-TYPE 
            13            354 
  ATIC MUTATED ATIC WILD-TYPE 
            13            354 
[1] "LMOD1 MUTATION ANALYSIS"
[1] 3
  LMOD1 MUTATED LMOD1 WILD-TYPE 
             12             355 
  LMOD1 MUTATED LMOD1 WILD-TYPE 
             12             355 
[1] "GAD2 MUTATION ANALYSIS"
[1] 3
  GAD2 MUTATED GAD2 WILD-TYPE 
            15            352 
  GAD2 MUTATED GAD2 WILD-TYPE 
            15            352 
[1] "SF3B2 MUTATION ANALYSIS"
[1] 3
  SF3B2 MUTATED SF3B2 WILD-TYPE 
             10             357 
  SF3B2 MUTATED SF3B2 WILD-TYPE 
             10             357 
[1] "EMR3 MUTATION ANALYSIS"
[1] 3
  EMR3 MUTATED EMR3 WILD-TYPE 
            16            351 
  EMR3 MUTATED EMR3 WILD-TYPE 
            16            351 
[1] "CYP4F11 MUTATION ANALYSIS"
[1] 3
  CYP4F11 MUTATED CYP4F11 WILD-TYPE 
                6               361 
  CYP4F11 MUTATED CYP4F11 WILD-TYPE 
                6               361 
[1] "USP9X MUTATION ANALYSIS"
[1] 3
  USP9X MUTATED USP9X WILD-TYPE 
             31             336 
  USP9X MUTATED USP9X WILD-TYPE 
             31             336 
[1] "ADH7 MUTATION ANALYSIS"
[1] 3
  ADH7 MUTATED ADH7 WILD-TYPE 
             7            360 
  ADH7 MUTATED ADH7 WILD-TYPE 
             7            360 
[1] "RUSC2 MUTATION ANALYSIS"
[1] 3
  RUSC2 MUTATED RUSC2 WILD-TYPE 
             12             355 
  RUSC2 MUTATED RUSC2 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] "C1ORF35 MUTATION ANALYSIS"
[1] 3
  C1ORF35 MUTATED C1ORF35 WILD-TYPE 
                4               363 
  C1ORF35 MUTATED C1ORF35 WILD-TYPE 
                4               363 
[1] "SLC30A8 MUTATION ANALYSIS"
[1] 3
  SLC30A8 MUTATED SLC30A8 WILD-TYPE 
               14               353 
  SLC30A8 MUTATED SLC30A8 WILD-TYPE 
               14               353 
[1] "NSUN6 MUTATION ANALYSIS"
[1] 3
  NSUN6 MUTATED NSUN6 WILD-TYPE 
              8             359 
  NSUN6 MUTATED NSUN6 WILD-TYPE 
              8             359 
[1] "SMARCB1 MUTATION ANALYSIS"
[1] 3
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
               23               344 
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
               23               344 
[1] "FAM155B MUTATION ANALYSIS"
[1] 3
  FAM155B MUTATED FAM155B WILD-TYPE 
                8               359 
  FAM155B MUTATED FAM155B 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] "TCF7 MUTATION ANALYSIS"
[1] 3
  TCF7 MUTATED TCF7 WILD-TYPE 
            11            356 
  TCF7 MUTATED TCF7 WILD-TYPE 
            11            356 
[1] "HEPACAM2 MUTATION ANALYSIS"
[1] 3
  HEPACAM2 MUTATED HEPACAM2 WILD-TYPE 
                13                354 
  HEPACAM2 MUTATED HEPACAM2 WILD-TYPE 
                13                354 
[1] "PSMB8 MUTATION ANALYSIS"
[1] 3
  PSMB8 MUTATED PSMB8 WILD-TYPE 
              6             361 
  PSMB8 MUTATED PSMB8 WILD-TYPE 
              6             361 
[1] "RDBP MUTATION ANALYSIS"
[1] 3
  RDBP MUTATED RDBP WILD-TYPE 
             6            361 
  RDBP MUTATED RDBP WILD-TYPE 
             6            361 
[1] "F2R MUTATION ANALYSIS"
[1] 3
  F2R MUTATED F2R WILD-TYPE 
           11           356 
  F2R MUTATED F2R WILD-TYPE 
           11           356 
[1] "TRYX3 MUTATION ANALYSIS"
[1] 3
  TRYX3 MUTATED TRYX3 WILD-TYPE 
              6             361 
  TRYX3 MUTATED TRYX3 WILD-TYPE 
              6             361 
[1] "SLC27A3 MUTATION ANALYSIS"
[1] 3
  SLC27A3 MUTATED SLC27A3 WILD-TYPE 
                6               361 
  SLC27A3 MUTATED SLC27A3 WILD-TYPE 
                6               361 
[1] "AKAP11 MUTATION ANALYSIS"
[1] 3
  AKAP11 MUTATED AKAP11 WILD-TYPE 
              22              345 
  AKAP11 MUTATED AKAP11 WILD-TYPE 
              22              345 
[1] "TRIM24 MUTATION ANALYSIS"
[1] 3
  TRIM24 MUTATED TRIM24 WILD-TYPE 
              17              350 
  TRIM24 MUTATED TRIM24 WILD-TYPE 
              17              350 
[1] "ASB18 MUTATION ANALYSIS"
[1] 3
  ASB18 MUTATED ASB18 WILD-TYPE 
              7             360 
  ASB18 MUTATED ASB18 WILD-TYPE 
              7             360 
[1] "RNASEL MUTATION ANALYSIS"
[1] 3
  RNASEL MUTATED RNASEL WILD-TYPE 
              12              355 
  RNASEL MUTATED RNASEL WILD-TYPE 
              12              355 
[1] "YES1 MUTATION ANALYSIS"
[1] 3
  YES1 MUTATED YES1 WILD-TYPE 
             9            358 
  YES1 MUTATED YES1 WILD-TYPE 
             9            358 
[1] "MAP3K10 MUTATION ANALYSIS"
[1] 3
  MAP3K10 MUTATED MAP3K10 WILD-TYPE 
               10               357 
  MAP3K10 MUTATED MAP3K10 WILD-TYPE 
               10               357 
[1] "SV2A MUTATION ANALYSIS"
[1] 3
  SV2A MUTATED SV2A WILD-TYPE 
            20            347 
  SV2A MUTATED SV2A WILD-TYPE 
            20            347 
[1] "RPN2 MUTATION ANALYSIS"
[1] 3
  RPN2 MUTATED RPN2 WILD-TYPE 
             5            362 
  RPN2 MUTATED RPN2 WILD-TYPE 
             5            362 
[1] "LRIG2 MUTATION ANALYSIS"
[1] 3
  LRIG2 MUTATED LRIG2 WILD-TYPE 
              9             358 
  LRIG2 MUTATED LRIG2 WILD-TYPE 
              9             358 
[1] "OR4A16 MUTATION ANALYSIS"
[1] 3
  OR4A16 MUTATED OR4A16 WILD-TYPE 
              14              353 
  OR4A16 MUTATED OR4A16 WILD-TYPE 
              14              353 
[1] "GAS6 MUTATION ANALYSIS"
[1] 3
  GAS6 MUTATED GAS6 WILD-TYPE 
             8            359 
  GAS6 MUTATED GAS6 WILD-TYPE 
             8            359 
[1] "MLL4 MUTATION ANALYSIS"
[1] 3
  MLL4 MUTATED MLL4 WILD-TYPE 
            33            334 
  MLL4 MUTATED MLL4 WILD-TYPE 
            33            334 
[1] "TAX1BP1 MUTATION ANALYSIS"
[1] 3
  TAX1BP1 MUTATED TAX1BP1 WILD-TYPE 
               12               355 
  TAX1BP1 MUTATED TAX1BP1 WILD-TYPE 
               12               355 
[1] "ASPG MUTATION ANALYSIS"
[1] 3
  ASPG MUTATED ASPG WILD-TYPE 
             7            360 
  ASPG MUTATED ASPG 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] "TUBB4 MUTATION ANALYSIS"
[1] 3
  TUBB4 MUTATED TUBB4 WILD-TYPE 
              5             362 
  TUBB4 MUTATED TUBB4 WILD-TYPE 
              5             362 
[1] "P2RX7 MUTATION ANALYSIS"
[1] 3
  P2RX7 MUTATED P2RX7 WILD-TYPE 
             12             355 
  P2RX7 MUTATED P2RX7 WILD-TYPE 
             12             355 
[1] "SNAPC2 MUTATION ANALYSIS"
[1] 3
  SNAPC2 MUTATED SNAPC2 WILD-TYPE 
               6              361 
  SNAPC2 MUTATED SNAPC2 WILD-TYPE 
               6              361 
[1] "USF1 MUTATION ANALYSIS"
[1] 3
  USF1 MUTATED USF1 WILD-TYPE 
             5            362 
  USF1 MUTATED USF1 WILD-TYPE 
             5            362 
[1] "CATSPER4 MUTATION ANALYSIS"
[1] 3
  CATSPER4 MUTATED CATSPER4 WILD-TYPE 
                11                356 
  CATSPER4 MUTATED CATSPER4 WILD-TYPE 
                11                356 
[1] "PIK3C3 MUTATION ANALYSIS"
[1] 3
  PIK3C3 MUTATED PIK3C3 WILD-TYPE 
              23              344 
  PIK3C3 MUTATED PIK3C3 WILD-TYPE 
              23              344 
[1] "IBTK MUTATION ANALYSIS"
[1] 3
  IBTK MUTATED IBTK WILD-TYPE 
            19            348 
  IBTK MUTATED IBTK WILD-TYPE 
            19            348 
[1] "C5ORF34 MUTATION ANALYSIS"
[1] 3
  C5ORF34 MUTATED C5ORF34 WILD-TYPE 
               10               357 
  C5ORF34 MUTATED C5ORF34 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] "UAP1L1 MUTATION ANALYSIS"
[1] 3
  UAP1L1 MUTATED UAP1L1 WILD-TYPE 
               6              361 
  UAP1L1 MUTATED UAP1L1 WILD-TYPE 
               6              361 
[1] "CDC7 MUTATION ANALYSIS"
[1] 3
  CDC7 MUTATED CDC7 WILD-TYPE 
            10            357 
  CDC7 MUTATED CDC7 WILD-TYPE 
            10            357 
[1] "ST8SIA6 MUTATION ANALYSIS"
[1] 3
  ST8SIA6 MUTATED ST8SIA6 WILD-TYPE 
               10               357 
  ST8SIA6 MUTATED ST8SIA6 WILD-TYPE 
               10               357 
[1] "MRPS18B MUTATION ANALYSIS"
[1] 3
  MRPS18B MUTATED MRPS18B WILD-TYPE 
                4               363 
  MRPS18B MUTATED MRPS18B WILD-TYPE 
                4               363 
[1] "ARHGAP28 MUTATION ANALYSIS"
[1] 3
  ARHGAP28 MUTATED ARHGAP28 WILD-TYPE 
                13                354 
  ARHGAP28 MUTATED ARHGAP28 WILD-TYPE 
                13                354 
[1] "SSX2IP MUTATION ANALYSIS"
[1] 3
  SSX2IP MUTATED SSX2IP WILD-TYPE 
               8              359 
  SSX2IP MUTATED SSX2IP WILD-TYPE 
               8              359 
[1] "SPOPL MUTATION ANALYSIS"
[1] 3
  SPOPL MUTATED SPOPL WILD-TYPE 
             10             357 
  SPOPL MUTATED SPOPL WILD-TYPE 
             10             357 
[1] "DACT1 MUTATION ANALYSIS"
[1] 3
  DACT1 MUTATED DACT1 WILD-TYPE 
             15             352 
  DACT1 MUTATED DACT1 WILD-TYPE 
             15             352 
[1] "FAM193A MUTATION ANALYSIS"
[1] 3
  FAM193A MUTATED FAM193A WILD-TYPE 
               17               350 
  FAM193A MUTATED FAM193A WILD-TYPE 
               17               350 
[1] "ZFP91 MUTATION ANALYSIS"
[1] 3
  ZFP91 MUTATED ZFP91 WILD-TYPE 
              7             360 
  ZFP91 MUTATED ZFP91 WILD-TYPE 
              7             360 
[1] "USP44 MUTATION ANALYSIS"
[1] 3
  USP44 MUTATED USP44 WILD-TYPE 
             16             351 
  USP44 MUTATED USP44 WILD-TYPE 
             16             351 
[1] "ZNF559 MUTATION ANALYSIS"
[1] 3
  ZNF559 MUTATED ZNF559 WILD-TYPE 
              15              352 
  ZNF559 MUTATED ZNF559 WILD-TYPE 
              15              352 
[1] "ATR MUTATION ANALYSIS"
[1] 3
  ATR MUTATED ATR WILD-TYPE 
           28           339 
  ATR MUTATED ATR WILD-TYPE 
           28           339 
[1] "FSHR MUTATION ANALYSIS"
[1] 3
  FSHR MUTATED FSHR WILD-TYPE 
            15            352 
  FSHR MUTATED FSHR WILD-TYPE 
            15            352 
[1] "HIF3A MUTATION ANALYSIS"
[1] 3
  HIF3A MUTATED HIF3A WILD-TYPE 
             15             352 
  HIF3A MUTATED HIF3A WILD-TYPE 
             15             352 
[1] "RUNX2 MUTATION ANALYSIS"
[1] 3
  RUNX2 MUTATED RUNX2 WILD-TYPE 
              8             359 
  RUNX2 MUTATED RUNX2 WILD-TYPE 
              8             359 
[1] "SNAPC1 MUTATION ANALYSIS"
[1] 3
  SNAPC1 MUTATED SNAPC1 WILD-TYPE 
               7              360 
  SNAPC1 MUTATED SNAPC1 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] "CD34 MUTATION ANALYSIS"
[1] 3
  CD34 MUTATED CD34 WILD-TYPE 
             6            361 
  CD34 MUTATED CD34 WILD-TYPE 
             6            361 
[1] "TPR MUTATION ANALYSIS"
[1] 3
  TPR MUTATED TPR WILD-TYPE 
           22           345 
  TPR MUTATED TPR WILD-TYPE 
           22           345 
[1] "OR9Q2 MUTATION ANALYSIS"
[1] 3
  OR9Q2 MUTATED OR9Q2 WILD-TYPE 
             14             353 
  OR9Q2 MUTATED OR9Q2 WILD-TYPE 
             14             353 
[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] "SERPINB7 MUTATION ANALYSIS"
[1] 3
  SERPINB7 MUTATED SERPINB7 WILD-TYPE 
                 8                359 
  SERPINB7 MUTATED SERPINB7 WILD-TYPE 
                 8                359 
[1] "IFNA2 MUTATION ANALYSIS"
[1] 3
  IFNA2 MUTATED IFNA2 WILD-TYPE 
              9             358 
  IFNA2 MUTATED IFNA2 WILD-TYPE 
              9             358 
[1] "SPARCL1 MUTATION ANALYSIS"
[1] 3
  SPARCL1 MUTATED SPARCL1 WILD-TYPE 
               14               353 
  SPARCL1 MUTATED SPARCL1 WILD-TYPE 
               14               353 
[1] "MRPL13 MUTATION ANALYSIS"
[1] 3
  MRPL13 MUTATED MRPL13 WILD-TYPE 
               6              361 
  MRPL13 MUTATED MRPL13 WILD-TYPE 
               6              361 
[1] "IL1RL1 MUTATION ANALYSIS"
[1] 3
  IL1RL1 MUTATED IL1RL1 WILD-TYPE 
              14              353 
  IL1RL1 MUTATED IL1RL1 WILD-TYPE 
              14              353 
[1] "C7ORF50 MUTATION ANALYSIS"
[1] 3
  C7ORF50 MUTATED C7ORF50 WILD-TYPE 
                5               362 
  C7ORF50 MUTATED C7ORF50 WILD-TYPE 
                5               362 
[1] "CEACAM6 MUTATION ANALYSIS"
[1] 3
  CEACAM6 MUTATED CEACAM6 WILD-TYPE 
                4               363 
  CEACAM6 MUTATED CEACAM6 WILD-TYPE 
                4               363 
[1] "CASP1 MUTATION ANALYSIS"
[1] 3
  CASP1 MUTATED CASP1 WILD-TYPE 
              6             361 
  CASP1 MUTATED CASP1 WILD-TYPE 
              6             361 
[1] "RANBP17 MUTATION ANALYSIS"
[1] 3
  RANBP17 MUTATED RANBP17 WILD-TYPE 
               11               356 
  RANBP17 MUTATED RANBP17 WILD-TYPE 
               11               356 
[1] "JAK3 MUTATION ANALYSIS"
[1] 3
  JAK3 MUTATED JAK3 WILD-TYPE 
            24            343 
  JAK3 MUTATED JAK3 WILD-TYPE 
            24            343 
[1] "NFKBIB MUTATION ANALYSIS"
[1] 3
  NFKBIB MUTATED NFKBIB WILD-TYPE 
               5              362 
  NFKBIB MUTATED NFKBIB WILD-TYPE 
               5              362 
[1] "CHD7 MUTATION ANALYSIS"
[1] 3
  CHD7 MUTATED CHD7 WILD-TYPE 
            37            330 
  CHD7 MUTATED CHD7 WILD-TYPE 
            37            330 
[1] "FBXO34 MUTATION ANALYSIS"
[1] 3
  FBXO34 MUTATED FBXO34 WILD-TYPE 
               9              358 
  FBXO34 MUTATED FBXO34 WILD-TYPE 
               9              358 
[1] "AP1G1 MUTATION ANALYSIS"
[1] 3
  AP1G1 MUTATED AP1G1 WILD-TYPE 
             11             356 
  AP1G1 MUTATED AP1G1 WILD-TYPE 
             11             356 
[1] "PLEKHH2 MUTATION ANALYSIS"
[1] 3
  PLEKHH2 MUTATED PLEKHH2 WILD-TYPE 
               19               348 
  PLEKHH2 MUTATED PLEKHH2 WILD-TYPE 
               19               348 
[1] "FBXL19 MUTATION ANALYSIS"
[1] 3
  FBXL19 MUTATED FBXL19 WILD-TYPE 
               8              359 
  FBXL19 MUTATED FBXL19 WILD-TYPE 
               8              359 
[1] "MFSD6 MUTATION ANALYSIS"
[1] 3
  MFSD6 MUTATED MFSD6 WILD-TYPE 
              7             360 
  MFSD6 MUTATED MFSD6 WILD-TYPE 
              7             360 
[1] "SBSN MUTATION ANALYSIS"
[1] 3
  SBSN MUTATED SBSN WILD-TYPE 
            10            357 
  SBSN MUTATED SBSN WILD-TYPE 
            10            357 
[1] "ZCWPW2 MUTATION ANALYSIS"
[1] 3
  ZCWPW2 MUTATED ZCWPW2 WILD-TYPE 
              11              356 
  ZCWPW2 MUTATED ZCWPW2 WILD-TYPE 
              11              356 
[1] "PAK4 MUTATION ANALYSIS"
[1] 3
  PAK4 MUTATED PAK4 WILD-TYPE 
             6            361 
  PAK4 MUTATED PAK4 WILD-TYPE 
             6            361 
[1] "NTRK2 MUTATION ANALYSIS"
[1] 3
  NTRK2 MUTATED NTRK2 WILD-TYPE 
             23             344 
  NTRK2 MUTATED NTRK2 WILD-TYPE 
             23             344 
[1] "FRMPD4 MUTATION ANALYSIS"
[1] 3
  FRMPD4 MUTATED FRMPD4 WILD-TYPE 
              24              343 
  FRMPD4 MUTATED FRMPD4 WILD-TYPE 
              24              343 
[1] "CCDC11 MUTATION ANALYSIS"
[1] 3
  CCDC11 MUTATED CCDC11 WILD-TYPE 
              10              357 
  CCDC11 MUTATED CCDC11 WILD-TYPE 
              10              357 
[1] "OSR1 MUTATION ANALYSIS"
[1] 3
  OSR1 MUTATED OSR1 WILD-TYPE 
             4            363 
  OSR1 MUTATED OSR1 WILD-TYPE 
             4            363 
[1] "CREG2 MUTATION ANALYSIS"
[1] 3
  CREG2 MUTATED CREG2 WILD-TYPE 
              5             362 
  CREG2 MUTATED CREG2 WILD-TYPE 
              5             362 
[1] "CDH22 MUTATION ANALYSIS"
[1] 3
  CDH22 MUTATED CDH22 WILD-TYPE 
             15             352 
  CDH22 MUTATED CDH22 WILD-TYPE 
             15             352 
[1] "GUCY2F MUTATION ANALYSIS"
[1] 3
  GUCY2F MUTATED GUCY2F WILD-TYPE 
              19              348 
  GUCY2F MUTATED GUCY2F WILD-TYPE 
              19              348 
[1] "CHMP4C MUTATION ANALYSIS"
[1] 3
  CHMP4C MUTATED CHMP4C WILD-TYPE 
               3              364 
  CHMP4C MUTATED CHMP4C WILD-TYPE 
               3              364 
[1] "CTSZ MUTATION ANALYSIS"
[1] 3
  CTSZ MUTATED CTSZ WILD-TYPE 
             6            361 
  CTSZ MUTATED CTSZ WILD-TYPE 
             6            361 
[1] "LRP2 MUTATION ANALYSIS"
[1] 3
  LRP2 MUTATED LRP2 WILD-TYPE 
            77            290 
  LRP2 MUTATED LRP2 WILD-TYPE 
            77            290 
[1] "DOCK7 MUTATION ANALYSIS"
[1] 3
  DOCK7 MUTATED DOCK7 WILD-TYPE 
             17             350 
  DOCK7 MUTATED DOCK7 WILD-TYPE 
             17             350 
[1] "DCLRE1A MUTATION ANALYSIS"
[1] 3
  DCLRE1A MUTATED DCLRE1A WILD-TYPE 
               10               357 
  DCLRE1A MUTATED DCLRE1A WILD-TYPE 
               10               357 
[1] "SLC44A4 MUTATION ANALYSIS"
[1] 3
  SLC44A4 MUTATED SLC44A4 WILD-TYPE 
               11               356 
  SLC44A4 MUTATED SLC44A4 WILD-TYPE 
               11               356 
[1] "SGOL2 MUTATION ANALYSIS"
[1] 3
  SGOL2 MUTATED SGOL2 WILD-TYPE 
             12             355 
  SGOL2 MUTATED SGOL2 WILD-TYPE 
             12             355 
[1] "MAGI1 MUTATION ANALYSIS"
[1] 3
  MAGI1 MUTATED MAGI1 WILD-TYPE 
             23             344 
  MAGI1 MUTATED MAGI1 WILD-TYPE 
             23             344 
[1] "EPHA2 MUTATION ANALYSIS"
[1] 3
  EPHA2 MUTATED EPHA2 WILD-TYPE 
             11             356 
  EPHA2 MUTATED EPHA2 WILD-TYPE 
             11             356 
[1] "STK38L MUTATION ANALYSIS"
[1] 3
  STK38L MUTATED STK38L WILD-TYPE 
               7              360 
  STK38L MUTATED STK38L WILD-TYPE 
               7              360 
[1] "YLPM1 MUTATION ANALYSIS"
[1] 3
  YLPM1 MUTATED YLPM1 WILD-TYPE 
             22             345 
  YLPM1 MUTATED YLPM1 WILD-TYPE 
             22             345 
[1] "FAM189B MUTATION ANALYSIS"
[1] 3
  FAM189B MUTATED FAM189B WILD-TYPE 
                9               358 
  FAM189B MUTATED FAM189B WILD-TYPE 
                9               358 
[1] "ATG10 MUTATION ANALYSIS"
[1] 3
  ATG10 MUTATED ATG10 WILD-TYPE 
              4             363 
  ATG10 MUTATED ATG10 WILD-TYPE 
              4             363 
[1] "OR5H15 MUTATION ANALYSIS"
[1] 3
  OR5H15 MUTATED OR5H15 WILD-TYPE 
               5              362 
  OR5H15 MUTATED OR5H15 WILD-TYPE 
               5              362 
[1] "CSGALNACT1 MUTATION ANALYSIS"
[1] 3
  CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE 
                   8                  359 
  CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE 
                   8                  359 
[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] "ATP11C MUTATION ANALYSIS"
[1] 3
  ATP11C MUTATED ATP11C WILD-TYPE 
              25              342 
  ATP11C MUTATED ATP11C WILD-TYPE 
              25              342 
[1] "MAGEA4 MUTATION ANALYSIS"
[1] 3
  MAGEA4 MUTATED MAGEA4 WILD-TYPE 
               6              361 
  MAGEA4 MUTATED MAGEA4 WILD-TYPE 
               6              361 
[1] "SMC1B MUTATION ANALYSIS"
[1] 3
  SMC1B MUTATED SMC1B WILD-TYPE 
             19             348 
  SMC1B MUTATED SMC1B WILD-TYPE 
             19             348 
[1] "BCAP29 MUTATION ANALYSIS"
[1] 3
  BCAP29 MUTATED BCAP29 WILD-TYPE 
               9              358 
  BCAP29 MUTATED BCAP29 WILD-TYPE 
               9              358 
[1] "MIPEP MUTATION ANALYSIS"
[1] 3
  MIPEP MUTATED MIPEP WILD-TYPE 
              8             359 
  MIPEP MUTATED MIPEP WILD-TYPE 
              8             359 
[1] "HMCN1 MUTATION ANALYSIS"
[1] 3
  HMCN1 MUTATED HMCN1 WILD-TYPE 
             70             297 
  HMCN1 MUTATED HMCN1 WILD-TYPE 
             70             297 
[1] "RAPGEF6 MUTATION ANALYSIS"
[1] 3
  RAPGEF6 MUTATED RAPGEF6 WILD-TYPE 
               17               350 
  RAPGEF6 MUTATED RAPGEF6 WILD-TYPE 
               17               350 
[1] "BAZ2B MUTATION ANALYSIS"
[1] 3
  BAZ2B MUTATED BAZ2B WILD-TYPE 
             15             352 
  BAZ2B MUTATED BAZ2B WILD-TYPE 
             15             352 
[1] "GLDN MUTATION ANALYSIS"
[1] 3
  GLDN MUTATED GLDN WILD-TYPE 
             7            360 
  GLDN MUTATED GLDN WILD-TYPE 
             7            360 
[1] "RNF215 MUTATION ANALYSIS"
[1] 3
  RNF215 MUTATED RNF215 WILD-TYPE 
               3              364 
  RNF215 MUTATED RNF215 WILD-TYPE 
               3              364 
[1] "TYW3 MUTATION ANALYSIS"
[1] 3
  TYW3 MUTATED TYW3 WILD-TYPE 
             6            361 
  TYW3 MUTATED TYW3 WILD-TYPE 
             6            361 
[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] "LRRN1 MUTATION ANALYSIS"
[1] 3
  LRRN1 MUTATED LRRN1 WILD-TYPE 
             17             350 
  LRRN1 MUTATED LRRN1 WILD-TYPE 
             17             350 
[1] "VASH1 MUTATION ANALYSIS"
[1] 3
  VASH1 MUTATED VASH1 WILD-TYPE 
              5             362 
  VASH1 MUTATED VASH1 WILD-TYPE 
              5             362 
[1] "PIGC MUTATION ANALYSIS"
[1] 3
  PIGC MUTATED PIGC WILD-TYPE 
             3            364 
  PIGC MUTATED PIGC WILD-TYPE 
             3            364 
[1] "VPS33A MUTATION ANALYSIS"
[1] 3
  VPS33A MUTATED VPS33A WILD-TYPE 
               8              359 
  VPS33A MUTATED VPS33A WILD-TYPE 
               8              359 
[1] "UPF2 MUTATION ANALYSIS"
[1] 3
  UPF2 MUTATED UPF2 WILD-TYPE 
            16            351 
  UPF2 MUTATED UPF2 WILD-TYPE 
            16            351 
[1] "TMEM92 MUTATION ANALYSIS"
[1] 3
  TMEM92 MUTATED TMEM92 WILD-TYPE 
               3              364 
  TMEM92 MUTATED TMEM92 WILD-TYPE 
               3              364 
[1] "MALT1 MUTATION ANALYSIS"
[1] 3
  MALT1 MUTATED MALT1 WILD-TYPE 
             11             356 
  MALT1 MUTATED MALT1 WILD-TYPE 
             11             356 
[1] "OR13C5 MUTATION ANALYSIS"
[1] 3
  OR13C5 MUTATED OR13C5 WILD-TYPE 
              11              356 
  OR13C5 MUTATED OR13C5 WILD-TYPE 
              11              356 
[1] "SPAG7 MUTATION ANALYSIS"
[1] 3
  SPAG7 MUTATED SPAG7 WILD-TYPE 
              3             364 
  SPAG7 MUTATED SPAG7 WILD-TYPE 
              3             364 
[1] "DEK MUTATION ANALYSIS"
[1] 3
  DEK MUTATED DEK WILD-TYPE 
            6           361 
  DEK MUTATED DEK WILD-TYPE 
            6           361 
[1] "DIAPH2 MUTATION ANALYSIS"
[1] 3
  DIAPH2 MUTATED DIAPH2 WILD-TYPE 
              21              346 
  DIAPH2 MUTATED DIAPH2 WILD-TYPE 
              21              346 
[1] "C10ORF81 MUTATION ANALYSIS"
[1] 3
  C10ORF81 MUTATED C10ORF81 WILD-TYPE 
                 6                361 
  C10ORF81 MUTATED C10ORF81 WILD-TYPE 
                 6                361 
[1] "DPCR1 MUTATION ANALYSIS"
[1] 3
  DPCR1 MUTATED DPCR1 WILD-TYPE 
             12             355 
  DPCR1 MUTATED DPCR1 WILD-TYPE 
             12             355 
[1] "ICA1 MUTATION ANALYSIS"
[1] 3
  ICA1 MUTATED ICA1 WILD-TYPE 
             6            361 
  ICA1 MUTATED ICA1 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] "TRAPPC10 MUTATION ANALYSIS"
[1] 3
  TRAPPC10 MUTATED TRAPPC10 WILD-TYPE 
                19                348 
  TRAPPC10 MUTATED TRAPPC10 WILD-TYPE 
                19                348 
[1] "STAG2 MUTATION ANALYSIS"
[1] 3
  STAG2 MUTATED STAG2 WILD-TYPE 
             13             354 
  STAG2 MUTATED STAG2 WILD-TYPE 
             13             354 
[1] "SFRS15 MUTATION ANALYSIS"
[1] 3
  SFRS15 MUTATED SFRS15 WILD-TYPE 
              18              349 
  SFRS15 MUTATED SFRS15 WILD-TYPE 
              18              349 
[1] "ABHD2 MUTATION ANALYSIS"
[1] 3
  ABHD2 MUTATED ABHD2 WILD-TYPE 
             10             357 
  ABHD2 MUTATED ABHD2 WILD-TYPE 
             10             357 
[1] "CRTC1 MUTATION ANALYSIS"
[1] 3
  CRTC1 MUTATED CRTC1 WILD-TYPE 
             13             354 
  CRTC1 MUTATED CRTC1 WILD-TYPE 
             13             354 
[1] "TMC8 MUTATION ANALYSIS"
[1] 3
  TMC8 MUTATED TMC8 WILD-TYPE 
             7            360 
  TMC8 MUTATED TMC8 WILD-TYPE 
             7            360 
[1] "LIX1 MUTATION ANALYSIS"
[1] 3
  LIX1 MUTATED LIX1 WILD-TYPE 
             9            358 
  LIX1 MUTATED LIX1 WILD-TYPE 
             9            358 
[1] "DBF4B MUTATION ANALYSIS"
[1] 3
  DBF4B MUTATED DBF4B WILD-TYPE 
              7             360 
  DBF4B MUTATED DBF4B WILD-TYPE 
              7             360 
[1] "C7ORF66 MUTATION ANALYSIS"
[1] 3
  C7ORF66 MUTATED C7ORF66 WILD-TYPE 
                7               360 
  C7ORF66 MUTATED C7ORF66 WILD-TYPE 
                7               360 
[1] "HIST1H1A MUTATION ANALYSIS"
[1] 3
  HIST1H1A MUTATED HIST1H1A WILD-TYPE 
                 9                358 
  HIST1H1A MUTATED HIST1H1A WILD-TYPE 
                 9                358 
[1] "OR51T1 MUTATION ANALYSIS"
[1] 3
  OR51T1 MUTATED OR51T1 WILD-TYPE 
              11              356 
  OR51T1 MUTATED OR51T1 WILD-TYPE 
              11              356 
[1] "KIAA0649 MUTATION ANALYSIS"
[1] 3
  KIAA0649 MUTATED KIAA0649 WILD-TYPE 
                10                357 
  KIAA0649 MUTATED KIAA0649 WILD-TYPE 
                10                357 
[1] "MSH4 MUTATION ANALYSIS"
[1] 3
  MSH4 MUTATED MSH4 WILD-TYPE 
            13            354 
  MSH4 MUTATED MSH4 WILD-TYPE 
            13            354 
[1] "TRAF3IP1 MUTATION ANALYSIS"
[1] 3
  TRAF3IP1 MUTATED TRAF3IP1 WILD-TYPE 
                 6                361 
  TRAF3IP1 MUTATED TRAF3IP1 WILD-TYPE 
                 6                361 
[1] "GPR160 MUTATION ANALYSIS"
[1] 3
  GPR160 MUTATED GPR160 WILD-TYPE 
               4              363 
  GPR160 MUTATED GPR160 WILD-TYPE 
               4              363 
[1] "KIAA1407 MUTATION ANALYSIS"
[1] 3
  KIAA1407 MUTATED KIAA1407 WILD-TYPE 
                11                356 
  KIAA1407 MUTATED KIAA1407 WILD-TYPE 
                11                356 
[1] "DTX3L MUTATION ANALYSIS"
[1] 3
  DTX3L MUTATED DTX3L WILD-TYPE 
             10             357 
  DTX3L MUTATED DTX3L WILD-TYPE 
             10             357 
[1] "DST MUTATION ANALYSIS"
[1] 3
  DST MUTATED DST WILD-TYPE 
           66           301 
  DST MUTATED DST WILD-TYPE 
           66           301 
[1] "KIRREL2 MUTATION ANALYSIS"
[1] 3
  KIRREL2 MUTATED KIRREL2 WILD-TYPE 
               13               354 
  KIRREL2 MUTATED KIRREL2 WILD-TYPE 
               13               354 
[1] "ICAM5 MUTATION ANALYSIS"
[1] 3
  ICAM5 MUTATED ICAM5 WILD-TYPE 
             10             357 
  ICAM5 MUTATED ICAM5 WILD-TYPE 
             10             357 
[1] "ACCN5 MUTATION ANALYSIS"
[1] 3
  ACCN5 MUTATED ACCN5 WILD-TYPE 
             13             354 
  ACCN5 MUTATED ACCN5 WILD-TYPE 
             13             354 
[1] "LUM MUTATION ANALYSIS"
[1] 3
  LUM MUTATED LUM WILD-TYPE 
           12           355 
  LUM MUTATED LUM 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] "DCAF6 MUTATION ANALYSIS"
[1] 3
  DCAF6 MUTATED DCAF6 WILD-TYPE 
             14             353 
  DCAF6 MUTATED DCAF6 WILD-TYPE 
             14             353 
[1] "SF1 MUTATION ANALYSIS"
[1] 3
  SF1 MUTATED SF1 WILD-TYPE 
           16           351 
  SF1 MUTATED SF1 WILD-TYPE 
           16           351 
[1] "NXF3 MUTATION ANALYSIS"
[1] 3
  NXF3 MUTATED NXF3 WILD-TYPE 
            10            357 
  NXF3 MUTATED NXF3 WILD-TYPE 
            10            357 
[1] "NUP205 MUTATION ANALYSIS"
[1] 3
  NUP205 MUTATED NUP205 WILD-TYPE 
              22              345 
  NUP205 MUTATED NUP205 WILD-TYPE 
              22              345 
[1] "DUSP7 MUTATION ANALYSIS"
[1] 3
  DUSP7 MUTATED DUSP7 WILD-TYPE 
              6             361 
  DUSP7 MUTATED DUSP7 WILD-TYPE 
              6             361 
[1] "PAK7 MUTATION ANALYSIS"
[1] 3
  PAK7 MUTATED PAK7 WILD-TYPE 
            20            347 
  PAK7 MUTATED PAK7 WILD-TYPE 
            20            347 
[1] "AFF1 MUTATION ANALYSIS"
[1] 3
  AFF1 MUTATED AFF1 WILD-TYPE 
            12            355 
  AFF1 MUTATED AFF1 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] "C5ORF42 MUTATION ANALYSIS"
[1] 3
  C5ORF42 MUTATED C5ORF42 WILD-TYPE 
               32               335 
  C5ORF42 MUTATED C5ORF42 WILD-TYPE 
               32               335 
[1] "ZNF622 MUTATION ANALYSIS"
[1] 3
  ZNF622 MUTATED ZNF622 WILD-TYPE 
               7              360 
  ZNF622 MUTATED ZNF622 WILD-TYPE 
               7              360 
[1] "OR8K3 MUTATION ANALYSIS"
[1] 3
  OR8K3 MUTATED OR8K3 WILD-TYPE 
             10             357 
  OR8K3 MUTATED OR8K3 WILD-TYPE 
             10             357 
[1] "METT5D1 MUTATION ANALYSIS"
[1] 3
  METT5D1 MUTATED METT5D1 WILD-TYPE 
                6               361 
  METT5D1 MUTATED METT5D1 WILD-TYPE 
                6               361 
[1] "ESCO1 MUTATION ANALYSIS"
[1] 3
  ESCO1 MUTATED ESCO1 WILD-TYPE 
             13             354 
  ESCO1 MUTATED ESCO1 WILD-TYPE 
             13             354 
[1] "PTCH2 MUTATION ANALYSIS"
[1] 3
  PTCH2 MUTATED PTCH2 WILD-TYPE 
             17             350 
  PTCH2 MUTATED PTCH2 WILD-TYPE 
             17             350 
[1] "RARG MUTATION ANALYSIS"
[1] 3
  RARG MUTATED RARG WILD-TYPE 
            10            357 
  RARG MUTATED RARG WILD-TYPE 
            10            357 
[1] "PPYR1 MUTATION ANALYSIS"
[1] 3
  PPYR1 MUTATED PPYR1 WILD-TYPE 
              5             362 
  PPYR1 MUTATED PPYR1 WILD-TYPE 
              5             362 
[1] "ERCC6 MUTATION ANALYSIS"
[1] 3
  ERCC6 MUTATED ERCC6 WILD-TYPE 
             27             340 
  ERCC6 MUTATED ERCC6 WILD-TYPE 
             27             340 
[1] "NHLRC2 MUTATION ANALYSIS"
[1] 3
  NHLRC2 MUTATED NHLRC2 WILD-TYPE 
               9              358 
  NHLRC2 MUTATED NHLRC2 WILD-TYPE 
               9              358 
[1] "NRAP MUTATION ANALYSIS"
[1] 3
  NRAP MUTATED NRAP WILD-TYPE 
            26            341 
  NRAP MUTATED NRAP WILD-TYPE 
            26            341 
[1] "FABP2 MUTATION ANALYSIS"
[1] 3
  FABP2 MUTATED FABP2 WILD-TYPE 
              8             359 
  FABP2 MUTATED FABP2 WILD-TYPE 
              8             359 
[1] "KIF16B MUTATION ANALYSIS"
[1] 3
  KIF16B MUTATED KIF16B WILD-TYPE 
              26              341 
  KIF16B MUTATED KIF16B WILD-TYPE 
              26              341 
[1] "TAB3 MUTATION ANALYSIS"
[1] 3
  TAB3 MUTATED TAB3 WILD-TYPE 
            10            357 
  TAB3 MUTATED TAB3 WILD-TYPE 
            10            357 
[1] "C16ORF45 MUTATION ANALYSIS"
[1] 3
  C16ORF45 MUTATED C16ORF45 WILD-TYPE 
                 5                362 
  C16ORF45 MUTATED C16ORF45 WILD-TYPE 
                 5                362 
[1] "A1CF MUTATION ANALYSIS"
[1] 3
  A1CF MUTATED A1CF WILD-TYPE 
             8            359 
  A1CF MUTATED A1CF WILD-TYPE 
             8            359 
[1] "NUPL2 MUTATION ANALYSIS"
[1] 3
  NUPL2 MUTATED NUPL2 WILD-TYPE 
             11             356 
  NUPL2 MUTATED NUPL2 WILD-TYPE 
             11             356 
[1] "MRPS22 MUTATION ANALYSIS"
[1] 3
  MRPS22 MUTATED MRPS22 WILD-TYPE 
              10              357 
  MRPS22 MUTATED MRPS22 WILD-TYPE 
              10              357 
[1] "STAU1 MUTATION ANALYSIS"
[1] 3
  STAU1 MUTATED STAU1 WILD-TYPE 
              7             360 
  STAU1 MUTATED STAU1 WILD-TYPE 
              7             360 
[1] "OR4N4 MUTATION ANALYSIS"
[1] 3
  OR4N4 MUTATED OR4N4 WILD-TYPE 
             12             355 
  OR4N4 MUTATED OR4N4 WILD-TYPE 
             12             355 
[1] "ATP12A MUTATION ANALYSIS"
[1] 3
  ATP12A MUTATED ATP12A WILD-TYPE 
              26              341 
  ATP12A MUTATED ATP12A WILD-TYPE 
              26              341 
[1] "SPATA16 MUTATION ANALYSIS"
[1] 3
  SPATA16 MUTATED SPATA16 WILD-TYPE 
               12               355 
  SPATA16 MUTATED SPATA16 WILD-TYPE 
               12               355 
[1] "BFSP1 MUTATION ANALYSIS"
[1] 3
  BFSP1 MUTATED BFSP1 WILD-TYPE 
              8             359 
  BFSP1 MUTATED BFSP1 WILD-TYPE 
              8             359 
[1] "NEUROD1 MUTATION ANALYSIS"
[1] 3
  NEUROD1 MUTATED NEUROD1 WILD-TYPE 
                9               358 
  NEUROD1 MUTATED NEUROD1 WILD-TYPE 
                9               358 
[1] "CCR8 MUTATION ANALYSIS"
[1] 3
  CCR8 MUTATED CCR8 WILD-TYPE 
             7            360 
  CCR8 MUTATED CCR8 WILD-TYPE 
             7            360 
[1] "DHX36 MUTATION ANALYSIS"
[1] 3
  DHX36 MUTATED DHX36 WILD-TYPE 
             12             355 
  DHX36 MUTATED DHX36 WILD-TYPE 
             12             355 
[1] "CACNA1D MUTATION ANALYSIS"
[1] 3
  CACNA1D MUTATED CACNA1D WILD-TYPE 
               22               345 
  CACNA1D MUTATED CACNA1D WILD-TYPE 
               22               345 
[1] "ACTL6B MUTATION ANALYSIS"
[1] 3
  ACTL6B MUTATED ACTL6B WILD-TYPE 
               8              359 
  ACTL6B MUTATED ACTL6B WILD-TYPE 
               8              359 
[1] "HERC1 MUTATION ANALYSIS"
[1] 3
  HERC1 MUTATED HERC1 WILD-TYPE 
             31             336 
  HERC1 MUTATED HERC1 WILD-TYPE 
             31             336 
[1] "MYLK4 MUTATION ANALYSIS"
[1] 3
  MYLK4 MUTATED MYLK4 WILD-TYPE 
             11             356 
  MYLK4 MUTATED MYLK4 WILD-TYPE 
             11             356 
[1] "UBE3C MUTATION ANALYSIS"
[1] 3
  UBE3C MUTATED UBE3C WILD-TYPE 
             18             349 
  UBE3C MUTATED UBE3C 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] "MCM9 MUTATION ANALYSIS"
[1] 3
  MCM9 MUTATED MCM9 WILD-TYPE 
             8            359 
  MCM9 MUTATED MCM9 WILD-TYPE 
             8            359 
[1] "ABCB6 MUTATION ANALYSIS"
[1] 3
  ABCB6 MUTATED ABCB6 WILD-TYPE 
              7             360 
  ABCB6 MUTATED ABCB6 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] "IGSF5 MUTATION ANALYSIS"
[1] 3
  IGSF5 MUTATED IGSF5 WILD-TYPE 
             14             353 
  IGSF5 MUTATED IGSF5 WILD-TYPE 
             14             353 
[1] "PEBP4 MUTATION ANALYSIS"
[1] 3
  PEBP4 MUTATED PEBP4 WILD-TYPE 
              7             360 
  PEBP4 MUTATED PEBP4 WILD-TYPE 
              7             360 
[1] "ATXN7L1 MUTATION ANALYSIS"
[1] 3
  ATXN7L1 MUTATED ATXN7L1 WILD-TYPE 
               11               356 
  ATXN7L1 MUTATED ATXN7L1 WILD-TYPE 
               11               356 
[1] "CDK14 MUTATION ANALYSIS"
[1] 3
  CDK14 MUTATED CDK14 WILD-TYPE 
             14             353 
  CDK14 MUTATED CDK14 WILD-TYPE 
             14             353 
[1] "CEPT1 MUTATION ANALYSIS"
[1] 3
  CEPT1 MUTATED CEPT1 WILD-TYPE 
              5             362 
  CEPT1 MUTATED CEPT1 WILD-TYPE 
              5             362 
[1] "OR9Q1 MUTATION ANALYSIS"
[1] 3
  OR9Q1 MUTATED OR9Q1 WILD-TYPE 
              6             361 
  OR9Q1 MUTATED OR9Q1 WILD-TYPE 
              6             361 
[1] "ZBTB24 MUTATION ANALYSIS"
[1] 3
  ZBTB24 MUTATED ZBTB24 WILD-TYPE 
               8              359 
  ZBTB24 MUTATED ZBTB24 WILD-TYPE 
               8              359 
[1] "NSUN2 MUTATION ANALYSIS"
[1] 3
  NSUN2 MUTATED NSUN2 WILD-TYPE 
             11             356 
  NSUN2 MUTATED NSUN2 WILD-TYPE 
             11             356 
[1] "PPP2R5E MUTATION ANALYSIS"
[1] 3
  PPP2R5E MUTATED PPP2R5E WILD-TYPE 
                8               359 
  PPP2R5E MUTATED PPP2R5E WILD-TYPE 
                8               359 
[1] "ABCF3 MUTATION ANALYSIS"
[1] 3
  ABCF3 MUTATED ABCF3 WILD-TYPE 
             15             352 
  ABCF3 MUTATED ABCF3 WILD-TYPE 
             15             352 
[1] "BEX5 MUTATION ANALYSIS"
[1] 3
  BEX5 MUTATED BEX5 WILD-TYPE 
             7            360 
  BEX5 MUTATED BEX5 WILD-TYPE 
             7            360 
[1] "GBA2 MUTATION ANALYSIS"
[1] 3
  GBA2 MUTATED GBA2 WILD-TYPE 
            15            352 
  GBA2 MUTATED GBA2 WILD-TYPE 
            15            352 
[1] "CYP2C9 MUTATION ANALYSIS"
[1] 3
  CYP2C9 MUTATED CYP2C9 WILD-TYPE 
               8              359 
  CYP2C9 MUTATED CYP2C9 WILD-TYPE 
               8              359 
[1] "SLFN12L MUTATION ANALYSIS"
[1] 3
  SLFN12L MUTATED SLFN12L WILD-TYPE 
                7               360 
  SLFN12L MUTATED SLFN12L WILD-TYPE 
                7               360 
[1] "HSPBAP1 MUTATION ANALYSIS"
[1] 3
  HSPBAP1 MUTATED HSPBAP1 WILD-TYPE 
                7               360 
  HSPBAP1 MUTATED HSPBAP1 WILD-TYPE 
                7               360 
[1] "METTL5 MUTATION ANALYSIS"
[1] 3
  METTL5 MUTATED METTL5 WILD-TYPE 
               5              362 
  METTL5 MUTATED METTL5 WILD-TYPE 
               5              362 
[1] "SULT1C4 MUTATION ANALYSIS"
[1] 3
  SULT1C4 MUTATED SULT1C4 WILD-TYPE 
                3               364 
  SULT1C4 MUTATED SULT1C4 WILD-TYPE 
                3               364 
[1] "COLEC12 MUTATION ANALYSIS"
[1] 3
  COLEC12 MUTATED COLEC12 WILD-TYPE 
               17               350 
  COLEC12 MUTATED COLEC12 WILD-TYPE 
               17               350 
[1] "MAOB MUTATION ANALYSIS"
[1] 3
  MAOB MUTATED MAOB WILD-TYPE 
             6            361 
  MAOB MUTATED MAOB WILD-TYPE 
             6            361 
[1] "LPAR6 MUTATION ANALYSIS"
[1] 3
  LPAR6 MUTATED LPAR6 WILD-TYPE 
              7             360 
  LPAR6 MUTATED LPAR6 WILD-TYPE 
              7             360 
[1] "ARHGEF1 MUTATION ANALYSIS"
[1] 3
  ARHGEF1 MUTATED ARHGEF1 WILD-TYPE 
               13               354 
  ARHGEF1 MUTATED ARHGEF1 WILD-TYPE 
               13               354 
[1] "ANXA11 MUTATION ANALYSIS"
[1] 3
  ANXA11 MUTATED ANXA11 WILD-TYPE 
               7              360 
  ANXA11 MUTATED ANXA11 WILD-TYPE 
               7              360 
[1] "AKAP7 MUTATION ANALYSIS"
[1] 3
  AKAP7 MUTATED AKAP7 WILD-TYPE 
              6             361 
  AKAP7 MUTATED AKAP7 WILD-TYPE 
              6             361 
[1] "USP16 MUTATION ANALYSIS"
[1] 3
  USP16 MUTATED USP16 WILD-TYPE 
              9             358 
  USP16 MUTATED USP16 WILD-TYPE 
              9             358 
[1] "GPR161 MUTATION ANALYSIS"
[1] 3
  GPR161 MUTATED GPR161 WILD-TYPE 
               9              358 
  GPR161 MUTATED GPR161 WILD-TYPE 
               9              358 
[1] "AHSA2 MUTATION ANALYSIS"
[1] 3
  AHSA2 MUTATED AHSA2 WILD-TYPE 
              3             364 
  AHSA2 MUTATED AHSA2 WILD-TYPE 
              3             364 
[1] "FAM167B MUTATION ANALYSIS"
[1] 3
  FAM167B MUTATED FAM167B WILD-TYPE 
                4               363 
  FAM167B MUTATED FAM167B WILD-TYPE 
                4               363 
[1] "MST1R MUTATION ANALYSIS"
[1] 3
  MST1R MUTATED MST1R WILD-TYPE 
             14             353 
  MST1R MUTATED MST1R WILD-TYPE 
             14             353 
[1] "MAP2K4 MUTATION ANALYSIS"
[1] 3
  MAP2K4 MUTATED MAP2K4 WILD-TYPE 
              30              337 
  MAP2K4 MUTATED MAP2K4 WILD-TYPE 
              30              337 
[1] "SCYL2 MUTATION ANALYSIS"
[1] 3
  SCYL2 MUTATED SCYL2 WILD-TYPE 
             16             351 
  SCYL2 MUTATED SCYL2 WILD-TYPE 
             16             351 
[1] "NSF MUTATION ANALYSIS"
[1] 3
  NSF MUTATED NSF WILD-TYPE 
            4           363 
  NSF MUTATED NSF WILD-TYPE 
            4           363 
[1] "PCDH20 MUTATION ANALYSIS"
[1] 3
  PCDH20 MUTATED PCDH20 WILD-TYPE 
              21              346 
  PCDH20 MUTATED PCDH20 WILD-TYPE 
              21              346 
[1] "ATF2 MUTATION ANALYSIS"
[1] 3
  ATF2 MUTATED ATF2 WILD-TYPE 
             6            361 
  ATF2 MUTATED ATF2 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] "HEPH MUTATION ANALYSIS"
[1] 3
  HEPH MUTATED HEPH WILD-TYPE 
            15            352 
  HEPH MUTATED HEPH WILD-TYPE 
            15            352 
[1] "ALAS1 MUTATION ANALYSIS"
[1] 3
  ALAS1 MUTATED ALAS1 WILD-TYPE 
              9             358 
  ALAS1 MUTATED ALAS1 WILD-TYPE 
              9             358 
[1] "KIAA0564 MUTATION ANALYSIS"
[1] 3
  KIAA0564 MUTATED KIAA0564 WILD-TYPE 
                22                345 
  KIAA0564 MUTATED KIAA0564 WILD-TYPE 
                22                345 
[1] "PDGFC MUTATION ANALYSIS"
[1] 3
  PDGFC MUTATED PDGFC WILD-TYPE 
              9             358 
  PDGFC MUTATED PDGFC WILD-TYPE 
              9             358 
[1] "MSLNL MUTATION ANALYSIS"
[1] 3
  MSLNL MUTATED MSLNL WILD-TYPE 
              6             361 
  MSLNL MUTATED MSLNL WILD-TYPE 
              6             361 
[1] "SENP8 MUTATION ANALYSIS"
[1] 3
  SENP8 MUTATED SENP8 WILD-TYPE 
              4             363 
  SENP8 MUTATED SENP8 WILD-TYPE 
              4             363 
[1] "STK11 MUTATION ANALYSIS"
[1] 3
  STK11 MUTATED STK11 WILD-TYPE 
             32             335 
  STK11 MUTATED STK11 WILD-TYPE 
             32             335 
[1] "BRD4 MUTATION ANALYSIS"
[1] 3
  BRD4 MUTATED BRD4 WILD-TYPE 
            20            347 
  BRD4 MUTATED BRD4 WILD-TYPE 
            20            347 
[1] "IGFN1 MUTATION ANALYSIS"
[1] 3
  IGFN1 MUTATED IGFN1 WILD-TYPE 
             15             352 
  IGFN1 MUTATED IGFN1 WILD-TYPE 
             15             352 
[1] "TOP2A MUTATION ANALYSIS"
[1] 3
  TOP2A MUTATED TOP2A WILD-TYPE 
             17             350 
  TOP2A MUTATED TOP2A WILD-TYPE 
             17             350 
[1] "MARCH5 MUTATION ANALYSIS"
[1] 3
  MARCH5 MUTATED MARCH5 WILD-TYPE 
               6              361 
  MARCH5 MUTATED MARCH5 WILD-TYPE 
               6              361 
[1] "SBDS MUTATION ANALYSIS"
[1] 3
  SBDS MUTATED SBDS WILD-TYPE 
             3            364 
  SBDS MUTATED SBDS WILD-TYPE 
             3            364 
[1] "SYNGR4 MUTATION ANALYSIS"
[1] 3
  SYNGR4 MUTATED SYNGR4 WILD-TYPE 
               6              361 
  SYNGR4 MUTATED SYNGR4 WILD-TYPE 
               6              361 
[1] "USP1 MUTATION ANALYSIS"
[1] 3
  USP1 MUTATED USP1 WILD-TYPE 
             9            358 
  USP1 MUTATED USP1 WILD-TYPE 
             9            358 
[1] "VANGL1 MUTATION ANALYSIS"
[1] 3
  VANGL1 MUTATED VANGL1 WILD-TYPE 
              10              357 
  VANGL1 MUTATED VANGL1 WILD-TYPE 
              10              357 
[1] "C10ORF119 MUTATION ANALYSIS"
[1] 3
  C10ORF119 MUTATED C10ORF119 WILD-TYPE 
                  9                 358 
  C10ORF119 MUTATED C10ORF119 WILD-TYPE 
                  9                 358 
[1] "FBXO38 MUTATION ANALYSIS"
[1] 3
  FBXO38 MUTATED FBXO38 WILD-TYPE 
              18              349 
  FBXO38 MUTATED FBXO38 WILD-TYPE 
              18              349 
[1] "CD47 MUTATION ANALYSIS"
[1] 3
  CD47 MUTATED CD47 WILD-TYPE 
             8            359 
  CD47 MUTATED CD47 WILD-TYPE 
             8            359 
[1] "FAM199X MUTATION ANALYSIS"
[1] 3
  FAM199X MUTATED FAM199X WILD-TYPE 
               10               357 
  FAM199X MUTATED FAM199X WILD-TYPE 
               10               357 
[1] "DPP8 MUTATION ANALYSIS"
[1] 3
  DPP8 MUTATED DPP8 WILD-TYPE 
            13            354 
  DPP8 MUTATED DPP8 WILD-TYPE 
            13            354 
[1] "TRIM45 MUTATION ANALYSIS"
[1] 3
  TRIM45 MUTATED TRIM45 WILD-TYPE 
              14              353 
  TRIM45 MUTATED TRIM45 WILD-TYPE 
              14              353 
[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] "KIF13A MUTATION ANALYSIS"
[1] 3
  KIF13A MUTATED KIF13A WILD-TYPE 
              21              346 
  KIF13A MUTATED KIF13A WILD-TYPE 
              21              346 
[1] "PTPRR MUTATION ANALYSIS"
[1] 3
  PTPRR MUTATED PTPRR WILD-TYPE 
             10             357 
  PTPRR MUTATED PTPRR WILD-TYPE 
             10             357 
[1] "CIZ1 MUTATION ANALYSIS"
[1] 3
  CIZ1 MUTATED CIZ1 WILD-TYPE 
            15            352 
  CIZ1 MUTATED CIZ1 WILD-TYPE 
            15            352 
[1] "TBX4 MUTATION ANALYSIS"
[1] 3
  TBX4 MUTATED TBX4 WILD-TYPE 
            11            356 
  TBX4 MUTATED TBX4 WILD-TYPE 
            11            356 
[1] "LPGAT1 MUTATION ANALYSIS"
[1] 3
  LPGAT1 MUTATED LPGAT1 WILD-TYPE 
               3              364 
  LPGAT1 MUTATED LPGAT1 WILD-TYPE 
               3              364 
[1] "PROM1 MUTATION ANALYSIS"
[1] 3
  PROM1 MUTATED PROM1 WILD-TYPE 
             12             355 
  PROM1 MUTATED PROM1 WILD-TYPE 
             12             355 
[1] "AP4B1 MUTATION ANALYSIS"
[1] 3
  AP4B1 MUTATED AP4B1 WILD-TYPE 
             11             356 
  AP4B1 MUTATED AP4B1 WILD-TYPE 
             11             356 
[1] "BTBD11 MUTATION ANALYSIS"
[1] 3
  BTBD11 MUTATED BTBD11 WILD-TYPE 
              21              346 
  BTBD11 MUTATED BTBD11 WILD-TYPE 
              21              346 
[1] "CALB2 MUTATION ANALYSIS"
[1] 3
  CALB2 MUTATED CALB2 WILD-TYPE 
              4             363 
  CALB2 MUTATED CALB2 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] "PAK1 MUTATION ANALYSIS"
[1] 3
  PAK1 MUTATED PAK1 WILD-TYPE 
            10            357 
  PAK1 MUTATED PAK1 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] "CXXC5 MUTATION ANALYSIS"
[1] 3
  CXXC5 MUTATED CXXC5 WILD-TYPE 
              6             361 
  CXXC5 MUTATED CXXC5 WILD-TYPE 
              6             361 
[1] "POLQ MUTATION ANALYSIS"
[1] 3
  POLQ MUTATED POLQ WILD-TYPE 
            29            338 
  POLQ MUTATED POLQ WILD-TYPE 
            29            338 
[1] "DSC2 MUTATION ANALYSIS"
[1] 3
  DSC2 MUTATED DSC2 WILD-TYPE 
            14            353 
  DSC2 MUTATED DSC2 WILD-TYPE 
            14            353 
[1] "CCDC110 MUTATION ANALYSIS"
[1] 3
  CCDC110 MUTATED CCDC110 WILD-TYPE 
               13               354 
  CCDC110 MUTATED CCDC110 WILD-TYPE 
               13               354 
[1] "KIAA1919 MUTATION ANALYSIS"
[1] 3
  KIAA1919 MUTATED KIAA1919 WILD-TYPE 
                 9                358 
  KIAA1919 MUTATED KIAA1919 WILD-TYPE 
                 9                358 
[1] "CCNH MUTATION ANALYSIS"
[1] 3
  CCNH MUTATED CCNH WILD-TYPE 
             7            360 
  CCNH MUTATED CCNH WILD-TYPE 
             7            360 
[1] "TRERF1 MUTATION ANALYSIS"
[1] 3
  TRERF1 MUTATED TRERF1 WILD-TYPE 
              20              347 
  TRERF1 MUTATED TRERF1 WILD-TYPE 
              20              347 
[1] "CACHD1 MUTATION ANALYSIS"
[1] 3
  CACHD1 MUTATED CACHD1 WILD-TYPE 
              21              346 
  CACHD1 MUTATED CACHD1 WILD-TYPE 
              21              346 
[1] "PRKCQ MUTATION ANALYSIS"
[1] 3
  PRKCQ MUTATED PRKCQ WILD-TYPE 
             15             352 
  PRKCQ MUTATED PRKCQ WILD-TYPE 
             15             352 
[1] "DNAJC11 MUTATION ANALYSIS"
[1] 3
  DNAJC11 MUTATED DNAJC11 WILD-TYPE 
                9               358 
  DNAJC11 MUTATED DNAJC11 WILD-TYPE 
                9               358 
[1] "FOXA2 MUTATION ANALYSIS"
[1] 3
  FOXA2 MUTATED FOXA2 WILD-TYPE 
              6             361 
  FOXA2 MUTATED FOXA2 WILD-TYPE 
              6             361 
[1] "ZNF14 MUTATION ANALYSIS"
[1] 3
  ZNF14 MUTATED ZNF14 WILD-TYPE 
             13             354 
  ZNF14 MUTATED ZNF14 WILD-TYPE 
             13             354 
[1] "FLNB MUTATION ANALYSIS"
[1] 3
  FLNB MUTATED FLNB WILD-TYPE 
            28            339 
  FLNB MUTATED FLNB WILD-TYPE 
            28            339 
[1] "DUSP9 MUTATION ANALYSIS"
[1] 3
  DUSP9 MUTATED DUSP9 WILD-TYPE 
              9             358 
  DUSP9 MUTATED DUSP9 WILD-TYPE 
              9             358 
[1] "PCDH9 MUTATION ANALYSIS"
[1] 3
  PCDH9 MUTATED PCDH9 WILD-TYPE 
             38             329 
  PCDH9 MUTATED PCDH9 WILD-TYPE 
             38             329 
[1] "MAP2 MUTATION ANALYSIS"
[1] 3
  MAP2 MUTATED MAP2 WILD-TYPE 
            36            331 
  MAP2 MUTATED MAP2 WILD-TYPE 
            36            331 
[1] "TRAF2 MUTATION ANALYSIS"
[1] 3
  TRAF2 MUTATED TRAF2 WILD-TYPE 
              7             360 
  TRAF2 MUTATED TRAF2 WILD-TYPE 
              7             360 
[1] "ZNF711 MUTATION ANALYSIS"
[1] 3
  ZNF711 MUTATED ZNF711 WILD-TYPE 
              10              357 
  ZNF711 MUTATED ZNF711 WILD-TYPE 
              10              357 
[1] "SYNJ1 MUTATION ANALYSIS"
[1] 3
  SYNJ1 MUTATED SYNJ1 WILD-TYPE 
             16             351 
  SYNJ1 MUTATED SYNJ1 WILD-TYPE 
             16             351 
[1] "BTBD3 MUTATION ANALYSIS"
[1] 3
  BTBD3 MUTATED BTBD3 WILD-TYPE 
             13             354 
  BTBD3 MUTATED BTBD3 WILD-TYPE 
             13             354 
[1] "MAGOHB MUTATION ANALYSIS"
[1] 3
  MAGOHB MUTATED MAGOHB WILD-TYPE 
               3              364 
  MAGOHB MUTATED MAGOHB WILD-TYPE 
               3              364 
[1] "CDH24 MUTATION ANALYSIS"
[1] 3
  CDH24 MUTATED CDH24 WILD-TYPE 
             11             356 
  CDH24 MUTATED CDH24 WILD-TYPE 
             11             356 
[1] "DIAPH3 MUTATION ANALYSIS"
[1] 3
  DIAPH3 MUTATED DIAPH3 WILD-TYPE 
              16              351 
  DIAPH3 MUTATED DIAPH3 WILD-TYPE 
              16              351 
[1] "BTF3L4 MUTATION ANALYSIS"
[1] 3
  BTF3L4 MUTATED BTF3L4 WILD-TYPE 
               5              362 
  BTF3L4 MUTATED BTF3L4 WILD-TYPE 
               5              362 
[1] "ADAMTS16 MUTATION ANALYSIS"
[1] 3
  ADAMTS16 MUTATED ADAMTS16 WILD-TYPE 
                30                337 
  ADAMTS16 MUTATED ADAMTS16 WILD-TYPE 
                30                337 
[1] "LAMB4 MUTATION ANALYSIS"
[1] 3
  LAMB4 MUTATED LAMB4 WILD-TYPE 
             26             341 
  LAMB4 MUTATED LAMB4 WILD-TYPE 
             26             341 
[1] "BTNL3 MUTATION ANALYSIS"
[1] 3
  BTNL3 MUTATED BTNL3 WILD-TYPE 
              7             360 
  BTNL3 MUTATED BTNL3 WILD-TYPE 
              7             360 
[1] "CLVS1 MUTATION ANALYSIS"
[1] 3
  CLVS1 MUTATED CLVS1 WILD-TYPE 
              9             358 
  CLVS1 MUTATED CLVS1 WILD-TYPE 
              9             358 
[1] "C4ORF29 MUTATION ANALYSIS"
[1] 3
  C4ORF29 MUTATED C4ORF29 WILD-TYPE 
                5               362 
  C4ORF29 MUTATED C4ORF29 WILD-TYPE 
                5               362 
[1] "CMTM2 MUTATION ANALYSIS"
[1] 3
  CMTM2 MUTATED CMTM2 WILD-TYPE 
              4             363 
  CMTM2 MUTATED CMTM2 WILD-TYPE 
              4             363 
[1] "PSMA2 MUTATION ANALYSIS"
[1] 3
  PSMA2 MUTATED PSMA2 WILD-TYPE 
              6             361 
  PSMA2 MUTATED PSMA2 WILD-TYPE 
              6             361 
[1] "AIM2 MUTATION ANALYSIS"
[1] 3
  AIM2 MUTATED AIM2 WILD-TYPE 
             9            358 
  AIM2 MUTATED AIM2 WILD-TYPE 
             9            358 
[1] "DLGAP3 MUTATION ANALYSIS"
[1] 3
  DLGAP3 MUTATED DLGAP3 WILD-TYPE 
              16              351 
  DLGAP3 MUTATED DLGAP3 WILD-TYPE 
              16              351 
[1] "RFXAP MUTATION ANALYSIS"
[1] 3
  RFXAP MUTATED RFXAP WILD-TYPE 
              5             362 
  RFXAP MUTATED RFXAP WILD-TYPE 
              5             362 
[1] "NCL MUTATION ANALYSIS"
[1] 3
  NCL MUTATED NCL WILD-TYPE 
           10           357 
  NCL MUTATED NCL WILD-TYPE 
           10           357 
[1] "PACS2 MUTATION ANALYSIS"
[1] 3
  PACS2 MUTATED PACS2 WILD-TYPE 
              5             362 
  PACS2 MUTATED PACS2 WILD-TYPE 
              5             362 
[1] "GNA11 MUTATION ANALYSIS"
[1] 3
  GNA11 MUTATED GNA11 WILD-TYPE 
              7             360 
  GNA11 MUTATED GNA11 WILD-TYPE 
              7             360 
[1] "MED13 MUTATION ANALYSIS"
[1] 3
  MED13 MUTATED MED13 WILD-TYPE 
             20             347 
  MED13 MUTATED MED13 WILD-TYPE 
             20             347 
[1] "TNNI3K MUTATION ANALYSIS"
[1] 3
  TNNI3K MUTATED TNNI3K WILD-TYPE 
              11              356 
  TNNI3K MUTATED TNNI3K WILD-TYPE 
              11              356 
[1] "FAM70A MUTATION ANALYSIS"
[1] 3
  FAM70A MUTATED FAM70A WILD-TYPE 
               7              360 
  FAM70A MUTATED FAM70A WILD-TYPE 
               7              360 
[1] "TMPRSS5 MUTATION ANALYSIS"
[1] 3
  TMPRSS5 MUTATED TMPRSS5 WILD-TYPE 
                7               360 
  TMPRSS5 MUTATED TMPRSS5 WILD-TYPE 
                7               360 
[1] "DMXL2 MUTATION ANALYSIS"
[1] 3
  DMXL2 MUTATED DMXL2 WILD-TYPE 
             33             334 
  DMXL2 MUTATED DMXL2 WILD-TYPE 
             33             334 
[1] "MED12L MUTATION ANALYSIS"
[1] 3
  MED12L MUTATED MED12L WILD-TYPE 
              28              339 
  MED12L MUTATED MED12L WILD-TYPE 
              28              339 
[1] "ATP6V0A4 MUTATION ANALYSIS"
[1] 3
  ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE 
                11                356 
  ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE 
                11                356 
[1] "TMSB15B MUTATION ANALYSIS"
[1] 3
  TMSB15B MUTATED TMSB15B WILD-TYPE 
                3               364 
  TMSB15B MUTATED TMSB15B WILD-TYPE 
                3               364 
[1] "TRIP12 MUTATION ANALYSIS"
[1] 3
  TRIP12 MUTATED TRIP12 WILD-TYPE 
              28              339 
  TRIP12 MUTATED TRIP12 WILD-TYPE 
              28              339 
[1] "STAT5B MUTATION ANALYSIS"
[1] 3
  STAT5B MUTATED STAT5B WILD-TYPE 
              12              355 
  STAT5B MUTATED STAT5B WILD-TYPE 
              12              355 
[1] "PLCG2 MUTATION ANALYSIS"
[1] 3
  PLCG2 MUTATED PLCG2 WILD-TYPE 
             18             349 
  PLCG2 MUTATED PLCG2 WILD-TYPE 
             18             349 
[1] "PTPRB MUTATION ANALYSIS"
[1] 3
  PTPRB MUTATED PTPRB WILD-TYPE 
             19             348 
  PTPRB MUTATED PTPRB WILD-TYPE 
             19             348 
[1] "PRPH2 MUTATION ANALYSIS"
[1] 3
  PRPH2 MUTATED PRPH2 WILD-TYPE 
             10             357 
  PRPH2 MUTATED PRPH2 WILD-TYPE 
             10             357 
[1] "ATAD1 MUTATION ANALYSIS"
[1] 3
  ATAD1 MUTATED ATAD1 WILD-TYPE 
              8             359 
  ATAD1 MUTATED ATAD1 WILD-TYPE 
              8             359 
[1] "EFCAB4B MUTATION ANALYSIS"
[1] 3
  EFCAB4B MUTATED EFCAB4B WILD-TYPE 
                5               362 
  EFCAB4B MUTATED EFCAB4B WILD-TYPE 
                5               362 
[1] "ZNF41 MUTATION ANALYSIS"
[1] 3
  ZNF41 MUTATED ZNF41 WILD-TYPE 
              9             358 
  ZNF41 MUTATED ZNF41 WILD-TYPE 
              9             358 
[1] "ZNF295 MUTATION ANALYSIS"
[1] 3
  ZNF295 MUTATED ZNF295 WILD-TYPE 
              10              357 
  ZNF295 MUTATED ZNF295 WILD-TYPE 
              10              357 
[1] "ZNF512 MUTATION ANALYSIS"
[1] 3
  ZNF512 MUTATED ZNF512 WILD-TYPE 
               3              364 
  ZNF512 MUTATED ZNF512 WILD-TYPE 
               3              364 
[1] "NCOA5 MUTATION ANALYSIS"
[1] 3
  NCOA5 MUTATED NCOA5 WILD-TYPE 
             11             356 
  NCOA5 MUTATED NCOA5 WILD-TYPE 
             11             356 
[1] "ZHX2 MUTATION ANALYSIS"
[1] 3
  ZHX2 MUTATED ZHX2 WILD-TYPE 
            17            350 
  ZHX2 MUTATED ZHX2 WILD-TYPE 
            17            350 
[1] "SKIV2L2 MUTATION ANALYSIS"
[1] 3
  SKIV2L2 MUTATED SKIV2L2 WILD-TYPE 
               11               356 
  SKIV2L2 MUTATED SKIV2L2 WILD-TYPE 
               11               356 
[1] "MYO3A MUTATION ANALYSIS"
[1] 3
  MYO3A MUTATED MYO3A WILD-TYPE 
             37             330 
  MYO3A MUTATED MYO3A WILD-TYPE 
             37             330 
[1] "APOBEC4 MUTATION ANALYSIS"
[1] 3
  APOBEC4 MUTATED APOBEC4 WILD-TYPE 
                7               360 
  APOBEC4 MUTATED APOBEC4 WILD-TYPE 
                7               360 
[1] "ACAN MUTATION ANALYSIS"
[1] 3
  ACAN MUTATED ACAN WILD-TYPE 
            27            340 
  ACAN MUTATED ACAN WILD-TYPE 
            27            340 
[1] "SLC16A5 MUTATION ANALYSIS"
[1] 3
  SLC16A5 MUTATED SLC16A5 WILD-TYPE 
               10               357 
  SLC16A5 MUTATED SLC16A5 WILD-TYPE 
               10               357 
[1] "FBXO40 MUTATION ANALYSIS"
[1] 3
  FBXO40 MUTATED FBXO40 WILD-TYPE 
              16              351 
  FBXO40 MUTATED FBXO40 WILD-TYPE 
              16              351 
[1] "GRK5 MUTATION ANALYSIS"
[1] 3
  GRK5 MUTATED GRK5 WILD-TYPE 
            11            356 
  GRK5 MUTATED GRK5 WILD-TYPE 
            11            356 
[1] "PTPN13 MUTATION ANALYSIS"
[1] 3
  PTPN13 MUTATED PTPN13 WILD-TYPE 
              22              345 
  PTPN13 MUTATED PTPN13 WILD-TYPE 
              22              345 
[1] "JAK1 MUTATION ANALYSIS"
[1] 3
  JAK1 MUTATED JAK1 WILD-TYPE 
            18            349 
  JAK1 MUTATED JAK1 WILD-TYPE 
            18            349 
[1] "C14ORF105 MUTATION ANALYSIS"
[1] 3
  C14ORF105 MUTATED C14ORF105 WILD-TYPE 
                  3                 364 
  C14ORF105 MUTATED C14ORF105 WILD-TYPE 
                  3                 364 
[1] "C9ORF102 MUTATION ANALYSIS"
[1] 3
  C9ORF102 MUTATED C9ORF102 WILD-TYPE 
                 8                359 
  C9ORF102 MUTATED C9ORF102 WILD-TYPE 
                 8                359 
[1] "OR11H12 MUTATION ANALYSIS"
[1] 3
  OR11H12 MUTATED OR11H12 WILD-TYPE 
                3               364 
  OR11H12 MUTATED OR11H12 WILD-TYPE 
                3               364 
[1] "STYK1 MUTATION ANALYSIS"
[1] 3
  STYK1 MUTATED STYK1 WILD-TYPE 
              7             360 
  STYK1 MUTATED STYK1 WILD-TYPE 
              7             360 
[1] "TTC13 MUTATION ANALYSIS"
[1] 3
  TTC13 MUTATED TTC13 WILD-TYPE 
              9             358 
  TTC13 MUTATED TTC13 WILD-TYPE 
              9             358 
[1] "OR2F2 MUTATION ANALYSIS"
[1] 3
  OR2F2 MUTATED OR2F2 WILD-TYPE 
              7             360 
  OR2F2 MUTATED OR2F2 WILD-TYPE 
              7             360 
[1] "GCC2 MUTATION ANALYSIS"
[1] 3
  GCC2 MUTATED GCC2 WILD-TYPE 
            10            357 
  GCC2 MUTATED GCC2 WILD-TYPE 
            10            357 
[1] "ZMIZ1 MUTATION ANALYSIS"
[1] 3
  ZMIZ1 MUTATED ZMIZ1 WILD-TYPE 
              9             358 
  ZMIZ1 MUTATED ZMIZ1 WILD-TYPE 
              9             358 
[1] "CCDC19 MUTATION ANALYSIS"
[1] 3
  CCDC19 MUTATED CCDC19 WILD-TYPE 
              15              352 
  CCDC19 MUTATED CCDC19 WILD-TYPE 
              15              352 
[1] "AGFG2 MUTATION ANALYSIS"
[1] 3
  AGFG2 MUTATED AGFG2 WILD-TYPE 
              9             358 
  AGFG2 MUTATED AGFG2 WILD-TYPE 
              9             358 
[1] "BATF3 MUTATION ANALYSIS"
[1] 3
  BATF3 MUTATED BATF3 WILD-TYPE 
              4             363 
  BATF3 MUTATED BATF3 WILD-TYPE 
              4             363 
[1] "ZNF124 MUTATION ANALYSIS"
[1] 3
  ZNF124 MUTATED ZNF124 WILD-TYPE 
               8              359 
  ZNF124 MUTATED ZNF124 WILD-TYPE 
               8              359 
[1] "TBCA MUTATION ANALYSIS"
[1] 3
  TBCA MUTATED TBCA WILD-TYPE 
             4            363 
  TBCA MUTATED TBCA WILD-TYPE 
             4            363 
[1] "LRRC6 MUTATION ANALYSIS"
[1] 3
  LRRC6 MUTATED LRRC6 WILD-TYPE 
              3             364 
  LRRC6 MUTATED LRRC6 WILD-TYPE 
              3             364 
[1] "NLRP13 MUTATION ANALYSIS"
[1] 3
  NLRP13 MUTATED NLRP13 WILD-TYPE 
              27              340 
  NLRP13 MUTATED NLRP13 WILD-TYPE 
              27              340 
[1] "TMEM62 MUTATION ANALYSIS"
[1] 3
  TMEM62 MUTATED TMEM62 WILD-TYPE 
               6              361 
  TMEM62 MUTATED TMEM62 WILD-TYPE 
               6              361 
[1] "ZNF385B MUTATION ANALYSIS"
[1] 3
  ZNF385B MUTATED ZNF385B WILD-TYPE 
                7               360 
  ZNF385B MUTATED ZNF385B WILD-TYPE 
                7               360 
[1] "SAFB MUTATION ANALYSIS"
[1] 3
  SAFB MUTATED SAFB WILD-TYPE 
            14            353 
  SAFB MUTATED SAFB WILD-TYPE 
            14            353 
[1] "C7ORF60 MUTATION ANALYSIS"
[1] 3
  C7ORF60 MUTATED C7ORF60 WILD-TYPE 
                6               361 
  C7ORF60 MUTATED C7ORF60 WILD-TYPE 
                6               361 
[1] "ZNF585B MUTATION ANALYSIS"
[1] 3
  ZNF585B MUTATED ZNF585B WILD-TYPE 
                7               360 
  ZNF585B MUTATED ZNF585B WILD-TYPE 
                7               360 
[1] "FAM151A MUTATION ANALYSIS"
[1] 3
  FAM151A MUTATED FAM151A WILD-TYPE 
                6               361 
  FAM151A MUTATED FAM151A WILD-TYPE 
                6               361 
[1] "CDK5RAP2 MUTATION ANALYSIS"
[1] 3
  CDK5RAP2 MUTATED CDK5RAP2 WILD-TYPE 
                23                344 
  CDK5RAP2 MUTATED CDK5RAP2 WILD-TYPE 
                23                344 
[1] "BRSK1 MUTATION ANALYSIS"
[1] 3
  BRSK1 MUTATED BRSK1 WILD-TYPE 
             16             351 
  BRSK1 MUTATED BRSK1 WILD-TYPE 
             16             351 
[1] "IRGQ MUTATION ANALYSIS"
[1] 3
  IRGQ MUTATED IRGQ WILD-TYPE 
             3            364 
  IRGQ MUTATED IRGQ WILD-TYPE 
             3            364 
[1] "POPDC3 MUTATION ANALYSIS"
[1] 3
  POPDC3 MUTATED POPDC3 WILD-TYPE 
               6              361 
  POPDC3 MUTATED POPDC3 WILD-TYPE 
               6              361 
[1] "SLC22A10 MUTATION ANALYSIS"
[1] 3
  SLC22A10 MUTATED SLC22A10 WILD-TYPE 
                15                352 
  SLC22A10 MUTATED SLC22A10 WILD-TYPE 
                15                352 
[1] "FKTN MUTATION ANALYSIS"
[1] 3
  FKTN MUTATED FKTN WILD-TYPE 
             7            360 
  FKTN MUTATED FKTN WILD-TYPE 
             7            360 
[1] "ENPP3 MUTATION ANALYSIS"
[1] 3
  ENPP3 MUTATED ENPP3 WILD-TYPE 
              9             358 
  ENPP3 MUTATED ENPP3 WILD-TYPE 
              9             358 
[1] "MYH9 MUTATION ANALYSIS"
[1] 3
  MYH9 MUTATED MYH9 WILD-TYPE 
            31            336 
  MYH9 MUTATED MYH9 WILD-TYPE 
            31            336 
[1] "ZNF643 MUTATION ANALYSIS"
[1] 3
  ZNF643 MUTATED ZNF643 WILD-TYPE 
               9              358 
  ZNF643 MUTATED ZNF643 WILD-TYPE 
               9              358 
[1] "SLC45A2 MUTATION ANALYSIS"
[1] 3
  SLC45A2 MUTATED SLC45A2 WILD-TYPE 
                9               358 
  SLC45A2 MUTATED SLC45A2 WILD-TYPE 
                9               358 
[1] "ERN1 MUTATION ANALYSIS"
[1] 3
  ERN1 MUTATED ERN1 WILD-TYPE 
             3            364 
  ERN1 MUTATED ERN1 WILD-TYPE 
             3            364 
[1] "DPF3 MUTATION ANALYSIS"
[1] 3
  DPF3 MUTATED DPF3 WILD-TYPE 
             6            361 
  DPF3 MUTATED DPF3 WILD-TYPE 
             6            361 
[1] "TRPC1 MUTATION ANALYSIS"
[1] 3
  TRPC1 MUTATED TRPC1 WILD-TYPE 
             13             354 
  TRPC1 MUTATED TRPC1 WILD-TYPE 
             13             354 
[1] "FSTL4 MUTATION ANALYSIS"
[1] 3
  FSTL4 MUTATED FSTL4 WILD-TYPE 
             15             352 
  FSTL4 MUTATED FSTL4 WILD-TYPE 
             15             352 
[1] "SETX MUTATION ANALYSIS"
[1] 3
  SETX MUTATED SETX WILD-TYPE 
            25            342 
  SETX MUTATED SETX WILD-TYPE 
            25            342 
[1] "SLC44A1 MUTATION ANALYSIS"
[1] 3
  SLC44A1 MUTATED SLC44A1 WILD-TYPE 
                9               358 
  SLC44A1 MUTATED SLC44A1 WILD-TYPE 
                9               358 
[1] "SYT2 MUTATION ANALYSIS"
[1] 3
  SYT2 MUTATED SYT2 WILD-TYPE 
             8            359 
  SYT2 MUTATED SYT2 WILD-TYPE 
             8            359 
[1] "LCN9 MUTATION ANALYSIS"
[1] 3
  LCN9 MUTATED LCN9 WILD-TYPE 
             4            363 
  LCN9 MUTATED LCN9 WILD-TYPE 
             4            363 
[1] "DDHD2 MUTATION ANALYSIS"
[1] 3
  DDHD2 MUTATED DDHD2 WILD-TYPE 
              9             358 
  DDHD2 MUTATED DDHD2 WILD-TYPE 
              9             358 
[1] "RBM15B MUTATION ANALYSIS"
[1] 3
  RBM15B MUTATED RBM15B WILD-TYPE 
               8              359 
  RBM15B MUTATED RBM15B WILD-TYPE 
               8              359 
[1] "DCLRE1C MUTATION ANALYSIS"
[1] 3
  DCLRE1C MUTATED DCLRE1C WILD-TYPE 
                9               358 
  DCLRE1C MUTATED DCLRE1C WILD-TYPE 
                9               358 
[1] "TAF4 MUTATION ANALYSIS"
[1] 3
  TAF4 MUTATED TAF4 WILD-TYPE 
             9            358 
  TAF4 MUTATED TAF4 WILD-TYPE 
             9            358 
[1] "IFITM5 MUTATION ANALYSIS"
[1] 3
  IFITM5 MUTATED IFITM5 WILD-TYPE 
               3              364 
  IFITM5 MUTATED IFITM5 WILD-TYPE 
               3              364 
[1] "ESRP2 MUTATION ANALYSIS"
[1] 3
  ESRP2 MUTATED ESRP2 WILD-TYPE 
              9             358 
  ESRP2 MUTATED ESRP2 WILD-TYPE 
              9             358 
[1] "FRY MUTATION ANALYSIS"
[1] 3
  FRY MUTATED FRY WILD-TYPE 
           38           329 
  FRY MUTATED FRY WILD-TYPE 
           38           329 
[1] "CTCFL MUTATION ANALYSIS"
[1] 3
  CTCFL MUTATED CTCFL WILD-TYPE 
             15             352 
  CTCFL MUTATED CTCFL WILD-TYPE 
             15             352 
[1] "HIST1H2BC MUTATION ANALYSIS"
[1] 3
  HIST1H2BC MUTATED HIST1H2BC WILD-TYPE 
                  4                 363 
  HIST1H2BC MUTATED HIST1H2BC WILD-TYPE 
                  4                 363 
[1] "CNOT10 MUTATION ANALYSIS"
[1] 3
  CNOT10 MUTATED CNOT10 WILD-TYPE 
               9              358 
  CNOT10 MUTATED CNOT10 WILD-TYPE 
               9              358 
[1] "GUCY1A3 MUTATION ANALYSIS"
[1] 3
  GUCY1A3 MUTATED GUCY1A3 WILD-TYPE 
               22               345 
  GUCY1A3 MUTATED GUCY1A3 WILD-TYPE 
               22               345 
[1] "CENPJ MUTATION ANALYSIS"
[1] 3
  CENPJ MUTATED CENPJ WILD-TYPE 
             21             346 
  CENPJ MUTATED CENPJ WILD-TYPE 
             21             346 
[1] "BAZ1B MUTATION ANALYSIS"
[1] 3
  BAZ1B MUTATED BAZ1B WILD-TYPE 
             21             346 
  BAZ1B MUTATED BAZ1B WILD-TYPE 
             21             346 
[1] "ESR1 MUTATION ANALYSIS"
[1] 3
  ESR1 MUTATED ESR1 WILD-TYPE 
            19            348 
  ESR1 MUTATED ESR1 WILD-TYPE 
            19            348 
[1] "LPIN2 MUTATION ANALYSIS"
[1] 3
  LPIN2 MUTATED LPIN2 WILD-TYPE 
              9             358 
  LPIN2 MUTATED LPIN2 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] "ANKRD26 MUTATION ANALYSIS"
[1] 3
  ANKRD26 MUTATED ANKRD26 WILD-TYPE 
               19               348 
  ANKRD26 MUTATED ANKRD26 WILD-TYPE 
               19               348 
[1] "SLC8A3 MUTATION ANALYSIS"
[1] 3
  SLC8A3 MUTATED SLC8A3 WILD-TYPE 
              11              356 
  SLC8A3 MUTATED SLC8A3 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] "CASP10 MUTATION ANALYSIS"
[1] 3
  CASP10 MUTATED CASP10 WILD-TYPE 
               7              360 
  CASP10 MUTATED CASP10 WILD-TYPE 
               7              360 
[1] "PLCL2 MUTATION ANALYSIS"
[1] 3
  PLCL2 MUTATED PLCL2 WILD-TYPE 
             19             348 
  PLCL2 MUTATED PLCL2 WILD-TYPE 
             19             348 
[1] "ADAM30 MUTATION ANALYSIS"
[1] 3
  ADAM30 MUTATED ADAM30 WILD-TYPE 
               8              359 
  ADAM30 MUTATED ADAM30 WILD-TYPE 
               8              359 
[1] "MICAL1 MUTATION ANALYSIS"
[1] 3
  MICAL1 MUTATED MICAL1 WILD-TYPE 
               9              358 
  MICAL1 MUTATED MICAL1 WILD-TYPE 
               9              358 
[1] "SUPT3H MUTATION ANALYSIS"
[1] 3
  SUPT3H MUTATED SUPT3H WILD-TYPE 
              11              356 
  SUPT3H MUTATED SUPT3H WILD-TYPE 
              11              356 
[1] "TMPRSS15 MUTATION ANALYSIS"
[1] 3
  TMPRSS15 MUTATED TMPRSS15 WILD-TYPE 
                18                349 
  TMPRSS15 MUTATED TMPRSS15 WILD-TYPE 
                18                349 
[1] "RNF219 MUTATION ANALYSIS"
[1] 3
  RNF219 MUTATED RNF219 WILD-TYPE 
              14              353 
  RNF219 MUTATED RNF219 WILD-TYPE 
              14              353 
[1] "SSRP1 MUTATION ANALYSIS"
[1] 3
  SSRP1 MUTATED SSRP1 WILD-TYPE 
             13             354 
  SSRP1 MUTATED SSRP1 WILD-TYPE 
             13             354 
[1] "IKBKE MUTATION ANALYSIS"
[1] 3
  IKBKE MUTATED IKBKE WILD-TYPE 
              7             360 
  IKBKE MUTATED IKBKE WILD-TYPE 
              7             360 
[1] "EHHADH MUTATION ANALYSIS"
[1] 3
  EHHADH MUTATED EHHADH WILD-TYPE 
              13              354 
  EHHADH MUTATED EHHADH WILD-TYPE 
              13              354 
[1] "ZNF564 MUTATION ANALYSIS"
[1] 3
  ZNF564 MUTATED ZNF564 WILD-TYPE 
              10              357 
  ZNF564 MUTATED ZNF564 WILD-TYPE 
              10              357 
[1] "ARHGEF38 MUTATION ANALYSIS"
[1] 3
  ARHGEF38 MUTATED ARHGEF38 WILD-TYPE 
                 4                363 
  ARHGEF38 MUTATED ARHGEF38 WILD-TYPE 
                 4                363 
[1] "PNPLA5 MUTATION ANALYSIS"
[1] 3
  PNPLA5 MUTATED PNPLA5 WILD-TYPE 
              10              357 
  PNPLA5 MUTATED PNPLA5 WILD-TYPE 
              10              357 
[1] "C1ORF85 MUTATION ANALYSIS"
[1] 3
  C1ORF85 MUTATED C1ORF85 WILD-TYPE 
                7               360 
  C1ORF85 MUTATED C1ORF85 WILD-TYPE 
                7               360 
[1] "PANK3 MUTATION ANALYSIS"
[1] 3
  PANK3 MUTATED PANK3 WILD-TYPE 
              6             361 
  PANK3 MUTATED PANK3 WILD-TYPE 
              6             361 
[1] "CHRM3 MUTATION ANALYSIS"
[1] 3
  CHRM3 MUTATED CHRM3 WILD-TYPE 
             13             354 
  CHRM3 MUTATED CHRM3 WILD-TYPE 
             13             354 
[1] "GFRAL MUTATION ANALYSIS"
[1] 3
  GFRAL MUTATED GFRAL WILD-TYPE 
              4             363 
  GFRAL MUTATED GFRAL WILD-TYPE 
              4             363 
[1] "CCDC6 MUTATION ANALYSIS"
[1] 3
  CCDC6 MUTATED CCDC6 WILD-TYPE 
             11             356 
  CCDC6 MUTATED CCDC6 WILD-TYPE 
             11             356 
[1] "CHRND MUTATION ANALYSIS"
[1] 3
  CHRND MUTATED CHRND WILD-TYPE 
             13             354 
  CHRND MUTATED CHRND WILD-TYPE 
             13             354 
[1] "WDR45L MUTATION ANALYSIS"
[1] 3
  WDR45L MUTATED WDR45L WILD-TYPE 
               7              360 
  WDR45L MUTATED WDR45L WILD-TYPE 
               7              360 
[1] "VEPH1 MUTATION ANALYSIS"
[1] 3
  VEPH1 MUTATED VEPH1 WILD-TYPE 
             17             350 
  VEPH1 MUTATED VEPH1 WILD-TYPE 
             17             350 
[1] "SUSD5 MUTATION ANALYSIS"
[1] 3
  SUSD5 MUTATED SUSD5 WILD-TYPE 
              9             358 
  SUSD5 MUTATED SUSD5 WILD-TYPE 
              9             358 
[1] "C20ORF43 MUTATION ANALYSIS"
[1] 3
  C20ORF43 MUTATED C20ORF43 WILD-TYPE 
                 3                364 
  C20ORF43 MUTATED C20ORF43 WILD-TYPE 
                 3                364 
[1] "HIST4H4 MUTATION ANALYSIS"
[1] 3
  HIST4H4 MUTATED HIST4H4 WILD-TYPE 
                3               364 
  HIST4H4 MUTATED HIST4H4 WILD-TYPE 
                3               364 
[1] "MDN1 MUTATION ANALYSIS"
[1] 3
  MDN1 MUTATED MDN1 WILD-TYPE 
            52            315 
  MDN1 MUTATED MDN1 WILD-TYPE 
            52            315 
[1] "PAK2 MUTATION ANALYSIS"
[1] 3
  PAK2 MUTATED PAK2 WILD-TYPE 
            10            357 
  PAK2 MUTATED PAK2 WILD-TYPE 
            10            357 
[1] "MBP MUTATION ANALYSIS"
[1] 3
  MBP MUTATED MBP WILD-TYPE 
            6           361 
  MBP MUTATED MBP WILD-TYPE 
            6           361 
[1] "CSF3R MUTATION ANALYSIS"
[1] 3
  CSF3R MUTATED CSF3R WILD-TYPE 
             14             353 
  CSF3R MUTATED CSF3R 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] "MMAA MUTATION ANALYSIS"
[1] 3
  MMAA MUTATED MMAA WILD-TYPE 
             9            358 
  MMAA MUTATED MMAA WILD-TYPE 
             9            358 
[1] "MAP7 MUTATION ANALYSIS"
[1] 3
  MAP7 MUTATED MAP7 WILD-TYPE 
            11            356 
  MAP7 MUTATED MAP7 WILD-TYPE 
            11            356 
[1] "ZNF167 MUTATION ANALYSIS"
[1] 3
  ZNF167 MUTATED ZNF167 WILD-TYPE 
              17              350 
  ZNF167 MUTATED ZNF167 WILD-TYPE 
              17              350 
[1] "LRRN3 MUTATION ANALYSIS"
[1] 3
  LRRN3 MUTATED LRRN3 WILD-TYPE 
             21             346 
  LRRN3 MUTATED LRRN3 WILD-TYPE 
             21             346 
[1] "HMG20A MUTATION ANALYSIS"
[1] 3
  HMG20A MUTATED HMG20A WILD-TYPE 
              11              356 
  HMG20A MUTATED HMG20A WILD-TYPE 
              11              356 
[1] "CCDC111 MUTATION ANALYSIS"
[1] 3
  CCDC111 MUTATED CCDC111 WILD-TYPE 
                7               360 
  CCDC111 MUTATED CCDC111 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] "ZNF286B MUTATION ANALYSIS"
[1] 3
  ZNF286B MUTATED ZNF286B WILD-TYPE 
                5               362 
  ZNF286B MUTATED ZNF286B WILD-TYPE 
                5               362 
[1] "TIFAB MUTATION ANALYSIS"
[1] 3
  TIFAB MUTATED TIFAB WILD-TYPE 
              3             364 
  TIFAB MUTATED TIFAB WILD-TYPE 
              3             364 
[1] "CPO MUTATION ANALYSIS"
[1] 3
  CPO MUTATED CPO WILD-TYPE 
            8           359 
  CPO MUTATED CPO WILD-TYPE 
            8           359 
[1] "SLC26A7 MUTATION ANALYSIS"
[1] 3
  SLC26A7 MUTATED SLC26A7 WILD-TYPE 
               16               351 
  SLC26A7 MUTATED SLC26A7 WILD-TYPE 
               16               351 
[1] "HECW2 MUTATION ANALYSIS"
[1] 3
  HECW2 MUTATED HECW2 WILD-TYPE 
             28             339 
  HECW2 MUTATED HECW2 WILD-TYPE 
             28             339 
[1] "GOLIM4 MUTATION ANALYSIS"
[1] 3
  GOLIM4 MUTATED GOLIM4 WILD-TYPE 
               9              358 
  GOLIM4 MUTATED GOLIM4 WILD-TYPE 
               9              358 
[1] "STK40 MUTATION ANALYSIS"
[1] 3
  STK40 MUTATED STK40 WILD-TYPE 
              7             360 
  STK40 MUTATED STK40 WILD-TYPE 
              7             360 
[1] "APBB1IP MUTATION ANALYSIS"
[1] 3
  APBB1IP MUTATED APBB1IP WILD-TYPE 
               18               349 
  APBB1IP MUTATED APBB1IP WILD-TYPE 
               18               349 
[1] "ZNF232 MUTATION ANALYSIS"
[1] 3
  ZNF232 MUTATED ZNF232 WILD-TYPE 
               4              363 
  ZNF232 MUTATED ZNF232 WILD-TYPE 
               4              363 
[1] "RNF38 MUTATION ANALYSIS"
[1] 3
  RNF38 MUTATED RNF38 WILD-TYPE 
              4             363 
  RNF38 MUTATED RNF38 WILD-TYPE 
              4             363 
[1] "CTR9 MUTATION ANALYSIS"
[1] 3
  CTR9 MUTATED CTR9 WILD-TYPE 
            17            350 
  CTR9 MUTATED CTR9 WILD-TYPE 
            17            350 
[1] "FAM175A MUTATION ANALYSIS"
[1] 3
  FAM175A MUTATED FAM175A WILD-TYPE 
                8               359 
  FAM175A MUTATED FAM175A WILD-TYPE 
                8               359 
[1] "KIAA0528 MUTATION ANALYSIS"
[1] 3
  KIAA0528 MUTATED KIAA0528 WILD-TYPE 
                15                352 
  KIAA0528 MUTATED KIAA0528 WILD-TYPE 
                15                352 
[1] "FGD4 MUTATION ANALYSIS"
[1] 3
  FGD4 MUTATED FGD4 WILD-TYPE 
             5            362 
  FGD4 MUTATED FGD4 WILD-TYPE 
             5            362 
[1] "IRF6 MUTATION ANALYSIS"
[1] 3
  IRF6 MUTATED IRF6 WILD-TYPE 
             6            361 
  IRF6 MUTATED IRF6 WILD-TYPE 
             6            361 
[1] "FANCD2 MUTATION ANALYSIS"
[1] 3
  FANCD2 MUTATED FANCD2 WILD-TYPE 
              15              352 
  FANCD2 MUTATED FANCD2 WILD-TYPE 
              15              352 
[1] "PSMD11 MUTATION ANALYSIS"
[1] 3
  PSMD11 MUTATED PSMD11 WILD-TYPE 
               8              359 
  PSMD11 MUTATED PSMD11 WILD-TYPE 
               8              359 
[1] "MTOR MUTATION ANALYSIS"
[1] 3
  MTOR MUTATED MTOR WILD-TYPE 
            34            333 
  MTOR MUTATED MTOR WILD-TYPE 
            34            333 
[1] "RNF10 MUTATION ANALYSIS"
[1] 3
  RNF10 MUTATED RNF10 WILD-TYPE 
             13             354 
  RNF10 MUTATED RNF10 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] "CREB3 MUTATION ANALYSIS"
[1] 3
  CREB3 MUTATED CREB3 WILD-TYPE 
              5             362 
  CREB3 MUTATED CREB3 WILD-TYPE 
              5             362 
[1] "MTIF2 MUTATION ANALYSIS"
[1] 3
  MTIF2 MUTATED MTIF2 WILD-TYPE 
              9             358 
  MTIF2 MUTATED MTIF2 WILD-TYPE 
              9             358 
[1] "MAP3K13 MUTATION ANALYSIS"
[1] 3
  MAP3K13 MUTATED MAP3K13 WILD-TYPE 
               18               349 
  MAP3K13 MUTATED MAP3K13 WILD-TYPE 
               18               349 
[1] "SETD7 MUTATION ANALYSIS"
[1] 3
  SETD7 MUTATED SETD7 WILD-TYPE 
              7             360 
  SETD7 MUTATED SETD7 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] "ETV1 MUTATION ANALYSIS"
[1] 3
  ETV1 MUTATED ETV1 WILD-TYPE 
            13            354 
  ETV1 MUTATED ETV1 WILD-TYPE 
            13            354 
[1] "WWC3 MUTATION ANALYSIS"
[1] 3
  WWC3 MUTATED WWC3 WILD-TYPE 
            22            345 
  WWC3 MUTATED WWC3 WILD-TYPE 
            22            345 
[1] "SMC3 MUTATION ANALYSIS"
[1] 3
  SMC3 MUTATED SMC3 WILD-TYPE 
            10            357 
  SMC3 MUTATED SMC3 WILD-TYPE 
            10            357 
[1] "ANKRD40 MUTATION ANALYSIS"
[1] 3
  ANKRD40 MUTATED ANKRD40 WILD-TYPE 
                8               359 
  ANKRD40 MUTATED ANKRD40 WILD-TYPE 
                8               359 
[1] "STAT3 MUTATION ANALYSIS"
[1] 3
  STAT3 MUTATED STAT3 WILD-TYPE 
              9             358 
  STAT3 MUTATED STAT3 WILD-TYPE 
              9             358 
[1] "WFDC10B MUTATION ANALYSIS"
[1] 3
  WFDC10B MUTATED WFDC10B WILD-TYPE 
                5               362 
  WFDC10B MUTATED WFDC10B WILD-TYPE 
                5               362 
[1] "OR10T2 MUTATION ANALYSIS"
[1] 3
  OR10T2 MUTATED OR10T2 WILD-TYPE 
               8              359 
  OR10T2 MUTATED OR10T2 WILD-TYPE 
               8              359 
[1] "KIAA0415 MUTATION ANALYSIS"
[1] 3
  KIAA0415 MUTATED KIAA0415 WILD-TYPE 
                12                355 
  KIAA0415 MUTATED KIAA0415 WILD-TYPE 
                12                355 
[1] "CD79A MUTATION ANALYSIS"
[1] 3
  CD79A MUTATED CD79A WILD-TYPE 
              6             361 
  CD79A MUTATED CD79A WILD-TYPE 
              6             361 
[1] "HCFC1R1 MUTATION ANALYSIS"
[1] 3
  HCFC1R1 MUTATED HCFC1R1 WILD-TYPE 
                5               362 
  HCFC1R1 MUTATED HCFC1R1 WILD-TYPE 
                5               362 
[1] "GPR113 MUTATION ANALYSIS"
[1] 3
  GPR113 MUTATED GPR113 WILD-TYPE 
              14              353 
  GPR113 MUTATED GPR113 WILD-TYPE 
              14              353 
[1] "HIST1H4L MUTATION ANALYSIS"
[1] 3
  HIST1H4L MUTATED HIST1H4L WILD-TYPE 
                 6                361 
  HIST1H4L MUTATED HIST1H4L WILD-TYPE 
                 6                361 
[1] "GRIN2B MUTATION ANALYSIS"
[1] 3
  GRIN2B MUTATED GRIN2B WILD-TYPE 
              26              341 
  GRIN2B MUTATED GRIN2B WILD-TYPE 
              26              341 
[1] "PON3 MUTATION ANALYSIS"
[1] 3
  PON3 MUTATED PON3 WILD-TYPE 
            10            357 
  PON3 MUTATED PON3 WILD-TYPE 
            10            357 
[1] "LGR4 MUTATION ANALYSIS"
[1] 3
  LGR4 MUTATED LGR4 WILD-TYPE 
            14            353 
  LGR4 MUTATED LGR4 WILD-TYPE 
            14            353 
[1] "MC3R MUTATION ANALYSIS"
[1] 3
  MC3R MUTATED MC3R WILD-TYPE 
            13            354 
  MC3R MUTATED MC3R WILD-TYPE 
            13            354 
[1] "IDI1 MUTATION ANALYSIS"
[1] 3
  IDI1 MUTATED IDI1 WILD-TYPE 
             4            363 
  IDI1 MUTATED IDI1 WILD-TYPE 
             4            363 
[1] "CCDC14 MUTATION ANALYSIS"
[1] 3
  CCDC14 MUTATED CCDC14 WILD-TYPE 
              11              356 
  CCDC14 MUTATED CCDC14 WILD-TYPE 
              11              356 
[1] "KLF12 MUTATION ANALYSIS"
[1] 3
  KLF12 MUTATED KLF12 WILD-TYPE 
              3             364 
  KLF12 MUTATED KLF12 WILD-TYPE 
              3             364 
[1] "ZNF556 MUTATION ANALYSIS"
[1] 3
  ZNF556 MUTATED ZNF556 WILD-TYPE 
               6              361 
  ZNF556 MUTATED ZNF556 WILD-TYPE 
               6              361 
[1] "PROKR2 MUTATION ANALYSIS"
[1] 3
  PROKR2 MUTATED PROKR2 WILD-TYPE 
               9              358 
  PROKR2 MUTATED PROKR2 WILD-TYPE 
               9              358 
[1] "ACTN1 MUTATION ANALYSIS"
[1] 3
  ACTN1 MUTATED ACTN1 WILD-TYPE 
              9             358 
  ACTN1 MUTATED ACTN1 WILD-TYPE 
              9             358 
[1] "KIAA2018 MUTATION ANALYSIS"
[1] 3
  KIAA2018 MUTATED KIAA2018 WILD-TYPE 
                21                346 
  KIAA2018 MUTATED KIAA2018 WILD-TYPE 
                21                346 
[1] "CCT4 MUTATION ANALYSIS"
[1] 3
  CCT4 MUTATED CCT4 WILD-TYPE 
            12            355 
  CCT4 MUTATED CCT4 WILD-TYPE 
            12            355 
[1] "IFLTD1 MUTATION ANALYSIS"
[1] 3
  IFLTD1 MUTATED IFLTD1 WILD-TYPE 
              13              354 
  IFLTD1 MUTATED IFLTD1 WILD-TYPE 
              13              354 
[1] "IL18R1 MUTATION ANALYSIS"
[1] 3
  IL18R1 MUTATED IL18R1 WILD-TYPE 
              13              354 
  IL18R1 MUTATED IL18R1 WILD-TYPE 
              13              354 
[1] "TRIM25 MUTATION ANALYSIS"
[1] 3
  TRIM25 MUTATED TRIM25 WILD-TYPE 
               4              363 
  TRIM25 MUTATED TRIM25 WILD-TYPE 
               4              363 
[1] "DONSON MUTATION ANALYSIS"
[1] 3
  DONSON MUTATED DONSON WILD-TYPE 
               4              363 
  DONSON MUTATED DONSON WILD-TYPE 
               4              363 
[1] "CALCOCO2 MUTATION ANALYSIS"
[1] 3
  CALCOCO2 MUTATED CALCOCO2 WILD-TYPE 
                 7                360 
  CALCOCO2 MUTATED CALCOCO2 WILD-TYPE 
                 7                360 
[1] "CBX8 MUTATION ANALYSIS"
[1] 3
  CBX8 MUTATED CBX8 WILD-TYPE 
            11            356 
  CBX8 MUTATED CBX8 WILD-TYPE 
            11            356 
[1] "C6ORF150 MUTATION ANALYSIS"
[1] 3
  C6ORF150 MUTATED C6ORF150 WILD-TYPE 
                 9                358 
  C6ORF150 MUTATED C6ORF150 WILD-TYPE 
                 9                358 
[1] "CDS2 MUTATION ANALYSIS"
[1] 3
  CDS2 MUTATED CDS2 WILD-TYPE 
             9            358 
  CDS2 MUTATED CDS2 WILD-TYPE 
             9            358 
[1] "IDE MUTATION ANALYSIS"
[1] 3
  IDE MUTATED IDE WILD-TYPE 
           10           357 
  IDE MUTATED IDE WILD-TYPE 
           10           357 
[1] "ARID5A MUTATION ANALYSIS"
[1] 3
  ARID5A MUTATED ARID5A WILD-TYPE 
               8              359 
  ARID5A MUTATED ARID5A WILD-TYPE 
               8              359 
[1] "CHD5 MUTATION ANALYSIS"
[1] 3
  CHD5 MUTATED CHD5 WILD-TYPE 
            26            341 
  CHD5 MUTATED CHD5 WILD-TYPE 
            26            341 
[1] "DNAJC18 MUTATION ANALYSIS"
[1] 3
  DNAJC18 MUTATED DNAJC18 WILD-TYPE 
                7               360 
  DNAJC18 MUTATED DNAJC18 WILD-TYPE 
                7               360 
[1] "CXCR7 MUTATION ANALYSIS"
[1] 3
  CXCR7 MUTATED CXCR7 WILD-TYPE 
             19             348 
  CXCR7 MUTATED CXCR7 WILD-TYPE 
             19             348 
[1] "LEMD1 MUTATION ANALYSIS"
[1] 3
  LEMD1 MUTATED LEMD1 WILD-TYPE 
              3             364 
  LEMD1 MUTATED LEMD1 WILD-TYPE 
              3             364 
[1] "FUT8 MUTATION ANALYSIS"
[1] 3
  FUT8 MUTATED FUT8 WILD-TYPE 
            10            357 
  FUT8 MUTATED FUT8 WILD-TYPE 
            10            357 
[1] "ANKRD12 MUTATION ANALYSIS"
[1] 3
  ANKRD12 MUTATED ANKRD12 WILD-TYPE 
               23               344 
  ANKRD12 MUTATED ANKRD12 WILD-TYPE 
               23               344 
[1] "FSCB MUTATION ANALYSIS"
[1] 3
  FSCB MUTATED FSCB WILD-TYPE 
            20            347 
  FSCB MUTATED FSCB WILD-TYPE 
            20            347 
[1] "SLC9A2 MUTATION ANALYSIS"
[1] 3
  SLC9A2 MUTATED SLC9A2 WILD-TYPE 
              10              357 
  SLC9A2 MUTATED SLC9A2 WILD-TYPE 
              10              357 
[1] "CASP5 MUTATION ANALYSIS"
[1] 3
  CASP5 MUTATED CASP5 WILD-TYPE 
             13             354 
  CASP5 MUTATED CASP5 WILD-TYPE 
             13             354 
[1] "TOMM70A MUTATION ANALYSIS"
[1] 3
  TOMM70A MUTATED TOMM70A WILD-TYPE 
               10               357 
  TOMM70A MUTATED TOMM70A WILD-TYPE 
               10               357 
[1] "GPX6 MUTATION ANALYSIS"
[1] 3
  GPX6 MUTATED GPX6 WILD-TYPE 
             8            359 
  GPX6 MUTATED GPX6 WILD-TYPE 
             8            359 
[1] "OR5H1 MUTATION ANALYSIS"
[1] 3
  OR5H1 MUTATED OR5H1 WILD-TYPE 
             10             357 
  OR5H1 MUTATED OR5H1 WILD-TYPE 
             10             357 
[1] "ESYT1 MUTATION ANALYSIS"
[1] 3
  ESYT1 MUTATED ESYT1 WILD-TYPE 
              9             358 
  ESYT1 MUTATED ESYT1 WILD-TYPE 
              9             358 
[1] "TSPAN7 MUTATION ANALYSIS"
[1] 3
  TSPAN7 MUTATED TSPAN7 WILD-TYPE 
               8              359 
  TSPAN7 MUTATED TSPAN7 WILD-TYPE 
               8              359 
[1] "OR4N2 MUTATION ANALYSIS"
[1] 3
  OR4N2 MUTATED OR4N2 WILD-TYPE 
             10             357 
  OR4N2 MUTATED OR4N2 WILD-TYPE 
             10             357 
[1] "OXA1L MUTATION ANALYSIS"
[1] 3
  OXA1L MUTATED OXA1L WILD-TYPE 
              5             362 
  OXA1L MUTATED OXA1L WILD-TYPE 
              5             362 
[1] "DLGAP5 MUTATION ANALYSIS"
[1] 3
  DLGAP5 MUTATED DLGAP5 WILD-TYPE 
               8              359 
  DLGAP5 MUTATED DLGAP5 WILD-TYPE 
               8              359 
[1] "NKTR MUTATION ANALYSIS"
[1] 3
  NKTR MUTATED NKTR WILD-TYPE 
            13            354 
  NKTR MUTATED NKTR WILD-TYPE 
            13            354 
[1] "TTLL13 MUTATION ANALYSIS"
[1] 3
  TTLL13 MUTATED TTLL13 WILD-TYPE 
               5              362 
  TTLL13 MUTATED TTLL13 WILD-TYPE 
               5              362 
[1] "VPS52 MUTATION ANALYSIS"
[1] 3
  VPS52 MUTATED VPS52 WILD-TYPE 
             11             356 
  VPS52 MUTATED VPS52 WILD-TYPE 
             11             356 
[1] "CDHR5 MUTATION ANALYSIS"
[1] 3
  CDHR5 MUTATED CDHR5 WILD-TYPE 
             11             356 
  CDHR5 MUTATED CDHR5 WILD-TYPE 
             11             356 
[1] "AVPR1A MUTATION ANALYSIS"
[1] 3
  AVPR1A MUTATED AVPR1A WILD-TYPE 
              11              356 
  AVPR1A MUTATED AVPR1A WILD-TYPE 
              11              356 
[1] "GRIN2A MUTATION ANALYSIS"
[1] 3
  GRIN2A MUTATED GRIN2A WILD-TYPE 
              41              326 
  GRIN2A MUTATED GRIN2A WILD-TYPE 
              41              326 
[1] "MFRP MUTATION ANALYSIS"
[1] 3
  MFRP MUTATED MFRP WILD-TYPE 
            11            356 
  MFRP MUTATED MFRP WILD-TYPE 
            11            356 
[1] "WIPI2 MUTATION ANALYSIS"
[1] 3
  WIPI2 MUTATED WIPI2 WILD-TYPE 
             10             357 
  WIPI2 MUTATED WIPI2 WILD-TYPE 
             10             357 
[1] "C9ORF125 MUTATION ANALYSIS"
[1] 3
  C9ORF125 MUTATED C9ORF125 WILD-TYPE 
                12                355 
  C9ORF125 MUTATED C9ORF125 WILD-TYPE 
                12                355 
[1] "PISD MUTATION ANALYSIS"
[1] 3
  PISD MUTATED PISD WILD-TYPE 
             5            362 
  PISD MUTATED PISD WILD-TYPE 
             5            362 
[1] "DYM MUTATION ANALYSIS"
[1] 3
  DYM MUTATED DYM WILD-TYPE 
           10           357 
  DYM MUTATED DYM 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] "MORC1 MUTATION ANALYSIS"
[1] 3
  MORC1 MUTATED MORC1 WILD-TYPE 
             13             354 
  MORC1 MUTATED MORC1 WILD-TYPE 
             13             354 
[1] "OR7D4 MUTATION ANALYSIS"
[1] 3
  OR7D4 MUTATED OR7D4 WILD-TYPE 
              9             358 
  OR7D4 MUTATED OR7D4 WILD-TYPE 
              9             358 
[1] "ST6GALNAC3 MUTATION ANALYSIS"
[1] 3
  ST6GALNAC3 MUTATED ST6GALNAC3 WILD-TYPE 
                  12                  355 
  ST6GALNAC3 MUTATED ST6GALNAC3 WILD-TYPE 
                  12                  355 
[1] "CCDC18 MUTATION ANALYSIS"
[1] 3
  CCDC18 MUTATED CCDC18 WILD-TYPE 
              11              356 
  CCDC18 MUTATED CCDC18 WILD-TYPE 
              11              356 
[1] "CLDN17 MUTATION ANALYSIS"
[1] 3
  CLDN17 MUTATED CLDN17 WILD-TYPE 
              13              354 
  CLDN17 MUTATED CLDN17 WILD-TYPE 
              13              354 
[1] "ENGASE MUTATION ANALYSIS"
[1] 3
  ENGASE MUTATED ENGASE WILD-TYPE 
               4              363 
  ENGASE MUTATED ENGASE WILD-TYPE 
               4              363 
[1] "TAPBP MUTATION ANALYSIS"
[1] 3
  TAPBP MUTATED TAPBP WILD-TYPE 
              4             363 
  TAPBP MUTATED TAPBP WILD-TYPE 
              4             363 
[1] "CAPZA3 MUTATION ANALYSIS"
[1] 3
  CAPZA3 MUTATED CAPZA3 WILD-TYPE 
               9              358 
  CAPZA3 MUTATED CAPZA3 WILD-TYPE 
               9              358 
[1] "BEND2 MUTATION ANALYSIS"
[1] 3
  BEND2 MUTATED BEND2 WILD-TYPE 
             23             344 
  BEND2 MUTATED BEND2 WILD-TYPE 
             23             344 
[1] "PIWIL1 MUTATION ANALYSIS"
[1] 3
  PIWIL1 MUTATED PIWIL1 WILD-TYPE 
              22              345 
  PIWIL1 MUTATED PIWIL1 WILD-TYPE 
              22              345 
[1] "SLC14A1 MUTATION ANALYSIS"
[1] 3
  SLC14A1 MUTATED SLC14A1 WILD-TYPE 
               10               357 
  SLC14A1 MUTATED SLC14A1 WILD-TYPE 
               10               357 
[1] "RIMS2 MUTATION ANALYSIS"
[1] 3
  RIMS2 MUTATED RIMS2 WILD-TYPE 
             36             331 
  RIMS2 MUTATED RIMS2 WILD-TYPE 
             36             331 
[1] "CEP164 MUTATION ANALYSIS"
[1] 3
  CEP164 MUTATED CEP164 WILD-TYPE 
              23              344 
  CEP164 MUTATED CEP164 WILD-TYPE 
              23              344 
[1] "PON1 MUTATION ANALYSIS"
[1] 3
  PON1 MUTATED PON1 WILD-TYPE 
             9            358 
  PON1 MUTATED PON1 WILD-TYPE 
             9            358 
[1] "CORO1C MUTATION ANALYSIS"
[1] 3
  CORO1C MUTATED CORO1C WILD-TYPE 
               6              361 
  CORO1C MUTATED CORO1C WILD-TYPE 
               6              361 
[1] "KIFC2 MUTATION ANALYSIS"
[1] 3
  KIFC2 MUTATED KIFC2 WILD-TYPE 
              6             361 
  KIFC2 MUTATED KIFC2 WILD-TYPE 
              6             361 
[1] "NOD2 MUTATION ANALYSIS"
[1] 3
  NOD2 MUTATED NOD2 WILD-TYPE 
            16            351 
  NOD2 MUTATED NOD2 WILD-TYPE 
            16            351 
[1] "KIAA0196 MUTATION ANALYSIS"
[1] 3
  KIAA0196 MUTATED KIAA0196 WILD-TYPE 
                10                357 
  KIAA0196 MUTATED KIAA0196 WILD-TYPE 
                10                357 
[1] "LRMP MUTATION ANALYSIS"
[1] 3
  LRMP MUTATED LRMP WILD-TYPE 
             6            361 
  LRMP MUTATED LRMP WILD-TYPE 
             6            361 
[1] "GSG2 MUTATION ANALYSIS"
[1] 3
  GSG2 MUTATED GSG2 WILD-TYPE 
             6            361 
  GSG2 MUTATED GSG2 WILD-TYPE 
             6            361 
[1] "GCNT4 MUTATION ANALYSIS"
[1] 3
  GCNT4 MUTATED GCNT4 WILD-TYPE 
             10             357 
  GCNT4 MUTATED GCNT4 WILD-TYPE 
             10             357 
[1] "ZSCAN20 MUTATION ANALYSIS"
[1] 3
  ZSCAN20 MUTATED ZSCAN20 WILD-TYPE 
               13               354 
  ZSCAN20 MUTATED ZSCAN20 WILD-TYPE 
               13               354 
[1] "NUDT16L1 MUTATION ANALYSIS"
[1] 3
  NUDT16L1 MUTATED NUDT16L1 WILD-TYPE 
                 3                364 
  NUDT16L1 MUTATED NUDT16L1 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] "OR9G4 MUTATION ANALYSIS"
[1] 3
  OR9G4 MUTATED OR9G4 WILD-TYPE 
              8             359 
  OR9G4 MUTATED OR9G4 WILD-TYPE 
              8             359 
[1] "LAMA3 MUTATION ANALYSIS"
[1] 3
  LAMA3 MUTATED LAMA3 WILD-TYPE 
             34             333 
  LAMA3 MUTATED LAMA3 WILD-TYPE 
             34             333 
[1] "TRAF3IP3 MUTATION ANALYSIS"
[1] 3
  TRAF3IP3 MUTATED TRAF3IP3 WILD-TYPE 
                12                355 
  TRAF3IP3 MUTATED TRAF3IP3 WILD-TYPE 
                12                355 
[1] "CTNNA3 MUTATION ANALYSIS"
[1] 3
  CTNNA3 MUTATED CTNNA3 WILD-TYPE 
              26              341 
  CTNNA3 MUTATED CTNNA3 WILD-TYPE 
              26              341 
[1] "KIAA0319 MUTATION ANALYSIS"
[1] 3
  KIAA0319 MUTATED KIAA0319 WILD-TYPE 
                15                352 
  KIAA0319 MUTATED KIAA0319 WILD-TYPE 
                15                352 
[1] "GLTSCR1 MUTATION ANALYSIS"
[1] 3
  GLTSCR1 MUTATED GLTSCR1 WILD-TYPE 
               11               356 
  GLTSCR1 MUTATED GLTSCR1 WILD-TYPE 
               11               356 
[1] "ZNF518A MUTATION ANALYSIS"
[1] 3
  ZNF518A MUTATED ZNF518A WILD-TYPE 
               18               349 
  ZNF518A MUTATED ZNF518A WILD-TYPE 
               18               349 
[1] "RCOR3 MUTATION ANALYSIS"
[1] 3
  RCOR3 MUTATED RCOR3 WILD-TYPE 
             12             355 
  RCOR3 MUTATED RCOR3 WILD-TYPE 
             12             355 
[1] "UVRAG MUTATION ANALYSIS"
[1] 3
  UVRAG MUTATED UVRAG WILD-TYPE 
              7             360 
  UVRAG MUTATED UVRAG WILD-TYPE 
              7             360 
[1] "IPPK MUTATION ANALYSIS"
[1] 3
  IPPK MUTATED IPPK WILD-TYPE 
             9            358 
  IPPK MUTATED IPPK WILD-TYPE 
             9            358 
[1] "SLC38A9 MUTATION ANALYSIS"
[1] 3
  SLC38A9 MUTATED SLC38A9 WILD-TYPE 
               11               356 
  SLC38A9 MUTATED SLC38A9 WILD-TYPE 
               11               356 
[1] "HIST1H3B MUTATION ANALYSIS"
[1] 3
  HIST1H3B MUTATED HIST1H3B WILD-TYPE 
                 4                363 
  HIST1H3B MUTATED HIST1H3B WILD-TYPE 
                 4                363 
[1] "PRKD1 MUTATION ANALYSIS"
[1] 3
  PRKD1 MUTATED PRKD1 WILD-TYPE 
             24             343 
  PRKD1 MUTATED PRKD1 WILD-TYPE 
             24             343 
[1] "IL34 MUTATION ANALYSIS"
[1] 3
  IL34 MUTATED IL34 WILD-TYPE 
             3            364 
  IL34 MUTATED IL34 WILD-TYPE 
             3            364 
[1] "YIF1A MUTATION ANALYSIS"
[1] 3
  YIF1A MUTATED YIF1A WILD-TYPE 
              7             360 
  YIF1A MUTATED YIF1A WILD-TYPE 
              7             360 
[1] "LCK MUTATION ANALYSIS"
[1] 3
  LCK MUTATED LCK WILD-TYPE 
            8           359 
  LCK MUTATED LCK WILD-TYPE 
            8           359 
[1] "ANK3 MUTATION ANALYSIS"
[1] 3
  ANK3 MUTATED ANK3 WILD-TYPE 
            49            318 
  ANK3 MUTATED ANK3 WILD-TYPE 
            49            318 
[1] "CTNND1 MUTATION ANALYSIS"
[1] 3
  CTNND1 MUTATED CTNND1 WILD-TYPE 
              19              348 
  CTNND1 MUTATED CTNND1 WILD-TYPE 
              19              348 
[1] "MR1 MUTATION ANALYSIS"
[1] 3
  MR1 MUTATED MR1 WILD-TYPE 
            5           362 
  MR1 MUTATED MR1 WILD-TYPE 
            5           362 
[1] "ARID4B MUTATION ANALYSIS"
[1] 3
  ARID4B MUTATED ARID4B WILD-TYPE 
              11              356 
  ARID4B MUTATED ARID4B WILD-TYPE 
              11              356 
[1] "G2E3 MUTATION ANALYSIS"
[1] 3
  G2E3 MUTATED G2E3 WILD-TYPE 
            12            355 
  G2E3 MUTATED G2E3 WILD-TYPE 
            12            355 
[1] "KCNC3 MUTATION ANALYSIS"
[1] 3
  KCNC3 MUTATED KCNC3 WILD-TYPE 
             11             356 
  KCNC3 MUTATED KCNC3 WILD-TYPE 
             11             356 
[1] "PUS7 MUTATION ANALYSIS"
[1] 3
  PUS7 MUTATED PUS7 WILD-TYPE 
            13            354 
  PUS7 MUTATED PUS7 WILD-TYPE 
            13            354 
[1] "RASGRF2 MUTATION ANALYSIS"
[1] 3
  RASGRF2 MUTATED RASGRF2 WILD-TYPE 
               17               350 
  RASGRF2 MUTATED RASGRF2 WILD-TYPE 
               17               350 
[1] "TET1 MUTATION ANALYSIS"
[1] 3
  TET1 MUTATED TET1 WILD-TYPE 
            23            344 
  TET1 MUTATED TET1 WILD-TYPE 
            23            344 
[1] "BRCA1 MUTATION ANALYSIS"
[1] 3
  BRCA1 MUTATED BRCA1 WILD-TYPE 
             26             341 
  BRCA1 MUTATED BRCA1 WILD-TYPE 
             26             341 
[1] "ACOX1 MUTATION ANALYSIS"
[1] 3
  ACOX1 MUTATED ACOX1 WILD-TYPE 
             11             356 
  ACOX1 MUTATED ACOX1 WILD-TYPE 
             11             356 
[1] "PIAS2 MUTATION ANALYSIS"
[1] 3
  PIAS2 MUTATED PIAS2 WILD-TYPE 
              4             363 
  PIAS2 MUTATED PIAS2 WILD-TYPE 
              4             363 
[1] "GATAD2A MUTATION ANALYSIS"
[1] 3
  GATAD2A MUTATED GATAD2A WILD-TYPE 
                9               358 
  GATAD2A MUTATED GATAD2A WILD-TYPE 
                9               358 
[1] "SECISBP2 MUTATION ANALYSIS"
[1] 3
  SECISBP2 MUTATED SECISBP2 WILD-TYPE 
                 8                359 
  SECISBP2 MUTATED SECISBP2 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] "AGBL5 MUTATION ANALYSIS"
[1] 3
  AGBL5 MUTATED AGBL5 WILD-TYPE 
             12             355 
  AGBL5 MUTATED AGBL5 WILD-TYPE 
             12             355 
[1] "DEFB129 MUTATION ANALYSIS"
[1] 3
  DEFB129 MUTATED DEFB129 WILD-TYPE 
                5               362 
  DEFB129 MUTATED DEFB129 WILD-TYPE 
                5               362 
[1] "SIX5 MUTATION ANALYSIS"
[1] 3
  SIX5 MUTATED SIX5 WILD-TYPE 
             5            362 
  SIX5 MUTATED SIX5 WILD-TYPE 
             5            362 
[1] "ZNF577 MUTATION ANALYSIS"
[1] 3
  ZNF577 MUTATED ZNF577 WILD-TYPE 
              12              355 
  ZNF577 MUTATED ZNF577 WILD-TYPE 
              12              355 
[1] "GPBP1 MUTATION ANALYSIS"
[1] 3
  GPBP1 MUTATED GPBP1 WILD-TYPE 
             12             355 
  GPBP1 MUTATED GPBP1 WILD-TYPE 
             12             355 
[1] "DOCK8 MUTATION ANALYSIS"
[1] 3
  DOCK8 MUTATED DOCK8 WILD-TYPE 
             20             347 
  DOCK8 MUTATED DOCK8 WILD-TYPE 
             20             347 
[1] "AKT1 MUTATION ANALYSIS"
[1] 3
  AKT1 MUTATED AKT1 WILD-TYPE 
            11            356 
  AKT1 MUTATED AKT1 WILD-TYPE 
            11            356 
[1] "GOLGA1 MUTATION ANALYSIS"
[1] 3
  GOLGA1 MUTATED GOLGA1 WILD-TYPE 
               7              360 
  GOLGA1 MUTATED GOLGA1 WILD-TYPE 
               7              360 
[1] "PDK1 MUTATION ANALYSIS"
[1] 3
  PDK1 MUTATED PDK1 WILD-TYPE 
             5            362 
  PDK1 MUTATED PDK1 WILD-TYPE 
             5            362 
[1] "NAE1 MUTATION ANALYSIS"
[1] 3
  NAE1 MUTATED NAE1 WILD-TYPE 
             5            362 
  NAE1 MUTATED NAE1 WILD-TYPE 
             5            362 
[1] "PLEKHA4 MUTATION ANALYSIS"
[1] 3
  PLEKHA4 MUTATED PLEKHA4 WILD-TYPE 
               10               357 
  PLEKHA4 MUTATED PLEKHA4 WILD-TYPE 
               10               357 
[1] "ARAF MUTATION ANALYSIS"
[1] 3
  ARAF MUTATED ARAF WILD-TYPE 
            10            357 
  ARAF MUTATED ARAF WILD-TYPE 
            10            357 
[1] "ZNF418 MUTATION ANALYSIS"
[1] 3
  ZNF418 MUTATED ZNF418 WILD-TYPE 
              14              353 
  ZNF418 MUTATED ZNF418 WILD-TYPE 
              14              353 
[1] "MGAT5 MUTATION ANALYSIS"
[1] 3
  MGAT5 MUTATED MGAT5 WILD-TYPE 
             14             353 
  MGAT5 MUTATED MGAT5 WILD-TYPE 
             14             353 
[1] "DCTN4 MUTATION ANALYSIS"
[1] 3
  DCTN4 MUTATED DCTN4 WILD-TYPE 
              6             361 
  DCTN4 MUTATED DCTN4 WILD-TYPE 
              6             361 
[1] "IRS4 MUTATION ANALYSIS"
[1] 3
  IRS4 MUTATED IRS4 WILD-TYPE 
            27            340 
  IRS4 MUTATED IRS4 WILD-TYPE 
            27            340 
[1] "HAUS3 MUTATION ANALYSIS"
[1] 3
  HAUS3 MUTATED HAUS3 WILD-TYPE 
              9             358 
  HAUS3 MUTATED HAUS3 WILD-TYPE 
              9             358 
[1] "ZNF451 MUTATION ANALYSIS"
[1] 3
  ZNF451 MUTATED ZNF451 WILD-TYPE 
              18              349 
  ZNF451 MUTATED ZNF451 WILD-TYPE 
              18              349 
[1] "CHST15 MUTATION ANALYSIS"
[1] 3
  CHST15 MUTATED CHST15 WILD-TYPE 
              19              348 
  CHST15 MUTATED CHST15 WILD-TYPE 
              19              348 
[1] "CCDC62 MUTATION ANALYSIS"
[1] 3
  CCDC62 MUTATED CCDC62 WILD-TYPE 
              11              356 
  CCDC62 MUTATED CCDC62 WILD-TYPE 
              11              356 
[1] "ERCC6L MUTATION ANALYSIS"
[1] 3
  ERCC6L MUTATED ERCC6L WILD-TYPE 
              12              355 
  ERCC6L MUTATED ERCC6L WILD-TYPE 
              12              355 
[1] "MCF2L2 MUTATION ANALYSIS"
[1] 3
  MCF2L2 MUTATED MCF2L2 WILD-TYPE 
              19              348 
  MCF2L2 MUTATED MCF2L2 WILD-TYPE 
              19              348 
[1] "KIF5B MUTATION ANALYSIS"
[1] 3
  KIF5B MUTATED KIF5B WILD-TYPE 
             14             353 
  KIF5B MUTATED KIF5B WILD-TYPE 
             14             353 
[1] "CDC14A MUTATION ANALYSIS"
[1] 3
  CDC14A MUTATED CDC14A WILD-TYPE 
              10              357 
  CDC14A MUTATED CDC14A 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] "PRDM14 MUTATION ANALYSIS"
[1] 3
  PRDM14 MUTATED PRDM14 WILD-TYPE 
              12              355 
  PRDM14 MUTATED PRDM14 WILD-TYPE 
              12              355 
[1] "LRRTM2 MUTATION ANALYSIS"
[1] 3
  LRRTM2 MUTATED LRRTM2 WILD-TYPE 
               5              362 
  LRRTM2 MUTATED LRRTM2 WILD-TYPE 
               5              362 
[1] "RAPGEF2 MUTATION ANALYSIS"
[1] 3
  RAPGEF2 MUTATED RAPGEF2 WILD-TYPE 
               21               346 
  RAPGEF2 MUTATED RAPGEF2 WILD-TYPE 
               21               346 
[1] "DDX11 MUTATION ANALYSIS"
[1] 3
  DDX11 MUTATED DDX11 WILD-TYPE 
              7             360 
  DDX11 MUTATED DDX11 WILD-TYPE 
              7             360 
[1] "CDHR3 MUTATION ANALYSIS"
[1] 3
  CDHR3 MUTATED CDHR3 WILD-TYPE 
             13             354 
  CDHR3 MUTATED CDHR3 WILD-TYPE 
             13             354 
[1] "P2RY11 MUTATION ANALYSIS"
[1] 3
  P2RY11 MUTATED P2RY11 WILD-TYPE 
               5              362 
  P2RY11 MUTATED P2RY11 WILD-TYPE 
               5              362 
[1] "TGIF1 MUTATION ANALYSIS"
[1] 3
  TGIF1 MUTATED TGIF1 WILD-TYPE 
              9             358 
  TGIF1 MUTATED TGIF1 WILD-TYPE 
              9             358 
[1] "HECTD2 MUTATION ANALYSIS"
[1] 3
  HECTD2 MUTATED HECTD2 WILD-TYPE 
              10              357 
  HECTD2 MUTATED HECTD2 WILD-TYPE 
              10              357 
[1] "VPRBP MUTATION ANALYSIS"
[1] 3
  VPRBP MUTATED VPRBP WILD-TYPE 
             13             354 
  VPRBP MUTATED VPRBP WILD-TYPE 
             13             354 
[1] "KPNA3 MUTATION ANALYSIS"
[1] 3
  KPNA3 MUTATED KPNA3 WILD-TYPE 
              5             362 
  KPNA3 MUTATED KPNA3 WILD-TYPE 
              5             362 
[1] "XRCC6 MUTATION ANALYSIS"
[1] 3
  XRCC6 MUTATED XRCC6 WILD-TYPE 
              7             360 
  XRCC6 MUTATED XRCC6 WILD-TYPE 
              7             360 
[1] "ZNF594 MUTATION ANALYSIS"
[1] 3
  ZNF594 MUTATED ZNF594 WILD-TYPE 
              14              353 
  ZNF594 MUTATED ZNF594 WILD-TYPE 
              14              353 
[1] "PPIL5 MUTATION ANALYSIS"
[1] 3
  PPIL5 MUTATED PPIL5 WILD-TYPE 
              5             362 
  PPIL5 MUTATED PPIL5 WILD-TYPE 
              5             362 
[1] "SESTD1 MUTATION ANALYSIS"
[1] 3
  SESTD1 MUTATED SESTD1 WILD-TYPE 
              16              351 
  SESTD1 MUTATED SESTD1 WILD-TYPE 
              16              351 
[1] "AGTPBP1 MUTATION ANALYSIS"
[1] 3
  AGTPBP1 MUTATED AGTPBP1 WILD-TYPE 
               17               350 
  AGTPBP1 MUTATED AGTPBP1 WILD-TYPE 
               17               350 
[1] "ATL2 MUTATION ANALYSIS"
[1] 3
  ATL2 MUTATED ATL2 WILD-TYPE 
             6            361 
  ATL2 MUTATED ATL2 WILD-TYPE 
             6            361 
[1] "SIGLEC14 MUTATION ANALYSIS"
[1] 3
  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
                 8                359 
  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
                 8                359 
[1] "OR5R1 MUTATION ANALYSIS"
[1] 3
  OR5R1 MUTATED OR5R1 WILD-TYPE 
             14             353 
  OR5R1 MUTATED OR5R1 WILD-TYPE 
             14             353 
[1] "ITGA5 MUTATION ANALYSIS"
[1] 3
  ITGA5 MUTATED ITGA5 WILD-TYPE 
             16             351 
  ITGA5 MUTATED ITGA5 WILD-TYPE 
             16             351 
[1] "VPS72 MUTATION ANALYSIS"
[1] 3
  VPS72 MUTATED VPS72 WILD-TYPE 
              8             359 
  VPS72 MUTATED VPS72 WILD-TYPE 
              8             359 
[1] "PKDREJ MUTATION ANALYSIS"
[1] 3
  PKDREJ MUTATED PKDREJ WILD-TYPE 
              31              336 
  PKDREJ MUTATED PKDREJ WILD-TYPE 
              31              336 
[1] "CUTC MUTATION ANALYSIS"
[1] 3
  CUTC MUTATED CUTC WILD-TYPE 
             5            362 
  CUTC MUTATED CUTC WILD-TYPE 
             5            362 
[1] "PYHIN1 MUTATION ANALYSIS"
[1] 3
  PYHIN1 MUTATED PYHIN1 WILD-TYPE 
              18              349 
  PYHIN1 MUTATED PYHIN1 WILD-TYPE 
              18              349 
[1] "SRL MUTATION ANALYSIS"
[1] 3
  SRL MUTATED SRL WILD-TYPE 
           12           355 
  SRL MUTATED SRL WILD-TYPE 
           12           355 
[1] "ATP13A3 MUTATION ANALYSIS"
[1] 3
  ATP13A3 MUTATED ATP13A3 WILD-TYPE 
               13               354 
  ATP13A3 MUTATED ATP13A3 WILD-TYPE 
               13               354 
[1] "CELSR1 MUTATION ANALYSIS"
[1] 3
  CELSR1 MUTATED CELSR1 WILD-TYPE 
              22              345 
  CELSR1 MUTATED CELSR1 WILD-TYPE 
              22              345 
[1] "OLFML1 MUTATION ANALYSIS"
[1] 3
  OLFML1 MUTATED OLFML1 WILD-TYPE 
              11              356 
  OLFML1 MUTATED OLFML1 WILD-TYPE 
              11              356 
[1] "GSTA5 MUTATION ANALYSIS"
[1] 3
  GSTA5 MUTATED GSTA5 WILD-TYPE 
              6             361 
  GSTA5 MUTATED GSTA5 WILD-TYPE 
              6             361 
[1] "TM7SF4 MUTATION ANALYSIS"
[1] 3
  TM7SF4 MUTATED TM7SF4 WILD-TYPE 
               7              360 
  TM7SF4 MUTATED TM7SF4 WILD-TYPE 
               7              360 
[1] "PLCB2 MUTATION ANALYSIS"
[1] 3
  PLCB2 MUTATED PLCB2 WILD-TYPE 
              9             358 
  PLCB2 MUTATED PLCB2 WILD-TYPE 
              9             358 
[1] "LRBA MUTATION ANALYSIS"
[1] 3
  LRBA MUTATED LRBA WILD-TYPE 
            26            341 
  LRBA MUTATED LRBA WILD-TYPE 
            26            341 
[1] "MED24 MUTATION ANALYSIS"
[1] 3
  MED24 MUTATED MED24 WILD-TYPE 
              9             358 
  MED24 MUTATED MED24 WILD-TYPE 
              9             358 
[1] "SRGAP3 MUTATION ANALYSIS"
[1] 3
  SRGAP3 MUTATED SRGAP3 WILD-TYPE 
              17              350 
  SRGAP3 MUTATED SRGAP3 WILD-TYPE 
              17              350 
[1] "AAMP MUTATION ANALYSIS"
[1] 3
  AAMP MUTATED AAMP WILD-TYPE 
             3            364 
  AAMP MUTATED AAMP WILD-TYPE 
             3            364 
[1] "TRAM1L1 MUTATION ANALYSIS"
[1] 3
  TRAM1L1 MUTATED TRAM1L1 WILD-TYPE 
               12               355 
  TRAM1L1 MUTATED TRAM1L1 WILD-TYPE 
               12               355 
[1] "HYDIN MUTATION ANALYSIS"
[1] 3
  HYDIN MUTATED HYDIN WILD-TYPE 
             80             287 
  HYDIN MUTATED HYDIN WILD-TYPE 
             80             287 
[1] "CARD6 MUTATION ANALYSIS"
[1] 3
  CARD6 MUTATED CARD6 WILD-TYPE 
             15             352 
  CARD6 MUTATED CARD6 WILD-TYPE 
             15             352 
[1] "C14ORF118 MUTATION ANALYSIS"
[1] 3
  C14ORF118 MUTATED C14ORF118 WILD-TYPE 
                  9                 358 
  C14ORF118 MUTATED C14ORF118 WILD-TYPE 
                  9                 358 
[1] "FAM83D MUTATION ANALYSIS"
[1] 3
  FAM83D MUTATED FAM83D WILD-TYPE 
              11              356 
  FAM83D MUTATED FAM83D WILD-TYPE 
              11              356 
[1] "GATA1 MUTATION ANALYSIS"
[1] 3
  GATA1 MUTATED GATA1 WILD-TYPE 
             16             351 
  GATA1 MUTATED GATA1 WILD-TYPE 
             16             351 
[1] "OR6C1 MUTATION ANALYSIS"
[1] 3
  OR6C1 MUTATED OR6C1 WILD-TYPE 
              7             360 
  OR6C1 MUTATED OR6C1 WILD-TYPE 
              7             360 
[1] "SEC31A MUTATION ANALYSIS"
[1] 3
  SEC31A MUTATED SEC31A WILD-TYPE 
              12              355 
  SEC31A MUTATED SEC31A WILD-TYPE 
              12              355 
[1] "SULF2 MUTATION ANALYSIS"
[1] 3
  SULF2 MUTATED SULF2 WILD-TYPE 
             22             345 
  SULF2 MUTATED SULF2 WILD-TYPE 
             22             345 
[1] "SLC8A2 MUTATION ANALYSIS"
[1] 3
  SLC8A2 MUTATED SLC8A2 WILD-TYPE 
              14              353 
  SLC8A2 MUTATED SLC8A2 WILD-TYPE 
              14              353 
[1] "C14ORF180 MUTATION ANALYSIS"
[1] 3
  C14ORF180 MUTATED C14ORF180 WILD-TYPE 
                  4                 363 
  C14ORF180 MUTATED C14ORF180 WILD-TYPE 
                  4                 363 
[1] "C3ORF63 MUTATION ANALYSIS"
[1] 3
  C3ORF63 MUTATED C3ORF63 WILD-TYPE 
               22               345 
  C3ORF63 MUTATED C3ORF63 WILD-TYPE 
               22               345 
[1] "XKR3 MUTATION ANALYSIS"
[1] 3
  XKR3 MUTATED XKR3 WILD-TYPE 
            12            355 
  XKR3 MUTATED XKR3 WILD-TYPE 
            12            355 
[1] "RBP3 MUTATION ANALYSIS"
[1] 3
  RBP3 MUTATED RBP3 WILD-TYPE 
            13            354 
  RBP3 MUTATED RBP3 WILD-TYPE 
            13            354 
[1] "ACADVL MUTATION ANALYSIS"
[1] 3
  ACADVL MUTATED ACADVL WILD-TYPE 
               6              361 
  ACADVL MUTATED ACADVL WILD-TYPE 
               6              361 
[1] "VCAN MUTATION ANALYSIS"
[1] 3
  VCAN MUTATED VCAN WILD-TYPE 
            37            330 
  VCAN MUTATED VCAN WILD-TYPE 
            37            330 
[1] "RIC8B MUTATION ANALYSIS"
[1] 3
  RIC8B MUTATED RIC8B WILD-TYPE 
              9             358 
  RIC8B MUTATED RIC8B WILD-TYPE 
              9             358 
[1] "FAM163A MUTATION ANALYSIS"
[1] 3
  FAM163A MUTATED FAM163A WILD-TYPE 
                5               362 
  FAM163A MUTATED FAM163A WILD-TYPE 
                5               362 
[1] "WNK4 MUTATION ANALYSIS"
[1] 3
  WNK4 MUTATED WNK4 WILD-TYPE 
            11            356 
  WNK4 MUTATED WNK4 WILD-TYPE 
            11            356 
[1] "S100A2 MUTATION ANALYSIS"
[1] 3
  S100A2 MUTATED S100A2 WILD-TYPE 
               7              360 
  S100A2 MUTATED S100A2 WILD-TYPE 
               7              360 
[1] "SPARC MUTATION ANALYSIS"
[1] 3
  SPARC MUTATED SPARC WILD-TYPE 
              8             359 
  SPARC MUTATED SPARC WILD-TYPE 
              8             359 
[1] "PKD2L1 MUTATION ANALYSIS"
[1] 3
  PKD2L1 MUTATED PKD2L1 WILD-TYPE 
              21              346 
  PKD2L1 MUTATED PKD2L1 WILD-TYPE 
              21              346 
[1] "NME7 MUTATION ANALYSIS"
[1] 3
  NME7 MUTATED NME7 WILD-TYPE 
             6            361 
  NME7 MUTATED NME7 WILD-TYPE 
             6            361 
[1] "C17ORF71 MUTATION ANALYSIS"
[1] 3
  C17ORF71 MUTATED C17ORF71 WILD-TYPE 
                 9                358 
  C17ORF71 MUTATED C17ORF71 WILD-TYPE 
                 9                358 
[1] "CCDC64B MUTATION ANALYSIS"
[1] 3
  CCDC64B MUTATED CCDC64B WILD-TYPE 
                5               362 
  CCDC64B MUTATED CCDC64B WILD-TYPE 
                5               362 
[1] "C12ORF24 MUTATION ANALYSIS"
[1] 3
  C12ORF24 MUTATED C12ORF24 WILD-TYPE 
                 4                363 
  C12ORF24 MUTATED C12ORF24 WILD-TYPE 
                 4                363 
[1] "GDF6 MUTATION ANALYSIS"
[1] 3
  GDF6 MUTATED GDF6 WILD-TYPE 
             6            361 
  GDF6 MUTATED GDF6 WILD-TYPE 
             6            361 
[1] "TARBP2 MUTATION ANALYSIS"
[1] 3
  TARBP2 MUTATED TARBP2 WILD-TYPE 
               9              358 
  TARBP2 MUTATED TARBP2 WILD-TYPE 
               9              358 
[1] "VWA5A MUTATION ANALYSIS"
[1] 3
  VWA5A MUTATED VWA5A WILD-TYPE 
             12             355 
  VWA5A MUTATED VWA5A WILD-TYPE 
             12             355 
[1] "BFAR MUTATION ANALYSIS"
[1] 3
  BFAR MUTATED BFAR WILD-TYPE 
             8            359 
  BFAR MUTATED BFAR WILD-TYPE 
             8            359 
[1] "ARSF MUTATION ANALYSIS"
[1] 3
  ARSF MUTATED ARSF WILD-TYPE 
            11            356 
  ARSF MUTATED ARSF WILD-TYPE 
            11            356 
[1] "OSBPL5 MUTATION ANALYSIS"
[1] 3
  OSBPL5 MUTATED OSBPL5 WILD-TYPE 
              14              353 
  OSBPL5 MUTATED OSBPL5 WILD-TYPE 
              14              353 
[1] "FMO1 MUTATION ANALYSIS"
[1] 3
  FMO1 MUTATED FMO1 WILD-TYPE 
             7            360 
  FMO1 MUTATED FMO1 WILD-TYPE 
             7            360 
[1] "ZNF286A MUTATION ANALYSIS"
[1] 3
  ZNF286A MUTATED ZNF286A WILD-TYPE 
                7               360 
  ZNF286A MUTATED ZNF286A WILD-TYPE 
                7               360 
[1] "CCDC66 MUTATION ANALYSIS"
[1] 3
  CCDC66 MUTATED CCDC66 WILD-TYPE 
               9              358 
  CCDC66 MUTATED CCDC66 WILD-TYPE 
               9              358 
[1] "NTSR2 MUTATION ANALYSIS"
[1] 3
  NTSR2 MUTATED NTSR2 WILD-TYPE 
              8             359 
  NTSR2 MUTATED NTSR2 WILD-TYPE 
              8             359 
[1] "XPOT MUTATION ANALYSIS"
[1] 3
  XPOT MUTATED XPOT WILD-TYPE 
             8            359 
  XPOT MUTATED XPOT 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] "MACROD1 MUTATION ANALYSIS"
[1] 3
  MACROD1 MUTATED MACROD1 WILD-TYPE 
                3               364 
  MACROD1 MUTATED MACROD1 WILD-TYPE 
                3               364 
[1] "CAPSL MUTATION ANALYSIS"
[1] 3
  CAPSL MUTATED CAPSL WILD-TYPE 
              7             360 
  CAPSL MUTATED CAPSL WILD-TYPE 
              7             360 
[1] "FAM55C MUTATION ANALYSIS"
[1] 3
  FAM55C MUTATED FAM55C WILD-TYPE 
               6              361 
  FAM55C MUTATED FAM55C WILD-TYPE 
               6              361 
[1] "TXNRD1 MUTATION ANALYSIS"
[1] 3
  TXNRD1 MUTATED TXNRD1 WILD-TYPE 
               8              359 
  TXNRD1 MUTATED TXNRD1 WILD-TYPE 
               8              359 
[1] "UST MUTATION ANALYSIS"
[1] 3
  UST MUTATED UST WILD-TYPE 
            9           358 
  UST MUTATED UST WILD-TYPE 
            9           358 
[1] "KCNJ16 MUTATION ANALYSIS"
[1] 3
  KCNJ16 MUTATED KCNJ16 WILD-TYPE 
               7              360 
  KCNJ16 MUTATED KCNJ16 WILD-TYPE 
               7              360 
[1] "REM1 MUTATION ANALYSIS"
[1] 3
  REM1 MUTATED REM1 WILD-TYPE 
             4            363 
  REM1 MUTATED REM1 WILD-TYPE 
             4            363 
[1] "TMEM171 MUTATION ANALYSIS"
[1] 3
  TMEM171 MUTATED TMEM171 WILD-TYPE 
                5               362 
  TMEM171 MUTATED TMEM171 WILD-TYPE 
                5               362 
[1] "TMEM229B MUTATION ANALYSIS"
[1] 3
  TMEM229B MUTATED TMEM229B WILD-TYPE 
                 4                363 
  TMEM229B MUTATED TMEM229B WILD-TYPE 
                 4                363 
[1] "IL8 MUTATION ANALYSIS"
[1] 3
  IL8 MUTATED IL8 WILD-TYPE 
            5           362 
  IL8 MUTATED IL8 WILD-TYPE 
            5           362 
[1] "KIF14 MUTATION ANALYSIS"
[1] 3
  KIF14 MUTATED KIF14 WILD-TYPE 
             11             356 
  KIF14 MUTATED KIF14 WILD-TYPE 
             11             356 
[1] "ZNF660 MUTATION ANALYSIS"
[1] 3
  ZNF660 MUTATED ZNF660 WILD-TYPE 
               7              360 
  ZNF660 MUTATED ZNF660 WILD-TYPE 
               7              360 
[1] "TRPC6 MUTATION ANALYSIS"
[1] 3
  TRPC6 MUTATED TRPC6 WILD-TYPE 
             22             345 
  TRPC6 MUTATED TRPC6 WILD-TYPE 
             22             345 
[1] "RXRA MUTATION ANALYSIS"
[1] 3
  RXRA MUTATED RXRA WILD-TYPE 
             8            359 
  RXRA MUTATED RXRA WILD-TYPE 
             8            359 
[1] "TMEM20 MUTATION ANALYSIS"
[1] 3
  TMEM20 MUTATED TMEM20 WILD-TYPE 
               3              364 
  TMEM20 MUTATED TMEM20 WILD-TYPE 
               3              364 
[1] "SLC16A1 MUTATION ANALYSIS"
[1] 3
  SLC16A1 MUTATED SLC16A1 WILD-TYPE 
                7               360 
  SLC16A1 MUTATED SLC16A1 WILD-TYPE 
                7               360 
[1] "MFSD9 MUTATION ANALYSIS"
[1] 3
  MFSD9 MUTATED MFSD9 WILD-TYPE 
             10             357 
  MFSD9 MUTATED MFSD9 WILD-TYPE 
             10             357 
[1] "LYST MUTATION ANALYSIS"
[1] 3
  LYST MUTATED LYST WILD-TYPE 
            34            333 
  LYST MUTATED LYST WILD-TYPE 
            34            333 
[1] "GLT8D1 MUTATION ANALYSIS"
[1] 3
  GLT8D1 MUTATED GLT8D1 WILD-TYPE 
               8              359 
  GLT8D1 MUTATED GLT8D1 WILD-TYPE 
               8              359 
[1] "RRP9 MUTATION ANALYSIS"
[1] 3
  RRP9 MUTATED RRP9 WILD-TYPE 
            12            355 
  RRP9 MUTATED RRP9 WILD-TYPE 
            12            355 
[1] "HSPA4L MUTATION ANALYSIS"
[1] 3
  HSPA4L MUTATED HSPA4L WILD-TYPE 
               8              359 
  HSPA4L MUTATED HSPA4L WILD-TYPE 
               8              359 
[1] "CASC4 MUTATION ANALYSIS"
[1] 3
  CASC4 MUTATED CASC4 WILD-TYPE 
              5             362 
  CASC4 MUTATED CASC4 WILD-TYPE 
              5             362 
[1] "RAG1 MUTATION ANALYSIS"
[1] 3
  RAG1 MUTATED RAG1 WILD-TYPE 
            14            353 
  RAG1 MUTATED RAG1 WILD-TYPE 
            14            353 
[1] "ZNF416 MUTATION ANALYSIS"
[1] 3
  ZNF416 MUTATED ZNF416 WILD-TYPE 
               8              359 
  ZNF416 MUTATED ZNF416 WILD-TYPE 
               8              359 
[1] "GRM1 MUTATION ANALYSIS"
[1] 3
  GRM1 MUTATED GRM1 WILD-TYPE 
            27            340 
  GRM1 MUTATED GRM1 WILD-TYPE 
            27            340 
[1] "CHMP4B MUTATION ANALYSIS"
[1] 3
  CHMP4B MUTATED CHMP4B WILD-TYPE 
               3              364 
  CHMP4B MUTATED CHMP4B WILD-TYPE 
               3              364 
[1] "CYP20A1 MUTATION ANALYSIS"
[1] 3
  CYP20A1 MUTATED CYP20A1 WILD-TYPE 
                8               359 
  CYP20A1 MUTATED CYP20A1 WILD-TYPE 
                8               359 
[1] "ZNF630 MUTATION ANALYSIS"
[1] 3
  ZNF630 MUTATED ZNF630 WILD-TYPE 
               7              360 
  ZNF630 MUTATED ZNF630 WILD-TYPE 
               7              360 
[1] "VEZF1 MUTATION ANALYSIS"
[1] 3
  VEZF1 MUTATED VEZF1 WILD-TYPE 
              6             361 
  VEZF1 MUTATED VEZF1 WILD-TYPE 
              6             361 
[1] "C16ORF88 MUTATION ANALYSIS"
[1] 3
  C16ORF88 MUTATED C16ORF88 WILD-TYPE 
                 7                360 
  C16ORF88 MUTATED C16ORF88 WILD-TYPE 
                 7                360 
[1] "CLGN MUTATION ANALYSIS"
[1] 3
  CLGN MUTATED CLGN WILD-TYPE 
            11            356 
  CLGN MUTATED CLGN WILD-TYPE 
            11            356 
[1] "MCM4 MUTATION ANALYSIS"
[1] 3
  MCM4 MUTATED MCM4 WILD-TYPE 
            12            355 
  MCM4 MUTATED MCM4 WILD-TYPE 
            12            355 
[1] "CLTCL1 MUTATION ANALYSIS"
[1] 3
  CLTCL1 MUTATED CLTCL1 WILD-TYPE 
              18              349 
  CLTCL1 MUTATED CLTCL1 WILD-TYPE 
              18              349 
[1] "MPZL1 MUTATION ANALYSIS"
[1] 3
  MPZL1 MUTATED MPZL1 WILD-TYPE 
              7             360 
  MPZL1 MUTATED MPZL1 WILD-TYPE 
              7             360 
[1] "PSMC3 MUTATION ANALYSIS"
[1] 3
  PSMC3 MUTATED PSMC3 WILD-TYPE 
             10             357 
  PSMC3 MUTATED PSMC3 WILD-TYPE 
             10             357 
[1] "HIST1H1B MUTATION ANALYSIS"
[1] 3
  HIST1H1B MUTATED HIST1H1B WILD-TYPE 
                 7                360 
  HIST1H1B MUTATED HIST1H1B WILD-TYPE 
                 7                360 
[1] "WNT8A MUTATION ANALYSIS"
[1] 3
  WNT8A MUTATED WNT8A WILD-TYPE 
              5             362 
  WNT8A MUTATED WNT8A WILD-TYPE 
              5             362 
[1] "RARS2 MUTATION ANALYSIS"
[1] 3
  RARS2 MUTATED RARS2 WILD-TYPE 
              7             360 
  RARS2 MUTATED RARS2 WILD-TYPE 
              7             360 
[1] "TEX11 MUTATION ANALYSIS"
[1] 3
  TEX11 MUTATED TEX11 WILD-TYPE 
             17             350 
  TEX11 MUTATED TEX11 WILD-TYPE 
             17             350 
[1] "VPS13C MUTATION ANALYSIS"
[1] 3
  VPS13C MUTATED VPS13C WILD-TYPE 
              24              343 
  VPS13C MUTATED VPS13C WILD-TYPE 
              24              343 
[1] "IGFBP3 MUTATION ANALYSIS"
[1] 3
  IGFBP3 MUTATED IGFBP3 WILD-TYPE 
               6              361 
  IGFBP3 MUTATED IGFBP3 WILD-TYPE 
               6              361 
[1] "HLA-DRA MUTATION ANALYSIS"
[1] 3
  HLA-DRA MUTATED HLA-DRA WILD-TYPE 
               11               356 
  HLA-DRA MUTATED HLA-DRA WILD-TYPE 
               11               356 
[1] "MUS81 MUTATION ANALYSIS"
[1] 3
  MUS81 MUTATED MUS81 WILD-TYPE 
              7             360 
  MUS81 MUTATED MUS81 WILD-TYPE 
              7             360 
[1] "PIGN MUTATION ANALYSIS"
[1] 3
  PIGN MUTATED PIGN WILD-TYPE 
             7            360 
  PIGN MUTATED PIGN WILD-TYPE 
             7            360 
[1] "ELANE MUTATION ANALYSIS"
[1] 3
  ELANE MUTATED ELANE WILD-TYPE 
              7             360 
  ELANE MUTATED ELANE WILD-TYPE 
              7             360 
[1] "C1ORF116 MUTATION ANALYSIS"
[1] 3
  C1ORF116 MUTATED C1ORF116 WILD-TYPE 
                 6                361 
  C1ORF116 MUTATED C1ORF116 WILD-TYPE 
                 6                361 
[1] "DEPDC5 MUTATION ANALYSIS"
[1] 3
  DEPDC5 MUTATED DEPDC5 WILD-TYPE 
              19              348 
  DEPDC5 MUTATED DEPDC5 WILD-TYPE 
              19              348 
[1] "SON MUTATION ANALYSIS"
[1] 3
  SON MUTATED SON WILD-TYPE 
           20           347 
  SON MUTATED SON WILD-TYPE 
           20           347 
[1] "LRRC15 MUTATION ANALYSIS"
[1] 3
  LRRC15 MUTATED LRRC15 WILD-TYPE 
               9              358 
  LRRC15 MUTATED LRRC15 WILD-TYPE 
               9              358 
[1] "POLA1 MUTATION ANALYSIS"
[1] 3
  POLA1 MUTATED POLA1 WILD-TYPE 
              9             358 
  POLA1 MUTATED POLA1 WILD-TYPE 
              9             358 
[1] "C3ORF27 MUTATION ANALYSIS"
[1] 3
  C3ORF27 MUTATED C3ORF27 WILD-TYPE 
                3               364 
  C3ORF27 MUTATED C3ORF27 WILD-TYPE 
                3               364 
[1] "ZNF821 MUTATION ANALYSIS"
[1] 3
  ZNF821 MUTATED ZNF821 WILD-TYPE 
               5              362 
  ZNF821 MUTATED ZNF821 WILD-TYPE 
               5              362 
[1] "TRHDE MUTATION ANALYSIS"
[1] 3
  TRHDE MUTATED TRHDE WILD-TYPE 
             27             340 
  TRHDE MUTATED TRHDE WILD-TYPE 
             27             340 
[1] "NT5C3L MUTATION ANALYSIS"
[1] 3
  NT5C3L MUTATED NT5C3L WILD-TYPE 
               5              362 
  NT5C3L MUTATED NT5C3L WILD-TYPE 
               5              362 
[1] "FAM133A MUTATION ANALYSIS"
[1] 3
  FAM133A MUTATED FAM133A WILD-TYPE 
               11               356 
  FAM133A MUTATED FAM133A WILD-TYPE 
               11               356 
[1] "SYT16 MUTATION ANALYSIS"
[1] 3
  SYT16 MUTATED SYT16 WILD-TYPE 
             13             354 
  SYT16 MUTATED SYT16 WILD-TYPE 
             13             354 
[1] "ZNF546 MUTATION ANALYSIS"
[1] 3
  ZNF546 MUTATED ZNF546 WILD-TYPE 
              15              352 
  ZNF546 MUTATED ZNF546 WILD-TYPE 
              15              352 
[1] "TTLL5 MUTATION ANALYSIS"
[1] 3
  TTLL5 MUTATED TTLL5 WILD-TYPE 
             11             356 
  TTLL5 MUTATED TTLL5 WILD-TYPE 
             11             356 
[1] "FOXF2 MUTATION ANALYSIS"
[1] 3
  FOXF2 MUTATED FOXF2 WILD-TYPE 
              4             363 
  FOXF2 MUTATED FOXF2 WILD-TYPE 
              4             363 
[1] "PKHD1 MUTATION ANALYSIS"
[1] 3
  PKHD1 MUTATED PKHD1 WILD-TYPE 
             57             310 
  PKHD1 MUTATED PKHD1 WILD-TYPE 
             57             310 
[1] "OR8K1 MUTATION ANALYSIS"
[1] 3
  OR8K1 MUTATED OR8K1 WILD-TYPE 
             10             357 
  OR8K1 MUTATED OR8K1 WILD-TYPE 
             10             357 
[1] "ITPRIPL1 MUTATION ANALYSIS"
[1] 3
  ITPRIPL1 MUTATED ITPRIPL1 WILD-TYPE 
                 7                360 
  ITPRIPL1 MUTATED ITPRIPL1 WILD-TYPE 
                 7                360 
[1] "LIPH MUTATION ANALYSIS"
[1] 3
  LIPH MUTATED LIPH WILD-TYPE 
             9            358 
  LIPH MUTATED LIPH WILD-TYPE 
             9            358 
[1] "MORC2 MUTATION ANALYSIS"
[1] 3
  MORC2 MUTATED MORC2 WILD-TYPE 
             12             355 
  MORC2 MUTATED MORC2 WILD-TYPE 
             12             355 
[1] "OR51E2 MUTATION ANALYSIS"
[1] 3
  OR51E2 MUTATED OR51E2 WILD-TYPE 
               5              362 
  OR51E2 MUTATED OR51E2 WILD-TYPE 
               5              362 
[1] "APAF1 MUTATION ANALYSIS"
[1] 3
  APAF1 MUTATED APAF1 WILD-TYPE 
             18             349 
  APAF1 MUTATED APAF1 WILD-TYPE 
             18             349 
[1] "TRIM34 MUTATION ANALYSIS"
[1] 3
  TRIM34 MUTATED TRIM34 WILD-TYPE 
               6              361 
  TRIM34 MUTATED TRIM34 WILD-TYPE 
               6              361 
[1] "PCDHGA4 MUTATION ANALYSIS"
[1] 3
  PCDHGA4 MUTATED PCDHGA4 WILD-TYPE 
               18               349 
  PCDHGA4 MUTATED PCDHGA4 WILD-TYPE 
               18               349 
[1] "DBF4 MUTATION ANALYSIS"
[1] 3
  DBF4 MUTATED DBF4 WILD-TYPE 
             7            360 
  DBF4 MUTATED DBF4 WILD-TYPE 
             7            360 
[1] "VIM MUTATION ANALYSIS"
[1] 3
  VIM MUTATED VIM WILD-TYPE 
            7           360 
  VIM MUTATED VIM WILD-TYPE 
            7           360 
[1] "SLIT1 MUTATION ANALYSIS"
[1] 3
  SLIT1 MUTATED SLIT1 WILD-TYPE 
             24             343 
  SLIT1 MUTATED SLIT1 WILD-TYPE 
             24             343 
[1] "PLEKHO2 MUTATION ANALYSIS"
[1] 3
  PLEKHO2 MUTATED PLEKHO2 WILD-TYPE 
                7               360 
  PLEKHO2 MUTATED PLEKHO2 WILD-TYPE 
                7               360 
[1] "C13ORF23 MUTATION ANALYSIS"
[1] 3
  C13ORF23 MUTATED C13ORF23 WILD-TYPE 
                12                355 
  C13ORF23 MUTATED C13ORF23 WILD-TYPE 
                12                355 
[1] "DNAJC6 MUTATION ANALYSIS"
[1] 3
  DNAJC6 MUTATED DNAJC6 WILD-TYPE 
               9              358 
  DNAJC6 MUTATED DNAJC6 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] "HBS1L MUTATION ANALYSIS"
[1] 3
  HBS1L MUTATED HBS1L WILD-TYPE 
             12             355 
  HBS1L MUTATED HBS1L WILD-TYPE 
             12             355 
[1] "TSC2 MUTATION ANALYSIS"
[1] 3
  TSC2 MUTATED TSC2 WILD-TYPE 
            15            352 
  TSC2 MUTATED TSC2 WILD-TYPE 
            15            352 
[1] "ABCG2 MUTATION ANALYSIS"
[1] 3
  ABCG2 MUTATED ABCG2 WILD-TYPE 
             11             356 
  ABCG2 MUTATED ABCG2 WILD-TYPE 
             11             356 
[1] "EFHD1 MUTATION ANALYSIS"
[1] 3
  EFHD1 MUTATED EFHD1 WILD-TYPE 
              5             362 
  EFHD1 MUTATED EFHD1 WILD-TYPE 
              5             362 
[1] "IFI35 MUTATION ANALYSIS"
[1] 3
  IFI35 MUTATED IFI35 WILD-TYPE 
              8             359 
  IFI35 MUTATED IFI35 WILD-TYPE 
              8             359 
[1] "RABGAP1 MUTATION ANALYSIS"
[1] 3
  RABGAP1 MUTATED RABGAP1 WILD-TYPE 
               12               355 
  RABGAP1 MUTATED RABGAP1 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] "RPS6KC1 MUTATION ANALYSIS"
[1] 3
  RPS6KC1 MUTATED RPS6KC1 WILD-TYPE 
               15               352 
  RPS6KC1 MUTATED RPS6KC1 WILD-TYPE 
               15               352 
[1] "AOX1 MUTATION ANALYSIS"
[1] 3
  AOX1 MUTATED AOX1 WILD-TYPE 
            11            356 
  AOX1 MUTATED AOX1 WILD-TYPE 
            11            356 
[1] "MTMR12 MUTATION ANALYSIS"
[1] 3
  MTMR12 MUTATED MTMR12 WILD-TYPE 
              12              355 
  MTMR12 MUTATED MTMR12 WILD-TYPE 
              12              355 
[1] "ADCY9 MUTATION ANALYSIS"
[1] 3
  ADCY9 MUTATED ADCY9 WILD-TYPE 
             18             349 
  ADCY9 MUTATED ADCY9 WILD-TYPE 
             18             349 
[1] "CLK4 MUTATION ANALYSIS"
[1] 3
  CLK4 MUTATED CLK4 WILD-TYPE 
             9            358 
  CLK4 MUTATED CLK4 WILD-TYPE 
             9            358 
[1] "PTPN14 MUTATION ANALYSIS"
[1] 3
  PTPN14 MUTATED PTPN14 WILD-TYPE 
              18              349 
  PTPN14 MUTATED PTPN14 WILD-TYPE 
              18              349 
[1] "PRSS48 MUTATION ANALYSIS"
[1] 3
  PRSS48 MUTATED PRSS48 WILD-TYPE 
               7              360 
  PRSS48 MUTATED PRSS48 WILD-TYPE 
               7              360 
[1] "TOX MUTATION ANALYSIS"
[1] 3
  TOX MUTATED TOX WILD-TYPE 
           15           352 
  TOX MUTATED TOX WILD-TYPE 
           15           352 
[1] "C6ORF203 MUTATION ANALYSIS"
[1] 3
  C6ORF203 MUTATED C6ORF203 WILD-TYPE 
                 4                363 
  C6ORF203 MUTATED C6ORF203 WILD-TYPE 
                 4                363 
[1] "TAP2 MUTATION ANALYSIS"
[1] 3
  TAP2 MUTATED TAP2 WILD-TYPE 
            14            353 
  TAP2 MUTATED TAP2 WILD-TYPE 
            14            353 
[1] "SCARA5 MUTATION ANALYSIS"
[1] 3
  SCARA5 MUTATED SCARA5 WILD-TYPE 
              12              355 
  SCARA5 MUTATED SCARA5 WILD-TYPE 
              12              355 
[1] "LARP7 MUTATION ANALYSIS"
[1] 3
  LARP7 MUTATED LARP7 WILD-TYPE 
              8             359 
  LARP7 MUTATED LARP7 WILD-TYPE 
              8             359 
[1] "CCPG1 MUTATION ANALYSIS"
[1] 3
  CCPG1 MUTATED CCPG1 WILD-TYPE 
             11             356 
  CCPG1 MUTATED CCPG1 WILD-TYPE 
             11             356 
[1] "YTHDF2 MUTATION ANALYSIS"
[1] 3
  YTHDF2 MUTATED YTHDF2 WILD-TYPE 
              10              357 
  YTHDF2 MUTATED YTHDF2 WILD-TYPE 
              10              357 
[1] "DNAH3 MUTATION ANALYSIS"
[1] 3
  DNAH3 MUTATED DNAH3 WILD-TYPE 
             45             322 
  DNAH3 MUTATED DNAH3 WILD-TYPE 
             45             322 
[1] "UGGT1 MUTATION ANALYSIS"
[1] 3
  UGGT1 MUTATED UGGT1 WILD-TYPE 
             17             350 
  UGGT1 MUTATED UGGT1 WILD-TYPE 
             17             350 
[1] "TEX13A MUTATION ANALYSIS"
[1] 3
  TEX13A MUTATED TEX13A WILD-TYPE 
               9              358 
  TEX13A MUTATED TEX13A WILD-TYPE 
               9              358 
[1] "CSNK1E MUTATION ANALYSIS"
[1] 3
  CSNK1E MUTATED CSNK1E WILD-TYPE 
               8              359 
  CSNK1E MUTATED CSNK1E 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] "C8ORF80 MUTATION ANALYSIS"
[1] 3
  C8ORF80 MUTATED C8ORF80 WILD-TYPE 
               14               353 
  C8ORF80 MUTATED C8ORF80 WILD-TYPE 
               14               353 
[1] "CPB2 MUTATION ANALYSIS"
[1] 3
  CPB2 MUTATED CPB2 WILD-TYPE 
             9            358 
  CPB2 MUTATED CPB2 WILD-TYPE 
             9            358 
[1] "GRAMD1C MUTATION ANALYSIS"
[1] 3
  GRAMD1C MUTATED GRAMD1C WILD-TYPE 
               11               356 
  GRAMD1C MUTATED GRAMD1C WILD-TYPE 
               11               356 
[1] "TSC1 MUTATION ANALYSIS"
[1] 3
  TSC1 MUTATED TSC1 WILD-TYPE 
            13            354 
  TSC1 MUTATED TSC1 WILD-TYPE 
            13            354 
[1] "FAM91A1 MUTATION ANALYSIS"
[1] 3
  FAM91A1 MUTATED FAM91A1 WILD-TYPE 
               10               357 
  FAM91A1 MUTATED FAM91A1 WILD-TYPE 
               10               357 
[1] "HDAC11 MUTATION ANALYSIS"
[1] 3
  HDAC11 MUTATED HDAC11 WILD-TYPE 
               8              359 
  HDAC11 MUTATED HDAC11 WILD-TYPE 
               8              359 
[1] "GANAB MUTATION ANALYSIS"
[1] 3
  GANAB MUTATED GANAB WILD-TYPE 
             13             354 
  GANAB MUTATED GANAB WILD-TYPE 
             13             354 
[1] "DDX55 MUTATION ANALYSIS"
[1] 3
  DDX55 MUTATED DDX55 WILD-TYPE 
             10             357 
  DDX55 MUTATED DDX55 WILD-TYPE 
             10             357 
[1] "EVI2A MUTATION ANALYSIS"
[1] 3
  EVI2A MUTATED EVI2A WILD-TYPE 
              8             359 
  EVI2A MUTATED EVI2A WILD-TYPE 
              8             359 
[1] "OR51B6 MUTATION ANALYSIS"
[1] 3
  OR51B6 MUTATED OR51B6 WILD-TYPE 
               3              364 
  OR51B6 MUTATED OR51B6 WILD-TYPE 
               3              364 
[1] "KIAA0020 MUTATION ANALYSIS"
[1] 3
  KIAA0020 MUTATED KIAA0020 WILD-TYPE 
                10                357 
  KIAA0020 MUTATED KIAA0020 WILD-TYPE 
                10                357 
[1] "ENC1 MUTATION ANALYSIS"
[1] 3
  ENC1 MUTATED ENC1 WILD-TYPE 
            12            355 
  ENC1 MUTATED ENC1 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] "ZFP3 MUTATION ANALYSIS"
[1] 3
  ZFP3 MUTATED ZFP3 WILD-TYPE 
            10            357 
  ZFP3 MUTATED ZFP3 WILD-TYPE 
            10            357 
[1] "S1PR1 MUTATION ANALYSIS"
[1] 3
  S1PR1 MUTATED S1PR1 WILD-TYPE 
             11             356 
  S1PR1 MUTATED S1PR1 WILD-TYPE 
             11             356 
[1] "UAP1 MUTATION ANALYSIS"
[1] 3
  UAP1 MUTATED UAP1 WILD-TYPE 
             6            361 
  UAP1 MUTATED UAP1 WILD-TYPE 
             6            361 
[1] "TACC2 MUTATION ANALYSIS"
[1] 3
  TACC2 MUTATED TACC2 WILD-TYPE 
             25             342 
  TACC2 MUTATED TACC2 WILD-TYPE 
             25             342 
[1] "GLRA1 MUTATION ANALYSIS"
[1] 3
  GLRA1 MUTATED GLRA1 WILD-TYPE 
             10             357 
  GLRA1 MUTATED GLRA1 WILD-TYPE 
             10             357 
[1] "CFP MUTATION ANALYSIS"
[1] 3
  CFP MUTATED CFP WILD-TYPE 
            7           360 
  CFP MUTATED CFP WILD-TYPE 
            7           360 
[1] "GNG12 MUTATION ANALYSIS"
[1] 3
  GNG12 MUTATED GNG12 WILD-TYPE 
              8             359 
  GNG12 MUTATED GNG12 WILD-TYPE 
              8             359 
[1] "SPATA6 MUTATION ANALYSIS"
[1] 3
  SPATA6 MUTATED SPATA6 WILD-TYPE 
               6              361 
  SPATA6 MUTATED SPATA6 WILD-TYPE 
               6              361 
[1] "BRD2 MUTATION ANALYSIS"
[1] 3
  BRD2 MUTATED BRD2 WILD-TYPE 
            10            357 
  BRD2 MUTATED BRD2 WILD-TYPE 
            10            357 
[1] "DSCAM MUTATION ANALYSIS"
[1] 3
  DSCAM MUTATED DSCAM WILD-TYPE 
             34             333 
  DSCAM MUTATED DSCAM WILD-TYPE 
             34             333 
[1] "SMPDL3B MUTATION ANALYSIS"
[1] 3
  SMPDL3B MUTATED SMPDL3B WILD-TYPE 
                9               358 
  SMPDL3B MUTATED SMPDL3B WILD-TYPE 
                9               358 
[1] "RNF20 MUTATION ANALYSIS"
[1] 3
  RNF20 MUTATED RNF20 WILD-TYPE 
             18             349 
  RNF20 MUTATED RNF20 WILD-TYPE 
             18             349 
[1] "ATP2B4 MUTATION ANALYSIS"
[1] 3
  ATP2B4 MUTATED ATP2B4 WILD-TYPE 
              18              349 
  ATP2B4 MUTATED ATP2B4 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] "TAS1R3 MUTATION ANALYSIS"
[1] 3
  TAS1R3 MUTATED TAS1R3 WILD-TYPE 
               7              360 
  TAS1R3 MUTATED TAS1R3 WILD-TYPE 
               7              360 
[1] "ZNF185 MUTATION ANALYSIS"
[1] 3
  ZNF185 MUTATED ZNF185 WILD-TYPE 
              10              357 
  ZNF185 MUTATED ZNF185 WILD-TYPE 
              10              357 
[1] "ZNF142 MUTATION ANALYSIS"
[1] 3
  ZNF142 MUTATED ZNF142 WILD-TYPE 
              14              353 
  ZNF142 MUTATED ZNF142 WILD-TYPE 
              14              353 
[1] "TBCE MUTATION ANALYSIS"
[1] 3
  TBCE MUTATED TBCE WILD-TYPE 
             3            364 
  TBCE MUTATED TBCE WILD-TYPE 
             3            364 
[1] "TIPARP MUTATION ANALYSIS"
[1] 3
  TIPARP MUTATED TIPARP WILD-TYPE 
               5              362 
  TIPARP MUTATED TIPARP WILD-TYPE 
               5              362 
[1] "LIMA1 MUTATION ANALYSIS"
[1] 3
  LIMA1 MUTATED LIMA1 WILD-TYPE 
             13             354 
  LIMA1 MUTATED LIMA1 WILD-TYPE 
             13             354 
[1] "SFTPB MUTATION ANALYSIS"
[1] 3
  SFTPB MUTATED SFTPB WILD-TYPE 
              9             358 
  SFTPB MUTATED SFTPB WILD-TYPE 
              9             358 
[1] "IL7R MUTATION ANALYSIS"
[1] 3
  IL7R MUTATED IL7R WILD-TYPE 
            11            356 
  IL7R MUTATED IL7R WILD-TYPE 
            11            356 
[1] "FAAH2 MUTATION ANALYSIS"
[1] 3
  FAAH2 MUTATED FAAH2 WILD-TYPE 
             11             356 
  FAAH2 MUTATED FAAH2 WILD-TYPE 
             11             356 
[1] "CNKSR3 MUTATION ANALYSIS"
[1] 3
  CNKSR3 MUTATED CNKSR3 WILD-TYPE 
               9              358 
  CNKSR3 MUTATED CNKSR3 WILD-TYPE 
               9              358 
[1] "KLF11 MUTATION ANALYSIS"
[1] 3
  KLF11 MUTATED KLF11 WILD-TYPE 
              7             360 
  KLF11 MUTATED KLF11 WILD-TYPE 
              7             360 
[1] "TRIB1 MUTATION ANALYSIS"
[1] 3
  TRIB1 MUTATED TRIB1 WILD-TYPE 
              7             360 
  TRIB1 MUTATED TRIB1 WILD-TYPE 
              7             360 
[1] "DAB2 MUTATION ANALYSIS"
[1] 3
  DAB2 MUTATED DAB2 WILD-TYPE 
            13            354 
  DAB2 MUTATED DAB2 WILD-TYPE 
            13            354 
[1] "ZNF557 MUTATION ANALYSIS"
[1] 3
  ZNF557 MUTATED ZNF557 WILD-TYPE 
               9              358 
  ZNF557 MUTATED ZNF557 WILD-TYPE 
               9              358 
[1] "OR5K2 MUTATION ANALYSIS"
[1] 3
  OR5K2 MUTATED OR5K2 WILD-TYPE 
              9             358 
  OR5K2 MUTATED OR5K2 WILD-TYPE 
              9             358 
[1] "PGAP3 MUTATION ANALYSIS"
[1] 3
  PGAP3 MUTATED PGAP3 WILD-TYPE 
              7             360 
  PGAP3 MUTATED PGAP3 WILD-TYPE 
              7             360 
[1] "TEK MUTATION ANALYSIS"
[1] 3
  TEK MUTATED TEK WILD-TYPE 
           28           339 
  TEK MUTATED TEK WILD-TYPE 
           28           339 
[1] "C5ORF36 MUTATION ANALYSIS"
[1] 3
  C5ORF36 MUTATED C5ORF36 WILD-TYPE 
               17               350 
  C5ORF36 MUTATED C5ORF36 WILD-TYPE 
               17               350 
[1] "CHRNA1 MUTATION ANALYSIS"
[1] 3
  CHRNA1 MUTATED CHRNA1 WILD-TYPE 
               9              358 
  CHRNA1 MUTATED CHRNA1 WILD-TYPE 
               9              358 
[1] "TRIM33 MUTATION ANALYSIS"
[1] 3
  TRIM33 MUTATED TRIM33 WILD-TYPE 
              15              352 
  TRIM33 MUTATED TRIM33 WILD-TYPE 
              15              352 
[1] "XRCC1 MUTATION ANALYSIS"
[1] 3
  XRCC1 MUTATED XRCC1 WILD-TYPE 
              8             359 
  XRCC1 MUTATED XRCC1 WILD-TYPE 
              8             359 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "NEOPLASM_DISEASESTAGE"                 
 [7] "PATHOLOGY_T_STAGE"                     
 [8] "PATHOLOGY_N_STAGE"                     
 [9] "PATHOLOGY_M_STAGE"                     
[10] "DCC_UPLOAD_DATE"                       
[11] "GENDER"                                
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[13] "DAYS_TO_LAST_KNOWN_ALIVE"              
[14] "RADIATION_THERAPY"                     
[15] "HISTOLOGICAL_TYPE"                     
[16] "RADIATIONS_RADIATION_REGIMENINDICATION"
[17] "COMPLETENESS_OF_RESECTION"             
[18] "NUMBER_OF_LYMPH_NODES"                 
[19] "RACE"                                  
[20] "ETHNICITY"                             
[21] "BATCH_NUMBER"                          

Input Data has 21 rows and 367 columns.

[1] "Batch" "21"   
[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=63,	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=232,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'NEOPLASM_DISEASESTAGE':	nDistinctValues=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCC_UPLOAD_DATE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'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 13:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 14:'RADIATION_THERAPY':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 15:'HISTOLOGICAL_TYPE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION excluded in the analysis because there is no case of (both >= 3) in the table below"
              NO      YES    
freq.values   "2"     "365"  
freq.contrast "365"   "2"    
both >= 3     "FALSE" "FALSE"
Variable 17:'COMPLETENESS_OF_RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=19,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'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"                "198"                 
freq.contrast "198"              "1"                   
both >= 3     "FALSE"            "FALSE"               
Variable 21:'BATCH_NUMBER':	nDistinctValues=21,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[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 10 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"            "NEOPLASM_DISEASESTAGE"    
 [3] "PATHOLOGY_T_STAGE"         "PATHOLOGY_N_STAGE"        
 [5] "PATHOLOGY_M_STAGE"         "GENDER"                   
 [7] "HISTOLOGICAL_TYPE"         "COMPLETENESS_OF_RESECTION"
 [9] "NUMBER_OF_LYMPH_NODES"     "RACE"                     
YEARS_TO_BIRTH, nv=58, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, 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  68 248  41 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
  9  68 248  41 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
  9  68 248  41 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
  9  68 248  41 
PATHOLOGY_N_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2 
220  80  66 
[1] "table(vv)"
vv
 N0  N1  N2 
220  80  66 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2 
220  80  66 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


 N0  N1  N2 
220  80  66 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=2, binary=FALSE, numeric=FALSE
COMPLETENESS_OF_RESECTION, 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   228  56
  APC WILD-TYPE  54  17
  APC MUTATED APC WILD-TYPE 
          284            71 
  APC MUTATED APC WILD-TYPE 
           56            17 
$`APC MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       43.76        43.76        24.33        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       36.53        32.91        31.63        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       23.61        22.09        22.06        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       23.87        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3530 TCGA-AA-3531 
       63.98         6.97         9.07        37.05        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01        12.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3710 
        5.98        37.05        19.00        36.00        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3837 
       19.04        19.04        35.05        33.04         0.99        38.99 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       17.03        10.06        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3870 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 
       29.98         2.01        12.99        24.00        33.01        24.00 
TCGA-AA-3952 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
        2.01        21.99        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       25.02        24.00        27.02        27.02         7.96        27.02 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       38.04        19.00        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
       27.02        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       32.02        31.00        31.00         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       33.04        35.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A03F 
        2.01         5.03        14.01         0.92        41.00        18.05 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37         4.21         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13        83.80        22.36        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        1.94         2.24         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        0.10        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 
       11.51        20.19        18.25         1.32        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       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        13.38        13.45        35.87 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6855 TCGA-F4-6856 
       29.59        16.24        33.67        13.25        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      107.67        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       45.11        36.72        36.00        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 
       91.79        46.75 

$`APC WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-4105 TCGA-A6-6648 
       46.65        42.90        42.28        16.57        14.53        25.18 
TCGA-A6-6780 TCGA-AA-3492 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       20.12         3.02         1.02        13.02        38.99         1.02 
TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3534 
       24.03        36.03         8.05        19.07         0.00        29.00 
TCGA-AA-3543 TCGA-AA-3560 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3696 TCGA-AA-3811 
        0.99        19.99        54.02         0.92         5.03        10.06 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3844 
       25.02         1.02        17.98        15.95        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
        0.00         0.00        24.03        27.02        18.05        31.00 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3986 
       26.01        20.98        34.03         2.01        16.08        19.07 
TCGA-AA-A004 TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A01D 
       13.94        30.02        34.03        42.02         0.99        10.98 
TCGA-AA-A01G TCGA-AA-A01P TCGA-AA-A01X TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-6889 
       12.00        38.07        26.01        39.98        40.96        56.55 
TCGA-AY-4070 TCGA-AZ-4323 TCGA-AZ-5403 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6719 
       16.31         1.41        62.79         3.06         3.25         1.35 
TCGA-CM-4747 TCGA-CM-6171 TCGA-D5-6534 TCGA-D5-6930 TCGA-F4-6570 TCGA-F4-6704 
       25.02        14.04        43.27         1.51         6.18         1.55 
TCGA-F4-6805 TCGA-F4-6854 TCGA-G4-6299 TCGA-G4-6321 TCGA-G4-6628 
       16.31         0.53        74.56        22.09        52.80 

  APC MUTATED APC WILD-TYPE 
            0             0 
  APC MUTATED APC WILD-TYPE 
       140.38         74.56 
  APC MUTATED APC WILD-TYPE 
       21.255        18.050 
[1] "0.0 - 140.4 (21.3)" "0.0 - 74.6 (18.1)" 
[1] "hr=" "1.6"
D1V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  APC MUTATED        51        1       19        86         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          12          9         35         23       30        11
  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            19             6
  STAGE IIA           86            23
  STAGE IIB            7             1
  STAGE IIC            1             0
  STAGE III           12             7
  STAGE IIIA           9             1
  STAGE IIIB          35             6
  STAGE IIIC          23             8
  STAGE IV            30             5
  STAGE IVA           11             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  53 200  34
  APC WILD-TYPE   2  15  48   7
D1V4, multiclass
    clus
vv   APC MUTATED APC WILD-TYPE
  T1           7             2
  T2          53            15
  T3         200            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  67  52
  APC WILD-TYPE  45  13  14
D1V5, multiclass
    clus
vv   APC MUTATED APC WILD-TYPE
  N0         175            45
  N1          67            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   222  41
  APC WILD-TYPE  61   7
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED    222   41
  APC WILD-TYPE   61    7
   clus
vv  APC MUTATED APC WILD-TYPE
  0         222            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   258  35
  APC WILD-TYPE  59  13
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED    258   35
  APC WILD-TYPE   59   13
                               clus
vv                              APC MUTATED APC WILD-TYPE
  COLON ADENOCARCINOMA                  258            59
  COLON MUCINOUS ADENOCARCINOMA          35            13
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  APC MUTATED   200   1  19  18
  APC WILD-TYPE  57   1   3   3
D1V9, multiclass
    clus
vv   APC MUTATED APC WILD-TYPE
  R0         200            57
  R1           1             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"
D1V10, 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
D1V11, 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   181  46
  TP53 WILD-TYPE 101  27
  TP53 MUTATED TP53 WILD-TYPE 
           227            128 
  TP53 MUTATED TP53 WILD-TYPE 
            46             27 
$`TP53 MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       43.76        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       36.53        14.53        32.91        30.44        29.19        23.61 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6651 
       22.06        27.09        22.52        25.08        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3510 
       24.69        23.87        20.28         3.02         1.02        63.98 
TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3526 
        6.97        38.99         9.07        24.03        36.03        19.07 
TCGA-AA-3531 TCGA-AA-3542 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 
       34.03        12.99        21.01        13.02        24.00        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       20.98        19.99        13.94        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 
        6.97         2.01        14.01        15.02         5.98        37.05 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3815 TCGA-AA-3842 TCGA-AA-3844 
       85.05        19.04        10.06        33.04        37.02        14.93 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       10.06        33.07         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 
       17.03        24.03        27.02        18.05         2.01        24.00 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3975 
       26.01        20.98        34.03        21.99        50.99        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-A004 
       26.01        25.02        24.00        27.02        27.02        13.94 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00W 
       19.00        30.02        34.03        38.04        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-6548 TCGA-AD-6888 TCGA-AD-6899 
       41.00        40.96         0.07        21.37         4.21         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        15.75         0.20        21.44         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5914 TCGA-CM-4743 TCGA-CM-4744 
      102.44        40.34        15.62        21.99        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       37.02        13.02        29.06        22.98        30.08        16.01 
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-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 
       14.04        11.01        13.05        11.08        11.08        10.06 
TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       12.26        13.51        11.51        18.25         1.32        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-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A0XF 
       13.41         1.51        12.00        11.38        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A285 TCGA-DM-A28E 
        7.50        44.32       131.51       135.65         6.12       119.93 
TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6703 
       35.97       117.07        98.24         8.61        13.38        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        91.79        46.75        52.80 

$`TP53 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2677 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-5657 TCGA-A6-5661 
       46.65        24.33        33.34        32.75        31.63        33.53 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6653 TCGA-A6-6780 
       22.09        32.71         8.38        25.18        24.39        20.12 
TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 
       19.66         7.04        35.01         1.02        13.02         1.02 
TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3532 TCGA-AA-3534 
       37.05         8.05         0.00        19.07        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3554 TCGA-AA-3555 
       26.01         0.99        14.01        33.99        17.95        29.95 
TCGA-AA-3562 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3680 
       19.99        54.02         0.92        50.04        47.01        11.01 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3812 
       19.00        36.00         5.03        26.99        19.04        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
        0.00        17.03         0.00         0.00        36.03        32.05 
TCGA-AA-3864 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3950 
       53.00        29.98        31.00        12.99        33.01        24.00 
TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3986 TCGA-AA-3989 
        2.01         2.01        16.08        13.05        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00Q 
       27.02        38.04        18.05        18.05         4.01        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01I TCGA-AA-A01P 
        0.99        17.03        21.99        15.02        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A029 
        1.02        35.01        35.01        26.01        39.06        51.98 
TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.92        39.98        18.05        56.55         0.79         0.72 
TCGA-AD-6964 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4682 TCGA-CA-5254 TCGA-CA-5255 
       10.88        17.82        58.39        22.36         2.24         3.06 
TCGA-CA-5796 TCGA-CA-6715 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 
        3.25         0.07        49.08        51.32        21.14         2.93 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4747 TCGA-CM-5344 TCGA-CM-5861 TCGA-CM-5863 
        2.01       124.27        25.02        22.03        15.02        15.02 
TCGA-CM-6170 TCGA-CM-6674 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 
       15.02        12.95        11.01        12.03        45.40        19.59 
TCGA-D5-6529 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6928 TCGA-D5-7000 TCGA-DM-A0X9 
       20.19        17.85         4.80        11.64        10.26       119.70 
TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28G TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6855 
      139.17        81.37        60.79        13.45         6.18        35.41 
TCGA-G4-6309 TCGA-G4-6588 
       51.75        26.17 

  TP53 MUTATED TP53 WILD-TYPE 
          0.07           0.00 
  TP53 MUTATED TP53 WILD-TYPE 
        140.38         139.17 
  TP53 MUTATED TP53 WILD-TYPE 
        20.980         19.825 
[1] "0.1 - 140.4 (21.0)" "0.0 - 139.2 (19.8)"
[1] "hr=" "1.2"
D2V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TP53 MUTATED        40        1       14        60         4         0
  TP53 WILD-TYPE      24        0       11        49         4         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TP53 MUTATED          11          9         27         24       24         9
  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             14             11
  STAGE IIA            60             49
  STAGE IIB             4              4
  STAGE IIC             0              1
  STAGE III            11              8
  STAGE IIIA            9              1
  STAGE IIIB           27             14
  STAGE IIIC           24              7
  STAGE IV             24             11
  STAGE IVA             9              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  44 155  24
  TP53 WILD-TYPE   3  24  93  17
D2V4, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  T1            6              3
  T2           44             24
  T3          155             93
  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   129  53  47
  TP53 WILD-TYPE  91  27  19
D2V5, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  N0          129             91
  N1           53             27
  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   175  33
  TP53 WILD-TYPE 108  15
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED    175   33
  TP53 WILD-TYPE  108   15
   clus
vv  TP53 MUTATED TP53 WILD-TYPE
  0          175            108
  1           33             15
[1] 2 2
[1] FALSE
D2V7, binary
                cls
clus               0   1
  TP53 MUTATED   102 128
  TP53 WILD-TYPE  68  69
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED    102  128
  TP53 WILD-TYPE   68   69
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE          102             68
  MALE            128             69
[1] 2 2
[1] FALSE
D2V8, binary
                cls
clus               0   1
  TP53 MUTATED   209  19
  TP53 WILD-TYPE 108  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED    209   19
  TP53 WILD-TYPE  108   29
                               clus
vv                              TP53 MUTATED TP53 WILD-TYPE
  COLON ADENOCARCINOMA                   209            108
  COLON MUCINOUS ADENOCARCINOMA           19             29
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TP53 MUTATED   158   2  13   8
  TP53 WILD-TYPE  99   0   9  13
D2V9, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  R0          158             99
  R1            2              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"
D2V10, 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   131
  TP53 WILD-TYPE                         6    45
D2V11, 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                                     131             45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = ARID1A MUTATION ANALYSIS
D3V1, survival
                  sevent
clus2                0   1
  ARID1A MUTATED    57  12
  ARID1A WILD-TYPE 225  61
  ARID1A MUTATED ARID1A WILD-TYPE 
              69              286 
  ARID1A MUTATED ARID1A WILD-TYPE 
              12               61 
$`ARID1A MUTATED`
TCGA-A6-2676 TCGA-A6-4105 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6780 TCGA-A6-6781 
       42.90        14.53        22.06         8.38        20.12        19.66 
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3554 TCGA-AA-3555 
        3.02         1.02         1.02        13.02        17.95        29.95 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3713 TCGA-AA-3831 TCGA-AA-3867 
       78.08         6.05         6.97        19.04        17.98        24.03 
TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00L TCGA-AA-A010 
       33.01        24.00        38.04        30.02        38.04        34.98 
TCGA-AA-A017 TCGA-AA-A01R TCGA-AD-6895 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 
       15.02        35.01         0.72         0.20        21.44        58.39 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 
        5.13        83.80        49.41         6.77       100.01        29.56 
TCGA-CA-5254 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CK-4952 TCGA-CK-5913 
        2.24         3.29         0.26         0.33        15.62        51.32 
TCGA-CK-6747 TCGA-CM-5864 TCGA-CM-6162 TCGA-CM-6166 TCGA-CM-6171 TCGA-CM-6172 
        2.93        15.02        12.00        21.99        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6679 TCGA-D5-5538 TCGA-D5-5541 TCGA-D5-6540 
       12.95        11.08        10.06        12.26        11.51        16.14 
TCGA-D5-6898 TCGA-D5-6930 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1HB TCGA-F4-6460 
        7.53         1.51        24.43        38.20       135.65        13.38 
TCGA-F4-6570 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6310 TCGA-G4-6317 
        6.18         0.53        19.43       107.67        45.11        36.00 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 
       35.80        26.17        52.80 

$`ARID1A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 
       34.65        33.34        32.75        36.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       30.44        29.19        33.53        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 
       27.09        22.52        25.08        25.18        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3502 
       24.69        24.39        23.87        20.28         7.04        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
       63.98         6.97        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 
       14.01        33.99        21.01        13.02        24.00        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3664 
       20.98        19.99        13.94        19.99        61.02        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
        0.99        25.02         1.02        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        53.00        17.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3952 
       31.00         2.01        12.99        24.00        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D 
       27.02        19.07         7.96        27.02        13.94        19.00 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        21.99        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S 
       12.00        31.00        31.00        38.07         1.02         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 
       17.82         1.41        22.36        62.79        61.41        12.10 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19         1.94         3.06         3.25 
TCGA-CA-6715 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       49.08        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        16.01        15.02         5.03        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 
       17.03        15.02        14.04        29.03        16.04        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 
       12.99        13.02        15.02        13.05        11.08        11.01 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6532 
       12.03        45.40        19.59        13.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       12.49        15.58        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-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       10.26       119.70       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       98.24         8.61        13.45        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6855 TCGA-G4-6299 
       29.59        16.24        33.67        13.25        35.41        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        51.75        36.72 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        91.79        46.75 

  ARID1A MUTATED ARID1A WILD-TYPE 
             0.2              0.0 
  ARID1A MUTATED ARID1A WILD-TYPE 
          135.65           140.38 
  ARID1A MUTATED ARID1A WILD-TYPE 
          17.950           21.255 
[1] "0.2 - 135.7 (17.9)" "0.0 - 140.4 (21.3)"
[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       19        78         5         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARID1A MUTATED           5          0          7          4        4
  ARID1A WILD-TYPE        14         10         34         27       31
                  vv
clus               STAGE IVA STAGE IVB
  ARID1A MUTATED           0         0
  ARID1A WILD-TYPE        13         1
D3V3, multiclass
            clus
vv           ARID1A MUTATED ARID1A WILD-TYPE
  STAGE I                10               54
  STAGE IA                0                1
  STAGE II                6               19
  STAGE IIA              31               78
  STAGE IIB               3                5
  STAGE IIC               0                1
  STAGE III               5               14
  STAGE IIIA              0               10
  STAGE IIIB              7               34
  STAGE IIIC              4               27
  STAGE IV                4               31
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ARID1A MUTATED     0  11  55   6
  ARID1A WILD-TYPE   9  57 193  35
D3V4, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  T1              0                9
  T2             11               57
  T3             55              193
  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  69  56
D3V5, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  N0             51              169
  N1             11               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"
D3V6, binary
                  cls
clus                 0   1
  ARID1A MUTATED    56   4
  ARID1A WILD-TYPE 227  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED     56    4
  ARID1A WILD-TYPE  227   44
   clus
vv  ARID1A MUTATED ARID1A WILD-TYPE
  0             56              227
  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    57  15
  ARID1A WILD-TYPE 260  33
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED     57   15
  ARID1A WILD-TYPE  260   33
                               clus
vv                              ARID1A MUTATED ARID1A WILD-TYPE
  COLON ADENOCARCINOMA                      57              260
  COLON MUCINOUS ADENOCARCINOMA             15               33
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ARID1A MUTATED    49   0   3   7
  ARID1A WILD-TYPE 208   2  19  14
D3V9, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  R0             49              208
  R1              0                2
  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"
D3V10, 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
D3V11, 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    37   8
  RNF43 WILD-TYPE 245  65
  RNF43 MUTATED RNF43 WILD-TYPE 
             45             310 
  RNF43 MUTATED RNF43 WILD-TYPE 
              8              65 
$`RNF43 MUTATED`
TCGA-A6-2671 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6649 TCGA-A6-6653 TCGA-A6-6781 
       43.76        33.53        22.06        24.16        24.39        19.66 
TCGA-AA-3492 TCGA-AA-3518 TCGA-AA-3555 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3710 
        3.02         1.02        29.95         6.97         0.92        26.99 
TCGA-AA-3715 TCGA-AA-3947 TCGA-AA-A00K TCGA-AA-A010 TCGA-AA-A01I TCGA-AA-A01P 
       19.04        33.01        18.05        34.98        31.00        38.07 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6964 TCGA-AU-6004 TCGA-AZ-6598 
        0.07        56.55         0.72        10.88        27.09        49.41 
TCGA-CA-5796 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CM-4743 TCGA-CM-4746 
        3.25        51.32        21.14         2.93        23.05        37.02 
TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6171 TCGA-CM-6674 TCGA-D5-6540 TCGA-D5-6928 
       15.02        12.00        14.04        12.95        16.14        11.64 
TCGA-D5-6930 TCGA-F4-6570 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6309 TCGA-G4-6315 
        1.51         6.18        19.43        74.56        51.75        36.72 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 
       35.80        26.17        52.80 

$`RNF43 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       31.63        30.44        29.19        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 
       27.09        22.52         8.38        25.08        25.18        21.76 
TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       24.69        23.87        20.12        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 
       37.05        19.00        36.00         5.03        85.05        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01Q 
       15.02        10.98        32.02        12.00        31.00         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        4.21         0.79         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
       17.56       102.44        40.34        15.62        49.08        21.99 
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        16.01         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-6172 
       21.99        14.99        12.99        13.02        15.02        11.01 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        15.58         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-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.38        13.45        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 
       16.24        33.67        13.25         0.53        35.41       107.67 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6317 
       65.85        53.62        44.68        55.04        45.11        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        91.79        46.75 

  RNF43 MUTATED RNF43 WILD-TYPE 
           0.07            0.00 
  RNF43 MUTATED RNF43 WILD-TYPE 
          74.56          140.38 
  RNF43 MUTATED RNF43 WILD-TYPE 
          22.06           20.07 
[1] "0.1 - 74.6 (22.1)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.1"
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       21        91         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RNF43 MUTATED           2          0          3          2        2         0
  RNF43 WILD-TYPE        17         10         38         29       33        13
                 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              21
  STAGE IIA             18              91
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             0              10
  STAGE IIIB             3              38
  STAGE IIIC             2              29
  STAGE IV               2              33
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RNF43 MUTATED     1   9  31   5
  RNF43 WILD-TYPE   8  59 217  36
D4V4, multiclass
    clus
vv   RNF43 MUTATED RNF43 WILD-TYPE
  T1             1               8
  T2             9              59
  T3            31             217
  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  72  63
D4V5, multiclass
    clus
vv   RNF43 MUTATED RNF43 WILD-TYPE
  N0            35             185
  N1             8              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"
D4V6, binary
                 cls
clus                0   1
  RNF43 MUTATED    36   2
  RNF43 WILD-TYPE 247  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF43 MUTATED     36    2
  RNF43 WILD-TYPE  247   46
   clus
vv  RNF43 MUTATED RNF43 WILD-TYPE
  0            36             247
  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    36  10
  RNF43 WILD-TYPE 281  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF43 MUTATED     36   10
  RNF43 WILD-TYPE  281   38
                               clus
vv                              RNF43 MUTATED RNF43 WILD-TYPE
  COLON ADENOCARCINOMA                     36             281
  COLON MUCINOUS ADENOCARCINOMA            10              38
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RNF43 MUTATED    36   0   0   4
  RNF43 WILD-TYPE 221   2  22  17
D4V9, multiclass
    clus
vv   RNF43 MUTATED RNF43 WILD-TYPE
  R0            36             221
  R1             0               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"
D4V10, 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
D4V11, 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    27   7
  SOX9 WILD-TYPE 255  66
  SOX9 MUTATED SOX9 WILD-TYPE 
            34            321 
  SOX9 MUTATED SOX9 WILD-TYPE 
             7             66 
$`SOX9 MUTATED`
TCGA-A6-4105 TCGA-A6-6141 TCGA-A6-6652 TCGA-AA-3492 TCGA-AA-3672 TCGA-AA-3713 
       14.53         8.38        24.69         3.02         0.92        19.04 
TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3939 TCGA-AA-3979 TCGA-AA-3989 TCGA-AA-A03F 
       25.02        17.98        12.99        24.00         7.96        18.05 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AY-6386 TCGA-AZ-4681 TCGA-AZ-6601 
       56.55         0.79         0.72        17.82        83.80       100.01 
TCGA-CA-5255 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4744 
        3.06        17.56        40.34         2.93       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       107.67        44.68 

$`SOX9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       24.16        21.76        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3821 
       19.04        10.06        35.05        33.04         0.99         1.02 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        25.02        27.02        27.02        19.07 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 
       14.01         0.92        41.00        39.98        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       21.37         4.21         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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        61.41        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5796 
        5.23        11.74         3.19         1.94         2.24         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      102.44        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
        2.01        23.05        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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-6678 TCGA-CM-6679 
       14.04        11.01        13.05        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       12.03        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        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-D5-6930 
       12.43        14.30         9.04         9.44        11.64         1.51 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38        10.26       119.70        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        53.62        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  SOX9 MUTATED SOX9 WILD-TYPE 
          0.72           0.00 
  SOX9 MUTATED SOX9 WILD-TYPE 
        124.27         140.38 
  SOX9 MUTATED SOX9 WILD-TYPE 
         17.90          21.01 
[1] "0.7 - 124.3 (17.9)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.1"
D5V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SOX9 MUTATED         3        0        2        18         0         0
  SOX9 WILD-TYPE      61        1       23        91         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SOX9 MUTATED           3          1          1          1        3         2
  SOX9 WILD-TYPE        16          9         40         30       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             23
  STAGE IIA            18             91
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             3             16
  STAGE IIIA            1              9
  STAGE IIIB            1             40
  STAGE IIIC            1             30
  STAGE IV              3             32
  STAGE IVA             2             11
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  64 219  39
D5V4, multiclass
    clus
vv   SOX9 MUTATED SOX9 WILD-TYPE
  T1            1              8
  T2            4             64
  T3           29            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
  SOX9 MUTATED    25   7   4
  SOX9 WILD-TYPE 195  73  62
D5V5, multiclass
    clus
vv   SOX9 MUTATED SOX9 WILD-TYPE
  N0           25            195
  N1            7             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"
D5V6, binary
                cls
clus               0   1
  SOX9 MUTATED    27   4
  SOX9 WILD-TYPE 256  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOX9 MUTATED     27    4
  SOX9 WILD-TYPE  256   44
   clus
vv  SOX9 MUTATED SOX9 WILD-TYPE
  0           27            256
  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    34   2
  SOX9 WILD-TYPE 283  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOX9 MUTATED     34    2
  SOX9 WILD-TYPE  283   46
                               clus
vv                              SOX9 MUTATED SOX9 WILD-TYPE
  COLON ADENOCARCINOMA                    34            283
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SOX9 MUTATED    20   1   2   5
  SOX9 WILD-TYPE 237   1  20  16
D5V9, multiclass
    clus
vv   SOX9 MUTATED SOX9 WILD-TYPE
  R0           20            237
  R1            1              1
  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"
D5V10, 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
D5V11, 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 = MUC4 MUTATION ANALYSIS
D6V1, survival
                sevent
clus2              0   1
  MUC4 MUTATED    77  15
  MUC4 WILD-TYPE 205  58
  MUC4 MUTATED MUC4 WILD-TYPE 
            92            263 
  MUC4 MUTATED MUC4 WILD-TYPE 
            15             58 
$`MUC4 MUTATED`
TCGA-A6-3809 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 
       32.75        14.53        32.91        33.53        22.09        22.06 
TCGA-A6-6137 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3492 
       27.09        25.18        21.76        19.66        20.28         3.02 
TCGA-AA-3510 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3697 TCGA-AA-3877 
       63.98        78.08         6.05         6.97        85.05        31.00 
TCGA-AA-3950 TCGA-AA-A00R TCGA-AA-A010 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6901 
       24.00         0.99        34.98         4.21         0.72        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4681 TCGA-AZ-6601 
       27.42        10.88        21.44        58.39        83.80       100.01 
TCGA-AZ-6603 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
       29.56         2.24         3.06         0.07         0.26         0.33 
TCGA-CA-6719 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 
        1.35         2.93         2.01        23.05        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5864 
       13.02        29.06        22.03        22.98        30.08        15.02 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6679 TCGA-CM-6680 
       14.99        12.99        14.04        12.95        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       45.40        19.59        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6927 TCGA-D5-6928 
       17.13        15.58         7.53        10.13         9.44        11.64 
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-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A285 TCGA-DM-A28C 
       12.59       140.38         7.50       131.51         6.12        81.37 
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        35.87        16.31 
TCGA-F4-6856 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       19.43        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6628 
       35.80        52.80 

$`MUC4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5657 TCGA-A6-5659 
       16.57        34.65        33.34        36.53        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       29.19        23.61        32.71        22.52         8.38        25.08 
TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-AA-3489 
       24.16        24.69        24.39        23.87        20.12         7.04 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3664 TCGA-AA-3666 
       19.99        13.94        19.99        61.02        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 
        5.98        37.05        19.00        36.00         5.03        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W 
       38.04         4.01        27.02        42.02        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96         0.07        21.37        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
        5.79         0.20        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 
       15.75         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-6605 
       62.79        61.41        49.41         6.77        12.10         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6718 
       11.74         3.19         1.94         3.25         3.29         0.10 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-5860 TCGA-CM-5861 
       21.99        21.14       124.27        20.02        16.01        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-6169 TCGA-CM-6170 TCGA-CM-6172 
       29.03        16.04        21.99        13.02        15.02        11.01 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5538 TCGA-D5-5540 
       13.05        11.08        11.08        11.01        12.26        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6539 TCGA-D5-6540 
       11.51        20.19        18.25         1.32        12.49        16.14 
TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6930 
       12.39        12.43        14.30         9.04        13.41         1.51 
TCGA-DM-A0X9 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1DB TCGA-DM-A1HB 
      119.70        92.75        49.91        13.32        44.32       135.65 
TCGA-DM-A282 TCGA-DM-A28F TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      139.17        35.97         8.61        13.38        13.45         6.18 
TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
        1.55        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.41       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       55.04        51.75        26.17        91.79        46.75 

  MUC4 MUTATED MUC4 WILD-TYPE 
          0.07           0.00 
  MUC4 MUTATED MUC4 WILD-TYPE 
        140.38         139.17 
  MUC4 MUTATED MUC4 WILD-TYPE 
         21.60          20.02 
[1] "0.1 - 140.4 (21.6)" "0.0 - 139.2 (20.0)"
[1] "hr=" "1.6"
D6V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MUC4 MUTATED        11        1        5        36         3         0
  MUC4 WILD-TYPE      53        0       20        73         5         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MUC4 MUTATED           2          3         11          9        4         2
  MUC4 WILD-TYPE        17          7         30         22       31        11
                vv
clus             STAGE IVB
  MUC4 MUTATED           0
  MUC4 WILD-TYPE         1
D6V3, multiclass
            clus
vv           MUC4 MUTATED MUC4 WILD-TYPE
  STAGE I              11             53
  STAGE IA              1              0
  STAGE II              5             20
  STAGE IIA            36             73
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             2             17
  STAGE IIIA            3              7
  STAGE IIIB           11             30
  STAGE IIIC            9             22
  STAGE IV              4             31
  STAGE IVA             2             11
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MUC4 MUTATED     1  14  68   9
  MUC4 WILD-TYPE   8  54 180  32
D6V4, multiclass
    clus
vv   MUC4 MUTATED MUC4 WILD-TYPE
  T1            1              8
  T2           14             54
  T3           68            180
  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
  MUC4 MUTATED    59  19  14
  MUC4 WILD-TYPE 161  61  52
D6V5, multiclass
    clus
vv   MUC4 MUTATED MUC4 WILD-TYPE
  N0           59            161
  N1           19             61
  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"
D6V6, binary
                cls
clus               0   1
  MUC4 MUTATED    68   6
  MUC4 WILD-TYPE 215  42
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC4 MUTATED     68    6
  MUC4 WILD-TYPE  215   42
   clus
vv  MUC4 MUTATED MUC4 WILD-TYPE
  0           68            215
  1            6             42
[1] 2 2
[1] FALSE
D6V7, binary
                cls
clus               0   1
  MUC4 MUTATED    39  54
  MUC4 WILD-TYPE 131 143
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC4 MUTATED     39   54
  MUC4 WILD-TYPE  131  143
        clus
vv       MUC4 MUTATED MUC4 WILD-TYPE
  FEMALE           39            131
  MALE             54            143
[1] 2 2
[1] FALSE
D6V8, binary
                cls
clus               0   1
  MUC4 MUTATED    79  14
  MUC4 WILD-TYPE 238  34
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC4 MUTATED     79   14
  MUC4 WILD-TYPE  238   34
                               clus
vv                              MUC4 MUTATED MUC4 WILD-TYPE
  COLON ADENOCARCINOMA                    79            238
  COLON MUCINOUS ADENOCARCINOMA           14             34
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MUC4 MUTATED    55   0   1  11
  MUC4 WILD-TYPE 202   2  21  10
D6V9, multiclass
    clus
vv   MUC4 MUTATED MUC4 WILD-TYPE
  R0           55            202
  R1            0              2
  R2            1             21
  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"
D6V10, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MUC4 MUTATED                                  0     6
  MUC4 WILD-TYPE                                1     4
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MUC4 MUTATED                           7    70
  MUC4 WILD-TYPE                        12   106
D6V11, multiclass
                                  clus
vv                                 MUC4 MUTATED MUC4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       6              4
  BLACK OR AFRICAN AMERICAN                   7             12
  WHITE                                      70            106
[1] 4 2
[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 = RBM38 MUTATION ANALYSIS
D7V1, survival
                 sevent
clus2               0   1
  RBM38 MUTATED    24  10
  RBM38 WILD-TYPE 258  63
  RBM38 MUTATED RBM38 WILD-TYPE 
             34             321 
  RBM38 MUTATED RBM38 WILD-TYPE 
             10              63 
$`RBM38 MUTATED`
TCGA-A6-5659 TCGA-AA-3715 TCGA-AD-6548 TCGA-AD-6888 TCGA-AY-5543 TCGA-AZ-4323 
       30.44        19.04        21.37         4.21        15.75         1.41 
TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 
        5.23         3.19        49.08        21.99        21.14         2.01 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5861 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6676 
       13.02        29.06        15.02        14.99        13.02        11.08 
TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6923 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       13.51        20.19        12.43         9.44        11.64         1.51 
TCGA-D5-7000 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A28F 
       10.26        92.75        13.32        44.32       131.51        35.97 
TCGA-DM-A28K TCGA-F4-6460 TCGA-G4-6306 TCGA-G4-6628 
       98.24        13.38        44.68        52.80 

$`RBM38 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         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         0.07        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 
       14.50        27.09        16.31         0.95         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82        58.39         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-6747 TCGA-CK-6751 
      102.44        40.34        15.62        51.32         2.93       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5344 TCGA-CM-5348 
       23.05        20.02        37.02        25.02        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        16.01         5.03        15.02        15.02        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-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-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       19.59        11.51        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 
        7.53        12.39        10.13        14.30         9.04        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-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A282 
       49.91        12.59       140.38         7.50       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 
        6.12        81.37       119.93        60.79       117.07         8.61 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 
      107.67        74.56        65.85        53.62        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       26.17        91.79        46.75 

  RBM38 MUTATED RBM38 WILD-TYPE 
           1.41            0.00 
  RBM38 MUTATED RBM38 WILD-TYPE 
         131.51          140.38 
  RBM38 MUTATED RBM38 WILD-TYPE 
         15.005          21.010 
[1] "1.4 - 131.5 (15.0)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.5"
D7V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RBM38 MUTATED         8        0        1        13         1         0
  RBM38 WILD-TYPE      56        1       24        96         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RBM38 MUTATED           0          1          5          2        3         1
  RBM38 WILD-TYPE        19          9         36         29       32        12
                 vv
clus              STAGE IVB
  RBM38 MUTATED           0
  RBM38 WILD-TYPE         1
D7V3, multiclass
            clus
vv           RBM38 MUTATED RBM38 WILD-TYPE
  STAGE I                8              56
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA             13              96
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             5              36
  STAGE IIIC             2              29
  STAGE IV               3              32
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RBM38 MUTATED     1  10  20   4
  RBM38 WILD-TYPE   8  58 228  37
D7V4, multiclass
    clus
vv   RBM38 MUTATED RBM38 WILD-TYPE
  T1             1               8
  T2            10              58
  T3            20             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
  RBM38 MUTATED    23   7   4
  RBM38 WILD-TYPE 197  73  62
D7V5, multiclass
    clus
vv   RBM38 MUTATED RBM38 WILD-TYPE
  N0            23             197
  N1             7              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"
D7V6, binary
                 cls
clus                0   1
  RBM38 MUTATED    28   4
  RBM38 WILD-TYPE 255  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM38 MUTATED     28    4
  RBM38 WILD-TYPE  255   44
   clus
vv  RBM38 MUTATED RBM38 WILD-TYPE
  0            28             255
  1             4              44
[1] 2 2
[1] FALSE
D7V7, binary
                 cls
clus                0   1
  RBM38 MUTATED    10  25
  RBM38 WILD-TYPE 160 172
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM38 MUTATED     10   25
  RBM38 WILD-TYPE  160  172
        clus
vv       RBM38 MUTATED RBM38 WILD-TYPE
  FEMALE            10             160
  MALE              25             172
[1] 2 2
[1] FALSE
D7V8, binary
                 cls
clus                0   1
  RBM38 MUTATED    30   5
  RBM38 WILD-TYPE 287  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM38 MUTATED     30    5
  RBM38 WILD-TYPE  287   43
                               clus
vv                              RBM38 MUTATED RBM38 WILD-TYPE
  COLON ADENOCARCINOMA                     30             287
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RBM38 MUTATED    21   0   0   5
  RBM38 WILD-TYPE 236   2  22  16
D7V9, multiclass
    clus
vv   RBM38 MUTATED RBM38 WILD-TYPE
  R0            21             236
  R1             0               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"
D7V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RBM38 MUTATED                                  0     0
  RBM38 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RBM38 MUTATED                           4    30
  RBM38 WILD-TYPE                        15   146
D7V11, multiclass
                                  clus
vv                                 RBM38 MUTATED RBM38 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              10
  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(8) Variable = ACVR1B MUTATION ANALYSIS
D8V1, survival
                  sevent
clus2                0   1
  ACVR1B MUTATED    20   4
  ACVR1B WILD-TYPE 262  69
  ACVR1B MUTATED ACVR1B WILD-TYPE 
              24              331 
  ACVR1B MUTATED ACVR1B WILD-TYPE 
               4               69 
$`ACVR1B MUTATED`
TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-6652 TCGA-AA-3715 TCGA-AA-3831 TCGA-AA-3833 
       34.65        32.75        24.69        19.04        17.98        15.95 
TCGA-AA-3877 TCGA-AA-3994 TCGA-AA-A00J TCGA-AA-A010 TCGA-AA-A01R TCGA-AA-A029 
       31.00        27.02        18.05        34.98        35.01        51.98 
TCGA-AA-A02J TCGA-AA-A03F TCGA-AZ-6601 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 
        5.03        18.05       100.01         0.07         0.33         0.10 
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        29.59 

$`ACVR1B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       16.57        33.34        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       24.16        21.76        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        0.99        25.02         1.02        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        27.02        19.07         7.96        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       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        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02K TCGA-AA-A02O 
       37.02        39.06        39.98         2.01        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 
        1.94         2.24         3.06         3.25         3.29         0.26 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4744 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 
       20.19        18.25         1.32        43.27        15.12         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
        1.55        16.31        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  ACVR1B MUTATED ACVR1B WILD-TYPE 
            0.07             0.00 
  ACVR1B MUTATED ACVR1B WILD-TYPE 
          124.27           140.38 
  ACVR1B MUTATED ACVR1B WILD-TYPE 
          21.045           20.190 
[1] "0.1 - 124.3 (21.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.3"
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       21       101         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ACVR1B MUTATED           2          0          3          1        1
  ACVR1B WILD-TYPE        17         10         38         30       34
                  vv
clus               STAGE IVA STAGE IVB
  ACVR1B MUTATED           1         0
  ACVR1B WILD-TYPE        12         1
D8V3, multiclass
            clus
vv           ACVR1B MUTATED ACVR1B WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                4               21
  STAGE IIA               8              101
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               2               17
  STAGE IIIA              0               10
  STAGE IIIB              3               38
  STAGE IIIC              1               30
  STAGE IV                1               34
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  65 230  37
D8V4, multiclass
    clus
vv   ACVR1B MUTATED ACVR1B WILD-TYPE
  T1              1                8
  T2              3               65
  T3             18              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
  ACVR1B MUTATED    20   3   3
  ACVR1B WILD-TYPE 200  77  63
D8V5, multiclass
    clus
vv   ACVR1B MUTATED ACVR1B WILD-TYPE
  N0             20              200
  N1              3               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"
D8V6, binary
                  cls
clus                 0   1
  ACVR1B MUTATED    22   2
  ACVR1B WILD-TYPE 261  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACVR1B MUTATED     22    2
  ACVR1B WILD-TYPE  261   46
   clus
vv  ACVR1B MUTATED ACVR1B WILD-TYPE
  0             22              261
  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    17   9
  ACVR1B WILD-TYPE 300  39
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACVR1B MUTATED     17    9
  ACVR1B WILD-TYPE  300   39
                               clus
vv                              ACVR1B MUTATED ACVR1B WILD-TYPE
  COLON ADENOCARCINOMA                      17              300
  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 239   2  21  16
D8V9, multiclass
    clus
vv   ACVR1B MUTATED ACVR1B WILD-TYPE
  R0             18              239
  R1              0                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"
D8V10, 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
D8V11, 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    12   3
  B2M WILD-TYPE 270  70
  B2M MUTATED B2M WILD-TYPE 
           15           340 
  B2M MUTATED B2M WILD-TYPE 
            3            70 
$`B2M MUTATED`
TCGA-A6-2672 TCGA-A6-3809 TCGA-A6-6653 TCGA-A6-6780 TCGA-AA-3510 TCGA-AA-3845 
       46.65        32.75        24.39        20.12        63.98         0.00 
TCGA-AA-A010 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5913 TCGA-D5-5538 
       34.98       100.01         0.33         0.10        51.32        12.26 
TCGA-DM-A28F TCGA-F4-6703 TCGA-G4-6628 
       35.97        35.87        52.80 

$`B2M WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       34.65        33.34        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 
       24.16        21.76        24.69        23.87        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 
        7.04         3.02         1.02        35.01         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       14.93        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07         0.26         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
       81.37       119.93        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.38        13.45         6.18         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       35.80        26.17        91.79        46.75 

  B2M MUTATED B2M WILD-TYPE 
            0             0 
  B2M MUTATED B2M WILD-TYPE 
       100.01        140.38 
  B2M MUTATED B2M WILD-TYPE 
        34.98         19.99 
[1] "0.0 - 100.0 (35.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.4"
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       23       103         5         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  B2M MUTATED           0          0          3          0        0         0
  B2M WILD-TYPE        19         10         38         31       35        13
               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            23
  STAGE IIA            6           103
  STAGE IIB            3             5
  STAGE IIC            0             1
  STAGE III            0            19
  STAGE IIIA           0            10
  STAGE IIIB           3            38
  STAGE IIIC           0            31
  STAGE IV             0            35
  STAGE IVA            0            13
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  B2M MUTATED     0   2  11   3
  B2M WILD-TYPE   9  66 237  38
D9V4, multiclass
    clus
vv   B2M MUTATED B2M WILD-TYPE
  T1           0             9
  T2           2            66
  T3          11           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
  B2M MUTATED    13   3   0
  B2M WILD-TYPE 207  77  66
D9V5, multiclass
    clus
vv   B2M MUTATED B2M WILD-TYPE
  N0          13           207
  N1           3            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"
D9V6, binary
               cls
clus              0   1
  B2M MUTATED    13   0
  B2M WILD-TYPE 270  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  B2M MUTATED     13    0
  B2M WILD-TYPE  270   48
   clus
vv  B2M MUTATED B2M WILD-TYPE
  0          13           270
  1           0            48
[1] 2 2
[1] FALSE
D9V7, binary
               cls
clus              0   1
  B2M MUTATED     7   9
  B2M WILD-TYPE 163 188
[1] "tbl2"
               cls
clus            [,1] [,2]
  B2M MUTATED      7    9
  B2M WILD-TYPE  163  188
        clus
vv       B2M MUTATED B2M WILD-TYPE
  FEMALE           7           163
  MALE             9           188
[1] 2 2
[1] FALSE
D9V8, binary
               cls
clus              0   1
  B2M MUTATED    13   3
  B2M WILD-TYPE 304  45
[1] "tbl2"
               cls
clus            [,1] [,2]
  B2M MUTATED     13    3
  B2M WILD-TYPE  304   45
                               clus
vv                              B2M MUTATED B2M WILD-TYPE
  COLON ADENOCARCINOMA                   13           304
  COLON MUCINOUS ADENOCARCINOMA           3            45
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  B2M MUTATED     8   0   0   4
  B2M WILD-TYPE 249   2  22  17
D9V9, multiclass
    clus
vv   B2M MUTATED B2M WILD-TYPE
  R0           8           249
  R1           0             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"
D9V10, 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    11
  B2M WILD-TYPE                        19   165
D9V11, 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                                     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(10) Variable = TXNDC2 MUTATION ANALYSIS
D10V1, survival
                  sevent
clus2                0   1
  TXNDC2 MUTATED    20   2
  TXNDC2 WILD-TYPE 262  71
  TXNDC2 MUTATED TXNDC2 WILD-TYPE 
              22              333 
  TXNDC2 MUTATED TXNDC2 WILD-TYPE 
               2               71 
$`TXNDC2 MUTATED`
TCGA-A6-5659 TCGA-A6-6142 TCGA-A6-6780 TCGA-AA-3660 TCGA-AA-3672 TCGA-AA-3713 
       30.44        25.08        20.12        78.08         0.92        19.04 
TCGA-AA-3977 TCGA-AD-6888 TCGA-AD-6901 TCGA-CA-6717 TCGA-CK-6747 TCGA-CK-6748 
       25.02         4.21        22.42         0.33         2.93         2.01 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6167 TCGA-CM-6170 TCGA-CM-6172 TCGA-D5-6533 
       15.02        14.04        14.99        15.02        11.01         1.32 
TCGA-D5-6538 TCGA-DM-A28C TCGA-G4-6321 TCGA-G4-6628 
       17.13        81.37        22.09        52.80 

$`TXNDC2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6648 
       22.06        32.71        27.09        22.52         8.38        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 
       24.16        21.76        24.69        24.39        23.87        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         0.72         5.79        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6751 
       15.62        49.08        51.32        21.99        21.14       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 
       15.02        15.02        17.03        12.00        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 
       21.99        12.99        13.02        14.04        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        13.51        11.51        20.19        18.25 
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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28E 
       44.32       131.51       135.65       139.17         6.12       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 
       51.75        45.11        36.72        36.00        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       26.17        91.79        46.75 

  TXNDC2 MUTATED TXNDC2 WILD-TYPE 
            0.33             0.00 
  TXNDC2 MUTATED TXNDC2 WILD-TYPE 
           81.37           140.38 
  TXNDC2 MUTATED TXNDC2 WILD-TYPE 
          16.075           20.980 
[1] "0.3 - 81.4 (16.1)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "2.1"
D10V2, 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       24       105         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TXNDC2 MUTATED           2          0          4          1        2
  TXNDC2 WILD-TYPE        17         10         37         30       33
                  vv
clus               STAGE IVA STAGE IVB
  TXNDC2 MUTATED           1         0
  TXNDC2 WILD-TYPE        12         1
D10V3, multiclass
            clus
vv           TXNDC2 MUTATED TXNDC2 WILD-TYPE
  STAGE I                 5               59
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               4              105
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               2               17
  STAGE IIIA              0               10
  STAGE IIIB              4               37
  STAGE IIIC              1               30
  STAGE IV                2               33
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TXNDC2 MUTATED     1   7  13   1
  TXNDC2 WILD-TYPE   8  61 235  40
D10V4, multiclass
    clus
vv   TXNDC2 MUTATED TXNDC2 WILD-TYPE
  T1              1                8
  T2              7               61
  T3             13              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   5   2
  TXNDC2 WILD-TYPE 206  75  64
D10V5, multiclass
    clus
vv   TXNDC2 MUTATED TXNDC2 WILD-TYPE
  N0             14              206
  N1              5               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"
D10V6, binary
                  cls
clus                 0   1
  TXNDC2 MUTATED    14   3
  TXNDC2 WILD-TYPE 269  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TXNDC2 MUTATED     14    3
  TXNDC2 WILD-TYPE  269   45
   clus
vv  TXNDC2 MUTATED TXNDC2 WILD-TYPE
  0             14              269
  1              3               45
[1] 2 2
[1] FALSE
D10V7, 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
D10V8, binary
                  cls
clus                 0   1
  TXNDC2 MUTATED    19   3
  TXNDC2 WILD-TYPE 298  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TXNDC2 MUTATED     19    3
  TXNDC2 WILD-TYPE  298   45
                               clus
vv                              TXNDC2 MUTATED TXNDC2 WILD-TYPE
  COLON ADENOCARCINOMA                      19              298
  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 244   2  21  18
D10V9, multiclass
    clus
vv   TXNDC2 MUTATED TXNDC2 WILD-TYPE
  R0             13              244
  R1              0                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"
D10V10, 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
D10V11, 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(11) Variable = SELPLG MUTATION ANALYSIS
D11V1, survival
                  sevent
clus2                0   1
  SELPLG MUTATED    15   1
  SELPLG WILD-TYPE 267  72
  SELPLG MUTATED SELPLG WILD-TYPE 
              16              339 
  SELPLG MUTATED SELPLG WILD-TYPE 
               1               72 
$`SELPLG MUTATED`
TCGA-A6-5660 TCGA-A6-5664 TCGA-AA-3864 TCGA-AZ-4315 TCGA-CA-5255 TCGA-CM-4752 
       29.19        22.09        53.00        58.39         3.06        13.02 
TCGA-CM-5864 TCGA-CM-6679 TCGA-D5-6533 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       15.02        10.06         1.32        17.85         4.80        17.13 
TCGA-F4-6855 TCGA-G4-6307 TCGA-G4-6317 TCGA-G4-6625 
       35.41        55.04        36.00        91.79 

$`SELPLG WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5665 
       32.91        31.63        30.44        33.53        23.61        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        2.24         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6539 
       11.51        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       51.75        45.11        36.72        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6628 
       26.17        46.75        52.80 

  SELPLG MUTATED SELPLG WILD-TYPE 
            1.32             0.00 
  SELPLG MUTATED SELPLG WILD-TYPE 
           91.79           140.38 
  SELPLG MUTATED SELPLG WILD-TYPE 
           19.97            20.19 
[1] "1.3 - 91.8 (20.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "3.8"
D11V2, 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       24       102         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SELPLG MUTATED           0          0          4          3        0
  SELPLG WILD-TYPE        19         10         37         28       35
                  vv
clus               STAGE IVA STAGE IVB
  SELPLG MUTATED           0         0
  SELPLG WILD-TYPE        13         1
D11V3, multiclass
            clus
vv           SELPLG MUTATED SELPLG WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               7              102
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              4               37
  STAGE IIIC              3               28
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SELPLG MUTATED     0   1  13   2
  SELPLG WILD-TYPE   9  67 235  39
D11V4, multiclass
    clus
vv   SELPLG MUTATED SELPLG WILD-TYPE
  T1              0                9
  T2              1               67
  T3             13              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
  SELPLG MUTATED    10   2   4
  SELPLG WILD-TYPE 210  78  62
D11V5, multiclass
    clus
vv   SELPLG MUTATED SELPLG WILD-TYPE
  N0             10              210
  N1              2               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"
D11V6, binary
                  cls
clus                 0   1
  SELPLG MUTATED    13   0
  SELPLG WILD-TYPE 270  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SELPLG MUTATED     13    0
  SELPLG WILD-TYPE  270   48
   clus
vv  SELPLG MUTATED SELPLG WILD-TYPE
  0             13              270
  1              0               48
[1] 2 2
[1] FALSE
D11V7, 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
D11V8, binary
                  cls
clus                 0   1
  SELPLG MUTATED    16   0
  SELPLG WILD-TYPE 301  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SELPLG MUTATED     16    0
  SELPLG WILD-TYPE  301   48
                               clus
vv                              SELPLG MUTATED SELPLG WILD-TYPE
  COLON ADENOCARCINOMA                      16              301
  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 244   2  22  20
D11V9, multiclass
    clus
vv   SELPLG MUTATED SELPLG WILD-TYPE
  R0             13              244
  R1              0                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"
D11V10, 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
D11V11, 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(12) Variable = FAM123B MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  FAM123B MUTATED    33  13
  FAM123B WILD-TYPE 249  60
  FAM123B MUTATED FAM123B WILD-TYPE 
               46               309 
  FAM123B MUTATED FAM123B WILD-TYPE 
               13                60 
$`FAM123B MUTATED`
TCGA-A6-3808 TCGA-A6-4105 TCGA-A6-6137 TCGA-AA-3492 TCGA-AA-3511 TCGA-AA-3516 
       33.34        14.53        27.09         3.02         6.97        13.02 
TCGA-AA-3530 TCGA-AA-3548 TCGA-AA-3554 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3666 
       19.07        33.99        17.95        61.02         6.97         2.01 
TCGA-AA-3680 TCGA-AA-3821 TCGA-AA-3845 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3939 
       11.01         1.02         0.00        53.00        27.02        12.99 
TCGA-AA-3977 TCGA-AA-A00A TCGA-AA-A010 TCGA-AA-A01D TCGA-AD-6890 TCGA-AD-6895 
       25.02        38.04        34.98        10.98         0.79         0.72 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-CA-6717 TCGA-CK-4947 TCGA-CK-6747 
       21.44        58.39        61.41         0.33        17.56         2.93 
TCGA-CM-4744 TCGA-CM-5860 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6677 
       20.02        16.01        14.99        12.99        14.04        11.08 
TCGA-D5-5537 TCGA-D5-6922 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A28H TCGA-DM-A28K 
       45.40        10.13        12.59       140.38       117.07        98.24 
TCGA-F4-6570 TCGA-F4-6809 TCGA-G4-6315 TCGA-G4-6626 
        6.18        13.25        36.72        46.75 

$`FAM123B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 
       16.57        34.65        32.75        36.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       32.71        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 
       20.28         7.04         1.02        35.01        63.98         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
        8.05        19.07         0.00        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3552 
       26.01        12.99         0.99        14.01        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 
       19.99        78.08         6.05        54.02        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       50.04        47.01        15.02         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 
       10.06        35.05        33.04         0.99        25.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02        14.93        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 
       31.07        31.07        30.05        17.03        24.03        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05        31.00         2.01        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       21.99        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        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6899 
       40.96         0.07        21.37         4.21        56.55         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        15.75         0.20        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13        83.80        22.36        62.79        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.26         0.10         1.35       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 
       49.08        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58         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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        13.38        13.45        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       29.59        16.24        33.67         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       51.75        45.11        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       26.17        91.79        52.80 

  FAM123B MUTATED FAM123B WILD-TYPE 
                0                 0 
  FAM123B MUTATED FAM123B WILD-TYPE 
           140.38            139.17 
  FAM123B MUTATED FAM123B WILD-TYPE 
            15.50             21.14 
[1] "0.0 - 140.4 (15.5)" "0.0 - 139.2 (21.1)"
[1] "hr=" "1.4"
D12V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FAM123B MUTATED         5        0        6        20         1         0
  FAM123B WILD-TYPE      59        1       19        89         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM123B MUTATED           2          1          1          4        3
  FAM123B WILD-TYPE        17          9         40         27       32
                   vv
clus                STAGE IVA STAGE IVB
  FAM123B MUTATED           2         0
  FAM123B WILD-TYPE        11         1
D12V3, multiclass
            clus
vv           FAM123B MUTATED FAM123B WILD-TYPE
  STAGE I                  5                59
  STAGE IA                 0                 1
  STAGE II                 6                19
  STAGE IIA               20                89
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                2                17
  STAGE IIIA               1                 9
  STAGE IIIB               1                40
  STAGE IIIC               4                27
  STAGE IV                 3                32
  STAGE IVA                2                11
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of 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   5  37   5
  FAM123B WILD-TYPE   7  63 211  36
D12V4, multiclass
    clus
vv   FAM123B MUTATED FAM123B WILD-TYPE
  T1               2                 7
  T2               5                63
  T3              37               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
  FAM123B MUTATED    33   8   8
  FAM123B WILD-TYPE 187  72  58
D12V5, multiclass
    clus
vv   FAM123B MUTATED FAM123B WILD-TYPE
  N0              33               187
  N1               8                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"
D12V6, binary
                   cls
clus                  0   1
  FAM123B MUTATED    38   4
  FAM123B WILD-TYPE 245  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM123B MUTATED     38    4
  FAM123B WILD-TYPE  245   44
   clus
vv  FAM123B MUTATED FAM123B WILD-TYPE
  0              38               245
  1               4                44
[1] 2 2
[1] FALSE
D12V7, binary
                   cls
clus                  0   1
  FAM123B MUTATED    22  27
  FAM123B WILD-TYPE 148 170
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM123B MUTATED     22   27
  FAM123B WILD-TYPE  148  170
        clus
vv       FAM123B MUTATED FAM123B WILD-TYPE
  FEMALE              22               148
  MALE                27               170
[1] 2 2
[1] FALSE
D12V8, binary
                   cls
clus                  0   1
  FAM123B MUTATED    44   5
  FAM123B WILD-TYPE 273  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM123B MUTATED     44    5
  FAM123B WILD-TYPE  273   43
                               clus
vv                              FAM123B MUTATED FAM123B WILD-TYPE
  COLON ADENOCARCINOMA                       44               273
  COLON MUCINOUS ADENOCARCINOMA               5                43
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  FAM123B MUTATED    32   0   2   4
  FAM123B WILD-TYPE 225   2  20  17
D12V9, multiclass
    clus
vv   FAM123B MUTATED FAM123B WILD-TYPE
  R0              32               225
  R1               0                 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"
D12V10, 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    24
  FAM123B WILD-TYPE                        17   152
D12V11, 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                                         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(13) Variable = RBMX MUTATION ANALYSIS
D13V1, survival
                sevent
clus2              0   1
  RBMX MUTATED    20   0
  RBMX WILD-TYPE 262  73
  RBMX MUTATED RBMX WILD-TYPE 
            20            335 
  RBMX MUTATED RBMX WILD-TYPE 
             0             73 
$`RBMX MUTATED`
TCGA-A6-5656 TCGA-A6-5664 TCGA-A6-6142 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3549 
       32.91        22.09        25.08        20.12        19.66        21.01 
TCGA-AD-5900 TCGA-AD-6889 TCGA-CA-6717 TCGA-CM-5860 TCGA-CM-6171 TCGA-D5-6898 
        0.07        56.55         0.33        16.01        14.04         7.53 
TCGA-D5-7000 TCGA-DM-A1HB TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6703 TCGA-F4-6855 
       10.26       135.65       117.07        98.24        35.87        35.41 
TCGA-F4-6856 TCGA-G4-6628 
       19.43        52.80 

$`RBMX WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5665 
       31.63        30.44        29.19        33.53        23.61        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 
       32.71        27.09        22.52         8.38        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 
       21.76        24.69        24.39        23.87        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        3.02         1.02        35.01        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       33.99        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        4.21         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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-6172 TCGA-CM-6674 TCGA-CM-6675 
       12.99        13.02        15.02        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        16.14        15.58        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        11.38       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       35.97        60.79         8.61        13.38        13.45         6.18 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
        0.53       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       13.78        35.80        26.17        91.79        46.75 

  RBMX MUTATED RBMX WILD-TYPE 
          0.07           0.00 
  RBMX MUTATED RBMX WILD-TYPE 
        135.65         140.38 
  RBMX MUTATED RBMX WILD-TYPE 
         21.55          20.02 
[1] "0.1 - 135.7 (21.6)" "0.0 - 140.4 (20.0)"
[1] "hr="     "7.6e+07"
D13V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RBMX MUTATED         8        0        0         7         1         0
  RBMX WILD-TYPE      56        1       25       102         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        19         10         40         28       35        12
                vv
clus             STAGE IVB
  RBMX MUTATED           0
  RBMX WILD-TYPE         1
D13V3, multiclass
            clus
vv           RBMX MUTATED RBMX WILD-TYPE
  STAGE I               8             56
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             7            102
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            3             28
  STAGE IV              0             35
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RBMX MUTATED     0   8  10   3
  RBMX WILD-TYPE   9  60 238  38
D13V4, multiclass
    clus
vv   RBMX MUTATED RBMX WILD-TYPE
  T1            0              9
  T2            8             60
  T3           10            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
  RBMX MUTATED    16   3   2
  RBMX WILD-TYPE 204  77  64
D13V5, multiclass
    clus
vv   RBMX MUTATED RBMX WILD-TYPE
  N0           16            204
  N1            3             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"
D13V6, binary
                cls
clus               0   1
  RBMX MUTATED    15   1
  RBMX WILD-TYPE 268  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBMX MUTATED     15    1
  RBMX WILD-TYPE  268   47
   clus
vv  RBMX MUTATED RBMX WILD-TYPE
  0           15            268
  1            1             47
[1] 2 2
[1] FALSE
D13V7, binary
                cls
clus               0   1
  RBMX MUTATED     6  15
  RBMX WILD-TYPE 164 182
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBMX MUTATED      6   15
  RBMX WILD-TYPE  164  182
        clus
vv       RBMX MUTATED RBMX WILD-TYPE
  FEMALE            6            164
  MALE             15            182
[1] 2 2
[1] FALSE
D13V8, binary
                cls
clus               0   1
  RBMX MUTATED    14   7
  RBMX WILD-TYPE 303  41
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBMX MUTATED     14    7
  RBMX WILD-TYPE  303   41
                               clus
vv                              RBMX MUTATED RBMX WILD-TYPE
  COLON ADENOCARCINOMA                    14            303
  COLON MUCINOUS ADENOCARCINOMA            7             41
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RBMX MUTATED    11   0   0   2
  RBMX WILD-TYPE 246   2  22  19
D13V9, multiclass
    clus
vv   RBMX MUTATED RBMX WILD-TYPE
  R0           11            246
  R1            0              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"
D13V10, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RBMX MUTATED                                  0     2
  RBMX WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RBMX MUTATED                           1    17
  RBMX WILD-TYPE                        18   159
D13V11, multiclass
                                  clus
vv                                 RBMX MUTATED RBMX 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(14) Variable = ZFP36L2 MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  ZFP36L2 MUTATED    10   3
  ZFP36L2 WILD-TYPE 272  70
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
               13               342 
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
                3                70 
$`ZFP36L2 MUTATED`
TCGA-A6-5666 TCGA-AA-3989 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6598 TCGA-CA-5797 
       32.71         7.96        10.88        83.80        49.41         3.29 
TCGA-CM-6171 TCGA-D5-6536 TCGA-D5-6540 TCGA-D5-6928 TCGA-DM-A1D9 TCGA-DM-A1HA 
       14.04        17.85        16.14        11.64       140.38       131.51 
TCGA-G4-6588 
       26.17 

$`ZFP36L2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        27.02        19.07        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-6601 
       22.36        62.79        61.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.06         3.25         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       15.12         4.80        17.13        12.49        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
       12.59         7.50        44.32       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        52.80 

  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
             3.29              0.00 
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
           140.38            139.17 
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
           17.850            20.235 
[1] "3.3 - 140.4 (17.9)" "0.0 - 139.2 (20.2)"
[1] "hr=" "1.3"
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       24       103         7         0
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZFP36L2 MUTATED           0          0          0          1        1
  ZFP36L2 WILD-TYPE        19         10         41         30       34
                   vv
clus                STAGE IVA STAGE IVB
  ZFP36L2 MUTATED           0         0
  ZFP36L2 WILD-TYPE        13         1
D14V3, multiclass
            clus
vv           ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                6               103
  STAGE IIB                1                 7
  STAGE IIC                1                 0
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               1                30
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ZFP36L2 MUTATED     0   2   9   3
  ZFP36L2 WILD-TYPE   9  66 239  38
D14V4, multiclass
    clus
vv   ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  T1               0                 9
  T2               2                66
  T3               9               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
  ZFP36L2 MUTATED    11   0   3
  ZFP36L2 WILD-TYPE 209  80  63
D14V5, multiclass
    clus
vv   ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  N0              11               209
  N1               0                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"
D14V6, binary
                   cls
clus                  0   1
  ZFP36L2 MUTATED    10   1
  ZFP36L2 WILD-TYPE 273  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFP36L2 MUTATED     10    1
  ZFP36L2 WILD-TYPE  273   47
   clus
vv  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  0              10               273
  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    12   2
  ZFP36L2 WILD-TYPE 305  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFP36L2 MUTATED     12    2
  ZFP36L2 WILD-TYPE  305   46
                               clus
vv                              ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  COLON ADENOCARCINOMA                       12               305
  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 250   2  21  20
D14V9, multiclass
    clus
vv   ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  R0               7               250
  R1               0                 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"
D14V10, 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
D14V11, 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 = BCOR MUTATION ANALYSIS
D15V1, survival
                sevent
clus2              0   1
  BCOR MUTATED    21   4
  BCOR WILD-TYPE 261  69
  BCOR MUTATED BCOR WILD-TYPE 
            25            330 
  BCOR MUTATED BCOR WILD-TYPE 
             4             69 
$`BCOR MUTATED`
TCGA-A6-3809 TCGA-A6-5661 TCGA-A6-6780 TCGA-AA-3555 TCGA-AA-3672 TCGA-AA-3930 
       32.75        33.53        20.12        29.95         0.92         2.01 
TCGA-AA-A010 TCGA-AD-6895 TCGA-AY-5543 TCGA-AY-6196 TCGA-AZ-4323 TCGA-AZ-6598 
       34.98         0.72        15.75         0.20         1.41        49.41 
TCGA-CM-5348 TCGA-CM-6162 TCGA-CM-6169 TCGA-CM-6171 TCGA-D5-6928 TCGA-D5-6930 
       22.98        12.00        13.02        14.04        11.64         1.51 
TCGA-D5-7000 TCGA-DM-A1HA TCGA-F4-6570 TCGA-F4-6805 TCGA-G4-6304 TCGA-G4-6317 
       10.26       131.51         6.18        16.31        53.62        36.00 
TCGA-G4-6588 
       26.17 

$`BCOR WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 
       24.16        21.76        24.69        24.39        23.87        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05        31.00        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        4.21        56.55         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82        58.39         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       13.45        35.87         1.55        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        52.80 

  BCOR MUTATED BCOR WILD-TYPE 
           0.2            0.0 
  BCOR MUTATED BCOR WILD-TYPE 
        131.51         140.38 
  BCOR MUTATED BCOR WILD-TYPE 
         15.75          20.98 
[1] "0.2 - 131.5 (15.8)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.1"
D15V2, 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       23       100         5         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BCOR MUTATED           1          0          2          3        2         1
  BCOR WILD-TYPE        18         10         39         28       33        12
                vv
clus             STAGE IVB
  BCOR MUTATED           0
  BCOR WILD-TYPE         1
D15V3, multiclass
            clus
vv           BCOR MUTATED BCOR WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             9            100
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            2             39
  STAGE IIIC            3             28
  STAGE IV              2             33
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  65 229  36
D15V4, multiclass
    clus
vv   BCOR MUTATED BCOR WILD-TYPE
  T1            0              9
  T2            3             65
  T3           19            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
  BCOR MUTATED    17   5   5
  BCOR WILD-TYPE 203  75  61
D15V5, multiclass
    clus
vv   BCOR MUTATED BCOR WILD-TYPE
  N0           17            203
  N1            5             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"
D15V6, binary
                cls
clus               0   1
  BCOR MUTATED    18   3
  BCOR WILD-TYPE 265  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCOR MUTATED     18    3
  BCOR WILD-TYPE  265   45
   clus
vv  BCOR MUTATED BCOR WILD-TYPE
  0           18            265
  1            3             45
[1] 2 2
[1] FALSE
D15V7, 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
D15V8, binary
                cls
clus               0   1
  BCOR MUTATED    19   8
  BCOR WILD-TYPE 298  40
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCOR MUTATED     19    8
  BCOR WILD-TYPE  298   40
                               clus
vv                              BCOR MUTATED BCOR WILD-TYPE
  COLON ADENOCARCINOMA                    19            298
  COLON MUCINOUS ADENOCARCINOMA            8             40
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  BCOR MUTATED    20   0   1   1
  BCOR WILD-TYPE 237   2  21  20
D15V9, multiclass
    clus
vv   BCOR MUTATED BCOR WILD-TYPE
  R0           20            237
  R1            0              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"
D15V10, 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
D15V11, 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(16) Variable = WNT1 MUTATION ANALYSIS
D16V1, survival
                sevent
clus2              0   1
  WNT1 MUTATED     4   2
  WNT1 WILD-TYPE 278  71
  WNT1 MUTATED WNT1 WILD-TYPE 
             6            349 
  WNT1 MUTATED WNT1 WILD-TYPE 
             2             71 
$`WNT1 MUTATED`
TCGA-AD-6889 TCGA-AZ-6598 TCGA-CK-5916 TCGA-CM-4743 TCGA-DM-A1HB TCGA-G4-6586 
       56.55        49.41        21.14        23.05       135.65        35.80 

$`WNT1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        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        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  WNT1 MUTATED WNT1 WILD-TYPE 
         21.14           0.00 
  WNT1 MUTATED WNT1 WILD-TYPE 
        135.65         140.38 
  WNT1 MUTATED WNT1 WILD-TYPE 
        42.605         19.990 
[1] "21.1 - 135.7 (42.6)" "0.0 - 140.4 (20.0)" 
[1] "hr=" "1.2"
D16V2, 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       23       106         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        19         10         40         31       35        13
                vv
clus             STAGE IVB
  WNT1 MUTATED           0
  WNT1 WILD-TYPE         1
D16V3, multiclass
            clus
vv           WNT1 MUTATED WNT1 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             3            106
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  WNT1 MUTATED     1   0   5   1
  WNT1 WILD-TYPE   8  68 243  40
D16V4, multiclass
    clus
vv   WNT1 MUTATED WNT1 WILD-TYPE
  T1            1              8
  T2            0             68
  T3            5            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
  WNT1 MUTATED     6   1   0
  WNT1 WILD-TYPE 214  79  66
D16V5, multiclass
    clus
vv   WNT1 MUTATED WNT1 WILD-TYPE
  N0            6            214
  N1            1             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"
D16V6, binary
                cls
clus               0   1
  WNT1 MUTATED     6   0
  WNT1 WILD-TYPE 277  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNT1 MUTATED      6    0
  WNT1 WILD-TYPE  277   48
   clus
vv  WNT1 MUTATED WNT1 WILD-TYPE
  0            6            277
  1            0             48
[1] 2 2
[1] FALSE
D16V7, 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
D16V8, binary
                cls
clus               0   1
  WNT1 MUTATED     7   0
  WNT1 WILD-TYPE 310  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNT1 MUTATED      7    0
  WNT1 WILD-TYPE  310   48
                               clus
vv                              WNT1 MUTATED WNT1 WILD-TYPE
  COLON ADENOCARCINOMA                     7            310
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  WNT1 MUTATED     3   0   0   1
  WNT1 WILD-TYPE 254   2  22  20
D16V9, multiclass
    clus
vv   WNT1 MUTATED WNT1 WILD-TYPE
  R0            3            254
  R1            0              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"
D16V10, 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
D16V11, 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(17) Variable = CDH1 MUTATION ANALYSIS
D17V1, survival
                sevent
clus2              0   1
  CDH1 MUTATED    61  12
  CDH1 WILD-TYPE 221  61
  CDH1 MUTATED CDH1 WILD-TYPE 
            73            282 
  CDH1 MUTATED CDH1 WILD-TYPE 
            12             61 
$`CDH1 MUTATED`
TCGA-A6-3809 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-6141 
       32.75        31.63        30.44        33.53        23.61         8.38 
TCGA-A6-6648 TCGA-A6-6780 TCGA-AA-3502 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3697 
       25.18        20.12        35.01         6.05         6.97        85.05 
TCGA-AA-3713 TCGA-AA-3821 TCGA-AA-A00N TCGA-AA-A00U TCGA-AA-A01R TCGA-AA-A02K 
       19.04         1.02         4.01        17.03        35.01        14.01 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6964 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-6197 
        0.07        56.55        10.88        14.50        27.09        21.44 
TCGA-AY-6386 TCGA-AZ-4616 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-CA-5797 
       17.82         5.13        49.41         6.77        12.10         3.29 
TCGA-CA-6715 TCGA-CA-6717 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
        0.07         0.33        40.34        15.62        49.08        21.99 
TCGA-CK-6747 TCGA-CM-4743 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
        2.93        23.05        13.02        22.03        22.98        30.08 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6678 
       17.03        15.02        15.02        14.04        11.01        11.01 
TCGA-CM-6679 TCGA-D5-6529 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 
       10.06        20.19        15.12        17.85         4.80        12.49 
TCGA-D5-6540 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6932 TCGA-DM-A1D4 TCGA-DM-A1HA 
       16.14        11.64         1.51        11.38        92.75       131.51 
TCGA-DM-A282 TCGA-DM-A28E TCGA-DM-A28F TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6856 
      139.17       119.93        35.97        13.38         6.18        19.43 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       53.62        44.68        45.11        36.00        22.09        13.78 
TCGA-G4-6586 
       35.80 

$`CDH1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5660 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       29.19        22.09        22.06        32.71        27.09        22.52 
TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3510 
       19.66        20.28         7.04         3.02         1.02        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       19.99        61.02        78.08        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 
       37.05        19.00        36.00         5.03        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 
       10.06        35.05        33.04         0.99        25.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       27.02        42.02         0.99        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       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        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        4.21         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AZ-4315 
        0.20        16.31         0.95        15.75         0.20        58.39 
TCGA-AZ-4323 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6601 
        1.41        83.80        22.36        62.79        61.41       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.06         3.25         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
      102.44        51.32        21.14         2.01       124.27        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       37.02        25.02        29.06        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 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-6674 TCGA-CM-6675 
       21.99        14.99        12.99        13.02        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.08        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6538 
       13.51        11.51        18.25         1.32        43.27        17.13 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 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-D5-7000 TCGA-DM-A0X9 
        9.04         9.44        13.41        12.00        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-A285 TCGA-DM-A28C 
      140.38         7.50        44.32       135.65         6.12        81.37 
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        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6307 
        0.53        35.41       107.67        74.56        65.85        55.04 
TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       51.75        36.72        26.17        91.79        46.75        52.80 

  CDH1 MUTATED CDH1 WILD-TYPE 
          0.07           0.00 
  CDH1 MUTATED CDH1 WILD-TYPE 
        139.17         140.38 
  CDH1 MUTATED CDH1 WILD-TYPE 
        17.820         21.255 
[1] "0.1 - 139.2 (17.8)" "0.0 - 140.4 (21.3)"
[1] "hr=" "1.3"
D17V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CDH1 MUTATED        13        1        2        24         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           4          2         13          2        5         4
  CDH1 WILD-TYPE        15          8         28         29       30         9
                vv
clus             STAGE IVB
  CDH1 MUTATED           0
  CDH1 WILD-TYPE         1
D17V3, multiclass
            clus
vv           CDH1 MUTATED CDH1 WILD-TYPE
  STAGE I              13             51
  STAGE IA              1              0
  STAGE II              2             23
  STAGE IIA            24             85
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             4             15
  STAGE IIIA            2              8
  STAGE IIIB           13             28
  STAGE IIIC            2             29
  STAGE IV              5             30
  STAGE IVA             4              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
  CDH1 MUTATED     0  15  48  10
  CDH1 WILD-TYPE   9  53 200  31
D17V4, multiclass
    clus
vv   CDH1 MUTATED CDH1 WILD-TYPE
  T1            0              9
  T2           15             53
  T3           48            200
  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  62  57
D17V5, multiclass
    clus
vv   CDH1 MUTATED CDH1 WILD-TYPE
  N0           47            173
  N1           18             62
  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"
D17V6, binary
                cls
clus               0   1
  CDH1 MUTATED    50   9
  CDH1 WILD-TYPE 233  39
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDH1 MUTATED     50    9
  CDH1 WILD-TYPE  233   39
   clus
vv  CDH1 MUTATED CDH1 WILD-TYPE
  0           50            233
  1            9             39
[1] 2 2
[1] FALSE
D17V7, 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
D17V8, binary
                cls
clus               0   1
  CDH1 MUTATED    62  12
  CDH1 WILD-TYPE 255  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDH1 MUTATED     62   12
  CDH1 WILD-TYPE  255   36
                               clus
vv                              CDH1 MUTATED CDH1 WILD-TYPE
  COLON ADENOCARCINOMA                    62            255
  COLON MUCINOUS ADENOCARCINOMA           12             36
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CDH1 MUTATED    47   1   3   8
  CDH1 WILD-TYPE 210   1  19  13
D17V9, multiclass
    clus
vv   CDH1 MUTATED CDH1 WILD-TYPE
  R0           47            210
  R1            1              1
  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"
D17V10, 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
D17V11, 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(18) Variable = NTAN1 MUTATION ANALYSIS
D18V1, survival
                 sevent
clus2               0   1
  NTAN1 MUTATED     8   2
  NTAN1 WILD-TYPE 274  71
  NTAN1 MUTATED NTAN1 WILD-TYPE 
             10             345 
  NTAN1 MUTATED NTAN1 WILD-TYPE 
              2              71 
$`NTAN1 MUTATED`
TCGA-A6-5665 TCGA-AA-3555 TCGA-AA-3663 TCGA-AA-3715 TCGA-AA-A00N TCGA-AD-5900 
       22.06        29.95         6.97        19.04         4.01         0.07 
TCGA-CM-4743 TCGA-D5-6540 TCGA-G4-6586 TCGA-G4-6628 
       23.05        16.14        35.80        52.80 

$`NTAN1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        17.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       26.17        91.79        46.75 

  NTAN1 MUTATED NTAN1 WILD-TYPE 
           0.07            0.00 
  NTAN1 MUTATED NTAN1 WILD-TYPE 
          52.80          140.38 
  NTAN1 MUTATED NTAN1 WILD-TYPE 
          20.55           20.19 
[1] "0.1 - 52.8 (20.5)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D18V2, 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       23       105         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        19         10         41         31       35        13
                 vv
clus              STAGE IVB
  NTAN1 MUTATED           0
  NTAN1 WILD-TYPE         1
D18V3, multiclass
            clus
vv           NTAN1 MUTATED NTAN1 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              4             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NTAN1 MUTATED     0   3   6   1
  NTAN1 WILD-TYPE   9  65 242  40
D18V4, multiclass
    clus
vv   NTAN1 MUTATED NTAN1 WILD-TYPE
  T1             0               9
  T2             3              65
  T3             6             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
  NTAN1 MUTATED    10   0   0
  NTAN1 WILD-TYPE 210  80  66
D18V5, multiclass
    clus
vv   NTAN1 MUTATED NTAN1 WILD-TYPE
  N0            10             210
  N1             0              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"
D18V6, binary
                 cls
clus                0   1
  NTAN1 MUTATED     9   0
  NTAN1 WILD-TYPE 274  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTAN1 MUTATED      9    0
  NTAN1 WILD-TYPE  274   48
   clus
vv  NTAN1 MUTATED NTAN1 WILD-TYPE
  0             9             274
  1             0              48
[1] 2 2
[1] FALSE
D18V7, 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
D18V8, binary
                 cls
clus                0   1
  NTAN1 MUTATED     6   4
  NTAN1 WILD-TYPE 311  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTAN1 MUTATED      6    4
  NTAN1 WILD-TYPE  311   44
                               clus
vv                              NTAN1 MUTATED NTAN1 WILD-TYPE
  COLON ADENOCARCINOMA                      6             311
  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 247   2  22  21
D18V9, multiclass
    clus
vv   NTAN1 MUTATED NTAN1 WILD-TYPE
  R0            10             247
  R1             0               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"
D18V10, 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
D18V11, 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(19) Variable = RHOA MUTATION ANALYSIS
D19V1, survival
                sevent
clus2              0   1
  RHOA MUTATED     9   3
  RHOA WILD-TYPE 273  70
  RHOA MUTATED RHOA WILD-TYPE 
            12            343 
  RHOA MUTATED RHOA WILD-TYPE 
             3             70 
$`RHOA MUTATED`
TCGA-AA-3845 TCGA-AA-3972 TCGA-AA-A01P TCGA-AA-A01R TCGA-AD-6895 TCGA-AD-6965 
        0.00        50.99        38.07        35.01         0.72         0.20 
TCGA-AZ-6598 TCGA-CK-4948 TCGA-CK-4950 TCGA-CM-6678 TCGA-D5-6536 TCGA-G4-6310 
       49.41       102.44        40.34        11.01        17.85        45.11 

$`RHOA WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        10.88        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       17.56        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        43.27        15.12         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        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        51.75        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  RHOA MUTATED RHOA WILD-TYPE 
             0              0 
  RHOA MUTATED RHOA WILD-TYPE 
        102.44         140.38 
  RHOA MUTATED RHOA WILD-TYPE 
         36.54          20.12 
[1] "0.0 - 102.4 (36.5)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1"  
D19V2, 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       24       107         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RHOA MUTATED           2          2          1          0        1         1
  RHOA WILD-TYPE        17          8         40         31       34        12
                vv
clus             STAGE IVB
  RHOA MUTATED           0
  RHOA WILD-TYPE         1
D19V3, multiclass
            clus
vv           RHOA MUTATED RHOA WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             2            107
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             2             17
  STAGE IIIA            2              8
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  68 238  39
D19V4, multiclass
    clus
vv   RHOA MUTATED RHOA WILD-TYPE
  T1            0              9
  T2            0             68
  T3           10            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
  RHOA MUTATED     3   7   2
  RHOA WILD-TYPE 217  73  64
D19V5, multiclass
    clus
vv   RHOA MUTATED RHOA WILD-TYPE
  N0            3            217
  N1            7             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"
D19V6, binary
                cls
clus               0   1
  RHOA MUTATED     7   2
  RHOA WILD-TYPE 276  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOA MUTATED      7    2
  RHOA WILD-TYPE  276   46
   clus
vv  RHOA MUTATED RHOA WILD-TYPE
  0            7            276
  1            2             46
[1] 2 2
[1] FALSE
D19V7, 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
D19V8, binary
                cls
clus               0   1
  RHOA MUTATED    11   1
  RHOA WILD-TYPE 306  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOA MUTATED     11    1
  RHOA WILD-TYPE  306   47
                               clus
vv                              RHOA MUTATED RHOA WILD-TYPE
  COLON ADENOCARCINOMA                    11            306
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RHOA MUTATED     7   1   1   0
  RHOA WILD-TYPE 250   1  21  21
D19V9, multiclass
    clus
vv   RHOA MUTATED RHOA WILD-TYPE
  R0            7            250
  R1            1              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"
D19V10, 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
D19V11, 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(20) Variable = BMPR2 MUTATION ANALYSIS
D20V1, survival
                 sevent
clus2               0   1
  BMPR2 MUTATED    28   6
  BMPR2 WILD-TYPE 254  67
  BMPR2 MUTATED BMPR2 WILD-TYPE 
             34             321 
  BMPR2 MUTATED BMPR2 WILD-TYPE 
              6              67 
$`BMPR2 MUTATED`
TCGA-A6-3809 TCGA-A6-5661 TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3516 TCGA-AA-3525 
       32.75        33.53        22.06         3.02        13.02         8.05 
TCGA-AA-3554 TCGA-AA-3672 TCGA-AA-3815 TCGA-AA-3950 TCGA-AA-A00E TCGA-AA-A00N 
       17.95         0.92        33.04        24.00        30.02         4.01 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6895 TCGA-AU-6004 TCGA-AY-6196 TCGA-AY-6197 
        0.07        56.55         0.72        27.09         0.20        21.44 
TCGA-AZ-4315 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-4952 TCGA-CK-6747 
       58.39        61.41        49.41         0.33        15.62         2.93 
TCGA-CM-6676 TCGA-D5-6540 TCGA-D5-6930 TCGA-DM-A1D6 TCGA-F4-6570 TCGA-F4-6808 
       11.08        16.14         1.51        49.91         6.18        33.67 
TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6586 TCGA-G4-6588 
       51.75        36.72        35.80        26.17 

$`BMPR2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       31.63        30.44        29.19        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
        1.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
       36.03        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F 
        7.96        27.02        13.94        38.04        19.00        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        4.21         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 
        0.20        14.50        16.31         0.95        15.75        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6599 
        1.41         5.13        83.80        22.36        62.79         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 
       49.08        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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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-A1D7 
      119.70        24.43        38.20       130.65        92.75        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      117.07        98.24         8.61        13.38        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 
        1.55        16.31        29.59        16.24        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       44.68        55.04        45.11        36.00        22.09        13.78 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  BMPR2 MUTATED BMPR2 WILD-TYPE 
           0.07            0.00 
  BMPR2 MUTATED BMPR2 WILD-TYPE 
          61.41          140.38 
  BMPR2 MUTATED BMPR2 WILD-TYPE 
          21.75           20.12 
[1] "0.1 - 61.4 (21.8)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.1"
D20V2, 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       23        93         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BMPR2 MUTATED           3          0          2          1        1         0
  BMPR2 WILD-TYPE        16         10         39         30       34        13
                 vv
clus              STAGE IVB
  BMPR2 MUTATED           0
  BMPR2 WILD-TYPE         1
D20V3, multiclass
            clus
vv           BMPR2 MUTATED BMPR2 WILD-TYPE
  STAGE I                6              58
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA             16              93
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              3              16
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  BMPR2 MUTATED     2   4  25   4
  BMPR2 WILD-TYPE   7  64 223  37
D20V4, multiclass
    clus
vv   BMPR2 MUTATED BMPR2 WILD-TYPE
  T1             2               7
  T2             4              64
  T3            25             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
  BMPR2 MUTATED    27   5   3
  BMPR2 WILD-TYPE 193  75  63
D20V5, multiclass
    clus
vv   BMPR2 MUTATED BMPR2 WILD-TYPE
  N0            27             193
  N1             5              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"
D20V6, binary
                 cls
clus                0   1
  BMPR2 MUTATED    27   1
  BMPR2 WILD-TYPE 256  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BMPR2 MUTATED     27    1
  BMPR2 WILD-TYPE  256   47
   clus
vv  BMPR2 MUTATED BMPR2 WILD-TYPE
  0            27             256
  1             1              47
[1] 2 2
[1] FALSE
D20V7, 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
D20V8, binary
                 cls
clus                0   1
  BMPR2 MUTATED    24  11
  BMPR2 WILD-TYPE 293  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BMPR2 MUTATED     24   11
  BMPR2 WILD-TYPE  293   37
                               clus
vv                              BMPR2 MUTATED BMPR2 WILD-TYPE
  COLON ADENOCARCINOMA                     24             293
  COLON MUCINOUS ADENOCARCINOMA            11              37
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  BMPR2 MUTATED    25   0   0   4
  BMPR2 WILD-TYPE 232   2  22  17
D20V9, multiclass
    clus
vv   BMPR2 MUTATED BMPR2 WILD-TYPE
  R0            25             232
  R1             0               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"
D20V10, 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
D20V11, 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(21) Variable = CRIPAK MUTATION ANALYSIS
D21V1, survival
                  sevent
clus2                0   1
  CRIPAK MUTATED    11   7
  CRIPAK WILD-TYPE 271  66
  CRIPAK MUTATED CRIPAK WILD-TYPE 
              18              337 
  CRIPAK MUTATED CRIPAK WILD-TYPE 
               7               66 
$`CRIPAK MUTATED`
TCGA-A6-6142 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3662 TCGA-AY-6196 TCGA-AY-6386 
       25.08         7.04         3.02         6.05         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         1.51        92.75        12.59       140.38         6.18 

$`CRIPAK WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.12        19.66        20.28         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        15.75        21.44 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       37.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       16.01        15.02         5.03        15.02        15.02        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-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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-A1D6 
       10.26       119.70        24.43        38.20       130.65        49.91 
TCGA-DM-A1D7 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       13.32         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        13.38        13.45        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  CRIPAK MUTATED CRIPAK WILD-TYPE 
             0.2              0.0 
  CRIPAK MUTATED CRIPAK WILD-TYPE 
          140.38           139.17 
  CRIPAK MUTATED CRIPAK WILD-TYPE 
           11.69            21.01 
[1] "0.2 - 140.4 (11.7)" "0.0 - 139.2 (21.0)"
[1] "hr=" "2.1"
D21V2, 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       22       102         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CRIPAK MUTATED           0          0          2          1        2
  CRIPAK WILD-TYPE        19         10         39         30       33
                  vv
clus               STAGE IVA STAGE IVB
  CRIPAK MUTATED           2         0
  CRIPAK WILD-TYPE        11         1
D21V3, multiclass
            clus
vv           CRIPAK MUTATED CRIPAK WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                3               22
  STAGE IIA               7              102
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              1               30
  STAGE IV                2               33
  STAGE IVA               2               11
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  68 233  38
D21V4, multiclass
    clus
vv   CRIPAK MUTATED CRIPAK WILD-TYPE
  T1              0                9
  T2              0               68
  T3             15              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
  CRIPAK MUTATED    10   5   3
  CRIPAK WILD-TYPE 210  75  63
D21V5, multiclass
    clus
vv   CRIPAK MUTATED CRIPAK WILD-TYPE
  N0             10              210
  N1              5               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"
D21V6, binary
                  cls
clus                 0   1
  CRIPAK MUTATED    11   4
  CRIPAK WILD-TYPE 272  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRIPAK MUTATED     11    4
  CRIPAK WILD-TYPE  272   44
   clus
vv  CRIPAK MUTATED CRIPAK WILD-TYPE
  0             11              272
  1              4               44
[1] 2 2
[1] FALSE
D21V7, 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
D21V8, binary
                  cls
clus                 0   1
  CRIPAK MUTATED    15   3
  CRIPAK WILD-TYPE 302  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRIPAK MUTATED     15    3
  CRIPAK WILD-TYPE  302   45
                               clus
vv                              CRIPAK MUTATED CRIPAK WILD-TYPE
  COLON ADENOCARCINOMA                      15              302
  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 246   2  21  21
D21V9, multiclass
    clus
vv   CRIPAK MUTATED CRIPAK WILD-TYPE
  R0             11              246
  R1              0                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"
D21V10, 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
D21V11, 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(22) Variable = MVK MUTATION ANALYSIS
D22V1, survival
               sevent
clus2             0   1
  MVK MUTATED    12   1
  MVK WILD-TYPE 270  72
  MVK MUTATED MVK WILD-TYPE 
           13           342 
  MVK MUTATED MVK WILD-TYPE 
            1            72 
$`MVK MUTATED`
TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3950 TCGA-AD-5900 TCGA-AD-6889 TCGA-CA-6717 
       22.06        19.66        24.00         0.07        56.55         0.33 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CM-4746 TCGA-CM-6162 TCGA-CM-6674 TCGA-D5-6540 
       51.32        21.14        37.02        12.00        12.95        16.14 
TCGA-G4-6588 
       26.17 

$`MVK WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       18.05        40.96        21.37         4.21         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99         2.93         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 
       16.01        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        52.80 

  MVK MUTATED MVK WILD-TYPE 
         0.07          0.00 
  MVK MUTATED MVK WILD-TYPE 
        56.55        140.38 
  MVK MUTATED MVK WILD-TYPE 
       21.140        20.155 
[1] "0.1 - 56.5 (21.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2.5"
D22V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MVK MUTATED         4        0        1         7         1         0
  MVK WILD-TYPE      60        1       24       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        19         10         40         30       35        13
               vv
clus            STAGE IVB
  MVK MUTATED           0
  MVK WILD-TYPE         1
D22V3, multiclass
            clus
vv           MVK MUTATED MVK WILD-TYPE
  STAGE I              4            60
  STAGE IA             0             1
  STAGE II             1            24
  STAGE IIA            7           102
  STAGE IIB            1             7
  STAGE IIC            0             1
  STAGE III            0            19
  STAGE IIIA           0            10
  STAGE IIIB           1            40
  STAGE IIIC           1            30
  STAGE IV             0            35
  STAGE IVA            0            13
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  MVK MUTATED     1   3   8   3
  MVK WILD-TYPE   8  65 240  38
D22V4, multiclass
    clus
vv   MVK MUTATED MVK WILD-TYPE
  T1           1             8
  T2           3            65
  T3           8           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
  MVK MUTATED    13   2   0
  MVK WILD-TYPE 207  78  66
D22V5, multiclass
    clus
vv   MVK MUTATED MVK WILD-TYPE
  N0          13           207
  N1           2            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"
D22V6, binary
               cls
clus              0   1
  MVK MUTATED    11   0
  MVK WILD-TYPE 272  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  MVK MUTATED     11    0
  MVK WILD-TYPE  272   48
   clus
vv  MVK MUTATED MVK WILD-TYPE
  0          11           272
  1           0            48
[1] 2 2
[1] FALSE
D22V7, binary
               cls
clus              0   1
  MVK MUTATED     8   7
  MVK WILD-TYPE 162 190
[1] "tbl2"
               cls
clus            [,1] [,2]
  MVK MUTATED      8    7
  MVK WILD-TYPE  162  190
        clus
vv       MVK MUTATED MVK WILD-TYPE
  FEMALE           8           162
  MALE             7           190
[1] 2 2
[1] FALSE
D22V8, binary
               cls
clus              0   1
  MVK MUTATED     9   6
  MVK WILD-TYPE 308  42
[1] "tbl2"
               cls
clus            [,1] [,2]
  MVK MUTATED      9    6
  MVK WILD-TYPE  308   42
                               clus
vv                              MVK MUTATED MVK WILD-TYPE
  COLON ADENOCARCINOMA                    9           308
  COLON MUCINOUS ADENOCARCINOMA           6            42
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  MVK MUTATED    10   0   0   4
  MVK WILD-TYPE 247   2  22  17
D22V9, multiclass
    clus
vv   MVK MUTATED MVK WILD-TYPE
  R0          10           247
  R1           0             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"
D22V10, 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    10
  MVK WILD-TYPE                        18   166
D22V11, 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                                     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(23) Variable = NF2 MUTATION ANALYSIS
D23V1, survival
               sevent
clus2             0   1
  NF2 MUTATED    53   8
  NF2 WILD-TYPE 229  65
  NF2 MUTATED NF2 WILD-TYPE 
           61           294 
  NF2 MUTATED NF2 WILD-TYPE 
            8            65 
$`NF2 MUTATED`
TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5666 TCGA-A6-6141 TCGA-A6-6142 TCGA-AA-3516 
       31.63        33.53        32.71         8.38        25.08        13.02 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3713 TCGA-AA-3950 TCGA-AA-3968 TCGA-AA-A01R 
        6.05         6.97        19.04        24.00        21.99        35.01 
TCGA-AD-6963 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-6598 
       27.42        14.50        27.09        17.82        58.39        49.41 
TCGA-AZ-6599 TCGA-AZ-6603 TCGA-CA-6716 TCGA-CA-6717 TCGA-CK-4947 TCGA-CK-4952 
        6.77        29.56         0.26         0.33        17.56        15.62 
TCGA-CK-5912 TCGA-CM-4743 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5864 
       49.08        23.05        13.02        22.03        30.08        15.02 
TCGA-CM-6161 TCGA-CM-6164 TCGA-CM-6167 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       15.02        29.03        14.99        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-D5-5538 TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6535 
       12.95        13.05        12.26        11.51        18.25        15.12 
TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6927 
       17.85        12.49        15.58        10.13         9.04         9.44 
TCGA-DM-A1DB TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6807 TCGA-F4-6856 TCGA-G4-6299 
       44.32         6.18        35.87        16.24        19.43        74.56 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       55.04        45.11        22.09        13.78        35.80        26.17 
TCGA-G4-6626 
       46.75 

$`NF2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       32.91        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 
       27.09        22.52        25.18        24.16        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 
       24.39        23.87        20.12        19.66        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        3.02         1.02        35.01        63.98         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
        2.01        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       22.42        10.88         0.20        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
        0.20        21.44         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 
       62.79        61.41        12.10       100.01         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 
        0.07         0.10         1.35       102.44        40.34        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
       21.99        21.14         2.93         2.01       124.27        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 
       37.02        25.02        29.06        22.98        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 
        5.03        15.02        17.03        12.00        14.04        16.04 
TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       21.99        12.99        13.02        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6529 
       10.06        12.03        45.40        19.59        13.51        20.19 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6898 
        1.32        43.27         4.80        17.13        16.14         7.53 
TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       12.39        12.43        14.30        11.64        13.41         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 
       13.38        13.45         1.55        16.31        29.59        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 
       13.25         0.53        35.41       107.67        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6625 TCGA-G4-6628 
       44.68        51.75        36.72        36.00        91.79        52.80 

  NF2 MUTATED NF2 WILD-TYPE 
         0.26          0.00 
  NF2 MUTATED NF2 WILD-TYPE 
        74.56        140.38 
  NF2 MUTATED NF2 WILD-TYPE 
       17.820        21.075 
[1] "0.3 - 74.6 (17.8)"  "0.0 - 140.4 (21.1)"
[1] "hr=" "1.5"
D23V2, 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       23        87         7         0
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NF2 MUTATED           4          3          9          3        2         2
  NF2 WILD-TYPE        15          7         32         28       33        11
               vv
clus            STAGE IVB
  NF2 MUTATED           1
  NF2 WILD-TYPE         0
D23V3, multiclass
            clus
vv           NF2 MUTATED NF2 WILD-TYPE
  STAGE I              9            55
  STAGE IA             1             0
  STAGE II             2            23
  STAGE IIA           22            87
  STAGE IIB            1             7
  STAGE IIC            1             0
  STAGE III            4            15
  STAGE IIIA           3             7
  STAGE IIIB           9            32
  STAGE IIIC           3            28
  STAGE IV             2            33
  STAGE IVA            2            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  57 204  35
D23V4, multiclass
    clus
vv   NF2 MUTATED NF2 WILD-TYPE
  T1           0             9
  T2          11            57
  T3          44           204
  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  65  58
D23V5, multiclass
    clus
vv   NF2 MUTATED NF2 WILD-TYPE
  N0          39           181
  N1          15            65
  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"
D23V6, binary
               cls
clus              0   1
  NF2 MUTATED    49   4
  NF2 WILD-TYPE 234  44
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF2 MUTATED     49    4
  NF2 WILD-TYPE  234   44
   clus
vv  NF2 MUTATED NF2 WILD-TYPE
  0          49           234
  1           4            44
[1] 2 2
[1] FALSE
D23V7, 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
D23V8, binary
               cls
clus              0   1
  NF2 MUTATED    56   6
  NF2 WILD-TYPE 261  42
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF2 MUTATED     56    6
  NF2 WILD-TYPE  261   42
                               clus
vv                              NF2 MUTATED NF2 WILD-TYPE
  COLON ADENOCARCINOMA                   56           261
  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 213   2  20  14
D23V9, multiclass
    clus
vv   NF2 MUTATED NF2 WILD-TYPE
  R0          44           213
  R1           0             2
  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"
D23V10, 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
D23V11, 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(24) Variable = C15ORF40 MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  C15ORF40 MUTATED    10   0
  C15ORF40 WILD-TYPE 272  73
  C15ORF40 MUTATED C15ORF40 WILD-TYPE 
                10                345 
  C15ORF40 MUTATED C15ORF40 WILD-TYPE 
                 0                 73 
$`C15ORF40 MUTATED`
TCGA-AA-3710 TCGA-AA-3815 TCGA-AA-3858 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-6162 
       26.99        33.04        31.07        30.08        15.02        12.00 
TCGA-CM-6166 TCGA-CM-6171 TCGA-G4-6315 TCGA-G4-6321 
       21.99        14.04        36.72        22.09 

$`C15ORF40 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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        16.01 
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-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       51.75        45.11        36.00        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  C15ORF40 MUTATED C15ORF40 WILD-TYPE 
                12                  0 
  C15ORF40 MUTATED C15ORF40 WILD-TYPE 
             36.72             140.38 
  C15ORF40 MUTATED C15ORF40 WILD-TYPE 
             24.54              20.02 
[1] "12.0 - 36.7 (24.5)" "0.0 - 140.4 (20.0)"
[1] "hr="     "9400000"
D24V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C15ORF40 MUTATED         3        0        0         4         0         0
  C15ORF40 WILD-TYPE      61        1       25       105         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C15ORF40 MUTATED           1          0          1          0        1
  C15ORF40 WILD-TYPE        18         10         40         31       34
                    vv
clus                 STAGE IVA STAGE IVB
  C15ORF40 MUTATED           0         0
  C15ORF40 WILD-TYPE        13         1
D24V3, multiclass
            clus
vv           C15ORF40 MUTATED C15ORF40 WILD-TYPE
  STAGE I                   3                 61
  STAGE IA                  0                  1
  STAGE II                  0                 25
  STAGE IIA                 4                105
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 1                 18
  STAGE IIIA                0                 10
  STAGE IIIB                1                 40
  STAGE IIIC                0                 31
  STAGE IV                  1                 34
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C15ORF40 MUTATED     0   4   6   0
  C15ORF40 WILD-TYPE   9  64 242  41
D24V4, multiclass
    clus
vv   C15ORF40 MUTATED C15ORF40 WILD-TYPE
  T1                0                  9
  T2                4                 64
  T3                6                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
  C15ORF40 MUTATED     7   3   0
  C15ORF40 WILD-TYPE 213  77  66
D24V5, multiclass
    clus
vv   C15ORF40 MUTATED C15ORF40 WILD-TYPE
  N0                7                213
  N1                3                 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"
D24V6, binary
                    cls
clus                   0   1
  C15ORF40 MUTATED     8   1
  C15ORF40 WILD-TYPE 275  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF40 MUTATED      8    1
  C15ORF40 WILD-TYPE  275   47
   clus
vv  C15ORF40 MUTATED C15ORF40 WILD-TYPE
  0                8                275
  1                1                 47
[1] 2 2
[1] FALSE
D24V7, binary
                    cls
clus                   0   1
  C15ORF40 MUTATED     8   2
  C15ORF40 WILD-TYPE 162 195
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF40 MUTATED      8    2
  C15ORF40 WILD-TYPE  162  195
        clus
vv       C15ORF40 MUTATED C15ORF40 WILD-TYPE
  FEMALE                8                162
  MALE                  2                195
[1] 2 2
[1] FALSE
D24V8, binary
                    cls
clus                   0   1
  C15ORF40 MUTATED     9   1
  C15ORF40 WILD-TYPE 308  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF40 MUTATED      9    1
  C15ORF40 WILD-TYPE  308   47
                               clus
vv                              C15ORF40 MUTATED C15ORF40 WILD-TYPE
  COLON ADENOCARCINOMA                         9                308
  COLON MUCINOUS ADENOCARCINOMA                1                 47
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C15ORF40 MUTATED    10   0   0   0
  C15ORF40 WILD-TYPE 247   2  22  21
D24V9, multiclass
    clus
vv   C15ORF40 MUTATED C15ORF40 WILD-TYPE
  R0               10                247
  R1                0                  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"
D24V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C15ORF40 MUTATED                                  0     0
  C15ORF40 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C15ORF40 MUTATED                           0     7
  C15ORF40 WILD-TYPE                        19   169
D24V11, multiclass
                                  clus
vv                                 C15ORF40 MUTATED C15ORF40 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(25) Variable = STARD3NL MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  STARD3NL MUTATED    12   1
  STARD3NL WILD-TYPE 270  72
  STARD3NL MUTATED STARD3NL WILD-TYPE 
                13                342 
  STARD3NL MUTATED STARD3NL WILD-TYPE 
                 1                 72 
$`STARD3NL MUTATED`
TCGA-A6-6781 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-A010 TCGA-AA-A01R TCGA-AY-6197 
       19.66         6.05         6.97        34.98        35.01        21.44 
TCGA-AZ-6599 TCGA-CK-4950 TCGA-CM-6167 TCGA-D5-5540 TCGA-D5-6536 TCGA-G4-6323 
        6.77        40.34        14.99        13.51        17.85        13.78 
TCGA-G4-6588 
       26.17 

$`STARD3NL WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       19.99        13.94        19.99        61.02        78.08        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       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        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       27.09        16.31         0.95        15.75         0.20        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41        49.41        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       102.44        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        43.27        15.12         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       36.00        22.09        35.80        91.79        46.75        52.80 

  STARD3NL MUTATED STARD3NL WILD-TYPE 
              6.05               0.00 
  STARD3NL MUTATED STARD3NL WILD-TYPE 
             40.34             140.38 
  STARD3NL MUTATED STARD3NL WILD-TYPE 
             17.85              20.63 
[1] "6.0 - 40.3 (17.9)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "2.1"
D25V2, 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       24       105         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  STARD3NL MUTATED           1          1          0          2        1
  STARD3NL WILD-TYPE        18          9         41         29       34
                    vv
clus                 STAGE IVA STAGE IVB
  STARD3NL MUTATED           0         0
  STARD3NL WILD-TYPE        13         1
D25V3, multiclass
            clus
vv           STARD3NL MUTATED STARD3NL WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  1                  0
  STAGE II                  1                 24
  STAGE IIA                 4                105
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 1                 18
  STAGE IIIA                1                  9
  STAGE IIIB                0                 41
  STAGE IIIC                2                 29
  STAGE IV                  1                 34
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  STARD3NL MUTATED     0   1   8   3
  STARD3NL WILD-TYPE   9  67 240  38
D25V4, multiclass
    clus
vv   STARD3NL MUTATED STARD3NL WILD-TYPE
  T1                0                  9
  T2                1                 67
  T3                8                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
  STARD3NL MUTATED     8   2   3
  STARD3NL WILD-TYPE 212  78  63
D25V5, multiclass
    clus
vv   STARD3NL MUTATED STARD3NL WILD-TYPE
  N0                8                212
  N1                2                 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"
D25V6, binary
                    cls
clus                   0   1
  STARD3NL MUTATED     8   1
  STARD3NL WILD-TYPE 275  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  STARD3NL MUTATED      8    1
  STARD3NL WILD-TYPE  275   47
   clus
vv  STARD3NL MUTATED STARD3NL WILD-TYPE
  0                8                275
  1                1                 47
[1] 2 2
[1] FALSE
D25V7, 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
D25V8, binary
                    cls
clus                   0   1
  STARD3NL MUTATED    11   2
  STARD3NL WILD-TYPE 306  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  STARD3NL MUTATED     11    2
  STARD3NL WILD-TYPE  306   46
                               clus
vv                              STARD3NL MUTATED STARD3NL WILD-TYPE
  COLON ADENOCARCINOMA                        11                306
  COLON MUCINOUS ADENOCARCINOMA                2                 46
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  STARD3NL MUTATED    10   1   1   0
  STARD3NL WILD-TYPE 247   1  21  21
D25V9, multiclass
    clus
vv   STARD3NL MUTATED STARD3NL WILD-TYPE
  R0               10                247
  R1                1                  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"
D25V10, 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
D25V11, 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(26) Variable = OR4D10 MUTATION ANALYSIS
D26V1, survival
                  sevent
clus2                0   1
  OR4D10 MUTATED    10   4
  OR4D10 WILD-TYPE 272  69
  OR4D10 MUTATED OR4D10 WILD-TYPE 
              14              341 
  OR4D10 MUTATED OR4D10 WILD-TYPE 
               4               69 
$`OR4D10 MUTATED`
TCGA-A6-5657 TCGA-AA-3864 TCGA-AA-A00N TCGA-AD-6899 TCGA-AY-5543 TCGA-AZ-4315 
       31.63        53.00         4.01         5.79        15.75        58.39 
TCGA-AZ-6601 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4752 TCGA-CM-5860 TCGA-CM-6161 
      100.01         0.33         0.10        13.02        16.01        15.02 
TCGA-D5-5537 TCGA-D5-6541 
       45.40        15.58 

$`OR4D10 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         0.72        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-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-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07         0.26         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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-5861 
       25.02        29.06        22.03        22.98        30.08        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        12.00        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  OR4D10 MUTATED OR4D10 WILD-TYPE 
             0.1              0.0 
  OR4D10 MUTATED OR4D10 WILD-TYPE 
          100.01           140.38 
  OR4D10 MUTATED OR4D10 WILD-TYPE 
          15.665           20.980 
[1] "0.1 - 100.0 (15.7)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.3"
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       23       102         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR4D10 MUTATED           0          0          1          1        0
  OR4D10 WILD-TYPE        19         10         40         30       35
                  vv
clus               STAGE IVA STAGE IVB
  OR4D10 MUTATED           1         0
  OR4D10 WILD-TYPE        12         1
D26V3, multiclass
            clus
vv           OR4D10 MUTATED OR4D10 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               7              102
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 237  39
D26V4, multiclass
    clus
vv   OR4D10 MUTATED OR4D10 WILD-TYPE
  T1              0                9
  T2              1               67
  T3             11              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
  OR4D10 MUTATED    10   2   2
  OR4D10 WILD-TYPE 210  78  64
D26V5, multiclass
    clus
vv   OR4D10 MUTATED OR4D10 WILD-TYPE
  N0             10              210
  N1              2               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"
D26V6, binary
                  cls
clus                 0   1
  OR4D10 MUTATED    11   1
  OR4D10 WILD-TYPE 272  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR4D10 MUTATED     11    1
  OR4D10 WILD-TYPE  272   47
   clus
vv  OR4D10 MUTATED OR4D10 WILD-TYPE
  0             11              272
  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    11   3
  OR4D10 WILD-TYPE 306  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR4D10 MUTATED     11    3
  OR4D10 WILD-TYPE  306   45
                               clus
vv                              OR4D10 MUTATED OR4D10 WILD-TYPE
  COLON ADENOCARCINOMA                      11              306
  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 248   2  22  18
D26V9, multiclass
    clus
vv   OR4D10 MUTATED OR4D10 WILD-TYPE
  R0              9              248
  R1              0                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"
D26V10, 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
D26V11, 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 = FMN2 MUTATION ANALYSIS
D27V1, survival
                sevent
clus2              0   1
  FMN2 MUTATED    39  10
  FMN2 WILD-TYPE 243  63
  FMN2 MUTATED FMN2 WILD-TYPE 
            49            306 
  FMN2 MUTATED FMN2 WILD-TYPE 
            10             63 
$`FMN2 MUTATED`
TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       31.63        33.53        22.06        24.69        24.39        23.87 
TCGA-AA-3713 TCGA-AA-3861 TCGA-AA-3956 TCGA-AA-3973 TCGA-AA-A00N TCGA-AA-A010 
       19.04        30.05        34.03        13.05         4.01        34.98 
TCGA-AD-6889 TCGA-AZ-6599 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-6717 TCGA-CA-6718 
       56.55         6.77        11.74         1.94         0.33         0.10 
TCGA-CK-4947 TCGA-CK-5916 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-5861 
       17.56        21.14       124.27        23.05        37.02        15.02 
TCGA-CM-5862 TCGA-CM-6161 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6679 
        5.03        15.02        13.02        14.04        11.01        10.06 
TCGA-CM-6680 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6540 
       12.03        20.19        18.25         1.32        43.27        16.14 
TCGA-D5-6927 TCGA-D5-7000 TCGA-DM-A1D4 TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        9.44        10.26        92.75       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-G4-6586 TCGA-G4-6588 
       81.37        13.38        13.45         6.18        35.80        26.17 
TCGA-G4-6628 
       52.80 

$`FMN2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       32.91        30.44        29.19        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       21.76        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3975 
       20.98         2.01        21.99        16.08        50.99        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        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        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 
       49.41        12.10       100.01        29.56         5.23         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
        1.35       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 
       21.99         2.93         2.01        20.02        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        16.01        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-6170 TCGA-CM-6674 TCGA-CM-6675 
       21.99        14.99        12.99        15.02        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.08        11.01        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       13.51        11.51        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-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04        11.64        13.41         1.51        12.00 
TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 
       11.38       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-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 
       36.72        36.00        22.09        13.78        91.79        46.75 

  FMN2 MUTATED FMN2 WILD-TYPE 
           0.1            0.0 
  FMN2 MUTATED FMN2 WILD-TYPE 
        139.17         140.38 
  FMN2 MUTATED FMN2 WILD-TYPE 
         18.25          20.98 
[1] "0.1 - 139.2 (18.2)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.1"
D27V2, 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       25        88         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FMN2 MUTATED           0          1          7          0        4         3
  FMN2 WILD-TYPE        19          9         34         31       31        10
                vv
clus             STAGE IVB
  FMN2 MUTATED           0
  FMN2 WILD-TYPE         1
D27V3, multiclass
            clus
vv           FMN2 MUTATED FMN2 WILD-TYPE
  STAGE I              11             53
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA            21             88
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            1              9
  STAGE IIIB            7             34
  STAGE IIIC            0             31
  STAGE IV              4             31
  STAGE IVA             3             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  57 217  35
D27V4, multiclass
    clus
vv   FMN2 MUTATED FMN2 WILD-TYPE
  T1            1              8
  T2           11             57
  T3           31            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
  FMN2 MUTATED    37   9   3
  FMN2 WILD-TYPE 183  71  63
D27V5, multiclass
    clus
vv   FMN2 MUTATED FMN2 WILD-TYPE
  N0           37            183
  N1            9             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"
D27V6, binary
                cls
clus               0   1
  FMN2 MUTATED    41   6
  FMN2 WILD-TYPE 242  42
[1] "tbl2"
                cls
clus             [,1] [,2]
  FMN2 MUTATED     41    6
  FMN2 WILD-TYPE  242   42
   clus
vv  FMN2 MUTATED FMN2 WILD-TYPE
  0           41            242
  1            6             42
[1] 2 2
[1] FALSE
D27V7, 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
D27V8, binary
                cls
clus               0   1
  FMN2 MUTATED    42   7
  FMN2 WILD-TYPE 275  41
[1] "tbl2"
                cls
clus             [,1] [,2]
  FMN2 MUTATED     42    7
  FMN2 WILD-TYPE  275   41
                               clus
vv                              FMN2 MUTATED FMN2 WILD-TYPE
  COLON ADENOCARCINOMA                    42            275
  COLON MUCINOUS ADENOCARCINOMA            7             41
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  FMN2 MUTATED    30   0   2   5
  FMN2 WILD-TYPE 227   2  20  16
D27V9, multiclass
    clus
vv   FMN2 MUTATED FMN2 WILD-TYPE
  R0           30            227
  R1            0              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"
D27V10, 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
D27V11, 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(28) Variable = MAPK6 MUTATION ANALYSIS
D28V1, survival
                 sevent
clus2               0   1
  MAPK6 MUTATED    14   4
  MAPK6 WILD-TYPE 268  69
  MAPK6 MUTATED MAPK6 WILD-TYPE 
             18             337 
  MAPK6 MUTATED MAPK6 WILD-TYPE 
              4              69 
$`MAPK6 MUTATED`
TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6648 TCGA-AA-3510 TCGA-AA-3672 TCGA-AA-3977 
       33.53        22.06        25.18        63.98         0.92        25.02 
TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CK-4950 TCGA-CK-4952 TCGA-CM-4752 
       49.41       100.01         0.33        40.34        15.62        13.02 
TCGA-CM-5344 TCGA-D5-5537 TCGA-F4-6704 TCGA-G4-6303 TCGA-G4-6321 TCGA-G4-6625 
       22.03        45.40         1.55        65.85        22.09        91.79 

$`MAPK6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6649 
       32.71        27.09        22.52         8.38        25.08        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       61.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45         6.18        35.87        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 
       36.72        36.00        13.78        35.80        26.17        46.75 
TCGA-G4-6628 
       52.80 

  MAPK6 MUTATED MAPK6 WILD-TYPE 
           0.33            0.00 
  MAPK6 MUTATED MAPK6 WILD-TYPE 
         100.01          140.38 
  MAPK6 MUTATED MAPK6 WILD-TYPE 
          25.10           19.99 
[1] "0.3 - 100.0 (25.1)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.3"
D28V2, 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       22       103         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MAPK6 MUTATED           3          1          1          1        1         1
  MAPK6 WILD-TYPE        16          9         40         30       34        12
                 vv
clus              STAGE IVB
  MAPK6 MUTATED           0
  MAPK6 WILD-TYPE         1
D28V3, multiclass
            clus
vv           MAPK6 MUTATED MAPK6 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              6             103
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              3              16
  STAGE IIIA             1               9
  STAGE IIIB             1              40
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 233  40
D28V4, multiclass
    clus
vv   MAPK6 MUTATED MAPK6 WILD-TYPE
  T1             0               9
  T2             2              66
  T3            15             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
  MAPK6 MUTATED    10   5   3
  MAPK6 WILD-TYPE 210  75  63
D28V5, multiclass
    clus
vv   MAPK6 MUTATED MAPK6 WILD-TYPE
  N0            10             210
  N1             5              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"
D28V6, binary
                 cls
clus                0   1
  MAPK6 MUTATED    11   2
  MAPK6 WILD-TYPE 272  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAPK6 MUTATED     11    2
  MAPK6 WILD-TYPE  272   46
   clus
vv  MAPK6 MUTATED MAPK6 WILD-TYPE
  0            11             272
  1             2              46
[1] 2 2
[1] FALSE
D28V7, 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
D28V8, binary
                 cls
clus                0   1
  MAPK6 MUTATED    15   3
  MAPK6 WILD-TYPE 302  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAPK6 MUTATED     15    3
  MAPK6 WILD-TYPE  302   45
                               clus
vv                              MAPK6 MUTATED MAPK6 WILD-TYPE
  COLON ADENOCARCINOMA                     15             302
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MAPK6 MUTATED    10   1   0   3
  MAPK6 WILD-TYPE 247   1  22  18
D28V9, multiclass
    clus
vv   MAPK6 MUTATED MAPK6 WILD-TYPE
  R0            10             247
  R1             1               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"
D28V10, 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
D28V11, 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(29) Variable = NR1H3 MUTATION ANALYSIS
D29V1, survival
                 sevent
clus2               0   1
  NR1H3 MUTATED    12   2
  NR1H3 WILD-TYPE 270  71
  NR1H3 MUTATED NR1H3 WILD-TYPE 
             14             341 
  NR1H3 MUTATED NR1H3 WILD-TYPE 
              2              71 
$`NR1H3 MUTATED`
TCGA-A6-6648 TCGA-AA-3660 TCGA-AA-3864 TCGA-AA-A00J TCGA-AA-A00R TCGA-AA-A02J 
       25.18        78.08        53.00        18.05         0.99         5.03 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CM-6163 TCGA-CM-6171 TCGA-CM-6674 TCGA-D5-6536 
       51.32        21.14        14.04        14.04        12.95        17.85 
TCGA-G4-6309 TCGA-G4-6628 
       51.75        52.80 

$`NR1H3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        61.02         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
       42.02        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02K 
       37.02        39.06        51.98        39.98         2.01        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99         2.93         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        16.01        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02        12.00        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6675 
       14.99        12.99        13.02        15.02        11.01        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        15.12         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       13.78        35.80        26.17        91.79        46.75 

  NR1H3 MUTATED NR1H3 WILD-TYPE 
           0.99            0.00 
  NR1H3 MUTATED NR1H3 WILD-TYPE 
          78.08          140.38 
  NR1H3 MUTATED NR1H3 WILD-TYPE 
         19.595          20.190 
[1] "1.0 - 78.1 (19.6)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.9"
D29V2, 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       23       106         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        19         10         39         31       34        12
                 vv
clus              STAGE IVB
  NR1H3 MUTATED           0
  NR1H3 WILD-TYPE         1
D29V3, multiclass
            clus
vv           NR1H3 MUTATED NR1H3 WILD-TYPE
  STAGE I                6              58
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              3             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  64 240  40
D29V4, multiclass
    clus
vv   NR1H3 MUTATED NR1H3 WILD-TYPE
  T1             2               7
  T2             4              64
  T3             8             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
  NR1H3 MUTATED    13   2   0
  NR1H3 WILD-TYPE 207  78  66
D29V5, multiclass
    clus
vv   NR1H3 MUTATED NR1H3 WILD-TYPE
  N0            13             207
  N1             2              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"
D29V6, binary
                 cls
clus                0   1
  NR1H3 MUTATED    11   2
  NR1H3 WILD-TYPE 272  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NR1H3 MUTATED     11    2
  NR1H3 WILD-TYPE  272   46
   clus
vv  NR1H3 MUTATED NR1H3 WILD-TYPE
  0            11             272
  1             2              46
[1] 2 2
[1] FALSE
D29V7, 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
D29V8, binary
                 cls
clus                0   1
  NR1H3 MUTATED    14   1
  NR1H3 WILD-TYPE 303  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NR1H3 MUTATED     14    1
  NR1H3 WILD-TYPE  303   47
                               clus
vv                              NR1H3 MUTATED NR1H3 WILD-TYPE
  COLON ADENOCARCINOMA                     14             303
  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 247   2  21  18
D29V9, multiclass
    clus
vv   NR1H3 MUTATED NR1H3 WILD-TYPE
  R0            10             247
  R1             0               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"
D29V10, 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
D29V11, 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(30) Variable = DIP2B MUTATION ANALYSIS
D30V1, survival
                 sevent
clus2               0   1
  DIP2B MUTATED    22   3
  DIP2B WILD-TYPE 260  70
  DIP2B MUTATED DIP2B WILD-TYPE 
             25             330 
  DIP2B MUTATED DIP2B WILD-TYPE 
              3              70 
$`DIP2B MUTATED`
TCGA-A6-2672 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-3496 TCGA-AA-3517 
       46.65        33.53        22.06        20.12         1.02        38.99 
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3973 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 
        6.05         0.92        13.05        18.05         4.01        34.98 
TCGA-AY-5543 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-CA-5254 TCGA-CK-4952 TCGA-D5-6926 
       15.75        58.39        61.41         2.24        15.62         9.04 
TCGA-F4-6570 TCGA-F4-6808 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6323 TCGA-G4-6588 
        6.18        33.67        55.04        36.72        13.78        26.17 
TCGA-G4-6626 
       46.75 

$`DIP2B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       31.63        30.44        29.19        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 
       21.76        24.69        24.39        23.87        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        7.04         3.02        35.01        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       13.02         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13        83.80        22.36        62.79        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        1.94         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-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        13.38        13.45        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       29.59        16.24        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 
      107.67        74.56        65.85        53.62        44.68        51.75 
TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 
       45.11        36.00        22.09        35.80        91.79        52.80 

  DIP2B MUTATED DIP2B WILD-TYPE 
           0.92            0.00 
  DIP2B MUTATED DIP2B WILD-TYPE 
          61.41          140.38 
  DIP2B MUTATED DIP2B WILD-TYPE 
         20.120          20.235 
[1] "0.9 - 61.4 (20.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.7"
D30V2, 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       24        99         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DIP2B MUTATED           2          1          3          0        4         1
  DIP2B WILD-TYPE        17          9         38         31       31        12
                 vv
clus              STAGE IVB
  DIP2B MUTATED           0
  DIP2B WILD-TYPE         1
D30V3, multiclass
            clus
vv           DIP2B MUTATED DIP2B WILD-TYPE
  STAGE I                2              62
  STAGE IA               1               0
  STAGE II               1              24
  STAGE IIA             10              99
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             1               9
  STAGE IIIB             3              38
  STAGE IIIC             0              31
  STAGE IV               4              31
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  68 232  33
D30V4, multiclass
    clus
vv   DIP2B MUTATED DIP2B WILD-TYPE
  T1             2               7
  T2             0              68
  T3            16             232
  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  72  63
D30V5, multiclass
    clus
vv   DIP2B MUTATED DIP2B WILD-TYPE
  N0            16             204
  N1             8              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"
D30V6, binary
                 cls
clus                0   1
  DIP2B MUTATED    20   5
  DIP2B WILD-TYPE 263  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DIP2B MUTATED     20    5
  DIP2B WILD-TYPE  263   43
   clus
vv  DIP2B MUTATED DIP2B WILD-TYPE
  0            20             263
  1             5              43
[1] 2 2
[1] FALSE
D30V7, 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
D30V8, binary
                 cls
clus                0   1
  DIP2B MUTATED    22   5
  DIP2B WILD-TYPE 295  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DIP2B MUTATED     22    5
  DIP2B WILD-TYPE  295   43
                               clus
vv                              DIP2B MUTATED DIP2B WILD-TYPE
  COLON ADENOCARCINOMA                     22             295
  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 237   2  19  19
D30V9, multiclass
    clus
vv   DIP2B MUTATED DIP2B WILD-TYPE
  R0            20             237
  R1             0               2
  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"
D30V10, 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
D30V11, 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(31) Variable = ATXN3L MUTATION ANALYSIS
D31V1, survival
                  sevent
clus2                0   1
  ATXN3L MUTATED    13   4
  ATXN3L WILD-TYPE 269  69
  ATXN3L MUTATED ATXN3L WILD-TYPE 
              17              338 
  ATXN3L MUTATED ATXN3L WILD-TYPE 
               4               69 
$`ATXN3L MUTATED`
TCGA-A6-2671 TCGA-A6-5661 TCGA-A6-5662 TCGA-AA-3713 TCGA-AA-3818 TCGA-AA-3947 
       43.76        33.53        23.61        19.04         0.99        33.01 
TCGA-AA-A00N TCGA-AY-6196 TCGA-CM-5348 TCGA-CM-5861 TCGA-CM-6166 TCGA-D5-6536 
        4.01         0.20        22.98        15.02        21.99        17.85 
TCGA-D5-6930 TCGA-DM-A1HA TCGA-F4-6809 TCGA-G4-6293 TCGA-G4-6310 
        1.51       131.51        13.25       107.67        45.11 

$`ATXN3L WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       31.63        30.44        29.19        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 
       18.05        31.00         2.01        12.99        24.00        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        15.75        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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 
       16.01         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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        15.12         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 
       16.24        33.67         0.53        35.41        19.43        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        51.75        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  ATXN3L MUTATED ATXN3L WILD-TYPE 
             0.2              0.0 
  ATXN3L MUTATED ATXN3L WILD-TYPE 
          131.51           140.38 
  ATXN3L MUTATED ATXN3L WILD-TYPE 
          21.990           20.155 
[1] "0.2 - 131.5 (22.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "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       25       104         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATXN3L MUTATED           1          0          2          2        2
  ATXN3L WILD-TYPE        18         10         39         29       33
                  vv
clus               STAGE IVA STAGE IVB
  ATXN3L MUTATED           2         0
  ATXN3L WILD-TYPE        11         1
D31V3, multiclass
            clus
vv           ATXN3L MUTATED ATXN3L WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               5              104
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              2               29
  STAGE IV                2               33
  STAGE IVA               2               11
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 234  39
D31V4, multiclass
    clus
vv   ATXN3L MUTATED ATXN3L WILD-TYPE
  T1              0                9
  T2              1               67
  T3             14              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
  ATXN3L MUTATED     9   4   4
  ATXN3L WILD-TYPE 211  76  62
D31V5, multiclass
    clus
vv   ATXN3L MUTATED ATXN3L WILD-TYPE
  N0              9              211
  N1              4               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"
D31V6, binary
                  cls
clus                 0   1
  ATXN3L MUTATED    12   4
  ATXN3L WILD-TYPE 271  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATXN3L MUTATED     12    4
  ATXN3L WILD-TYPE  271   44
   clus
vv  ATXN3L MUTATED ATXN3L WILD-TYPE
  0             12              271
  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    13   4
  ATXN3L WILD-TYPE 304  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATXN3L MUTATED     13    4
  ATXN3L WILD-TYPE  304   44
                               clus
vv                              ATXN3L MUTATED ATXN3L WILD-TYPE
  COLON ADENOCARCINOMA                      13              304
  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 243   2  21  21
D31V9, multiclass
    clus
vv   ATXN3L MUTATED ATXN3L WILD-TYPE
  R0             14              243
  R1              0                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"
D31V10, 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
D31V11, 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 = ALPK2 MUTATION ANALYSIS
D32V1, survival
                 sevent
clus2               0   1
  ALPK2 MUTATED    35   6
  ALPK2 WILD-TYPE 247  67
  ALPK2 MUTATED ALPK2 WILD-TYPE 
             41             314 
  ALPK2 MUTATED ALPK2 WILD-TYPE 
              6              67 
$`ALPK2 MUTATED`
TCGA-A6-5661 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6780 
       33.53        32.71        27.09         8.38        25.18        20.12 
TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3525 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3697 
       19.66         3.02         8.05        78.08         6.97        85.05 
TCGA-AA-3821 TCGA-AA-3844 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-5900 
        1.02        14.93        25.02         4.01        34.98         0.07 
TCGA-AU-6004 TCGA-AY-6197 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-CA-5255 TCGA-CA-6717 
       27.09        21.44        49.41         6.77         3.06         0.33 
TCGA-CA-6718 TCGA-CK-4952 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4752 TCGA-CM-5861 
        0.10        15.62        23.05        20.02        13.02        15.02 
TCGA-CM-6162 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-D5-5540 
       12.00        12.99        15.02        14.04        11.01        13.51 
TCGA-D5-6540 TCGA-DM-A28G TCGA-F4-6809 TCGA-G4-6309 TCGA-G4-6588 
       16.14        60.79        13.25        51.75        26.17 

$`ALPK2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 
       22.06        22.52        25.08        24.16        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       24.39        23.87        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 
        9.07        24.03        37.05        36.03        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       19.99        61.02         6.05        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 
       37.05        19.00        36.00         5.03        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 
       17.98        15.95        38.99        37.02         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        15.75         0.20        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 
        5.13        83.80        22.36        62.79        61.41        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        2.24         3.25         3.29         0.07         0.26         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       102.44        40.34        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4746 TCGA-CM-4747 
       21.14         2.93         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        16.01         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 
       12.26        19.59        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
      119.93        35.97       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       16.24        33.67         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       74.56        65.85        53.62        44.68        55.04        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  ALPK2 MUTATED ALPK2 WILD-TYPE 
           0.07            0.00 
  ALPK2 MUTATED ALPK2 WILD-TYPE 
          85.05          140.38 
  ALPK2 MUTATED ALPK2 WILD-TYPE 
         15.020          21.255 
[1] "0.1 - 85.0 (15.0)"  "0.0 - 140.4 (21.3)"
[1] "hr=" "1.2"
D32V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ALPK2 MUTATED         8        0        4        15         2         1
  ALPK2 WILD-TYPE      56        1       21        94         6         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ALPK2 MUTATED           2          0          5          2        0         2
  ALPK2 WILD-TYPE        17         10         36         29       35        11
                 vv
clus              STAGE IVB
  ALPK2 MUTATED           0
  ALPK2 WILD-TYPE         1
D32V3, multiclass
            clus
vv           ALPK2 MUTATED ALPK2 WILD-TYPE
  STAGE I                8              56
  STAGE IA               0               1
  STAGE II               4              21
  STAGE IIA             15              94
  STAGE IIB              2               6
  STAGE IIC              1               0
  STAGE III              2              17
  STAGE IIIA             0              10
  STAGE IIIB             5              36
  STAGE IIIC             2              29
  STAGE IV               0              35
  STAGE IVA              2              11
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  59 220  36
D32V4, multiclass
    clus
vv   ALPK2 MUTATED ALPK2 WILD-TYPE
  T1             0               9
  T2             9              59
  T3            28             220
  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  73  64
D32V5, multiclass
    clus
vv   ALPK2 MUTATED ALPK2 WILD-TYPE
  N0            33             187
  N1             7              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"
D32V6, binary
                 cls
clus                0   1
  ALPK2 MUTATED    33   2
  ALPK2 WILD-TYPE 250  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALPK2 MUTATED     33    2
  ALPK2 WILD-TYPE  250   46
   clus
vv  ALPK2 MUTATED ALPK2 WILD-TYPE
  0            33             250
  1             2              46
[1] 2 2
[1] FALSE
D32V7, 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
D32V8, binary
                 cls
clus                0   1
  ALPK2 MUTATED    33   9
  ALPK2 WILD-TYPE 284  39
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALPK2 MUTATED     33    9
  ALPK2 WILD-TYPE  284   39
                               clus
vv                              ALPK2 MUTATED ALPK2 WILD-TYPE
  COLON ADENOCARCINOMA                     33             284
  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 228   2  22  17
D32V9, multiclass
    clus
vv   ALPK2 MUTATED ALPK2 WILD-TYPE
  R0            29             228
  R1             0               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"
D32V10, 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
D32V11, 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(33) Variable = P2RY13 MUTATION ANALYSIS
D33V1, survival
                  sevent
clus2                0   1
  P2RY13 MUTATED    12   1
  P2RY13 WILD-TYPE 270  72
  P2RY13 MUTATED P2RY13 WILD-TYPE 
              13              342 
  P2RY13 MUTATED P2RY13 WILD-TYPE 
               1               72 
$`P2RY13 MUTATED`
TCGA-A6-6780 TCGA-AA-3496 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3713 TCGA-AA-3977 
       20.12         1.02         6.05         6.97        19.04        25.02 
TCGA-AD-6889 TCGA-CA-6717 TCGA-CM-6678 TCGA-D5-6539 TCGA-DM-A28G TCGA-DM-A28H 
       56.55         0.33        11.01        12.49        60.79       117.07 
TCGA-F4-6569 
       13.45 

$`P2RY13 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       23.87        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       13.94        19.99        61.02        78.08        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        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        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28K 
      139.17         6.12        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        13.38         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  P2RY13 MUTATED P2RY13 WILD-TYPE 
            0.33             0.00 
  P2RY13 MUTATED P2RY13 WILD-TYPE 
          117.07           140.38 
  P2RY13 MUTATED P2RY13 WILD-TYPE 
           13.45            20.98 
[1] "0.3 - 117.1 (13.4)" "0.0 - 140.4 (21.0)"
[1] "hr=" "2.9"
D33V2, 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       23       104         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  P2RY13 MUTATED           0          1          0          1        2
  P2RY13 WILD-TYPE        19          9         41         30       33
                  vv
clus               STAGE IVA STAGE IVB
  P2RY13 MUTATED           1         0
  P2RY13 WILD-TYPE        12         1
D33V3, multiclass
            clus
vv           P2RY13 MUTATED P2RY13 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               5              104
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              1                9
  STAGE IIIB              0               41
  STAGE IIIC              1               30
  STAGE IV                2               33
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 238  38
D33V4, multiclass
    clus
vv   P2RY13 MUTATED P2RY13 WILD-TYPE
  T1              0                9
  T2              2               66
  T3             10              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
  P2RY13 MUTATED    12   1   2
  P2RY13 WILD-TYPE 208  79  64
D33V5, multiclass
    clus
vv   P2RY13 MUTATED P2RY13 WILD-TYPE
  N0             12              208
  N1              1               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"
D33V6, binary
                  cls
clus                 0   1
  P2RY13 MUTATED     9   3
  P2RY13 WILD-TYPE 274  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  P2RY13 MUTATED      9    3
  P2RY13 WILD-TYPE  274   45
   clus
vv  P2RY13 MUTATED P2RY13 WILD-TYPE
  0              9              274
  1              3               45
[1] 2 2
[1] FALSE
D33V7, 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
D33V8, binary
                  cls
clus                 0   1
  P2RY13 MUTATED    13   2
  P2RY13 WILD-TYPE 304  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  P2RY13 MUTATED     13    2
  P2RY13 WILD-TYPE  304   46
                               clus
vv                              P2RY13 MUTATED P2RY13 WILD-TYPE
  COLON ADENOCARCINOMA                      13              304
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  P2RY13 MUTATED     6   0   2   2
  P2RY13 WILD-TYPE 251   2  20  19
D33V9, multiclass
    clus
vv   P2RY13 MUTATED P2RY13 WILD-TYPE
  R0              6              251
  R1              0                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"
D33V10, 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
D33V11, 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(34) Variable = ALG12 MUTATION ANALYSIS
D34V1, survival
                 sevent
clus2               0   1
  ALG12 MUTATED     5   2
  ALG12 WILD-TYPE 277  71
  ALG12 MUTATED ALG12 WILD-TYPE 
              7             348 
  ALG12 MUTATED ALG12 WILD-TYPE 
              2              71 
$`ALG12 MUTATED`
TCGA-AA-3713 TCGA-AA-3989 TCGA-AA-A00J TCGA-AZ-6598 TCGA-CM-4746 TCGA-CM-5861 
       19.04         7.96        18.05        49.41        37.02        15.02 
TCGA-DM-A1HB 
      135.65 

$`ALG12 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        27.02        19.07        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  ALG12 MUTATED ALG12 WILD-TYPE 
           7.96            0.00 
  ALG12 MUTATED ALG12 WILD-TYPE 
         135.65          140.38 
  ALG12 MUTATED ALG12 WILD-TYPE 
         19.040          20.235 
[1] "8.0 - 135.7 (19.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1"  
D34V2, 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       24       108         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        19         10         39         31       33        13
                 vv
clus              STAGE IVB
  ALG12 MUTATED           0
  ALG12 WILD-TYPE         1
D34V3, multiclass
            clus
vv           ALG12 MUTATED ALG12 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              1             108
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               2              33
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ALG12 MUTATED     0   1   5   1
  ALG12 WILD-TYPE   9  67 243  40
D34V4, multiclass
    clus
vv   ALG12 MUTATED ALG12 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             5             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
  ALG12 MUTATED     4   2   1
  ALG12 WILD-TYPE 216  78  65
D34V5, multiclass
    clus
vv   ALG12 MUTATED ALG12 WILD-TYPE
  N0             4             216
  N1             2              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"
D34V6, binary
                 cls
clus                0   1
  ALG12 MUTATED     4   2
  ALG12 WILD-TYPE 279  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALG12 MUTATED      4    2
  ALG12 WILD-TYPE  279   46
   clus
vv  ALG12 MUTATED ALG12 WILD-TYPE
  0             4             279
  1             2              46
[1] 2 2
[1] FALSE
D34V7, 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
D34V8, binary
                 cls
clus                0   1
  ALG12 MUTATED     6   1
  ALG12 WILD-TYPE 311  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALG12 MUTATED      6    1
  ALG12 WILD-TYPE  311   47
                               clus
vv                              ALG12 MUTATED ALG12 WILD-TYPE
  COLON ADENOCARCINOMA                      6             311
  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 254   2  20  21
D34V9, multiclass
    clus
vv   ALG12 MUTATED ALG12 WILD-TYPE
  R0             3             254
  R1             0               2
  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"
D34V10, 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
D34V11, 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(35) Variable = UBQLN2 MUTATION ANALYSIS
D35V1, survival
                  sevent
clus2                0   1
  UBQLN2 MUTATED     9   0
  UBQLN2 WILD-TYPE 273  73
  UBQLN2 MUTATED UBQLN2 WILD-TYPE 
               9              346 
  UBQLN2 MUTATED UBQLN2 WILD-TYPE 
               0               73 
$`UBQLN2 MUTATED`
TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3672 TCGA-AA-A01Q TCGA-CM-5861 TCGA-CM-6168 
       24.39        19.66         0.92         1.02        15.02        12.99 
TCGA-D5-6920 TCGA-G4-6586 TCGA-G4-6588 
       12.39        35.80        26.17 

$`UBQLN2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        91.79        46.75        52.80 

  UBQLN2 MUTATED UBQLN2 WILD-TYPE 
            0.92             0.00 
  UBQLN2 MUTATED UBQLN2 WILD-TYPE 
           35.80           140.38 
  UBQLN2 MUTATED UBQLN2 WILD-TYPE 
           15.02            20.63 
[1] "0.9 - 35.8 (15.0)"  "0.0 - 140.4 (20.6)"
[1] "hr="     "9200000"
D35V2, 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       24       104         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  UBQLN2 MUTATED           1          0          0          1        0
  UBQLN2 WILD-TYPE        18         10         41         30       35
                  vv
clus               STAGE IVA STAGE IVB
  UBQLN2 MUTATED           0         0
  UBQLN2 WILD-TYPE        13         1
D35V3, multiclass
            clus
vv           UBQLN2 MUTATED UBQLN2 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               5              104
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  UBQLN2 MUTATED     0   1   7   2
  UBQLN2 WILD-TYPE   9  67 241  39
D35V4, multiclass
    clus
vv   UBQLN2 MUTATED UBQLN2 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              7              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
  UBQLN2 MUTATED     8   2   0
  UBQLN2 WILD-TYPE 212  78  66
D35V5, multiclass
    clus
vv   UBQLN2 MUTATED UBQLN2 WILD-TYPE
  N0              8              212
  N1              2               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"
D35V6, binary
                  cls
clus                 0   1
  UBQLN2 MUTATED     8   0
  UBQLN2 WILD-TYPE 275  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UBQLN2 MUTATED      8    0
  UBQLN2 WILD-TYPE  275   48
   clus
vv  UBQLN2 MUTATED UBQLN2 WILD-TYPE
  0              8              275
  1              0               48
[1] 2 2
[1] FALSE
D35V7, 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
D35V8, binary
                  cls
clus                 0   1
  UBQLN2 MUTATED     9   1
  UBQLN2 WILD-TYPE 308  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UBQLN2 MUTATED      9    1
  UBQLN2 WILD-TYPE  308   47
                               clus
vv                              UBQLN2 MUTATED UBQLN2 WILD-TYPE
  COLON ADENOCARCINOMA                       9              308
  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 249   2  22  20
D35V9, multiclass
    clus
vv   UBQLN2 MUTATED UBQLN2 WILD-TYPE
  R0              8              249
  R1              0                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"
D35V10, 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
D35V11, 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(36) Variable = TPRKB MUTATION ANALYSIS
D36V1, survival
                 sevent
clus2               0   1
  TPRKB MUTATED     8   2
  TPRKB WILD-TYPE 274  71
  TPRKB MUTATED TPRKB WILD-TYPE 
             10             345 
  TPRKB MUTATED TPRKB WILD-TYPE 
              2              71 
$`TPRKB MUTATED`
TCGA-AZ-6601 TCGA-CA-6717 TCGA-CK-4952 TCGA-CM-5348 TCGA-CM-5861 TCGA-D5-5539 
      100.01         0.33        15.62        22.98        15.02        19.59 
TCGA-D5-6538 TCGA-D5-6928 TCGA-D5-7000 TCGA-DM-A28C 
       17.13        11.64        10.26        81.37 

$`TPRKB WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      102.44        40.34        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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        16.01 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12        17.85         4.80        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00        11.38 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      135.65       139.17         6.12       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  TPRKB MUTATED TPRKB WILD-TYPE 
           0.33            0.00 
  TPRKB MUTATED TPRKB WILD-TYPE 
         100.01          140.38 
  TPRKB MUTATED TPRKB WILD-TYPE 
         16.375          20.980 
[1] "0.3 - 100.0 (16.4)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.3"
D36V2, 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       24       105         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TPRKB MUTATED           1          1          2          0        0         0
  TPRKB WILD-TYPE        18          9         39         31       35        13
                 vv
clus              STAGE IVB
  TPRKB MUTATED           0
  TPRKB WILD-TYPE         1
D36V3, multiclass
            clus
vv           TPRKB MUTATED TPRKB WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              4             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             1               9
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TPRKB MUTATED     0   1   8   1
  TPRKB WILD-TYPE   9  67 240  40
D36V4, multiclass
    clus
vv   TPRKB MUTATED TPRKB WILD-TYPE
  T1             0               9
  T2             1              67
  T3             8             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
  TPRKB MUTATED     6   2   2
  TPRKB WILD-TYPE 214  78  64
D36V5, multiclass
    clus
vv   TPRKB MUTATED TPRKB WILD-TYPE
  N0             6             214
  N1             2              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"
D36V6, binary
                 cls
clus                0   1
  TPRKB MUTATED    10   0
  TPRKB WILD-TYPE 273  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TPRKB MUTATED     10    0
  TPRKB WILD-TYPE  273   48
   clus
vv  TPRKB MUTATED TPRKB WILD-TYPE
  0            10             273
  1             0              48
[1] 2 2
[1] FALSE
D36V7, 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
D36V8, binary
                 cls
clus                0   1
  TPRKB MUTATED     5   5
  TPRKB WILD-TYPE 312  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TPRKB MUTATED      5    5
  TPRKB WILD-TYPE  312   43
                               clus
vv                              TPRKB MUTATED TPRKB WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  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 251   2  22  19
D36V9, multiclass
    clus
vv   TPRKB MUTATED TPRKB WILD-TYPE
  R0             6             251
  R1             0               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"
D36V10, 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
D36V11, 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(37) Variable = PLAGL2 MUTATION ANALYSIS
D37V1, survival
                  sevent
clus2                0   1
  PLAGL2 MUTATED     5   1
  PLAGL2 WILD-TYPE 277  72
  PLAGL2 MUTATED PLAGL2 WILD-TYPE 
               6              349 
  PLAGL2 MUTATED PLAGL2 WILD-TYPE 
               1               72 
$`PLAGL2 MUTATED`
TCGA-A6-5665 TCGA-AA-3713 TCGA-AY-6197 TCGA-AZ-6598 TCGA-CM-4743 TCGA-G4-6586 
       22.06        19.04        21.44        49.41        23.05        35.80 

$`PLAGL2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  PLAGL2 MUTATED PLAGL2 WILD-TYPE 
           19.04             0.00 
  PLAGL2 MUTATED PLAGL2 WILD-TYPE 
           49.41           140.38 
  PLAGL2 MUTATED PLAGL2 WILD-TYPE 
          22.555           20.020 
[1] "19.0 - 49.4 (22.6)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.4"
D37V2, 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       24       105         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLAGL2 MUTATED           0          0          0          0        1
  PLAGL2 WILD-TYPE        19         10         41         31       34
                  vv
clus               STAGE IVA STAGE IVB
  PLAGL2 MUTATED           0         0
  PLAGL2 WILD-TYPE        13         1
D37V3, multiclass
            clus
vv           PLAGL2 MUTATED PLAGL2 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               4              105
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PLAGL2 MUTATED     0   0   6   0
  PLAGL2 WILD-TYPE   9  68 242  41
D37V4, multiclass
    clus
vv   PLAGL2 MUTATED PLAGL2 WILD-TYPE
  T1              0                9
  T2              0               68
  T3              6              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
  PLAGL2 MUTATED     6   0   0
  PLAGL2 WILD-TYPE 214  80  66
D37V5, multiclass
    clus
vv   PLAGL2 MUTATED PLAGL2 WILD-TYPE
  N0              6              214
  N1              0               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"
D37V6, binary
                  cls
clus                 0   1
  PLAGL2 MUTATED     3   1
  PLAGL2 WILD-TYPE 280  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLAGL2 MUTATED      3    1
  PLAGL2 WILD-TYPE  280   47
   clus
vv  PLAGL2 MUTATED PLAGL2 WILD-TYPE
  0              3              280
  1              1               47
[1] 2 2
[1] FALSE
D37V7, 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
D37V8, binary
                  cls
clus                 0   1
  PLAGL2 MUTATED     6   0
  PLAGL2 WILD-TYPE 311  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLAGL2 MUTATED      6    0
  PLAGL2 WILD-TYPE  311   48
                               clus
vv                              PLAGL2 MUTATED PLAGL2 WILD-TYPE
  COLON ADENOCARCINOMA                       6              311
  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 253   2  21  21
D37V9, multiclass
    clus
vv   PLAGL2 MUTATED PLAGL2 WILD-TYPE
  R0              4              253
  R1              0                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"
D37V10, 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
D37V11, 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(38) Variable = MGA MUTATION ANALYSIS
D38V1, survival
               sevent
clus2             0   1
  MGA MUTATED    28   6
  MGA WILD-TYPE 254  67
  MGA MUTATED MGA WILD-TYPE 
           34           321 
  MGA MUTATED MGA WILD-TYPE 
            6            67 
$`MGA MUTATED`
TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6141 TCGA-A6-6781 TCGA-AA-3492 
       33.53        22.06        32.71         8.38        19.66         3.02 
TCGA-AA-3510 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3715 TCGA-AA-3811 
       63.98        78.08         6.97         0.92        19.04        10.06 
TCGA-AA-3812 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R TCGA-AA-A024 TCGA-AD-6895 
       35.05         4.01        34.98        35.01        39.06         0.72 
TCGA-AU-6004 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-5407 TCGA-CA-6717 TCGA-CK-5913 
       27.09         0.20        21.44        61.41         0.33        51.32 
TCGA-CM-5348 TCGA-CM-5861 TCGA-CM-5863 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6927 
       22.98        15.02        15.02        17.13        16.14         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-DM-A1DB TCGA-G4-6306 
       11.64         1.51        44.32        44.68 

$`MGA WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 
       27.09        22.52        25.08        25.18        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 
       24.69        24.39        23.87        20.12        20.28         7.04 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3664 
       19.99        13.94        19.99        61.02         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       26.99        19.04        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       26.01        37.02        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
        0.07        21.37         4.21        56.55         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        15.75        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        21.99        21.14         2.93         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-5864 TCGA-CM-5868 
       22.03        30.08        16.01         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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 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-D5-6929 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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        53.62        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  MGA MUTATED MGA WILD-TYPE 
          0.2           0.0 
  MGA MUTATED MGA WILD-TYPE 
        78.08        140.38 
  MGA MUTATED MGA WILD-TYPE 
        19.35         20.28 
[1] "0.2 - 78.1 (19.4)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.1"
D38V2, 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       18        95         6         0
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MGA MUTATED           3          0          3          2        0         0
  MGA WILD-TYPE        16         10         38         29       35        13
               vv
clus            STAGE IVB
  MGA MUTATED           0
  MGA WILD-TYPE         1
D38V3, multiclass
            clus
vv           MGA MUTATED MGA WILD-TYPE
  STAGE I              3            61
  STAGE IA             0             1
  STAGE II             7            18
  STAGE IIA           14            95
  STAGE IIB            2             6
  STAGE IIC            1             0
  STAGE III            3            16
  STAGE IIIA           0            10
  STAGE IIIB           3            38
  STAGE IIIC           2            29
  STAGE IV             0            35
  STAGE IVA            0            13
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  MGA MUTATED     1   3  27   5
  MGA WILD-TYPE   8  65 221  36
D38V4, multiclass
    clus
vv   MGA MUTATED MGA WILD-TYPE
  T1           1             8
  T2           3            65
  T3          27           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    27   5   4
  MGA WILD-TYPE 193  75  62
D38V5, multiclass
    clus
vv   MGA MUTATED MGA WILD-TYPE
  N0          27           193
  N1           5            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"
D38V6, binary
               cls
clus              0   1
  MGA MUTATED    31   0
  MGA WILD-TYPE 252  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  MGA MUTATED     31    0
  MGA WILD-TYPE  252   48
   clus
vv  MGA MUTATED MGA WILD-TYPE
  0          31           252
  1           0            48
[1] 2 2
[1] FALSE
D38V7, binary
               cls
clus              0   1
  MGA MUTATED    16  20
  MGA WILD-TYPE 154 177
[1] "tbl2"
               cls
clus            [,1] [,2]
  MGA MUTATED     16   20
  MGA WILD-TYPE  154  177
        clus
vv       MGA MUTATED MGA WILD-TYPE
  FEMALE          16           154
  MALE            20           177
[1] 2 2
[1] FALSE
D38V8, binary
               cls
clus              0   1
  MGA MUTATED    26  10
  MGA WILD-TYPE 291  38
[1] "tbl2"
               cls
clus            [,1] [,2]
  MGA MUTATED     26   10
  MGA WILD-TYPE  291   38
                               clus
vv                              MGA MUTATED MGA WILD-TYPE
  COLON ADENOCARCINOMA                   26           291
  COLON MUCINOUS ADENOCARCINOMA          10            38
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  MGA MUTATED    29   0   0   2
  MGA WILD-TYPE 228   2  22  19
D38V9, multiclass
    clus
vv   MGA MUTATED MGA WILD-TYPE
  R0          29           228
  R1           0             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"
D38V10, 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    19
  MGA WILD-TYPE                        17   157
D38V11, 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                                     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(39) Variable = C14ORF184 MUTATION ANALYSIS
D39V1, survival
                     sevent
clus2                   0   1
  C14ORF184 MUTATED     4   2
  C14ORF184 WILD-TYPE 278  71
  C14ORF184 MUTATED C14ORF184 WILD-TYPE 
                  6                 349 
  C14ORF184 MUTATED C14ORF184 WILD-TYPE 
                  2                  71 
$`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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       12.59       140.38        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  C14ORF184 MUTATED C14ORF184 WILD-TYPE 
                7.5                 0.0 
  C14ORF184 MUTATED C14ORF184 WILD-TYPE 
              61.02              140.38 
  C14ORF184 MUTATED C14ORF184 WILD-TYPE 
              23.11               20.19 
[1] "7.5 - 61.0 (23.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.3"
D39V2, 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       24       108         8         1
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C14ORF184 MUTATED           0          0          1          1        1
  C14ORF184 WILD-TYPE        19         10         40         30       34
                     vv
clus                  STAGE IVA STAGE IVB
  C14ORF184 MUTATED           0         0
  C14ORF184 WILD-TYPE        13         1
D39V3, multiclass
            clus
vv           C14ORF184 MUTATED C14ORF184 WILD-TYPE
  STAGE I                    1                  63
  STAGE IA                   0                   1
  STAGE II                   1                  24
  STAGE IIA                  1                 108
  STAGE IIB                  0                   8
  STAGE IIC                  0                   1
  STAGE III                  0                  19
  STAGE IIIA                 0                  10
  STAGE IIIB                 1                  40
  STAGE IIIC                 1                  30
  STAGE IV                   1                  34
  STAGE IVA                  0                  13
  STAGE IVB                  0                   1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2  T3  T4
  C14ORF184 MUTATED     0   1   4   1
  C14ORF184 WILD-TYPE   9  67 244  40
D39V4, multiclass
    clus
vv   C14ORF184 MUTATED C14ORF184 WILD-TYPE
  T1                 0                   9
  T2                 1                  67
  T3                 4                 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
  C14ORF184 MUTATED     3   2   1
  C14ORF184 WILD-TYPE 217  78  65
D39V5, multiclass
    clus
vv   C14ORF184 MUTATED C14ORF184 WILD-TYPE
  N0                 3                 217
  N1                 2                  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"
D39V6, binary
                     cls
clus                    0   1
  C14ORF184 MUTATED     5   1
  C14ORF184 WILD-TYPE 278  47
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF184 MUTATED      5    1
  C14ORF184 WILD-TYPE  278   47
   clus
vv  C14ORF184 MUTATED C14ORF184 WILD-TYPE
  0                 5                 278
  1                 1                  47
[1] 2 2
[1] FALSE
D39V7, 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
D39V8, binary
                     cls
clus                    0   1
  C14ORF184 MUTATED     5   1
  C14ORF184 WILD-TYPE 312  47
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF184 MUTATED      5    1
  C14ORF184 WILD-TYPE  312   47
                               clus
vv                              C14ORF184 MUTATED C14ORF184 WILD-TYPE
  COLON ADENOCARCINOMA                          5                 312
  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 253   2  22  21
D39V9, multiclass
    clus
vv   C14ORF184 MUTATED C14ORF184 WILD-TYPE
  R0                 4                 253
  R1                 0                   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"
D39V10, 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
D39V11, 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(40) Variable = FBXW7 MUTATION ANALYSIS
D40V1, survival
                 sevent
clus2               0   1
  FBXW7 MUTATED    77  23
  FBXW7 WILD-TYPE 205  50
  FBXW7 MUTATED FBXW7 WILD-TYPE 
            100             255 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             23              50 
$`FBXW7 MUTATED`
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-5656 
       46.65        42.90        24.33        34.65        32.75        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-6137 TCGA-A6-6142 TCGA-A6-6651 
       31.63        30.44        33.53        27.09        25.08        21.76 
TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3524 TCGA-AA-3543 TCGA-AA-3560 TCGA-AA-3655 
       13.02         1.02        36.03         0.99        19.99        61.02 
TCGA-AA-3672 TCGA-AA-3681 TCGA-AA-3713 TCGA-AA-3815 TCGA-AA-3831 TCGA-AA-3833 
        0.92         5.98        19.04        33.04        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3949 
       38.99         0.00        10.06         0.00         0.00        26.01 
TCGA-AA-3982 TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01Z TCGA-AA-A024 
       27.02        31.00         1.02        35.01        37.02        39.06 
TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6899 TCGA-AD-6964 
       18.05         0.07        21.37        56.55         5.79        10.88 
TCGA-AU-6004 TCGA-AY-6386 TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
       27.09        17.82        83.80        62.79        61.41        49.41 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4948 TCGA-CK-4950 
      100.01         1.94         0.33         0.10       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4744 
       15.62        49.08        51.32         2.93         2.01        20.02 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5864 
       22.03        22.98        30.08        15.02         5.03        15.02 
TCGA-CM-6171 TCGA-CM-6676 TCGA-CM-6677 TCGA-D5-6532 TCGA-D5-6541 TCGA-D5-6898 
       14.04        11.08        11.08        18.25        15.58         7.53 
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         1.51        12.00 
TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-DM-A1DB 
       10.26        24.43       130.65        49.91         7.50        44.32 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6703 TCGA-F4-6704 
      135.65       139.17        60.79       117.07        35.87         1.55 
TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      107.67        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6588 
       36.72        36.00        22.09        26.17 

$`FBXW7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3808 TCGA-A6-3810 
       43.76        43.76        42.28        16.57        33.34        36.53 
TCGA-A6-4105 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       14.53        29.19        23.61        22.09        22.06        32.71 
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 
       22.52         8.38        25.18        24.16        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        1.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
        9.07        24.03        37.05         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 
       29.95        23.01        20.98        13.94        19.99        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
        6.05         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       47.01        15.02        11.01        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
        0.99        25.02         1.02        37.02        14.93        17.03 
TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
       33.07        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       24.00        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       12.00        31.00        38.07         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       26.01        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-6888 TCGA-AD-6890 
        0.92        41.00        39.98        40.96         4.21         0.79 
TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
        0.72        22.42        27.42         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
        5.13        22.36         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-5914 TCGA-CK-5916 
        0.07         0.26         1.35        17.56        21.99        21.14 
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-5860 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       16.01        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-6678 TCGA-CM-6679 
       15.02        11.01        12.95        13.05        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       17.13        12.49        16.14        12.39        10.13        12.43 
TCGA-D5-6926 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D7 
        9.04        11.38       119.70        38.20        92.75        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       12.59       140.38       131.51         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       35.97        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6310 TCGA-G4-6323 TCGA-G4-6586 
       35.41        19.43        74.56        45.11        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  FBXW7 MUTATED FBXW7 WILD-TYPE 
              0               0 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
         139.17          140.38 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
          24.38           19.07 
[1] "0.0 - 139.2 (24.4)" "0.0 - 140.4 (19.1)"
[1] "hr=" "1.1"
D40V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FBXW7 MUTATED        15        0        9        33         4         0
  FBXW7 WILD-TYPE      49        1       16        76         4         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FBXW7 MUTATED           8          3         12         11        5         2
  FBXW7 WILD-TYPE        11          7         29         20       30        11
                 vv
clus              STAGE IVB
  FBXW7 MUTATED           0
  FBXW7 WILD-TYPE         1
D40V3, multiclass
            clus
vv           FBXW7 MUTATED FBXW7 WILD-TYPE
  STAGE I               15              49
  STAGE IA               0               1
  STAGE II               9              16
  STAGE IIA             33              76
  STAGE IIB              4               4
  STAGE IIC              0               1
  STAGE III              8              11
  STAGE IIIA             3               7
  STAGE IIIB            12              29
  STAGE IIIC            11              20
  STAGE IV               5              30
  STAGE IVA              2              11
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  51 172  32
D40V4, multiclass
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  T1             1               8
  T2            17              51
  T3            76             172
  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  55  50
D40V5, multiclass
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  N0            62             158
  N1            25              55
  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"
D40V6, binary
                 cls
clus                0   1
  FBXW7 MUTATED    83   7
  FBXW7 WILD-TYPE 200  41
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED     83    7
  FBXW7 WILD-TYPE  200   41
   clus
vv  FBXW7 MUTATED FBXW7 WILD-TYPE
  0            83             200
  1             7              41
[1] 2 2
[1] FALSE
D40V7, 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
D40V8, binary
                 cls
clus                0   1
  FBXW7 MUTATED    84  19
  FBXW7 WILD-TYPE 233  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED     84   19
  FBXW7 WILD-TYPE  233   29
                               clus
vv                              FBXW7 MUTATED FBXW7 WILD-TYPE
  COLON ADENOCARCINOMA                     84             233
  COLON MUCINOUS ADENOCARCINOMA            19              29
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  FBXW7 MUTATED    70   1   1   8
  FBXW7 WILD-TYPE 187   1  21  13
D40V9, multiclass
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  R0            70             187
  R1             1               1
  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"
D40V10, 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
D40V11, 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(41) Variable = RPTN MUTATION ANALYSIS
D41V1, survival
                sevent
clus2              0   1
  RPTN MUTATED    12   1
  RPTN WILD-TYPE 270  72
  RPTN MUTATED RPTN WILD-TYPE 
            13            342 
  RPTN MUTATED RPTN WILD-TYPE 
             1             72 
$`RPTN MUTATED`
TCGA-AA-3663 TCGA-AA-3713 TCGA-AZ-6601 TCGA-CA-6716 TCGA-CA-6717 TCGA-CM-5344 
        6.97        19.04       100.01         0.26         0.33        22.03 
TCGA-CM-6166 TCGA-CM-6171 TCGA-CM-6679 TCGA-D5-6932 TCGA-F4-6704 TCGA-G4-6323 
       21.99        14.04        10.06        11.38         1.55        13.78 
TCGA-G4-6628 
       52.80 

$`RPTN WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       35.87        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        35.80        26.17        91.79        46.75 

  RPTN MUTATED RPTN WILD-TYPE 
          0.26           0.00 
  RPTN MUTATED RPTN WILD-TYPE 
        100.01         140.38 
  RPTN MUTATED RPTN WILD-TYPE 
         13.78          20.98 
[1] "0.3 - 100.0 (13.8)" "0.0 - 140.4 (21.0)"
[1] "hr=" "2.5"
D41V2, 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       23       105         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        19         10         40         30       34        13
                vv
clus             STAGE IVB
  RPTN MUTATED           0
  RPTN WILD-TYPE         1
D41V3, multiclass
            clus
vv           RPTN MUTATED RPTN WILD-TYPE
  STAGE I               3             61
  STAGE IA              1              0
  STAGE II              2             23
  STAGE IIA             4            105
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            1             30
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RPTN MUTATED     0   3   9   0
  RPTN WILD-TYPE   9  65 239  41
D41V4, multiclass
    clus
vv   RPTN MUTATED RPTN WILD-TYPE
  T1            0              9
  T2            3             65
  T3            9            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
  RPTN MUTATED    11   1   1
  RPTN WILD-TYPE 209  79  65
D41V5, multiclass
    clus
vv   RPTN MUTATED RPTN WILD-TYPE
  N0           11            209
  N1            1             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"
D41V6, binary
                cls
clus               0   1
  RPTN MUTATED    10   1
  RPTN WILD-TYPE 273  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPTN MUTATED     10    1
  RPTN WILD-TYPE  273   47
   clus
vv  RPTN MUTATED RPTN WILD-TYPE
  0           10            273
  1            1             47
[1] 2 2
[1] FALSE
D41V7, 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
D41V8, binary
                cls
clus               0   1
  RPTN MUTATED    11   2
  RPTN WILD-TYPE 306  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPTN MUTATED     11    2
  RPTN WILD-TYPE  306   46
                               clus
vv                              RPTN MUTATED RPTN WILD-TYPE
  COLON ADENOCARCINOMA                    11            306
  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 248   2  21  19
D41V9, multiclass
    clus
vv   RPTN MUTATED RPTN WILD-TYPE
  R0            9            248
  R1            0              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"
D41V10, 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
D41V11, 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(42) Variable = ZBTB20 MUTATION ANALYSIS
D42V1, survival
                  sevent
clus2                0   1
  ZBTB20 MUTATED    15   4
  ZBTB20 WILD-TYPE 267  69
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
              19              336 
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
               4               69 
$`ZBTB20 MUTATED`
TCGA-A6-5661 TCGA-A6-6653 TCGA-A6-6780 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3815 
       33.53        24.39        20.12         6.97         0.92        33.04 
TCGA-AA-3845 TCGA-AA-3950 TCGA-AA-3966 TCGA-AD-6964 TCGA-AY-6197 TCGA-CK-5913 
        0.00        24.00         2.01        10.88        21.44        51.32 
TCGA-CK-5916 TCGA-CM-6171 TCGA-D5-6538 TCGA-D5-6922 TCGA-F4-6570 TCGA-F4-6856 
       21.14        14.04        17.13        10.13         6.18        19.43 
TCGA-G4-6588 
       26.17 

$`ZBTB20 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6781 
       25.18        24.16        21.76        24.69        23.87        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       19.04        19.04        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       49.08        21.99         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        12.49        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       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        13.38        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        35.41       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        52.80 

  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
               0                0 
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
           51.32           140.38 
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
           19.43            20.63 
[1] "0.0 - 51.3 (19.4)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "1.4"
D42V2, 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       24        99         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZBTB20 MUTATED           1          1          1          0        0
  ZBTB20 WILD-TYPE        18          9         40         31       35
                  vv
clus               STAGE IVA STAGE IVB
  ZBTB20 MUTATED           0         0
  ZBTB20 WILD-TYPE        13         1
D42V3, multiclass
            clus
vv           ZBTB20 MUTATED ZBTB20 WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA              10               99
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              1                9
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZBTB20 MUTATED     1   3  14   2
  ZBTB20 WILD-TYPE   8  65 234  39
D42V4, multiclass
    clus
vv   ZBTB20 MUTATED ZBTB20 WILD-TYPE
  T1              1                8
  T2              3               65
  T3             14              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
  ZBTB20 MUTATED    16   2   2
  ZBTB20 WILD-TYPE 204  78  64
D42V5, multiclass
    clus
vv   ZBTB20 MUTATED ZBTB20 WILD-TYPE
  N0             16              204
  N1              2               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"
D42V6, binary
                  cls
clus                 0   1
  ZBTB20 MUTATED    15   0
  ZBTB20 WILD-TYPE 268  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB20 MUTATED     15    0
  ZBTB20 WILD-TYPE  268   48
   clus
vv  ZBTB20 MUTATED ZBTB20 WILD-TYPE
  0             15              268
  1              0               48
[1] 2 2
[1] FALSE
D42V7, 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
D42V8, binary
                  cls
clus                 0   1
  ZBTB20 MUTATED    16   4
  ZBTB20 WILD-TYPE 301  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB20 MUTATED     16    4
  ZBTB20 WILD-TYPE  301   44
                               clus
vv                              ZBTB20 MUTATED ZBTB20 WILD-TYPE
  COLON ADENOCARCINOMA                      16              301
  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 244   2  22  18
D42V9, multiclass
    clus
vv   ZBTB20 MUTATED ZBTB20 WILD-TYPE
  R0             13              244
  R1              0                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"
D42V10, 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
D42V11, 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(43) Variable = TOP2B MUTATION ANALYSIS
D43V1, survival
                 sevent
clus2               0   1
  TOP2B MUTATED    18   3
  TOP2B WILD-TYPE 264  70
  TOP2B MUTATED TOP2B WILD-TYPE 
             21             334 
  TOP2B MUTATED TOP2B WILD-TYPE 
              3              70 
$`TOP2B MUTATED`
TCGA-A6-5661 TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3815 TCGA-AA-3855 TCGA-AA-3864 
       33.53        22.06        63.98        33.04        32.05        53.00 
TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-6889 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CK-5912 
       34.98        35.01        56.55        58.39        49.41        49.08 
TCGA-CM-4743 TCGA-CM-5861 TCGA-CM-6161 TCGA-CM-6165 TCGA-D5-6536 TCGA-DM-A0XD 
       23.05        15.02        15.02        16.04        17.85        24.43 
TCGA-F4-6856 TCGA-G4-6315 TCGA-G4-6628 
       19.43        36.72        52.80 

$`TOP2B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
       33.07         0.00        36.03         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        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         2.93         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        16.01         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 
       17.03        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        43.27        15.12         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.41       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        51.75        45.11        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       35.80        26.17        91.79        46.75 

  TOP2B MUTATED TOP2B WILD-TYPE 
          15.02            0.00 
  TOP2B MUTATED TOP2B WILD-TYPE 
          63.98          140.38 
  TOP2B MUTATED TOP2B WILD-TYPE 
         33.530          19.625 
[1] "15.0 - 64.0 (33.5)" "0.0 - 140.4 (19.6)"
[1] "hr=" "2.1"
D43V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TOP2B MUTATED         5        0        4        10         1         0
  TOP2B WILD-TYPE      59        1       21        99         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        18         10         41         31       34        13
                 vv
clus              STAGE IVB
  TOP2B MUTATED           0
  TOP2B WILD-TYPE         1
D43V3, multiclass
            clus
vv           TOP2B MUTATED TOP2B WILD-TYPE
  STAGE I                5              59
  STAGE IA               0               1
  STAGE II               4              21
  STAGE IIA             10              99
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TOP2B MUTATED     0   5  15   2
  TOP2B WILD-TYPE   9  63 233  39
D43V4, multiclass
    clus
vv   TOP2B MUTATED TOP2B WILD-TYPE
  T1             0               9
  T2             5              63
  T3            15             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    20   1   1
  TOP2B WILD-TYPE 200  79  65
D43V5, multiclass
    clus
vv   TOP2B MUTATED TOP2B WILD-TYPE
  N0            20             200
  N1             1              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"
D43V6, binary
                 cls
clus                0   1
  TOP2B MUTATED    19   1
  TOP2B WILD-TYPE 264  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TOP2B MUTATED     19    1
  TOP2B WILD-TYPE  264   47
   clus
vv  TOP2B MUTATED TOP2B WILD-TYPE
  0            19             264
  1             1              47
[1] 2 2
[1] FALSE
D43V7, binary
                 cls
clus                0   1
  TOP2B MUTATED     8  14
  TOP2B WILD-TYPE 162 183
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TOP2B MUTATED      8   14
  TOP2B WILD-TYPE  162  183
        clus
vv       TOP2B MUTATED TOP2B WILD-TYPE
  FEMALE             8             162
  MALE              14             183
[1] 2 2
[1] FALSE
D43V8, binary
                 cls
clus                0   1
  TOP2B MUTATED    20   2
  TOP2B WILD-TYPE 297  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TOP2B MUTATED     20    2
  TOP2B WILD-TYPE  297   46
                               clus
vv                              TOP2B MUTATED TOP2B WILD-TYPE
  COLON ADENOCARCINOMA                     20             297
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TOP2B MUTATED    18   0   0   1
  TOP2B WILD-TYPE 239   2  22  20
D43V9, multiclass
    clus
vv   TOP2B MUTATED TOP2B WILD-TYPE
  R0            18             239
  R1             0               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"
D43V10, 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    13
  TOP2B WILD-TYPE                        18   163
D43V11, 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                                       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(44) Variable = SMAD2 MUTATION ANALYSIS
D44V1, survival
                 sevent
clus2               0   1
  SMAD2 MUTATED    11   4
  SMAD2 WILD-TYPE 271  69
  SMAD2 MUTATED SMAD2 WILD-TYPE 
             15             340 
  SMAD2 MUTATED SMAD2 WILD-TYPE 
              4              69 
$`SMAD2 MUTATED`
TCGA-A6-6780 TCGA-AA-3510 TCGA-AA-3520 TCGA-AA-3663 TCGA-AA-3696 TCGA-AA-3842 
       20.12        63.98        24.03         6.97         5.03        37.02 
TCGA-AA-3864 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A01V TCGA-AA-A024 TCGA-AA-A029 
       53.00        25.02         4.01        35.01        39.06        51.98 
TCGA-AZ-6600 TCGA-CM-6168 TCGA-CM-6169 
       12.10        12.99        13.02 

$`SMAD2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
        9.07        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3710 
        5.98        37.05        19.00        36.00        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3844 
       25.02         1.02        17.98        15.95        38.99        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A01X TCGA-AA-A01Z TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       26.01        37.02        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41        49.41         6.77       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       16.04        21.99        14.99        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  SMAD2 MUTATED SMAD2 WILD-TYPE 
           4.01            0.00 
  SMAD2 MUTATED SMAD2 WILD-TYPE 
          63.98          140.38 
  SMAD2 MUTATED SMAD2 WILD-TYPE 
         24.030          20.105 
[1] "4.0 - 64.0 (24.0)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.2"
D44V2, 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       19       106         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        19          9         41         31       32        13
                 vv
clus              STAGE IVB
  SMAD2 MUTATED           0
  SMAD2 WILD-TYPE         1
D44V3, multiclass
            clus
vv           SMAD2 MUTATED SMAD2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               6              19
  STAGE IIA              3             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               3              32
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SMAD2 MUTATED     0   3  10   3
  SMAD2 WILD-TYPE   9  65 238  38
D44V4, multiclass
    clus
vv   SMAD2 MUTATED SMAD2 WILD-TYPE
  T1             0               9
  T2             3              65
  T3            10             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
  SMAD2 MUTATED    12   3   1
  SMAD2 WILD-TYPE 208  77  65
D44V5, multiclass
    clus
vv   SMAD2 MUTATED SMAD2 WILD-TYPE
  N0            12             208
  N1             3              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"
D44V6, binary
                 cls
clus                0   1
  SMAD2 MUTATED    11   3
  SMAD2 WILD-TYPE 272  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD2 MUTATED     11    3
  SMAD2 WILD-TYPE  272   45
   clus
vv  SMAD2 MUTATED SMAD2 WILD-TYPE
  0            11             272
  1             3              45
[1] 2 2
[1] FALSE
D44V7, 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
D44V8, binary
                 cls
clus                0   1
  SMAD2 MUTATED    12   4
  SMAD2 WILD-TYPE 305  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD2 MUTATED     12    4
  SMAD2 WILD-TYPE  305   44
                               clus
vv                              SMAD2 MUTATED SMAD2 WILD-TYPE
  COLON ADENOCARCINOMA                     12             305
  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 246   2  20  21
D44V9, multiclass
    clus
vv   SMAD2 MUTATED SMAD2 WILD-TYPE
  R0            11             246
  R1             0               2
  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"
D44V10, 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
D44V11, 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(45) Variable = GMPS MUTATION ANALYSIS
D45V1, survival
                sevent
clus2              0   1
  GMPS MUTATED    15   1
  GMPS WILD-TYPE 267  72
  GMPS MUTATED GMPS WILD-TYPE 
            16            339 
  GMPS MUTATED GMPS WILD-TYPE 
             1             72 
$`GMPS MUTATED`
TCGA-A6-3809 TCGA-AA-3710 TCGA-AA-3977 TCGA-AA-A010 TCGA-AA-A01I TCGA-AD-6890 
       32.75        26.99        25.02        34.98        31.00         0.79 
TCGA-AZ-4315 TCGA-AZ-6600 TCGA-CA-6717 TCGA-CM-4752 TCGA-CM-5864 TCGA-D5-6540 
       58.39        12.10         0.33        13.02        15.02        16.14 
TCGA-D5-6922 TCGA-D5-6930 TCGA-F4-6569 TCGA-G4-6588 
       10.13         1.51        13.45        26.17 

$`GMPS WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01P 
       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        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37         4.21        56.55         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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        16.01 
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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 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-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  GMPS MUTATED GMPS WILD-TYPE 
          0.33           0.00 
  GMPS MUTATED GMPS WILD-TYPE 
         58.39         140.38 
  GMPS MUTATED GMPS WILD-TYPE 
         15.58          20.28 
[1] "0.3 - 58.4 (15.6)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "2.6"
D45V2, 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       25       102         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        19          9         41         31       34        13
                vv
clus             STAGE IVB
  GMPS MUTATED           0
  GMPS WILD-TYPE         1
D45V3, multiclass
            clus
vv           GMPS MUTATED GMPS WILD-TYPE
  STAGE I               4             60
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             7            102
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            1              9
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GMPS MUTATED     1   5   8   3
  GMPS WILD-TYPE   8  63 240  38
D45V4, multiclass
    clus
vv   GMPS MUTATED GMPS WILD-TYPE
  T1            1              8
  T2            5             63
  T3            8            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
  GMPS MUTATED    15   2   0
  GMPS WILD-TYPE 205  78  66
D45V5, multiclass
    clus
vv   GMPS MUTATED GMPS WILD-TYPE
  N0           15            205
  N1            2             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"
D45V6, binary
                cls
clus               0   1
  GMPS MUTATED    14   1
  GMPS WILD-TYPE 269  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  GMPS MUTATED     14    1
  GMPS WILD-TYPE  269   47
   clus
vv  GMPS MUTATED GMPS WILD-TYPE
  0           14            269
  1            1             47
[1] 2 2
[1] FALSE
D45V7, 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
D45V8, binary
                cls
clus               0   1
  GMPS MUTATED    13   4
  GMPS WILD-TYPE 304  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  GMPS MUTATED     13    4
  GMPS WILD-TYPE  304   44
                               clus
vv                              GMPS MUTATED GMPS WILD-TYPE
  COLON ADENOCARCINOMA                    13            304
  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 244   2  22  20
D45V9, multiclass
    clus
vv   GMPS MUTATED GMPS WILD-TYPE
  R0           13            244
  R1            0              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"
D45V10, 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
D45V11, 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(46) Variable = SETD2 MUTATION ANALYSIS
D46V1, survival
                 sevent
clus2               0   1
  SETD2 MUTATED    34   6
  SETD2 WILD-TYPE 248  67
  SETD2 MUTATED SETD2 WILD-TYPE 
             40             315 
  SETD2 MUTATED SETD2 WILD-TYPE 
              6              67 
$`SETD2 MUTATED`
TCGA-A6-2672 TCGA-A6-5659 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6141 TCGA-AA-3525 
       46.65        30.44        22.09        22.06         8.38         8.05 
TCGA-AA-3543 TCGA-AA-3663 TCGA-AA-3680 TCGA-AA-3710 TCGA-AA-3851 TCGA-AA-A00E 
        0.99         6.97        11.01        26.99        33.07        30.02 
TCGA-AA-A00N TCGA-AD-6548 TCGA-AD-6889 TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-6386 
        4.01        21.37        56.55        27.09        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-6599 TCGA-CA-6717 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 
       58.39         6.77         0.33        40.34        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        16.01        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        12.26        13.51        18.25        16.14 
TCGA-DM-A28F TCGA-F4-6570 TCGA-F4-6805 TCGA-F4-6809 
       35.97         6.18        16.31        13.25 

$`SETD2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-6137 
       31.63        29.19        33.53        23.61        32.71        27.09 
TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 
       22.52        25.08        25.18        24.16        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 
       24.39        23.87        20.12        19.66        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        3.02         1.02        35.01        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
       36.03        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01        12.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       15.02         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J 
       27.02        13.94        38.04        19.00        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6888 
       41.00        39.98        18.05        40.96         0.07         4.21 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.20        14.50        16.31         0.95        15.75         0.20 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4744 
       49.08        21.99        21.14         2.93         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-5862 TCGA-CM-5863 TCGA-CM-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-D5-5537 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 
       11.01        10.06        45.40        19.59        11.51        20.19 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
       81.37       119.93        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6807 
       13.38        13.45        35.87         1.55        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       33.67         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  SETD2 MUTATED SETD2 WILD-TYPE 
           0.33            0.00 
  SETD2 MUTATED SETD2 WILD-TYPE 
         124.27          140.38 
  SETD2 MUTATED SETD2 WILD-TYPE 
         17.065          20.980 
[1] "0.3 - 124.3 (17.1)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.3"
D46V2, 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       24        91         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SETD2 MUTATED           1          1          7          1        1         1
  SETD2 WILD-TYPE        18          9         34         30       34        12
                 vv
clus              STAGE IVB
  SETD2 MUTATED           0
  SETD2 WILD-TYPE         1
D46V3, multiclass
            clus
vv           SETD2 MUTATED SETD2 WILD-TYPE
  STAGE I                9              55
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA             18              91
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             1               9
  STAGE IIIB             7              34
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  60 220  37
D46V4, multiclass
    clus
vv   SETD2 MUTATED SETD2 WILD-TYPE
  T1             1               8
  T2             8              60
  T3            28             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
  SETD2 MUTATED    29   8   4
  SETD2 WILD-TYPE 191  72  62
D46V5, multiclass
    clus
vv   SETD2 MUTATED SETD2 WILD-TYPE
  N0            29             191
  N1             8              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"
D46V6, binary
                 cls
clus                0   1
  SETD2 MUTATED    34   2
  SETD2 WILD-TYPE 249  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED     34    2
  SETD2 WILD-TYPE  249   46
   clus
vv  SETD2 MUTATED SETD2 WILD-TYPE
  0            34             249
  1             2              46
[1] 2 2
[1] FALSE
D46V7, 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
D46V8, binary
                 cls
clus                0   1
  SETD2 MUTATED    35   6
  SETD2 WILD-TYPE 282  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED     35    6
  SETD2 WILD-TYPE  282   42
                               clus
vv                              SETD2 MUTATED SETD2 WILD-TYPE
  COLON ADENOCARCINOMA                     35             282
  COLON MUCINOUS ADENOCARCINOMA             6              42
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SETD2 MUTATED    30   1   1   4
  SETD2 WILD-TYPE 227   1  21  17
D46V9, multiclass
    clus
vv   SETD2 MUTATED SETD2 WILD-TYPE
  R0            30             227
  R1             1               1
  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"
D46V10, 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
D46V11, 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(47) Variable = PTGDR MUTATION ANALYSIS
D47V1, survival
                 sevent
clus2               0   1
  PTGDR MUTATED     6   0
  PTGDR WILD-TYPE 276  73
  PTGDR MUTATED PTGDR WILD-TYPE 
              6             349 
  PTGDR MUTATED PTGDR WILD-TYPE 
              0              73 
$`PTGDR MUTATED`
TCGA-AA-3510 TCGA-AY-6197 TCGA-CM-4752 TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6930 
       63.98        21.44        13.02        15.12        17.13         1.51 

$`PTGDR WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        15.75         0.20        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 
       20.19        18.25         1.32        43.27        17.85         4.80 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 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-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  PTGDR MUTATED PTGDR WILD-TYPE 
           1.51            0.00 
  PTGDR MUTATED PTGDR WILD-TYPE 
          63.98          140.38 
  PTGDR MUTATED PTGDR WILD-TYPE 
         16.125          20.280 
[1] "1.5 - 64.0 (16.1)"  "0.0 - 140.4 (20.3)"
[1] "hr="     "9200000"
D47V2, 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       24       106         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        18         10         39         31       35        13
                 vv
clus              STAGE IVB
  PTGDR MUTATED           0
  PTGDR WILD-TYPE         1
D47V3, multiclass
            clus
vv           PTGDR MUTATED PTGDR WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              3             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PTGDR MUTATED     0   0   7   0
  PTGDR WILD-TYPE   9  68 241  41
D47V4, multiclass
    clus
vv   PTGDR MUTATED PTGDR WILD-TYPE
  T1             0               9
  T2             0              68
  T3             7             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
  PTGDR MUTATED     4   1   2
  PTGDR WILD-TYPE 216  79  64
D47V5, multiclass
    clus
vv   PTGDR MUTATED PTGDR WILD-TYPE
  N0             4             216
  N1             1              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"
D47V6, binary
                 cls
clus                0   1
  PTGDR MUTATED     5   0
  PTGDR WILD-TYPE 278  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTGDR MUTATED      5    0
  PTGDR WILD-TYPE  278   48
   clus
vv  PTGDR MUTATED PTGDR WILD-TYPE
  0             5             278
  1             0              48
[1] 2 2
[1] FALSE
D47V7, 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
D47V8, binary
                 cls
clus                0   1
  PTGDR MUTATED     6   1
  PTGDR WILD-TYPE 311  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTGDR MUTATED      6    1
  PTGDR WILD-TYPE  311   47
                               clus
vv                              PTGDR MUTATED PTGDR WILD-TYPE
  COLON ADENOCARCINOMA                      6             311
  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 251   2  22  20
D47V9, multiclass
    clus
vv   PTGDR MUTATED PTGDR WILD-TYPE
  R0             6             251
  R1             0               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"
D47V10, 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
D47V11, 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(48) Variable = PLEKHF2 MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  PLEKHF2 MUTATED     7   2
  PLEKHF2 WILD-TYPE 275  71
  PLEKHF2 MUTATED PLEKHF2 WILD-TYPE 
                9               346 
  PLEKHF2 MUTATED PLEKHF2 WILD-TYPE 
                2                71 
$`PLEKHF2 MUTATED`
TCGA-A6-5665 TCGA-AA-3713 TCGA-AA-3977 TCGA-D5-6533 TCGA-D5-6541 TCGA-G4-6303 
       22.06        19.04        25.02         1.32        15.58        65.85 
TCGA-G4-6309 TCGA-G4-6323 TCGA-G4-6626 
       51.75        13.78        46.75 

$`PLEKHF2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
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-D5-6898 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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 
        0.53        35.41        19.43       107.67        74.56        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        45.11        36.72        36.00        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       35.80        26.17        91.79        52.80 

  PLEKHF2 MUTATED PLEKHF2 WILD-TYPE 
             1.32              0.00 
  PLEKHF2 MUTATED PLEKHF2 WILD-TYPE 
            65.85            140.38 
  PLEKHF2 MUTATED PLEKHF2 WILD-TYPE 
           22.060            20.155 
[1] "1.3 - 65.8 (22.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D48V2, 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       25       106         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLEKHF2 MUTATED           0          0          2          0        2
  PLEKHF2 WILD-TYPE        19         10         39         31       33
                   vv
clus                STAGE IVA STAGE IVB
  PLEKHF2 MUTATED           0         0
  PLEKHF2 WILD-TYPE        13         1
D48V3, multiclass
            clus
vv           PLEKHF2 MUTATED PLEKHF2 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 1                 0
  STAGE II                 0                25
  STAGE IIA                3               106
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               2                39
  STAGE IIIC               0                31
  STAGE IV                 2                33
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PLEKHF2 MUTATED     0   2   6   1
  PLEKHF2 WILD-TYPE   9  66 242  40
D48V4, multiclass
    clus
vv   PLEKHF2 MUTATED PLEKHF2 WILD-TYPE
  T1               0                 9
  T2               2                66
  T3               6               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
  PLEKHF2 MUTATED     8   2   0
  PLEKHF2 WILD-TYPE 212  78  66
D48V5, multiclass
    clus
vv   PLEKHF2 MUTATED PLEKHF2 WILD-TYPE
  N0               8               212
  N1               2                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"
D48V6, binary
                   cls
clus                  0   1
  PLEKHF2 MUTATED     5   2
  PLEKHF2 WILD-TYPE 278  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHF2 MUTATED      5    2
  PLEKHF2 WILD-TYPE  278   46
   clus
vv  PLEKHF2 MUTATED PLEKHF2 WILD-TYPE
  0               5               278
  1               2                46
[1] 2 2
[1] FALSE
D48V7, 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
D48V8, binary
                   cls
clus                  0   1
  PLEKHF2 MUTATED    10   0
  PLEKHF2 WILD-TYPE 307  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHF2 MUTATED     10    0
  PLEKHF2 WILD-TYPE  307   48
                               clus
vv                              PLEKHF2 MUTATED PLEKHF2 WILD-TYPE
  COLON ADENOCARCINOMA                       10               307
  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 250   2  21  20
D48V9, multiclass
    clus
vv   PLEKHF2 MUTATED PLEKHF2 WILD-TYPE
  R0               7               250
  R1               0                 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"
D48V10, 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
D48V11, 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(49) Variable = ASXL1 MUTATION ANALYSIS
D49V1, survival
                 sevent
clus2               0   1
  ASXL1 MUTATED    27  11
  ASXL1 WILD-TYPE 255  62
  ASXL1 MUTATED ASXL1 WILD-TYPE 
             38             317 
  ASXL1 MUTATED ASXL1 WILD-TYPE 
             11              62 
$`ASXL1 MUTATED`
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3542 TCGA-AA-3561 
       31.63        29.19        22.06        63.98        12.99        13.94 
TCGA-AA-3672 TCGA-AA-3680 TCGA-AA-3715 TCGA-AA-3864 TCGA-AA-A00E TCGA-AA-A010 
        0.92        11.01        19.04        53.00        30.02        34.98 
TCGA-AD-5900 TCGA-AD-6901 TCGA-AD-6964 TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-4323 
        0.07        22.42        10.88        27.09        58.39         1.41 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-CA-6718 TCGA-CA-6719 TCGA-CM-5860 
       61.41         6.77       100.01         0.10         1.35        16.01 
TCGA-CM-5861 TCGA-CM-6164 TCGA-CM-6172 TCGA-D5-5540 TCGA-D5-6535 TCGA-DM-A282 
       15.02        29.03        11.01        13.51        15.12       139.17 
TCGA-DM-A28F TCGA-F4-6570 TCGA-F4-6806 TCGA-F4-6809 TCGA-G4-6304 TCGA-G4-6323 
       35.97         6.18        29.59        13.25        53.62        13.78 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

$`ASXL1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       32.91        30.44        33.53        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 
       34.03        29.00        29.00        26.01         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       23.01        20.98        19.99        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
        6.05         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       47.01        15.02         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F 
        7.96        27.02        13.94        38.04        19.00        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 
        4.21        56.55         0.79         0.72         5.79        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.20        14.50        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       21.44        17.82         5.13        83.80        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-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.26         0.33        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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-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-D5-5541 TCGA-D5-6529 
       12.03        45.40        12.26        19.59        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        43.27        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A285 
      140.38         7.50        44.32       131.51       135.65         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
       81.37       119.93        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 
       13.38        13.45        35.87         1.55        16.31        16.24 
TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       33.67         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        35.80        26.17        91.79 

  ASXL1 MUTATED ASXL1 WILD-TYPE 
           0.07            0.00 
  ASXL1 MUTATED ASXL1 WILD-TYPE 
         139.17          140.38 
  ASXL1 MUTATED ASXL1 WILD-TYPE 
          20.55           20.19 
[1] "0.1 - 139.2 (20.5)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.3"
D49V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ASXL1 MUTATED         7        1        4        13         2         0
  ASXL1 WILD-TYPE      57        0       21        96         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        18         10         37         29       33        12
                 vv
clus              STAGE IVB
  ASXL1 MUTATED           0
  ASXL1 WILD-TYPE         1
D49V3, multiclass
            clus
vv           ASXL1 MUTATED ASXL1 WILD-TYPE
  STAGE I                7              57
  STAGE IA               1               0
  STAGE II               4              21
  STAGE IIA             13              96
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             4              37
  STAGE IIIC             2              29
  STAGE IV               2              33
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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   6  26   5
  ASXL1 WILD-TYPE   8  62 222  36
D49V4, multiclass
    clus
vv   ASXL1 MUTATED ASXL1 WILD-TYPE
  T1             1               8
  T2             6              62
  T3            26             222
  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    28   6   5
  ASXL1 WILD-TYPE 192  74  61
D49V5, multiclass
    clus
vv   ASXL1 MUTATED ASXL1 WILD-TYPE
  N0            28             192
  N1             6              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"
D49V6, binary
                 cls
clus                0   1
  ASXL1 MUTATED    29   3
  ASXL1 WILD-TYPE 254  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASXL1 MUTATED     29    3
  ASXL1 WILD-TYPE  254   45
   clus
vv  ASXL1 MUTATED ASXL1 WILD-TYPE
  0            29             254
  1             3              45
[1] 2 2
[1] FALSE
D49V7, binary
                 cls
clus                0   1
  ASXL1 MUTATED    15  24
  ASXL1 WILD-TYPE 155 173
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASXL1 MUTATED     15   24
  ASXL1 WILD-TYPE  155  173
        clus
vv       ASXL1 MUTATED ASXL1 WILD-TYPE
  FEMALE            15             155
  MALE              24             173
[1] 2 2
[1] FALSE
D49V8, binary
                 cls
clus                0   1
  ASXL1 MUTATED    38   1
  ASXL1 WILD-TYPE 279  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASXL1 MUTATED     38    1
  ASXL1 WILD-TYPE  279   47
                               clus
vv                              ASXL1 MUTATED ASXL1 WILD-TYPE
  COLON ADENOCARCINOMA                     38             279
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ASXL1 MUTATED    25   0   1   4
  ASXL1 WILD-TYPE 232   2  21  17
D49V9, multiclass
    clus
vv   ASXL1 MUTATED ASXL1 WILD-TYPE
  R0            25             232
  R1             0               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"
D49V10, 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    25
  ASXL1 WILD-TYPE                        16   151
D49V11, 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                                       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(50) Variable = HPS3 MUTATION ANALYSIS
D50V1, survival
                sevent
clus2              0   1
  HPS3 MUTATED    16   4
  HPS3 WILD-TYPE 266  69
  HPS3 MUTATED HPS3 WILD-TYPE 
            20            335 
  HPS3 MUTATED HPS3 WILD-TYPE 
             4             69 
$`HPS3 MUTATED`
TCGA-A6-5659 TCGA-AA-3510 TCGA-AA-3660 TCGA-AA-3697 TCGA-AA-3950 TCGA-AA-3977 
       30.44        63.98        78.08        85.05        24.00        25.02 
TCGA-AA-A00N TCGA-AA-A01Q TCGA-AD-6548 TCGA-AD-6895 TCGA-AZ-4315 TCGA-AZ-4682 
        4.01         1.02        21.37         0.72        58.39        22.36 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-CA-5797 TCGA-CK-4950 TCGA-CM-6172 TCGA-G4-6307 
       49.41         6.77         3.29        40.34        11.01        55.04 
TCGA-G4-6321 TCGA-G4-6588 
       22.09        26.17 

$`HPS3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96         0.07         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-5403 
       21.44        17.82         1.41         5.13        83.80        62.79 
TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       61.41        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 
        3.19         1.94         2.24         3.06         3.25         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        51.75        45.11        36.72        36.00 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        91.79        46.75        52.80 

  HPS3 MUTATED HPS3 WILD-TYPE 
          0.72           0.00 
  HPS3 MUTATED HPS3 WILD-TYPE 
         85.05         140.38 
  HPS3 MUTATED HPS3 WILD-TYPE 
         24.51          19.99 
[1] "0.7 - 85.0 (24.5)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1.3"
D50V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HPS3 MUTATED         3        0        4         4         1         0
  HPS3 WILD-TYPE      61        1       21       105         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HPS3 MUTATED           2          1          2          0        0         1
  HPS3 WILD-TYPE        17          9         39         31       35        12
                vv
clus             STAGE IVB
  HPS3 MUTATED           0
  HPS3 WILD-TYPE         1
D50V3, multiclass
            clus
vv           HPS3 MUTATED HPS3 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              4             21
  STAGE IIA             4            105
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             2             17
  STAGE IIIA            1              9
  STAGE IIIB            2             39
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  63 234  40
D50V4, multiclass
    clus
vv   HPS3 MUTATED HPS3 WILD-TYPE
  T1            0              9
  T2            5             63
  T3           14            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
  HPS3 MUTATED    15   5   0
  HPS3 WILD-TYPE 205  75  66
D50V5, multiclass
    clus
vv   HPS3 MUTATED HPS3 WILD-TYPE
  N0           15            205
  N1            5             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"
D50V6, binary
                cls
clus               0   1
  HPS3 MUTATED    14   1
  HPS3 WILD-TYPE 269  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  HPS3 MUTATED     14    1
  HPS3 WILD-TYPE  269   47
   clus
vv  HPS3 MUTATED HPS3 WILD-TYPE
  0           14            269
  1            1             47
[1] 2 2
[1] FALSE
D50V7, 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
D50V8, binary
                cls
clus               0   1
  HPS3 MUTATED    18   2
  HPS3 WILD-TYPE 299  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  HPS3 MUTATED     18    2
  HPS3 WILD-TYPE  299   46
                               clus
vv                              HPS3 MUTATED HPS3 WILD-TYPE
  COLON ADENOCARCINOMA                    18            299
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  HPS3 MUTATED    15   1   0   0
  HPS3 WILD-TYPE 242   1  22  21
D50V9, multiclass
    clus
vv   HPS3 MUTATED HPS3 WILD-TYPE
  R0           15            242
  R1            1              1
  R2            0             22
  RX            0             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V10, 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
D50V11, 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(51) Variable = IDH1 MUTATION ANALYSIS
D51V1, survival
                sevent
clus2              0   1
  IDH1 MUTATED    16   2
  IDH1 WILD-TYPE 266  71
  IDH1 MUTATED IDH1 WILD-TYPE 
            18            337 
  IDH1 MUTATED IDH1 WILD-TYPE 
             2             71 
$`IDH1 MUTATED`
TCGA-AA-3555 TCGA-AA-3947 TCGA-AA-3949 TCGA-AD-5900 TCGA-AD-6889 TCGA-AY-6386 
       29.95        33.01        26.01         0.07        56.55        17.82 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-CA-5796 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-6168 
       49.41        12.10         3.25         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        11.51        20.19        10.13       139.17        13.38 

$`IDH1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        17.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
        2.01        12.99        24.00        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       18.05        40.96        21.37         4.21         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       61.41         6.77       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5797 TCGA-CA-6715 
        3.19         1.94         2.24         3.06         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        2.93       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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       13.51        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  IDH1 MUTATED IDH1 WILD-TYPE 
          0.07           0.00 
  IDH1 MUTATED IDH1 WILD-TYPE 
        139.17         140.38 
  IDH1 MUTATED IDH1 WILD-TYPE 
         15.60          20.98 
[1] "0.1 - 139.2 (15.6)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.9"
D51V2, 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       24       101         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        19          9         37         31       33        13
                vv
clus             STAGE IVB
  IDH1 MUTATED           0
  IDH1 WILD-TYPE         1
D51V3, multiclass
            clus
vv           IDH1 MUTATED IDH1 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             8            101
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            1              9
  STAGE IIIB            4             37
  STAGE IIIC            0             31
  STAGE IV              2             33
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  IDH1 MUTATED     0   1  15   2
  IDH1 WILD-TYPE   9  67 233  39
D51V4, multiclass
    clus
vv   IDH1 MUTATED IDH1 WILD-TYPE
  T1            0              9
  T2            1             67
  T3           15            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
  IDH1 MUTATED    11   7   0
  IDH1 WILD-TYPE 209  73  66
D51V5, multiclass
    clus
vv   IDH1 MUTATED IDH1 WILD-TYPE
  N0           11            209
  N1            7             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"
D51V6, binary
                cls
clus               0   1
  IDH1 MUTATED    14   2
  IDH1 WILD-TYPE 269  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED     14    2
  IDH1 WILD-TYPE  269   46
   clus
vv  IDH1 MUTATED IDH1 WILD-TYPE
  0           14            269
  1            2             46
[1] 2 2
[1] FALSE
D51V7, 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
D51V8, binary
                cls
clus               0   1
  IDH1 MUTATED    12   6
  IDH1 WILD-TYPE 305  42
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED     12    6
  IDH1 WILD-TYPE  305   42
                               clus
vv                              IDH1 MUTATED IDH1 WILD-TYPE
  COLON ADENOCARCINOMA                    12            305
  COLON MUCINOUS ADENOCARCINOMA            6             42
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  IDH1 MUTATED    13   0   0   1
  IDH1 WILD-TYPE 244   2  22  20
D51V9, multiclass
    clus
vv   IDH1 MUTATED IDH1 WILD-TYPE
  R0           13            244
  R1            0              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"
D51V10, 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
D51V11, 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(52) Variable = PIK3R1 MUTATION ANALYSIS
D52V1, survival
                  sevent
clus2                0   1
  PIK3R1 MUTATED    36   7
  PIK3R1 WILD-TYPE 246  66
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
              43              312 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
               7               66 
$`PIK3R1 MUTATED`
TCGA-A6-5656 TCGA-A6-5660 TCGA-A6-5665 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3511 
       32.91        29.19        22.06        20.12        19.66         6.97 
TCGA-AA-3552 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3697 TCGA-AA-3833 TCGA-AA-A010 
       13.02         6.05        54.02        85.05        15.95        34.98 
TCGA-AD-6895 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-5543 TCGA-AZ-4315 TCGA-AZ-6608 
        0.72        14.50        27.09        15.75        58.39         1.94 
TCGA-CA-5255 TCGA-CA-6717 TCGA-CK-4950 TCGA-CK-5914 TCGA-CK-5916 TCGA-CM-4752 
        3.06         0.33        40.34        21.99        21.14        13.02 
TCGA-CM-5862 TCGA-CM-6161 TCGA-CM-6164 TCGA-CM-6167 TCGA-CM-6171 TCGA-CM-6674 
        5.03        15.02        29.03        14.99        14.04        12.95 
TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6922 TCGA-D5-6927 TCGA-DM-A0XD TCGA-DM-A1D9 
       11.51        18.25        10.13         9.44        24.43       140.38 
TCGA-DM-A1DB TCGA-DM-A1HB TCGA-F4-6460 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 
       44.32       135.65        13.38        55.04        51.75        36.72 
TCGA-G4-6626 
       46.75 

$`PIK3R1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       31.63        30.44        33.53        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 
       21.76        24.69        24.39        23.87        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 
        3.02         1.02        35.01        63.98         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       21.01        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       19.99        13.94        19.99        61.02        78.08         6.97 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 
        0.99        25.02         1.02        17.98        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        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        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21        56.55         0.79         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 
       27.42        10.88         0.20        16.31         0.95         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5796 
       29.56         5.23        11.74         3.19         2.24         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-6747 TCGA-CK-6748 
      102.44        15.62        49.08        51.32         2.93         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-5863 
       22.03        22.98        30.08        16.01        15.02        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 
       15.02        17.03        12.00        14.04        16.04        21.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 
       12.99        13.02        15.02        11.01        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       19.59        13.51        20.19         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 
        7.53        12.39        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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
        7.50       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 
       35.97        60.79       117.07        98.24         8.61        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6310 TCGA-G4-6317 
       74.56        65.85        53.62        44.68        45.11        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       22.09        13.78        35.80        26.17        91.79        52.80 

  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
            0.33             0.00 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
          140.38           139.17 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
           19.66            20.63 
[1] "0.3 - 140.4 (19.7)" "0.0 - 139.2 (20.6)"
[1] "hr=" "1.4"
D52V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PIK3R1 MUTATED         5        0        2        17         1         0
  PIK3R1 WILD-TYPE      59        1       23        92         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PIK3R1 MUTATED           1          3          6          4        2
  PIK3R1 WILD-TYPE        18          7         35         27       33
                  vv
clus               STAGE IVA STAGE IVB
  PIK3R1 MUTATED           2         0
  PIK3R1 WILD-TYPE        11         1
D52V3, multiclass
            clus
vv           PIK3R1 MUTATED PIK3R1 WILD-TYPE
  STAGE I                 5               59
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA              17               92
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              3                7
  STAGE IIIB              6               35
  STAGE IIIC              4               27
  STAGE IV                2               33
  STAGE IVA               2               11
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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   5  34   4
  PIK3R1 WILD-TYPE   8  63 214  37
D52V4, multiclass
    clus
vv   PIK3R1 MUTATED PIK3R1 WILD-TYPE
  T1              1                8
  T2              5               63
  T3             34              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
  PIK3R1 MUTATED    26  14   4
  PIK3R1 WILD-TYPE 194  66  62
D52V5, multiclass
    clus
vv   PIK3R1 MUTATED PIK3R1 WILD-TYPE
  N0             26              194
  N1             14               66
  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"
D52V6, binary
                  cls
clus                 0   1
  PIK3R1 MUTATED    36   4
  PIK3R1 WILD-TYPE 247  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R1 MUTATED     36    4
  PIK3R1 WILD-TYPE  247   44
   clus
vv  PIK3R1 MUTATED PIK3R1 WILD-TYPE
  0             36              247
  1              4               44
[1] 2 2
[1] FALSE
D52V7, binary
                  cls
clus                 0   1
  PIK3R1 MUTATED    20  24
  PIK3R1 WILD-TYPE 150 173
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R1 MUTATED     20   24
  PIK3R1 WILD-TYPE  150  173
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  FEMALE             20              150
  MALE               24              173
[1] 2 2
[1] FALSE
D52V8, binary
                  cls
clus                 0   1
  PIK3R1 MUTATED    41   3
  PIK3R1 WILD-TYPE 276  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R1 MUTATED     41    3
  PIK3R1 WILD-TYPE  276   45
                               clus
vv                              PIK3R1 MUTATED PIK3R1 WILD-TYPE
  COLON ADENOCARCINOMA                      41              276
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PIK3R1 MUTATED    29   1   1   4
  PIK3R1 WILD-TYPE 228   1  21  17
D52V9, multiclass
    clus
vv   PIK3R1 MUTATED PIK3R1 WILD-TYPE
  R0             29              228
  R1              1                1
  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"
D52V10, 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    28
  PIK3R1 WILD-TYPE                        13   148
D52V11, 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                                        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(53) Variable = TCF7L2 MUTATION ANALYSIS
D53V1, survival
                  sevent
clus2                0   1
  TCF7L2 MUTATED    24   3
  TCF7L2 WILD-TYPE 258  70
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
              27              328 
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
               3               70 
$`TCF7L2 MUTATED`
TCGA-A6-6137 TCGA-A6-6781 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3955 
       27.09        19.66         6.97         0.92        50.04        20.98 
TCGA-AA-3977 TCGA-AA-A00K TCGA-AA-A010 TCGA-AA-A01I TCGA-AA-A01T TCGA-AU-6004 
       25.02        18.05        34.98        31.00        33.04        27.09 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-5403 TCGA-AZ-6601 TCGA-CK-4947 TCGA-CK-4950 
       21.44        58.39        62.79       100.01        17.56        40.34 
TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-6165 TCGA-CM-6171 TCGA-CM-6678 TCGA-D5-6922 
       30.08        15.02        16.04        14.04        11.01        10.13 
TCGA-DM-A282 TCGA-DM-A28F TCGA-F4-6855 
      139.17        35.97        35.41 

$`TCF7L2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        32.71        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-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-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01        24.00         2.01        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K 
       21.99        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X 
       38.07         1.02        35.01         1.02        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        15.75         0.20        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13        83.80        22.36        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 
        0.33         0.10         1.35       102.44        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01         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-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-6679 TCGA-CM-6680 TCGA-D5-5537 
       13.05        11.08        11.08        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 
       12.49        16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       135.65         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
      119.93        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 
       16.24        33.67        13.25         0.53        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
            0.92             0.00 
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
          139.17           140.38 
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
           27.09            19.99 
[1] "0.9 - 139.2 (27.1)" "0.0 - 140.4 (20.0)"
[1] "hr=" "2.4"
D53V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TCF7L2 MUTATED         4        0        5         9         1         0
  TCF7L2 WILD-TYPE      60        1       20       100         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TCF7L2 MUTATED           2          2          3          1        1
  TCF7L2 WILD-TYPE        17          8         38         30       34
                  vv
clus               STAGE IVA STAGE IVB
  TCF7L2 MUTATED           2         0
  TCF7L2 WILD-TYPE        11         1
D53V3, multiclass
            clus
vv           TCF7L2 MUTATED TCF7L2 WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                5               20
  STAGE IIA               9              100
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               2               17
  STAGE IIIA              2                8
  STAGE IIIB              3               38
  STAGE IIIC              1               30
  STAGE IV                1               34
  STAGE IVA               2               11
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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   6  20   5
  TCF7L2 WILD-TYPE   9  62 228  36
D53V4, multiclass
    clus
vv   TCF7L2 MUTATED TCF7L2 WILD-TYPE
  T1              0                9
  T2              6               62
  T3             20              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
  TCF7L2 MUTATED    20   9   2
  TCF7L2 WILD-TYPE 200  71  64
D53V5, multiclass
    clus
vv   TCF7L2 MUTATED TCF7L2 WILD-TYPE
  N0             20              200
  N1              9               71
  N2              2               64
[1] 3 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
  TCF7L2 MUTATED    24   2
  TCF7L2 WILD-TYPE 259  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCF7L2 MUTATED     24    2
  TCF7L2 WILD-TYPE  259   46
   clus
vv  TCF7L2 MUTATED TCF7L2 WILD-TYPE
  0             24              259
  1              2               46
[1] 2 2
[1] FALSE
D53V7, binary
                  cls
clus                 0   1
  TCF7L2 MUTATED    16  15
  TCF7L2 WILD-TYPE 154 182
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCF7L2 MUTATED     16   15
  TCF7L2 WILD-TYPE  154  182
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  FEMALE             16              154
  MALE               15              182
[1] 2 2
[1] FALSE
D53V8, binary
                  cls
clus                 0   1
  TCF7L2 MUTATED    30   1
  TCF7L2 WILD-TYPE 287  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCF7L2 MUTATED     30    1
  TCF7L2 WILD-TYPE  287   47
                               clus
vv                              TCF7L2 MUTATED TCF7L2 WILD-TYPE
  COLON ADENOCARCINOMA                      30              287
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TCF7L2 MUTATED    21   1   1   2
  TCF7L2 WILD-TYPE 236   1  21  19
D53V9, multiclass
    clus
vv   TCF7L2 MUTATED TCF7L2 WILD-TYPE
  R0             21              236
  R1              1                1
  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"
D53V10, 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                           1    18
  TCF7L2 WILD-TYPE                        18   158
D53V11, multiclass
                                  clus
vv                                 TCF7L2 MUTATED TCF7L2 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(54) Variable = NLRC4 MUTATION ANALYSIS
D54V1, survival
                 sevent
clus2               0   1
  NLRC4 MUTATED    20   4
  NLRC4 WILD-TYPE 262  69
  NLRC4 MUTATED NLRC4 WILD-TYPE 
             24             331 
  NLRC4 MUTATED NLRC4 WILD-TYPE 
              4              69 
$`NLRC4 MUTATED`
TCGA-A6-6141 TCGA-A6-6781 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3966 
        8.38        19.66        85.05        19.04        19.04         2.01 
TCGA-AA-3977 TCGA-AA-A010 TCGA-AD-6895 TCGA-AD-6901 TCGA-AU-3779 TCGA-AY-6196 
       25.02        34.98         0.72        22.42        14.50         0.20 
TCGA-CA-5796 TCGA-CA-6717 TCGA-CK-5916 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5349 
        3.25         0.33        21.14        13.02        22.03        30.08 
TCGA-D5-6536 TCGA-D5-6928 TCGA-DM-A1DA TCGA-G4-6293 TCGA-G4-6317 TCGA-G4-6588 
       17.85        11.64         7.50       107.67        36.00        26.17 

$`NLRC4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
        5.03        26.99        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       26.01        24.00         2.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
       56.55         0.79         5.79        27.42        10.88         0.20 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        15.75        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 
       33.67        13.25         0.53        35.41        19.43        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.72        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 
       52.80 

  NLRC4 MUTATED NLRC4 WILD-TYPE 
            0.2             0.0 
  NLRC4 MUTATED NLRC4 WILD-TYPE 
         107.67          140.38 
  NLRC4 MUTATED NLRC4 WILD-TYPE 
          19.04           20.98 
[1] "0.2 - 107.7 (19.0)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.1"
D54V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NLRC4 MUTATED         1        0        1        10         1         0
  NLRC4 WILD-TYPE      63        1       24        99         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NLRC4 MUTATED           2          0          1          4        1         0
  NLRC4 WILD-TYPE        17         10         40         27       34        13
                 vv
clus              STAGE IVB
  NLRC4 MUTATED           0
  NLRC4 WILD-TYPE         1
D54V3, multiclass
            clus
vv           NLRC4 MUTATED NLRC4 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA             10              99
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             4              27
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NLRC4 MUTATED     1   1  20   2
  NLRC4 WILD-TYPE   8  67 228  39
D54V4, multiclass
    clus
vv   NLRC4 MUTATED NLRC4 WILD-TYPE
  T1             1               8
  T2             1              67
  T3            20             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
  NLRC4 MUTATED    17   4   3
  NLRC4 WILD-TYPE 203  76  63
D54V5, multiclass
    clus
vv   NLRC4 MUTATED NLRC4 WILD-TYPE
  N0            17             203
  N1             4              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"
D54V6, binary
                 cls
clus                0   1
  NLRC4 MUTATED    17   1
  NLRC4 WILD-TYPE 266  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRC4 MUTATED     17    1
  NLRC4 WILD-TYPE  266   47
   clus
vv  NLRC4 MUTATED NLRC4 WILD-TYPE
  0            17             266
  1             1              47
[1] 2 2
[1] FALSE
D54V7, 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
D54V8, binary
                 cls
clus                0   1
  NLRC4 MUTATED    18   6
  NLRC4 WILD-TYPE 299  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRC4 MUTATED     18    6
  NLRC4 WILD-TYPE  299   42
                               clus
vv                              NLRC4 MUTATED NLRC4 WILD-TYPE
  COLON ADENOCARCINOMA                     18             299
  COLON MUCINOUS ADENOCARCINOMA             6              42
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  NLRC4 MUTATED    15   0   1   2
  NLRC4 WILD-TYPE 242   2  21  19
D54V9, multiclass
    clus
vv   NLRC4 MUTATED NLRC4 WILD-TYPE
  R0            15             242
  R1             0               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"
D54V10, 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
D54V11, 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(55) Variable = DDX26B MUTATION ANALYSIS
D55V1, survival
                  sevent
clus2                0   1
  DDX26B MUTATED    12   2
  DDX26B WILD-TYPE 270  71
  DDX26B MUTATED DDX26B WILD-TYPE 
              14              341 
  DDX26B MUTATED DDX26B WILD-TYPE 
               2               71 
$`DDX26B MUTATED`
TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-3713 TCGA-AA-3950 TCGA-AU-6004 
       33.53        22.06        20.12        19.04        24.00        27.09 
TCGA-CA-6717 TCGA-CK-5913 TCGA-CK-5916 TCGA-CM-6162 TCGA-CM-6674 TCGA-D5-6536 
        0.33        51.32        21.14        12.00        12.95        17.85 
TCGA-F4-6570 TCGA-G4-6586 
        6.18        35.80 

$`DDX26B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 
       24.16        21.76        24.69        24.39        23.87        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
       17.56       102.44        40.34        15.62        49.08        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        15.12         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-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        13.38        13.45        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        26.17        91.79        46.75        52.80 

  DDX26B MUTATED DDX26B WILD-TYPE 
            0.33             0.00 
  DDX26B MUTATED DDX26B WILD-TYPE 
           51.32           140.38 
  DDX26B MUTATED DDX26B WILD-TYPE 
           20.63            20.19 
[1] "0.3 - 51.3 (20.6)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
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       25        99         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DDX26B MUTATED           0          0          1          0        1
  DDX26B WILD-TYPE        19         10         40         31       34
                  vv
clus               STAGE IVA STAGE IVB
  DDX26B MUTATED           0         0
  DDX26B WILD-TYPE        13         1
D55V3, multiclass
            clus
vv           DDX26B MUTATED DDX26B WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA              10               99
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  DDX26B MUTATED     1   1  12   1
  DDX26B WILD-TYPE   8  67 236  40
D55V4, multiclass
    clus
vv   DDX26B MUTATED DDX26B WILD-TYPE
  T1              1                8
  T2              1               67
  T3             12              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
  DDX26B MUTATED    14   1   0
  DDX26B WILD-TYPE 206  79  66
D55V5, multiclass
    clus
vv   DDX26B MUTATED DDX26B WILD-TYPE
  N0             14              206
  N1              1               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"
D55V6, binary
                  cls
clus                 0   1
  DDX26B MUTATED    11   1
  DDX26B WILD-TYPE 272  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DDX26B MUTATED     11    1
  DDX26B WILD-TYPE  272   47
   clus
vv  DDX26B MUTATED DDX26B WILD-TYPE
  0             11              272
  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    11   4
  DDX26B WILD-TYPE 306  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DDX26B MUTATED     11    4
  DDX26B WILD-TYPE  306   44
                               clus
vv                              DDX26B MUTATED DDX26B WILD-TYPE
  COLON ADENOCARCINOMA                      11              306
  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 248   2  21  17
D55V9, multiclass
    clus
vv   DDX26B MUTATED DDX26B WILD-TYPE
  R0              9              248
  R1              0                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"
D55V10, 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
D55V11, 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 = FYN MUTATION ANALYSIS
D56V1, survival
               sevent
clus2             0   1
  FYN MUTATED    12   2
  FYN WILD-TYPE 270  71
  FYN MUTATED FYN WILD-TYPE 
           14           341 
  FYN MUTATED FYN WILD-TYPE 
            2            71 
$`FYN MUTATED`
TCGA-A6-2671 TCGA-A6-5666 TCGA-A6-6141 TCGA-A6-6653 TCGA-AA-3713 TCGA-AA-3815 
       43.76        32.71         8.38        24.39        19.04        33.04 
TCGA-AA-3994 TCGA-AA-A010 TCGA-AA-A01P TCGA-AZ-4315 TCGA-CM-5341 TCGA-CM-6162 
       27.02        34.98        38.07        58.39        29.06        12.00 
TCGA-G4-6293 TCGA-G4-6323 
      107.67        13.78 

$`FYN WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       22.06        27.09        22.52        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       21.76        24.69        23.87        20.12        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        7.04         3.02         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       26.99        19.04        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 
       24.00        27.02        27.02        19.07         7.96        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       13.02        22.03        22.98        30.08        16.01        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.41        19.43        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  FYN MUTATED FYN WILD-TYPE 
         8.38          0.00 
  FYN MUTATED FYN WILD-TYPE 
       107.67        140.38 
  FYN MUTATED FYN WILD-TYPE 
       30.885        19.990 
[1] "8.4 - 107.7 (30.9)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.9"
D56V2, 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       25       105         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        17          9         39         31       33        13
               vv
clus            STAGE IVB
  FYN MUTATED           0
  FYN WILD-TYPE         1
D56V3, multiclass
            clus
vv           FYN MUTATED FYN WILD-TYPE
  STAGE I              1            63
  STAGE IA             1             0
  STAGE II             0            25
  STAGE IIA            4           105
  STAGE IIB            1             7
  STAGE IIC            1             0
  STAGE III            2            17
  STAGE IIIA           1             9
  STAGE IIIB           2            39
  STAGE IIIC           0            31
  STAGE IV             2            33
  STAGE IVA            0            13
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  FYN MUTATED     0   2  10   2
  FYN WILD-TYPE   9  66 238  39
D56V4, multiclass
    clus
vv   FYN MUTATED FYN WILD-TYPE
  T1           0             9
  T2           2            66
  T3          10           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
  FYN MUTATED     9   5   1
  FYN WILD-TYPE 211  75  65
D56V5, multiclass
    clus
vv   FYN MUTATED FYN WILD-TYPE
  N0           9           211
  N1           5            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"
D56V6, binary
               cls
clus              0   1
  FYN MUTATED    12   2
  FYN WILD-TYPE 271  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  FYN MUTATED     12    2
  FYN WILD-TYPE  271   46
   clus
vv  FYN MUTATED FYN WILD-TYPE
  0          12           271
  1           2            46
[1] 2 2
[1] FALSE
D56V7, 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
D56V8, binary
               cls
clus              0   1
  FYN MUTATED    13   2
  FYN WILD-TYPE 304  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  FYN MUTATED     13    2
  FYN WILD-TYPE  304   46
                               clus
vv                              FYN MUTATED FYN WILD-TYPE
  COLON ADENOCARCINOMA                   13           304
  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 246   2  21  21
D56V9, multiclass
    clus
vv   FYN MUTATED FYN WILD-TYPE
  R0          11           246
  R1           0             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"
D56V10, 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
D56V11, 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(57) Variable = ATP6V1B1 MUTATION ANALYSIS
D57V1, survival
                    sevent
clus2                  0   1
  ATP6V1B1 MUTATED    12   1
  ATP6V1B1 WILD-TYPE 270  72
  ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE 
                13                342 
  ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE 
                 1                 72 
$`ATP6V1B1 MUTATED`
TCGA-A6-3809 TCGA-A6-6781 TCGA-AA-3664 TCGA-AA-3713 TCGA-AA-3877 TCGA-AA-3950 
       32.75        19.66        54.02        19.04        31.00        24.00 
TCGA-AA-3966 TCGA-AD-5900 TCGA-AD-6548 TCGA-CA-6716 TCGA-CK-5916 TCGA-CM-5861 
        2.01         0.07        21.37         0.26        21.14        15.02 
TCGA-G4-6309 
       51.75 

$`ATP6V1B1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       26.01         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6888 TCGA-AD-6889 
       41.00        39.98        18.05        40.96         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        51.32        21.99         2.93         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        16.01         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE 
              0.07               0.00 
  ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE 
             54.02             140.38 
  ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE 
            21.140             20.155 
[1] "0.1 - 54.0 (21.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2.5"
D57V2, 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       24       104         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP6V1B1 MUTATED           0          0          1          1        1
  ATP6V1B1 WILD-TYPE        19         10         40         30       34
                    vv
clus                 STAGE IVA STAGE IVB
  ATP6V1B1 MUTATED           0         0
  ATP6V1B1 WILD-TYPE        13         1
D57V3, multiclass
            clus
vv           ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE
  STAGE I                   4                 60
  STAGE IA                  0                  1
  STAGE II                  1                 24
  STAGE IIA                 5                104
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                0                 10
  STAGE IIIB                1                 40
  STAGE IIIC                1                 30
  STAGE IV                  1                 34
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  ATP6V1B1 MUTATED     2   2   8   2
  ATP6V1B1 WILD-TYPE   7  66 240  39
D57V4, multiclass
    clus
vv   ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE
  T1                2                  7
  T2                2                 66
  T3                8                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
  ATP6V1B1 MUTATED    12   2   0
  ATP6V1B1 WILD-TYPE 208  78  66
D57V5, multiclass
    clus
vv   ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE
  N0               12                208
  N1                2                 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"
D57V6, binary
                    cls
clus                   0   1
  ATP6V1B1 MUTATED    11   1
  ATP6V1B1 WILD-TYPE 272  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ATP6V1B1 MUTATED     11    1
  ATP6V1B1 WILD-TYPE  272   47
   clus
vv  ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE
  0               11                272
  1                1                 47
[1] 2 2
[1] FALSE
D57V7, 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
D57V8, binary
                    cls
clus                   0   1
  ATP6V1B1 MUTATED     8   6
  ATP6V1B1 WILD-TYPE 309  42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ATP6V1B1 MUTATED      8    6
  ATP6V1B1 WILD-TYPE  309   42
                               clus
vv                              ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE
  COLON ADENOCARCINOMA                         8                309
  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 247   2  21  19
D57V9, multiclass
    clus
vv   ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE
  R0               10                247
  R1                0                  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"
D57V10, 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
D57V11, 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(58) Variable = NF1 MUTATION ANALYSIS
D58V1, survival
               sevent
clus2             0   1
  NF1 MUTATED    68  19
  NF1 WILD-TYPE 214  54
  NF1 MUTATED NF1 WILD-TYPE 
           87           268 
  NF1 MUTATED NF1 WILD-TYPE 
           19            54 
$`NF1 MUTATED`
TCGA-A6-2671 TCGA-A6-3809 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5665 
       43.76        32.75        31.63        33.53        23.61        22.06 
TCGA-A6-5666 TCGA-A6-6142 TCGA-A6-6652 TCGA-A6-6781 TCGA-AA-3496 TCGA-AA-3555 
       32.71        25.08        24.69        19.66         1.02        29.95 
TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3950 TCGA-AA-3956 
       61.02         6.05        85.05        19.04        24.00        34.03 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6890 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        4.01        34.98         0.79         0.20        14.50        27.09 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4616 TCGA-AZ-5407 
       15.75        21.44        17.82        58.39         5.13        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6607 
       49.41         6.77        12.10       100.01         5.23         3.19 
TCGA-CA-5255 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4952 TCGA-CK-5912 
        3.06         0.07         0.33         1.35        15.62        49.08 
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-A285 TCGA-DM-A28H 
       13.32         7.50        44.32       135.65         6.12       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6807 
       98.24         8.61        13.38         6.18         1.55        16.24 
TCGA-G4-6293 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
      107.67        44.68        55.04        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 
       35.80        91.79        52.80 

$`NF1 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5659 
       34.65        33.34        36.53        14.53        32.91        30.44 
TCGA-A6-5660 TCGA-A6-5664 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6648 
       29.19        22.09        27.09        22.52         8.38        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 
       24.16        21.76        24.39        23.87        20.12        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        7.04         3.02        35.01        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 
       33.99        21.01        13.02        24.00        17.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3663 
       20.98        19.99        13.94        19.99        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.03        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01         2.01        20.98         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.72         5.79        22.42        27.42        10.88 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AZ-4323 TCGA-AZ-4681 TCGA-AZ-4682 
       16.31         0.95         0.20         1.41        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5796 
       62.79        29.56        11.74         1.94         2.24         3.25 
TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        3.29         0.26         0.10        17.56       102.44        40.34 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 
       21.99        21.14         2.93         2.01        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5860 TCGA-CM-5863 
       25.02        13.02        29.06        22.03        16.01        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 
       15.02        17.03        15.02        12.00        16.04        21.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       12.99        13.02        15.02        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 
       11.01        10.06        12.03        45.40        12.26        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6541 
       11.51        20.19        18.25         1.32        43.27        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 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-D5-7000 TCGA-DM-A0X9 
        9.44        11.64         1.51        12.00        10.26       119.70 
TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1HA 
       38.20        92.75        49.91        12.59       140.38       131.51 
TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-F4-6569 
      139.17        81.37       119.93        35.97        60.79        13.45 
TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       35.87        16.31        29.59        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6309 
       35.41        19.43        74.56        65.85        53.62        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6588 TCGA-G4-6626 
       45.11        36.72        26.17        46.75 

  NF1 MUTATED NF1 WILD-TYPE 
         0.07          0.00 
  NF1 MUTATED NF1 WILD-TYPE 
       135.65        140.38 
  NF1 MUTATED NF1 WILD-TYPE 
        19.59         20.63 
[1] "0.1 - 135.7 (19.6)" "0.0 - 140.4 (20.6)"
[1] "hr=" "1.1"
D58V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NF1 MUTATED         9        1        4        29         3         1
  NF1 WILD-TYPE      55        0       21        80         5         0
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NF1 MUTATED           4          2         13          7        8         5
  NF1 WILD-TYPE        15          8         28         24       27         8
               vv
clus            STAGE IVB
  NF1 MUTATED           0
  NF1 WILD-TYPE         1
D58V3, multiclass
            clus
vv           NF1 MUTATED NF1 WILD-TYPE
  STAGE I              9            55
  STAGE IA             1             0
  STAGE II             4            21
  STAGE IIA           29            80
  STAGE IIB            3             5
  STAGE IIC            1             0
  STAGE III            4            15
  STAGE IIIA           2             8
  STAGE IIIB          13            28
  STAGE IIIC           7            24
  STAGE IV             8            27
  STAGE IVA            5             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
  NF1 MUTATED     3   9  64  11
  NF1 WILD-TYPE   6  59 184  30
D58V4, multiclass
    clus
vv   NF1 MUTATED NF1 WILD-TYPE
  T1           3             6
  T2           9            59
  T3          64           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    52  20  16
  NF1 WILD-TYPE 168  60  50
D58V5, multiclass
    clus
vv   NF1 MUTATED NF1 WILD-TYPE
  N0          52           168
  N1          20            60
  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"
D58V6, binary
               cls
clus              0   1
  NF1 MUTATED    60  13
  NF1 WILD-TYPE 223  35
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED     60   13
  NF1 WILD-TYPE  223   35
   clus
vv  NF1 MUTATED NF1 WILD-TYPE
  0          60           223
  1          13            35
[1] 2 2
[1] FALSE
D58V7, binary
               cls
clus              0   1
  NF1 MUTATED    43  45
  NF1 WILD-TYPE 127 152
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED     43   45
  NF1 WILD-TYPE  127  152
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  FEMALE          43           127
  MALE            45           152
[1] 2 2
[1] FALSE
D58V8, binary
               cls
clus              0   1
  NF1 MUTATED    75  13
  NF1 WILD-TYPE 242  35
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED     75   13
  NF1 WILD-TYPE  242   35
                               clus
vv                              NF1 MUTATED NF1 WILD-TYPE
  COLON ADENOCARCINOMA                   75           242
  COLON MUCINOUS ADENOCARCINOMA          13            35
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  NF1 MUTATED    54   0   2   9
  NF1 WILD-TYPE 203   2  20  12
D58V9, multiclass
    clus
vv   NF1 MUTATED NF1 WILD-TYPE
  R0          54           203
  R1           0             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"
D58V10, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NF1 MUTATED                                  1     4
  NF1 WILD-TYPE                                0     6
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  NF1 MUTATED                           8    64
  NF1 WILD-TYPE                        11   112
D58V11, multiclass
                                  clus
vv                                 NF1 MUTATED NF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           1             0
  ASIAN                                      4             6
  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(59) Variable = ROS1 MUTATION ANALYSIS
D59V1, survival
                sevent
clus2              0   1
  ROS1 MUTATED    37   7
  ROS1 WILD-TYPE 245  66
  ROS1 MUTATED ROS1 WILD-TYPE 
            44            311 
  ROS1 MUTATED ROS1 WILD-TYPE 
             7             66 
$`ROS1 MUTATED`
TCGA-A6-5657 TCGA-A6-6781 TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3662 
       31.63        19.66         1.02        63.98        29.95         6.05 
TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3821 TCGA-AA-3864 TCGA-AA-3875 TCGA-AA-3950 
        6.97         0.92         1.02        53.00        18.05        24.00 
TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6895 TCGA-AD-6964 TCGA-AD-6965 
       25.02         4.01        34.98         0.72        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-6196 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-AZ-6598 
       14.50        27.09         0.20        58.39        61.41        49.41 
TCGA-AZ-6600 TCGA-AZ-6607 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4952 TCGA-CK-5916 
       12.10         3.19         0.33         0.10        15.62        21.14 
TCGA-CM-4743 TCGA-CM-5344 TCGA-CM-6165 TCGA-CM-6171 TCGA-D5-6533 TCGA-D5-6535 
       23.05        22.03        16.04        14.04         1.32        15.12 
TCGA-D5-6538 TCGA-D5-6541 TCGA-F4-6570 TCGA-F4-6856 TCGA-G4-6317 TCGA-G4-6321 
       17.13        15.58         6.18        19.43        36.00        22.09 
TCGA-G4-6586 TCGA-G4-6588 
       35.80        26.17 

$`ROS1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3511 
       20.12        20.28         7.04         3.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
       78.08        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 
       35.05        33.04         0.99        25.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AY-4070 TCGA-AY-4071 
        0.79         5.79        22.42        27.42        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       15.75        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       22.36        62.79         6.77       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07         0.26         1.35        17.56       102.44        40.34 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32        21.99         2.93         2.01       124.27 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 
       20.02        37.02        25.02        13.02        29.06        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        16.01        15.02         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-6172 TCGA-CM-6674 
       14.99        12.99        13.02        15.02        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 
       18.25        43.27        17.85         4.80        12.49        16.14 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 
       33.67        13.25         0.53        35.41       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       36.72        13.78        91.79        46.75        52.80 

  ROS1 MUTATED ROS1 WILD-TYPE 
           0.1            0.0 
  ROS1 MUTATED ROS1 WILD-TYPE 
         63.98         140.38 
  ROS1 MUTATED ROS1 WILD-TYPE 
        16.585         21.010 
[1] "0.1 - 64.0 (16.6)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1"  
D59V2, 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       19        96         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ROS1 MUTATED           4          0          5          3        3         0
  ROS1 WILD-TYPE        15         10         36         28       32        13
                vv
clus             STAGE IVB
  ROS1 MUTATED           0
  ROS1 WILD-TYPE         1
D59V3, multiclass
            clus
vv           ROS1 MUTATED ROS1 WILD-TYPE
  STAGE I               7             57
  STAGE IA              0              1
  STAGE II              6             19
  STAGE IIA            13             96
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             4             15
  STAGE IIIA            0             10
  STAGE IIIB            5             36
  STAGE IIIC            3             28
  STAGE IV              3             32
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ROS1 MUTATED     3   6  27  11
  ROS1 WILD-TYPE   6  62 221  30
D59V4, multiclass
    clus
vv   ROS1 MUTATED ROS1 WILD-TYPE
  T1            3              6
  T2            6             62
  T3           27            221
  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  72  57
D59V5, multiclass
    clus
vv   ROS1 MUTATED ROS1 WILD-TYPE
  N0           30            190
  N1            8             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"
D59V6, binary
                cls
clus               0   1
  ROS1 MUTATED    34   3
  ROS1 WILD-TYPE 249  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  ROS1 MUTATED     34    3
  ROS1 WILD-TYPE  249   45
   clus
vv  ROS1 MUTATED ROS1 WILD-TYPE
  0           34            249
  1            3             45
[1] 2 2
[1] FALSE
D59V7, 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
D59V8, binary
                cls
clus               0   1
  ROS1 MUTATED    38   9
  ROS1 WILD-TYPE 279  39
[1] "tbl2"
                cls
clus             [,1] [,2]
  ROS1 MUTATED     38    9
  ROS1 WILD-TYPE  279   39
                               clus
vv                              ROS1 MUTATED ROS1 WILD-TYPE
  COLON ADENOCARCINOMA                    38            279
  COLON MUCINOUS ADENOCARCINOMA            9             39
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ROS1 MUTATED    33   0   1   5
  ROS1 WILD-TYPE 224   2  21  16
D59V9, multiclass
    clus
vv   ROS1 MUTATED ROS1 WILD-TYPE
  R0           33            224
  R1            0              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"
D59V10, 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
D59V11, 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(60) Variable = KCNK1 MUTATION ANALYSIS
D60V1, survival
                 sevent
clus2               0   1
  KCNK1 MUTATED     8   2
  KCNK1 WILD-TYPE 274  71
  KCNK1 MUTATED KCNK1 WILD-TYPE 
             10             345 
  KCNK1 MUTATED KCNK1 WILD-TYPE 
              2              71 
$`KCNK1 MUTATED`
TCGA-A6-5661 TCGA-AA-3845 TCGA-AD-6964 TCGA-CM-4747 TCGA-CM-5344 TCGA-CM-5864 
       33.53         0.00        10.88        25.02        22.03        15.02 
TCGA-CM-6163 TCGA-CM-6679 TCGA-G4-6315 TCGA-G4-6588 
       14.04        10.06        36.72        26.17 

$`KCNK1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
       17.98        15.95        38.99        37.02        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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        16.01        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       51.75        45.11        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  KCNK1 MUTATED KCNK1 WILD-TYPE 
              0               0 
  KCNK1 MUTATED KCNK1 WILD-TYPE 
          36.72          140.38 
  KCNK1 MUTATED KCNK1 WILD-TYPE 
         18.525          20.190 
[1] "0.0 - 36.7 (18.5)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.3"
D60V2, 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       25       105         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        19         10         40         31       34        12
                 vv
clus              STAGE IVB
  KCNK1 MUTATED           0
  KCNK1 WILD-TYPE         1
D60V3, multiclass
            clus
vv           KCNK1 MUTATED KCNK1 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              4             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 242  39
D60V4, multiclass
    clus
vv   KCNK1 MUTATED KCNK1 WILD-TYPE
  T1             1               8
  T2             1              67
  T3             6             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
  KCNK1 MUTATED     6   3   1
  KCNK1 WILD-TYPE 214  77  65
D60V5, multiclass
    clus
vv   KCNK1 MUTATED KCNK1 WILD-TYPE
  N0             6             214
  N1             3              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"
D60V6, binary
                 cls
clus                0   1
  KCNK1 MUTATED     7   2
  KCNK1 WILD-TYPE 276  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNK1 MUTATED      7    2
  KCNK1 WILD-TYPE  276   46
   clus
vv  KCNK1 MUTATED KCNK1 WILD-TYPE
  0             7             276
  1             2              46
[1] 2 2
[1] FALSE
D60V7, 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
D60V8, binary
                 cls
clus                0   1
  KCNK1 MUTATED    10   0
  KCNK1 WILD-TYPE 307  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNK1 MUTATED     10    0
  KCNK1 WILD-TYPE  307   48
                               clus
vv                              KCNK1 MUTATED KCNK1 WILD-TYPE
  COLON ADENOCARCINOMA                     10             307
  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 248   2  22  21
D60V9, multiclass
    clus
vv   KCNK1 MUTATED KCNK1 WILD-TYPE
  R0             9             248
  R1             0               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"
D60V10, 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
D60V11, 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(61) Variable = MPHOSPH10 MUTATION ANALYSIS
D61V1, survival
                     sevent
clus2                   0   1
  MPHOSPH10 MUTATED    13   4
  MPHOSPH10 WILD-TYPE 269  69
  MPHOSPH10 MUTATED MPHOSPH10 WILD-TYPE 
                 17                 338 
  MPHOSPH10 MUTATED MPHOSPH10 WILD-TYPE 
                  4                  69 
$`MPHOSPH10 MUTATED`
TCGA-A6-6651 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-A00K TCGA-AD-6895 TCGA-AD-6901 
       21.76        20.12        19.66        18.05         0.72        22.42 
TCGA-AD-6964 TCGA-AU-6004 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6718 
       10.88        27.09        21.44        58.39        49.41         0.10 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-5344 TCGA-D5-6927 TCGA-DM-A285 
      124.27        23.05        22.03         9.44         6.12 

$`MPHOSPH10 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        24.16        24.69        24.39        23.87 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
        5.79        27.42         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       15.75         0.20        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4744 
       51.32        21.99        21.14         2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  MPHOSPH10 MUTATED MPHOSPH10 WILD-TYPE 
                0.1                 0.0 
  MPHOSPH10 MUTATED MPHOSPH10 WILD-TYPE 
             124.27              140.38 
  MPHOSPH10 MUTATED MPHOSPH10 WILD-TYPE 
             21.440              20.105 
[1] "0.1 - 124.3 (21.4)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.1"
D61V2, 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       24       101         8         1
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MPHOSPH10 MUTATED           0          0          2          1        1
  MPHOSPH10 WILD-TYPE        19         10         39         30       34
                     vv
clus                  STAGE IVA STAGE IVB
  MPHOSPH10 MUTATED           0         0
  MPHOSPH10 WILD-TYPE        13         1
D61V3, multiclass
            clus
vv           MPHOSPH10 MUTATED MPHOSPH10 WILD-TYPE
  STAGE I                    2                  62
  STAGE IA                   0                   1
  STAGE II                   1                  24
  STAGE IIA                  8                 101
  STAGE IIB                  0                   8
  STAGE IIC                  0                   1
  STAGE III                  0                  19
  STAGE IIIA                 0                  10
  STAGE IIIB                 2                  39
  STAGE IIIC                 1                  30
  STAGE IV                   1                  34
  STAGE IVA                  0                  13
  STAGE IVB                  0                   1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2  T3  T4
  MPHOSPH10 MUTATED     0   2  14   2
  MPHOSPH10 WILD-TYPE   9  66 234  39
D61V4, multiclass
    clus
vv   MPHOSPH10 MUTATED MPHOSPH10 WILD-TYPE
  T1                 0                   9
  T2                 2                  66
  T3                14                 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
  MPHOSPH10 MUTATED    12   4   2
  MPHOSPH10 WILD-TYPE 208  76  64
D61V5, multiclass
    clus
vv   MPHOSPH10 MUTATED MPHOSPH10 WILD-TYPE
  N0                12                 208
  N1                 4                  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"
D61V6, binary
                     cls
clus                    0   1
  MPHOSPH10 MUTATED     8   1
  MPHOSPH10 WILD-TYPE 275  47
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  MPHOSPH10 MUTATED      8    1
  MPHOSPH10 WILD-TYPE  275   47
   clus
vv  MPHOSPH10 MUTATED MPHOSPH10 WILD-TYPE
  0                 8                 275
  1                 1                  47
[1] 2 2
[1] FALSE
D61V7, 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
D61V8, binary
                     cls
clus                    0   1
  MPHOSPH10 MUTATED    14   4
  MPHOSPH10 WILD-TYPE 303  44
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  MPHOSPH10 MUTATED     14    4
  MPHOSPH10 WILD-TYPE  303   44
                               clus
vv                              MPHOSPH10 MUTATED MPHOSPH10 WILD-TYPE
  COLON ADENOCARCINOMA                         14                 303
  COLON MUCINOUS ADENOCARCINOMA                 4                  44
[1] 2 2
[1] FALSE
                     vv
clus                   R0  R1  R2  RX
  MPHOSPH10 MUTATED     9   0   0   2
  MPHOSPH10 WILD-TYPE 248   2  22  19
D61V9, multiclass
    clus
vv   MPHOSPH10 MUTATED MPHOSPH10 WILD-TYPE
  R0                 9                 248
  R1                 0                   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"
D61V10, 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
D61V11, 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(62) Variable = CDK12 MUTATION ANALYSIS
D62V1, survival
                 sevent
clus2               0   1
  CDK12 MUTATED    21   5
  CDK12 WILD-TYPE 261  68
  CDK12 MUTATED CDK12 WILD-TYPE 
             26             329 
  CDK12 MUTATED CDK12 WILD-TYPE 
              5              68 
$`CDK12 MUTATED`
TCGA-A6-5659 TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-3492 TCGA-AA-3660 TCGA-AA-3663 
       30.44        22.06        20.12         3.02        78.08         6.97 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3815 TCGA-AA-3864 TCGA-AA-3989 TCGA-AA-A010 
       85.05        19.04        33.04        53.00         7.96        34.98 
TCGA-AA-A01P TCGA-AY-5543 TCGA-AZ-4315 TCGA-CK-4948 TCGA-CK-4950 TCGA-CM-4746 
       38.07        15.75        58.39       102.44        40.34        37.02 
TCGA-CM-5861 TCGA-D5-6928 TCGA-F4-6459 TCGA-F4-6570 TCGA-G4-6309 TCGA-G4-6586 
       15.02        11.64         8.61         6.18        51.75        35.80 
TCGA-G4-6588 TCGA-G4-6628 
       26.17        52.80 

$`CDK12 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 
       24.16        21.76        24.69        24.39        23.87        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       61.02         6.05        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       19.00        36.00         5.03        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4952 
        0.26         0.33         0.10         1.35        17.56        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 
       35.97        60.79       117.07        98.24        13.38        13.45 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        91.79        46.75 

  CDK12 MUTATED CDK12 WILD-TYPE 
           3.02            0.00 
  CDK12 MUTATED CDK12 WILD-TYPE 
         102.44          140.38 
  CDK12 MUTATED CDK12 WILD-TYPE 
          31.74           19.99 
[1] "3.0 - 102.4 (31.7)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.5"
D62V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CDK12 MUTATED         3        0        4        10         1         0
  CDK12 WILD-TYPE      61        1       21        99         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CDK12 MUTATED           2          2          2          0        3         1
  CDK12 WILD-TYPE        17          8         39         31       32        12
                 vv
clus              STAGE IVB
  CDK12 MUTATED           0
  CDK12 WILD-TYPE         1
D62V3, multiclass
            clus
vv           CDK12 MUTATED CDK12 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               4              21
  STAGE IIA             10              99
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             2               8
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               3              32
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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   3  23   2
  CDK12 WILD-TYPE   9  65 225  39
D62V4, multiclass
    clus
vv   CDK12 MUTATED CDK12 WILD-TYPE
  T1             0               9
  T2             3              65
  T3            23             225
  T4             2              39
[1] 4 2
[1] TRUE
[1] "dimension 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    20   6   2
  CDK12 WILD-TYPE 200  74  64
D62V5, multiclass
    clus
vv   CDK12 MUTATED CDK12 WILD-TYPE
  N0            20             200
  N1             6              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"
D62V6, binary
                 cls
clus                0   1
  CDK12 MUTATED    23   4
  CDK12 WILD-TYPE 260  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK12 MUTATED     23    4
  CDK12 WILD-TYPE  260   44
   clus
vv  CDK12 MUTATED CDK12 WILD-TYPE
  0            23             260
  1             4              44
[1] 2 2
[1] FALSE
D62V7, binary
                 cls
clus                0   1
  CDK12 MUTATED    17  11
  CDK12 WILD-TYPE 153 186
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK12 MUTATED     17   11
  CDK12 WILD-TYPE  153  186
        clus
vv       CDK12 MUTATED CDK12 WILD-TYPE
  FEMALE            17             153
  MALE              11             186
[1] 2 2
[1] FALSE
D62V8, binary
                 cls
clus                0   1
  CDK12 MUTATED    26   2
  CDK12 WILD-TYPE 291  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK12 MUTATED     26    2
  CDK12 WILD-TYPE  291   46
                               clus
vv                              CDK12 MUTATED CDK12 WILD-TYPE
  COLON ADENOCARCINOMA                     26             291
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CDK12 MUTATED    23   1   3   0
  CDK12 WILD-TYPE 234   1  19  21
D62V9, multiclass
    clus
vv   CDK12 MUTATED CDK12 WILD-TYPE
  R0            23             234
  R1             1               1
  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"
D62V10, 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
D62V11, 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(63) Variable = CLSPN MUTATION ANALYSIS
D63V1, survival
                 sevent
clus2               0   1
  CLSPN MUTATED    24   5
  CLSPN WILD-TYPE 258  68
  CLSPN MUTATED CLSPN WILD-TYPE 
             29             326 
  CLSPN MUTATED CLSPN WILD-TYPE 
              5              68 
$`CLSPN MUTATED`
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-6782 TCGA-AA-3496 TCGA-AA-3664 
        8.38        25.08        21.76        20.28         1.02        54.02 
TCGA-AA-A00A TCGA-AA-A02J TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-CA-5797 
       38.04         5.03        58.39        49.41        12.10         3.29 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CK-4948 TCGA-CM-5348 TCGA-CM-6166 TCGA-CM-6678 
        0.26         0.33       102.44        22.98        21.99        11.01 
TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6931 TCGA-DM-A0X9 TCGA-DM-A282 TCGA-F4-6460 
       17.13        16.14        12.00       119.70       139.17        13.38 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6809 TCGA-G4-6586 TCGA-G4-6626 
       13.45        35.87        13.25        35.80        46.75 

$`CLSPN WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6648 
       22.09        22.06        32.71        27.09        22.52        25.18 
TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       24.16        24.69        24.39        23.87        20.12        19.66 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        7.04         3.02        35.01        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       78.08         6.05         6.97         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       13.94        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       51.98        39.98         2.01        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 
       83.80        22.36        62.79        61.41         6.77       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.06         3.25         0.07         0.10         1.35        17.56 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
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         1.51        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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       98.24         8.61         6.18         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       16.24        33.67         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 
       45.11        36.72        36.00        22.09        13.78        26.17 
TCGA-G4-6625 TCGA-G4-6628 
       91.79        52.80 

  CLSPN MUTATED CLSPN WILD-TYPE 
           0.26            0.00 
  CLSPN MUTATED CLSPN WILD-TYPE 
         139.17          140.38 
  CLSPN MUTATED CLSPN WILD-TYPE 
         20.280          20.155 
[1] "0.3 - 139.2 (20.3)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.5"
D63V2, 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       22        97         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CLSPN MUTATED           0          1          4          1        2         3
  CLSPN WILD-TYPE        19          9         37         30       33        10
                 vv
clus              STAGE IVB
  CLSPN MUTATED           0
  CLSPN WILD-TYPE         1
D63V3, multiclass
            clus
vv           CLSPN MUTATED CLSPN WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA             12              97
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             4              37
  STAGE IIIC             1              30
  STAGE IV               2              33
  STAGE IVA              3              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
  CLSPN MUTATED     0   3  23   4
  CLSPN WILD-TYPE   9  65 225  37
D63V4, multiclass
    clus
vv   CLSPN MUTATED CLSPN WILD-TYPE
  T1             0               9
  T2             3              65
  T3            23             225
  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  72  64
D63V5, multiclass
    clus
vv   CLSPN MUTATED CLSPN WILD-TYPE
  N0            20             200
  N1             8              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"
D63V6, binary
                 cls
clus                0   1
  CLSPN MUTATED    22   5
  CLSPN WILD-TYPE 261  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLSPN MUTATED     22    5
  CLSPN WILD-TYPE  261   43
   clus
vv  CLSPN MUTATED CLSPN WILD-TYPE
  0            22             261
  1             5              43
[1] 2 2
[1] FALSE
D63V7, 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
D63V8, binary
                 cls
clus                0   1
  CLSPN MUTATED    28   2
  CLSPN WILD-TYPE 289  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLSPN MUTATED     28    2
  CLSPN WILD-TYPE  289   46
                               clus
vv                              CLSPN MUTATED CLSPN WILD-TYPE
  COLON ADENOCARCINOMA                     28             289
  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 238   2  21  19
D63V9, multiclass
    clus
vv   CLSPN MUTATED CLSPN WILD-TYPE
  R0            19             238
  R1             0               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"
D63V10, 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
D63V11, 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(64) Variable = EGR1 MUTATION ANALYSIS
D64V1, survival
                sevent
clus2              0   1
  EGR1 MUTATED     8   1
  EGR1 WILD-TYPE 274  72
  EGR1 MUTATED EGR1 WILD-TYPE 
             9            346 
  EGR1 MUTATED EGR1 WILD-TYPE 
             1             72 
$`EGR1 MUTATED`
TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-3663 TCGA-AA-3877 TCGA-AA-3994 TCGA-AZ-6598 
       22.06        20.12         6.97        31.00        27.02        49.41 
TCGA-CM-4743 TCGA-G4-6588 TCGA-G4-6628 
       23.05        26.17        52.80 

$`EGR1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       27.02        29.98        18.05         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
        7.96        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       13.78        35.80        91.79        46.75 

  EGR1 MUTATED EGR1 WILD-TYPE 
          6.97           0.00 
  EGR1 MUTATED EGR1 WILD-TYPE 
         52.80         140.38 
  EGR1 MUTATED EGR1 WILD-TYPE 
         26.17          19.99 
[1] "7.0 - 52.8 (26.2)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "2.2"
D64V2, 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       23       105         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        19         10         40         31       35        13
                vv
clus             STAGE IVB
  EGR1 MUTATED           0
  EGR1 WILD-TYPE         1
D64V3, multiclass
            clus
vv           EGR1 MUTATED EGR1 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             4            105
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  EGR1 MUTATED     1   1   7   0
  EGR1 WILD-TYPE   8  67 241  41
D64V4, multiclass
    clus
vv   EGR1 MUTATED EGR1 WILD-TYPE
  T1            1              8
  T2            1             67
  T3            7            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
  EGR1 MUTATED     8   1   0
  EGR1 WILD-TYPE 212  79  66
D64V5, multiclass
    clus
vv   EGR1 MUTATED EGR1 WILD-TYPE
  N0            8            212
  N1            1             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"
D64V6, binary
                cls
clus               0   1
  EGR1 MUTATED     7   0
  EGR1 WILD-TYPE 276  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGR1 MUTATED      7    0
  EGR1 WILD-TYPE  276   48
   clus
vv  EGR1 MUTATED EGR1 WILD-TYPE
  0            7            276
  1            0             48
[1] 2 2
[1] FALSE
D64V7, 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
D64V8, binary
                cls
clus               0   1
  EGR1 MUTATED     6   3
  EGR1 WILD-TYPE 311  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGR1 MUTATED      6    3
  EGR1 WILD-TYPE  311   45
                               clus
vv                              EGR1 MUTATED EGR1 WILD-TYPE
  COLON ADENOCARCINOMA                     6            311
  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 250   2  22  21
D64V9, multiclass
    clus
vv   EGR1 MUTATED EGR1 WILD-TYPE
  R0            7            250
  R1            0              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"
D64V10, 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
D64V11, 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(65) Variable = CHD3 MUTATION ANALYSIS
D65V1, survival
                sevent
clus2              0   1
  CHD3 MUTATED    17   6
  CHD3 WILD-TYPE 265  67
  CHD3 MUTATED CHD3 WILD-TYPE 
            23            332 
  CHD3 MUTATED CHD3 WILD-TYPE 
             6             67 
$`CHD3 MUTATED`
TCGA-A6-2676 TCGA-A6-5661 TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3710 
       42.90        33.53        24.39        19.66         3.02        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3845 TCGA-AA-3864 TCGA-AA-A00J TCGA-AA-A00N 
       19.04        19.04         0.00        53.00        18.05         4.01 
TCGA-AA-A010 TCGA-AA-A01Q TCGA-AD-6895 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6601 
       34.98         1.02         0.72        21.44        58.39       100.01 
TCGA-D5-6927 TCGA-DM-A1HB TCGA-F4-6854 TCGA-G4-6309 TCGA-G4-6588 
        9.44       135.65         0.53        51.75        26.17 

$`CHD3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 
       24.16        21.76        24.69        23.87        20.12        20.28 
TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        7.04         1.02        35.01        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3811 
       37.05        19.00        36.00         5.03        85.05        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02        14.93        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
        0.20        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        61.41        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       16.24        33.67        13.25        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       74.56        65.85        53.62        44.68        55.04        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  CHD3 MUTATED CHD3 WILD-TYPE 
             0              0 
  CHD3 MUTATED CHD3 WILD-TYPE 
        135.65         140.38 
  CHD3 MUTATED CHD3 WILD-TYPE 
        21.440         20.155 
[1] "0.0 - 135.7 (21.4)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D65V2, 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       20       101         4         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CHD3 MUTATED           0          0          3          1        1         0
  CHD3 WILD-TYPE        19         10         38         30       34        13
                vv
clus             STAGE IVB
  CHD3 MUTATED           0
  CHD3 WILD-TYPE         1
D65V3, multiclass
            clus
vv           CHD3 MUTATED CHD3 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              5             20
  STAGE IIA             8            101
  STAGE IIB             4              4
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            3             38
  STAGE IIIC            1             30
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CHD3 MUTATED     0   1  17   6
  CHD3 WILD-TYPE   9  67 231  35
D65V4, multiclass
    clus
vv   CHD3 MUTATED CHD3 WILD-TYPE
  T1            0              9
  T2            1             67
  T3           17            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
  CHD3 MUTATED    19   5   0
  CHD3 WILD-TYPE 201  75  66
D65V5, multiclass
    clus
vv   CHD3 MUTATED CHD3 WILD-TYPE
  N0           19            201
  N1            5             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"
D65V6, binary
                cls
clus               0   1
  CHD3 MUTATED    19   1
  CHD3 WILD-TYPE 264  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD3 MUTATED     19    1
  CHD3 WILD-TYPE  264   47
   clus
vv  CHD3 MUTATED CHD3 WILD-TYPE
  0           19            264
  1            1             47
[1] 2 2
[1] FALSE
D65V7, 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
D65V8, binary
                cls
clus               0   1
  CHD3 MUTATED    21   3
  CHD3 WILD-TYPE 296  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD3 MUTATED     21    3
  CHD3 WILD-TYPE  296   45
                               clus
vv                              CHD3 MUTATED CHD3 WILD-TYPE
  COLON ADENOCARCINOMA                    21            296
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CHD3 MUTATED    18   0   1   1
  CHD3 WILD-TYPE 239   2  21  20
D65V9, multiclass
    clus
vv   CHD3 MUTATED CHD3 WILD-TYPE
  R0           18            239
  R1            0              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"
D65V10, 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
D65V11, 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(66) Variable = ALDH1A3 MUTATION ANALYSIS
D66V1, survival
                   sevent
clus2                 0   1
  ALDH1A3 MUTATED    12   4
  ALDH1A3 WILD-TYPE 270  69
  ALDH1A3 MUTATED ALDH1A3 WILD-TYPE 
               16               339 
  ALDH1A3 MUTATED ALDH1A3 WILD-TYPE 
                4                69 
$`ALDH1A3 MUTATED`
TCGA-A6-6654 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3655 TCGA-AA-3950 
       23.87        63.98        29.95        20.98        61.02        24.00 
TCGA-AA-3977 TCGA-AD-6964 TCGA-AZ-6598 TCGA-CK-4952 TCGA-CK-5916 TCGA-D5-6539 
       25.02        10.88        49.41        15.62        21.14        12.49 
TCGA-D5-6930 TCGA-DM-A1D6 TCGA-G4-6304 TCGA-G4-6309 
        1.51        49.91        53.62        51.75 

$`ALDH1A3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       24.00        17.95        23.01        19.99        13.94        19.99 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13        83.80        22.36        62.79        61.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       40.34        49.08        51.32        21.99         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
      107.67        74.56        65.85        44.68        55.04        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  ALDH1A3 MUTATED ALDH1A3 WILD-TYPE 
             1.51              0.00 
  ALDH1A3 MUTATED ALDH1A3 WILD-TYPE 
            63.98            140.38 
  ALDH1A3 MUTATED ALDH1A3 WILD-TYPE 
            24.51             19.99 
[1] "1.5 - 64.0 (24.5)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1.1"
D66V2, 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       22       104         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ALDH1A3 MUTATED           1          1          2          0        0
  ALDH1A3 WILD-TYPE        18          9         39         31       35
                   vv
clus                STAGE IVA STAGE IVB
  ALDH1A3 MUTATED           0         0
  ALDH1A3 WILD-TYPE        13         1
D66V3, multiclass
            clus
vv           ALDH1A3 MUTATED ALDH1A3 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 3                22
  STAGE IIA                5               104
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               1                 9
  STAGE IIIB               2                39
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ALDH1A3 MUTATED     1   2  11   4
  ALDH1A3 WILD-TYPE   8  66 237  37
D66V4, multiclass
    clus
vv   ALDH1A3 MUTATED ALDH1A3 WILD-TYPE
  T1               1                 8
  T2               2                66
  T3              11               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
  ALDH1A3 MUTATED    14   2   2
  ALDH1A3 WILD-TYPE 206  78  64
D66V5, multiclass
    clus
vv   ALDH1A3 MUTATED ALDH1A3 WILD-TYPE
  N0              14               206
  N1               2                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"
D66V6, binary
                   cls
clus                  0   1
  ALDH1A3 MUTATED    14   0
  ALDH1A3 WILD-TYPE 269  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ALDH1A3 MUTATED     14    0
  ALDH1A3 WILD-TYPE  269   48
   clus
vv  ALDH1A3 MUTATED ALDH1A3 WILD-TYPE
  0              14               269
  1               0                48
[1] 2 2
[1] FALSE
D66V7, 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
D66V8, binary
                   cls
clus                  0   1
  ALDH1A3 MUTATED    13   5
  ALDH1A3 WILD-TYPE 304  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ALDH1A3 MUTATED     13    5
  ALDH1A3 WILD-TYPE  304   43
                               clus
vv                              ALDH1A3 MUTATED ALDH1A3 WILD-TYPE
  COLON ADENOCARCINOMA                       13               304
  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 248   2  21  18
D66V9, multiclass
    clus
vv   ALDH1A3 MUTATED ALDH1A3 WILD-TYPE
  R0               9               248
  R1               0                 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"
D66V10, 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
D66V11, 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(67) Variable = CYSLTR2 MUTATION ANALYSIS
D67V1, survival
                   sevent
clus2                 0   1
  CYSLTR2 MUTATED    14   1
  CYSLTR2 WILD-TYPE 268  72
  CYSLTR2 MUTATED CYSLTR2 WILD-TYPE 
               15               340 
  CYSLTR2 MUTATED CYSLTR2 WILD-TYPE 
                1                72 
$`CYSLTR2 MUTATED`
TCGA-A6-2671 TCGA-A6-6781 TCGA-AA-3496 TCGA-AA-3525 TCGA-AA-A00J TCGA-AA-A00O 
       43.76        19.66         1.02         8.05        18.05        27.02 
TCGA-AD-6548 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4752 TCGA-CM-6676 TCGA-CM-6680 
       21.37         0.33         0.10        13.02        11.08        12.03 
TCGA-D5-5539 TCGA-DM-A28K TCGA-G4-6310 
       19.59        98.24        45.11 

$`CYSLTR2 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 
       20.12        20.28         7.04         3.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       24.03        37.05        36.03        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        38.04         4.01        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07         0.26         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 
      119.93        35.97        60.79       117.07         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       51.75        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  CYSLTR2 MUTATED CYSLTR2 WILD-TYPE 
              0.1               0.0 
  CYSLTR2 MUTATED CYSLTR2 WILD-TYPE 
            98.24            140.38 
  CYSLTR2 MUTATED CYSLTR2 WILD-TYPE 
            18.05             20.98 
[1] "0.1 - 98.2 (18.1)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "2.8"
D67V2, 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       24       105         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CYSLTR2 MUTATED           0          1          4          2        1
  CYSLTR2 WILD-TYPE        19          9         37         29       34
                   vv
clus                STAGE IVA STAGE IVB
  CYSLTR2 MUTATED           0         0
  CYSLTR2 WILD-TYPE        13         1
D67V3, multiclass
            clus
vv           CYSLTR2 MUTATED CYSLTR2 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                4               105
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               1                 9
  STAGE IIIB               4                37
  STAGE IIIC               2                29
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CYSLTR2 MUTATED     0   2  11   2
  CYSLTR2 WILD-TYPE   9  66 237  39
D67V4, multiclass
    clus
vv   CYSLTR2 MUTATED CYSLTR2 WILD-TYPE
  T1               0                 9
  T2               2                66
  T3              11               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
  CYSLTR2 MUTATED     7   5   3
  CYSLTR2 WILD-TYPE 213  75  63
D67V5, multiclass
    clus
vv   CYSLTR2 MUTATED CYSLTR2 WILD-TYPE
  N0               7               213
  N1               5                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"
D67V6, binary
                   cls
clus                  0   1
  CYSLTR2 MUTATED    13   1
  CYSLTR2 WILD-TYPE 270  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYSLTR2 MUTATED     13    1
  CYSLTR2 WILD-TYPE  270   47
   clus
vv  CYSLTR2 MUTATED CYSLTR2 WILD-TYPE
  0              13               270
  1               1                47
[1] 2 2
[1] FALSE
D67V7, 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
D67V8, binary
                   cls
clus                  0   1
  CYSLTR2 MUTATED    10   5
  CYSLTR2 WILD-TYPE 307  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYSLTR2 MUTATED     10    5
  CYSLTR2 WILD-TYPE  307   43
                               clus
vv                              CYSLTR2 MUTATED CYSLTR2 WILD-TYPE
  COLON ADENOCARCINOMA                       10               307
  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 245   2  22  19
D67V9, multiclass
    clus
vv   CYSLTR2 MUTATED CYSLTR2 WILD-TYPE
  R0              12               245
  R1               0                 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"
D67V10, 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
D67V11, 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(68) Variable = GGTLC2 MUTATION ANALYSIS
D68V1, survival
                  sevent
clus2                0   1
  GGTLC2 MUTATED     6   0
  GGTLC2 WILD-TYPE 276  73
  GGTLC2 MUTATED GGTLC2 WILD-TYPE 
               6              349 
  GGTLC2 MUTATED GGTLC2 WILD-TYPE 
               0               73 
$`GGTLC2 MUTATED`
TCGA-AU-3779 TCGA-D5-6535 TCGA-G4-6306 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       14.50        15.12        44.68        22.09        35.80        26.17 

$`GGTLC2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 
      107.67        74.56        65.85        53.62        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 
       45.11        36.72        36.00        13.78        91.79        46.75 
TCGA-G4-6628 
       52.80 

  GGTLC2 MUTATED GGTLC2 WILD-TYPE 
            14.5              0.0 
  GGTLC2 MUTATED GGTLC2 WILD-TYPE 
           44.68           140.38 
  GGTLC2 MUTATED GGTLC2 WILD-TYPE 
           24.13            20.12 
[1] "14.5 - 44.7 (24.1)" "0.0 - 140.4 (20.1)"
[1] "hr="     "9200000"
D68V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GGTLC2 MUTATED         0        0        0         4         1         0
  GGTLC2 WILD-TYPE      64        1       25       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        18         10         40         31       35
                  vv
clus               STAGE IVA STAGE IVB
  GGTLC2 MUTATED           0         0
  GGTLC2 WILD-TYPE        13         1
D68V3, multiclass
            clus
vv           GGTLC2 MUTATED GGTLC2 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               4              105
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GGTLC2 MUTATED     0   2   4   1
  GGTLC2 WILD-TYPE   9  66 244  40
D68V4, multiclass
    clus
vv   GGTLC2 MUTATED GGTLC2 WILD-TYPE
  T1              0                9
  T2              2               66
  T3              4              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
  GGTLC2 MUTATED     5   2   0
  GGTLC2 WILD-TYPE 215  78  66
D68V5, multiclass
    clus
vv   GGTLC2 MUTATED GGTLC2 WILD-TYPE
  N0              5              215
  N1              2               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"
D68V6, binary
                  cls
clus                 0   1
  GGTLC2 MUTATED     4   0
  GGTLC2 WILD-TYPE 279  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GGTLC2 MUTATED      4    0
  GGTLC2 WILD-TYPE  279   48
   clus
vv  GGTLC2 MUTATED GGTLC2 WILD-TYPE
  0              4              279
  1              0               48
[1] 2 2
[1] FALSE
D68V7, 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
D68V8, binary
                  cls
clus                 0   1
  GGTLC2 MUTATED     7   0
  GGTLC2 WILD-TYPE 310  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GGTLC2 MUTATED      7    0
  GGTLC2 WILD-TYPE  310   48
                               clus
vv                              GGTLC2 MUTATED GGTLC2 WILD-TYPE
  COLON ADENOCARCINOMA                       7              310
  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 252   2  22  19
D68V9, multiclass
    clus
vv   GGTLC2 MUTATED GGTLC2 WILD-TYPE
  R0              5              252
  R1              0                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"
D68V10, 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
D68V11, 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(69) Variable = IQCD MUTATION ANALYSIS
D69V1, survival
                sevent
clus2              0   1
  IQCD MUTATED     9   1
  IQCD WILD-TYPE 273  72
  IQCD MUTATED IQCD WILD-TYPE 
            10            345 
  IQCD MUTATED IQCD WILD-TYPE 
             1             72 
$`IQCD MUTATED`
TCGA-A6-6141 TCGA-A6-6654 TCGA-AA-3538 TCGA-AA-3672 TCGA-AY-6196 TCGA-AZ-6599 
        8.38        23.87        26.01         0.92         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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 
        0.00        19.07        34.03        29.00        29.00        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        15.75        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41        49.41        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        16.01         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       45.11        36.72        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  IQCD MUTATED IQCD WILD-TYPE 
           0.2            0.0 
  IQCD MUTATED IQCD WILD-TYPE 
         36.00         140.38 
  IQCD MUTATED IQCD WILD-TYPE 
         14.53          20.98 
[1] "0.2 - 36.0 (14.5)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.3"
D69V2, 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       25       107         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        18         10         40         29       35        13
                vv
clus             STAGE IVB
  IQCD MUTATED           0
  IQCD WILD-TYPE         1
D69V3, multiclass
            clus
vv           IQCD MUTATED IQCD WILD-TYPE
  STAGE I               4             60
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             2            107
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            2             29
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  IQCD MUTATED     0   4   6   0
  IQCD WILD-TYPE   9  64 242  41
D69V4, multiclass
    clus
vv   IQCD MUTATED IQCD WILD-TYPE
  T1            0              9
  T2            4             64
  T3            6            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
  IQCD MUTATED     6   2   2
  IQCD WILD-TYPE 214  78  64
D69V5, multiclass
    clus
vv   IQCD MUTATED IQCD WILD-TYPE
  N0            6            214
  N1            2             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"
D69V6, binary
                cls
clus               0   1
  IQCD MUTATED     7   0
  IQCD WILD-TYPE 276  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  IQCD MUTATED      7    0
  IQCD WILD-TYPE  276   48
   clus
vv  IQCD MUTATED IQCD WILD-TYPE
  0            7            276
  1            0             48
[1] 2 2
[1] FALSE
D69V7, 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
D69V8, binary
                cls
clus               0   1
  IQCD MUTATED     9   1
  IQCD WILD-TYPE 308  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  IQCD MUTATED      9    1
  IQCD WILD-TYPE  308   47
                               clus
vv                              IQCD MUTATED IQCD WILD-TYPE
  COLON ADENOCARCINOMA                     9            308
  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 250   2  22  21
D69V9, multiclass
    clus
vv   IQCD MUTATED IQCD WILD-TYPE
  R0            7            250
  R1            0              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"
D69V10, 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
D69V11, 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(70) Variable = PRPS1 MUTATION ANALYSIS
D70V1, survival
                 sevent
clus2               0   1
  PRPS1 MUTATED     7   1
  PRPS1 WILD-TYPE 275  72
  PRPS1 MUTATED PRPS1 WILD-TYPE 
              8             347 
  PRPS1 MUTATED PRPS1 WILD-TYPE 
              1              72 
$`PRPS1 MUTATED`
TCGA-A6-5660 TCGA-A6-6781 TCGA-AA-3713 TCGA-AZ-6598 TCGA-CM-4752 TCGA-CM-5348 
       29.19        19.66        19.04        49.41        13.02        22.98 
TCGA-D5-6539 TCGA-DM-A1HB 
       12.49       135.65 

$`PRPS1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.03        30.08        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 
       43.27        15.12        17.85         4.80        17.13        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  PRPS1 MUTATED PRPS1 WILD-TYPE 
          12.49            0.00 
  PRPS1 MUTATED PRPS1 WILD-TYPE 
         135.65          140.38 
  PRPS1 MUTATED PRPS1 WILD-TYPE 
          21.32           20.19 
[1] "12.5 - 135.7 (21.3)" "0.0 - 140.4 (20.2)" 
[1] "hr=" "2.3"
D70V2, 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       24       108         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PRPS1 MUTATED           0          1          2          2        1         0
  PRPS1 WILD-TYPE        19          9         39         29       34        13
                 vv
clus              STAGE IVB
  PRPS1 MUTATED           0
  PRPS1 WILD-TYPE         1
D70V3, multiclass
            clus
vv           PRPS1 MUTATED PRPS1 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              1             108
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             2              39
  STAGE IIIC             2              29
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PRPS1 MUTATED     0   0   7   1
  PRPS1 WILD-TYPE   9  68 241  40
D70V4, multiclass
    clus
vv   PRPS1 MUTATED PRPS1 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             7             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
  PRPS1 MUTATED     4   3   1
  PRPS1 WILD-TYPE 216  77  65
D70V5, multiclass
    clus
vv   PRPS1 MUTATED PRPS1 WILD-TYPE
  N0             4             216
  N1             3              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"
D70V6, binary
                 cls
clus                0   1
  PRPS1 MUTATED     5   1
  PRPS1 WILD-TYPE 278  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRPS1 MUTATED      5    1
  PRPS1 WILD-TYPE  278   47
   clus
vv  PRPS1 MUTATED PRPS1 WILD-TYPE
  0             5             278
  1             1              47
[1] 2 2
[1] FALSE
D70V7, 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
D70V8, binary
                 cls
clus                0   1
  PRPS1 MUTATED     7   1
  PRPS1 WILD-TYPE 310  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRPS1 MUTATED      7    1
  PRPS1 WILD-TYPE  310   47
                               clus
vv                              PRPS1 MUTATED PRPS1 WILD-TYPE
  COLON ADENOCARCINOMA                      7             310
  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 253   2  21  21
D70V9, multiclass
    clus
vv   PRPS1 MUTATED PRPS1 WILD-TYPE
  R0             4             253
  R1             0               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"
D70V10, 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
D70V11, 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(71) Variable = CAB39L MUTATION ANALYSIS
D71V1, survival
                  sevent
clus2                0   1
  CAB39L MUTATED     8   1
  CAB39L WILD-TYPE 274  72
  CAB39L MUTATED CAB39L WILD-TYPE 
               9              346 
  CAB39L MUTATED CAB39L WILD-TYPE 
               1               72 
$`CAB39L MUTATED`
TCGA-A6-5661 TCGA-A6-6653 TCGA-A6-6780 TCGA-AA-A010 TCGA-AD-5900 TCGA-AY-6197 
       33.53        24.39        20.12        34.98         0.07        21.44 
TCGA-CK-5916 TCGA-F4-6856 TCGA-G4-6588 
       21.14        19.43        26.17 

$`CAB39L WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6781 
       25.18        24.16        21.76        24.69        23.87        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       27.09        16.31         0.95        15.75         0.20        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        91.79        46.75        52.80 

  CAB39L MUTATED CAB39L WILD-TYPE 
            0.07             0.00 
  CAB39L MUTATED CAB39L WILD-TYPE 
           34.98           140.38 
  CAB39L MUTATED CAB39L WILD-TYPE 
          21.440           20.005 
[1] "0.1 - 35.0 (21.4)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1.5"
D71V2, 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       25       105         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CAB39L MUTATED           0          0          0          0        0
  CAB39L WILD-TYPE        19         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  CAB39L MUTATED           0         0
  CAB39L WILD-TYPE        13         1
D71V3, multiclass
            clus
vv           CAB39L MUTATED CAB39L WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               4              105
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CAB39L MUTATED     1   3   4   1
  CAB39L WILD-TYPE   8  65 244  40
D71V4, multiclass
    clus
vv   CAB39L MUTATED CAB39L WILD-TYPE
  T1              1                8
  T2              3               65
  T3              4              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
  CAB39L MUTATED     9   0   0
  CAB39L WILD-TYPE 211  80  66
D71V5, multiclass
    clus
vv   CAB39L MUTATED CAB39L WILD-TYPE
  N0              9              211
  N1              0               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
  CAB39L MUTATED     6   0
  CAB39L WILD-TYPE 277  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CAB39L MUTATED      6    0
  CAB39L WILD-TYPE  277   48
   clus
vv  CAB39L MUTATED CAB39L WILD-TYPE
  0              6              277
  1              0               48
[1] 2 2
[1] FALSE
D71V7, 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
D71V8, binary
                  cls
clus                 0   1
  CAB39L MUTATED     6   3
  CAB39L WILD-TYPE 311  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CAB39L MUTATED      6    3
  CAB39L WILD-TYPE  311   45
                               clus
vv                              CAB39L MUTATED CAB39L WILD-TYPE
  COLON ADENOCARCINOMA                       6              311
  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 251   2  22  20
D71V9, multiclass
    clus
vv   CAB39L MUTATED CAB39L WILD-TYPE
  R0              6              251
  R1              0                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"
D71V10, 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
D71V11, 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(72) Variable = MLH1 MUTATION ANALYSIS
D72V1, survival
                sevent
clus2              0   1
  MLH1 MUTATED    35  10
  MLH1 WILD-TYPE 247  63
  MLH1 MUTATED MLH1 WILD-TYPE 
            45            310 
  MLH1 MUTATED MLH1 WILD-TYPE 
            10             63 
$`MLH1 MUTATED`
TCGA-A6-2671 TCGA-A6-3809 TCGA-A6-4105 TCGA-A6-6138 TCGA-A6-6780 TCGA-A6-6781 
       43.76        32.75        14.53        22.52        20.12        19.66 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3864 TCGA-AA-A01P TCGA-AD-6889 
       85.05        19.04        19.04        53.00        38.07        56.55 
TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-5403 TCGA-AZ-6599 
       27.09        15.75         0.20        17.82        62.79         6.77 
TCGA-AZ-6601 TCGA-CA-6719 TCGA-CK-5916 TCGA-CM-4746 TCGA-CM-4752 TCGA-CM-5344 
      100.01         1.35        21.14        37.02        13.02        22.03 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5868 TCGA-CM-6167 TCGA-CM-6171 TCGA-CM-6172 
       30.08        16.01        17.03        14.99        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6678 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 
       12.95        11.01         1.32        43.27        15.12         4.80 
TCGA-D5-6540 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6809 TCGA-F4-6856 TCGA-G4-6293 
       16.14        16.31        29.59        13.25        19.43       107.67 
TCGA-G4-6306 TCGA-G4-6310 TCGA-G4-6586 
       44.68        45.11        35.80 

$`MLH1 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       34.65        33.34        36.53        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       29.19        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 
       27.09         8.38        25.08        25.18        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.69        24.39        23.87        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
       19.00        36.00         5.03        26.99        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       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        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37         4.21         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.95        21.44        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       22.36        61.41        49.41        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 
        3.29         0.07         0.26         0.33         0.10        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 
        2.93         2.01       124.27        23.05        20.02        25.02 
TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       29.06        22.98        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-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       12.99        13.02        15.02        13.05        11.08        11.08 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 
       11.51        20.19        18.25        17.85        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6807 
       13.38        13.45         6.18        35.87         1.55        16.24 
TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       33.67         0.53        35.41        74.56        65.85        53.62 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        51.75        36.72        36.00        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  MLH1 MUTATED MLH1 WILD-TYPE 
           0.2            0.0 
  MLH1 MUTATED MLH1 WILD-TYPE 
        107.67         140.38 
  MLH1 MUTATED MLH1 WILD-TYPE 
         19.43          20.98 
[1] "0.2 - 107.7 (19.4)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1"  
D72V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MLH1 MUTATED        10        0        4        12         2         0
  MLH1 WILD-TYPE      54        1       21        97         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MLH1 MUTATED           4          0          7          3        2         4
  MLH1 WILD-TYPE        15         10         34         28       33         9
                vv
clus             STAGE IVB
  MLH1 MUTATED           0
  MLH1 WILD-TYPE         1
D72V3, multiclass
            clus
vv           MLH1 MUTATED MLH1 WILD-TYPE
  STAGE I              10             54
  STAGE IA              0              1
  STAGE II              4             21
  STAGE IIA            12             97
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             4             15
  STAGE IIIA            0             10
  STAGE IIIB            7             34
  STAGE IIIC            3             28
  STAGE IV              2             33
  STAGE IVA             4              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
  MLH1 MUTATED     1  10  31   6
  MLH1 WILD-TYPE   8  58 217  35
D72V4, multiclass
    clus
vv   MLH1 MUTATED MLH1 WILD-TYPE
  T1            1              8
  T2           10             58
  T3           31            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
  MLH1 MUTATED    31  13   4
  MLH1 WILD-TYPE 189  67  62
D72V5, multiclass
    clus
vv   MLH1 MUTATED MLH1 WILD-TYPE
  N0           31            189
  N1           13             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"
D72V6, binary
                cls
clus               0   1
  MLH1 MUTATED    33   6
  MLH1 WILD-TYPE 250  42
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLH1 MUTATED     33    6
  MLH1 WILD-TYPE  250   42
   clus
vv  MLH1 MUTATED MLH1 WILD-TYPE
  0           33            250
  1            6             42
[1] 2 2
[1] FALSE
D72V7, binary
                cls
clus               0   1
  MLH1 MUTATED    22  26
  MLH1 WILD-TYPE 148 171
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLH1 MUTATED     22   26
  MLH1 WILD-TYPE  148  171
        clus
vv       MLH1 MUTATED MLH1 WILD-TYPE
  FEMALE           22            148
  MALE             26            171
[1] 2 2
[1] FALSE
D72V8, binary
                cls
clus               0   1
  MLH1 MUTATED    41   7
  MLH1 WILD-TYPE 276  41
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLH1 MUTATED     41    7
  MLH1 WILD-TYPE  276   41
                               clus
vv                              MLH1 MUTATED MLH1 WILD-TYPE
  COLON ADENOCARCINOMA                    41            276
  COLON MUCINOUS ADENOCARCINOMA            7             41
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MLH1 MUTATED    35   0   1   5
  MLH1 WILD-TYPE 222   2  21  16
D72V9, multiclass
    clus
vv   MLH1 MUTATED MLH1 WILD-TYPE
  R0           35            222
  R1            0              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"
D72V10, 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                           5    35
  MLH1 WILD-TYPE                        14   141
D72V11, multiclass
                                  clus
vv                                 MLH1 MUTATED MLH1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  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(73) Variable = CD58 MUTATION ANALYSIS
D73V1, survival
                sevent
clus2              0   1
  CD58 MUTATED    11   3
  CD58 WILD-TYPE 271  70
  CD58 MUTATED CD58 WILD-TYPE 
            14            341 
  CD58 MUTATED CD58 WILD-TYPE 
             3             70 
$`CD58 MUTATED`
TCGA-A6-5665 TCGA-AA-3663 TCGA-AA-A010 TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6895 
       22.06         6.97        34.98         0.07        56.55         0.72 
TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-5916 TCGA-CM-5861 TCGA-F4-6570 
       58.39        49.41         0.33        21.14        15.02         6.18 
TCGA-G4-6625 TCGA-G4-6628 
       91.79        52.80 

$`CD58 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        21.37         4.21         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
       40.34        15.62        49.08        51.32        21.99         2.93 
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        16.01 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        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        13.38        13.45        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        46.75 

  CD58 MUTATED CD58 WILD-TYPE 
          0.07           0.00 
  CD58 MUTATED CD58 WILD-TYPE 
         91.79         140.38 
  CD58 MUTATED CD58 WILD-TYPE 
         21.60          20.12 
[1] "0.1 - 91.8 (21.6)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.1"
D73V2, 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       23       102         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CD58 MUTATED           0          0          0          0        0         0
  CD58 WILD-TYPE        19         10         41         31       35        13
                vv
clus             STAGE IVB
  CD58 MUTATED           0
  CD58 WILD-TYPE         1
D73V3, multiclass
            clus
vv           CD58 MUTATED CD58 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             7            102
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CD58 MUTATED     1   2  10   1
  CD58 WILD-TYPE   8  66 238  40
D73V4, multiclass
    clus
vv   CD58 MUTATED CD58 WILD-TYPE
  T1            1              8
  T2            2             66
  T3           10            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
  CD58 MUTATED    13   1   0
  CD58 WILD-TYPE 207  79  66
D73V5, multiclass
    clus
vv   CD58 MUTATED CD58 WILD-TYPE
  N0           13            207
  N1            1             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
  CD58 MUTATED    11   0
  CD58 WILD-TYPE 272  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD58 MUTATED     11    0
  CD58 WILD-TYPE  272   48
   clus
vv  CD58 MUTATED CD58 WILD-TYPE
  0           11            272
  1            0             48
[1] 2 2
[1] FALSE
D73V7, 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
D73V8, binary
                cls
clus               0   1
  CD58 MUTATED    12   2
  CD58 WILD-TYPE 305  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD58 MUTATED     12    2
  CD58 WILD-TYPE  305   46
                               clus
vv                              CD58 MUTATED CD58 WILD-TYPE
  COLON ADENOCARCINOMA                    12            305
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CD58 MUTATED     9   0   0   2
  CD58 WILD-TYPE 248   2  22  19
D73V9, multiclass
    clus
vv   CD58 MUTATED CD58 WILD-TYPE
  R0            9            248
  R1            0              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"
D73V10, 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
D73V11, 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(74) Variable = BCL9 MUTATION ANALYSIS
D74V1, survival
                sevent
clus2              0   1
  BCL9 MUTATED    16   6
  BCL9 WILD-TYPE 266  67
  BCL9 MUTATED BCL9 WILD-TYPE 
            22            333 
  BCL9 MUTATED BCL9 WILD-TYPE 
             6             67 
$`BCL9 MUTATED`
TCGA-A6-5661 TCGA-A6-6781 TCGA-AA-3555 TCGA-AA-3663 TCGA-AA-3715 TCGA-AA-3815 
       33.53        19.66        29.95         6.97        19.04        33.04 
TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R 
       33.01        24.00        25.02         4.01        34.98        35.01 
TCGA-AD-6964 TCGA-AZ-6601 TCGA-CA-6718 TCGA-CM-6678 TCGA-DM-A0X9 TCGA-DM-A282 
       10.88       100.01         0.10        11.01       119.70       139.17 
TCGA-DM-A285 TCGA-F4-6570 TCGA-F4-6854 TCGA-G4-6586 
        6.12         6.18         0.53        35.80 

$`BCL9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       26.99        19.04        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3952 
       31.00         2.01        12.99        24.00        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.33         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.38        13.45        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       16.24        33.67        13.25        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 
       45.11        36.72        36.00        22.09        13.78        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  BCL9 MUTATED BCL9 WILD-TYPE 
           0.1            0.0 
  BCL9 MUTATED BCL9 WILD-TYPE 
        139.17         140.38 
  BCL9 MUTATED BCL9 WILD-TYPE 
         24.51          20.12 
[1] "0.1 - 139.2 (24.5)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.2"
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       22        99         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        18         10         41         30       34        12
                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             22
  STAGE IIA            10             99
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            1             30
  STAGE IV              1             34
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 233  35
D74V4, multiclass
    clus
vv   BCL9 MUTATED BCL9 WILD-TYPE
  T1            0              9
  T2            1             67
  T3           15            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
  BCL9 MUTATED    17   2   3
  BCL9 WILD-TYPE 203  78  63
D74V5, multiclass
    clus
vv   BCL9 MUTATED BCL9 WILD-TYPE
  N0           17            203
  N1            2             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"
D74V6, binary
                cls
clus               0   1
  BCL9 MUTATED    17   2
  BCL9 WILD-TYPE 266  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCL9 MUTATED     17    2
  BCL9 WILD-TYPE  266   46
   clus
vv  BCL9 MUTATED BCL9 WILD-TYPE
  0           17            266
  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    15   7
  BCL9 WILD-TYPE 302  41
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCL9 MUTATED     15    7
  BCL9 WILD-TYPE  302   41
                               clus
vv                              BCL9 MUTATED BCL9 WILD-TYPE
  COLON ADENOCARCINOMA                    15            302
  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 242   2  22  20
D74V9, multiclass
    clus
vv   BCL9 MUTATED BCL9 WILD-TYPE
  R0           15            242
  R1            0              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"
D74V10, 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
D74V11, 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 = NEFH MUTATION ANALYSIS
D75V1, survival
                sevent
clus2              0   1
  NEFH MUTATED    12   1
  NEFH WILD-TYPE 270  72
  NEFH MUTATED NEFH WILD-TYPE 
            13            342 
  NEFH MUTATED NEFH WILD-TYPE 
             1             72 
$`NEFH MUTATED`
TCGA-A6-6142 TCGA-AA-3947 TCGA-AA-A010 TCGA-AA-A02K TCGA-AD-6965 TCGA-AY-6197 
       25.08        33.01        34.98        14.01         0.20        21.44 
TCGA-AZ-4315 TCGA-CK-4948 TCGA-CM-6161 TCGA-D5-6920 TCGA-DM-A28K TCGA-F4-6856 
       58.39       102.44        15.02        12.39        98.24        19.43 
TCGA-G4-6588 
       26.17 

$`NEFH WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AU-3779 
        0.72         5.79        22.42        27.42        10.88        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       27.09        16.31         0.95        15.75         0.20        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
      117.07         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        35.41       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        52.80 

  NEFH MUTATED NEFH WILD-TYPE 
           0.2            0.0 
  NEFH MUTATED NEFH WILD-TYPE 
        102.44         140.38 
  NEFH MUTATED NEFH WILD-TYPE 
         25.08          20.07 
[1] "0.2 - 102.4 (25.1)" "0.0 - 140.4 (20.1)"
[1] "hr=" "3.7"
D75V2, 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       25       104         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NEFH MUTATED           0          1          0          0        1         1
  NEFH WILD-TYPE        19          9         41         31       34        12
                vv
clus             STAGE IVB
  NEFH MUTATED           0
  NEFH WILD-TYPE         1
D75V3, multiclass
            clus
vv           NEFH MUTATED NEFH WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             5            104
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            1              9
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 241  37
D75V4, multiclass
    clus
vv   NEFH MUTATED NEFH WILD-TYPE
  T1            0              9
  T2            2             66
  T3            7            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
  NEFH MUTATED     9   2   2
  NEFH WILD-TYPE 211  78  64
D75V5, multiclass
    clus
vv   NEFH MUTATED NEFH WILD-TYPE
  N0            9            211
  N1            2             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"
D75V6, binary
                cls
clus               0   1
  NEFH MUTATED     9   2
  NEFH WILD-TYPE 274  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED      9    2
  NEFH WILD-TYPE  274   46
   clus
vv  NEFH MUTATED NEFH WILD-TYPE
  0            9            274
  1            2             46
[1] 2 2
[1] FALSE
D75V7, 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
D75V8, binary
                cls
clus               0   1
  NEFH MUTATED    10   3
  NEFH WILD-TYPE 307  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED     10    3
  NEFH WILD-TYPE  307   45
                               clus
vv                              NEFH MUTATED NEFH WILD-TYPE
  COLON ADENOCARCINOMA                    10            307
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  NEFH MUTATED     9   0   1   0
  NEFH WILD-TYPE 248   2  21  21
D75V9, multiclass
    clus
vv   NEFH MUTATED NEFH WILD-TYPE
  R0            9            248
  R1            0              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"
D75V10, 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
D75V11, 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(76) Variable = XYLT2 MUTATION ANALYSIS
D76V1, survival
                 sevent
clus2               0   1
  XYLT2 MUTATED    12   2
  XYLT2 WILD-TYPE 270  71
  XYLT2 MUTATED XYLT2 WILD-TYPE 
             14             341 
  XYLT2 MUTATED XYLT2 WILD-TYPE 
              2              71 
$`XYLT2 MUTATED`
TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3663 TCGA-AA-3672 TCGA-AD-5900 
       33.53        22.06        19.66         6.97         0.92         0.07 
TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CM-4746 TCGA-CM-5861 TCGA-D5-6923 TCGA-F4-6570 
       58.39        49.41        37.02        15.02        12.43         6.18 
TCGA-G4-6586 TCGA-G4-6588 
       35.80        26.17 

$`XYLT2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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 
       16.01         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        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        13.38        13.45        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        91.79        46.75        52.80 

  XYLT2 MUTATED XYLT2 WILD-TYPE 
           0.07            0.00 
  XYLT2 MUTATED XYLT2 WILD-TYPE 
          58.39          140.38 
  XYLT2 MUTATED XYLT2 WILD-TYPE 
          20.86           20.19 
[1] "0.1 - 58.4 (20.9)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.3"
D76V2, 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       23       102         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        18         10         41         30       35        13
                 vv
clus              STAGE IVB
  XYLT2 MUTATED           0
  XYLT2 WILD-TYPE         1
D76V3, multiclass
            clus
vv           XYLT2 MUTATED XYLT2 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              7             102
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  XYLT2 MUTATED     0   3  10   1
  XYLT2 WILD-TYPE   9  65 238  40
D76V4, multiclass
    clus
vv   XYLT2 MUTATED XYLT2 WILD-TYPE
  T1             0               9
  T2             3              65
  T3            10             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
  XYLT2 MUTATED    12   2   0
  XYLT2 WILD-TYPE 208  78  66
D76V5, multiclass
    clus
vv   XYLT2 MUTATED XYLT2 WILD-TYPE
  N0            12             208
  N1             2              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"
D76V6, binary
                 cls
clus                0   1
  XYLT2 MUTATED    11   0
  XYLT2 WILD-TYPE 272  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XYLT2 MUTATED     11    0
  XYLT2 WILD-TYPE  272   48
   clus
vv  XYLT2 MUTATED XYLT2 WILD-TYPE
  0            11             272
  1             0              48
[1] 2 2
[1] FALSE
D76V7, 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
D76V8, binary
                 cls
clus                0   1
  XYLT2 MUTATED    12   2
  XYLT2 WILD-TYPE 305  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XYLT2 MUTATED     12    2
  XYLT2 WILD-TYPE  305   46
                               clus
vv                              XYLT2 MUTATED XYLT2 WILD-TYPE
  COLON ADENOCARCINOMA                     12             305
  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 244   2  22  21
D76V9, multiclass
    clus
vv   XYLT2 MUTATED XYLT2 WILD-TYPE
  R0            13             244
  R1             0               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"
D76V10, 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
D76V11, 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(77) Variable = GRB2 MUTATION ANALYSIS
D77V1, survival
                sevent
clus2              0   1
  GRB2 MUTATED     5   3
  GRB2 WILD-TYPE 277  70
  GRB2 MUTATED GRB2 WILD-TYPE 
             8            347 
  GRB2 MUTATED GRB2 WILD-TYPE 
             3             70 
$`GRB2 MUTATED`
TCGA-A6-5661 TCGA-AA-3543 TCGA-AA-A00N TCGA-AD-6964 TCGA-AY-6197 TCGA-D5-6538 
       33.53         0.99         4.01        10.88        21.44        17.13 
TCGA-DM-A1DA TCGA-G4-6625 
        7.50        91.79 

$`GRB2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       26.01        12.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 
        1.32        43.27        15.12        17.85         4.80        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        46.75        52.80 

  GRB2 MUTATED GRB2 WILD-TYPE 
          0.99           0.00 
  GRB2 MUTATED GRB2 WILD-TYPE 
         91.79         140.38 
  GRB2 MUTATED GRB2 WILD-TYPE 
        14.005         20.280 
[1] "1.0 - 91.8 (14.0)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "2.1"
D77V2, 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       25       106         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        18         10         40         30       35        13
                vv
clus             STAGE IVB
  GRB2 MUTATED           0
  GRB2 WILD-TYPE         1
D77V3, multiclass
            clus
vv           GRB2 MUTATED GRB2 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             3            106
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            1             30
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GRB2 MUTATED     0   1   6   2
  GRB2 WILD-TYPE   9  67 242  39
D77V4, multiclass
    clus
vv   GRB2 MUTATED GRB2 WILD-TYPE
  T1            0              9
  T2            1             67
  T3            6            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
  GRB2 MUTATED     5   0   4
  GRB2 WILD-TYPE 215  80  62
D77V5, multiclass
    clus
vv   GRB2 MUTATED GRB2 WILD-TYPE
  N0            5            215
  N1            0             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"
D77V6, binary
                cls
clus               0   1
  GRB2 MUTATED     7   0
  GRB2 WILD-TYPE 276  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRB2 MUTATED      7    0
  GRB2 WILD-TYPE  276   48
   clus
vv  GRB2 MUTATED GRB2 WILD-TYPE
  0            7            276
  1            0             48
[1] 2 2
[1] FALSE
D77V7, 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
D77V8, binary
                cls
clus               0   1
  GRB2 MUTATED     7   2
  GRB2 WILD-TYPE 310  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRB2 MUTATED      7    2
  GRB2 WILD-TYPE  310   46
                               clus
vv                              GRB2 MUTATED GRB2 WILD-TYPE
  COLON ADENOCARCINOMA                     7            310
  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 250   2  22  21
D77V9, multiclass
    clus
vv   GRB2 MUTATED GRB2 WILD-TYPE
  R0            7            250
  R1            0              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"
D77V10, 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
D77V11, 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(78) Variable = L1TD1 MUTATION ANALYSIS
D78V1, survival
                 sevent
clus2               0   1
  L1TD1 MUTATED    14   2
  L1TD1 WILD-TYPE 268  71
  L1TD1 MUTATED L1TD1 WILD-TYPE 
             16             339 
  L1TD1 MUTATED L1TD1 WILD-TYPE 
              2              71 
$`L1TD1 MUTATED`
TCGA-A6-3809 TCGA-A6-6654 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3525 
       32.75        23.87        19.66         3.02        63.98         8.05 
TCGA-AA-3663 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 TCGA-CA-5254 TCGA-CA-6717 
        6.97        18.05         4.01        34.98         2.24         0.33 
TCGA-CM-6166 TCGA-D5-6929 TCGA-G4-6309 TCGA-G4-6588 
       21.99        13.41        51.75        26.17 

$`L1TD1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        24.39        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 
       20.28         7.04         1.02        35.01         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
       36.03        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  L1TD1 MUTATED L1TD1 WILD-TYPE 
           0.33            0.00 
  L1TD1 MUTATED L1TD1 WILD-TYPE 
          63.98          140.38 
  L1TD1 MUTATED L1TD1 WILD-TYPE 
         18.855          20.280 
[1] "0.3 - 64.0 (18.9)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.4"
D78V2, 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       22       105         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        19         10         37         30       34        13
                 vv
clus              STAGE IVB
  L1TD1 MUTATED           0
  L1TD1 WILD-TYPE         1
D78V3, multiclass
            clus
vv           L1TD1 MUTATED L1TD1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              4             105
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             4              37
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  L1TD1 MUTATED     0   1  11   5
  L1TD1 WILD-TYPE   9  67 237  36
D78V4, multiclass
    clus
vv   L1TD1 MUTATED L1TD1 WILD-TYPE
  T1             0               9
  T2             1              67
  T3            11             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
  L1TD1 MUTATED    11   6   0
  L1TD1 WILD-TYPE 209  74  66
D78V5, multiclass
    clus
vv   L1TD1 MUTATED L1TD1 WILD-TYPE
  N0            11             209
  N1             6              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"
D78V6, binary
                 cls
clus                0   1
  L1TD1 MUTATED    15   1
  L1TD1 WILD-TYPE 268  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  L1TD1 MUTATED     15    1
  L1TD1 WILD-TYPE  268   47
   clus
vv  L1TD1 MUTATED L1TD1 WILD-TYPE
  0            15             268
  1             1              47
[1] 2 2
[1] FALSE
D78V7, 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
D78V8, binary
                 cls
clus                0   1
  L1TD1 MUTATED    12   5
  L1TD1 WILD-TYPE 305  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  L1TD1 MUTATED     12    5
  L1TD1 WILD-TYPE  305   43
                               clus
vv                              L1TD1 MUTATED L1TD1 WILD-TYPE
  COLON ADENOCARCINOMA                     12             305
  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 243   2  22  19
D78V9, multiclass
    clus
vv   L1TD1 MUTATED L1TD1 WILD-TYPE
  R0            14             243
  R1             0               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"
D78V10, 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
D78V11, 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(79) Variable = TMEM126A MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                  0   1
  TMEM126A MUTATED     4   3
  TMEM126A WILD-TYPE 278  70
  TMEM126A MUTATED TMEM126A WILD-TYPE 
                 7                348 
  TMEM126A MUTATED TMEM126A WILD-TYPE 
                 3                 70 
$`TMEM126A MUTATED`
TCGA-AA-3662 TCGA-AD-6895 TCGA-AZ-6603 TCGA-AZ-6608 TCGA-DM-A1HA TCGA-DM-A28G 
        6.05         0.72        29.56         1.94       131.51        60.79 
TCGA-DM-A28K 
       98.24 

$`TMEM126A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        4.21        56.55         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10       100.01         5.23        11.74         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 
       12.59       140.38         7.50        44.32       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-F4-6459 
        6.12        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 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  TMEM126A MUTATED TMEM126A WILD-TYPE 
              0.72               0.00 
  TMEM126A MUTATED TMEM126A WILD-TYPE 
            131.51             140.38 
  TMEM126A MUTATED TMEM126A WILD-TYPE 
            29.560             20.155 
[1] "0.7 - 131.5 (29.6)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.3"
D79V2, 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       25       107         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM126A MUTATED           0          1          0          1        1
  TMEM126A WILD-TYPE        19          9         41         30       34
                    vv
clus                 STAGE IVA STAGE IVB
  TMEM126A MUTATED           0         0
  TMEM126A WILD-TYPE        13         1
D79V3, multiclass
            clus
vv           TMEM126A MUTATED TMEM126A WILD-TYPE
  STAGE I                   0                 64
  STAGE IA                  0                  1
  STAGE II                  0                 25
  STAGE IIA                 2                107
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                1                  9
  STAGE IIIB                0                 41
  STAGE IIIC                1                 30
  STAGE IV                  1                 34
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  TMEM126A MUTATED     0   2   4   1
  TMEM126A WILD-TYPE   9  66 244  40
D79V4, multiclass
    clus
vv   TMEM126A MUTATED TMEM126A WILD-TYPE
  T1                0                  9
  T2                2                 66
  T3                4                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
  TMEM126A MUTATED     2   3   2
  TMEM126A WILD-TYPE 218  77  64
D79V5, multiclass
    clus
vv   TMEM126A MUTATED TMEM126A WILD-TYPE
  N0                2                218
  N1                3                 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"
D79V6, binary
                    cls
clus                   0   1
  TMEM126A MUTATED     4   1
  TMEM126A WILD-TYPE 279  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMEM126A MUTATED      4    1
  TMEM126A WILD-TYPE  279   47
   clus
vv  TMEM126A MUTATED TMEM126A WILD-TYPE
  0                4                279
  1                1                 47
[1] 2 2
[1] FALSE
D79V7, 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
D79V8, binary
                    cls
clus                   0   1
  TMEM126A MUTATED     6   1
  TMEM126A WILD-TYPE 311  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMEM126A MUTATED      6    1
  TMEM126A WILD-TYPE  311   47
                               clus
vv                              TMEM126A MUTATED TMEM126A WILD-TYPE
  COLON ADENOCARCINOMA                         6                311
  COLON MUCINOUS ADENOCARCINOMA                1                 47
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  TMEM126A MUTATED     0   0   1   0
  TMEM126A WILD-TYPE 257   2  21  21
D79V9, multiclass
[1] "Remove cluster labels:" "TMEM126A MUTATED"      
clus
  TMEM126A MUTATED TMEM126A WILD-TYPE 
                 1                301 
        TCGA-A6-2671         TCGA-A6-2672         TCGA-A6-2674 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-A6-2676         TCGA-A6-2677         TCGA-A6-2678 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-A6-2683         TCGA-A6-3807         TCGA-A6-3808 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-A6-3809         TCGA-A6-3810         TCGA-A6-5657 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-A6-5659         TCGA-A6-5661         TCGA-A6-5665 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-A6-6781         TCGA-AA-3489         TCGA-AA-3492 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3496         TCGA-AA-3502         TCGA-AA-3510 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3511         TCGA-AA-3514         TCGA-AA-3517 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3518         TCGA-AA-3519         TCGA-AA-3520 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3521         TCGA-AA-3522         TCGA-AA-3524 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3525         TCGA-AA-3526         TCGA-AA-3527 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3529         TCGA-AA-3530         TCGA-AA-3531 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3532         TCGA-AA-3534         TCGA-AA-3538 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3542         TCGA-AA-3543         TCGA-AA-3544 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3548         TCGA-AA-3549         TCGA-AA-3552 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3553         TCGA-AA-3554         TCGA-AA-3555 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3556         TCGA-AA-3558         TCGA-AA-3560 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3561         TCGA-AA-3562         TCGA-AA-3655 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3660         TCGA-AA-3663         TCGA-AA-3664 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3666         TCGA-AA-3667         TCGA-AA-3672 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3673         TCGA-AA-3678         TCGA-AA-3679 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3680         TCGA-AA-3681         TCGA-AA-3684 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3685         TCGA-AA-3688         TCGA-AA-3692 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3693         TCGA-AA-3695         TCGA-AA-3696 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3697         TCGA-AA-3710         TCGA-AA-3712 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3713         TCGA-AA-3715         TCGA-AA-3811 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3812         TCGA-AA-3814         TCGA-AA-3815 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3818         TCGA-AA-3819         TCGA-AA-3821 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3831         TCGA-AA-3833         TCGA-AA-3837 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3842         TCGA-AA-3844         TCGA-AA-3845 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3846         TCGA-AA-3848         TCGA-AA-3850 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3851         TCGA-AA-3852         TCGA-AA-3854 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3855         TCGA-AA-3856         TCGA-AA-3858 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3860         TCGA-AA-3861         TCGA-AA-3864 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3866         TCGA-AA-3867         TCGA-AA-3869 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3870         TCGA-AA-3872         TCGA-AA-3875 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3877         TCGA-AA-3930         TCGA-AA-3939 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3941         TCGA-AA-3947         TCGA-AA-3949 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3950         TCGA-AA-3952         TCGA-AA-3955 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3956         TCGA-AA-3968         TCGA-AA-3971 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3972         TCGA-AA-3973         TCGA-AA-3975 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3976         TCGA-AA-3979         TCGA-AA-3984 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3986         TCGA-AA-3989         TCGA-AA-3994 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-A004         TCGA-AA-A00A         TCGA-AA-A00D 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-A00E         TCGA-AA-A00F         TCGA-AA-A00J 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-A00K         TCGA-AA-A00L         TCGA-AA-A00N 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-A00O         TCGA-AA-A00Q         TCGA-AA-A00R 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-A00U         TCGA-AA-A00W         TCGA-AA-A00Z 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-A010         TCGA-AA-A017         TCGA-AA-A01D 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-A01F         TCGA-AA-A01G         TCGA-AA-A01I 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-A01K         TCGA-AA-A01P         TCGA-AA-A01Q 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-A01R         TCGA-AA-A01S         TCGA-AA-A01T 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-A01V         TCGA-AA-A01X         TCGA-AA-A01Z 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-A022         TCGA-AA-A024         TCGA-AA-A029 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-A02F         TCGA-AA-A02H         TCGA-AA-A02J 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-A02K         TCGA-AA-A02O         TCGA-AA-A02W 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-A02Y         TCGA-AA-A03F         TCGA-AA-A03J 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AD-5900         TCGA-AD-6548         TCGA-AD-6888 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AU-3779         TCGA-AU-6004         TCGA-AY-4070 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AY-4071         TCGA-AY-5543         TCGA-AY-6196 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AY-6197         TCGA-AY-6386         TCGA-AZ-4315 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AZ-4681         TCGA-AZ-4682         TCGA-CA-5254 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-CA-5255         TCGA-CA-5796         TCGA-CA-5797 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-CA-6715         TCGA-CA-6716         TCGA-CA-6717 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-CA-6718         TCGA-CA-6719         TCGA-CK-4947 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-CK-4948         TCGA-CK-4950         TCGA-CK-4952 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-CK-5912         TCGA-CK-5913         TCGA-CK-5914 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-CK-5915         TCGA-CK-5916         TCGA-CK-6746 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-CK-6747         TCGA-CK-6748         TCGA-CK-6751 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-CM-4743         TCGA-CM-4744         TCGA-CM-4746 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-CM-4747         TCGA-CM-4752         TCGA-CM-5341 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-CM-5344         TCGA-CM-5348         TCGA-CM-5349 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-CM-5860         TCGA-CM-5861         TCGA-CM-5862 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-CM-5863         TCGA-CM-5864         TCGA-CM-5868 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-CM-6161         TCGA-CM-6162         TCGA-CM-6163 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-CM-6164         TCGA-CM-6165         TCGA-CM-6166 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-CM-6167         TCGA-CM-6168         TCGA-CM-6169 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-CM-6170         TCGA-CM-6171         TCGA-CM-6172 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-CM-6674         TCGA-CM-6675         TCGA-CM-6676 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-CM-6677         TCGA-CM-6678         TCGA-CM-6679 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-CM-6680         TCGA-D5-5537         TCGA-D5-5538 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-D5-5539         TCGA-D5-5540         TCGA-D5-5541 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-D5-6529         TCGA-D5-6532         TCGA-D5-6533 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-D5-6534         TCGA-D5-6535         TCGA-D5-6536 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-D5-6537         TCGA-D5-6538         TCGA-D5-6539 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-D5-6540         TCGA-D5-6541         TCGA-D5-6898 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-D5-6920         TCGA-D5-6922         TCGA-D5-6923 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-D5-6924         TCGA-D5-6926         TCGA-D5-6927 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-D5-6928         TCGA-D5-6929         TCGA-D5-6930 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-D5-6931         TCGA-D5-6932         TCGA-D5-7000 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-F4-6459         TCGA-F4-6460         TCGA-F4-6569 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-F4-6570         TCGA-F4-6703         TCGA-F4-6704 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-F4-6805         TCGA-F4-6806         TCGA-F4-6807 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-F4-6808         TCGA-F4-6809         TCGA-F4-6854 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-F4-6855         TCGA-F4-6856         TCGA-G4-6293 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-G4-6299         TCGA-G4-6303         TCGA-G4-6304 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-G4-6306         TCGA-G4-6307         TCGA-G4-6309 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-G4-6310         TCGA-G4-6315         TCGA-G4-6317 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-G4-6321         TCGA-G4-6323         TCGA-G4-6586 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-G4-6588         TCGA-G4-6625         TCGA-G4-6626 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-G4-6628 
"TMEM126A WILD-TYPE" 
D79V10, 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
D79V11, 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(80) Variable = KCTD3 MUTATION ANALYSIS
D80V1, survival
                 sevent
clus2               0   1
  KCTD3 MUTATED    12   4
  KCTD3 WILD-TYPE 270  69
  KCTD3 MUTATED KCTD3 WILD-TYPE 
             16             339 
  KCTD3 MUTATED KCTD3 WILD-TYPE 
              4              69 
$`KCTD3 MUTATED`
TCGA-A6-5664 TCGA-A6-6649 TCGA-A6-6653 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-5900 
       22.09        24.16        24.39         4.01        34.98         0.07 
TCGA-AD-6964 TCGA-AZ-4682 TCGA-CA-6718 TCGA-CM-4743 TCGA-CM-6171 TCGA-F4-6570 
       10.88        22.36         0.10        23.05        14.04         6.18 
TCGA-G4-6309 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 
       51.75        35.80        26.17        52.80 

$`KCTD3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       25.18        21.76        24.69        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        1.41         5.13        83.80        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.33         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        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        13.38        13.45        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 
       13.78        91.79        46.75 

  KCTD3 MUTATED KCTD3 WILD-TYPE 
           0.07            0.00 
  KCTD3 MUTATED KCTD3 WILD-TYPE 
          52.80          140.38 
  KCTD3 MUTATED KCTD3 WILD-TYPE 
         22.705          20.020 
[1] "0.1 - 52.8 (22.7)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1.4"
D80V2, 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       24       104         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        19         10         39         30       35        12
                 vv
clus              STAGE IVB
  KCTD3 MUTATED           0
  KCTD3 WILD-TYPE         1
D80V3, multiclass
            clus
vv           KCTD3 MUTATED KCTD3 WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              5             104
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  64 240  36
D80V4, multiclass
    clus
vv   KCTD3 MUTATED KCTD3 WILD-TYPE
  T1             0               9
  T2             4              64
  T3             8             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
  KCTD3 MUTATED    13   2   2
  KCTD3 WILD-TYPE 207  78  64
D80V5, multiclass
    clus
vv   KCTD3 MUTATED KCTD3 WILD-TYPE
  N0            13             207
  N1             2              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"
D80V6, binary
                 cls
clus                0   1
  KCTD3 MUTATED    13   1
  KCTD3 WILD-TYPE 270  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCTD3 MUTATED     13    1
  KCTD3 WILD-TYPE  270   47
   clus
vv  KCTD3 MUTATED KCTD3 WILD-TYPE
  0            13             270
  1             1              47
[1] 2 2
[1] FALSE
D80V7, 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
D80V8, binary
                 cls
clus                0   1
  KCTD3 MUTATED    15   2
  KCTD3 WILD-TYPE 302  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCTD3 MUTATED     15    2
  KCTD3 WILD-TYPE  302   46
                               clus
vv                              KCTD3 MUTATED KCTD3 WILD-TYPE
  COLON ADENOCARCINOMA                     15             302
  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 245   2  22  20
D80V9, multiclass
    clus
vv   KCTD3 MUTATED KCTD3 WILD-TYPE
  R0            12             245
  R1             0               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"
D80V10, 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
D80V11, 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(81) Variable = PRKDC MUTATION ANALYSIS
D81V1, survival
                 sevent
clus2               0   1
  PRKDC MUTATED    47  12
  PRKDC WILD-TYPE 235  61
  PRKDC MUTATED PRKDC WILD-TYPE 
             59             296 
  PRKDC MUTATED PRKDC WILD-TYPE 
             12              61 
$`PRKDC MUTATED`
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6141 TCGA-A6-6653 
       31.63        30.44        22.06        32.71         8.38        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3715 
       20.12        19.66        63.98        61.02         6.97        19.04 
TCGA-AA-3811 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-A00N TCGA-AA-A010 
       10.06        53.00        31.00         2.01         4.01        34.98 
TCGA-AA-A01P TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6964 TCGA-AU-3779 TCGA-AU-6004 
       38.07         0.07        56.55        10.88        14.50        27.09 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6601 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-6717 
       21.44        58.39       100.01         3.19         1.94         0.33 
TCGA-CA-6718 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 TCGA-CM-5349 TCGA-CM-5860 
        0.10       102.44        15.62        51.32        30.08        16.01 
TCGA-CM-6161 TCGA-CM-6166 TCGA-CM-6171 TCGA-CM-6676 TCGA-D5-6532 TCGA-D5-6535 
       15.02        21.99        14.04        11.08        18.25        15.12 
TCGA-D5-6537 TCGA-D5-6923 TCGA-D5-6927 TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6703 
        4.80        12.43         9.44       117.07        98.24        35.87 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 
       13.25         0.53        19.43       107.67        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6315 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       44.68        36.72        26.17        91.79        52.80 

$`PRKDC WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-6137 
       32.91        29.19        33.53        23.61        22.09        27.09 
TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 
       22.52        25.08        25.18        24.16        21.76        24.69 
TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       23.87        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       19.99        78.08         6.05        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 
       24.03        27.02        29.98        18.05        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37         4.21 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        15.75         0.20        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5254 
        6.77        12.10        29.56         5.23        11.74         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07         0.26         1.35 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       17.56        40.34        49.08        21.99        21.14         2.93 
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-5861 TCGA-CM-5862 
       13.02        29.06        22.03        22.98        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-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-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
        1.32        43.27        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-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64        13.41         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 
       60.79         8.61        13.38        13.45         6.18         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6855 TCGA-G4-6299 
       16.31        29.59        16.24        33.67        35.41        74.56 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        51.75        45.11        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6626 
       35.80        46.75 

  PRKDC MUTATED PRKDC WILD-TYPE 
           0.07            0.00 
  PRKDC MUTATED PRKDC WILD-TYPE 
         117.07          140.38 
  PRKDC MUTATED PRKDC WILD-TYPE 
         21.990          20.005 
[1] "0.1 - 117.1 (22.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.4"
D81V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PRKDC MUTATED        12        0        6        21         3         1
  PRKDC WILD-TYPE      52        1       19        88         5         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PRKDC MUTATED           4          2          3          2        4         1
  PRKDC WILD-TYPE        15          8         38         29       31        12
                 vv
clus              STAGE IVB
  PRKDC MUTATED           0
  PRKDC WILD-TYPE         1
D81V3, multiclass
            clus
vv           PRKDC MUTATED PRKDC WILD-TYPE
  STAGE I               12              52
  STAGE IA               0               1
  STAGE II               6              19
  STAGE IIA             21              88
  STAGE IIB              3               5
  STAGE IIC              1               0
  STAGE III              4              15
  STAGE IIIA             2               8
  STAGE IIIB             3              38
  STAGE IIIC             2              29
  STAGE IV               4              31
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  13  38   8
  PRKDC WILD-TYPE   8  55 210  33
D81V4, multiclass
    clus
vv   PRKDC MUTATED PRKDC WILD-TYPE
  T1             1               8
  T2            13              55
  T3            38             210
  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
  PRKDC MUTATED    43  11   6
  PRKDC WILD-TYPE 177  69  60
D81V5, multiclass
    clus
vv   PRKDC MUTATED PRKDC WILD-TYPE
  N0            43             177
  N1            11              69
  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"
D81V6, binary
                 cls
clus                0   1
  PRKDC MUTATED    47   5
  PRKDC WILD-TYPE 236  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKDC MUTATED     47    5
  PRKDC WILD-TYPE  236   43
   clus
vv  PRKDC MUTATED PRKDC WILD-TYPE
  0            47             236
  1             5              43
[1] 2 2
[1] FALSE
D81V7, binary
                 cls
clus                0   1
  PRKDC MUTATED    24  36
  PRKDC WILD-TYPE 146 161
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKDC MUTATED     24   36
  PRKDC WILD-TYPE  146  161
        clus
vv       PRKDC MUTATED PRKDC WILD-TYPE
  FEMALE            24             146
  MALE              36             161
[1] 2 2
[1] FALSE
D81V8, binary
                 cls
clus                0   1
  PRKDC MUTATED    51   9
  PRKDC WILD-TYPE 266  39
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKDC MUTATED     51    9
  PRKDC WILD-TYPE  266   39
                               clus
vv                              PRKDC MUTATED PRKDC WILD-TYPE
  COLON ADENOCARCINOMA                     51             266
  COLON MUCINOUS ADENOCARCINOMA             9              39
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PRKDC MUTATED    43   0   1   5
  PRKDC WILD-TYPE 214   2  21  16
D81V9, multiclass
    clus
vv   PRKDC MUTATED PRKDC WILD-TYPE
  R0            43             214
  R1             0               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"
D81V10, 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    43
  PRKDC WILD-TYPE                        17   133
D81V11, 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                                       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(82) Variable = PCBP1 MUTATION ANALYSIS
D82V1, survival
                 sevent
clus2               0   1
  PCBP1 MUTATED     9   0
  PCBP1 WILD-TYPE 273  73
  PCBP1 MUTATED PCBP1 WILD-TYPE 
              9             346 
  PCBP1 MUTATED PCBP1 WILD-TYPE 
              0              73 
$`PCBP1 MUTATED`
TCGA-AA-3941 TCGA-AA-3979 TCGA-AA-A01I TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 
       24.00        24.00        31.00         0.10        17.56        40.34 
TCGA-CK-6751 TCGA-CM-6680 TCGA-D5-6529 
      124.27        12.03        20.19 

$`PCBP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        25.02        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 
        0.26         0.33         1.35       102.44        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       11.51        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  PCBP1 MUTATED PCBP1 WILD-TYPE 
            0.1             0.0 
  PCBP1 MUTATED PCBP1 WILD-TYPE 
         124.27          140.38 
  PCBP1 MUTATED PCBP1 WILD-TYPE 
          24.00           20.07 
[1] "0.1 - 124.3 (24.0)" "0.0 - 140.4 (20.1)"
[1] "hr="     "2.5e+07"
D82V2, 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       25       105         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PCBP1 MUTATED           0          1          1          0        0         2
  PCBP1 WILD-TYPE        19          9         40         31       35        11
                 vv
clus              STAGE IVB
  PCBP1 MUTATED           0
  PCBP1 WILD-TYPE         1
D82V3, multiclass
            clus
vv           PCBP1 MUTATED PCBP1 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              4             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              2              11
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 242  39
D82V4, multiclass
    clus
vv   PCBP1 MUTATED PCBP1 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             6             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
  PCBP1 MUTATED     6   3   1
  PCBP1 WILD-TYPE 214  77  65
D82V5, multiclass
    clus
vv   PCBP1 MUTATED PCBP1 WILD-TYPE
  N0             6             214
  N1             3              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"
D82V6, binary
                 cls
clus                0   1
  PCBP1 MUTATED     8   1
  PCBP1 WILD-TYPE 275  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCBP1 MUTATED      8    1
  PCBP1 WILD-TYPE  275   47
   clus
vv  PCBP1 MUTATED PCBP1 WILD-TYPE
  0             8             275
  1             1              47
[1] 2 2
[1] FALSE
D82V7, 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
D82V8, binary
                 cls
clus                0   1
  PCBP1 MUTATED     9   1
  PCBP1 WILD-TYPE 308  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCBP1 MUTATED      9    1
  PCBP1 WILD-TYPE  308   47
                               clus
vv                              PCBP1 MUTATED PCBP1 WILD-TYPE
  COLON ADENOCARCINOMA                      9             308
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PCBP1 MUTATED     6   1   0   3
  PCBP1 WILD-TYPE 251   1  22  18
D82V9, multiclass
    clus
vv   PCBP1 MUTATED PCBP1 WILD-TYPE
  R0             6             251
  R1             1               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"
D82V10, 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
D82V11, 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(83) Variable = ECT2 MUTATION ANALYSIS
D83V1, survival
                sevent
clus2              0   1
  ECT2 MUTATED    13   5
  ECT2 WILD-TYPE 269  68
  ECT2 MUTATED ECT2 WILD-TYPE 
            18            337 
  ECT2 MUTATED ECT2 WILD-TYPE 
             5             68 
$`ECT2 MUTATED`
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-6781 TCGA-AA-3713 TCGA-AA-3950 TCGA-AA-A00D 
       46.65        42.90        19.66        19.04        24.00        19.00 
TCGA-AA-A00N TCGA-AZ-5403 TCGA-AZ-6608 TCGA-CK-5913 TCGA-CM-5861 TCGA-CM-6170 
        4.01        62.79         1.94        51.32        15.02        15.02 
TCGA-D5-6926 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6586 TCGA-G4-6628 
        9.04        65.85        53.62        51.75        35.80        52.80 

$`ECT2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       43.76        43.76        24.33        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       33.34        32.75        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       27.02        13.94        38.04        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 
        1.41         5.13        83.80        22.36        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       40.34        15.62        49.08        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       19.43       107.67        74.56        44.68        55.04        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        26.17        91.79 
TCGA-G4-6626 
       46.75 

  ECT2 MUTATED ECT2 WILD-TYPE 
          1.94           0.00 
  ECT2 MUTATED ECT2 WILD-TYPE 
         65.85         140.38 
  ECT2 MUTATED ECT2 WILD-TYPE 
         29.90          20.12 
[1] "1.9 - 65.8 (29.9)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1"  
D83V2, 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       24       105         5         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ECT2 MUTATED           0          2          2          1        2         0
  ECT2 WILD-TYPE        19          8         39         30       33        13
                vv
clus             STAGE IVB
  ECT2 MUTATED           0
  ECT2 WILD-TYPE         1
D83V3, multiclass
            clus
vv           ECT2 MUTATED ECT2 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             4            105
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            2              8
  STAGE IIIB            2             39
  STAGE IIIC            1             30
  STAGE IV              2             33
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ECT2 MUTATED     0   4   9   5
  ECT2 WILD-TYPE   9  64 239  36
D83V4, multiclass
    clus
vv   ECT2 MUTATED ECT2 WILD-TYPE
  T1            0              9
  T2            4             64
  T3            9            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
  ECT2 MUTATED    12   6   0
  ECT2 WILD-TYPE 208  74  66
D83V5, multiclass
    clus
vv   ECT2 MUTATED ECT2 WILD-TYPE
  N0           12            208
  N1            6             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"
D83V6, binary
                cls
clus               0   1
  ECT2 MUTATED    13   2
  ECT2 WILD-TYPE 270  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  ECT2 MUTATED     13    2
  ECT2 WILD-TYPE  270   46
   clus
vv  ECT2 MUTATED ECT2 WILD-TYPE
  0           13            270
  1            2             46
[1] 2 2
[1] FALSE
D83V7, 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
D83V8, binary
                cls
clus               0   1
  ECT2 MUTATED    15   3
  ECT2 WILD-TYPE 302  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  ECT2 MUTATED     15    3
  ECT2 WILD-TYPE  302   45
                               clus
vv                              ECT2 MUTATED ECT2 WILD-TYPE
  COLON ADENOCARCINOMA                    15            302
  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 243   2  21  20
D83V9, multiclass
    clus
vv   ECT2 MUTATED ECT2 WILD-TYPE
  R0           14            243
  R1            0              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"
D83V10, 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
D83V11, 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(84) Variable = RLIM MUTATION ANALYSIS
D84V1, survival
                sevent
clus2              0   1
  RLIM MUTATED    12   2
  RLIM WILD-TYPE 270  71
  RLIM MUTATED RLIM WILD-TYPE 
            14            341 
  RLIM MUTATED RLIM WILD-TYPE 
             2             71 
$`RLIM MUTATED`
TCGA-A6-6651 TCGA-AA-3678 TCGA-AA-3947 TCGA-AZ-5407 TCGA-CK-4952 TCGA-CM-4752 
       21.76        47.01        33.01        61.41        15.62        13.02 
TCGA-D5-5540 TCGA-F4-6570 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6321 
       13.51         6.18        35.41       107.67        65.85        22.09 
TCGA-G4-6586 TCGA-G4-6625 
       35.80        91.79 

$`RLIM WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        24.16        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       19.59        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.38        13.45        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6299 
       16.24        33.67        13.25         0.53        19.43        74.56 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6628 
       36.00        13.78        26.17        46.75        52.80 

  RLIM MUTATED RLIM WILD-TYPE 
          6.18           0.00 
  RLIM MUTATED RLIM WILD-TYPE 
        107.67         140.38 
  RLIM MUTATED RLIM WILD-TYPE 
         34.21          19.99 
[1] "6.2 - 107.7 (34.2)" "0.0 - 140.4 (20.0)"
[1] "hr=" "2.3"
D84V2, 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       25       103         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RLIM MUTATED           4          0          1          0        1         0
  RLIM WILD-TYPE        15         10         40         31       34        13
                vv
clus             STAGE IVB
  RLIM MUTATED           0
  RLIM WILD-TYPE         1
D84V3, multiclass
            clus
vv           RLIM MUTATED RLIM WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             6            103
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             4             15
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RLIM MUTATED     1   2   9   2
  RLIM WILD-TYPE   8  66 239  39
D84V4, multiclass
    clus
vv   RLIM MUTATED RLIM WILD-TYPE
  T1            1              8
  T2            2             66
  T3            9            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
  RLIM MUTATED     8   5   1
  RLIM WILD-TYPE 212  75  65
D84V5, multiclass
    clus
vv   RLIM MUTATED RLIM WILD-TYPE
  N0            8            212
  N1            5             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"
D84V6, binary
                cls
clus               0   1
  RLIM MUTATED    11   1
  RLIM WILD-TYPE 272  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  RLIM MUTATED     11    1
  RLIM WILD-TYPE  272   47
   clus
vv  RLIM MUTATED RLIM WILD-TYPE
  0           11            272
  1            1             47
[1] 2 2
[1] FALSE
D84V7, 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
D84V8, binary
                cls
clus               0   1
  RLIM MUTATED    12   2
  RLIM WILD-TYPE 305  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  RLIM MUTATED     12    2
  RLIM WILD-TYPE  305   46
                               clus
vv                              RLIM MUTATED RLIM WILD-TYPE
  COLON ADENOCARCINOMA                    12            305
  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 246   2  22  20
D84V9, multiclass
    clus
vv   RLIM MUTATED RLIM WILD-TYPE
  R0           11            246
  R1            0              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"
D84V10, 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
D84V11, 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(85) Variable = BIRC3 MUTATION ANALYSIS
D85V1, survival
                 sevent
clus2               0   1
  BIRC3 MUTATED    11   0
  BIRC3 WILD-TYPE 271  73
  BIRC3 MUTATED BIRC3 WILD-TYPE 
             11             344 
  BIRC3 MUTATED BIRC3 WILD-TYPE 
              0              73 
$`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        15.75 
TCGA-AY-6196 TCGA-CA-6718 TCGA-CM-5868 TCGA-D5-6929 TCGA-F4-6808 
        0.20         0.10        17.03        13.41        33.67 

$`BIRC3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       33.04         0.99        25.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       27.09        16.31         0.95        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.33         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 
       35.87         1.55        16.31        29.59        16.24        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  BIRC3 MUTATED BIRC3 WILD-TYPE 
            0.1             0.0 
  BIRC3 MUTATED BIRC3 WILD-TYPE 
          34.98          140.38 
  BIRC3 MUTATED BIRC3 WILD-TYPE 
          15.75           20.63 
[1] "0.1 - 35.0 (15.8)"  "0.0 - 140.4 (20.6)"
[1] "hr="     "9300000"
D85V2, 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       24       107         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        19         10         41         30       34        11
                 vv
clus              STAGE IVB
  BIRC3 MUTATED           0
  BIRC3 WILD-TYPE         1
D85V3, multiclass
            clus
vv           BIRC3 MUTATED BIRC3 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              2             107
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              2              11
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 242  38
D85V4, multiclass
    clus
vv   BIRC3 MUTATED BIRC3 WILD-TYPE
  T1             1               8
  T2             1              67
  T3             6             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
  BIRC3 MUTATED     7   3   1
  BIRC3 WILD-TYPE 213  77  65
D85V5, multiclass
    clus
vv   BIRC3 MUTATED BIRC3 WILD-TYPE
  N0             7             213
  N1             3              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"
D85V6, binary
                 cls
clus                0   1
  BIRC3 MUTATED     7   3
  BIRC3 WILD-TYPE 276  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BIRC3 MUTATED      7    3
  BIRC3 WILD-TYPE  276   45
   clus
vv  BIRC3 MUTATED BIRC3 WILD-TYPE
  0             7             276
  1             3              45
[1] 2 2
[1] FALSE
D85V7, 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
D85V8, binary
                 cls
clus                0   1
  BIRC3 MUTATED     8   3
  BIRC3 WILD-TYPE 309  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BIRC3 MUTATED      8    3
  BIRC3 WILD-TYPE  309   45
                               clus
vv                              BIRC3 MUTATED BIRC3 WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  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 247   2  22  20
D85V9, multiclass
    clus
vv   BIRC3 MUTATED BIRC3 WILD-TYPE
  R0            10             247
  R1             0               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"
D85V10, 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
D85V11, 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(86) Variable = BCORL1 MUTATION ANALYSIS
D86V1, survival
                  sevent
clus2                0   1
  BCORL1 MUTATED    18   6
  BCORL1 WILD-TYPE 264  67
  BCORL1 MUTATED BCORL1 WILD-TYPE 
              24              331 
  BCORL1 MUTATED BCORL1 WILD-TYPE 
               6               67 
$`BCORL1 MUTATED`
TCGA-A6-2676 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3713 TCGA-AA-3811 
       42.90        22.06        19.66        63.98        19.04        10.06 
TCGA-AA-3861 TCGA-AA-A010 TCGA-AD-6889 TCGA-AD-6895 TCGA-AU-6004 TCGA-AY-6197 
       30.05        34.98        56.55         0.72        27.09        21.44 
TCGA-AZ-4323 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5916 TCGA-CM-5861 TCGA-CM-6162 
        1.41        83.80         1.94        21.14        15.02        12.00 
TCGA-CM-6674 TCGA-D5-6533 TCGA-D5-6538 TCGA-DM-A1DA TCGA-DM-A28H TCGA-G4-6588 
       12.95         1.32        17.13         7.50       117.07        26.17 

$`BCORL1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       26.99        19.04        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       14.50        16.31         0.95        15.75         0.20        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        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
       40.34        15.62        49.08        51.32        21.99         2.93 
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        16.01 
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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 
       13.51        11.51        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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32        12.59       140.38        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 
       52.80 

  BCORL1 MUTATED BCORL1 WILD-TYPE 
            0.72             0.00 
  BCORL1 MUTATED BCORL1 WILD-TYPE 
          117.07           140.38 
  BCORL1 MUTATED BCORL1 WILD-TYPE 
           20.40            20.19 
[1] "0.7 - 117.1 (20.4)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D86V2, 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       24       101         5         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BCORL1 MUTATED           1          1          3          3        2
  BCORL1 WILD-TYPE        18          9         38         28       33
                  vv
clus               STAGE IVA STAGE IVB
  BCORL1 MUTATED           0         0
  BCORL1 WILD-TYPE        13         1
D86V3, multiclass
            clus
vv           BCORL1 MUTATED BCORL1 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               8              101
  STAGE IIB               3                5
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              1                9
  STAGE IIIB              3               38
  STAGE IIIC              3               28
  STAGE IV                2               33
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  BCORL1 MUTATED     1   2  16   6
  BCORL1 WILD-TYPE   8  66 232  35
D86V4, multiclass
    clus
vv   BCORL1 MUTATED BCORL1 WILD-TYPE
  T1              1                8
  T2              2               66
  T3             16              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
  BCORL1 MUTATED    16   4   5
  BCORL1 WILD-TYPE 204  76  61
D86V5, multiclass
    clus
vv   BCORL1 MUTATED BCORL1 WILD-TYPE
  N0             16              204
  N1              4               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"
D86V6, binary
                  cls
clus                 0   1
  BCORL1 MUTATED    19   2
  BCORL1 WILD-TYPE 264  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCORL1 MUTATED     19    2
  BCORL1 WILD-TYPE  264   46
   clus
vv  BCORL1 MUTATED BCORL1 WILD-TYPE
  0             19              264
  1              2               46
[1] 2 2
[1] FALSE
D86V7, 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
D86V8, binary
                  cls
clus                 0   1
  BCORL1 MUTATED    23   2
  BCORL1 WILD-TYPE 294  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCORL1 MUTATED     23    2
  BCORL1 WILD-TYPE  294   46
                               clus
vv                              BCORL1 MUTATED BCORL1 WILD-TYPE
  COLON ADENOCARCINOMA                      23              294
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  BCORL1 MUTATED    16   0   1   2
  BCORL1 WILD-TYPE 241   2  21  19
D86V9, multiclass
    clus
vv   BCORL1 MUTATED BCORL1 WILD-TYPE
  R0             16              241
  R1              0                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"
D86V10, 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
D86V11, 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(87) Variable = SLK MUTATION ANALYSIS
D87V1, survival
               sevent
clus2             0   1
  SLK MUTATED    19   2
  SLK WILD-TYPE 263  71
  SLK MUTATED SLK WILD-TYPE 
           21           334 
  SLK MUTATED SLK WILD-TYPE 
            2            71 
$`SLK MUTATED`
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6651 TCGA-A6-6782 TCGA-AA-3510 TCGA-AA-3663 
       22.06        32.71        21.76        20.28        63.98         6.97 
TCGA-AA-3710 TCGA-AA-3877 TCGA-AA-A010 TCGA-AA-A01I TCGA-AD-6889 TCGA-AU-6004 
       26.99        31.00        34.98        31.00        56.55        27.09 
TCGA-AZ-4315 TCGA-AZ-6603 TCGA-CA-6717 TCGA-CM-6172 TCGA-D5-6533 TCGA-D5-6924 
       58.39        29.56         0.33        11.01         1.32        14.30 
TCGA-D5-7000 TCGA-G4-6303 TCGA-G4-6321 
       10.26        65.85        22.09 

$`SLK WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.09        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       24.16        24.69        24.39        23.87        20.12        19.66 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 
        7.04         3.02         1.02        35.01         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       78.08         6.05        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K 
       21.99        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        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37         4.21         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10       100.01         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        11.38       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       19.43       107.67        74.56        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 
       51.75        45.11        36.72        36.00        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  SLK MUTATED SLK WILD-TYPE 
         0.33          0.00 
  SLK MUTATED SLK WILD-TYPE 
        65.85        140.38 
  SLK MUTATED SLK WILD-TYPE 
       26.990        19.825 
[1] "0.3 - 65.8 (27.0)"  "0.0 - 140.4 (19.8)"
[1] "hr=" "2.5"
D87V2, 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       22       103         6         0
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SLK MUTATED           1          0          3          0        1         0
  SLK WILD-TYPE        18         10         38         31       34        13
               vv
clus            STAGE IVB
  SLK MUTATED           0
  SLK WILD-TYPE         1
D87V3, multiclass
            clus
vv           SLK MUTATED SLK WILD-TYPE
  STAGE I              5            59
  STAGE IA             0             1
  STAGE II             3            22
  STAGE IIA            6           103
  STAGE IIB            2             6
  STAGE IIC            1             0
  STAGE III            1            18
  STAGE IIIA           0            10
  STAGE IIIB           3            38
  STAGE IIIC           0            31
  STAGE IV             1            34
  STAGE IVA            0            13
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  SLK MUTATED     1   6  11   5
  SLK WILD-TYPE   8  62 237  36
D87V4, multiclass
    clus
vv   SLK MUTATED SLK WILD-TYPE
  T1           1             8
  T2           6            62
  T3          11           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
  SLK MUTATED    18   5   0
  SLK WILD-TYPE 202  75  66
D87V5, multiclass
    clus
vv   SLK MUTATED SLK WILD-TYPE
  N0          18           202
  N1           5            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"
D87V6, binary
               cls
clus              0   1
  SLK MUTATED    17   1
  SLK WILD-TYPE 266  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  SLK MUTATED     17    1
  SLK WILD-TYPE  266   47
   clus
vv  SLK MUTATED SLK WILD-TYPE
  0          17           266
  1           1            47
[1] 2 2
[1] FALSE
D87V7, 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
D87V8, binary
               cls
clus              0   1
  SLK MUTATED    20   3
  SLK WILD-TYPE 297  45
[1] "tbl2"
               cls
clus            [,1] [,2]
  SLK MUTATED     20    3
  SLK WILD-TYPE  297   45
                               clus
vv                              SLK MUTATED SLK WILD-TYPE
  COLON ADENOCARCINOMA                   20           297
  COLON MUCINOUS ADENOCARCINOMA           3            45
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  SLK MUTATED    16   0   0   2
  SLK WILD-TYPE 241   2  22  19
D87V9, multiclass
    clus
vv   SLK MUTATED SLK WILD-TYPE
  R0          16           241
  R1           0             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"
D87V10, 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
D87V11, 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(88) Variable = C15ORF52 MUTATION ANALYSIS
D88V1, survival
                    sevent
clus2                  0   1
  C15ORF52 MUTATED     8   4
  C15ORF52 WILD-TYPE 274  69
  C15ORF52 MUTATED C15ORF52 WILD-TYPE 
                12                343 
  C15ORF52 MUTATED C15ORF52 WILD-TYPE 
                 4                 69 
$`C15ORF52 MUTATED`
TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6653 TCGA-AA-3492 TCGA-AA-3663 TCGA-AA-3672 
       22.06         8.38        24.39         3.02         6.97         0.92 
TCGA-AA-3845 TCGA-AA-3950 TCGA-AD-6889 TCGA-AD-6964 TCGA-CK-5913 TCGA-DM-A28G 
        0.00        24.00        56.55        10.88        51.32        60.79 

$`C15ORF52 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.09        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       24.16        21.76        24.69        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.05        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K 
        6.12        81.37       119.93        35.97       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  C15ORF52 MUTATED C15ORF52 WILD-TYPE 
                 0                  0 
  C15ORF52 MUTATED C15ORF52 WILD-TYPE 
             60.79             140.38 
  C15ORF52 MUTATED C15ORF52 WILD-TYPE 
             16.47              20.19 
[1] "0.0 - 60.8 (16.5)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.8"
D88V2, 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       23       102         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C15ORF52 MUTATED           1          0          0          0        0
  C15ORF52 WILD-TYPE        18         10         41         31       35
                    vv
clus                 STAGE IVA STAGE IVB
  C15ORF52 MUTATED           0         0
  C15ORF52 WILD-TYPE        13         1
D88V3, multiclass
            clus
vv           C15ORF52 MUTATED C15ORF52 WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  2                 23
  STAGE IIA                 7                102
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 1                 18
  STAGE IIIA                0                 10
  STAGE IIIB                0                 41
  STAGE IIIC                0                 31
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C15ORF52 MUTATED     0   1  10   1
  C15ORF52 WILD-TYPE   9  67 238  40
D88V4, multiclass
    clus
vv   C15ORF52 MUTATED C15ORF52 WILD-TYPE
  T1                0                  9
  T2                1                 67
  T3               10                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
  C15ORF52 MUTATED    10   1   1
  C15ORF52 WILD-TYPE 210  79  65
D88V5, multiclass
    clus
vv   C15ORF52 MUTATED C15ORF52 WILD-TYPE
  N0               10                210
  N1                1                 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"
D88V6, binary
                    cls
clus                   0   1
  C15ORF52 MUTATED    10   0
  C15ORF52 WILD-TYPE 273  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF52 MUTATED     10    0
  C15ORF52 WILD-TYPE  273   48
   clus
vv  C15ORF52 MUTATED C15ORF52 WILD-TYPE
  0               10                273
  1                0                 48
[1] 2 2
[1] FALSE
D88V7, 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
D88V8, binary
                    cls
clus                   0   1
  C15ORF52 MUTATED    11   1
  C15ORF52 WILD-TYPE 306  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF52 MUTATED     11    1
  C15ORF52 WILD-TYPE  306   47
                               clus
vv                              C15ORF52 MUTATED C15ORF52 WILD-TYPE
  COLON ADENOCARCINOMA                        11                306
  COLON MUCINOUS ADENOCARCINOMA                1                 47
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C15ORF52 MUTATED     6   0   0   1
  C15ORF52 WILD-TYPE 251   2  22  20
D88V9, multiclass
    clus
vv   C15ORF52 MUTATED C15ORF52 WILD-TYPE
  R0                6                251
  R1                0                  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"
D88V10, 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
D88V11, 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(89) Variable = TAF7L MUTATION ANALYSIS
D89V1, survival
                 sevent
clus2               0   1
  TAF7L MUTATED     8   3
  TAF7L WILD-TYPE 274  70
  TAF7L MUTATED TAF7L WILD-TYPE 
             11             344 
  TAF7L MUTATED TAF7L WILD-TYPE 
              3              70 
$`TAF7L MUTATED`
TCGA-A6-4105 TCGA-A6-5665 TCGA-AA-3875 TCGA-AA-A010 TCGA-CM-4743 TCGA-D5-6929 
       14.53        22.06        18.05        34.98        23.05        13.41 
TCGA-F4-6570 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6321 
        6.18        65.85        44.68        51.75        22.09 

$`TAF7L WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-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        13.38        13.45        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6310 
       19.43       107.67        74.56        53.62        55.04        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.72        36.00        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  TAF7L MUTATED TAF7L WILD-TYPE 
           6.18            0.00 
  TAF7L MUTATED TAF7L WILD-TYPE 
          65.85          140.38 
  TAF7L MUTATED TAF7L WILD-TYPE 
          22.09           20.07 
[1] "6.2 - 65.8 (22.1)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.1"
D89V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TAF7L MUTATED         1        0        0         5         1         0
  TAF7L WILD-TYPE      63        1       25       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        18         10         40         31       33        13
                 vv
clus              STAGE IVB
  TAF7L MUTATED           0
  TAF7L WILD-TYPE         1
D89V3, multiclass
            clus
vv           TAF7L MUTATED TAF7L WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              5             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               2              33
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TAF7L MUTATED     1   2   7   1
  TAF7L WILD-TYPE   8  66 241  40
D89V4, multiclass
    clus
vv   TAF7L MUTATED TAF7L WILD-TYPE
  T1             1               8
  T2             2              66
  T3             7             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
  TAF7L MUTATED     7   4   0
  TAF7L WILD-TYPE 213  76  66
D89V5, multiclass
    clus
vv   TAF7L MUTATED TAF7L WILD-TYPE
  N0             7             213
  N1             4              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"
D89V6, binary
                 cls
clus                0   1
  TAF7L MUTATED     8   2
  TAF7L WILD-TYPE 275  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF7L MUTATED      8    2
  TAF7L WILD-TYPE  275   46
   clus
vv  TAF7L MUTATED TAF7L WILD-TYPE
  0             8             275
  1             2              46
[1] 2 2
[1] FALSE
D89V7, 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
D89V8, binary
                 cls
clus                0   1
  TAF7L MUTATED    11   0
  TAF7L WILD-TYPE 306  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF7L MUTATED     11    0
  TAF7L WILD-TYPE  306   48
                               clus
vv                              TAF7L MUTATED TAF7L WILD-TYPE
  COLON ADENOCARCINOMA                     11             306
  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 247   2  22  21
D89V9, multiclass
    clus
vv   TAF7L MUTATED TAF7L WILD-TYPE
  R0            10             247
  R1             0               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"
D89V10, 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
D89V11, 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(90) Variable = TPM4 MUTATION ANALYSIS
D90V1, survival
                sevent
clus2              0   1
  TPM4 MUTATED     8   0
  TPM4 WILD-TYPE 274  73
  TPM4 MUTATED TPM4 WILD-TYPE 
             8            347 
  TPM4 MUTATED TPM4 WILD-TYPE 
             0             73 
$`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 
        0.07        15.62 

$`TPM4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 
       35.05        33.04         0.99        25.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       102.44        40.34        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  TPM4 MUTATED TPM4 WILD-TYPE 
          0.07           0.00 
  TPM4 MUTATED TPM4 WILD-TYPE 
         63.98         140.38 
  TPM4 MUTATED TPM4 WILD-TYPE 
        24.705         20.120 
[1] "0.1 - 64.0 (24.7)"  "0.0 - 140.4 (20.1)"
[1] "hr="     "9300000"
D90V2, 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       23       109         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TPM4 MUTATED           1          0          1          0        0         0
  TPM4 WILD-TYPE        18         10         40         31       35        13
                vv
clus             STAGE IVB
  TPM4 MUTATED           0
  TPM4 WILD-TYPE         1
D90V3, multiclass
            clus
vv           TPM4 MUTATED TPM4 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             0            109
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TPM4 MUTATED     0   4   3   1
  TPM4 WILD-TYPE   9  64 245  40
D90V4, multiclass
    clus
vv   TPM4 MUTATED TPM4 WILD-TYPE
  T1            0              9
  T2            4             64
  T3            3            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
  TPM4 MUTATED     6   1   1
  TPM4 WILD-TYPE 214  79  65
D90V5, multiclass
    clus
vv   TPM4 MUTATED TPM4 WILD-TYPE
  N0            6            214
  N1            1             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"
D90V6, binary
                cls
clus               0   1
  TPM4 MUTATED     7   0
  TPM4 WILD-TYPE 276  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPM4 MUTATED      7    0
  TPM4 WILD-TYPE  276   48
   clus
vv  TPM4 MUTATED TPM4 WILD-TYPE
  0            7            276
  1            0             48
[1] 2 2
[1] FALSE
D90V7, 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
D90V8, binary
                cls
clus               0   1
  TPM4 MUTATED     6   2
  TPM4 WILD-TYPE 311  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPM4 MUTATED      6    2
  TPM4 WILD-TYPE  311   46
                               clus
vv                              TPM4 MUTATED TPM4 WILD-TYPE
  COLON ADENOCARCINOMA                     6            311
  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 253   2  22  19
D90V9, multiclass
    clus
vv   TPM4 MUTATED TPM4 WILD-TYPE
  R0            4            253
  R1            0              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"
D90V10, 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
D90V11, 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(91) Variable = OR5V1 MUTATION ANALYSIS
D91V1, survival
                 sevent
clus2               0   1
  OR5V1 MUTATED    13   1
  OR5V1 WILD-TYPE 269  72
  OR5V1 MUTATED OR5V1 WILD-TYPE 
             14             341 
  OR5V1 MUTATED OR5V1 WILD-TYPE 
              1              72 
$`OR5V1 MUTATED`
TCGA-AA-3866 TCGA-AA-3977 TCGA-AU-3779 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4950 
       17.03        25.02        14.50         0.33         1.35        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CM-6164 TCGA-CM-6676 TCGA-D5-6535 TCGA-D5-6928 
       15.62        49.08        29.03        11.08        15.12        11.64 
TCGA-DM-A1HB TCGA-G4-6321 
      135.65        22.09 

$`OR5V1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       53.00        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-5913 TCGA-CK-5914 
        0.26         0.10        17.56       102.44        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        43.27        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       55.04        51.75        45.11        36.72        36.00        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  OR5V1 MUTATED OR5V1 WILD-TYPE 
           0.33            0.00 
  OR5V1 MUTATED OR5V1 WILD-TYPE 
         135.65          140.38 
  OR5V1 MUTATED OR5V1 WILD-TYPE 
         16.325          20.280 
[1] "0.3 - 135.7 (16.3)" "0.0 - 140.4 (20.3)"
[1] "hr=" "3"  
D91V2, 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       25       104         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR5V1 MUTATED           2          1          2          0        0         0
  OR5V1 WILD-TYPE        17          9         39         31       35        13
                 vv
clus              STAGE IVB
  OR5V1 MUTATED           0
  OR5V1 WILD-TYPE         1
D91V3, multiclass
            clus
vv           OR5V1 MUTATED OR5V1 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              5             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             1               9
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR5V1 MUTATED     0   5   8   1
  OR5V1 WILD-TYPE   9  63 240  40
D91V4, multiclass
    clus
vv   OR5V1 MUTATED OR5V1 WILD-TYPE
  T1             0               9
  T2             5              63
  T3             8             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
  OR5V1 MUTATED     9   4   1
  OR5V1 WILD-TYPE 211  76  65
D91V5, multiclass
    clus
vv   OR5V1 MUTATED OR5V1 WILD-TYPE
  N0             9             211
  N1             4              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"
D91V6, binary
                 cls
clus                0   1
  OR5V1 MUTATED    10   0
  OR5V1 WILD-TYPE 273  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5V1 MUTATED     10    0
  OR5V1 WILD-TYPE  273   48
   clus
vv  OR5V1 MUTATED OR5V1 WILD-TYPE
  0            10             273
  1             0              48
[1] 2 2
[1] FALSE
D91V7, 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
D91V8, binary
                 cls
clus                0   1
  OR5V1 MUTATED    11   3
  OR5V1 WILD-TYPE 306  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5V1 MUTATED     11    3
  OR5V1 WILD-TYPE  306   45
                               clus
vv                              OR5V1 MUTATED OR5V1 WILD-TYPE
  COLON ADENOCARCINOMA                     11             306
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  OR5V1 MUTATED     6   1   0   5
  OR5V1 WILD-TYPE 251   1  22  16
D91V9, multiclass
    clus
vv   OR5V1 MUTATED OR5V1 WILD-TYPE
  R0             6             251
  R1             1               1
  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"
D91V10, 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
D91V11, 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(92) Variable = KDM6A MUTATION ANALYSIS
D92V1, survival
                 sevent
clus2               0   1
  KDM6A MUTATED    21   5
  KDM6A WILD-TYPE 261  68
  KDM6A MUTATED KDM6A WILD-TYPE 
             26             329 
  KDM6A MUTATED KDM6A WILD-TYPE 
              5              68 
$`KDM6A MUTATED`
TCGA-A6-3809 TCGA-A6-5666 TCGA-AA-3713 TCGA-AA-A010 TCGA-AD-6964 TCGA-AZ-4315 
       32.75        32.71        19.04        34.98        10.88        58.39 
TCGA-CK-5914 TCGA-CM-4747 TCGA-CM-5348 TCGA-CM-6164 TCGA-CM-6168 TCGA-CM-6169 
       21.99        25.02        22.98        29.03        12.99        13.02 
TCGA-CM-6676 TCGA-D5-6529 TCGA-D5-6535 TCGA-D5-6540 TCGA-D5-6926 TCGA-D5-6929 
       11.08        20.19        15.12        16.14         9.04        13.41 
TCGA-D5-7000 TCGA-DM-A0XF TCGA-DM-A1HB TCGA-DM-A28C TCGA-DM-A28F TCGA-F4-6805 
       10.26        38.20       135.65        81.37        35.97        16.31 
TCGA-G4-6303 TCGA-G4-6586 
       65.85        35.80 

$`KDM6A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
        0.72         5.79        22.42        27.42         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.14         2.93         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 
       20.02        37.02        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 
       16.01        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-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 
       13.51        11.51        18.25         1.32        43.27        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 
       12.00        11.38       119.70        24.43       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
      131.51       139.17         6.12       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        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
        1.55        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 
       35.41        19.43       107.67        74.56        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        26.17        91.79        46.75        52.80 

  KDM6A MUTATED KDM6A WILD-TYPE 
           9.04            0.00 
  KDM6A MUTATED KDM6A WILD-TYPE 
         135.65          140.38 
  KDM6A MUTATED KDM6A WILD-TYPE 
         22.485          20.020 
[1] "9.0 - 135.7 (22.5)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.3"
D92V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KDM6A MUTATED         3        0        0         8         2         1
  KDM6A WILD-TYPE      61        1       25       101         6         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KDM6A MUTATED           0          1          5          1        3         1
  KDM6A WILD-TYPE        19          9         36         30       32        12
                 vv
clus              STAGE IVB
  KDM6A MUTATED           0
  KDM6A WILD-TYPE         1
D92V3, multiclass
            clus
vv           KDM6A MUTATED KDM6A WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              8             101
  STAGE IIB              2               6
  STAGE IIC              1               0
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             5              36
  STAGE IIIC             1              30
  STAGE IV               3              32
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  17   6
  KDM6A WILD-TYPE   9  65 231  35
D92V4, multiclass
    clus
vv   KDM6A MUTATED KDM6A WILD-TYPE
  T1             0               9
  T2             3              65
  T3            17             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    15   9   2
  KDM6A WILD-TYPE 205  71  64
D92V5, multiclass
    clus
vv   KDM6A MUTATED KDM6A WILD-TYPE
  N0            15             205
  N1             9              71
  N2             2              64
[1] 3 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
  KDM6A MUTATED    19   4
  KDM6A WILD-TYPE 264  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED     19    4
  KDM6A WILD-TYPE  264   44
   clus
vv  KDM6A MUTATED KDM6A WILD-TYPE
  0            19             264
  1             4              44
[1] 2 2
[1] FALSE
D92V7, binary
                 cls
clus                0   1
  KDM6A MUTATED    11  15
  KDM6A WILD-TYPE 159 182
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED     11   15
  KDM6A WILD-TYPE  159  182
        clus
vv       KDM6A MUTATED KDM6A WILD-TYPE
  FEMALE            11             159
  MALE              15             182
[1] 2 2
[1] FALSE
D92V8, binary
                 cls
clus                0   1
  KDM6A MUTATED    22   4
  KDM6A WILD-TYPE 295  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED     22    4
  KDM6A WILD-TYPE  295   44
                               clus
vv                              KDM6A MUTATED KDM6A WILD-TYPE
  COLON ADENOCARCINOMA                     22             295
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  KDM6A MUTATED    17   0   1   2
  KDM6A WILD-TYPE 240   2  21  19
D92V9, multiclass
    clus
vv   KDM6A MUTATED KDM6A WILD-TYPE
  R0            17             240
  R1             0               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"
D92V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KDM6A MUTATED                                  0     0
  KDM6A WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KDM6A MUTATED                           2    22
  KDM6A WILD-TYPE                        17   154
D92V11, multiclass
                                  clus
vv                                 KDM6A MUTATED KDM6A 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(93) Variable = C2ORF29 MUTATION ANALYSIS
D93V1, survival
                   sevent
clus2                 0   1
  C2ORF29 MUTATED    14   2
  C2ORF29 WILD-TYPE 268  71
  C2ORF29 MUTATED C2ORF29 WILD-TYPE 
               16               339 
  C2ORF29 MUTATED C2ORF29 WILD-TYPE 
                2                71 
$`C2ORF29 MUTATED`
TCGA-A6-4105 TCGA-AA-A010 TCGA-AZ-6599 TCGA-CA-5255 TCGA-CK-4952 TCGA-CM-5348 
       14.53        34.98         6.77         3.06        15.62        22.98 
TCGA-CM-6163 TCGA-CM-6171 TCGA-CM-6677 TCGA-D5-6529 TCGA-D5-6540 TCGA-D5-6929 
       14.04        14.04        11.08        20.19        16.14        13.41 
TCGA-DM-A1HA TCGA-F4-6460 TCGA-G4-6293 TCGA-G4-6309 
      131.51        13.38       107.67        51.75 

$`C2ORF29 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        1.94         2.24         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 
       15.02        15.02        17.03        15.02        12.00        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 
       11.01        12.95        13.05        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        13.51        11.51 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       74.56        65.85        53.62        44.68        55.04        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  C2ORF29 MUTATED C2ORF29 WILD-TYPE 
             3.06              0.00 
  C2ORF29 MUTATED C2ORF29 WILD-TYPE 
           131.51            140.38 
  C2ORF29 MUTATED C2ORF29 WILD-TYPE 
           15.075            20.980 
[1] "3.1 - 131.5 (15.1)" "0.0 - 140.4 (21.0)"
[1] "hr=" "2"  
D93V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C2ORF29 MUTATED         4        0        0         4         1         0
  C2ORF29 WILD-TYPE      60        1       25       105         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C2ORF29 MUTATED           2          0          3          1        1
  C2ORF29 WILD-TYPE        17         10         38         30       34
                   vv
clus                STAGE IVA STAGE IVB
  C2ORF29 MUTATED           0         0
  C2ORF29 WILD-TYPE        13         1
D93V3, multiclass
            clus
vv           C2ORF29 MUTATED C2ORF29 WILD-TYPE
  STAGE I                  4                60
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                4               105
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                2                17
  STAGE IIIA               0                10
  STAGE IIIB               3                38
  STAGE IIIC               1                30
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C2ORF29 MUTATED     1   3  10   2
  C2ORF29 WILD-TYPE   8  65 238  39
D93V4, multiclass
    clus
vv   C2ORF29 MUTATED C2ORF29 WILD-TYPE
  T1               1                 8
  T2               3                65
  T3              10               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     9   5   2
  C2ORF29 WILD-TYPE 211  75  64
D93V5, multiclass
    clus
vv   C2ORF29 MUTATED C2ORF29 WILD-TYPE
  N0               9               211
  N1               5                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"
D93V6, binary
                   cls
clus                  0   1
  C2ORF29 MUTATED    14   1
  C2ORF29 WILD-TYPE 269  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF29 MUTATED     14    1
  C2ORF29 WILD-TYPE  269   47
   clus
vv  C2ORF29 MUTATED C2ORF29 WILD-TYPE
  0              14               269
  1               1                47
[1] 2 2
[1] FALSE
D93V7, binary
                   cls
clus                  0   1
  C2ORF29 MUTATED     8   8
  C2ORF29 WILD-TYPE 162 189
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF29 MUTATED      8    8
  C2ORF29 WILD-TYPE  162  189
        clus
vv       C2ORF29 MUTATED C2ORF29 WILD-TYPE
  FEMALE               8               162
  MALE                 8               189
[1] 2 2
[1] FALSE
D93V8, binary
                   cls
clus                  0   1
  C2ORF29 MUTATED    14   2
  C2ORF29 WILD-TYPE 303  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF29 MUTATED     14    2
  C2ORF29 WILD-TYPE  303   46
                               clus
vv                              C2ORF29 MUTATED C2ORF29 WILD-TYPE
  COLON ADENOCARCINOMA                       14               303
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  C2ORF29 MUTATED    11   0   0   2
  C2ORF29 WILD-TYPE 246   2  22  19
D93V9, multiclass
    clus
vv   C2ORF29 MUTATED C2ORF29 WILD-TYPE
  R0              11               246
  R1               0                 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"
D93V10, 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                           1    13
  C2ORF29 WILD-TYPE                        18   163
D93V11, multiclass
                                  clus
vv                                 C2ORF29 MUTATED C2ORF29 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(94) Variable = GGT1 MUTATION ANALYSIS
D94V1, survival
                sevent
clus2              0   1
  GGT1 MUTATED     6   2
  GGT1 WILD-TYPE 276  71
  GGT1 MUTATED GGT1 WILD-TYPE 
             8            347 
  GGT1 MUTATED GGT1 WILD-TYPE 
             2             71 
$`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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        33.53        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99        21.14         2.93       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-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        16.01        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-6171 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        13.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 
       18.25         1.32        43.27        15.12        17.85        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 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-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 
       19.43       107.67        74.56        65.85        53.62        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  GGT1 MUTATED GGT1 WILD-TYPE 
          2.01           0.00 
  GGT1 MUTATED GGT1 WILD-TYPE 
        130.65         140.38 
  GGT1 MUTATED GGT1 WILD-TYPE 
        16.075         20.280 
[1] "2.0 - 130.7 (16.1)" "0.0 - 140.4 (20.3)"
[1] "hr=" "1.1"
D94V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GGT1 MUTATED         1        0        0         2         0         0
  GGT1 WILD-TYPE      63        1       25       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        19         10         39         31       34        11
                vv
clus             STAGE IVB
  GGT1 MUTATED           0
  GGT1 WILD-TYPE         1
D94V3, multiclass
            clus
vv           GGT1 MUTATED GGT1 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             2            107
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            2             39
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             2             11
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 242  41
D94V4, multiclass
    clus
vv   GGT1 MUTATED GGT1 WILD-TYPE
  T1            0              9
  T2            2             66
  T3            6            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
  GGT1 MUTATED     3   3   2
  GGT1 WILD-TYPE 217  77  64
D94V5, multiclass
    clus
vv   GGT1 MUTATED GGT1 WILD-TYPE
  N0            3            217
  N1            3             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"
D94V6, binary
                cls
clus               0   1
  GGT1 MUTATED     4   3
  GGT1 WILD-TYPE 279  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  GGT1 MUTATED      4    3
  GGT1 WILD-TYPE  279   45
   clus
vv  GGT1 MUTATED GGT1 WILD-TYPE
  0            4            279
  1            3             45
[1] 2 2
[1] FALSE
D94V7, 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
D94V8, binary
                cls
clus               0   1
  GGT1 MUTATED     7   1
  GGT1 WILD-TYPE 310  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  GGT1 MUTATED      7    1
  GGT1 WILD-TYPE  310   47
                               clus
vv                              GGT1 MUTATED GGT1 WILD-TYPE
  COLON ADENOCARCINOMA                     7            310
  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 252   2  22  20
D94V9, multiclass
    clus
vv   GGT1 MUTATED GGT1 WILD-TYPE
  R0            5            252
  R1            0              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"
D94V10, 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
D94V11, 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(95) Variable = PIK3IP1 MUTATION ANALYSIS
D95V1, survival
                   sevent
clus2                 0   1
  PIK3IP1 MUTATED     7   1
  PIK3IP1 WILD-TYPE 275  72
  PIK3IP1 MUTATED PIK3IP1 WILD-TYPE 
                8               347 
  PIK3IP1 MUTATED PIK3IP1 WILD-TYPE 
                1                72 
$`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       107.67 

$`PIK3IP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       15.75        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        43.27        15.12         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        92.75        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       19.43        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  PIK3IP1 MUTATED PIK3IP1 WILD-TYPE 
              0.2               0.0 
  PIK3IP1 MUTATED PIK3IP1 WILD-TYPE 
           107.67            140.38 
  PIK3IP1 MUTATED PIK3IP1 WILD-TYPE 
           16.995            20.280 
[1] "0.2 - 107.7 (17.0)" "0.0 - 140.4 (20.3)"
[1] "hr=" "2.1"
D95V2, 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       24       107         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PIK3IP1 MUTATED           1          0          0          2        0
  PIK3IP1 WILD-TYPE        18         10         41         29       35
                   vv
clus                STAGE IVA STAGE IVB
  PIK3IP1 MUTATED           0         0
  PIK3IP1 WILD-TYPE        13         1
D95V3, multiclass
            clus
vv           PIK3IP1 MUTATED PIK3IP1 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                2               107
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               2                29
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PIK3IP1 MUTATED     0   2   6   0
  PIK3IP1 WILD-TYPE   9  66 242  41
D95V4, multiclass
    clus
vv   PIK3IP1 MUTATED PIK3IP1 WILD-TYPE
  T1               0                 9
  T2               2                66
  T3               6               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
  PIK3IP1 MUTATED     5   1   2
  PIK3IP1 WILD-TYPE 215  79  64
D95V5, multiclass
    clus
vv   PIK3IP1 MUTATED PIK3IP1 WILD-TYPE
  N0               5               215
  N1               1                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"
D95V6, binary
                   cls
clus                  0   1
  PIK3IP1 MUTATED     7   0
  PIK3IP1 WILD-TYPE 276  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PIK3IP1 MUTATED      7    0
  PIK3IP1 WILD-TYPE  276   48
   clus
vv  PIK3IP1 MUTATED PIK3IP1 WILD-TYPE
  0               7               276
  1               0                48
[1] 2 2
[1] FALSE
D95V7, 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
D95V8, binary
                   cls
clus                  0   1
  PIK3IP1 MUTATED     5   3
  PIK3IP1 WILD-TYPE 312  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PIK3IP1 MUTATED      5    3
  PIK3IP1 WILD-TYPE  312   45
                               clus
vv                              PIK3IP1 MUTATED PIK3IP1 WILD-TYPE
  COLON ADENOCARCINOMA                        5               312
  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 250   2  22  21
D95V9, multiclass
    clus
vv   PIK3IP1 MUTATED PIK3IP1 WILD-TYPE
  R0               7               250
  R1               0                 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"
D95V10, 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
D95V11, 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(96) Variable = PRDM1 MUTATION ANALYSIS
D96V1, survival
                 sevent
clus2               0   1
  PRDM1 MUTATED    15   4
  PRDM1 WILD-TYPE 267  69
  PRDM1 MUTATED PRDM1 WILD-TYPE 
             19             336 
  PRDM1 MUTATED PRDM1 WILD-TYPE 
              4              69 
$`PRDM1 MUTATED`
TCGA-A6-5666 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3968 TCGA-AA-A00J TCGA-AA-A00N 
       32.71         6.05         6.97        21.99        18.05         4.01 
TCGA-AU-6004 TCGA-AY-6197 TCGA-AZ-6599 TCGA-CK-4950 TCGA-CM-4746 TCGA-CM-6164 
       27.09        21.44         6.77        40.34        37.02        29.03 
TCGA-CM-6171 TCGA-D5-5541 TCGA-D5-6540 TCGA-DM-A1D6 TCGA-F4-6570 TCGA-G4-6293 
       14.04        11.51        16.14        49.91         6.18       107.67 
TCGA-G4-6307 
       55.04 

$`PRDM1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       19.99        13.94        19.99        61.02        78.08        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        15.75         0.20        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-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-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       13.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 
      119.70        24.43        38.20       130.65        92.75        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      117.07        98.24         8.61        13.38        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        35.41        19.43        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  PRDM1 MUTATED PRDM1 WILD-TYPE 
           4.01            0.00 
  PRDM1 MUTATED PRDM1 WILD-TYPE 
         107.67          140.38 
  PRDM1 MUTATED PRDM1 WILD-TYPE 
         21.440          20.155 
[1] "4.0 - 107.7 (21.4)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1"  
D96V2, 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       24       105         6         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PRDM1 MUTATED           1          1          3          0        1         0
  PRDM1 WILD-TYPE        18          9         38         31       34        13
                 vv
clus              STAGE IVB
  PRDM1 MUTATED           0
  PRDM1 WILD-TYPE         1
D96V3, multiclass
            clus
vv           PRDM1 MUTATED PRDM1 WILD-TYPE
  STAGE I                6              58
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              4             105
  STAGE IIB              2               6
  STAGE IIC              1               0
  STAGE III              1              18
  STAGE IIIA             1               9
  STAGE IIIB             3              38
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PRDM1 MUTATED     0   6   9   5
  PRDM1 WILD-TYPE   9  62 239  36
D96V4, multiclass
    clus
vv   PRDM1 MUTATED PRDM1 WILD-TYPE
  T1             0               9
  T2             6              62
  T3             9             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
  PRDM1 MUTATED    14   5   1
  PRDM1 WILD-TYPE 206  75  65
D96V5, multiclass
    clus
vv   PRDM1 MUTATED PRDM1 WILD-TYPE
  N0            14             206
  N1             5              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"
D96V6, binary
                 cls
clus                0   1
  PRDM1 MUTATED    16   1
  PRDM1 WILD-TYPE 267  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRDM1 MUTATED     16    1
  PRDM1 WILD-TYPE  267   47
   clus
vv  PRDM1 MUTATED PRDM1 WILD-TYPE
  0            16             267
  1             1              47
[1] 2 2
[1] FALSE
D96V7, 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
D96V8, binary
                 cls
clus                0   1
  PRDM1 MUTATED    16   4
  PRDM1 WILD-TYPE 301  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRDM1 MUTATED     16    4
  PRDM1 WILD-TYPE  301   44
                               clus
vv                              PRDM1 MUTATED PRDM1 WILD-TYPE
  COLON ADENOCARCINOMA                     16             301
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PRDM1 MUTATED    14   1   1   1
  PRDM1 WILD-TYPE 243   1  21  20
D96V9, multiclass
    clus
vv   PRDM1 MUTATED PRDM1 WILD-TYPE
  R0            14             243
  R1             1               1
  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"
D96V10, 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
D96V11, 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(97) Variable = ZDHHC7 MUTATION ANALYSIS
D97V1, survival
                  sevent
clus2                0   1
  ZDHHC7 MUTATED     9   2
  ZDHHC7 WILD-TYPE 273  71
  ZDHHC7 MUTATED ZDHHC7 WILD-TYPE 
              11              344 
  ZDHHC7 MUTATED ZDHHC7 WILD-TYPE 
               2               71 
$`ZDHHC7 MUTATED`
TCGA-A6-6653 TCGA-AA-3662 TCGA-AA-3811 TCGA-AA-3947 TCGA-AA-3949 TCGA-AU-6004 
       24.39         6.05        10.06        33.01        26.01        27.09 
TCGA-AZ-4315 TCGA-D5-6930 TCGA-DM-A28F TCGA-G4-6304 TCGA-G4-6628 
       58.39         1.51        35.97        53.62        52.80 

$`ZDHHC7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       19.99        13.94        19.99        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        19.04        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 
       91.79        46.75 

  ZDHHC7 MUTATED ZDHHC7 WILD-TYPE 
            1.51             0.00 
  ZDHHC7 MUTATED ZDHHC7 WILD-TYPE 
           58.39           140.38 
  ZDHHC7 MUTATED ZDHHC7 WILD-TYPE 
          27.090           20.005 
[1] "1.5 - 58.4 (27.1)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1.3"
D97V2, 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       25       106         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZDHHC7 MUTATED           1          0          2          0        1
  ZDHHC7 WILD-TYPE        18         10         39         31       34
                  vv
clus               STAGE IVA STAGE IVB
  ZDHHC7 MUTATED           0         0
  ZDHHC7 WILD-TYPE        13         1
D97V3, multiclass
            clus
vv           ZDHHC7 MUTATED ZDHHC7 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               3              106
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZDHHC7 MUTATED     0   3   6   3
  ZDHHC7 WILD-TYPE   9  65 242  38
D97V4, multiclass
    clus
vv   ZDHHC7 MUTATED ZDHHC7 WILD-TYPE
  T1              0                9
  T2              3               65
  T3              6              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
  ZDHHC7 MUTATED     8   2   2
  ZDHHC7 WILD-TYPE 212  78  64
D97V5, multiclass
    clus
vv   ZDHHC7 MUTATED ZDHHC7 WILD-TYPE
  N0              8              212
  N1              2               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"
D97V6, binary
                  cls
clus                 0   1
  ZDHHC7 MUTATED    11   1
  ZDHHC7 WILD-TYPE 272  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZDHHC7 MUTATED     11    1
  ZDHHC7 WILD-TYPE  272   47
   clus
vv  ZDHHC7 MUTATED ZDHHC7 WILD-TYPE
  0             11              272
  1              1               47
[1] 2 2
[1] FALSE
D97V7, 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
D97V8, binary
                  cls
clus                 0   1
  ZDHHC7 MUTATED     9   3
  ZDHHC7 WILD-TYPE 308  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZDHHC7 MUTATED      9    3
  ZDHHC7 WILD-TYPE  308   45
                               clus
vv                              ZDHHC7 MUTATED ZDHHC7 WILD-TYPE
  COLON ADENOCARCINOMA                       9              308
  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 248   2  21  21
D97V9, multiclass
    clus
vv   ZDHHC7 MUTATED ZDHHC7 WILD-TYPE
  R0              9              248
  R1              0                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"
D97V10, 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
D97V11, 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(98) Variable = ZFYVE26 MUTATION ANALYSIS
D98V1, survival
                   sevent
clus2                 0   1
  ZFYVE26 MUTATED    21   6
  ZFYVE26 WILD-TYPE 261  67
  ZFYVE26 MUTATED ZFYVE26 WILD-TYPE 
               27               328 
  ZFYVE26 MUTATED ZFYVE26 WILD-TYPE 
                6                67 
$`ZFYVE26 MUTATED`
TCGA-A6-3809 TCGA-A6-6137 TCGA-A6-6651 TCGA-A6-6653 TCGA-AA-3555 TCGA-AA-3864 
       32.75        27.09        21.76        24.39        29.95        53.00 
TCGA-AA-3947 TCGA-AA-3977 TCGA-AA-A00N TCGA-AD-6889 TCGA-AU-3779 TCGA-AY-6197 
       33.01        25.02         4.01        56.55        14.50        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6605 TCGA-AZ-6608 
       17.82        58.39        49.41        12.10         5.23         1.94 
TCGA-CK-4952 TCGA-CM-5861 TCGA-CM-6171 TCGA-D5-6538 TCGA-D5-6928 TCGA-DM-A28H 
       15.62        15.02        14.04        17.13        11.64       117.07 
TCGA-F4-6570 TCGA-G4-6588 TCGA-G4-6628 
        6.18        26.17        52.80 

$`ZFYVE26 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.16        24.69        23.87        20.12        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        7.04         3.02         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37         4.21         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AZ-4323 
       27.09        16.31         0.95        15.75         0.20         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13        83.80        22.36        62.79        61.41         6.77 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
      100.01        29.56        11.74         3.19         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 
        1.35        17.56       102.44        40.34        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K 
        6.12        81.37       119.93        35.97        60.79        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        13.38        13.45        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       13.78        35.80        91.79        46.75 

  ZFYVE26 MUTATED ZFYVE26 WILD-TYPE 
             1.94              0.00 
  ZFYVE26 MUTATED ZFYVE26 WILD-TYPE 
           117.07            140.38 
  ZFYVE26 MUTATED ZFYVE26 WILD-TYPE 
            21.76             20.07 
[1] "1.9 - 117.1 (21.8)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1"  
D98V2, 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       23        99         5         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZFYVE26 MUTATED           1          1          5          1        1
  ZFYVE26 WILD-TYPE        18          9         36         30       34
                   vv
clus                STAGE IVA STAGE IVB
  ZFYVE26 MUTATED           0         0
  ZFYVE26 WILD-TYPE        13         1
D98V3, multiclass
            clus
vv           ZFYVE26 MUTATED ZFYVE26 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 2                23
  STAGE IIA               10                99
  STAGE IIB                3                 5
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               1                 9
  STAGE IIIB               5                36
  STAGE IIIC               1                30
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ZFYVE26 MUTATED     0   5  17   6
  ZFYVE26 WILD-TYPE   9  63 231  35
D98V4, multiclass
    clus
vv   ZFYVE26 MUTATED ZFYVE26 WILD-TYPE
  T1               0                 9
  T2               5                63
  T3              17               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
  ZFYVE26 MUTATED    19   6   3
  ZFYVE26 WILD-TYPE 201  74  63
D98V5, multiclass
    clus
vv   ZFYVE26 MUTATED ZFYVE26 WILD-TYPE
  N0              19               201
  N1               6                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"
D98V6, binary
                   cls
clus                  0   1
  ZFYVE26 MUTATED    23   1
  ZFYVE26 WILD-TYPE 260  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFYVE26 MUTATED     23    1
  ZFYVE26 WILD-TYPE  260   47
   clus
vv  ZFYVE26 MUTATED ZFYVE26 WILD-TYPE
  0              23               260
  1               1                47
[1] 2 2
[1] FALSE
D98V7, 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
D98V8, binary
                   cls
clus                  0   1
  ZFYVE26 MUTATED    22   6
  ZFYVE26 WILD-TYPE 295  42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFYVE26 MUTATED     22    6
  ZFYVE26 WILD-TYPE  295   42
                               clus
vv                              ZFYVE26 MUTATED ZFYVE26 WILD-TYPE
  COLON ADENOCARCINOMA                       22               295
  COLON MUCINOUS ADENOCARCINOMA               6                42
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ZFYVE26 MUTATED    17   0   0   1
  ZFYVE26 WILD-TYPE 240   2  22  20
D98V9, multiclass
    clus
vv   ZFYVE26 MUTATED ZFYVE26 WILD-TYPE
  R0              17               240
  R1               0                 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"
D98V10, 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
D98V11, 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(99) Variable = ST3GAL6 MUTATION ANALYSIS
D99V1, survival
                   sevent
clus2                 0   1
  ST3GAL6 MUTATED     8   4
  ST3GAL6 WILD-TYPE 274  69
  ST3GAL6 MUTATED ST3GAL6 WILD-TYPE 
               12               343 
  ST3GAL6 MUTATED ST3GAL6 WILD-TYPE 
                4                69 
$`ST3GAL6 MUTATED`
TCGA-AA-3663 TCGA-AA-3715 TCGA-AA-3947 TCGA-AA-A00N TCGA-AA-A00R TCGA-AD-6895 
        6.97        19.04        33.01         4.01         0.99         0.72 
TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-5916 TCGA-CM-5864 TCGA-D5-5540 TCGA-G4-6628 
       49.41         0.33        21.14        15.02        13.51        52.80 

$`ST3GAL6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
       42.02        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
        0.07        21.37         4.21        56.55         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        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-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       45.40        12.26        19.59        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 
       46.75 

  ST3GAL6 MUTATED ST3GAL6 WILD-TYPE 
             0.33              0.00 
  ST3GAL6 MUTATED ST3GAL6 WILD-TYPE 
            52.80            140.38 
  ST3GAL6 MUTATED ST3GAL6 WILD-TYPE 
           14.265            20.980 
[1] "0.3 - 52.8 (14.3)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "2.2"
D99V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ST3GAL6 MUTATED         4        0        3         2         2         0
  ST3GAL6 WILD-TYPE      60        1       22       107         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ST3GAL6 MUTATED           0          0          0          0        0
  ST3GAL6 WILD-TYPE        19         10         41         31       35
                   vv
clus                STAGE IVA STAGE IVB
  ST3GAL6 MUTATED           0         0
  ST3GAL6 WILD-TYPE        13         1
D99V3, multiclass
            clus
vv           ST3GAL6 MUTATED ST3GAL6 WILD-TYPE
  STAGE I                  4                60
  STAGE IA                 0                 1
  STAGE II                 3                22
  STAGE IIA                2               107
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ST3GAL6 MUTATED     1   3   6   2
  ST3GAL6 WILD-TYPE   8  65 242  39
D99V4, multiclass
    clus
vv   ST3GAL6 MUTATED ST3GAL6 WILD-TYPE
  T1               1                 8
  T2               3                65
  T3               6               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
  ST3GAL6 MUTATED    11   1   0
  ST3GAL6 WILD-TYPE 209  79  66
D99V5, multiclass
    clus
vv   ST3GAL6 MUTATED ST3GAL6 WILD-TYPE
  N0              11               209
  N1               1                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"
D99V6, binary
                   cls
clus                  0   1
  ST3GAL6 MUTATED    10   0
  ST3GAL6 WILD-TYPE 273  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ST3GAL6 MUTATED     10    0
  ST3GAL6 WILD-TYPE  273   48
   clus
vv  ST3GAL6 MUTATED ST3GAL6 WILD-TYPE
  0              10               273
  1               0                48
[1] 2 2
[1] FALSE
D99V7, binary
                   cls
clus                  0   1
  ST3GAL6 MUTATED     4   8
  ST3GAL6 WILD-TYPE 166 189
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ST3GAL6 MUTATED      4    8
  ST3GAL6 WILD-TYPE  166  189
        clus
vv       ST3GAL6 MUTATED ST3GAL6 WILD-TYPE
  FEMALE               4               166
  MALE                 8               189
[1] 2 2
[1] FALSE
D99V8, binary
                   cls
clus                  0   1
  ST3GAL6 MUTATED     9   3
  ST3GAL6 WILD-TYPE 308  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ST3GAL6 MUTATED      9    3
  ST3GAL6 WILD-TYPE  308   45
                               clus
vv                              ST3GAL6 MUTATED ST3GAL6 WILD-TYPE
  COLON ADENOCARCINOMA                        9               308
  COLON MUCINOUS ADENOCARCINOMA               3                45
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ST3GAL6 MUTATED     8   0   0   2
  ST3GAL6 WILD-TYPE 249   2  22  19
D99V9, multiclass
    clus
vv   ST3GAL6 MUTATED ST3GAL6 WILD-TYPE
  R0               8               249
  R1               0                 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"
D99V10, 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     6
  ST3GAL6 WILD-TYPE                        19   170
D99V11, 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                                          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(100) Variable = CDX2 MUTATION ANALYSIS
D100V1, survival
                sevent
clus2              0   1
  CDX2 MUTATED     5   1
  CDX2 WILD-TYPE 277  72
  CDX2 MUTATED CDX2 WILD-TYPE 
             6            349 
  CDX2 MUTATED CDX2 WILD-TYPE 
             1             72 
$`CDX2 MUTATED`
TCGA-A6-2672 TCGA-AA-3713 TCGA-AD-6889 TCGA-AZ-6598 TCGA-D5-6927 TCGA-G4-6586 
       46.65        19.04        56.55        49.41         9.44        35.80 

$`CDX2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  CDX2 MUTATED CDX2 WILD-TYPE 
          9.44           0.00 
  CDX2 MUTATED CDX2 WILD-TYPE 
         56.55         140.38 
  CDX2 MUTATED CDX2 WILD-TYPE 
        41.225         20.120 
[1] "9.4 - 56.5 (41.2)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.8"
D100V2, 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       24       106         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        19         10         40         31       34        13
                vv
clus             STAGE IVB
  CDX2 MUTATED           0
  CDX2 WILD-TYPE         1
D100V3, multiclass
            clus
vv           CDX2 MUTATED CDX2 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             3            106
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CDX2 MUTATED     0   0   6   0
  CDX2 WILD-TYPE   9  68 242  41
D100V4, multiclass
    clus
vv   CDX2 MUTATED CDX2 WILD-TYPE
  T1            0              9
  T2            0             68
  T3            6            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
  CDX2 MUTATED     5   1   0
  CDX2 WILD-TYPE 215  79  66
D100V5, multiclass
    clus
vv   CDX2 MUTATED CDX2 WILD-TYPE
  N0            5            215
  N1            1             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"
D100V6, binary
                cls
clus               0   1
  CDX2 MUTATED     4   1
  CDX2 WILD-TYPE 279  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDX2 MUTATED      4    1
  CDX2 WILD-TYPE  279   47
   clus
vv  CDX2 MUTATED CDX2 WILD-TYPE
  0            4            279
  1            1             47
[1] 2 2
[1] FALSE
D100V7, 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
D100V8, binary
                cls
clus               0   1
  CDX2 MUTATED     6   0
  CDX2 WILD-TYPE 311  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDX2 MUTATED      6    0
  CDX2 WILD-TYPE  311   48
                               clus
vv                              CDX2 MUTATED CDX2 WILD-TYPE
  COLON ADENOCARCINOMA                     6            311
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CDX2 MUTATED     3   0   1   0
  CDX2 WILD-TYPE 254   2  21  21
D100V9, multiclass
    clus
vv   CDX2 MUTATED CDX2 WILD-TYPE
  R0            3            254
  R1            0              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"
D100V10, 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
D100V11, 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(101) Variable = PTK2 MUTATION ANALYSIS
D101V1, survival
                sevent
clus2              0   1
  PTK2 MUTATED    18   4
  PTK2 WILD-TYPE 264  69
  PTK2 MUTATED PTK2 WILD-TYPE 
            22            333 
  PTK2 MUTATED PTK2 WILD-TYPE 
             4             69 
$`PTK2 MUTATED`
TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-3510 TCGA-AA-3526 TCGA-AA-3821 TCGA-AA-3877 
       22.06        20.12        63.98        19.07         1.02        31.00 
TCGA-AA-A010 TCGA-AY-5543 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-CA-6717 
       34.98        15.75        61.41         6.77       100.01         0.33 
TCGA-CA-6718 TCGA-CK-6747 TCGA-CM-5861 TCGA-CM-6171 TCGA-D5-5538 TCGA-D5-6920 
        0.10         2.93        15.02        14.04        12.26        12.39 
TCGA-D5-6931 TCGA-DM-A0XF TCGA-G4-6299 TCGA-G4-6303 
       12.00        38.20        74.56        65.85 

$`PTK2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3529 TCGA-AA-3530 
       24.03        37.05        36.03         8.05         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
        0.99        25.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 
        5.13        83.80        22.36        62.79        49.41        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07         0.26         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        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        16.01         5.03        15.02        15.02        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-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       45.40        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 
       12.49        16.14        15.58         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         1.51 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38        10.26       119.70        24.43       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
      107.67        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  PTK2 MUTATED PTK2 WILD-TYPE 
           0.1            0.0 
  PTK2 MUTATED PTK2 WILD-TYPE 
        100.01         140.38 
  PTK2 MUTATED PTK2 WILD-TYPE 
         17.41          20.98 
[1] "0.1 - 100.0 (17.4)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.3"
D101V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PTK2 MUTATED         6        0        2         7         1         0
  PTK2 WILD-TYPE      58        1       23       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        19         10         40         28       34        12
                vv
clus             STAGE IVB
  PTK2 MUTATED           0
  PTK2 WILD-TYPE         1
D101V3, multiclass
            clus
vv           PTK2 MUTATED PTK2 WILD-TYPE
  STAGE I               6             58
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             7            102
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            3             28
  STAGE IV              1             34
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  14   2
  PTK2 WILD-TYPE   7  64 234  39
D101V4, multiclass
    clus
vv   PTK2 MUTATED PTK2 WILD-TYPE
  T1            2              7
  T2            4             64
  T3           14            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
  PTK2 MUTATED    16   3   3
  PTK2 WILD-TYPE 204  77  63
D101V5, multiclass
    clus
vv   PTK2 MUTATED PTK2 WILD-TYPE
  N0           16            204
  N1            3             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"
D101V6, binary
                cls
clus               0   1
  PTK2 MUTATED    17   2
  PTK2 WILD-TYPE 266  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTK2 MUTATED     17    2
  PTK2 WILD-TYPE  266   46
   clus
vv  PTK2 MUTATED PTK2 WILD-TYPE
  0           17            266
  1            2             46
[1] 2 2
[1] FALSE
D101V7, binary
                cls
clus               0   1
  PTK2 MUTATED    13   9
  PTK2 WILD-TYPE 157 188
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTK2 MUTATED     13    9
  PTK2 WILD-TYPE  157  188
        clus
vv       PTK2 MUTATED PTK2 WILD-TYPE
  FEMALE           13            157
  MALE              9            188
[1] 2 2
[1] FALSE
D101V8, binary
                cls
clus               0   1
  PTK2 MUTATED    17   5
  PTK2 WILD-TYPE 300  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTK2 MUTATED     17    5
  PTK2 WILD-TYPE  300   43
                               clus
vv                              PTK2 MUTATED PTK2 WILD-TYPE
  COLON ADENOCARCINOMA                    17            300
  COLON MUCINOUS ADENOCARCINOMA            5             43
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PTK2 MUTATED    14   0   0   3
  PTK2 WILD-TYPE 243   2  22  18
D101V9, multiclass
    clus
vv   PTK2 MUTATED PTK2 WILD-TYPE
  R0           14            243
  R1            0              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"
D101V10, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTK2 MUTATED                                  0     2
  PTK2 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PTK2 MUTATED                           1    14
  PTK2 WILD-TYPE                        18   162
D101V11, multiclass
                                  clus
vv                                 PTK2 MUTATED PTK2 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(102) Variable = KLK10 MUTATION ANALYSIS
D102V1, survival
                 sevent
clus2               0   1
  KLK10 MUTATED     4   2
  KLK10 WILD-TYPE 278  71
  KLK10 MUTATED KLK10 WILD-TYPE 
              6             349 
  KLK10 MUTATED KLK10 WILD-TYPE 
              2              71 
$`KLK10 MUTATED`
TCGA-A6-6651 TCGA-AA-3815 TCGA-AZ-6601 TCGA-D5-6540 TCGA-DM-A1DA TCGA-DM-A1HB 
       21.76        33.04       100.01        16.14         7.50       135.65 

$`KLK10 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        24.16        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-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-A282 TCGA-DM-A285 
       12.59       140.38        44.32       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  KLK10 MUTATED KLK10 WILD-TYPE 
            7.5             0.0 
  KLK10 MUTATED KLK10 WILD-TYPE 
         135.65          140.38 
  KLK10 MUTATED KLK10 WILD-TYPE 
          27.40           20.12 
[1] "7.5 - 135.7 (27.4)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.1"
D102V2, 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       24       108         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        19         10         39         30       35        13
                 vv
clus              STAGE IVB
  KLK10 MUTATED           0
  KLK10 WILD-TYPE         1
D102V3, multiclass
            clus
vv           KLK10 MUTATED KLK10 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              1             108
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KLK10 MUTATED     0   2   5   0
  KLK10 WILD-TYPE   9  66 243  41
D102V4, multiclass
    clus
vv   KLK10 MUTATED KLK10 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             5             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
  KLK10 MUTATED     4   2   1
  KLK10 WILD-TYPE 216  78  65
D102V5, multiclass
    clus
vv   KLK10 MUTATED KLK10 WILD-TYPE
  N0             4             216
  N1             2              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"
D102V6, binary
                 cls
clus                0   1
  KLK10 MUTATED     5   0
  KLK10 WILD-TYPE 278  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLK10 MUTATED      5    0
  KLK10 WILD-TYPE  278   48
   clus
vv  KLK10 MUTATED KLK10 WILD-TYPE
  0             5             278
  1             0              48
[1] 2 2
[1] FALSE
D102V7, 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
D102V8, binary
                 cls
clus                0   1
  KLK10 MUTATED     6   1
  KLK10 WILD-TYPE 311  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLK10 MUTATED      6    1
  KLK10 WILD-TYPE  311   47
                               clus
vv                              KLK10 MUTATED KLK10 WILD-TYPE
  COLON ADENOCARCINOMA                      6             311
  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 255   2  22  20
D102V9, multiclass
    clus
vv   KLK10 MUTATED KLK10 WILD-TYPE
  R0             2             255
  R1             0               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"
D102V10, 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
D102V11, 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(103) Variable = SVIL MUTATION ANALYSIS
D103V1, survival
                sevent
clus2              0   1
  SVIL MUTATED    21   9
  SVIL WILD-TYPE 261  64
  SVIL MUTATED SVIL WILD-TYPE 
            30            325 
  SVIL MUTATED SVIL WILD-TYPE 
             9             64 
$`SVIL MUTATED`
TCGA-A6-3809 TCGA-A6-5665 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3518 
       32.75        22.06        24.39        20.12        19.66         1.02 
TCGA-AA-3696 TCGA-AA-3713 TCGA-AA-3845 TCGA-AA-3864 TCGA-AD-5900 TCGA-AD-6889 
        5.03        19.04         0.00        53.00         0.07        56.55 
TCGA-AD-6964 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CK-5916 
       10.88        21.44        58.39        49.41       100.01        21.14 
TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6171 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6541 
       15.02        12.00        14.04         4.80        16.14        15.58 
TCGA-DM-A1HB TCGA-F4-6459 TCGA-F4-6570 TCGA-G4-6307 TCGA-G4-6588 TCGA-G4-6628 
      135.65         8.61         6.18        55.04        26.17        52.80 

$`SVIL WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 
       24.16        21.76        24.69        23.87        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        3.02         1.02        35.01        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       13.02        38.99         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       19.00        36.00        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02        14.93        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       40.96        21.37         4.21         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        15.75         0.20        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32        21.99         2.93         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        16.01         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-6172 
       21.99        14.99        12.99        13.02        15.02        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 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-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 
      119.93        35.97        60.79       117.07        98.24        13.38 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        53.62        44.68        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 
       46.75 

  SVIL MUTATED SVIL WILD-TYPE 
             0              0 
  SVIL MUTATED SVIL WILD-TYPE 
        135.65         140.38 
  SVIL MUTATED SVIL WILD-TYPE 
         19.89          20.28 
[1] "0.0 - 135.7 (19.9)" "0.0 - 140.4 (20.3)"
[1] "hr=" "1.3"
D103V2, 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       21        97         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        19         10         36         30       33        13
                vv
clus             STAGE IVB
  SVIL MUTATED           0
  SVIL WILD-TYPE         1
D103V3, multiclass
            clus
vv           SVIL MUTATED SVIL WILD-TYPE
  STAGE I               6             58
  STAGE IA              0              1
  STAGE II              4             21
  STAGE IIA            12             97
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            5             36
  STAGE IIIC            1             30
  STAGE IV              2             33
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SVIL MUTATED     1   5  22   4
  SVIL WILD-TYPE   8  63 226  37
D103V4, multiclass
    clus
vv   SVIL MUTATED SVIL WILD-TYPE
  T1            1              8
  T2            5             63
  T3           22            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
  SVIL MUTATED    24   6   2
  SVIL WILD-TYPE 196  74  64
D103V5, multiclass
    clus
vv   SVIL MUTATED SVIL WILD-TYPE
  N0           24            196
  N1            6             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"
D103V6, binary
                cls
clus               0   1
  SVIL MUTATED    23   2
  SVIL WILD-TYPE 260  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  SVIL MUTATED     23    2
  SVIL WILD-TYPE  260   46
   clus
vv  SVIL MUTATED SVIL WILD-TYPE
  0           23            260
  1            2             46
[1] 2 2
[1] FALSE
D103V7, 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
D103V8, binary
                cls
clus               0   1
  SVIL MUTATED    26   6
  SVIL WILD-TYPE 291  42
[1] "tbl2"
                cls
clus             [,1] [,2]
  SVIL MUTATED     26    6
  SVIL WILD-TYPE  291   42
                               clus
vv                              SVIL MUTATED SVIL WILD-TYPE
  COLON ADENOCARCINOMA                    26            291
  COLON MUCINOUS ADENOCARCINOMA            6             42
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SVIL MUTATED    22   0   2   1
  SVIL WILD-TYPE 235   2  20  20
D103V9, multiclass
    clus
vv   SVIL MUTATED SVIL WILD-TYPE
  R0           22            235
  R1            0              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"
D103V10, 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
D103V11, 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(104) Variable = CEP135 MUTATION ANALYSIS
D104V1, survival
                  sevent
clus2                0   1
  CEP135 MUTATED    13   6
  CEP135 WILD-TYPE 269  67
  CEP135 MUTATED CEP135 WILD-TYPE 
              19              336 
  CEP135 MUTATED CEP135 WILD-TYPE 
               6               67 
$`CEP135 MUTATED`
TCGA-A6-6782 TCGA-AA-3554 TCGA-AA-3811 TCGA-AA-3977 TCGA-AA-A00E TCGA-AA-A00N 
       20.28        17.95        10.06        25.02        30.02         4.01 
TCGA-AZ-4315 TCGA-AZ-6601 TCGA-CA-6715 TCGA-CA-6717 TCGA-CM-6676 TCGA-CM-6679 
       58.39       100.01         0.07         0.33        11.08        10.06 
TCGA-D5-6538 TCGA-DM-A1D8 TCGA-DM-A1DB TCGA-DM-A1HB TCGA-F4-6570 TCGA-G4-6586 
       17.13        12.59        44.32       135.65         6.18        35.80 
TCGA-G4-6628 
       52.80 

$`CEP135 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        19.66         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        19.04        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F 
        7.96        27.02        13.94        38.04        19.00        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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-6680 TCGA-D5-5537 TCGA-D5-5538 
       13.05        11.08        11.01        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12        17.85         4.80        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-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-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       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        13.38        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 

  CEP135 MUTATED CEP135 WILD-TYPE 
            0.07             0.00 
  CEP135 MUTATED CEP135 WILD-TYPE 
          135.65           140.38 
  CEP135 MUTATED CEP135 WILD-TYPE 
          17.950           20.585 
[1] "0.1 - 135.7 (17.9)" "0.0 - 140.4 (20.6)"
[1] "hr=" "1.3"
D104V2, 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       24       100         5         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CEP135 MUTATED           1          0          3          0        0
  CEP135 WILD-TYPE        18         10         38         31       35
                  vv
clus               STAGE IVA STAGE IVB
  CEP135 MUTATED           0         0
  CEP135 WILD-TYPE        13         1
D104V3, multiclass
            clus
vv           CEP135 MUTATED CEP135 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               9              100
  STAGE IIB               3                5
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              3               38
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CEP135 MUTATED     0   3  15   3
  CEP135 WILD-TYPE   9  65 233  38
D104V4, multiclass
    clus
vv   CEP135 MUTATED CEP135 WILD-TYPE
  T1              0                9
  T2              3               65
  T3             15              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
  CEP135 MUTATED    16   3   2
  CEP135 WILD-TYPE 204  77  64
D104V5, multiclass
    clus
vv   CEP135 MUTATED CEP135 WILD-TYPE
  N0             16              204
  N1              3               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"
D104V6, binary
                  cls
clus                 0   1
  CEP135 MUTATED    17   0
  CEP135 WILD-TYPE 266  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP135 MUTATED     17    0
  CEP135 WILD-TYPE  266   48
   clus
vv  CEP135 MUTATED CEP135 WILD-TYPE
  0             17              266
  1              0               48
[1] 2 2
[1] FALSE
D104V7, 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
D104V8, binary
                  cls
clus                 0   1
  CEP135 MUTATED    19   2
  CEP135 WILD-TYPE 298  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP135 MUTATED     19    2
  CEP135 WILD-TYPE  298   46
                               clus
vv                              CEP135 MUTATED CEP135 WILD-TYPE
  COLON ADENOCARCINOMA                      19              298
  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 245   2  22  18
D104V9, multiclass
    clus
vv   CEP135 MUTATED CEP135 WILD-TYPE
  R0             12              245
  R1              0                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"
D104V10, 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
D104V11, 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(105) Variable = RNF128 MUTATION ANALYSIS
D105V1, survival
                  sevent
clus2                0   1
  RNF128 MUTATED    11   2
  RNF128 WILD-TYPE 271  71
  RNF128 MUTATED RNF128 WILD-TYPE 
              13              342 
  RNF128 MUTATED RNF128 WILD-TYPE 
               2               71 
$`RNF128 MUTATED`
TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3697 TCGA-AD-6548 TCGA-AD-6895 TCGA-AD-6964 
       22.06         3.02        85.05        21.37         0.72        10.88 
TCGA-AZ-4315 TCGA-CM-4746 TCGA-D5-6928 TCGA-DM-A0X9 TCGA-G4-6586 TCGA-G4-6588 
       58.39        37.02        11.64       119.70        35.80        26.17 
TCGA-G4-6628 
       52.80 

$`RNF128 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96         0.07         4.21        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38        10.26 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 
       36.72        36.00        22.09        13.78        91.79        46.75 

  RNF128 MUTATED RNF128 WILD-TYPE 
            0.72             0.00 
  RNF128 MUTATED RNF128 WILD-TYPE 
          119.70           140.38 
  RNF128 MUTATED RNF128 WILD-TYPE 
          26.170           20.005 
[1] "0.7 - 119.7 (26.2)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.9"
D105V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RNF128 MUTATED         3        0        1         6         1         0
  RNF128 WILD-TYPE      61        1       24       103         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RNF128 MUTATED           1          0          0          0        0
  RNF128 WILD-TYPE        18         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  RNF128 MUTATED           0         0
  RNF128 WILD-TYPE        13         1
D105V3, multiclass
            clus
vv           RNF128 MUTATED RNF128 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               6              103
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  RNF128 MUTATED     0   3   9   2
  RNF128 WILD-TYPE   9  65 239  39
D105V4, multiclass
    clus
vv   RNF128 MUTATED RNF128 WILD-TYPE
  T1              0                9
  T2              3               65
  T3              9              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
  RNF128 MUTATED    12   1   1
  RNF128 WILD-TYPE 208  79  65
D105V5, multiclass
    clus
vv   RNF128 MUTATED RNF128 WILD-TYPE
  N0             12              208
  N1              1               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"
D105V6, binary
                  cls
clus                 0   1
  RNF128 MUTATED    11   0
  RNF128 WILD-TYPE 272  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF128 MUTATED     11    0
  RNF128 WILD-TYPE  272   48
   clus
vv  RNF128 MUTATED RNF128 WILD-TYPE
  0             11              272
  1              0               48
[1] 2 2
[1] FALSE
D105V7, 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
D105V8, binary
                  cls
clus                 0   1
  RNF128 MUTATED    13   1
  RNF128 WILD-TYPE 304  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF128 MUTATED     13    1
  RNF128 WILD-TYPE  304   47
                               clus
vv                              RNF128 MUTATED RNF128 WILD-TYPE
  COLON ADENOCARCINOMA                      13              304
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  RNF128 MUTATED    10   0   0   1
  RNF128 WILD-TYPE 247   2  22  20
D105V9, multiclass
    clus
vv   RNF128 MUTATED RNF128 WILD-TYPE
  R0             10              247
  R1              0                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"
D105V10, 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
D105V11, 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(106) Variable = PTCH1 MUTATION ANALYSIS
D106V1, survival
                 sevent
clus2               0   1
  PTCH1 MUTATED    69  19
  PTCH1 WILD-TYPE 213  54
  PTCH1 MUTATED PTCH1 WILD-TYPE 
             88             267 
  PTCH1 MUTATED PTCH1 WILD-TYPE 
             19              54 
$`PTCH1 MUTATED`
TCGA-A6-3809 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6649 
       32.75        29.19        23.61        22.09        22.06        24.16 
TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6781 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3660 
       24.69        23.87        19.66         0.99        17.95        78.08 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3950 
       85.05        19.04        19.04        30.05        53.00        24.00 
TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A02K TCGA-AD-5900 
        0.99        34.98        38.07        35.01        14.01         0.07 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6964 TCGA-AU-3779 TCGA-AU-6004 
       56.55         0.79        22.42        10.88        14.50        27.09 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-AZ-6599 
       15.75         0.20        21.44        58.39        61.41         6.77 
TCGA-AZ-6601 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CM-4743 
      100.01       102.44        15.62        49.08        21.99        23.05 
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        16.01        15.02 
TCGA-CM-6164 TCGA-CM-6168 TCGA-CM-6172 TCGA-CM-6676 TCGA-D5-5537 TCGA-D5-5538 
       29.03        12.99        11.01        11.08        45.40        12.26 
TCGA-D5-5539 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 
       19.59        18.25         1.32        43.27        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6924 TCGA-D5-6927 
       17.13        12.49        16.14        15.58        14.30         9.44 
TCGA-D5-6929 TCGA-D5-6930 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D4 TCGA-DM-A1D8 
       13.41         1.51       119.70        24.43        92.75        12.59 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A285 TCGA-DM-A28F TCGA-DM-A28K TCGA-F4-6570 
        7.50        44.32         6.12        35.97        98.24         6.18 
TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       53.62        55.04        51.75        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 
       13.78        35.80        26.17        46.75 

$`PTCH1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       31.63        30.44        33.53        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 
        8.38        25.08        25.18        21.76        24.39        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3555 
       14.01        33.99        21.01        13.02        24.00        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
       19.00        36.00         5.03        26.99        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        31.07        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U 
       18.05        38.04         4.01        27.02        42.02        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 
       21.37         4.21         0.72         5.79        27.42         0.20 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       16.31         0.95        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       22.36        62.79        49.41        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       17.56        40.34        51.32        21.14         2.93         2.01 
TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5862 
      124.27        20.02        37.02        25.02        29.06         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00        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-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.01        10.06        12.03 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6535 TCGA-D5-6898 TCGA-D5-6920 
       13.51        11.51        20.19        15.12         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6931 TCGA-D5-6932 
       10.13        12.43         9.04        11.64        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 
       10.26        38.20       130.65        49.91        13.32       140.38 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G 
      131.51       135.65       139.17        81.37       119.93        60.79 
TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
      117.07         8.61        13.38        13.45        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 
       35.41        19.43       107.67        74.56        65.85        44.68 
TCGA-G4-6310 TCGA-G4-6625 TCGA-G4-6628 
       45.11        91.79        52.80 

  PTCH1 MUTATED PTCH1 WILD-TYPE 
           0.07            0.00 
  PTCH1 MUTATED PTCH1 WILD-TYPE 
         119.70          140.38 
  PTCH1 MUTATED PTCH1 WILD-TYPE 
         22.075          19.990 
[1] "0.1 - 119.7 (22.1)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.1"
D106V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PTCH1 MUTATED         9        1        4        32         4         0
  PTCH1 WILD-TYPE      55        0       21        77         4         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PTCH1 MUTATED           5          3         13          6        5         3
  PTCH1 WILD-TYPE        14          7         28         25       30        10
                 vv
clus              STAGE IVB
  PTCH1 MUTATED           0
  PTCH1 WILD-TYPE         1
D106V3, multiclass
            clus
vv           PTCH1 MUTATED PTCH1 WILD-TYPE
  STAGE I                9              55
  STAGE IA               1               0
  STAGE II               4              21
  STAGE IIA             32              77
  STAGE IIB              4               4
  STAGE IIC              0               1
  STAGE III              5              14
  STAGE IIIA             3               7
  STAGE IIIB            13              28
  STAGE IIIC             6              25
  STAGE IV               5              30
  STAGE IVA              3              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
  PTCH1 MUTATED     2   9  67  10
  PTCH1 WILD-TYPE   7  59 181  31
D106V4, multiclass
    clus
vv   PTCH1 MUTATED PTCH1 WILD-TYPE
  T1             2               7
  T2             9              59
  T3            67             181
  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  60  53
D106V5, multiclass
    clus
vv   PTCH1 MUTATED PTCH1 WILD-TYPE
  N0            56             164
  N1            20              60
  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"
D106V6, binary
                 cls
clus                0   1
  PTCH1 MUTATED    63   8
  PTCH1 WILD-TYPE 220  40
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTCH1 MUTATED     63    8
  PTCH1 WILD-TYPE  220   40
   clus
vv  PTCH1 MUTATED PTCH1 WILD-TYPE
  0            63             220
  1             8              40
[1] 2 2
[1] FALSE
D106V7, 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
D106V8, binary
                 cls
clus                0   1
  PTCH1 MUTATED    75  14
  PTCH1 WILD-TYPE 242  34
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTCH1 MUTATED     75   14
  PTCH1 WILD-TYPE  242   34
                               clus
vv                              PTCH1 MUTATED PTCH1 WILD-TYPE
  COLON ADENOCARCINOMA                     75             242
  COLON MUCINOUS ADENOCARCINOMA            14              34
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PTCH1 MUTATED    60   0   2   5
  PTCH1 WILD-TYPE 197   2  20  16
D106V9, multiclass
    clus
vv   PTCH1 MUTATED PTCH1 WILD-TYPE
  R0            60             197
  R1             0               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"
D106V10, 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
D106V11, 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(107) Variable = ADAM28 MUTATION ANALYSIS
D107V1, survival
                  sevent
clus2                0   1
  ADAM28 MUTATED     9   6
  ADAM28 WILD-TYPE 273  67
  ADAM28 MUTATED ADAM28 WILD-TYPE 
              15              340 
  ADAM28 MUTATED ADAM28 WILD-TYPE 
               6               67 
$`ADAM28 MUTATED`
TCGA-A6-5660 TCGA-A6-6652 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3543 TCGA-AA-A00N 
       29.19        24.69         3.02        63.98         0.99         4.01 
TCGA-AZ-6599 TCGA-AZ-6605 TCGA-CK-5913 TCGA-CM-5344 TCGA-CM-5863 TCGA-D5-6928 
        6.77         5.23        51.32        22.03        15.02        11.64 
TCGA-DM-A28F TCGA-F4-6569 TCGA-G4-6626 
       35.97        13.45        46.75 

$`ADAM28 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       19.66        20.28         7.04         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
       34.03        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 
       61.41        49.41        12.10       100.01        29.56        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 
      102.44        40.34        15.62        49.08        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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        16.01 
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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
       81.37       119.93        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.38         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       35.80        26.17        91.79        52.80 

  ADAM28 MUTATED ADAM28 WILD-TYPE 
            0.99             0.00 
  ADAM28 MUTATED ADAM28 WILD-TYPE 
           63.98           140.38 
  ADAM28 MUTATED ADAM28 WILD-TYPE 
          15.020           20.235 
[1] "1.0 - 64.0 (15.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2.2"
D107V2, 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       23       105         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ADAM28 MUTATED           0          0          4          1        0
  ADAM28 WILD-TYPE        19         10         37         30       35
                  vv
clus               STAGE IVA STAGE IVB
  ADAM28 MUTATED           1         0
  ADAM28 WILD-TYPE        12         1
D107V3, multiclass
            clus
vv           ADAM28 MUTATED ADAM28 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               4              105
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              4               37
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  65 237  38
D107V4, multiclass
    clus
vv   ADAM28 MUTATED ADAM28 WILD-TYPE
  T1              0                9
  T2              3               65
  T3             11              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
  ADAM28 MUTATED    12   4   1
  ADAM28 WILD-TYPE 208  76  65
D107V5, multiclass
    clus
vv   ADAM28 MUTATED ADAM28 WILD-TYPE
  N0             12              208
  N1              4               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"
D107V6, binary
                  cls
clus                 0   1
  ADAM28 MUTATED    13   1
  ADAM28 WILD-TYPE 270  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM28 MUTATED     13    1
  ADAM28 WILD-TYPE  270   47
   clus
vv  ADAM28 MUTATED ADAM28 WILD-TYPE
  0             13              270
  1              1               47
[1] 2 2
[1] FALSE
D107V7, 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
D107V8, binary
                  cls
clus                 0   1
  ADAM28 MUTATED    13   4
  ADAM28 WILD-TYPE 304  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM28 MUTATED     13    4
  ADAM28 WILD-TYPE  304   44
                               clus
vv                              ADAM28 MUTATED ADAM28 WILD-TYPE
  COLON ADENOCARCINOMA                      13              304
  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 247   2  22  19
D107V9, multiclass
    clus
vv   ADAM28 MUTATED ADAM28 WILD-TYPE
  R0             10              247
  R1              0                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"
D107V10, 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
D107V11, 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(108) Variable = WEE1 MUTATION ANALYSIS
D108V1, survival
                sevent
clus2              0   1
  WEE1 MUTATED     8   3
  WEE1 WILD-TYPE 274  70
  WEE1 MUTATED WEE1 WILD-TYPE 
            11            344 
  WEE1 MUTATED WEE1 WILD-TYPE 
             3             70 
$`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 
        2.24        22.98        15.02        81.37       107.67 

$`WEE1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 
       10.06        35.05        33.04         0.99        25.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       22.36        62.79        61.41        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19         1.94         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        16.01         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      135.65       139.17         6.12       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        35.41        19.43        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  WEE1 MUTATED WEE1 WILD-TYPE 
          1.02           0.00 
  WEE1 MUTATED WEE1 WILD-TYPE 
        107.67         140.38 
  WEE1 MUTATED WEE1 WILD-TYPE 
         27.09          20.07 
[1] "1.0 - 107.7 (27.1)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.2"
D108V2, 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       22       105         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        18         10         40         31       35        13
                vv
clus             STAGE IVB
  WEE1 MUTATED           0
  WEE1 WILD-TYPE         1
D108V3, multiclass
            clus
vv           WEE1 MUTATED WEE1 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              3             22
  STAGE IIA             4            105
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  WEE1 MUTATED     0   3   8   1
  WEE1 WILD-TYPE   9  65 240  40
D108V4, multiclass
    clus
vv   WEE1 MUTATED WEE1 WILD-TYPE
  T1            0              9
  T2            3             65
  T3            8            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
  WEE1 MUTATED    10   2   0
  WEE1 WILD-TYPE 210  78  66
D108V5, multiclass
    clus
vv   WEE1 MUTATED WEE1 WILD-TYPE
  N0           10            210
  N1            2             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"
D108V6, binary
                cls
clus               0   1
  WEE1 MUTATED    10   0
  WEE1 WILD-TYPE 273  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  WEE1 MUTATED     10    0
  WEE1 WILD-TYPE  273   48
   clus
vv  WEE1 MUTATED WEE1 WILD-TYPE
  0           10            273
  1            0             48
[1] 2 2
[1] FALSE
D108V7, 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
D108V8, binary
                cls
clus               0   1
  WEE1 MUTATED    11   1
  WEE1 WILD-TYPE 306  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  WEE1 MUTATED     11    1
  WEE1 WILD-TYPE  306   47
                               clus
vv                              WEE1 MUTATED WEE1 WILD-TYPE
  COLON ADENOCARCINOMA                    11            306
  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 249   2  22  20
D108V9, multiclass
    clus
vv   WEE1 MUTATED WEE1 WILD-TYPE
  R0            8            249
  R1            0              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"
D108V10, 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
D108V11, 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(109) Variable = TNFRSF9 MUTATION ANALYSIS
D109V1, survival
                   sevent
clus2                 0   1
  TNFRSF9 MUTATED     8   1
  TNFRSF9 WILD-TYPE 274  72
  TNFRSF9 MUTATED TNFRSF9 WILD-TYPE 
                9               346 
  TNFRSF9 MUTATED TNFRSF9 WILD-TYPE 
                1                72 
$`TNFRSF9 MUTATED`
TCGA-A6-5666 TCGA-A6-6653 TCGA-AA-A00J TCGA-AA-A01P TCGA-CA-5796 TCGA-CA-6717 
       32.71        24.39        18.05        38.07         3.25         0.33 
TCGA-CM-5341 TCGA-CM-6167 TCGA-D5-6538 
       29.06        14.99        17.13 

$`TNFRSF9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        2.24         3.06         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  TNFRSF9 MUTATED TNFRSF9 WILD-TYPE 
             0.33              0.00 
  TNFRSF9 MUTATED TNFRSF9 WILD-TYPE 
            38.07            140.38 
  TNFRSF9 MUTATED TNFRSF9 WILD-TYPE 
           18.050            20.235 
[1] "0.3 - 38.1 (18.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.4"
D109V2, 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       25       107         8         0
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TNFRSF9 MUTATED           1          1          2          1        0
  TNFRSF9 WILD-TYPE        18          9         39         30       35
                   vv
clus                STAGE IVA STAGE IVB
  TNFRSF9 MUTATED           0         0
  TNFRSF9 WILD-TYPE        13         1
D109V3, multiclass
            clus
vv           TNFRSF9 MUTATED TNFRSF9 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                2               107
  STAGE IIB                0                 8
  STAGE IIC                1                 0
  STAGE III                1                18
  STAGE IIIA               1                 9
  STAGE IIIB               2                39
  STAGE IIIC               1                30
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TNFRSF9 MUTATED     0   2   5   2
  TNFRSF9 WILD-TYPE   9  66 243  39
D109V4, multiclass
    clus
vv   TNFRSF9 MUTATED TNFRSF9 WILD-TYPE
  T1               0                 9
  T2               2                66
  T3               5               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
  TNFRSF9 MUTATED     4   3   2
  TNFRSF9 WILD-TYPE 216  77  64
D109V5, multiclass
    clus
vv   TNFRSF9 MUTATED TNFRSF9 WILD-TYPE
  N0               4               216
  N1               3                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"
D109V6, binary
                   cls
clus                  0   1
  TNFRSF9 MUTATED     9   0
  TNFRSF9 WILD-TYPE 274  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFRSF9 MUTATED      9    0
  TNFRSF9 WILD-TYPE  274   48
   clus
vv  TNFRSF9 MUTATED TNFRSF9 WILD-TYPE
  0               9               274
  1               0                48
[1] 2 2
[1] FALSE
D109V7, 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
D109V8, binary
                   cls
clus                  0   1
  TNFRSF9 MUTATED     6   3
  TNFRSF9 WILD-TYPE 311  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFRSF9 MUTATED      6    3
  TNFRSF9 WILD-TYPE  311   45
                               clus
vv                              TNFRSF9 MUTATED TNFRSF9 WILD-TYPE
  COLON ADENOCARCINOMA                        6               311
  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 251   2  22  20
D109V9, multiclass
    clus
vv   TNFRSF9 MUTATED TNFRSF9 WILD-TYPE
  R0               6               251
  R1               0                 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"
D109V10, 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
D109V11, 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(110) Variable = HTR2A MUTATION ANALYSIS
D110V1, survival
                 sevent
clus2               0   1
  HTR2A MUTATED    14   5
  HTR2A WILD-TYPE 268  68
  HTR2A MUTATED HTR2A WILD-TYPE 
             19             336 
  HTR2A MUTATED HTR2A WILD-TYPE 
              5              68 
$`HTR2A MUTATED`
TCGA-A6-5660 TCGA-A6-5665 TCGA-A6-6651 TCGA-AA-A00N TCGA-AA-A010 TCGA-CA-5255 
       29.19        22.06        21.76         4.01        34.98         3.06 
TCGA-CA-6717 TCGA-CK-4952 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-6161 TCGA-D5-5539 
        0.33        15.62        16.01         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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       24.16        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       102.44        40.34        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 
       30.08        15.02        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-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       12.26        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 
       43.27        17.85         4.80        17.13        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-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-A1HB 
       49.91        12.59       140.38         7.50        44.32       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
      139.17         6.12       119.93        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.41        19.43       107.67        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  HTR2A MUTATED HTR2A WILD-TYPE 
           0.33            0.00 
  HTR2A MUTATED HTR2A WILD-TYPE 
         131.51          140.38 
  HTR2A MUTATED HTR2A WILD-TYPE 
          16.01           20.63 
[1] "0.3 - 131.5 (16.0)" "0.0 - 140.4 (20.6)"
[1] "hr=" "1.2"
D110V2, 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       25       103         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HTR2A MUTATED           1          2          3          3        0         1
  HTR2A WILD-TYPE        18          8         38         28       35        12
                 vv
clus              STAGE IVB
  HTR2A MUTATED           0
  HTR2A WILD-TYPE         1
D110V3, multiclass
            clus
vv           HTR2A MUTATED HTR2A WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              6             103
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             2               8
  STAGE IIIB             3              38
  STAGE IIIC             3              28
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 233  38
D110V4, multiclass
    clus
vv   HTR2A MUTATED HTR2A WILD-TYPE
  T1             0               9
  T2             1              67
  T3            15             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
  HTR2A MUTATED    10   5   4
  HTR2A WILD-TYPE 210  75  62
D110V5, multiclass
    clus
vv   HTR2A MUTATED HTR2A WILD-TYPE
  N0            10             210
  N1             5              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"
D110V6, binary
                 cls
clus                0   1
  HTR2A MUTATED    16   1
  HTR2A WILD-TYPE 267  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HTR2A MUTATED     16    1
  HTR2A WILD-TYPE  267   47
   clus
vv  HTR2A MUTATED HTR2A WILD-TYPE
  0            16             267
  1             1              47
[1] 2 2
[1] FALSE
D110V7, 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
D110V8, binary
                 cls
clus                0   1
  HTR2A MUTATED    15   4
  HTR2A WILD-TYPE 302  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HTR2A MUTATED     15    4
  HTR2A WILD-TYPE  302   44
                               clus
vv                              HTR2A MUTATED HTR2A WILD-TYPE
  COLON ADENOCARCINOMA                     15             302
  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 248   2  22  17
D110V9, multiclass
    clus
vv   HTR2A MUTATED HTR2A WILD-TYPE
  R0             9             248
  R1             0               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"
D110V10, 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
D110V11, 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(111) Variable = EHBP1 MUTATION ANALYSIS
D111V1, survival
                 sevent
clus2               0   1
  EHBP1 MUTATED    18   3
  EHBP1 WILD-TYPE 264  70
  EHBP1 MUTATED EHBP1 WILD-TYPE 
             21             334 
  EHBP1 MUTATED EHBP1 WILD-TYPE 
              3              70 
$`EHBP1 MUTATED`
TCGA-A6-5666 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3845 TCGA-AA-3864 TCGA-AA-3977 
       32.71         1.02        35.01         0.00        53.00        25.02 
TCGA-AD-6889 TCGA-AU-6004 TCGA-CK-5913 TCGA-CK-5914 TCGA-CM-6167 TCGA-D5-5538 
       56.55        27.09        51.32        21.99        14.99        12.26 
TCGA-D5-6532 TCGA-D5-6535 TCGA-D5-6540 TCGA-DM-A1D7 TCGA-DM-A28H TCGA-F4-6570 
       18.25        15.12        16.14        13.32       117.07         6.18 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6588 
       55.04        45.11        26.17 

$`EHBP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3510 
       20.12        19.66        20.28         7.04         3.02        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       38.99        37.02        14.93        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5916 TCGA-CK-6747 
      102.44        40.34        15.62        49.08        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        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-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-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-D5-6533 TCGA-D5-6534 
       19.59        13.51        11.51        20.19         1.32        43.27 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        13.38        13.45        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       44.68        51.75        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        91.79        46.75        52.80 

  EHBP1 MUTATED EHBP1 WILD-TYPE 
              0               0 
  EHBP1 MUTATED EHBP1 WILD-TYPE 
         117.07          140.38 
  EHBP1 MUTATED EHBP1 WILD-TYPE 
          25.02           20.07 
[1] "0.0 - 117.1 (25.0)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.8"
D111V2, 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       23       101         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        19         10         36         29       35        13
                 vv
clus              STAGE IVB
  EHBP1 MUTATED           0
  EHBP1 WILD-TYPE         1
D111V3, multiclass
            clus
vv           EHBP1 MUTATED EHBP1 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              8             101
  STAGE IIB              0               8
  STAGE IIC              1               0
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             5              36
  STAGE IIIC             2              29
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EHBP1 MUTATED     0   4  17   1
  EHBP1 WILD-TYPE   9  64 231  40
D111V4, multiclass
    clus
vv   EHBP1 MUTATED EHBP1 WILD-TYPE
  T1             0               9
  T2             4              64
  T3            17             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
  EHBP1 MUTATED    15   5   2
  EHBP1 WILD-TYPE 205  75  64
D111V5, multiclass
    clus
vv   EHBP1 MUTATED EHBP1 WILD-TYPE
  N0            15             205
  N1             5              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"
D111V6, binary
                 cls
clus                0   1
  EHBP1 MUTATED    18   0
  EHBP1 WILD-TYPE 265  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EHBP1 MUTATED     18    0
  EHBP1 WILD-TYPE  265   48
   clus
vv  EHBP1 MUTATED EHBP1 WILD-TYPE
  0            18             265
  1             0              48
[1] 2 2
[1] FALSE
D111V7, 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
D111V8, binary
                 cls
clus                0   1
  EHBP1 MUTATED    21   1
  EHBP1 WILD-TYPE 296  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EHBP1 MUTATED     21    1
  EHBP1 WILD-TYPE  296   47
                               clus
vv                              EHBP1 MUTATED EHBP1 WILD-TYPE
  COLON ADENOCARCINOMA                     21             296
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  EHBP1 MUTATED    14   0   0   3
  EHBP1 WILD-TYPE 243   2  22  18
D111V9, multiclass
    clus
vv   EHBP1 MUTATED EHBP1 WILD-TYPE
  R0            14             243
  R1             0               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"
D111V10, 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
D111V11, 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(112) Variable = UQCRC2 MUTATION ANALYSIS
D112V1, survival
                  sevent
clus2                0   1
  UQCRC2 MUTATED     5   3
  UQCRC2 WILD-TYPE 277  70
  UQCRC2 MUTATED UQCRC2 WILD-TYPE 
               8              347 
  UQCRC2 MUTATED UQCRC2 WILD-TYPE 
               3               70 
$`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-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.33         0.10         1.35       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 
       81.37       119.93        35.97        60.79       117.07         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       19.43       107.67        74.56        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  UQCRC2 MUTATED UQCRC2 WILD-TYPE 
            5.03             0.00 
  UQCRC2 MUTATED UQCRC2 WILD-TYPE 
           98.24           140.38 
  UQCRC2 MUTATED UQCRC2 WILD-TYPE 
          29.685           20.120 
[1] "5.0 - 98.2 (29.7)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.3"
D112V2, 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       25       108         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  UQCRC2 MUTATED           0          0          1          0        2
  UQCRC2 WILD-TYPE        19         10         40         31       33
                  vv
clus               STAGE IVA STAGE IVB
  UQCRC2 MUTATED           2         0
  UQCRC2 WILD-TYPE        11         1
D112V3, multiclass
            clus
vv           UQCRC2 MUTATED UQCRC2 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               1              108
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                2               33
  STAGE IVA               2               11
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 243  39
D112V4, multiclass
    clus
vv   UQCRC2 MUTATED UQCRC2 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              5              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
  UQCRC2 MUTATED     3   4   1
  UQCRC2 WILD-TYPE 217  76  65
D112V5, multiclass
    clus
vv   UQCRC2 MUTATED UQCRC2 WILD-TYPE
  N0              3              217
  N1              4               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"
D112V6, binary
                  cls
clus                 0   1
  UQCRC2 MUTATED     4   3
  UQCRC2 WILD-TYPE 279  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UQCRC2 MUTATED      4    3
  UQCRC2 WILD-TYPE  279   45
   clus
vv  UQCRC2 MUTATED UQCRC2 WILD-TYPE
  0              4              279
  1              3               45
[1] 2 2
[1] FALSE
D112V7, 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
D112V8, binary
                  cls
clus                 0   1
  UQCRC2 MUTATED     7   1
  UQCRC2 WILD-TYPE 310  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UQCRC2 MUTATED      7    1
  UQCRC2 WILD-TYPE  310   47
                               clus
vv                              UQCRC2 MUTATED UQCRC2 WILD-TYPE
  COLON ADENOCARCINOMA                       7              310
  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 253   2  22  19
D112V9, multiclass
    clus
vv   UQCRC2 MUTATED UQCRC2 WILD-TYPE
  R0              4              253
  R1              0                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"
D112V10, 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
D112V11, 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(113) Variable = LINGO4 MUTATION ANALYSIS
D113V1, survival
                  sevent
clus2                0   1
  LINGO4 MUTATED     5   4
  LINGO4 WILD-TYPE 277  69
  LINGO4 MUTATED LINGO4 WILD-TYPE 
               9              346 
  LINGO4 MUTATED LINGO4 WILD-TYPE 
               4               69 
$`LINGO4 MUTATED`
TCGA-A6-2671 TCGA-AA-3672 TCGA-AA-3864 TCGA-AA-3950 TCGA-AA-A00N TCGA-AZ-6598 
       43.76         0.92        53.00        24.00         4.01        49.41 
TCGA-CM-6171 TCGA-D5-6537 TCGA-D5-6930 
       14.04         4.80         1.51 

$`LINGO4 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  LINGO4 MUTATED LINGO4 WILD-TYPE 
            0.92             0.00 
  LINGO4 MUTATED LINGO4 WILD-TYPE 
           53.00           140.38 
  LINGO4 MUTATED LINGO4 WILD-TYPE 
          14.040           20.235 
[1] "0.9 - 53.0 (14.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2.5"
D113V2, 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       22       107         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LINGO4 MUTATED           1          0          1          0        1
  LINGO4 WILD-TYPE        18         10         40         31       34
                  vv
clus               STAGE IVA STAGE IVB
  LINGO4 MUTATED           0         0
  LINGO4 WILD-TYPE        13         1
D113V3, multiclass
            clus
vv           LINGO4 MUTATED LINGO4 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                3               22
  STAGE IIA               2              107
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  LINGO4 MUTATED     0   1   7   2
  LINGO4 WILD-TYPE   9  67 241  39
D113V4, multiclass
    clus
vv   LINGO4 MUTATED LINGO4 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              7              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
  LINGO4 MUTATED     7   2   1
  LINGO4 WILD-TYPE 213  78  65
D113V5, multiclass
    clus
vv   LINGO4 MUTATED LINGO4 WILD-TYPE
  N0              7              213
  N1              2               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"
D113V6, binary
                  cls
clus                 0   1
  LINGO4 MUTATED     7   1
  LINGO4 WILD-TYPE 276  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LINGO4 MUTATED      7    1
  LINGO4 WILD-TYPE  276   47
   clus
vv  LINGO4 MUTATED LINGO4 WILD-TYPE
  0              7              276
  1              1               47
[1] 2 2
[1] FALSE
D113V7, 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
D113V8, binary
                  cls
clus                 0   1
  LINGO4 MUTATED     7   3
  LINGO4 WILD-TYPE 310  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LINGO4 MUTATED      7    3
  LINGO4 WILD-TYPE  310   45
                               clus
vv                              LINGO4 MUTATED LINGO4 WILD-TYPE
  COLON ADENOCARCINOMA                       7              310
  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 248   2  22  21
D113V9, multiclass
    clus
vv   LINGO4 MUTATED LINGO4 WILD-TYPE
  R0              9              248
  R1              0                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"
D113V10, 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
D113V11, 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(114) Variable = DCLK2 MUTATION ANALYSIS
D114V1, survival
                 sevent
clus2               0   1
  DCLK2 MUTATED    13   0
  DCLK2 WILD-TYPE 269  73
  DCLK2 MUTATED DCLK2 WILD-TYPE 
             13             342 
  DCLK2 MUTATED DCLK2 WILD-TYPE 
              0              73 
$`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        61.41 
TCGA-CM-5868 TCGA-CM-6679 TCGA-D5-6533 TCGA-D5-6539 TCGA-D5-6928 TCGA-F4-6703 
       17.03        10.06         1.32        12.49        11.64        35.87 
TCGA-G4-6306 
       44.68 

$`DCLK2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 
       10.06        35.05         0.99        25.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        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-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       11.01        12.03        45.40        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       11.51        20.19        18.25        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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        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        13.38        13.45         6.18         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  DCLK2 MUTATED DCLK2 WILD-TYPE 
           1.02            0.00 
  DCLK2 MUTATED DCLK2 WILD-TYPE 
          61.41          140.38 
  DCLK2 MUTATED DCLK2 WILD-TYPE 
         17.030          20.235 
[1] "1.0 - 61.4 (17.0)"  "0.0 - 140.4 (20.2)"
[1] "hr="     "2.6e+07"
D114V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DCLK2 MUTATED         2        0        1         7         1         0
  DCLK2 WILD-TYPE      62        1       24       102         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DCLK2 MUTATED           0          1          1          0        0         1
  DCLK2 WILD-TYPE        19          9         40         31       35        12
                 vv
clus              STAGE IVB
  DCLK2 MUTATED           0
  DCLK2 WILD-TYPE         1
D114V3, multiclass
            clus
vv           DCLK2 MUTATED DCLK2 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              7             102
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 240  38
D114V4, multiclass
    clus
vv   DCLK2 MUTATED DCLK2 WILD-TYPE
  T1             1               8
  T2             2              66
  T3             8             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
  DCLK2 MUTATED    13   1   0
  DCLK2 WILD-TYPE 207  79  66
D114V5, multiclass
    clus
vv   DCLK2 MUTATED DCLK2 WILD-TYPE
  N0            13             207
  N1             1              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"
D114V6, binary
                 cls
clus                0   1
  DCLK2 MUTATED    13   1
  DCLK2 WILD-TYPE 270  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DCLK2 MUTATED     13    1
  DCLK2 WILD-TYPE  270   47
   clus
vv  DCLK2 MUTATED DCLK2 WILD-TYPE
  0            13             270
  1             1              47
[1] 2 2
[1] FALSE
D114V7, 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
D114V8, binary
                 cls
clus                0   1
  DCLK2 MUTATED    11   3
  DCLK2 WILD-TYPE 306  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DCLK2 MUTATED     11    3
  DCLK2 WILD-TYPE  306   45
                               clus
vv                              DCLK2 MUTATED DCLK2 WILD-TYPE
  COLON ADENOCARCINOMA                     11             306
  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 244   2  22  21
D114V9, multiclass
    clus
vv   DCLK2 MUTATED DCLK2 WILD-TYPE
  R0            13             244
  R1             0               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"
D114V10, 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
D114V11, 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(115) Variable = NCAPD2 MUTATION ANALYSIS
D115V1, survival
                  sevent
clus2                0   1
  NCAPD2 MUTATED    17   1
  NCAPD2 WILD-TYPE 265  72
  NCAPD2 MUTATED NCAPD2 WILD-TYPE 
              18              337 
  NCAPD2 MUTATED NCAPD2 WILD-TYPE 
               1               72 
$`NCAPD2 MUTATED`
TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3950 TCGA-AA-A00K 
       24.39        19.66        63.98         6.97        24.00        18.05 
TCGA-AA-A010 TCGA-AA-A01Q TCGA-AZ-4315 TCGA-AZ-6601 TCGA-CM-4743 TCGA-CM-6162 
       34.98         1.02        58.39       100.01        23.05        12.00 
TCGA-D5-6930 TCGA-DM-A28K TCGA-G4-6293 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6628 
        1.51        98.24       107.67        53.62        44.68        52.80 

$`NCAPD2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 
      119.93        35.97        60.79       117.07         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       74.56        65.85        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 
       46.75 

  NCAPD2 MUTATED NCAPD2 WILD-TYPE 
            1.02             0.00 
  NCAPD2 MUTATED NCAPD2 WILD-TYPE 
          107.67           140.38 
  NCAPD2 MUTATED NCAPD2 WILD-TYPE 
          29.685           19.990 
[1] "1.0 - 107.7 (29.7)" "0.0 - 140.4 (20.0)"
[1] "hr=" "6.6"
D115V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NCAPD2 MUTATED         2        0        4         8         3         0
  NCAPD2 WILD-TYPE      62        1       21       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        18         10         40         30       35
                  vv
clus               STAGE IVA STAGE IVB
  NCAPD2 MUTATED           0         0
  NCAPD2 WILD-TYPE        13         1
D115V3, multiclass
            clus
vv           NCAPD2 MUTATED NCAPD2 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                4               21
  STAGE IIA               8              101
  STAGE IIB               3                5
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  NCAPD2 MUTATED     0   3  13   4
  NCAPD2 WILD-TYPE   9  65 235  37
D115V4, multiclass
    clus
vv   NCAPD2 MUTATED NCAPD2 WILD-TYPE
  T1              0                9
  T2              3               65
  T3             13              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
  NCAPD2 MUTATED    17   3   0
  NCAPD2 WILD-TYPE 203  77  66
D115V5, multiclass
    clus
vv   NCAPD2 MUTATED NCAPD2 WILD-TYPE
  N0             17              203
  N1              3               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"
D115V6, binary
                  cls
clus                 0   1
  NCAPD2 MUTATED    18   0
  NCAPD2 WILD-TYPE 265  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NCAPD2 MUTATED     18    0
  NCAPD2 WILD-TYPE  265   48
   clus
vv  NCAPD2 MUTATED NCAPD2 WILD-TYPE
  0             18              265
  1              0               48
[1] 2 2
[1] FALSE
D115V7, 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
D115V8, binary
                  cls
clus                 0   1
  NCAPD2 MUTATED    15   5
  NCAPD2 WILD-TYPE 302  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NCAPD2 MUTATED     15    5
  NCAPD2 WILD-TYPE  302   43
                               clus
vv                              NCAPD2 MUTATED NCAPD2 WILD-TYPE
  COLON ADENOCARCINOMA                      15              302
  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 241   2  22  20
D115V9, multiclass
    clus
vv   NCAPD2 MUTATED NCAPD2 WILD-TYPE
  R0             16              241
  R1              0                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"
D115V10, 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
D115V11, 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(116) Variable = RSPH3 MUTATION ANALYSIS
D116V1, survival
                 sevent
clus2               0   1
  RSPH3 MUTATED     7   3
  RSPH3 WILD-TYPE 275  70
  RSPH3 MUTATED RSPH3 WILD-TYPE 
             10             345 
  RSPH3 MUTATED RSPH3 WILD-TYPE 
              3              70 
$`RSPH3 MUTATED`
TCGA-A6-6652 TCGA-A6-6653 TCGA-AA-A010 TCGA-AD-6895 TCGA-AD-6965 TCGA-AZ-6599 
       24.69        24.39        34.98         0.72         0.20         6.77 
TCGA-AZ-6601 TCGA-DM-A1DA TCGA-DM-A28H TCGA-G4-6309 
      100.01         7.50       117.07        51.75 

$`RSPH3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-6780 
       25.08        25.18        24.16        21.76        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AU-3779 
        0.79         5.79        22.42        27.42        10.88        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       62.79        61.41        49.41        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB 
       92.75        49.91        13.32        12.59       140.38        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       35.97        60.79        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       74.56        65.85        53.62        44.68        55.04        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  RSPH3 MUTATED RSPH3 WILD-TYPE 
            0.2             0.0 
  RSPH3 MUTATED RSPH3 WILD-TYPE 
         117.07          140.38 
  RSPH3 MUTATED RSPH3 WILD-TYPE 
          24.54           20.12 
[1] "0.2 - 117.1 (24.5)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1"  
D116V2, 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       24       109         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RSPH3 MUTATED           0          0          1          2        0         1
  RSPH3 WILD-TYPE        19         10         40         29       35        12
                 vv
clus              STAGE IVB
  RSPH3 MUTATED           0
  RSPH3 WILD-TYPE         1
D116V3, multiclass
            clus
vv           RSPH3 MUTATED RSPH3 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              0             109
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             2              29
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 242  39
D116V4, multiclass
    clus
vv   RSPH3 MUTATED RSPH3 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             6             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
  RSPH3 MUTATED     5   2   3
  RSPH3 WILD-TYPE 215  78  63
D116V5, multiclass
    clus
vv   RSPH3 MUTATED RSPH3 WILD-TYPE
  N0             5             215
  N1             2              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"
D116V6, binary
                 cls
clus                0   1
  RSPH3 MUTATED     6   1
  RSPH3 WILD-TYPE 277  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RSPH3 MUTATED      6    1
  RSPH3 WILD-TYPE  277   47
   clus
vv  RSPH3 MUTATED RSPH3 WILD-TYPE
  0             6             277
  1             1              47
[1] 2 2
[1] FALSE
D116V7, 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
D116V8, binary
                 cls
clus                0   1
  RSPH3 MUTATED    10   0
  RSPH3 WILD-TYPE 307  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RSPH3 MUTATED     10    0
  RSPH3 WILD-TYPE  307   48
                               clus
vv                              RSPH3 MUTATED RSPH3 WILD-TYPE
  COLON ADENOCARCINOMA                     10             307
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RSPH3 MUTATED     2   0   0   0
  RSPH3 WILD-TYPE 255   2  22  21
D116V9, multiclass
[1] "Remove cluster labels:" "RSPH3 MUTATED"         
clus
  RSPH3 MUTATED RSPH3 WILD-TYPE 
              2             300 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-5657 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-A6-5659      TCGA-A6-5661      TCGA-A6-5665      TCGA-A6-6781 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-AA-3489      TCGA-AA-3492      TCGA-AA-3496      TCGA-AA-3502 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-AA-3510      TCGA-AA-3511      TCGA-AA-3514      TCGA-AA-3517 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-AA-3518      TCGA-AA-3519      TCGA-AA-3520      TCGA-AA-3521 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-AA-3522      TCGA-AA-3524      TCGA-AA-3525      TCGA-AA-3526 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-AA-3527      TCGA-AA-3529      TCGA-AA-3530      TCGA-AA-3531 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-AA-3532      TCGA-AA-3534      TCGA-AA-3538      TCGA-AA-3542 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-AA-3543      TCGA-AA-3544      TCGA-AA-3548      TCGA-AA-3549 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-AA-3552      TCGA-AA-3553      TCGA-AA-3554      TCGA-AA-3555 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-AA-3556      TCGA-AA-3558      TCGA-AA-3560      TCGA-AA-3561 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-AA-3562      TCGA-AA-3655      TCGA-AA-3660      TCGA-AA-3662 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-AA-3663      TCGA-AA-3664      TCGA-AA-3666      TCGA-AA-3667 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-AA-3672      TCGA-AA-3673      TCGA-AA-3678      TCGA-AA-3679 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-AA-3680      TCGA-AA-3681      TCGA-AA-3684      TCGA-AA-3685 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-AA-3688      TCGA-AA-3692      TCGA-AA-3693      TCGA-AA-3695 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-AA-3696      TCGA-AA-3697      TCGA-AA-3710      TCGA-AA-3712 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-AA-3713      TCGA-AA-3715      TCGA-AA-3811      TCGA-AA-3812 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-AA-3814      TCGA-AA-3815      TCGA-AA-3818      TCGA-AA-3819 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-AA-3821      TCGA-AA-3831      TCGA-AA-3833      TCGA-AA-3837 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-AA-3842      TCGA-AA-3844      TCGA-AA-3845      TCGA-AA-3846 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-AA-3848      TCGA-AA-3850      TCGA-AA-3851      TCGA-AA-3852 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-AA-3854      TCGA-AA-3855      TCGA-AA-3856      TCGA-AA-3858 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-AA-3860      TCGA-AA-3861      TCGA-AA-3864      TCGA-AA-3866 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-AA-3867      TCGA-AA-3869      TCGA-AA-3870      TCGA-AA-3872 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-AA-3875      TCGA-AA-3877      TCGA-AA-3930      TCGA-AA-3939 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-AA-3941      TCGA-AA-3947      TCGA-AA-3949      TCGA-AA-3950 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-AA-3952      TCGA-AA-3955      TCGA-AA-3956      TCGA-AA-3968 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-AA-3971      TCGA-AA-3972      TCGA-AA-3973      TCGA-AA-3975 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-AA-3976      TCGA-AA-3979      TCGA-AA-3984      TCGA-AA-3986 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-AA-3989      TCGA-AA-3994      TCGA-AA-A004      TCGA-AA-A00A 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-AA-A00D      TCGA-AA-A00E      TCGA-AA-A00F      TCGA-AA-A00J 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-AA-A00K      TCGA-AA-A00L      TCGA-AA-A00N      TCGA-AA-A00O 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-AA-A00Q      TCGA-AA-A00R      TCGA-AA-A00U      TCGA-AA-A00W 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-AA-A00Z      TCGA-AA-A017      TCGA-AA-A01D      TCGA-AA-A01F 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-AA-A01G      TCGA-AA-A01I      TCGA-AA-A01K      TCGA-AA-A01P 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-AA-A01Q      TCGA-AA-A01R      TCGA-AA-A01S      TCGA-AA-A01T 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-AA-A01V      TCGA-AA-A01X      TCGA-AA-A01Z      TCGA-AA-A022 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-AA-A024      TCGA-AA-A029      TCGA-AA-A02F      TCGA-AA-A02H 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-AA-A02J      TCGA-AA-A02K      TCGA-AA-A02O      TCGA-AA-A02W 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-AA-A02Y      TCGA-AA-A03F      TCGA-AA-A03J      TCGA-AD-5900 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-AD-6548      TCGA-AD-6888      TCGA-AU-3779      TCGA-AU-6004 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-AY-4070      TCGA-AY-4071      TCGA-AY-5543      TCGA-AY-6196 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-AY-6197      TCGA-AY-6386      TCGA-AZ-4315      TCGA-AZ-4681 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-AZ-4682      TCGA-CA-5254      TCGA-CA-5255      TCGA-CA-5796 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-CA-5797      TCGA-CA-6715      TCGA-CA-6716      TCGA-CA-6717 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-CA-6718      TCGA-CA-6719      TCGA-CK-4947      TCGA-CK-4948 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-CK-4950      TCGA-CK-4952      TCGA-CK-5912      TCGA-CK-5913 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-CK-5914      TCGA-CK-5915      TCGA-CK-5916      TCGA-CK-6746 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-CK-6747      TCGA-CK-6748      TCGA-CK-6751      TCGA-CM-4743 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-CM-4744      TCGA-CM-4746      TCGA-CM-4747      TCGA-CM-4752 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-CM-5341      TCGA-CM-5344      TCGA-CM-5348      TCGA-CM-5349 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-CM-5860      TCGA-CM-5861      TCGA-CM-5862      TCGA-CM-5863 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-CM-5864      TCGA-CM-5868      TCGA-CM-6161      TCGA-CM-6162 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-CM-6163      TCGA-CM-6164      TCGA-CM-6165      TCGA-CM-6166 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-CM-6167      TCGA-CM-6168      TCGA-CM-6169      TCGA-CM-6170 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-CM-6171      TCGA-CM-6172      TCGA-CM-6674      TCGA-CM-6675 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-CM-6676      TCGA-CM-6677      TCGA-CM-6678      TCGA-CM-6679 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-CM-6680      TCGA-D5-5537      TCGA-D5-5538      TCGA-D5-5539 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-D5-5540      TCGA-D5-5541      TCGA-D5-6529      TCGA-D5-6532 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-D5-6533      TCGA-D5-6534      TCGA-D5-6535      TCGA-D5-6536 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-D5-6537      TCGA-D5-6538      TCGA-D5-6539      TCGA-D5-6540 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-D5-6541      TCGA-D5-6898      TCGA-D5-6920      TCGA-D5-6922 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-D5-6923      TCGA-D5-6924      TCGA-D5-6926      TCGA-D5-6927 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-D5-6928      TCGA-D5-6929      TCGA-D5-6930      TCGA-D5-6931 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-D5-6932      TCGA-D5-7000      TCGA-F4-6459      TCGA-F4-6460 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-F4-6805      TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-G4-6306      TCGA-G4-6307      TCGA-G4-6310      TCGA-G4-6315 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323      TCGA-G4-6586 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
     TCGA-G4-6588      TCGA-G4-6625      TCGA-G4-6626      TCGA-G4-6628 
"RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" "RSPH3 WILD-TYPE" 
D116V10, 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
D116V11, 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(117) Variable = OXSM MUTATION ANALYSIS
D117V1, survival
                sevent
clus2              0   1
  OXSM MUTATED     9   1
  OXSM WILD-TYPE 273  72
  OXSM MUTATED OXSM WILD-TYPE 
            10            345 
  OXSM MUTATED OXSM WILD-TYPE 
             1             72 
$`OXSM MUTATED`
TCGA-AA-3710 TCGA-AA-3977 TCGA-AA-A00E TCGA-AA-A00N TCGA-AD-5900 TCGA-CM-4744 
       26.99        25.02        30.02         4.01         0.07        20.02 
TCGA-CM-4746 TCGA-D5-6923 TCGA-DM-A1D9 TCGA-G4-6304 
       37.02        12.43       140.38        53.62 

$`OXSM WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       19.00        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
      124.27        23.05        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 
       15.58         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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32        12.59         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  OXSM MUTATED OXSM WILD-TYPE 
          0.07           0.00 
  OXSM MUTATED OXSM WILD-TYPE 
        140.38         139.17 
  OXSM MUTATED OXSM WILD-TYPE 
        26.005         20.120 
[1] "0.1 - 140.4 (26.0)" "0.0 - 139.2 (20.1)"
[1] "hr=" "2.5"
D117V2, 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       25       106         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        19         10         41         31       35        13
                vv
clus             STAGE IVB
  OXSM MUTATED           0
  OXSM WILD-TYPE         1
D117V3, multiclass
            clus
vv           OXSM MUTATED OXSM WILD-TYPE
  STAGE I               4             60
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             3            106
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  OXSM MUTATED     0   5   3   2
  OXSM WILD-TYPE   9  63 245  39
D117V4, multiclass
    clus
vv   OXSM MUTATED OXSM WILD-TYPE
  T1            0              9
  T2            5             63
  T3            3            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
  OXSM MUTATED    10   0   0
  OXSM WILD-TYPE 210  80  66
D117V5, multiclass
    clus
vv   OXSM MUTATED OXSM WILD-TYPE
  N0           10            210
  N1            0             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"
D117V6, binary
                cls
clus               0   1
  OXSM MUTATED     8   0
  OXSM WILD-TYPE 275  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  OXSM MUTATED      8    0
  OXSM WILD-TYPE  275   48
   clus
vv  OXSM MUTATED OXSM WILD-TYPE
  0            8            275
  1            0             48
[1] 2 2
[1] FALSE
D117V7, 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
D117V8, binary
                cls
clus               0   1
  OXSM MUTATED     8   2
  OXSM WILD-TYPE 309  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  OXSM MUTATED      8    2
  OXSM WILD-TYPE  309   46
                               clus
vv                              OXSM MUTATED OXSM WILD-TYPE
  COLON ADENOCARCINOMA                     8            309
  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 249   2  22  21
D117V9, multiclass
    clus
vv   OXSM MUTATED OXSM WILD-TYPE
  R0            8            249
  R1            0              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"
D117V10, 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
D117V11, 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(118) Variable = SENP6 MUTATION ANALYSIS
D118V1, survival
                 sevent
clus2               0   1
  SENP6 MUTATED    11   3
  SENP6 WILD-TYPE 271  70
  SENP6 MUTATED SENP6 WILD-TYPE 
             14             341 
  SENP6 MUTATED SENP6 WILD-TYPE 
              3              70 
$`SENP6 MUTATED`
TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3663 TCGA-AA-A00N TCGA-AU-6004 TCGA-AY-6197 
       22.06        19.66         6.97         4.01        27.09        21.44 
TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-5912 TCGA-CM-5348 TCGA-D5-5539 TCGA-D5-5540 
       49.41         0.33        49.08        22.98        19.59        13.51 
TCGA-DM-A1HB TCGA-G4-6588 
      135.65        26.17 

$`SENP6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       14.50        16.31         0.95        15.75         0.20        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      102.44        40.34        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 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        91.79        46.75        52.80 

  SENP6 MUTATED SENP6 WILD-TYPE 
           0.33            0.00 
  SENP6 MUTATED SENP6 WILD-TYPE 
         135.65          140.38 
  SENP6 MUTATED SENP6 WILD-TYPE 
          21.75           20.12 
[1] "0.3 - 135.7 (21.8)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.1"
D118V2, 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       23       104         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        19          9         39         30       35        13
                 vv
clus              STAGE IVB
  SENP6 MUTATED           0
  SENP6 WILD-TYPE         1
D118V3, multiclass
            clus
vv           SENP6 MUTATED SENP6 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              5             104
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             2              39
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SENP6 MUTATED     0   2  10   3
  SENP6 WILD-TYPE   9  66 238  38
D118V4, multiclass
    clus
vv   SENP6 MUTATED SENP6 WILD-TYPE
  T1             0               9
  T2             2              66
  T3            10             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
  SENP6 MUTATED    11   4   0
  SENP6 WILD-TYPE 209  76  66
D118V5, multiclass
    clus
vv   SENP6 MUTATED SENP6 WILD-TYPE
  N0            11             209
  N1             4              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"
D118V6, binary
                 cls
clus                0   1
  SENP6 MUTATED    10   0
  SENP6 WILD-TYPE 273  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SENP6 MUTATED     10    0
  SENP6 WILD-TYPE  273   48
   clus
vv  SENP6 MUTATED SENP6 WILD-TYPE
  0            10             273
  1             0              48
[1] 2 2
[1] FALSE
D118V7, 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
D118V8, binary
                 cls
clus                0   1
  SENP6 MUTATED    11   4
  SENP6 WILD-TYPE 306  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SENP6 MUTATED     11    4
  SENP6 WILD-TYPE  306   44
                               clus
vv                              SENP6 MUTATED SENP6 WILD-TYPE
  COLON ADENOCARCINOMA                     11             306
  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 247   2  22  18
D118V9, multiclass
    clus
vv   SENP6 MUTATED SENP6 WILD-TYPE
  R0            10             247
  R1             0               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"
D118V10, 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
D118V11, 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(119) Variable = GNPAT MUTATION ANALYSIS
D119V1, survival
                 sevent
clus2               0   1
  GNPAT MUTATED    13   4
  GNPAT WILD-TYPE 269  69
  GNPAT MUTATED GNPAT WILD-TYPE 
             17             338 
  GNPAT MUTATED GNPAT WILD-TYPE 
              4              69 
$`GNPAT MUTATED`
TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3710 TCGA-AY-6197 TCGA-AZ-6598 TCGA-CA-5797 
       22.06        19.66        26.99        21.44        49.41         3.29 
TCGA-CA-6717 TCGA-CK-5914 TCGA-CK-5916 TCGA-CM-6163 TCGA-CM-6675 TCGA-D5-5541 
        0.33        21.99        21.14        14.04        13.05        11.51 
TCGA-DM-A1D4 TCGA-F4-6460 TCGA-F4-6570 TCGA-G4-6315 TCGA-G4-6321 
       92.75        13.38         6.18        36.72        22.09 

$`GNPAT WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.06         3.25         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        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 
       12.26        19.59        13.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       45.11        36.00        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  GNPAT MUTATED GNPAT WILD-TYPE 
           0.33            0.00 
  GNPAT MUTATED GNPAT WILD-TYPE 
          92.75          140.38 
  GNPAT MUTATED GNPAT WILD-TYPE 
         21.140          20.155 
[1] "0.3 - 92.8 (21.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D119V2, 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       24       102         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        18         10         38         30       34        13
                 vv
clus              STAGE IVB
  GNPAT MUTATED           1
  GNPAT WILD-TYPE         0
D119V3, multiclass
            clus
vv           GNPAT MUTATED GNPAT WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              7             102
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             3              38
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              0              13
  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  67 235  40
D119V4, multiclass
    clus
vv   GNPAT MUTATED GNPAT WILD-TYPE
  T1             2               7
  T2             1              67
  T3            13             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
  GNPAT MUTATED    10   6   1
  GNPAT WILD-TYPE 210  74  65
D119V5, multiclass
    clus
vv   GNPAT MUTATED GNPAT WILD-TYPE
  N0            10             210
  N1             6              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"
D119V6, binary
                 cls
clus                0   1
  GNPAT MUTATED    10   2
  GNPAT WILD-TYPE 273  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNPAT MUTATED     10    2
  GNPAT WILD-TYPE  273   46
   clus
vv  GNPAT MUTATED GNPAT WILD-TYPE
  0            10             273
  1             2              46
[1] 2 2
[1] FALSE
D119V7, 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
D119V8, binary
                 cls
clus                0   1
  GNPAT MUTATED    15   2
  GNPAT WILD-TYPE 302  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNPAT MUTATED     15    2
  GNPAT WILD-TYPE  302   46
                               clus
vv                              GNPAT MUTATED GNPAT WILD-TYPE
  COLON ADENOCARCINOMA                     15             302
  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 245   2  22  18
D119V9, multiclass
    clus
vv   GNPAT MUTATED GNPAT WILD-TYPE
  R0            12             245
  R1             0               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"
D119V10, 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
D119V11, 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(120) Variable = GPR174 MUTATION ANALYSIS
D120V1, survival
                  sevent
clus2                0   1
  GPR174 MUTATED     8   0
  GPR174 WILD-TYPE 274  73
  GPR174 MUTATED GPR174 WILD-TYPE 
               8              347 
  GPR174 MUTATED GPR174 WILD-TYPE 
               0               73 
$`GPR174 MUTATED`
TCGA-A6-5659 TCGA-AA-3543 TCGA-AA-3955 TCGA-CA-6718 TCGA-CM-6679 TCGA-D5-5538 
       30.44         0.99        20.98         0.10        10.06        12.26 
TCGA-D5-6539 TCGA-G4-6625 
       12.49        91.79 

$`GPR174 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       26.01        12.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.33         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 
       43.27        15.12        17.85         4.80        17.13        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        46.75        52.80 

  GPR174 MUTATED GPR174 WILD-TYPE 
             0.1              0.0 
  GPR174 MUTATED GPR174 WILD-TYPE 
           91.79           140.38 
  GPR174 MUTATED GPR174 WILD-TYPE 
          12.375           20.280 
[1] "0.1 - 91.8 (12.4)"  "0.0 - 140.4 (20.3)"
[1] "hr="     "9200000"
D120V2, 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       25       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPR174 MUTATED           0          1          2          0        0
  GPR174 WILD-TYPE        19          9         39         31       35
                  vv
clus               STAGE IVA STAGE IVB
  GPR174 MUTATED           0         0
  GPR174 WILD-TYPE        13         1
D120V3, multiclass
            clus
vv           GPR174 MUTATED GPR174 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               3              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              1                9
  STAGE IIIB              2               39
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GPR174 MUTATED     0   3   5   0
  GPR174 WILD-TYPE   9  65 243  41
D120V4, multiclass
    clus
vv   GPR174 MUTATED GPR174 WILD-TYPE
  T1              0                9
  T2              3               65
  T3              5              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
  GPR174 MUTATED     6   1   1
  GPR174 WILD-TYPE 214  79  65
D120V5, multiclass
    clus
vv   GPR174 MUTATED GPR174 WILD-TYPE
  N0              6              214
  N1              1               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"
D120V6, binary
                  cls
clus                 0   1
  GPR174 MUTATED     8   0
  GPR174 WILD-TYPE 275  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR174 MUTATED      8    0
  GPR174 WILD-TYPE  275   48
   clus
vv  GPR174 MUTATED GPR174 WILD-TYPE
  0              8              275
  1              0               48
[1] 2 2
[1] FALSE
D120V7, 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
D120V8, binary
                  cls
clus                 0   1
  GPR174 MUTATED     7   1
  GPR174 WILD-TYPE 310  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR174 MUTATED      7    1
  GPR174 WILD-TYPE  310   47
                               clus
vv                              GPR174 MUTATED GPR174 WILD-TYPE
  COLON ADENOCARCINOMA                       7              310
  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 250   2  22  20
D120V9, multiclass
    clus
vv   GPR174 MUTATED GPR174 WILD-TYPE
  R0              7              250
  R1              0                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"
D120V10, 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
D120V11, 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(121) Variable = NOTCH2NL MUTATION ANALYSIS
D121V1, survival
                    sevent
clus2                  0   1
  NOTCH2NL MUTATED     5   1
  NOTCH2NL WILD-TYPE 277  72
  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE 
                 6                349 
  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE 
                 1                 72 
$`NOTCH2NL MUTATED`
TCGA-A6-6649 TCGA-AA-3520 TCGA-AA-A00N TCGA-AZ-4315 TCGA-D5-6923 TCGA-G4-6588 
       24.16        24.03         4.01        58.39        12.43        26.17 

$`NOTCH2NL WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        1.02         9.07        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 
       52.80 

  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE 
              4.01               0.00 
  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE 
             58.39             140.38 
  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE 
            24.095             20.120 
[1] "4.0 - 58.4 (24.1)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.2"
D121V2, 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       24       107         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NOTCH2NL MUTATED           0          0          1          0        0
  NOTCH2NL WILD-TYPE        19         10         40         31       35
                    vv
clus                 STAGE IVA STAGE IVB
  NOTCH2NL MUTATED           0         0
  NOTCH2NL WILD-TYPE        13         1
D121V3, multiclass
            clus
vv           NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  1                 24
  STAGE IIA                 2                107
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                0                 10
  STAGE IIIB                1                 40
  STAGE IIIC                0                 31
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  NOTCH2NL MUTATED     0   1   4   1
  NOTCH2NL WILD-TYPE   9  67 244  40
D121V4, multiclass
    clus
vv   NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  T1                0                  9
  T2                1                 67
  T3                4                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
  NOTCH2NL MUTATED     5   1   0
  NOTCH2NL WILD-TYPE 215  79  66
D121V5, multiclass
    clus
vv   NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  N0                5                215
  N1                1                 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"
D121V6, binary
                    cls
clus                   0   1
  NOTCH2NL MUTATED     6   0
  NOTCH2NL WILD-TYPE 277  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  NOTCH2NL MUTATED      6    0
  NOTCH2NL WILD-TYPE  277   48
   clus
vv  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  0                6                277
  1                0                 48
[1] 2 2
[1] FALSE
D121V7, 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
D121V8, binary
                    cls
clus                   0   1
  NOTCH2NL MUTATED     5   1
  NOTCH2NL WILD-TYPE 312  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  NOTCH2NL MUTATED      5    1
  NOTCH2NL WILD-TYPE  312   47
                               clus
vv                              NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  COLON ADENOCARCINOMA                         5                312
  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 252   2  22  21
D121V9, multiclass
    clus
vv   NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  R0                5                252
  R1                0                  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"
D121V10, 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
D121V11, 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(122) Variable = PLXNA3 MUTATION ANALYSIS
D122V1, survival
                  sevent
clus2                0   1
  PLXNA3 MUTATED    16   1
  PLXNA3 WILD-TYPE 266  72
  PLXNA3 MUTATED PLXNA3 WILD-TYPE 
              17              338 
  PLXNA3 MUTATED PLXNA3 WILD-TYPE 
               1               72 
$`PLXNA3 MUTATED`
TCGA-A6-5661 TCGA-A6-5665 TCGA-AA-3663 TCGA-AA-3713 TCGA-AA-3947 TCGA-AD-5900 
       33.53        22.06         6.97        19.04        33.01         0.07 
TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-6386 TCGA-CA-5797 TCGA-CK-5916 TCGA-CM-4746 
       27.09        21.44        17.82         3.29        21.14        37.02 
TCGA-CM-5861 TCGA-CM-6171 TCGA-F4-6460 TCGA-G4-6309 TCGA-G4-6628 
       15.02        14.04        13.38        51.75        52.80 

$`PLXNA3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        15.75         0.20        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 
        1.94         2.24         3.06         3.25         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        51.32        21.99         2.93         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        16.01         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 
       35.97        60.79       117.07        98.24         8.61        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       74.56        65.85        53.62        44.68        55.04        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 
       91.79        46.75 

  PLXNA3 MUTATED PLXNA3 WILD-TYPE 
            0.07             0.00 
  PLXNA3 MUTATED PLXNA3 WILD-TYPE 
           52.80           140.38 
  PLXNA3 MUTATED PLXNA3 WILD-TYPE 
          21.140           20.155 
[1] "0.1 - 52.8 (21.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "3.3"
D122V2, 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       24       104         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLXNA3 MUTATED           0          0          3          0        1
  PLXNA3 WILD-TYPE        19         10         38         31       34
                  vv
clus               STAGE IVA STAGE IVB
  PLXNA3 MUTATED           0         0
  PLXNA3 WILD-TYPE        13         1
D122V3, multiclass
            clus
vv           PLXNA3 MUTATED PLXNA3 WILD-TYPE
  STAGE I                 6               58
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               5              104
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              3               38
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PLXNA3 MUTATED     1   5  10   1
  PLXNA3 WILD-TYPE   8  63 238  40
D122V4, multiclass
    clus
vv   PLXNA3 MUTATED PLXNA3 WILD-TYPE
  T1              1                8
  T2              5               63
  T3             10              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
  PLXNA3 MUTATED    14   3   0
  PLXNA3 WILD-TYPE 206  77  66
D122V5, multiclass
    clus
vv   PLXNA3 MUTATED PLXNA3 WILD-TYPE
  N0             14              206
  N1              3               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"
D122V6, binary
                  cls
clus                 0   1
  PLXNA3 MUTATED    14   1
  PLXNA3 WILD-TYPE 269  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLXNA3 MUTATED     14    1
  PLXNA3 WILD-TYPE  269   47
   clus
vv  PLXNA3 MUTATED PLXNA3 WILD-TYPE
  0             14              269
  1              1               47
[1] 2 2
[1] FALSE
D122V7, 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
D122V8, binary
                  cls
clus                 0   1
  PLXNA3 MUTATED    15   2
  PLXNA3 WILD-TYPE 302  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLXNA3 MUTATED     15    2
  PLXNA3 WILD-TYPE  302   46
                               clus
vv                              PLXNA3 MUTATED PLXNA3 WILD-TYPE
  COLON ADENOCARCINOMA                      15              302
  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 242   2  21  20
D122V9, multiclass
    clus
vv   PLXNA3 MUTATED PLXNA3 WILD-TYPE
  R0             15              242
  R1              0                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"
D122V10, 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
D122V11, 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(123) Variable = GPATCH8 MUTATION ANALYSIS
D123V1, survival
                   sevent
clus2                 0   1
  GPATCH8 MUTATED    12   2
  GPATCH8 WILD-TYPE 270  71
  GPATCH8 MUTATED GPATCH8 WILD-TYPE 
               14               341 
  GPATCH8 MUTATED GPATCH8 WILD-TYPE 
                2                71 
$`GPATCH8 MUTATED`
TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3947 TCGA-AA-3977 
       24.39        19.66        19.04        10.06        33.01        25.02 
TCGA-AD-5900 TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CM-5860 
        0.07        27.09        58.39        49.41         0.33        16.01 
TCGA-G4-6321 TCGA-G4-6586 
       22.09        35.80 

$`GPATCH8 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 
        5.03        85.05        26.99        19.04        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        26.17        91.79        46.75        52.80 

  GPATCH8 MUTATED GPATCH8 WILD-TYPE 
             0.07              0.00 
  GPATCH8 MUTATED GPATCH8 WILD-TYPE 
            58.39            140.38 
  GPATCH8 MUTATED GPATCH8 WILD-TYPE 
            23.24             20.12 
[1] "0.1 - 58.4 (23.2)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.4"
D123V2, 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       24       105         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPATCH8 MUTATED           2          0          0          1        1
  GPATCH8 WILD-TYPE        17         10         41         30       34
                   vv
clus                STAGE IVA STAGE IVB
  GPATCH8 MUTATED           0         0
  GPATCH8 WILD-TYPE        13         1
D123V3, multiclass
            clus
vv           GPATCH8 MUTATED GPATCH8 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                4               105
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                2                17
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               1                30
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  GPATCH8 MUTATED     0   5   7   2
  GPATCH8 WILD-TYPE   9  63 241  39
D123V4, multiclass
    clus
vv   GPATCH8 MUTATED GPATCH8 WILD-TYPE
  T1               0                 9
  T2               5                63
  T3               7               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
  GPATCH8 MUTATED    11   2   1
  GPATCH8 WILD-TYPE 209  78  65
D123V5, multiclass
    clus
vv   GPATCH8 MUTATED GPATCH8 WILD-TYPE
  N0              11               209
  N1               2                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"
D123V6, binary
                   cls
clus                  0   1
  GPATCH8 MUTATED     8   1
  GPATCH8 WILD-TYPE 275  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPATCH8 MUTATED      8    1
  GPATCH8 WILD-TYPE  275   47
   clus
vv  GPATCH8 MUTATED GPATCH8 WILD-TYPE
  0               8               275
  1               1                47
[1] 2 2
[1] FALSE
D123V7, 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
D123V8, binary
                   cls
clus                  0   1
  GPATCH8 MUTATED    10   4
  GPATCH8 WILD-TYPE 307  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPATCH8 MUTATED     10    4
  GPATCH8 WILD-TYPE  307   44
                               clus
vv                              GPATCH8 MUTATED GPATCH8 WILD-TYPE
  COLON ADENOCARCINOMA                       10               307
  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 248   2  21  20
D123V9, multiclass
    clus
vv   GPATCH8 MUTATED GPATCH8 WILD-TYPE
  R0               9               248
  R1               0                 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"
D123V10, 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
D123V11, 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(124) Variable = FHOD3 MUTATION ANALYSIS
D124V1, survival
                 sevent
clus2               0   1
  FHOD3 MUTATED    19   6
  FHOD3 WILD-TYPE 263  67
  FHOD3 MUTATED FHOD3 WILD-TYPE 
             25             330 
  FHOD3 MUTATED FHOD3 WILD-TYPE 
              6              67 
$`FHOD3 MUTATED`
TCGA-A6-5661 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3525 TCGA-AA-3930 
       33.53        19.66         3.02        35.01         8.05         2.01 
TCGA-AA-3947 TCGA-AA-3966 TCGA-AA-A00A TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q 
       33.01         2.01        38.04         4.01        34.98         1.02 
TCGA-AY-6197 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4743 TCGA-CM-6162 
       21.44        49.41         0.33         0.10        23.05        12.00 
TCGA-D5-6536 TCGA-D5-6927 TCGA-DM-A28C TCGA-F4-6570 TCGA-G4-6309 TCGA-G4-6588 
       17.85         9.44        81.37         6.18        51.75        26.17 
TCGA-G4-6628 
       52.80 

$`FHOD3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3511 
       20.12        20.28         7.04         1.02        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       37.05        36.03        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       18.05        31.00        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D 
       27.02        19.07         7.96        27.02        13.94        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        15.75         0.20        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07         0.26         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28E TCGA-DM-A28F 
      131.51       135.65       139.17         6.12       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 

  FHOD3 MUTATED FHOD3 WILD-TYPE 
            0.1             0.0 
  FHOD3 MUTATED FHOD3 WILD-TYPE 
          81.37          140.38 
  FHOD3 MUTATED FHOD3 WILD-TYPE 
         19.660          20.235 
[1] "0.1 - 81.4 (19.7)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.3"
D124V2, 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       22        96         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        19         10         38         30       34        13
                 vv
clus              STAGE IVB
  FHOD3 MUTATED           0
  FHOD3 WILD-TYPE         1
D124V3, multiclass
            clus
vv           FHOD3 MUTATED FHOD3 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA             13              96
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             3              38
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FHOD3 MUTATED     0   3  20   4
  FHOD3 WILD-TYPE   9  65 228  37
D124V4, multiclass
    clus
vv   FHOD3 MUTATED FHOD3 WILD-TYPE
  T1             0               9
  T2             3              65
  T3            20             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
  FHOD3 MUTATED    22   4   1
  FHOD3 WILD-TYPE 198  76  65
D124V5, multiclass
    clus
vv   FHOD3 MUTATED FHOD3 WILD-TYPE
  N0            22             198
  N1             4              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"
D124V6, binary
                 cls
clus                0   1
  FHOD3 MUTATED    22   1
  FHOD3 WILD-TYPE 261  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FHOD3 MUTATED     22    1
  FHOD3 WILD-TYPE  261   47
   clus
vv  FHOD3 MUTATED FHOD3 WILD-TYPE
  0            22             261
  1             1              47
[1] 2 2
[1] FALSE
D124V7, 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
D124V8, binary
                 cls
clus                0   1
  FHOD3 MUTATED    21   6
  FHOD3 WILD-TYPE 296  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FHOD3 MUTATED     21    6
  FHOD3 WILD-TYPE  296   42
                               clus
vv                              FHOD3 MUTATED FHOD3 WILD-TYPE
  COLON ADENOCARCINOMA                     21             296
  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 237   2  21  18
D124V9, multiclass
    clus
vv   FHOD3 MUTATED FHOD3 WILD-TYPE
  R0            20             237
  R1             0               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"
D124V10, 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
D124V11, 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(125) Variable = OR7C2 MUTATION ANALYSIS
D125V1, survival
                 sevent
clus2               0   1
  OR7C2 MUTATED     9   1
  OR7C2 WILD-TYPE 273  72
  OR7C2 MUTATED OR7C2 WILD-TYPE 
             10             345 
  OR7C2 MUTATED OR7C2 WILD-TYPE 
              1              72 
$`OR7C2 MUTATED`
TCGA-A6-6781 TCGA-AA-3950 TCGA-AA-A010 TCGA-AU-3779 TCGA-AZ-5407 TCGA-AZ-6601 
       19.66        24.00        34.98        14.50        61.41       100.01 
TCGA-CA-6717 TCGA-D5-5540 TCGA-D5-6926 TCGA-G4-6588 
        0.33        13.51         9.04        26.17 

$`OR7C2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.20        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       22.36        62.79        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 
        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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  OR7C2 MUTATED OR7C2 WILD-TYPE 
           0.33            0.00 
  OR7C2 MUTATED OR7C2 WILD-TYPE 
         100.01          140.38 
  OR7C2 MUTATED OR7C2 WILD-TYPE 
          21.83           20.19 
[1] "0.3 - 100.0 (21.8)" "0.0 - 140.4 (20.2)"
[1] "hr=" "2.5"
D125V2, 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       24       104         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR7C2 MUTATED           0          1          0          1        0         0
  OR7C2 WILD-TYPE        19          9         41         30       35        13
                 vv
clus              STAGE IVB
  OR7C2 MUTATED           0
  OR7C2 WILD-TYPE         1
D125V3, multiclass
            clus
vv           OR7C2 MUTATED OR7C2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              5             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR7C2 MUTATED     1   0   6   3
  OR7C2 WILD-TYPE   8  68 242  38
D125V4, multiclass
    clus
vv   OR7C2 MUTATED OR7C2 WILD-TYPE
  T1             1               8
  T2             0              68
  T3             6             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
  OR7C2 MUTATED     8   2   0
  OR7C2 WILD-TYPE 212  78  66
D125V5, multiclass
    clus
vv   OR7C2 MUTATED OR7C2 WILD-TYPE
  N0             8             212
  N1             2              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"
D125V6, binary
                 cls
clus                0   1
  OR7C2 MUTATED     9   0
  OR7C2 WILD-TYPE 274  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR7C2 MUTATED      9    0
  OR7C2 WILD-TYPE  274   48
   clus
vv  OR7C2 MUTATED OR7C2 WILD-TYPE
  0             9             274
  1             0              48
[1] 2 2
[1] FALSE
D125V7, 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
D125V8, binary
                 cls
clus                0   1
  OR7C2 MUTATED     7   3
  OR7C2 WILD-TYPE 310  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR7C2 MUTATED      7    3
  OR7C2 WILD-TYPE  310   45
                               clus
vv                              OR7C2 MUTATED OR7C2 WILD-TYPE
  COLON ADENOCARCINOMA                      7             310
  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 250   2  22  20
D125V9, multiclass
    clus
vv   OR7C2 MUTATED OR7C2 WILD-TYPE
  R0             7             250
  R1             0               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"
D125V10, 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
D125V11, 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(126) Variable = NUP188 MUTATION ANALYSIS
D126V1, survival
                  sevent
clus2                0   1
  NUP188 MUTATED    13   5
  NUP188 WILD-TYPE 269  68
  NUP188 MUTATED NUP188 WILD-TYPE 
              18              337 
  NUP188 MUTATED NUP188 WILD-TYPE 
               5               68 
$`NUP188 MUTATED`
TCGA-A6-5657 TCGA-A6-6653 TCGA-AA-3510 TCGA-AA-3713 TCGA-AA-3955 TCGA-AA-A00R 
       31.63        24.39        63.98        19.04        20.98         0.99 
TCGA-AA-A010 TCGA-AA-A01Q TCGA-AD-6895 TCGA-AZ-4315 TCGA-AZ-5403 TCGA-AZ-6601 
       34.98         1.02         0.72        58.39        62.79       100.01 
TCGA-CM-6171 TCGA-D5-6923 TCGA-DM-A1DA TCGA-F4-6459 TCGA-F4-6570 TCGA-F4-6856 
       14.04        12.43         7.50         8.61         6.18        19.43 

$`NUP188 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01        24.00         2.01        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       22.36        61.41        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 
       15.58         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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
       60.79       117.07        98.24        13.38        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        35.41       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  NUP188 MUTATED NUP188 WILD-TYPE 
            0.72             0.00 
  NUP188 MUTATED NUP188 WILD-TYPE 
          100.01           140.38 
  NUP188 MUTATED NUP188 WILD-TYPE 
          19.235           20.280 
[1] "0.7 - 100.0 (19.2)" "0.0 - 140.4 (20.3)"
[1] "hr=" "1.3"
D126V2, 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       21       106         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NUP188 MUTATED           0          0          3          1        1
  NUP188 WILD-TYPE        19         10         38         30       34
                  vv
clus               STAGE IVA STAGE IVB
  NUP188 MUTATED           0         0
  NUP188 WILD-TYPE        13         1
D126V3, multiclass
            clus
vv           NUP188 MUTATED NUP188 WILD-TYPE
  STAGE I                 5               59
  STAGE IA                0                1
  STAGE II                4               21
  STAGE IIA               3              106
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              3               38
  STAGE IIIC              1               30
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  NUP188 MUTATED     0   6  12   1
  NUP188 WILD-TYPE   9  62 236  40
D126V4, multiclass
    clus
vv   NUP188 MUTATED NUP188 WILD-TYPE
  T1              0                9
  T2              6               62
  T3             12              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
  NUP188 MUTATED    14   2   3
  NUP188 WILD-TYPE 206  78  63
D126V5, multiclass
    clus
vv   NUP188 MUTATED NUP188 WILD-TYPE
  N0             14              206
  N1              2               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"
D126V6, binary
                  cls
clus                 0   1
  NUP188 MUTATED    16   1
  NUP188 WILD-TYPE 267  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUP188 MUTATED     16    1
  NUP188 WILD-TYPE  267   47
   clus
vv  NUP188 MUTATED NUP188 WILD-TYPE
  0             16              267
  1              1               47
[1] 2 2
[1] FALSE
D126V7, 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
D126V8, binary
                  cls
clus                 0   1
  NUP188 MUTATED    18   1
  NUP188 WILD-TYPE 299  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUP188 MUTATED     18    1
  NUP188 WILD-TYPE  299   47
                               clus
vv                              NUP188 MUTATED NUP188 WILD-TYPE
  COLON ADENOCARCINOMA                      18              299
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  NUP188 MUTATED    13   0   1   0
  NUP188 WILD-TYPE 244   2  21  21
D126V9, multiclass
    clus
vv   NUP188 MUTATED NUP188 WILD-TYPE
  R0             13              244
  R1              0                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"
D126V10, 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
D126V11, 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(127) Variable = ZNF486 MUTATION ANALYSIS
D127V1, survival
                  sevent
clus2                0   1
  ZNF486 MUTATED     6   5
  ZNF486 WILD-TYPE 276  68
  ZNF486 MUTATED ZNF486 WILD-TYPE 
              11              344 
  ZNF486 MUTATED ZNF486 WILD-TYPE 
               5               68 
$`ZNF486 MUTATED`
TCGA-A6-4105 TCGA-A6-5661 TCGA-AA-3864 TCGA-AA-3949 TCGA-AA-A01P TCGA-AD-6895 
       14.53        33.53        53.00        26.01        38.07         0.72 
TCGA-CK-5912 TCGA-CM-5861 TCGA-DM-A0XD TCGA-DM-A285 TCGA-G4-6588 
       49.08        15.02        24.43         6.12        26.17 

$`ZNF486 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       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        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
        0.07        21.37         4.21        56.55         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 
        1.35        17.56       102.44        40.34        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         2.93         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        16.01         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       10.26       119.70        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-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        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  ZNF486 MUTATED ZNF486 WILD-TYPE 
            0.72             0.00 
  ZNF486 MUTATED ZNF486 WILD-TYPE 
           53.00           140.38 
  ZNF486 MUTATED ZNF486 WILD-TYPE 
           26.01            20.07 
[1] "0.7 - 53.0 (26.0)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "2.2"
D127V2, 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       24       104         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF486 MUTATED           1          0          1          0        1
  ZNF486 WILD-TYPE        18         10         40         31       34
                  vv
clus               STAGE IVA STAGE IVB
  ZNF486 MUTATED           0         0
  ZNF486 WILD-TYPE        13         1
D127V3, multiclass
            clus
vv           ZNF486 MUTATED ZNF486 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               5              104
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF486 MUTATED     0   1  10   1
  ZNF486 WILD-TYPE   9  67 238  40
D127V4, multiclass
    clus
vv   ZNF486 MUTATED ZNF486 WILD-TYPE
  T1              0                9
  T2              1               67
  T3             10              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
  ZNF486 MUTATED     8   3   1
  ZNF486 WILD-TYPE 212  77  65
D127V5, multiclass
    clus
vv   ZNF486 MUTATED ZNF486 WILD-TYPE
  N0              8              212
  N1              3               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"
D127V6, binary
                  cls
clus                 0   1
  ZNF486 MUTATED     8   1
  ZNF486 WILD-TYPE 275  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF486 MUTATED      8    1
  ZNF486 WILD-TYPE  275   47
   clus
vv  ZNF486 MUTATED ZNF486 WILD-TYPE
  0              8              275
  1              1               47
[1] 2 2
[1] FALSE
D127V7, 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
D127V8, binary
                  cls
clus                 0   1
  ZNF486 MUTATED    10   2
  ZNF486 WILD-TYPE 307  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF486 MUTATED     10    2
  ZNF486 WILD-TYPE  307   46
                               clus
vv                              ZNF486 MUTATED ZNF486 WILD-TYPE
  COLON ADENOCARCINOMA                      10              307
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF486 MUTATED     6   0   0   2
  ZNF486 WILD-TYPE 251   2  22  19
D127V9, multiclass
    clus
vv   ZNF486 MUTATED ZNF486 WILD-TYPE
  R0              6              251
  R1              0                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"
D127V10, 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
D127V11, 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(128) Variable = SLAMF7 MUTATION ANALYSIS
D128V1, survival
                  sevent
clus2                0   1
  SLAMF7 MUTATED     9   2
  SLAMF7 WILD-TYPE 273  71
  SLAMF7 MUTATED SLAMF7 WILD-TYPE 
              11              344 
  SLAMF7 MUTATED SLAMF7 WILD-TYPE 
               2               71 
$`SLAMF7 MUTATED`
TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3662 TCGA-AA-A00N TCGA-AA-A010 TCGA-CK-6748 
       22.06        63.98         6.05         4.01        34.98         2.01 
TCGA-CM-5348 TCGA-CM-6168 TCGA-D5-6541 TCGA-F4-6809 TCGA-G4-6588 
       22.98        12.99        15.58        13.25        26.17 

$`SLAMF7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 
       49.08        51.32        21.99        21.14         2.93       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        16.14         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       33.67         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  SLAMF7 MUTATED SLAMF7 WILD-TYPE 
            2.01             0.00 
  SLAMF7 MUTATED SLAMF7 WILD-TYPE 
           63.98           140.38 
  SLAMF7 MUTATED SLAMF7 WILD-TYPE 
          15.580           20.235 
[1] "2.0 - 64.0 (15.6)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D128V2, 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       24       105         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLAMF7 MUTATED           0          0          1          0        2
  SLAMF7 WILD-TYPE        19         10         40         31       33
                  vv
clus               STAGE IVA STAGE IVB
  SLAMF7 MUTATED           1         0
  SLAMF7 WILD-TYPE        12         1
D128V3, multiclass
            clus
vv           SLAMF7 MUTATED SLAMF7 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               4              105
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                2               33
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  68 240  38
D128V4, multiclass
    clus
vv   SLAMF7 MUTATED SLAMF7 WILD-TYPE
  T1              0                9
  T2              0               68
  T3              8              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
  SLAMF7 MUTATED     7   3   1
  SLAMF7 WILD-TYPE 213  77  65
D128V5, multiclass
    clus
vv   SLAMF7 MUTATED SLAMF7 WILD-TYPE
  N0              7              213
  N1              3               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"
D128V6, binary
                  cls
clus                 0   1
  SLAMF7 MUTATED     8   3
  SLAMF7 WILD-TYPE 275  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLAMF7 MUTATED      8    3
  SLAMF7 WILD-TYPE  275   45
   clus
vv  SLAMF7 MUTATED SLAMF7 WILD-TYPE
  0              8              275
  1              3               45
[1] 2 2
[1] FALSE
D128V7, 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
D128V8, binary
                  cls
clus                 0   1
  SLAMF7 MUTATED     9   2
  SLAMF7 WILD-TYPE 308  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLAMF7 MUTATED      9    2
  SLAMF7 WILD-TYPE  308   46
                               clus
vv                              SLAMF7 MUTATED SLAMF7 WILD-TYPE
  COLON ADENOCARCINOMA                       9              308
  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 248   2  21  20
D128V9, multiclass
    clus
vv   SLAMF7 MUTATED SLAMF7 WILD-TYPE
  R0              9              248
  R1              0                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"
D128V10, 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
D128V11, 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(129) Variable = FNDC7 MUTATION ANALYSIS
D129V1, survival
                 sevent
clus2               0   1
  FNDC7 MUTATED     8   1
  FNDC7 WILD-TYPE 274  72
  FNDC7 MUTATED FNDC7 WILD-TYPE 
              9             346 
  FNDC7 MUTATED FNDC7 WILD-TYPE 
              1              72 
$`FNDC7 MUTATED`
TCGA-A6-5660 TCGA-A6-5665 TCGA-AA-3663 TCGA-AA-3947 TCGA-AD-6895 TCGA-AZ-4315 
       29.19        22.06         6.97        33.01         0.72        58.39 
TCGA-AZ-6599 TCGA-CM-6162 TCGA-CM-6164 
        6.77        12.00        29.03 

$`FNDC7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41        49.41        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  FNDC7 MUTATED FNDC7 WILD-TYPE 
           0.72            0.00 
  FNDC7 MUTATED FNDC7 WILD-TYPE 
          58.39          140.38 
  FNDC7 MUTATED FNDC7 WILD-TYPE 
         22.060          20.155 
[1] "0.7 - 58.4 (22.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.6"
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       24       106         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FNDC7 MUTATED           0          0          1          1        0         0
  FNDC7 WILD-TYPE        19         10         40         30       35        13
                 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              24
  STAGE IIA              3             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FNDC7 MUTATED     0   1   7   1
  FNDC7 WILD-TYPE   9  67 241  40
D129V4, multiclass
    clus
vv   FNDC7 MUTATED FNDC7 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             7             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
  FNDC7 MUTATED     6   2   1
  FNDC7 WILD-TYPE 214  78  65
D129V5, multiclass
    clus
vv   FNDC7 MUTATED FNDC7 WILD-TYPE
  N0             6             214
  N1             2              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"
D129V6, binary
                 cls
clus                0   1
  FNDC7 MUTATED     7   0
  FNDC7 WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FNDC7 MUTATED      7    0
  FNDC7 WILD-TYPE  276   48
   clus
vv  FNDC7 MUTATED FNDC7 WILD-TYPE
  0             7             276
  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     7   2
  FNDC7 WILD-TYPE 310  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FNDC7 MUTATED      7    2
  FNDC7 WILD-TYPE  310   46
                               clus
vv                              FNDC7 MUTATED FNDC7 WILD-TYPE
  COLON ADENOCARCINOMA                      7             310
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  FNDC7 MUTATED     6   0   0   0
  FNDC7 WILD-TYPE 251   2  22  21
D129V9, multiclass
    clus
vv   FNDC7 MUTATED FNDC7 WILD-TYPE
  R0             6             251
  R1             0               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"
D129V10, 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
D129V11, 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 = B4GALNT4 MUTATION ANALYSIS
D130V1, survival
                    sevent
clus2                  0   1
  B4GALNT4 MUTATED     7   3
  B4GALNT4 WILD-TYPE 275  70
  B4GALNT4 MUTATED B4GALNT4 WILD-TYPE 
                10                345 
  B4GALNT4 MUTATED B4GALNT4 WILD-TYPE 
                 3                 70 
$`B4GALNT4 MUTATED`
TCGA-A6-2672 TCGA-AA-3510 TCGA-AD-6964 TCGA-AU-6004 TCGA-AZ-6598 TCGA-CK-5916 
       46.65        63.98        10.88        27.09        49.41        21.14 
TCGA-CM-4743 TCGA-D5-6928 TCGA-DM-A1HB TCGA-G4-6588 
       23.05        11.64       135.65        26.17 

$`B4GALNT4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.20        14.50        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32        21.99         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  B4GALNT4 MUTATED B4GALNT4 WILD-TYPE 
             10.88               0.00 
  B4GALNT4 MUTATED B4GALNT4 WILD-TYPE 
            135.65             140.38 
  B4GALNT4 MUTATED B4GALNT4 WILD-TYPE 
             26.63              19.99 
[1] "10.9 - 135.7 (26.6)" "0.0 - 140.4 (20.0)" 
[1] "hr=" "1.1"
D130V2, 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       23       106         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  B4GALNT4 MUTATED           0          0          2          0        0
  B4GALNT4 WILD-TYPE        19         10         39         31       35
                    vv
clus                 STAGE IVA STAGE IVB
  B4GALNT4 MUTATED           0         0
  B4GALNT4 WILD-TYPE        13         1
D130V3, multiclass
            clus
vv           B4GALNT4 MUTATED B4GALNT4 WILD-TYPE
  STAGE I                   2                 62
  STAGE IA                  0                  1
  STAGE II                  2                 23
  STAGE IIA                 3                106
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                0                 10
  STAGE IIIB                2                 39
  STAGE IIIC                0                 31
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  B4GALNT4 MUTATED     1   1   7   2
  B4GALNT4 WILD-TYPE   8  67 241  39
D130V4, multiclass
    clus
vv   B4GALNT4 MUTATED B4GALNT4 WILD-TYPE
  T1                1                  8
  T2                1                 67
  T3                7                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
  B4GALNT4 MUTATED     8   2   1
  B4GALNT4 WILD-TYPE 212  78  65
D130V5, multiclass
    clus
vv   B4GALNT4 MUTATED B4GALNT4 WILD-TYPE
  N0                8                212
  N1                2                 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"
D130V6, binary
                    cls
clus                   0   1
  B4GALNT4 MUTATED     8   0
  B4GALNT4 WILD-TYPE 275  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  B4GALNT4 MUTATED      8    0
  B4GALNT4 WILD-TYPE  275   48
   clus
vv  B4GALNT4 MUTATED B4GALNT4 WILD-TYPE
  0                8                275
  1                0                 48
[1] 2 2
[1] FALSE
D130V7, 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
D130V8, binary
                    cls
clus                   0   1
  B4GALNT4 MUTATED    10   1
  B4GALNT4 WILD-TYPE 307  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  B4GALNT4 MUTATED     10    1
  B4GALNT4 WILD-TYPE  307   47
                               clus
vv                              B4GALNT4 MUTATED B4GALNT4 WILD-TYPE
  COLON ADENOCARCINOMA                        10                307
  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 251   2  22  19
D130V9, multiclass
    clus
vv   B4GALNT4 MUTATED B4GALNT4 WILD-TYPE
  R0                6                251
  R1                0                  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"
D130V10, 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
D130V11, 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(131) Variable = MIER3 MUTATION ANALYSIS
D131V1, survival
                 sevent
clus2               0   1
  MIER3 MUTATED    10   1
  MIER3 WILD-TYPE 272  72
  MIER3 MUTATED MIER3 WILD-TYPE 
             11             344 
  MIER3 MUTATED MIER3 WILD-TYPE 
              1              72 
$`MIER3 MUTATED`
TCGA-A6-2672 TCGA-A6-5665 TCGA-AA-3526 TCGA-AA-3555 TCGA-AA-3672 TCGA-AA-3715 
       46.65        22.06        19.07        29.95         0.92        19.04 
TCGA-AA-3864 TCGA-AA-3977 TCGA-AA-A010 TCGA-AU-6004 TCGA-CM-5861 
       53.00        25.02        34.98        27.09        15.02 

$`MIER3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3529 
        9.07        24.03        37.05        36.03         8.05         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.20        14.50        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  MIER3 MUTATED MIER3 WILD-TYPE 
           0.92            0.00 
  MIER3 MUTATED MIER3 WILD-TYPE 
          53.00          140.38 
  MIER3 MUTATED MIER3 WILD-TYPE 
          25.02           20.07 
[1] "0.9 - 53.0 (25.0)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "2.4"
D131V2, 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       22       105         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        18         10         40         31       35        13
                 vv
clus              STAGE IVB
  MIER3 MUTATED           0
  MIER3 WILD-TYPE         1
D131V3, multiclass
            clus
vv           MIER3 MUTATED MIER3 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              4             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MIER3 MUTATED     0   3   8   2
  MIER3 WILD-TYPE   9  65 240  39
D131V4, multiclass
    clus
vv   MIER3 MUTATED MIER3 WILD-TYPE
  T1             0               9
  T2             3              65
  T3             8             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
  MIER3 MUTATED    11   2   0
  MIER3 WILD-TYPE 209  78  66
D131V5, multiclass
    clus
vv   MIER3 MUTATED MIER3 WILD-TYPE
  N0            11             209
  N1             2              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"
D131V6, binary
                 cls
clus                0   1
  MIER3 MUTATED    12   0
  MIER3 WILD-TYPE 271  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MIER3 MUTATED     12    0
  MIER3 WILD-TYPE  271   48
   clus
vv  MIER3 MUTATED MIER3 WILD-TYPE
  0            12             271
  1             0              48
[1] 2 2
[1] FALSE
D131V7, 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
D131V8, binary
                 cls
clus                0   1
  MIER3 MUTATED    12   1
  MIER3 WILD-TYPE 305  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MIER3 MUTATED     12    1
  MIER3 WILD-TYPE  305   47
                               clus
vv                              MIER3 MUTATED MIER3 WILD-TYPE
  COLON ADENOCARCINOMA                     12             305
  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 245   2  22  21
D131V9, multiclass
    clus
vv   MIER3 MUTATED MIER3 WILD-TYPE
  R0            12             245
  R1             0               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"
D131V10, 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
D131V11, 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(132) Variable = ATM MUTATION ANALYSIS
D132V1, survival
               sevent
clus2             0   1
  ATM MUTATED   104  24
  ATM WILD-TYPE 178  49
  ATM MUTATED ATM WILD-TYPE 
          128           227 
  ATM MUTATED ATM WILD-TYPE 
           24            49 
$`ATM MUTATED`
TCGA-A6-4105 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6141 
       14.53        29.19        33.53        22.09        22.06         8.38 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       24.39        20.12        19.66         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3522 TCGA-AA-3530 TCGA-AA-3555 
       63.98        13.02         1.02        37.05        19.07        29.95 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3678 
       61.02        78.08         6.05         6.97        54.02        47.01 
TCGA-AA-3679 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3819 
       15.02        85.05        26.99        19.04        10.06        25.02 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00N 
       31.07        30.05        24.00         2.01        25.02         4.01 
TCGA-AA-A010 TCGA-AA-A01R TCGA-AA-A02Y TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 
       34.98        35.01        39.98        21.37        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-6196 
        5.79        22.42        27.42        14.50        27.09         0.20 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
       21.44        58.39        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6608 TCGA-CA-6715 TCGA-CA-6717 
        6.77       100.01        29.56         1.94         0.07         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
        0.10         1.35        17.56        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4752 TCGA-CM-5348 
       21.99         2.01       124.27        23.05        13.02        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 
       30.08        16.01        15.02         5.03        15.02        17.03 
TCGA-CM-6164 TCGA-CM-6171 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 
       29.03        14.04        11.08        10.06        12.03        12.26 
TCGA-D5-5539 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 
       19.59        20.19        18.25         1.32        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-7000 
       12.39        12.43        14.30        11.64        13.41        10.26 
TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A28C TCGA-DM-A28E 
       38.20        92.75        44.32       135.65        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6570 TCGA-F4-6807 
       35.97        60.79       117.07        98.24         6.18        16.24 
TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6304 TCGA-G4-6306 
       33.67         0.53        19.43       107.67        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 
       55.04        51.75        36.72        36.00        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6628 
       26.17        52.80 

$`ATM WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       31.63        30.44        23.61        32.71        27.09        22.52 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 
       20.28         7.04         6.97         1.02        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3531 
       24.03        36.03         8.05        19.07         0.00        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 
       33.99        21.01        13.02        24.00        17.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3667 
       20.98        19.99        13.94        19.99         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
        0.92        50.04        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       36.00         5.03        19.04        35.05        33.04         0.99 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       18.05        40.96         0.07         4.21         0.72        10.88 
TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 
        0.20        16.31         0.95        15.75        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-6600 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        5.13        83.80        12.10         5.23        11.74         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CK-4948 
        2.24         3.06         3.25         3.29         0.26       102.44 
TCGA-CK-4950 TCGA-CK-5916 TCGA-CK-6747 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       40.34        21.14         2.93        20.02        37.02        25.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       29.06        22.03        15.02        15.02        12.00        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-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-D5-5537 
       11.01        12.95        13.05        11.08        11.01        45.40 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6534 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6927 
       13.51        11.51        43.27        10.13         9.04         9.44 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 
        1.51        12.00        11.38       119.70        24.43       130.65 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38         7.50       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      139.17         6.12         8.61        13.38        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6809 TCGA-F4-6855 TCGA-G4-6299 
        1.55        16.31        29.59        13.25        35.41        74.56 
TCGA-G4-6303 TCGA-G4-6310 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 
       65.85        45.11        13.78        91.79        46.75 

  ATM MUTATED ATM WILD-TYPE 
         0.07          0.00 
  ATM MUTATED ATM WILD-TYPE 
       135.65        140.38 
  ATM MUTATED ATM WILD-TYPE 
       21.715        19.990 
[1] "0.1 - 135.7 (21.7)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.5"
D132V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATM MUTATED        19        0       11        49         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           8          3         14          9        6         4
  ATM WILD-TYPE        11          7         27         22       29         9
               vv
clus            STAGE IVB
  ATM MUTATED           0
  ATM WILD-TYPE         1
D132V3, multiclass
            clus
vv           ATM MUTATED ATM WILD-TYPE
  STAGE I             19            45
  STAGE IA             0             1
  STAGE II            11            14
  STAGE IIA           49            60
  STAGE IIB            4             4
  STAGE IIC            0             1
  STAGE III            8            11
  STAGE IIIA           3             7
  STAGE IIIB          14            27
  STAGE IIIC           9            22
  STAGE IV             6            29
  STAGE IVA            4             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  45 155  28
D132V4, multiclass
    clus
vv   ATM MUTATED ATM WILD-TYPE
  T1           3             6
  T2          23            45
  T3          93           155
  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  56  50
D132V5, multiclass
    clus
vv   ATM MUTATED ATM WILD-TYPE
  N0          92           128
  N1          24            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"
D132V6, binary
               cls
clus              0   1
  ATM MUTATED   100   9
  ATM WILD-TYPE 183  39
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED    100    9
  ATM WILD-TYPE  183   39
   clus
vv  ATM MUTATED ATM WILD-TYPE
  0         100           183
  1           9            39
[1] 2 2
[1] FALSE
D132V7, 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
D132V8, binary
               cls
clus              0   1
  ATM MUTATED   111  21
  ATM WILD-TYPE 206  27
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED    111   21
  ATM WILD-TYPE  206   27
                               clus
vv                              ATM MUTATED ATM WILD-TYPE
  COLON ADENOCARCINOMA                  111           206
  COLON MUCINOUS ADENOCARCINOMA          21            27
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  ATM MUTATED    85   0   3  13
  ATM WILD-TYPE 172   2  19   8
D132V9, multiclass
    clus
vv   ATM MUTATED ATM WILD-TYPE
  R0          85           172
  R1           0             2
  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"
D132V10, 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
D132V11, 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(133) Variable = CHRM2 MUTATION ANALYSIS
D133V1, survival
                 sevent
clus2               0   1
  CHRM2 MUTATED    17   3
  CHRM2 WILD-TYPE 265  70
  CHRM2 MUTATED CHRM2 WILD-TYPE 
             20             335 
  CHRM2 MUTATED CHRM2 WILD-TYPE 
              3              70 
$`CHRM2 MUTATED`
TCGA-A6-5664 TCGA-A6-6141 TCGA-A6-6651 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3688 
       22.09         8.38        21.76         3.02        63.98        19.00 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6889 
       26.99        19.04        19.04         4.01        34.98        56.55 
TCGA-CA-6717 TCGA-CK-5913 TCGA-CM-6172 TCGA-D5-6923 TCGA-D5-6931 TCGA-DM-A1HA 
        0.33        51.32        11.01        12.43        12.00       131.51 
TCGA-G4-6293 TCGA-G4-6304 
      107.67        53.62 

$`CHRM2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       24.16        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 
       20.28         7.04         1.02        35.01         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3812 
       37.05        36.00         5.03        85.05        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37         4.21         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
       17.56       102.44        40.34        15.62        49.08        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         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-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.41         1.51        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 
       35.41        19.43        74.56        65.85        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  CHRM2 MUTATED CHRM2 WILD-TYPE 
           0.33            0.00 
  CHRM2 MUTATED CHRM2 WILD-TYPE 
         131.51          140.38 
  CHRM2 MUTATED CHRM2 WILD-TYPE 
          20.40           20.19 
[1] "0.3 - 131.5 (20.4)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.9"
D133V2, 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       21       104         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        18         10         39         28       31        13
                 vv
clus              STAGE IVB
  CHRM2 MUTATED           0
  CHRM2 WILD-TYPE         1
D133V3, multiclass
            clus
vv           CHRM2 MUTATED CHRM2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               4              21
  STAGE IIA              5             104
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             3              28
  STAGE IV               4              31
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CHRM2 MUTATED     0   1  15   7
  CHRM2 WILD-TYPE   9  67 233  34
D133V4, multiclass
    clus
vv   CHRM2 MUTATED CHRM2 WILD-TYPE
  T1             0               9
  T2             1              67
  T3            15             233
  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  76  61
D133V5, multiclass
    clus
vv   CHRM2 MUTATED CHRM2 WILD-TYPE
  N0            14             206
  N1             4              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"
D133V6, binary
                 cls
clus                0   1
  CHRM2 MUTATED    16   4
  CHRM2 WILD-TYPE 267  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHRM2 MUTATED     16    4
  CHRM2 WILD-TYPE  267   44
   clus
vv  CHRM2 MUTATED CHRM2 WILD-TYPE
  0            16             267
  1             4              44
[1] 2 2
[1] FALSE
D133V7, 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
D133V8, binary
                 cls
clus                0   1
  CHRM2 MUTATED    20   3
  CHRM2 WILD-TYPE 297  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHRM2 MUTATED     20    3
  CHRM2 WILD-TYPE  297   45
                               clus
vv                              CHRM2 MUTATED CHRM2 WILD-TYPE
  COLON ADENOCARCINOMA                     20             297
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CHRM2 MUTATED    12   0   4   2
  CHRM2 WILD-TYPE 245   2  18  19
D133V9, multiclass
    clus
vv   CHRM2 MUTATED CHRM2 WILD-TYPE
  R0            12             245
  R1             0               2
  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"
D133V10, 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
D133V11, 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(134) Variable = CASP8 MUTATION ANALYSIS
D134V1, survival
                 sevent
clus2               0   1
  CASP8 MUTATED    12   4
  CASP8 WILD-TYPE 270  69
  CASP8 MUTATED CASP8 WILD-TYPE 
             16             339 
  CASP8 MUTATED CASP8 WILD-TYPE 
              4              69 
$`CASP8 MUTATED`
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3518 TCGA-AA-3543 TCGA-AA-3710 TCGA-AA-3715 
        7.04         3.02         1.02         0.99        26.99        19.04 
TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-A00A TCGA-AA-A00J TCGA-AA-A00R TCGA-AD-6895 
       53.00        33.01        38.04        18.05         0.99         0.72 
TCGA-AY-6197 TCGA-CA-6717 TCGA-CM-4746 TCGA-DM-A28F 
       21.44         0.33        37.02        35.97 

$`CASP8 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3496 TCGA-AA-3502 
       23.87        20.12        19.66        20.28         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 
       63.98         6.97         1.02        13.02        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D 
       27.02        19.07         7.96        27.02        13.94        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
       42.02        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
        0.07        21.37         4.21        56.55         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        15.75         0.20        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G 
      135.65       139.17         6.12        81.37       119.93        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  CASP8 MUTATED CASP8 WILD-TYPE 
           0.33            0.00 
  CASP8 MUTATED CASP8 WILD-TYPE 
          53.00          140.38 
  CASP8 MUTATED CASP8 WILD-TYPE 
         18.545          20.280 
[1] "0.3 - 53.0 (18.5)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.8"
D134V2, 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       20       104         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CASP8 MUTATED           0          0          2          0        0         0
  CASP8 WILD-TYPE        19         10         39         31       35        13
                 vv
clus              STAGE IVB
  CASP8 MUTATED           0
  CASP8 WILD-TYPE         1
D134V3, multiclass
            clus
vv           CASP8 MUTATED CASP8 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               5              20
  STAGE IIA              5             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CASP8 MUTATED     0   3  11   3
  CASP8 WILD-TYPE   9  65 237  38
D134V4, multiclass
    clus
vv   CASP8 MUTATED CASP8 WILD-TYPE
  T1             0               9
  T2             3              65
  T3            11             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
  CASP8 MUTATED    14   3   0
  CASP8 WILD-TYPE 206  77  66
D134V5, multiclass
    clus
vv   CASP8 MUTATED CASP8 WILD-TYPE
  N0            14             206
  N1             3              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"
D134V6, binary
                 cls
clus                0   1
  CASP8 MUTATED    15   0
  CASP8 WILD-TYPE 268  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED     15    0
  CASP8 WILD-TYPE  268   48
   clus
vv  CASP8 MUTATED CASP8 WILD-TYPE
  0            15             268
  1             0              48
[1] 2 2
[1] FALSE
D134V7, 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
D134V8, binary
                 cls
clus                0   1
  CASP8 MUTATED    13   4
  CASP8 WILD-TYPE 304  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED     13    4
  CASP8 WILD-TYPE  304   44
                               clus
vv                              CASP8 MUTATED CASP8 WILD-TYPE
  COLON ADENOCARCINOMA                     13             304
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CASP8 MUTATED    14   0   0   1
  CASP8 WILD-TYPE 243   2  22  20
D134V9, multiclass
    clus
vv   CASP8 MUTATED CASP8 WILD-TYPE
  R0            14             243
  R1             0               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"
D134V10, 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
D134V11, 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(135) Variable = INTS4 MUTATION ANALYSIS
D135V1, survival
                 sevent
clus2               0   1
  INTS4 MUTATED    12   5
  INTS4 WILD-TYPE 270  68
  INTS4 MUTATED INTS4 WILD-TYPE 
             17             338 
  INTS4 MUTATED INTS4 WILD-TYPE 
              5              68 
$`INTS4 MUTATED`
TCGA-A6-5660 TCGA-A6-5664 TCGA-AA-3525 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3672 
       29.19        22.09         8.05         6.05         6.97         0.92 
TCGA-AZ-4315 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-6718 TCGA-CM-5868 
       58.39        62.79        49.41       100.01         0.10        17.03 
TCGA-CM-6171 TCGA-D5-6537 TCGA-D5-6930 TCGA-F4-6459 TCGA-G4-6306 
       14.04         4.80         1.51         8.61        44.68 

$`INTS4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5665 
       32.91        31.63        30.44        33.53        23.61        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 
        9.07        24.03        37.05        36.03        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       19.99        61.02        78.08        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6599 
        1.41         5.13        83.80        22.36        61.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.33         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        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-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79       117.07        98.24        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  INTS4 MUTATED INTS4 WILD-TYPE 
            0.1             0.0 
  INTS4 MUTATED INTS4 WILD-TYPE 
         100.01          140.38 
  INTS4 MUTATED INTS4 WILD-TYPE 
          14.04           20.63 
[1] "0.1 - 100.0 (14.0)" "0.0 - 140.4 (20.6)"
[1] "hr=" "1.4"
D135V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  INTS4 MUTATED         2        0        4         4         0         0
  INTS4 WILD-TYPE      62        1       21       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        18         10         38         29       34        12
                 vv
clus              STAGE IVB
  INTS4 MUTATED           0
  INTS4 WILD-TYPE         1
D135V3, multiclass
            clus
vv           INTS4 MUTATED INTS4 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               4              21
  STAGE IIA              4             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             3              38
  STAGE IIIC             2              29
  STAGE IV               1              34
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  65 236  38
D135V4, multiclass
    clus
vv   INTS4 MUTATED INTS4 WILD-TYPE
  T1             0               9
  T2             3              65
  T3            12             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
  INTS4 MUTATED    10   4   4
  INTS4 WILD-TYPE 210  76  62
D135V5, multiclass
    clus
vv   INTS4 MUTATED INTS4 WILD-TYPE
  N0            10             210
  N1             4              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"
D135V6, binary
                 cls
clus                0   1
  INTS4 MUTATED    11   2
  INTS4 WILD-TYPE 272  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INTS4 MUTATED     11    2
  INTS4 WILD-TYPE  272   46
   clus
vv  INTS4 MUTATED INTS4 WILD-TYPE
  0            11             272
  1             2              46
[1] 2 2
[1] FALSE
D135V7, 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
D135V8, binary
                 cls
clus                0   1
  INTS4 MUTATED    17   1
  INTS4 WILD-TYPE 300  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INTS4 MUTATED     17    1
  INTS4 WILD-TYPE  300   47
                               clus
vv                              INTS4 MUTATED INTS4 WILD-TYPE
  COLON ADENOCARCINOMA                     17             300
  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 247   2  21  19
D135V9, multiclass
    clus
vv   INTS4 MUTATED INTS4 WILD-TYPE
  R0            10             247
  R1             0               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"
D135V10, 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
D135V11, 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(136) Variable = MMP8 MUTATION ANALYSIS
D136V1, survival
                sevent
clus2              0   1
  MMP8 MUTATED     9   3
  MMP8 WILD-TYPE 273  70
  MMP8 MUTATED MMP8 WILD-TYPE 
            12            343 
  MMP8 MUTATED MMP8 WILD-TYPE 
             3             70 
$`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 
        2.24        51.32        21.99        37.02        12.99         6.18 

$`MMP8 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       22.36        61.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19         1.94         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5916 
       17.56       102.44        40.34        15.62        49.08        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        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        13.38        13.45        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  MMP8 MUTATED MMP8 WILD-TYPE 
          2.24           0.00 
  MMP8 MUTATED MMP8 WILD-TYPE 
         63.98         140.38 
  MMP8 MUTATED MMP8 WILD-TYPE 
        28.535         19.990 
[1] "2.2 - 64.0 (28.5)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1.1"
D136V2, 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       22       104         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        19         10         40         30       35        13
                vv
clus             STAGE IVB
  MMP8 MUTATED           0
  MMP8 WILD-TYPE         1
D136V3, multiclass
            clus
vv           MMP8 MUTATED MMP8 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              3             22
  STAGE IIA             5            104
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            1             30
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MMP8 MUTATED     0   1   9   2
  MMP8 WILD-TYPE   9  67 239  39
D136V4, multiclass
    clus
vv   MMP8 MUTATED MMP8 WILD-TYPE
  T1            0              9
  T2            1             67
  T3            9            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
  MMP8 MUTATED    10   1   1
  MMP8 WILD-TYPE 210  79  65
D136V5, multiclass
    clus
vv   MMP8 MUTATED MMP8 WILD-TYPE
  N0           10            210
  N1            1             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"
D136V6, binary
                cls
clus               0   1
  MMP8 MUTATED     6   0
  MMP8 WILD-TYPE 277  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMP8 MUTATED      6    0
  MMP8 WILD-TYPE  277   48
   clus
vv  MMP8 MUTATED MMP8 WILD-TYPE
  0            6            277
  1            0             48
[1] 2 2
[1] FALSE
D136V7, 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
D136V8, binary
                cls
clus               0   1
  MMP8 MUTATED    11   1
  MMP8 WILD-TYPE 306  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMP8 MUTATED     11    1
  MMP8 WILD-TYPE  306   47
                               clus
vv                              MMP8 MUTATED MMP8 WILD-TYPE
  COLON ADENOCARCINOMA                    11            306
  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 252   2  22  18
D136V9, multiclass
    clus
vv   MMP8 MUTATED MMP8 WILD-TYPE
  R0            5            252
  R1            0              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"
D136V10, 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
D136V11, 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(137) Variable = LDHA MUTATION ANALYSIS
D137V1, survival
                sevent
clus2              0   1
  LDHA MUTATED     7   2
  LDHA WILD-TYPE 275  71
  LDHA MUTATED LDHA WILD-TYPE 
             9            346 
  LDHA MUTATED LDHA WILD-TYPE 
             2             71 
$`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       107.67 

$`LDHA WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
       40.34        15.62        49.08        51.32        21.99         2.93 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        15.12         4.80        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 
      119.93        35.97        60.79       117.07         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  LDHA MUTATED LDHA WILD-TYPE 
          1.02           0.00 
  LDHA MUTATED LDHA WILD-TYPE 
        107.67         140.38 
  LDHA MUTATED LDHA WILD-TYPE 
        21.140         20.155 
[1] "1.0 - 107.7 (21.1)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.3"
D137V2, 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       24       106         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        18         10         41         31       33        13
                vv
clus             STAGE IVB
  LDHA MUTATED           0
  LDHA WILD-TYPE         1
D137V3, multiclass
            clus
vv           LDHA MUTATED LDHA WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             3            106
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              2             33
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  LDHA MUTATED     1   2   7   0
  LDHA WILD-TYPE   8  66 241  41
D137V4, multiclass
    clus
vv   LDHA MUTATED LDHA WILD-TYPE
  T1            1              8
  T2            2             66
  T3            7            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
  LDHA MUTATED     7   2   1
  LDHA WILD-TYPE 213  78  65
D137V5, multiclass
    clus
vv   LDHA MUTATED LDHA WILD-TYPE
  N0            7            213
  N1            2             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"
D137V6, binary
                cls
clus               0   1
  LDHA MUTATED     7   2
  LDHA WILD-TYPE 276  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  LDHA MUTATED      7    2
  LDHA WILD-TYPE  276   46
   clus
vv  LDHA MUTATED LDHA WILD-TYPE
  0            7            276
  1            2             46
[1] 2 2
[1] FALSE
D137V7, 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
D137V8, binary
                cls
clus               0   1
  LDHA MUTATED     7   3
  LDHA WILD-TYPE 310  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  LDHA MUTATED      7    3
  LDHA WILD-TYPE  310   45
                               clus
vv                              LDHA MUTATED LDHA WILD-TYPE
  COLON ADENOCARCINOMA                     7            310
  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 251   2  22  18
D137V9, multiclass
    clus
vv   LDHA MUTATED LDHA WILD-TYPE
  R0            6            251
  R1            0              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"
D137V10, 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
D137V11, 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(138) Variable = NAA25 MUTATION ANALYSIS
D138V1, survival
                 sevent
clus2               0   1
  NAA25 MUTATED    10   2
  NAA25 WILD-TYPE 272  71
  NAA25 MUTATED NAA25 WILD-TYPE 
             12             343 
  NAA25 MUTATED NAA25 WILD-TYPE 
              2              71 
$`NAA25 MUTATED`
TCGA-A6-3809 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-6780 TCGA-AA-3710 TCGA-AA-3715 
       32.75        33.53        22.09        20.12        26.99        19.04 
TCGA-AA-3864 TCGA-AA-3950 TCGA-AA-A00N TCGA-AA-A010 TCGA-CM-6678 TCGA-F4-6808 
       53.00        24.00         4.01        34.98        11.01        33.67 

$`NAA25 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5665 TCGA-A6-5666 
       31.63        30.44        29.19        23.61        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 
       21.76        24.69        24.39        23.87        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        7.04         3.02         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 
        1.55        16.31        29.59        16.24        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  NAA25 MUTATED NAA25 WILD-TYPE 
           4.01            0.00 
  NAA25 MUTATED NAA25 WILD-TYPE 
          53.00          140.38 
  NAA25 MUTATED NAA25 WILD-TYPE 
         25.495          19.990 
[1] "4.0 - 53.0 (25.5)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1.2"
D138V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NAA25 MUTATED         1        0        2         5         3         0
  NAA25 WILD-TYPE      63        1       23       104         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        19         10         41         30       35        12
                 vv
clus              STAGE IVB
  NAA25 MUTATED           0
  NAA25 WILD-TYPE         1
D138V3, multiclass
            clus
vv           NAA25 MUTATED NAA25 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              5             104
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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   7   5
  NAA25 WILD-TYPE   8  68 241  36
D138V4, multiclass
    clus
vv   NAA25 MUTATED NAA25 WILD-TYPE
  T1             1               8
  T2             0              68
  T3             7             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    11   1   1
  NAA25 WILD-TYPE 209  79  65
D138V5, multiclass
    clus
vv   NAA25 MUTATED NAA25 WILD-TYPE
  N0            11             209
  N1             1              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
  NAA25 MUTATED    10   1
  NAA25 WILD-TYPE 273  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA25 MUTATED     10    1
  NAA25 WILD-TYPE  273   47
   clus
vv  NAA25 MUTATED NAA25 WILD-TYPE
  0            10             273
  1             1              47
[1] 2 2
[1] FALSE
D138V7, binary
                 cls
clus                0   1
  NAA25 MUTATED     8   5
  NAA25 WILD-TYPE 162 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA25 MUTATED      8    5
  NAA25 WILD-TYPE  162  192
        clus
vv       NAA25 MUTATED NAA25 WILD-TYPE
  FEMALE             8             162
  MALE               5             192
[1] 2 2
[1] FALSE
D138V8, binary
                 cls
clus                0   1
  NAA25 MUTATED     9   4
  NAA25 WILD-TYPE 308  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA25 MUTATED      9    4
  NAA25 WILD-TYPE  308   44
                               clus
vv                              NAA25 MUTATED NAA25 WILD-TYPE
  COLON ADENOCARCINOMA                      9             308
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  NAA25 MUTATED    11   0   0   0
  NAA25 WILD-TYPE 246   2  22  21
D138V9, multiclass
    clus
vv   NAA25 MUTATED NAA25 WILD-TYPE
  R0            11             246
  R1             0               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"
D138V10, 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
D138V11, 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(139) Variable = C11ORF30 MUTATION ANALYSIS
D139V1, survival
                    sevent
clus2                  0   1
  C11ORF30 MUTATED    17   3
  C11ORF30 WILD-TYPE 265  70
  C11ORF30 MUTATED C11ORF30 WILD-TYPE 
                20                335 
  C11ORF30 MUTATED C11ORF30 WILD-TYPE 
                 3                 70 
$`C11ORF30 MUTATED`
TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-3554 TCGA-AA-3672 TCGA-AA-3947 TCGA-AA-3949 
       22.06        20.12        17.95         0.92        33.01        26.01 
TCGA-AA-3977 TCGA-AA-A00N TCGA-AD-6889 TCGA-AD-6895 TCGA-AZ-4315 TCGA-AZ-6599 
       25.02         4.01        56.55         0.72        58.39         6.77 
TCGA-CA-6715 TCGA-CA-6717 TCGA-CM-6161 TCGA-D5-6541 TCGA-D5-6927 TCGA-DM-A0XD 
        0.07         0.33        15.02        15.58         9.44        24.43 
TCGA-F4-6807 TCGA-G4-6586 
       16.24        35.80 

$`C11ORF30 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41        49.41        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        16.14         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 
        1.51        12.00        11.38        10.26       119.70        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       16.31        29.59        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        26.17        91.79        46.75        52.80 

  C11ORF30 MUTATED C11ORF30 WILD-TYPE 
              0.07               0.00 
  C11ORF30 MUTATED C11ORF30 WILD-TYPE 
             58.39             140.38 
  C11ORF30 MUTATED C11ORF30 WILD-TYPE 
            17.095             20.980 
[1] "0.1 - 58.4 (17.1)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.1"
D139V2, 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       25        98         6         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C11ORF30 MUTATED           1          0          2          1        0
  C11ORF30 WILD-TYPE        18         10         39         30       35
                    vv
clus                 STAGE IVA STAGE IVB
  C11ORF30 MUTATED           0         0
  C11ORF30 WILD-TYPE        13         1
D139V3, multiclass
            clus
vv           C11ORF30 MUTATED C11ORF30 WILD-TYPE
  STAGE I                   2                 62
  STAGE IA                  0                  1
  STAGE II                  0                 25
  STAGE IIA                11                 98
  STAGE IIB                 2                  6
  STAGE IIC                 0                  1
  STAGE III                 1                 18
  STAGE IIIA                0                 10
  STAGE IIIB                2                 39
  STAGE IIIC                1                 30
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C11ORF30 MUTATED     0   3  16   2
  C11ORF30 WILD-TYPE   9  65 232  39
D139V4, multiclass
    clus
vv   C11ORF30 MUTATED C11ORF30 WILD-TYPE
  T1                0                  9
  T2                3                 65
  T3               16                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
  C11ORF30 MUTATED    16   4   1
  C11ORF30 WILD-TYPE 204  76  65
D139V5, multiclass
    clus
vv   C11ORF30 MUTATED C11ORF30 WILD-TYPE
  N0               16                204
  N1                4                 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"
D139V6, binary
                    cls
clus                   0   1
  C11ORF30 MUTATED    17   0
  C11ORF30 WILD-TYPE 266  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF30 MUTATED     17    0
  C11ORF30 WILD-TYPE  266   48
   clus
vv  C11ORF30 MUTATED C11ORF30 WILD-TYPE
  0               17                266
  1                0                 48
[1] 2 2
[1] FALSE
D139V7, 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
D139V8, binary
                    cls
clus                   0   1
  C11ORF30 MUTATED    16   5
  C11ORF30 WILD-TYPE 301  43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF30 MUTATED     16    5
  C11ORF30 WILD-TYPE  301   43
                               clus
vv                              C11ORF30 MUTATED C11ORF30 WILD-TYPE
  COLON ADENOCARCINOMA                        16                301
  COLON MUCINOUS ADENOCARCINOMA                5                 43
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C11ORF30 MUTATED    13   0   0   2
  C11ORF30 WILD-TYPE 244   2  22  19
D139V9, multiclass
    clus
vv   C11ORF30 MUTATED C11ORF30 WILD-TYPE
  R0               13                244
  R1                0                  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"
D139V10, 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
D139V11, 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(140) Variable = ASNSD1 MUTATION ANALYSIS
D140V1, survival
                  sevent
clus2                0   1
  ASNSD1 MUTATED     6   2
  ASNSD1 WILD-TYPE 276  71
  ASNSD1 MUTATED ASNSD1 WILD-TYPE 
               8              347 
  ASNSD1 MUTATED ASNSD1 WILD-TYPE 
               2               71 
$`ASNSD1 MUTATED`
TCGA-A6-6780 TCGA-AA-3510 TCGA-AA-3715 TCGA-AA-3864 TCGA-AA-3947 TCGA-AD-6964 
       20.12        63.98        19.04        53.00        33.01        10.88 
TCGA-AY-6196 TCGA-CA-6717 
        0.20         0.33 

$`ASNSD1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        15.75        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  ASNSD1 MUTATED ASNSD1 WILD-TYPE 
             0.2              0.0 
  ASNSD1 MUTATED ASNSD1 WILD-TYPE 
           63.98           140.38 
  ASNSD1 MUTATED ASNSD1 WILD-TYPE 
           19.58            20.28 
[1] "0.2 - 64.0 (19.6)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.2"
D140V2, 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       22       106         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ASNSD1 MUTATED           0          0          0          1        0
  ASNSD1 WILD-TYPE        19         10         41         30       35
                  vv
clus               STAGE IVA STAGE IVB
  ASNSD1 MUTATED           0         0
  ASNSD1 WILD-TYPE        13         1
D140V3, multiclass
            clus
vv           ASNSD1 MUTATED ASNSD1 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                3               22
  STAGE IIA               3              106
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ASNSD1 MUTATED     0   0   7   2
  ASNSD1 WILD-TYPE   9  68 241  39
D140V4, multiclass
    clus
vv   ASNSD1 MUTATED ASNSD1 WILD-TYPE
  T1              0                9
  T2              0               68
  T3              7              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
  ASNSD1 MUTATED     7   0   2
  ASNSD1 WILD-TYPE 213  80  64
D140V5, multiclass
    clus
vv   ASNSD1 MUTATED ASNSD1 WILD-TYPE
  N0              7              213
  N1              0               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"
D140V6, binary
                  cls
clus                 0   1
  ASNSD1 MUTATED     6   0
  ASNSD1 WILD-TYPE 277  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ASNSD1 MUTATED      6    0
  ASNSD1 WILD-TYPE  277   48
   clus
vv  ASNSD1 MUTATED ASNSD1 WILD-TYPE
  0              6              277
  1              0               48
[1] 2 2
[1] FALSE
D140V7, 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
D140V8, binary
                  cls
clus                 0   1
  ASNSD1 MUTATED     5   4
  ASNSD1 WILD-TYPE 312  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ASNSD1 MUTATED      5    4
  ASNSD1 WILD-TYPE  312   44
                               clus
vv                              ASNSD1 MUTATED ASNSD1 WILD-TYPE
  COLON ADENOCARCINOMA                       5              312
  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 251   2  22  20
D140V9, multiclass
    clus
vv   ASNSD1 MUTATED ASNSD1 WILD-TYPE
  R0              6              251
  R1              0                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"
D140V10, 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
D140V11, 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(141) Variable = ALG9 MUTATION ANALYSIS
D141V1, survival
                sevent
clus2              0   1
  ALG9 MUTATED     6   1
  ALG9 WILD-TYPE 276  72
  ALG9 MUTATED ALG9 WILD-TYPE 
             7            348 
  ALG9 MUTATED ALG9 WILD-TYPE 
             1             72 
$`ALG9 MUTATED`
TCGA-AA-3496 TCGA-AA-3715 TCGA-AU-6004 TCGA-CK-6751 TCGA-CM-6165 TCGA-D5-6932 
        1.02        19.04        27.09       124.27        16.04        11.38 
TCGA-F4-6569 
       13.45 

$`ALG9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        13.38         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  ALG9 MUTATED ALG9 WILD-TYPE 
          1.02           0.00 
  ALG9 MUTATED ALG9 WILD-TYPE 
        124.27         140.38 
  ALG9 MUTATED ALG9 WILD-TYPE 
         16.04          20.63 
[1] "1.0 - 124.3 (16.0)" "0.0 - 140.4 (20.6)"
[1] "hr=" "1.6"
D141V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ALG9 MUTATED         3        0        2         2         0         0
  ALG9 WILD-TYPE      61        1       23       107         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        19         10         41         31       35        13
                vv
clus             STAGE IVB
  ALG9 MUTATED           0
  ALG9 WILD-TYPE         1
D141V3, multiclass
            clus
vv           ALG9 MUTATED ALG9 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             2            107
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ALG9 MUTATED     0   3   4   0
  ALG9 WILD-TYPE   9  65 244  41
D141V4, multiclass
    clus
vv   ALG9 MUTATED ALG9 WILD-TYPE
  T1            0              9
  T2            3             65
  T3            4            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
  ALG9 MUTATED     7   0   0
  ALG9 WILD-TYPE 213  80  66
D141V5, multiclass
    clus
vv   ALG9 MUTATED ALG9 WILD-TYPE
  N0            7            213
  N1            0             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"
D141V6, binary
                cls
clus               0   1
  ALG9 MUTATED     6   0
  ALG9 WILD-TYPE 277  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  ALG9 MUTATED      6    0
  ALG9 WILD-TYPE  277   48
   clus
vv  ALG9 MUTATED ALG9 WILD-TYPE
  0            6            277
  1            0             48
[1] 2 2
[1] FALSE
D141V7, binary
                cls
clus               0   1
  ALG9 MUTATED     3   4
  ALG9 WILD-TYPE 167 193
[1] "tbl2"
                cls
clus             [,1] [,2]
  ALG9 MUTATED      3    4
  ALG9 WILD-TYPE  167  193
        clus
vv       ALG9 MUTATED ALG9 WILD-TYPE
  FEMALE            3            167
  MALE              4            193
[1] 2 2
[1] FALSE
D141V8, binary
                cls
clus               0   1
  ALG9 MUTATED     6   1
  ALG9 WILD-TYPE 311  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  ALG9 MUTATED      6    1
  ALG9 WILD-TYPE  311   47
                               clus
vv                              ALG9 MUTATED ALG9 WILD-TYPE
  COLON ADENOCARCINOMA                     6            311
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ALG9 MUTATED     6   0   0   1
  ALG9 WILD-TYPE 251   2  22  20
D141V9, multiclass
    clus
vv   ALG9 MUTATED ALG9 WILD-TYPE
  R0            6            251
  R1            0              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"
D141V10, 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     5
  ALG9 WILD-TYPE                        19   171
D141V11, multiclass
                                  clus
vv                                 ALG9 MUTATED ALG9 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(142) Variable = TUBE1 MUTATION ANALYSIS
D142V1, survival
                 sevent
clus2               0   1
  TUBE1 MUTATED     8   3
  TUBE1 WILD-TYPE 274  70
  TUBE1 MUTATED TUBE1 WILD-TYPE 
             11             344 
  TUBE1 MUTATED TUBE1 WILD-TYPE 
              3              70 
$`TUBE1 MUTATED`
TCGA-A6-2677 TCGA-A6-5661 TCGA-AA-3516 TCGA-AA-3663 TCGA-AA-A010 TCGA-CA-6717 
       24.33        33.53        13.02         6.97        34.98         0.33 
TCGA-CK-4950 TCGA-CM-6162 TCGA-CM-6171 TCGA-DM-A1HB TCGA-DM-A28G 
       40.34        12.00        14.04       135.65        60.79 

$`TUBE1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        42.90        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
        1.35        17.56       102.44        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        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-6172 
       21.99        14.99        12.99        13.02        15.02        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H 
      139.17         6.12        81.37       119.93        35.97       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  TUBE1 MUTATED TUBE1 WILD-TYPE 
           0.33            0.00 
  TUBE1 MUTATED TUBE1 WILD-TYPE 
         135.65          140.38 
  TUBE1 MUTATED TUBE1 WILD-TYPE 
         24.330          20.155 
[1] "0.3 - 135.7 (24.3)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D142V2, 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       24       106         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TUBE1 MUTATED           1          1          2          1        0         0
  TUBE1 WILD-TYPE        18          9         39         30       35        13
                 vv
clus              STAGE IVB
  TUBE1 MUTATED           0
  TUBE1 WILD-TYPE         1
D142V3, multiclass
            clus
vv           TUBE1 MUTATED TUBE1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              3             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             1               9
  STAGE IIIB             2              39
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TUBE1 MUTATED     0   1   9   1
  TUBE1 WILD-TYPE   9  67 239  40
D142V4, multiclass
    clus
vv   TUBE1 MUTATED TUBE1 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             9             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
  TUBE1 MUTATED     6   3   2
  TUBE1 WILD-TYPE 214  77  64
D142V5, multiclass
    clus
vv   TUBE1 MUTATED TUBE1 WILD-TYPE
  N0             6             214
  N1             3              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"
D142V6, binary
                 cls
clus                0   1
  TUBE1 MUTATED    11   0
  TUBE1 WILD-TYPE 272  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TUBE1 MUTATED     11    0
  TUBE1 WILD-TYPE  272   48
   clus
vv  TUBE1 MUTATED TUBE1 WILD-TYPE
  0            11             272
  1             0              48
[1] 2 2
[1] FALSE
D142V7, 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
D142V8, binary
                 cls
clus                0   1
  TUBE1 MUTATED     8   3
  TUBE1 WILD-TYPE 309  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TUBE1 MUTATED      8    3
  TUBE1 WILD-TYPE  309   45
                               clus
vv                              TUBE1 MUTATED TUBE1 WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TUBE1 MUTATED     6   1   0   1
  TUBE1 WILD-TYPE 251   1  22  20
D142V9, multiclass
    clus
vv   TUBE1 MUTATED TUBE1 WILD-TYPE
  R0             6             251
  R1             1               1
  R2             0              22
  RX             1              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D142V10, 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
D142V11, 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(143) Variable = MEN1 MUTATION ANALYSIS
D143V1, survival
                sevent
clus2              0   1
  MEN1 MUTATED    16   7
  MEN1 WILD-TYPE 266  66
  MEN1 MUTATED MEN1 WILD-TYPE 
            23            332 
  MEN1 MUTATED MEN1 WILD-TYPE 
             7             66 
$`MEN1 MUTATED`
TCGA-A6-2676 TCGA-A6-4105 TCGA-A6-6137 TCGA-AA-3492 TCGA-AA-3662 TCGA-AY-5543 
       42.90        14.53        27.09         3.02         6.05        15.75 
TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CM-6168 
       49.41       100.01       102.44        40.34        15.62        12.99 
TCGA-D5-5537 TCGA-D5-6533 TCGA-D5-6540 TCGA-D5-6922 TCGA-DM-A1D6 TCGA-F4-6460 
       45.40         1.32        16.14        10.13        49.91        13.38 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       19.43       107.67        22.09        35.80        26.17 

$`MEN1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 
       34.65        33.34        32.75        36.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       32.71        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-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-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       61.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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-D5-5538 TCGA-D5-5539 
       11.08        11.01        10.06        12.03        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 
       13.51        11.51        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-D5-6920 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43        38.20       130.65        92.75        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       35.41        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6625 
       51.75        45.11        36.72        36.00        13.78        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  MEN1 MUTATED MEN1 WILD-TYPE 
          1.32           0.00 
  MEN1 MUTATED MEN1 WILD-TYPE 
        107.67         140.38 
  MEN1 MUTATED MEN1 WILD-TYPE 
        22.090         20.155 
[1] "1.3 - 107.7 (22.1)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D143V2, 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       22       103         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MEN1 MUTATED           4          3          3          0        1         1
  MEN1 WILD-TYPE        15          7         38         31       34        12
                vv
clus             STAGE IVB
  MEN1 MUTATED           0
  MEN1 WILD-TYPE         1
D143V3, multiclass
            clus
vv           MEN1 MUTATED MEN1 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              3             22
  STAGE IIA             6            103
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             4             15
  STAGE IIIA            3              7
  STAGE IIIB            3             38
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  65 231  37
D143V4, multiclass
    clus
vv   MEN1 MUTATED MEN1 WILD-TYPE
  T1            0              9
  T2            3             65
  T3           17            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
  MEN1 MUTATED    12   8   4
  MEN1 WILD-TYPE 208  72  62
D143V5, multiclass
    clus
vv   MEN1 MUTATED MEN1 WILD-TYPE
  N0           12            208
  N1            8             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"
D143V6, binary
                cls
clus               0   1
  MEN1 MUTATED    19   2
  MEN1 WILD-TYPE 264  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  MEN1 MUTATED     19    2
  MEN1 WILD-TYPE  264   46
   clus
vv  MEN1 MUTATED MEN1 WILD-TYPE
  0           19            264
  1            2             46
[1] 2 2
[1] FALSE
D143V7, 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
D143V8, binary
                cls
clus               0   1
  MEN1 MUTATED    20   4
  MEN1 WILD-TYPE 297  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  MEN1 MUTATED     20    4
  MEN1 WILD-TYPE  297   44
                               clus
vv                              MEN1 MUTATED MEN1 WILD-TYPE
  COLON ADENOCARCINOMA                    20            297
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MEN1 MUTATED    15   1   1   2
  MEN1 WILD-TYPE 242   1  21  19
D143V9, multiclass
    clus
vv   MEN1 MUTATED MEN1 WILD-TYPE
  R0           15            242
  R1            1              1
  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"
D143V10, 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
D143V11, 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(144) Variable = GIGYF2 MUTATION ANALYSIS
D144V1, survival
                  sevent
clus2                0   1
  GIGYF2 MUTATED    21   4
  GIGYF2 WILD-TYPE 261  69
  GIGYF2 MUTATED GIGYF2 WILD-TYPE 
              25              330 
  GIGYF2 MUTATED GIGYF2 WILD-TYPE 
               4               69 
$`GIGYF2 MUTATED`
TCGA-A6-5661 TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3672 TCGA-AA-3877 TCGA-AA-3949 
       33.53        22.06         3.02         0.92        31.00        26.01 
TCGA-AA-A00J TCGA-AA-A010 TCGA-AD-6895 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-5403 
       18.05        34.98         0.72         0.20        21.44        62.79 
TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CM-4743 TCGA-CM-5863 TCGA-CM-6163 TCGA-CM-6172 
       49.41       100.01        23.05        15.02        14.04        11.01 
TCGA-D5-6536 TCGA-D5-6920 TCGA-D5-6928 TCGA-D5-6929 TCGA-DM-A28H TCGA-F4-6856 
       17.85        12.39        11.64        13.41       117.07        19.43 
TCGA-G4-6628 
       52.80 

$`GIGYF2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05         2.01        12.99        24.00        33.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       61.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14         2.93         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 
       16.01        15.02         5.03        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       12.00        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        14.04        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        35.41       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 

  GIGYF2 MUTATED GIGYF2 WILD-TYPE 
             0.2              0.0 
  GIGYF2 MUTATED GIGYF2 WILD-TYPE 
          117.07           140.38 
  GIGYF2 MUTATED GIGYF2 WILD-TYPE 
          19.430           20.235 
[1] "0.2 - 117.1 (19.4)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.5"
D144V2, 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       21       101         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GIGYF2 MUTATED           1          0          4          2        1
  GIGYF2 WILD-TYPE        18         10         37         29       34
                  vv
clus               STAGE IVA STAGE IVB
  GIGYF2 MUTATED           0         0
  GIGYF2 WILD-TYPE        13         1
D144V3, multiclass
            clus
vv           GIGYF2 MUTATED GIGYF2 WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                4               21
  STAGE IIA               8              101
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              4               37
  STAGE IIIC              2               29
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GIGYF2 MUTATED     2   2  20   2
  GIGYF2 WILD-TYPE   7  66 228  39
D144V4, multiclass
    clus
vv   GIGYF2 MUTATED GIGYF2 WILD-TYPE
  T1              2                7
  T2              2               66
  T3             20              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
  GIGYF2 MUTATED    17   7   2
  GIGYF2 WILD-TYPE 203  73  64
D144V5, multiclass
    clus
vv   GIGYF2 MUTATED GIGYF2 WILD-TYPE
  N0             17              203
  N1              7               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"
D144V6, binary
                  cls
clus                 0   1
  GIGYF2 MUTATED    20   1
  GIGYF2 WILD-TYPE 263  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GIGYF2 MUTATED     20    1
  GIGYF2 WILD-TYPE  263   47
   clus
vv  GIGYF2 MUTATED GIGYF2 WILD-TYPE
  0             20              263
  1              1               47
[1] 2 2
[1] FALSE
D144V7, 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
D144V8, binary
                  cls
clus                 0   1
  GIGYF2 MUTATED    19   7
  GIGYF2 WILD-TYPE 298  41
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GIGYF2 MUTATED     19    7
  GIGYF2 WILD-TYPE  298   41
                               clus
vv                              GIGYF2 MUTATED GIGYF2 WILD-TYPE
  COLON ADENOCARCINOMA                      19              298
  COLON MUCINOUS ADENOCARCINOMA              7               41
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  GIGYF2 MUTATED    21   0   0   0
  GIGYF2 WILD-TYPE 236   2  22  21
D144V9, multiclass
    clus
vv   GIGYF2 MUTATED GIGYF2 WILD-TYPE
  R0             21              236
  R1              0                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"
D144V10, 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
D144V11, 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(145) Variable = SMAD4 MUTATION ANALYSIS
D145V1, survival
                 sevent
clus2               0   1
  SMAD4 MUTATED    91  25
  SMAD4 WILD-TYPE 191  48
  SMAD4 MUTATED SMAD4 WILD-TYPE 
            116             239 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             25              48 
$`SMAD4 MUTATED`
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-3809 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 
       42.90        42.28        32.75        32.91        30.44        29.19 
TCGA-A6-5664 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       22.09        27.09        22.52        21.76        24.69        23.87 
TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3530 TCGA-AA-3555 TCGA-AA-3558 
        1.02        24.03        37.05        19.07        29.95        20.98 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 
       78.08         6.05         2.01        36.00        85.05        19.04 
TCGA-AA-3811 TCGA-AA-3821 TCGA-AA-3845 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3950 
       10.06         1.02         0.00        30.05        53.00        24.00 
TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-A00K TCGA-AA-A01D TCGA-AA-A02O TCGA-AD-6888 
       21.99        13.05        18.05        10.98         0.92         4.21 
TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-6196 
        5.79        27.42        10.88        14.50        27.09         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-6598 
       21.44        17.82         5.13        83.80        62.79        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 
        6.77        12.10       100.01        29.56         5.23         3.19 
TCGA-CA-5796 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4950 
        3.25         0.26         0.33         0.10         1.35        40.34 
TCGA-CK-5914 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       21.99        13.02        22.03        22.98        30.08        16.01 
TCGA-CM-5861 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-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 
       15.02        14.04        11.01        12.03        12.26        19.59 
TCGA-D5-5540 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6541 
       13.51        18.25         1.32        43.27        17.85        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
        7.53        12.39        14.30         9.44        11.64         1.51 
TCGA-D5-7000 TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB 
       10.26        38.20        92.75        12.59       140.38        44.32 
TCGA-DM-A285 TCGA-DM-A28H TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6805 
        6.12       117.07        13.38        13.45         6.18        16.31 
TCGA-F4-6807 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       16.24        35.41       107.67        74.56        65.85        53.62 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       51.75        45.11        36.00        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

$`SMAD4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2683 TCGA-A6-3807 
       43.76        46.65        43.76        24.33        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 
       33.34        36.53        14.53        31.63        33.53        23.61 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       22.06        32.71         8.38        25.08        25.18        24.16 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
        1.02         9.07        36.03         8.05        19.07         0.00 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3663 
       23.01        19.99        13.94        19.99        61.02         6.97 
TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3710 
       11.01         5.98        37.05        19.00         5.03        26.99 
TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 
       19.04        35.05        33.04         0.99        25.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02        14.93        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        31.07        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 
       26.01         2.01        20.98        34.03         2.01        16.08 
TCGA-AA-3972 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       50.99        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       34.98        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        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03        14.01        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 
        0.07        21.37        56.55         0.79         0.72        22.42 
TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AZ-4315 TCGA-AZ-4323 
        0.20        16.31         0.95        15.75        58.39         1.41 
TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
       22.36        61.41        11.74         1.94         2.24         3.06 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 
        3.29         0.07        17.56       102.44        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.14         2.93         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5862 TCGA-CM-5863 
       20.02        37.02        25.02        29.06         5.03        15.02 
TCGA-CM-5864 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       15.02        12.00        29.03        14.99        12.99        13.02 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-D5-5537 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       45.40        11.51        20.19        15.12         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6929 
       12.49        16.14        10.13        12.43         9.04        13.41 
TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D6 
       12.00        11.38       119.70        24.43       130.65        49.91 
TCGA-DM-A1D7 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C 
       13.32         7.50       131.51       135.65       139.17        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6703 
      119.93        35.97        60.79        98.24         8.61        35.87 
TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 
        1.55        29.59        33.67        13.25         0.53        19.43 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6588 
       44.68        55.04        36.72        22.09        26.17 

  SMAD4 MUTATED SMAD4 WILD-TYPE 
              0               0 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
         140.38          139.17 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
         18.645          21.010 
[1] "0.0 - 140.4 (18.6)" "0.0 - 139.2 (21.0)"
[1] "hr=" "1"  
D145V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SMAD4 MUTATED        19        1        8        39         4         0
  SMAD4 WILD-TYPE      45        0       17        70         4         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SMAD4 MUTATED           4          2         17         10        9         2
  SMAD4 WILD-TYPE        15          8         24         21       26        11
                 vv
clus              STAGE IVB
  SMAD4 MUTATED           0
  SMAD4 WILD-TYPE         1
D145V3, multiclass
            clus
vv           SMAD4 MUTATED SMAD4 WILD-TYPE
  STAGE I               19              45
  STAGE IA               1               0
  STAGE II               8              17
  STAGE IIA             39              70
  STAGE IIB              4               4
  STAGE IIC              0               1
  STAGE III              4              15
  STAGE IIIA             2               8
  STAGE IIIB            17              24
  STAGE IIIC            10              21
  STAGE IV               9              26
  STAGE IVA              2              11
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  20  83  14
  SMAD4 WILD-TYPE   8  48 165  27
D145V4, multiclass
    clus
vv   SMAD4 MUTATED SMAD4 WILD-TYPE
  T1             1               8
  T2            20              48
  T3            83             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  24  18
  SMAD4 WILD-TYPE 144  56  48
D145V5, multiclass
    clus
vv   SMAD4 MUTATED SMAD4 WILD-TYPE
  N0            76             144
  N1            24              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"
D145V6, binary
                 cls
clus                0   1
  SMAD4 MUTATED    91  11
  SMAD4 WILD-TYPE 192  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED     91   11
  SMAD4 WILD-TYPE  192   37
   clus
vv  SMAD4 MUTATED SMAD4 WILD-TYPE
  0            91             192
  1            11              37
[1] 2 2
[1] FALSE
D145V7, 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
D145V8, binary
                 cls
clus                0   1
  SMAD4 MUTATED   102  17
  SMAD4 WILD-TYPE 215  31
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED    102   17
  SMAD4 WILD-TYPE  215   31
                               clus
vv                              SMAD4 MUTATED SMAD4 WILD-TYPE
  COLON ADENOCARCINOMA                    102             215
  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 178   1  17  14
D145V9, multiclass
    clus
vv   SMAD4 MUTATED SMAD4 WILD-TYPE
  R0            79             178
  R1             1               1
  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"
D145V10, 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
D145V11, 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(146) Variable = TNMD MUTATION ANALYSIS
D146V1, survival
                sevent
clus2              0   1
  TNMD MUTATED     9   2
  TNMD WILD-TYPE 273  71
  TNMD MUTATED TNMD WILD-TYPE 
            11            344 
  TNMD MUTATED TNMD WILD-TYPE 
             2             71 
$`TNMD MUTATED`
TCGA-A6-5665 TCGA-A6-6141 TCGA-AA-3502 TCGA-AA-3542 TCGA-AA-3815 TCGA-AA-3864 
       22.06         8.38        35.01        12.99        33.04        53.00 
TCGA-AA-3977 TCGA-AZ-6598 TCGA-CK-5916 TCGA-D5-6930 TCGA-G4-6586 
       25.02        49.41        21.14         1.51        35.80 

$`TNMD WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.09        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3510 
       19.66        20.28         7.04         3.02         1.02        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 
       19.07        34.03        29.00        29.00        26.01         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  TNMD MUTATED TNMD WILD-TYPE 
          1.51           0.00 
  TNMD MUTATED TNMD WILD-TYPE 
         53.00         140.38 
  TNMD MUTATED TNMD WILD-TYPE 
        25.020         20.005 
[1] "1.5 - 53.0 (25.0)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1.2"
D146V2, 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       23       104         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        19         10         41         30       35        13
                vv
clus             STAGE IVB
  TNMD MUTATED           0
  TNMD WILD-TYPE         1
D146V3, multiclass
            clus
vv           TNMD MUTATED TNMD WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             5            104
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            1             30
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TNMD MUTATED     1   2   8   0
  TNMD WILD-TYPE   8  66 240  41
D146V4, multiclass
    clus
vv   TNMD MUTATED TNMD WILD-TYPE
  T1            1              8
  T2            2             66
  T3            8            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
  TNMD MUTATED    10   0   1
  TNMD WILD-TYPE 210  80  65
D146V5, multiclass
    clus
vv   TNMD MUTATED TNMD WILD-TYPE
  N0           10            210
  N1            0             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"
D146V6, binary
                cls
clus               0   1
  TNMD MUTATED     9   0
  TNMD WILD-TYPE 274  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  TNMD MUTATED      9    0
  TNMD WILD-TYPE  274   48
   clus
vv  TNMD MUTATED TNMD WILD-TYPE
  0            9            274
  1            0             48
[1] 2 2
[1] FALSE
D146V7, 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
D146V8, binary
                cls
clus               0   1
  TNMD MUTATED    10   1
  TNMD WILD-TYPE 307  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  TNMD MUTATED     10    1
  TNMD WILD-TYPE  307   47
                               clus
vv                              TNMD MUTATED TNMD WILD-TYPE
  COLON ADENOCARCINOMA                    10            307
  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 250   2  22  20
D146V9, multiclass
    clus
vv   TNMD MUTATED TNMD WILD-TYPE
  R0            7            250
  R1            0              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"
D146V10, 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
D146V11, 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(147) Variable = PAQR5 MUTATION ANALYSIS
D147V1, survival
                 sevent
clus2               0   1
  PAQR5 MUTATED     6   2
  PAQR5 WILD-TYPE 276  71
  PAQR5 MUTATED PAQR5 WILD-TYPE 
              8             347 
  PAQR5 MUTATED PAQR5 WILD-TYPE 
              2              71 
$`PAQR5 MUTATED`
TCGA-A6-4105 TCGA-AA-3663 TCGA-AD-6895 TCGA-AY-5543 TCGA-CK-5912 TCGA-D5-5541 
       14.53         6.97         0.72        15.75        49.08        11.51 
TCGA-D5-6540 TCGA-D5-6541 
       16.14        15.58 

$`PAQR5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 
        0.20        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-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
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         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 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-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64        13.41         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  PAQR5 MUTATED PAQR5 WILD-TYPE 
           0.72            0.00 
  PAQR5 MUTATED PAQR5 WILD-TYPE 
          49.08          140.38 
  PAQR5 MUTATED PAQR5 WILD-TYPE 
         15.055          20.980 
[1] "0.7 - 49.1 (15.1)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.7"
D147V2, 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       24       107         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PAQR5 MUTATED           0          0          1          0        0         1
  PAQR5 WILD-TYPE        19         10         40         31       35        12
                 vv
clus              STAGE IVB
  PAQR5 MUTATED           0
  PAQR5 WILD-TYPE         1
D147V3, multiclass
            clus
vv           PAQR5 MUTATED PAQR5 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              2             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 242  41
D147V4, multiclass
    clus
vv   PAQR5 MUTATED PAQR5 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             6             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
  PAQR5 MUTATED     5   3   0
  PAQR5 WILD-TYPE 215  77  66
D147V5, multiclass
    clus
vv   PAQR5 MUTATED PAQR5 WILD-TYPE
  N0             5             215
  N1             3              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"
D147V6, binary
                 cls
clus                0   1
  PAQR5 MUTATED     5   1
  PAQR5 WILD-TYPE 278  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAQR5 MUTATED      5    1
  PAQR5 WILD-TYPE  278   47
   clus
vv  PAQR5 MUTATED PAQR5 WILD-TYPE
  0             5             278
  1             1              47
[1] 2 2
[1] FALSE
D147V7, 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
D147V8, binary
                 cls
clus                0   1
  PAQR5 MUTATED     7   1
  PAQR5 WILD-TYPE 310  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAQR5 MUTATED      7    1
  PAQR5 WILD-TYPE  310   47
                               clus
vv                              PAQR5 MUTATED PAQR5 WILD-TYPE
  COLON ADENOCARCINOMA                      7             310
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PAQR5 MUTATED     5   0   0   1
  PAQR5 WILD-TYPE 252   2  22  20
D147V9, multiclass
    clus
vv   PAQR5 MUTATED PAQR5 WILD-TYPE
  R0             5             252
  R1             0               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"
D147V10, 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
D147V11, 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(148) Variable = ATG5 MUTATION ANALYSIS
D148V1, survival
                sevent
clus2              0   1
  ATG5 MUTATED     7   0
  ATG5 WILD-TYPE 275  73
  ATG5 MUTATED ATG5 WILD-TYPE 
             7            348 
  ATG5 MUTATED ATG5 WILD-TYPE 
             0             73 
$`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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        34.98        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  ATG5 MUTATED ATG5 WILD-TYPE 
         13.41           0.00 
  ATG5 MUTATED ATG5 WILD-TYPE 
         25.02         140.38 
  ATG5 MUTATED ATG5 WILD-TYPE 
         18.25          20.63 
[1] "13.4 - 25.0 (18.2)" "0.0 - 140.4 (20.6)"
[1] "hr="     "9200000"
D148V2, 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       25       106         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        19         10         41         31       34        13
                vv
clus             STAGE IVB
  ATG5 MUTATED           0
  ATG5 WILD-TYPE         1
D148V3, multiclass
            clus
vv           ATG5 MUTATED ATG5 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             3            106
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ATG5 MUTATED     0   3   4   1
  ATG5 WILD-TYPE   9  65 244  40
D148V4, multiclass
    clus
vv   ATG5 MUTATED ATG5 WILD-TYPE
  T1            0              9
  T2            3             65
  T3            4            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
  ATG5 MUTATED     7   1   0
  ATG5 WILD-TYPE 213  79  66
D148V5, multiclass
    clus
vv   ATG5 MUTATED ATG5 WILD-TYPE
  N0            7            213
  N1            1             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"
D148V6, binary
                cls
clus               0   1
  ATG5 MUTATED     4   1
  ATG5 WILD-TYPE 279  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATG5 MUTATED      4    1
  ATG5 WILD-TYPE  279   47
   clus
vv  ATG5 MUTATED ATG5 WILD-TYPE
  0            4            279
  1            1             47
[1] 2 2
[1] FALSE
D148V7, 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
D148V8, binary
                cls
clus               0   1
  ATG5 MUTATED     7   1
  ATG5 WILD-TYPE 310  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATG5 MUTATED      7    1
  ATG5 WILD-TYPE  310   47
                               clus
vv                              ATG5 MUTATED ATG5 WILD-TYPE
  COLON ADENOCARCINOMA                     7            310
  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 251   2  22  20
D148V9, multiclass
    clus
vv   ATG5 MUTATED ATG5 WILD-TYPE
  R0            6            251
  R1            0              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"
D148V10, 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
D148V11, 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(149) Variable = CLEC4F MUTATION ANALYSIS
D149V1, survival
                  sevent
clus2                0   1
  CLEC4F MUTATED    16   3
  CLEC4F WILD-TYPE 266  70
  CLEC4F MUTATED CLEC4F WILD-TYPE 
              19              336 
  CLEC4F MUTATED CLEC4F WILD-TYPE 
               3               70 
$`CLEC4F MUTATED`
TCGA-A6-6653 TCGA-AA-3510 TCGA-AA-3534 TCGA-AA-3713 TCGA-AA-3864 TCGA-AA-A00N 
       24.39        63.98        29.00        19.04        53.00         4.01 
TCGA-AD-5900 TCGA-AD-6964 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-CA-6717 
        0.07        10.88        15.75        17.82        58.39         0.33 
TCGA-CA-6718 TCGA-CM-4743 TCGA-CM-4752 TCGA-D5-6529 TCGA-D5-6532 TCGA-DM-A28C 
        0.10        23.05        13.02        20.19        18.25        81.37 
TCGA-G4-6588 
       26.17 

$`CLEC4F WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 
        0.00        19.07        34.03        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
        0.20        21.44         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07         0.26         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
       21.99        21.14         2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
        6.12       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        52.80 

  CLEC4F MUTATED CLEC4F WILD-TYPE 
            0.07             0.00 
  CLEC4F MUTATED CLEC4F WILD-TYPE 
           81.37           140.38 
  CLEC4F MUTATED CLEC4F WILD-TYPE 
           19.04            20.63 
[1] "0.1 - 81.4 (19.0)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "1.4"
D149V2, 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       23        99         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CLEC4F MUTATED           0          0          1          0        1
  CLEC4F WILD-TYPE        19         10         40         31       34
                  vv
clus               STAGE IVA STAGE IVB
  CLEC4F MUTATED           1         0
  CLEC4F WILD-TYPE        12         1
D149V3, multiclass
            clus
vv           CLEC4F MUTATED CLEC4F WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA              10               99
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 233  39
D149V4, multiclass
    clus
vv   CLEC4F MUTATED CLEC4F WILD-TYPE
  T1              0                9
  T2              2               66
  T3             15              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
  CLEC4F MUTATED    16   2   1
  CLEC4F WILD-TYPE 204  78  65
D149V5, multiclass
    clus
vv   CLEC4F MUTATED CLEC4F WILD-TYPE
  N0             16              204
  N1              2               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"
D149V6, binary
                  cls
clus                 0   1
  CLEC4F MUTATED    15   2
  CLEC4F WILD-TYPE 268  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLEC4F MUTATED     15    2
  CLEC4F WILD-TYPE  268   46
   clus
vv  CLEC4F MUTATED CLEC4F WILD-TYPE
  0             15              268
  1              2               46
[1] 2 2
[1] FALSE
D149V7, 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
D149V8, binary
                  cls
clus                 0   1
  CLEC4F MUTATED    16   3
  CLEC4F WILD-TYPE 301  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLEC4F MUTATED     16    3
  CLEC4F WILD-TYPE  301   45
                               clus
vv                              CLEC4F MUTATED CLEC4F WILD-TYPE
  COLON ADENOCARCINOMA                      16              301
  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 244   2  21  19
D149V9, multiclass
    clus
vv   CLEC4F MUTATED CLEC4F WILD-TYPE
  R0             13              244
  R1              0                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"
D149V10, 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
D149V11, 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(150) Variable = MKL2 MUTATION ANALYSIS
D150V1, survival
                sevent
clus2              0   1
  MKL2 MUTATED     6   4
  MKL2 WILD-TYPE 276  69
  MKL2 MUTATED MKL2 WILD-TYPE 
            10            345 
  MKL2 MUTATED MKL2 WILD-TYPE 
             4             69 
$`MKL2 MUTATED`
TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3518 TCGA-AD-5900 TCGA-AD-6963 TCGA-AD-6964 
       22.06         3.02         1.02         0.07        27.42        10.88 
TCGA-AU-6004 TCGA-CK-5916 TCGA-F4-6570 TCGA-G4-6307 
       27.09        21.14         6.18        55.04 

$`MKL2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 
       63.98         6.97         1.02        13.02        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
        0.72         5.79        22.42         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        53.62        44.68        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  MKL2 MUTATED MKL2 WILD-TYPE 
          0.07           0.00 
  MKL2 MUTATED MKL2 WILD-TYPE 
         55.04         140.38 
  MKL2 MUTATED MKL2 WILD-TYPE 
         16.01          20.19 
[1] "0.1 - 55.0 (16.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2.8"
D150V2, 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       24       106         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        19         10         40         31       35        13
                vv
clus             STAGE IVB
  MKL2 MUTATED           0
  MKL2 WILD-TYPE         1
D150V3, multiclass
            clus
vv           MKL2 MUTATED MKL2 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             3            106
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MKL2 MUTATED     1   2   6   1
  MKL2 WILD-TYPE   8  66 242  40
D150V4, multiclass
    clus
vv   MKL2 MUTATED MKL2 WILD-TYPE
  T1            1              8
  T2            2             66
  T3            6            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
  MKL2 MUTATED     8   1   1
  MKL2 WILD-TYPE 212  79  65
D150V5, multiclass
    clus
vv   MKL2 MUTATED MKL2 WILD-TYPE
  N0            8            212
  N1            1             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"
D150V6, binary
                cls
clus               0   1
  MKL2 MUTATED     7   0
  MKL2 WILD-TYPE 276  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  MKL2 MUTATED      7    0
  MKL2 WILD-TYPE  276   48
   clus
vv  MKL2 MUTATED MKL2 WILD-TYPE
  0            7            276
  1            0             48
[1] 2 2
[1] FALSE
D150V7, 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
D150V8, binary
                cls
clus               0   1
  MKL2 MUTATED     9   1
  MKL2 WILD-TYPE 308  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  MKL2 MUTATED      9    1
  MKL2 WILD-TYPE  308   47
                               clus
vv                              MKL2 MUTATED MKL2 WILD-TYPE
  COLON ADENOCARCINOMA                     9            308
  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 250   2  22  20
D150V9, multiclass
    clus
vv   MKL2 MUTATED MKL2 WILD-TYPE
  R0            7            250
  R1            0              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"
D150V10, 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
D150V11, 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(151) Variable = RAF1 MUTATION ANALYSIS
D151V1, survival
                sevent
clus2              0   1
  RAF1 MUTATED    11   2
  RAF1 WILD-TYPE 271  71
  RAF1 MUTATED RAF1 WILD-TYPE 
            13            342 
  RAF1 MUTATED RAF1 WILD-TYPE 
             2             71 
$`RAF1 MUTATED`
TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3562 TCGA-AA-A00N TCGA-AA-A01V TCGA-AZ-4315 
       63.98        13.02        19.99         4.01        35.01        58.39 
TCGA-AZ-5407 TCGA-CA-6717 TCGA-CM-4746 TCGA-CM-6162 TCGA-DM-A28H TCGA-F4-6856 
       61.41         0.33        37.02        12.00       117.07        19.43 
TCGA-G4-6306 
       44.68 

$`RAF1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        1.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01X 
       38.07         1.02        35.01         1.02        33.04        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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 
       16.01        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        35.41       107.67        74.56        65.85        53.62 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  RAF1 MUTATED RAF1 WILD-TYPE 
          0.33           0.00 
  RAF1 MUTATED RAF1 WILD-TYPE 
        117.07         140.38 
  RAF1 MUTATED RAF1 WILD-TYPE 
        35.010         20.155 
[1] "0.3 - 117.1 (35.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.9"
D151V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RAF1 MUTATED         4        0        1         3         1         0
  RAF1 WILD-TYPE      60        1       24       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        18         10         40         29       35        13
                vv
clus             STAGE IVB
  RAF1 MUTATED           0
  RAF1 WILD-TYPE         1
D151V3, multiclass
            clus
vv           RAF1 MUTATED RAF1 WILD-TYPE
  STAGE I               4             60
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             3            106
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            2             29
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RAF1 MUTATED     1   4   7   1
  RAF1 WILD-TYPE   8  64 241  40
D151V4, multiclass
    clus
vv   RAF1 MUTATED RAF1 WILD-TYPE
  T1            1              8
  T2            4             64
  T3            7            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
  RAF1 MUTATED     9   1   3
  RAF1 WILD-TYPE 211  79  63
D151V5, multiclass
    clus
vv   RAF1 MUTATED RAF1 WILD-TYPE
  N0            9            211
  N1            1             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"
D151V6, binary
                cls
clus               0   1
  RAF1 MUTATED    13   0
  RAF1 WILD-TYPE 270  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAF1 MUTATED     13    0
  RAF1 WILD-TYPE  270   48
   clus
vv  RAF1 MUTATED RAF1 WILD-TYPE
  0           13            270
  1            0             48
[1] 2 2
[1] FALSE
D151V7, 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
D151V8, binary
                cls
clus               0   1
  RAF1 MUTATED     8   5
  RAF1 WILD-TYPE 309  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAF1 MUTATED      8    5
  RAF1 WILD-TYPE  309   43
                               clus
vv                              RAF1 MUTATED RAF1 WILD-TYPE
  COLON ADENOCARCINOMA                     8            309
  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 248   2  22  20
D151V9, multiclass
    clus
vv   RAF1 MUTATED RAF1 WILD-TYPE
  R0            9            248
  R1            0              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"
D151V10, 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
D151V11, 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(152) Variable = KLHL10 MUTATION ANALYSIS
D152V1, survival
                  sevent
clus2                0   1
  KLHL10 MUTATED    13   5
  KLHL10 WILD-TYPE 269  68
  KLHL10 MUTATED KLHL10 WILD-TYPE 
              18              337 
  KLHL10 MUTATED KLHL10 WILD-TYPE 
               5               68 
$`KLHL10 MUTATED`
TCGA-A6-5659 TCGA-A6-5660 TCGA-AA-3663 TCGA-AD-6964 TCGA-AU-6004 TCGA-AY-6196 
       30.44        29.19         6.97        10.88        27.09         0.20 
TCGA-AY-6197 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CA-6718 TCGA-CM-4743 TCGA-CM-5868 
       21.44       100.01         1.94         0.10        23.05        17.03 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6928 TCGA-DM-A1D4 TCGA-G4-6588 TCGA-G4-6626 
        1.32        15.12        11.64        92.75        26.17        46.75 

$`KLHL10 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       32.91        31.63        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 
       14.50        16.31         0.95        15.75        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
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         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.33         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 
       19.59        13.51        11.51        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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        24.43        38.20       130.65        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6628 
       52.80 

  KLHL10 MUTATED KLHL10 WILD-TYPE 
             0.1              0.0 
  KLHL10 MUTATED KLHL10 WILD-TYPE 
          100.01           140.38 
  KLHL10 MUTATED KLHL10 WILD-TYPE 
          19.235           20.190 
[1] "0.1 - 100.0 (19.2)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.4"
D152V2, 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       23       102         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KLHL10 MUTATED           0          1          2          2        1
  KLHL10 WILD-TYPE        19          9         39         29       34
                  vv
clus               STAGE IVA STAGE IVB
  KLHL10 MUTATED           1         0
  KLHL10 WILD-TYPE        12         1
D152V3, multiclass
            clus
vv           KLHL10 MUTATED KLHL10 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               7              102
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              1                9
  STAGE IIIB              2               39
  STAGE IIIC              2               29
  STAGE IV                1               34
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  65 235  38
D152V4, multiclass
    clus
vv   KLHL10 MUTATED KLHL10 WILD-TYPE
  T1              0                9
  T2              3               65
  T3             13              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
  KLHL10 MUTATED    12   3   4
  KLHL10 WILD-TYPE 208  77  62
D152V5, multiclass
    clus
vv   KLHL10 MUTATED KLHL10 WILD-TYPE
  N0             12              208
  N1              3               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"
D152V6, binary
                  cls
clus                 0   1
  KLHL10 MUTATED    13   2
  KLHL10 WILD-TYPE 270  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KLHL10 MUTATED     13    2
  KLHL10 WILD-TYPE  270   46
   clus
vv  KLHL10 MUTATED KLHL10 WILD-TYPE
  0             13              270
  1              2               46
[1] 2 2
[1] FALSE
D152V7, 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
D152V8, binary
                  cls
clus                 0   1
  KLHL10 MUTATED    17   2
  KLHL10 WILD-TYPE 300  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KLHL10 MUTATED     17    2
  KLHL10 WILD-TYPE  300   46
                               clus
vv                              KLHL10 MUTATED KLHL10 WILD-TYPE
  COLON ADENOCARCINOMA                      17              300
  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 246   2  21  19
D152V9, multiclass
    clus
vv   KLHL10 MUTATED KLHL10 WILD-TYPE
  R0             11              246
  R1              0                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"
D152V10, 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
D152V11, 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(153) Variable = SLC12A6 MUTATION ANALYSIS
D153V1, survival
                   sevent
clus2                 0   1
  SLC12A6 MUTATED    16   4
  SLC12A6 WILD-TYPE 266  69
  SLC12A6 MUTATED SLC12A6 WILD-TYPE 
               20               335 
  SLC12A6 MUTATED SLC12A6 WILD-TYPE 
                4                69 
$`SLC12A6 MUTATED`
TCGA-A6-5665 TCGA-AA-3518 TCGA-AA-3662 TCGA-AA-3715 TCGA-AA-A010 TCGA-AA-A01I 
       22.06         1.02         6.05        19.04        34.98        31.00 
TCGA-AD-5900 TCGA-AU-6004 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6601 
        0.07        27.09        21.44        58.39        49.41       100.01 
TCGA-CM-4744 TCGA-CM-6162 TCGA-CM-6680 TCGA-D5-6536 TCGA-DM-A28H TCGA-F4-6570 
       20.02        12.00        12.03        17.85       117.07         6.18 
TCGA-G4-6323 TCGA-G4-6588 
       13.78        26.17 

$`SLC12A6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        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        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       15.75         0.20        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       22.36        62.79        61.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 
       20.19        18.25         1.32        43.27        15.12         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        13.38        13.45        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        35.80        91.79        46.75        52.80 

  SLC12A6 MUTATED SLC12A6 WILD-TYPE 
             0.07              0.00 
  SLC12A6 MUTATED SLC12A6 WILD-TYPE 
           117.07            140.38 
  SLC12A6 MUTATED SLC12A6 WILD-TYPE 
            20.73             20.19 
[1] "0.1 - 117.1 (20.7)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D153V2, 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       22       102         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC12A6 MUTATED           0          0          2          1        1
  SLC12A6 WILD-TYPE        19         10         39         30       34
                   vv
clus                STAGE IVA STAGE IVB
  SLC12A6 MUTATED           0         0
  SLC12A6 WILD-TYPE        13         1
D153V3, multiclass
            clus
vv           SLC12A6 MUTATED SLC12A6 WILD-TYPE
  STAGE I                  4                60
  STAGE IA                 1                 0
  STAGE II                 3                22
  STAGE IIA                7               102
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               2                39
  STAGE IIIC               1                30
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC12A6 MUTATED     0   4  13   2
  SLC12A6 WILD-TYPE   9  64 235  39
D153V4, multiclass
    clus
vv   SLC12A6 MUTATED SLC12A6 WILD-TYPE
  T1               0                 9
  T2               4                64
  T3              13               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
  SLC12A6 MUTATED    16   1   3
  SLC12A6 WILD-TYPE 204  79  63
D153V5, multiclass
    clus
vv   SLC12A6 MUTATED SLC12A6 WILD-TYPE
  N0              16               204
  N1               1                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"
D153V6, binary
                   cls
clus                  0   1
  SLC12A6 MUTATED    15   1
  SLC12A6 WILD-TYPE 268  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC12A6 MUTATED     15    1
  SLC12A6 WILD-TYPE  268   47
   clus
vv  SLC12A6 MUTATED SLC12A6 WILD-TYPE
  0              15               268
  1               1                47
[1] 2 2
[1] FALSE
D153V7, 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
D153V8, binary
                   cls
clus                  0   1
  SLC12A6 MUTATED    18   2
  SLC12A6 WILD-TYPE 299  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC12A6 MUTATED     18    2
  SLC12A6 WILD-TYPE  299   46
                               clus
vv                              SLC12A6 MUTATED SLC12A6 WILD-TYPE
  COLON ADENOCARCINOMA                       18               299
  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 241   2  21  21
D153V9, multiclass
    clus
vv   SLC12A6 MUTATED SLC12A6 WILD-TYPE
  R0              16               241
  R1               0                 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"
D153V10, 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
D153V11, 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(154) Variable = GNAS MUTATION ANALYSIS
D154V1, survival
                sevent
clus2              0   1
  GNAS MUTATED    26   7
  GNAS WILD-TYPE 256  66
  GNAS MUTATED GNAS WILD-TYPE 
            33            322 
  GNAS MUTATED GNAS WILD-TYPE 
             7             66 
$`GNAS MUTATED`
TCGA-A6-2678 TCGA-A6-6141 TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3518 TCGA-AA-3660 
       42.28         8.38         7.04        35.01         1.02        78.08 
TCGA-AA-3663 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3713 TCGA-AA-3815 TCGA-AA-3861 
        6.97        15.02         5.98        19.04        33.04        30.05 
TCGA-AA-3869 TCGA-AA-3989 TCGA-AD-5900 TCGA-AD-6889 TCGA-AU-6004 TCGA-AZ-6598 
       27.02         7.96         0.07        56.55        27.09        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-CA-6718 TCGA-CK-4952 TCGA-CM-4743 
        6.77        12.10        29.56         0.10        15.62        23.05 
TCGA-CM-6675 TCGA-D5-6928 TCGA-DM-A1HA TCGA-G4-6306 TCGA-G4-6315 TCGA-G4-6317 
       13.05        11.64       131.51        44.68        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       22.09        35.80        26.17 

$`GNAS WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2683 
       43.76        46.65        43.76        42.90        24.33        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3511 
       19.66        20.28         3.02         1.02        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
        1.02        13.02        38.99         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       47.01        11.01        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       85.05        26.99        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       53.00        17.03        24.03        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        27.02        19.07        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       39.98        18.05        40.96        21.37         4.21         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       62.79        61.41       100.01         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.33         1.35        17.56       102.44        40.34 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        53.62        55.04        51.75        45.11 
TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        91.79        46.75        52.80 

  GNAS MUTATED GNAS WILD-TYPE 
          0.07           0.00 
  GNAS MUTATED GNAS WILD-TYPE 
        131.51         140.38 
  GNAS MUTATED GNAS WILD-TYPE 
         23.05          20.07 
[1] "0.1 - 131.5 (23.1)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1"  
D154V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GNAS MUTATED         4        0        4        11         0         0
  GNAS WILD-TYPE      60        1       21        98         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GNAS MUTATED           3          0          1          2        6         0
  GNAS WILD-TYPE        16         10         40         29       29        13
                vv
clus             STAGE IVB
  GNAS MUTATED           1
  GNAS WILD-TYPE         0
D154V3, multiclass
            clus
vv           GNAS MUTATED GNAS WILD-TYPE
  STAGE I               4             60
  STAGE IA              0              1
  STAGE II              4             21
  STAGE IIA            11             98
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             3             16
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            2             29
  STAGE IV              6             29
  STAGE IVA             0             13
  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  23   3
  GNAS WILD-TYPE   9  61 225  38
D154V4, multiclass
    clus
vv   GNAS MUTATED GNAS WILD-TYPE
  T1            0              9
  T2            7             61
  T3           23            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
  GNAS MUTATED    20   6   7
  GNAS WILD-TYPE 200  74  59
D154V5, multiclass
    clus
vv   GNAS MUTATED GNAS WILD-TYPE
  N0           20            200
  N1            6             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"
D154V6, binary
                cls
clus               0   1
  GNAS MUTATED    20   7
  GNAS WILD-TYPE 263  41
[1] "tbl2"
                cls
clus             [,1] [,2]
  GNAS MUTATED     20    7
  GNAS WILD-TYPE  263   41
   clus
vv  GNAS MUTATED GNAS WILD-TYPE
  0           20            263
  1            7             41
[1] 2 2
[1] FALSE
D154V7, binary
                cls
clus               0   1
  GNAS MUTATED    13  20
  GNAS WILD-TYPE 157 177
[1] "tbl2"
                cls
clus             [,1] [,2]
  GNAS MUTATED     13   20
  GNAS WILD-TYPE  157  177
        clus
vv       GNAS MUTATED GNAS WILD-TYPE
  FEMALE           13            157
  MALE             20            177
[1] 2 2
[1] FALSE
D154V8, binary
                cls
clus               0   1
  GNAS MUTATED    30   3
  GNAS WILD-TYPE 287  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  GNAS MUTATED     30    3
  GNAS WILD-TYPE  287   45
                               clus
vv                              GNAS MUTATED GNAS WILD-TYPE
  COLON ADENOCARCINOMA                    30            287
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  GNAS MUTATED    20   0   4   2
  GNAS WILD-TYPE 237   2  18  19
D154V9, multiclass
    clus
vv   GNAS MUTATED GNAS WILD-TYPE
  R0           20            237
  R1            0              2
  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"
D154V10, 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
D154V11, 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(155) Variable = USP24 MUTATION ANALYSIS
D155V1, survival
                 sevent
clus2               0   1
  USP24 MUTATED    21   6
  USP24 WILD-TYPE 261  67
  USP24 MUTATED USP24 WILD-TYPE 
             27             328 
  USP24 MUTATED USP24 WILD-TYPE 
              6              67 
$`USP24 MUTATED`
TCGA-A6-5661 TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3663 
       33.53        24.39        19.66        63.98         6.97         6.97 
TCGA-AA-3815 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6964 
       33.04        37.02         0.00         4.01        34.98        10.88 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6606 TCGA-CA-5797 TCGA-CK-4950 TCGA-CM-6167 
       61.41        49.41        11.74         3.29        40.34        14.99 
TCGA-CM-6680 TCGA-D5-5540 TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       12.03        13.51        15.12        17.13        12.49        16.14 
TCGA-DM-A1D8 TCGA-DM-A282 TCGA-G4-6323 
       12.59       139.17        13.78 

$`USP24 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3514 
       20.28         7.04         3.02         1.02        35.01         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       78.08         6.05        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       17.98        15.95        38.99        14.93        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 
        6.77        12.10       100.01        29.56         5.23         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 
        1.94         2.24         3.06         3.25         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 
        0.33         0.10         1.35        17.56       102.44        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        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        12.26        19.59 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 
       11.51        20.19        18.25         1.32        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        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-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       135.65         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 
       51.75        45.11        36.72        36.00        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  USP24 MUTATED USP24 WILD-TYPE 
              0               0 
  USP24 MUTATED USP24 WILD-TYPE 
         139.17          140.38 
  USP24 MUTATED USP24 WILD-TYPE 
         15.120          20.995 
[1] "0.0 - 139.2 (15.1)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.1"
D155V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  USP24 MUTATED         3        1        4         6         3         0
  USP24 WILD-TYPE      61        0       21       103         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  USP24 MUTATED           0          3          3          2        1         0
  USP24 WILD-TYPE        19          7         38         29       34        13
                 vv
clus              STAGE IVB
  USP24 MUTATED           0
  USP24 WILD-TYPE         1
D155V3, multiclass
            clus
vv           USP24 MUTATED USP24 WILD-TYPE
  STAGE I                3              61
  STAGE IA               1               0
  STAGE II               4              21
  STAGE IIA              6             103
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             3               7
  STAGE IIIB             3              38
  STAGE IIIC             2              29
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  USP24 MUTATED     1   3  16   7
  USP24 WILD-TYPE   8  65 232  34
D155V4, multiclass
    clus
vv   USP24 MUTATED USP24 WILD-TYPE
  T1             1               8
  T2             3              65
  T3            16             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
  USP24 MUTATED    18   5   5
  USP24 WILD-TYPE 202  75  61
D155V5, multiclass
    clus
vv   USP24 MUTATED USP24 WILD-TYPE
  N0            18             202
  N1             5              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"
D155V6, binary
                 cls
clus                0   1
  USP24 MUTATED    20   1
  USP24 WILD-TYPE 263  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP24 MUTATED     20    1
  USP24 WILD-TYPE  263   47
   clus
vv  USP24 MUTATED USP24 WILD-TYPE
  0            20             263
  1             1              47
[1] 2 2
[1] FALSE
D155V7, binary
                 cls
clus                0   1
  USP24 MUTATED    15  13
  USP24 WILD-TYPE 155 184
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP24 MUTATED     15   13
  USP24 WILD-TYPE  155  184
        clus
vv       USP24 MUTATED USP24 WILD-TYPE
  FEMALE            15             155
  MALE              13             184
[1] 2 2
[1] FALSE
D155V8, binary
                 cls
clus                0   1
  USP24 MUTATED    25   3
  USP24 WILD-TYPE 292  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP24 MUTATED     25    3
  USP24 WILD-TYPE  292   45
                               clus
vv                              USP24 MUTATED USP24 WILD-TYPE
  COLON ADENOCARCINOMA                     25             292
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  USP24 MUTATED    18   1   0   2
  USP24 WILD-TYPE 239   1  22  19
D155V9, multiclass
    clus
vv   USP24 MUTATED USP24 WILD-TYPE
  R0            18             239
  R1             1               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"
D155V10, 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    15
  USP24 WILD-TYPE                        15   161
D155V11, 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                                       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(156) Variable = FAM179A MUTATION ANALYSIS
D156V1, survival
                   sevent
clus2                 0   1
  FAM179A MUTATED    21   6
  FAM179A WILD-TYPE 261  67
  FAM179A MUTATED FAM179A WILD-TYPE 
               27               328 
  FAM179A MUTATED FAM179A WILD-TYPE 
                6                67 
$`FAM179A MUTATED`
TCGA-A6-3809 TCGA-A6-6137 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3949 TCGA-AA-3950 
       32.75        27.09        19.66        63.98        26.01        24.00 
TCGA-AA-3977 TCGA-AA-A01R TCGA-AD-5900 TCGA-AD-6889 TCGA-AY-6197 TCGA-AZ-4315 
       25.02        35.01         0.07        56.55        21.44        58.39 
TCGA-AZ-6598 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-6717 TCGA-CK-4952 TCGA-CK-5916 
       49.41         3.19         2.24         0.33        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        16.24        53.62 

$`FAM179A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       39.98        18.05        40.96        21.37         4.21         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
       11.74         1.94         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32        21.99         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        16.14         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        24.43        38.20        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       12.59       140.38        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K 
        6.12        81.37       119.93        35.97       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        13.38        13.45        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       29.59        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      107.67        74.56        65.85        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  FAM179A MUTATED FAM179A WILD-TYPE 
             0.07              0.00 
  FAM179A MUTATED FAM179A WILD-TYPE 
           130.65            140.38 
  FAM179A MUTATED FAM179A WILD-TYPE 
           23.050            20.005 
[1] "0.1 - 130.7 (23.1)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.1"
D156V2, 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       23        98         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM179A MUTATED           2          0          2          3        1
  FAM179A WILD-TYPE        17         10         39         28       34
                   vv
clus                STAGE IVA STAGE IVB
  FAM179A MUTATED           0         0
  FAM179A WILD-TYPE        13         1
D156V3, multiclass
            clus
vv           FAM179A MUTATED FAM179A WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 2                23
  STAGE IIA               11                98
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                2                17
  STAGE IIIA               0                10
  STAGE IIIB               2                39
  STAGE IIIC               3                28
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  FAM179A MUTATED     1   3  18   5
  FAM179A WILD-TYPE   8  65 230  36
D156V4, multiclass
    clus
vv   FAM179A MUTATED FAM179A WILD-TYPE
  T1               1                 8
  T2               3                65
  T3              18               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
  FAM179A MUTATED    19   3   5
  FAM179A WILD-TYPE 201  77  61
D156V5, multiclass
    clus
vv   FAM179A MUTATED FAM179A WILD-TYPE
  N0              19               201
  N1               3                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"
D156V6, binary
                   cls
clus                  0   1
  FAM179A MUTATED    21   1
  FAM179A WILD-TYPE 262  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM179A MUTATED     21    1
  FAM179A WILD-TYPE  262   47
   clus
vv  FAM179A MUTATED FAM179A WILD-TYPE
  0              21               262
  1               1                47
[1] 2 2
[1] FALSE
D156V7, 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
D156V8, binary
                   cls
clus                  0   1
  FAM179A MUTATED    19   8
  FAM179A WILD-TYPE 298  40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM179A MUTATED     19    8
  FAM179A WILD-TYPE  298   40
                               clus
vv                              FAM179A MUTATED FAM179A WILD-TYPE
  COLON ADENOCARCINOMA                       19               298
  COLON MUCINOUS ADENOCARCINOMA               8                40
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  FAM179A MUTATED    15   0   0   4
  FAM179A WILD-TYPE 242   2  22  17
D156V9, multiclass
    clus
vv   FAM179A MUTATED FAM179A WILD-TYPE
  R0              15               242
  R1               0                 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"
D156V10, 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
D156V11, 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(157) Variable = FAM9A MUTATION ANALYSIS
D157V1, survival
                 sevent
clus2               0   1
  FAM9A MUTATED     5   5
  FAM9A WILD-TYPE 277  68
  FAM9A MUTATED FAM9A WILD-TYPE 
             10             345 
  FAM9A MUTATED FAM9A WILD-TYPE 
              5              68 
$`FAM9A MUTATED`
TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3815 TCGA-AD-6964 TCGA-AZ-6598 TCGA-AZ-6601 
       20.12        19.66        33.04        10.88        49.41       100.01 
TCGA-AZ-6603 TCGA-CK-5913 TCGA-F4-6570 TCGA-G4-6588 
       29.56        51.32         6.18        26.17 

$`FAM9A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       23.87        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6605 
       22.36        62.79        61.41         6.77        12.10         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
       17.56       102.44        40.34        15.62        49.08        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  FAM9A MUTATED FAM9A WILD-TYPE 
           6.18            0.00 
  FAM9A MUTATED FAM9A WILD-TYPE 
         100.01          140.38 
  FAM9A MUTATED FAM9A WILD-TYPE 
         27.865          20.020 
[1] "6.2 - 100.0 (27.9)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.8"
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       23       103         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        19         10         41         30       35        13
                 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              23
  STAGE IIA              6             103
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FAM9A MUTATED     0   1   8   2
  FAM9A WILD-TYPE   9  67 240  39
D157V4, multiclass
    clus
vv   FAM9A MUTATED FAM9A WILD-TYPE
  T1             0               9
  T2             1              67
  T3             8             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
  FAM9A MUTATED     8   2   1
  FAM9A WILD-TYPE 212  78  65
D157V5, multiclass
    clus
vv   FAM9A MUTATED FAM9A WILD-TYPE
  N0             8             212
  N1             2              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"
D157V6, binary
                 cls
clus                0   1
  FAM9A MUTATED     5   0
  FAM9A WILD-TYPE 278  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FAM9A MUTATED      5    0
  FAM9A WILD-TYPE  278   48
   clus
vv  FAM9A MUTATED FAM9A WILD-TYPE
  0             5             278
  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     9   2
  FAM9A WILD-TYPE 308  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FAM9A MUTATED      9    2
  FAM9A WILD-TYPE  308   46
                               clus
vv                              FAM9A MUTATED FAM9A WILD-TYPE
  COLON ADENOCARCINOMA                      9             308
  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 252   2  22  20
D157V9, multiclass
    clus
vv   FAM9A MUTATED FAM9A WILD-TYPE
  R0             5             252
  R1             0               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"
D157V10, 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
D157V11, 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 = RBM44 MUTATION ANALYSIS
D158V1, survival
                 sevent
clus2               0   1
  RBM44 MUTATED    10   2
  RBM44 WILD-TYPE 272  71
  RBM44 MUTATED RBM44 WILD-TYPE 
             12             343 
  RBM44 MUTATED RBM44 WILD-TYPE 
              2              71 
$`RBM44 MUTATED`
TCGA-A6-6141 TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3672 TCGA-AA-3811 
        8.38        24.39        19.66        63.98         0.92        10.06 
TCGA-AA-A00N TCGA-AA-A010 TCGA-CA-6717 TCGA-CM-4746 TCGA-F4-6703 TCGA-G4-6588 
        4.01        34.98         0.33        37.02        35.87        26.17 

$`RBM44 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        19.04        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 
       52.80 

  RBM44 MUTATED RBM44 WILD-TYPE 
           0.33            0.00 
  RBM44 MUTATED RBM44 WILD-TYPE 
          63.98          140.38 
  RBM44 MUTATED RBM44 WILD-TYPE 
         22.025          20.190 
[1] "0.3 - 64.0 (22.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1"  
D158V2, 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       24       104         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        17         10         41         30       35        13
                 vv
clus              STAGE IVB
  RBM44 MUTATED           0
  RBM44 WILD-TYPE         1
D158V3, multiclass
            clus
vv           RBM44 MUTATED RBM44 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              5             104
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RBM44 MUTATED     0   2   8   3
  RBM44 WILD-TYPE   9  66 240  38
D158V4, multiclass
    clus
vv   RBM44 MUTATED RBM44 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             8             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
  RBM44 MUTATED    10   2   1
  RBM44 WILD-TYPE 210  78  65
D158V5, multiclass
    clus
vv   RBM44 MUTATED RBM44 WILD-TYPE
  N0            10             210
  N1             2              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"
D158V6, binary
                 cls
clus                0   1
  RBM44 MUTATED    12   0
  RBM44 WILD-TYPE 271  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM44 MUTATED     12    0
  RBM44 WILD-TYPE  271   48
   clus
vv  RBM44 MUTATED RBM44 WILD-TYPE
  0            12             271
  1             0              48
[1] 2 2
[1] FALSE
D158V7, 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
D158V8, binary
                 cls
clus                0   1
  RBM44 MUTATED    10   3
  RBM44 WILD-TYPE 307  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM44 MUTATED     10    3
  RBM44 WILD-TYPE  307   45
                               clus
vv                              RBM44 MUTATED RBM44 WILD-TYPE
  COLON ADENOCARCINOMA                     10             307
  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 247   2  22  20
D158V9, multiclass
    clus
vv   RBM44 MUTATED RBM44 WILD-TYPE
  R0            10             247
  R1             0               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"
D158V10, 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
D158V11, 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(159) Variable = KRT2 MUTATION ANALYSIS
D159V1, survival
                sevent
clus2              0   1
  KRT2 MUTATED    13   0
  KRT2 WILD-TYPE 269  73
  KRT2 MUTATED KRT2 WILD-TYPE 
            13            342 
  KRT2 MUTATED KRT2 WILD-TYPE 
             0             73 
$`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         0.33         1.35 
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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.09        32.71        27.09         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        0.10        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 
       15.12        17.85         4.80        17.13        12.49         7.53 
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-A0XD TCGA-DM-A0XF 
        1.51        12.00        11.38        10.26        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-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 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  KRT2 MUTATED KRT2 WILD-TYPE 
          0.33           0.00 
  KRT2 MUTATED KRT2 WILD-TYPE 
        119.70         140.38 
  KRT2 MUTATED KRT2 WILD-TYPE 
         16.14          20.98 
[1] "0.3 - 119.7 (16.1)" "0.0 - 140.4 (21.0)"
[1] "hr="     "2.6e+07"
D159V2, 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       24       101         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KRT2 MUTATED           0          1          0          1        0         1
  KRT2 WILD-TYPE        19          9         41         30       35        12
                vv
clus             STAGE IVB
  KRT2 MUTATED           0
  KRT2 WILD-TYPE         1
D159V3, multiclass
            clus
vv           KRT2 MUTATED KRT2 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             8            101
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            1              9
  STAGE IIIB            0             41
  STAGE IIIC            1             30
  STAGE IV              0             35
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 240  37
D159V4, multiclass
    clus
vv   KRT2 MUTATED KRT2 WILD-TYPE
  T1            0              9
  T2            2             66
  T3            8            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
  KRT2 MUTATED    11   3   0
  KRT2 WILD-TYPE 209  77  66
D159V5, multiclass
    clus
vv   KRT2 MUTATED KRT2 WILD-TYPE
  N0           11            209
  N1            3             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"
D159V6, binary
                cls
clus               0   1
  KRT2 MUTATED    12   1
  KRT2 WILD-TYPE 271  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRT2 MUTATED     12    1
  KRT2 WILD-TYPE  271   47
   clus
vv  KRT2 MUTATED KRT2 WILD-TYPE
  0           12            271
  1            1             47
[1] 2 2
[1] FALSE
D159V7, 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
D159V8, binary
                cls
clus               0   1
  KRT2 MUTATED    10   4
  KRT2 WILD-TYPE 307  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRT2 MUTATED     10    4
  KRT2 WILD-TYPE  307   44
                               clus
vv                              KRT2 MUTATED KRT2 WILD-TYPE
  COLON ADENOCARCINOMA                    10            307
  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 248   2  22  19
D159V9, multiclass
    clus
vv   KRT2 MUTATED KRT2 WILD-TYPE
  R0            9            248
  R1            0              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"
D159V10, 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
D159V11, 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(160) Variable = TNRC6C MUTATION ANALYSIS
D160V1, survival
                  sevent
clus2                0   1
  TNRC6C MUTATED    12   4
  TNRC6C WILD-TYPE 270  69
  TNRC6C MUTATED TNRC6C WILD-TYPE 
              16              339 
  TNRC6C MUTATED TNRC6C WILD-TYPE 
               4               69 
$`TNRC6C MUTATED`
TCGA-A6-3809 TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3815 TCGA-AA-3845 TCGA-AA-3950 
       32.75        22.06         3.02        33.04         0.00        24.00 
TCGA-AA-3966 TCGA-AA-A01P TCGA-AD-5900 TCGA-AU-6004 TCGA-AY-6197 TCGA-CA-6717 
        2.01        38.07         0.07        27.09        21.44         0.33 
TCGA-CK-5913 TCGA-CM-6171 TCGA-F4-6570 TCGA-F4-6856 
       51.32        14.04         6.18        19.43 

$`TNRC6C WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02        14.93        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       26.01         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.20        14.50        16.31         0.95        15.75         0.20 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 
       33.67        13.25         0.53        35.41       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  TNRC6C MUTATED TNRC6C WILD-TYPE 
               0                0 
  TNRC6C MUTATED TNRC6C WILD-TYPE 
           51.32           140.38 
  TNRC6C MUTATED TNRC6C WILD-TYPE 
          20.435           20.190 
[1] "0.0 - 51.3 (20.4)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.7"
D160V2, 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       24        99         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TNRC6C MUTATED           1          0          0          0        0
  TNRC6C WILD-TYPE        18         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  TNRC6C MUTATED           0         0
  TNRC6C WILD-TYPE        13         1
D160V3, multiclass
            clus
vv           TNRC6C MUTATED TNRC6C WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA              10               99
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TNRC6C MUTATED     0   4  12   2
  TNRC6C WILD-TYPE   9  64 236  39
D160V4, multiclass
    clus
vv   TNRC6C MUTATED TNRC6C WILD-TYPE
  T1              0                9
  T2              4               64
  T3             12              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
  TNRC6C MUTATED    17   1   0
  TNRC6C WILD-TYPE 203  79  66
D160V5, multiclass
    clus
vv   TNRC6C MUTATED TNRC6C WILD-TYPE
  N0             17              203
  N1              1               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"
D160V6, binary
                  cls
clus                 0   1
  TNRC6C MUTATED    14   0
  TNRC6C WILD-TYPE 269  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNRC6C MUTATED     14    0
  TNRC6C WILD-TYPE  269   48
   clus
vv  TNRC6C MUTATED TNRC6C WILD-TYPE
  0             14              269
  1              0               48
[1] 2 2
[1] FALSE
D160V7, 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
D160V8, binary
                  cls
clus                 0   1
  TNRC6C MUTATED    12   6
  TNRC6C WILD-TYPE 305  42
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNRC6C MUTATED     12    6
  TNRC6C WILD-TYPE  305   42
                               clus
vv                              TNRC6C MUTATED TNRC6C WILD-TYPE
  COLON ADENOCARCINOMA                      12              305
  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 243   2  22  18
D160V9, multiclass
    clus
vv   TNRC6C MUTATED TNRC6C WILD-TYPE
  R0             14              243
  R1              0                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"
D160V10, 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
D160V11, 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(161) Variable = ZNF583 MUTATION ANALYSIS
D161V1, survival
                  sevent
clus2                0   1
  ZNF583 MUTATED    13   2
  ZNF583 WILD-TYPE 269  71
  ZNF583 MUTATED ZNF583 WILD-TYPE 
              15              340 
  ZNF583 MUTATED ZNF583 WILD-TYPE 
               2               71 
$`ZNF583 MUTATED`
TCGA-A6-6138 TCGA-AA-3939 TCGA-AA-3977 TCGA-AA-A00O TCGA-AA-A010 TCGA-AD-5900 
       22.52        12.99        25.02        27.02        34.98         0.07 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CK-4952 TCGA-CK-5913 
        0.72        10.88        58.39         0.33        15.62        51.32 
TCGA-CM-5862 TCGA-CM-5868 TCGA-DM-A1HB 
        5.03        17.03       135.65 

$`ZNF583 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        32.71        27.09         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21        56.55         0.79         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        21.99        21.14         2.93         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        16.01        15.02        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  ZNF583 MUTATED ZNF583 WILD-TYPE 
            0.07             0.00 
  ZNF583 MUTATED ZNF583 WILD-TYPE 
          135.65           140.38 
  ZNF583 MUTATED ZNF583 WILD-TYPE 
          17.030           20.235 
[1] "0.1 - 135.7 (17.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.6"
D161V2, 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       25       105         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF583 MUTATED           1          0          1          1        0
  ZNF583 WILD-TYPE        18         10         40         30       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF583 MUTATED           2         0
  ZNF583 WILD-TYPE        11         1
D161V3, multiclass
            clus
vv           ZNF583 MUTATED ZNF583 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               4              105
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               2               11
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  65 240  37
D161V4, multiclass
    clus
vv   ZNF583 MUTATED ZNF583 WILD-TYPE
  T1              0                9
  T2              3               65
  T3              8              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
  ZNF583 MUTATED     8   4   3
  ZNF583 WILD-TYPE 212  76  63
D161V5, multiclass
    clus
vv   ZNF583 MUTATED ZNF583 WILD-TYPE
  N0              8              212
  N1              4               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"
D161V6, binary
                  cls
clus                 0   1
  ZNF583 MUTATED     8   2
  ZNF583 WILD-TYPE 275  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF583 MUTATED      8    2
  ZNF583 WILD-TYPE  275   46
   clus
vv  ZNF583 MUTATED ZNF583 WILD-TYPE
  0              8              275
  1              2               46
[1] 2 2
[1] FALSE
D161V7, 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
D161V8, binary
                  cls
clus                 0   1
  ZNF583 MUTATED    12   3
  ZNF583 WILD-TYPE 305  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF583 MUTATED     12    3
  ZNF583 WILD-TYPE  305   45
                               clus
vv                              ZNF583 MUTATED ZNF583 WILD-TYPE
  COLON ADENOCARCINOMA                      12              305
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF583 MUTATED     7   0   0   3
  ZNF583 WILD-TYPE 250   2  22  18
D161V9, multiclass
    clus
vv   ZNF583 MUTATED ZNF583 WILD-TYPE
  R0              7              250
  R1              0                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"
D161V10, 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
D161V11, 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(162) Variable = PRRG1 MUTATION ANALYSIS
D162V1, survival
                 sevent
clus2               0   1
  PRRG1 MUTATED     9   2
  PRRG1 WILD-TYPE 273  71
  PRRG1 MUTATED PRRG1 WILD-TYPE 
             11             344 
  PRRG1 MUTATED PRRG1 WILD-TYPE 
              2              71 
$`PRRG1 MUTATED`
TCGA-A6-5661 TCGA-AD-5900 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-5913 TCGA-CM-6162 
       33.53         0.07        49.41         0.33        51.32        12.00 
TCGA-CM-6171 TCGA-D5-5538 TCGA-DM-A28K TCGA-G4-6303 TCGA-G4-6586 
       14.04        12.26        98.24        65.85        35.80 

$`PRRG1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13        83.80        22.36        62.79        61.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        21.99        21.14         2.93         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        16.01        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        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       35.97        60.79       117.07         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  PRRG1 MUTATED PRRG1 WILD-TYPE 
           0.07            0.00 
  PRRG1 MUTATED PRRG1 WILD-TYPE 
          98.24          140.38 
  PRRG1 MUTATED PRRG1 WILD-TYPE 
         33.530          20.155 
[1] "0.1 - 98.2 (33.5)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.6"
D162V2, 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       24       104         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        19         10         39         31       34        13
                 vv
clus              STAGE IVB
  PRRG1 MUTATED           0
  PRRG1 WILD-TYPE         1
D162V3, multiclass
            clus
vv           PRRG1 MUTATED PRRG1 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              5             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PRRG1 MUTATED     0   2   9   0
  PRRG1 WILD-TYPE   9  66 239  41
D162V4, multiclass
    clus
vv   PRRG1 MUTATED PRRG1 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             9             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
  PRRG1 MUTATED     8   3   0
  PRRG1 WILD-TYPE 212  77  66
D162V5, multiclass
    clus
vv   PRRG1 MUTATED PRRG1 WILD-TYPE
  N0             8             212
  N1             3              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"
D162V6, binary
                 cls
clus                0   1
  PRRG1 MUTATED     7   1
  PRRG1 WILD-TYPE 276  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRRG1 MUTATED      7    1
  PRRG1 WILD-TYPE  276   47
   clus
vv  PRRG1 MUTATED PRRG1 WILD-TYPE
  0             7             276
  1             1              47
[1] 2 2
[1] FALSE
D162V7, 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
D162V8, binary
                 cls
clus                0   1
  PRRG1 MUTATED     7   4
  PRRG1 WILD-TYPE 310  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRRG1 MUTATED      7    4
  PRRG1 WILD-TYPE  310   44
                               clus
vv                              PRRG1 MUTATED PRRG1 WILD-TYPE
  COLON ADENOCARCINOMA                      7             310
  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 250   2  22  19
D162V9, multiclass
    clus
vv   PRRG1 MUTATED PRRG1 WILD-TYPE
  R0             7             250
  R1             0               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"
D162V10, 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
D162V11, 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(163) Variable = RGS22 MUTATION ANALYSIS
D163V1, survival
                 sevent
clus2               0   1
  RGS22 MUTATED    20   4
  RGS22 WILD-TYPE 262  69
  RGS22 MUTATED RGS22 WILD-TYPE 
             24             331 
  RGS22 MUTATED RGS22 WILD-TYPE 
              4              69 
$`RGS22 MUTATED`
TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3713 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6895 
       22.06        63.98        19.04         4.01        34.98         0.72 
TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4952 
       27.09        58.39        49.41         0.33         0.10        15.62 
TCGA-CK-5913 TCGA-CM-5348 TCGA-CM-6172 TCGA-D5-6536 TCGA-D5-6930 TCGA-DM-A1D6 
       51.32        22.98        11.01        17.85         1.51        49.91 
TCGA-DM-A1HA TCGA-DM-A28G TCGA-F4-6569 TCGA-G4-6309 TCGA-G4-6586 TCGA-G4-6628 
      131.51        60.79        13.45        51.75        35.80        52.80 

$`RGS22 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
        0.07        21.37         4.21        56.55         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13        83.80        22.36        62.79        61.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 
        0.26         1.35        17.56       102.44        40.34        49.08 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 
       20.19        18.25         1.32        43.27        15.12         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         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-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-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
      119.93        35.97       117.07        98.24         8.61        13.38 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       74.56        65.85        53.62        44.68        55.04        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        26.17        91.79 
TCGA-G4-6626 
       46.75 

  RGS22 MUTATED RGS22 WILD-TYPE 
            0.1             0.0 
  RGS22 MUTATED RGS22 WILD-TYPE 
         131.51          140.38 
  RGS22 MUTATED RGS22 WILD-TYPE 
         25.035          20.020 
[1] "0.1 - 131.5 (25.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.7"
D163V2, 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       23        99         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RGS22 MUTATED           1          0          3          1        1         0
  RGS22 WILD-TYPE        18         10         38         30       34        13
                 vv
clus              STAGE IVB
  RGS22 MUTATED           0
  RGS22 WILD-TYPE         1
D163V3, multiclass
            clus
vv           RGS22 MUTATED RGS22 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA             10              99
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             3              38
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RGS22 MUTATED     0   3  18   3
  RGS22 WILD-TYPE   9  65 230  38
D163V4, multiclass
    clus
vv   RGS22 MUTATED RGS22 WILD-TYPE
  T1             0               9
  T2             3              65
  T3            18             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
  RGS22 MUTATED    18   4   2
  RGS22 WILD-TYPE 202  76  64
D163V5, multiclass
    clus
vv   RGS22 MUTATED RGS22 WILD-TYPE
  N0            18             202
  N1             4              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"
D163V6, binary
                 cls
clus                0   1
  RGS22 MUTATED    20   1
  RGS22 WILD-TYPE 263  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RGS22 MUTATED     20    1
  RGS22 WILD-TYPE  263   47
   clus
vv  RGS22 MUTATED RGS22 WILD-TYPE
  0            20             263
  1             1              47
[1] 2 2
[1] FALSE
D163V7, 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
D163V8, binary
                 cls
clus                0   1
  RGS22 MUTATED    19   5
  RGS22 WILD-TYPE 298  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RGS22 MUTATED     19    5
  RGS22 WILD-TYPE  298   43
                               clus
vv                              RGS22 MUTATED RGS22 WILD-TYPE
  COLON ADENOCARCINOMA                     19             298
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RGS22 MUTATED    14   0   1   4
  RGS22 WILD-TYPE 243   2  21  17
D163V9, multiclass
    clus
vv   RGS22 MUTATED RGS22 WILD-TYPE
  R0            14             243
  R1             0               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"
D163V10, 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
D163V11, 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(164) Variable = RB1 MUTATION ANALYSIS
D164V1, survival
               sevent
clus2             0   1
  RB1 MUTATED    71  16
  RB1 WILD-TYPE 211  57
  RB1 MUTATED RB1 WILD-TYPE 
           87           268 
  RB1 MUTATED RB1 WILD-TYPE 
           16            57 
$`RB1 MUTATED`
TCGA-A6-4105 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6141 
       14.53        33.53        23.61        22.06        32.71         8.38 
TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6780 TCGA-AA-3496 TCGA-AA-3502 
       25.08        24.16        24.69        20.12         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
       63.98        61.02         6.05        85.05        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3968 TCGA-AA-A010 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6901 
       10.06        21.99        34.98        56.55         0.72        22.42 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-6197 TCGA-AZ-4323 TCGA-AZ-6598 TCGA-AZ-6599 
       14.50        27.09        21.44         1.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6719 
       12.10       100.01        29.56         3.29         0.33         1.35 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CM-4743 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       40.34        15.62        23.05        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-6161 TCGA-CM-6162 
       22.03        22.98        30.08        16.01        15.02        12.00 
TCGA-CM-6165 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6678 
       16.04        13.02        14.04        11.01        12.95        11.01 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       12.26        19.59        18.25         1.32        43.27        15.12 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6923 TCGA-D5-6927 TCGA-D5-6932 
       12.49        16.14         7.53        12.43         9.44        11.38 
TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A1D4 TCGA-DM-A1HB TCGA-DM-A28C TCGA-DM-A28F 
       10.26        24.43        92.75       135.65        81.37        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6570 TCGA-F4-6806 TCGA-G4-6293 TCGA-G4-6299 
       60.79       117.07         6.18        29.59       107.67        74.56 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       53.62        44.68        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       35.80        26.17        91.79 

$`RB1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5664 TCGA-A6-6137 TCGA-A6-6138 
       31.63        30.44        29.19        22.09        27.09        22.52 
TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 
       25.18        21.76        24.39        23.87        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        7.04         3.02         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       19.99        13.94        19.99        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       26.99        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03         2.01        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37         4.21         0.79 
TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-4071 
        5.79        27.42        10.88         0.20        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4616 TCGA-AZ-4681 
       15.75         0.20        17.82        58.39         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       22.36        62.79        61.41         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 
        1.94         2.24         3.06         3.25         0.07         0.26 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
        0.10        17.56       102.44        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14         2.93         2.01       124.27        20.02        37.02 
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-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6675 
       29.03        21.99        14.99        12.99        15.02        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5540 
       11.08        11.08        10.06        12.03        45.40        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6541 
       11.51        20.19        17.85         4.80        17.13        15.58 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 
       12.39        10.13        14.30         9.04        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 
        1.51        12.00       119.70        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-A282 TCGA-DM-A285 TCGA-DM-A28E TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
      139.17         6.12       119.93        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 
       13.45        35.87         1.55        16.31        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6303 TCGA-G4-6307 
       13.25         0.53        35.41        19.43        65.85        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6626 TCGA-G4-6628 
       51.75        45.11        46.75        52.80 

  RB1 MUTATED RB1 WILD-TYPE 
         0.33          0.00 
  RB1 MUTATED RB1 WILD-TYPE 
       135.65        140.38 
  RB1 MUTATED RB1 WILD-TYPE 
        22.03         19.99 
[1] "0.3 - 135.7 (22.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.4"
D164V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RB1 MUTATED        11        1        6        31         2         1
  RB1 WILD-TYPE      53        0       19        78         6         0
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RB1 MUTATED           5          4         10          3        5         5
  RB1 WILD-TYPE        14          6         31         28       30         8
               vv
clus            STAGE IVB
  RB1 MUTATED           0
  RB1 WILD-TYPE         1
D164V3, multiclass
            clus
vv           RB1 MUTATED RB1 WILD-TYPE
  STAGE I             11            53
  STAGE IA             1             0
  STAGE II             6            19
  STAGE IIA           31            78
  STAGE IIB            2             6
  STAGE IIC            1             0
  STAGE III            5            14
  STAGE IIIA           4             6
  STAGE IIIB          10            31
  STAGE IIIC           3            28
  STAGE IV             5            30
  STAGE IVA            5             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
  RB1 MUTATED     0  15  61  10
  RB1 WILD-TYPE   9  53 187  31
D164V4, multiclass
    clus
vv   RB1 MUTATED RB1 WILD-TYPE
  T1           0             9
  T2          15            53
  T3          61           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    58  21   8
  RB1 WILD-TYPE 162  59  58
D164V5, multiclass
    clus
vv   RB1 MUTATED RB1 WILD-TYPE
  N0          58           162
  N1          21            59
  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"
D164V6, binary
               cls
clus              0   1
  RB1 MUTATED    66  10
  RB1 WILD-TYPE 217  38
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED     66   10
  RB1 WILD-TYPE  217   38
   clus
vv  RB1 MUTATED RB1 WILD-TYPE
  0          66           217
  1          10            38
[1] 2 2
[1] FALSE
D164V7, binary
               cls
clus              0   1
  RB1 MUTATED    38  49
  RB1 WILD-TYPE 132 148
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED     38   49
  RB1 WILD-TYPE  132  148
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  FEMALE          38           132
  MALE            49           148
[1] 2 2
[1] FALSE
D164V8, binary
               cls
clus              0   1
  RB1 MUTATED    79   8
  RB1 WILD-TYPE 238  40
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED     79    8
  RB1 WILD-TYPE  238   40
                               clus
vv                              RB1 MUTATED RB1 WILD-TYPE
  COLON ADENOCARCINOMA                   79           238
  COLON MUCINOUS ADENOCARCINOMA           8            40
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  RB1 MUTATED    56   1   2   4
  RB1 WILD-TYPE 201   1  20  17
D164V9, multiclass
    clus
vv   RB1 MUTATED RB1 WILD-TYPE
  R0          56           201
  R1           1             1
  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"
D164V10, 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    64
  RB1 WILD-TYPE                        11   112
D164V11, 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                                     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(165) Variable = TFE3 MUTATION ANALYSIS
D165V1, survival
                sevent
clus2              0   1
  TFE3 MUTATED    11   0
  TFE3 WILD-TYPE 271  73
  TFE3 MUTATED TFE3 WILD-TYPE 
            11            344 
  TFE3 MUTATED TFE3 WILD-TYPE 
             0             73 
$`TFE3 MUTATED`
TCGA-AA-3532 TCGA-AA-3710 TCGA-AA-3947 TCGA-AD-6889 TCGA-AY-6197 TCGA-CK-5913 
       29.00        26.99        33.01        56.55        21.44        51.32 
TCGA-CM-6171 TCGA-D5-6920 TCGA-D5-6928 TCGA-F4-6703 TCGA-G4-6588 
       14.04        12.39        11.64        35.87        26.17 

$`TFE3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37         4.21         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58         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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  TFE3 MUTATED TFE3 WILD-TYPE 
         11.64           0.00 
  TFE3 MUTATED TFE3 WILD-TYPE 
         56.55         140.38 
  TFE3 MUTATED TFE3 WILD-TYPE 
        26.990         20.005 
[1] "11.6 - 56.5 (27.0)" "0.0 - 140.4 (20.0)"
[1] "hr="     "2.6e+07"
D165V2, 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       25       100         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        19         10         41         31       35        13
                vv
clus             STAGE IVB
  TFE3 MUTATED           0
  TFE3 WILD-TYPE         1
D165V3, multiclass
            clus
vv           TFE3 MUTATED TFE3 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             9            100
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TFE3 MUTATED     0   1   9   1
  TFE3 WILD-TYPE   9  67 239  40
D165V4, multiclass
    clus
vv   TFE3 MUTATED TFE3 WILD-TYPE
  T1            0              9
  T2            1             67
  T3            9            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
  TFE3 MUTATED    11   0   0
  TFE3 WILD-TYPE 209  80  66
D165V5, multiclass
    clus
vv   TFE3 MUTATED TFE3 WILD-TYPE
  N0           11            209
  N1            0             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"
D165V6, binary
                cls
clus               0   1
  TFE3 MUTATED     9   0
  TFE3 WILD-TYPE 274  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  TFE3 MUTATED      9    0
  TFE3 WILD-TYPE  274   48
   clus
vv  TFE3 MUTATED TFE3 WILD-TYPE
  0            9            274
  1            0             48
[1] 2 2
[1] FALSE
D165V7, 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
D165V8, binary
                cls
clus               0   1
  TFE3 MUTATED     9   2
  TFE3 WILD-TYPE 308  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  TFE3 MUTATED      9    2
  TFE3 WILD-TYPE  308   46
                               clus
vv                              TFE3 MUTATED TFE3 WILD-TYPE
  COLON ADENOCARCINOMA                     9            308
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TFE3 MUTATED     9   0   0   1
  TFE3 WILD-TYPE 248   2  22  20
D165V9, multiclass
    clus
vv   TFE3 MUTATED TFE3 WILD-TYPE
  R0            9            248
  R1            0              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"
D165V10, 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
D165V11, 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(166) Variable = AKR1C4 MUTATION ANALYSIS
D166V1, survival
                  sevent
clus2                0   1
  AKR1C4 MUTATED     7   2
  AKR1C4 WILD-TYPE 275  71
  AKR1C4 MUTATED AKR1C4 WILD-TYPE 
               9              346 
  AKR1C4 MUTATED AKR1C4 WILD-TYPE 
               2               71 
$`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         0.10        40.34        15.12 
TCGA-DM-A0XF TCGA-F4-6809 TCGA-G4-6306 
       38.20        13.25        44.68 

$`AKR1C4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        61.02         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04         4.01        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 
        0.26         0.33         1.35        17.56       102.44        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 
       12.00        11.38        10.26       119.70        24.43       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       29.59        16.24        33.67         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 
      107.67        74.56        65.85        53.62        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  AKR1C4 MUTATED AKR1C4 WILD-TYPE 
             0.1              0.0 
  AKR1C4 MUTATED AKR1C4 WILD-TYPE 
           78.08           140.38 
  AKR1C4 MUTATED AKR1C4 WILD-TYPE 
           35.01            20.07 
[1] "0.1 - 78.1 (35.0)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.1"
D166V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AKR1C4 MUTATED         0        0        1         2         0         0
  AKR1C4 WILD-TYPE      64        1       24       107         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AKR1C4 MUTATED           1          1          1          2        0
  AKR1C4 WILD-TYPE        18          9         40         29       35
                  vv
clus               STAGE IVA STAGE IVB
  AKR1C4 MUTATED           1         0
  AKR1C4 WILD-TYPE        12         1
D166V3, multiclass
            clus
vv           AKR1C4 MUTATED AKR1C4 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               2              107
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              1                9
  STAGE IIIB              1               40
  STAGE IIIC              2               29
  STAGE IV                0               35
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 240  41
D166V4, multiclass
    clus
vv   AKR1C4 MUTATED AKR1C4 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              8              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
  AKR1C4 MUTATED     3   3   3
  AKR1C4 WILD-TYPE 217  77  63
D166V5, multiclass
    clus
vv   AKR1C4 MUTATED AKR1C4 WILD-TYPE
  N0              3              217
  N1              3               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"
D166V6, binary
                  cls
clus                 0   1
  AKR1C4 MUTATED     7   1
  AKR1C4 WILD-TYPE 276  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKR1C4 MUTATED      7    1
  AKR1C4 WILD-TYPE  276   47
   clus
vv  AKR1C4 MUTATED AKR1C4 WILD-TYPE
  0              7              276
  1              1               47
[1] 2 2
[1] FALSE
D166V7, 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
D166V8, binary
                  cls
clus                 0   1
  AKR1C4 MUTATED     7   2
  AKR1C4 WILD-TYPE 310  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKR1C4 MUTATED      7    2
  AKR1C4 WILD-TYPE  310   46
                               clus
vv                              AKR1C4 MUTATED AKR1C4 WILD-TYPE
  COLON ADENOCARCINOMA                       7              310
  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 252   1  22  19
D166V9, multiclass
    clus
vv   AKR1C4 MUTATED AKR1C4 WILD-TYPE
  R0              5              252
  R1              1                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"
D166V10, 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
D166V11, 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(167) Variable = OR52A4 MUTATION ANALYSIS
D167V1, survival
                  sevent
clus2                0   1
  OR52A4 MUTATED     9   0
  OR52A4 WILD-TYPE 273  73
  OR52A4 MUTATED OR52A4 WILD-TYPE 
               9              346 
  OR52A4 MUTATED OR52A4 WILD-TYPE 
               0               73 
$`OR52A4 MUTATED`
TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-3861 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-6171 
       22.06        20.12        30.05        23.05        37.02        14.04 
TCGA-D5-6898 TCGA-G4-6304 TCGA-G4-6586 
        7.53        53.62        35.80 

$`OR52A4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 
        2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       16.14        15.58        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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 
       19.43       107.67        74.56        65.85        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  OR52A4 MUTATED OR52A4 WILD-TYPE 
            7.53             0.00 
  OR52A4 MUTATED OR52A4 WILD-TYPE 
           53.62           140.38 
  OR52A4 MUTATED OR52A4 WILD-TYPE 
          23.050           20.005 
[1] "7.5 - 53.6 (23.1)"  "0.0 - 140.4 (20.0)"
[1] "hr="     "9300000"
D167V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR52A4 MUTATED         3        0        0         5         1         0
  OR52A4 WILD-TYPE      61        1       25       104         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR52A4 MUTATED           0          0          0          0        0
  OR52A4 WILD-TYPE        19         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  OR52A4 MUTATED           0         0
  OR52A4 WILD-TYPE        13         1
D167V3, multiclass
            clus
vv           OR52A4 MUTATED OR52A4 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               5              104
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  OR52A4 MUTATED     0   3   5   1
  OR52A4 WILD-TYPE   9  65 243  40
D167V4, multiclass
    clus
vv   OR52A4 MUTATED OR52A4 WILD-TYPE
  T1              0                9
  T2              3               65
  T3              5              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
  OR52A4 MUTATED     9   0   0
  OR52A4 WILD-TYPE 211  80  66
D167V5, multiclass
    clus
vv   OR52A4 MUTATED OR52A4 WILD-TYPE
  N0              9              211
  N1              0               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"
D167V6, binary
                  cls
clus                 0   1
  OR52A4 MUTATED     8   0
  OR52A4 WILD-TYPE 275  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR52A4 MUTATED      8    0
  OR52A4 WILD-TYPE  275   48
   clus
vv  OR52A4 MUTATED OR52A4 WILD-TYPE
  0              8              275
  1              0               48
[1] 2 2
[1] FALSE
D167V7, binary
                  cls
clus                 0   1
  OR52A4 MUTATED     5   4
  OR52A4 WILD-TYPE 165 193
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR52A4 MUTATED      5    4
  OR52A4 WILD-TYPE  165  193
        clus
vv       OR52A4 MUTATED OR52A4 WILD-TYPE
  FEMALE              5              165
  MALE                4              193
[1] 2 2
[1] FALSE
D167V8, binary
                  cls
clus                 0   1
  OR52A4 MUTATED     8   1
  OR52A4 WILD-TYPE 309  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR52A4 MUTATED      8    1
  OR52A4 WILD-TYPE  309   47
                               clus
vv                              OR52A4 MUTATED OR52A4 WILD-TYPE
  COLON ADENOCARCINOMA                       8              309
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  OR52A4 MUTATED     8   0   0   0
  OR52A4 WILD-TYPE 249   2  22  21
D167V9, multiclass
    clus
vv   OR52A4 MUTATED OR52A4 WILD-TYPE
  R0              8              249
  R1              0                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"
D167V10, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR52A4 MUTATED                                  0     0
  OR52A4 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  OR52A4 MUTATED                           1     7
  OR52A4 WILD-TYPE                        18   169
D167V11, multiclass
                                  clus
vv                                 OR52A4 MUTATED OR52A4 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(168) Variable = TIAL1 MUTATION ANALYSIS
D168V1, survival
                 sevent
clus2               0   1
  TIAL1 MUTATED     8   3
  TIAL1 WILD-TYPE 274  70
  TIAL1 MUTATED TIAL1 WILD-TYPE 
             11             344 
  TIAL1 MUTATED TIAL1 WILD-TYPE 
              3              70 
$`TIAL1 MUTATED`
TCGA-AA-3663 TCGA-AA-3715 TCGA-AA-3864 TCGA-AA-A00J TCGA-AZ-6599 TCGA-CA-6718 
        6.97        19.04        53.00        18.05         6.77         0.10 
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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41        49.41        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        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-6676 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        12.95        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        7.53        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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  TIAL1 MUTATED TIAL1 WILD-TYPE 
            0.1             0.0 
  TIAL1 MUTATED TIAL1 WILD-TYPE 
         135.65          140.38 
  TIAL1 MUTATED TIAL1 WILD-TYPE 
         12.390          20.995 
[1] "0.1 - 135.7 (12.4)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.4"
D168V2, 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       22       106         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        19         10         39         31       35        12
                 vv
clus              STAGE IVB
  TIAL1 MUTATED           1
  TIAL1 WILD-TYPE         0
D168V3, multiclass
            clus
vv           TIAL1 MUTATED TIAL1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              3             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              1              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
  TIAL1 MUTATED     0   1   9   2
  TIAL1 WILD-TYPE   9  67 239  39
D168V4, multiclass
    clus
vv   TIAL1 MUTATED TIAL1 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             9             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
  TIAL1 MUTATED     8   3   1
  TIAL1 WILD-TYPE 212  77  65
D168V5, multiclass
    clus
vv   TIAL1 MUTATED TIAL1 WILD-TYPE
  N0             8             212
  N1             3              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"
D168V6, binary
                 cls
clus                0   1
  TIAL1 MUTATED     8   2
  TIAL1 WILD-TYPE 275  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TIAL1 MUTATED      8    2
  TIAL1 WILD-TYPE  275   46
   clus
vv  TIAL1 MUTATED TIAL1 WILD-TYPE
  0             8             275
  1             2              46
[1] 2 2
[1] FALSE
D168V7, 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
D168V8, binary
                 cls
clus                0   1
  TIAL1 MUTATED    10   2
  TIAL1 WILD-TYPE 307  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TIAL1 MUTATED     10    2
  TIAL1 WILD-TYPE  307   46
                               clus
vv                              TIAL1 MUTATED TIAL1 WILD-TYPE
  COLON ADENOCARCINOMA                     10             307
  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 249   2  22  19
D168V9, multiclass
    clus
vv   TIAL1 MUTATED TIAL1 WILD-TYPE
  R0             8             249
  R1             0               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"
D168V10, 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
D168V11, 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(169) Variable = HNF1B MUTATION ANALYSIS
D169V1, survival
                 sevent
clus2               0   1
  HNF1B MUTATED     7   2
  HNF1B WILD-TYPE 275  71
  HNF1B MUTATED HNF1B WILD-TYPE 
              9             346 
  HNF1B MUTATED HNF1B WILD-TYPE 
              2              71 
$`HNF1B MUTATED`
TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-6141 TCGA-AA-3819 TCGA-AD-6889 TCGA-AD-6899 
       14.53        32.91         8.38        25.02        56.55         5.79 
TCGA-AD-6965 TCGA-D5-6540 TCGA-G4-6586 
        0.20        16.14        35.80 

$`HNF1B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5657 
       16.57        34.65        33.34        32.75        36.53        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       32.71        27.09        22.52        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       33.04         0.99         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37         4.21         0.79         0.72 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        10.88        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  HNF1B MUTATED HNF1B WILD-TYPE 
            0.2             0.0 
  HNF1B MUTATED HNF1B WILD-TYPE 
          56.55          140.38 
  HNF1B MUTATED HNF1B WILD-TYPE 
         16.140          20.235 
[1] "0.2 - 56.5 (16.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.3"
D169V2, 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       25       104         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HNF1B MUTATED           0          0          0          1        0         0
  HNF1B WILD-TYPE        19         10         41         30       35        13
                 vv
clus              STAGE IVB
  HNF1B MUTATED           0
  HNF1B WILD-TYPE         1
D169V3, multiclass
            clus
vv           HNF1B MUTATED HNF1B WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              5             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HNF1B MUTATED     0   2   5   2
  HNF1B WILD-TYPE   9  66 243  39
D169V4, multiclass
    clus
vv   HNF1B MUTATED HNF1B WILD-TYPE
  T1             0               9
  T2             2              66
  T3             5             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
  HNF1B MUTATED     7   0   2
  HNF1B WILD-TYPE 213  80  64
D169V5, multiclass
    clus
vv   HNF1B MUTATED HNF1B WILD-TYPE
  N0             7             213
  N1             0              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"
D169V6, binary
                 cls
clus                0   1
  HNF1B MUTATED     7   0
  HNF1B WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HNF1B MUTATED      7    0
  HNF1B WILD-TYPE  276   48
   clus
vv  HNF1B MUTATED HNF1B WILD-TYPE
  0             7             276
  1             0              48
[1] 2 2
[1] FALSE
D169V7, 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
D169V8, binary
                 cls
clus                0   1
  HNF1B MUTATED     7   2
  HNF1B WILD-TYPE 310  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HNF1B MUTATED      7    2
  HNF1B WILD-TYPE  310   46
                               clus
vv                              HNF1B MUTATED HNF1B WILD-TYPE
  COLON ADENOCARCINOMA                      7             310
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  HNF1B MUTATED     3   0   0   0
  HNF1B WILD-TYPE 254   2  22  21
D169V9, multiclass
    clus
vv   HNF1B MUTATED HNF1B WILD-TYPE
  R0             3             254
  R1             0               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"
D169V10, 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
D169V11, 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(170) Variable = PSD MUTATION ANALYSIS
D170V1, survival
               sevent
clus2             0   1
  PSD MUTATED    11   4
  PSD WILD-TYPE 271  69
  PSD MUTATED PSD WILD-TYPE 
           15           340 
  PSD MUTATED PSD WILD-TYPE 
            4            69 
$`PSD MUTATED`
TCGA-A6-5665 TCGA-AA-3516 TCGA-AA-3663 TCGA-AA-3696 TCGA-AA-3815 TCGA-AA-A00E 
       22.06        13.02         6.97         5.03        33.04        30.02 
TCGA-AZ-4315 TCGA-AZ-4681 TCGA-CA-6717 TCGA-CK-5913 TCGA-CK-5916 TCGA-CM-5860 
       58.39        83.80         0.33        51.32        21.14        16.01 
TCGA-D5-6540 TCGA-DM-A1D8 TCGA-G4-6309 
       16.14        12.59        51.75 

$`PSD WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       11.01         5.98        37.05        19.00        36.00        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J 
       27.02        13.94        38.04        19.00        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         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        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       40.34        15.62        49.08        21.99         2.93         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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        49.91        13.32       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  PSD MUTATED PSD WILD-TYPE 
         0.33          0.00 
  PSD MUTATED PSD WILD-TYPE 
        83.80        140.38 
  PSD MUTATED PSD WILD-TYPE 
       21.140        20.155 
[1] "0.3 - 83.8 (21.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D170V2, 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       23       101         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        18         10         40         31       34        13
               vv
clus            STAGE IVB
  PSD MUTATED           0
  PSD WILD-TYPE         1
D170V3, multiclass
            clus
vv           PSD MUTATED PSD WILD-TYPE
  STAGE I              2            62
  STAGE IA             0             1
  STAGE II             2            23
  STAGE IIA            8           101
  STAGE IIB            0             8
  STAGE IIC            0             1
  STAGE III            1            18
  STAGE IIIA           0            10
  STAGE IIIB           1            40
  STAGE IIIC           0            31
  STAGE IV             1            34
  STAGE IVA            0            13
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  PSD MUTATED     1   1  13   1
  PSD WILD-TYPE   8  67 235  40
D170V4, multiclass
    clus
vv   PSD MUTATED PSD WILD-TYPE
  T1           1             8
  T2           1            67
  T3          13           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
  PSD MUTATED    12   3   1
  PSD WILD-TYPE 208  77  65
D170V5, multiclass
    clus
vv   PSD MUTATED PSD WILD-TYPE
  N0          12           208
  N1           3            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"
D170V6, binary
               cls
clus              0   1
  PSD MUTATED    13   1
  PSD WILD-TYPE 270  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  PSD MUTATED     13    1
  PSD WILD-TYPE  270   47
   clus
vv  PSD MUTATED PSD WILD-TYPE
  0          13           270
  1           1            47
[1] 2 2
[1] FALSE
D170V7, 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
D170V8, binary
               cls
clus              0   1
  PSD MUTATED    13   3
  PSD WILD-TYPE 304  45
[1] "tbl2"
               cls
clus            [,1] [,2]
  PSD MUTATED     13    3
  PSD WILD-TYPE  304   45
                               clus
vv                              PSD MUTATED PSD WILD-TYPE
  COLON ADENOCARCINOMA                   13           304
  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 247   2  21  18
D170V9, multiclass
    clus
vv   PSD MUTATED PSD WILD-TYPE
  R0          10           247
  R1           0             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"
D170V10, 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
D170V11, 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(171) Variable = MBD6 MUTATION ANALYSIS
D171V1, survival
                sevent
clus2              0   1
  MBD6 MUTATED     9   6
  MBD6 WILD-TYPE 273  67
  MBD6 MUTATED MBD6 WILD-TYPE 
            15            340 
  MBD6 MUTATED MBD6 WILD-TYPE 
             6             67 
$`MBD6 MUTATED`
TCGA-AA-3492 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-6895 TCGA-AU-6004 
        3.02         4.01        34.98        35.01         0.72        27.09 
TCGA-AZ-6598 TCGA-AZ-6608 TCGA-CK-5913 TCGA-CM-6171 TCGA-D5-6537 TCGA-D5-6928 
       49.41         1.94        51.32        14.04         4.80        11.64 
TCGA-D5-6930 TCGA-F4-6570 TCGA-G4-6304 
        1.51         6.18        53.62 

$`MBD6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 
      102.44        40.34        15.62        49.08        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 
       18.25         1.32        43.27        15.12        17.85        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.38        13.45        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      107.67        74.56        65.85        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  MBD6 MUTATED MBD6 WILD-TYPE 
          0.72           0.00 
  MBD6 MUTATED MBD6 WILD-TYPE 
         53.62         140.38 
  MBD6 MUTATED MBD6 WILD-TYPE 
         11.64          20.63 
[1] "0.7 - 53.6 (11.6)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "2.5"
D171V2, 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       23       105         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        17          9         40         31       35        13
                vv
clus             STAGE IVB
  MBD6 MUTATED           0
  MBD6 WILD-TYPE         1
D171V3, multiclass
            clus
vv           MBD6 MUTATED MBD6 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             4            105
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             2             17
  STAGE IIIA            1              9
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MBD6 MUTATED     0   3  10   3
  MBD6 WILD-TYPE   9  65 238  38
D171V4, multiclass
    clus
vv   MBD6 MUTATED MBD6 WILD-TYPE
  T1            0              9
  T2            3             65
  T3           10            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
  MBD6 MUTATED    11   3   2
  MBD6 WILD-TYPE 209  77  64
D171V5, multiclass
    clus
vv   MBD6 MUTATED MBD6 WILD-TYPE
  N0           11            209
  N1            3             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"
D171V6, binary
                cls
clus               0   1
  MBD6 MUTATED    12   0
  MBD6 WILD-TYPE 271  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  MBD6 MUTATED     12    0
  MBD6 WILD-TYPE  271   48
   clus
vv  MBD6 MUTATED MBD6 WILD-TYPE
  0           12            271
  1            0             48
[1] 2 2
[1] FALSE
D171V7, binary
                cls
clus               0   1
  MBD6 MUTATED     9   7
  MBD6 WILD-TYPE 161 190
[1] "tbl2"
                cls
clus             [,1] [,2]
  MBD6 MUTATED      9    7
  MBD6 WILD-TYPE  161  190
        clus
vv       MBD6 MUTATED MBD6 WILD-TYPE
  FEMALE            9            161
  MALE              7            190
[1] 2 2
[1] FALSE
D171V8, binary
                cls
clus               0   1
  MBD6 MUTATED    12   4
  MBD6 WILD-TYPE 305  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  MBD6 MUTATED     12    4
  MBD6 WILD-TYPE  305   44
                               clus
vv                              MBD6 MUTATED MBD6 WILD-TYPE
  COLON ADENOCARCINOMA                    12            305
  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 245   2  22  20
D171V9, multiclass
    clus
vv   MBD6 MUTATED MBD6 WILD-TYPE
  R0           12            245
  R1            0              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"
D171V10, 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    11
  MBD6 WILD-TYPE                        19   165
D171V11, 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                                      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(172) Variable = PARG MUTATION ANALYSIS
D172V1, survival
                sevent
clus2              0   1
  PARG MUTATED    10   2
  PARG WILD-TYPE 272  71
  PARG MUTATED PARG WILD-TYPE 
            12            343 
  PARG MUTATED PARG WILD-TYPE 
             2             71 
$`PARG MUTATED`
TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3662 TCGA-AA-A010 TCGA-CA-6717 
       22.06         3.02        63.98         6.05        34.98         0.33 
TCGA-CM-6171 TCGA-CM-6674 TCGA-D5-6529 TCGA-D5-6928 TCGA-F4-6459 TCGA-G4-6588 
       14.04        12.95        20.19        11.64         8.61        26.17 

$`PARG WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        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        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       11.51        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
      117.07        98.24        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 
       52.80 

  PARG MUTATED PARG WILD-TYPE 
          0.33           0.00 
  PARG MUTATED PARG WILD-TYPE 
         63.98         140.38 
  PARG MUTATED PARG WILD-TYPE 
        13.495         20.980 
[1] "0.3 - 64.0 (13.5)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.1"
D172V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PARG MUTATED         1        0        2         6         1         0
  PARG WILD-TYPE      63        1       23       103         7         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        19         10         40         31       34        13
                vv
clus             STAGE IVB
  PARG MUTATED           0
  PARG WILD-TYPE         1
D172V3, multiclass
            clus
vv           PARG MUTATED PARG WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             6            103
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PARG MUTATED     0   1   9   2
  PARG WILD-TYPE   9  67 239  39
D172V4, multiclass
    clus
vv   PARG MUTATED PARG WILD-TYPE
  T1            0              9
  T2            1             67
  T3            9            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
  PARG MUTATED    10   0   2
  PARG WILD-TYPE 210  80  64
D172V5, multiclass
    clus
vv   PARG MUTATED PARG WILD-TYPE
  N0           10            210
  N1            0             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"
D172V6, binary
                cls
clus               0   1
  PARG MUTATED    11   1
  PARG WILD-TYPE 272  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  PARG MUTATED     11    1
  PARG WILD-TYPE  272   47
   clus
vv  PARG MUTATED PARG WILD-TYPE
  0           11            272
  1            1             47
[1] 2 2
[1] FALSE
D172V7, binary
                cls
clus               0   1
  PARG MUTATED     7   5
  PARG WILD-TYPE 163 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  PARG MUTATED      7    5
  PARG WILD-TYPE  163  192
        clus
vv       PARG MUTATED PARG WILD-TYPE
  FEMALE            7            163
  MALE              5            192
[1] 2 2
[1] FALSE
D172V8, binary
                cls
clus               0   1
  PARG MUTATED    10   2
  PARG WILD-TYPE 307  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  PARG MUTATED     10    2
  PARG WILD-TYPE  307   46
                               clus
vv                              PARG MUTATED PARG WILD-TYPE
  COLON ADENOCARCINOMA                    10            307
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PARG MUTATED    10   0   1   1
  PARG WILD-TYPE 247   2  21  20
D172V9, multiclass
    clus
vv   PARG MUTATED PARG WILD-TYPE
  R0           10            247
  R1            0              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"
D172V10, 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
D172V11, 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(173) Variable = FAM134A MUTATION ANALYSIS
D173V1, survival
                   sevent
clus2                 0   1
  FAM134A MUTATED     5   3
  FAM134A WILD-TYPE 277  70
  FAM134A MUTATED FAM134A WILD-TYPE 
                8               347 
  FAM134A MUTATED FAM134A WILD-TYPE 
                3                70 
$`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        15.75        49.41        40.34 
TCGA-CM-5861 TCGA-DM-A1D7 
       15.02        13.32 

$`FAM134A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
        1.02        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 
        0.20        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-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 
        0.10         1.35        17.56       102.44        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        49.91        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  FAM134A MUTATED FAM134A WILD-TYPE 
             4.01              0.00 
  FAM134A MUTATED FAM134A WILD-TYPE 
            49.41            140.38 
  FAM134A MUTATED FAM134A WILD-TYPE 
            15.85             20.98 
[1] "4.0 - 49.4 (15.8)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "2"  
D173V2, 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       24       105         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM134A MUTATED           0          1          0          0        0
  FAM134A WILD-TYPE        19          9         41         31       35
                   vv
clus                STAGE IVA STAGE IVB
  FAM134A MUTATED           1         0
  FAM134A WILD-TYPE        12         1
D173V3, multiclass
            clus
vv           FAM134A MUTATED FAM134A WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                4               105
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               1                 9
  STAGE IIIB               0                41
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                1                12
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of 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  68 241  40
D173V4, multiclass
    clus
vv   FAM134A MUTATED FAM134A WILD-TYPE
  T1               0                 9
  T2               0                68
  T3               7               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
  FAM134A MUTATED     6   2   0
  FAM134A WILD-TYPE 214  78  66
D173V5, multiclass
    clus
vv   FAM134A MUTATED FAM134A WILD-TYPE
  N0               6               214
  N1               2                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"
D173V6, binary
                   cls
clus                  0   1
  FAM134A MUTATED     6   1
  FAM134A WILD-TYPE 277  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM134A MUTATED      6    1
  FAM134A WILD-TYPE  277   47
   clus
vv  FAM134A MUTATED FAM134A WILD-TYPE
  0               6               277
  1               1                47
[1] 2 2
[1] FALSE
D173V7, 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
D173V8, binary
                   cls
clus                  0   1
  FAM134A MUTATED     7   1
  FAM134A WILD-TYPE 310  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM134A MUTATED      7    1
  FAM134A WILD-TYPE  310   47
                               clus
vv                              FAM134A MUTATED FAM134A WILD-TYPE
  COLON ADENOCARCINOMA                        7               310
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  FAM134A MUTATED     5   1   0   0
  FAM134A WILD-TYPE 252   1  22  21
D173V9, multiclass
    clus
vv   FAM134A MUTATED FAM134A WILD-TYPE
  R0               5               252
  R1               1                 1
  R2               0                22
  RX               0                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D173V10, 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
D173V11, 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(174) Variable = PTEN MUTATION ANALYSIS
D174V1, survival
                sevent
clus2              0   1
  PTEN MUTATED   123  28
  PTEN WILD-TYPE 159  45
  PTEN MUTATED PTEN WILD-TYPE 
           151            204 
  PTEN MUTATED PTEN WILD-TYPE 
            28             45 
$`PTEN MUTATED`
TCGA-A6-2671 TCGA-A6-3809 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       43.76        32.75        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6648 TCGA-A6-6649 
       33.53        23.61        22.09        32.71        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3496 TCGA-AA-3502 
       21.76        24.69        20.12        19.66         1.02        35.01 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3815 
       61.02        78.08         6.97        36.00        19.04        33.04 
TCGA-AA-3864 TCGA-AA-3950 TCGA-AA-3968 TCGA-AA-3977 TCGA-AA-A010 TCGA-AD-5900 
       53.00        24.00        21.99        25.02        34.98         0.07 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-6004 
        4.21        56.55         0.72        22.42         0.20        27.09 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4682 TCGA-AZ-5403 
       15.75        21.44        17.82        58.39        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41        49.41         6.77       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6716 
       11.74         1.94         2.24         3.06         3.25         0.26 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        0.10        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4746 
       51.32        21.99         2.93         2.01        23.05        37.02 
TCGA-CM-4747 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       25.02        22.03        22.98        30.08        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 
        5.03        15.02        17.03        12.00        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-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-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       19.59        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6898 TCGA-D5-6922 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-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       13.41        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       49.91        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-A28K 
      139.17        81.37       119.93        35.97        60.79        98.24 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45         6.18        35.87        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
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        51.75        36.72 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

$`PTEN WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5665 TCGA-A6-6137 
       34.65        33.34        36.53        14.53        22.06        27.09 
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6782 
       22.52         8.38        25.08        24.39        23.87        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        7.04         3.02        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3664 
       20.98        19.99        13.94        19.99         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3697 
       11.01         5.98        37.05        19.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       26.99        19.04        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03         2.01        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AU-3779 
       21.37         0.79         5.79        27.42        10.88        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       16.31         0.95         0.20         1.41         5.13        83.80 
TCGA-AZ-6600 TCGA-AZ-6607 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6719 
       12.10         3.19         3.29         0.07         0.33         1.35 
TCGA-CK-5916 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5863 
       21.14       124.27        20.02        13.02        29.06        15.02 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6674 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 
       15.02        14.04        12.95        10.06        45.40        12.26 
TCGA-D5-5540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6926 TCGA-D5-6930 TCGA-D5-6931 
       13.51        15.58        12.39         9.04         1.51        12.00 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A285 TCGA-DM-A28H 
      130.65        92.75        13.32       140.38         6.12       117.07 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6704 TCGA-G4-6304 TCGA-G4-6310 TCGA-G4-6321 
        8.61        13.38         1.55        53.62        45.11        22.09 

  PTEN MUTATED PTEN WILD-TYPE 
          0.07           0.00 
  PTEN MUTATED PTEN WILD-TYPE 
        139.17         140.38 
  PTEN MUTATED PTEN WILD-TYPE 
         21.99          19.07 
[1] "0.1 - 139.2 (22.0)" "0.0 - 140.4 (19.1)"
[1] "hr=" "1.6"
D174V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PTEN MUTATED        25        1        8        50         3         1
  PTEN WILD-TYPE      39        0       17        59         5         0
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PTEN MUTATED           3          6         21         10        8        11
  PTEN WILD-TYPE        16          4         20         21       27         2
                vv
clus             STAGE IVB
  PTEN MUTATED           1
  PTEN WILD-TYPE         0
D174V3, multiclass
            clus
vv           PTEN MUTATED PTEN WILD-TYPE
  STAGE I              25             39
  STAGE IA              1              0
  STAGE II              8             17
  STAGE IIA            50             59
  STAGE IIB             3              5
  STAGE IIC             1              0
  STAGE III             3             16
  STAGE IIIA            6              4
  STAGE IIIB           21             20
  STAGE IIIC           10             21
  STAGE IV              8             27
  STAGE IVA            11              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  28 108  15
  PTEN WILD-TYPE   7  40 140  26
D174V4, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  T1            2              7
  T2           28             40
  T3          108            140
  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    96  38  19
  PTEN WILD-TYPE 124  42  47
D174V5, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  N0           96            124
  N1           38             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"
D174V6, binary
                cls
clus               0   1
  PTEN MUTATED   110  19
  PTEN WILD-TYPE 173  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED    110   19
  PTEN WILD-TYPE  173   29
   clus
vv  PTEN MUTATED PTEN WILD-TYPE
  0          110            173
  1           19             29
[1] 2 2
[1] FALSE
D174V7, binary
                cls
clus               0   1
  PTEN MUTATED    72  82
  PTEN WILD-TYPE  98 115
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED     72   82
  PTEN WILD-TYPE   98  115
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  FEMALE           72             98
  MALE             82            115
[1] 2 2
[1] FALSE
D174V8, binary
                cls
clus               0   1
  PTEN MUTATED   135  19
  PTEN WILD-TYPE 182  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED    135   19
  PTEN WILD-TYPE  182   29
                               clus
vv                              PTEN MUTATED PTEN WILD-TYPE
  COLON ADENOCARCINOMA                   135            182
  COLON MUCINOUS ADENOCARCINOMA           19             29
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PTEN MUTATED    98   1   2  14
  PTEN WILD-TYPE 159   1  20   7
D174V9, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  R0           98            159
  R1            1              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"
D174V10, 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   119
  PTEN WILD-TYPE                         4    57
D174V11, 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                                     119             57
[1] 4 2
[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 = HIPK2 MUTATION ANALYSIS
D175V1, survival
                 sevent
clus2               0   1
  HIPK2 MUTATED    18   6
  HIPK2 WILD-TYPE 264  67
  HIPK2 MUTATED HIPK2 WILD-TYPE 
             24             331 
  HIPK2 MUTATED HIPK2 WILD-TYPE 
              6              67 
$`HIPK2 MUTATED`
TCGA-A6-6654 TCGA-AA-3492 TCGA-AA-3811 TCGA-AA-3947 TCGA-AA-A02O TCGA-AD-6901 
       23.87         3.02        10.06        33.01         0.92        22.42 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-6197 TCGA-CK-4950 TCGA-CM-5861 TCGA-CM-6163 
       14.50        27.09        21.44        40.34        15.02        14.04 
TCGA-CM-6171 TCGA-D5-6533 TCGA-D5-6539 TCGA-D5-6541 TCGA-DM-A1D6 TCGA-DM-A1DB 
       14.04         1.32        12.49        15.58        49.91        44.32 
TCGA-F4-6856 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 
       19.43        65.85        53.62        35.80        26.17        52.80 

$`HIPK2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        19.04        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03        14.01        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-4071 
        5.79        27.42        10.88         0.20        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       15.75         0.20        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 
       13.51        11.51        20.19        18.25        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 
       17.85         4.80        17.13        16.14         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43        38.20       130.65        92.75        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       35.41       107.67        74.56        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 
       45.11        36.72        36.00        22.09        13.78        91.79 
TCGA-G4-6626 
       46.75 

  HIPK2 MUTATED HIPK2 WILD-TYPE 
           0.92            0.00 
  HIPK2 MUTATED HIPK2 WILD-TYPE 
          65.85          140.38 
  HIPK2 MUTATED HIPK2 WILD-TYPE 
          21.93           20.12 
[1] "0.9 - 65.8 (21.9)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.2"
D175V2, 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       23       101         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HIPK2 MUTATED           1          2          2          0        1         0
  HIPK2 WILD-TYPE        18          8         39         31       34        13
                 vv
clus              STAGE IVB
  HIPK2 MUTATED           0
  HIPK2 WILD-TYPE         1
D175V3, multiclass
            clus
vv           HIPK2 MUTATED HIPK2 WILD-TYPE
  STAGE I                5              59
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              8             101
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             2               8
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HIPK2 MUTATED     1   4  16   3
  HIPK2 WILD-TYPE   8  64 232  38
D175V4, multiclass
    clus
vv   HIPK2 MUTATED HIPK2 WILD-TYPE
  T1             1               8
  T2             4              64
  T3            16             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
  HIPK2 MUTATED    20   3   1
  HIPK2 WILD-TYPE 200  77  65
D175V5, multiclass
    clus
vv   HIPK2 MUTATED HIPK2 WILD-TYPE
  N0            20             200
  N1             3              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"
D175V6, binary
                 cls
clus                0   1
  HIPK2 MUTATED    21   1
  HIPK2 WILD-TYPE 262  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HIPK2 MUTATED     21    1
  HIPK2 WILD-TYPE  262   47
   clus
vv  HIPK2 MUTATED HIPK2 WILD-TYPE
  0            21             262
  1             1              47
[1] 2 2
[1] FALSE
D175V7, 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
D175V8, binary
                 cls
clus                0   1
  HIPK2 MUTATED    21   3
  HIPK2 WILD-TYPE 296  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HIPK2 MUTATED     21    3
  HIPK2 WILD-TYPE  296   45
                               clus
vv                              HIPK2 MUTATED HIPK2 WILD-TYPE
  COLON ADENOCARCINOMA                     21             296
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  HIPK2 MUTATED    19   1   0   0
  HIPK2 WILD-TYPE 238   1  22  21
D175V9, multiclass
    clus
vv   HIPK2 MUTATED HIPK2 WILD-TYPE
  R0            19             238
  R1             1               1
  R2             0              22
  RX             0              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D175V10, 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
D175V11, 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(176) Variable = TUBA4A MUTATION ANALYSIS
D176V1, survival
                  sevent
clus2                0   1
  TUBA4A MUTATED     7   2
  TUBA4A WILD-TYPE 275  71
  TUBA4A MUTATED TUBA4A WILD-TYPE 
               9              346 
  TUBA4A MUTATED TUBA4A WILD-TYPE 
               2               71 
$`TUBA4A MUTATED`
TCGA-A6-5665 TCGA-AA-3662 TCGA-AA-3977 TCGA-AZ-6601 TCGA-CK-4950 TCGA-CK-4952 
       22.06         6.05        25.02       100.01        40.34        15.62 
TCGA-CK-5916 TCGA-DM-A282 TCGA-F4-6856 
       21.14       139.17        19.43 

$`TUBA4A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       19.99        13.94        19.99        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-5912 
        0.33         0.10         1.35        17.56       102.44        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       135.65         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 
       16.24        33.67        13.25         0.53        35.41       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  TUBA4A MUTATED TUBA4A WILD-TYPE 
            6.05             0.00 
  TUBA4A MUTATED TUBA4A WILD-TYPE 
          139.17           140.38 
  TUBA4A MUTATED TUBA4A WILD-TYPE 
           22.06            20.07 
[1] "6.0 - 139.2 (22.1)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.4"
D176V2, 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       24       107         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TUBA4A MUTATED           1          1          0          0        1
  TUBA4A WILD-TYPE        18          9         41         31       34
                  vv
clus               STAGE IVA STAGE IVB
  TUBA4A MUTATED           0         0
  TUBA4A WILD-TYPE        13         1
D176V3, multiclass
            clus
vv           TUBA4A MUTATED TUBA4A WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               2              107
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              1                9
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TUBA4A MUTATED     1   2   4   2
  TUBA4A WILD-TYPE   8  66 244  39
D176V4, multiclass
    clus
vv   TUBA4A MUTATED TUBA4A WILD-TYPE
  T1              1                8
  T2              2               66
  T3              4              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
  TUBA4A MUTATED     6   1   2
  TUBA4A WILD-TYPE 214  79  64
D176V5, multiclass
    clus
vv   TUBA4A MUTATED TUBA4A WILD-TYPE
  N0              6              214
  N1              1               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"
D176V6, binary
                  cls
clus                 0   1
  TUBA4A MUTATED     7   1
  TUBA4A WILD-TYPE 276  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TUBA4A MUTATED      7    1
  TUBA4A WILD-TYPE  276   47
   clus
vv  TUBA4A MUTATED TUBA4A WILD-TYPE
  0              7              276
  1              1               47
[1] 2 2
[1] FALSE
D176V7, 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
D176V8, binary
                  cls
clus                 0   1
  TUBA4A MUTATED     7   2
  TUBA4A WILD-TYPE 310  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TUBA4A MUTATED      7    2
  TUBA4A WILD-TYPE  310   46
                               clus
vv                              TUBA4A MUTATED TUBA4A WILD-TYPE
  COLON ADENOCARCINOMA                       7              310
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TUBA4A MUTATED     2   1   1   2
  TUBA4A WILD-TYPE 255   1  21  19
D176V9, multiclass
    clus
vv   TUBA4A MUTATED TUBA4A WILD-TYPE
  R0              2              255
  R1              1                1
  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"
D176V10, 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
D176V11, 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(177) Variable = OR2M3 MUTATION ANALYSIS
D177V1, survival
                 sevent
clus2               0   1
  OR2M3 MUTATED    12   2
  OR2M3 WILD-TYPE 270  71
  OR2M3 MUTATED OR2M3 WILD-TYPE 
             14             341 
  OR2M3 MUTATED OR2M3 WILD-TYPE 
              2              71 
$`OR2M3 MUTATED`
TCGA-AA-3949 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5912 TCGA-CM-4744 
       26.01        58.39         0.33         0.10        49.08        20.02 
TCGA-CM-5349 TCGA-CM-6163 TCGA-CM-6168 TCGA-D5-6540 TCGA-DM-A1D7 TCGA-F4-6805 
       30.08        14.04        12.99        16.14        13.32        16.31 
TCGA-F4-6855 TCGA-G4-6628 
       35.41        52.80 

$`OR2M3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        33.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07         0.26         1.35        17.56       102.44        40.34 
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         2.93         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        16.01        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 
       24.43        38.20       130.65        92.75        49.91        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
        1.55        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       13.78        35.80        26.17        91.79        46.75 

  OR2M3 MUTATED OR2M3 WILD-TYPE 
            0.1             0.0 
  OR2M3 MUTATED OR2M3 WILD-TYPE 
          58.39          140.38 
  OR2M3 MUTATED OR2M3 WILD-TYPE 
         18.165          20.280 
[1] "0.1 - 58.4 (18.2)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.5"
D177V2, 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       24       101         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        19         10         40         31       35        13
                 vv
clus              STAGE IVB
  OR2M3 MUTATED           0
  OR2M3 WILD-TYPE         1
D177V3, multiclass
            clus
vv           OR2M3 MUTATED OR2M3 WILD-TYPE
  STAGE I                5              59
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              8             101
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR2M3 MUTATED     1   4   9   1
  OR2M3 WILD-TYPE   8  64 239  40
D177V4, multiclass
    clus
vv   OR2M3 MUTATED OR2M3 WILD-TYPE
  T1             1               8
  T2             4              64
  T3             9             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
  OR2M3 MUTATED    14   1   0
  OR2M3 WILD-TYPE 206  79  66
D177V5, multiclass
    clus
vv   OR2M3 MUTATED OR2M3 WILD-TYPE
  N0            14             206
  N1             1              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"
D177V6, binary
                 cls
clus                0   1
  OR2M3 MUTATED    14   0
  OR2M3 WILD-TYPE 269  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2M3 MUTATED     14    0
  OR2M3 WILD-TYPE  269   48
   clus
vv  OR2M3 MUTATED OR2M3 WILD-TYPE
  0            14             269
  1             0              48
[1] 2 2
[1] FALSE
D177V7, 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
D177V8, binary
                 cls
clus                0   1
  OR2M3 MUTATED    12   3
  OR2M3 WILD-TYPE 305  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2M3 MUTATED     12    3
  OR2M3 WILD-TYPE  305   45
                               clus
vv                              OR2M3 MUTATED OR2M3 WILD-TYPE
  COLON ADENOCARCINOMA                     12             305
  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 246   2  22  18
D177V9, multiclass
    clus
vv   OR2M3 MUTATED OR2M3 WILD-TYPE
  R0            11             246
  R1             0               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"
D177V10, 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
D177V11, 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(178) Variable = ATP11B MUTATION ANALYSIS
D178V1, survival
                  sevent
clus2                0   1
  ATP11B MUTATED    14   2
  ATP11B WILD-TYPE 268  71
  ATP11B MUTATED ATP11B WILD-TYPE 
              16              339 
  ATP11B MUTATED ATP11B WILD-TYPE 
               2               71 
$`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         0.33         0.10 
TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-5861 TCGA-CM-6170 TCGA-D5-6533 TCGA-DM-A0XD 
       23.05        37.02        15.02        15.02         1.32        24.43 
TCGA-F4-6569 TCGA-F4-6808 TCGA-G4-6304 TCGA-G4-6315 
       13.45        33.67        53.62        36.72 

$`ATP11B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        1.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51        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 
        1.51        12.00        11.38        10.26       119.70        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        13.38         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       29.59        16.24        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      107.67        74.56        65.85        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       45.11        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  ATP11B MUTATED ATP11B WILD-TYPE 
             0.1              0.0 
  ATP11B MUTATED ATP11B WILD-TYPE 
           58.39           140.38 
  ATP11B MUTATED ATP11B WILD-TYPE 
           17.03            20.28 
[1] "0.1 - 58.4 (17.0)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.4"
D178V2, 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       25       102         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP11B MUTATED           2          0          1          0        2
  ATP11B WILD-TYPE        17         10         40         31       33
                  vv
clus               STAGE IVA STAGE IVB
  ATP11B MUTATED           0         0
  ATP11B WILD-TYPE        13         1
D178V3, multiclass
            clus
vv           ATP11B MUTATED ATP11B WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               7              102
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               2               17
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                2               33
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ATP11B MUTATED     1   3  11   2
  ATP11B WILD-TYPE   8  65 237  39
D178V4, multiclass
    clus
vv   ATP11B MUTATED ATP11B WILD-TYPE
  T1              1                8
  T2              3               65
  T3             11              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
  ATP11B MUTATED    14   2   1
  ATP11B WILD-TYPE 206  78  65
D178V5, multiclass
    clus
vv   ATP11B MUTATED ATP11B WILD-TYPE
  N0             14              206
  N1              2               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
  ATP11B MUTATED    15   2
  ATP11B WILD-TYPE 268  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP11B MUTATED     15    2
  ATP11B WILD-TYPE  268   46
   clus
vv  ATP11B MUTATED ATP11B WILD-TYPE
  0             15              268
  1              2               46
[1] 2 2
[1] FALSE
D178V7, 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
D178V8, binary
                  cls
clus                 0   1
  ATP11B MUTATED    15   2
  ATP11B WILD-TYPE 302  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP11B MUTATED     15    2
  ATP11B WILD-TYPE  302   46
                               clus
vv                              ATP11B MUTATED ATP11B WILD-TYPE
  COLON ADENOCARCINOMA                      15              302
  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 245   2  21  19
D178V9, multiclass
    clus
vv   ATP11B MUTATED ATP11B WILD-TYPE
  R0             12              245
  R1              0                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"
D178V10, 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
D178V11, 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(179) Variable = TRIM13 MUTATION ANALYSIS
D179V1, survival
                  sevent
clus2                0   1
  TRIM13 MUTATED     6   1
  TRIM13 WILD-TYPE 276  72
  TRIM13 MUTATED TRIM13 WILD-TYPE 
               7              348 
  TRIM13 MUTATED TRIM13 WILD-TYPE 
               1               72 
$`TRIM13 MUTATED`
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3848 TCGA-AA-3950 TCGA-AA-3977 TCGA-AY-5543 
       78.08         6.05        10.06        24.00        25.02        15.75 
TCGA-G4-6293 
      107.67 

$`TRIM13 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3663 
       20.98        19.99        13.94        19.99        61.02         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-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-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.41        19.43        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  TRIM13 MUTATED TRIM13 WILD-TYPE 
            6.05             0.00 
  TRIM13 MUTATED TRIM13 WILD-TYPE 
          107.67           140.38 
  TRIM13 MUTATED TRIM13 WILD-TYPE 
          24.000           20.155 
[1] "6.0 - 107.7 (24.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "2.1"
D179V2, 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       24       108         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRIM13 MUTATED           1          0          0          1        1
  TRIM13 WILD-TYPE        18         10         41         30       34
                  vv
clus               STAGE IVA STAGE IVB
  TRIM13 MUTATED           1         0
  TRIM13 WILD-TYPE        12         1
D179V3, multiclass
            clus
vv           TRIM13 MUTATED TRIM13 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               1              108
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              1               30
  STAGE IV                1               34
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 243  40
D179V4, multiclass
    clus
vv   TRIM13 MUTATED TRIM13 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              5              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
  TRIM13 MUTATED     3   2   2
  TRIM13 WILD-TYPE 217  78  64
D179V5, multiclass
    clus
vv   TRIM13 MUTATED TRIM13 WILD-TYPE
  N0              3              217
  N1              2               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"
D179V6, binary
                  cls
clus                 0   1
  TRIM13 MUTATED     4   2
  TRIM13 WILD-TYPE 279  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM13 MUTATED      4    2
  TRIM13 WILD-TYPE  279   46
   clus
vv  TRIM13 MUTATED TRIM13 WILD-TYPE
  0              4              279
  1              2               46
[1] 2 2
[1] FALSE
D179V7, 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
D179V8, binary
                  cls
clus                 0   1
  TRIM13 MUTATED     6   1
  TRIM13 WILD-TYPE 311  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM13 MUTATED      6    1
  TRIM13 WILD-TYPE  311   47
                               clus
vv                              TRIM13 MUTATED TRIM13 WILD-TYPE
  COLON ADENOCARCINOMA                       6              311
  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 252   2  21  21
D179V9, multiclass
    clus
vv   TRIM13 MUTATED TRIM13 WILD-TYPE
  R0              5              252
  R1              0                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"
D179V10, 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
D179V11, multiclass
[1] "Remove cluster labels:" "TRIM13 MUTATED"        
clus
  TRIM13 MUTATED TRIM13 WILD-TYPE 
               2              204 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-4105 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-A6-5661       TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5665 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-A6-5666       TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-A6-6142       TCGA-A6-6648       TCGA-A6-6649       TCGA-A6-6651 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-A6-6652       TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-A6-6781       TCGA-A6-6782       TCGA-AD-5900       TCGA-AD-6548 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-AD-6888       TCGA-AD-6889       TCGA-AD-6890       TCGA-AD-6895 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-AD-6899       TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6964 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-AD-6965       TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-AY-4071       TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-AZ-4315       TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4681 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-AZ-4682       TCGA-AZ-5403       TCGA-AZ-5407       TCGA-AZ-6598 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-AZ-6599       TCGA-AZ-6600       TCGA-AZ-6601       TCGA-AZ-6603 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-AZ-6605       TCGA-AZ-6606       TCGA-AZ-6607       TCGA-AZ-6608 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-CA-5254       TCGA-CA-5255       TCGA-CA-5796       TCGA-CA-5797 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-CA-6715       TCGA-CA-6716       TCGA-CA-6717       TCGA-CA-6718 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-CA-6719       TCGA-CK-4947       TCGA-CK-4948       TCGA-CK-4950 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-CK-4952       TCGA-CK-5912       TCGA-CK-5913       TCGA-CK-5914 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-CK-5915       TCGA-CK-5916       TCGA-CK-6746       TCGA-CK-6747 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-CK-6748       TCGA-CK-6751       TCGA-CM-4743       TCGA-CM-4744 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-CM-4746       TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-CM-5344       TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-CM-5861       TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-CM-5868       TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-CM-6164       TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-CM-6168       TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-CM-6172       TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-CM-6677       TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-D5-5537       TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-D5-5541       TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-D5-6534       TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-D5-6538       TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-D5-6898       TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-D5-6924       TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-D5-6929       TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-D5-7000       TCGA-DM-A0X9       TCGA-DM-A0XD       TCGA-DM-A0XF 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-DM-A1D0       TCGA-DM-A1D4       TCGA-DM-A1D6       TCGA-DM-A1D7 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-DM-A1D8       TCGA-DM-A1D9       TCGA-DM-A1DA       TCGA-DM-A1DB 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-DM-A1HA       TCGA-DM-A1HB       TCGA-DM-A282       TCGA-DM-A285 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-DM-A28C       TCGA-DM-A28E       TCGA-DM-A28F       TCGA-DM-A28G 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-DM-A28H       TCGA-DM-A28K       TCGA-F4-6459       TCGA-F4-6460 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-F4-6569       TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-F4-6805       TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-F4-6809       TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304       TCGA-G4-6306 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310       TCGA-G4-6315 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323       TCGA-G4-6586 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 

Clustering(180) Variable = THOC5 MUTATION ANALYSIS
D180V1, survival
                 sevent
clus2               0   1
  THOC5 MUTATED    10   4
  THOC5 WILD-TYPE 272  69
  THOC5 MUTATED THOC5 WILD-TYPE 
             14             341 
  THOC5 MUTATED THOC5 WILD-TYPE 
              4              69 
$`THOC5 MUTATED`
TCGA-AA-3492 TCGA-AA-3518 TCGA-AA-3663 TCGA-AA-A00N TCGA-AA-A010 TCGA-AY-6197 
        3.02         1.02         6.97         4.01        34.98        21.44 
TCGA-AZ-4681 TCGA-AZ-6600 TCGA-CA-6718 TCGA-CK-4950 TCGA-CK-6747 TCGA-CM-6171 
       83.80        12.10         0.10        40.34         2.93        14.04 
TCGA-DM-A285 TCGA-G4-6309 
        6.12        51.75 

$`THOC5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       27.09        16.31         0.95        15.75         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        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.33         1.35        17.56       102.44 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 
       15.62        49.08        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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        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 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  THOC5 MUTATED THOC5 WILD-TYPE 
            0.1             0.0 
  THOC5 MUTATED THOC5 WILD-TYPE 
          83.80          140.38 
  THOC5 MUTATED THOC5 WILD-TYPE 
          9.535          20.980 
[1] "0.1 - 83.8 (9.5)"   "0.0 - 140.4 (21.0)"
[1] "hr=" "1.7"
D180V2, 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       23       104         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  THOC5 MUTATED           0          1          1          0        2         0
  THOC5 WILD-TYPE        19          9         40         31       33        13
                 vv
clus              STAGE IVB
  THOC5 MUTATED           0
  THOC5 WILD-TYPE         1
D180V3, multiclass
            clus
vv           THOC5 MUTATED THOC5 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              5             104
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               2              33
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  THOC5 MUTATED     0   1  10   3
  THOC5 WILD-TYPE   9  67 238  38
D180V4, multiclass
    clus
vv   THOC5 MUTATED THOC5 WILD-TYPE
  T1             0               9
  T2             1              67
  T3            10             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
  THOC5 MUTATED    10   3   1
  THOC5 WILD-TYPE 210  77  65
D180V5, multiclass
    clus
vv   THOC5 MUTATED THOC5 WILD-TYPE
  N0            10             210
  N1             3              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
  THOC5 MUTATED    10   2
  THOC5 WILD-TYPE 273  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THOC5 MUTATED     10    2
  THOC5 WILD-TYPE  273   46
   clus
vv  THOC5 MUTATED THOC5 WILD-TYPE
  0            10             273
  1             2              46
[1] 2 2
[1] FALSE
D180V7, 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
D180V8, binary
                 cls
clus                0   1
  THOC5 MUTATED    12   2
  THOC5 WILD-TYPE 305  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THOC5 MUTATED     12    2
  THOC5 WILD-TYPE  305   46
                               clus
vv                              THOC5 MUTATED THOC5 WILD-TYPE
  COLON ADENOCARCINOMA                     12             305
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  THOC5 MUTATED     9   1   0   2
  THOC5 WILD-TYPE 248   1  22  19
D180V9, multiclass
    clus
vv   THOC5 MUTATED THOC5 WILD-TYPE
  R0             9             248
  R1             1               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"
D180V10, 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
D180V11, 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(181) Variable = GTF2B MUTATION ANALYSIS
D181V1, survival
                 sevent
clus2               0   1
  GTF2B MUTATED    10   0
  GTF2B WILD-TYPE 272  73
  GTF2B MUTATED GTF2B WILD-TYPE 
             10             345 
  GTF2B MUTATED GTF2B WILD-TYPE 
              0              73 
$`GTF2B MUTATED`
TCGA-AA-3510 TCGA-AA-3660 TCGA-AA-3713 TCGA-AA-3877 TCGA-AZ-4315 TCGA-AZ-4681 
       63.98        78.08        19.04        31.00        58.39        83.80 
TCGA-CM-5344 TCGA-DM-A1HB TCGA-G4-6323 TCGA-G4-6586 
       22.03       135.65        13.78        35.80 

$`GTF2B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        61.02         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       27.02        29.98        18.05         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         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-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6588 
       51.75        45.11        36.72        36.00        22.09        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  GTF2B MUTATED GTF2B WILD-TYPE 
          13.78            0.00 
  GTF2B MUTATED GTF2B WILD-TYPE 
         135.65          140.38 
  GTF2B MUTATED GTF2B WILD-TYPE 
         47.095          19.990 
[1] "13.8 - 135.7 (47.1)" "0.0 - 140.4 (20.0)" 
[1] "hr="     "2.7e+07"
D181V2, 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       23       106         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        19         10         39         31       34        13
                 vv
clus              STAGE IVB
  GTF2B MUTATED           0
  GTF2B WILD-TYPE         1
D181V3, multiclass
            clus
vv           GTF2B MUTATED GTF2B WILD-TYPE
  STAGE I                1              63
  STAGE IA               1               0
  STAGE II               2              23
  STAGE IIA              3             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GTF2B MUTATED     1   0   8   1
  GTF2B WILD-TYPE   8  68 240  40
D181V4, multiclass
    clus
vv   GTF2B MUTATED GTF2B WILD-TYPE
  T1             1               8
  T2             0              68
  T3             8             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
  GTF2B MUTATED     9   2   0
  GTF2B WILD-TYPE 211  78  66
D181V5, multiclass
    clus
vv   GTF2B MUTATED GTF2B WILD-TYPE
  N0             9             211
  N1             2              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
  GTF2B MUTATED     8   1
  GTF2B WILD-TYPE 275  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GTF2B MUTATED      8    1
  GTF2B WILD-TYPE  275   47
   clus
vv  GTF2B MUTATED GTF2B WILD-TYPE
  0             8             275
  1             1              47
[1] 2 2
[1] FALSE
D181V7, 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
D181V8, binary
                 cls
clus                0   1
  GTF2B MUTATED    10   1
  GTF2B WILD-TYPE 307  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GTF2B MUTATED     10    1
  GTF2B WILD-TYPE  307   47
                               clus
vv                              GTF2B MUTATED GTF2B WILD-TYPE
  COLON ADENOCARCINOMA                     10             307
  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 249   2  21  20
D181V9, multiclass
    clus
vv   GTF2B MUTATED GTF2B WILD-TYPE
  R0             8             249
  R1             0               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"
D181V10, 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
D181V11, 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(182) Variable = PPP1R12B MUTATION ANALYSIS
D182V1, survival
                    sevent
clus2                  0   1
  PPP1R12B MUTATED    10   2
  PPP1R12B WILD-TYPE 272  71
  PPP1R12B MUTATED PPP1R12B WILD-TYPE 
                12                343 
  PPP1R12B MUTATED PPP1R12B WILD-TYPE 
                 2                 71 
$`PPP1R12B MUTATED`
TCGA-AA-3842 TCGA-AA-3867 TCGA-AA-A00N TCGA-AZ-4315 TCGA-CM-5344 TCGA-CM-5348 
       37.02        24.03         4.01        58.39        22.03        22.98 
TCGA-CM-6162 TCGA-D5-6529 TCGA-D5-6536 TCGA-DM-A1D4 TCGA-G4-6310 TCGA-G4-6588 
       12.00        20.19        17.85        92.75        45.11        26.17 

$`PPP1R12B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3844 TCGA-AA-3845 
        1.02        17.98        15.95        38.99        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       17.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       13.02        29.06        30.08        16.01        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       13.51        11.51        18.25         1.32        43.27        15.12 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        24.43        38.20       130.65        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        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        51.75        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 
       52.80 

  PPP1R12B MUTATED PPP1R12B WILD-TYPE 
              4.01               0.00 
  PPP1R12B MUTATED PPP1R12B WILD-TYPE 
             92.75             140.38 
  PPP1R12B MUTATED PPP1R12B WILD-TYPE 
            23.505             19.990 
[1] "4.0 - 92.8 (23.5)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1.5"
D182V2, 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       25       104         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PPP1R12B MUTATED           0          1          4          0        1
  PPP1R12B WILD-TYPE        19          9         37         31       34
                    vv
clus                 STAGE IVA STAGE IVB
  PPP1R12B MUTATED           0         0
  PPP1R12B WILD-TYPE        13         1
D182V3, multiclass
            clus
vv           PPP1R12B MUTATED PPP1R12B WILD-TYPE
  STAGE I                   0                 64
  STAGE IA                  0                  1
  STAGE II                  0                 25
  STAGE IIA                 5                104
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                1                  9
  STAGE IIIB                4                 37
  STAGE IIIC                0                 31
  STAGE IV                  1                 34
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  PPP1R12B MUTATED     0   1  10   1
  PPP1R12B WILD-TYPE   9  67 238  40
D182V4, multiclass
    clus
vv   PPP1R12B MUTATED PPP1R12B WILD-TYPE
  T1                0                  9
  T2                1                 67
  T3               10                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
  PPP1R12B MUTATED     6   5   1
  PPP1R12B WILD-TYPE 214  75  65
D182V5, multiclass
    clus
vv   PPP1R12B MUTATED PPP1R12B WILD-TYPE
  N0                6                214
  N1                5                 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"
D182V6, binary
                    cls
clus                   0   1
  PPP1R12B MUTATED    11   1
  PPP1R12B WILD-TYPE 272  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R12B MUTATED     11    1
  PPP1R12B WILD-TYPE  272   47
   clus
vv  PPP1R12B MUTATED PPP1R12B WILD-TYPE
  0               11                272
  1                1                 47
[1] 2 2
[1] FALSE
D182V7, 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
D182V8, binary
                    cls
clus                   0   1
  PPP1R12B MUTATED    10   2
  PPP1R12B WILD-TYPE 307  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R12B MUTATED     10    2
  PPP1R12B WILD-TYPE  307   46
                               clus
vv                              PPP1R12B MUTATED PPP1R12B WILD-TYPE
  COLON ADENOCARCINOMA                        10                307
  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 247   2  21  21
D182V9, multiclass
    clus
vv   PPP1R12B MUTATED PPP1R12B WILD-TYPE
  R0               10                247
  R1                0                  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"
D182V10, 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
D182V11, 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(183) Variable = C1ORF59 MUTATION ANALYSIS
D183V1, survival
                   sevent
clus2                 0   1
  C1ORF59 MUTATED     7   3
  C1ORF59 WILD-TYPE 275  70
  C1ORF59 MUTATED C1ORF59 WILD-TYPE 
               10               345 
  C1ORF59 MUTATED C1ORF59 WILD-TYPE 
                3                70 
$`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         1.35 
TCGA-CM-4752 TCGA-CM-5348 TCGA-D5-5540 TCGA-DM-A0XD 
       13.02        22.98        13.51        24.43 

$`C1ORF59 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        0.10        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  C1ORF59 MUTATED C1ORF59 WILD-TYPE 
             1.35              0.00 
  C1ORF59 MUTATED C1ORF59 WILD-TYPE 
            62.79            140.38 
  C1ORF59 MUTATED C1ORF59 WILD-TYPE 
            21.32             20.19 
[1] "1.4 - 62.8 (21.3)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.4"
D183V2, 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       24       104         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C1ORF59 MUTATED           0          0          1          2        0
  C1ORF59 WILD-TYPE        19         10         40         29       35
                   vv
clus                STAGE IVA STAGE IVB
  C1ORF59 MUTATED           0         0
  C1ORF59 WILD-TYPE        13         1
D183V3, multiclass
            clus
vv           C1ORF59 MUTATED C1ORF59 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                5               104
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               2                29
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C1ORF59 MUTATED     0   0   8   2
  C1ORF59 WILD-TYPE   9  68 240  39
D183V4, multiclass
    clus
vv   C1ORF59 MUTATED C1ORF59 WILD-TYPE
  T1               0                 9
  T2               0                68
  T3               8               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
  C1ORF59 MUTATED     7   2   1
  C1ORF59 WILD-TYPE 213  78  65
D183V5, multiclass
    clus
vv   C1ORF59 MUTATED C1ORF59 WILD-TYPE
  N0               7               213
  N1               2                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"
D183V6, binary
                   cls
clus                  0   1
  C1ORF59 MUTATED     8   0
  C1ORF59 WILD-TYPE 275  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1ORF59 MUTATED      8    0
  C1ORF59 WILD-TYPE  275   48
   clus
vv  C1ORF59 MUTATED C1ORF59 WILD-TYPE
  0               8               275
  1               0                48
[1] 2 2
[1] FALSE
D183V7, 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
D183V8, binary
                   cls
clus                  0   1
  C1ORF59 MUTATED     8   2
  C1ORF59 WILD-TYPE 309  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1ORF59 MUTATED      8    2
  C1ORF59 WILD-TYPE  309   46
                               clus
vv                              C1ORF59 MUTATED C1ORF59 WILD-TYPE
  COLON ADENOCARCINOMA                        8               309
  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 251   2  22  20
D183V9, multiclass
    clus
vv   C1ORF59 MUTATED C1ORF59 WILD-TYPE
  R0               6               251
  R1               0                 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"
D183V10, 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
D183V11, 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(184) Variable = PDCD5 MUTATION ANALYSIS
D184V1, survival
                 sevent
clus2               0   1
  PDCD5 MUTATED     8   0
  PDCD5 WILD-TYPE 274  73
  PDCD5 MUTATED PDCD5 WILD-TYPE 
              8             347 
  PDCD5 MUTATED PDCD5 WILD-TYPE 
              0              73 
$`PDCD5 MUTATED`
TCGA-A6-6651 TCGA-AA-3502 TCGA-AA-3672 TCGA-AD-6895 TCGA-AZ-4315 TCGA-CK-5914 
       21.76        35.01         0.92         0.72        58.39        21.99 
TCGA-D5-6920 TCGA-F4-6855 
       12.39        35.41 

$`PDCD5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        24.16        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 
       29.59        16.24        33.67        13.25         0.53        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  PDCD5 MUTATED PDCD5 WILD-TYPE 
           0.72            0.00 
  PDCD5 MUTATED PDCD5 WILD-TYPE 
          58.39          140.38 
  PDCD5 MUTATED PDCD5 WILD-TYPE 
         21.875          20.120 
[1] "0.7 - 58.4 (21.9)"  "0.0 - 140.4 (20.1)"
[1] "hr="     "9200000"
D184V2, 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       25       106         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PDCD5 MUTATED           1          0          2          0        0         0
  PDCD5 WILD-TYPE        18         10         39         31       35        13
                 vv
clus              STAGE IVB
  PDCD5 MUTATED           0
  PDCD5 WILD-TYPE         1
D184V3, multiclass
            clus
vv           PDCD5 MUTATED PDCD5 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              3             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PDCD5 MUTATED     0   1   7   0
  PDCD5 WILD-TYPE   9  67 241  41
D184V4, multiclass
    clus
vv   PDCD5 MUTATED PDCD5 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             7             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
  PDCD5 MUTATED     4   4   0
  PDCD5 WILD-TYPE 216  76  66
D184V5, multiclass
    clus
vv   PDCD5 MUTATED PDCD5 WILD-TYPE
  N0             4             216
  N1             4              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"
D184V6, binary
                 cls
clus                0   1
  PDCD5 MUTATED     5   0
  PDCD5 WILD-TYPE 278  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDCD5 MUTATED      5    0
  PDCD5 WILD-TYPE  278   48
   clus
vv  PDCD5 MUTATED PDCD5 WILD-TYPE
  0             5             278
  1             0              48
[1] 2 2
[1] FALSE
D184V7, 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
D184V8, binary
                 cls
clus                0   1
  PDCD5 MUTATED     8   0
  PDCD5 WILD-TYPE 309  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDCD5 MUTATED      8    0
  PDCD5 WILD-TYPE  309   48
                               clus
vv                              PDCD5 MUTATED PDCD5 WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PDCD5 MUTATED     5   0   0   1
  PDCD5 WILD-TYPE 252   2  22  20
D184V9, multiclass
    clus
vv   PDCD5 MUTATED PDCD5 WILD-TYPE
  R0             5             252
  R1             0               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"
D184V10, 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
D184V11, 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(185) Variable = STBD1 MUTATION ANALYSIS
D185V1, survival
                 sevent
clus2               0   1
  STBD1 MUTATED     5   1
  STBD1 WILD-TYPE 277  72
  STBD1 MUTATED STBD1 WILD-TYPE 
              6             349 
  STBD1 MUTATED STBD1 WILD-TYPE 
              1              72 
$`STBD1 MUTATED`
TCGA-A6-5666 TCGA-AA-3678 TCGA-CK-4948 TCGA-D5-6541 TCGA-DM-A1DB TCGA-F4-6856 
       32.71        47.01       102.44        15.58        44.32        19.43 

$`STBD1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        16.14         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       12.59       140.38         7.50       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        35.41       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  STBD1 MUTATED STBD1 WILD-TYPE 
          15.58            0.00 
  STBD1 MUTATED STBD1 WILD-TYPE 
         102.44          140.38 
  STBD1 MUTATED STBD1 WILD-TYPE 
         38.515          20.120 
[1] "15.6 - 102.4 (38.5)" "0.0 - 140.4 (20.1)" 
[1] "hr=" "2.1"
D185V2, 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       25       107         8         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  STBD1 MUTATED           1          1          0          0        0         0
  STBD1 WILD-TYPE        18          9         41         31       35        13
                 vv
clus              STAGE IVB
  STBD1 MUTATED           0
  STBD1 WILD-TYPE         1
D185V3, multiclass
            clus
vv           STBD1 MUTATED STBD1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              2             107
  STAGE IIB              0               8
  STAGE IIC              1               0
  STAGE III              1              18
  STAGE IIIA             1               9
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  STBD1 MUTATED     0   2   3   1
  STBD1 WILD-TYPE   9  66 245  40
D185V4, multiclass
    clus
vv   STBD1 MUTATED STBD1 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             3             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
  STBD1 MUTATED     4   2   0
  STBD1 WILD-TYPE 216  78  66
D185V5, multiclass
    clus
vv   STBD1 MUTATED STBD1 WILD-TYPE
  N0             4             216
  N1             2              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"
D185V6, binary
                 cls
clus                0   1
  STBD1 MUTATED     6   0
  STBD1 WILD-TYPE 277  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STBD1 MUTATED      6    0
  STBD1 WILD-TYPE  277   48
   clus
vv  STBD1 MUTATED STBD1 WILD-TYPE
  0             6             277
  1             0              48
[1] 2 2
[1] FALSE
D185V7, 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
D185V8, binary
                 cls
clus                0   1
  STBD1 MUTATED     5   1
  STBD1 WILD-TYPE 312  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STBD1 MUTATED      5    1
  STBD1 WILD-TYPE  312   47
                               clus
vv                              STBD1 MUTATED STBD1 WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  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 253   2  22  21
D185V9, multiclass
    clus
vv   STBD1 MUTATED STBD1 WILD-TYPE
  R0             4             253
  R1             0               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"
D185V10, 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
D185V11, 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(186) Variable = SNTN MUTATION ANALYSIS
D186V1, survival
                sevent
clus2              0   1
  SNTN MUTATED     5   0
  SNTN WILD-TYPE 277  73
  SNTN MUTATED SNTN WILD-TYPE 
             5            350 
  SNTN MUTATED SNTN WILD-TYPE 
             0             73 
$`SNTN MUTATED`
TCGA-AA-3496 TCGA-CA-6716 TCGA-CM-6676 TCGA-DM-A1HA TCGA-F4-6806 
        1.02         0.26        11.08       131.51        29.59 

$`SNTN WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB 
       13.32        12.59       140.38         7.50        44.32       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       35.87         1.55        16.31        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  SNTN MUTATED SNTN WILD-TYPE 
          0.26           0.00 
  SNTN MUTATED SNTN WILD-TYPE 
        131.51         140.38 
  SNTN MUTATED SNTN WILD-TYPE 
        11.080         20.235 
[1] "0.3 - 131.5 (11.1)" "0.0 - 140.4 (20.2)"
[1] "hr="     "9300000"
D186V2, 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       24       108         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        19         10         41         30       35        13
                vv
clus             STAGE IVB
  SNTN MUTATED           0
  SNTN WILD-TYPE         1
D186V3, multiclass
            clus
vv           SNTN MUTATED SNTN WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             1            108
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            1             30
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SNTN MUTATED     0   2   3   1
  SNTN WILD-TYPE   9  66 245  40
D186V4, multiclass
    clus
vv   SNTN MUTATED SNTN WILD-TYPE
  T1            0              9
  T2            2             66
  T3            3            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
  SNTN MUTATED     5   0   1
  SNTN WILD-TYPE 215  80  65
D186V5, multiclass
    clus
vv   SNTN MUTATED SNTN WILD-TYPE
  N0            5            215
  N1            0             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"
D186V6, binary
                cls
clus               0   1
  SNTN MUTATED     5   0
  SNTN WILD-TYPE 278  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  SNTN MUTATED      5    0
  SNTN WILD-TYPE  278   48
   clus
vv  SNTN MUTATED SNTN WILD-TYPE
  0            5            278
  1            0             48
[1] 2 2
[1] FALSE
D186V7, 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
D186V8, binary
                cls
clus               0   1
  SNTN MUTATED     6   0
  SNTN WILD-TYPE 311  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  SNTN MUTATED      6    0
  SNTN WILD-TYPE  311   48
                               clus
vv                              SNTN MUTATED SNTN WILD-TYPE
  COLON ADENOCARCINOMA                     6            311
  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 254   2  22  19
D186V9, multiclass
    clus
vv   SNTN MUTATED SNTN WILD-TYPE
  R0            3            254
  R1            0              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"
D186V10, 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
D186V11, 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(187) Variable = FGFR2 MUTATION ANALYSIS
D187V1, survival
                 sevent
clus2               0   1
  FGFR2 MUTATED    31  14
  FGFR2 WILD-TYPE 251  59
  FGFR2 MUTATED FGFR2 WILD-TYPE 
             45             310 
  FGFR2 MUTATED FGFR2 WILD-TYPE 
             14              59 
$`FGFR2 MUTATED`
TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6142 TCGA-AA-3489 
       29.19        23.61        32.71        22.52        25.08         7.04 
TCGA-AA-3510 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3710 TCGA-AA-3713 TCGA-AD-6889 
       63.98        78.08         6.97        26.99        19.04        56.55 
TCGA-AD-6901 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.42         0.20        17.82        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-CA-6717 TCGA-CK-4950 TCGA-CK-4952 TCGA-CM-4743 TCGA-CM-4752 
      100.01         0.33        40.34        15.62        23.05        13.02 
TCGA-CM-5348 TCGA-CM-5862 TCGA-CM-6168 TCGA-D5-6529 TCGA-D5-6535 TCGA-D5-6537 
       22.98         5.03        12.99        20.19        15.12         4.80 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-DM-A0XF TCGA-DM-A1D6 TCGA-DM-A1DB 
       12.49        16.14         7.53        38.20        49.91        44.32 
TCGA-DM-A28F TCGA-DM-A28G TCGA-F4-6570 TCGA-G4-6304 TCGA-G4-6317 TCGA-G4-6323 
       35.97        60.79         6.18        53.62        36.00        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       26.17        91.79        52.80 

$`FGFR2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 
       32.91        31.63        30.44        33.53        22.09        22.06 
TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 
       27.09         8.38        25.18        24.16        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3492 
       24.39        23.87        20.12        19.66        20.28         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3664 
       19.99        13.94        19.99        61.02         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       85.05        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37         4.21         0.79         0.72         5.79 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        15.75        21.44        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6603 TCGA-AZ-6605 
       83.80        22.36        62.79        61.41        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
      102.44        49.08        51.32        21.99        21.14         2.93 
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-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 
       22.03        30.08        16.01        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-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       21.99        14.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        13.51        11.51 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6541 
       18.25         1.32        43.27        17.85        17.13        15.58 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 
      119.70        24.43       130.65        92.75        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       81.37       119.93       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6626 
       36.72        22.09        35.80        46.75 

  FGFR2 MUTATED FGFR2 WILD-TYPE 
            0.2             0.0 
  FGFR2 MUTATED FGFR2 WILD-TYPE 
         100.01          140.38 
  FGFR2 MUTATED FGFR2 WILD-TYPE 
          22.98           19.99 
[1] "0.2 - 100.0 (23.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.4"
D187V2, 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       19        96         7         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FGFR2 MUTATED           1          2          5          4        2         3
  FGFR2 WILD-TYPE        18          8         36         27       33        10
                 vv
clus              STAGE IVB
  FGFR2 MUTATED           0
  FGFR2 WILD-TYPE         1
D187V3, multiclass
            clus
vv           FGFR2 MUTATED FGFR2 WILD-TYPE
  STAGE I                5              59
  STAGE IA               1               0
  STAGE II               6              19
  STAGE IIA             13              96
  STAGE IIB              1               7
  STAGE IIC              1               0
  STAGE III              1              18
  STAGE IIIA             2               8
  STAGE IIIB             5              36
  STAGE IIIC             4              27
  STAGE IV               2              33
  STAGE IVA              3              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
  FGFR2 MUTATED     0   5  35   4
  FGFR2 WILD-TYPE   9  63 213  37
D187V4, multiclass
    clus
vv   FGFR2 MUTATED FGFR2 WILD-TYPE
  T1             0               9
  T2             5              63
  T3            35             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
  FGFR2 MUTATED    30   9   6
  FGFR2 WILD-TYPE 190  71  60
D187V5, multiclass
    clus
vv   FGFR2 MUTATED FGFR2 WILD-TYPE
  N0            30             190
  N1             9              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"
D187V6, binary
                 cls
clus                0   1
  FGFR2 MUTATED    32   5
  FGFR2 WILD-TYPE 251  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGFR2 MUTATED     32    5
  FGFR2 WILD-TYPE  251   43
   clus
vv  FGFR2 MUTATED FGFR2 WILD-TYPE
  0            32             251
  1             5              43
[1] 2 2
[1] FALSE
D187V7, 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
D187V8, binary
                 cls
clus                0   1
  FGFR2 MUTATED    39   6
  FGFR2 WILD-TYPE 278  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGFR2 MUTATED     39    6
  FGFR2 WILD-TYPE  278   42
                               clus
vv                              FGFR2 MUTATED FGFR2 WILD-TYPE
  COLON ADENOCARCINOMA                     39             278
  COLON MUCINOUS ADENOCARCINOMA             6              42
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  FGFR2 MUTATED    24   1   1   3
  FGFR2 WILD-TYPE 233   1  21  18
D187V9, multiclass
    clus
vv   FGFR2 MUTATED FGFR2 WILD-TYPE
  R0            24             233
  R1             1               1
  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"
D187V10, 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
D187V11, 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(188) Variable = NBPF7 MUTATION ANALYSIS
D188V1, survival
                 sevent
clus2               0   1
  NBPF7 MUTATED    10   1
  NBPF7 WILD-TYPE 272  72
  NBPF7 MUTATED NBPF7 WILD-TYPE 
             11             344 
  NBPF7 MUTATED NBPF7 WILD-TYPE 
              1              72 
$`NBPF7 MUTATED`
TCGA-AA-3496 TCGA-AA-3663 TCGA-AA-3977 TCGA-AA-A010 TCGA-AD-5900 TCGA-AZ-6598 
        1.02         6.97        25.02        34.98         0.07        49.41 
TCGA-CA-6718 TCGA-CM-6164 TCGA-CM-6676 TCGA-G4-6310 TCGA-G4-6628 
        0.10        29.03        11.08        45.11        52.80 

$`NBPF7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.33         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        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-6677 TCGA-CM-6678 TCGA-CM-6679 
       11.01        12.95        13.05        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 
       91.79        46.75 

  NBPF7 MUTATED NBPF7 WILD-TYPE 
           0.07            0.00 
  NBPF7 MUTATED NBPF7 WILD-TYPE 
          52.80          140.38 
  NBPF7 MUTATED NBPF7 WILD-TYPE 
         25.020          20.155 
[1] "0.1 - 52.8 (25.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2.1"
D188V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NBPF7 MUTATED         3        0        3         2         1         0
  NBPF7 WILD-TYPE      61        1       22       107         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NBPF7 MUTATED           0          0          1          0        0         0
  NBPF7 WILD-TYPE        19         10         40         31       35        13
                 vv
clus              STAGE IVB
  NBPF7 MUTATED           0
  NBPF7 WILD-TYPE         1
D188V3, multiclass
            clus
vv           NBPF7 MUTATED NBPF7 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              2             107
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NBPF7 MUTATED     0   4   6   1
  NBPF7 WILD-TYPE   9  64 242  40
D188V4, multiclass
    clus
vv   NBPF7 MUTATED NBPF7 WILD-TYPE
  T1             0               9
  T2             4              64
  T3             6             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
  NBPF7 MUTATED    10   1   0
  NBPF7 WILD-TYPE 210  79  66
D188V5, multiclass
    clus
vv   NBPF7 MUTATED NBPF7 WILD-TYPE
  N0            10             210
  N1             1              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"
D188V6, binary
                 cls
clus                0   1
  NBPF7 MUTATED     8   0
  NBPF7 WILD-TYPE 275  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF7 MUTATED      8    0
  NBPF7 WILD-TYPE  275   48
   clus
vv  NBPF7 MUTATED NBPF7 WILD-TYPE
  0             8             275
  1             0              48
[1] 2 2
[1] FALSE
D188V7, binary
                 cls
clus                0   1
  NBPF7 MUTATED     4   7
  NBPF7 WILD-TYPE 166 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF7 MUTATED      4    7
  NBPF7 WILD-TYPE  166  190
        clus
vv       NBPF7 MUTATED NBPF7 WILD-TYPE
  FEMALE             4             166
  MALE               7             190
[1] 2 2
[1] FALSE
D188V8, binary
                 cls
clus                0   1
  NBPF7 MUTATED    10   1
  NBPF7 WILD-TYPE 307  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF7 MUTATED     10    1
  NBPF7 WILD-TYPE  307   47
                               clus
vv                              NBPF7 MUTATED NBPF7 WILD-TYPE
  COLON ADENOCARCINOMA                     10             307
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  NBPF7 MUTATED     8   0   0   1
  NBPF7 WILD-TYPE 249   2  22  20
D188V9, multiclass
    clus
vv   NBPF7 MUTATED NBPF7 WILD-TYPE
  R0             8             249
  R1             0               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"
D188V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NBPF7 MUTATED                                  0     1
  NBPF7 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NBPF7 MUTATED                           0     6
  NBPF7 WILD-TYPE                        19   170
D188V11, multiclass
                                  clus
vv                                 NBPF7 MUTATED NBPF7 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(189) Variable = LATS1 MUTATION ANALYSIS
D189V1, survival
                 sevent
clus2               0   1
  LATS1 MUTATED     8   9
  LATS1 WILD-TYPE 274  64
  LATS1 MUTATED LATS1 WILD-TYPE 
             17             338 
  LATS1 MUTATED LATS1 WILD-TYPE 
              9              64 
$`LATS1 MUTATED`
TCGA-A6-2676 TCGA-AA-3492 TCGA-AA-3516 TCGA-AA-3681 TCGA-AA-A00N TCGA-AA-A02H 
       42.90         3.02        13.02         5.98         4.01         2.01 
TCGA-AD-6889 TCGA-AD-6964 TCGA-AZ-6598 TCGA-CK-4950 TCGA-CK-5916 TCGA-CM-6168 
       56.55        10.88        49.41        40.34        21.14        12.99 
TCGA-D5-6536 TCGA-DM-A1HB TCGA-F4-6570 TCGA-G4-6321 TCGA-G4-6588 
       17.85       135.65         6.18        22.09        26.17 

$`LATS1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
       11.01        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02K 
       37.02        39.06        51.98        39.98         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13        83.80        22.36        62.79        61.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        51.32        21.99         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       45.11        36.72        36.00        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  LATS1 MUTATED LATS1 WILD-TYPE 
           2.01            0.00 
  LATS1 MUTATED LATS1 WILD-TYPE 
         135.65          140.38 
  LATS1 MUTATED LATS1 WILD-TYPE 
         17.850          20.235 
[1] "2.0 - 135.7 (17.9)" "0.0 - 140.4 (20.2)"
[1] "hr=" "2.7"
D189V2, 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       23       103         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LATS1 MUTATED           3          1          1          0        1         0
  LATS1 WILD-TYPE        16          9         40         31       34        13
                 vv
clus              STAGE IVB
  LATS1 MUTATED           0
  LATS1 WILD-TYPE         1
D189V3, multiclass
            clus
vv           LATS1 MUTATED LATS1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              6             103
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              3              16
  STAGE IIIA             1               9
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LATS1 MUTATED     1   1  13   3
  LATS1 WILD-TYPE   8  67 235  38
D189V4, multiclass
    clus
vv   LATS1 MUTATED LATS1 WILD-TYPE
  T1             1               8
  T2             1              67
  T3            13             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
  LATS1 MUTATED    11   4   3
  LATS1 WILD-TYPE 209  76  63
D189V5, multiclass
    clus
vv   LATS1 MUTATED LATS1 WILD-TYPE
  N0            11             209
  N1             4              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"
D189V6, binary
                 cls
clus                0   1
  LATS1 MUTATED    14   1
  LATS1 WILD-TYPE 269  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LATS1 MUTATED     14    1
  LATS1 WILD-TYPE  269   47
   clus
vv  LATS1 MUTATED LATS1 WILD-TYPE
  0            14             269
  1             1              47
[1] 2 2
[1] FALSE
D189V7, 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
D189V8, binary
                 cls
clus                0   1
  LATS1 MUTATED    16   2
  LATS1 WILD-TYPE 301  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LATS1 MUTATED     16    2
  LATS1 WILD-TYPE  301   46
                               clus
vv                              LATS1 MUTATED LATS1 WILD-TYPE
  COLON ADENOCARCINOMA                     16             301
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  LATS1 MUTATED    10   1   1   1
  LATS1 WILD-TYPE 247   1  21  20
D189V9, multiclass
    clus
vv   LATS1 MUTATED LATS1 WILD-TYPE
  R0            10             247
  R1             1               1
  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"
D189V10, 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
D189V11, 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(190) Variable = KIAA1586 MUTATION ANALYSIS
D190V1, survival
                    sevent
clus2                  0   1
  KIAA1586 MUTATED     7   2
  KIAA1586 WILD-TYPE 275  71
  KIAA1586 MUTATED KIAA1586 WILD-TYPE 
                 9                346 
  KIAA1586 MUTATED KIAA1586 WILD-TYPE 
                 2                 71 
$`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         0.33         0.10 
TCGA-CK-6748 TCGA-DM-A1D7 TCGA-F4-6570 
        2.01        13.32         6.18 

$`KIAA1586 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99        21.14         2.93       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        49.91        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  KIAA1586 MUTATED KIAA1586 WILD-TYPE 
               0.1                0.0 
  KIAA1586 MUTATED KIAA1586 WILD-TYPE 
             63.98             140.38 
  KIAA1586 MUTATED KIAA1586 WILD-TYPE 
            13.320             20.235 
[1] "0.1 - 64.0 (13.3)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D190V2, 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       24       102         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1586 MUTATED           0          0          0          0        1
  KIAA1586 WILD-TYPE        19         10         41         31       34
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA1586 MUTATED           0         0
  KIAA1586 WILD-TYPE        13         1
D190V3, multiclass
            clus
vv           KIAA1586 MUTATED KIAA1586 WILD-TYPE
  STAGE I                   0                 64
  STAGE IA                  0                  1
  STAGE II                  1                 24
  STAGE IIA                 7                102
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                0                 10
  STAGE IIIB                0                 41
  STAGE IIIC                0                 31
  STAGE IV                  1                 34
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA1586 MUTATED     0   1   9   1
  KIAA1586 WILD-TYPE   9  67 239  40
D190V4, multiclass
    clus
vv   KIAA1586 MUTATED KIAA1586 WILD-TYPE
  T1                0                  9
  T2                1                 67
  T3                9                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
  KIAA1586 MUTATED    10   1   0
  KIAA1586 WILD-TYPE 210  79  66
D190V5, multiclass
    clus
vv   KIAA1586 MUTATED KIAA1586 WILD-TYPE
  N0               10                210
  N1                1                 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"
D190V6, binary
                    cls
clus                   0   1
  KIAA1586 MUTATED     8   1
  KIAA1586 WILD-TYPE 275  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1586 MUTATED      8    1
  KIAA1586 WILD-TYPE  275   47
   clus
vv  KIAA1586 MUTATED KIAA1586 WILD-TYPE
  0                8                275
  1                1                 47
[1] 2 2
[1] FALSE
D190V7, 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
D190V8, binary
                    cls
clus                   0   1
  KIAA1586 MUTATED     9   2
  KIAA1586 WILD-TYPE 308  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1586 MUTATED      9    2
  KIAA1586 WILD-TYPE  308   46
                               clus
vv                              KIAA1586 MUTATED KIAA1586 WILD-TYPE
  COLON ADENOCARCINOMA                         9                308
  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 252   2  22  17
D190V9, multiclass
    clus
vv   KIAA1586 MUTATED KIAA1586 WILD-TYPE
  R0                5                252
  R1                0                  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"
D190V10, 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
D190V11, 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(191) Variable = FKBP9 MUTATION ANALYSIS
D191V1, survival
                 sevent
clus2               0   1
  FKBP9 MUTATED    15   2
  FKBP9 WILD-TYPE 267  71
  FKBP9 MUTATED FKBP9 WILD-TYPE 
             17             338 
  FKBP9 MUTATED FKBP9 WILD-TYPE 
              2              71 
$`FKBP9 MUTATED`
TCGA-A6-6780 TCGA-AA-3697 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q 
       20.12        85.05        25.02         4.01        34.98         1.02 
TCGA-AD-6889 TCGA-AZ-4315 TCGA-AZ-6601 TCGA-CK-5913 TCGA-CM-5348 TCGA-CM-5861 
       56.55        58.39       100.01        51.32        22.98        15.02 
TCGA-CM-6678 TCGA-D5-6930 TCGA-DM-A28H TCGA-G4-6588 TCGA-G4-6628 
       11.01         1.51       117.07        26.17        52.80 

$`FKBP9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        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        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       40.34        15.62        49.08        21.99        21.14         2.93 
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-5862 
       13.02        29.06        22.03        30.08        16.01         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       35.97        60.79        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 
       91.79        46.75 

  FKBP9 MUTATED FKBP9 WILD-TYPE 
           1.02            0.00 
  FKBP9 MUTATED FKBP9 WILD-TYPE 
         117.07          140.38 
  FKBP9 MUTATED FKBP9 WILD-TYPE 
          26.17           19.99 
[1] "1.0 - 117.1 (26.2)" "0.0 - 140.4 (20.0)"
[1] "hr=" "2.9"
D191V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FKBP9 MUTATED         1        0        2         7         2         0
  FKBP9 WILD-TYPE      63        1       23       102         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FKBP9 MUTATED           1          0          1          1        0         1
  FKBP9 WILD-TYPE        18         10         40         30       35        12
                 vv
clus              STAGE IVB
  FKBP9 MUTATED           0
  FKBP9 WILD-TYPE         1
D191V3, multiclass
            clus
vv           FKBP9 MUTATED FKBP9 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              7             102
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 236  38
D191V4, multiclass
    clus
vv   FKBP9 MUTATED FKBP9 WILD-TYPE
  T1             0               9
  T2             2              66
  T3            12             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
  FKBP9 MUTATED    14   2   1
  FKBP9 WILD-TYPE 206  78  65
D191V5, multiclass
    clus
vv   FKBP9 MUTATED FKBP9 WILD-TYPE
  N0            14             206
  N1             2              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"
D191V6, binary
                 cls
clus                0   1
  FKBP9 MUTATED    13   1
  FKBP9 WILD-TYPE 270  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FKBP9 MUTATED     13    1
  FKBP9 WILD-TYPE  270   47
   clus
vv  FKBP9 MUTATED FKBP9 WILD-TYPE
  0            13             270
  1             1              47
[1] 2 2
[1] FALSE
D191V7, 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
D191V8, binary
                 cls
clus                0   1
  FKBP9 MUTATED    14   3
  FKBP9 WILD-TYPE 303  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FKBP9 MUTATED     14    3
  FKBP9 WILD-TYPE  303   45
                               clus
vv                              FKBP9 MUTATED FKBP9 WILD-TYPE
  COLON ADENOCARCINOMA                     14             303
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  FKBP9 MUTATED    11   0   0   1
  FKBP9 WILD-TYPE 246   2  22  20
D191V9, multiclass
    clus
vv   FKBP9 MUTATED FKBP9 WILD-TYPE
  R0            11             246
  R1             0               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"
D191V10, 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
D191V11, 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(192) Variable = SCD5 MUTATION ANALYSIS
D192V1, survival
                sevent
clus2              0   1
  SCD5 MUTATED     6   3
  SCD5 WILD-TYPE 276  70
  SCD5 MUTATED SCD5 WILD-TYPE 
             9            346 
  SCD5 MUTATED SCD5 WILD-TYPE 
             3             70 
$`SCD5 MUTATED`
TCGA-AA-3663 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-A00E TCGA-AD-6964 TCGA-CM-6162 
        6.97         5.03        26.99        30.02        10.88        12.00 
TCGA-DM-A28K TCGA-G4-6586 TCGA-G4-6626 
       98.24        35.80        46.75 

$`SCD5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       36.00        85.05        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
        0.72         5.79        22.42        27.42         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 
       81.37       119.93        35.97        60.79       117.07         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       13.78        26.17        91.79        52.80 

  SCD5 MUTATED SCD5 WILD-TYPE 
          5.03           0.00 
  SCD5 MUTATED SCD5 WILD-TYPE 
         98.24         140.38 
  SCD5 MUTATED SCD5 WILD-TYPE 
        26.990         20.155 
[1] "5.0 - 98.2 (27.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.5"
D192V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SCD5 MUTATED         0        0        1         5         0         0
  SCD5 WILD-TYPE      64        1       24       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        19         10         40         31       34        13
                vv
clus             STAGE IVB
  SCD5 MUTATED           0
  SCD5 WILD-TYPE         1
D192V3, multiclass
            clus
vv           SCD5 MUTATED SCD5 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             5            104
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SCD5 MUTATED     0   0   8   1
  SCD5 WILD-TYPE   9  68 240  40
D192V4, multiclass
    clus
vv   SCD5 MUTATED SCD5 WILD-TYPE
  T1            0              9
  T2            0             68
  T3            8            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
  SCD5 MUTATED     6   2   1
  SCD5 WILD-TYPE 214  78  65
D192V5, multiclass
    clus
vv   SCD5 MUTATED SCD5 WILD-TYPE
  N0            6            214
  N1            2             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"
D192V6, binary
                cls
clus               0   1
  SCD5 MUTATED     7   1
  SCD5 WILD-TYPE 276  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  SCD5 MUTATED      7    1
  SCD5 WILD-TYPE  276   47
   clus
vv  SCD5 MUTATED SCD5 WILD-TYPE
  0            7            276
  1            1             47
[1] 2 2
[1] FALSE
D192V7, binary
                cls
clus               0   1
  SCD5 MUTATED     4   5
  SCD5 WILD-TYPE 166 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  SCD5 MUTATED      4    5
  SCD5 WILD-TYPE  166  192
        clus
vv       SCD5 MUTATED SCD5 WILD-TYPE
  FEMALE            4            166
  MALE              5            192
[1] 2 2
[1] FALSE
D192V8, binary
                cls
clus               0   1
  SCD5 MUTATED     7   2
  SCD5 WILD-TYPE 310  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  SCD5 MUTATED      7    2
  SCD5 WILD-TYPE  310   46
                               clus
vv                              SCD5 MUTATED SCD5 WILD-TYPE
  COLON ADENOCARCINOMA                     7            310
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SCD5 MUTATED     6   0   1   0
  SCD5 WILD-TYPE 251   2  21  21
D192V9, multiclass
    clus
vv   SCD5 MUTATED SCD5 WILD-TYPE
  R0            6            251
  R1            0              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"
D192V10, 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
D192V11, 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(193) Variable = SHROOM4 MUTATION ANALYSIS
D193V1, survival
                   sevent
clus2                 0   1
  SHROOM4 MUTATED    14   4
  SHROOM4 WILD-TYPE 268  69
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
               18               337 
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
                4                69 
$`SHROOM4 MUTATED`
TCGA-A6-5661 TCGA-AA-3811 TCGA-AA-3815 TCGA-AA-3947 TCGA-AA-A00N TCGA-AD-6889 
       33.53        10.06        33.04        33.01         4.01        56.55 
TCGA-CA-5796 TCGA-CK-5913 TCGA-CM-6164 TCGA-CM-6678 TCGA-D5-6537 TCGA-D5-6540 
        3.25        51.32        29.03        11.01         4.80        16.14 
TCGA-D5-6922 TCGA-D5-7000 TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28E TCGA-F4-6570 
       10.13        10.26       135.65       139.17       119.93         6.18 

$`SHROOM4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37         4.21         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
       17.56       102.44        40.34        15.62        49.08        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        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-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.08        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 
       18.25         1.32        43.27        15.12        17.85        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 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-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64        13.41         1.51        12.00 
TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
      131.51         6.12        81.37        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        13.38        13.45        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
             3.25              0.00 
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
           139.17            140.38 
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
           22.585            20.190 
[1] "3.2 - 139.2 (22.6)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.3"
D193V2, 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       25        99         5         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SHROOM4 MUTATED           1          1          2          0        0
  SHROOM4 WILD-TYPE        18          9         39         31       35
                   vv
clus                STAGE IVA STAGE IVB
  SHROOM4 MUTATED           1         0
  SHROOM4 WILD-TYPE        12         1
D193V3, multiclass
            clus
vv           SHROOM4 MUTATED SHROOM4 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA               10                99
  STAGE IIB                3                 5
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               1                 9
  STAGE IIIB               2                39
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                1                12
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of 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  65 234  37
D193V4, multiclass
    clus
vv   SHROOM4 MUTATED SHROOM4 WILD-TYPE
  T1               0                 9
  T2               3                65
  T3              14               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
  SHROOM4 MUTATED    16   4   1
  SHROOM4 WILD-TYPE 204  76  65
D193V5, multiclass
    clus
vv   SHROOM4 MUTATED SHROOM4 WILD-TYPE
  N0              16               204
  N1               4                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"
D193V6, binary
                   cls
clus                  0   1
  SHROOM4 MUTATED    16   1
  SHROOM4 WILD-TYPE 267  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SHROOM4 MUTATED     16    1
  SHROOM4 WILD-TYPE  267   47
   clus
vv  SHROOM4 MUTATED SHROOM4 WILD-TYPE
  0              16               267
  1               1                47
[1] 2 2
[1] FALSE
D193V7, 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
D193V8, binary
                   cls
clus                  0   1
  SHROOM4 MUTATED    16   5
  SHROOM4 WILD-TYPE 301  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SHROOM4 MUTATED     16    5
  SHROOM4 WILD-TYPE  301   43
                               clus
vv                              SHROOM4 MUTATED SHROOM4 WILD-TYPE
  COLON ADENOCARCINOMA                       16               301
  COLON MUCINOUS ADENOCARCINOMA               5                43
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SHROOM4 MUTATED    14   0   0   3
  SHROOM4 WILD-TYPE 243   2  22  18
D193V9, multiclass
    clus
vv   SHROOM4 MUTATED SHROOM4 WILD-TYPE
  R0              14               243
  R1               0                 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"
D193V10, 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
D193V11, 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(194) Variable = SNAI2 MUTATION ANALYSIS
D194V1, survival
                 sevent
clus2               0   1
  SNAI2 MUTATED     7   1
  SNAI2 WILD-TYPE 275  72
  SNAI2 MUTATED SNAI2 WILD-TYPE 
              8             347 
  SNAI2 MUTATED SNAI2 WILD-TYPE 
              1              72 
$`SNAI2 MUTATED`
TCGA-AA-3655 TCGA-AA-A00N TCGA-CA-6717 TCGA-CK-4952 TCGA-CM-4752 TCGA-G4-6306 
       61.02         4.01         0.33        15.62        13.02        44.68 
TCGA-G4-6321 TCGA-G4-6323 
       22.09        13.78 

$`SNAI2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       40.34        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  SNAI2 MUTATED SNAI2 WILD-TYPE 
           0.33            0.00 
  SNAI2 MUTATED SNAI2 WILD-TYPE 
          61.02          140.38 
  SNAI2 MUTATED SNAI2 WILD-TYPE 
          14.70           20.28 
[1] "0.3 - 61.0 (14.7)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.5"
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       24       106         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SNAI2 MUTATED           2          0          0          0        0         0
  SNAI2 WILD-TYPE        17         10         41         31       35        13
                 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              24
  STAGE IIA              3             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SNAI2 MUTATED     0   2   3   2
  SNAI2 WILD-TYPE   9  66 245  39
D194V4, multiclass
    clus
vv   SNAI2 MUTATED SNAI2 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             3             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
  SNAI2 MUTATED     6   1   1
  SNAI2 WILD-TYPE 214  79  65
D194V5, multiclass
    clus
vv   SNAI2 MUTATED SNAI2 WILD-TYPE
  N0             6             214
  N1             1              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     6   0
  SNAI2 WILD-TYPE 277  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SNAI2 MUTATED      6    0
  SNAI2 WILD-TYPE  277   48
   clus
vv  SNAI2 MUTATED SNAI2 WILD-TYPE
  0             6             277
  1             0              48
[1] 2 2
[1] FALSE
D194V7, binary
                 cls
clus                0   1
  SNAI2 MUTATED     2   6
  SNAI2 WILD-TYPE 168 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SNAI2 MUTATED      2    6
  SNAI2 WILD-TYPE  168  191
        clus
vv       SNAI2 MUTATED SNAI2 WILD-TYPE
  FEMALE             2             168
  MALE               6             191
[1] 2 2
[1] FALSE
D194V8, binary
                 cls
clus                0   1
  SNAI2 MUTATED     5   3
  SNAI2 WILD-TYPE 312  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SNAI2 MUTATED      5    3
  SNAI2 WILD-TYPE  312   45
                               clus
vv                              SNAI2 MUTATED SNAI2 WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SNAI2 MUTATED     6   0   0   2
  SNAI2 WILD-TYPE 251   2  22  19
D194V9, multiclass
    clus
vv   SNAI2 MUTATED SNAI2 WILD-TYPE
  R0             6             251
  R1             0               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"
D194V10, 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     3
  SNAI2 WILD-TYPE                        17   173
D194V11, 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                                        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(195) Variable = C14ORF43 MUTATION ANALYSIS
D195V1, survival
                    sevent
clus2                  0   1
  C14ORF43 MUTATED    15   3
  C14ORF43 WILD-TYPE 267  70
  C14ORF43 MUTATED C14ORF43 WILD-TYPE 
                18                337 
  C14ORF43 MUTATED C14ORF43 WILD-TYPE 
                 3                 70 
$`C14ORF43 MUTATED`
TCGA-A6-3809 TCGA-AA-3518 TCGA-AA-3663 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3864 
       32.75         1.02         6.97        26.99        19.04        53.00 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CK-5916 
        0.07        56.55        49.41       100.01         0.33        21.14 
TCGA-CM-6170 TCGA-CM-6171 TCGA-D5-6930 TCGA-G4-6309 TCGA-G4-6588 TCGA-G4-6625 
       15.02        14.04         1.51        51.75        26.17        91.79 

$`C14ORF43 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       85.05        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        4.21         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13        83.80        22.36        62.79        61.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32        21.99         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       74.56        65.85        53.62        44.68        55.04        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6626 
       36.72        36.00        22.09        13.78        35.80        46.75 
TCGA-G4-6628 
       52.80 

  C14ORF43 MUTATED C14ORF43 WILD-TYPE 
              0.07               0.00 
  C14ORF43 MUTATED C14ORF43 WILD-TYPE 
            100.01             140.38 
  C14ORF43 MUTATED C14ORF43 WILD-TYPE 
            23.655             20.120 
[1] "0.1 - 100.0 (23.7)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.6"
D195V2, 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       21       102         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C14ORF43 MUTATED           0          0          1          0        1
  C14ORF43 WILD-TYPE        19         10         40         31       34
                    vv
clus                 STAGE IVA STAGE IVB
  C14ORF43 MUTATED           0         0
  C14ORF43 WILD-TYPE        13         1
D195V3, multiclass
            clus
vv           C14ORF43 MUTATED C14ORF43 WILD-TYPE
  STAGE I                   4                 60
  STAGE IA                  0                  1
  STAGE II                  4                 21
  STAGE IIA                 7                102
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                0                 10
  STAGE IIIB                1                 40
  STAGE IIIC                0                 31
  STAGE IV                  1                 34
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C14ORF43 MUTATED     1   3  13   1
  C14ORF43 WILD-TYPE   8  65 235  40
D195V4, multiclass
    clus
vv   C14ORF43 MUTATED C14ORF43 WILD-TYPE
  T1                1                  8
  T2                3                 65
  T3               13                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
  C14ORF43 MUTATED    17   1   0
  C14ORF43 WILD-TYPE 203  79  66
D195V5, multiclass
    clus
vv   C14ORF43 MUTATED C14ORF43 WILD-TYPE
  N0               17                203
  N1                1                 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"
D195V6, binary
                    cls
clus                   0   1
  C14ORF43 MUTATED    15   1
  C14ORF43 WILD-TYPE 268  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF43 MUTATED     15    1
  C14ORF43 WILD-TYPE  268   47
   clus
vv  C14ORF43 MUTATED C14ORF43 WILD-TYPE
  0               15                268
  1                1                 47
[1] 2 2
[1] FALSE
D195V7, 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
D195V8, binary
                    cls
clus                   0   1
  C14ORF43 MUTATED    14   4
  C14ORF43 WILD-TYPE 303  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF43 MUTATED     14    4
  C14ORF43 WILD-TYPE  303   44
                               clus
vv                              C14ORF43 MUTATED C14ORF43 WILD-TYPE
  COLON ADENOCARCINOMA                        14                303
  COLON MUCINOUS ADENOCARCINOMA                4                 44
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C14ORF43 MUTATED    12   0   1   2
  C14ORF43 WILD-TYPE 245   2  21  19
D195V9, multiclass
    clus
vv   C14ORF43 MUTATED C14ORF43 WILD-TYPE
  R0               12                245
  R1                0                  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"
D195V10, 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
D195V11, 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(196) Variable = SMARCA4 MUTATION ANALYSIS
D196V1, survival
                   sevent
clus2                 0   1
  SMARCA4 MUTATED    24   5
  SMARCA4 WILD-TYPE 258  68
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
               29               326 
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
                5                68 
$`SMARCA4 MUTATED`
TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3518 TCGA-AA-3524 TCGA-AA-3529 
       24.39        19.66         3.02         1.02        36.03         0.00 
TCGA-AA-3558 TCGA-AA-3663 TCGA-AA-3815 TCGA-AA-3977 TCGA-AA-A010 TCGA-AD-6889 
       20.98         6.97        33.04        25.02        34.98        56.55 
TCGA-AD-6964 TCGA-AY-6197 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CK-4950 
       10.88        21.44        49.41       100.01         0.33        40.34 
TCGA-CM-4746 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-6161 TCGA-CM-6674 
       37.02        13.02        22.03        22.98        15.02        12.95 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6928 TCGA-G4-6310 TCGA-G4-6588 
       43.27        17.85        11.64        45.11        26.17 

$`SMARCA4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.12        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 
        6.97         1.02        13.02        38.99         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
       37.05         8.05        19.07        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37         4.21         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        15.75         0.20        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13        83.80        22.36        62.79        61.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 
        0.10         1.35        17.56       102.44        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5349 TCGA-CM-5860 
       23.05        20.02        25.02        29.06        30.08        16.01 
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-6675 TCGA-CM-6676 
       13.02        15.02        14.04        11.01        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
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-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44        13.41         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
                0                 0 
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
           100.01            140.38 
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
           22.030            20.005 
[1] "0.0 - 100.0 (22.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.2"
D196V2, 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       20        98         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SMARCA4 MUTATED           1          1          3          2        0
  SMARCA4 WILD-TYPE        18          9         38         29       35
                   vv
clus                STAGE IVA STAGE IVB
  SMARCA4 MUTATED           0         0
  SMARCA4 WILD-TYPE        13         1
D196V3, multiclass
            clus
vv           SMARCA4 MUTATED SMARCA4 WILD-TYPE
  STAGE I                  4                60
  STAGE IA                 0                 1
  STAGE II                 5                20
  STAGE IIA               11                98
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               1                 9
  STAGE IIIB               3                38
  STAGE IIIC               2                29
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SMARCA4 MUTATED     0   5  22   3
  SMARCA4 WILD-TYPE   9  63 226  38
D196V4, multiclass
    clus
vv   SMARCA4 MUTATED SMARCA4 WILD-TYPE
  T1               0                 9
  T2               5                63
  T3              22               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
  SMARCA4 MUTATED    22   5   3
  SMARCA4 WILD-TYPE 198  75  63
D196V5, multiclass
    clus
vv   SMARCA4 MUTATED SMARCA4 WILD-TYPE
  N0              22               198
  N1               5                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"
D196V6, binary
                   cls
clus                  0   1
  SMARCA4 MUTATED    25   0
  SMARCA4 WILD-TYPE 258  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA4 MUTATED     25    0
  SMARCA4 WILD-TYPE  258   48
   clus
vv  SMARCA4 MUTATED SMARCA4 WILD-TYPE
  0              25               258
  1               0                48
[1] 2 2
[1] FALSE
D196V7, 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
D196V8, binary
                   cls
clus                  0   1
  SMARCA4 MUTATED    26   4
  SMARCA4 WILD-TYPE 291  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA4 MUTATED     26    4
  SMARCA4 WILD-TYPE  291   44
                               clus
vv                              SMARCA4 MUTATED SMARCA4 WILD-TYPE
  COLON ADENOCARCINOMA                       26               291
  COLON MUCINOUS ADENOCARCINOMA               4                44
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SMARCA4 MUTATED    21   1   1   1
  SMARCA4 WILD-TYPE 236   1  21  20
D196V9, multiclass
    clus
vv   SMARCA4 MUTATED SMARCA4 WILD-TYPE
  R0              21               236
  R1               1                 1
  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"
D196V10, 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
D196V11, 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(197) Variable = DNAH12 MUTATION ANALYSIS
D197V1, survival
                  sevent
clus2                0   1
  DNAH12 MUTATED    20   3
  DNAH12 WILD-TYPE 262  70
  DNAH12 MUTATED DNAH12 WILD-TYPE 
              23              332 
  DNAH12 MUTATED DNAH12 WILD-TYPE 
               3               70 
$`DNAH12 MUTATED`
TCGA-A6-3809 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6780 TCGA-AA-3489 TCGA-AA-3502 
       32.75        22.06         8.38        20.12         7.04        35.01 
TCGA-AA-3510 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3815 TCGA-AA-3877 TCGA-AA-3950 
       63.98        19.04        10.06        33.04        31.00        24.00 
TCGA-AA-A010 TCGA-AD-6895 TCGA-AY-6197 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 
       34.98         0.72        21.44        58.39         0.33         0.10 
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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       32.71        27.09        22.52        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 
       21.76        24.69        24.39        23.87        19.66        20.28 
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        3.02         1.02         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3812 
       36.00         5.03        85.05        26.99        19.04        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        4.21        56.55         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       15.75         0.20        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 
       15.58         7.53        12.39        10.13        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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      117.07        98.24         8.61        13.38        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  DNAH12 MUTATED DNAH12 WILD-TYPE 
             0.1              0.0 
  DNAH12 MUTATED DNAH12 WILD-TYPE 
          135.65           140.38 
  DNAH12 MUTATED DNAH12 WILD-TYPE 
          21.440           20.105 
[1] "0.1 - 135.7 (21.4)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.6"
D197V2, 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       23        98         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DNAH12 MUTATED           1          1          1          0        1
  DNAH12 WILD-TYPE        18          9         40         31       34
                  vv
clus               STAGE IVA STAGE IVB
  DNAH12 MUTATED           0         0
  DNAH12 WILD-TYPE        13         1
D197V3, multiclass
            clus
vv           DNAH12 MUTATED DNAH12 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA              11               98
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              1                9
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  DNAH12 MUTATED     1   3  17   2
  DNAH12 WILD-TYPE   8  65 231  39
D197V4, multiclass
    clus
vv   DNAH12 MUTATED DNAH12 WILD-TYPE
  T1              1                8
  T2              3               65
  T3             17              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
  DNAH12 MUTATED    19   3   1
  DNAH12 WILD-TYPE 201  77  65
D197V5, multiclass
    clus
vv   DNAH12 MUTATED DNAH12 WILD-TYPE
  N0             19              201
  N1              3               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
  DNAH12 MUTATED    19   1
  DNAH12 WILD-TYPE 264  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAH12 MUTATED     19    1
  DNAH12 WILD-TYPE  264   47
   clus
vv  DNAH12 MUTATED DNAH12 WILD-TYPE
  0             19              264
  1              1               47
[1] 2 2
[1] FALSE
D197V7, 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
D197V8, binary
                  cls
clus                 0   1
  DNAH12 MUTATED    18   5
  DNAH12 WILD-TYPE 299  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAH12 MUTATED     18    5
  DNAH12 WILD-TYPE  299   43
                               clus
vv                              DNAH12 MUTATED DNAH12 WILD-TYPE
  COLON ADENOCARCINOMA                      18              299
  COLON MUCINOUS ADENOCARCINOMA              5               43
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  DNAH12 MUTATED    16   0   1   2
  DNAH12 WILD-TYPE 241   2  21  19
D197V9, multiclass
    clus
vv   DNAH12 MUTATED DNAH12 WILD-TYPE
  R0             16              241
  R1              0                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"
D197V10, 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
D197V11, 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(198) Variable = OSBPL2 MUTATION ANALYSIS
D198V1, survival
                  sevent
clus2                0   1
  OSBPL2 MUTATED    10   1
  OSBPL2 WILD-TYPE 272  72
  OSBPL2 MUTATED OSBPL2 WILD-TYPE 
              11              344 
  OSBPL2 MUTATED OSBPL2 WILD-TYPE 
               1               72 
$`OSBPL2 MUTATED`
TCGA-A6-5661 TCGA-A6-6654 TCGA-AU-6004 TCGA-AZ-4315 TCGA-CA-6715 TCGA-CK-5913 
       33.53        23.87        27.09        58.39         0.07        51.32 
TCGA-CM-5349 TCGA-CM-5862 TCGA-D5-7000 TCGA-DM-A28K TCGA-G4-6293 
       30.08         5.03        10.26        98.24       107.67 

$`OSBPL2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 
        2.24         3.06         3.25         3.29         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        21.99        21.14         2.93         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-5863 TCGA-CM-5864 
       22.03        22.98        16.01        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79       117.07         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        35.41        19.43        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  OSBPL2 MUTATED OSBPL2 WILD-TYPE 
            0.07             0.00 
  OSBPL2 MUTATED OSBPL2 WILD-TYPE 
          107.67           140.38 
  OSBPL2 MUTATED OSBPL2 WILD-TYPE 
          30.080           20.005 
[1] "0.1 - 107.7 (30.1)" "0.0 - 140.4 (20.0)"
[1] "hr=" "3.6"
D198V2, 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       25       104         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OSBPL2 MUTATED           1          0          2          0        0
  OSBPL2 WILD-TYPE        18         10         39         31       35
                  vv
clus               STAGE IVA STAGE IVB
  OSBPL2 MUTATED           1         0
  OSBPL2 WILD-TYPE        12         1
D198V3, multiclass
            clus
vv           OSBPL2 MUTATED OSBPL2 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               5              104
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 239  41
D198V4, multiclass
    clus
vv   OSBPL2 MUTATED OSBPL2 WILD-TYPE
  T1              0                9
  T2              2               66
  T3              9              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
  OSBPL2 MUTATED     7   4   0
  OSBPL2 WILD-TYPE 213  76  66
D198V5, multiclass
    clus
vv   OSBPL2 MUTATED OSBPL2 WILD-TYPE
  N0              7              213
  N1              4               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"
D198V6, binary
                  cls
clus                 0   1
  OSBPL2 MUTATED     9   1
  OSBPL2 WILD-TYPE 274  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OSBPL2 MUTATED      9    1
  OSBPL2 WILD-TYPE  274   47
   clus
vv  OSBPL2 MUTATED OSBPL2 WILD-TYPE
  0              9              274
  1              1               47
[1] 2 2
[1] FALSE
D198V7, 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
D198V8, binary
                  cls
clus                 0   1
  OSBPL2 MUTATED     9   2
  OSBPL2 WILD-TYPE 308  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OSBPL2 MUTATED      9    2
  OSBPL2 WILD-TYPE  308   46
                               clus
vv                              OSBPL2 MUTATED OSBPL2 WILD-TYPE
  COLON ADENOCARCINOMA                       9              308
  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 250   2  22  19
D198V9, multiclass
    clus
vv   OSBPL2 MUTATED OSBPL2 WILD-TYPE
  R0              7              250
  R1              0                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"
D198V10, 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
D198V11, 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(199) Variable = MAGEA1 MUTATION ANALYSIS
D199V1, survival
                  sevent
clus2                0   1
  MAGEA1 MUTATED    10   3
  MAGEA1 WILD-TYPE 272  70
  MAGEA1 MUTATED MAGEA1 WILD-TYPE 
              13              342 
  MAGEA1 MUTATED MAGEA1 WILD-TYPE 
               3               70 
$`MAGEA1 MUTATED`
TCGA-AA-3510 TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4616 TCGA-AZ-5403 TCGA-CK-4948 
       63.98        15.75        21.44         5.13        62.79       102.44 
TCGA-CK-5914 TCGA-CK-6748 TCGA-D5-6539 TCGA-F4-6805 TCGA-G4-6303 TCGA-G4-6588 
       21.99         2.01        12.49        16.31        65.85        26.17 
TCGA-G4-6628 
       52.80 

$`MAGEA1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4681 
        0.95         0.20        17.82        58.39         1.41        83.80 
TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        0.10         1.35        17.56        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       51.32        21.14         2.93       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18        35.87         1.55        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 

  MAGEA1 MUTATED MAGEA1 WILD-TYPE 
            2.01             0.00 
  MAGEA1 MUTATED MAGEA1 WILD-TYPE 
          102.44           140.38 
  MAGEA1 MUTATED MAGEA1 WILD-TYPE 
           21.99            20.07 
[1] "2.0 - 102.4 (22.0)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.4"
D199V2, 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       23       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAGEA1 MUTATED           0          2          1          0        3
  MAGEA1 WILD-TYPE        19          8         40         31       32
                  vv
clus               STAGE IVA STAGE IVB
  MAGEA1 MUTATED           1         0
  MAGEA1 WILD-TYPE        12         1
D199V3, multiclass
            clus
vv           MAGEA1 MUTATED MAGEA1 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               3              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              2                8
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                3               32
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 236  41
D199V4, multiclass
    clus
vv   MAGEA1 MUTATED MAGEA1 WILD-TYPE
  T1              0                9
  T2              1               67
  T3             12              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
  MAGEA1 MUTATED     7   5   1
  MAGEA1 WILD-TYPE 213  75  65
D199V5, multiclass
    clus
vv   MAGEA1 MUTATED MAGEA1 WILD-TYPE
  N0              7              213
  N1              5               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"
D199V6, binary
                  cls
clus                 0   1
  MAGEA1 MUTATED     6   4
  MAGEA1 WILD-TYPE 277  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGEA1 MUTATED      6    4
  MAGEA1 WILD-TYPE  277   44
   clus
vv  MAGEA1 MUTATED MAGEA1 WILD-TYPE
  0              6              277
  1              4               44
[1] 2 2
[1] FALSE
D199V7, 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
D199V8, binary
                  cls
clus                 0   1
  MAGEA1 MUTATED    12   1
  MAGEA1 WILD-TYPE 305  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGEA1 MUTATED     12    1
  MAGEA1 WILD-TYPE  305   47
                               clus
vv                              MAGEA1 MUTATED MAGEA1 WILD-TYPE
  COLON ADENOCARCINOMA                      12              305
  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 248   2  22  19
D199V9, multiclass
    clus
vv   MAGEA1 MUTATED MAGEA1 WILD-TYPE
  R0              9              248
  R1              0                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"
D199V10, 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
D199V11, 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(200) Variable = C9ORF84 MUTATION ANALYSIS
D200V1, survival
                   sevent
clus2                 0   1
  C9ORF84 MUTATED    15   4
  C9ORF84 WILD-TYPE 267  69
  C9ORF84 MUTATED C9ORF84 WILD-TYPE 
               19               336 
  C9ORF84 MUTATED C9ORF84 WILD-TYPE 
                4                69 
$`C9ORF84 MUTATED`
TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3715 TCGA-AA-3845 TCGA-AA-A00J TCGA-AA-A010 
       19.66         7.04        19.04         0.00        18.05        34.98 
TCGA-AD-5900 TCGA-AD-6889 TCGA-CA-5796 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-6751 
        0.07        56.55         3.25         0.33         0.10       124.27 
TCGA-CM-4746 TCGA-D5-6923 TCGA-F4-6809 TCGA-F4-6856 TCGA-G4-6304 TCGA-G4-6307 
       37.02        12.43        13.25        19.43        53.62        55.04 
TCGA-G4-6310 
       45.11 

$`C9ORF84 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       23.87        20.12        20.28         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       38.99        37.02        14.93        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        4.21         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5797 TCGA-CA-6715 
        3.19         1.94         2.24         3.06         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.26         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 
       15.58         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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 
       16.24        33.67         0.53        35.41       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       65.85        44.68        51.75        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  C9ORF84 MUTATED C9ORF84 WILD-TYPE 
                0                 0 
  C9ORF84 MUTATED C9ORF84 WILD-TYPE 
           124.27            140.38 
  C9ORF84 MUTATED C9ORF84 WILD-TYPE 
            19.04             20.98 
[1] "0.0 - 124.3 (19.0)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1"  
D200V2, 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       23       103         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C9ORF84 MUTATED           0          0          3          1        0
  C9ORF84 WILD-TYPE        19         10         38         30       35
                   vv
clus                STAGE IVA STAGE IVB
  C9ORF84 MUTATED           1         0
  C9ORF84 WILD-TYPE        12         1
D200V3, multiclass
            clus
vv           C9ORF84 MUTATED C9ORF84 WILD-TYPE
  STAGE I                  5                59
  STAGE IA                 0                 1
  STAGE II                 2                23
  STAGE IIA                6               103
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               3                38
  STAGE IIIC               1                30
  STAGE IV                 0                35
  STAGE IVA                1                12
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of 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  63 237  37
D200V4, multiclass
    clus
vv   C9ORF84 MUTATED C9ORF84 WILD-TYPE
  T1               0                 9
  T2               5                63
  T3              11               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
  C9ORF84 MUTATED    15   5   0
  C9ORF84 WILD-TYPE 205  75  66
D200V5, multiclass
    clus
vv   C9ORF84 MUTATED C9ORF84 WILD-TYPE
  N0              15               205
  N1               5                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"
D200V6, binary
                   cls
clus                  0   1
  C9ORF84 MUTATED    16   1
  C9ORF84 WILD-TYPE 267  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF84 MUTATED     16    1
  C9ORF84 WILD-TYPE  267   47
   clus
vv  C9ORF84 MUTATED C9ORF84 WILD-TYPE
  0              16               267
  1               1                47
[1] 2 2
[1] FALSE
D200V7, 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
D200V8, binary
                   cls
clus                  0   1
  C9ORF84 MUTATED    13   7
  C9ORF84 WILD-TYPE 304  41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF84 MUTATED     13    7
  C9ORF84 WILD-TYPE  304   41
                               clus
vv                              C9ORF84 MUTATED C9ORF84 WILD-TYPE
  COLON ADENOCARCINOMA                       13               304
  COLON MUCINOUS ADENOCARCINOMA               7                41
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  C9ORF84 MUTATED    16   0   0   3
  C9ORF84 WILD-TYPE 241   2  22  18
D200V9, multiclass
    clus
vv   C9ORF84 MUTATED C9ORF84 WILD-TYPE
  R0              16               241
  R1               0                 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"
D200V10, 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
D200V11, 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(201) Variable = NT5DC3 MUTATION ANALYSIS
D201V1, survival
                  sevent
clus2                0   1
  NT5DC3 MUTATED     9   3
  NT5DC3 WILD-TYPE 273  70
  NT5DC3 MUTATED NT5DC3 WILD-TYPE 
              12              343 
  NT5DC3 MUTATED NT5DC3 WILD-TYPE 
               3               70 
$`NT5DC3 MUTATED`
TCGA-A6-2672 TCGA-A6-6780 TCGA-AA-3502 TCGA-AA-3697 TCGA-AZ-6598 TCGA-AZ-6601 
       46.65        20.12        35.01        85.05        49.41       100.01 
TCGA-CM-6171 TCGA-D5-5539 TCGA-D5-6541 TCGA-D5-6929 TCGA-F4-6570 TCGA-G4-6310 
       14.04        19.59        15.58        13.41         6.18        45.11 

$`NT5DC3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3510 
       19.66        20.28         7.04         3.02         1.02        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       22.36        62.79        61.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        16.14         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       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        13.38        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        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        51.75        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  NT5DC3 MUTATED NT5DC3 WILD-TYPE 
            6.18             0.00 
  NT5DC3 MUTATED NT5DC3 WILD-TYPE 
          100.01           140.38 
  NT5DC3 MUTATED NT5DC3 WILD-TYPE 
          27.565           20.190 
[1] "6.2 - 100.0 (27.6)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D201V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NT5DC3 MUTATED         2        0        2         3         0         0
  NT5DC3 WILD-TYPE      62        1       23       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NT5DC3 MUTATED           1          1          2          0        1
  NT5DC3 WILD-TYPE        18          9         39         31       34
                  vv
clus               STAGE IVA STAGE IVB
  NT5DC3 MUTATED           0         0
  NT5DC3 WILD-TYPE        13         1
D201V3, multiclass
            clus
vv           NT5DC3 MUTATED NT5DC3 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               3              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              1                9
  STAGE IIIB              2               39
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  NT5DC3 MUTATED     0   2  10   0
  NT5DC3 WILD-TYPE   9  66 238  41
D201V4, multiclass
    clus
vv   NT5DC3 MUTATED NT5DC3 WILD-TYPE
  T1              0                9
  T2              2               66
  T3             10              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
  NT5DC3 MUTATED     8   4   0
  NT5DC3 WILD-TYPE 212  76  66
D201V5, multiclass
    clus
vv   NT5DC3 MUTATED NT5DC3 WILD-TYPE
  N0              8              212
  N1              4               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"
D201V6, binary
                  cls
clus                 0   1
  NT5DC3 MUTATED     9   1
  NT5DC3 WILD-TYPE 274  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NT5DC3 MUTATED      9    1
  NT5DC3 WILD-TYPE  274   47
   clus
vv  NT5DC3 MUTATED NT5DC3 WILD-TYPE
  0              9              274
  1              1               47
[1] 2 2
[1] FALSE
D201V7, 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
D201V8, binary
                  cls
clus                 0   1
  NT5DC3 MUTATED    10   2
  NT5DC3 WILD-TYPE 307  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NT5DC3 MUTATED     10    2
  NT5DC3 WILD-TYPE  307   46
                               clus
vv                              NT5DC3 MUTATED NT5DC3 WILD-TYPE
  COLON ADENOCARCINOMA                      10              307
  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 248   2  22  21
D201V9, multiclass
    clus
vv   NT5DC3 MUTATED NT5DC3 WILD-TYPE
  R0              9              248
  R1              0                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"
D201V10, 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
D201V11, 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(202) Variable = GLI1 MUTATION ANALYSIS
D202V1, survival
                sevent
clus2              0   1
  GLI1 MUTATED    14   4
  GLI1 WILD-TYPE 268  69
  GLI1 MUTATED GLI1 WILD-TYPE 
            18            337 
  GLI1 MUTATED GLI1 WILD-TYPE 
             4             69 
$`GLI1 MUTATED`
TCGA-A6-4105 TCGA-AA-3555 TCGA-AA-A00N TCGA-AA-A010 TCGA-AU-6004 TCGA-AZ-4315 
       14.53        29.95         4.01        34.98        27.09        58.39 
TCGA-AZ-6600 TCGA-CA-6718 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CM-5341 
       12.10         0.10        15.62        51.32        21.14        29.06 
TCGA-CM-5860 TCGA-CM-6161 TCGA-CM-6171 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6628 
       16.01        15.02        14.04        19.43       107.67        52.80 

$`GLI1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        17.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41        49.41         6.77       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.33         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
      102.44        40.34        49.08        21.99         2.93         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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6299 TCGA-G4-6303 
       33.67        13.25         0.53        35.41        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 
       46.75 

  GLI1 MUTATED GLI1 WILD-TYPE 
           0.1            0.0 
  GLI1 MUTATED GLI1 WILD-TYPE 
        107.67         140.38 
  GLI1 MUTATED GLI1 WILD-TYPE 
        20.285         20.190 
[1] "0.1 - 107.7 (20.3)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D202V2, 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       25       103         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GLI1 MUTATED           2          1          0          0        1         0
  GLI1 WILD-TYPE        17          9         41         31       34        13
                vv
clus             STAGE IVB
  GLI1 MUTATED           0
  GLI1 WILD-TYPE         1
D202V3, multiclass
            clus
vv           GLI1 MUTATED GLI1 WILD-TYPE
  STAGE I               6             58
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             6            103
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             2             17
  STAGE IIIA            1              9
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GLI1 MUTATED     1   6   7   4
  GLI1 WILD-TYPE   8  62 241  37
D202V4, multiclass
    clus
vv   GLI1 MUTATED GLI1 WILD-TYPE
  T1            1              8
  T2            6             62
  T3            7            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
  GLI1 MUTATED    14   3   1
  GLI1 WILD-TYPE 206  77  65
D202V5, multiclass
    clus
vv   GLI1 MUTATED GLI1 WILD-TYPE
  N0           14            206
  N1            3             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"
D202V6, binary
                cls
clus               0   1
  GLI1 MUTATED    16   1
  GLI1 WILD-TYPE 267  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLI1 MUTATED     16    1
  GLI1 WILD-TYPE  267   47
   clus
vv  GLI1 MUTATED GLI1 WILD-TYPE
  0           16            267
  1            1             47
[1] 2 2
[1] FALSE
D202V7, 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
D202V8, binary
                cls
clus               0   1
  GLI1 MUTATED    14   4
  GLI1 WILD-TYPE 303  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLI1 MUTATED     14    4
  GLI1 WILD-TYPE  303   44
                               clus
vv                              GLI1 MUTATED GLI1 WILD-TYPE
  COLON ADENOCARCINOMA                    14            303
  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 245   2  22  17
D202V9, multiclass
    clus
vv   GLI1 MUTATED GLI1 WILD-TYPE
  R0           12            245
  R1            0              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"
D202V10, 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
D202V11, 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(203) Variable = ZFX MUTATION ANALYSIS
D203V1, survival
               sevent
clus2             0   1
  ZFX MUTATED     9   4
  ZFX WILD-TYPE 273  69
  ZFX MUTATED ZFX WILD-TYPE 
           13           342 
  ZFX MUTATED ZFX WILD-TYPE 
            4            69 
$`ZFX MUTATED`
TCGA-A6-2676 TCGA-A6-5656 TCGA-A6-5662 TCGA-AA-3492 TCGA-AA-3516 TCGA-AA-3949 
       42.90        32.91        23.61         3.02        13.02        26.01 
TCGA-AA-3966 TCGA-AA-A010 TCGA-AD-6889 TCGA-AY-6196 TCGA-AZ-6599 TCGA-CM-5860 
        2.01        34.98        56.55         0.20         6.77        16.01 
TCGA-G4-6588 
       26.17 

$`ZFX WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5657 
       34.65        33.34        32.75        36.53        14.53        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       30.44        29.19        33.53        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
        1.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41        49.41        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        52.80 

  ZFX MUTATED ZFX WILD-TYPE 
          0.2           0.0 
  ZFX MUTATED ZFX WILD-TYPE 
        56.55        140.38 
  ZFX MUTATED ZFX WILD-TYPE 
       23.610        20.155 
[1] "0.2 - 56.5 (23.6)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.8"
D203V2, 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       24       105         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        18         10         40         30       35        12
               vv
clus            STAGE IVB
  ZFX MUTATED           0
  ZFX WILD-TYPE         1
D203V3, multiclass
            clus
vv           ZFX MUTATED ZFX WILD-TYPE
  STAGE I              2            62
  STAGE IA             0             1
  STAGE II             1            24
  STAGE IIA            4           105
  STAGE IIB            2             6
  STAGE IIC            0             1
  STAGE III            1            18
  STAGE IIIA           0            10
  STAGE IIIB           1            40
  STAGE IIIC           1            30
  STAGE IV             0            35
  STAGE IVA            1            12
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 239  39
D203V4, multiclass
    clus
vv   ZFX MUTATED ZFX WILD-TYPE
  T1           0             9
  T2           2            66
  T3           9           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
  ZFX MUTATED     9   1   3
  ZFX WILD-TYPE 211  79  63
D203V5, multiclass
    clus
vv   ZFX MUTATED ZFX WILD-TYPE
  N0           9           211
  N1           1            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"
D203V6, binary
               cls
clus              0   1
  ZFX MUTATED    10   1
  ZFX WILD-TYPE 273  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  ZFX MUTATED     10    1
  ZFX WILD-TYPE  273   47
   clus
vv  ZFX MUTATED ZFX WILD-TYPE
  0          10           273
  1           1            47
[1] 2 2
[1] FALSE
D203V7, 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
D203V8, binary
               cls
clus              0   1
  ZFX MUTATED     9   4
  ZFX WILD-TYPE 308  44
[1] "tbl2"
               cls
clus            [,1] [,2]
  ZFX MUTATED      9    4
  ZFX WILD-TYPE  308   44
                               clus
vv                              ZFX MUTATED ZFX WILD-TYPE
  COLON ADENOCARCINOMA                    9           308
  COLON MUCINOUS ADENOCARCINOMA           4            44
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  ZFX MUTATED     7   0   0   0
  ZFX WILD-TYPE 250   2  22  21
D203V9, multiclass
    clus
vv   ZFX MUTATED ZFX WILD-TYPE
  R0           7           250
  R1           0             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"
D203V10, 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
D203V11, 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(204) Variable = F2RL1 MUTATION ANALYSIS
D204V1, survival
                 sevent
clus2               0   1
  F2RL1 MUTATED     6   0
  F2RL1 WILD-TYPE 276  73
  F2RL1 MUTATED F2RL1 WILD-TYPE 
              6             349 
  F2RL1 MUTATED F2RL1 WILD-TYPE 
              0              73 
$`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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        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-6679 TCGA-CM-6680 TCGA-D5-5537 
       12.95        13.05        11.08        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       12.26        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  F2RL1 MUTATED F2RL1 WILD-TYPE 
          11.01            0.00 
  F2RL1 MUTATED F2RL1 WILD-TYPE 
          58.39          140.38 
  F2RL1 MUTATED F2RL1 WILD-TYPE 
         16.815          20.980 
[1] "11.0 - 58.4 (16.8)" "0.0 - 140.4 (21.0)"
[1] "hr="     "9200000"
D204V2, 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       25       107         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        19          9         41         31       35        12
                 vv
clus              STAGE IVB
  F2RL1 MUTATED           0
  F2RL1 WILD-TYPE         1
D204V3, multiclass
            clus
vv           F2RL1 MUTATED F2RL1 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              2             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 245  40
D204V4, multiclass
    clus
vv   F2RL1 MUTATED F2RL1 WILD-TYPE
  T1             1               8
  T2             2              66
  T3             3             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
  F2RL1 MUTATED     5   2   0
  F2RL1 WILD-TYPE 215  78  66
D204V5, multiclass
    clus
vv   F2RL1 MUTATED F2RL1 WILD-TYPE
  N0             5             215
  N1             2              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"
D204V6, binary
                 cls
clus                0   1
  F2RL1 MUTATED     5   1
  F2RL1 WILD-TYPE 278  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  F2RL1 MUTATED      5    1
  F2RL1 WILD-TYPE  278   47
   clus
vv  F2RL1 MUTATED F2RL1 WILD-TYPE
  0             5             278
  1             1              47
[1] 2 2
[1] FALSE
D204V7, 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
D204V8, binary
                 cls
clus                0   1
  F2RL1 MUTATED     6   1
  F2RL1 WILD-TYPE 311  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  F2RL1 MUTATED      6    1
  F2RL1 WILD-TYPE  311   47
                               clus
vv                              F2RL1 MUTATED F2RL1 WILD-TYPE
  COLON ADENOCARCINOMA                      6             311
  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 251   2  22  20
D204V9, multiclass
    clus
vv   F2RL1 MUTATED F2RL1 WILD-TYPE
  R0             6             251
  R1             0               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"
D204V10, 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
D204V11, 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(205) Variable = KCNH7 MUTATION ANALYSIS
D205V1, survival
                 sevent
clus2               0   1
  KCNH7 MUTATED    23   9
  KCNH7 WILD-TYPE 259  64
  KCNH7 MUTATED KCNH7 WILD-TYPE 
             32             323 
  KCNH7 MUTATED KCNH7 WILD-TYPE 
              9              64 
$`KCNH7 MUTATED`
TCGA-A6-2676 TCGA-A6-6141 TCGA-AA-3510 TCGA-AA-3554 TCGA-AA-3715 TCGA-AA-3845 
       42.90         8.38        63.98        17.95        19.04         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         0.33         0.10        40.34        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 
        1.51       130.65        13.45         6.18        19.43        36.00 
TCGA-G4-6586 TCGA-G4-6626 
       35.80        46.75 

$`KCNH7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       14.93        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 
       58.39         1.41         5.13        83.80        22.36        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07         0.26         1.35        17.56       102.44 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        51.32        21.99         2.93         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-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       29.06        22.03        16.01        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-6171 TCGA-CM-6172 
       21.99        14.99        12.99        13.02        14.04        11.01 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       13.05        11.08        11.08        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        35.41       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       22.09        13.78        26.17        91.79        52.80 

  KCNH7 MUTATED KCNH7 WILD-TYPE 
              0               0 
  KCNH7 MUTATED KCNH7 WILD-TYPE 
         130.65          140.38 
  KCNH7 MUTATED KCNH7 WILD-TYPE 
         16.535          20.980 
[1] "0.0 - 130.7 (16.5)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.6"
D205V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KCNH7 MUTATED         6        0        3        15         2         0
  KCNH7 WILD-TYPE      58        1       22        94         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KCNH7 MUTATED           1          1          2          1        0         2
  KCNH7 WILD-TYPE        18          9         39         30       35        11
                 vv
clus              STAGE IVB
  KCNH7 MUTATED           0
  KCNH7 WILD-TYPE         1
D205V3, multiclass
            clus
vv           KCNH7 MUTATED KCNH7 WILD-TYPE
  STAGE I                6              58
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA             15              94
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             1               9
  STAGE IIIB             2              39
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              2              11
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  23   4
  KCNH7 WILD-TYPE   7  64 225  37
D205V4, multiclass
    clus
vv   KCNH7 MUTATED KCNH7 WILD-TYPE
  T1             2               7
  T2             4              64
  T3            23             225
  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    26   5   2
  KCNH7 WILD-TYPE 194  75  64
D205V5, multiclass
    clus
vv   KCNH7 MUTATED KCNH7 WILD-TYPE
  N0            26             194
  N1             5              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"
D205V6, binary
                 cls
clus                0   1
  KCNH7 MUTATED    27   2
  KCNH7 WILD-TYPE 256  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNH7 MUTATED     27    2
  KCNH7 WILD-TYPE  256   46
   clus
vv  KCNH7 MUTATED KCNH7 WILD-TYPE
  0            27             256
  1             2              46
[1] 2 2
[1] FALSE
D205V7, binary
                 cls
clus                0   1
  KCNH7 MUTATED    19  14
  KCNH7 WILD-TYPE 151 183
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNH7 MUTATED     19   14
  KCNH7 WILD-TYPE  151  183
        clus
vv       KCNH7 MUTATED KCNH7 WILD-TYPE
  FEMALE            19             151
  MALE              14             183
[1] 2 2
[1] FALSE
D205V8, binary
                 cls
clus                0   1
  KCNH7 MUTATED    26   6
  KCNH7 WILD-TYPE 291  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNH7 MUTATED     26    6
  KCNH7 WILD-TYPE  291   42
                               clus
vv                              KCNH7 MUTATED KCNH7 WILD-TYPE
  COLON ADENOCARCINOMA                     26             291
  COLON MUCINOUS ADENOCARCINOMA             6              42
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  KCNH7 MUTATED    24   1   0   4
  KCNH7 WILD-TYPE 233   1  22  17
D205V9, multiclass
    clus
vv   KCNH7 MUTATED KCNH7 WILD-TYPE
  R0            24             233
  R1             1               1
  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"
D205V10, 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                           2    20
  KCNH7 WILD-TYPE                        17   156
D205V11, multiclass
                                  clus
vv                                 KCNH7 MUTATED KCNH7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  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(206) Variable = COLEC10 MUTATION ANALYSIS
D206V1, survival
                   sevent
clus2                 0   1
  COLEC10 MUTATED     6   2
  COLEC10 WILD-TYPE 276  71
  COLEC10 MUTATED COLEC10 WILD-TYPE 
                8               347 
  COLEC10 MUTATED COLEC10 WILD-TYPE 
                2                71 
$`COLEC10 MUTATED`
TCGA-A6-5660 TCGA-AA-3715 TCGA-AA-3821 TCGA-AZ-4681 TCGA-CM-5348 TCGA-CM-5862 
       29.19        19.04         1.02        83.80        22.98         5.03 
TCGA-D5-5541 TCGA-DM-A1HA 
       11.51       131.51 

$`COLEC10 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 
       35.05        33.04         0.99        25.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       19.59        13.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  COLEC10 MUTATED COLEC10 WILD-TYPE 
             1.02              0.00 
  COLEC10 MUTATED COLEC10 WILD-TYPE 
           131.51            140.38 
  COLEC10 MUTATED COLEC10 WILD-TYPE 
            21.01             20.19 
[1] "1.0 - 131.5 (21.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D206V2, 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       24       108         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  COLEC10 MUTATED           0          0          2          2        0
  COLEC10 WILD-TYPE        19         10         39         29       35
                   vv
clus                STAGE IVA STAGE IVB
  COLEC10 MUTATED           1         0
  COLEC10 WILD-TYPE        12         1
D206V3, multiclass
            clus
vv           COLEC10 MUTATED COLEC10 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                1               108
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               2                39
  STAGE IIIC               2                29
  STAGE IV                 0                35
  STAGE IVA                1                12
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 241  41
D206V4, multiclass
    clus
vv   COLEC10 MUTATED COLEC10 WILD-TYPE
  T1               0                 9
  T2               1                67
  T3               7               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
  COLEC10 MUTATED     3   3   2
  COLEC10 WILD-TYPE 217  77  64
D206V5, multiclass
    clus
vv   COLEC10 MUTATED COLEC10 WILD-TYPE
  N0               3               217
  N1               3                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"
D206V6, binary
                   cls
clus                  0   1
  COLEC10 MUTATED     7   1
  COLEC10 WILD-TYPE 276  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COLEC10 MUTATED      7    1
  COLEC10 WILD-TYPE  276   47
   clus
vv  COLEC10 MUTATED COLEC10 WILD-TYPE
  0               7               276
  1               1                47
[1] 2 2
[1] FALSE
D206V7, 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
D206V8, binary
                   cls
clus                  0   1
  COLEC10 MUTATED     7   1
  COLEC10 WILD-TYPE 310  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COLEC10 MUTATED      7    1
  COLEC10 WILD-TYPE  310   47
                               clus
vv                              COLEC10 MUTATED COLEC10 WILD-TYPE
  COLON ADENOCARCINOMA                        7               310
  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 251   2  22  21
D206V9, multiclass
    clus
vv   COLEC10 MUTATED COLEC10 WILD-TYPE
  R0               6               251
  R1               0                 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"
D206V10, 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
D206V11, 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(207) Variable = IVL MUTATION ANALYSIS
D207V1, survival
               sevent
clus2             0   1
  IVL MUTATED    12   4
  IVL WILD-TYPE 270  69
  IVL MUTATED IVL WILD-TYPE 
           16           339 
  IVL MUTATED IVL WILD-TYPE 
            4            69 
$`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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01         0.92        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        1.41         5.13        83.80        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 
        0.07         0.26         0.33         0.10         1.35       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 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-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64        13.41         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28F 
       44.32       131.51       135.65       139.17         6.12        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  IVL MUTATED IVL WILD-TYPE 
         6.97          0.00 
  IVL MUTATED IVL WILD-TYPE 
       119.93        140.38 
  IVL MUTATED IVL WILD-TYPE 
        22.39         20.12 
[1] "7.0 - 119.9 (22.4)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.1"
D207V2, 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       23       105         8         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IVL MUTATED           1          1          0          1        1         2
  IVL WILD-TYPE        18          9         41         30       34        11
               vv
clus            STAGE IVB
  IVL MUTATED           0
  IVL WILD-TYPE         1
D207V3, multiclass
            clus
vv           IVL MUTATED IVL WILD-TYPE
  STAGE I              3            61
  STAGE IA             0             1
  STAGE II             2            23
  STAGE IIA            4           105
  STAGE IIB            0             8
  STAGE IIC            0             1
  STAGE III            1            18
  STAGE IIIA           1             9
  STAGE IIIB           0            41
  STAGE IIIC           1            30
  STAGE IV             1            34
  STAGE IVA            2            11
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of 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  64 237  39
D207V4, multiclass
    clus
vv   IVL MUTATED IVL WILD-TYPE
  T1           0             9
  T2           4            64
  T3          11           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
  IVL MUTATED    12   4   1
  IVL WILD-TYPE 208  76  65
D207V5, multiclass
    clus
vv   IVL MUTATED IVL WILD-TYPE
  N0          12           208
  N1           4            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"
D207V6, binary
               cls
clus              0   1
  IVL MUTATED    12   2
  IVL WILD-TYPE 271  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  IVL MUTATED     12    2
  IVL WILD-TYPE  271   46
   clus
vv  IVL MUTATED IVL WILD-TYPE
  0          12           271
  1           2            46
[1] 2 2
[1] FALSE
D207V7, 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
D207V8, binary
               cls
clus              0   1
  IVL MUTATED    15   2
  IVL WILD-TYPE 302  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  IVL MUTATED     15    2
  IVL WILD-TYPE  302   46
                               clus
vv                              IVL MUTATED IVL WILD-TYPE
  COLON ADENOCARCINOMA                   15           302
  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 246   2  22  20
D207V9, multiclass
    clus
vv   IVL MUTATED IVL WILD-TYPE
  R0          11           246
  R1           0             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"
D207V10, 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
D207V11, 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(208) Variable = FAHD2B MUTATION ANALYSIS
D208V1, survival
                  sevent
clus2                0   1
  FAHD2B MUTATED     5   0
  FAHD2B WILD-TYPE 277  73
  FAHD2B MUTATED FAHD2B WILD-TYPE 
               5              350 
  FAHD2B MUTATED FAHD2B WILD-TYPE 
               0               73 
$`FAHD2B MUTATED`
TCGA-A6-5665 TCGA-A6-6780 TCGA-AD-5900 TCGA-AU-6004 TCGA-CM-5861 
       22.06        20.12         0.07        27.09        15.02 

$`FAHD2B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.20        14.50        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  FAHD2B MUTATED FAHD2B WILD-TYPE 
            0.07             0.00 
  FAHD2B MUTATED FAHD2B WILD-TYPE 
           27.09           140.38 
  FAHD2B MUTATED FAHD2B WILD-TYPE 
          20.120           20.235 
[1] "0.1 - 27.1 (20.1)"  "0.0 - 140.4 (20.2)"
[1] "hr="     "3300000"
D208V2, 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       25       106         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAHD2B MUTATED           0          0          0          0        0
  FAHD2B WILD-TYPE        19         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  FAHD2B MUTATED           0         0
  FAHD2B WILD-TYPE        13         1
D208V3, multiclass
            clus
vv           FAHD2B MUTATED FAHD2B WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               3              106
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FAHD2B MUTATED     0   2   3   1
  FAHD2B WILD-TYPE   9  66 245  40
D208V4, multiclass
    clus
vv   FAHD2B MUTATED FAHD2B WILD-TYPE
  T1              0                9
  T2              2               66
  T3              3              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
  FAHD2B MUTATED     6   0   0
  FAHD2B WILD-TYPE 214  80  66
D208V5, multiclass
    clus
vv   FAHD2B MUTATED FAHD2B WILD-TYPE
  N0              6              214
  N1              0               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"
D208V6, binary
                  cls
clus                 0   1
  FAHD2B MUTATED     3   0
  FAHD2B WILD-TYPE 280  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAHD2B MUTATED      3    0
  FAHD2B WILD-TYPE  280   48
   clus
vv  FAHD2B MUTATED FAHD2B WILD-TYPE
  0              3              280
  1              0               48
[1] 2 2
[1] FALSE
D208V7, 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
D208V8, binary
                  cls
clus                 0   1
  FAHD2B MUTATED     4   2
  FAHD2B WILD-TYPE 313  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAHD2B MUTATED      4    2
  FAHD2B WILD-TYPE  313   46
                               clus
vv                              FAHD2B MUTATED FAHD2B WILD-TYPE
  COLON ADENOCARCINOMA                       4              313
  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 253   2  22  20
D208V9, multiclass
    clus
vv   FAHD2B MUTATED FAHD2B WILD-TYPE
  R0              4              253
  R1              0                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"
D208V10, 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
D208V11, 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(209) Variable = TRIP11 MUTATION ANALYSIS
D209V1, survival
                  sevent
clus2                0   1
  TRIP11 MUTATED    16   2
  TRIP11 WILD-TYPE 266  71
  TRIP11 MUTATED TRIP11 WILD-TYPE 
              18              337 
  TRIP11 MUTATED TRIP11 WILD-TYPE 
               2               71 
$`TRIP11 MUTATED`
TCGA-A6-5661 TCGA-A6-5665 TCGA-AA-3663 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00N 
       33.53        22.06         6.97         2.01        25.02         4.01 
TCGA-AA-A010 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-6603 TCGA-CA-6717 
       34.98        21.44        17.82        58.39        29.56         0.33 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CM-6168 TCGA-D5-6532 TCGA-D5-6540 TCGA-G4-6628 
       51.32        21.99        12.99        18.25        16.14        52.80 

$`TRIP11 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.95        15.75         0.20         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
      100.01         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 
       46.75 

  TRIP11 MUTATED TRIP11 WILD-TYPE 
            0.33             0.00 
  TRIP11 MUTATED TRIP11 WILD-TYPE 
           58.39           140.38 
  TRIP11 MUTATED TRIP11 WILD-TYPE 
          21.715           20.120 
[1] "0.3 - 58.4 (21.7)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.8"
D209V2, 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       24        99         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRIP11 MUTATED           0          0          2          0        0
  TRIP11 WILD-TYPE        19         10         39         31       35
                  vv
clus               STAGE IVA STAGE IVB
  TRIP11 MUTATED           0         0
  TRIP11 WILD-TYPE        13         1
D209V3, multiclass
            clus
vv           TRIP11 MUTATED TRIP11 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA              10               99
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TRIP11 MUTATED     0   4  13   2
  TRIP11 WILD-TYPE   9  64 235  39
D209V4, multiclass
    clus
vv   TRIP11 MUTATED TRIP11 WILD-TYPE
  T1              0                9
  T2              4               64
  T3             13              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
  TRIP11 MUTATED    16   3   0
  TRIP11 WILD-TYPE 204  77  66
D209V5, multiclass
    clus
vv   TRIP11 MUTATED TRIP11 WILD-TYPE
  N0             16              204
  N1              3               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"
D209V6, binary
                  cls
clus                 0   1
  TRIP11 MUTATED    14   0
  TRIP11 WILD-TYPE 269  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIP11 MUTATED     14    0
  TRIP11 WILD-TYPE  269   48
   clus
vv  TRIP11 MUTATED TRIP11 WILD-TYPE
  0             14              269
  1              0               48
[1] 2 2
[1] FALSE
D209V7, 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
D209V8, binary
                  cls
clus                 0   1
  TRIP11 MUTATED    15   4
  TRIP11 WILD-TYPE 302  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIP11 MUTATED     15    4
  TRIP11 WILD-TYPE  302   44
                               clus
vv                              TRIP11 MUTATED TRIP11 WILD-TYPE
  COLON ADENOCARCINOMA                      15              302
  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 244   2  22  18
D209V9, multiclass
    clus
vv   TRIP11 MUTATED TRIP11 WILD-TYPE
  R0             13              244
  R1              0                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"
D209V10, 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
D209V11, 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(210) Variable = MLL3 MUTATION ANALYSIS
D210V1, survival
                sevent
clus2              0   1
  MLL3 MUTATED    44  12
  MLL3 WILD-TYPE 238  61
  MLL3 MUTATED MLL3 WILD-TYPE 
            56            299 
  MLL3 MUTATED MLL3 WILD-TYPE 
            12             61 
$`MLL3 MUTATED`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 
       43.76        46.65        22.06        32.71        22.52         8.38 
TCGA-A6-6654 TCGA-A6-6781 TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3525 TCGA-AA-3660 
       23.87        19.66         1.02        63.98         8.05        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3710 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3869 
        6.05         6.97        26.99         0.00        17.03        27.02 
TCGA-AA-3950 TCGA-AA-3977 TCGA-AA-A00N TCGA-AD-6899 TCGA-AD-6964 TCGA-AU-3779 
       24.00        25.02         4.01         5.79        10.88        14.50 
TCGA-AZ-4315 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6603 TCGA-AZ-6608 TCGA-CA-6717 
       58.39        61.41        49.41        29.56         1.94         0.33 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CM-5344 TCGA-CM-5861 TCGA-CM-5862 
       40.34        15.62        51.32        22.03        15.02         5.03 
TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6167 TCGA-CM-6674 TCGA-D5-5539 TCGA-D5-6532 
       17.03        12.00        14.99        12.95        19.59        18.25 
TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6928 TCGA-D5-6929 TCGA-DM-A1D0 
       16.14        12.39        12.43        11.64        13.41       130.65 
TCGA-DM-A1D7 TCGA-DM-A28C TCGA-G4-6293 TCGA-G4-6310 TCGA-G4-6586 TCGA-G4-6588 
       13.32        81.37       107.67        45.11        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 
       91.79        52.80 

$`MLL3 WILD-TYPE`
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       43.76        42.90        24.33        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       33.34        32.75        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-6137 
       30.44        29.19        33.53        23.61        22.09        27.09 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3511 
       20.12        20.28         7.04         3.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       37.05        36.03        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       38.99        37.02        14.93        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3875 
       30.05        53.00        17.03        24.03        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 
        0.79         0.72        22.42        27.42         0.20        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6599 
        1.41         5.13        83.80        22.36        62.79         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
       12.10       100.01         5.23        11.74         3.19         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 
        1.35        17.56       102.44        49.08        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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        16.01 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        15.02        15.02        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-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 
       45.40        12.26        13.51        11.51        20.19         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       15.58         7.53        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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       38.20        92.75        49.91        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28E 
       44.32       131.51       135.65       139.17         6.12       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6626 
       36.72        36.00        22.09        13.78        46.75 

  MLL3 MUTATED MLL3 WILD-TYPE 
             0              0 
  MLL3 MUTATED MLL3 WILD-TYPE 
        130.65         140.38 
  MLL3 MUTATED MLL3 WILD-TYPE 
        19.625         20.280 
[1] "0.0 - 130.7 (19.6)" "0.0 - 140.4 (20.3)"
[1] "hr=" "1.1"
D210V2, 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       20        87         6         0
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MLL3 MUTATED           2          3          6          3        4         2
  MLL3 WILD-TYPE        17          7         35         28       31        11
                vv
clus             STAGE IVB
  MLL3 MUTATED           0
  MLL3 WILD-TYPE         1
D210V3, multiclass
            clus
vv           MLL3 MUTATED MLL3 WILD-TYPE
  STAGE I               5             59
  STAGE IA              0              1
  STAGE II              5             20
  STAGE IIA            22             87
  STAGE IIB             2              6
  STAGE IIC             1              0
  STAGE III             2             17
  STAGE IIIA            3              7
  STAGE IIIB            6             35
  STAGE IIIC            3             28
  STAGE IV              4             31
  STAGE IVA             2             11
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  61 208  31
D210V4, multiclass
    clus
vv   MLL3 MUTATED MLL3 WILD-TYPE
  T1            1              8
  T2            7             61
  T3           40            208
  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  65  59
D210V5, multiclass
    clus
vv   MLL3 MUTATED MLL3 WILD-TYPE
  N0           36            184
  N1           15             65
  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"
D210V6, binary
                cls
clus               0   1
  MLL3 MUTATED    44   6
  MLL3 WILD-TYPE 239  42
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL3 MUTATED     44    6
  MLL3 WILD-TYPE  239   42
   clus
vv  MLL3 MUTATED MLL3 WILD-TYPE
  0           44            239
  1            6             42
[1] 2 2
[1] FALSE
D210V7, 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
D210V8, binary
                cls
clus               0   1
  MLL3 MUTATED    48  10
  MLL3 WILD-TYPE 269  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL3 MUTATED     48   10
  MLL3 WILD-TYPE  269   38
                               clus
vv                              MLL3 MUTATED MLL3 WILD-TYPE
  COLON ADENOCARCINOMA                    48            269
  COLON MUCINOUS ADENOCARCINOMA           10             38
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MLL3 MUTATED    37   1   2   4
  MLL3 WILD-TYPE 220   1  20  17
D210V9, multiclass
    clus
vv   MLL3 MUTATED MLL3 WILD-TYPE
  R0           37            220
  R1            1              1
  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"
D210V10, 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
D210V11, 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(211) Variable = CBL MUTATION ANALYSIS
D211V1, survival
               sevent
clus2             0   1
  CBL MUTATED    28   6
  CBL WILD-TYPE 254  67
  CBL MUTATED CBL WILD-TYPE 
           34           321 
  CBL MUTATED CBL WILD-TYPE 
            6            67 
$`CBL MUTATED`
TCGA-A6-5657 TCGA-A6-5662 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3518 TCGA-AA-3662 
       31.63        23.61        63.98         6.97         1.02         6.05 
TCGA-AA-3968 TCGA-AA-A010 TCGA-AD-5900 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 
       21.99        34.98         0.07        15.75        17.82        58.39 
TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6608 TCGA-CA-6718 
       61.41        12.10       100.01        29.56         1.94         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CM-4743 TCGA-CM-4752 TCGA-CM-5862 TCGA-CM-6164 
        1.35        17.56        23.05        13.02         5.03        29.03 
TCGA-CM-6172 TCGA-CM-6676 TCGA-D5-6533 TCGA-D5-6923 TCGA-DM-A1DB TCGA-DM-A28E 
       11.01        11.08         1.32        12.43        44.32       119.93 
TCGA-DM-A28K TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6628 
       98.24        51.75        45.11        52.80 

$`CBL WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 
       32.91        30.44        29.19        33.53        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
        1.02        13.02        38.99         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       78.08         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 
       24.00         2.01        20.98        34.03         2.01        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 
        0.20        14.50        27.09        16.31         0.95         0.20 
TCGA-AY-6197 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       21.44         1.41         5.13        83.80        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         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14         2.93         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        16.01 
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-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-6677 TCGA-CM-6678 
       15.02        14.04        12.95        13.05        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       11.51        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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       12.59       140.38         7.50       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 
        6.12        81.37        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 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       55.04        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       26.17        91.79        46.75 

  CBL MUTATED CBL WILD-TYPE 
         0.07          0.00 
  CBL MUTATED CBL WILD-TYPE 
       119.93        140.38 
  CBL MUTATED CBL WILD-TYPE 
       19.905        20.190 
[1] "0.1 - 119.9 (19.9)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.4"
D211V2, 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       22        99         7         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CBL MUTATED           0          1          6          0        2         4
  CBL WILD-TYPE        19          9         35         31       33         9
               vv
clus            STAGE IVB
  CBL MUTATED           0
  CBL WILD-TYPE         1
D211V3, multiclass
            clus
vv           CBL MUTATED CBL WILD-TYPE
  STAGE I              6            58
  STAGE IA             0             1
  STAGE II             3            22
  STAGE IIA           10            99
  STAGE IIB            1             7
  STAGE IIC            0             1
  STAGE III            0            19
  STAGE IIIA           1             9
  STAGE IIIB           6            35
  STAGE IIIC           0            31
  STAGE IV             2            33
  STAGE IVA            4             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  61 228  35
D211V4, multiclass
    clus
vv   CBL MUTATED CBL WILD-TYPE
  T1           1             8
  T2           7            61
  T3          20           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
  CBL MUTATED    21  11   2
  CBL WILD-TYPE 199  69  64
D211V5, multiclass
    clus
vv   CBL MUTATED CBL WILD-TYPE
  N0          21           199
  N1          11            69
  N2           2            64
[1] 3 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
  CBL MUTATED    27   5
  CBL WILD-TYPE 256  43
[1] "tbl2"
               cls
clus            [,1] [,2]
  CBL MUTATED     27    5
  CBL WILD-TYPE  256   43
   clus
vv  CBL MUTATED CBL WILD-TYPE
  0          27           256
  1           5            43
[1] 2 2
[1] FALSE
D211V7, 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
D211V8, binary
               cls
clus              0   1
  CBL MUTATED    32   2
  CBL WILD-TYPE 285  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  CBL MUTATED     32    2
  CBL WILD-TYPE  285   46
                               clus
vv                              CBL MUTATED CBL WILD-TYPE
  COLON ADENOCARCINOMA                   32           285
  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 236   2  21  18
D211V9, multiclass
    clus
vv   CBL MUTATED CBL WILD-TYPE
  R0          21           236
  R1           0             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"
D211V10, 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
D211V11, 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(212) Variable = MAGEC1 MUTATION ANALYSIS
D212V1, survival
                  sevent
clus2                0   1
  MAGEC1 MUTATED    22   4
  MAGEC1 WILD-TYPE 260  69
  MAGEC1 MUTATED MAGEC1 WILD-TYPE 
              26              329 
  MAGEC1 MUTATED MAGEC1 WILD-TYPE 
               4               69 
$`MAGEC1 MUTATED`
TCGA-A6-2672 TCGA-A6-3809 TCGA-A6-5664 TCGA-A6-5666 TCGA-AA-3502 TCGA-AA-3662 
       46.65        32.75        22.09        32.71        35.01         6.05 
TCGA-AA-3955 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-A00N TCGA-AA-A010 
       20.98        34.06        25.02        27.02         4.01        34.98 
TCGA-AD-6889 TCGA-AD-6901 TCGA-CA-6717 TCGA-D5-5538 TCGA-D5-6538 TCGA-D5-6898 
       56.55        22.42         0.33        12.26        17.13         7.53 
TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-F4-6808 TCGA-F4-6855 
       12.00        11.38        24.43        38.20        33.67        35.41 
TCGA-G4-6304 TCGA-G4-6586 
       53.62        35.80 

$`MAGEC1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       34.65        33.34        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5665 TCGA-A6-6137 
       30.44        29.19        33.53        23.61        22.06        27.09 
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 
       22.52         8.38        25.08        25.18        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        7.04         3.02         1.02        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       78.08         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 
       50.99        13.05        26.01        24.00        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 
       21.37         4.21         0.79         0.72         5.79        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 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         1.51 
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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 
       35.87         1.55        16.31        29.59        16.24        13.25 
TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 
        0.53        19.43       107.67        74.56        65.85        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        26.17        91.79        46.75        52.80 

  MAGEC1 MUTATED MAGEC1 WILD-TYPE 
            0.33             0.00 
  MAGEC1 MUTATED MAGEC1 WILD-TYPE 
           56.55           140.38 
  MAGEC1 MUTATED MAGEC1 WILD-TYPE 
           26.02            19.66 
[1] "0.3 - 56.5 (26.0)"  "0.0 - 140.4 (19.7)"
[1] "hr=" "1.3"
D212V2, 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       25       102         4         0
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAGEC1 MUTATED           0          0          4          3        2
  MAGEC1 WILD-TYPE        19         10         37         28       33
                  vv
clus               STAGE IVA STAGE IVB
  MAGEC1 MUTATED           0         0
  MAGEC1 WILD-TYPE        13         1
D212V3, multiclass
            clus
vv           MAGEC1 MUTATED MAGEC1 WILD-TYPE
  STAGE I                 5               59
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               7              102
  STAGE IIB               4                4
  STAGE IIC               1                0
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              4               37
  STAGE IIIC              3               28
  STAGE IV                2               33
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MAGEC1 MUTATED     1   6  12   9
  MAGEC1 WILD-TYPE   8  62 236  32
D212V4, multiclass
    clus
vv   MAGEC1 MUTATED MAGEC1 WILD-TYPE
  T1              1                8
  T2              6               62
  T3             12              236
  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  77  60
D212V5, multiclass
    clus
vv   MAGEC1 MUTATED MAGEC1 WILD-TYPE
  N0             19              201
  N1              3               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"
D212V6, binary
                  cls
clus                 0   1
  MAGEC1 MUTATED    23   2
  MAGEC1 WILD-TYPE 260  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGEC1 MUTATED     23    2
  MAGEC1 WILD-TYPE  260   46
   clus
vv  MAGEC1 MUTATED MAGEC1 WILD-TYPE
  0             23              260
  1              2               46
[1] 2 2
[1] FALSE
D212V7, 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
D212V8, binary
                  cls
clus                 0   1
  MAGEC1 MUTATED    24   4
  MAGEC1 WILD-TYPE 293  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGEC1 MUTATED     24    4
  MAGEC1 WILD-TYPE  293   44
                               clus
vv                              MAGEC1 MUTATED MAGEC1 WILD-TYPE
  COLON ADENOCARCINOMA                      24              293
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  MAGEC1 MUTATED    17   0   2   1
  MAGEC1 WILD-TYPE 240   2  20  20
D212V9, multiclass
    clus
vv   MAGEC1 MUTATED MAGEC1 WILD-TYPE
  R0             17              240
  R1              0                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"
D212V10, 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
D212V11, 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(213) Variable = PCSK1 MUTATION ANALYSIS
D213V1, survival
                 sevent
clus2               0   1
  PCSK1 MUTATED    12   4
  PCSK1 WILD-TYPE 270  69
  PCSK1 MUTATED PCSK1 WILD-TYPE 
             16             339 
  PCSK1 MUTATED PCSK1 WILD-TYPE 
              4              69 
$`PCSK1 MUTATED`
TCGA-AA-3555 TCGA-AA-3663 TCGA-AA-3966 TCGA-AA-A010 TCGA-AD-6899 TCGA-AD-6963 
       29.95         6.97         2.01        34.98         5.79        27.42 
TCGA-AD-6964 TCGA-AZ-4315 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-CA-5254 TCGA-CA-6717 
       10.88        58.39        62.79        49.41         2.24         0.33 
TCGA-CK-4950 TCGA-CM-4746 TCGA-D5-6536 TCGA-G4-6628 
       40.34        37.02        17.85        52.80 

$`PCSK1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        17.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
        0.72        22.42         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
        5.13        83.80        22.36        61.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
        1.35        17.56       102.44        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       26.17        91.79        46.75 

  PCSK1 MUTATED PCSK1 WILD-TYPE 
           0.33            0.00 
  PCSK1 MUTATED PCSK1 WILD-TYPE 
          62.79          140.38 
  PCSK1 MUTATED PCSK1 WILD-TYPE 
         28.685          20.120 
[1] "0.3 - 62.8 (28.7)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.1"
D213V2, 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       22       103         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PCSK1 MUTATED           0          1          0          1        0         0
  PCSK1 WILD-TYPE        19          9         41         30       35        13
                 vv
clus              STAGE IVB
  PCSK1 MUTATED           0
  PCSK1 WILD-TYPE         1
D213V3, multiclass
            clus
vv           PCSK1 MUTATED PCSK1 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              6             103
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PCSK1 MUTATED     0   2  11   3
  PCSK1 WILD-TYPE   9  66 237  38
D213V4, multiclass
    clus
vv   PCSK1 MUTATED PCSK1 WILD-TYPE
  T1             0               9
  T2             2              66
  T3            11             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
  PCSK1 MUTATED    13   1   2
  PCSK1 WILD-TYPE 207  79  64
D213V5, multiclass
    clus
vv   PCSK1 MUTATED PCSK1 WILD-TYPE
  N0            13             207
  N1             1              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"
D213V6, binary
                 cls
clus                0   1
  PCSK1 MUTATED    11   0
  PCSK1 WILD-TYPE 272  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCSK1 MUTATED     11    0
  PCSK1 WILD-TYPE  272   48
   clus
vv  PCSK1 MUTATED PCSK1 WILD-TYPE
  0            11             272
  1             0              48
[1] 2 2
[1] FALSE
D213V7, 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
D213V8, binary
                 cls
clus                0   1
  PCSK1 MUTATED    12   4
  PCSK1 WILD-TYPE 305  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCSK1 MUTATED     12    4
  PCSK1 WILD-TYPE  305   44
                               clus
vv                              PCSK1 MUTATED PCSK1 WILD-TYPE
  COLON ADENOCARCINOMA                     12             305
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PCSK1 MUTATED     7   1   0   2
  PCSK1 WILD-TYPE 250   1  22  19
D213V9, multiclass
    clus
vv   PCSK1 MUTATED PCSK1 WILD-TYPE
  R0             7             250
  R1             1               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"
D213V10, 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
D213V11, 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(214) Variable = RASA2 MUTATION ANALYSIS
D214V1, survival
                 sevent
clus2               0   1
  RASA2 MUTATED    13   2
  RASA2 WILD-TYPE 269  71
  RASA2 MUTATED RASA2 WILD-TYPE 
             15             340 
  RASA2 MUTATED RASA2 WILD-TYPE 
              2              71 
$`RASA2 MUTATED`
TCGA-A6-6141 TCGA-AA-3510 TCGA-AA-3655 TCGA-AA-3697 TCGA-AA-A010 TCGA-AD-5900 
        8.38        63.98        61.02        85.05        34.98         0.07 
TCGA-AD-6889 TCGA-AD-6964 TCGA-AZ-4315 TCGA-CK-6751 TCGA-CM-5344 TCGA-D5-6926 
       56.55        10.88        58.39       124.27        22.03         9.04 
TCGA-DM-A1D6 TCGA-F4-6703 TCGA-G4-6321 
       49.91        35.87        22.09 

$`RASA2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        92.75        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.38        13.45         6.18         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 
       51.75        45.11        36.72        36.00        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  RASA2 MUTATED RASA2 WILD-TYPE 
           0.07            0.00 
  RASA2 MUTATED RASA2 WILD-TYPE 
         124.27          140.38 
  RASA2 MUTATED RASA2 WILD-TYPE 
          35.87           19.99 
[1] "0.1 - 124.3 (35.9)" "0.0 - 140.4 (20.0)"
[1] "hr=" "2.7"
D214V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RASA2 MUTATED         2        0        2         5         1         0
  RASA2 WILD-TYPE      62        1       23       104         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RASA2 MUTATED           2          1          1          0        0         0
  RASA2 WILD-TYPE        17          9         40         31       35        13
                 vv
clus              STAGE IVB
  RASA2 MUTATED           0
  RASA2 WILD-TYPE         1
D214V3, multiclass
            clus
vv           RASA2 MUTATED RASA2 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              5             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             1               9
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RASA2 MUTATED     0   3   9   3
  RASA2 WILD-TYPE   9  65 239  38
D214V4, multiclass
    clus
vv   RASA2 MUTATED RASA2 WILD-TYPE
  T1             0               9
  T2             3              65
  T3             9             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
  RASA2 MUTATED    11   3   1
  RASA2 WILD-TYPE 209  77  65
D214V5, multiclass
    clus
vv   RASA2 MUTATED RASA2 WILD-TYPE
  N0            11             209
  N1             3              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"
D214V6, binary
                 cls
clus                0   1
  RASA2 MUTATED    11   0
  RASA2 WILD-TYPE 272  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RASA2 MUTATED     11    0
  RASA2 WILD-TYPE  272   48
   clus
vv  RASA2 MUTATED RASA2 WILD-TYPE
  0            11             272
  1             0              48
[1] 2 2
[1] FALSE
D214V7, 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
D214V8, binary
                 cls
clus                0   1
  RASA2 MUTATED    12   3
  RASA2 WILD-TYPE 305  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RASA2 MUTATED     12    3
  RASA2 WILD-TYPE  305   45
                               clus
vv                              RASA2 MUTATED RASA2 WILD-TYPE
  COLON ADENOCARCINOMA                     12             305
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RASA2 MUTATED    10   0   0   1
  RASA2 WILD-TYPE 247   2  22  20
D214V9, multiclass
    clus
vv   RASA2 MUTATED RASA2 WILD-TYPE
  R0            10             247
  R1             0               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"
D214V10, 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
D214V11, 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(215) Variable = LARP4B MUTATION ANALYSIS
D215V1, survival
                  sevent
clus2                0   1
  LARP4B MUTATED    25   3
  LARP4B WILD-TYPE 257  70
  LARP4B MUTATED LARP4B WILD-TYPE 
              28              327 
  LARP4B MUTATED LARP4B WILD-TYPE 
               3               70 
$`LARP4B MUTATED`
TCGA-A6-5666 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3815 TCGA-AA-3821 
       32.71         6.97         0.92        19.04        33.04         1.02 
TCGA-AA-3845 TCGA-AA-3877 TCGA-AA-3949 TCGA-AA-3977 TCGA-AA-A01Q TCGA-AA-A02O 
        0.00        31.00        26.01        25.02         1.02         0.92 
TCGA-AY-5543 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CK-4950 TCGA-CM-4743 
       15.75        49.41       100.01         0.33        40.34        23.05 
TCGA-CM-4752 TCGA-CM-5861 TCGA-CM-6162 TCGA-D5-6540 TCGA-D5-6930 TCGA-DM-A1HB 
       13.02        15.02        12.00        16.14         1.51       135.65 
TCGA-F4-6856 TCGA-G4-6309 TCGA-G4-6586 TCGA-G4-6588 
       19.43        51.75        35.80        26.17 

$`LARP4B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       85.05        26.99        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
       25.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       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        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
       14.01        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 
        0.26         0.10         1.35        17.56       102.44        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        16.01         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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         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-A282 TCGA-DM-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.41       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  LARP4B MUTATED LARP4B WILD-TYPE 
               0                0 
  LARP4B MUTATED LARP4B WILD-TYPE 
          135.65           140.38 
  LARP4B MUTATED LARP4B WILD-TYPE 
          19.235           20.280 
[1] "0.0 - 135.7 (19.2)" "0.0 - 140.4 (20.3)"
[1] "hr=" "2"  
D215V2, 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       20        99         8         0
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LARP4B MUTATED           1          1          4          0        1
  LARP4B WILD-TYPE        18          9         37         31       34
                  vv
clus               STAGE IVA STAGE IVB
  LARP4B MUTATED           1         0
  LARP4B WILD-TYPE        12         1
D215V3, multiclass
            clus
vv           LARP4B MUTATED LARP4B WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                5               20
  STAGE IIA              10               99
  STAGE IIB               0                8
  STAGE IIC               1                0
  STAGE III               1               18
  STAGE IIIA              1                9
  STAGE IIIB              4               37
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  64 225  40
D215V4, multiclass
    clus
vv   LARP4B MUTATED LARP4B WILD-TYPE
  T1              1                8
  T2              4               64
  T3             23              225
  T4              1               40
[1] 4 2
[1] TRUE
[1] "dimension 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  73  66
D215V5, multiclass
    clus
vv   LARP4B MUTATED LARP4B WILD-TYPE
  N0             22              198
  N1              7               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"
D215V6, binary
                  cls
clus                 0   1
  LARP4B MUTATED    25   2
  LARP4B WILD-TYPE 258  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LARP4B MUTATED     25    2
  LARP4B WILD-TYPE  258   46
   clus
vv  LARP4B MUTATED LARP4B WILD-TYPE
  0             25              258
  1              2               46
[1] 2 2
[1] FALSE
D215V7, 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
D215V8, binary
                  cls
clus                 0   1
  LARP4B MUTATED    21   8
  LARP4B WILD-TYPE 296  40
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LARP4B MUTATED     21    8
  LARP4B WILD-TYPE  296   40
                               clus
vv                              LARP4B MUTATED LARP4B WILD-TYPE
  COLON ADENOCARCINOMA                      21              296
  COLON MUCINOUS ADENOCARCINOMA              8               40
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  LARP4B MUTATED    21   1   1   1
  LARP4B WILD-TYPE 236   1  21  20
D215V9, multiclass
    clus
vv   LARP4B MUTATED LARP4B WILD-TYPE
  R0             21              236
  R1              1                1
  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"
D215V10, 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
D215V11, 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(216) Variable = TWISTNB MUTATION ANALYSIS
D216V1, survival
                   sevent
clus2                 0   1
  TWISTNB MUTATED     7   1
  TWISTNB WILD-TYPE 275  72
  TWISTNB MUTATED TWISTNB WILD-TYPE 
                8               347 
  TWISTNB MUTATED TWISTNB WILD-TYPE 
                1                72 
$`TWISTNB MUTATED`
TCGA-AA-3977 TCGA-AZ-6603 TCGA-CM-4743 TCGA-CM-5344 TCGA-D5-6926 TCGA-DM-A28H 
       25.02        29.56        23.05        22.03         9.04       117.07 
TCGA-G4-6309 TCGA-G4-6625 
       51.75        91.79 

$`TWISTNB WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10       100.01         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14         2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K 
        6.12        81.37       119.93        35.97        60.79        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        46.75        52.80 

  TWISTNB MUTATED TWISTNB WILD-TYPE 
             9.04              0.00 
  TWISTNB MUTATED TWISTNB WILD-TYPE 
           117.07            140.38 
  TWISTNB MUTATED TWISTNB WILD-TYPE 
            27.29             19.99 
[1] "9.0 - 117.1 (27.3)" "0.0 - 140.4 (20.0)"
[1] "hr=" "2.9"
D216V2, 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       25       107         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TWISTNB MUTATED           0          1          2          1        0
  TWISTNB WILD-TYPE        19          9         39         30       35
                   vv
clus                STAGE IVA STAGE IVB
  TWISTNB MUTATED           0         0
  TWISTNB WILD-TYPE        13         1
D216V3, multiclass
            clus
vv           TWISTNB MUTATED TWISTNB WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                2               107
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               1                 9
  STAGE IIIB               2                39
  STAGE IIIC               1                30
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TWISTNB MUTATED     0   2   5   1
  TWISTNB WILD-TYPE   9  66 243  40
D216V4, multiclass
    clus
vv   TWISTNB MUTATED TWISTNB WILD-TYPE
  T1               0                 9
  T2               2                66
  T3               5               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
  TWISTNB MUTATED     3   4   1
  TWISTNB WILD-TYPE 217  76  65
D216V5, multiclass
    clus
vv   TWISTNB MUTATED TWISTNB WILD-TYPE
  N0               3               217
  N1               4                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"
D216V6, binary
                   cls
clus                  0   1
  TWISTNB MUTATED     6   0
  TWISTNB WILD-TYPE 277  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TWISTNB MUTATED      6    0
  TWISTNB WILD-TYPE  277   48
   clus
vv  TWISTNB MUTATED TWISTNB WILD-TYPE
  0               6               277
  1               0                48
[1] 2 2
[1] FALSE
D216V7, 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
D216V8, binary
                   cls
clus                  0   1
  TWISTNB MUTATED     8   0
  TWISTNB WILD-TYPE 309  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TWISTNB MUTATED      8    0
  TWISTNB WILD-TYPE  309   48
                               clus
vv                              TWISTNB MUTATED TWISTNB WILD-TYPE
  COLON ADENOCARCINOMA                        8               309
  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 252   2  22  21
D216V9, multiclass
    clus
vv   TWISTNB MUTATED TWISTNB WILD-TYPE
  R0               5               252
  R1               0                 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"
D216V10, 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
D216V11, 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(217) Variable = BRCA2 MUTATION ANALYSIS
D217V1, survival
                 sevent
clus2               0   1
  BRCA2 MUTATED    41   7
  BRCA2 WILD-TYPE 241  66
  BRCA2 MUTATED BRCA2 WILD-TYPE 
             48             307 
  BRCA2 MUTATED BRCA2 WILD-TYPE 
              7              66 
$`BRCA2 MUTATED`
TCGA-A6-5656 TCGA-A6-5665 TCGA-A6-6654 TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3518 
       32.91        22.06        23.87         1.02        63.98         1.02 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.99         6.05         6.97        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6964 TCGA-AU-6004 TCGA-AZ-4315 
       19.04         4.01        34.98        10.88        27.09        58.39 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 
       49.41         6.77       100.01         0.07         0.33         0.10 
TCGA-CK-5913 TCGA-CM-4743 TCGA-CM-4752 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6162 
       51.32        23.05        13.02        15.02        17.03        12.00 
TCGA-CM-6172 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-6533 TCGA-D5-6536 
       11.01        11.08        11.01        10.06         1.32        17.85 
TCGA-D5-6540 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6930 TCGA-DM-A0XD 
       16.14        12.43         9.04        13.41         1.51        24.43 
TCGA-DM-A1D9 TCGA-F4-6460 TCGA-F4-6703 TCGA-G4-6307 TCGA-G4-6588 TCGA-G4-6628 
      140.38        13.38        35.87        55.04        26.17        52.80 

$`BRCA2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       24.16        21.76        24.69        24.39        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 
       20.28         7.04         3.02        35.01         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       13.02        38.99         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       20.98        19.99        13.94        61.02        78.08        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       61.41        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 
        1.94         2.24         3.06         3.25         3.29         0.26 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
       21.99        21.14         2.93         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-5864 TCGA-CM-6161 TCGA-CM-6163 
       16.01        15.02         5.03        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-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6680 
       15.02        14.04        12.95        13.05        11.08        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        13.51        11.51        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-D5-6924 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-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45         6.18         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        53.62        44.68        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 
       46.75 

  BRCA2 MUTATED BRCA2 WILD-TYPE 
           0.07            0.00 
  BRCA2 MUTATED BRCA2 WILD-TYPE 
         140.38          139.17 
  BRCA2 MUTATED BRCA2 WILD-TYPE 
         16.585          21.140 
[1] "0.1 - 140.4 (16.6)" "0.0 - 139.2 (21.1)"
[1] "hr=" "1.5"
D217V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BRCA2 MUTATED         6        0        6        17         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           2          1          8          1        3         2
  BRCA2 WILD-TYPE        17          9         33         30       32        11
                 vv
clus              STAGE IVB
  BRCA2 MUTATED           0
  BRCA2 WILD-TYPE         1
D217V3, multiclass
            clus
vv           BRCA2 MUTATED BRCA2 WILD-TYPE
  STAGE I                6              58
  STAGE IA               0               1
  STAGE II               6              19
  STAGE IIA             17              92
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             1               9
  STAGE IIIB             8              33
  STAGE IIIC             1              30
  STAGE IV               3              32
  STAGE IVA              2              11
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  35   8
  BRCA2 WILD-TYPE   9  62 213  33
D217V4, multiclass
    clus
vv   BRCA2 MUTATED BRCA2 WILD-TYPE
  T1             0               9
  T2             6              62
  T3            35             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
  BRCA2 MUTATED    34  11   4
  BRCA2 WILD-TYPE 186  69  62
D217V5, multiclass
    clus
vv   BRCA2 MUTATED BRCA2 WILD-TYPE
  N0            34             186
  N1            11              69
  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"
D217V6, binary
                 cls
clus                0   1
  BRCA2 MUTATED    40   5
  BRCA2 WILD-TYPE 243  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRCA2 MUTATED     40    5
  BRCA2 WILD-TYPE  243   43
   clus
vv  BRCA2 MUTATED BRCA2 WILD-TYPE
  0            40             243
  1             5              43
[1] 2 2
[1] FALSE
D217V7, binary
                 cls
clus                0   1
  BRCA2 MUTATED    22  27
  BRCA2 WILD-TYPE 148 170
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRCA2 MUTATED     22   27
  BRCA2 WILD-TYPE  148  170
        clus
vv       BRCA2 MUTATED BRCA2 WILD-TYPE
  FEMALE            22             148
  MALE              27             170
[1] 2 2
[1] FALSE
D217V8, binary
                 cls
clus                0   1
  BRCA2 MUTATED    43   6
  BRCA2 WILD-TYPE 274  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRCA2 MUTATED     43    6
  BRCA2 WILD-TYPE  274   42
                               clus
vv                              BRCA2 MUTATED BRCA2 WILD-TYPE
  COLON ADENOCARCINOMA                     43             274
  COLON MUCINOUS ADENOCARCINOMA             6              42
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  BRCA2 MUTATED    35   0   2   4
  BRCA2 WILD-TYPE 222   2  20  17
D217V9, multiclass
    clus
vv   BRCA2 MUTATED BRCA2 WILD-TYPE
  R0            35             222
  R1             0               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"
D217V10, 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    32
  BRCA2 WILD-TYPE                        18   144
D217V11, 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                                       32             144
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(218) Variable = IFT57 MUTATION ANALYSIS
D218V1, survival
                 sevent
clus2               0   1
  IFT57 MUTATED     8   2
  IFT57 WILD-TYPE 274  71
  IFT57 MUTATED IFT57 WILD-TYPE 
             10             345 
  IFT57 MUTATED IFT57 WILD-TYPE 
              2              71 
$`IFT57 MUTATED`
TCGA-A6-5665 TCGA-A6-5666 TCGA-AA-A00N TCGA-AZ-4315 TCGA-CM-4743 TCGA-CM-5868 
       22.06        32.71         4.01        58.39        23.05        17.03 
TCGA-CM-6162 TCGA-DM-A1DA TCGA-G4-6323 TCGA-G4-6588 
       12.00         7.50        13.78        26.17 

$`IFT57 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.09        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB 
       92.75        49.91        13.32        12.59       140.38        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 
       51.75        45.11        36.72        36.00        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  IFT57 MUTATED IFT57 WILD-TYPE 
           4.01            0.00 
  IFT57 MUTATED IFT57 WILD-TYPE 
          58.39          140.38 
  IFT57 MUTATED IFT57 WILD-TYPE 
         19.545          20.190 
[1] "4.0 - 58.4 (19.5)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D218V2, 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       25       105         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        19         10         40         30       35        12
                 vv
clus              STAGE IVB
  IFT57 MUTATED           0
  IFT57 WILD-TYPE         1
D218V3, multiclass
            clus
vv           IFT57 MUTATED IFT57 WILD-TYPE
  STAGE I                0              64
  STAGE IA               1               0
  STAGE II               0              25
  STAGE IIA              4             105
  STAGE IIB              1               7
  STAGE IIC              1               0
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  68 242  38
D218V4, multiclass
    clus
vv   IFT57 MUTATED IFT57 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             6             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
  IFT57 MUTATED     7   2   1
  IFT57 WILD-TYPE 213  78  65
D218V5, multiclass
    clus
vv   IFT57 MUTATED IFT57 WILD-TYPE
  N0             7             213
  N1             2              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"
D218V6, binary
                 cls
clus                0   1
  IFT57 MUTATED     8   1
  IFT57 WILD-TYPE 275  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFT57 MUTATED      8    1
  IFT57 WILD-TYPE  275   47
   clus
vv  IFT57 MUTATED IFT57 WILD-TYPE
  0             8             275
  1             1              47
[1] 2 2
[1] FALSE
D218V7, 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
D218V8, binary
                 cls
clus                0   1
  IFT57 MUTATED     8   2
  IFT57 WILD-TYPE 309  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFT57 MUTATED      8    2
  IFT57 WILD-TYPE  309   46
                               clus
vv                              IFT57 MUTATED IFT57 WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  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 249   2  22  21
D218V9, multiclass
    clus
vv   IFT57 MUTATED IFT57 WILD-TYPE
  R0             8             249
  R1             0               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"
D218V10, 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
D218V11, 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(219) Variable = SPR MUTATION ANALYSIS
D219V1, survival
               sevent
clus2             0   1
  SPR MUTATED     4   3
  SPR WILD-TYPE 278  70
  SPR MUTATED SPR WILD-TYPE 
            7           348 
  SPR MUTATED SPR WILD-TYPE 
            3            70 
$`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 
      107.67 

$`SPR WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       40.34        49.08        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.41        19.43        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  SPR MUTATED SPR WILD-TYPE 
         3.02          0.00 
  SPR MUTATED SPR WILD-TYPE 
       107.67        140.38 
  SPR MUTATED SPR WILD-TYPE 
        14.53         20.63 
[1] "3.0 - 107.7 (14.5)" "0.0 - 140.4 (20.6)"
[1] "hr=" "1.7"
D219V2, 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       24       106         8         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SPR MUTATED           2          0          0          0        0         0
  SPR WILD-TYPE        17         10         41         31       35        13
               vv
clus            STAGE IVB
  SPR MUTATED           0
  SPR WILD-TYPE         1
D219V3, multiclass
            clus
vv           SPR MUTATED SPR WILD-TYPE
  STAGE I              1            63
  STAGE IA             0             1
  STAGE II             1            24
  STAGE IIA            3           106
  STAGE IIB            0             8
  STAGE IIC            0             1
  STAGE III            2            17
  STAGE IIIA           0            10
  STAGE IIIB           0            41
  STAGE IIIC           0            31
  STAGE IV             0            35
  STAGE IVA            0            13
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  SPR MUTATED     0   1   5   1
  SPR WILD-TYPE   9  67 243  40
D219V4, multiclass
    clus
vv   SPR MUTATED SPR WILD-TYPE
  T1           0             9
  T2           1            67
  T3           5           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
  SPR MUTATED     5   1   1
  SPR WILD-TYPE 215  79  65
D219V5, multiclass
    clus
vv   SPR MUTATED SPR WILD-TYPE
  N0           5           215
  N1           1            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"
D219V6, binary
               cls
clus              0   1
  SPR MUTATED     5   0
  SPR WILD-TYPE 278  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  SPR MUTATED      5    0
  SPR WILD-TYPE  278   48
   clus
vv  SPR MUTATED SPR WILD-TYPE
  0           5           278
  1           0            48
[1] 2 2
[1] FALSE
D219V7, 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
D219V8, binary
               cls
clus              0   1
  SPR MUTATED     5   2
  SPR WILD-TYPE 312  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  SPR MUTATED      5    2
  SPR WILD-TYPE  312   46
                               clus
vv                              SPR MUTATED SPR WILD-TYPE
  COLON ADENOCARCINOMA                    5           312
  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 254   2  22  19
D219V9, multiclass
    clus
vv   SPR MUTATED SPR WILD-TYPE
  R0           3           254
  R1           0             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"
D219V10, 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
D219V11, 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(220) Variable = ARFGEF1 MUTATION ANALYSIS
D220V1, survival
                   sevent
clus2                 0   1
  ARFGEF1 MUTATED    24   7
  ARFGEF1 WILD-TYPE 258  66
  ARFGEF1 MUTATED ARFGEF1 WILD-TYPE 
               31               324 
  ARFGEF1 MUTATED ARFGEF1 WILD-TYPE 
                7                66 
$`ARFGEF1 MUTATED`
TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3526 TCGA-AA-3555 TCGA-AA-3660 TCGA-AA-3662 
       22.06         3.02        19.07        29.95        78.08         6.05 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3852 TCGA-AA-3864 TCGA-AA-3977 TCGA-AA-A00N 
       85.05        19.04         0.00        53.00        25.02         4.01 
TCGA-AA-A010 TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-CA-5797 TCGA-CA-6717 
       34.98        83.80        62.79        49.41         3.29         0.33 
TCGA-CA-6718 TCGA-CK-5912 TCGA-CK-6747 TCGA-CM-4743 TCGA-CM-5344 TCGA-CM-6171 
        0.10        49.08         2.93        23.05        22.03        14.04 
TCGA-D5-6930 TCGA-DM-A0X9 TCGA-DM-A282 TCGA-DM-A28C TCGA-F4-6460 TCGA-F4-6704 
        1.51       119.70       139.17        81.37        13.38         1.55 
TCGA-G4-6586 
       35.80 

$`ARFGEF1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3529 
        9.07        24.03        37.05        36.03         8.05         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       61.02         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       19.00        36.00         5.03        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       10.06         0.00        33.07        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
        1.41         5.13        22.36        61.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        2.24         3.06         3.25         0.07         0.26         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
       17.56       102.44        40.34        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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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-A285 TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      131.51       135.65         6.12       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        13.45         6.18        35.87 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        26.17        91.79        46.75        52.80 

  ARFGEF1 MUTATED ARFGEF1 WILD-TYPE 
                0                 0 
  ARFGEF1 MUTATED ARFGEF1 WILD-TYPE 
           139.17            140.38 
  ARFGEF1 MUTATED ARFGEF1 WILD-TYPE 
            22.06             20.07 
[1] "0.0 - 139.2 (22.1)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.2"
D220V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ARFGEF1 MUTATED         3        0        5        15         2         0
  ARFGEF1 WILD-TYPE      61        1       20        94         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARFGEF1 MUTATED           2          0          2          1        2
  ARFGEF1 WILD-TYPE        17         10         39         30       33
                   vv
clus                STAGE IVA STAGE IVB
  ARFGEF1 MUTATED           0         0
  ARFGEF1 WILD-TYPE        13         1
D220V3, multiclass
            clus
vv           ARFGEF1 MUTATED ARFGEF1 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 5                20
  STAGE IIA               15                94
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                2                17
  STAGE IIIA               0                10
  STAGE IIIB               2                39
  STAGE IIIC               1                30
  STAGE IV                 2                33
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ARFGEF1 MUTATED     0   4  26   3
  ARFGEF1 WILD-TYPE   9  64 222  38
D220V4, multiclass
    clus
vv   ARFGEF1 MUTATED ARFGEF1 WILD-TYPE
  T1               0                 9
  T2               4                64
  T3              26               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    28   2   3
  ARFGEF1 WILD-TYPE 192  78  63
D220V5, multiclass
    clus
vv   ARFGEF1 MUTATED ARFGEF1 WILD-TYPE
  N0              28               192
  N1               2                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"
D220V6, binary
                   cls
clus                  0   1
  ARFGEF1 MUTATED    25   2
  ARFGEF1 WILD-TYPE 258  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARFGEF1 MUTATED     25    2
  ARFGEF1 WILD-TYPE  258   46
   clus
vv  ARFGEF1 MUTATED ARFGEF1 WILD-TYPE
  0              25               258
  1               2                46
[1] 2 2
[1] FALSE
D220V7, binary
                   cls
clus                  0   1
  ARFGEF1 MUTATED    16  17
  ARFGEF1 WILD-TYPE 154 180
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARFGEF1 MUTATED     16   17
  ARFGEF1 WILD-TYPE  154  180
        clus
vv       ARFGEF1 MUTATED ARFGEF1 WILD-TYPE
  FEMALE              16               154
  MALE                17               180
[1] 2 2
[1] FALSE
D220V8, binary
                   cls
clus                  0   1
  ARFGEF1 MUTATED    27   6
  ARFGEF1 WILD-TYPE 290  42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARFGEF1 MUTATED     27    6
  ARFGEF1 WILD-TYPE  290   42
                               clus
vv                              ARFGEF1 MUTATED ARFGEF1 WILD-TYPE
  COLON ADENOCARCINOMA                       27               290
  COLON MUCINOUS ADENOCARCINOMA               6                42
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ARFGEF1 MUTATED    21   0   2   4
  ARFGEF1 WILD-TYPE 236   2  20  17
D220V9, multiclass
    clus
vv   ARFGEF1 MUTATED ARFGEF1 WILD-TYPE
  R0              21               236
  R1               0                 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"
D220V10, 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    15
  ARFGEF1 WILD-TYPE                        19   161
D220V11, 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                                         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(221) Variable = DOCK10 MUTATION ANALYSIS
D221V1, survival
                  sevent
clus2                0   1
  DOCK10 MUTATED    17   6
  DOCK10 WILD-TYPE 265  67
  DOCK10 MUTATED DOCK10 WILD-TYPE 
              23              332 
  DOCK10 MUTATED DOCK10 WILD-TYPE 
               6               67 
$`DOCK10 MUTATED`
TCGA-A6-3809 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3697 
       32.75        24.16         1.02        14.01         0.92        85.05 
TCGA-AA-3713 TCGA-AA-3821 TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-A00N TCGA-AA-A010 
       19.04         1.02        25.02        19.07         4.01        34.98 
TCGA-AD-5900 TCGA-AD-6901 TCGA-AY-6197 TCGA-AZ-6600 TCGA-CA-6717 TCGA-CA-6718 
        0.07        22.42        21.44        12.10         0.33         0.10 
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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.18        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         3.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        2.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 
       37.05        19.00        36.00         5.03        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 
       10.06        35.05        33.04         0.99        25.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 
        4.21        56.55         0.79         0.72         5.79        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       15.75         0.20        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-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-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
      130.65        49.91        13.32       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  DOCK10 MUTATED DOCK10 WILD-TYPE 
            0.07             0.00 
  DOCK10 MUTATED DOCK10 WILD-TYPE 
          135.65           140.38 
  DOCK10 MUTATED DOCK10 WILD-TYPE 
           19.04            20.63 
[1] "0.1 - 135.7 (19.0)" "0.0 - 140.4 (20.6)"
[1] "hr=" "1.3"
D221V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DOCK10 MUTATED         4        0        2         6         3         0
  DOCK10 WILD-TYPE      60        1       23       103         5         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DOCK10 MUTATED           2          0          3          0        2
  DOCK10 WILD-TYPE        17         10         38         31       33
                  vv
clus               STAGE IVA STAGE IVB
  DOCK10 MUTATED           0         0
  DOCK10 WILD-TYPE        13         1
D221V3, multiclass
            clus
vv           DOCK10 MUTATED DOCK10 WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               6              103
  STAGE IIB               3                5
  STAGE IIC               0                1
  STAGE III               2               17
  STAGE IIIA              0               10
  STAGE IIIB              3               38
  STAGE IIIC              0               31
  STAGE IV                2               33
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  DOCK10 MUTATED     0   5  15   5
  DOCK10 WILD-TYPE   9  63 233  36
D221V4, multiclass
    clus
vv   DOCK10 MUTATED DOCK10 WILD-TYPE
  T1              0                9
  T2              5               63
  T3             15              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
  DOCK10 MUTATED    19   6   0
  DOCK10 WILD-TYPE 201  74  66
D221V5, multiclass
    clus
vv   DOCK10 MUTATED DOCK10 WILD-TYPE
  N0             19              201
  N1              6               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"
D221V6, binary
                  cls
clus                 0   1
  DOCK10 MUTATED    18   2
  DOCK10 WILD-TYPE 265  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DOCK10 MUTATED     18    2
  DOCK10 WILD-TYPE  265   46
   clus
vv  DOCK10 MUTATED DOCK10 WILD-TYPE
  0             18              265
  1              2               46
[1] 2 2
[1] FALSE
D221V7, 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
D221V8, binary
                  cls
clus                 0   1
  DOCK10 MUTATED    20   5
  DOCK10 WILD-TYPE 297  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DOCK10 MUTATED     20    5
  DOCK10 WILD-TYPE  297   43
                               clus
vv                              DOCK10 MUTATED DOCK10 WILD-TYPE
  COLON ADENOCARCINOMA                      20              297
  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 242   2  21  19
D221V9, multiclass
    clus
vv   DOCK10 MUTATED DOCK10 WILD-TYPE
  R0             15              242
  R1              0                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"
D221V10, 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
D221V11, 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(222) Variable = EP400 MUTATION ANALYSIS
D222V1, survival
                 sevent
clus2               0   1
  EP400 MUTATED    27   7
  EP400 WILD-TYPE 255  66
  EP400 MUTATED EP400 WILD-TYPE 
             34             321 
  EP400 MUTATED EP400 WILD-TYPE 
              7              66 
$`EP400 MUTATED`
TCGA-A6-2672 TCGA-A6-5661 TCGA-AA-3492 TCGA-AA-3511 TCGA-AA-3555 TCGA-AA-3663 
       46.65        33.53         3.02         6.97        29.95         6.97 
TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3850 TCGA-AA-3864 TCGA-AA-3977 TCGA-AA-A00E 
        0.92        19.04         0.00        53.00        25.02        30.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q TCGA-AA-A01R TCGA-AD-6888 TCGA-AY-6386 
        4.01        34.98         1.02        35.01         4.21        17.82 
TCGA-AZ-6598 TCGA-CK-4952 TCGA-CK-5913 TCGA-CM-4744 TCGA-CM-4752 TCGA-CM-5341 
       49.41        15.62        51.32        20.02        13.02        29.06 
TCGA-CM-5348 TCGA-CM-5349 TCGA-D5-6532 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-7000 
       22.98        30.08        18.25        16.14         7.53        10.26 
TCGA-DM-A1D8 TCGA-DM-A1DB TCGA-F4-6809 TCGA-G4-6588 
       12.59        44.32        13.25        26.17 

$`EP400 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       78.08         6.05        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       10.06        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J 
       27.02        13.94        38.04        19.00        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        31.00        38.07         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 
       17.56       102.44        40.34        49.08        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 
        2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       11.51        20.19         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 
        4.80        17.13        12.49        15.58        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 
        1.51        12.00        11.38       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        92.75        49.91        13.32       140.38         7.50 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       16.24        33.67         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  EP400 MUTATED EP400 WILD-TYPE 
              0               0 
  EP400 MUTATED EP400 WILD-TYPE 
          53.00          140.38 
  EP400 MUTATED EP400 WILD-TYPE 
         18.645          20.980 
[1] "0.0 - 53.0 (18.6)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.2"
D222V2, 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       19        99         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EP400 MUTATED           3          1          4          0        1         1
  EP400 WILD-TYPE        16          9         37         31       34        12
                 vv
clus              STAGE IVB
  EP400 MUTATED           0
  EP400 WILD-TYPE         1
D222V3, multiclass
            clus
vv           EP400 MUTATED EP400 WILD-TYPE
  STAGE I                5              59
  STAGE IA               0               1
  STAGE II               6              19
  STAGE IIA             10              99
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              3              16
  STAGE IIIA             1               9
  STAGE IIIB             4              37
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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   8  23   5
  EP400 WILD-TYPE   9  60 225  36
D222V4, multiclass
    clus
vv   EP400 MUTATED EP400 WILD-TYPE
  T1             0               9
  T2             8              60
  T3            23             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   7   2
  EP400 WILD-TYPE 194  73  64
D222V5, multiclass
    clus
vv   EP400 MUTATED EP400 WILD-TYPE
  N0            26             194
  N1             7              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"
D222V6, binary
                 cls
clus                0   1
  EP400 MUTATED    29   2
  EP400 WILD-TYPE 254  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP400 MUTATED     29    2
  EP400 WILD-TYPE  254   46
   clus
vv  EP400 MUTATED EP400 WILD-TYPE
  0            29             254
  1             2              46
[1] 2 2
[1] FALSE
D222V7, 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
D222V8, binary
                 cls
clus                0   1
  EP400 MUTATED    30   6
  EP400 WILD-TYPE 287  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP400 MUTATED     30    6
  EP400 WILD-TYPE  287   42
                               clus
vv                              EP400 MUTATED EP400 WILD-TYPE
  COLON ADENOCARCINOMA                     30             287
  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 229   2  21  18
D222V9, multiclass
    clus
vv   EP400 MUTATED EP400 WILD-TYPE
  R0            28             229
  R1             0               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"
D222V10, 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
D222V11, 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(223) Variable = C12ORF5 MUTATION ANALYSIS
D223V1, survival
                   sevent
clus2                 0   1
  C12ORF5 MUTATED     6   0
  C12ORF5 WILD-TYPE 276  73
  C12ORF5 MUTATED C12ORF5 WILD-TYPE 
                6               349 
  C12ORF5 MUTATED C12ORF5 WILD-TYPE 
                0                73 
$`C12ORF5 MUTATED`
TCGA-A6-5660 TCGA-AZ-4315 TCGA-CM-6164 TCGA-D5-5538 TCGA-G4-6293 TCGA-G4-6306 
       29.19        58.39        29.03        12.26       107.67        44.68 

$`C12ORF5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        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-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       12.03        45.40        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        35.41        19.43        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  C12ORF5 MUTATED C12ORF5 WILD-TYPE 
            12.26              0.00 
  C12ORF5 MUTATED C12ORF5 WILD-TYPE 
           107.67            140.38 
  C12ORF5 MUTATED C12ORF5 WILD-TYPE 
           36.935            20.020 
[1] "12.3 - 107.7 (36.9)" "0.0 - 140.4 (20.0)" 
[1] "hr="     "2.6e+07"
D223V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C12ORF5 MUTATED         0        0        0         3         0         0
  C12ORF5 WILD-TYPE      64        1       25       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        18         10         40         30       35
                   vv
clus                STAGE IVA STAGE IVB
  C12ORF5 MUTATED           0         0
  C12ORF5 WILD-TYPE        13         1
D223V3, multiclass
            clus
vv           C12ORF5 MUTATED C12ORF5 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                3               106
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               1                30
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C12ORF5 MUTATED     0   1   5   0
  C12ORF5 WILD-TYPE   9  67 243  41
D223V4, multiclass
    clus
vv   C12ORF5 MUTATED C12ORF5 WILD-TYPE
  T1               0                 9
  T2               1                67
  T3               5               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
  C12ORF5 MUTATED     3   2   1
  C12ORF5 WILD-TYPE 217  78  65
D223V5, multiclass
    clus
vv   C12ORF5 MUTATED C12ORF5 WILD-TYPE
  N0               3               217
  N1               2                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"
D223V6, binary
                   cls
clus                  0   1
  C12ORF5 MUTATED     6   0
  C12ORF5 WILD-TYPE 277  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C12ORF5 MUTATED      6    0
  C12ORF5 WILD-TYPE  277   48
   clus
vv  C12ORF5 MUTATED C12ORF5 WILD-TYPE
  0               6               277
  1               0                48
[1] 2 2
[1] FALSE
D223V7, 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
D223V8, binary
                   cls
clus                  0   1
  C12ORF5 MUTATED     6   0
  C12ORF5 WILD-TYPE 311  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C12ORF5 MUTATED      6    0
  C12ORF5 WILD-TYPE  311   48
                               clus
vv                              C12ORF5 MUTATED C12ORF5 WILD-TYPE
  COLON ADENOCARCINOMA                        6               311
  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 252   2  22  21
D223V9, multiclass
    clus
vv   C12ORF5 MUTATED C12ORF5 WILD-TYPE
  R0               5               252
  R1               0                 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"
D223V10, 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
D223V11, 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(224) Variable = ERCC5 MUTATION ANALYSIS
D224V1, survival
                 sevent
clus2               0   1
  ERCC5 MUTATED    15   8
  ERCC5 WILD-TYPE 267  65
  ERCC5 MUTATED ERCC5 WILD-TYPE 
             23             332 
  ERCC5 MUTATED ERCC5 WILD-TYPE 
              8              65 
$`ERCC5 MUTATED`
TCGA-A6-2672 TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-3492 TCGA-AA-3655 TCGA-AA-3815 
       46.65        22.06        20.12         3.02        61.02        33.04 
TCGA-AA-A004 TCGA-AA-A00N TCGA-AA-A017 TCGA-AA-A01R TCGA-AZ-4315 TCGA-AZ-6598 
       13.94         4.01        15.02        35.01        58.39        49.41 
TCGA-AZ-6608 TCGA-CM-5861 TCGA-CM-6171 TCGA-CM-6674 TCGA-D5-5537 TCGA-D5-5540 
        1.94        15.02        14.04        12.95        45.40        13.51 
TCGA-DM-A0XD TCGA-DM-A282 TCGA-DM-A28F TCGA-F4-6806 TCGA-F4-6809 
       24.43       139.17        35.97        29.59        13.25 

$`ERCC5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 
       24.16        21.76        24.69        24.39        23.87        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       19.04        19.04        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        34.98        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07         1.02         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01         5.03        15.02        15.02 
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-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       12.26        19.59        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        11.38        10.26       119.70        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       135.65         6.12        81.37       119.93 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 
        6.18        35.87         1.55        16.31        16.24        33.67 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  ERCC5 MUTATED ERCC5 WILD-TYPE 
           1.94            0.00 
  ERCC5 MUTATED ERCC5 WILD-TYPE 
         139.17          140.38 
  ERCC5 MUTATED ERCC5 WILD-TYPE 
         22.060          20.105 
[1] "1.9 - 139.2 (22.1)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.5"
D224V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ERCC5 MUTATED         2        0        3        13         1         0
  ERCC5 WILD-TYPE      62        1       22        96         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ERCC5 MUTATED           1          1          2          0        0         1
  ERCC5 WILD-TYPE        18          9         39         31       35        12
                 vv
clus              STAGE IVB
  ERCC5 MUTATED           0
  ERCC5 WILD-TYPE         1
D224V3, multiclass
            clus
vv           ERCC5 MUTATED ERCC5 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA             13              96
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             1               9
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  20   1
  ERCC5 WILD-TYPE   9  65 228  40
D224V4, multiclass
    clus
vv   ERCC5 MUTATED ERCC5 WILD-TYPE
  T1             0               9
  T2             3              65
  T3            20             228
  T4             1              40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ERCC5 MUTATED    18   4   2
  ERCC5 WILD-TYPE 202  76  64
D224V5, multiclass
    clus
vv   ERCC5 MUTATED ERCC5 WILD-TYPE
  N0            18             202
  N1             4              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"
D224V6, binary
                 cls
clus                0   1
  ERCC5 MUTATED    20   1
  ERCC5 WILD-TYPE 263  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC5 MUTATED     20    1
  ERCC5 WILD-TYPE  263   47
   clus
vv  ERCC5 MUTATED ERCC5 WILD-TYPE
  0            20             263
  1             1              47
[1] 2 2
[1] FALSE
D224V7, binary
                 cls
clus                0   1
  ERCC5 MUTATED    13  11
  ERCC5 WILD-TYPE 157 186
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC5 MUTATED     13   11
  ERCC5 WILD-TYPE  157  186
        clus
vv       ERCC5 MUTATED ERCC5 WILD-TYPE
  FEMALE            13             157
  MALE              11             186
[1] 2 2
[1] FALSE
D224V8, binary
                 cls
clus                0   1
  ERCC5 MUTATED    21   3
  ERCC5 WILD-TYPE 296  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC5 MUTATED     21    3
  ERCC5 WILD-TYPE  296   45
                               clus
vv                              ERCC5 MUTATED ERCC5 WILD-TYPE
  COLON ADENOCARCINOMA                     21             296
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ERCC5 MUTATED    17   0   0   1
  ERCC5 WILD-TYPE 240   2  22  20
D224V9, multiclass
    clus
vv   ERCC5 MUTATED ERCC5 WILD-TYPE
  R0            17             240
  R1             0               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"
D224V10, 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
D224V11, 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(225) Variable = C12ORF40 MUTATION ANALYSIS
D225V1, survival
                    sevent
clus2                  0   1
  C12ORF40 MUTATED    16   4
  C12ORF40 WILD-TYPE 266  69
  C12ORF40 MUTATED C12ORF40 WILD-TYPE 
                20                335 
  C12ORF40 MUTATED C12ORF40 WILD-TYPE 
                 4                 69 
$`C12ORF40 MUTATED`
TCGA-A6-5661 TCGA-A6-6648 TCGA-AA-3713 TCGA-AA-A00N TCGA-AD-6889 TCGA-AU-3779 
       33.53        25.18        19.04         4.01        56.55        14.50 
TCGA-AU-6004 TCGA-AY-6196 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-4947 TCGA-CK-5912 
       27.09         0.20        49.41         0.33        17.56        49.08 
TCGA-CK-6748 TCGA-CM-5344 TCGA-CM-6171 TCGA-CM-6676 TCGA-D5-6931 TCGA-DM-A1D6 
        2.01        22.03        14.04        11.08        12.00        49.91 
TCGA-DM-A1HB TCGA-G4-6588 
      135.65        26.17 

$`C12ORF40 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37         4.21         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AY-4070 
        5.79        22.42        27.42        10.88         0.20        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        15.75        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13        83.80        22.36        62.79        61.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.26         0.10         1.35       102.44        40.34        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         2.93       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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20       130.65        92.75        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        91.79        46.75        52.80 

  C12ORF40 MUTATED C12ORF40 WILD-TYPE 
               0.2                0.0 
  C12ORF40 MUTATED C12ORF40 WILD-TYPE 
            135.65             140.38 
  C12ORF40 MUTATED C12ORF40 WILD-TYPE 
            20.535             20.190 
[1] "0.2 - 135.7 (20.5)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D225V2, 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       24       103         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C12ORF40 MUTATED           0          0          2          2        3
  C12ORF40 WILD-TYPE        19         10         39         29       32
                    vv
clus                 STAGE IVA STAGE IVB
  C12ORF40 MUTATED           2         0
  C12ORF40 WILD-TYPE        11         1
D225V3, multiclass
            clus
vv           C12ORF40 MUTATED C12ORF40 WILD-TYPE
  STAGE I                   4                 60
  STAGE IA                  0                  1
  STAGE II                  1                 24
  STAGE IIA                 6                103
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                0                 10
  STAGE IIIB                2                 39
  STAGE IIIC                2                 29
  STAGE IV                  3                 32
  STAGE IVA                 2                 11
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of 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  64 235  37
D225V4, multiclass
    clus
vv   C12ORF40 MUTATED C12ORF40 WILD-TYPE
  T1                0                  9
  T2                4                 64
  T3               13                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
  C12ORF40 MUTATED    14   4   3
  C12ORF40 WILD-TYPE 206  76  63
D225V5, multiclass
    clus
vv   C12ORF40 MUTATED C12ORF40 WILD-TYPE
  N0               14                206
  N1                4                 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"
D225V6, binary
                    cls
clus                   0   1
  C12ORF40 MUTATED    14   4
  C12ORF40 WILD-TYPE 269  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF40 MUTATED     14    4
  C12ORF40 WILD-TYPE  269   44
   clus
vv  C12ORF40 MUTATED C12ORF40 WILD-TYPE
  0               14                269
  1                4                 44
[1] 2 2
[1] FALSE
D225V7, 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
D225V8, binary
                    cls
clus                   0   1
  C12ORF40 MUTATED    16   5
  C12ORF40 WILD-TYPE 301  43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF40 MUTATED     16    5
  C12ORF40 WILD-TYPE  301   43
                               clus
vv                              C12ORF40 MUTATED C12ORF40 WILD-TYPE
  COLON ADENOCARCINOMA                        16                301
  COLON MUCINOUS ADENOCARCINOMA                5                 43
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C12ORF40 MUTATED    10   0   2   4
  C12ORF40 WILD-TYPE 247   2  20  17
D225V9, multiclass
    clus
vv   C12ORF40 MUTATED C12ORF40 WILD-TYPE
  R0               10                247
  R1                0                  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"
D225V10, 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
D225V11, 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(226) Variable = MYL1 MUTATION ANALYSIS
D226V1, survival
                sevent
clus2              0   1
  MYL1 MUTATED     5   2
  MYL1 WILD-TYPE 277  71
  MYL1 MUTATED MYL1 WILD-TYPE 
             7            348 
  MYL1 MUTATED MYL1 WILD-TYPE 
             2             71 
$`MYL1 MUTATED`
TCGA-A6-5662 TCGA-AA-3979 TCGA-CK-5916 TCGA-CM-5862 TCGA-CM-6163 TCGA-CM-6172 
       23.61        24.00        21.14         5.03        14.04        11.01 
TCGA-D5-5540 
       13.51 

$`MYL1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        33.53        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        25.02        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02        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-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        14.04        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       19.59        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  MYL1 MUTATED MYL1 WILD-TYPE 
          5.03           0.00 
  MYL1 MUTATED MYL1 WILD-TYPE 
         24.00         140.38 
  MYL1 MUTATED MYL1 WILD-TYPE 
        14.040         20.235 
[1] "5.0 - 24.0 (14.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2.1"
D226V2, 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       25       107         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        19         10         40         31       35        11
                vv
clus             STAGE IVB
  MYL1 MUTATED           0
  MYL1 WILD-TYPE         1
D226V3, multiclass
            clus
vv           MYL1 MUTATED MYL1 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             2            107
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             2             11
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 243  41
D226V4, multiclass
    clus
vv   MYL1 MUTATED MYL1 WILD-TYPE
  T1            2              7
  T2            1             67
  T3            5            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
  MYL1 MUTATED     5   2   1
  MYL1 WILD-TYPE 215  78  65
D226V5, multiclass
    clus
vv   MYL1 MUTATED MYL1 WILD-TYPE
  N0            5            215
  N1            2             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"
D226V6, binary
                cls
clus               0   1
  MYL1 MUTATED     5   2
  MYL1 WILD-TYPE 278  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYL1 MUTATED      5    2
  MYL1 WILD-TYPE  278   46
   clus
vv  MYL1 MUTATED MYL1 WILD-TYPE
  0            5            278
  1            2             46
[1] 2 2
[1] FALSE
D226V7, 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
D226V8, binary
                cls
clus               0   1
  MYL1 MUTATED     8   0
  MYL1 WILD-TYPE 309  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYL1 MUTATED      8    0
  MYL1 WILD-TYPE  309   48
                               clus
vv                              MYL1 MUTATED MYL1 WILD-TYPE
  COLON ADENOCARCINOMA                     8            309
  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 252   2  22  19
D226V9, multiclass
    clus
vv   MYL1 MUTATED MYL1 WILD-TYPE
  R0            5            252
  R1            0              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"
D226V10, 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
D226V11, 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(227) Variable = GPR141 MUTATION ANALYSIS
D227V1, survival
                  sevent
clus2                0   1
  GPR141 MUTATED     9   2
  GPR141 WILD-TYPE 273  71
  GPR141 MUTATED GPR141 WILD-TYPE 
              11              344 
  GPR141 MUTATED GPR141 WILD-TYPE 
               2               71 
$`GPR141 MUTATED`
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3877 TCGA-AA-3947 TCGA-AZ-6601 TCGA-CA-6718 
       19.04        19.04        31.00        33.01       100.01         0.10 
TCGA-D5-5539 TCGA-D5-6930 TCGA-DM-A1HB TCGA-DM-A28E TCGA-G4-6306 
       19.59         1.51       135.65       119.93        44.68 

$`GPR141 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3811 
       19.00        36.00         5.03        85.05        26.99        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        18.05         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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-A285 TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G 
      131.51       139.17         6.12        81.37        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  GPR141 MUTATED GPR141 WILD-TYPE 
             0.1              0.0 
  GPR141 MUTATED GPR141 WILD-TYPE 
          135.65           140.38 
  GPR141 MUTATED GPR141 WILD-TYPE 
          31.000           20.155 
[1] "0.1 - 135.7 (31.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.9"
D227V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GPR141 MUTATED         1        0        2         4         1         0
  GPR141 WILD-TYPE      63        1       23       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        19          9         40         31       34
                  vv
clus               STAGE IVA STAGE IVB
  GPR141 MUTATED           0         0
  GPR141 WILD-TYPE        13         1
D227V3, multiclass
            clus
vv           GPR141 MUTATED GPR141 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               4              105
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              1                9
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GPR141 MUTATED     1   1   8   1
  GPR141 WILD-TYPE   8  67 240  40
D227V4, multiclass
    clus
vv   GPR141 MUTATED GPR141 WILD-TYPE
  T1              1                8
  T2              1               67
  T3              8              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
  GPR141 MUTATED     9   2   0
  GPR141 WILD-TYPE 211  78  66
D227V5, multiclass
    clus
vv   GPR141 MUTATED GPR141 WILD-TYPE
  N0              9              211
  N1              2               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"
D227V6, binary
                  cls
clus                 0   1
  GPR141 MUTATED    10   1
  GPR141 WILD-TYPE 273  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR141 MUTATED     10    1
  GPR141 WILD-TYPE  273   47
   clus
vv  GPR141 MUTATED GPR141 WILD-TYPE
  0             10              273
  1              1               47
[1] 2 2
[1] FALSE
D227V7, 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
D227V8, binary
                  cls
clus                 0   1
  GPR141 MUTATED     7   4
  GPR141 WILD-TYPE 310  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR141 MUTATED      7    4
  GPR141 WILD-TYPE  310   44
                               clus
vv                              GPR141 MUTATED GPR141 WILD-TYPE
  COLON ADENOCARCINOMA                       7              310
  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 251   2  21  20
D227V9, multiclass
    clus
vv   GPR141 MUTATED GPR141 WILD-TYPE
  R0              6              251
  R1              0                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"
D227V10, 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
D227V11, 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(228) Variable = AKAP3 MUTATION ANALYSIS
D228V1, survival
                 sevent
clus2               0   1
  AKAP3 MUTATED    19   2
  AKAP3 WILD-TYPE 263  71
  AKAP3 MUTATED AKAP3 WILD-TYPE 
             21             334 
  AKAP3 MUTATED AKAP3 WILD-TYPE 
              2              71 
$`AKAP3 MUTATED`
TCGA-A6-6141 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3655 TCGA-AA-3713 TCGA-AA-3968 
        8.38         3.02        35.01        61.02        19.04        21.99 
TCGA-AA-3977 TCGA-AA-A010 TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A02F TCGA-AD-6963 
       25.02        34.98         1.02        35.01        39.98        27.42 
TCGA-AZ-4315 TCGA-AZ-6600 TCGA-CA-6717 TCGA-CK-4952 TCGA-CM-5348 TCGA-CM-5860 
       58.39        12.10         0.33        15.62        22.98        16.01 
TCGA-CM-5861 TCGA-D5-6931 TCGA-G4-6588 
       15.02        12.00        26.17 

$`AKAP3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3510 
       20.12        19.66        20.28         7.04         1.02        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        31.00        38.07         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02H TCGA-AA-A02J 
       26.01        37.02        39.06        51.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       40.34        49.08        51.32        21.99        21.14         2.93 
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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        91.79        46.75        52.80 

  AKAP3 MUTATED AKAP3 WILD-TYPE 
           0.33            0.00 
  AKAP3 MUTATED AKAP3 WILD-TYPE 
          61.02          140.38 
  AKAP3 MUTATED AKAP3 WILD-TYPE 
         21.990          20.155 
[1] "0.3 - 61.0 (22.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2"  
D228V2, 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       22       103         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AKAP3 MUTATED           2          0          1          1        3         0
  AKAP3 WILD-TYPE        17         10         40         30       32        13
                 vv
clus              STAGE IVB
  AKAP3 MUTATED           0
  AKAP3 WILD-TYPE         1
D228V3, multiclass
            clus
vv           AKAP3 MUTATED AKAP3 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              6             103
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             1              30
  STAGE IV               3              32
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  AKAP3 MUTATED     0   3  14   4
  AKAP3 WILD-TYPE   9  65 234  37
D228V4, multiclass
    clus
vv   AKAP3 MUTATED AKAP3 WILD-TYPE
  T1             0               9
  T2             3              65
  T3            14             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
  AKAP3 MUTATED    15   3   3
  AKAP3 WILD-TYPE 205  77  63
D228V5, multiclass
    clus
vv   AKAP3 MUTATED AKAP3 WILD-TYPE
  N0            15             205
  N1             3              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"
D228V6, binary
                 cls
clus                0   1
  AKAP3 MUTATED    16   3
  AKAP3 WILD-TYPE 267  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AKAP3 MUTATED     16    3
  AKAP3 WILD-TYPE  267   45
   clus
vv  AKAP3 MUTATED AKAP3 WILD-TYPE
  0            16             267
  1             3              45
[1] 2 2
[1] FALSE
D228V7, 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
D228V8, binary
                 cls
clus                0   1
  AKAP3 MUTATED    18   3
  AKAP3 WILD-TYPE 299  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AKAP3 MUTATED     18    3
  AKAP3 WILD-TYPE  299   45
                               clus
vv                              AKAP3 MUTATED AKAP3 WILD-TYPE
  COLON ADENOCARCINOMA                     18             299
  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 244   2  20  19
D228V9, multiclass
    clus
vv   AKAP3 MUTATED AKAP3 WILD-TYPE
  R0            13             244
  R1             0               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"
D228V10, 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
D228V11, 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(229) Variable = HELQ MUTATION ANALYSIS
D229V1, survival
                sevent
clus2              0   1
  HELQ MUTATED    13   3
  HELQ WILD-TYPE 269  70
  HELQ MUTATED HELQ WILD-TYPE 
            16            339 
  HELQ MUTATED HELQ WILD-TYPE 
             3             70 
$`HELQ MUTATED`
TCGA-AA-3510 TCGA-AA-3660 TCGA-AA-3821 TCGA-AA-3966 TCGA-AA-A00N TCGA-AA-A010 
       63.98        78.08         1.02         2.01         4.01        34.98 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 
        0.07        56.55         0.79        58.39        49.41         0.33 
TCGA-CM-5861 TCGA-CM-6165 TCGA-F4-6459 TCGA-G4-6628 
       15.02        16.04         8.61        52.80 

$`HELQ WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        61.02         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 
       35.05        33.04         0.99        25.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        4.21         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 
       35.97        60.79       117.07        98.24        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       26.17        91.79        46.75 

  HELQ MUTATED HELQ WILD-TYPE 
          0.07           0.00 
  HELQ MUTATED HELQ WILD-TYPE 
         78.08         140.38 
  HELQ MUTATED HELQ WILD-TYPE 
         15.53          20.28 
[1] "0.1 - 78.1 (15.5)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.3"
D229V2, 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       22       103         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        18         10         40         31       35        13
                vv
clus             STAGE IVB
  HELQ MUTATED           0
  HELQ WILD-TYPE         1
D229V3, multiclass
            clus
vv           HELQ MUTATED HELQ WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              3             22
  STAGE IIA             6            103
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  HELQ MUTATED     1   3  11   3
  HELQ WILD-TYPE   8  65 237  38
D229V4, multiclass
    clus
vv   HELQ MUTATED HELQ WILD-TYPE
  T1            1              8
  T2            3             65
  T3           11            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
  HELQ MUTATED    16   0   2
  HELQ WILD-TYPE 204  80  64
D229V5, multiclass
    clus
vv   HELQ MUTATED HELQ WILD-TYPE
  N0           16            204
  N1            0             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"
D229V6, binary
                cls
clus               0   1
  HELQ MUTATED    14   0
  HELQ WILD-TYPE 269  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  HELQ MUTATED     14    0
  HELQ WILD-TYPE  269   48
   clus
vv  HELQ MUTATED HELQ WILD-TYPE
  0           14            269
  1            0             48
[1] 2 2
[1] FALSE
D229V7, 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
D229V8, binary
                cls
clus               0   1
  HELQ MUTATED    13   5
  HELQ WILD-TYPE 304  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  HELQ MUTATED     13    5
  HELQ WILD-TYPE  304   43
                               clus
vv                              HELQ MUTATED HELQ WILD-TYPE
  COLON ADENOCARCINOMA                    13            304
  COLON MUCINOUS ADENOCARCINOMA            5             43
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  HELQ MUTATED    12   0   0   2
  HELQ WILD-TYPE 245   2  22  19
D229V9, multiclass
    clus
vv   HELQ MUTATED HELQ WILD-TYPE
  R0           12            245
  R1            0              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"
D229V10, 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
D229V11, 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(230) Variable = GLI2 MUTATION ANALYSIS
D230V1, survival
                sevent
clus2              0   1
  GLI2 MUTATED    14   5
  GLI2 WILD-TYPE 268  68
  GLI2 MUTATED GLI2 WILD-TYPE 
            19            336 
  GLI2 MUTATED GLI2 WILD-TYPE 
             5             68 
$`GLI2 MUTATED`
TCGA-AA-3492 TCGA-AA-A01P TCGA-AY-5543 TCGA-AY-6196 TCGA-CA-5255 TCGA-CA-6717 
        3.02        38.07        15.75         0.20         3.06         0.33 
TCGA-CA-6718 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6171 TCGA-D5-6537 
        0.10         5.03        15.02        14.04        14.04         4.80 
TCGA-D5-6539 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6928 TCGA-DM-A1DA TCGA-G4-6625 
       12.49        10.13        12.43        11.64         7.50        91.79 
TCGA-G4-6628 
       52.80 

$`GLI2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        2.24         3.25         3.29         0.07         0.26         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02        12.00        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       12.99        13.02        15.02        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6540 
        1.32        43.27        15.12        17.85        17.13        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       15.58         7.53        12.39        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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       12.59       140.38        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        26.17        46.75 

  GLI2 MUTATED GLI2 WILD-TYPE 
           0.1            0.0 
  GLI2 MUTATED GLI2 WILD-TYPE 
         91.79         140.38 
  GLI2 MUTATED GLI2 WILD-TYPE 
        11.640         21.405 
[1] "0.1 - 91.8 (11.6)"  "0.0 - 140.4 (21.4)"
[1] "hr=" "1.9"
D230V2, 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       23       104         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GLI2 MUTATED           1          2          1          2        0         2
  GLI2 WILD-TYPE        18          8         40         29       35        11
                vv
clus             STAGE IVB
  GLI2 MUTATED           0
  GLI2 WILD-TYPE         1
D230V3, multiclass
            clus
vv           GLI2 MUTATED GLI2 WILD-TYPE
  STAGE I               5             59
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             5            104
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            2              8
  STAGE IIIB            1             40
  STAGE IIIC            2             29
  STAGE IV              0             35
  STAGE IVA             2             11
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  64 234  40
D230V4, multiclass
    clus
vv   GLI2 MUTATED GLI2 WILD-TYPE
  T1            1              8
  T2            4             64
  T3           14            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
  GLI2 MUTATED    13   5   2
  GLI2 WILD-TYPE 207  75  64
D230V5, multiclass
    clus
vv   GLI2 MUTATED GLI2 WILD-TYPE
  N0           13            207
  N1            5             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"
D230V6, binary
                cls
clus               0   1
  GLI2 MUTATED    16   2
  GLI2 WILD-TYPE 267  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLI2 MUTATED     16    2
  GLI2 WILD-TYPE  267   46
   clus
vv  GLI2 MUTATED GLI2 WILD-TYPE
  0           16            267
  1            2             46
[1] 2 2
[1] FALSE
D230V7, 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
D230V8, binary
                cls
clus               0   1
  GLI2 MUTATED    17   3
  GLI2 WILD-TYPE 300  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLI2 MUTATED     17    3
  GLI2 WILD-TYPE  300   45
                               clus
vv                              GLI2 MUTATED GLI2 WILD-TYPE
  COLON ADENOCARCINOMA                    17            300
  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 241   2  22  18
D230V9, multiclass
    clus
vv   GLI2 MUTATED GLI2 WILD-TYPE
  R0           16            241
  R1            0              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"
D230V10, 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
D230V11, 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(231) Variable = SULT6B1 MUTATION ANALYSIS
D231V1, survival
                   sevent
clus2                 0   1
  SULT6B1 MUTATED     7   1
  SULT6B1 WILD-TYPE 275  72
  SULT6B1 MUTATED SULT6B1 WILD-TYPE 
                8               347 
  SULT6B1 MUTATED SULT6B1 WILD-TYPE 
                1                72 
$`SULT6B1 MUTATED`
TCGA-AA-3510 TCGA-AA-A010 TCGA-AY-6196 TCGA-AZ-4315 TCGA-CM-4743 TCGA-D5-6539 
       63.98        34.98         0.20        58.39        23.05        12.49 
TCGA-DM-A1DB TCGA-G4-6310 
       44.32        45.11 

$`SULT6B1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       15.75        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        51.75        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  SULT6B1 MUTATED SULT6B1 WILD-TYPE 
              0.2               0.0 
  SULT6B1 MUTATED SULT6B1 WILD-TYPE 
            63.98            140.38 
  SULT6B1 MUTATED SULT6B1 WILD-TYPE 
            39.65             20.02 
[1] "0.2 - 64.0 (39.6)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "2.3"
D231V2, 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       24       105         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SULT6B1 MUTATED           0          1          1          1        0
  SULT6B1 WILD-TYPE        19          9         40         30       35
                   vv
clus                STAGE IVA STAGE IVB
  SULT6B1 MUTATED           0         0
  SULT6B1 WILD-TYPE        13         1
D231V3, multiclass
            clus
vv           SULT6B1 MUTATED SULT6B1 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                4               105
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               1                 9
  STAGE IIIB               1                40
  STAGE IIIC               1                30
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SULT6B1 MUTATED     0   0   8   1
  SULT6B1 WILD-TYPE   9  68 240  40
D231V4, multiclass
    clus
vv   SULT6B1 MUTATED SULT6B1 WILD-TYPE
  T1               0                 9
  T2               0                68
  T3               8               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
  SULT6B1 MUTATED     7   1   1
  SULT6B1 WILD-TYPE 213  79  65
D231V5, multiclass
    clus
vv   SULT6B1 MUTATED SULT6B1 WILD-TYPE
  N0               7               213
  N1               1                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"
D231V6, binary
                   cls
clus                  0   1
  SULT6B1 MUTATED     8   0
  SULT6B1 WILD-TYPE 275  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SULT6B1 MUTATED      8    0
  SULT6B1 WILD-TYPE  275   48
   clus
vv  SULT6B1 MUTATED SULT6B1 WILD-TYPE
  0               8               275
  1               0                48
[1] 2 2
[1] FALSE
D231V7, 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
D231V8, binary
                   cls
clus                  0   1
  SULT6B1 MUTATED     8   1
  SULT6B1 WILD-TYPE 309  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SULT6B1 MUTATED      8    1
  SULT6B1 WILD-TYPE  309   47
                               clus
vv                              SULT6B1 MUTATED SULT6B1 WILD-TYPE
  COLON ADENOCARCINOMA                        8               309
  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 249   2  22  21
D231V9, multiclass
    clus
vv   SULT6B1 MUTATED SULT6B1 WILD-TYPE
  R0               8               249
  R1               0                 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"
D231V10, 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
D231V11, 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(232) Variable = LNPEP MUTATION ANALYSIS
D232V1, survival
                 sevent
clus2               0   1
  LNPEP MUTATED    13   4
  LNPEP WILD-TYPE 269  69
  LNPEP MUTATED LNPEP WILD-TYPE 
             17             338 
  LNPEP MUTATED LNPEP WILD-TYPE 
              4              69 
$`LNPEP MUTATED`
TCGA-AA-3492 TCGA-AA-3663 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3966 TCGA-AA-A00A 
        3.02         6.97        19.04        19.04         2.01        38.04 
TCGA-AA-A00J TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-CA-6718 
       18.05        34.98        58.39        61.41        49.41         0.10 
TCGA-CK-6747 TCGA-D5-6536 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6626 
        2.93        17.85        51.75        45.11        46.75 

$`LNPEP WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.03        85.05        26.99        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K 
       27.02        13.94        19.00        30.02        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       83.80        22.36        62.79         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 
       91.79        52.80 

  LNPEP MUTATED LNPEP WILD-TYPE 
            0.1             0.0 
  LNPEP MUTATED LNPEP WILD-TYPE 
          61.41          140.38 
  LNPEP MUTATED LNPEP WILD-TYPE 
         19.040          20.235 
[1] "0.1 - 61.4 (19.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1"  
D232V2, 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       21       101         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        19         10         38         31       34        13
                 vv
clus              STAGE IVB
  LNPEP MUTATED           0
  LNPEP WILD-TYPE         1
D232V3, multiclass
            clus
vv           LNPEP MUTATED LNPEP WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               4              21
  STAGE IIA              8             101
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             3              38
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LNPEP MUTATED     1   0  15   2
  LNPEP WILD-TYPE   8  68 233  39
D232V4, multiclass
    clus
vv   LNPEP MUTATED LNPEP WILD-TYPE
  T1             1               8
  T2             0              68
  T3            15             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
  LNPEP MUTATED    15   3   0
  LNPEP WILD-TYPE 205  77  66
D232V5, multiclass
    clus
vv   LNPEP MUTATED LNPEP WILD-TYPE
  N0            15             205
  N1             3              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"
D232V6, binary
                 cls
clus                0   1
  LNPEP MUTATED    15   1
  LNPEP WILD-TYPE 268  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LNPEP MUTATED     15    1
  LNPEP WILD-TYPE  268   47
   clus
vv  LNPEP MUTATED LNPEP WILD-TYPE
  0            15             268
  1             1              47
[1] 2 2
[1] FALSE
D232V7, 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
D232V8, binary
                 cls
clus                0   1
  LNPEP MUTATED    16   2
  LNPEP WILD-TYPE 301  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LNPEP MUTATED     16    2
  LNPEP WILD-TYPE  301   46
                               clus
vv                              LNPEP MUTATED LNPEP WILD-TYPE
  COLON ADENOCARCINOMA                     16             301
  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 245   2  21  19
D232V9, multiclass
    clus
vv   LNPEP MUTATED LNPEP WILD-TYPE
  R0            12             245
  R1             0               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"
D232V10, 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
D232V11, 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(233) Variable = OR1J2 MUTATION ANALYSIS
D233V1, survival
                 sevent
clus2               0   1
  OR1J2 MUTATED     9   0
  OR1J2 WILD-TYPE 273  73
  OR1J2 MUTATED OR1J2 WILD-TYPE 
              9             346 
  OR1J2 MUTATED OR1J2 WILD-TYPE 
              0              73 
$`OR1J2 MUTATED`
TCGA-A6-6780 TCGA-AA-3663 TCGA-AY-5543 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
       20.12         6.97        15.75         3.25         3.29         0.07 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CM-6170 
       21.99         2.93        15.02 

$`OR1J2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        1.94         2.24         3.06         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       51.32        21.14         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  OR1J2 MUTATED OR1J2 WILD-TYPE 
           0.07            0.00 
  OR1J2 MUTATED OR1J2 WILD-TYPE 
          21.99          140.38 
  OR1J2 MUTATED OR1J2 WILD-TYPE 
          6.970          20.995 
[1] "0.1 - 22.0 (7.0)"   "0.0 - 140.4 (21.0)"
[1] "hr="     "9200000"
D233V2, 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       24       105         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        18         10         39         31       35        12
                 vv
clus              STAGE IVB
  OR1J2 MUTATED           0
  OR1J2 WILD-TYPE         1
D233V3, multiclass
            clus
vv           OR1J2 MUTATED OR1J2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              4             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 239  41
D233V4, multiclass
    clus
vv   OR1J2 MUTATED OR1J2 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             9             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
  OR1J2 MUTATED     6   3   1
  OR1J2 WILD-TYPE 214  77  65
D233V5, multiclass
    clus
vv   OR1J2 MUTATED OR1J2 WILD-TYPE
  N0             6             214
  N1             3              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"
D233V6, binary
                 cls
clus                0   1
  OR1J2 MUTATED     6   1
  OR1J2 WILD-TYPE 277  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1J2 MUTATED      6    1
  OR1J2 WILD-TYPE  277   47
   clus
vv  OR1J2 MUTATED OR1J2 WILD-TYPE
  0             6             277
  1             1              47
[1] 2 2
[1] FALSE
D233V7, 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
D233V8, binary
                 cls
clus                0   1
  OR1J2 MUTATED     8   2
  OR1J2 WILD-TYPE 309  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1J2 MUTATED      8    2
  OR1J2 WILD-TYPE  309   46
                               clus
vv                              OR1J2 MUTATED OR1J2 WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  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 251   2  22  18
D233V9, multiclass
    clus
vv   OR1J2 MUTATED OR1J2 WILD-TYPE
  R0             6             251
  R1             0               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"
D233V10, 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
D233V11, 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(234) Variable = PRKCH MUTATION ANALYSIS
D234V1, survival
                 sevent
clus2               0   1
  PRKCH MUTATED    10   2
  PRKCH WILD-TYPE 272  71
  PRKCH MUTATED PRKCH WILD-TYPE 
             12             343 
  PRKCH MUTATED PRKCH WILD-TYPE 
              2              71 
$`PRKCH MUTATED`
TCGA-A6-5665 TCGA-AA-3502 TCGA-AA-3989 TCGA-AD-6889 TCGA-AU-6004 TCGA-AZ-6601 
       22.06        35.01         7.96        56.55        27.09       100.01 
TCGA-CA-6717 TCGA-CM-5864 TCGA-CM-6167 TCGA-D5-5540 TCGA-F4-6460 TCGA-G4-6586 
        0.33        15.02        14.99        13.51        13.38        35.80 

$`PRKCH WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       27.02        19.07        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37         4.21         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        61.41        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        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        12.26        19.59        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
      117.07        98.24         8.61        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  PRKCH MUTATED PRKCH WILD-TYPE 
           0.33            0.00 
  PRKCH MUTATED PRKCH WILD-TYPE 
         100.01          140.38 
  PRKCH MUTATED PRKCH WILD-TYPE 
          18.54           20.19 
[1] "0.3 - 100.0 (18.5)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.4"
D234V2, 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       24       103         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        19         10         40         30       34        13
                 vv
clus              STAGE IVB
  PRKCH MUTATED           0
  PRKCH WILD-TYPE         1
D234V3, multiclass
            clus
vv           PRKCH MUTATED PRKCH WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              6             103
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PRKCH MUTATED     0   3  10   0
  PRKCH WILD-TYPE   9  65 238  41
D234V4, multiclass
    clus
vv   PRKCH MUTATED PRKCH WILD-TYPE
  T1             0               9
  T2             3              65
  T3            10             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
  PRKCH MUTATED    10   1   2
  PRKCH WILD-TYPE 210  79  64
D234V5, multiclass
    clus
vv   PRKCH MUTATED PRKCH WILD-TYPE
  N0            10             210
  N1             1              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"
D234V6, binary
                 cls
clus                0   1
  PRKCH MUTATED    12   1
  PRKCH WILD-TYPE 271  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCH MUTATED     12    1
  PRKCH WILD-TYPE  271   47
   clus
vv  PRKCH MUTATED PRKCH WILD-TYPE
  0            12             271
  1             1              47
[1] 2 2
[1] FALSE
D234V7, 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
D234V8, binary
                 cls
clus                0   1
  PRKCH MUTATED    12   1
  PRKCH WILD-TYPE 305  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCH MUTATED     12    1
  PRKCH WILD-TYPE  305   47
                               clus
vv                              PRKCH MUTATED PRKCH WILD-TYPE
  COLON ADENOCARCINOMA                     12             305
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PRKCH MUTATED     9   0   1   1
  PRKCH WILD-TYPE 248   2  21  20
D234V9, multiclass
    clus
vv   PRKCH MUTATED PRKCH WILD-TYPE
  R0             9             248
  R1             0               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"
D234V10, 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
D234V11, 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(235) Variable = PPARGC1A MUTATION ANALYSIS
D235V1, survival
                    sevent
clus2                  0   1
  PPARGC1A MUTATED    17   5
  PPARGC1A WILD-TYPE 265  68
  PPARGC1A MUTATED PPARGC1A WILD-TYPE 
                22                333 
  PPARGC1A MUTATED PPARGC1A WILD-TYPE 
                 5                 68 
$`PPARGC1A MUTATED`
TCGA-A6-3809 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6648 TCGA-A6-6780 TCGA-A6-6782 
       32.75        22.06        32.71        25.18        20.12        20.28 
TCGA-AA-3662 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3864 TCGA-AA-3947 
        6.05        26.99        19.04        19.04        53.00        33.01 
TCGA-AD-6889 TCGA-AY-6386 TCGA-AZ-6598 TCGA-AZ-6606 TCGA-CA-6717 TCGA-CA-6718 
       56.55        17.82        49.41        11.74         0.33         0.10 
TCGA-CM-6162 TCGA-D5-6537 TCGA-D5-6923 TCGA-G4-6626 
       12.00         4.80        12.43        46.75 

$`PPARGC1A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6651 
       27.09        22.52         8.38        25.08        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3492 
       24.69        24.39        23.87        19.66         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       36.00         5.03        85.05        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 
       18.05        31.00         2.01        12.99        24.00        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        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        15.75         0.20        21.44        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13        83.80        22.36        62.79        61.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10       100.01        29.56         5.23         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       26.17        91.79        52.80 

  PPARGC1A MUTATED PPARGC1A WILD-TYPE 
               0.1                0.0 
  PPARGC1A MUTATED PPARGC1A WILD-TYPE 
             56.55             140.38 
  PPARGC1A MUTATED PPARGC1A WILD-TYPE 
             20.20              20.19 
[1] "0.1 - 56.5 (20.2)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D235V2, 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       21       102         5         0
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PPARGC1A MUTATED           0          0          3          0        3
  PPARGC1A WILD-TYPE        19         10         38         31       32
                    vv
clus                 STAGE IVA STAGE IVB
  PPARGC1A MUTATED           1         0
  PPARGC1A WILD-TYPE        12         1
D235V3, multiclass
            clus
vv           PPARGC1A MUTATED PPARGC1A WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  4                 21
  STAGE IIA                 7                102
  STAGE IIB                 3                  5
  STAGE IIC                 1                  0
  STAGE III                 0                 19
  STAGE IIIA                0                 10
  STAGE IIIB                3                 38
  STAGE IIIC                0                 31
  STAGE IV                  3                 32
  STAGE IVA                 1                 12
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 233  34
D235V4, multiclass
    clus
vv   PPARGC1A MUTATED PPARGC1A WILD-TYPE
  T1                0                  9
  T2                1                 67
  T3               15                233
  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  77  64
D235V5, multiclass
    clus
vv   PPARGC1A MUTATED PPARGC1A WILD-TYPE
  N0               18                202
  N1                3                 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"
D235V6, binary
                    cls
clus                   0   1
  PPARGC1A MUTATED    15   4
  PPARGC1A WILD-TYPE 268  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPARGC1A MUTATED     15    4
  PPARGC1A WILD-TYPE  268   44
   clus
vv  PPARGC1A MUTATED PPARGC1A WILD-TYPE
  0               15                268
  1                4                 44
[1] 2 2
[1] FALSE
D235V7, 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
D235V8, binary
                    cls
clus                   0   1
  PPARGC1A MUTATED    18   5
  PPARGC1A WILD-TYPE 299  43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPARGC1A MUTATED     18    5
  PPARGC1A WILD-TYPE  299   43
                               clus
vv                              PPARGC1A MUTATED PPARGC1A WILD-TYPE
  COLON ADENOCARCINOMA                        18                299
  COLON MUCINOUS ADENOCARCINOMA                5                 43
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  PPARGC1A MUTATED    12   0   2   2
  PPARGC1A WILD-TYPE 245   2  20  19
D235V9, multiclass
    clus
vv   PPARGC1A MUTATED PPARGC1A WILD-TYPE
  R0               12                245
  R1                0                  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"
D235V10, 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
D235V11, 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(236) Variable = DHRS7 MUTATION ANALYSIS
D236V1, survival
                 sevent
clus2               0   1
  DHRS7 MUTATED     9   1
  DHRS7 WILD-TYPE 273  72
  DHRS7 MUTATED DHRS7 WILD-TYPE 
             10             345 
  DHRS7 MUTATED DHRS7 WILD-TYPE 
              1              72 
$`DHRS7 MUTATED`
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3950 TCGA-AU-6004 
       33.53        23.61        19.66        63.98        24.00        27.09 
TCGA-AY-6197 TCGA-AZ-6601 TCGA-CK-4950 TCGA-CM-6172 
       21.44       100.01        40.34        11.01 

$`DHRS7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5664 TCGA-A6-5665 
       32.91        31.63        30.44        29.19        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        15.75         0.20        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      102.44        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  DHRS7 MUTATED DHRS7 WILD-TYPE 
          11.01            0.00 
  DHRS7 MUTATED DHRS7 WILD-TYPE 
         100.01          140.38 
  DHRS7 MUTATED DHRS7 WILD-TYPE 
         25.545          19.990 
[1] "11.0 - 100.0 (25.5)" "0.0 - 140.4 (20.0)" 
[1] "hr=" "3"  
D236V2, 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       23       106         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DHRS7 MUTATED           0          1          1          1        0         1
  DHRS7 WILD-TYPE        19          9         40         30       35        12
                 vv
clus              STAGE IVB
  DHRS7 MUTATED           0
  DHRS7 WILD-TYPE         1
D236V3, multiclass
            clus
vv           DHRS7 MUTATED DHRS7 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              3             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             1              40
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 240  40
D236V4, multiclass
    clus
vv   DHRS7 MUTATED DHRS7 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             8             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
  DHRS7 MUTATED     6   3   1
  DHRS7 WILD-TYPE 214  77  65
D236V5, multiclass
    clus
vv   DHRS7 MUTATED DHRS7 WILD-TYPE
  N0             6             214
  N1             3              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"
D236V6, binary
                 cls
clus                0   1
  DHRS7 MUTATED     7   1
  DHRS7 WILD-TYPE 276  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHRS7 MUTATED      7    1
  DHRS7 WILD-TYPE  276   47
   clus
vv  DHRS7 MUTATED DHRS7 WILD-TYPE
  0             7             276
  1             1              47
[1] 2 2
[1] FALSE
D236V7, 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
D236V8, binary
                 cls
clus                0   1
  DHRS7 MUTATED     8   2
  DHRS7 WILD-TYPE 309  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHRS7 MUTATED      8    2
  DHRS7 WILD-TYPE  309   46
                               clus
vv                              DHRS7 MUTATED DHRS7 WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DHRS7 MUTATED     7   1   0   0
  DHRS7 WILD-TYPE 250   1  22  21
D236V9, multiclass
    clus
vv   DHRS7 MUTATED DHRS7 WILD-TYPE
  R0             7             250
  R1             1               1
  R2             0              22
  RX             0              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D236V10, 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
D236V11, 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(237) Variable = HAS2 MUTATION ANALYSIS
D237V1, survival
                sevent
clus2              0   1
  HAS2 MUTATED     7   2
  HAS2 WILD-TYPE 275  71
  HAS2 MUTATED HAS2 WILD-TYPE 
             9            346 
  HAS2 MUTATED HAS2 WILD-TYPE 
             2             71 
$`HAS2 MUTATED`
TCGA-A6-6780 TCGA-AA-3492 TCGA-AA-3821 TCGA-AA-A00N TCGA-AD-6889 TCGA-AY-6197 
       20.12         3.02         1.02         4.01        56.55        21.44 
TCGA-AY-6386 TCGA-CA-6716 TCGA-G4-6306 
       17.82         0.26        44.68 

$`HAS2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       23.87        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 
       35.05        33.04         0.99        25.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37         4.21         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AZ-4315 
       27.09        16.31         0.95        15.75         0.20        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 
      107.67        74.56        65.85        53.62        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  HAS2 MUTATED HAS2 WILD-TYPE 
          0.26           0.00 
  HAS2 MUTATED HAS2 WILD-TYPE 
         56.55         140.38 
  HAS2 MUTATED HAS2 WILD-TYPE 
         17.82          20.63 
[1] "0.3 - 56.5 (17.8)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "1.4"
D237V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HAS2 MUTATED         1        0        1         5         1         0
  HAS2 WILD-TYPE      63        1       24       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        19         10         40         31       35        13
                vv
clus             STAGE IVB
  HAS2 MUTATED           0
  HAS2 WILD-TYPE         1
D237V3, multiclass
            clus
vv           HAS2 MUTATED HAS2 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             5            104
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  HAS2 MUTATED     0   2   6   1
  HAS2 WILD-TYPE   9  66 242  40
D237V4, multiclass
    clus
vv   HAS2 MUTATED HAS2 WILD-TYPE
  T1            0              9
  T2            2             66
  T3            6            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
  HAS2 MUTATED     8   1   0
  HAS2 WILD-TYPE 212  79  66
D237V5, multiclass
    clus
vv   HAS2 MUTATED HAS2 WILD-TYPE
  N0            8            212
  N1            1             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"
D237V6, binary
                cls
clus               0   1
  HAS2 MUTATED     7   0
  HAS2 WILD-TYPE 276  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  HAS2 MUTATED      7    0
  HAS2 WILD-TYPE  276   48
   clus
vv  HAS2 MUTATED HAS2 WILD-TYPE
  0            7            276
  1            0             48
[1] 2 2
[1] FALSE
D237V7, 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
D237V8, binary
                cls
clus               0   1
  HAS2 MUTATED     6   3
  HAS2 WILD-TYPE 311  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  HAS2 MUTATED      6    3
  HAS2 WILD-TYPE  311   45
                               clus
vv                              HAS2 MUTATED HAS2 WILD-TYPE
  COLON ADENOCARCINOMA                     6            311
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  HAS2 MUTATED     6   0   0   1
  HAS2 WILD-TYPE 251   2  22  20
D237V9, multiclass
    clus
vv   HAS2 MUTATED HAS2 WILD-TYPE
  R0            6            251
  R1            0              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"
D237V10, 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
D237V11, 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(238) Variable = ANKRD36B MUTATION ANALYSIS
D238V1, survival
                    sevent
clus2                  0   1
  ANKRD36B MUTATED     7   1
  ANKRD36B WILD-TYPE 275  72
  ANKRD36B MUTATED ANKRD36B WILD-TYPE 
                 8                347 
  ANKRD36B MUTATED ANKRD36B WILD-TYPE 
                 1                 72 
$`ANKRD36B MUTATED`
TCGA-A6-5660 TCGA-AA-A010 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-6170 TCGA-D5-6923 
       29.19        34.98         0.33         0.10        15.02        12.43 
TCGA-F4-6570 TCGA-G4-6293 
        6.18       107.67 

$`ANKRD36B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07         0.26         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-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        13.38        13.45        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       19.43        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  ANKRD36B MUTATED ANKRD36B WILD-TYPE 
               0.1                0.0 
  ANKRD36B MUTATED ANKRD36B WILD-TYPE 
            107.67             140.38 
  ANKRD36B MUTATED ANKRD36B WILD-TYPE 
            13.725             20.280 
[1] "0.1 - 107.7 (13.7)" "0.0 - 140.4 (20.3)"
[1] "hr=" "1.6"
D238V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ANKRD36B MUTATED         2        0        0         3         1         0
  ANKRD36B WILD-TYPE      62        1       25       106         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANKRD36B MUTATED           1          0          0          1        0
  ANKRD36B WILD-TYPE        18         10         41         30       35
                    vv
clus                 STAGE IVA STAGE IVB
  ANKRD36B MUTATED           0         0
  ANKRD36B WILD-TYPE        13         1
D238V3, multiclass
            clus
vv           ANKRD36B MUTATED ANKRD36B WILD-TYPE
  STAGE I                   2                 62
  STAGE IA                  0                  1
  STAGE II                  0                 25
  STAGE IIA                 3                106
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 1                 18
  STAGE IIIA                0                 10
  STAGE IIIB                0                 41
  STAGE IIIC                1                 30
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  ANKRD36B MUTATED     0   2   5   1
  ANKRD36B WILD-TYPE   9  66 243  40
D238V4, multiclass
    clus
vv   ANKRD36B MUTATED ANKRD36B WILD-TYPE
  T1                0                  9
  T2                2                 66
  T3                5                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
  ANKRD36B MUTATED     6   1   1
  ANKRD36B WILD-TYPE 214  79  65
D238V5, multiclass
    clus
vv   ANKRD36B MUTATED ANKRD36B WILD-TYPE
  N0                6                214
  N1                1                 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"
D238V6, binary
                    cls
clus                   0   1
  ANKRD36B MUTATED     8   0
  ANKRD36B WILD-TYPE 275  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ANKRD36B MUTATED      8    0
  ANKRD36B WILD-TYPE  275   48
   clus
vv  ANKRD36B MUTATED ANKRD36B WILD-TYPE
  0                8                275
  1                0                 48
[1] 2 2
[1] FALSE
D238V7, binary
                    cls
clus                   0   1
  ANKRD36B MUTATED     4   4
  ANKRD36B WILD-TYPE 166 193
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ANKRD36B MUTATED      4    4
  ANKRD36B WILD-TYPE  166  193
        clus
vv       ANKRD36B MUTATED ANKRD36B WILD-TYPE
  FEMALE                4                166
  MALE                  4                193
[1] 2 2
[1] FALSE
D238V8, binary
                    cls
clus                   0   1
  ANKRD36B MUTATED     7   1
  ANKRD36B WILD-TYPE 310  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ANKRD36B MUTATED      7    1
  ANKRD36B WILD-TYPE  310   47
                               clus
vv                              ANKRD36B MUTATED ANKRD36B WILD-TYPE
  COLON ADENOCARCINOMA                         7                310
  COLON MUCINOUS ADENOCARCINOMA                1                 47
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  ANKRD36B MUTATED     5   0   0   2
  ANKRD36B WILD-TYPE 252   2  22  19
D238V9, multiclass
    clus
vv   ANKRD36B MUTATED ANKRD36B WILD-TYPE
  R0                5                252
  R1                0                  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"
D238V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ANKRD36B MUTATED                                  0     2
  ANKRD36B WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  ANKRD36B MUTATED                           1     4
  ANKRD36B WILD-TYPE                        18   172
D238V11, multiclass
                                  clus
vv                                 ANKRD36B MUTATED ANKRD36B 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(239) Variable = ZNF280B MUTATION ANALYSIS
D239V1, survival
                   sevent
clus2                 0   1
  ZNF280B MUTATED    11   0
  ZNF280B WILD-TYPE 271  73
  ZNF280B MUTATED ZNF280B WILD-TYPE 
               11               344 
  ZNF280B MUTATED ZNF280B WILD-TYPE 
                0                73 
$`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         0.26         0.33 
TCGA-CK-5913 TCGA-CM-6161 TCGA-D5-6930 TCGA-G4-6293 TCGA-G4-6299 
       51.32        15.02         1.51       107.67        74.56 

$`ZNF280B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
        2.01        12.99        24.00        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6718 
        2.24         3.06         3.25         3.29         0.07         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6303 
       33.67        13.25         0.53        35.41        19.43        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  ZNF280B MUTATED ZNF280B WILD-TYPE 
             0.26              0.00 
  ZNF280B MUTATED ZNF280B WILD-TYPE 
           107.67            140.38 
  ZNF280B MUTATED ZNF280B WILD-TYPE 
            26.01             20.07 
[1] "0.3 - 107.7 (26.0)" "0.0 - 140.4 (20.1)"
[1] "hr="     "2.6e+07"
D239V2, 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       25       104         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF280B MUTATED           1          0          1          1        0
  ZNF280B WILD-TYPE        18         10         40         30       35
                   vv
clus                STAGE IVA STAGE IVB
  ZNF280B MUTATED           1         0
  ZNF280B WILD-TYPE        12         1
D239V3, multiclass
            clus
vv           ZNF280B MUTATED ZNF280B WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                5               104
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               1                30
  STAGE IV                 0                35
  STAGE IVA                1                12
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 239  39
D239V4, multiclass
    clus
vv   ZNF280B MUTATED ZNF280B WILD-TYPE
  T1               0                 9
  T2               1                67
  T3               9               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
  ZNF280B MUTATED     8   3   1
  ZNF280B WILD-TYPE 212  77  65
D239V5, multiclass
    clus
vv   ZNF280B MUTATED ZNF280B WILD-TYPE
  N0               8               212
  N1               3                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
  ZNF280B MUTATED    10   1
  ZNF280B WILD-TYPE 273  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF280B MUTATED     10    1
  ZNF280B WILD-TYPE  273   47
   clus
vv  ZNF280B MUTATED ZNF280B WILD-TYPE
  0              10               273
  1               1                47
[1] 2 2
[1] FALSE
D239V7, 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
D239V8, binary
                   cls
clus                  0   1
  ZNF280B MUTATED     8   4
  ZNF280B WILD-TYPE 309  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF280B MUTATED      8    4
  ZNF280B WILD-TYPE  309   44
                               clus
vv                              ZNF280B MUTATED ZNF280B WILD-TYPE
  COLON ADENOCARCINOMA                        8               309
  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 249   2  22  18
D239V9, multiclass
    clus
vv   ZNF280B MUTATED ZNF280B WILD-TYPE
  R0               8               249
  R1               0                 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"
D239V10, 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
D239V11, 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(240) Variable = MPO MUTATION ANALYSIS
D240V1, survival
               sevent
clus2             0   1
  MPO MUTATED     9   2
  MPO WILD-TYPE 273  71
  MPO MUTATED MPO WILD-TYPE 
           11           344 
  MPO MUTATED MPO WILD-TYPE 
            2            71 
$`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         0.33 
TCGA-CM-6164 TCGA-CM-6167 TCGA-DM-A1HB TCGA-F4-6807 TCGA-F4-6809 
       29.03        14.99       135.65        16.24        13.25 

$`MPO WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       16.04        21.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 
        6.18        35.87         1.55        16.31        29.59        33.67 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  MPO MUTATED MPO WILD-TYPE 
         0.33          0.00 
  MPO MUTATED MPO WILD-TYPE 
       135.65        140.38 
  MPO MUTATED MPO WILD-TYPE 
       20.120        20.235 
[1] "0.3 - 135.7 (20.1)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.3"
D240V2, 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       25       104         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        19         10         40         29       34        12
               vv
clus            STAGE IVB
  MPO MUTATED           0
  MPO WILD-TYPE         1
D240V3, multiclass
            clus
vv           MPO MUTATED MPO WILD-TYPE
  STAGE I              1            63
  STAGE IA             0             1
  STAGE II             0            25
  STAGE IIA            5           104
  STAGE IIB            0             8
  STAGE IIC            0             1
  STAGE III            0            19
  STAGE IIIA           0            10
  STAGE IIIB           1            40
  STAGE IIIC           2            29
  STAGE IV             1            34
  STAGE IVA            1            12
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 239  40
D240V4, multiclass
    clus
vv   MPO MUTATED MPO WILD-TYPE
  T1           1             8
  T2           1            67
  T3           9           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
  MPO MUTATED     7   2   3
  MPO WILD-TYPE 213  78  63
D240V5, multiclass
    clus
vv   MPO MUTATED MPO WILD-TYPE
  N0           7           213
  N1           2            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"
D240V6, binary
               cls
clus              0   1
  MPO MUTATED     8   2
  MPO WILD-TYPE 275  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  MPO MUTATED      8    2
  MPO WILD-TYPE  275   46
   clus
vv  MPO MUTATED MPO WILD-TYPE
  0           8           275
  1           2            46
[1] 2 2
[1] FALSE
D240V7, 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
D240V8, binary
               cls
clus              0   1
  MPO MUTATED     9   3
  MPO WILD-TYPE 308  45
[1] "tbl2"
               cls
clus            [,1] [,2]
  MPO MUTATED      9    3
  MPO WILD-TYPE  308   45
                               clus
vv                              MPO MUTATED MPO WILD-TYPE
  COLON ADENOCARCINOMA                    9           308
  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 250   2  21  20
D240V9, multiclass
    clus
vv   MPO MUTATED MPO WILD-TYPE
  R0           7           250
  R1           0             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"
D240V10, 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
D240V11, 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(241) Variable = EIF5B MUTATION ANALYSIS
D241V1, survival
                 sevent
clus2               0   1
  EIF5B MUTATED    10   5
  EIF5B WILD-TYPE 272  68
  EIF5B MUTATED EIF5B WILD-TYPE 
             15             340 
  EIF5B MUTATED EIF5B WILD-TYPE 
              5              68 
$`EIF5B MUTATED`
TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3715 TCGA-AA-3977 TCGA-AD-6889 TCGA-AZ-6598 
        3.02        63.98        19.04        25.02        56.55        49.41 
TCGA-CA-6717 TCGA-CK-4950 TCGA-CK-5916 TCGA-D5-5538 TCGA-DM-A28K TCGA-F4-6570 
        0.33        40.34        21.14        12.26        98.24         6.18 
TCGA-F4-6856 TCGA-G4-6586 TCGA-G4-6588 
       19.43        35.80        26.17 

$`EIF5B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37         4.21         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       102.44        15.62        49.08        51.32        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
      117.07         8.61        13.38        13.45        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.41       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        91.79        46.75        52.80 

  EIF5B MUTATED EIF5B WILD-TYPE 
           0.33            0.00 
  EIF5B MUTATED EIF5B WILD-TYPE 
          98.24          140.38 
  EIF5B MUTATED EIF5B WILD-TYPE 
          25.02           20.07 
[1] "0.3 - 98.2 (25.0)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.3"
D241V2, 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       20       103         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EIF5B MUTATED           0          1          1          0        0         0
  EIF5B WILD-TYPE        19          9         40         31       35        13
                 vv
clus              STAGE IVB
  EIF5B MUTATED           0
  EIF5B WILD-TYPE         1
D241V3, multiclass
            clus
vv           EIF5B MUTATED EIF5B WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               5              20
  STAGE IIA              6             103
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EIF5B MUTATED     1   2  12   1
  EIF5B WILD-TYPE   8  66 236  40
D241V4, multiclass
    clus
vv   EIF5B MUTATED EIF5B WILD-TYPE
  T1             1               8
  T2             2              66
  T3            12             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
  EIF5B MUTATED    14   2   0
  EIF5B WILD-TYPE 206  78  66
D241V5, multiclass
    clus
vv   EIF5B MUTATED EIF5B WILD-TYPE
  N0            14             206
  N1             2              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"
D241V6, binary
                 cls
clus                0   1
  EIF5B MUTATED    14   0
  EIF5B WILD-TYPE 269  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EIF5B MUTATED     14    0
  EIF5B WILD-TYPE  269   48
   clus
vv  EIF5B MUTATED EIF5B WILD-TYPE
  0            14             269
  1             0              48
[1] 2 2
[1] FALSE
D241V7, 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
D241V8, binary
                 cls
clus                0   1
  EIF5B MUTATED    13   3
  EIF5B WILD-TYPE 304  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EIF5B MUTATED     13    3
  EIF5B WILD-TYPE  304   45
                               clus
vv                              EIF5B MUTATED EIF5B WILD-TYPE
  COLON ADENOCARCINOMA                     13             304
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  EIF5B MUTATED     9   1   0   2
  EIF5B WILD-TYPE 248   1  22  19
D241V9, multiclass
    clus
vv   EIF5B MUTATED EIF5B WILD-TYPE
  R0             9             248
  R1             1               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"
D241V10, 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
D241V11, 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(242) Variable = PALB2 MUTATION ANALYSIS
D242V1, survival
                 sevent
clus2               0   1
  PALB2 MUTATED    17   2
  PALB2 WILD-TYPE 265  71
  PALB2 MUTATED PALB2 WILD-TYPE 
             19             336 
  PALB2 MUTATED PALB2 WILD-TYPE 
              2              71 
$`PALB2 MUTATED`
TCGA-A6-4105 TCGA-A6-5661 TCGA-A6-6653 TCGA-AA-3510 TCGA-AA-3543 TCGA-AA-3660 
       14.53        33.53        24.39        63.98         0.99        78.08 
TCGA-AA-3819 TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3947 TCGA-AZ-6599 TCGA-CA-6716 
       25.02        36.03        53.00        33.01         6.77         0.26 
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 
       19.43 

$`PALB2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       24.16        21.76        24.69        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
       34.03        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3821 
       19.04        10.06        35.05        33.04         0.99         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3855 
       17.03        10.06         0.00        33.07         0.00        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41        49.41        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 
       51.32        21.99        21.14         2.93         2.01        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        16.01        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 
       17.03        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.41       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  PALB2 MUTATED PALB2 WILD-TYPE 
           0.26            0.00 
  PALB2 MUTATED PALB2 WILD-TYPE 
         124.27          140.38 
  PALB2 MUTATED PALB2 WILD-TYPE 
         21.990          20.155 
[1] "0.3 - 124.3 (22.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "2.4"
D242V2, 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       22       104         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        19         10         40         31       35        13
                 vv
clus              STAGE IVB
  PALB2 MUTATED           0
  PALB2 WILD-TYPE         1
D242V3, multiclass
            clus
vv           PALB2 MUTATED PALB2 WILD-TYPE
  STAGE I                9              55
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              5             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PALB2 MUTATED     0   9   9   1
  PALB2 WILD-TYPE   9  59 239  40
D242V4, multiclass
    clus
vv   PALB2 MUTATED PALB2 WILD-TYPE
  T1             0               9
  T2             9              59
  T3             9             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
  PALB2 MUTATED    18   1   0
  PALB2 WILD-TYPE 202  79  66
D242V5, multiclass
    clus
vv   PALB2 MUTATED PALB2 WILD-TYPE
  N0            18             202
  N1             1              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"
D242V6, binary
                 cls
clus                0   1
  PALB2 MUTATED    17   0
  PALB2 WILD-TYPE 266  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PALB2 MUTATED     17    0
  PALB2 WILD-TYPE  266   48
   clus
vv  PALB2 MUTATED PALB2 WILD-TYPE
  0            17             266
  1             0              48
[1] 2 2
[1] FALSE
D242V7, 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
D242V8, binary
                 cls
clus                0   1
  PALB2 MUTATED    13   6
  PALB2 WILD-TYPE 304  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PALB2 MUTATED     13    6
  PALB2 WILD-TYPE  304   42
                               clus
vv                              PALB2 MUTATED PALB2 WILD-TYPE
  COLON ADENOCARCINOMA                     13             304
  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 243   2  22  19
D242V9, multiclass
    clus
vv   PALB2 MUTATED PALB2 WILD-TYPE
  R0            14             243
  R1             0               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"
D242V10, 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
D242V11, 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(243) Variable = NBEA MUTATION ANALYSIS
D243V1, survival
                sevent
clus2              0   1
  NBEA MUTATED    37   6
  NBEA WILD-TYPE 245  67
  NBEA MUTATED NBEA WILD-TYPE 
            43            312 
  NBEA MUTATED NBEA WILD-TYPE 
             6             67 
$`NBEA MUTATED`
TCGA-A6-5665 TCGA-A6-6653 TCGA-A6-6780 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3688 
       22.06        24.39        20.12         3.02        63.98        19.00 
TCGA-AA-3713 TCGA-AA-3949 TCGA-AA-3971 TCGA-AA-3977 TCGA-AA-3994 TCGA-AA-A00N 
       19.04        26.01        16.08        25.02        27.02         4.01 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AD-5900 TCGA-AD-6899 TCGA-AU-3779 TCGA-AU-6004 
       34.98        15.02         0.07         5.79        14.50        27.09 
TCGA-AY-4070 TCGA-AZ-4315 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-6716 TCGA-CA-6717 
       16.31        58.39        11.74         1.94         0.26         0.33 
TCGA-CA-6718 TCGA-CK-6747 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5864 TCGA-CM-6162 
        0.10         2.93        22.98        16.01        15.02        12.00 
TCGA-CM-6166 TCGA-CM-6170 TCGA-CM-6172 TCGA-D5-6529 TCGA-D5-6922 TCGA-D5-6927 
       21.99        15.02        11.01        20.19        10.13         9.44 
TCGA-D5-6932 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6806 TCGA-G4-6293 TCGA-G4-6299 
       11.38        13.45        35.87        29.59       107.67        74.56 
TCGA-G4-6625 
       91.79 

$`NBEA WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6781 
       25.18        24.16        21.76        24.69        23.87        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 
       20.28         7.04         1.02        35.01         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       37.05        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03         2.01        21.99        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
        7.96        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        21.99        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         0.72        22.42        27.42        10.88         0.20 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 
        6.77        12.10       100.01        29.56         5.23         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6719 
        2.24         3.06         3.25         3.29         0.07         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        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-5349 
       37.02        25.02        13.02        29.06        22.03        30.08 
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-6171 
       29.03        16.04        14.99        12.99        13.02        14.04 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        13.51        11.51 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       12.43        14.30         9.04        11.64        13.41         1.51 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 
       13.38         6.18         1.55        16.31        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6303 TCGA-G4-6304 
       13.25         0.53        35.41        19.43        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        26.17        46.75        52.80 

  NBEA MUTATED NBEA WILD-TYPE 
          0.07           0.00 
  NBEA MUTATED NBEA WILD-TYPE 
        107.67         140.38 
  NBEA MUTATED NBEA WILD-TYPE 
        16.080         21.255 
[1] "0.1 - 107.7 (16.1)" "0.0 - 140.4 (21.3)"
[1] "hr=" "1.4"
D243V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NBEA MUTATED         8        0        2        16         3         0
  NBEA WILD-TYPE      56        1       23        93         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        17          8         36         28       32        13
                vv
clus             STAGE IVB
  NBEA MUTATED           0
  NBEA WILD-TYPE         1
D243V3, multiclass
            clus
vv           NBEA MUTATED NBEA WILD-TYPE
  STAGE I               8             56
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA            16             93
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             2             17
  STAGE IIIA            2              8
  STAGE IIIB            5             36
  STAGE IIIC            3             28
  STAGE IV              3             32
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NBEA MUTATED     0  10  30   5
  NBEA WILD-TYPE   9  58 218  36
D243V4, multiclass
    clus
vv   NBEA MUTATED NBEA WILD-TYPE
  T1            0              9
  T2           10             58
  T3           30            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    31  10   4
  NBEA WILD-TYPE 189  70  62
D243V5, multiclass
    clus
vv   NBEA MUTATED NBEA WILD-TYPE
  N0           31            189
  N1           10             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"
D243V6, binary
                cls
clus               0   1
  NBEA MUTATED    36   3
  NBEA WILD-TYPE 247  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  NBEA MUTATED     36    3
  NBEA WILD-TYPE  247   45
   clus
vv  NBEA MUTATED NBEA WILD-TYPE
  0           36            247
  1            3             45
[1] 2 2
[1] FALSE
D243V7, binary
                cls
clus               0   1
  NBEA MUTATED    19  26
  NBEA WILD-TYPE 151 171
[1] "tbl2"
                cls
clus             [,1] [,2]
  NBEA MUTATED     19   26
  NBEA WILD-TYPE  151  171
        clus
vv       NBEA MUTATED NBEA WILD-TYPE
  FEMALE           19            151
  MALE             26            171
[1] 2 2
[1] FALSE
D243V8, binary
                cls
clus               0   1
  NBEA MUTATED    37   8
  NBEA WILD-TYPE 280  40
[1] "tbl2"
                cls
clus             [,1] [,2]
  NBEA MUTATED     37    8
  NBEA WILD-TYPE  280   40
                               clus
vv                              NBEA MUTATED NBEA WILD-TYPE
  COLON ADENOCARCINOMA                    37            280
  COLON MUCINOUS ADENOCARCINOMA            8             40
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  NBEA MUTATED    31   1   2   5
  NBEA WILD-TYPE 226   1  20  16
D243V9, multiclass
    clus
vv   NBEA MUTATED NBEA WILD-TYPE
  R0           31            226
  R1            1              1
  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"
D243V10, 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    29
  NBEA WILD-TYPE                        18   147
D243V11, 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                                      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(244) Variable = RASAL2 MUTATION ANALYSIS
D244V1, survival
                  sevent
clus2                0   1
  RASAL2 MUTATED    10   4
  RASAL2 WILD-TYPE 272  69
  RASAL2 MUTATED RASAL2 WILD-TYPE 
              14              341 
  RASAL2 MUTATED RASAL2 WILD-TYPE 
               4               69 
$`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         0.33         0.10        21.14         5.03        15.02 
TCGA-CM-6162 TCGA-DM-A28K 
       12.00        98.24 

$`RASAL2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07         0.26         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
       40.34        15.62        49.08        51.32        21.99         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        15.02        17.03        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 
      119.93        35.97        60.79       117.07         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  RASAL2 MUTATED RASAL2 WILD-TYPE 
             0.1              0.0 
  RASAL2 MUTATED RASAL2 WILD-TYPE 
           98.24           140.38 
  RASAL2 MUTATED RASAL2 WILD-TYPE 
           13.51            20.28 
[1] "0.1 - 98.2 (13.5)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.7"
D244V2, 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       23       105         5         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RASAL2 MUTATED           0          0          1          0        1
  RASAL2 WILD-TYPE        19         10         40         31       34
                  vv
clus               STAGE IVA STAGE IVB
  RASAL2 MUTATED           1         0
  RASAL2 WILD-TYPE        12         1
D244V3, multiclass
            clus
vv           RASAL2 MUTATED RASAL2 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               4              105
  STAGE IIB               3                5
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 240  37
D244V4, multiclass
    clus
vv   RASAL2 MUTATED RASAL2 WILD-TYPE
  T1              2                7
  T2              1               67
  T3              8              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
  RASAL2 MUTATED    12   2   1
  RASAL2 WILD-TYPE 208  78  65
D244V5, multiclass
    clus
vv   RASAL2 MUTATED RASAL2 WILD-TYPE
  N0             12              208
  N1              2               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"
D244V6, binary
                  cls
clus                 0   1
  RASAL2 MUTATED    12   2
  RASAL2 WILD-TYPE 271  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RASAL2 MUTATED     12    2
  RASAL2 WILD-TYPE  271   46
   clus
vv  RASAL2 MUTATED RASAL2 WILD-TYPE
  0             12              271
  1              2               46
[1] 2 2
[1] FALSE
D244V7, 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
D244V8, binary
                  cls
clus                 0   1
  RASAL2 MUTATED     9   5
  RASAL2 WILD-TYPE 308  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RASAL2 MUTATED      9    5
  RASAL2 WILD-TYPE  308   43
                               clus
vv                              RASAL2 MUTATED RASAL2 WILD-TYPE
  COLON ADENOCARCINOMA                       9              308
  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 247   2  21  18
D244V9, multiclass
    clus
vv   RASAL2 MUTATED RASAL2 WILD-TYPE
  R0             10              247
  R1              0                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"
D244V10, 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
D244V11, 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(245) Variable = C12ORF10 MUTATION ANALYSIS
D245V1, survival
                    sevent
clus2                  0   1
  C12ORF10 MUTATED     2   2
  C12ORF10 WILD-TYPE 280  71
  C12ORF10 MUTATED C12ORF10 WILD-TYPE 
                 4                351 
  C12ORF10 MUTATED C12ORF10 WILD-TYPE 
                 2                 71 
$`C12ORF10 MUTATED`
TCGA-A6-4105 TCGA-CM-5861 TCGA-F4-6570 TCGA-G4-6293 
       14.53        15.02         6.18       107.67 

$`C12ORF10 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 
       33.67        13.25         0.53        35.41        19.43        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  C12ORF10 MUTATED C12ORF10 WILD-TYPE 
              6.18               0.00 
  C12ORF10 MUTATED C12ORF10 WILD-TYPE 
            107.67             140.38 
  C12ORF10 MUTATED C12ORF10 WILD-TYPE 
            14.775             20.280 
[1] "6.2 - 107.7 (14.8)" "0.0 - 140.4 (20.3)"
[1] "hr=" "1.7"
D245V2, 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       25       106         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C12ORF10 MUTATED           1          0          0          0        0
  C12ORF10 WILD-TYPE        18         10         41         31       35
                    vv
clus                 STAGE IVA STAGE IVB
  C12ORF10 MUTATED           0         0
  C12ORF10 WILD-TYPE        13         1
D245V3, multiclass
            clus
vv           C12ORF10 MUTATED C12ORF10 WILD-TYPE
  STAGE I                   0                 64
  STAGE IA                  0                  1
  STAGE II                  0                 25
  STAGE IIA                 3                106
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 1                 18
  STAGE IIIA                0                 10
  STAGE IIIB                0                 41
  STAGE IIIC                0                 31
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C12ORF10 MUTATED     0   0   4   0
  C12ORF10 WILD-TYPE   9  68 244  41
D245V4, multiclass
    clus
vv   C12ORF10 MUTATED C12ORF10 WILD-TYPE
  T1                0                  9
  T2                0                 68
  T3                4                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
  C12ORF10 MUTATED     3   1   0
  C12ORF10 WILD-TYPE 217  79  66
D245V5, multiclass
    clus
vv   C12ORF10 MUTATED C12ORF10 WILD-TYPE
  N0                3                217
  N1                1                 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"
D245V6, binary
                    cls
clus                   0   1
  C12ORF10 MUTATED     4   0
  C12ORF10 WILD-TYPE 279  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF10 MUTATED      4    0
  C12ORF10 WILD-TYPE  279   48
   clus
vv  C12ORF10 MUTATED C12ORF10 WILD-TYPE
  0                4                279
  1                0                 48
[1] 2 2
[1] FALSE
D245V7, 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
D245V8, binary
                    cls
clus                   0   1
  C12ORF10 MUTATED     4   0
  C12ORF10 WILD-TYPE 313  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF10 MUTATED      4    0
  C12ORF10 WILD-TYPE  313   48
                               clus
vv                              C12ORF10 MUTATED C12ORF10 WILD-TYPE
  COLON ADENOCARCINOMA                         4                313
  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 254   2  22  21
D245V9, multiclass
    clus
vv   C12ORF10 MUTATED C12ORF10 WILD-TYPE
  R0                3                254
  R1                0                  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"
D245V10, 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
D245V11, 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(246) Variable = ANAPC4 MUTATION ANALYSIS
D246V1, survival
                  sevent
clus2                0   1
  ANAPC4 MUTATED     8   2
  ANAPC4 WILD-TYPE 274  71
  ANAPC4 MUTATED ANAPC4 WILD-TYPE 
              10              345 
  ANAPC4 MUTATED ANAPC4 WILD-TYPE 
               2               71 
$`ANAPC4 MUTATED`
TCGA-A6-6141 TCGA-AA-3697 TCGA-AA-A00N TCGA-AD-5900 TCGA-CA-6717 TCGA-CK-4950 
        8.38        85.05         4.01         0.07         0.33        40.34 
TCGA-CM-6676 TCGA-D5-6538 TCGA-DM-A1D4 TCGA-G4-6315 
       11.08        17.13        92.75        36.72 

$`ANAPC4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 
        0.10         1.35        17.56       102.44        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85         4.80        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 
       10.26       119.70        24.43        38.20       130.65        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       45.11        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  ANAPC4 MUTATED ANAPC4 WILD-TYPE 
            0.07             0.00 
  ANAPC4 MUTATED ANAPC4 WILD-TYPE 
           92.75           140.38 
  ANAPC4 MUTATED ANAPC4 WILD-TYPE 
          14.105           20.280 
[1] "0.1 - 92.8 (14.1)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.2"
D246V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ANAPC4 MUTATED         2        0        0         3         1         0
  ANAPC4 WILD-TYPE      62        1       25       106         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANAPC4 MUTATED           1          1          1          0        1
  ANAPC4 WILD-TYPE        18          9         40         31       34
                  vv
clus               STAGE IVA STAGE IVB
  ANAPC4 MUTATED           0         0
  ANAPC4 WILD-TYPE        13         1
D246V3, multiclass
            clus
vv           ANAPC4 MUTATED ANAPC4 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               3              106
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              1                9
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ANAPC4 MUTATED     0   2   7   1
  ANAPC4 WILD-TYPE   9  66 241  40
D246V4, multiclass
    clus
vv   ANAPC4 MUTATED ANAPC4 WILD-TYPE
  T1              0                9
  T2              2               66
  T3              7              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
  ANAPC4 MUTATED     7   2   1
  ANAPC4 WILD-TYPE 213  78  65
D246V5, multiclass
    clus
vv   ANAPC4 MUTATED ANAPC4 WILD-TYPE
  N0              7              213
  N1              2               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"
D246V6, binary
                  cls
clus                 0   1
  ANAPC4 MUTATED     8   1
  ANAPC4 WILD-TYPE 275  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANAPC4 MUTATED      8    1
  ANAPC4 WILD-TYPE  275   47
   clus
vv  ANAPC4 MUTATED ANAPC4 WILD-TYPE
  0              8              275
  1              1               47
[1] 2 2
[1] FALSE
D246V7, 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
D246V8, binary
                  cls
clus                 0   1
  ANAPC4 MUTATED     7   3
  ANAPC4 WILD-TYPE 310  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANAPC4 MUTATED      7    3
  ANAPC4 WILD-TYPE  310   45
                               clus
vv                              ANAPC4 MUTATED ANAPC4 WILD-TYPE
  COLON ADENOCARCINOMA                       7              310
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ANAPC4 MUTATED     6   1   0   1
  ANAPC4 WILD-TYPE 251   1  22  20
D246V9, multiclass
    clus
vv   ANAPC4 MUTATED ANAPC4 WILD-TYPE
  R0              6              251
  R1              1                1
  R2              0               22
  RX              1               20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D246V10, 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
D246V11, 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(247) Variable = ARNT2 MUTATION ANALYSIS
D247V1, survival
                 sevent
clus2               0   1
  ARNT2 MUTATED     8   3
  ARNT2 WILD-TYPE 274  70
  ARNT2 MUTATED ARNT2 WILD-TYPE 
             11             344 
  ARNT2 MUTATED ARNT2 WILD-TYPE 
              3              70 
$`ARNT2 MUTATED`
TCGA-AA-3663 TCGA-AA-3811 TCGA-AA-A00E TCGA-AA-A00J TCGA-AZ-5407 TCGA-AZ-6601 
        6.97        10.06        30.02        18.05        61.41       100.01 
TCGA-CA-6717 TCGA-D5-6928 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6588 
        0.33        11.64        74.56        65.85        26.17 

$`ARNT2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       19.00        34.03        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       22.36        62.79        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
      107.67        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  ARNT2 MUTATED ARNT2 WILD-TYPE 
           0.33            0.00 
  ARNT2 MUTATED ARNT2 WILD-TYPE 
         100.01          140.38 
  ARNT2 MUTATED ARNT2 WILD-TYPE 
         26.170          20.155 
[1] "0.3 - 100.0 (26.2)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D247V2, 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       23       104         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        18         10         40         30       34        13
                 vv
clus              STAGE IVB
  ARNT2 MUTATED           0
  ARNT2 WILD-TYPE         1
D247V3, multiclass
            clus
vv           ARNT2 MUTATED ARNT2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              5             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ARNT2 MUTATED     1   0  10   1
  ARNT2 WILD-TYPE   8  68 238  40
D247V4, multiclass
    clus
vv   ARNT2 MUTATED ARNT2 WILD-TYPE
  T1             1               8
  T2             0              68
  T3            10             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
  ARNT2 MUTATED     8   2   2
  ARNT2 WILD-TYPE 212  78  64
D247V5, multiclass
    clus
vv   ARNT2 MUTATED ARNT2 WILD-TYPE
  N0             8             212
  N1             2              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"
D247V6, binary
                 cls
clus                0   1
  ARNT2 MUTATED    11   1
  ARNT2 WILD-TYPE 272  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARNT2 MUTATED     11    1
  ARNT2 WILD-TYPE  272   47
   clus
vv  ARNT2 MUTATED ARNT2 WILD-TYPE
  0            11             272
  1             1              47
[1] 2 2
[1] FALSE
D247V7, 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
D247V8, binary
                 cls
clus                0   1
  ARNT2 MUTATED     9   3
  ARNT2 WILD-TYPE 308  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARNT2 MUTATED      9    3
  ARNT2 WILD-TYPE  308   45
                               clus
vv                              ARNT2 MUTATED ARNT2 WILD-TYPE
  COLON ADENOCARCINOMA                      9             308
  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 248   2  22  20
D247V9, multiclass
    clus
vv   ARNT2 MUTATED ARNT2 WILD-TYPE
  R0             9             248
  R1             0               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"
D247V10, 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
D247V11, 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(248) Variable = AURKA MUTATION ANALYSIS
D248V1, survival
                 sevent
clus2               0   1
  AURKA MUTATED     5   3
  AURKA WILD-TYPE 277  70
  AURKA MUTATED AURKA WILD-TYPE 
              8             347 
  AURKA MUTATED AURKA WILD-TYPE 
              3              70 
$`AURKA MUTATED`
TCGA-AA-3864 TCGA-AA-A00J TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CM-6674 TCGA-CM-6677 
       53.00        18.05         5.23         1.94        12.95        11.08 
TCGA-DM-A28H TCGA-G4-6626 
      117.07        46.75 

$`AURKA WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10       100.01        29.56        11.74         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 
       81.37       119.93        35.97        60.79        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        52.80 

  AURKA MUTATED AURKA WILD-TYPE 
           1.94            0.00 
  AURKA MUTATED AURKA WILD-TYPE 
         117.07          140.38 
  AURKA MUTATED AURKA WILD-TYPE 
          15.50           20.28 
[1] "1.9 - 117.1 (15.5)" "0.0 - 140.4 (20.3)"
[1] "hr=" "1.4"
D248V2, 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       24       106         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AURKA MUTATED           0          1          2          1        0         0
  AURKA WILD-TYPE        19          9         39         30       35        13
                 vv
clus              STAGE IVB
  AURKA MUTATED           0
  AURKA WILD-TYPE         1
D248V3, multiclass
            clus
vv           AURKA MUTATED AURKA WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              3             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             2              39
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  AURKA MUTATED     0   1   5   2
  AURKA WILD-TYPE   9  67 243  39
D248V4, multiclass
    clus
vv   AURKA MUTATED AURKA WILD-TYPE
  T1             0               9
  T2             1              67
  T3             5             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
  AURKA MUTATED     4   3   1
  AURKA WILD-TYPE 216  77  65
D248V5, multiclass
    clus
vv   AURKA MUTATED AURKA WILD-TYPE
  N0             4             216
  N1             3              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"
D248V6, binary
                 cls
clus                0   1
  AURKA MUTATED     8   0
  AURKA WILD-TYPE 275  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AURKA MUTATED      8    0
  AURKA WILD-TYPE  275   48
   clus
vv  AURKA MUTATED AURKA WILD-TYPE
  0             8             275
  1             0              48
[1] 2 2
[1] FALSE
D248V7, binary
                 cls
clus                0   1
  AURKA MUTATED     2   6
  AURKA WILD-TYPE 168 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AURKA MUTATED      2    6
  AURKA WILD-TYPE  168  191
        clus
vv       AURKA MUTATED AURKA WILD-TYPE
  FEMALE             2             168
  MALE               6             191
[1] 2 2
[1] FALSE
D248V8, binary
                 cls
clus                0   1
  AURKA MUTATED     7   1
  AURKA WILD-TYPE 310  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AURKA MUTATED      7    1
  AURKA WILD-TYPE  310   47
                               clus
vv                              AURKA MUTATED AURKA WILD-TYPE
  COLON ADENOCARCINOMA                      7             310
  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 252   2  22  21
D248V9, multiclass
    clus
vv   AURKA MUTATED AURKA WILD-TYPE
  R0             5             252
  R1             0               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"
D248V10, 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     6
  AURKA WILD-TYPE                        19   170
D248V11, 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                                        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 = WNT16 MUTATION ANALYSIS
D249V1, survival
                 sevent
clus2               0   1
  WNT16 MUTATED     5   2
  WNT16 WILD-TYPE 277  71
  WNT16 MUTATED WNT16 WILD-TYPE 
              7             348 
  WNT16 MUTATED WNT16 WILD-TYPE 
              2              71 
$`WNT16 MUTATED`
TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3660 TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-5403 
       19.66         3.02        78.08        34.98        58.39        62.79 
TCGA-D5-6928 
       11.64 

$`WNT16 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       23.87        20.12        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  WNT16 MUTATED WNT16 WILD-TYPE 
           3.02            0.00 
  WNT16 MUTATED WNT16 WILD-TYPE 
          78.08          140.38 
  WNT16 MUTATED WNT16 WILD-TYPE 
         34.980          20.155 
[1] "3.0 - 78.1 (35.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D249V2, 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       22       107         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        19         10         41         30       35        13
                 vv
clus              STAGE IVB
  WNT16 MUTATED           0
  WNT16 WILD-TYPE         1
D249V3, multiclass
            clus
vv           WNT16 MUTATED WNT16 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              2             107
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  WNT16 MUTATED     0   0   5   3
  WNT16 WILD-TYPE   9  68 243  38
D249V4, multiclass
    clus
vv   WNT16 MUTATED WNT16 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             5             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
  WNT16 MUTATED     7   1   0
  WNT16 WILD-TYPE 213  79  66
D249V5, multiclass
    clus
vv   WNT16 MUTATED WNT16 WILD-TYPE
  N0             7             213
  N1             1              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"
D249V6, binary
                 cls
clus                0   1
  WNT16 MUTATED     5   0
  WNT16 WILD-TYPE 278  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WNT16 MUTATED      5    0
  WNT16 WILD-TYPE  278   48
   clus
vv  WNT16 MUTATED WNT16 WILD-TYPE
  0             5             278
  1             0              48
[1] 2 2
[1] FALSE
D249V7, 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
D249V8, binary
                 cls
clus                0   1
  WNT16 MUTATED     6   2
  WNT16 WILD-TYPE 311  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WNT16 MUTATED      6    2
  WNT16 WILD-TYPE  311   46
                               clus
vv                              WNT16 MUTATED WNT16 WILD-TYPE
  COLON ADENOCARCINOMA                      6             311
  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 251   2  22  20
D249V9, multiclass
    clus
vv   WNT16 MUTATED WNT16 WILD-TYPE
  R0             6             251
  R1             0               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"
D249V10, 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
D249V11, 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(250) Variable = VAV2 MUTATION ANALYSIS
D250V1, survival
                sevent
clus2              0   1
  VAV2 MUTATED    14   3
  VAV2 WILD-TYPE 268  70
  VAV2 MUTATED VAV2 WILD-TYPE 
            17            338 
  VAV2 MUTATED VAV2 WILD-TYPE 
             3             70 
$`VAV2 MUTATED`
TCGA-A6-6781 TCGA-AA-3534 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-A01R TCGA-CK-4947 
       19.66        29.00         6.05         6.97        35.01        17.56 
TCGA-CM-4743 TCGA-CM-5861 TCGA-CM-5862 TCGA-D5-6533 TCGA-D5-6536 TCGA-D5-6537 
       23.05        15.02         5.03         1.32        17.85         4.80 
TCGA-D5-6541 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       15.58        35.80        91.79        46.75        52.80 

$`VAV2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 
       19.07         0.00        19.07        34.03        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       13.94        19.99        61.02        78.08        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       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        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        0.10         1.35       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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-5863 TCGA-CM-5864 TCGA-CM-5868 
       22.98        30.08        16.01        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6539 
       20.19        18.25        43.27        15.12        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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6588 
       13.78        26.17 

  VAV2 MUTATED VAV2 WILD-TYPE 
          1.32           0.00 
  VAV2 MUTATED VAV2 WILD-TYPE 
         91.79         140.38 
  VAV2 MUTATED VAV2 WILD-TYPE 
         17.85          20.63 
[1] "1.3 - 91.8 (17.9)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "1.1"
D250V2, 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       24       101         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  VAV2 MUTATED           1          0          2          1        1         2
  VAV2 WILD-TYPE        18         10         39         30       34        11
                vv
clus             STAGE IVB
  VAV2 MUTATED           0
  VAV2 WILD-TYPE         1
D250V3, multiclass
            clus
vv           VAV2 MUTATED VAV2 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             8            101
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            2             39
  STAGE IIIC            1             30
  STAGE IV              1             34
  STAGE IVA             2             11
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 236  37
D250V4, multiclass
    clus
vv   VAV2 MUTATED VAV2 WILD-TYPE
  T1            0              9
  T2            1             67
  T3           12            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
  VAV2 MUTATED    11   4   2
  VAV2 WILD-TYPE 209  76  64
D250V5, multiclass
    clus
vv   VAV2 MUTATED VAV2 WILD-TYPE
  N0           11            209
  N1            4             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"
D250V6, binary
                cls
clus               0   1
  VAV2 MUTATED    13   2
  VAV2 WILD-TYPE 270  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  VAV2 MUTATED     13    2
  VAV2 WILD-TYPE  270   46
   clus
vv  VAV2 MUTATED VAV2 WILD-TYPE
  0           13            270
  1            2             46
[1] 2 2
[1] FALSE
D250V7, 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
D250V8, binary
                cls
clus               0   1
  VAV2 MUTATED    15   2
  VAV2 WILD-TYPE 302  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  VAV2 MUTATED     15    2
  VAV2 WILD-TYPE  302   46
                               clus
vv                              VAV2 MUTATED VAV2 WILD-TYPE
  COLON ADENOCARCINOMA                    15            302
  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 242   2  21  20
D250V9, multiclass
    clus
vv   VAV2 MUTATED VAV2 WILD-TYPE
  R0           15            242
  R1            0              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"
D250V10, 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
D250V11, 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(251) Variable = CENPF MUTATION ANALYSIS
D251V1, survival
                 sevent
clus2               0   1
  CENPF MUTATED    36   5
  CENPF WILD-TYPE 246  68
  CENPF MUTATED CENPF WILD-TYPE 
             41             314 
  CENPF MUTATED CENPF WILD-TYPE 
              5              68 
$`CENPF MUTATED`
TCGA-A6-2676 TCGA-A6-3809 TCGA-A6-5656 TCGA-A6-5661 TCGA-A6-6648 TCGA-AA-3510 
       42.90        32.75        32.91        33.53        25.18        63.98 
TCGA-AA-3525 TCGA-AA-3555 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3815 TCGA-AA-3845 
        8.05        29.95        78.08         6.97        33.04         0.00 
TCGA-AA-3977 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01Q 
       25.02        18.05         4.01         0.99        34.98         1.02 
TCGA-AA-A02O TCGA-AD-5900 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4952 
        0.92         0.07        58.39         0.33         1.35        15.62 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4752 TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6675 
        2.93       124.27        13.02        15.02        12.00        13.05 
TCGA-D5-6535 TCGA-D5-6540 TCGA-D5-6898 TCGA-DM-A1D7 TCGA-F4-6569 TCGA-F4-6808 
       15.12        16.14         7.53        13.32        13.45        33.67 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6625 
       19.43       107.67        65.85        55.04        91.79 

$`CENPF WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5657 TCGA-A6-5659 
       34.65        33.34        36.53        14.53        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 
       29.19        23.61        22.09        22.06        32.71        27.09 
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 
       22.52         8.38        25.08        24.16        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 
       24.39        23.87        20.12        19.66        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        3.02         1.02        35.01         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        17.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       13.94        19.99        61.02         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       14.93        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       27.02        42.02        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 
        0.26         0.10        17.56       102.44        40.34        49.08 
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 
       16.01         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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       43.27        17.85         4.80        17.13        12.49        15.58 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6703 
      117.07        98.24         8.61        13.38         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 
        1.55        16.31        29.59        16.24        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 
       35.41        74.56        53.62        44.68        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  CENPF MUTATED CENPF WILD-TYPE 
              0               0 
  CENPF MUTATED CENPF WILD-TYPE 
         124.27          140.38 
  CENPF MUTATED CENPF WILD-TYPE 
          16.14           20.98 
[1] "0.0 - 124.3 (16.1)" "0.0 - 140.4 (21.0)"
[1] "hr=" "2"  
D251V2, 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       20        97         4         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CENPF MUTATED           2          0          5          0        1         1
  CENPF WILD-TYPE        17         10         36         31       34        12
                 vv
clus              STAGE IVB
  CENPF MUTATED           1
  CENPF WILD-TYPE         0
D251V3, multiclass
            clus
vv           CENPF MUTATED CENPF WILD-TYPE
  STAGE I                9              55
  STAGE IA               0               1
  STAGE II               5              20
  STAGE IIA             12              97
  STAGE IIB              4               4
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             0              10
  STAGE IIIB             5              36
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              1              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
  CENPF MUTATED     1   9  25   6
  CENPF WILD-TYPE   8  59 223  35
D251V4, multiclass
    clus
vv   CENPF MUTATED CENPF WILD-TYPE
  T1             1               8
  T2             9              59
  T3            25             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
  CENPF MUTATED    32   7   2
  CENPF WILD-TYPE 188  73  64
D251V5, multiclass
    clus
vv   CENPF MUTATED CENPF WILD-TYPE
  N0            32             188
  N1             7              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"
D251V6, binary
                 cls
clus                0   1
  CENPF MUTATED    33   3
  CENPF WILD-TYPE 250  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CENPF MUTATED     33    3
  CENPF WILD-TYPE  250   45
   clus
vv  CENPF MUTATED CENPF WILD-TYPE
  0            33             250
  1             3              45
[1] 2 2
[1] FALSE
D251V7, 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
D251V8, binary
                 cls
clus                0   1
  CENPF MUTATED    30  11
  CENPF WILD-TYPE 287  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CENPF MUTATED     30   11
  CENPF WILD-TYPE  287   37
                               clus
vv                              CENPF MUTATED CENPF WILD-TYPE
  COLON ADENOCARCINOMA                     30             287
  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 226   2  22  15
D251V9, multiclass
    clus
vv   CENPF MUTATED CENPF WILD-TYPE
  R0            31             226
  R1             0               2
  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"
D251V10, 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
D251V11, 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(252) Variable = TOB1 MUTATION ANALYSIS
D252V1, survival
                sevent
clus2              0   1
  TOB1 MUTATED     6   0
  TOB1 WILD-TYPE 276  73
  TOB1 MUTATED TOB1 WILD-TYPE 
             6            349 
  TOB1 MUTATED TOB1 WILD-TYPE 
             0             73 
$`TOB1 MUTATED`
TCGA-A6-6780 TCGA-CK-4952 TCGA-CK-6751 TCGA-CM-5863 TCGA-G4-6310 TCGA-G4-6586 
       20.12        15.62       124.27        15.02        45.11        35.80 

$`TOB1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       102.44        40.34        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14         2.93         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-5864 TCGA-CM-5868 TCGA-CM-6161 
       16.01        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        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        51.75        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  TOB1 MUTATED TOB1 WILD-TYPE 
         15.02           0.00 
  TOB1 MUTATED TOB1 WILD-TYPE 
        124.27         140.38 
  TOB1 MUTATED TOB1 WILD-TYPE 
         27.96          20.19 
[1] "15.0 - 124.3 (28.0)" "0.0 - 140.4 (20.2)" 
[1] "hr="     "9300000"
D252V2, 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       25       107         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TOB1 MUTATED           1          0          2          0        0         0
  TOB1 WILD-TYPE        18         10         39         31       35        13
                vv
clus             STAGE IVB
  TOB1 MUTATED           0
  TOB1 WILD-TYPE         1
D252V3, multiclass
            clus
vv           TOB1 MUTATED TOB1 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             2            107
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            2             39
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TOB1 MUTATED     0   1   4   1
  TOB1 WILD-TYPE   9  67 244  40
D252V4, multiclass
    clus
vv   TOB1 MUTATED TOB1 WILD-TYPE
  T1            0              9
  T2            1             67
  T3            4            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
  TOB1 MUTATED     3   2   1
  TOB1 WILD-TYPE 217  78  65
D252V5, multiclass
    clus
vv   TOB1 MUTATED TOB1 WILD-TYPE
  N0            3            217
  N1            2             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"
D252V6, binary
                cls
clus               0   1
  TOB1 MUTATED     4   0
  TOB1 WILD-TYPE 279  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  TOB1 MUTATED      4    0
  TOB1 WILD-TYPE  279   48
   clus
vv  TOB1 MUTATED TOB1 WILD-TYPE
  0            4            279
  1            0             48
[1] 2 2
[1] FALSE
D252V7, 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
D252V8, binary
                cls
clus               0   1
  TOB1 MUTATED     2   4
  TOB1 WILD-TYPE 315  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  TOB1 MUTATED      2    4
  TOB1 WILD-TYPE  315   44
                               clus
vv                              TOB1 MUTATED TOB1 WILD-TYPE
  COLON ADENOCARCINOMA                     2            315
  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 254   2  22  19
D252V9, multiclass
    clus
vv   TOB1 MUTATED TOB1 WILD-TYPE
  R0            3            254
  R1            0              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"
D252V10, 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
D252V11, 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(253) Variable = SLC4A10 MUTATION ANALYSIS
D253V1, survival
                   sevent
clus2                 0   1
  SLC4A10 MUTATED    20   6
  SLC4A10 WILD-TYPE 262  67
  SLC4A10 MUTATED SLC4A10 WILD-TYPE 
               26               329 
  SLC4A10 MUTATED SLC4A10 WILD-TYPE 
                6                67 
$`SLC4A10 MUTATED`
TCGA-A6-3809 TCGA-A6-5659 TCGA-A6-6141 TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-6901 
       32.75        30.44         8.38        34.98        35.01        22.42 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4681 TCGA-AZ-6606 TCGA-CK-6747 TCGA-CM-5860 
       17.82        58.39        83.80        11.74         2.93        16.01 
TCGA-CM-5864 TCGA-CM-6162 TCGA-D5-6536 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.02        12.00        17.85        10.13        12.43        14.30 
TCGA-D5-6930 TCGA-DM-A1D6 TCGA-DM-A285 TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6570 
        1.51        49.91         6.12        60.79        98.24         6.18 
TCGA-F4-6856 TCGA-G4-6293 
       19.43       107.67 

$`SLC4A10 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       32.71        27.09        22.52        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       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        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4323 
       16.31         0.95        15.75         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        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10       100.01        29.56         5.23         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 
       15.62        49.08        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         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        13.38        13.45        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       35.41        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  SLC4A10 MUTATED SLC4A10 WILD-TYPE 
             1.51              0.00 
  SLC4A10 MUTATED SLC4A10 WILD-TYPE 
           107.67            140.38 
  SLC4A10 MUTATED SLC4A10 WILD-TYPE 
           17.835            20.980 
[1] "1.5 - 107.7 (17.8)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.1"
D253V2, 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       25        97         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC4A10 MUTATED           2          1          2          0        3
  SLC4A10 WILD-TYPE        17          9         39         31       32
                   vv
clus                STAGE IVA STAGE IVB
  SLC4A10 MUTATED           0         0
  SLC4A10 WILD-TYPE        13         1
D253V3, multiclass
            clus
vv           SLC4A10 MUTATED SLC4A10 WILD-TYPE
  STAGE I                  4                60
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA               12                97
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                2                17
  STAGE IIIA               1                 9
  STAGE IIIB               2                39
  STAGE IIIC               0                31
  STAGE IV                 3                32
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC4A10 MUTATED     0   4  20   3
  SLC4A10 WILD-TYPE   9  64 228  38
D253V4, multiclass
    clus
vv   SLC4A10 MUTATED SLC4A10 WILD-TYPE
  T1               0                 9
  T2               4                64
  T3              20               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
  SLC4A10 MUTATED    19   4   4
  SLC4A10 WILD-TYPE 201  76  62
D253V5, multiclass
    clus
vv   SLC4A10 MUTATED SLC4A10 WILD-TYPE
  N0              19               201
  N1               4                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"
D253V6, binary
                   cls
clus                  0   1
  SLC4A10 MUTATED    22   3
  SLC4A10 WILD-TYPE 261  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC4A10 MUTATED     22    3
  SLC4A10 WILD-TYPE  261   45
   clus
vv  SLC4A10 MUTATED SLC4A10 WILD-TYPE
  0              22               261
  1               3                45
[1] 2 2
[1] FALSE
D253V7, 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
D253V8, binary
                   cls
clus                  0   1
  SLC4A10 MUTATED    19   8
  SLC4A10 WILD-TYPE 298  40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC4A10 MUTATED     19    8
  SLC4A10 WILD-TYPE  298   40
                               clus
vv                              SLC4A10 MUTATED SLC4A10 WILD-TYPE
  COLON ADENOCARCINOMA                       19               298
  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 239   2  21  20
D253V9, multiclass
    clus
vv   SLC4A10 MUTATED SLC4A10 WILD-TYPE
  R0              18               239
  R1               0                 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"
D253V10, 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
D253V11, 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(254) Variable = KIR2DL3 MUTATION ANALYSIS
D254V1, survival
                   sevent
clus2                 0   1
  KIR2DL3 MUTATED    12   5
  KIR2DL3 WILD-TYPE 270  68
  KIR2DL3 MUTATED KIR2DL3 WILD-TYPE 
               17               338 
  KIR2DL3 MUTATED KIR2DL3 WILD-TYPE 
                5                68 
$`KIR2DL3 MUTATED`
TCGA-A6-4105 TCGA-A6-5665 TCGA-A6-6648 TCGA-A6-6651 TCGA-AA-3815 TCGA-AY-5543 
       14.53        22.06        25.18        21.76        33.04        15.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6601 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       22.36        62.79       100.01        25.02        13.02        29.06 
TCGA-CM-6163 TCGA-CM-6168 TCGA-D5-6537 TCGA-D5-6928 TCGA-DM-A28H 
       14.04        12.99         4.80        11.64       117.07 

$`KIR2DL3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6649 
       32.71        27.09        22.52         8.38        25.08        24.16 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        7.04         3.02         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-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-4681 TCGA-AZ-5407 TCGA-AZ-6598 
       58.39         1.41         5.13        83.80        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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        16.01        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  KIR2DL3 MUTATED KIR2DL3 WILD-TYPE 
              4.8               0.0 
  KIR2DL3 MUTATED KIR2DL3 WILD-TYPE 
           117.07            140.38 
  KIR2DL3 MUTATED KIR2DL3 WILD-TYPE 
            22.06             20.07 
[1] "4.8 - 117.1 (22.1)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.2"
D254V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIR2DL3 MUTATED         1        0        2         7         0         0
  KIR2DL3 WILD-TYPE      63        1       23       102         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIR2DL3 MUTATED           0          1          2          1        0
  KIR2DL3 WILD-TYPE        19          9         39         30       35
                   vv
clus                STAGE IVA STAGE IVB
  KIR2DL3 MUTATED           4         0
  KIR2DL3 WILD-TYPE         9         1
D254V3, multiclass
            clus
vv           KIR2DL3 MUTATED KIR2DL3 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 2                23
  STAGE IIA                7               102
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               1                 9
  STAGE IIIB               2                39
  STAGE IIIC               1                30
  STAGE IV                 0                35
  STAGE IVA                4                 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
  KIR2DL3 MUTATED     1   1  15   1
  KIR2DL3 WILD-TYPE   8  67 233  40
D254V4, multiclass
    clus
vv   KIR2DL3 MUTATED KIR2DL3 WILD-TYPE
  T1               1                 8
  T2               1                67
  T3              15               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    12   5   1
  KIR2DL3 WILD-TYPE 208  75  65
D254V5, multiclass
    clus
vv   KIR2DL3 MUTATED KIR2DL3 WILD-TYPE
  N0              12               208
  N1               5                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"
D254V6, binary
                   cls
clus                  0   1
  KIR2DL3 MUTATED    11   4
  KIR2DL3 WILD-TYPE 272  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KIR2DL3 MUTATED     11    4
  KIR2DL3 WILD-TYPE  272   44
   clus
vv  KIR2DL3 MUTATED KIR2DL3 WILD-TYPE
  0              11               272
  1               4                44
[1] 2 2
[1] FALSE
D254V7, binary
                   cls
clus                  0   1
  KIR2DL3 MUTATED     7  11
  KIR2DL3 WILD-TYPE 163 186
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KIR2DL3 MUTATED      7   11
  KIR2DL3 WILD-TYPE  163  186
        clus
vv       KIR2DL3 MUTATED KIR2DL3 WILD-TYPE
  FEMALE               7               163
  MALE                11               186
[1] 2 2
[1] FALSE
D254V8, binary
                   cls
clus                  0   1
  KIR2DL3 MUTATED    17   1
  KIR2DL3 WILD-TYPE 300  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KIR2DL3 MUTATED     17    1
  KIR2DL3 WILD-TYPE  300   47
                               clus
vv                              KIR2DL3 MUTATED KIR2DL3 WILD-TYPE
  COLON ADENOCARCINOMA                       17               300
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  KIR2DL3 MUTATED    12   0   0   0
  KIR2DL3 WILD-TYPE 245   2  22  21
D254V9, multiclass
    clus
vv   KIR2DL3 MUTATED KIR2DL3 WILD-TYPE
  R0              12               245
  R1               0                 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"
D254V10, 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
D254V11, 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(255) Variable = ZNF789 MUTATION ANALYSIS
D255V1, survival
                  sevent
clus2                0   1
  ZNF789 MUTATED     5   2
  ZNF789 WILD-TYPE 277  71
  ZNF789 MUTATED ZNF789 WILD-TYPE 
               7              348 
  ZNF789 MUTATED ZNF789 WILD-TYPE 
               2               71 
$`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         0.33        30.08        14.04 
TCGA-G4-6626 
       46.75 

$`ZNF789 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       22.09        13.78        35.80        26.17        91.79        52.80 

  ZNF789 MUTATED ZNF789 WILD-TYPE 
            0.33             0.00 
  ZNF789 MUTATED ZNF789 WILD-TYPE 
           58.39           140.38 
  ZNF789 MUTATED ZNF789 WILD-TYPE 
          25.020           20.155 
[1] "0.3 - 58.4 (25.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.4"
D255V2, 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       25       105         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF789 MUTATED           0          0          0          0        0
  ZNF789 WILD-TYPE        19         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF789 MUTATED           0         0
  ZNF789 WILD-TYPE        13         1
D255V3, multiclass
            clus
vv           ZNF789 MUTATED ZNF789 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               4              105
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF789 MUTATED     0   2   4   1
  ZNF789 WILD-TYPE   9  66 244  40
D255V4, multiclass
    clus
vv   ZNF789 MUTATED ZNF789 WILD-TYPE
  T1              0                9
  T2              2               66
  T3              4              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
  ZNF789 MUTATED     7   0   0
  ZNF789 WILD-TYPE 213  80  66
D255V5, multiclass
    clus
vv   ZNF789 MUTATED ZNF789 WILD-TYPE
  N0              7              213
  N1              0               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"
D255V6, binary
                  cls
clus                 0   1
  ZNF789 MUTATED     6   0
  ZNF789 WILD-TYPE 277  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF789 MUTATED      6    0
  ZNF789 WILD-TYPE  277   48
   clus
vv  ZNF789 MUTATED ZNF789 WILD-TYPE
  0              6              277
  1              0               48
[1] 2 2
[1] FALSE
D255V7, 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
D255V8, binary
                  cls
clus                 0   1
  ZNF789 MUTATED     5   2
  ZNF789 WILD-TYPE 312  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF789 MUTATED      5    2
  ZNF789 WILD-TYPE  312   46
                               clus
vv                              ZNF789 MUTATED ZNF789 WILD-TYPE
  COLON ADENOCARCINOMA                       5              312
  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 252   2  22  20
D255V9, multiclass
    clus
vv   ZNF789 MUTATED ZNF789 WILD-TYPE
  R0              5              252
  R1              0                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"
D255V10, 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
D255V11, 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(256) Variable = SYNRG MUTATION ANALYSIS
D256V1, survival
                 sevent
clus2               0   1
  SYNRG MUTATED    11   3
  SYNRG WILD-TYPE 271  70
  SYNRG MUTATED SYNRG WILD-TYPE 
             14             341 
  SYNRG MUTATED SYNRG WILD-TYPE 
              3              70 
$`SYNRG MUTATED`
TCGA-A6-6781 TCGA-AA-3864 TCGA-AA-3949 TCGA-AA-3950 TCGA-AU-6004 TCGA-AZ-6598 
       19.66        53.00        26.01        24.00        27.09        49.41 
TCGA-AZ-6601 TCGA-CA-6717 TCGA-CK-6751 TCGA-CM-4752 TCGA-D5-6539 TCGA-DM-A1D6 
      100.01         0.33       124.27        13.02        12.49        49.91 
TCGA-DM-A1D9 TCGA-G4-6628 
      140.38        52.80 

$`SYNRG WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       12.99        24.00        33.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       62.79        61.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14         2.93         2.01        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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       13.78        35.80        26.17        91.79        46.75 

  SYNRG MUTATED SYNRG WILD-TYPE 
           0.33            0.00 
  SYNRG MUTATED SYNRG WILD-TYPE 
         140.38          139.17 
  SYNRG MUTATED SYNRG WILD-TYPE 
          38.25           19.99 
[1] "0.3 - 140.4 (38.2)" "0.0 - 139.2 (20.0)"
[1] "hr=" "1.9"
D256V2, 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       22       104         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SYNRG MUTATED           0          1          1          1        0         0
  SYNRG WILD-TYPE        19          9         40         30       35        13
                 vv
clus              STAGE IVB
  SYNRG MUTATED           0
  SYNRG WILD-TYPE         1
D256V3, multiclass
            clus
vv           SYNRG MUTATED SYNRG WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              5             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             1              40
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SYNRG MUTATED     0   3  10   1
  SYNRG WILD-TYPE   9  65 238  40
D256V4, multiclass
    clus
vv   SYNRG MUTATED SYNRG WILD-TYPE
  T1             0               9
  T2             3              65
  T3            10             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
  SYNRG MUTATED    12   2   0
  SYNRG WILD-TYPE 208  78  66
D256V5, multiclass
    clus
vv   SYNRG MUTATED SYNRG WILD-TYPE
  N0            12             208
  N1             2              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"
D256V6, binary
                 cls
clus                0   1
  SYNRG MUTATED    11   0
  SYNRG WILD-TYPE 272  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYNRG MUTATED     11    0
  SYNRG WILD-TYPE  272   48
   clus
vv  SYNRG MUTATED SYNRG WILD-TYPE
  0            11             272
  1             0              48
[1] 2 2
[1] FALSE
D256V7, binary
                 cls
clus                0   1
  SYNRG MUTATED     7   7
  SYNRG WILD-TYPE 163 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYNRG MUTATED      7    7
  SYNRG WILD-TYPE  163  190
        clus
vv       SYNRG MUTATED SYNRG WILD-TYPE
  FEMALE             7             163
  MALE               7             190
[1] 2 2
[1] FALSE
D256V8, binary
                 cls
clus                0   1
  SYNRG MUTATED     8   6
  SYNRG WILD-TYPE 309  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYNRG MUTATED      8    6
  SYNRG WILD-TYPE  309   42
                               clus
vv                              SYNRG MUTATED SYNRG WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  COLON MUCINOUS ADENOCARCINOMA             6              42
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SYNRG MUTATED     8   0   0   2
  SYNRG WILD-TYPE 249   2  22  19
D256V9, multiclass
    clus
vv   SYNRG MUTATED SYNRG WILD-TYPE
  R0             8             249
  R1             0               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"
D256V10, 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
D256V11, 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(257) Variable = MLL2 MUTATION ANALYSIS
D257V1, survival
                sevent
clus2              0   1
  MLL2 MUTATED    40  11
  MLL2 WILD-TYPE 242  62
  MLL2 MUTATED MLL2 WILD-TYPE 
            51            304 
  MLL2 MUTATED MLL2 WILD-TYPE 
            11             62 
$`MLL2 MUTATED`
TCGA-A6-3808 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 
       33.34        33.53        22.06        25.18        24.16        24.69 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3672 
       24.39        20.12        19.66        63.98         6.97         0.92 
TCGA-AA-3681 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3833 
        5.98        85.05        26.99        19.04        10.06        15.95 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-5900 TCGA-AD-6964 TCGA-AY-6197 
        4.01        34.98        35.01         0.07        10.88        21.44 
TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-CA-6715 TCGA-CA-6717 
       58.39        49.41        12.10       100.01         0.07         0.33 
TCGA-CA-6718 TCGA-CK-5916 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4747 TCGA-CM-4752 
        0.10        21.14       124.27        23.05        25.02        13.02 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 
       14.99        12.99        14.04        18.25         1.32        15.12 
TCGA-D5-6538 TCGA-D5-6540 TCGA-DM-A1D6 TCGA-DM-A285 TCGA-F4-6570 TCGA-F4-6703 
       17.13        16.14        49.91         6.12         6.18        35.87 
TCGA-G4-6315 TCGA-G4-6586 TCGA-G4-6628 
       36.72        35.80        52.80 

$`MLL2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       31.63        30.44        29.19        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-6654 
       27.09        22.52         8.38        25.08        21.76        23.87 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.05        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3688 
       50.04        47.01        15.02        11.01        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3713 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       36.00         5.03        19.04        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
       25.02         1.02        17.98        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
        0.72         5.79        22.42        27.42         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       27.09        16.31         0.95        15.75         0.20        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
        6.77        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6719 
        2.24         3.06         3.25         3.29         0.26         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-5341 
       21.99         2.93         2.01        20.02        37.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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-6169 TCGA-CM-6170 TCGA-CM-6172 
       29.03        16.04        21.99        13.02        15.02        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6541 
       20.19        43.27        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-D5-6931 TCGA-D5-6932 
        9.44        11.64        13.41         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-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-F4-6704 
      117.07        98.24         8.61        13.38        13.45         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        51.75        45.11        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       13.78        26.17        91.79        46.75 

  MLL2 MUTATED MLL2 WILD-TYPE 
          0.07           0.00 
  MLL2 MUTATED MLL2 WILD-TYPE 
        124.27         140.38 
  MLL2 MUTATED MLL2 WILD-TYPE 
        20.120         20.235 
[1] "0.1 - 124.3 (20.1)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1"  
D257V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MLL2 MUTATED         7        0        5        18         3         0
  MLL2 WILD-TYPE      57        1       20        91         5         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MLL2 MUTATED           5          0          5          2        3         3
  MLL2 WILD-TYPE        14         10         36         29       32        10
                vv
clus             STAGE IVB
  MLL2 MUTATED           0
  MLL2 WILD-TYPE         1
D257V3, multiclass
            clus
vv           MLL2 MUTATED MLL2 WILD-TYPE
  STAGE I               7             57
  STAGE IA              0              1
  STAGE II              5             20
  STAGE IIA            18             91
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             5             14
  STAGE IIIA            0             10
  STAGE IIIB            5             36
  STAGE IIIC            2             29
  STAGE IV              3             32
  STAGE IVA             3             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
  MLL2 MUTATED     1   6  37   8
  MLL2 WILD-TYPE   8  62 211  33
D257V4, multiclass
    clus
vv   MLL2 MUTATED MLL2 WILD-TYPE
  T1            1              8
  T2            6             62
  T3           37            211
  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  71  60
D257V5, multiclass
    clus
vv   MLL2 MUTATED MLL2 WILD-TYPE
  N0           37            183
  N1            9             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"
D257V6, binary
                cls
clus               0   1
  MLL2 MUTATED    37   6
  MLL2 WILD-TYPE 246  42
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED     37    6
  MLL2 WILD-TYPE  246   42
   clus
vv  MLL2 MUTATED MLL2 WILD-TYPE
  0           37            246
  1            6             42
[1] 2 2
[1] FALSE
D257V7, 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
D257V8, binary
                cls
clus               0   1
  MLL2 MUTATED    42  10
  MLL2 WILD-TYPE 275  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED     42   10
  MLL2 WILD-TYPE  275   38
                               clus
vv                              MLL2 MUTATED MLL2 WILD-TYPE
  COLON ADENOCARCINOMA                    42            275
  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 223   2  22  14
D257V9, multiclass
    clus
vv   MLL2 MUTATED MLL2 WILD-TYPE
  R0           34            223
  R1            0              2
  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"
D257V10, 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
D257V11, 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(258) Variable = ANKHD1 MUTATION ANALYSIS
D258V1, survival
                  sevent
clus2                0   1
  ANKHD1 MUTATED    18   5
  ANKHD1 WILD-TYPE 264  68
  ANKHD1 MUTATED ANKHD1 WILD-TYPE 
              23              332 
  ANKHD1 MUTATED ANKHD1 WILD-TYPE 
               5               68 
$`ANKHD1 MUTATED`
TCGA-A6-5666 TCGA-A6-6141 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3660 
       32.71         8.38         7.04         1.02        63.98        78.08 
TCGA-AA-3950 TCGA-AD-5900 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6599 
       24.00         0.07        21.44        58.39        49.41         6.77 
TCGA-AZ-6601 TCGA-CA-6717 TCGA-CM-5348 TCGA-CM-6162 TCGA-CM-6674 TCGA-D5-6533 
      100.01         0.33        22.98        12.00        12.95         1.32 
TCGA-DM-A1D7 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6323 TCGA-G4-6588 
       13.32        53.62        51.75        13.78        26.17 

$`ANKHD1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.09        22.06        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 
       19.66        20.28         3.02        35.01         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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-4681 
       15.75         0.20        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       22.36        62.79        61.41        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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 
       16.01        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 
       12.26        19.59        13.51        11.51        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        92.75        49.91        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 
       19.43       107.67        74.56        65.85        44.68        55.04 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 
       45.11        36.72        36.00        22.09        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  ANKHD1 MUTATED ANKHD1 WILD-TYPE 
            0.07             0.00 
  ANKHD1 MUTATED ANKHD1 WILD-TYPE 
          100.01           140.38 
  ANKHD1 MUTATED ANKHD1 WILD-TYPE 
          21.440           20.155 
[1] "0.1 - 100.0 (21.4)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D258V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ANKHD1 MUTATED         2        1        6         8         1         1
  ANKHD1 WILD-TYPE      62        0       19       101         7         0
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANKHD1 MUTATED           0          0          4          0        0
  ANKHD1 WILD-TYPE        19         10         37         31       35
                  vv
clus               STAGE IVA STAGE IVB
  ANKHD1 MUTATED           0         0
  ANKHD1 WILD-TYPE        13         1
D258V3, multiclass
            clus
vv           ANKHD1 MUTATED ANKHD1 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                1                0
  STAGE II                6               19
  STAGE IIA               8              101
  STAGE IIB               1                7
  STAGE IIC               1                0
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              4               37
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ANKHD1 MUTATED     0   2  17   3
  ANKHD1 WILD-TYPE   9  66 231  38
D258V4, multiclass
    clus
vv   ANKHD1 MUTATED ANKHD1 WILD-TYPE
  T1              0                9
  T2              2               66
  T3             17              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
  ANKHD1 MUTATED    20   3   0
  ANKHD1 WILD-TYPE 200  77  66
D258V5, multiclass
    clus
vv   ANKHD1 MUTATED ANKHD1 WILD-TYPE
  N0             20              200
  N1              3               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"
D258V6, binary
                  cls
clus                 0   1
  ANKHD1 MUTATED    18   0
  ANKHD1 WILD-TYPE 265  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANKHD1 MUTATED     18    0
  ANKHD1 WILD-TYPE  265   48
   clus
vv  ANKHD1 MUTATED ANKHD1 WILD-TYPE
  0             18              265
  1              0               48
[1] 2 2
[1] FALSE
D258V7, binary
                  cls
clus                 0   1
  ANKHD1 MUTATED     9  14
  ANKHD1 WILD-TYPE 161 183
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANKHD1 MUTATED      9   14
  ANKHD1 WILD-TYPE  161  183
        clus
vv       ANKHD1 MUTATED ANKHD1 WILD-TYPE
  FEMALE              9              161
  MALE               14              183
[1] 2 2
[1] FALSE
D258V8, binary
                  cls
clus                 0   1
  ANKHD1 MUTATED    19   4
  ANKHD1 WILD-TYPE 298  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANKHD1 MUTATED     19    4
  ANKHD1 WILD-TYPE  298   44
                               clus
vv                              ANKHD1 MUTATED ANKHD1 WILD-TYPE
  COLON ADENOCARCINOMA                      19              298
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ANKHD1 MUTATED    16   0   0   1
  ANKHD1 WILD-TYPE 241   2  22  20
D258V9, multiclass
    clus
vv   ANKHD1 MUTATED ANKHD1 WILD-TYPE
  R0             16              241
  R1              0                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"
D258V10, 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    14
  ANKHD1 WILD-TYPE                        16   162
D258V11, 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                                        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(259) Variable = CXORF38 MUTATION ANALYSIS
D259V1, survival
                   sevent
clus2                 0   1
  CXORF38 MUTATED     5   0
  CXORF38 WILD-TYPE 277  73
  CXORF38 MUTATED CXORF38 WILD-TYPE 
                5               350 
  CXORF38 MUTATED CXORF38 WILD-TYPE 
                0                73 
$`CXORF38 MUTATED`
TCGA-AY-6197 TCGA-AZ-4315 TCGA-CM-5349 TCGA-G4-6309 TCGA-G4-6588 
       21.44        58.39        30.08        51.75        26.17 

$`CXORF38 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        15.75         0.20        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       74.56        65.85        53.62        44.68        55.04        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  CXORF38 MUTATED CXORF38 WILD-TYPE 
            21.44              0.00 
  CXORF38 MUTATED CXORF38 WILD-TYPE 
            58.39            140.38 
  CXORF38 MUTATED CXORF38 WILD-TYPE 
           30.080            20.005 
[1] "21.4 - 58.4 (30.1)" "0.0 - 140.4 (20.0)"
[1] "hr="     "9300000"
D259V2, 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       25       105         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CXORF38 MUTATED           0          0          1          0        0
  CXORF38 WILD-TYPE        19         10         40         31       35
                   vv
clus                STAGE IVA STAGE IVB
  CXORF38 MUTATED           0         0
  CXORF38 WILD-TYPE        13         1
D259V3, multiclass
            clus
vv           CXORF38 MUTATED CXORF38 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                4               105
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CXORF38 MUTATED     0   0   5   0
  CXORF38 WILD-TYPE   9  68 243  41
D259V4, multiclass
    clus
vv   CXORF38 MUTATED CXORF38 WILD-TYPE
  T1               0                 9
  T2               0                68
  T3               5               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
  CXORF38 MUTATED     4   1   0
  CXORF38 WILD-TYPE 216  79  66
D259V5, multiclass
    clus
vv   CXORF38 MUTATED CXORF38 WILD-TYPE
  N0               4               216
  N1               1                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"
D259V6, binary
                   cls
clus                  0   1
  CXORF38 MUTATED     4   0
  CXORF38 WILD-TYPE 279  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CXORF38 MUTATED      4    0
  CXORF38 WILD-TYPE  279   48
   clus
vv  CXORF38 MUTATED CXORF38 WILD-TYPE
  0               4               279
  1               0                48
[1] 2 2
[1] FALSE
D259V7, 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
D259V8, binary
                   cls
clus                  0   1
  CXORF38 MUTATED     5   0
  CXORF38 WILD-TYPE 312  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CXORF38 MUTATED      5    0
  CXORF38 WILD-TYPE  312   48
                               clus
vv                              CXORF38 MUTATED CXORF38 WILD-TYPE
  COLON ADENOCARCINOMA                        5               312
  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 252   2  22  21
D259V9, multiclass
    clus
vv   CXORF38 MUTATED CXORF38 WILD-TYPE
  R0               5               252
  R1               0                 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"
D259V10, 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
D259V11, 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(260) Variable = CLCNKA MUTATION ANALYSIS
D260V1, survival
                  sevent
clus2                0   1
  CLCNKA MUTATED     6   3
  CLCNKA WILD-TYPE 276  70
  CLCNKA MUTATED CLCNKA WILD-TYPE 
               9              346 
  CLCNKA MUTATED CLCNKA WILD-TYPE 
               3               70 
$`CLCNKA MUTATED`
TCGA-AA-3492 TCGA-AA-3663 TCGA-AA-3672 TCGA-AY-6197 TCGA-AZ-6598 TCGA-DM-A1D6 
        3.02         6.97         0.92        21.44        49.41        49.91 
TCGA-DM-A1D9 TCGA-F4-6856 TCGA-G4-6628 
      140.38        19.43        52.80 

$`CLCNKA WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       35.80        26.17        91.79        46.75 

  CLCNKA MUTATED CLCNKA WILD-TYPE 
            0.92             0.00 
  CLCNKA MUTATED CLCNKA WILD-TYPE 
          140.38           139.17 
  CLCNKA MUTATED CLCNKA WILD-TYPE 
          21.440           20.155 
[1] "0.9 - 140.4 (21.4)" "0.0 - 139.2 (20.2)"
[1] "hr=" "1.1"
D260V2, 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       22       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CLCNKA MUTATED           1          0          0          0        0
  CLCNKA WILD-TYPE        18         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  CLCNKA MUTATED           0         0
  CLCNKA WILD-TYPE        13         1
D260V3, multiclass
            clus
vv           CLCNKA MUTATED CLCNKA WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                3               22
  STAGE IIA               3              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CLCNKA MUTATED     0   3   7   0
  CLCNKA WILD-TYPE   9  65 241  41
D260V4, multiclass
    clus
vv   CLCNKA MUTATED CLCNKA WILD-TYPE
  T1              0                9
  T2              3               65
  T3              7              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
  CLCNKA MUTATED     9   1   0
  CLCNKA WILD-TYPE 211  79  66
D260V5, multiclass
    clus
vv   CLCNKA MUTATED CLCNKA WILD-TYPE
  N0              9              211
  N1              1               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"
D260V6, binary
                  cls
clus                 0   1
  CLCNKA MUTATED     7   0
  CLCNKA WILD-TYPE 276  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLCNKA MUTATED      7    0
  CLCNKA WILD-TYPE  276   48
   clus
vv  CLCNKA MUTATED CLCNKA WILD-TYPE
  0              7              276
  1              0               48
[1] 2 2
[1] FALSE
D260V7, 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
D260V8, binary
                  cls
clus                 0   1
  CLCNKA MUTATED     8   2
  CLCNKA WILD-TYPE 309  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLCNKA MUTATED      8    2
  CLCNKA WILD-TYPE  309   46
                               clus
vv                              CLCNKA MUTATED CLCNKA WILD-TYPE
  COLON ADENOCARCINOMA                       8              309
  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 251   2  22  20
D260V9, multiclass
    clus
vv   CLCNKA MUTATED CLCNKA WILD-TYPE
  R0              6              251
  R1              0                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"
D260V10, 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
D260V11, 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(261) Variable = ETAA1 MUTATION ANALYSIS
D261V1, survival
                 sevent
clus2               0   1
  ETAA1 MUTATED    14   2
  ETAA1 WILD-TYPE 268  71
  ETAA1 MUTATED ETAA1 WILD-TYPE 
             16             339 
  ETAA1 MUTATED ETAA1 WILD-TYPE 
              2              71 
$`ETAA1 MUTATED`
TCGA-AA-3492 TCGA-AA-3525 TCGA-AA-3663 TCGA-AA-3866 TCGA-AA-3977 TCGA-AA-A010 
        3.02         8.05         6.97        17.03        25.02        34.98 
TCGA-AD-5900 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-CA-6717 TCGA-D5-5541 TCGA-D5-6539 
        0.07        58.39        61.41         0.33        11.51        12.49 
TCGA-D5-6927 TCGA-DM-A1HA TCGA-F4-6459 TCGA-G4-6588 
        9.44       131.51         8.61        26.17 

$`ETAA1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 
        1.02         9.07        24.03        37.05        36.03        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        53.00        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13        83.80        22.36        62.79        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 
       35.97        60.79       117.07        98.24        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  ETAA1 MUTATED ETAA1 WILD-TYPE 
           0.07            0.00 
  ETAA1 MUTATED ETAA1 WILD-TYPE 
         131.51          140.38 
  ETAA1 MUTATED ETAA1 WILD-TYPE 
          12.00           20.98 
[1] "0.1 - 131.5 (12.0)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.6"
D261V2, 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       23       105         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ETAA1 MUTATED           0          1          3          1        0         0
  ETAA1 WILD-TYPE        19          9         38         30       35        13
                 vv
clus              STAGE IVB
  ETAA1 MUTATED           0
  ETAA1 WILD-TYPE         1
D261V3, multiclass
            clus
vv           ETAA1 MUTATED ETAA1 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              4             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             3              38
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ETAA1 MUTATED     1   3  11   1
  ETAA1 WILD-TYPE   8  65 237  40
D261V4, multiclass
    clus
vv   ETAA1 MUTATED ETAA1 WILD-TYPE
  T1             1               8
  T2             3              65
  T3            11             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
  ETAA1 MUTATED    12   2   2
  ETAA1 WILD-TYPE 208  78  64
D261V5, multiclass
    clus
vv   ETAA1 MUTATED ETAA1 WILD-TYPE
  N0            12             208
  N1             2              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"
D261V6, binary
                 cls
clus                0   1
  ETAA1 MUTATED    14   0
  ETAA1 WILD-TYPE 269  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ETAA1 MUTATED     14    0
  ETAA1 WILD-TYPE  269   48
   clus
vv  ETAA1 MUTATED ETAA1 WILD-TYPE
  0            14             269
  1             0              48
[1] 2 2
[1] FALSE
D261V7, 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
D261V8, binary
                 cls
clus                0   1
  ETAA1 MUTATED    14   2
  ETAA1 WILD-TYPE 303  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ETAA1 MUTATED     14    2
  ETAA1 WILD-TYPE  303   46
                               clus
vv                              ETAA1 MUTATED ETAA1 WILD-TYPE
  COLON ADENOCARCINOMA                     14             303
  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 245   2  22  20
D261V9, multiclass
    clus
vv   ETAA1 MUTATED ETAA1 WILD-TYPE
  R0            12             245
  R1             0               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"
D261V10, 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
D261V11, 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(262) Variable = TTF1 MUTATION ANALYSIS
D262V1, survival
                sevent
clus2              0   1
  TTF1 MUTATED     7   1
  TTF1 WILD-TYPE 275  72
  TTF1 MUTATED TTF1 WILD-TYPE 
             8            347 
  TTF1 MUTATED TTF1 WILD-TYPE 
             1             72 
$`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         0.33         0.10 
TCGA-CM-5861 TCGA-CM-6680 
       15.02        12.03 

$`TTF1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       32.91        31.63        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       32.71        27.09        22.52        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  TTF1 MUTATED TTF1 WILD-TYPE 
           0.1            0.0 
  TTF1 MUTATED TTF1 WILD-TYPE 
         33.53         140.38 
  TTF1 MUTATED TTF1 WILD-TYPE 
        10.205         20.980 
[1] "0.1 - 33.5 (10.2)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.2"
D262V2, 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       24       104         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        19         10         40         31       35        13
                vv
clus             STAGE IVB
  TTF1 MUTATED           0
  TTF1 WILD-TYPE         1
D262V3, multiclass
            clus
vv           TTF1 MUTATED TTF1 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             5            104
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TTF1 MUTATED     0   1   7   1
  TTF1 WILD-TYPE   9  67 241  40
D262V4, multiclass
    clus
vv   TTF1 MUTATED TTF1 WILD-TYPE
  T1            0              9
  T2            1             67
  T3            7            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
  TTF1 MUTATED     8   0   1
  TTF1 WILD-TYPE 212  80  65
D262V5, multiclass
    clus
vv   TTF1 MUTATED TTF1 WILD-TYPE
  N0            8            212
  N1            0             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"
D262V6, binary
                cls
clus               0   1
  TTF1 MUTATED     8   0
  TTF1 WILD-TYPE 275  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  TTF1 MUTATED      8    0
  TTF1 WILD-TYPE  275   48
   clus
vv  TTF1 MUTATED TTF1 WILD-TYPE
  0            8            275
  1            0             48
[1] 2 2
[1] FALSE
D262V7, 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
D262V8, binary
                cls
clus               0   1
  TTF1 MUTATED     8   1
  TTF1 WILD-TYPE 309  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  TTF1 MUTATED      8    1
  TTF1 WILD-TYPE  309   47
                               clus
vv                              TTF1 MUTATED TTF1 WILD-TYPE
  COLON ADENOCARCINOMA                     8            309
  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 252   2  22  18
D262V9, multiclass
    clus
vv   TTF1 MUTATED TTF1 WILD-TYPE
  R0            5            252
  R1            0              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"
D262V10, 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
D262V11, 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(263) Variable = USP26 MUTATION ANALYSIS
D263V1, survival
                 sevent
clus2               0   1
  USP26 MUTATED    19   2
  USP26 WILD-TYPE 263  71
  USP26 MUTATED USP26 WILD-TYPE 
             21             334 
  USP26 MUTATED USP26 WILD-TYPE 
              2              71 
$`USP26 MUTATED`
TCGA-A6-2672 TCGA-A6-5665 TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3864 
       46.65        22.06        24.39        19.66        63.98        53.00 
TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-A00E TCGA-AA-A010 TCGA-AU-6004 TCGA-AY-6197 
       33.01        24.00        30.02        34.98        27.09        21.44 
TCGA-AZ-4315 TCGA-AZ-6599 TCGA-CA-6717 TCGA-CM-6171 TCGA-D5-6928 TCGA-D5-6932 
       58.39         6.77         0.33        14.04        11.64        11.38 
TCGA-F4-6570 TCGA-F4-6806 TCGA-F4-6856 
        6.18        29.59        19.43 

$`USP26 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 
       24.16        21.76        24.69        23.87        20.12        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 
        7.04         3.02         1.02        35.01         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3952 
       31.00         2.01        12.99        24.00        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       14.50        16.31         0.95        15.75         0.20        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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 
        1.51        12.00        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        13.38        13.45        35.87         1.55        16.31 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 
       16.24        33.67        13.25         0.53        35.41       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  USP26 MUTATED USP26 WILD-TYPE 
           0.33            0.00 
  USP26 MUTATED USP26 WILD-TYPE 
          63.98          140.38 
  USP26 MUTATED USP26 WILD-TYPE 
         24.000          20.005 
[1] "0.3 - 64.0 (24.0)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "2.3"
D263V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  USP26 MUTATED         6        0        2        10         2         0
  USP26 WILD-TYPE      58        1       23        99         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        19         10         40         30       35        13
                 vv
clus              STAGE IVB
  USP26 MUTATED           0
  USP26 WILD-TYPE         1
D263V3, multiclass
            clus
vv           USP26 MUTATED USP26 WILD-TYPE
  STAGE I                6              58
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA             10              99
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  USP26 MUTATED     0   6  13   3
  USP26 WILD-TYPE   9  62 235  38
D263V4, multiclass
    clus
vv   USP26 MUTATED USP26 WILD-TYPE
  T1             0               9
  T2             6              62
  T3            13             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    20   2   0
  USP26 WILD-TYPE 200  78  66
D263V5, multiclass
    clus
vv   USP26 MUTATED USP26 WILD-TYPE
  N0            20             200
  N1             2              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"
D263V6, binary
                 cls
clus                0   1
  USP26 MUTATED    19   0
  USP26 WILD-TYPE 264  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP26 MUTATED     19    0
  USP26 WILD-TYPE  264   48
   clus
vv  USP26 MUTATED USP26 WILD-TYPE
  0            19             264
  1             0              48
[1] 2 2
[1] FALSE
D263V7, binary
                 cls
clus                0   1
  USP26 MUTATED    10  12
  USP26 WILD-TYPE 160 185
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP26 MUTATED     10   12
  USP26 WILD-TYPE  160  185
        clus
vv       USP26 MUTATED USP26 WILD-TYPE
  FEMALE            10             160
  MALE              12             185
[1] 2 2
[1] FALSE
D263V8, binary
                 cls
clus                0   1
  USP26 MUTATED    16   6
  USP26 WILD-TYPE 301  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP26 MUTATED     16    6
  USP26 WILD-TYPE  301   42
                               clus
vv                              USP26 MUTATED USP26 WILD-TYPE
  COLON ADENOCARCINOMA                     16             301
  COLON MUCINOUS ADENOCARCINOMA             6              42
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  USP26 MUTATED    19   0   0   1
  USP26 WILD-TYPE 238   2  22  20
D263V9, multiclass
    clus
vv   USP26 MUTATED USP26 WILD-TYPE
  R0            19             238
  R1             0               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"
D263V10, 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
D263V11, 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(264) Variable = RAB28 MUTATION ANALYSIS
D264V1, survival
                 sevent
clus2               0   1
  RAB28 MUTATED     4   2
  RAB28 WILD-TYPE 278  71
  RAB28 MUTATED RAB28 WILD-TYPE 
              6             349 
  RAB28 MUTATED RAB28 WILD-TYPE 
              2              71 
$`RAB28 MUTATED`
TCGA-AY-6197 TCGA-AZ-6598 TCGA-D5-6541 TCGA-DM-A28G TCGA-F4-6856 TCGA-G4-6588 
       21.44        49.41        15.58        60.79        19.43        26.17 

$`RAB28 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        15.75         0.20        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        16.14         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        35.41       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 
       52.80 

  RAB28 MUTATED RAB28 WILD-TYPE 
          15.58            0.00 
  RAB28 MUTATED RAB28 WILD-TYPE 
          60.79          140.38 
  RAB28 MUTATED RAB28 WILD-TYPE 
         23.805          20.120 
[1] "15.6 - 60.8 (23.8)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.2"
D264V2, 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       24       105         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        19         10         41         31       35        13
                 vv
clus              STAGE IVB
  RAB28 MUTATED           0
  RAB28 WILD-TYPE         1
D264V3, multiclass
            clus
vv           RAB28 MUTATED RAB28 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              4             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RAB28 MUTATED     0   1   5   0
  RAB28 WILD-TYPE   9  67 243  41
D264V4, multiclass
    clus
vv   RAB28 MUTATED RAB28 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             5             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
  RAB28 MUTATED     6   0   0
  RAB28 WILD-TYPE 214  80  66
D264V5, multiclass
    clus
vv   RAB28 MUTATED RAB28 WILD-TYPE
  N0             6             214
  N1             0              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"
D264V6, binary
                 cls
clus                0   1
  RAB28 MUTATED     4   0
  RAB28 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB28 MUTATED      4    0
  RAB28 WILD-TYPE  279   48
   clus
vv  RAB28 MUTATED RAB28 WILD-TYPE
  0             4             279
  1             0              48
[1] 2 2
[1] FALSE
D264V7, 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
D264V8, binary
                 cls
clus                0   1
  RAB28 MUTATED     5   1
  RAB28 WILD-TYPE 312  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB28 MUTATED      5    1
  RAB28 WILD-TYPE  312   47
                               clus
vv                              RAB28 MUTATED RAB28 WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  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 253   2  22  21
D264V9, multiclass
    clus
vv   RAB28 MUTATED RAB28 WILD-TYPE
  R0             4             253
  R1             0               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"
D264V10, 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
D264V11, 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(265) Variable = MST4 MUTATION ANALYSIS
D265V1, survival
                sevent
clus2              0   1
  MST4 MUTATED     5   2
  MST4 WILD-TYPE 277  71
  MST4 MUTATED MST4 WILD-TYPE 
             7            348 
  MST4 MUTATED MST4 WILD-TYPE 
             2             71 
$`MST4 MUTATED`
TCGA-A6-4105 TCGA-A6-5661 TCGA-A6-5662 TCGA-AA-3496 TCGA-AA-A00N TCGA-AU-6004 
       14.53        33.53        23.61         1.02         4.01        27.09 
TCGA-DM-A28K 
       98.24 

$`MST4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       31.63        30.44        29.19        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         3.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 
       81.37       119.93        35.97        60.79       117.07         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  MST4 MUTATED MST4 WILD-TYPE 
          1.02           0.00 
  MST4 MUTATED MST4 WILD-TYPE 
         98.24         140.38 
  MST4 MUTATED MST4 WILD-TYPE 
        23.610         20.155 
[1] "1.0 - 98.2 (23.6)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.3"
D265V2, 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       24       106         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        19         10         41         31       35        12
                vv
clus             STAGE IVB
  MST4 MUTATED           0
  MST4 WILD-TYPE         1
D265V3, multiclass
            clus
vv           MST4 MUTATED MST4 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             3            106
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 243  40
D265V4, multiclass
    clus
vv   MST4 MUTATED MST4 WILD-TYPE
  T1            0              9
  T2            1             67
  T3            5            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
  MST4 MUTATED     6   0   1
  MST4 WILD-TYPE 214  80  65
D265V5, multiclass
    clus
vv   MST4 MUTATED MST4 WILD-TYPE
  N0            6            214
  N1            0             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"
D265V6, binary
                cls
clus               0   1
  MST4 MUTATED     6   1
  MST4 WILD-TYPE 277  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  MST4 MUTATED      6    1
  MST4 WILD-TYPE  277   47
   clus
vv  MST4 MUTATED MST4 WILD-TYPE
  0            6            277
  1            1             47
[1] 2 2
[1] FALSE
D265V7, 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
D265V8, binary
                cls
clus               0   1
  MST4 MUTATED     5   2
  MST4 WILD-TYPE 312  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  MST4 MUTATED      5    2
  MST4 WILD-TYPE  312   46
                               clus
vv                              MST4 MUTATED MST4 WILD-TYPE
  COLON ADENOCARCINOMA                     5            312
  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 253   2  22  21
D265V9, multiclass
    clus
vv   MST4 MUTATED MST4 WILD-TYPE
  R0            4            253
  R1            0              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"
D265V10, 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
D265V11, 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(266) Variable = FAM133B MUTATION ANALYSIS
D266V1, survival
                   sevent
clus2                 0   1
  FAM133B MUTATED     4   1
  FAM133B WILD-TYPE 278  72
  FAM133B MUTATED FAM133B WILD-TYPE 
                5               350 
  FAM133B MUTATED FAM133B WILD-TYPE 
                1                72 
$`FAM133B MUTATED`
TCGA-A6-3809 TCGA-CK-5916 TCGA-CM-6167 TCGA-G4-6309 TCGA-G4-6628 
       32.75        21.14        14.99        51.75        52.80 

$`FAM133B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       74.56        65.85        53.62        44.68        55.04        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 
       91.79        46.75 

  FAM133B MUTATED FAM133B WILD-TYPE 
            14.99              0.00 
  FAM133B MUTATED FAM133B WILD-TYPE 
            52.80            140.38 
  FAM133B MUTATED FAM133B WILD-TYPE 
            32.75             20.07 
[1] "15.0 - 52.8 (32.8)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.5"
D266V2, 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       25       109         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM133B MUTATED           0          0          1          1        0
  FAM133B WILD-TYPE        19         10         40         30       35
                   vv
clus                STAGE IVA STAGE IVB
  FAM133B MUTATED           0         0
  FAM133B WILD-TYPE        13         1
D266V3, multiclass
            clus
vv           FAM133B MUTATED FAM133B WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                0               109
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               1                30
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  FAM133B MUTATED     1   1   2   1
  FAM133B WILD-TYPE   8  67 246  40
D266V4, multiclass
    clus
vv   FAM133B MUTATED FAM133B WILD-TYPE
  T1               1                 8
  T2               1                67
  T3               2               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
  FAM133B MUTATED     3   1   1
  FAM133B WILD-TYPE 217  79  65
D266V5, multiclass
    clus
vv   FAM133B MUTATED FAM133B WILD-TYPE
  N0               3               217
  N1               1                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"
D266V6, binary
                   cls
clus                  0   1
  FAM133B MUTATED     5   0
  FAM133B WILD-TYPE 278  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM133B MUTATED      5    0
  FAM133B WILD-TYPE  278   48
   clus
vv  FAM133B MUTATED FAM133B WILD-TYPE
  0               5               278
  1               0                48
[1] 2 2
[1] FALSE
D266V7, 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
D266V8, binary
                   cls
clus                  0   1
  FAM133B MUTATED     4   1
  FAM133B WILD-TYPE 313  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM133B MUTATED      4    1
  FAM133B WILD-TYPE  313   47
                               clus
vv                              FAM133B MUTATED FAM133B WILD-TYPE
  COLON ADENOCARCINOMA                        4               313
  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 253   2  22  20
D266V9, multiclass
    clus
vv   FAM133B MUTATED FAM133B WILD-TYPE
  R0               4               253
  R1               0                 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"
D266V10, 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
D266V11, 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(267) Variable = TRIM32 MUTATION ANALYSIS
D267V1, survival
                  sevent
clus2                0   1
  TRIM32 MUTATED     8   3
  TRIM32 WILD-TYPE 274  70
  TRIM32 MUTATED TRIM32 WILD-TYPE 
              11              344 
  TRIM32 MUTATED TRIM32 WILD-TYPE 
               3               70 
$`TRIM32 MUTATED`
TCGA-AA-3516 TCGA-AA-3522 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3968 TCGA-AA-A01R 
       13.02        37.05        26.99        19.04        21.99        35.01 
TCGA-AZ-5403 TCGA-F4-6808 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6315 
       62.79        33.67        74.56        53.62        36.72 

$`TRIM32 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        1.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        1.02         9.07        24.03        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.03        85.05        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
        2.01        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 
       58.39         1.41         5.13        83.80        22.36        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       29.59        16.24        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
      107.67        65.85        44.68        55.04        51.75        45.11 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  TRIM32 MUTATED TRIM32 WILD-TYPE 
           13.02             0.00 
  TRIM32 MUTATED TRIM32 WILD-TYPE 
           74.56           140.38 
  TRIM32 MUTATED TRIM32 WILD-TYPE 
           35.01            19.99 
[1] "13.0 - 74.6 (35.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.1"
D267V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TRIM32 MUTATED         2        0        2         2         1         0
  TRIM32 WILD-TYPE      62        1       23       107         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRIM32 MUTATED           2          0          0          1        1
  TRIM32 WILD-TYPE        17         10         41         30       34
                  vv
clus               STAGE IVA STAGE IVB
  TRIM32 MUTATED           0         0
  TRIM32 WILD-TYPE        13         1
D267V3, multiclass
            clus
vv           TRIM32 MUTATED TRIM32 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               2              107
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               2               17
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              1               30
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TRIM32 MUTATED     1   1   8   1
  TRIM32 WILD-TYPE   8  67 240  40
D267V4, multiclass
    clus
vv   TRIM32 MUTATED TRIM32 WILD-TYPE
  T1              1                8
  T2              1               67
  T3              8              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
  TRIM32 MUTATED     7   1   3
  TRIM32 WILD-TYPE 213  79  63
D267V5, multiclass
    clus
vv   TRIM32 MUTATED TRIM32 WILD-TYPE
  N0              7              213
  N1              1               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"
D267V6, binary
                  cls
clus                 0   1
  TRIM32 MUTATED     9   1
  TRIM32 WILD-TYPE 274  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM32 MUTATED      9    1
  TRIM32 WILD-TYPE  274   47
   clus
vv  TRIM32 MUTATED TRIM32 WILD-TYPE
  0              9              274
  1              1               47
[1] 2 2
[1] FALSE
D267V7, binary
                  cls
clus                 0   1
  TRIM32 MUTATED     5   6
  TRIM32 WILD-TYPE 165 191
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM32 MUTATED      5    6
  TRIM32 WILD-TYPE  165  191
        clus
vv       TRIM32 MUTATED TRIM32 WILD-TYPE
  FEMALE              5              165
  MALE                6              191
[1] 2 2
[1] FALSE
D267V8, binary
                  cls
clus                 0   1
  TRIM32 MUTATED     9   2
  TRIM32 WILD-TYPE 308  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM32 MUTATED      9    2
  TRIM32 WILD-TYPE  308   46
                               clus
vv                              TRIM32 MUTATED TRIM32 WILD-TYPE
  COLON ADENOCARCINOMA                       9              308
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TRIM32 MUTATED     9   0   0   0
  TRIM32 WILD-TYPE 248   2  22  21
D267V9, multiclass
    clus
vv   TRIM32 MUTATED TRIM32 WILD-TYPE
  R0              9              248
  R1              0                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"
D267V10, 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     5
  TRIM32 WILD-TYPE                        19   171
D267V11, 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                                         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 = GOLPH3L MUTATION ANALYSIS
D268V1, survival
                   sevent
clus2                 0   1
  GOLPH3L MUTATED     2   3
  GOLPH3L WILD-TYPE 280  70
  GOLPH3L MUTATED GOLPH3L WILD-TYPE 
                5               350 
  GOLPH3L MUTATED GOLPH3L WILD-TYPE 
                3                70 
$`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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
        8.05        19.07        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        15.75         0.20        21.44         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        24.43        38.20       130.65        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  GOLPH3L MUTATED GOLPH3L WILD-TYPE 
                0                 0 
  GOLPH3L MUTATED GOLPH3L WILD-TYPE 
            92.75            140.38 
  GOLPH3L MUTATED GOLPH3L WILD-TYPE 
           58.390            20.155 
[1] "0.0 - 92.8 (58.4)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.6"
D268V2, 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       25       107         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GOLPH3L MUTATED           0          0          1          1        1
  GOLPH3L WILD-TYPE        19         10         40         30       34
                   vv
clus                STAGE IVA STAGE IVB
  GOLPH3L MUTATED           0         0
  GOLPH3L WILD-TYPE        13         1
D268V3, multiclass
            clus
vv           GOLPH3L MUTATED GOLPH3L WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                2               107
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               1                30
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  GOLPH3L MUTATED     0   0   5   0
  GOLPH3L WILD-TYPE   9  68 243  41
D268V4, multiclass
    clus
vv   GOLPH3L MUTATED GOLPH3L WILD-TYPE
  T1               0                 9
  T2               0                68
  T3               5               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
  GOLPH3L MUTATED     2   2   1
  GOLPH3L WILD-TYPE 218  78  65
D268V5, multiclass
    clus
vv   GOLPH3L MUTATED GOLPH3L WILD-TYPE
  N0               2               218
  N1               2                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"
D268V6, binary
                   cls
clus                  0   1
  GOLPH3L MUTATED     4   1
  GOLPH3L WILD-TYPE 279  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GOLPH3L MUTATED      4    1
  GOLPH3L WILD-TYPE  279   47
   clus
vv  GOLPH3L MUTATED GOLPH3L WILD-TYPE
  0               4               279
  1               1                47
[1] 2 2
[1] FALSE
D268V7, 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
D268V8, binary
                   cls
clus                  0   1
  GOLPH3L MUTATED     5   0
  GOLPH3L WILD-TYPE 312  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GOLPH3L MUTATED      5    0
  GOLPH3L WILD-TYPE  312   48
                               clus
vv                              GOLPH3L MUTATED GOLPH3L WILD-TYPE
  COLON ADENOCARCINOMA                        5               312
  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 253   2  22  21
D268V9, multiclass
    clus
vv   GOLPH3L MUTATED GOLPH3L WILD-TYPE
  R0               4               253
  R1               0                 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"
D268V10, 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
D268V11, 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(269) Variable = ACP6 MUTATION ANALYSIS
D269V1, survival
                sevent
clus2              0   1
  ACP6 MUTATED     5   1
  ACP6 WILD-TYPE 277  72
  ACP6 MUTATED ACP6 WILD-TYPE 
             6            349 
  ACP6 MUTATED ACP6 WILD-TYPE 
             1             72 
$`ACP6 MUTATED`
TCGA-A6-6648 TCGA-AA-3713 TCGA-AD-6964 TCGA-CK-4948 TCGA-F4-6460 TCGA-G4-6588 
       25.18        19.04        10.88       102.44        13.38        26.17 

$`ACP6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 
        0.26         0.33         0.10         1.35        17.56        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
      117.07        98.24         8.61        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 
       52.80 

  ACP6 MUTATED ACP6 WILD-TYPE 
         10.88           0.00 
  ACP6 MUTATED ACP6 WILD-TYPE 
        102.44         140.38 
  ACP6 MUTATED ACP6 WILD-TYPE 
         22.11          20.19 
[1] "10.9 - 102.4 (22.1)" "0.0 - 140.4 (20.2)" 
[1] "hr=" "1.6"
D269V2, 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       25       108         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ACP6 MUTATED           0          1          1          0        1         1
  ACP6 WILD-TYPE        19          9         40         31       34        12
                vv
clus             STAGE IVB
  ACP6 MUTATED           0
  ACP6 WILD-TYPE         1
D269V3, multiclass
            clus
vv           ACP6 MUTATED ACP6 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             1            108
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            1              9
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  68 243  40
D269V4, multiclass
    clus
vv   ACP6 MUTATED ACP6 WILD-TYPE
  T1            0              9
  T2            0             68
  T3            5            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
  ACP6 MUTATED     3   2   1
  ACP6 WILD-TYPE 217  78  65
D269V5, multiclass
    clus
vv   ACP6 MUTATED ACP6 WILD-TYPE
  N0            3            217
  N1            2             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"
D269V6, binary
                cls
clus               0   1
  ACP6 MUTATED     3   2
  ACP6 WILD-TYPE 280  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  ACP6 MUTATED      3    2
  ACP6 WILD-TYPE  280   46
   clus
vv  ACP6 MUTATED ACP6 WILD-TYPE
  0            3            280
  1            2             46
[1] 2 2
[1] FALSE
D269V7, 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
D269V8, binary
                cls
clus               0   1
  ACP6 MUTATED     6   0
  ACP6 WILD-TYPE 311  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  ACP6 MUTATED      6    0
  ACP6 WILD-TYPE  311   48
                               clus
vv                              ACP6 MUTATED ACP6 WILD-TYPE
  COLON ADENOCARCINOMA                     6            311
  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 254   2  21  21
D269V9, multiclass
    clus
vv   ACP6 MUTATED ACP6 WILD-TYPE
  R0            3            254
  R1            0              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"
D269V10, 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
D269V11, 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(270) Variable = PPP2R1A MUTATION ANALYSIS
D270V1, survival
                   sevent
clus2                 0   1
  PPP2R1A MUTATED    12   2
  PPP2R1A WILD-TYPE 270  71
  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
               14               341 
  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
                2                71 
$`PPP2R1A MUTATED`
TCGA-A6-6653 TCGA-AA-3514 TCGA-AA-3663 TCGA-AA-3846 TCGA-AA-A01R TCGA-AA-A02O 
       24.39         1.02         6.97        17.03        35.01         0.92 
TCGA-AD-5900 TCGA-AZ-5407 TCGA-AZ-6601 TCGA-CK-4952 TCGA-D5-6540 TCGA-D5-6928 
        0.07        61.41       100.01        15.62        16.14        11.64 
TCGA-G4-6588 TCGA-G4-6626 
       26.17        46.75 

$`PPP2R1A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         6.97        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 
       38.99        37.02        14.93         0.00        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       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        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
       14.01        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 
        1.41         5.13        83.80        22.36        62.79        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       40.34        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        52.80 

  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
             0.07              0.00 
  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
           100.01            140.38 
  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
           16.585            20.280 
[1] "0.1 - 100.0 (16.6)" "0.0 - 140.4 (20.3)"
[1] "hr=" "1.5"
D270V2, 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       22       105         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PPP2R1A MUTATED           2          0          0          0        0
  PPP2R1A WILD-TYPE        17         10         41         31       35
                   vv
clus                STAGE IVA STAGE IVB
  PPP2R1A MUTATED           0         0
  PPP2R1A WILD-TYPE        13         1
D270V3, multiclass
            clus
vv           PPP2R1A MUTATED PPP2R1A WILD-TYPE
  STAGE I                  5                59
  STAGE IA                 0                 1
  STAGE II                 3                22
  STAGE IIA                4               105
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                2                17
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PPP2R1A MUTATED     1   4   8   1
  PPP2R1A WILD-TYPE   8  64 240  40
D270V4, multiclass
    clus
vv   PPP2R1A MUTATED PPP2R1A WILD-TYPE
  T1               1                 8
  T2               4                64
  T3               8               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
  PPP2R1A MUTATED    12   0   2
  PPP2R1A WILD-TYPE 208  80  64
D270V5, multiclass
    clus
vv   PPP2R1A MUTATED PPP2R1A WILD-TYPE
  N0              12               208
  N1               0                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"
D270V6, binary
                   cls
clus                  0   1
  PPP2R1A MUTATED    13   0
  PPP2R1A WILD-TYPE 270  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP2R1A MUTATED     13    0
  PPP2R1A WILD-TYPE  270   48
   clus
vv  PPP2R1A MUTATED PPP2R1A WILD-TYPE
  0              13               270
  1               0                48
[1] 2 2
[1] FALSE
D270V7, 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
D270V8, binary
                   cls
clus                  0   1
  PPP2R1A MUTATED     9   5
  PPP2R1A WILD-TYPE 308  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP2R1A MUTATED      9    5
  PPP2R1A WILD-TYPE  308   43
                               clus
vv                              PPP2R1A MUTATED PPP2R1A WILD-TYPE
  COLON ADENOCARCINOMA                        9               308
  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 247   2  22  20
D270V9, multiclass
    clus
vv   PPP2R1A MUTATED PPP2R1A WILD-TYPE
  R0              10               247
  R1               0                 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"
D270V10, 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
D270V11, 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(271) Variable = INSM2 MUTATION ANALYSIS
D271V1, survival
                 sevent
clus2               0   1
  INSM2 MUTATED     9   1
  INSM2 WILD-TYPE 273  72
  INSM2 MUTATED INSM2 WILD-TYPE 
             10             345 
  INSM2 MUTATED INSM2 WILD-TYPE 
              1              72 
$`INSM2 MUTATED`
TCGA-A6-6781 TCGA-AD-6895 TCGA-AY-6386 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-4952 
       19.66         0.72        17.82        49.41         0.33        15.62 
TCGA-CM-4743 TCGA-CM-4744 TCGA-G4-6299 TCGA-G4-6628 
       23.05        20.02        74.56        52.80 

$`INSM2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        4.21        56.55         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       15.75         0.20        21.44        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 
        0.10         1.35        17.56       102.44        40.34        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      107.67        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       26.17        91.79        46.75 

  INSM2 MUTATED INSM2 WILD-TYPE 
           0.33            0.00 
  INSM2 MUTATED INSM2 WILD-TYPE 
          74.56          140.38 
  INSM2 MUTATED INSM2 WILD-TYPE 
          19.84           20.28 
[1] "0.3 - 74.6 (19.8)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "2.4"
D271V2, 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       24       107         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  INSM2 MUTATED           1          0          1          2        0         0
  INSM2 WILD-TYPE        18         10         40         29       35        13
                 vv
clus              STAGE IVB
  INSM2 MUTATED           0
  INSM2 WILD-TYPE         1
D271V3, multiclass
            clus
vv           INSM2 MUTATED INSM2 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              2             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             2              29
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  INSM2 MUTATED     0   2   6   2
  INSM2 WILD-TYPE   9  66 242  39
D271V4, multiclass
    clus
vv   INSM2 MUTATED INSM2 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             6             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
  INSM2 MUTATED     5   3   2
  INSM2 WILD-TYPE 215  77  64
D271V5, multiclass
    clus
vv   INSM2 MUTATED INSM2 WILD-TYPE
  N0             5             215
  N1             3              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"
D271V6, binary
                 cls
clus                0   1
  INSM2 MUTATED     7   0
  INSM2 WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INSM2 MUTATED      7    0
  INSM2 WILD-TYPE  276   48
   clus
vv  INSM2 MUTATED INSM2 WILD-TYPE
  0             7             276
  1             0              48
[1] 2 2
[1] FALSE
D271V7, 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
D271V8, binary
                 cls
clus                0   1
  INSM2 MUTATED     7   3
  INSM2 WILD-TYPE 310  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INSM2 MUTATED      7    3
  INSM2 WILD-TYPE  310   45
                               clus
vv                              INSM2 MUTATED INSM2 WILD-TYPE
  COLON ADENOCARCINOMA                      7             310
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  INSM2 MUTATED     6   0   0   2
  INSM2 WILD-TYPE 251   2  22  19
D271V9, multiclass
    clus
vv   INSM2 MUTATED INSM2 WILD-TYPE
  R0             6             251
  R1             0               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"
D271V10, 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
D271V11, 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(272) Variable = TSHR MUTATION ANALYSIS
D272V1, survival
                sevent
clus2              0   1
  TSHR MUTATED    32  12
  TSHR WILD-TYPE 250  61
  TSHR MUTATED TSHR WILD-TYPE 
            44            311 
  TSHR MUTATED TSHR WILD-TYPE 
            12             61 
$`TSHR MUTATED`
TCGA-A6-5665 TCGA-A6-6141 TCGA-AA-3516 TCGA-AA-3555 TCGA-AA-3660 TCGA-AA-3663 
       22.06         8.38        13.02        29.95        78.08         6.97 
TCGA-AA-3947 TCGA-AA-A010 TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A02K TCGA-AD-6890 
       33.01        34.98        38.07         1.02        14.01         0.79 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6603 
       17.82        58.39        62.79        49.41         6.77        29.56 
TCGA-CA-6717 TCGA-CK-5912 TCGA-CM-5868 TCGA-CM-6164 TCGA-CM-6172 TCGA-D5-5538 
        0.33        49.08        17.03        29.03        11.01        12.26 
TCGA-D5-6536 TCGA-D5-6541 TCGA-D5-6926 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0XF 
       17.85        15.58         9.04        12.00        10.26        38.20 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28H TCGA-F4-6460 TCGA-F4-6703 
      139.17         6.12        81.37       117.07        13.38        35.87 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 
       44.68        55.04        51.75        13.78        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

$`TSHR WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.09        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       61.02         6.05        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        31.00        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37         4.21        56.55         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4323 
       16.31         0.95        15.75         0.20        21.44         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6601 
        5.13        83.80        22.36        61.41        12.10       100.01 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
       17.56       102.44        40.34        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         2.93         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        16.01        15.02         5.03        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-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-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12         4.80        17.13        12.49        16.14 
TCGA-D5-6898 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-D5-6932 TCGA-DM-A0X9 TCGA-DM-A0XD 
       11.64        13.41         1.51        11.38       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-A28E TCGA-DM-A28F 
        7.50        44.32       131.51       135.65       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 
       60.79        98.24         8.61        13.45         6.18         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        35.80 

  TSHR MUTATED TSHR WILD-TYPE 
          0.33           0.00 
  TSHR MUTATED TSHR WILD-TYPE 
        139.17         140.38 
  TSHR MUTATED TSHR WILD-TYPE 
         27.60          20.02 
[1] "0.3 - 139.2 (27.6)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1"  
D272V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TSHR MUTATED         4        1        5        15         2         0
  TSHR WILD-TYPE      60        0       20        94         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TSHR MUTATED           2          1          6          3        2         1
  TSHR WILD-TYPE        17          9         35         28       33        12
                vv
clus             STAGE IVB
  TSHR MUTATED           0
  TSHR WILD-TYPE         1
D272V3, multiclass
            clus
vv           TSHR MUTATED TSHR WILD-TYPE
  STAGE I               4             60
  STAGE IA              1              0
  STAGE II              5             20
  STAGE IIA            15             94
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             2             17
  STAGE IIIA            1              9
  STAGE IIIB            6             35
  STAGE IIIC            3             28
  STAGE IV              2             33
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  62 218  35
D272V4, multiclass
    clus
vv   TSHR MUTATED TSHR WILD-TYPE
  T1            1              8
  T2            6             62
  T3           30            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
  TSHR MUTATED    28  10   6
  TSHR WILD-TYPE 192  70  60
D272V5, multiclass
    clus
vv   TSHR MUTATED TSHR WILD-TYPE
  N0           28            192
  N1           10             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"
D272V6, binary
                cls
clus               0   1
  TSHR MUTATED    34   3
  TSHR WILD-TYPE 249  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  TSHR MUTATED     34    3
  TSHR WILD-TYPE  249   45
   clus
vv  TSHR MUTATED TSHR WILD-TYPE
  0           34            249
  1            3             45
[1] 2 2
[1] FALSE
D272V7, 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
D272V8, binary
                cls
clus               0   1
  TSHR MUTATED    37   7
  TSHR WILD-TYPE 280  41
[1] "tbl2"
                cls
clus             [,1] [,2]
  TSHR MUTATED     37    7
  TSHR WILD-TYPE  280   41
                               clus
vv                              TSHR MUTATED TSHR WILD-TYPE
  COLON ADENOCARCINOMA                    37            280
  COLON MUCINOUS ADENOCARCINOMA            7             41
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TSHR MUTATED    29   0   1   2
  TSHR WILD-TYPE 228   2  21  19
D272V9, multiclass
    clus
vv   TSHR MUTATED TSHR WILD-TYPE
  R0           29            228
  R1            0              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"
D272V10, 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
D272V11, 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(273) Variable = USP34 MUTATION ANALYSIS
D273V1, survival
                 sevent
clus2               0   1
  USP34 MUTATED    30  10
  USP34 WILD-TYPE 252  63
  USP34 MUTATED USP34 WILD-TYPE 
             40             315 
  USP34 MUTATED USP34 WILD-TYPE 
             10              63 
$`USP34 MUTATED`
TCGA-A6-6781 TCGA-AA-3663 TCGA-AA-3673 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3815 
       19.66         6.97        50.04        19.04        19.04        33.04 
TCGA-AA-3867 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3977 TCGA-AA-A00N TCGA-AD-5900 
       24.03        33.01        20.98        25.02         4.01         0.07 
TCGA-AD-6889 TCGA-AD-6895 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-AZ-6606 
       56.55         0.72        58.39        49.41       100.01        11.74 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4950 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4752 
        0.33         0.10        40.34         2.01        23.05        13.02 
TCGA-CM-6167 TCGA-CM-6171 TCGA-D5-6535 TCGA-D5-6540 TCGA-D5-6927 TCGA-D5-6932 
       14.99        14.04        15.12        16.14         9.44        11.38 
TCGA-DM-A1D7 TCGA-DM-A1DA TCGA-F4-6570 TCGA-G4-6303 TCGA-G4-6309 TCGA-G4-6315 
       13.32         7.50         6.18        65.85        51.75        36.72 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6626 TCGA-G4-6628 
       22.09        35.80        46.75        52.80 

$`USP34 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01         0.92        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       85.05        26.99        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       53.00        17.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        26.01        24.00         2.01 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       21.37         4.21         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07         0.26         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      102.44        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 
        2.93       124.27        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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 
       11.51        20.19        18.25         1.32        43.27        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         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-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
        1.51        12.00        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB 
      130.65        92.75        49.91        12.59       140.38        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6317 
       74.56        53.62        44.68        55.04        45.11        36.00 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 
       13.78        26.17        91.79 

  USP34 MUTATED USP34 WILD-TYPE 
           0.07            0.00 
  USP34 MUTATED USP34 WILD-TYPE 
         100.01          140.38 
  USP34 MUTATED USP34 WILD-TYPE 
          19.35           20.28 
[1] "0.1 - 100.0 (19.4)" "0.0 - 140.4 (20.3)"
[1] "hr=" "1.2"
D273V2, 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       20        96         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  USP34 MUTATED           1          1          3          3        6         0
  USP34 WILD-TYPE        18          9         38         28       29        13
                 vv
clus              STAGE IVB
  USP34 MUTATED           0
  USP34 WILD-TYPE         1
D273V3, multiclass
            clus
vv           USP34 MUTATED USP34 WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               5              20
  STAGE IIA             13              96
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             1               9
  STAGE IIIB             3              38
  STAGE IIIC             3              28
  STAGE IV               6              29
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  USP34 MUTATED     0   7  29   5
  USP34 WILD-TYPE   9  61 219  36
D273V4, multiclass
    clus
vv   USP34 MUTATED USP34 WILD-TYPE
  T1             0               9
  T2             7              61
  T3            29             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   9   5
  USP34 WILD-TYPE 193  71  61
D273V5, multiclass
    clus
vv   USP34 MUTATED USP34 WILD-TYPE
  N0            27             193
  N1             9              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"
D273V6, binary
                 cls
clus                0   1
  USP34 MUTATED    27   6
  USP34 WILD-TYPE 256  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP34 MUTATED     27    6
  USP34 WILD-TYPE  256   42
   clus
vv  USP34 MUTATED USP34 WILD-TYPE
  0            27             256
  1             6              42
[1] 2 2
[1] FALSE
D273V7, binary
                 cls
clus                0   1
  USP34 MUTATED    16  25
  USP34 WILD-TYPE 154 172
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP34 MUTATED     16   25
  USP34 WILD-TYPE  154  172
        clus
vv       USP34 MUTATED USP34 WILD-TYPE
  FEMALE            16             154
  MALE              25             172
[1] 2 2
[1] FALSE
D273V8, binary
                 cls
clus                0   1
  USP34 MUTATED    34   7
  USP34 WILD-TYPE 283  41
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP34 MUTATED     34    7
  USP34 WILD-TYPE  283   41
                               clus
vv                              USP34 MUTATED USP34 WILD-TYPE
  COLON ADENOCARCINOMA                     34             283
  COLON MUCINOUS ADENOCARCINOMA             7              41
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  USP34 MUTATED    25   1   2   5
  USP34 WILD-TYPE 232   1  20  16
D273V9, multiclass
    clus
vv   USP34 MUTATED USP34 WILD-TYPE
  R0            25             232
  R1             1               1
  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"
D273V10, 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    24
  USP34 WILD-TYPE                        15   152
D273V11, 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                                       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(274) Variable = C14ORF159 MUTATION ANALYSIS
D274V1, survival
                     sevent
clus2                   0   1
  C14ORF159 MUTATED     7   1
  C14ORF159 WILD-TYPE 275  72
  C14ORF159 MUTATED C14ORF159 WILD-TYPE 
                  8                 347 
  C14ORF159 MUTATED C14ORF159 WILD-TYPE 
                  1                  72 
$`C14ORF159 MUTATED`
TCGA-A6-5660 TCGA-AA-A010 TCGA-AU-3779 TCGA-AZ-6601 TCGA-D5-6927 TCGA-DM-A1D9 
       29.19        34.98        14.50       100.01         9.44       140.38 
TCGA-DM-A1HB TCGA-F4-6808 
      135.65        33.67 

$`C14ORF159 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       29.59        16.24        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  C14ORF159 MUTATED C14ORF159 WILD-TYPE 
               9.44                0.00 
  C14ORF159 MUTATED C14ORF159 WILD-TYPE 
             140.38              139.17 
  C14ORF159 MUTATED C14ORF159 WILD-TYPE 
             34.325              20.020 
[1] "9.4 - 140.4 (34.3)" "0.0 - 139.2 (20.0)"
[1] "hr=" "3.5"
D274V2, 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       24       106         7         1
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C14ORF159 MUTATED           0          0          1          1        0
  C14ORF159 WILD-TYPE        19         10         40         30       35
                     vv
clus                  STAGE IVA STAGE IVB
  C14ORF159 MUTATED           0         0
  C14ORF159 WILD-TYPE        13         1
D274V3, multiclass
            clus
vv           C14ORF159 MUTATED C14ORF159 WILD-TYPE
  STAGE I                    2                  62
  STAGE IA                   0                   1
  STAGE II                   1                  24
  STAGE IIA                  3                 106
  STAGE IIB                  1                   7
  STAGE IIC                  0                   1
  STAGE III                  0                  19
  STAGE IIIA                 0                  10
  STAGE IIIB                 1                  40
  STAGE IIIC                 1                  30
  STAGE IV                   0                  35
  STAGE IVA                  0                  13
  STAGE IVB                  0                   1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2  T3  T4
  C14ORF159 MUTATED     1   1   6   1
  C14ORF159 WILD-TYPE   8  67 242  40
D274V4, multiclass
    clus
vv   C14ORF159 MUTATED C14ORF159 WILD-TYPE
  T1                 1                   8
  T2                 1                  67
  T3                 6                 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
  C14ORF159 MUTATED     7   1   1
  C14ORF159 WILD-TYPE 213  79  65
D274V5, multiclass
    clus
vv   C14ORF159 MUTATED C14ORF159 WILD-TYPE
  N0                 7                 213
  N1                 1                  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"
D274V6, binary
                     cls
clus                    0   1
  C14ORF159 MUTATED     8   0
  C14ORF159 WILD-TYPE 275  48
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF159 MUTATED      8    0
  C14ORF159 WILD-TYPE  275   48
   clus
vv  C14ORF159 MUTATED C14ORF159 WILD-TYPE
  0                 8                 275
  1                 0                  48
[1] 2 2
[1] FALSE
D274V7, 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
D274V8, binary
                     cls
clus                    0   1
  C14ORF159 MUTATED     9   0
  C14ORF159 WILD-TYPE 308  48
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF159 MUTATED      9    0
  C14ORF159 WILD-TYPE  308   48
                               clus
vv                              C14ORF159 MUTATED C14ORF159 WILD-TYPE
  COLON ADENOCARCINOMA                          9                 308
  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 253   2  22  20
D274V9, multiclass
    clus
vv   C14ORF159 MUTATED C14ORF159 WILD-TYPE
  R0                 4                 253
  R1                 0                   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"
D274V10, 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
D274V11, 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(275) Variable = KRAS MUTATION ANALYSIS
D275V1, survival
                sevent
clus2              0   1
  KRAS MUTATED   130  36
  KRAS WILD-TYPE 152  37
  KRAS MUTATED KRAS WILD-TYPE 
           166            189 
  KRAS MUTATED KRAS WILD-TYPE 
            36             37 
$`KRAS MUTATED`
TCGA-A6-2683 TCGA-A6-3808 TCGA-A6-4105 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 
       16.57        33.34        14.53        31.63        30.44        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        22.06        32.71        22.52         8.38 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       24.39        23.87        20.28        35.01        63.98         6.97 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3530 TCGA-AA-3532 TCGA-AA-3548 TCGA-AA-3555 
       24.03        37.05        19.07        29.00        33.99        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       23.01        20.98        19.99        13.94        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 
        6.97         0.92        50.04        11.01         5.98         5.03 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3818 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
       19.04        19.04         0.99        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3861 
        0.00        10.06        33.07         0.00        36.03        30.05 
TCGA-AA-3864 TCGA-AA-3870 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3975 
       53.00        29.98         2.01        12.99        24.00        34.06 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00K 
       25.02        24.00        19.07        27.02        38.04        18.05 
TCGA-AA-A00N TCGA-AA-A00Q TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        4.01        42.02        32.02        12.00        31.00        31.00 
TCGA-AA-A01R TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02K TCGA-AA-A02O 
       35.01        26.01        37.02        51.98        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6889 
       41.00        39.98        18.05        40.96        21.37        56.55 
TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 TCGA-AY-5543 TCGA-AY-6386 
        0.72        22.42        10.88         0.20        15.75        17.82 
TCGA-AZ-4315 TCGA-AZ-4616 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       58.39         5.13        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 
      100.01         5.23        11.74         3.19         1.94         3.06 
TCGA-CA-5796 TCGA-CA-6716 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        3.25         0.26         0.10        17.56       102.44        40.34 
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-5862 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 
        5.03        15.02        15.02        14.04        29.03        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6678 TCGA-D5-5537 
       14.99        12.99        14.04        12.95        11.01        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6535 
       12.26        19.59        13.51        20.19        18.25        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6923 
       17.85         4.80        17.13        12.49        15.58        12.43 
TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-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-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28E 
      140.38        44.32       131.51       139.17         6.12       119.93 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 
       60.79       117.07        98.24        35.87        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6304 TCGA-G4-6306 
       16.24         0.53        35.41        19.43        53.62        44.68 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       13.78        35.80        91.79        46.75 

$`KRAS WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5660 TCGA-A6-6137 
       34.65        32.75        36.53        32.91        29.19        27.09 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6780 
       25.08        25.18        24.16        21.76        24.69        20.12 
TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3514 TCGA-AA-3516 
       19.66         7.04         3.02         1.02         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
       38.99         1.02         9.07        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
        0.00        34.03        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3562 
       14.01        21.01        13.02        24.00        17.95        19.99 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3678 TCGA-AA-3679 
        6.05        54.02         2.01        14.01        47.01        15.02 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3811 
       37.05        19.00        36.00        85.05        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-3846 TCGA-AA-3850 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
       17.03         0.00        32.05         0.99        31.07        31.07 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3947 
       17.03        24.03        27.02        18.05        31.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3976 TCGA-AA-3980 
       21.99        16.08        50.99        13.05        26.01        27.02 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02         7.96        13.94        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       18.05        38.04        27.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01P TCGA-AA-A01Q 
       21.99        34.98        15.02        10.98        38.07         1.02 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A024 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        33.04        35.01        39.06        39.98         2.01 
TCGA-AA-A02J TCGA-AD-5900 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 
        5.03         0.07         4.21         0.79         5.79        27.42 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6603 TCGA-CA-5254 
        1.41        83.80        22.36        62.79        29.56         2.24 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4952 TCGA-CK-5912 
        3.29         0.07         0.33         1.35        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CM-4752 TCGA-CM-5341 
       51.32        21.99        21.14         2.93        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5864 
       22.03        22.98        30.08        16.01        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       17.03        12.00        16.04        13.02        15.02        11.01 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5541 
       13.05        11.08        11.08        10.06        12.03        11.51 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
        1.32        43.27        16.14         7.53        12.39        10.13 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-DM-A0XF TCGA-DM-A1DA 
       14.30         9.04        11.64        13.41        38.20         7.50 
TCGA-DM-A1HB TCGA-DM-A28C TCGA-DM-A28F TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
      135.65        81.37        35.97         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6808 TCGA-F4-6809 TCGA-G4-6293 TCGA-G4-6299 
        6.18         1.55        33.67        13.25       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       65.85        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6628 
       22.09        26.17        52.80 

  KRAS MUTATED KRAS WILD-TYPE 
             0              0 
  KRAS MUTATED KRAS WILD-TYPE 
        140.38         135.65 
  KRAS MUTATED KRAS WILD-TYPE 
        21.175         19.660 
[1] "0.0 - 140.4 (21.2)" "0.0 - 135.7 (19.7)"
[1] "hr=" "1.1"
D275V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KRAS MUTATED        28        1       15        60         3         1
  KRAS WILD-TYPE      36        0       10        49         5         0
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KRAS MUTATED           5          6         12         11       14         7
  KRAS WILD-TYPE        14          4         29         20       21         6
                vv
clus             STAGE IVB
  KRAS MUTATED           0
  KRAS WILD-TYPE         1
D275V3, multiclass
            clus
vv           KRAS MUTATED KRAS WILD-TYPE
  STAGE I              28             36
  STAGE IA              1              0
  STAGE II             15             10
  STAGE IIA            60             49
  STAGE IIB             3              5
  STAGE IIC             1              0
  STAGE III             5             14
  STAGE IIIA            6              4
  STAGE IIIB           12             29
  STAGE IIIC           11             20
  STAGE IV             14             21
  STAGE IVA             7              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  31 114  21
  KRAS WILD-TYPE   7  37 134  20
D275V4, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  T1            2              7
  T2           31             37
  T3          114            134
  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   112  30  27
  KRAS WILD-TYPE 108  50  39
D275V5, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  N0          112            108
  N1           30             50
  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"
D275V6, binary
                cls
clus               0   1
  KRAS MUTATED   134  20
  KRAS WILD-TYPE 149  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED    134   20
  KRAS WILD-TYPE  149   28
   clus
vv  KRAS MUTATED KRAS WILD-TYPE
  0          134            149
  1           20             28
[1] 2 2
[1] FALSE
D275V7, binary
                cls
clus               0   1
  KRAS MUTATED    70  99
  KRAS WILD-TYPE 100  98
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED     70   99
  KRAS WILD-TYPE  100   98
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  FEMALE           70            100
  MALE             99             98
[1] 2 2
[1] FALSE
D275V8, binary
                cls
clus               0   1
  KRAS MUTATED   148  20
  KRAS WILD-TYPE 169  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED    148   20
  KRAS WILD-TYPE  169   28
                               clus
vv                              KRAS MUTATED KRAS WILD-TYPE
  COLON ADENOCARCINOMA                   148            169
  COLON MUCINOUS ADENOCARCINOMA           20             28
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  KRAS MUTATED   111   1   7   9
  KRAS WILD-TYPE 146   1  15  12
D275V9, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  R0          111            146
  R1            1              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"
D275V10, 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
D275V11, 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(276) Variable = WASH1 MUTATION ANALYSIS
D276V1, survival
                 sevent
clus2               0   1
  WASH1 MUTATED     5   1
  WASH1 WILD-TYPE 277  72
  WASH1 MUTATED WASH1 WILD-TYPE 
              6             349 
  WASH1 MUTATED WASH1 WILD-TYPE 
              1              72 
$`WASH1 MUTATED`
TCGA-A6-6138 TCGA-AA-3510 TCGA-AA-3697 TCGA-CK-5913 TCGA-D5-6537 TCGA-D5-6927 
       22.52        63.98        85.05        51.32         4.80         9.44 

$`WASH1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        32.71        27.09         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       40.34        15.62        49.08        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 
       18.25         1.32        43.27        15.12        17.85        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  WASH1 MUTATED WASH1 WILD-TYPE 
            4.8             0.0 
  WASH1 MUTATED WASH1 WILD-TYPE 
          85.05          140.38 
  WASH1 MUTATED WASH1 WILD-TYPE 
          36.92           20.12 
[1] "4.8 - 85.0 (36.9)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "2"  
D276V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  WASH1 MUTATED         2        0        1         2         0         0
  WASH1 WILD-TYPE      62        1       24       107         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  WASH1 MUTATED           1          0          1          0        0         0
  WASH1 WILD-TYPE        18         10         40         31       35        13
                 vv
clus              STAGE IVB
  WASH1 MUTATED           0
  WASH1 WILD-TYPE         1
D276V3, multiclass
            clus
vv           WASH1 MUTATED WASH1 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              2             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  WASH1 MUTATED     0   2   5   0
  WASH1 WILD-TYPE   9  66 243  41
D276V4, multiclass
    clus
vv   WASH1 MUTATED WASH1 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             5             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
  WASH1 MUTATED     6   1   0
  WASH1 WILD-TYPE 214  79  66
D276V5, multiclass
    clus
vv   WASH1 MUTATED WASH1 WILD-TYPE
  N0             6             214
  N1             1              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"
D276V6, binary
                 cls
clus                0   1
  WASH1 MUTATED     4   0
  WASH1 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WASH1 MUTATED      4    0
  WASH1 WILD-TYPE  279   48
   clus
vv  WASH1 MUTATED WASH1 WILD-TYPE
  0             4             279
  1             0              48
[1] 2 2
[1] FALSE
D276V7, binary
                 cls
clus                0   1
  WASH1 MUTATED     1   6
  WASH1 WILD-TYPE 169 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WASH1 MUTATED      1    6
  WASH1 WILD-TYPE  169  191
        clus
vv       WASH1 MUTATED WASH1 WILD-TYPE
  FEMALE             1             169
  MALE               6             191
[1] 2 2
[1] FALSE
D276V8, binary
                 cls
clus                0   1
  WASH1 MUTATED     7   0
  WASH1 WILD-TYPE 310  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WASH1 MUTATED      7    0
  WASH1 WILD-TYPE  310   48
                               clus
vv                              WASH1 MUTATED WASH1 WILD-TYPE
  COLON ADENOCARCINOMA                      7             310
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  WASH1 MUTATED     4   0   0   2
  WASH1 WILD-TYPE 253   2  22  19
D276V9, multiclass
    clus
vv   WASH1 MUTATED WASH1 WILD-TYPE
  R0             4             253
  R1             0               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"
D276V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  WASH1 MUTATED                                  0     0
  WASH1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  WASH1 MUTATED                           0     5
  WASH1 WILD-TYPE                        19   171
D276V11, multiclass
                                  clus
vv                                 WASH1 MUTATED WASH1 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(277) Variable = ZNF189 MUTATION ANALYSIS
D277V1, survival
                  sevent
clus2                0   1
  ZNF189 MUTATED    17   0
  ZNF189 WILD-TYPE 265  73
  ZNF189 MUTATED ZNF189 WILD-TYPE 
              17              338 
  ZNF189 MUTATED ZNF189 WILD-TYPE 
               0               73 
$`ZNF189 MUTATED`
TCGA-A6-5659 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3815 TCGA-AD-5900 
       30.44        22.06        19.66        63.98        33.04         0.07 
TCGA-AZ-4315 TCGA-AZ-4681 TCGA-CA-6716 TCGA-CA-6717 TCGA-CM-6164 TCGA-CM-6168 
       58.39        83.80         0.26         0.33        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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         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        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 
       12.00        14.04        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       13.51        11.51        20.19         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 
       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-D5-6927 TCGA-D5-6928 
       12.39        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-A0X9 
       13.41         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.72        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  ZNF189 MUTATED ZNF189 WILD-TYPE 
            0.07             0.00 
  ZNF189 MUTATED ZNF189 WILD-TYPE 
           83.80           140.38 
  ZNF189 MUTATED ZNF189 WILD-TYPE 
          19.660           20.235 
[1] "0.1 - 83.8 (19.7)"  "0.0 - 140.4 (20.2)"
[1] "hr="     "2.6e+07"
D277V2, 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       24        99         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF189 MUTATED           0          1          1          2        0
  ZNF189 WILD-TYPE        19          9         40         29       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF189 MUTATED           0         0
  ZNF189 WILD-TYPE        13         1
D277V3, multiclass
            clus
vv           ZNF189 MUTATED ZNF189 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA              10               99
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              1                9
  STAGE IIIB              1               40
  STAGE IIIC              2               29
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF189 MUTATED     0   2  13   2
  ZNF189 WILD-TYPE   9  66 235  39
D277V4, multiclass
    clus
vv   ZNF189 MUTATED ZNF189 WILD-TYPE
  T1              0                9
  T2              2               66
  T3             13              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
  ZNF189 MUTATED    13   3   1
  ZNF189 WILD-TYPE 207  77  65
D277V5, multiclass
    clus
vv   ZNF189 MUTATED ZNF189 WILD-TYPE
  N0             13              207
  N1              3               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"
D277V6, binary
                  cls
clus                 0   1
  ZNF189 MUTATED    14   0
  ZNF189 WILD-TYPE 269  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF189 MUTATED     14    0
  ZNF189 WILD-TYPE  269   48
   clus
vv  ZNF189 MUTATED ZNF189 WILD-TYPE
  0             14              269
  1              0               48
[1] 2 2
[1] FALSE
D277V7, 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
D277V8, binary
                  cls
clus                 0   1
  ZNF189 MUTATED    14   3
  ZNF189 WILD-TYPE 303  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF189 MUTATED     14    3
  ZNF189 WILD-TYPE  303   45
                               clus
vv                              ZNF189 MUTATED ZNF189 WILD-TYPE
  COLON ADENOCARCINOMA                      14              303
  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 242   2  22  19
D277V9, multiclass
    clus
vv   ZNF189 MUTATED ZNF189 WILD-TYPE
  R0             15              242
  R1              0                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"
D277V10, 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
D277V11, 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(278) Variable = ZNF438 MUTATION ANALYSIS
D278V1, survival
                  sevent
clus2                0   1
  ZNF438 MUTATED     7   3
  ZNF438 WILD-TYPE 275  70
  ZNF438 MUTATED ZNF438 WILD-TYPE 
              10              345 
  ZNF438 MUTATED ZNF438 WILD-TYPE 
               3               70 
$`ZNF438 MUTATED`
TCGA-A6-2671 TCGA-A6-6137 TCGA-AA-3845 TCGA-AA-A00N TCGA-CA-6717 TCGA-CK-4952 
       43.76        27.09         0.00         4.01         0.33        15.62 
TCGA-CM-6167 TCGA-D5-6541 TCGA-D5-6927 TCGA-G4-6588 
       14.99        15.58         9.44        26.17 

$`ZNF438 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02        14.93        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 
        0.10         1.35        17.56       102.44        40.34        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  ZNF438 MUTATED ZNF438 WILD-TYPE 
               0                0 
  ZNF438 MUTATED ZNF438 WILD-TYPE 
           43.76           140.38 
  ZNF438 MUTATED ZNF438 WILD-TYPE 
          15.285           20.980 
[1] "0.0 - 43.8 (15.3)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "2.3"
D278V2, 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       25       104         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF438 MUTATED           2          0          1          1        1
  ZNF438 WILD-TYPE        17         10         40         30       34
                  vv
clus               STAGE IVA STAGE IVB
  ZNF438 MUTATED           0         0
  ZNF438 WILD-TYPE        13         1
D278V3, multiclass
            clus
vv           ZNF438 MUTATED ZNF438 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               5              104
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               2               17
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              1               30
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF438 MUTATED     0   1   9   2
  ZNF438 WILD-TYPE   9  67 239  39
D278V4, multiclass
    clus
vv   ZNF438 MUTATED ZNF438 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              9              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
  ZNF438 MUTATED     7   1   4
  ZNF438 WILD-TYPE 213  79  62
D278V5, multiclass
    clus
vv   ZNF438 MUTATED ZNF438 WILD-TYPE
  N0              7              213
  N1              1               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"
D278V6, binary
                  cls
clus                 0   1
  ZNF438 MUTATED    10   1
  ZNF438 WILD-TYPE 273  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF438 MUTATED     10    1
  ZNF438 WILD-TYPE  273   47
   clus
vv  ZNF438 MUTATED ZNF438 WILD-TYPE
  0             10              273
  1              1               47
[1] 2 2
[1] FALSE
D278V7, 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
D278V8, binary
                  cls
clus                 0   1
  ZNF438 MUTATED     9   3
  ZNF438 WILD-TYPE 308  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF438 MUTATED      9    3
  ZNF438 WILD-TYPE  308   45
                               clus
vv                              ZNF438 MUTATED ZNF438 WILD-TYPE
  COLON ADENOCARCINOMA                       9              308
  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 249   2  22  18
D278V9, multiclass
    clus
vv   ZNF438 MUTATED ZNF438 WILD-TYPE
  R0              8              249
  R1              0                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"
D278V10, 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
D278V11, 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(279) Variable = WNK1 MUTATION ANALYSIS
D279V1, survival
                sevent
clus2              0   1
  WNK1 MUTATED    18   4
  WNK1 WILD-TYPE 264  69
  WNK1 MUTATED WNK1 WILD-TYPE 
            22            333 
  WNK1 MUTATED WNK1 WILD-TYPE 
             4             69 
$`WNK1 MUTATED`
TCGA-A6-5661 TCGA-A6-6648 TCGA-AA-3655 TCGA-AA-3815 TCGA-AA-3845 TCGA-AA-3977 
       33.53        25.18        61.02        33.04         0.00        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-6895 TCGA-AZ-4315 TCGA-AZ-6598 
        4.01        34.98        35.01         0.72        58.39        49.41 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-6717 TCGA-CM-5861 TCGA-CM-6168 TCGA-CM-6677 
        1.94         2.24         0.33        15.02        12.99        11.08 
TCGA-D5-6535 TCGA-DM-A28K TCGA-F4-6806 TCGA-G4-6588 
       15.12        98.24        29.59        26.17 

$`WNK1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02        14.93        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41         6.77        12.10       100.01        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         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 
      119.93        35.97        60.79       117.07         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 
       13.45         6.18        35.87         1.55        16.31        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  WNK1 MUTATED WNK1 WILD-TYPE 
             0              0 
  WNK1 MUTATED WNK1 WILD-TYPE 
         98.24         140.38 
  WNK1 MUTATED WNK1 WILD-TYPE 
         25.10          20.12 
[1] "0.0 - 98.2 (25.1)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.1"
D279V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  WNK1 MUTATED         2        0        2        11         2         0
  WNK1 WILD-TYPE      62        1       23        98         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  WNK1 MUTATED           1          1          1          0        0         1
  WNK1 WILD-TYPE        18          9         40         31       35        12
                vv
clus             STAGE IVB
  WNK1 MUTATED           0
  WNK1 WILD-TYPE         1
D279V3, multiclass
            clus
vv           WNK1 MUTATED WNK1 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA            11             98
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            1              9
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  17   2
  WNK1 WILD-TYPE   9  64 231  39
D279V4, multiclass
    clus
vv   WNK1 MUTATED WNK1 WILD-TYPE
  T1            0              9
  T2            4             64
  T3           17            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
  WNK1 MUTATED    19   3   1
  WNK1 WILD-TYPE 201  77  65
D279V5, multiclass
    clus
vv   WNK1 MUTATED WNK1 WILD-TYPE
  N0           19            201
  N1            3             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"
D279V6, binary
                cls
clus               0   1
  WNK1 MUTATED    17   1
  WNK1 WILD-TYPE 266  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNK1 MUTATED     17    1
  WNK1 WILD-TYPE  266   47
   clus
vv  WNK1 MUTATED WNK1 WILD-TYPE
  0           17            266
  1            1             47
[1] 2 2
[1] FALSE
D279V7, binary
                cls
clus               0   1
  WNK1 MUTATED    13  10
  WNK1 WILD-TYPE 157 187
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNK1 MUTATED     13   10
  WNK1 WILD-TYPE  157  187
        clus
vv       WNK1 MUTATED WNK1 WILD-TYPE
  FEMALE           13            157
  MALE             10            187
[1] 2 2
[1] FALSE
D279V8, binary
                cls
clus               0   1
  WNK1 MUTATED    19   4
  WNK1 WILD-TYPE 298  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNK1 MUTATED     19    4
  WNK1 WILD-TYPE  298   44
                               clus
vv                              WNK1 MUTATED WNK1 WILD-TYPE
  COLON ADENOCARCINOMA                    19            298
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  WNK1 MUTATED    13   0   0   4
  WNK1 WILD-TYPE 244   2  22  17
D279V9, multiclass
    clus
vv   WNK1 MUTATED WNK1 WILD-TYPE
  R0           13            244
  R1            0              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"
D279V10, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  WNK1 MUTATED                                  0     2
  WNK1 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  WNK1 MUTATED                           2    12
  WNK1 WILD-TYPE                        17   164
D279V11, multiclass
                                  clus
vv                                 WNK1 MUTATED WNK1 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(280) Variable = GATA3 MUTATION ANALYSIS
D280V1, survival
                 sevent
clus2               0   1
  GATA3 MUTATED     9   4
  GATA3 WILD-TYPE 273  69
  GATA3 MUTATED GATA3 WILD-TYPE 
             13             342 
  GATA3 MUTATED GATA3 WILD-TYPE 
              4              69 
$`GATA3 MUTATED`
TCGA-A6-5665 TCGA-A6-6141 TCGA-AA-3492 TCGA-AA-3821 TCGA-AA-3930 TCGA-AA-A00Q 
       22.06         8.38         3.02         1.02         2.01        42.02 
TCGA-AD-6895 TCGA-AD-6901 TCGA-AY-6197 TCGA-AZ-6601 TCGA-DM-A0X9 TCGA-G4-6293 
        0.72        22.42        21.44       100.01       119.70       107.67 
TCGA-G4-6307 
       55.04 

$`GATA3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.09        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       33.04         0.99        25.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05        31.00        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R 
       18.05        18.05        38.04         4.01        27.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 
       21.37         4.21        56.55         0.79         5.79        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       15.75         0.20        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        35.41        19.43        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  GATA3 MUTATED GATA3 WILD-TYPE 
           0.72            0.00 
  GATA3 MUTATED GATA3 WILD-TYPE 
         119.70          140.38 
  GATA3 MUTATED GATA3 WILD-TYPE 
          22.06           20.07 
[1] "0.7 - 119.7 (22.1)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1"  
D280V2, 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       23       105         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GATA3 MUTATED           2          0          2          0        1         0
  GATA3 WILD-TYPE        17         10         39         31       34        13
                 vv
clus              STAGE IVB
  GATA3 MUTATED           0
  GATA3 WILD-TYPE         1
D280V3, multiclass
            clus
vv           GATA3 MUTATED GATA3 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              4             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GATA3 MUTATED     0   2  12   2
  GATA3 WILD-TYPE   9  66 236  39
D280V4, multiclass
    clus
vv   GATA3 MUTATED GATA3 WILD-TYPE
  T1             0               9
  T2             2              66
  T3            12             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
  GATA3 MUTATED    10   4   2
  GATA3 WILD-TYPE 210  76  64
D280V5, multiclass
    clus
vv   GATA3 MUTATED GATA3 WILD-TYPE
  N0            10             210
  N1             4              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"
D280V6, binary
                 cls
clus                0   1
  GATA3 MUTATED    10   1
  GATA3 WILD-TYPE 273  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GATA3 MUTATED     10    1
  GATA3 WILD-TYPE  273   47
   clus
vv  GATA3 MUTATED GATA3 WILD-TYPE
  0            10             273
  1             1              47
[1] 2 2
[1] FALSE
D280V7, 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
D280V8, binary
                 cls
clus                0   1
  GATA3 MUTATED    15   1
  GATA3 WILD-TYPE 302  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GATA3 MUTATED     15    1
  GATA3 WILD-TYPE  302   47
                               clus
vv                              GATA3 MUTATED GATA3 WILD-TYPE
  COLON ADENOCARCINOMA                     15             302
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  GATA3 MUTATED     8   0   1   2
  GATA3 WILD-TYPE 249   2  21  19
D280V9, multiclass
    clus
vv   GATA3 MUTATED GATA3 WILD-TYPE
  R0             8             249
  R1             0               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"
D280V10, 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
D280V11, 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(281) Variable = CATSPER1 MUTATION ANALYSIS
D281V1, survival
                    sevent
clus2                  0   1
  CATSPER1 MUTATED    11   4
  CATSPER1 WILD-TYPE 271  69
  CATSPER1 MUTATED CATSPER1 WILD-TYPE 
                15                340 
  CATSPER1 MUTATED CATSPER1 WILD-TYPE 
                 4                 69 
$`CATSPER1 MUTATED`
TCGA-A6-5666 TCGA-A6-6780 TCGA-AA-3530 TCGA-AA-3555 TCGA-AA-3710 TCGA-AA-3713 
       32.71        20.12        19.07        29.95        26.99        19.04 
TCGA-AA-3815 TCGA-AZ-5403 TCGA-AZ-6608 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6171 
       33.04        62.79         1.94        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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
        0.00        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 
        1.41         5.13        83.80        22.36        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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-6161 TCGA-CM-6162 
       16.01        15.02         5.03        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        11.38        10.26       119.70        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
      119.93        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       16.24        33.67        13.25        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  CATSPER1 MUTATED CATSPER1 WILD-TYPE 
              0.53               0.00 
  CATSPER1 MUTATED CATSPER1 WILD-TYPE 
             62.79             140.38 
  CATSPER1 MUTATED CATSPER1 WILD-TYPE 
            20.120             20.235 
[1] "0.5 - 62.8 (20.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.5"
D281V2, 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       24       102         8         0
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CATSPER1 MUTATED           0          1          1          0        1
  CATSPER1 WILD-TYPE        19          9         40         31       34
                    vv
clus                 STAGE IVA STAGE IVB
  CATSPER1 MUTATED           1         0
  CATSPER1 WILD-TYPE        12         1
D281V3, multiclass
            clus
vv           CATSPER1 MUTATED CATSPER1 WILD-TYPE
  STAGE I                   3                 61
  STAGE IA                  0                  1
  STAGE II                  1                 24
  STAGE IIA                 7                102
  STAGE IIB                 0                  8
  STAGE IIC                 1                  0
  STAGE III                 0                 19
  STAGE IIIA                1                  9
  STAGE IIIB                1                 40
  STAGE IIIC                0                 31
  STAGE IV                  1                 34
  STAGE IVA                 1                 12
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of 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  64 238  39
D281V4, multiclass
    clus
vv   CATSPER1 MUTATED CATSPER1 WILD-TYPE
  T1                0                  9
  T2                4                 64
  T3               10                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
  CATSPER1 MUTATED    13   3   0
  CATSPER1 WILD-TYPE 207  77  66
D281V5, multiclass
    clus
vv   CATSPER1 MUTATED CATSPER1 WILD-TYPE
  N0               13                207
  N1                3                 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"
D281V6, binary
                    cls
clus                   0   1
  CATSPER1 MUTATED    12   2
  CATSPER1 WILD-TYPE 271  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CATSPER1 MUTATED     12    2
  CATSPER1 WILD-TYPE  271   46
   clus
vv  CATSPER1 MUTATED CATSPER1 WILD-TYPE
  0               12                271
  1                2                 46
[1] 2 2
[1] FALSE
D281V7, 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
D281V8, binary
                    cls
clus                   0   1
  CATSPER1 MUTATED    14   2
  CATSPER1 WILD-TYPE 303  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CATSPER1 MUTATED     14    2
  CATSPER1 WILD-TYPE  303   46
                               clus
vv                              CATSPER1 MUTATED CATSPER1 WILD-TYPE
  COLON ADENOCARCINOMA                        14                303
  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 248   2  21  21
D281V9, multiclass
    clus
vv   CATSPER1 MUTATED CATSPER1 WILD-TYPE
  R0                9                248
  R1                0                  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"
D281V10, 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
D281V11, 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(282) Variable = C14ORF102 MUTATION ANALYSIS
D282V1, survival
                     sevent
clus2                   0   1
  C14ORF102 MUTATED    13   4
  C14ORF102 WILD-TYPE 269  69
  C14ORF102 MUTATED C14ORF102 WILD-TYPE 
                 17                 338 
  C14ORF102 MUTATED C14ORF102 WILD-TYPE 
                  4                  69 
$`C14ORF102 MUTATED`
TCGA-A6-5661 TCGA-A6-5664 TCGA-AA-3516 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3815 
       33.53        22.09        13.02         6.97        54.02        33.04 
TCGA-AA-A00J TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6716 TCGA-CA-6717 
       18.05        34.98        58.39        49.41         0.26         0.33 
TCGA-CA-6718 TCGA-CM-6171 TCGA-D5-6537 TCGA-F4-6459 TCGA-G4-6310 
        0.10        14.04         4.80         8.61        45.11 

$`C14ORF102 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5665 
       32.91        31.63        30.44        29.19        23.61        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3667 
       19.99        61.02        78.08         6.05         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       19.04        19.04        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6719 
        2.24         3.06         3.25         3.29         0.07         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79       117.07        98.24        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        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        51.75        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  C14ORF102 MUTATED C14ORF102 WILD-TYPE 
                0.1                 0.0 
  C14ORF102 MUTATED C14ORF102 WILD-TYPE 
              58.39              140.38 
  C14ORF102 MUTATED C14ORF102 WILD-TYPE 
             18.050              20.235 
[1] "0.1 - 58.4 (18.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.3"
D282V2, 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       22       103         7         1
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C14ORF102 MUTATED           1          0          4          1        0
  C14ORF102 WILD-TYPE        18         10         37         30       35
                     vv
clus                  STAGE IVA STAGE IVB
  C14ORF102 MUTATED           0         0
  C14ORF102 WILD-TYPE        13         1
D282V3, multiclass
            clus
vv           C14ORF102 MUTATED C14ORF102 WILD-TYPE
  STAGE I                    1                  63
  STAGE IA                   0                   1
  STAGE II                   3                  22
  STAGE IIA                  6                 103
  STAGE IIB                  1                   7
  STAGE IIC                  0                   1
  STAGE III                  1                  18
  STAGE IIIA                 0                  10
  STAGE IIIB                 4                  37
  STAGE IIIC                 1                  30
  STAGE IV                   0                  35
  STAGE IVA                  0                  13
  STAGE IVB                  0                   1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2  T3  T4
  C14ORF102 MUTATED     0   1  13   3
  C14ORF102 WILD-TYPE   9  67 235  38
D282V4, multiclass
    clus
vv   C14ORF102 MUTATED C14ORF102 WILD-TYPE
  T1                 0                   9
  T2                 1                  67
  T3                13                 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
  C14ORF102 MUTATED    11   3   3
  C14ORF102 WILD-TYPE 209  77  63
D282V5, multiclass
    clus
vv   C14ORF102 MUTATED C14ORF102 WILD-TYPE
  N0                11                 209
  N1                 3                  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"
D282V6, binary
                     cls
clus                    0   1
  C14ORF102 MUTATED    14   0
  C14ORF102 WILD-TYPE 269  48
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF102 MUTATED     14    0
  C14ORF102 WILD-TYPE  269   48
   clus
vv  C14ORF102 MUTATED C14ORF102 WILD-TYPE
  0                14                 269
  1                 0                  48
[1] 2 2
[1] FALSE
D282V7, 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
D282V8, binary
                     cls
clus                    0   1
  C14ORF102 MUTATED    14   3
  C14ORF102 WILD-TYPE 303  45
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF102 MUTATED     14    3
  C14ORF102 WILD-TYPE  303   45
                               clus
vv                              C14ORF102 MUTATED C14ORF102 WILD-TYPE
  COLON ADENOCARCINOMA                         14                 303
  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 246   2  22  18
D282V9, multiclass
    clus
vv   C14ORF102 MUTATED C14ORF102 WILD-TYPE
  R0                11                 246
  R1                 0                   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"
D282V10, 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
D282V11, 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(283) Variable = RBM7 MUTATION ANALYSIS
D283V1, survival
                sevent
clus2              0   1
  RBM7 MUTATED     6   4
  RBM7 WILD-TYPE 276  69
  RBM7 MUTATED RBM7 WILD-TYPE 
            10            345 
  RBM7 MUTATED RBM7 WILD-TYPE 
             4             69 
$`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         0.33 
TCGA-CK-4952 TCGA-CM-6678 TCGA-D5-6535 TCGA-G4-6303 
       15.62        11.01        15.12        65.85 

$`RBM7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
        1.02        17.98        15.95        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41        49.41        12.10 
TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
      100.01         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 
        1.35        17.56       102.44        40.34        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 
       11.51        20.19        18.25         1.32        43.27        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  RBM7 MUTATED RBM7 WILD-TYPE 
          0.33           0.00 
  RBM7 MUTATED RBM7 WILD-TYPE 
         65.85         140.38 
  RBM7 MUTATED RBM7 WILD-TYPE 
         15.37          20.28 
[1] "0.3 - 65.8 (15.4)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "2"  
D283V2, 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       25       106         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RBM7 MUTATED           1          0          1          0        1         1
  RBM7 WILD-TYPE        18         10         40         31       34        12
                vv
clus             STAGE IVB
  RBM7 MUTATED           0
  RBM7 WILD-TYPE         1
D283V3, multiclass
            clus
vv           RBM7 MUTATED RBM7 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             3            106
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 243  38
D283V4, multiclass
    clus
vv   RBM7 MUTATED RBM7 WILD-TYPE
  T1            0              9
  T2            2             66
  T3            5            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
  RBM7 MUTATED     5   4   1
  RBM7 WILD-TYPE 215  76  65
D283V5, multiclass
    clus
vv   RBM7 MUTATED RBM7 WILD-TYPE
  N0            5            215
  N1            4             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"
D283V6, binary
                cls
clus               0   1
  RBM7 MUTATED     5   2
  RBM7 WILD-TYPE 278  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBM7 MUTATED      5    2
  RBM7 WILD-TYPE  278   46
   clus
vv  RBM7 MUTATED RBM7 WILD-TYPE
  0            5            278
  1            2             46
[1] 2 2
[1] FALSE
D283V7, 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
D283V8, binary
                cls
clus               0   1
  RBM7 MUTATED     6   4
  RBM7 WILD-TYPE 311  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBM7 MUTATED      6    4
  RBM7 WILD-TYPE  311   44
                               clus
vv                              RBM7 MUTATED RBM7 WILD-TYPE
  COLON ADENOCARCINOMA                     6            311
  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 252   2  22  18
D283V9, multiclass
    clus
vv   RBM7 MUTATED RBM7 WILD-TYPE
  R0            5            252
  R1            0              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"
D283V10, 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
D283V11, 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(284) Variable = GMCL1 MUTATION ANALYSIS
D284V1, survival
                 sevent
clus2               0   1
  GMCL1 MUTATED     7   2
  GMCL1 WILD-TYPE 275  71
  GMCL1 MUTATED GMCL1 WILD-TYPE 
              9             346 
  GMCL1 MUTATED GMCL1 WILD-TYPE 
              2              71 
$`GMCL1 MUTATED`
TCGA-AD-6548 TCGA-AZ-4315 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-CM-5863 TCGA-CM-6161 
       21.37        58.39       100.01         5.23        15.02        15.02 
TCGA-DM-A1D9 TCGA-G4-6307 TCGA-G4-6625 
      140.38        55.04        91.79 

$`GMCL1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
        6.77        12.10        29.56        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA 
      130.65        92.75        49.91        13.32        12.59         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        46.75        52.80 

  GMCL1 MUTATED GMCL1 WILD-TYPE 
           5.23            0.00 
  GMCL1 MUTATED GMCL1 WILD-TYPE 
         140.38          139.17 
  GMCL1 MUTATED GMCL1 WILD-TYPE 
          55.04           20.07 
[1] "5.2 - 140.4 (55.0)" "0.0 - 139.2 (20.1)"
[1] "hr=" "1.9"
D284V2, 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       24       106         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        19         10         38         31       35        13
                 vv
clus              STAGE IVB
  GMCL1 MUTATED           0
  GMCL1 WILD-TYPE         1
D284V3, multiclass
            clus
vv           GMCL1 MUTATED GMCL1 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              3             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             3              38
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GMCL1 MUTATED     0   2   6   2
  GMCL1 WILD-TYPE   9  66 242  39
D284V4, multiclass
    clus
vv   GMCL1 MUTATED GMCL1 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             6             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
  GMCL1 MUTATED     7   3   0
  GMCL1 WILD-TYPE 213  77  66
D284V5, multiclass
    clus
vv   GMCL1 MUTATED GMCL1 WILD-TYPE
  N0             7             213
  N1             3              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"
D284V6, binary
                 cls
clus                0   1
  GMCL1 MUTATED     9   0
  GMCL1 WILD-TYPE 274  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GMCL1 MUTATED      9    0
  GMCL1 WILD-TYPE  274   48
   clus
vv  GMCL1 MUTATED GMCL1 WILD-TYPE
  0             9             274
  1             0              48
[1] 2 2
[1] FALSE
D284V7, 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
D284V8, binary
                 cls
clus                0   1
  GMCL1 MUTATED     9   1
  GMCL1 WILD-TYPE 308  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GMCL1 MUTATED      9    1
  GMCL1 WILD-TYPE  308   47
                               clus
vv                              GMCL1 MUTATED GMCL1 WILD-TYPE
  COLON ADENOCARCINOMA                      9             308
  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 251   2  22  20
D284V9, multiclass
    clus
vv   GMCL1 MUTATED GMCL1 WILD-TYPE
  R0             6             251
  R1             0               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"
D284V10, 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
D284V11, 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(285) Variable = IKZF4 MUTATION ANALYSIS
D285V1, survival
                 sevent
clus2               0   1
  IKZF4 MUTATED     9   3
  IKZF4 WILD-TYPE 273  70
  IKZF4 MUTATED IKZF4 WILD-TYPE 
             12             343 
  IKZF4 MUTATED IKZF4 WILD-TYPE 
              3              70 
$`IKZF4 MUTATED`
TCGA-A6-6141 TCGA-A6-6654 TCGA-AA-3977 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-6600 
        8.38        23.87        25.02        21.44        17.82        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-CK-5914 TCGA-CM-5861 TCGA-D5-6924 TCGA-G4-6306 
      100.01        29.56        21.99        15.02        14.30        44.68 

$`IKZF4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
        0.20        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6605 TCGA-AZ-6606 
       62.79        61.41        49.41         6.77         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 
      102.44        40.34        15.62        49.08        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  IKZF4 MUTATED IKZF4 WILD-TYPE 
           8.38            0.00 
  IKZF4 MUTATED IKZF4 WILD-TYPE 
         100.01          140.38 
  IKZF4 MUTATED IKZF4 WILD-TYPE 
         21.715          20.120 
[1] "8.4 - 100.0 (21.7)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.1"
D285V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IKZF4 MUTATED         0        0        1         5         0         0
  IKZF4 WILD-TYPE      64        1       24       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        18         10         38         31       34        13
                 vv
clus              STAGE IVB
  IKZF4 MUTATED           0
  IKZF4 WILD-TYPE         1
D285V3, multiclass
            clus
vv           IKZF4 MUTATED IKZF4 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              5             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             3              38
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  IKZF4 MUTATED     0   3   9   1
  IKZF4 WILD-TYPE   9  65 239  40
D285V4, multiclass
    clus
vv   IKZF4 MUTATED IKZF4 WILD-TYPE
  T1             0               9
  T2             3              65
  T3             9             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
  IKZF4 MUTATED     7   5   1
  IKZF4 WILD-TYPE 213  75  65
D285V5, multiclass
    clus
vv   IKZF4 MUTATED IKZF4 WILD-TYPE
  N0             7             213
  N1             5              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"
D285V6, binary
                 cls
clus                0   1
  IKZF4 MUTATED     8   1
  IKZF4 WILD-TYPE 275  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IKZF4 MUTATED      8    1
  IKZF4 WILD-TYPE  275   47
   clus
vv  IKZF4 MUTATED IKZF4 WILD-TYPE
  0             8             275
  1             1              47
[1] 2 2
[1] FALSE
D285V7, 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
D285V8, binary
                 cls
clus                0   1
  IKZF4 MUTATED    13   0
  IKZF4 WILD-TYPE 304  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IKZF4 MUTATED     13    0
  IKZF4 WILD-TYPE  304   48
                               clus
vv                              IKZF4 MUTATED IKZF4 WILD-TYPE
  COLON ADENOCARCINOMA                     13             304
  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 251   2  22  20
D285V9, multiclass
    clus
vv   IKZF4 MUTATED IKZF4 WILD-TYPE
  R0             6             251
  R1             0               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"
D285V10, 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
D285V11, 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(286) Variable = ANKRD50 MUTATION ANALYSIS
D286V1, survival
                   sevent
clus2                 0   1
  ANKRD50 MUTATED     7   7
  ANKRD50 WILD-TYPE 275  66
  ANKRD50 MUTATED ANKRD50 WILD-TYPE 
               14               341 
  ANKRD50 MUTATED ANKRD50 WILD-TYPE 
                7                66 
$`ANKRD50 MUTATED`
TCGA-AA-3492 TCGA-AA-3516 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3977 TCGA-AA-A00E 
        3.02        13.02        19.04        19.04        25.02        30.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01P TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CK-4948 
        4.01        34.98        38.07        49.41       100.01       102.44 
TCGA-CM-6171 TCGA-DM-A1HB 
       14.04       135.65 

$`ANKRD50 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.03        85.05        26.99        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J 
       27.02        13.94        38.04        19.00        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        0.10         1.35        17.56        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  ANKRD50 MUTATED ANKRD50 WILD-TYPE 
             3.02              0.00 
  ANKRD50 MUTATED ANKRD50 WILD-TYPE 
           135.65            140.38 
  ANKRD50 MUTATED ANKRD50 WILD-TYPE 
            27.52             20.12 
[1] "3.0 - 135.7 (27.5)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.7"
D286V2, 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       20       108         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANKRD50 MUTATED           2          1          1          0        1
  ANKRD50 WILD-TYPE        17          9         40         31       34
                   vv
clus                STAGE IVA STAGE IVB
  ANKRD50 MUTATED           0         0
  ANKRD50 WILD-TYPE        13         1
D286V3, multiclass
            clus
vv           ANKRD50 MUTATED ANKRD50 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 5                20
  STAGE IIA                1               108
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                2                17
  STAGE IIIA               1                 9
  STAGE IIIB               1                40
  STAGE IIIC               0                31
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ANKRD50 MUTATED     0   2  10   3
  ANKRD50 WILD-TYPE   9  66 238  38
D286V4, multiclass
    clus
vv   ANKRD50 MUTATED ANKRD50 WILD-TYPE
  T1               0                 9
  T2               2                66
  T3              10               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
  ANKRD50 MUTATED    11   3   1
  ANKRD50 WILD-TYPE 209  77  65
D286V5, multiclass
    clus
vv   ANKRD50 MUTATED ANKRD50 WILD-TYPE
  N0              11               209
  N1               3                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"
D286V6, binary
                   cls
clus                  0   1
  ANKRD50 MUTATED    12   1
  ANKRD50 WILD-TYPE 271  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD50 MUTATED     12    1
  ANKRD50 WILD-TYPE  271   47
   clus
vv  ANKRD50 MUTATED ANKRD50 WILD-TYPE
  0              12               271
  1               1                47
[1] 2 2
[1] FALSE
D286V7, 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
D286V8, binary
                   cls
clus                  0   1
  ANKRD50 MUTATED    13   2
  ANKRD50 WILD-TYPE 304  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD50 MUTATED     13    2
  ANKRD50 WILD-TYPE  304   46
                               clus
vv                              ANKRD50 MUTATED ANKRD50 WILD-TYPE
  COLON ADENOCARCINOMA                       13               304
  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 248   2  21  21
D286V9, multiclass
    clus
vv   ANKRD50 MUTATED ANKRD50 WILD-TYPE
  R0               9               248
  R1               0                 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"
D286V10, 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
D286V11, 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(287) Variable = LHCGR MUTATION ANALYSIS
D287V1, survival
                 sevent
clus2               0   1
  LHCGR MUTATED    19   4
  LHCGR WILD-TYPE 263  69
  LHCGR MUTATED LHCGR WILD-TYPE 
             23             332 
  LHCGR MUTATED LHCGR WILD-TYPE 
              4              69 
$`LHCGR MUTATED`
TCGA-A6-3808 TCGA-AA-3510 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-A00O TCGA-AA-A029 
       33.34        63.98        61.02         6.05        27.02        51.98 
TCGA-AD-6965 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-CA-6716 TCGA-CA-6717 
        0.20        58.39        49.41         6.77         0.26         0.33 
TCGA-CA-6718 TCGA-CK-6748 TCGA-CM-5344 TCGA-CM-5860 TCGA-CM-6166 TCGA-D5-6541 
        0.10         2.01        22.03        16.01        21.99        15.58 
TCGA-D5-6932 TCGA-DM-A28G TCGA-F4-6570 TCGA-F4-6807 TCGA-G4-6586 
       11.38        60.79         6.18        16.24        35.80 

$`LHCGR WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        19.99        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04         4.01        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       37.02        39.06        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        10.88        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 
        5.13        83.80        22.36        62.79        61.41        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6719 
        2.24         3.06         3.25         3.29         0.07         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99        21.14         2.93       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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        16.14         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         1.51 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
      119.93        35.97       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 
       13.45        35.87         1.55        16.31        29.59        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  LHCGR MUTATED LHCGR WILD-TYPE 
            0.1             0.0 
  LHCGR MUTATED LHCGR WILD-TYPE 
          63.98          140.38 
  LHCGR MUTATED LHCGR WILD-TYPE 
         16.240          20.235 
[1] "0.1 - 64.0 (16.2)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D287V2, 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       21        97         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LHCGR MUTATED           0          0          1          2        2         0
  LHCGR WILD-TYPE        19         10         40         29       33        13
                 vv
clus              STAGE IVB
  LHCGR MUTATED           0
  LHCGR WILD-TYPE         1
D287V3, multiclass
            clus
vv           LHCGR MUTATED LHCGR WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               4              21
  STAGE IIA             12              97
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             2              29
  STAGE IV               2              33
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LHCGR MUTATED     0   2  20   2
  LHCGR WILD-TYPE   9  66 228  39
D287V4, multiclass
    clus
vv   LHCGR MUTATED LHCGR WILD-TYPE
  T1             0               9
  T2             2              66
  T3            20             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
  LHCGR MUTATED    18   2   4
  LHCGR WILD-TYPE 202  78  62
D287V5, multiclass
    clus
vv   LHCGR MUTATED LHCGR WILD-TYPE
  N0            18             202
  N1             2              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"
D287V6, binary
                 cls
clus                0   1
  LHCGR MUTATED    19   2
  LHCGR WILD-TYPE 264  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LHCGR MUTATED     19    2
  LHCGR WILD-TYPE  264   46
   clus
vv  LHCGR MUTATED LHCGR WILD-TYPE
  0            19             264
  1             2              46
[1] 2 2
[1] FALSE
D287V7, 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
D287V8, binary
                 cls
clus                0   1
  LHCGR MUTATED    22   2
  LHCGR WILD-TYPE 295  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LHCGR MUTATED     22    2
  LHCGR WILD-TYPE  295   46
                               clus
vv                              LHCGR MUTATED LHCGR WILD-TYPE
  COLON ADENOCARCINOMA                     22             295
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  LHCGR MUTATED    15   0   1   4
  LHCGR WILD-TYPE 242   2  21  17
D287V9, multiclass
    clus
vv   LHCGR MUTATED LHCGR WILD-TYPE
  R0            15             242
  R1             0               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"
D287V10, 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
D287V11, 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(288) Variable = RUNX1 MUTATION ANALYSIS
D288V1, survival
                 sevent
clus2               0   1
  RUNX1 MUTATED    29   7
  RUNX1 WILD-TYPE 253  66
  RUNX1 MUTATED RUNX1 WILD-TYPE 
             36             319 
  RUNX1 MUTATED RUNX1 WILD-TYPE 
              7              66 
$`RUNX1 MUTATED`
TCGA-A6-4105 TCGA-A6-5657 TCGA-A6-6781 TCGA-AA-3672 TCGA-AA-3697 TCGA-AA-3713 
       14.53        31.63        19.66         0.92        85.05        19.04 
TCGA-AA-3818 TCGA-AA-3861 TCGA-AA-3950 TCGA-AA-A01T TCGA-AD-6889 TCGA-AY-5543 
        0.99        30.05        24.00        33.04        56.55        15.75 
TCGA-AZ-4315 TCGA-AZ-4681 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6603 TCGA-CK-4950 
       58.39        83.80        49.41         6.77        29.56        40.34 
TCGA-CK-4952 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-6168 TCGA-CM-6171 
       15.62        30.08        16.01        15.02        12.99        14.04 
TCGA-D5-6533 TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6569 
        1.32        44.32       135.65       117.07        98.24        13.45 
TCGA-G4-6293 TCGA-G4-6304 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6628 
      107.67        53.62        36.00        13.78        46.75        52.80 

$`RUNX1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 
        5.98        37.05        19.00        36.00         5.03        26.99 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3819 TCGA-AA-3821 
       19.04        10.06        35.05        33.04        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A01V 
       31.00        38.07         1.02        35.01         1.02        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37         4.21         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       27.09        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-6600 
        1.41         5.13        22.36        62.79        61.41        12.10 
TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
      100.01         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-5913 
        0.10         1.35        17.56       102.44        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 
       19.59        13.51        11.51        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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       60.79         8.61        13.38         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 
       35.41        19.43        74.56        65.85        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       51.75        45.11        36.72        22.09        35.80        26.17 
TCGA-G4-6625 
       91.79 

  RUNX1 MUTATED RUNX1 WILD-TYPE 
           0.92            0.00 
  RUNX1 MUTATED RUNX1 WILD-TYPE 
         135.65          140.38 
  RUNX1 MUTATED RUNX1 WILD-TYPE 
         30.065          19.990 
[1] "0.9 - 135.7 (30.1)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.7"
D288V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RUNX1 MUTATED         4        1        1        14         1         0
  RUNX1 WILD-TYPE      60        0       24        95         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RUNX1 MUTATED           6          1          3          3        1         1
  RUNX1 WILD-TYPE        13          9         38         28       34        12
                 vv
clus              STAGE IVB
  RUNX1 MUTATED           0
  RUNX1 WILD-TYPE         1
D288V3, multiclass
            clus
vv           RUNX1 MUTATED RUNX1 WILD-TYPE
  STAGE I                4              60
  STAGE IA               1               0
  STAGE II               1              24
  STAGE IIA             14              95
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              6              13
  STAGE IIIA             1               9
  STAGE IIIB             3              38
  STAGE IIIC             3              28
  STAGE IV               1              34
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  63 221  37
D288V4, multiclass
    clus
vv   RUNX1 MUTATED RUNX1 WILD-TYPE
  T1             0               9
  T2             5              63
  T3            27             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
  RUNX1 MUTATED    24   9   4
  RUNX1 WILD-TYPE 196  71  62
D288V5, multiclass
    clus
vv   RUNX1 MUTATED RUNX1 WILD-TYPE
  N0            24             196
  N1             9              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"
D288V6, binary
                 cls
clus                0   1
  RUNX1 MUTATED    29   2
  RUNX1 WILD-TYPE 254  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUNX1 MUTATED     29    2
  RUNX1 WILD-TYPE  254   46
   clus
vv  RUNX1 MUTATED RUNX1 WILD-TYPE
  0            29             254
  1             2              46
[1] 2 2
[1] FALSE
D288V7, 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
D288V8, binary
                 cls
clus                0   1
  RUNX1 MUTATED    33   4
  RUNX1 WILD-TYPE 284  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUNX1 MUTATED     33    4
  RUNX1 WILD-TYPE  284   44
                               clus
vv                              RUNX1 MUTATED RUNX1 WILD-TYPE
  COLON ADENOCARCINOMA                     33             284
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RUNX1 MUTATED    25   1   1   1
  RUNX1 WILD-TYPE 232   1  21  20
D288V9, multiclass
    clus
vv   RUNX1 MUTATED RUNX1 WILD-TYPE
  R0            25             232
  R1             1               1
  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"
D288V10, 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
D288V11, 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(289) Variable = OR51E1 MUTATION ANALYSIS
D289V1, survival
                  sevent
clus2                0   1
  OR51E1 MUTATED     9   4
  OR51E1 WILD-TYPE 273  69
  OR51E1 MUTATED OR51E1 WILD-TYPE 
              13              342 
  OR51E1 MUTATED OR51E1 WILD-TYPE 
               4               69 
$`OR51E1 MUTATED`
TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3866 TCGA-AA-3950 TCGA-AY-6197 TCGA-CK-5913 
       22.06         3.02        17.03        24.00        21.44        51.32 
TCGA-CM-5348 TCGA-CM-5862 TCGA-CM-6164 TCGA-DM-A1D7 TCGA-DM-A1HB TCGA-DM-A28F 
       22.98         5.03        29.03        13.32       135.65        35.97 
TCGA-G4-6299 
       74.56 

$`OR51E1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        53.00        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        21.99        21.14         2.93         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-5863 TCGA-CM-5864 
       22.03        30.08        16.01        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-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-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
        6.12        81.37       119.93        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.41        19.43       107.67        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  OR51E1 MUTATED OR51E1 WILD-TYPE 
            3.02             0.00 
  OR51E1 MUTATED OR51E1 WILD-TYPE 
          135.65           140.38 
  OR51E1 MUTATED OR51E1 WILD-TYPE 
          22.980           20.005 
[1] "3.0 - 135.7 (23.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.2"
D289V2, 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       24       103         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR51E1 MUTATED           0          0          3          1        0
  OR51E1 WILD-TYPE        19         10         38         30       35
                  vv
clus               STAGE IVA STAGE IVB
  OR51E1 MUTATED           1         0
  OR51E1 WILD-TYPE        12         1
D289V3, multiclass
            clus
vv           OR51E1 MUTATED OR51E1 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               6              103
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              3               38
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 236  41
D289V4, multiclass
    clus
vv   OR51E1 MUTATED OR51E1 WILD-TYPE
  T1              0                9
  T2              1               67
  T3             12              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
  OR51E1 MUTATED     8   4   1
  OR51E1 WILD-TYPE 212  76  65
D289V5, multiclass
    clus
vv   OR51E1 MUTATED OR51E1 WILD-TYPE
  N0              8              212
  N1              4               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"
D289V6, binary
                  cls
clus                 0   1
  OR51E1 MUTATED    10   1
  OR51E1 WILD-TYPE 273  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51E1 MUTATED     10    1
  OR51E1 WILD-TYPE  273   47
   clus
vv  OR51E1 MUTATED OR51E1 WILD-TYPE
  0             10              273
  1              1               47
[1] 2 2
[1] FALSE
D289V7, 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
D289V8, binary
                  cls
clus                 0   1
  OR51E1 MUTATED    12   1
  OR51E1 WILD-TYPE 305  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51E1 MUTATED     12    1
  OR51E1 WILD-TYPE  305   47
                               clus
vv                              OR51E1 MUTATED OR51E1 WILD-TYPE
  COLON ADENOCARCINOMA                      12              305
  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 248   2  22  20
D289V9, multiclass
    clus
vv   OR51E1 MUTATED OR51E1 WILD-TYPE
  R0              9              248
  R1              0                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"
D289V10, 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
D289V11, 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(290) Variable = NEXN MUTATION ANALYSIS
D290V1, survival
                sevent
clus2              0   1
  NEXN MUTATED    13   4
  NEXN WILD-TYPE 269  69
  NEXN MUTATED NEXN WILD-TYPE 
            17            338 
  NEXN MUTATED NEXN WILD-TYPE 
             4             69 
$`NEXN MUTATED`
TCGA-A6-5661 TCGA-AA-3510 TCGA-AA-3976 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01I 
       33.53        63.98        26.01         4.01        34.98        31.00 
TCGA-AZ-6603 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-6747 TCGA-CM-6171 TCGA-CM-6679 
       29.56         0.33         1.35         2.93        14.04        10.06 
TCGA-D5-6920 TCGA-DM-A285 TCGA-F4-6805 TCGA-G4-6293 TCGA-G4-6303 
       12.39         6.12        16.31       107.67        65.85 

$`NEXN WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        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        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 
       61.41        49.41         6.77        12.10       100.01         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07         0.26         0.10        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        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        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6807 
       13.45         6.18        35.87         1.55        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 
       33.67        13.25         0.53        35.41        19.43        74.56 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  NEXN MUTATED NEXN WILD-TYPE 
          0.33           0.00 
  NEXN MUTATED NEXN WILD-TYPE 
        107.67         140.38 
  NEXN MUTATED NEXN WILD-TYPE 
        16.310         20.235 
[1] "0.3 - 107.7 (16.3)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D290V2, 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       24       102         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        18          9         41         31       33        13
                vv
clus             STAGE IVB
  NEXN MUTATED           0
  NEXN WILD-TYPE         1
D290V3, multiclass
            clus
vv           NEXN MUTATED NEXN WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             7            102
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            1              9
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              2             33
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NEXN MUTATED     0   4  11   2
  NEXN WILD-TYPE   9  64 237  39
D290V4, multiclass
    clus
vv   NEXN MUTATED NEXN WILD-TYPE
  T1            0              9
  T2            4             64
  T3           11            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
  NEXN MUTATED    12   4   1
  NEXN WILD-TYPE 208  76  65
D290V5, multiclass
    clus
vv   NEXN MUTATED NEXN WILD-TYPE
  N0           12            208
  N1            4             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"
D290V6, binary
                cls
clus               0   1
  NEXN MUTATED    13   2
  NEXN WILD-TYPE 270  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEXN MUTATED     13    2
  NEXN WILD-TYPE  270   46
   clus
vv  NEXN MUTATED NEXN WILD-TYPE
  0           13            270
  1            2             46
[1] 2 2
[1] FALSE
D290V7, 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
D290V8, binary
                cls
clus               0   1
  NEXN MUTATED    14   3
  NEXN WILD-TYPE 303  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEXN MUTATED     14    3
  NEXN WILD-TYPE  303   45
                               clus
vv                              NEXN MUTATED NEXN WILD-TYPE
  COLON ADENOCARCINOMA                    14            303
  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 245   2  22  18
D290V9, multiclass
    clus
vv   NEXN MUTATED NEXN WILD-TYPE
  R0           12            245
  R1            0              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"
D290V10, 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
D290V11, 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(291) Variable = EIF4A2 MUTATION ANALYSIS
D291V1, survival
                  sevent
clus2                0   1
  EIF4A2 MUTATED     9   0
  EIF4A2 WILD-TYPE 273  73
  EIF4A2 MUTATED EIF4A2 WILD-TYPE 
               9              346 
  EIF4A2 MUTATED EIF4A2 WILD-TYPE 
               0               73 
$`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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3833 
       35.05        33.04         0.99        25.02         1.02        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        50.99        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45         6.18        35.87        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  EIF4A2 MUTATED EIF4A2 WILD-TYPE 
            1.55             0.00 
  EIF4A2 MUTATED EIF4A2 WILD-TYPE 
          135.65           140.38 
  EIF4A2 MUTATED EIF4A2 WILD-TYPE 
           15.02            20.63 
[1] "1.6 - 135.7 (15.0)" "0.0 - 140.4 (20.6)"
[1] "hr="     "2.5e+07"
D291V2, 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       25       106         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EIF4A2 MUTATED           0          0          2          1        1
  EIF4A2 WILD-TYPE        19         10         39         30       34
                  vv
clus               STAGE IVA STAGE IVB
  EIF4A2 MUTATED           0         0
  EIF4A2 WILD-TYPE        13         1
D291V3, multiclass
            clus
vv           EIF4A2 MUTATED EIF4A2 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               3              106
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              1               30
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  EIF4A2 MUTATED     0   2   6   2
  EIF4A2 WILD-TYPE   9  66 242  39
D291V4, multiclass
    clus
vv   EIF4A2 MUTATED EIF4A2 WILD-TYPE
  T1              0                9
  T2              2               66
  T3              6              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
  EIF4A2 MUTATED     6   3   1
  EIF4A2 WILD-TYPE 214  77  65
D291V5, multiclass
    clus
vv   EIF4A2 MUTATED EIF4A2 WILD-TYPE
  N0              6              214
  N1              3               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"
D291V6, binary
                  cls
clus                 0   1
  EIF4A2 MUTATED     7   1
  EIF4A2 WILD-TYPE 276  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF4A2 MUTATED      7    1
  EIF4A2 WILD-TYPE  276   47
   clus
vv  EIF4A2 MUTATED EIF4A2 WILD-TYPE
  0              7              276
  1              1               47
[1] 2 2
[1] FALSE
D291V7, 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
D291V8, binary
                  cls
clus                 0   1
  EIF4A2 MUTATED     9   1
  EIF4A2 WILD-TYPE 308  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF4A2 MUTATED      9    1
  EIF4A2 WILD-TYPE  308   47
                               clus
vv                              EIF4A2 MUTATED EIF4A2 WILD-TYPE
  COLON ADENOCARCINOMA                       9              308
  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 251   2  21  20
D291V9, multiclass
    clus
vv   EIF4A2 MUTATED EIF4A2 WILD-TYPE
  R0              6              251
  R1              0                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"
D291V10, 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
D291V11, 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(292) Variable = MYEOV MUTATION ANALYSIS
D292V1, survival
                 sevent
clus2               0   1
  MYEOV MUTATED     6   0
  MYEOV WILD-TYPE 276  73
  MYEOV MUTATED MYEOV WILD-TYPE 
              6             349 
  MYEOV MUTATED MYEOV WILD-TYPE 
              0              73 
$`MYEOV MUTATED`
TCGA-A6-5661 TCGA-AA-A00E TCGA-AD-6889 TCGA-AU-6004 TCGA-D5-6923 TCGA-G4-6588 
       33.53        30.02        56.55        27.09        12.43        26.17 

$`MYEOV WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.20        14.50        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 
       52.80 

  MYEOV MUTATED MYEOV WILD-TYPE 
          12.43            0.00 
  MYEOV MUTATED MYEOV WILD-TYPE 
          56.55          140.38 
  MYEOV MUTATED MYEOV WILD-TYPE 
         28.555          20.020 
[1] "12.4 - 56.5 (28.6)" "0.0 - 140.4 (20.0)"
[1] "hr="     "9200000"
D292V2, 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       25       105         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        19         10         41         31       35        13
                 vv
clus              STAGE IVB
  MYEOV MUTATED           0
  MYEOV WILD-TYPE         1
D292V3, multiclass
            clus
vv           MYEOV MUTATED MYEOV WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              4             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MYEOV MUTATED     0   2   4   0
  MYEOV WILD-TYPE   9  66 244  41
D292V4, multiclass
    clus
vv   MYEOV MUTATED MYEOV WILD-TYPE
  T1             0               9
  T2             2              66
  T3             4             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
  MYEOV MUTATED     6   0   0
  MYEOV WILD-TYPE 214  80  66
D292V5, multiclass
    clus
vv   MYEOV MUTATED MYEOV WILD-TYPE
  N0             6             214
  N1             0              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
  MYEOV MUTATED     6   0
  MYEOV WILD-TYPE 277  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYEOV MUTATED      6    0
  MYEOV WILD-TYPE  277   48
   clus
vv  MYEOV MUTATED MYEOV WILD-TYPE
  0             6             277
  1             0              48
[1] 2 2
[1] FALSE
D292V7, 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
D292V8, binary
                 cls
clus                0   1
  MYEOV MUTATED     6   0
  MYEOV WILD-TYPE 311  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYEOV MUTATED      6    0
  MYEOV WILD-TYPE  311   48
                               clus
vv                              MYEOV MUTATED MYEOV WILD-TYPE
  COLON ADENOCARCINOMA                      6             311
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MYEOV MUTATED     5   0   0   0
  MYEOV WILD-TYPE 252   2  22  21
D292V9, multiclass
    clus
vv   MYEOV MUTATED MYEOV WILD-TYPE
  R0             5             252
  R1             0               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"
D292V10, 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
D292V11, 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(293) Variable = IGFBP7 MUTATION ANALYSIS
D293V1, survival
                  sevent
clus2                0   1
  IGFBP7 MUTATED     4   0
  IGFBP7 WILD-TYPE 278  73
  IGFBP7 MUTATED IGFBP7 WILD-TYPE 
               4              351 
  IGFBP7 MUTATED IGFBP7 WILD-TYPE 
               0               73 
$`IGFBP7 MUTATED`
TCGA-A6-5657 TCGA-AA-3815 TCGA-D5-5541 TCGA-F4-6808 
       31.63        33.04        11.51        33.67 

$`IGFBP7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  IGFBP7 MUTATED IGFBP7 WILD-TYPE 
           11.51             0.00 
  IGFBP7 MUTATED IGFBP7 WILD-TYPE 
           33.67           140.38 
  IGFBP7 MUTATED IGFBP7 WILD-TYPE 
          32.335           20.120 
[1] "11.5 - 33.7 (32.3)" "0.0 - 140.4 (20.1)"
[1] "hr="     "9100000"
D293V2, 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       25       108         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IGFBP7 MUTATED           0          0          2          0        0
  IGFBP7 WILD-TYPE        19         10         39         31       35
                  vv
clus               STAGE IVA STAGE IVB
  IGFBP7 MUTATED           0         0
  IGFBP7 WILD-TYPE        13         1
D293V3, multiclass
            clus
vv           IGFBP7 MUTATED IGFBP7 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               1              108
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  IGFBP7 MUTATED     1   0   3   0
  IGFBP7 WILD-TYPE   8  68 245  41
D293V4, multiclass
    clus
vv   IGFBP7 MUTATED IGFBP7 WILD-TYPE
  T1              1                8
  T2              0               68
  T3              3              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
  IGFBP7 MUTATED     2   2   0
  IGFBP7 WILD-TYPE 218  78  66
D293V5, multiclass
    clus
vv   IGFBP7 MUTATED IGFBP7 WILD-TYPE
  N0              2              218
  N1              2               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"
D293V6, binary
                  cls
clus                 0   1
  IGFBP7 MUTATED     4   0
  IGFBP7 WILD-TYPE 279  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGFBP7 MUTATED      4    0
  IGFBP7 WILD-TYPE  279   48
   clus
vv  IGFBP7 MUTATED IGFBP7 WILD-TYPE
  0              4              279
  1              0               48
[1] 2 2
[1] FALSE
D293V7, 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
D293V8, binary
                  cls
clus                 0   1
  IGFBP7 MUTATED     4   0
  IGFBP7 WILD-TYPE 313  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGFBP7 MUTATED      4    0
  IGFBP7 WILD-TYPE  313   48
                               clus
vv                              IGFBP7 MUTATED IGFBP7 WILD-TYPE
  COLON ADENOCARCINOMA                       4              313
  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 253   2  22  21
D293V9, multiclass
    clus
vv   IGFBP7 MUTATED IGFBP7 WILD-TYPE
  R0              4              253
  R1              0                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"
D293V10, 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
D293V11, 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(294) Variable = RNF182 MUTATION ANALYSIS
D294V1, survival
                  sevent
clus2                0   1
  RNF182 MUTATED    12   1
  RNF182 WILD-TYPE 270  72
  RNF182 MUTATED RNF182 WILD-TYPE 
              13              342 
  RNF182 MUTATED RNF182 WILD-TYPE 
               1               72 
$`RNF182 MUTATED`
TCGA-A6-3810 TCGA-AA-3558 TCGA-AA-3655 TCGA-AA-3713 TCGA-AD-6888 TCGA-AZ-4315 
       36.53        20.98        61.02        19.04         4.21        58.39 
TCGA-AZ-5407 TCGA-D5-5540 TCGA-D5-6540 TCGA-D5-6931 TCGA-DM-A1HB TCGA-DM-A282 
       61.41        13.51        16.14        12.00       135.65       139.17 
TCGA-F4-6809 
       13.25 

$`RNF182 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3560 
       13.02        24.00        17.95        29.95        23.01        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A285 
       12.59       140.38         7.50        44.32       131.51         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 
       16.31        29.59        16.24        33.67         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  RNF182 MUTATED RNF182 WILD-TYPE 
            4.21             0.00 
  RNF182 MUTATED RNF182 WILD-TYPE 
          139.17           140.38 
  RNF182 MUTATED RNF182 WILD-TYPE 
          20.980           20.155 
[1] "4.2 - 139.2 (21.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "4.5"
D294V2, 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       24       105         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RNF182 MUTATED           0          0          2          1        1
  RNF182 WILD-TYPE        19         10         39         30       34
                  vv
clus               STAGE IVA STAGE IVB
  RNF182 MUTATED           1         0
  RNF182 WILD-TYPE        12         1
D294V3, multiclass
            clus
vv           RNF182 MUTATED RNF182 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               4              105
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              1               30
  STAGE IV                1               34
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  RNF182 MUTATED     1   3   8   1
  RNF182 WILD-TYPE   8  65 240  40
D294V4, multiclass
    clus
vv   RNF182 MUTATED RNF182 WILD-TYPE
  T1              1                8
  T2              3               65
  T3              8              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   2   1
  RNF182 WILD-TYPE 211  78  65
D294V5, multiclass
    clus
vv   RNF182 MUTATED RNF182 WILD-TYPE
  N0              9              211
  N1              2               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"
D294V6, binary
                  cls
clus                 0   1
  RNF182 MUTATED    11   2
  RNF182 WILD-TYPE 272  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF182 MUTATED     11    2
  RNF182 WILD-TYPE  272   46
   clus
vv  RNF182 MUTATED RNF182 WILD-TYPE
  0             11              272
  1              2               46
[1] 2 2
[1] FALSE
D294V7, 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
D294V8, binary
                  cls
clus                 0   1
  RNF182 MUTATED    12   1
  RNF182 WILD-TYPE 305  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF182 MUTATED     12    1
  RNF182 WILD-TYPE  305   47
                               clus
vv                              RNF182 MUTATED RNF182 WILD-TYPE
  COLON ADENOCARCINOMA                      12              305
  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 249   2  20  21
D294V9, multiclass
    clus
vv   RNF182 MUTATED RNF182 WILD-TYPE
  R0              8              249
  R1              0                2
  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"
D294V10, 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
D294V11, 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(295) Variable = SYNCRIP MUTATION ANALYSIS
D295V1, survival
                   sevent
clus2                 0   1
  SYNCRIP MUTATED     9   1
  SYNCRIP WILD-TYPE 273  72
  SYNCRIP MUTATED SYNCRIP WILD-TYPE 
               10               345 
  SYNCRIP MUTATED SYNCRIP WILD-TYPE 
                1                72 
$`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         0.33         0.10        22.98 
TCGA-CM-6171 TCGA-D5-6535 TCGA-D5-6536 TCGA-F4-6460 
       14.04        15.12        17.85        13.38 

$`SYNCRIP WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        21.99        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.26         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6537 TCGA-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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 
       60.79       117.07        98.24         8.61        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  SYNCRIP MUTATED SYNCRIP WILD-TYPE 
              0.1               0.0 
  SYNCRIP MUTATED SYNCRIP WILD-TYPE 
            34.98            140.38 
  SYNCRIP MUTATED SYNCRIP WILD-TYPE 
            14.53             20.98 
[1] "0.1 - 35.0 (14.5)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.2"
D295V2, 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       25       105         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SYNCRIP MUTATED           0          0          3          0        0
  SYNCRIP WILD-TYPE        19         10         38         31       35
                   vv
clus                STAGE IVA STAGE IVB
  SYNCRIP MUTATED           0         0
  SYNCRIP WILD-TYPE        13         1
D295V3, multiclass
            clus
vv           SYNCRIP MUTATED SYNCRIP WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                4               105
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               3                38
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SYNCRIP MUTATED     0   2   7   1
  SYNCRIP WILD-TYPE   9  66 241  40
D295V4, multiclass
    clus
vv   SYNCRIP MUTATED SYNCRIP WILD-TYPE
  T1               0                 9
  T2               2                66
  T3               7               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
  SYNCRIP MUTATED     7   3   0
  SYNCRIP WILD-TYPE 213  77  66
D295V5, multiclass
    clus
vv   SYNCRIP MUTATED SYNCRIP WILD-TYPE
  N0               7               213
  N1               3                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"
D295V6, binary
                   cls
clus                  0   1
  SYNCRIP MUTATED     8   0
  SYNCRIP WILD-TYPE 275  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SYNCRIP MUTATED      8    0
  SYNCRIP WILD-TYPE  275   48
   clus
vv  SYNCRIP MUTATED SYNCRIP WILD-TYPE
  0               8               275
  1               0                48
[1] 2 2
[1] FALSE
D295V7, 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
D295V8, binary
                   cls
clus                  0   1
  SYNCRIP MUTATED     9   1
  SYNCRIP WILD-TYPE 308  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SYNCRIP MUTATED      9    1
  SYNCRIP WILD-TYPE  308   47
                               clus
vv                              SYNCRIP MUTATED SYNCRIP WILD-TYPE
  COLON ADENOCARCINOMA                        9               308
  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 251   2  22  18
D295V9, multiclass
    clus
vv   SYNCRIP MUTATED SYNCRIP WILD-TYPE
  R0               6               251
  R1               0                 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"
D295V10, 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
D295V11, 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(296) Variable = SLC9A10 MUTATION ANALYSIS
D296V1, survival
                   sevent
clus2                 0   1
  SLC9A10 MUTATED    16   2
  SLC9A10 WILD-TYPE 266  71
  SLC9A10 MUTATED SLC9A10 WILD-TYPE 
               18               337 
  SLC9A10 MUTATED SLC9A10 WILD-TYPE 
                2                71 
$`SLC9A10 MUTATED`
TCGA-A6-6780 TCGA-AA-3534 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-A010 TCGA-AA-A01Q 
       20.12        29.00        26.99        19.04        34.98         1.02 
TCGA-AZ-4315 TCGA-CA-6717 TCGA-CK-5916 TCGA-CM-4743 TCGA-CM-6161 TCGA-CM-6164 
       58.39         0.33        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        35.87 

$`SLC9A10 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 
       19.07         0.00        19.07        34.03        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.03        85.05        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93         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        16.01 
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-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-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32        12.59         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
      139.17         6.12        81.37       119.93        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 
       98.24         8.61        13.38        13.45         6.18         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  SLC9A10 MUTATED SLC9A10 WILD-TYPE 
             0.33              0.00 
  SLC9A10 MUTATED SLC9A10 WILD-TYPE 
           140.38            139.17 
  SLC9A10 MUTATED SLC9A10 WILD-TYPE 
           22.095            20.020 
[1] "0.3 - 140.4 (22.1)" "0.0 - 139.2 (20.0)"
[1] "hr=" "1.9"
D296V2, 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       24        98         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC9A10 MUTATED           0          0          1          0        1
  SLC9A10 WILD-TYPE        19         10         40         31       34
                   vv
clus                STAGE IVA STAGE IVB
  SLC9A10 MUTATED           0         0
  SLC9A10 WILD-TYPE        13         1
D296V3, multiclass
            clus
vv           SLC9A10 MUTATED SLC9A10 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA               11                98
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               0                31
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC9A10 MUTATED     1   2  14   1
  SLC9A10 WILD-TYPE   8  66 234  40
D296V4, multiclass
    clus
vv   SLC9A10 MUTATED SLC9A10 WILD-TYPE
  T1               1                 8
  T2               2                66
  T3              14               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
  SLC9A10 MUTATED    17   1   0
  SLC9A10 WILD-TYPE 203  79  66
D296V5, multiclass
    clus
vv   SLC9A10 MUTATED SLC9A10 WILD-TYPE
  N0              17               203
  N1               1                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"
D296V6, binary
                   cls
clus                  0   1
  SLC9A10 MUTATED    16   1
  SLC9A10 WILD-TYPE 267  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC9A10 MUTATED     16    1
  SLC9A10 WILD-TYPE  267   47
   clus
vv  SLC9A10 MUTATED SLC9A10 WILD-TYPE
  0              16               267
  1               1                47
[1] 2 2
[1] FALSE
D296V7, 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
D296V8, binary
                   cls
clus                  0   1
  SLC9A10 MUTATED    15   3
  SLC9A10 WILD-TYPE 302  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC9A10 MUTATED     15    3
  SLC9A10 WILD-TYPE  302   45
                               clus
vv                              SLC9A10 MUTATED SLC9A10 WILD-TYPE
  COLON ADENOCARCINOMA                       15               302
  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 245   2  21  19
D296V9, multiclass
    clus
vv   SLC9A10 MUTATED SLC9A10 WILD-TYPE
  R0              12               245
  R1               0                 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"
D296V10, 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
D296V11, 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(297) Variable = PDGFRA MUTATION ANALYSIS
D297V1, survival
                  sevent
clus2                0   1
  PDGFRA MUTATED    36  10
  PDGFRA WILD-TYPE 246  63
  PDGFRA MUTATED PDGFRA WILD-TYPE 
              46              309 
  PDGFRA MUTATED PDGFRA WILD-TYPE 
              10               63 
$`PDGFRA MUTATED`
TCGA-A6-5659 TCGA-A6-5665 TCGA-A6-5666 TCGA-AA-3510 TCGA-AA-3660 TCGA-AA-3662 
       30.44        22.06        32.71        63.98        78.08         6.05 
TCGA-AA-3666 TCGA-AA-3672 TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-3952 TCGA-AA-A00N 
        2.01         0.92        53.00        33.01         2.01         4.01 
TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-6895 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       34.98        35.01         0.72         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-5407 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
       58.39         1.41        61.41         0.07         0.26         0.33 
TCGA-CK-4950 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5868 TCGA-CM-6172 TCGA-CM-6675 
       40.34        22.03        30.08        17.03        11.01        13.05 
TCGA-D5-6539 TCGA-D5-6922 TCGA-D5-6928 TCGA-D5-7000 TCGA-DM-A0XF TCGA-DM-A1D4 
       12.49        10.13        11.64        10.26        38.20        92.75 
TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A282 TCGA-F4-6459 
       13.32       140.38         7.50       135.65       139.17         8.61 
TCGA-F4-6460 TCGA-F4-6570 TCGA-G4-6310 TCGA-G4-6586 
       13.38         6.18        45.11        35.80 

$`PDGFRA WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
       61.02         6.97        54.02        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        26.01        24.00        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13        83.80        22.36        62.79        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6718 
        1.94         2.24         3.06         3.25         3.29         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
        1.35        17.56       102.44        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 
       16.01        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-6674 TCGA-CM-6676 
       12.99        13.02        15.02        14.04        12.95        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 
       43.27        15.12        17.85         4.80        17.13        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58         7.53        12.39        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 
        9.44        13.41         1.51        12.00        11.38       119.70 
TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1DB TCGA-DM-A1HA 
       24.43       130.65        49.91        12.59        44.32       131.51 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       98.24        13.45        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 
       51.75        36.72        36.00        22.09        13.78        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  PDGFRA MUTATED PDGFRA WILD-TYPE 
            0.07             0.00 
  PDGFRA MUTATED PDGFRA WILD-TYPE 
          140.38           131.51 
  PDGFRA MUTATED PDGFRA WILD-TYPE 
          17.425           20.280 
[1] "0.1 - 140.4 (17.4)" "0.0 - 131.5 (20.3)"
[1] "hr=" "1.1"
D297V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PDGFRA MUTATED         3        0        3        14         3         1
  PDGFRA WILD-TYPE      61        1       22        95         5         0
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PDGFRA MUTATED           3          3          8          4        2
  PDGFRA WILD-TYPE        16          7         33         27       33
                  vv
clus               STAGE IVA STAGE IVB
  PDGFRA MUTATED           1         1
  PDGFRA WILD-TYPE        12         0
D297V3, multiclass
            clus
vv           PDGFRA MUTATED PDGFRA WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                3               22
  STAGE IIA              14               95
  STAGE IIB               3                5
  STAGE IIC               1                0
  STAGE III               3               16
  STAGE IIIA              3                7
  STAGE IIIB              8               33
  STAGE IIIC              4               27
  STAGE IV                2               33
  STAGE IVA               1               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
  PDGFRA MUTATED     1   2  37   7
  PDGFRA WILD-TYPE   8  66 211  34
D297V4, multiclass
    clus
vv   PDGFRA MUTATED PDGFRA WILD-TYPE
  T1              1                8
  T2              2               66
  T3             37              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    25  13   9
  PDGFRA WILD-TYPE 195  67  57
D297V5, multiclass
    clus
vv   PDGFRA MUTATED PDGFRA WILD-TYPE
  N0             25              195
  N1             13               67
  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"
D297V6, binary
                  cls
clus                 0   1
  PDGFRA MUTATED    40   4
  PDGFRA WILD-TYPE 243  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PDGFRA MUTATED     40    4
  PDGFRA WILD-TYPE  243   44
   clus
vv  PDGFRA MUTATED PDGFRA WILD-TYPE
  0             40              243
  1              4               44
[1] 2 2
[1] FALSE
D297V7, binary
                  cls
clus                 0   1
  PDGFRA MUTATED    24  23
  PDGFRA WILD-TYPE 146 174
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PDGFRA MUTATED     24   23
  PDGFRA WILD-TYPE  146  174
        clus
vv       PDGFRA MUTATED PDGFRA WILD-TYPE
  FEMALE             24              146
  MALE               23              174
[1] 2 2
[1] FALSE
D297V8, binary
                  cls
clus                 0   1
  PDGFRA MUTATED    39   8
  PDGFRA WILD-TYPE 278  40
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PDGFRA MUTATED     39    8
  PDGFRA WILD-TYPE  278   40
                               clus
vv                              PDGFRA MUTATED PDGFRA WILD-TYPE
  COLON ADENOCARCINOMA                      39              278
  COLON MUCINOUS ADENOCARCINOMA              8               40
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PDGFRA MUTATED    31   1   1   3
  PDGFRA WILD-TYPE 226   1  21  18
D297V9, multiclass
    clus
vv   PDGFRA MUTATED PDGFRA WILD-TYPE
  R0             31              226
  R1              1                1
  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"
D297V10, 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                           3    29
  PDGFRA WILD-TYPE                        16   147
D297V11, multiclass
                                  clus
vv                                 PDGFRA MUTATED PDGFRA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         3                7
  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(298) Variable = ECM2 MUTATION ANALYSIS
D298V1, survival
                sevent
clus2              0   1
  ECM2 MUTATED    13   3
  ECM2 WILD-TYPE 269  70
  ECM2 MUTATED ECM2 WILD-TYPE 
            16            339 
  ECM2 MUTATED ECM2 WILD-TYPE 
             3             70 
$`ECM2 MUTATED`
TCGA-A6-3808 TCGA-A6-6653 TCGA-AA-3510 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3815 
       33.34        24.39        63.98        19.04        10.06        33.04 
TCGA-AA-A00N TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-6196 TCGA-AZ-4315 TCGA-AZ-5407 
        4.01        14.50        27.09         0.20        58.39        61.41 
TCGA-AZ-6599 TCGA-CA-6717 TCGA-CM-4752 TCGA-CM-6164 
        6.77         0.33        13.02        29.03 

$`ECM2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       85.05        26.99        19.04        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       27.42        10.88         0.20        16.31         0.95        15.75 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       62.79        49.41        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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 
       16.01        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  ECM2 MUTATED ECM2 WILD-TYPE 
           0.2            0.0 
  ECM2 MUTATED ECM2 WILD-TYPE 
         63.98         140.38 
  ECM2 MUTATED ECM2 WILD-TYPE 
        21.715         20.190 
[1] "0.2 - 64.0 (21.7)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D298V2, 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       24       102         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        18         10         41         30       34        13
                vv
clus             STAGE IVB
  ECM2 MUTATED           0
  ECM2 WILD-TYPE         1
D298V3, multiclass
            clus
vv           ECM2 MUTATED ECM2 WILD-TYPE
  STAGE I               4             60
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             7            102
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            1             30
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ECM2 MUTATED     1   3  11   2
  ECM2 WILD-TYPE   8  65 237  39
D298V4, multiclass
    clus
vv   ECM2 MUTATED ECM2 WILD-TYPE
  T1            1              8
  T2            3             65
  T3           11            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
  ECM2 MUTATED    15   0   2
  ECM2 WILD-TYPE 205  80  64
D298V5, multiclass
    clus
vv   ECM2 MUTATED ECM2 WILD-TYPE
  N0           15            205
  N1            0             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"
D298V6, binary
                cls
clus               0   1
  ECM2 MUTATED    13   1
  ECM2 WILD-TYPE 270  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  ECM2 MUTATED     13    1
  ECM2 WILD-TYPE  270   47
   clus
vv  ECM2 MUTATED ECM2 WILD-TYPE
  0           13            270
  1            1             47
[1] 2 2
[1] FALSE
D298V7, 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
D298V8, binary
                cls
clus               0   1
  ECM2 MUTATED    14   3
  ECM2 WILD-TYPE 303  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  ECM2 MUTATED     14    3
  ECM2 WILD-TYPE  303   45
                               clus
vv                              ECM2 MUTATED ECM2 WILD-TYPE
  COLON ADENOCARCINOMA                    14            303
  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 246   2  21  19
D298V9, multiclass
    clus
vv   ECM2 MUTATED ECM2 WILD-TYPE
  R0           11            246
  R1            0              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"
D298V10, 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
D298V11, 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(299) Variable = MYST4 MUTATION ANALYSIS
D299V1, survival
                 sevent
clus2               0   1
  MYST4 MUTATED    20   3
  MYST4 WILD-TYPE 262  70
  MYST4 MUTATED MYST4 WILD-TYPE 
             23             332 
  MYST4 MUTATED MYST4 WILD-TYPE 
              3              70 
$`MYST4 MUTATED`
TCGA-A6-4105 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3710 
       14.53         3.02        35.01        17.95        29.95        26.99 
TCGA-AA-3864 TCGA-AA-3950 TCGA-AA-3966 TCGA-AD-6895 TCGA-AU-6004 TCGA-AY-6197 
       53.00        24.00         2.01         0.72        27.09        21.44 
TCGA-AZ-4315 TCGA-AZ-5407 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4744 
       58.39        61.41       100.01         0.33         0.10        20.02 
TCGA-CM-5344 TCGA-CM-5348 TCGA-D5-6532 TCGA-F4-6856 TCGA-G4-6309 
       22.03        22.98        18.25        19.43        51.75 

$`MYST4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3510 
       20.12        19.66        20.28         7.04         1.02        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 
       37.05        19.00        36.00         5.03        85.05        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       14.50        16.31         0.95        15.75         0.20        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 
        1.41         5.13        83.80        22.36        62.79        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.26         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       11.51        20.19         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 
       33.67        13.25         0.53        35.41       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  MYST4 MUTATED MYST4 WILD-TYPE 
            0.1             0.0 
  MYST4 MUTATED MYST4 WILD-TYPE 
         100.01          140.38 
  MYST4 MUTATED MYST4 WILD-TYPE 
         22.030          20.055 
[1] "0.1 - 100.0 (22.0)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.8"
D299V2, 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       22        98         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MYST4 MUTATED           0          0          3          0        0         0
  MYST4 WILD-TYPE        19         10         38         31       35        13
                 vv
clus              STAGE IVB
  MYST4 MUTATED           0
  MYST4 WILD-TYPE         1
D299V3, multiclass
            clus
vv           MYST4 MUTATED MYST4 WILD-TYPE
  STAGE I                5              59
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA             11              98
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             3              38
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MYST4 MUTATED     1   4  18   0
  MYST4 WILD-TYPE   8  64 230  41
D299V4, multiclass
    clus
vv   MYST4 MUTATED MYST4 WILD-TYPE
  T1             1               8
  T2             4              64
  T3            18             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
  MYST4 MUTATED    19   4   0
  MYST4 WILD-TYPE 201  76  66
D299V5, multiclass
    clus
vv   MYST4 MUTATED MYST4 WILD-TYPE
  N0            19             201
  N1             4              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"
D299V6, binary
                 cls
clus                0   1
  MYST4 MUTATED    21   0
  MYST4 WILD-TYPE 262  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYST4 MUTATED     21    0
  MYST4 WILD-TYPE  262   48
   clus
vv  MYST4 MUTATED MYST4 WILD-TYPE
  0            21             262
  1             0              48
[1] 2 2
[1] FALSE
D299V7, 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
D299V8, binary
                 cls
clus                0   1
  MYST4 MUTATED    18   5
  MYST4 WILD-TYPE 299  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYST4 MUTATED     18    5
  MYST4 WILD-TYPE  299   43
                               clus
vv                              MYST4 MUTATED MYST4 WILD-TYPE
  COLON ADENOCARCINOMA                     18             299
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MYST4 MUTATED    16   0   0   2
  MYST4 WILD-TYPE 241   2  22  19
D299V9, multiclass
    clus
vv   MYST4 MUTATED MYST4 WILD-TYPE
  R0            16             241
  R1             0               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"
D299V10, 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
D299V11, 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(300) Variable = CARD11 MUTATION ANALYSIS
D300V1, survival
                  sevent
clus2                0   1
  CARD11 MUTATED    32   7
  CARD11 WILD-TYPE 250  66
  CARD11 MUTATED CARD11 WILD-TYPE 
              39              316 
  CARD11 MUTATED CARD11 WILD-TYPE 
               7               66 
$`CARD11 MUTATED`
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-6651 TCGA-A6-6652 TCGA-AA-3663 TCGA-AA-3715 
       32.91        30.44        21.76        24.69         6.97        19.04 
TCGA-AA-3864 TCGA-AA-3950 TCGA-AA-3980 TCGA-AA-A00R TCGA-AD-6964 TCGA-AY-4071 
       53.00        24.00        27.02         0.99        10.88         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-CA-5796 TCGA-CA-5797 
       15.75        21.44        58.39         1.41         3.25         3.29 
TCGA-CA-6716 TCGA-CK-4948 TCGA-CK-4950 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-5344 
        0.26       102.44        40.34        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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.16        24.39        23.87        20.12        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        7.04         3.02         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.05        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       27.02        42.02        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
        0.72         5.79        22.42        27.42         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4616 TCGA-AZ-4681 
       27.09        16.31         0.20        17.82         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        2.24         3.06         0.07         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       17.56        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4747 TCGA-CM-4752 
        2.93         2.01       124.27        23.05        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        16.01        15.02         5.03 
TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 
       15.02        15.02        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6540 
        1.32        43.27        15.12        17.85        17.13        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 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-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44        13.41         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        24.43        38.20       130.65        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       12.59         7.50       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 
       13.38        13.45         6.18        35.87        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 
       51.75        45.11        36.72        36.00        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  CARD11 MUTATED CARD11 WILD-TYPE 
            0.26             0.00 
  CARD11 MUTATED CARD11 WILD-TYPE 
          140.38           139.17 
  CARD11 MUTATED CARD11 WILD-TYPE 
           19.04            20.63 
[1] "0.3 - 140.4 (19.0)" "0.0 - 139.2 (20.6)"
[1] "hr=" "1.3"
D300V2, 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       22        97         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CARD11 MUTATED           1          4          5          2        1
  CARD11 WILD-TYPE        18          6         36         29       34
                  vv
clus               STAGE IVA STAGE IVB
  CARD11 MUTATED           3         0
  CARD11 WILD-TYPE        10         1
D300V3, multiclass
            clus
vv           CARD11 MUTATED CARD11 WILD-TYPE
  STAGE I                 8               56
  STAGE IA                1                0
  STAGE II                3               22
  STAGE IIA              12               97
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              4                6
  STAGE IIIB              5               36
  STAGE IIIC              2               29
  STAGE IV                1               34
  STAGE IVA               3               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
  CARD11 MUTATED     1   7  28   4
  CARD11 WILD-TYPE   8  61 220  37
D300V4, multiclass
    clus
vv   CARD11 MUTATED CARD11 WILD-TYPE
  T1              1                8
  T2              7               61
  T3             28              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
  CARD11 MUTATED    26  10   5
  CARD11 WILD-TYPE 194  70  61
D300V5, multiclass
    clus
vv   CARD11 MUTATED CARD11 WILD-TYPE
  N0             26              194
  N1             10               70
  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"
D300V6, binary
                  cls
clus                 0   1
  CARD11 MUTATED    30   4
  CARD11 WILD-TYPE 253  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CARD11 MUTATED     30    4
  CARD11 WILD-TYPE  253   44
   clus
vv  CARD11 MUTATED CARD11 WILD-TYPE
  0             30              253
  1              4               44
[1] 2 2
[1] FALSE
D300V7, 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
D300V8, binary
                  cls
clus                 0   1
  CARD11 MUTATED    34   6
  CARD11 WILD-TYPE 283  42
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CARD11 MUTATED     34    6
  CARD11 WILD-TYPE  283   42
                               clus
vv                              CARD11 MUTATED CARD11 WILD-TYPE
  COLON ADENOCARCINOMA                      34              283
  COLON MUCINOUS ADENOCARCINOMA              6               42
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CARD11 MUTATED    29   1   0   1
  CARD11 WILD-TYPE 228   1  22  20
D300V9, multiclass
    clus
vv   CARD11 MUTATED CARD11 WILD-TYPE
  R0             29              228
  R1              1                1
  R2              0               22
  RX              1               20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D300V10, 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
D300V11, 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(301) Variable = PLCH2 MUTATION ANALYSIS
D301V1, survival
                 sevent
clus2               0   1
  PLCH2 MUTATED    14   5
  PLCH2 WILD-TYPE 268  68
  PLCH2 MUTATED PLCH2 WILD-TYPE 
             19             336 
  PLCH2 MUTATED PLCH2 WILD-TYPE 
              5              68 
$`PLCH2 MUTATED`
TCGA-A6-6782 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3994 TCGA-AZ-6599 TCGA-AZ-6600 
       20.28        35.01         6.97        27.02         6.77        12.10 
TCGA-AZ-6603 TCGA-CK-4947 TCGA-CK-4952 TCGA-CM-6167 TCGA-D5-6928 TCGA-DM-A1D0 
       29.56        17.56        15.62        14.99        11.64       130.65 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A28F TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6303 
      131.51       135.65        35.97        35.41        19.43        65.85 
TCGA-G4-6628 
       52.80 

$`PLCH2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        19.66         7.04         3.02         1.02 
TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       19.07         7.96        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-AZ-6605 
       22.36        62.79        61.41        49.41       100.01         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      102.44        40.34        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
        7.50        44.32       139.17         6.12        81.37       119.93 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 
       33.67        13.25         0.53       107.67        74.56        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 

  PLCH2 MUTATED PLCH2 WILD-TYPE 
           6.77            0.00 
  PLCH2 MUTATED PLCH2 WILD-TYPE 
         135.65          140.38 
  PLCH2 MUTATED PLCH2 WILD-TYPE 
          27.02           20.07 
[1] "6.8 - 135.7 (27.0)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.2"
D301V2, 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       24       106         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PLCH2 MUTATED           1          0          3          2        2         1
  PLCH2 WILD-TYPE        18         10         38         29       33        12
                 vv
clus              STAGE IVB
  PLCH2 MUTATED           0
  PLCH2 WILD-TYPE         1
D301V3, multiclass
            clus
vv           PLCH2 MUTATED PLCH2 WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              3             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             3              38
  STAGE IIIC             2              29
  STAGE IV               2              33
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  63 239  36
D301V4, multiclass
    clus
vv   PLCH2 MUTATED PLCH2 WILD-TYPE
  T1             0               9
  T2             5              63
  T3             9             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
  PLCH2 MUTATED     9   7   3
  PLCH2 WILD-TYPE 211  73  63
D301V5, multiclass
    clus
vv   PLCH2 MUTATED PLCH2 WILD-TYPE
  N0             9             211
  N1             7              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"
D301V6, binary
                 cls
clus                0   1
  PLCH2 MUTATED    14   2
  PLCH2 WILD-TYPE 269  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLCH2 MUTATED     14    2
  PLCH2 WILD-TYPE  269   46
   clus
vv  PLCH2 MUTATED PLCH2 WILD-TYPE
  0            14             269
  1             2              46
[1] 2 2
[1] FALSE
D301V7, 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
D301V8, binary
                 cls
clus                0   1
  PLCH2 MUTATED    15   4
  PLCH2 WILD-TYPE 302  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLCH2 MUTATED     15    4
  PLCH2 WILD-TYPE  302   44
                               clus
vv                              PLCH2 MUTATED PLCH2 WILD-TYPE
  COLON ADENOCARCINOMA                     15             302
  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 248   2  22  19
D301V9, multiclass
    clus
vv   PLCH2 MUTATED PLCH2 WILD-TYPE
  R0             9             248
  R1             0               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"
D301V10, 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
D301V11, 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(302) Variable = C2ORF77 MUTATION ANALYSIS
D302V1, survival
                   sevent
clus2                 0   1
  C2ORF77 MUTATED     8   0
  C2ORF77 WILD-TYPE 274  73
  C2ORF77 MUTATED C2ORF77 WILD-TYPE 
                8               347 
  C2ORF77 MUTATED C2ORF77 WILD-TYPE 
                0                73 
$`C2ORF77 MUTATED`
TCGA-AA-3713 TCGA-AA-3866 TCGA-AA-3950 TCGA-AA-A010 TCGA-AD-5900 TCGA-CA-6717 
       19.04        17.03        24.00        34.98         0.07         0.33 
TCGA-D5-6928 TCGA-G4-6586 
       11.64        35.80 

$`C2ORF77 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        26.17        91.79        46.75        52.80 

  C2ORF77 MUTATED C2ORF77 WILD-TYPE 
             0.07              0.00 
  C2ORF77 MUTATED C2ORF77 WILD-TYPE 
            35.80            140.38 
  C2ORF77 MUTATED C2ORF77 WILD-TYPE 
           18.035            20.280 
[1] "0.1 - 35.8 (18.0)"  "0.0 - 140.4 (20.3)"
[1] "hr="     "9200000"
D302V2, 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       25       105         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C2ORF77 MUTATED           0          0          0          0        1
  C2ORF77 WILD-TYPE        19         10         41         31       34
                   vv
clus                STAGE IVA STAGE IVB
  C2ORF77 MUTATED           0         0
  C2ORF77 WILD-TYPE        13         1
D302V3, multiclass
            clus
vv           C2ORF77 MUTATED C2ORF77 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                4               105
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               0                31
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C2ORF77 MUTATED     0   2   5   1
  C2ORF77 WILD-TYPE   9  66 243  40
D302V4, multiclass
    clus
vv   C2ORF77 MUTATED C2ORF77 WILD-TYPE
  T1               0                 9
  T2               2                66
  T3               5               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
  C2ORF77 MUTATED     8   0   0
  C2ORF77 WILD-TYPE 212  80  66
D302V5, multiclass
    clus
vv   C2ORF77 MUTATED C2ORF77 WILD-TYPE
  N0               8               212
  N1               0                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"
D302V6, binary
                   cls
clus                  0   1
  C2ORF77 MUTATED     6   1
  C2ORF77 WILD-TYPE 277  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF77 MUTATED      6    1
  C2ORF77 WILD-TYPE  277   47
   clus
vv  C2ORF77 MUTATED C2ORF77 WILD-TYPE
  0               6               277
  1               1                47
[1] 2 2
[1] FALSE
D302V7, 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
D302V8, binary
                   cls
clus                  0   1
  C2ORF77 MUTATED     4   4
  C2ORF77 WILD-TYPE 313  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF77 MUTATED      4    4
  C2ORF77 WILD-TYPE  313   44
                               clus
vv                              C2ORF77 MUTATED C2ORF77 WILD-TYPE
  COLON ADENOCARCINOMA                        4               313
  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 251   2  21  20
D302V9, multiclass
    clus
vv   C2ORF77 MUTATED C2ORF77 WILD-TYPE
  R0               6               251
  R1               0                 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"
D302V10, 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
D302V11, 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(303) Variable = TIFA MUTATION ANALYSIS
D303V1, survival
                sevent
clus2              0   1
  TIFA MUTATED     5   0
  TIFA WILD-TYPE 277  73
  TIFA MUTATED TIFA WILD-TYPE 
             5            350 
  TIFA MUTATED TIFA WILD-TYPE 
             0             73 
$`TIFA MUTATED`
TCGA-AA-3663 TCGA-CA-6715 TCGA-CM-5348 TCGA-D5-5541 TCGA-G4-6317 
        6.97         0.07        22.98        11.51        36.00 

$`TIFA WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.72        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  TIFA MUTATED TIFA WILD-TYPE 
          0.07           0.00 
  TIFA MUTATED TIFA WILD-TYPE 
         36.00         140.38 
  TIFA MUTATED TIFA WILD-TYPE 
        11.510         20.235 
[1] "0.1 - 36.0 (11.5)"  "0.0 - 140.4 (20.2)"
[1] "hr="     "3300000"
D303V2, 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       24       108         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        19         10         38         30       35        13
                vv
clus             STAGE IVB
  TIFA MUTATED           0
  TIFA WILD-TYPE         1
D303V3, multiclass
            clus
vv           TIFA MUTATED TIFA WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             1            108
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            3             38
  STAGE IIIC            1             30
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TIFA MUTATED     0   0   6   0
  TIFA WILD-TYPE   9  68 242  41
D303V4, multiclass
    clus
vv   TIFA MUTATED TIFA WILD-TYPE
  T1            0              9
  T2            0             68
  T3            6            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
  TIFA MUTATED     2   3   1
  TIFA WILD-TYPE 218  77  65
D303V5, multiclass
    clus
vv   TIFA MUTATED TIFA WILD-TYPE
  N0            2            218
  N1            3             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"
D303V6, binary
                cls
clus               0   1
  TIFA MUTATED     5   0
  TIFA WILD-TYPE 278  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  TIFA MUTATED      5    0
  TIFA WILD-TYPE  278   48
   clus
vv  TIFA MUTATED TIFA WILD-TYPE
  0            5            278
  1            0             48
[1] 2 2
[1] FALSE
D303V7, 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
D303V8, binary
                cls
clus               0   1
  TIFA MUTATED     6   0
  TIFA WILD-TYPE 311  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  TIFA MUTATED      6    0
  TIFA WILD-TYPE  311   48
                               clus
vv                              TIFA MUTATED TIFA WILD-TYPE
  COLON ADENOCARCINOMA                     6            311
  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 252   2  22  20
D303V9, multiclass
    clus
vv   TIFA MUTATED TIFA WILD-TYPE
  R0            5            252
  R1            0              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"
D303V10, 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
D303V11, 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(304) Variable = PIK3C2A MUTATION ANALYSIS
D304V1, survival
                   sevent
clus2                 0   1
  PIK3C2A MUTATED    13   1
  PIK3C2A WILD-TYPE 269  72
  PIK3C2A MUTATED PIK3C2A WILD-TYPE 
               14               341 
  PIK3C2A MUTATED PIK3C2A WILD-TYPE 
                1                72 
$`PIK3C2A MUTATED`
TCGA-A6-5660 TCGA-A6-6141 TCGA-AA-3496 TCGA-AA-3660 TCGA-AA-3877 TCGA-AA-3977 
       29.19         8.38         1.02        78.08        31.00        25.02 
TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-4950 TCGA-CM-5861 TCGA-CM-6674 TCGA-D5-6540 
       49.41         0.33        40.34        15.02        12.95        16.14 
TCGA-G4-6309 TCGA-G4-6315 
       51.75        36.72 

$`PIK3C2A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         3.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      102.44        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       44.68        55.04        45.11        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  PIK3C2A MUTATED PIK3C2A WILD-TYPE 
             0.33              0.00 
  PIK3C2A MUTATED PIK3C2A WILD-TYPE 
            78.08            140.38 
  PIK3C2A MUTATED PIK3C2A WILD-TYPE 
           27.105            20.120 
[1] "0.3 - 78.1 (27.1)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "3.3"
D304V2, 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       22       105         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PIK3C2A MUTATED           0          1          1          1        1
  PIK3C2A WILD-TYPE        19          9         40         30       34
                   vv
clus                STAGE IVA STAGE IVB
  PIK3C2A MUTATED           0         0
  PIK3C2A WILD-TYPE        13         1
D304V3, multiclass
            clus
vv           PIK3C2A MUTATED PIK3C2A WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 3                22
  STAGE IIA                4               105
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               1                 9
  STAGE IIIB               1                40
  STAGE IIIC               1                30
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PIK3C2A MUTATED     1   2  11   0
  PIK3C2A WILD-TYPE   8  66 237  41
D304V4, multiclass
    clus
vv   PIK3C2A MUTATED PIK3C2A WILD-TYPE
  T1               1                 8
  T2               2                66
  T3              11               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
  PIK3C2A MUTATED    10   3   1
  PIK3C2A WILD-TYPE 210  77  65
D304V5, multiclass
    clus
vv   PIK3C2A MUTATED PIK3C2A WILD-TYPE
  N0              10               210
  N1               3                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"
D304V6, binary
                   cls
clus                  0   1
  PIK3C2A MUTATED    11   1
  PIK3C2A WILD-TYPE 272  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PIK3C2A MUTATED     11    1
  PIK3C2A WILD-TYPE  272   47
   clus
vv  PIK3C2A MUTATED PIK3C2A WILD-TYPE
  0              11               272
  1               1                47
[1] 2 2
[1] FALSE
D304V7, 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
D304V8, binary
                   cls
clus                  0   1
  PIK3C2A MUTATED    11   3
  PIK3C2A WILD-TYPE 306  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PIK3C2A MUTATED     11    3
  PIK3C2A WILD-TYPE  306   45
                               clus
vv                              PIK3C2A MUTATED PIK3C2A WILD-TYPE
  COLON ADENOCARCINOMA                       11               306
  COLON MUCINOUS ADENOCARCINOMA               3                45
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  PIK3C2A MUTATED     8   1   0   1
  PIK3C2A WILD-TYPE 249   1  22  20
D304V9, multiclass
    clus
vv   PIK3C2A MUTATED PIK3C2A WILD-TYPE
  R0               8               249
  R1               1                 1
  R2               0                22
  RX               1                20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D304V10, 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
D304V11, 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(305) Variable = OR11G2 MUTATION ANALYSIS
D305V1, survival
                  sevent
clus2                0   1
  OR11G2 MUTATED     3   2
  OR11G2 WILD-TYPE 279  71
  OR11G2 MUTATED OR11G2 WILD-TYPE 
               5              350 
  OR11G2 MUTATED OR11G2 WILD-TYPE 
               2               71 
$`OR11G2 MUTATED`
TCGA-AA-3489 TCGA-AA-A00N TCGA-D5-5541 TCGA-DM-A28E TCGA-G4-6307 
        7.04         4.01        11.51       119.93        55.04 

$`OR11G2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G 
      135.65       139.17         6.12        81.37        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  OR11G2 MUTATED OR11G2 WILD-TYPE 
            4.01             0.00 
  OR11G2 MUTATED OR11G2 WILD-TYPE 
          119.93           140.38 
  OR11G2 MUTATED OR11G2 WILD-TYPE 
          11.510           20.235 
[1] "4.0 - 119.9 (11.5)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.3"
D305V2, 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       24       108         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR11G2 MUTATED           0          0          2          0        0
  OR11G2 WILD-TYPE        19         10         39         31       35
                  vv
clus               STAGE IVA STAGE IVB
  OR11G2 MUTATED           0         0
  OR11G2 WILD-TYPE        13         1
D305V3, multiclass
            clus
vv           OR11G2 MUTATED OR11G2 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               1              108
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  OR11G2 MUTATED     0   0   4   1
  OR11G2 WILD-TYPE   9  68 244  40
D305V4, multiclass
    clus
vv   OR11G2 MUTATED OR11G2 WILD-TYPE
  T1              0                9
  T2              0               68
  T3              4              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
  OR11G2 MUTATED     3   2   0
  OR11G2 WILD-TYPE 217  78  66
D305V5, multiclass
    clus
vv   OR11G2 MUTATED OR11G2 WILD-TYPE
  N0              3              217
  N1              2               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"
D305V6, binary
                  cls
clus                 0   1
  OR11G2 MUTATED     5   0
  OR11G2 WILD-TYPE 278  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR11G2 MUTATED      5    0
  OR11G2 WILD-TYPE  278   48
   clus
vv  OR11G2 MUTATED OR11G2 WILD-TYPE
  0              5              278
  1              0               48
[1] 2 2
[1] FALSE
D305V7, 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
D305V8, binary
                  cls
clus                 0   1
  OR11G2 MUTATED     4   1
  OR11G2 WILD-TYPE 313  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR11G2 MUTATED      4    1
  OR11G2 WILD-TYPE  313   47
                               clus
vv                              OR11G2 MUTATED OR11G2 WILD-TYPE
  COLON ADENOCARCINOMA                       4              313
  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 253   2  22  21
D305V9, multiclass
    clus
vv   OR11G2 MUTATED OR11G2 WILD-TYPE
  R0              4              253
  R1              0                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"
D305V10, 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
D305V11, 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(306) Variable = TRIM23 MUTATION ANALYSIS
D306V1, survival
                  sevent
clus2                0   1
  TRIM23 MUTATED     8   2
  TRIM23 WILD-TYPE 274  71
  TRIM23 MUTATED TRIM23 WILD-TYPE 
              10              345 
  TRIM23 MUTATED TRIM23 WILD-TYPE 
               2               71 
$`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 
      107.67        74.56        36.72        36.00 

$`TRIM23 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20       130.65        92.75        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       35.41        19.43        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       51.75        45.11        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  TRIM23 MUTATED TRIM23 WILD-TYPE 
            1.02             0.00 
  TRIM23 MUTATED TRIM23 WILD-TYPE 
          107.67           140.38 
  TRIM23 MUTATED TRIM23 WILD-TYPE 
           36.36            19.99 
[1] "1.0 - 107.7 (36.4)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.7"
D306V2, 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       23       107         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRIM23 MUTATED           1          0          1          2        1
  TRIM23 WILD-TYPE        18         10         40         29       34
                  vv
clus               STAGE IVA STAGE IVB
  TRIM23 MUTATED           0         0
  TRIM23 WILD-TYPE        13         1
D306V3, multiclass
            clus
vv           TRIM23 MUTATED TRIM23 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               2              107
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              2               29
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TRIM23 MUTATED     0   2   9   0
  TRIM23 WILD-TYPE   9  66 239  41
D306V4, multiclass
    clus
vv   TRIM23 MUTATED TRIM23 WILD-TYPE
  T1              0                9
  T2              2               66
  T3              9              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
  TRIM23 MUTATED     6   3   2
  TRIM23 WILD-TYPE 214  77  64
D306V5, multiclass
    clus
vv   TRIM23 MUTATED TRIM23 WILD-TYPE
  N0              6              214
  N1              3               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"
D306V6, binary
                  cls
clus                 0   1
  TRIM23 MUTATED     7   1
  TRIM23 WILD-TYPE 276  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM23 MUTATED      7    1
  TRIM23 WILD-TYPE  276   47
   clus
vv  TRIM23 MUTATED TRIM23 WILD-TYPE
  0              7              276
  1              1               47
[1] 2 2
[1] FALSE
D306V7, 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
D306V8, binary
                  cls
clus                 0   1
  TRIM23 MUTATED     9   2
  TRIM23 WILD-TYPE 308  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM23 MUTATED      9    2
  TRIM23 WILD-TYPE  308   46
                               clus
vv                              TRIM23 MUTATED TRIM23 WILD-TYPE
  COLON ADENOCARCINOMA                       9              308
  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 249   2  22  21
D306V9, multiclass
    clus
vv   TRIM23 MUTATED TRIM23 WILD-TYPE
  R0              8              249
  R1              0                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"
D306V10, 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
D306V11, 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(307) Variable = IL1RAPL1 MUTATION ANALYSIS
D307V1, survival
                    sevent
clus2                  0   1
  IL1RAPL1 MUTATED    15   5
  IL1RAPL1 WILD-TYPE 267  68
  IL1RAPL1 MUTATED IL1RAPL1 WILD-TYPE 
                20                335 
  IL1RAPL1 MUTATED IL1RAPL1 WILD-TYPE 
                 5                 68 
$`IL1RAPL1 MUTATED`
TCGA-A6-5661 TCGA-AA-3518 TCGA-AA-3554 TCGA-AA-3663 TCGA-AA-3977 TCGA-AZ-6598 
       33.53         1.02        17.95         6.97        25.02        49.41 
TCGA-AZ-6607 TCGA-CA-6717 TCGA-CM-6162 TCGA-CM-6164 TCGA-D5-6532 TCGA-D5-6533 
        3.19         0.33        12.00        29.03        18.25         1.32 
TCGA-DM-A1DA TCGA-DM-A285 TCGA-DM-A28E TCGA-DM-A28G TCGA-F4-6855 TCGA-G4-6304 
        7.50         6.12       119.93        60.79        35.41        53.62 
TCGA-G4-6307 TCGA-G4-6628 
       55.04        52.80 

$`IL1RAPL1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        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-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        13.51        11.51        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-D5-6540 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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-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-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        19.43       107.67        74.56        65.85 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       13.78        35.80        26.17        91.79        46.75 

  IL1RAPL1 MUTATED IL1RAPL1 WILD-TYPE 
              0.33               0.00 
  IL1RAPL1 MUTATED IL1RAPL1 WILD-TYPE 
            119.93             140.38 
  IL1RAPL1 MUTATED IL1RAPL1 WILD-TYPE 
            21.635             20.190 
[1] "0.3 - 119.9 (21.6)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D307V2, 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       23        98         6         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IL1RAPL1 MUTATED           0          0          3          1        2
  IL1RAPL1 WILD-TYPE        19         10         38         30       33
                    vv
clus                 STAGE IVA STAGE IVB
  IL1RAPL1 MUTATED           0         0
  IL1RAPL1 WILD-TYPE        13         1
D307V3, multiclass
            clus
vv           IL1RAPL1 MUTATED IL1RAPL1 WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  2                 23
  STAGE IIA                11                 98
  STAGE IIB                 2                  6
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                0                 10
  STAGE IIIB                3                 38
  STAGE IIIC                1                 30
  STAGE IV                  2                 33
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  IL1RAPL1 MUTATED     0   2  17   4
  IL1RAPL1 WILD-TYPE   9  66 231  37
D307V4, multiclass
    clus
vv   IL1RAPL1 MUTATED IL1RAPL1 WILD-TYPE
  T1                0                  9
  T2                2                 66
  T3               17                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
  IL1RAPL1 MUTATED    18   2   3
  IL1RAPL1 WILD-TYPE 202  78  63
D307V5, multiclass
    clus
vv   IL1RAPL1 MUTATED IL1RAPL1 WILD-TYPE
  N0               18                202
  N1                2                 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"
D307V6, binary
                    cls
clus                   0   1
  IL1RAPL1 MUTATED    18   2
  IL1RAPL1 WILD-TYPE 265  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  IL1RAPL1 MUTATED     18    2
  IL1RAPL1 WILD-TYPE  265   46
   clus
vv  IL1RAPL1 MUTATED IL1RAPL1 WILD-TYPE
  0               18                265
  1                2                 46
[1] 2 2
[1] FALSE
D307V7, 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
D307V8, binary
                    cls
clus                   0   1
  IL1RAPL1 MUTATED    20   3
  IL1RAPL1 WILD-TYPE 297  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  IL1RAPL1 MUTATED     20    3
  IL1RAPL1 WILD-TYPE  297   45
                               clus
vv                              IL1RAPL1 MUTATED IL1RAPL1 WILD-TYPE
  COLON ADENOCARCINOMA                        20                297
  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 243   2  22  19
D307V9, multiclass
    clus
vv   IL1RAPL1 MUTATED IL1RAPL1 WILD-TYPE
  R0               14                243
  R1                0                  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"
D307V10, 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
D307V11, 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(308) Variable = GPR87 MUTATION ANALYSIS
D308V1, survival
                 sevent
clus2               0   1
  GPR87 MUTATED     8   1
  GPR87 WILD-TYPE 274  72
  GPR87 MUTATED GPR87 WILD-TYPE 
              9             346 
  GPR87 MUTATED GPR87 WILD-TYPE 
              1              72 
$`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         0.33         5.03 
TCGA-CM-6674 TCGA-D5-6540 TCGA-F4-6806 
       12.95        16.14        29.59 

$`GPR87 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        17.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       33.04        35.01        26.01        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.20        14.50        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        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-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        14.04        11.01        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 
       13.45         6.18        35.87         1.55        16.31        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  GPR87 MUTATED GPR87 WILD-TYPE 
           0.33            0.00 
  GPR87 MUTATED GPR87 WILD-TYPE 
          37.02          140.38 
  GPR87 MUTATED GPR87 WILD-TYPE 
         25.020          20.155 
[1] "0.3 - 37.0 (25.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.4"
D308V2, 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       24       106         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        19         10         41         31       34        12
                 vv
clus              STAGE IVB
  GPR87 MUTATED           0
  GPR87 WILD-TYPE         1
D308V3, multiclass
            clus
vv           GPR87 MUTATED GPR87 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              3             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  64 243  40
D308V4, multiclass
    clus
vv   GPR87 MUTATED GPR87 WILD-TYPE
  T1             0               9
  T2             4              64
  T3             5             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
  GPR87 MUTATED     8   1   1
  GPR87 WILD-TYPE 212  79  65
D308V5, multiclass
    clus
vv   GPR87 MUTATED GPR87 WILD-TYPE
  N0             8             212
  N1             1              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"
D308V6, binary
                 cls
clus                0   1
  GPR87 MUTATED     7   2
  GPR87 WILD-TYPE 276  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR87 MUTATED      7    2
  GPR87 WILD-TYPE  276   46
   clus
vv  GPR87 MUTATED GPR87 WILD-TYPE
  0             7             276
  1             2              46
[1] 2 2
[1] FALSE
D308V7, 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
D308V8, binary
                 cls
clus                0   1
  GPR87 MUTATED     6   4
  GPR87 WILD-TYPE 311  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR87 MUTATED      6    4
  GPR87 WILD-TYPE  311   44
                               clus
vv                              GPR87 MUTATED GPR87 WILD-TYPE
  COLON ADENOCARCINOMA                      6             311
  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 250   2  21  20
D308V9, multiclass
    clus
vv   GPR87 MUTATED GPR87 WILD-TYPE
  R0             7             250
  R1             0               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"
D308V10, 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
D308V11, 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(309) Variable = KPNA5 MUTATION ANALYSIS
D309V1, survival
                 sevent
clus2               0   1
  KPNA5 MUTATED     7   3
  KPNA5 WILD-TYPE 275  70
  KPNA5 MUTATED KPNA5 WILD-TYPE 
             10             345 
  KPNA5 MUTATED KPNA5 WILD-TYPE 
              3              70 
$`KPNA5 MUTATED`
TCGA-AA-3524 TCGA-AA-3713 TCGA-AA-3973 TCGA-AA-A00N TCGA-AZ-6608 TCGA-CK-5913 
       36.03        19.04        13.05         4.01         1.94        51.32 
TCGA-D5-6930 TCGA-DM-A28E TCGA-G4-6315 TCGA-G4-6626 
        1.51       119.93        36.72        46.75 

$`KPNA5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 
       38.99         1.02         9.07        24.03        37.05         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
      100.01        29.56         5.23        11.74         3.19         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       51.75        45.11        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       26.17        91.79        52.80 

  KPNA5 MUTATED KPNA5 WILD-TYPE 
           1.51            0.00 
  KPNA5 MUTATED KPNA5 WILD-TYPE 
         119.93          140.38 
  KPNA5 MUTATED KPNA5 WILD-TYPE 
         27.535          20.190 
[1] "1.5 - 119.9 (27.5)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D309V2, 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       24       105         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        19          9         41         31       32        13
                 vv
clus              STAGE IVB
  KPNA5 MUTATED           0
  KPNA5 WILD-TYPE         1
D309V3, multiclass
            clus
vv           KPNA5 MUTATED KPNA5 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              4             105
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               3              32
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KPNA5 MUTATED     0   1   7   3
  KPNA5 WILD-TYPE   9  67 241  38
D309V4, multiclass
    clus
vv   KPNA5 MUTATED KPNA5 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             7             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
  KPNA5 MUTATED     8   3   0
  KPNA5 WILD-TYPE 212  77  66
D309V5, multiclass
    clus
vv   KPNA5 MUTATED KPNA5 WILD-TYPE
  N0             8             212
  N1             3              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"
D309V6, binary
                 cls
clus                0   1
  KPNA5 MUTATED     6   3
  KPNA5 WILD-TYPE 277  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KPNA5 MUTATED      6    3
  KPNA5 WILD-TYPE  277   45
   clus
vv  KPNA5 MUTATED KPNA5 WILD-TYPE
  0             6             277
  1             3              45
[1] 2 2
[1] FALSE
D309V7, 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
D309V8, binary
                 cls
clus                0   1
  KPNA5 MUTATED     9   2
  KPNA5 WILD-TYPE 308  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KPNA5 MUTATED      9    2
  KPNA5 WILD-TYPE  308   46
                               clus
vv                              KPNA5 MUTATED KPNA5 WILD-TYPE
  COLON ADENOCARCINOMA                      9             308
  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 252   2  20  19
D309V9, multiclass
    clus
vv   KPNA5 MUTATED KPNA5 WILD-TYPE
  R0             5             252
  R1             0               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"
D309V10, 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
D309V11, 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(310) Variable = GPNMB MUTATION ANALYSIS
D310V1, survival
                 sevent
clus2               0   1
  GPNMB MUTATED     9   2
  GPNMB WILD-TYPE 273  71
  GPNMB MUTATED GPNMB WILD-TYPE 
             11             344 
  GPNMB MUTATED GPNMB WILD-TYPE 
              2              71 
$`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         0.33         0.10        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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.26         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-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-A285 TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      131.51       139.17         6.12       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        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  GPNMB MUTATED GPNMB WILD-TYPE 
            0.1             0.0 
  GPNMB MUTATED GPNMB WILD-TYPE 
         135.65          140.38 
  GPNMB MUTATED GPNMB WILD-TYPE 
         17.850          20.235 
[1] "0.1 - 135.7 (17.9)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.6"
D310V2, 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       24       104         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        17         10         40         30       35        12
                 vv
clus              STAGE IVB
  GPNMB MUTATED           0
  GPNMB WILD-TYPE         1
D310V3, multiclass
            clus
vv           GPNMB MUTATED GPNMB WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              5             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 238  39
D310V4, multiclass
    clus
vv   GPNMB MUTATED GPNMB WILD-TYPE
  T1             0               9
  T2             1              67
  T3            10             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
  GPNMB MUTATED     8   3   2
  GPNMB WILD-TYPE 212  77  64
D310V5, multiclass
    clus
vv   GPNMB MUTATED GPNMB WILD-TYPE
  N0             8             212
  N1             3              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"
D310V6, binary
                 cls
clus                0   1
  GPNMB MUTATED    10   1
  GPNMB WILD-TYPE 273  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPNMB MUTATED     10    1
  GPNMB WILD-TYPE  273   47
   clus
vv  GPNMB MUTATED GPNMB WILD-TYPE
  0            10             273
  1             1              47
[1] 2 2
[1] FALSE
D310V7, 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
D310V8, binary
                 cls
clus                0   1
  GPNMB MUTATED    12   1
  GPNMB WILD-TYPE 305  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPNMB MUTATED     12    1
  GPNMB WILD-TYPE  305   47
                               clus
vv                              GPNMB MUTATED GPNMB WILD-TYPE
  COLON ADENOCARCINOMA                     12             305
  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 252   2  22  18
D310V9, multiclass
    clus
vv   GPNMB MUTATED GPNMB WILD-TYPE
  R0             5             252
  R1             0               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"
D310V10, 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
D310V11, 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(311) Variable = BAG4 MUTATION ANALYSIS
D311V1, survival
                sevent
clus2              0   1
  BAG4 MUTATED     8   0
  BAG4 WILD-TYPE 274  73
  BAG4 MUTATED BAG4 WILD-TYPE 
             8            347 
  BAG4 MUTATED BAG4 WILD-TYPE 
             0             73 
$`BAG4 MUTATED`
TCGA-A6-5665 TCGA-AA-3555 TCGA-AA-3977 TCGA-AD-6890 TCGA-CA-6717 TCGA-CK-4952 
       22.06        29.95        25.02         0.79         0.33        15.62 
TCGA-CM-4744 TCGA-G4-6323 
       20.02        13.78 

$`BAG4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        17.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 
        0.10         1.35        17.56       102.44        40.34        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  BAG4 MUTATED BAG4 WILD-TYPE 
          0.33           0.00 
  BAG4 MUTATED BAG4 WILD-TYPE 
         29.95         140.38 
  BAG4 MUTATED BAG4 WILD-TYPE 
         17.82          20.28 
[1] "0.3 - 29.9 (17.8)"  "0.0 - 140.4 (20.3)"
[1] "hr="     "9200000"
D311V2, 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       25       106         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BAG4 MUTATED           1          0          0          0        0         0
  BAG4 WILD-TYPE        18         10         41         31       35        13
                vv
clus             STAGE IVB
  BAG4 MUTATED           0
  BAG4 WILD-TYPE         1
D311V3, multiclass
            clus
vv           BAG4 MUTATED BAG4 WILD-TYPE
  STAGE I               1             63
  STAGE IA              1              0
  STAGE II              0             25
  STAGE IIA             3            106
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  BAG4 MUTATED     1   2   3   1
  BAG4 WILD-TYPE   8  66 245  40
D311V4, multiclass
    clus
vv   BAG4 MUTATED BAG4 WILD-TYPE
  T1            1              8
  T2            2             66
  T3            3            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
  BAG4 MUTATED     7   0   1
  BAG4 WILD-TYPE 213  80  65
D311V5, multiclass
    clus
vv   BAG4 MUTATED BAG4 WILD-TYPE
  N0            7            213
  N1            0             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"
D311V6, binary
                cls
clus               0   1
  BAG4 MUTATED     5   0
  BAG4 WILD-TYPE 278  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAG4 MUTATED      5    0
  BAG4 WILD-TYPE  278   48
   clus
vv  BAG4 MUTATED BAG4 WILD-TYPE
  0            5            278
  1            0             48
[1] 2 2
[1] FALSE
D311V7, 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
D311V8, binary
                cls
clus               0   1
  BAG4 MUTATED     5   3
  BAG4 WILD-TYPE 312  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAG4 MUTATED      5    3
  BAG4 WILD-TYPE  312   45
                               clus
vv                              BAG4 MUTATED BAG4 WILD-TYPE
  COLON ADENOCARCINOMA                     5            312
  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 253   2  22  19
D311V9, multiclass
    clus
vv   BAG4 MUTATED BAG4 WILD-TYPE
  R0            4            253
  R1            0              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"
D311V10, 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
D311V11, 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(312) Variable = NRAS MUTATION ANALYSIS
D312V1, survival
                sevent
clus2              0   1
  NRAS MUTATED    27   6
  NRAS WILD-TYPE 255  67
  NRAS MUTATED NRAS WILD-TYPE 
            33            322 
  NRAS MUTATED NRAS WILD-TYPE 
             6             67 
$`NRAS MUTATED`
TCGA-A6-2678 TCGA-A6-5656 TCGA-A6-5666 TCGA-AA-3549 TCGA-AA-3558 TCGA-AA-3666 
       42.28        32.91        32.71        21.01        20.98         2.01 
TCGA-AA-3713 TCGA-AA-3819 TCGA-AA-3850 TCGA-AA-3864 TCGA-AA-3972 TCGA-AA-3973 
       19.04        25.02         0.00        53.00        50.99        13.05 
TCGA-AA-3976 TCGA-AA-A00F TCGA-AA-A00N TCGA-AA-A01V TCGA-AA-A024 TCGA-AA-A02F 
       26.01        34.03         4.01        35.01        39.06        39.98 
TCGA-AY-5543 TCGA-CA-5797 TCGA-CM-5864 TCGA-CM-6162 TCGA-CM-6680 TCGA-D5-5538 
       15.75         3.29        15.02        12.00        12.03        12.26 
TCGA-D5-6539 TCGA-D5-6922 TCGA-D5-6932 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-F4-6809 
       12.49        10.13        11.38       140.38         7.50        13.25 
TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6315 
       53.62        55.04        36.72 

$`NRAS WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2683 
       43.76        46.65        43.76        42.90        24.33        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5657 
       34.65        33.34        32.75        36.53        14.53        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
        0.99        14.01        33.99        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       29.95        23.01        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 
       78.08         6.05         6.97        54.02        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05        33.04         0.99         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       10.06        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3979 
        2.01        21.99        16.08        34.06        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       26.01        37.02        51.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        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-D5-5537 
       13.05        11.08        11.08        11.01        10.06        45.40 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 
       43.27        15.12        17.85         4.80        17.13        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 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-D5-7000 
        9.44        11.64        13.41         1.51        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-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       13.32        12.59        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 
        1.55        16.31        29.59        16.24        33.67         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 
       35.41        19.43       107.67        74.56        65.85        44.68 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       51.75        45.11        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  NRAS MUTATED NRAS WILD-TYPE 
             0              0 
  NRAS MUTATED NRAS WILD-TYPE 
        140.38         139.17 
  NRAS MUTATED NRAS WILD-TYPE 
        20.980         20.155 
[1] "0.0 - 140.4 (21.0)" "0.0 - 139.2 (20.2)"
[1] "hr=" "1.2"
D312V2, 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       23       105         6         0
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NRAS MUTATED           1          3          5          2        5         2
  NRAS WILD-TYPE        18          7         36         29       30        11
                vv
clus             STAGE IVB
  NRAS MUTATED           0
  NRAS WILD-TYPE         1
D312V3, multiclass
            clus
vv           NRAS MUTATED NRAS WILD-TYPE
  STAGE I               6             58
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             4            105
  STAGE IIB             2              6
  STAGE IIC             1              0
  STAGE III             1             18
  STAGE IIIA            3              7
  STAGE IIIB            5             36
  STAGE IIIC            2             29
  STAGE IV              5             30
  STAGE IVA             2             11
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  61 226  37
D312V4, multiclass
    clus
vv   NRAS MUTATED NRAS WILD-TYPE
  T1            0              9
  T2            7             61
  T3           22            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
  NRAS MUTATED    17  13   3
  NRAS WILD-TYPE 203  67  63
D312V5, multiclass
    clus
vv   NRAS MUTATED NRAS WILD-TYPE
  N0           17            203
  N1           13             67
  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"
D312V6, binary
                cls
clus               0   1
  NRAS MUTATED    26   7
  NRAS WILD-TYPE 257  41
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED     26    7
  NRAS WILD-TYPE  257   41
   clus
vv  NRAS MUTATED NRAS WILD-TYPE
  0           26            257
  1            7             41
[1] 2 2
[1] FALSE
D312V7, 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
D312V8, binary
                cls
clus               0   1
  NRAS MUTATED    30   3
  NRAS WILD-TYPE 287  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED     30    3
  NRAS WILD-TYPE  287   45
                               clus
vv                              NRAS MUTATED NRAS WILD-TYPE
  COLON ADENOCARCINOMA                    30            287
  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 233   2  17  21
D312V9, multiclass
    clus
vv   NRAS MUTATED NRAS WILD-TYPE
  R0           24            233
  R1            0              2
  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"
D312V10, 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
D312V11, 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(313) Variable = DDX43 MUTATION ANALYSIS
D313V1, survival
                 sevent
clus2               0   1
  DDX43 MUTATED     9   2
  DDX43 WILD-TYPE 273  71
  DDX43 MUTATED DDX43 WILD-TYPE 
             11             344 
  DDX43 MUTATED DDX43 WILD-TYPE 
              2              71 
$`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        51.75        46.75 

$`DDX43 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6648 
       22.09        22.06        32.71        27.09        22.52        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       24.16        21.76        24.69        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 
       11.51        20.19        18.25         1.32        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       74.56        65.85        53.62        44.68        55.04        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 
       91.79        52.80 

  DDX43 MUTATED DDX43 WILD-TYPE 
           8.38            0.00 
  DDX43 MUTATED DDX43 WILD-TYPE 
          63.98          140.38 
  DDX43 MUTATED DDX43 WILD-TYPE 
          33.04           19.99 
[1] "8.4 - 64.0 (33.0)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1.6"
D313V2, 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       24       104         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        19         10         40         31       35        12
                 vv
clus              STAGE IVB
  DDX43 MUTATED           0
  DDX43 WILD-TYPE         1
D313V3, multiclass
            clus
vv           DDX43 MUTATED DDX43 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              5             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 240  41
D313V4, multiclass
    clus
vv   DDX43 MUTATED DDX43 WILD-TYPE
  T1             1               8
  T2             2              66
  T3             8             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
  DDX43 MUTATED     9   2   0
  DDX43 WILD-TYPE 211  78  66
D313V5, multiclass
    clus
vv   DDX43 MUTATED DDX43 WILD-TYPE
  N0             9             211
  N1             2              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"
D313V6, binary
                 cls
clus                0   1
  DDX43 MUTATED    10   1
  DDX43 WILD-TYPE 273  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX43 MUTATED     10    1
  DDX43 WILD-TYPE  273   47
   clus
vv  DDX43 MUTATED DDX43 WILD-TYPE
  0            10             273
  1             1              47
[1] 2 2
[1] FALSE
D313V7, 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
D313V8, binary
                 cls
clus                0   1
  DDX43 MUTATED    10   1
  DDX43 WILD-TYPE 307  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX43 MUTATED     10    1
  DDX43 WILD-TYPE  307   47
                               clus
vv                              DDX43 MUTATED DDX43 WILD-TYPE
  COLON ADENOCARCINOMA                     10             307
  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 250   2  22  20
D313V9, multiclass
    clus
vv   DDX43 MUTATED DDX43 WILD-TYPE
  R0             7             250
  R1             0               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"
D313V10, 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
D313V11, 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(314) Variable = LIG1 MUTATION ANALYSIS
D314V1, survival
                sevent
clus2              0   1
  LIG1 MUTATED    11   4
  LIG1 WILD-TYPE 271  69
  LIG1 MUTATED LIG1 WILD-TYPE 
            15            340 
  LIG1 MUTATED LIG1 WILD-TYPE 
             4             69 
$`LIG1 MUTATED`
TCGA-A6-5665 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-6600 
       22.06        30.05        53.00         4.01        34.98        12.10 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CM-6171 TCGA-D5-6536 TCGA-D5-6540 TCGA-F4-6460 
        3.19         1.94        14.04        17.85        16.14        13.38 
TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6306 
       19.43        74.56        44.68 

$`LIG1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 
       32.05         0.99        31.07        31.07        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41        49.41         6.77       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        5.23        11.74         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 
       20.19        18.25         1.32        43.27        15.12         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 
       35.41       107.67        65.85        53.62        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  LIG1 MUTATED LIG1 WILD-TYPE 
          1.94           0.00 
  LIG1 MUTATED LIG1 WILD-TYPE 
         74.56         140.38 
  LIG1 MUTATED LIG1 WILD-TYPE 
         17.85          20.63 
[1] "1.9 - 74.6 (17.9)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "1.4"
D314V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LIG1 MUTATED         3        0        2         4         2         0
  LIG1 WILD-TYPE      61        1       23       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        19          9         40         30       33        13
                vv
clus             STAGE IVB
  LIG1 MUTATED           0
  LIG1 WILD-TYPE         1
D314V3, multiclass
            clus
vv           LIG1 MUTATED LIG1 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             4            105
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            1              9
  STAGE IIIB            1             40
  STAGE IIIC            1             30
  STAGE IV              2             33
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  LIG1 MUTATED     0   5   6   5
  LIG1 WILD-TYPE   9  63 242  36
D314V4, multiclass
    clus
vv   LIG1 MUTATED LIG1 WILD-TYPE
  T1            0              9
  T2            5             63
  T3            6            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
  LIG1 MUTATED    11   3   2
  LIG1 WILD-TYPE 209  77  64
D314V5, multiclass
    clus
vv   LIG1 MUTATED LIG1 WILD-TYPE
  N0           11            209
  N1            3             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"
D314V6, binary
                cls
clus               0   1
  LIG1 MUTATED    14   2
  LIG1 WILD-TYPE 269  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIG1 MUTATED     14    2
  LIG1 WILD-TYPE  269   46
   clus
vv  LIG1 MUTATED LIG1 WILD-TYPE
  0           14            269
  1            2             46
[1] 2 2
[1] FALSE
D314V7, 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
D314V8, binary
                cls
clus               0   1
  LIG1 MUTATED    13   3
  LIG1 WILD-TYPE 304  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIG1 MUTATED     13    3
  LIG1 WILD-TYPE  304   45
                               clus
vv                              LIG1 MUTATED LIG1 WILD-TYPE
  COLON ADENOCARCINOMA                    13            304
  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 244   2  22  21
D314V9, multiclass
    clus
vv   LIG1 MUTATED LIG1 WILD-TYPE
  R0           13            244
  R1            0              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"
D314V10, 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
D314V11, 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(315) Variable = PRB4 MUTATION ANALYSIS
D315V1, survival
                sevent
clus2              0   1
  PRB4 MUTATED    10   0
  PRB4 WILD-TYPE 272  73
  PRB4 MUTATED PRB4 WILD-TYPE 
            10            345 
  PRB4 MUTATED PRB4 WILD-TYPE 
             0             73 
$`PRB4 MUTATED`
TCGA-A6-6651 TCGA-AA-3812 TCGA-AA-3855 TCGA-AA-A010 TCGA-CA-6717 TCGA-CM-6169 
       21.76        35.05        32.05        34.98         0.33        13.02 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6898 TCGA-G4-6625 
       18.25         1.32         7.53        91.79 

$`PRB4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        24.16        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 
       10.06         0.00        33.07         0.00        36.03         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6534 TCGA-D5-6535 
       19.59        13.51        11.51        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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6628 
       26.17        46.75        52.80 

  PRB4 MUTATED PRB4 WILD-TYPE 
          0.33           0.00 
  PRB4 MUTATED PRB4 WILD-TYPE 
         91.79         140.38 
  PRB4 MUTATED PRB4 WILD-TYPE 
        20.005         20.190 
[1] "0.3 - 91.8 (20.0)"  "0.0 - 140.4 (20.2)"
[1] "hr="     "9300000"
D315V2, 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       25       104         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PRB4 MUTATED           0          0          2          0        0         0
  PRB4 WILD-TYPE        19         10         39         31       35        13
                vv
clus             STAGE IVB
  PRB4 MUTATED           0
  PRB4 WILD-TYPE         1
D315V3, multiclass
            clus
vv           PRB4 MUTATED PRB4 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             5            104
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            2             39
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PRB4 MUTATED     0   2   6   2
  PRB4 WILD-TYPE   9  66 242  39
D315V4, multiclass
    clus
vv   PRB4 MUTATED PRB4 WILD-TYPE
  T1            0              9
  T2            2             66
  T3            6            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
  PRB4 MUTATED     9   1   0
  PRB4 WILD-TYPE 211  79  66
D315V5, multiclass
    clus
vv   PRB4 MUTATED PRB4 WILD-TYPE
  N0            9            211
  N1            1             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"
D315V6, binary
                cls
clus               0   1
  PRB4 MUTATED     9   0
  PRB4 WILD-TYPE 274  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRB4 MUTATED      9    0
  PRB4 WILD-TYPE  274   48
   clus
vv  PRB4 MUTATED PRB4 WILD-TYPE
  0            9            274
  1            0             48
[1] 2 2
[1] FALSE
D315V7, 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
D315V8, binary
                cls
clus               0   1
  PRB4 MUTATED     9   1
  PRB4 WILD-TYPE 308  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRB4 MUTATED      9    1
  PRB4 WILD-TYPE  308   47
                               clus
vv                              PRB4 MUTATED PRB4 WILD-TYPE
  COLON ADENOCARCINOMA                     9            308
  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 249   2  22  20
D315V9, multiclass
    clus
vv   PRB4 MUTATED PRB4 WILD-TYPE
  R0            8            249
  R1            0              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"
D315V10, 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
D315V11, 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(316) Variable = WDR78 MUTATION ANALYSIS
D316V1, survival
                 sevent
clus2               0   1
  WDR78 MUTATED    11   1
  WDR78 WILD-TYPE 271  72
  WDR78 MUTATED WDR78 WILD-TYPE 
             12             343 
  WDR78 MUTATED WDR78 WILD-TYPE 
              1              72 
$`WDR78 MUTATED`
TCGA-AA-3672 TCGA-AA-3680 TCGA-AA-3713 TCGA-AA-3977 TCGA-AZ-4315 TCGA-CA-6717 
        0.92        11.01        19.04        25.02        58.39         0.33 
TCGA-CA-6718 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6923 TCGA-G4-6304 TCGA-G4-6307 
        0.10        13.51        20.19        12.43        53.62        55.04 

$`WDR78 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
        6.05         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       47.01        15.02         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07         0.26         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       11.51        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       65.85        44.68        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  WDR78 MUTATED WDR78 WILD-TYPE 
            0.1             0.0 
  WDR78 MUTATED WDR78 WILD-TYPE 
          58.39          140.38 
  WDR78 MUTATED WDR78 WILD-TYPE 
         16.275          20.980 
[1] "0.1 - 58.4 (16.3)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "2.4"
D316V2, 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       25       104         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        18         10         40         31       33        13
                 vv
clus              STAGE IVB
  WDR78 MUTATED           0
  WDR78 WILD-TYPE         1
D316V3, multiclass
            clus
vv           WDR78 MUTATED WDR78 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              5             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               2              33
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  WDR78 MUTATED     0   2   8   2
  WDR78 WILD-TYPE   9  66 240  39
D316V4, multiclass
    clus
vv   WDR78 MUTATED WDR78 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             8             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
  WDR78 MUTATED     9   2   1
  WDR78 WILD-TYPE 211  78  65
D316V5, multiclass
    clus
vv   WDR78 MUTATED WDR78 WILD-TYPE
  N0             9             211
  N1             2              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"
D316V6, binary
                 cls
clus                0   1
  WDR78 MUTATED     9   2
  WDR78 WILD-TYPE 274  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR78 MUTATED      9    2
  WDR78 WILD-TYPE  274   46
   clus
vv  WDR78 MUTATED WDR78 WILD-TYPE
  0             9             274
  1             2              46
[1] 2 2
[1] FALSE
D316V7, 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
D316V8, binary
                 cls
clus                0   1
  WDR78 MUTATED    11   1
  WDR78 WILD-TYPE 306  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR78 MUTATED     11    1
  WDR78 WILD-TYPE  306   47
                               clus
vv                              WDR78 MUTATED WDR78 WILD-TYPE
  COLON ADENOCARCINOMA                     11             306
  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 250   2  20  19
D316V9, multiclass
    clus
vv   WDR78 MUTATED WDR78 WILD-TYPE
  R0             7             250
  R1             0               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"
D316V10, 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
D316V11, 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(317) Variable = CYLD MUTATION ANALYSIS
D317V1, survival
                sevent
clus2              0   1
  CYLD MUTATED    16   3
  CYLD WILD-TYPE 266  70
  CYLD MUTATED CYLD WILD-TYPE 
            19            336 
  CYLD MUTATED CYLD WILD-TYPE 
             3             70 
$`CYLD MUTATED`
TCGA-A6-5657 TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3660 TCGA-AA-3715 TCGA-AA-3815 
       31.63         1.02        63.98        78.08        19.04        33.04 
TCGA-AA-3973 TCGA-AA-A010 TCGA-AD-6889 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CM-5348 
       13.05        34.98        56.55        58.39         0.33        22.98 
TCGA-CM-5860 TCGA-CM-6171 TCGA-CM-6677 TCGA-D5-5539 TCGA-D5-6539 TCGA-G4-6303 
       16.01        14.04        11.08        19.59        12.49        65.85 
TCGA-G4-6626 
       46.75 

$`CYLD WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       26.99        19.04        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       16.08        50.99        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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-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-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       12.03        45.40        12.26        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 
        0.53        35.41        19.43       107.67        74.56        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       22.09        13.78        35.80        26.17        91.79        52.80 

  CYLD MUTATED CYLD WILD-TYPE 
          0.33           0.00 
  CYLD MUTATED CYLD WILD-TYPE 
         78.08         140.38 
  CYLD MUTATED CYLD WILD-TYPE 
        22.980         20.155 
[1] "0.3 - 78.1 (23.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.7"
D317V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CYLD MUTATED         1        0        4         7         1         0
  CYLD WILD-TYPE      63        1       21       102         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CYLD MUTATED           0          2          2          0        2         0
  CYLD WILD-TYPE        19          8         39         31       33        13
                vv
clus             STAGE IVB
  CYLD MUTATED           0
  CYLD WILD-TYPE         1
D317V3, multiclass
            clus
vv           CYLD MUTATED CYLD WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              4             21
  STAGE IIA             7            102
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            2              8
  STAGE IIIB            2             39
  STAGE IIIC            0             31
  STAGE IV              2             33
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CYLD MUTATED     0   1  16   2
  CYLD WILD-TYPE   9  67 232  39
D317V4, multiclass
    clus
vv   CYLD MUTATED CYLD WILD-TYPE
  T1            0              9
  T2            1             67
  T3           16            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
  CYLD MUTATED    14   5   0
  CYLD WILD-TYPE 206  75  66
D317V5, multiclass
    clus
vv   CYLD MUTATED CYLD WILD-TYPE
  N0           14            206
  N1            5             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"
D317V6, binary
                cls
clus               0   1
  CYLD MUTATED    17   2
  CYLD WILD-TYPE 266  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  CYLD MUTATED     17    2
  CYLD WILD-TYPE  266   46
   clus
vv  CYLD MUTATED CYLD WILD-TYPE
  0           17            266
  1            2             46
[1] 2 2
[1] FALSE
D317V7, binary
                cls
clus               0   1
  CYLD MUTATED     8  11
  CYLD WILD-TYPE 162 186
[1] "tbl2"
                cls
clus             [,1] [,2]
  CYLD MUTATED      8   11
  CYLD WILD-TYPE  162  186
        clus
vv       CYLD MUTATED CYLD WILD-TYPE
  FEMALE            8            162
  MALE             11            186
[1] 2 2
[1] FALSE
D317V8, binary
                cls
clus               0   1
  CYLD MUTATED    17   2
  CYLD WILD-TYPE 300  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  CYLD MUTATED     17    2
  CYLD WILD-TYPE  300   46
                               clus
vv                              CYLD MUTATED CYLD WILD-TYPE
  COLON ADENOCARCINOMA                    17            300
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CYLD MUTATED    16   0   1   1
  CYLD WILD-TYPE 241   2  21  20
D317V9, multiclass
    clus
vv   CYLD MUTATED CYLD WILD-TYPE
  R0           16            241
  R1            0              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"
D317V10, 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     9
  CYLD WILD-TYPE                        18   167
D317V11, 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                                       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(318) Variable = ZNF182 MUTATION ANALYSIS
D318V1, survival
                  sevent
clus2                0   1
  ZNF182 MUTATED    11   1
  ZNF182 WILD-TYPE 271  72
  ZNF182 MUTATED ZNF182 WILD-TYPE 
              12              343 
  ZNF182 MUTATED ZNF182 WILD-TYPE 
               1               72 
$`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        61.41 
TCGA-CA-6717 TCGA-CK-5913 TCGA-CM-5348 TCGA-CM-5349 TCGA-DM-A1HB TCGA-G4-6303 
        0.33        51.32        22.98        30.08       135.65        65.85 

$`ZNF182 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
       17.56       102.44        40.34        15.62        49.08        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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-5860 
       37.02        25.02        13.02        29.06        22.03        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 
        0.53        35.41        19.43       107.67        74.56        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  ZNF182 MUTATED ZNF182 WILD-TYPE 
            0.33             0.00 
  ZNF182 MUTATED ZNF182 WILD-TYPE 
          135.65           140.38 
  ZNF182 MUTATED ZNF182 WILD-TYPE 
          31.805           19.660 
[1] "0.3 - 135.7 (31.8)" "0.0 - 140.4 (19.7)"
[1] "hr=" "4"  
D318V2, 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       25       103         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF182 MUTATED           0          0          3          0        1
  ZNF182 WILD-TYPE        19         10         38         31       34
                  vv
clus               STAGE IVA STAGE IVB
  ZNF182 MUTATED           0         0
  ZNF182 WILD-TYPE        13         1
D318V3, multiclass
            clus
vv           ZNF182 MUTATED ZNF182 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               6              103
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              3               38
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF182 MUTATED     1   1  10   1
  ZNF182 WILD-TYPE   8  67 238  40
D318V4, multiclass
    clus
vv   ZNF182 MUTATED ZNF182 WILD-TYPE
  T1              1                8
  T2              1               67
  T3             10              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
  ZNF182 MUTATED     9   4   0
  ZNF182 WILD-TYPE 211  76  66
D318V5, multiclass
    clus
vv   ZNF182 MUTATED ZNF182 WILD-TYPE
  N0              9              211
  N1              4               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"
D318V6, binary
                  cls
clus                 0   1
  ZNF182 MUTATED     9   1
  ZNF182 WILD-TYPE 274  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF182 MUTATED      9    1
  ZNF182 WILD-TYPE  274   47
   clus
vv  ZNF182 MUTATED ZNF182 WILD-TYPE
  0              9              274
  1              1               47
[1] 2 2
[1] FALSE
D318V7, 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
D318V8, binary
                  cls
clus                 0   1
  ZNF182 MUTATED    11   2
  ZNF182 WILD-TYPE 306  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF182 MUTATED     11    2
  ZNF182 WILD-TYPE  306   46
                               clus
vv                              ZNF182 MUTATED ZNF182 WILD-TYPE
  COLON ADENOCARCINOMA                      11              306
  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 250   2  22  19
D318V9, multiclass
    clus
vv   ZNF182 MUTATED ZNF182 WILD-TYPE
  R0              7              250
  R1              0                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"
D318V10, 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
D318V11, 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(319) Variable = MAP4K3 MUTATION ANALYSIS
D319V1, survival
                  sevent
clus2                0   1
  MAP4K3 MUTATED    12   3
  MAP4K3 WILD-TYPE 270  70
  MAP4K3 MUTATED MAP4K3 WILD-TYPE 
              15              340 
  MAP4K3 MUTATED MAP4K3 WILD-TYPE 
               3               70 
$`MAP4K3 MUTATED`
TCGA-A6-5661 TCGA-AA-3489 TCGA-AA-3663 TCGA-AA-3947 TCGA-AA-A00N TCGA-AA-A010 
       33.53         7.04         6.97        33.01         4.01        34.98 
TCGA-AD-6889 TCGA-AZ-6605 TCGA-CA-6717 TCGA-CM-6169 TCGA-CM-6679 TCGA-DM-A28H 
       56.55         5.23         0.33        13.02        10.06       117.07 
TCGA-F4-6569 TCGA-G4-6588 TCGA-G4-6628 
       13.45        26.17        52.80 

$`MAP4K3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        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        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 
       49.41         6.77        12.10       100.01        29.56        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K 
        6.12        81.37       119.93        35.97        60.79        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        13.38         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       13.78        35.80        91.79        46.75 

  MAP4K3 MUTATED MAP4K3 WILD-TYPE 
            0.33             0.00 
  MAP4K3 MUTATED MAP4K3 WILD-TYPE 
          117.07           140.38 
  MAP4K3 MUTATED MAP4K3 WILD-TYPE 
          13.450           20.235 
[1] "0.3 - 117.1 (13.4)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D319V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MAP4K3 MUTATED         2        0        2         6         4         0
  MAP4K3 WILD-TYPE      62        1       23       103         4         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAP4K3 MUTATED           0          0          1          1        0
  MAP4K3 WILD-TYPE        19         10         40         30       35
                  vv
clus               STAGE IVA STAGE IVB
  MAP4K3 MUTATED           0         0
  MAP4K3 WILD-TYPE        13         1
D319V3, multiclass
            clus
vv           MAP4K3 MUTATED MAP4K3 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               6              103
  STAGE IIB               4                4
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MAP4K3 MUTATED     0   2   9   5
  MAP4K3 WILD-TYPE   9  66 239  36
D319V4, multiclass
    clus
vv   MAP4K3 MUTATED MAP4K3 WILD-TYPE
  T1              0                9
  T2              2               66
  T3              9              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    14   1   1
  MAP4K3 WILD-TYPE 206  79  65
D319V5, multiclass
    clus
vv   MAP4K3 MUTATED MAP4K3 WILD-TYPE
  N0             14              206
  N1              1               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"
D319V6, binary
                  cls
clus                 0   1
  MAP4K3 MUTATED    15   0
  MAP4K3 WILD-TYPE 268  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP4K3 MUTATED     15    0
  MAP4K3 WILD-TYPE  268   48
   clus
vv  MAP4K3 MUTATED MAP4K3 WILD-TYPE
  0             15              268
  1              0               48
[1] 2 2
[1] FALSE
D319V7, binary
                  cls
clus                 0   1
  MAP4K3 MUTATED     5  11
  MAP4K3 WILD-TYPE 165 186
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP4K3 MUTATED      5   11
  MAP4K3 WILD-TYPE  165  186
        clus
vv       MAP4K3 MUTATED MAP4K3 WILD-TYPE
  FEMALE              5              165
  MALE               11              186
[1] 2 2
[1] FALSE
D319V8, binary
                  cls
clus                 0   1
  MAP4K3 MUTATED    13   3
  MAP4K3 WILD-TYPE 304  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP4K3 MUTATED     13    3
  MAP4K3 WILD-TYPE  304   45
                               clus
vv                              MAP4K3 MUTATED MAP4K3 WILD-TYPE
  COLON ADENOCARCINOMA                      13              304
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  MAP4K3 MUTATED    11   0   0   2
  MAP4K3 WILD-TYPE 246   2  22  19
D319V9, multiclass
    clus
vv   MAP4K3 MUTATED MAP4K3 WILD-TYPE
  R0             11              246
  R1              0                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"
D319V10, 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     7
  MAP4K3 WILD-TYPE                        17   169
D319V11, 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                                         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(320) Variable = DDB1 MUTATION ANALYSIS
D320V1, survival
                sevent
clus2              0   1
  DDB1 MUTATED     8   5
  DDB1 WILD-TYPE 274  68
  DDB1 MUTATED DDB1 WILD-TYPE 
            13            342 
  DDB1 MUTATED DDB1 WILD-TYPE 
             5             68 
$`DDB1 MUTATED`
TCGA-A6-5661 TCGA-A6-6780 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3949 TCGA-AA-A01Q 
       33.53        20.12         1.02        13.02        26.01         1.02 
TCGA-AD-6964 TCGA-AZ-6599 TCGA-CM-5862 TCGA-D5-6537 TCGA-D5-7000 TCGA-DM-A1HB 
       10.88         6.77         5.03         4.80        10.26       135.65 
TCGA-F4-6460 
       13.38 

$`DDB1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         3.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        6.97         1.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         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         1.51        12.00        11.38       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-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        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  DDB1 MUTATED DDB1 WILD-TYPE 
          1.02           0.00 
  DDB1 MUTATED DDB1 WILD-TYPE 
        135.65         140.38 
  DDB1 MUTATED DDB1 WILD-TYPE 
        10.880         20.995 
[1] "1.0 - 135.7 (10.9)" "0.0 - 140.4 (21.0)"
[1] "hr=" "2.5"
D320V2, 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       23       107         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        18         10         37         31       35        12
                vv
clus             STAGE IVB
  DDB1 MUTATED           0
  DDB1 WILD-TYPE         1
D320V3, multiclass
            clus
vv           DDB1 MUTATED DDB1 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             2            107
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            4             37
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 238  40
D320V4, multiclass
    clus
vv   DDB1 MUTATED DDB1 WILD-TYPE
  T1            0              9
  T2            2             66
  T3           10            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
  DDB1 MUTATED     6   5   2
  DDB1 WILD-TYPE 214  75  64
D320V5, multiclass
    clus
vv   DDB1 MUTATED DDB1 WILD-TYPE
  N0            6            214
  N1            5             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"
D320V6, binary
                cls
clus               0   1
  DDB1 MUTATED     8   1
  DDB1 WILD-TYPE 275  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDB1 MUTATED      8    1
  DDB1 WILD-TYPE  275   47
   clus
vv  DDB1 MUTATED DDB1 WILD-TYPE
  0            8            275
  1            1             47
[1] 2 2
[1] FALSE
D320V7, 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
D320V8, binary
                cls
clus               0   1
  DDB1 MUTATED     9   4
  DDB1 WILD-TYPE 308  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDB1 MUTATED      9    4
  DDB1 WILD-TYPE  308   44
                               clus
vv                              DDB1 MUTATED DDB1 WILD-TYPE
  COLON ADENOCARCINOMA                     9            308
  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 249   2  22  21
D320V9, multiclass
    clus
vv   DDB1 MUTATED DDB1 WILD-TYPE
  R0            8            249
  R1            0              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"
D320V10, 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
D320V11, 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(321) Variable = ITGAV MUTATION ANALYSIS
D321V1, survival
                 sevent
clus2               0   1
  ITGAV MUTATED    13   2
  ITGAV WILD-TYPE 269  71
  ITGAV MUTATED ITGAV WILD-TYPE 
             15             340 
  ITGAV MUTATED ITGAV WILD-TYPE 
              2              71 
$`ITGAV MUTATED`
TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3950 TCGA-AY-4070 TCGA-AY-6197 TCGA-AZ-4315 
       61.02         6.97        24.00        16.31        21.44        58.39 
TCGA-AZ-6601 TCGA-CA-6717 TCGA-CK-4948 TCGA-CM-5861 TCGA-CM-6674 TCGA-D5-6923 
      100.01         0.33       102.44        15.02        12.95        12.43 
TCGA-F4-6856 TCGA-G4-6306 TCGA-G4-6628 
       19.43        44.68        52.80 

$`ITGAV WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.20        14.50        27.09         0.95        15.75         0.20 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 
       35.41       107.67        74.56        65.85        53.62        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       35.80        26.17        91.79        46.75 

  ITGAV MUTATED ITGAV WILD-TYPE 
           0.33            0.00 
  ITGAV MUTATED ITGAV WILD-TYPE 
         102.44          140.38 
  ITGAV MUTATED ITGAV WILD-TYPE 
         21.440          20.155 
[1] "0.3 - 102.4 (21.4)" "0.0 - 140.4 (20.2)"
[1] "hr=" "2.4"
D321V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ITGAV MUTATED         3        0        3         7         0         0
  ITGAV WILD-TYPE      61        1       22       102         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ITGAV MUTATED           0          1          0          1        0         0
  ITGAV WILD-TYPE        19          9         41         30       35        13
                 vv
clus              STAGE IVB
  ITGAV MUTATED           0
  ITGAV WILD-TYPE         1
D321V3, multiclass
            clus
vv           ITGAV MUTATED ITGAV WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              7             102
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ITGAV MUTATED     0   4  11   0
  ITGAV WILD-TYPE   9  64 237  41
D321V4, multiclass
    clus
vv   ITGAV MUTATED ITGAV WILD-TYPE
  T1             0               9
  T2             4              64
  T3            11             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
  ITGAV MUTATED    13   1   1
  ITGAV WILD-TYPE 207  79  65
D321V5, multiclass
    clus
vv   ITGAV MUTATED ITGAV WILD-TYPE
  N0            13             207
  N1             1              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"
D321V6, binary
                 cls
clus                0   1
  ITGAV MUTATED    14   0
  ITGAV WILD-TYPE 269  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGAV MUTATED     14    0
  ITGAV WILD-TYPE  269   48
   clus
vv  ITGAV MUTATED ITGAV WILD-TYPE
  0            14             269
  1             0              48
[1] 2 2
[1] FALSE
D321V7, 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
D321V8, binary
                 cls
clus                0   1
  ITGAV MUTATED    12   3
  ITGAV WILD-TYPE 305  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGAV MUTATED     12    3
  ITGAV WILD-TYPE  305   45
                               clus
vv                              ITGAV MUTATED ITGAV WILD-TYPE
  COLON ADENOCARCINOMA                     12             305
  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 245   1  22  20
D321V9, multiclass
    clus
vv   ITGAV MUTATED ITGAV WILD-TYPE
  R0            12             245
  R1             1               1
  R2             0              22
  RX             1              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D321V10, 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
D321V11, 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(322) Variable = F8 MUTATION ANALYSIS
D322V1, survival
              sevent
clus2            0   1
  F8 MUTATED    25   7
  F8 WILD-TYPE 257  66
  F8 MUTATED F8 WILD-TYPE 
          32          323 
  F8 MUTATED F8 WILD-TYPE 
           7           66 
$`F8 MUTATED`
TCGA-A6-5656 TCGA-A6-5660 TCGA-A6-6142 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3502 
       32.91        29.19        25.08        19.66         3.02        35.01 
TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3710 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 
       63.98        29.95        26.99        33.01        24.00         2.01 
TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6964 
       25.02         4.01        34.98        56.55         0.72        10.88 
TCGA-AY-6197 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
       21.44        49.41       100.01         3.25         3.29         0.07 
TCGA-CA-6717 TCGA-CM-4743 TCGA-CM-6172 TCGA-D5-6930 TCGA-DM-A1D6 TCGA-G4-6309 
        0.33        23.05        11.01         1.51        49.91        51.75 
TCGA-G4-6586 TCGA-G4-6588 
       35.80        26.17 

$`F8 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 
       32.71        27.09        22.52         8.38        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 
       21.76        24.69        24.39        23.87        20.12        20.28 
TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        7.04         1.02         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        17.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37         4.21         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        15.75         0.20        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        1.94         2.24         3.06         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        91.79        46.75        52.80 

  F8 MUTATED F8 WILD-TYPE 
        0.07         0.00 
  F8 MUTATED F8 WILD-TYPE 
      100.01       140.38 
  F8 MUTATED F8 WILD-TYPE 
       25.05        19.99 
[1] "0.1 - 100.0 (25.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.1"
D322V2, continuous
              vv
clus           STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  F8 MUTATED         2        0        4        14         3         0
  F8 WILD-TYPE      62        1       21        95         5         1
              vv
clus           STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  F8 MUTATED           0          0          3          3        0         1
  F8 WILD-TYPE        19         10         38         28       35        12
              vv
clus           STAGE IVB
  F8 MUTATED           0
  F8 WILD-TYPE         1
D322V3, multiclass
            clus
vv           F8 MUTATED F8 WILD-TYPE
  STAGE I             2           62
  STAGE IA            0            1
  STAGE II            4           21
  STAGE IIA          14           95
  STAGE IIB           3            5
  STAGE IIC           0            1
  STAGE III           0           19
  STAGE IIIA          0           10
  STAGE IIIB          3           38
  STAGE IIIC          3           28
  STAGE IV            0           35
  STAGE IVA           1           12
  STAGE IVB           0            1
[1] 13  2
[1] TRUE
[1] "dimension of 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  25   5
  F8 WILD-TYPE   9  65 223  36
D322V4, multiclass
    clus
vv   F8 MUTATED F8 WILD-TYPE
  T1          0            9
  T2          3           65
  T3         25          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
  F8 MUTATED    24   6   3
  F8 WILD-TYPE 196  74  63
D322V5, multiclass
    clus
vv   F8 MUTATED F8 WILD-TYPE
  N0         24          196
  N1          6           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"
D322V6, binary
              cls
clus             0   1
  F8 MUTATED    26   1
  F8 WILD-TYPE 257  47
[1] "tbl2"
              cls
clus           [,1] [,2]
  F8 MUTATED     26    1
  F8 WILD-TYPE  257   47
   clus
vv  F8 MUTATED F8 WILD-TYPE
  0         26          257
  1          1           47
[1] 2 2
[1] FALSE
D322V7, binary
              cls
clus             0   1
  F8 MUTATED    14  19
  F8 WILD-TYPE 156 178
[1] "tbl2"
              cls
clus           [,1] [,2]
  F8 MUTATED     14   19
  F8 WILD-TYPE  156  178
        clus
vv       F8 MUTATED F8 WILD-TYPE
  FEMALE         14          156
  MALE           19          178
[1] 2 2
[1] FALSE
D322V8, binary
              cls
clus             0   1
  F8 MUTATED    24   9
  F8 WILD-TYPE 293  39
[1] "tbl2"
              cls
clus           [,1] [,2]
  F8 MUTATED     24    9
  F8 WILD-TYPE  293   39
                               clus
vv                              F8 MUTATED F8 WILD-TYPE
  COLON ADENOCARCINOMA                  24          293
  COLON MUCINOUS ADENOCARCINOMA          9           39
[1] 2 2
[1] FALSE
              vv
clus            R0  R1  R2  RX
  F8 MUTATED    21   0   0   2
  F8 WILD-TYPE 236   2  22  19
D322V9, multiclass
    clus
vv   F8 MUTATED F8 WILD-TYPE
  R0         21          236
  R1          0            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"
D322V10, 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      14
  F8 WILD-TYPE   162
D322V11, 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                                    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(323) Variable = MBTD1 MUTATION ANALYSIS
D323V1, survival
                 sevent
clus2               0   1
  MBTD1 MUTATED     7   2
  MBTD1 WILD-TYPE 275  71
  MBTD1 MUTATED MBTD1 WILD-TYPE 
              9             346 
  MBTD1 MUTATED MBTD1 WILD-TYPE 
              2              71 
$`MBTD1 MUTATED`
TCGA-AA-3492 TCGA-AD-6889 TCGA-AZ-6601 TCGA-CK-4948 TCGA-CK-5913 TCGA-CK-6747 
        3.02        56.55       100.01       102.44        51.32         2.93 
TCGA-D5-5539 TCGA-D5-6922 TCGA-G4-6628 
       19.59        10.13        52.80 

$`MBTD1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        4.21         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 
        0.26         0.33         0.10         1.35        17.56        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 
       15.62        49.08        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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58         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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       35.80        26.17        91.79        46.75 

  MBTD1 MUTATED MBTD1 WILD-TYPE 
           2.93            0.00 
  MBTD1 MUTATED MBTD1 WILD-TYPE 
         102.44          140.38 
  MBTD1 MUTATED MBTD1 WILD-TYPE 
         51.320          20.155 
[1] "2.9 - 102.4 (51.3)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.7"
D323V2, 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       23       106         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MBTD1 MUTATED           0          3          0          0        0         0
  MBTD1 WILD-TYPE        19          7         41         31       35        13
                 vv
clus              STAGE IVB
  MBTD1 MUTATED           0
  MBTD1 WILD-TYPE         1
D323V3, multiclass
            clus
vv           MBTD1 MUTATED MBTD1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              3             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             3               7
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MBTD1 MUTATED     0   1   8   0
  MBTD1 WILD-TYPE   9  67 240  41
D323V4, multiclass
    clus
vv   MBTD1 MUTATED MBTD1 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             8             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
  MBTD1 MUTATED     6   3   0
  MBTD1 WILD-TYPE 214  77  66
D323V5, multiclass
    clus
vv   MBTD1 MUTATED MBTD1 WILD-TYPE
  N0             6             214
  N1             3              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"
D323V6, binary
                 cls
clus                0   1
  MBTD1 MUTATED     7   0
  MBTD1 WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MBTD1 MUTATED      7    0
  MBTD1 WILD-TYPE  276   48
   clus
vv  MBTD1 MUTATED MBTD1 WILD-TYPE
  0             7             276
  1             0              48
[1] 2 2
[1] FALSE
D323V7, 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
D323V8, binary
                 cls
clus                0   1
  MBTD1 MUTATED     8   1
  MBTD1 WILD-TYPE 309  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MBTD1 MUTATED      8    1
  MBTD1 WILD-TYPE  309   47
                               clus
vv                              MBTD1 MUTATED MBTD1 WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MBTD1 MUTATED     5   0   0   2
  MBTD1 WILD-TYPE 252   2  22  19
D323V9, multiclass
    clus
vv   MBTD1 MUTATED MBTD1 WILD-TYPE
  R0             5             252
  R1             0               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"
D323V10, 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
D323V11, 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(324) Variable = OR1I1 MUTATION ANALYSIS
D324V1, survival
                 sevent
clus2               0   1
  OR1I1 MUTATED     9   1
  OR1I1 WILD-TYPE 273  72
  OR1I1 MUTATED OR1I1 WILD-TYPE 
             10             345 
  OR1I1 MUTATED OR1I1 WILD-TYPE 
              1              72 
$`OR1I1 MUTATED`
TCGA-A6-5659 TCGA-AA-3864 TCGA-AU-3779 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CM-5861 
       30.44        53.00        14.50       100.01         0.33        15.02 
TCGA-D5-6930 TCGA-F4-6569 TCGA-G4-6293 TCGA-G4-6625 
        1.51        13.45       107.67        91.79 

$`OR1I1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.38         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6628 
       26.17        46.75        52.80 

  OR1I1 MUTATED OR1I1 WILD-TYPE 
           0.33            0.00 
  OR1I1 MUTATED OR1I1 WILD-TYPE 
         107.67          140.38 
  OR1I1 MUTATED OR1I1 WILD-TYPE 
          22.73           20.19 
[1] "0.3 - 107.7 (22.7)" "0.0 - 140.4 (20.2)"
[1] "hr=" "3.6"
D324V2, 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       23       104         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        18         10         41         31       35        13
                 vv
clus              STAGE IVB
  OR1I1 MUTATED           0
  OR1I1 WILD-TYPE         1
D324V3, multiclass
            clus
vv           OR1I1 MUTATED OR1I1 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              5             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR1I1 MUTATED     0   2   8   0
  OR1I1 WILD-TYPE   9  66 240  41
D324V4, multiclass
    clus
vv   OR1I1 MUTATED OR1I1 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             8             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
  OR1I1 MUTATED     9   1   0
  OR1I1 WILD-TYPE 211  79  66
D324V5, multiclass
    clus
vv   OR1I1 MUTATED OR1I1 WILD-TYPE
  N0             9             211
  N1             1              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"
D324V6, binary
                 cls
clus                0   1
  OR1I1 MUTATED    10   0
  OR1I1 WILD-TYPE 273  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1I1 MUTATED     10    0
  OR1I1 WILD-TYPE  273   48
   clus
vv  OR1I1 MUTATED OR1I1 WILD-TYPE
  0            10             273
  1             0              48
[1] 2 2
[1] FALSE
D324V7, 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
D324V8, binary
                 cls
clus                0   1
  OR1I1 MUTATED     8   2
  OR1I1 WILD-TYPE 309  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1I1 MUTATED      8    2
  OR1I1 WILD-TYPE  309   46
                               clus
vv                              OR1I1 MUTATED OR1I1 WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  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 249   2  22  20
D324V9, multiclass
    clus
vv   OR1I1 MUTATED OR1I1 WILD-TYPE
  R0             8             249
  R1             0               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"
D324V10, 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
D324V11, 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(325) Variable = IFIT2 MUTATION ANALYSIS
D325V1, survival
                 sevent
clus2               0   1
  IFIT2 MUTATED     6   1
  IFIT2 WILD-TYPE 276  72
  IFIT2 MUTATED IFIT2 WILD-TYPE 
              7             348 
  IFIT2 MUTATED IFIT2 WILD-TYPE 
              1              72 
$`IFIT2 MUTATED`
TCGA-AA-3492 TCGA-AA-3950 TCGA-AA-3977 TCGA-CA-6717 TCGA-CA-6718 TCGA-D5-6534 
        3.02        24.00        25.02         0.33         0.10        43.27 
TCGA-G4-6309 
       51.75 

$`IFIT2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.26         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  IFIT2 MUTATED IFIT2 WILD-TYPE 
            0.1             0.0 
  IFIT2 MUTATED IFIT2 WILD-TYPE 
          51.75          140.38 
  IFIT2 MUTATED IFIT2 WILD-TYPE 
         24.000          20.155 
[1] "0.1 - 51.8 (24.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D325V2, 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       24       105         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        19         10         40         31       35        13
                 vv
clus              STAGE IVB
  IFIT2 MUTATED           0
  IFIT2 WILD-TYPE         1
D325V3, multiclass
            clus
vv           IFIT2 MUTATED IFIT2 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              4             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  IFIT2 MUTATED     0   1   6   0
  IFIT2 WILD-TYPE   9  67 242  41
D325V4, multiclass
    clus
vv   IFIT2 MUTATED IFIT2 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             6             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
  IFIT2 MUTATED     6   1   0
  IFIT2 WILD-TYPE 214  79  66
D325V5, multiclass
    clus
vv   IFIT2 MUTATED IFIT2 WILD-TYPE
  N0             6             214
  N1             1              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"
D325V6, binary
                 cls
clus                0   1
  IFIT2 MUTATED     6   0
  IFIT2 WILD-TYPE 277  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFIT2 MUTATED      6    0
  IFIT2 WILD-TYPE  277   48
   clus
vv  IFIT2 MUTATED IFIT2 WILD-TYPE
  0             6             277
  1             0              48
[1] 2 2
[1] FALSE
D325V7, 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
D325V8, binary
                 cls
clus                0   1
  IFIT2 MUTATED     4   3
  IFIT2 WILD-TYPE 313  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFIT2 MUTATED      4    3
  IFIT2 WILD-TYPE  313   45
                               clus
vv                              IFIT2 MUTATED IFIT2 WILD-TYPE
  COLON ADENOCARCINOMA                      4             313
  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 253   2  22  19
D325V9, multiclass
    clus
vv   IFIT2 MUTATED IFIT2 WILD-TYPE
  R0             4             253
  R1             0               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"
D325V10, 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
D325V11, 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(326) Variable = NUP54 MUTATION ANALYSIS
D326V1, survival
                 sevent
clus2               0   1
  NUP54 MUTATED     6   2
  NUP54 WILD-TYPE 276  71
  NUP54 MUTATED NUP54 WILD-TYPE 
              8             347 
  NUP54 MUTATED NUP54 WILD-TYPE 
              2              71 
$`NUP54 MUTATED`
TCGA-A6-6141 TCGA-AA-3510 TCGA-AA-A010 TCGA-AZ-6600 TCGA-CM-5864 TCGA-CM-6678 
        8.38        63.98        34.98        12.10        15.02        11.01 
TCGA-DM-A1D4 TCGA-G4-6321 
       92.75        22.09 

$`NUP54 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       55.04        51.75        45.11        36.72        36.00        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  NUP54 MUTATED NUP54 WILD-TYPE 
           8.38            0.00 
  NUP54 MUTATED NUP54 WILD-TYPE 
          92.75          140.38 
  NUP54 MUTATED NUP54 WILD-TYPE 
         18.555          20.190 
[1] "8.4 - 92.8 (18.6)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D326V2, 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       24       107         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        18         10         41         31       34        12
                 vv
clus              STAGE IVB
  NUP54 MUTATED           0
  NUP54 WILD-TYPE         1
D326V3, multiclass
            clus
vv           NUP54 MUTATED NUP54 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              2             107
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 245  38
D326V4, multiclass
    clus
vv   NUP54 MUTATED NUP54 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             3             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
  NUP54 MUTATED     5   3   0
  NUP54 WILD-TYPE 215  77  66
D326V5, multiclass
    clus
vv   NUP54 MUTATED NUP54 WILD-TYPE
  N0             5             215
  N1             3              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"
D326V6, binary
                 cls
clus                0   1
  NUP54 MUTATED     5   2
  NUP54 WILD-TYPE 278  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUP54 MUTATED      5    2
  NUP54 WILD-TYPE  278   46
   clus
vv  NUP54 MUTATED NUP54 WILD-TYPE
  0             5             278
  1             2              46
[1] 2 2
[1] FALSE
D326V7, 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
D326V8, binary
                 cls
clus                0   1
  NUP54 MUTATED     8   0
  NUP54 WILD-TYPE 309  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUP54 MUTATED      8    0
  NUP54 WILD-TYPE  309   48
                               clus
vv                              NUP54 MUTATED NUP54 WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  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 252   2  22  21
D326V9, multiclass
    clus
vv   NUP54 MUTATED NUP54 WILD-TYPE
  R0             5             252
  R1             0               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"
D326V10, 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
D326V11, 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(327) Variable = DMRTB1 MUTATION ANALYSIS
D327V1, survival
                  sevent
clus2                0   1
  DMRTB1 MUTATED     5   1
  DMRTB1 WILD-TYPE 277  72
  DMRTB1 MUTATED DMRTB1 WILD-TYPE 
               6              349 
  DMRTB1 MUTATED DMRTB1 WILD-TYPE 
               1               72 
$`DMRTB1 MUTATED`
TCGA-AA-3713 TCGA-AA-3846 TCGA-CK-5916 TCGA-CM-5341 TCGA-D5-6928 TCGA-G4-6588 
       19.04        17.03        21.14        29.06        11.64        26.17 

$`DMRTB1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 
       52.80 

  DMRTB1 MUTATED DMRTB1 WILD-TYPE 
           11.64             0.00 
  DMRTB1 MUTATED DMRTB1 WILD-TYPE 
           29.06           140.38 
  DMRTB1 MUTATED DMRTB1 WILD-TYPE 
           20.09            20.19 
[1] "11.6 - 29.1 (20.1)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1"  
D327V2, 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       25       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DMRTB1 MUTATED           0          1          0          0        1
  DMRTB1 WILD-TYPE        19          9         41         31       34
                  vv
clus               STAGE IVA STAGE IVB
  DMRTB1 MUTATED           0         0
  DMRTB1 WILD-TYPE        13         1
D327V3, multiclass
            clus
vv           DMRTB1 MUTATED DMRTB1 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               3              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              1                9
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  DMRTB1 MUTATED     1   1   4   0
  DMRTB1 WILD-TYPE   8  67 244  41
D327V4, multiclass
    clus
vv   DMRTB1 MUTATED DMRTB1 WILD-TYPE
  T1              1                8
  T2              1               67
  T3              4              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
  DMRTB1 MUTATED     5   1   0
  DMRTB1 WILD-TYPE 215  79  66
D327V5, multiclass
    clus
vv   DMRTB1 MUTATED DMRTB1 WILD-TYPE
  N0              5              215
  N1              1               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"
D327V6, binary
                  cls
clus                 0   1
  DMRTB1 MUTATED     5   1
  DMRTB1 WILD-TYPE 278  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DMRTB1 MUTATED      5    1
  DMRTB1 WILD-TYPE  278   47
   clus
vv  DMRTB1 MUTATED DMRTB1 WILD-TYPE
  0              5              278
  1              1               47
[1] 2 2
[1] FALSE
D327V7, 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
D327V8, binary
                  cls
clus                 0   1
  DMRTB1 MUTATED     5   1
  DMRTB1 WILD-TYPE 312  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DMRTB1 MUTATED      5    1
  DMRTB1 WILD-TYPE  312   47
                               clus
vv                              DMRTB1 MUTATED DMRTB1 WILD-TYPE
  COLON ADENOCARCINOMA                       5              312
  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 253   2  21  20
D327V9, multiclass
    clus
vv   DMRTB1 MUTATED DMRTB1 WILD-TYPE
  R0              4              253
  R1              0                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"
D327V10, 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
D327V11, 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(328) Variable = SLC28A2 MUTATION ANALYSIS
D328V1, survival
                   sevent
clus2                 0   1
  SLC28A2 MUTATED    10   1
  SLC28A2 WILD-TYPE 272  72
  SLC28A2 MUTATED SLC28A2 WILD-TYPE 
               11               344 
  SLC28A2 MUTATED SLC28A2 WILD-TYPE 
                1                72 
$`SLC28A2 MUTATED`
TCGA-AA-3655 TCGA-AA-3672 TCGA-AA-A02F TCGA-AZ-6601 TCGA-CA-6717 TCGA-CK-4950 
       61.02         0.92        39.98       100.01         0.33        40.34 
TCGA-CM-6168 TCGA-CM-6674 TCGA-D5-5538 TCGA-G4-6293 TCGA-G4-6588 
       12.99        12.95        12.26       107.67        26.17 

$`SLC28A2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 
        0.10         1.35        17.56       102.44        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 
       33.67        13.25         0.53        35.41        19.43        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  SLC28A2 MUTATED SLC28A2 WILD-TYPE 
             0.33              0.00 
  SLC28A2 MUTATED SLC28A2 WILD-TYPE 
           107.67            140.38 
  SLC28A2 MUTATED SLC28A2 WILD-TYPE 
           26.170            20.155 
[1] "0.3 - 107.7 (26.2)" "0.0 - 140.4 (20.2)"
[1] "hr=" "3.4"
D328V2, 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       23       105         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC28A2 MUTATED           3          1          1          0        1
  SLC28A2 WILD-TYPE        16          9         40         31       34
                   vv
clus                STAGE IVA STAGE IVB
  SLC28A2 MUTATED           0         0
  SLC28A2 WILD-TYPE        13         1
D328V3, multiclass
            clus
vv           SLC28A2 MUTATED SLC28A2 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 2                23
  STAGE IIA                4               105
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                3                16
  STAGE IIIA               1                 9
  STAGE IIIB               1                40
  STAGE IIIC               0                31
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC28A2 MUTATED     0   0  12   1
  SLC28A2 WILD-TYPE   9  68 236  40
D328V4, multiclass
    clus
vv   SLC28A2 MUTATED SLC28A2 WILD-TYPE
  T1               0                 9
  T2               0                68
  T3              12               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
  SLC28A2 MUTATED     7   5   1
  SLC28A2 WILD-TYPE 213  75  65
D328V5, multiclass
    clus
vv   SLC28A2 MUTATED SLC28A2 WILD-TYPE
  N0               7               213
  N1               5                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"
D328V6, binary
                   cls
clus                  0   1
  SLC28A2 MUTATED    11   1
  SLC28A2 WILD-TYPE 272  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC28A2 MUTATED     11    1
  SLC28A2 WILD-TYPE  272   47
   clus
vv  SLC28A2 MUTATED SLC28A2 WILD-TYPE
  0              11               272
  1               1                47
[1] 2 2
[1] FALSE
D328V7, 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
D328V8, binary
                   cls
clus                  0   1
  SLC28A2 MUTATED    12   1
  SLC28A2 WILD-TYPE 305  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC28A2 MUTATED     12    1
  SLC28A2 WILD-TYPE  305   47
                               clus
vv                              SLC28A2 MUTATED SLC28A2 WILD-TYPE
  COLON ADENOCARCINOMA                       12               305
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SLC28A2 MUTATED     8   1   1   2
  SLC28A2 WILD-TYPE 249   1  21  19
D328V9, multiclass
    clus
vv   SLC28A2 MUTATED SLC28A2 WILD-TYPE
  R0               8               249
  R1               1                 1
  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"
D328V10, 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
D328V11, 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(329) Variable = MSH2 MUTATION ANALYSIS
D329V1, survival
                sevent
clus2              0   1
  MSH2 MUTATED    25   7
  MSH2 WILD-TYPE 257  66
  MSH2 MUTATED MSH2 WILD-TYPE 
            32            323 
  MSH2 MUTATED MSH2 WILD-TYPE 
             7             66 
$`MSH2 MUTATED`
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3968 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 
        3.02         1.02        21.99        25.02         4.01        34.98 
TCGA-AD-6889 TCGA-AD-6895 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-6386 
       56.55         0.72        14.50        27.09        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4681 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       58.39        83.80        49.41         6.77        12.10       100.01 
TCGA-AZ-6605 TCGA-CA-6717 TCGA-CK-5914 TCGA-CM-4746 TCGA-CM-5348 TCGA-CM-6162 
        5.23         0.33        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         1.51       135.65       117.07        29.59 
TCGA-G4-6307 TCGA-G4-6315 
       55.04        36.72 

$`MSH2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3502 
       23.87        20.12        19.66        20.28         7.04        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03         2.01        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       21.37         4.21         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       10.88         0.20        16.31         0.95        15.75         0.20 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6603 
        1.41         5.13        22.36        62.79        61.41        29.56 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 
      102.44        40.34        15.62        49.08        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 
        2.93         2.01       124.27        23.05        20.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       13.02        29.06        22.03        30.08        16.01        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-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       15.02        14.04        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
        1.55        16.31        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       44.68        51.75        45.11        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  MSH2 MUTATED MSH2 WILD-TYPE 
          0.33           0.00 
  MSH2 MUTATED MSH2 WILD-TYPE 
        135.65         140.38 
  MSH2 MUTATED MSH2 WILD-TYPE 
         21.99          20.02 
[1] "0.3 - 135.7 (22.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.2"
D329V2, 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       21       101         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MSH2 MUTATED           1          0          8          1        2         0
  MSH2 WILD-TYPE        18         10         33         30       33        13
                vv
clus             STAGE IVB
  MSH2 MUTATED           0
  MSH2 WILD-TYPE         1
D329V3, multiclass
            clus
vv           MSH2 MUTATED MSH2 WILD-TYPE
  STAGE I               5             59
  STAGE IA              0              1
  STAGE II              4             21
  STAGE IIA             8            101
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            8             33
  STAGE IIIC            1             30
  STAGE IV              2             33
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MSH2 MUTATED     0   6  23   4
  MSH2 WILD-TYPE   9  62 225  37
D329V4, multiclass
    clus
vv   MSH2 MUTATED MSH2 WILD-TYPE
  T1            0              9
  T2            6             62
  T3           23            225
  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  69  64
D329V5, multiclass
    clus
vv   MSH2 MUTATED MSH2 WILD-TYPE
  N0           20            200
  N1           11             69
  N2            2             64
[1] 3 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
  MSH2 MUTATED    25   2
  MSH2 WILD-TYPE 258  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH2 MUTATED     25    2
  MSH2 WILD-TYPE  258   46
   clus
vv  MSH2 MUTATED MSH2 WILD-TYPE
  0           25            258
  1            2             46
[1] 2 2
[1] FALSE
D329V7, 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
D329V8, binary
                cls
clus               0   1
  MSH2 MUTATED    29   4
  MSH2 WILD-TYPE 288  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH2 MUTATED     29    4
  MSH2 WILD-TYPE  288   44
                               clus
vv                              MSH2 MUTATED MSH2 WILD-TYPE
  COLON ADENOCARCINOMA                    29            288
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MSH2 MUTATED    21   0   0   2
  MSH2 WILD-TYPE 236   2  22  19
D329V9, multiclass
    clus
vv   MSH2 MUTATED MSH2 WILD-TYPE
  R0           21            236
  R1            0              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"
D329V10, 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
D329V11, 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(330) Variable = ATP8B1 MUTATION ANALYSIS
D330V1, survival
                  sevent
clus2                0   1
  ATP8B1 MUTATED    19   3
  ATP8B1 WILD-TYPE 263  70
  ATP8B1 MUTATED ATP8B1 WILD-TYPE 
              22              333 
  ATP8B1 MUTATED ATP8B1 WILD-TYPE 
               3               70 
$`ATP8B1 MUTATED`
TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-3554 TCGA-AA-3672 TCGA-AA-3877 TCGA-AA-A010 
       22.06        20.12        17.95         0.92        31.00        34.98 
TCGA-AA-A01K TCGA-AD-5900 TCGA-AY-6197 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-6717 
       31.00         0.07        21.44        49.41       100.01         0.33 
TCGA-CA-6718 TCGA-CM-4752 TCGA-CM-5349 TCGA-CM-6165 TCGA-CM-6674 TCGA-D5-6529 
        0.10        13.02        30.08        16.04        12.95        20.19 
TCGA-D5-6534 TCGA-DM-A28H TCGA-G4-6625 TCGA-G4-6626 
       43.27       117.07        91.79        46.75 

$`ATP8B1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07         0.26         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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 
       16.01        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 
       12.26        19.59        13.51        11.51        18.25         1.32 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
      119.93        35.97        60.79        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 
       35.80        26.17        52.80 

  ATP8B1 MUTATED ATP8B1 WILD-TYPE 
            0.07             0.00 
  ATP8B1 MUTATED ATP8B1 WILD-TYPE 
          117.07           140.38 
  ATP8B1 MUTATED ATP8B1 WILD-TYPE 
           21.75            19.99 
[1] "0.1 - 117.1 (21.8)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.9"
D330V2, 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       23        94         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP8B1 MUTATED           1          0          0          2        0
  ATP8B1 WILD-TYPE        18         10         41         29       35
                  vv
clus               STAGE IVA STAGE IVB
  ATP8B1 MUTATED           0         0
  ATP8B1 WILD-TYPE        13         1
D330V3, multiclass
            clus
vv           ATP8B1 MUTATED ATP8B1 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA              15               94
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              2               29
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ATP8B1 MUTATED     1   1  20   1
  ATP8B1 WILD-TYPE   8  67 228  40
D330V4, multiclass
    clus
vv   ATP8B1 MUTATED ATP8B1 WILD-TYPE
  T1              1                8
  T2              1               67
  T3             20              228
  T4              1               40
[1] 4 2
[1] TRUE
[1] "dimension 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  79  64
D330V5, multiclass
    clus
vv   ATP8B1 MUTATED ATP8B1 WILD-TYPE
  N0             20              200
  N1              1               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"
D330V6, binary
                  cls
clus                 0   1
  ATP8B1 MUTATED    19   0
  ATP8B1 WILD-TYPE 264  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP8B1 MUTATED     19    0
  ATP8B1 WILD-TYPE  264   48
   clus
vv  ATP8B1 MUTATED ATP8B1 WILD-TYPE
  0             19              264
  1              0               48
[1] 2 2
[1] FALSE
D330V7, 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
D330V8, binary
                  cls
clus                 0   1
  ATP8B1 MUTATED    18   5
  ATP8B1 WILD-TYPE 299  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP8B1 MUTATED     18    5
  ATP8B1 WILD-TYPE  299   43
                               clus
vv                              ATP8B1 MUTATED ATP8B1 WILD-TYPE
  COLON ADENOCARCINOMA                      18              299
  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 240   2  22  19
D330V9, multiclass
    clus
vv   ATP8B1 MUTATED ATP8B1 WILD-TYPE
  R0             17              240
  R1              0                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"
D330V10, 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
D330V11, 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(331) Variable = DAXX MUTATION ANALYSIS
D331V1, survival
                sevent
clus2              0   1
  DAXX MUTATED     9   2
  DAXX WILD-TYPE 273  71
  DAXX MUTATED DAXX WILD-TYPE 
            11            344 
  DAXX MUTATED DAXX WILD-TYPE 
             2             71 
$`DAXX MUTATED`
TCGA-A6-5657 TCGA-A6-5661 TCGA-AU-6004 TCGA-CK-5916 TCGA-CM-5862 TCGA-CM-5868 
       31.63        33.53        27.09        21.14         5.03        17.03 
TCGA-CM-6166 TCGA-D5-6536 TCGA-G4-6309 TCGA-G4-6317 TCGA-G4-6586 
       21.99        17.85        51.75        36.00        35.80 

$`DAXX WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       32.91        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
       40.34        15.62        49.08        51.32        21.99         2.93 
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        16.01 
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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 
       45.11        36.72        22.09        13.78        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  DAXX MUTATED DAXX WILD-TYPE 
          5.03           0.00 
  DAXX MUTATED DAXX WILD-TYPE 
         51.75         140.38 
  DAXX MUTATED DAXX WILD-TYPE 
        27.090         20.005 
[1] "5.0 - 51.8 (27.1)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1.1"
D331V2, 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       25       106         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        18         10         39         30       35        11
                vv
clus             STAGE IVB
  DAXX MUTATED           0
  DAXX WILD-TYPE         1
D331V3, multiclass
            clus
vv           DAXX MUTATED DAXX WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             3            106
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            2             39
  STAGE IIIC            1             30
  STAGE IV              0             35
  STAGE IVA             2             11
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 240  40
D331V4, multiclass
    clus
vv   DAXX MUTATED DAXX WILD-TYPE
  T1            1              8
  T2            2             66
  T3            8            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
  DAXX MUTATED     6   4   2
  DAXX WILD-TYPE 214  76  64
D331V5, multiclass
    clus
vv   DAXX MUTATED DAXX WILD-TYPE
  N0            6            214
  N1            4             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"
D331V6, binary
                cls
clus               0   1
  DAXX MUTATED     9   2
  DAXX WILD-TYPE 274  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  DAXX MUTATED      9    2
  DAXX WILD-TYPE  274   46
   clus
vv  DAXX MUTATED DAXX WILD-TYPE
  0            9            274
  1            2             46
[1] 2 2
[1] FALSE
D331V7, 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
D331V8, binary
                cls
clus               0   1
  DAXX MUTATED    12   0
  DAXX WILD-TYPE 305  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  DAXX MUTATED     12    0
  DAXX WILD-TYPE  305   48
                               clus
vv                              DAXX MUTATED DAXX WILD-TYPE
  COLON ADENOCARCINOMA                    12            305
  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 246   2  22  20
D331V9, multiclass
    clus
vv   DAXX MUTATED DAXX WILD-TYPE
  R0           11            246
  R1            0              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"
D331V10, 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
D331V11, 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(332) Variable = CSNK1D MUTATION ANALYSIS
D332V1, survival
                  sevent
clus2                0   1
  CSNK1D MUTATED    13   1
  CSNK1D WILD-TYPE 269  72
  CSNK1D MUTATED CSNK1D WILD-TYPE 
              14              341 
  CSNK1D MUTATED CSNK1D WILD-TYPE 
               1               72 
$`CSNK1D MUTATED`
TCGA-A6-5661 TCGA-A6-5662 TCGA-AA-3821 TCGA-AA-3864 TCGA-AA-A00R TCGA-AY-5543 
       33.53        23.61         1.02        53.00         0.99        15.75 
TCGA-AZ-4315 TCGA-AZ-6605 TCGA-CA-6717 TCGA-CM-5861 TCGA-CM-6679 TCGA-D5-6533 
       58.39         5.23         0.33        15.02        10.06         1.32 
TCGA-D5-6928 TCGA-G4-6628 
       11.64        52.80 

$`CSNK1D WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5664 TCGA-A6-5665 
       32.91        31.63        30.44        29.19        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 
       35.05        33.04         0.99        25.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
       42.02        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 
       49.41         6.77        12.10       100.01        29.56        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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 
       12.26        19.59        13.51        11.51        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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       13.78        35.80        26.17        91.79        46.75 

  CSNK1D MUTATED CSNK1D WILD-TYPE 
            0.33             0.00 
  CSNK1D MUTATED CSNK1D WILD-TYPE 
           58.39           140.38 
  CSNK1D MUTATED CSNK1D WILD-TYPE 
           13.33            20.98 
[1] "0.3 - 58.4 (13.3)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "2.5"
D332V2, 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       24       103         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CSNK1D MUTATED           0          0          2          0        0
  CSNK1D WILD-TYPE        19         10         39         31       35
                  vv
clus               STAGE IVA STAGE IVB
  CSNK1D MUTATED           2         0
  CSNK1D WILD-TYPE        11         1
D332V3, multiclass
            clus
vv           CSNK1D MUTATED CSNK1D WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               6              103
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               2               11
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  65 239  39
D332V4, multiclass
    clus
vv   CSNK1D MUTATED CSNK1D WILD-TYPE
  T1              0                9
  T2              3               65
  T3              9              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
  CSNK1D MUTATED    11   2   1
  CSNK1D WILD-TYPE 209  78  65
D332V5, multiclass
    clus
vv   CSNK1D MUTATED CSNK1D WILD-TYPE
  N0             11              209
  N1              2               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"
D332V6, binary
                  cls
clus                 0   1
  CSNK1D MUTATED    12   2
  CSNK1D WILD-TYPE 271  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CSNK1D MUTATED     12    2
  CSNK1D WILD-TYPE  271   46
   clus
vv  CSNK1D MUTATED CSNK1D WILD-TYPE
  0             12              271
  1              2               46
[1] 2 2
[1] FALSE
D332V7, 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
D332V8, binary
                  cls
clus                 0   1
  CSNK1D MUTATED    11   3
  CSNK1D WILD-TYPE 306  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CSNK1D MUTATED     11    3
  CSNK1D WILD-TYPE  306   45
                               clus
vv                              CSNK1D MUTATED CSNK1D WILD-TYPE
  COLON ADENOCARCINOMA                      11              306
  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 246   2  22  20
D332V9, multiclass
    clus
vv   CSNK1D MUTATED CSNK1D WILD-TYPE
  R0             11              246
  R1              0                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"
D332V10, 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
D332V11, 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(333) Variable = UBR4 MUTATION ANALYSIS
D333V1, survival
                sevent
clus2              0   1
  UBR4 MUTATED    30   7
  UBR4 WILD-TYPE 252  66
  UBR4 MUTATED UBR4 WILD-TYPE 
            37            318 
  UBR4 MUTATED UBR4 WILD-TYPE 
             7             66 
$`UBR4 MUTATED`
TCGA-A6-2676 TCGA-A6-5660 TCGA-A6-6780 TCGA-AA-3516 TCGA-AA-3542 TCGA-AA-3663 
       42.90        29.19        20.12        13.02        12.99         6.97 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3864 TCGA-AA-3950 
       85.05        26.99        19.04        10.06        53.00        24.00 
TCGA-AA-A010 TCGA-AA-A02K TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 TCGA-AY-5543 
       34.98        14.01         0.72        27.42        10.88        15.75 
TCGA-AZ-4315 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CM-4743 TCGA-CM-5863 TCGA-CM-6171 
       58.39       100.01         0.33        23.05        15.02        14.04 
TCGA-CM-6674 TCGA-CM-6676 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6540 
       12.95        11.08        18.25         1.32        15.12        16.14 
TCGA-D5-6927 TCGA-D5-7000 TCGA-DM-A1HB TCGA-F4-6570 TCGA-F4-6856 TCGA-G4-6304 
        9.44        10.26       135.65         6.18        19.43        53.62 
TCGA-G4-6588 
       26.17 

$`UBR4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 
       24.16        21.76        24.69        24.39        23.87        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        6.97         1.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 
       34.03        29.00        29.00        26.01         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       78.08         6.05        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 
       19.00        36.00         5.03        19.04        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W 
       51.98        39.98         2.01         5.03         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 
       56.55         0.79         5.79        22.42         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93         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        16.01 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       11.51        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         1.51        12.00 
TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        35.41       107.67        74.56        65.85 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        52.80 

  UBR4 MUTATED UBR4 WILD-TYPE 
          0.33           0.00 
  UBR4 MUTATED UBR4 WILD-TYPE 
        135.65         140.38 
  UBR4 MUTATED UBR4 WILD-TYPE 
        16.140         21.075 
[1] "0.3 - 135.7 (16.1)" "0.0 - 140.4 (21.1)"
[1] "hr=" "1.2"
D333V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  UBR4 MUTATED         5        0        3        12         4         0
  UBR4 WILD-TYPE      59        1       22        97         4         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  UBR4 MUTATED           3          0          4          2        2         1
  UBR4 WILD-TYPE        16         10         37         29       33        12
                vv
clus             STAGE IVB
  UBR4 MUTATED           0
  UBR4 WILD-TYPE         1
D333V3, multiclass
            clus
vv           UBR4 MUTATED UBR4 WILD-TYPE
  STAGE I               5             59
  STAGE IA              0              1
  STAGE II              3             22
  STAGE IIA            12             97
  STAGE IIB             4              4
  STAGE IIC             0              1
  STAGE III             3             16
  STAGE IIIA            0             10
  STAGE IIIB            4             37
  STAGE IIIC            2             29
  STAGE IV              2             33
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  63 221  34
D333V4, multiclass
    clus
vv   UBR4 MUTATED UBR4 WILD-TYPE
  T1            0              9
  T2            5             63
  T3           27            221
  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  75  60
D333V5, multiclass
    clus
vv   UBR4 MUTATED UBR4 WILD-TYPE
  N0           28            192
  N1            5             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"
D333V6, binary
                cls
clus               0   1
  UBR4 MUTATED    30   3
  UBR4 WILD-TYPE 253  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  UBR4 MUTATED     30    3
  UBR4 WILD-TYPE  253   45
   clus
vv  UBR4 MUTATED UBR4 WILD-TYPE
  0           30            253
  1            3             45
[1] 2 2
[1] FALSE
D333V7, 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
D333V8, binary
                cls
clus               0   1
  UBR4 MUTATED    31   8
  UBR4 WILD-TYPE 286  40
[1] "tbl2"
                cls
clus             [,1] [,2]
  UBR4 MUTATED     31    8
  UBR4 WILD-TYPE  286   40
                               clus
vv                              UBR4 MUTATED UBR4 WILD-TYPE
  COLON ADENOCARCINOMA                    31            286
  COLON MUCINOUS ADENOCARCINOMA            8             40
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  UBR4 MUTATED    26   0   2   3
  UBR4 WILD-TYPE 231   2  20  18
D333V9, multiclass
    clus
vv   UBR4 MUTATED UBR4 WILD-TYPE
  R0           26            231
  R1            0              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"
D333V10, 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
D333V11, 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(334) Variable = PRAMEF12 MUTATION ANALYSIS
D334V1, survival
                    sevent
clus2                  0   1
  PRAMEF12 MUTATED     3   3
  PRAMEF12 WILD-TYPE 279  70
  PRAMEF12 MUTATED PRAMEF12 WILD-TYPE 
                 6                349 
  PRAMEF12 MUTATED PRAMEF12 WILD-TYPE 
                 3                 70 
$`PRAMEF12 MUTATED`
TCGA-AA-3715 TCGA-AZ-6603 TCGA-CM-6171 TCGA-DM-A1HB TCGA-DM-A28F TCGA-G4-6309 
       19.04        29.56        14.04       135.65        35.97        51.75 

$`PRAMEF12 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10       100.01         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
      139.17         6.12        81.37       119.93        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  PRAMEF12 MUTATED PRAMEF12 WILD-TYPE 
             14.04               0.00 
  PRAMEF12 MUTATED PRAMEF12 WILD-TYPE 
            135.65             140.38 
  PRAMEF12 MUTATED PRAMEF12 WILD-TYPE 
            32.765             20.120 
[1] "14.0 - 135.7 (32.8)" "0.0 - 140.4 (20.1)" 
[1] "hr=" "1.5"
D334V2, 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       24       109         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PRAMEF12 MUTATED           0          0          3          0        0
  PRAMEF12 WILD-TYPE        19         10         38         31       35
                    vv
clus                 STAGE IVA STAGE IVB
  PRAMEF12 MUTATED           0         0
  PRAMEF12 WILD-TYPE        13         1
D334V3, multiclass
            clus
vv           PRAMEF12 MUTATED PRAMEF12 WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  1                 24
  STAGE IIA                 0                109
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                0                 10
  STAGE IIIB                3                 38
  STAGE IIIC                0                 31
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  PRAMEF12 MUTATED     0   2   4   0
  PRAMEF12 WILD-TYPE   9  66 244  41
D334V4, multiclass
    clus
vv   PRAMEF12 MUTATED PRAMEF12 WILD-TYPE
  T1                0                  9
  T2                2                 66
  T3                4                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
  PRAMEF12 MUTATED     2   4   0
  PRAMEF12 WILD-TYPE 218  76  66
D334V5, multiclass
    clus
vv   PRAMEF12 MUTATED PRAMEF12 WILD-TYPE
  N0                2                218
  N1                4                 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"
D334V6, binary
                    cls
clus                   0   1
  PRAMEF12 MUTATED     5   0
  PRAMEF12 WILD-TYPE 278  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PRAMEF12 MUTATED      5    0
  PRAMEF12 WILD-TYPE  278   48
   clus
vv  PRAMEF12 MUTATED PRAMEF12 WILD-TYPE
  0                5                278
  1                0                 48
[1] 2 2
[1] FALSE
D334V7, binary
                    cls
clus                   0   1
  PRAMEF12 MUTATED     3   3
  PRAMEF12 WILD-TYPE 167 194
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PRAMEF12 MUTATED      3    3
  PRAMEF12 WILD-TYPE  167  194
        clus
vv       PRAMEF12 MUTATED PRAMEF12 WILD-TYPE
  FEMALE                3                167
  MALE                  3                194
[1] 2 2
[1] FALSE
D334V8, binary
                    cls
clus                   0   1
  PRAMEF12 MUTATED     6   0
  PRAMEF12 WILD-TYPE 311  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PRAMEF12 MUTATED      6    0
  PRAMEF12 WILD-TYPE  311   48
                               clus
vv                              PRAMEF12 MUTATED PRAMEF12 WILD-TYPE
  COLON ADENOCARCINOMA                         6                311
  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 254   2  22  21
D334V9, multiclass
    clus
vv   PRAMEF12 MUTATED PRAMEF12 WILD-TYPE
  R0                3                254
  R1                0                  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"
D334V10, 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     4
  PRAMEF12 WILD-TYPE                        18   172
D334V11, 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                                           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(335) Variable = ARHGAP5 MUTATION ANALYSIS
D335V1, survival
                   sevent
clus2                 0   1
  ARHGAP5 MUTATED    15   4
  ARHGAP5 WILD-TYPE 267  69
  ARHGAP5 MUTATED ARHGAP5 WILD-TYPE 
               19               336 
  ARHGAP5 MUTATED ARHGAP5 WILD-TYPE 
                4                69 
$`ARHGAP5 MUTATED`
TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3821 TCGA-AA-3845 TCGA-AA-3973 
        3.02        63.98        29.95         1.02         0.00        13.05 
TCGA-AA-A01R TCGA-AD-6889 TCGA-AD-6899 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5913 
       35.01        56.55         5.79         0.33         0.10        51.32 
TCGA-CM-5860 TCGA-CM-6678 TCGA-D5-6540 TCGA-D5-6930 TCGA-DM-A1HB TCGA-F4-6570 
       16.01        11.01        16.14         1.51       135.65         6.18 
TCGA-G4-6628 
       52.80 

$`ARHGAP5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       33.04         0.99        25.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02        14.93        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       21.99        16.08        50.99        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        4.21         0.79         0.72        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.26         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        21.99        21.14         2.93         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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        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        13.38        13.45        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 

  ARHGAP5 MUTATED ARHGAP5 WILD-TYPE 
                0                 0 
  ARHGAP5 MUTATED ARHGAP5 WILD-TYPE 
           135.65            140.38 
  ARHGAP5 MUTATED ARHGAP5 WILD-TYPE 
            13.05             20.98 
[1] "0.0 - 135.7 (13.1)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1"  
D335V2, 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       23       100         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARHGAP5 MUTATED           1          0          1          1        1
  ARHGAP5 WILD-TYPE        18         10         40         30       34
                   vv
clus                STAGE IVA STAGE IVB
  ARHGAP5 MUTATED           1         0
  ARHGAP5 WILD-TYPE        12         1
D335V3, multiclass
            clus
vv           ARHGAP5 MUTATED ARHGAP5 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 2                23
  STAGE IIA                9               100
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               1                30
  STAGE IV                 1                34
  STAGE IVA                1                12
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of 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  65 235  38
D335V4, multiclass
    clus
vv   ARHGAP5 MUTATED ARHGAP5 WILD-TYPE
  T1               0                 9
  T2               3                65
  T3              13               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
  ARHGAP5 MUTATED    14   3   2
  ARHGAP5 WILD-TYPE 206  77  64
D335V5, multiclass
    clus
vv   ARHGAP5 MUTATED ARHGAP5 WILD-TYPE
  N0              14               206
  N1               3                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"
D335V6, binary
                   cls
clus                  0   1
  ARHGAP5 MUTATED    15   2
  ARHGAP5 WILD-TYPE 268  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGAP5 MUTATED     15    2
  ARHGAP5 WILD-TYPE  268   46
   clus
vv  ARHGAP5 MUTATED ARHGAP5 WILD-TYPE
  0              15               268
  1               2                46
[1] 2 2
[1] FALSE
D335V7, 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
D335V8, binary
                   cls
clus                  0   1
  ARHGAP5 MUTATED    12   7
  ARHGAP5 WILD-TYPE 305  41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGAP5 MUTATED     12    7
  ARHGAP5 WILD-TYPE  305   41
                               clus
vv                              ARHGAP5 MUTATED ARHGAP5 WILD-TYPE
  COLON ADENOCARCINOMA                       12               305
  COLON MUCINOUS ADENOCARCINOMA               7                41
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ARHGAP5 MUTATED    12   0   1   3
  ARHGAP5 WILD-TYPE 245   2  21  18
D335V9, multiclass
    clus
vv   ARHGAP5 MUTATED ARHGAP5 WILD-TYPE
  R0              12               245
  R1               0                 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"
D335V10, 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
D335V11, 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(336) Variable = PCDHGA11 MUTATION ANALYSIS
D336V1, survival
                    sevent
clus2                  0   1
  PCDHGA11 MUTATED    14   5
  PCDHGA11 WILD-TYPE 268  68
  PCDHGA11 MUTATED PCDHGA11 WILD-TYPE 
                19                336 
  PCDHGA11 MUTATED PCDHGA11 WILD-TYPE 
                 5                 68 
$`PCDHGA11 MUTATED`
TCGA-A6-6141 TCGA-AA-3492 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3837 TCGA-AA-3864 
        8.38         3.02        85.05        19.04        38.99        53.00 
TCGA-AA-3966 TCGA-AA-A00N TCGA-AA-A02F TCGA-AD-6888 TCGA-AD-6890 TCGA-AY-6197 
        2.01         4.01        39.98         4.21         0.79        21.44 
TCGA-CK-5916 TCGA-CM-6677 TCGA-D5-6540 TCGA-DM-A1DA TCGA-F4-6570 TCGA-G4-6625 
       21.14        11.08        16.14         7.50         6.18        91.79 
TCGA-G4-6628 
       52.80 

$`PCDHGA11 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.03        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3842 
        0.99        25.02         1.02        17.98        15.95        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6895 
       18.05        40.96         0.07        21.37        56.55         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       27.09        16.31         0.95        15.75         0.20        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32        12.59       140.38        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      117.07        98.24         8.61        13.38        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        26.17        46.75 

  PCDHGA11 MUTATED PCDHGA11 WILD-TYPE 
              0.79               0.00 
  PCDHGA11 MUTATED PCDHGA11 WILD-TYPE 
             91.79             140.38 
  PCDHGA11 MUTATED PCDHGA11 WILD-TYPE 
             16.14              20.63 
[1] "0.8 - 91.8 (16.1)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "1.3"
D336V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PCDHGA11 MUTATED         3        0        2         7         1         0
  PCDHGA11 WILD-TYPE      61        1       23       102         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PCDHGA11 MUTATED           1          0          1          1        2
  PCDHGA11 WILD-TYPE        18         10         40         30       33
                    vv
clus                 STAGE IVA STAGE IVB
  PCDHGA11 MUTATED           0         0
  PCDHGA11 WILD-TYPE        13         1
D336V3, multiclass
            clus
vv           PCDHGA11 MUTATED PCDHGA11 WILD-TYPE
  STAGE I                   3                 61
  STAGE IA                  0                  1
  STAGE II                  2                 23
  STAGE IIA                 7                102
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 1                 18
  STAGE IIIA                0                 10
  STAGE IIIB                1                 40
  STAGE IIIC                1                 30
  STAGE IV                  2                 33
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  PCDHGA11 MUTATED     2   3  13   1
  PCDHGA11 WILD-TYPE   7  65 235  40
D336V4, multiclass
    clus
vv   PCDHGA11 MUTATED PCDHGA11 WILD-TYPE
  T1                2                  7
  T2                3                 65
  T3               13                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
  PCDHGA11 MUTATED    16   1   1
  PCDHGA11 WILD-TYPE 204  79  65
D336V5, multiclass
    clus
vv   PCDHGA11 MUTATED PCDHGA11 WILD-TYPE
  N0               16                204
  N1                1                 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"
D336V6, binary
                    cls
clus                   0   1
  PCDHGA11 MUTATED    15   2
  PCDHGA11 WILD-TYPE 268  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PCDHGA11 MUTATED     15    2
  PCDHGA11 WILD-TYPE  268   46
   clus
vv  PCDHGA11 MUTATED PCDHGA11 WILD-TYPE
  0               15                268
  1                2                 46
[1] 2 2
[1] FALSE
D336V7, binary
                    cls
clus                   0   1
  PCDHGA11 MUTATED     8  11
  PCDHGA11 WILD-TYPE 162 186
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PCDHGA11 MUTATED      8   11
  PCDHGA11 WILD-TYPE  162  186
        clus
vv       PCDHGA11 MUTATED PCDHGA11 WILD-TYPE
  FEMALE                8                162
  MALE                 11                186
[1] 2 2
[1] FALSE
D336V8, binary
                    cls
clus                   0   1
  PCDHGA11 MUTATED    15   4
  PCDHGA11 WILD-TYPE 302  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PCDHGA11 MUTATED     15    4
  PCDHGA11 WILD-TYPE  302   44
                               clus
vv                              PCDHGA11 MUTATED PCDHGA11 WILD-TYPE
  COLON ADENOCARCINOMA                        15                302
  COLON MUCINOUS ADENOCARCINOMA                4                 44
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  PCDHGA11 MUTATED    12   0   2   1
  PCDHGA11 WILD-TYPE 245   2  20  20
D336V9, multiclass
    clus
vv   PCDHGA11 MUTATED PCDHGA11 WILD-TYPE
  R0               12                245
  R1                0                  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"
D336V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PCDHGA11 MUTATED                                  0     0
  PCDHGA11 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  PCDHGA11 MUTATED                           1    10
  PCDHGA11 WILD-TYPE                        18   166
D336V11, multiclass
                                  clus
vv                                 PCDHGA11 MUTATED PCDHGA11 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(337) Variable = HIST1H1T MUTATION ANALYSIS
D337V1, survival
                    sevent
clus2                  0   1
  HIST1H1T MUTATED     7   2
  HIST1H1T WILD-TYPE 275  71
  HIST1H1T MUTATED HIST1H1T WILD-TYPE 
                 9                346 
  HIST1H1T MUTATED HIST1H1T WILD-TYPE 
                 2                 71 
$`HIST1H1T MUTATED`
TCGA-A6-5661 TCGA-A6-6141 TCGA-AA-3663 TCGA-D5-5538 TCGA-D5-6533 TCGA-D5-6922 
       33.53         8.38         6.97        12.26         1.32        10.13 
TCGA-D5-6930 TCGA-DM-A1D4 TCGA-DM-A1D6 
        1.51        92.75        49.91 

$`HIST1H1T WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        13.51        11.51        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-D5-6923 
       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-D5-6931 
       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-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  HIST1H1T MUTATED HIST1H1T WILD-TYPE 
              1.32               0.00 
  HIST1H1T MUTATED HIST1H1T WILD-TYPE 
             92.75             140.38 
  HIST1H1T MUTATED HIST1H1T WILD-TYPE 
             10.13              20.63 
[1] "1.3 - 92.8 (10.1)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "1.1"
D337V2, 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       24       104         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HIST1H1T MUTATED           0          1          2          0        0
  HIST1H1T WILD-TYPE        19          9         39         31       35
                    vv
clus                 STAGE IVA STAGE IVB
  HIST1H1T MUTATED           0         0
  HIST1H1T WILD-TYPE        13         1
D337V3, multiclass
            clus
vv           HIST1H1T MUTATED HIST1H1T WILD-TYPE
  STAGE I                   0                 64
  STAGE IA                  0                  1
  STAGE II                  1                 24
  STAGE IIA                 5                104
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                1                  9
  STAGE IIIB                2                 39
  STAGE IIIC                0                 31
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  HIST1H1T MUTATED     0   0   8   1
  HIST1H1T WILD-TYPE   9  68 240  40
D337V4, multiclass
    clus
vv   HIST1H1T MUTATED HIST1H1T WILD-TYPE
  T1                0                  9
  T2                0                 68
  T3                8                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
  HIST1H1T MUTATED     7   2   0
  HIST1H1T WILD-TYPE 213  78  66
D337V5, multiclass
    clus
vv   HIST1H1T MUTATED HIST1H1T WILD-TYPE
  N0                7                213
  N1                2                 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"
D337V6, binary
                    cls
clus                   0   1
  HIST1H1T MUTATED     9   0
  HIST1H1T WILD-TYPE 274  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1T MUTATED      9    0
  HIST1H1T WILD-TYPE  274   48
   clus
vv  HIST1H1T MUTATED HIST1H1T WILD-TYPE
  0                9                274
  1                0                 48
[1] 2 2
[1] FALSE
D337V7, 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
D337V8, binary
                    cls
clus                   0   1
  HIST1H1T MUTATED     7   2
  HIST1H1T WILD-TYPE 310  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1T MUTATED      7    2
  HIST1H1T WILD-TYPE  310   46
                               clus
vv                              HIST1H1T MUTATED HIST1H1T WILD-TYPE
  COLON ADENOCARCINOMA                         7                310
  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 251   2  22  21
D337V9, multiclass
    clus
vv   HIST1H1T MUTATED HIST1H1T WILD-TYPE
  R0                6                251
  R1                0                  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"
D337V10, 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
D337V11, 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(338) Variable = DOCK1 MUTATION ANALYSIS
D338V1, survival
                 sevent
clus2               0   1
  DOCK1 MUTATED    19   4
  DOCK1 WILD-TYPE 263  69
  DOCK1 MUTATED DOCK1 WILD-TYPE 
             23             332 
  DOCK1 MUTATED DOCK1 WILD-TYPE 
              4              69 
$`DOCK1 MUTATED`
TCGA-A6-5661 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3715 TCGA-AA-3950 TCGA-AA-A004 
       33.53        78.08        54.02        19.04        24.00        13.94 
TCGA-AA-A010 TCGA-AD-5900 TCGA-AD-6889 TCGA-AU-3779 TCGA-AY-6196 TCGA-AZ-4315 
       34.98         0.07        56.55        14.50         0.20        58.39 
TCGA-CA-6717 TCGA-CK-4948 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-6166 TCGA-CM-6171 
        0.33       102.44        23.05        37.02        21.99        14.04 
TCGA-D5-6537 TCGA-DM-A0XD TCGA-F4-6570 TCGA-G4-6307 TCGA-G4-6588 
        4.80        24.43         6.18        55.04        26.17 

$`DOCK1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        61.02         6.05         6.97 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       27.02        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37         4.21 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        27.09        16.31         0.95        15.75        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4747 
       21.14         2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12        17.85        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38        10.26       119.70        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        53.62        44.68        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  DOCK1 MUTATED DOCK1 WILD-TYPE 
           0.07            0.00 
  DOCK1 MUTATED DOCK1 WILD-TYPE 
         102.44          140.38 
  DOCK1 MUTATED DOCK1 WILD-TYPE 
         24.000          20.005 
[1] "0.1 - 102.4 (24.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.4"
D338V2, 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       22        97         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DOCK1 MUTATED           0          1          2          1        0         0
  DOCK1 WILD-TYPE        19          9         39         30       35        13
                 vv
clus              STAGE IVB
  DOCK1 MUTATED           0
  DOCK1 WILD-TYPE         1
D338V3, multiclass
            clus
vv           DOCK1 MUTATED DOCK1 WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA             12              97
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             2              39
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DOCK1 MUTATED     0   4  19   1
  DOCK1 WILD-TYPE   9  64 229  40
D338V4, multiclass
    clus
vv   DOCK1 MUTATED DOCK1 WILD-TYPE
  T1             0               9
  T2             4              64
  T3            19             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
  DOCK1 MUTATED    20   3   1
  DOCK1 WILD-TYPE 200  77  65
D338V5, multiclass
    clus
vv   DOCK1 MUTATED DOCK1 WILD-TYPE
  N0            20             200
  N1             3              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"
D338V6, binary
                 cls
clus                0   1
  DOCK1 MUTATED    21   0
  DOCK1 WILD-TYPE 262  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK1 MUTATED     21    0
  DOCK1 WILD-TYPE  262   48
   clus
vv  DOCK1 MUTATED DOCK1 WILD-TYPE
  0            21             262
  1             0              48
[1] 2 2
[1] FALSE
D338V7, 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
D338V8, binary
                 cls
clus                0   1
  DOCK1 MUTATED    20   4
  DOCK1 WILD-TYPE 297  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK1 MUTATED     20    4
  DOCK1 WILD-TYPE  297   44
                               clus
vv                              DOCK1 MUTATED DOCK1 WILD-TYPE
  COLON ADENOCARCINOMA                     20             297
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DOCK1 MUTATED    21   0   0   1
  DOCK1 WILD-TYPE 236   2  22  20
D338V9, multiclass
    clus
vv   DOCK1 MUTATED DOCK1 WILD-TYPE
  R0            21             236
  R1             0               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"
D338V10, 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
D338V11, 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(339) Variable = ABCC4 MUTATION ANALYSIS
D339V1, survival
                 sevent
clus2               0   1
  ABCC4 MUTATED    13   4
  ABCC4 WILD-TYPE 269  69
  ABCC4 MUTATED ABCC4 WILD-TYPE 
             17             338 
  ABCC4 MUTATED ABCC4 WILD-TYPE 
              4              69 
$`ABCC4 MUTATED`
TCGA-A6-5666 TCGA-AA-3516 TCGA-AA-3534 TCGA-AA-3955 TCGA-AA-A00N TCGA-AA-A010 
       32.71        13.02        29.00        20.98         4.01        34.98 
TCGA-AA-A01R TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-6601 TCGA-CA-5797 TCGA-CK-6747 
       35.01        27.09        58.39       100.01         3.29         2.93 
TCGA-CM-4743 TCGA-D5-5539 TCGA-D5-6534 TCGA-DM-A285 TCGA-G4-6306 
       23.05        19.59        43.27         6.12        44.68 

$`ABCC4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 
        0.00        19.07        34.03        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3956 
       24.00        33.01        26.01        24.00         2.01        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        2.24         3.06         3.25         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 
       49.08        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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 
       11.51        20.19        18.25         1.32        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  ABCC4 MUTATED ABCC4 WILD-TYPE 
           2.93            0.00 
  ABCC4 MUTATED ABCC4 WILD-TYPE 
         100.01          140.38 
  ABCC4 MUTATED ABCC4 WILD-TYPE 
         27.090          20.005 
[1] "2.9 - 100.0 (27.1)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1"  
D339V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ABCC4 MUTATED         1        0        2         8         3         1
  ABCC4 WILD-TYPE      63        1       23       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        17          9         40         31       34        13
                 vv
clus              STAGE IVB
  ABCC4 MUTATED           0
  ABCC4 WILD-TYPE         1
D339V3, multiclass
            clus
vv           ABCC4 MUTATED ABCC4 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              8             101
  STAGE IIB              3               5
  STAGE IIC              1               0
  STAGE III              2              17
  STAGE IIIA             1               9
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ABCC4 MUTATED     0   3  12   5
  ABCC4 WILD-TYPE   9  65 236  36
D339V4, multiclass
    clus
vv   ABCC4 MUTATED ABCC4 WILD-TYPE
  T1             0               9
  T2             3              65
  T3            12             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
  ABCC4 MUTATED    15   1   4
  ABCC4 WILD-TYPE 205  79  62
D339V5, multiclass
    clus
vv   ABCC4 MUTATED ABCC4 WILD-TYPE
  N0            15             205
  N1             1              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"
D339V6, binary
                 cls
clus                0   1
  ABCC4 MUTATED    17   1
  ABCC4 WILD-TYPE 266  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCC4 MUTATED     17    1
  ABCC4 WILD-TYPE  266   47
   clus
vv  ABCC4 MUTATED ABCC4 WILD-TYPE
  0            17             266
  1             1              47
[1] 2 2
[1] FALSE
D339V7, 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
D339V8, binary
                 cls
clus                0   1
  ABCC4 MUTATED    14   6
  ABCC4 WILD-TYPE 303  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCC4 MUTATED     14    6
  ABCC4 WILD-TYPE  303   42
                               clus
vv                              ABCC4 MUTATED ABCC4 WILD-TYPE
  COLON ADENOCARCINOMA                     14             303
  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 243   2  22  19
D339V9, multiclass
    clus
vv   ABCC4 MUTATED ABCC4 WILD-TYPE
  R0            14             243
  R1             0               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"
D339V10, 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
D339V11, 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(340) Variable = MOBKL2B MUTATION ANALYSIS
D340V1, survival
                   sevent
clus2                 0   1
  MOBKL2B MUTATED     6   1
  MOBKL2B WILD-TYPE 276  72
  MOBKL2B MUTATED MOBKL2B WILD-TYPE 
                7               348 
  MOBKL2B MUTATED MOBKL2B WILD-TYPE 
                1                72 
$`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         2.93 
TCGA-DM-A1HA 
      131.51 

$`MOBKL2B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W 
       51.98        39.98         2.01         5.03         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 
       56.55         0.79         0.72         5.79        22.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 
       15.62        49.08        51.32        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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  MOBKL2B MUTATED MOBKL2B WILD-TYPE 
             2.93              0.00 
  MOBKL2B MUTATED MOBKL2B WILD-TYPE 
           131.51            140.38 
  MOBKL2B MUTATED MOBKL2B WILD-TYPE 
           19.660            20.235 
[1] "2.9 - 131.5 (19.7)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.7"
D340V2, 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       25       108         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MOBKL2B MUTATED           0          0          2          2        1
  MOBKL2B WILD-TYPE        19         10         39         29       34
                   vv
clus                STAGE IVA STAGE IVB
  MOBKL2B MUTATED           0         0
  MOBKL2B WILD-TYPE        13         1
D340V3, multiclass
            clus
vv           MOBKL2B MUTATED MOBKL2B WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                1               108
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               2                39
  STAGE IIIC               2                29
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  MOBKL2B MUTATED     0   0   5   2
  MOBKL2B WILD-TYPE   9  68 243  39
D340V4, multiclass
    clus
vv   MOBKL2B MUTATED MOBKL2B WILD-TYPE
  T1               0                 9
  T2               0                68
  T3               5               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
  MOBKL2B MUTATED     2   3   2
  MOBKL2B WILD-TYPE 218  77  64
D340V5, multiclass
    clus
vv   MOBKL2B MUTATED MOBKL2B WILD-TYPE
  N0               2               218
  N1               3                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"
D340V6, binary
                   cls
clus                  0   1
  MOBKL2B MUTATED     2   1
  MOBKL2B WILD-TYPE 281  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MOBKL2B MUTATED      2    1
  MOBKL2B WILD-TYPE  281   47
   clus
vv  MOBKL2B MUTATED MOBKL2B WILD-TYPE
  0               2               281
  1               1                47
[1] 2 2
[1] FALSE
D340V7, 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
D340V8, binary
                   cls
clus                  0   1
  MOBKL2B MUTATED     6   1
  MOBKL2B WILD-TYPE 311  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MOBKL2B MUTATED      6    1
  MOBKL2B WILD-TYPE  311   47
                               clus
vv                              MOBKL2B MUTATED MOBKL2B WILD-TYPE
  COLON ADENOCARCINOMA                        6               311
  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 255   2  21  19
D340V9, multiclass
    clus
vv   MOBKL2B MUTATED MOBKL2B WILD-TYPE
  R0               2               255
  R1               0                 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"
D340V10, 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
D340V11, 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(341) Variable = TXNDC15 MUTATION ANALYSIS
D341V1, survival
                   sevent
clus2                 0   1
  TXNDC15 MUTATED     4   2
  TXNDC15 WILD-TYPE 278  71
  TXNDC15 MUTATED TXNDC15 WILD-TYPE 
                6               349 
  TXNDC15 MUTATED TXNDC15 WILD-TYPE 
                2                71 
$`TXNDC15 MUTATED`
TCGA-AA-3950 TCGA-AA-A00N TCGA-CM-4746 TCGA-CM-6163 TCGA-DM-A285 TCGA-G4-6307 
       24.00         4.01        37.02        14.04         6.12        55.04 

$`TXNDC15 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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 
       16.01        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02        12.00        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  TXNDC15 MUTATED TXNDC15 WILD-TYPE 
             4.01              0.00 
  TXNDC15 MUTATED TXNDC15 WILD-TYPE 
            55.04            140.38 
  TXNDC15 MUTATED TXNDC15 WILD-TYPE 
            19.02             20.19 
[1] "4.0 - 55.0 (19.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.8"
D341V2, 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       25       108         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TXNDC15 MUTATED           0          0          1          0        1
  TXNDC15 WILD-TYPE        19         10         40         31       34
                   vv
clus                STAGE IVA STAGE IVB
  TXNDC15 MUTATED           0         0
  TXNDC15 WILD-TYPE        13         1
D341V3, multiclass
            clus
vv           TXNDC15 MUTATED TXNDC15 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                1               108
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               0                31
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TXNDC15 MUTATED     1   1   3   1
  TXNDC15 WILD-TYPE   8  67 245  40
D341V4, multiclass
    clus
vv   TXNDC15 MUTATED TXNDC15 WILD-TYPE
  T1               1                 8
  T2               1                67
  T3               3               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
  TXNDC15 MUTATED     4   1   1
  TXNDC15 WILD-TYPE 216  79  65
D341V5, multiclass
    clus
vv   TXNDC15 MUTATED TXNDC15 WILD-TYPE
  N0               4               216
  N1               1                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"
D341V6, binary
                   cls
clus                  0   1
  TXNDC15 MUTATED     5   1
  TXNDC15 WILD-TYPE 278  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TXNDC15 MUTATED      5    1
  TXNDC15 WILD-TYPE  278   47
   clus
vv  TXNDC15 MUTATED TXNDC15 WILD-TYPE
  0               5               278
  1               1                47
[1] 2 2
[1] FALSE
D341V7, 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
D341V8, binary
                   cls
clus                  0   1
  TXNDC15 MUTATED     3   3
  TXNDC15 WILD-TYPE 314  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TXNDC15 MUTATED      3    3
  TXNDC15 WILD-TYPE  314   45
                               clus
vv                              TXNDC15 MUTATED TXNDC15 WILD-TYPE
  COLON ADENOCARCINOMA                        3               314
  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 252   2  22  21
D341V9, multiclass
    clus
vv   TXNDC15 MUTATED TXNDC15 WILD-TYPE
  R0               5               252
  R1               0                 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"
D341V10, 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
D341V11, 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(342) Variable = GTF2IRD2 MUTATION ANALYSIS
D342V1, survival
                    sevent
clus2                  0   1
  GTF2IRD2 MUTATED     6   0
  GTF2IRD2 WILD-TYPE 276  73
  GTF2IRD2 MUTATED GTF2IRD2 WILD-TYPE 
                 6                349 
  GTF2IRD2 MUTATED GTF2IRD2 WILD-TYPE 
                 0                 73 
$`GTF2IRD2 MUTATED`
TCGA-CA-5797 TCGA-CA-6717 TCGA-CM-5860 TCGA-CM-6165 TCGA-F4-6856 TCGA-G4-6588 
        3.29         0.33        16.01        16.04        19.43        26.17 

$`GTF2IRD2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.25         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        35.41       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 
       52.80 

  GTF2IRD2 MUTATED GTF2IRD2 WILD-TYPE 
              0.33               0.00 
  GTF2IRD2 MUTATED GTF2IRD2 WILD-TYPE 
             26.17             140.38 
  GTF2IRD2 MUTATED GTF2IRD2 WILD-TYPE 
            16.025             20.980 
[1] "0.3 - 26.2 (16.0)"  "0.0 - 140.4 (21.0)"
[1] "hr="     "9100000"
D342V2, 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       25       104         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GTF2IRD2 MUTATED           0          0          0          0        0
  GTF2IRD2 WILD-TYPE        19         10         41         31       35
                    vv
clus                 STAGE IVA STAGE IVB
  GTF2IRD2 MUTATED           0         0
  GTF2IRD2 WILD-TYPE        13         1
D342V3, multiclass
            clus
vv           GTF2IRD2 MUTATED GTF2IRD2 WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  0                 25
  STAGE IIA                 5                104
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                0                 10
  STAGE IIIB                0                 41
  STAGE IIIC                0                 31
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  GTF2IRD2 MUTATED     0   1   5   0
  GTF2IRD2 WILD-TYPE   9  67 243  41
D342V4, multiclass
    clus
vv   GTF2IRD2 MUTATED GTF2IRD2 WILD-TYPE
  T1                0                  9
  T2                1                 67
  T3                5                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
  GTF2IRD2 MUTATED     6   0   0
  GTF2IRD2 WILD-TYPE 214  80  66
D342V5, multiclass
    clus
vv   GTF2IRD2 MUTATED GTF2IRD2 WILD-TYPE
  N0                6                214
  N1                0                 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"
D342V6, binary
                    cls
clus                   0   1
  GTF2IRD2 MUTATED     6   0
  GTF2IRD2 WILD-TYPE 277  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  GTF2IRD2 MUTATED      6    0
  GTF2IRD2 WILD-TYPE  277   48
   clus
vv  GTF2IRD2 MUTATED GTF2IRD2 WILD-TYPE
  0                6                277
  1                0                 48
[1] 2 2
[1] FALSE
D342V7, 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
D342V8, binary
                    cls
clus                   0   1
  GTF2IRD2 MUTATED     4   2
  GTF2IRD2 WILD-TYPE 313  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  GTF2IRD2 MUTATED      4    2
  GTF2IRD2 WILD-TYPE  313   46
                               clus
vv                              GTF2IRD2 MUTATED GTF2IRD2 WILD-TYPE
  COLON ADENOCARCINOMA                         4                313
  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 252   2  22  20
D342V9, multiclass
    clus
vv   GTF2IRD2 MUTATED GTF2IRD2 WILD-TYPE
  R0                5                252
  R1                0                  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"
D342V10, 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
D342V11, 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(343) Variable = KDM5B MUTATION ANALYSIS
D343V1, survival
                 sevent
clus2               0   1
  KDM5B MUTATED    14   8
  KDM5B WILD-TYPE 268  65
  KDM5B MUTATED KDM5B WILD-TYPE 
             22             333 
  KDM5B MUTATED KDM5B WILD-TYPE 
              8              65 
$`KDM5B MUTATED`
TCGA-A6-3809 TCGA-A6-5661 TCGA-AA-3510 TCGA-AA-3715 TCGA-AA-3818 TCGA-AA-3864 
       32.75        33.53        63.98        19.04         0.99        53.00 
TCGA-AA-3877 TCGA-AA-3947 TCGA-AY-6197 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CM-6161 
       31.00        33.01        21.44       100.01         0.33        15.02 
TCGA-CM-6677 TCGA-D5-5541 TCGA-DM-A0XD TCGA-DM-A1D4 TCGA-DM-A1D9 TCGA-DM-A1DA 
       11.08        11.51        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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        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-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       13.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 
       10.26       119.70        38.20       130.65        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
       12.59        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-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 
       13.38        13.45        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      107.67        74.56        65.85        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       26.17        91.79        52.80 

  KDM5B MUTATED KDM5B WILD-TYPE 
           0.33            0.00 
  KDM5B MUTATED KDM5B WILD-TYPE 
         140.38          139.17 
  KDM5B MUTATED KDM5B WILD-TYPE 
         31.875          19.990 
[1] "0.3 - 140.4 (31.9)" "0.0 - 139.2 (20.0)"
[1] "hr=" "1.2"
D343V2, 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       21        98         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        19         10         40         29       35        13
                 vv
clus              STAGE IVB
  KDM5B MUTATED           0
  KDM5B WILD-TYPE         1
D343V3, multiclass
            clus
vv           KDM5B MUTATED KDM5B WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               4              21
  STAGE IIA             11              98
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             2              29
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KDM5B MUTATED     1   1  18   3
  KDM5B WILD-TYPE   8  67 230  38
D343V4, multiclass
    clus
vv   KDM5B MUTATED KDM5B WILD-TYPE
  T1             1               8
  T2             1              67
  T3            18             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
  KDM5B MUTATED    20   1   2
  KDM5B WILD-TYPE 200  79  64
D343V5, multiclass
    clus
vv   KDM5B MUTATED KDM5B WILD-TYPE
  N0            20             200
  N1             1              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"
D343V6, binary
                 cls
clus                0   1
  KDM5B MUTATED    22   0
  KDM5B WILD-TYPE 261  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM5B MUTATED     22    0
  KDM5B WILD-TYPE  261   48
   clus
vv  KDM5B MUTATED KDM5B WILD-TYPE
  0            22             261
  1             0              48
[1] 2 2
[1] FALSE
D343V7, 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
D343V8, binary
                 cls
clus                0   1
  KDM5B MUTATED    19   4
  KDM5B WILD-TYPE 298  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM5B MUTATED     19    4
  KDM5B WILD-TYPE  298   44
                               clus
vv                              KDM5B MUTATED KDM5B WILD-TYPE
  COLON ADENOCARCINOMA                     19             298
  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 241   2  22  20
D343V9, multiclass
    clus
vv   KDM5B MUTATED KDM5B WILD-TYPE
  R0            16             241
  R1             0               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"
D343V10, 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
D343V11, 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(344) Variable = CRY1 MUTATION ANALYSIS
D344V1, survival
                sevent
clus2              0   1
  CRY1 MUTATED     9   3
  CRY1 WILD-TYPE 273  70
  CRY1 MUTATED CRY1 WILD-TYPE 
            12            343 
  CRY1 MUTATED CRY1 WILD-TYPE 
             3             70 
$`CRY1 MUTATED`
TCGA-A6-6651 TCGA-AA-3492 TCGA-AA-3511 TCGA-AA-3672 TCGA-AA-3713 TCGA-AD-6895 
       21.76         3.02         6.97         0.92        19.04         0.72 
TCGA-CA-6717 TCGA-CM-6168 TCGA-D5-5537 TCGA-DM-A1HB TCGA-G4-6317 TCGA-G4-6626 
        0.33        12.99        45.40       135.65        36.00        46.75 

$`CRY1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        24.16        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
        0.07        21.37         4.21        56.55         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.72        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6628 
       52.80 

  CRY1 MUTATED CRY1 WILD-TYPE 
          0.33           0.00 
  CRY1 MUTATED CRY1 WILD-TYPE 
        135.65         140.38 
  CRY1 MUTATED CRY1 WILD-TYPE 
        16.015         20.280 
[1] "0.3 - 135.7 (16.0)" "0.0 - 140.4 (20.3)"
[1] "hr=" "1.2"
D344V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CRY1 MUTATED         0        0        2         4         0         0
  CRY1 WILD-TYPE      64        1       23       105         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CRY1 MUTATED           1          0          2          1        1         0
  CRY1 WILD-TYPE        18         10         39         30       34        13
                vv
clus             STAGE IVB
  CRY1 MUTATED           0
  CRY1 WILD-TYPE         1
D344V3, multiclass
            clus
vv           CRY1 MUTATED CRY1 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             4            105
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            2             39
  STAGE IIIC            1             30
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CRY1 MUTATED     0   0  11   1
  CRY1 WILD-TYPE   9  68 237  40
D344V4, multiclass
    clus
vv   CRY1 MUTATED CRY1 WILD-TYPE
  T1            0              9
  T2            0             68
  T3           11            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     6   4   2
  CRY1 WILD-TYPE 214  76  64
D344V5, multiclass
    clus
vv   CRY1 MUTATED CRY1 WILD-TYPE
  N0            6            214
  N1            4             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"
D344V6, binary
                cls
clus               0   1
  CRY1 MUTATED     7   1
  CRY1 WILD-TYPE 276  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  CRY1 MUTATED      7    1
  CRY1 WILD-TYPE  276   47
   clus
vv  CRY1 MUTATED CRY1 WILD-TYPE
  0            7            276
  1            1             47
[1] 2 2
[1] FALSE
D344V7, binary
                cls
clus               0   1
  CRY1 MUTATED     5   7
  CRY1 WILD-TYPE 165 190
[1] "tbl2"
                cls
clus             [,1] [,2]
  CRY1 MUTATED      5    7
  CRY1 WILD-TYPE  165  190
        clus
vv       CRY1 MUTATED CRY1 WILD-TYPE
  FEMALE            5            165
  MALE              7            190
[1] 2 2
[1] FALSE
D344V8, binary
                cls
clus               0   1
  CRY1 MUTATED    11   1
  CRY1 WILD-TYPE 306  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  CRY1 MUTATED     11    1
  CRY1 WILD-TYPE  306   47
                               clus
vv                              CRY1 MUTATED CRY1 WILD-TYPE
  COLON ADENOCARCINOMA                    11            306
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CRY1 MUTATED     6   0   1   2
  CRY1 WILD-TYPE 251   2  21  19
D344V9, multiclass
    clus
vv   CRY1 MUTATED CRY1 WILD-TYPE
  R0            6            251
  R1            0              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"
D344V10, 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     6
  CRY1 WILD-TYPE                        18   170
D344V11, 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                                       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(345) Variable = FBLN5 MUTATION ANALYSIS
D345V1, survival
                 sevent
clus2               0   1
  FBLN5 MUTATED     4   4
  FBLN5 WILD-TYPE 278  69
  FBLN5 MUTATED FBLN5 WILD-TYPE 
              8             347 
  FBLN5 MUTATED FBLN5 WILD-TYPE 
              4              69 
$`FBLN5 MUTATED`
TCGA-AY-5543 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-4952 TCGA-DM-A0XF 
       15.75        61.41        49.41         0.33        15.62        38.20 
TCGA-DM-A1DB TCGA-G4-6626 
       44.32        46.75 

$`FBLN5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6599 
        1.41         5.13        83.80        22.36        62.79         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        52.80 

  FBLN5 MUTATED FBLN5 WILD-TYPE 
           0.33            0.00 
  FBLN5 MUTATED FBLN5 WILD-TYPE 
          61.41          140.38 
  FBLN5 MUTATED FBLN5 WILD-TYPE 
          41.26           20.12 
[1] "0.3 - 61.4 (41.3)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.8"
D345V2, 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       24       106         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FBLN5 MUTATED           1          0          0          1        0         1
  FBLN5 WILD-TYPE        18         10         41         30       35        12
                 vv
clus              STAGE IVB
  FBLN5 MUTATED           0
  FBLN5 WILD-TYPE         1
D345V3, multiclass
            clus
vv           FBLN5 MUTATED FBLN5 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              3             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  68 242  40
D345V4, multiclass
    clus
vv   FBLN5 MUTATED FBLN5 WILD-TYPE
  T1             1               8
  T2             0              68
  T3             6             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
  FBLN5 MUTATED     5   1   2
  FBLN5 WILD-TYPE 215  79  64
D345V5, multiclass
    clus
vv   FBLN5 MUTATED FBLN5 WILD-TYPE
  N0             5             215
  N1             1              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"
D345V6, binary
                 cls
clus                0   1
  FBLN5 MUTATED     6   1
  FBLN5 WILD-TYPE 277  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBLN5 MUTATED      6    1
  FBLN5 WILD-TYPE  277   47
   clus
vv  FBLN5 MUTATED FBLN5 WILD-TYPE
  0             6             277
  1             1              47
[1] 2 2
[1] FALSE
D345V7, 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
D345V8, binary
                 cls
clus                0   1
  FBLN5 MUTATED     5   3
  FBLN5 WILD-TYPE 312  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBLN5 MUTATED      5    3
  FBLN5 WILD-TYPE  312   45
                               clus
vv                              FBLN5 MUTATED FBLN5 WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  FBLN5 MUTATED     2   0   0   2
  FBLN5 WILD-TYPE 255   2  22  19
D345V9, multiclass
    clus
vv   FBLN5 MUTATED FBLN5 WILD-TYPE
  R0             2             255
  R1             0               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"
D345V10, 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
D345V11, 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(346) Variable = EFHC2 MUTATION ANALYSIS
D346V1, survival
                 sevent
clus2               0   1
  EFHC2 MUTATED    12   3
  EFHC2 WILD-TYPE 270  70
  EFHC2 MUTATED EFHC2 WILD-TYPE 
             15             340 
  EFHC2 MUTATED EFHC2 WILD-TYPE 
              3              70 
$`EFHC2 MUTATED`
TCGA-AA-3492 TCGA-AA-3877 TCGA-AA-3977 TCGA-AA-A00N TCGA-AD-5900 TCGA-AZ-4315 
        3.02        31.00        25.02         4.01         0.07        58.39 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4952 TCGA-CM-5860 TCGA-CM-6161 TCGA-CM-6170 
        0.33         0.10        15.62        16.01        15.02        15.02 
TCGA-D5-6535 TCGA-DM-A1DB TCGA-F4-6856 
       15.12        44.32        19.43 

$`EFHC2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07         0.26         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      102.44        40.34        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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-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-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 
       16.24        33.67        13.25         0.53        35.41       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  EFHC2 MUTATED EFHC2 WILD-TYPE 
           0.07            0.00 
  EFHC2 MUTATED EFHC2 WILD-TYPE 
          58.39          140.38 
  EFHC2 MUTATED EFHC2 WILD-TYPE 
         15.120          20.995 
[1] "0.1 - 58.4 (15.1)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.4"
D346V2, 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       24       104         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EFHC2 MUTATED           1          0          1          0        0         0
  EFHC2 WILD-TYPE        18         10         40         31       35        13
                 vv
clus              STAGE IVB
  EFHC2 MUTATED           0
  EFHC2 WILD-TYPE         1
D346V3, multiclass
            clus
vv           EFHC2 MUTATED EFHC2 WILD-TYPE
  STAGE I                5              59
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              5             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EFHC2 MUTATED     1   5   7   2
  EFHC2 WILD-TYPE   8  63 241  39
D346V4, multiclass
    clus
vv   EFHC2 MUTATED EFHC2 WILD-TYPE
  T1             1               8
  T2             5              63
  T3             7             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
  EFHC2 MUTATED    13   1   1
  EFHC2 WILD-TYPE 207  79  65
D346V5, multiclass
    clus
vv   EFHC2 MUTATED EFHC2 WILD-TYPE
  N0            13             207
  N1             1              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"
D346V6, binary
                 cls
clus                0   1
  EFHC2 MUTATED    12   0
  EFHC2 WILD-TYPE 271  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHC2 MUTATED     12    0
  EFHC2 WILD-TYPE  271   48
   clus
vv  EFHC2 MUTATED EFHC2 WILD-TYPE
  0            12             271
  1             0              48
[1] 2 2
[1] FALSE
D346V7, 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
D346V8, binary
                 cls
clus                0   1
  EFHC2 MUTATED     9   6
  EFHC2 WILD-TYPE 308  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHC2 MUTATED      9    6
  EFHC2 WILD-TYPE  308   42
                               clus
vv                              EFHC2 MUTATED EFHC2 WILD-TYPE
  COLON ADENOCARCINOMA                      9             308
  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 248   2  22  17
D346V9, multiclass
    clus
vv   EFHC2 MUTATED EFHC2 WILD-TYPE
  R0             9             248
  R1             0               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"
D346V10, 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
D346V11, 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(347) Variable = E2F7 MUTATION ANALYSIS
D347V1, survival
                sevent
clus2              0   1
  E2F7 MUTATED    13   6
  E2F7 WILD-TYPE 269  67
  E2F7 MUTATED E2F7 WILD-TYPE 
            19            336 
  E2F7 MUTATED E2F7 WILD-TYPE 
             6             67 
$`E2F7 MUTATED`
TCGA-A6-5659 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3697 
       30.44        13.02         1.02         6.97         0.92        85.05 
TCGA-AA-3715 TCGA-AA-3821 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-5900 TCGA-AD-6964 
       19.04         1.02         4.01        34.98         0.07        10.88 
TCGA-CK-4952 TCGA-CK-5916 TCGA-CM-5862 TCGA-D5-5541 TCGA-D5-6930 TCGA-G4-6310 
       15.62        21.14         5.03        11.51         1.51        45.11 
TCGA-G4-6586 
       35.80 

$`E2F7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 
       35.01        63.98         6.97         1.02        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 
       37.05        19.00        36.00         5.03        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 
       10.06        35.05        33.04         0.99        25.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 
        1.35        17.56       102.44        40.34        49.08        51.32 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99         2.93         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        16.01        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-D5-6529 
       12.03        45.40        12.26        19.59        13.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        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        51.75        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        26.17        91.79        46.75        52.80 

  E2F7 MUTATED E2F7 WILD-TYPE 
          0.07           0.00 
  E2F7 MUTATED E2F7 WILD-TYPE 
         85.05         140.38 
  E2F7 MUTATED E2F7 WILD-TYPE 
        11.510         20.995 
[1] "0.1 - 85.0 (11.5)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "2.3"
D347V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  E2F7 MUTATED         4        0        2         4         3         0
  E2F7 WILD-TYPE      60        1       23       105         5         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  E2F7 MUTATED           4          0          2          0        0         1
  E2F7 WILD-TYPE        15         10         39         31       35        12
                vv
clus             STAGE IVB
  E2F7 MUTATED           0
  E2F7 WILD-TYPE         1
D347V3, multiclass
            clus
vv           E2F7 MUTATED E2F7 WILD-TYPE
  STAGE I               4             60
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             4            105
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             4             15
  STAGE IIIA            0             10
  STAGE IIIB            2             39
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  65 236  36
D347V4, multiclass
    clus
vv   E2F7 MUTATED E2F7 WILD-TYPE
  T1            1              8
  T2            3             65
  T3           12            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
  E2F7 MUTATED    14   4   3
  E2F7 WILD-TYPE 206  76  63
D347V5, multiclass
    clus
vv   E2F7 MUTATED E2F7 WILD-TYPE
  N0           14            206
  N1            4             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"
D347V6, binary
                cls
clus               0   1
  E2F7 MUTATED    17   1
  E2F7 WILD-TYPE 266  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  E2F7 MUTATED     17    1
  E2F7 WILD-TYPE  266   47
   clus
vv  E2F7 MUTATED E2F7 WILD-TYPE
  0           17            266
  1            1             47
[1] 2 2
[1] FALSE
D347V7, 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
D347V8, binary
                cls
clus               0   1
  E2F7 MUTATED    15   6
  E2F7 WILD-TYPE 302  42
[1] "tbl2"
                cls
clus             [,1] [,2]
  E2F7 MUTATED     15    6
  E2F7 WILD-TYPE  302   42
                               clus
vv                              E2F7 MUTATED E2F7 WILD-TYPE
  COLON ADENOCARCINOMA                    15            302
  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 241   2  22  18
D347V9, multiclass
    clus
vv   E2F7 MUTATED E2F7 WILD-TYPE
  R0           16            241
  R1            0              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"
D347V10, 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
D347V11, 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(348) Variable = MSH6 MUTATION ANALYSIS
D348V1, survival
                sevent
clus2              0   1
  MSH6 MUTATED    33   6
  MSH6 WILD-TYPE 249  67
  MSH6 MUTATED MSH6 WILD-TYPE 
            39            316 
  MSH6 MUTATED MSH6 WILD-TYPE 
             6             67 
$`MSH6 MUTATED`
TCGA-A6-3809 TCGA-A6-5662 TCGA-AA-3525 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3710 
       32.75        23.61         8.05        61.02        78.08        26.99 
TCGA-AA-3715 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3968 TCGA-AA-3977 TCGA-AA-A00N 
       19.04        26.01        24.00        21.99        25.02         4.01 
TCGA-AA-A010 TCGA-AD-6890 TCGA-AD-6963 TCGA-AU-3779 TCGA-AZ-4315 TCGA-AZ-5403 
       34.98         0.79        27.42        14.50        58.39        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-CA-5255 TCGA-CA-6717 
       61.41        49.41        12.10       100.01         3.06         0.33 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-6751 TCGA-CM-5344 TCGA-CM-6164 
      102.44        40.34        15.62       124.27        22.03        29.03 
TCGA-CM-6169 TCGA-D5-6533 TCGA-D5-6541 TCGA-D5-6929 TCGA-D5-6930 TCGA-DM-A1HB 
       13.02         1.32        15.58        13.41         1.51       135.65 
TCGA-DM-A28H TCGA-G4-6307 TCGA-G4-6321 
      117.07        55.04        22.09 

$`MSH6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        33.53        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 
        9.07        24.03        37.05        36.03        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       19.99         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 
       37.05        19.00        36.00         5.03        85.05        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3952 TCGA-AA-3955 
        2.01        12.99        24.00        33.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 
        4.21        56.55         0.72         5.79        22.42        10.88 
TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.20        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
        6.77        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        2.24         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
        1.35        17.56        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 
       13.51        11.51        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-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-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 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 
       51.75        45.11        36.72        36.00        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  MSH6 MUTATED MSH6 WILD-TYPE 
          0.33           0.00 
  MSH6 MUTATED MSH6 WILD-TYPE 
        135.65         140.38 
  MSH6 MUTATED MSH6 WILD-TYPE 
        25.020         19.625 
[1] "0.3 - 135.7 (25.0)" "0.0 - 140.4 (19.6)"
[1] "hr=" "2.1"
D348V2, 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       19        99         5         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MSH6 MUTATED           2          2          6          1        2         1
  MSH6 WILD-TYPE        17          8         35         30       33        12
                vv
clus             STAGE IVB
  MSH6 MUTATED           0
  MSH6 WILD-TYPE         1
D348V3, multiclass
            clus
vv           MSH6 MUTATED MSH6 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              6             19
  STAGE IIA            10             99
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             2             17
  STAGE IIIA            2              8
  STAGE IIIB            6             35
  STAGE IIIC            1             30
  STAGE IV              2             33
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  64 221  35
D348V4, multiclass
    clus
vv   MSH6 MUTATED MSH6 WILD-TYPE
  T1            2              7
  T2            4             64
  T3           27            221
  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  70  63
D348V5, multiclass
    clus
vv   MSH6 MUTATED MSH6 WILD-TYPE
  N0           26            194
  N1           10             70
  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
  MSH6 MUTATED    29   3
  MSH6 WILD-TYPE 254  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH6 MUTATED     29    3
  MSH6 WILD-TYPE  254   45
   clus
vv  MSH6 MUTATED MSH6 WILD-TYPE
  0           29            254
  1            3             45
[1] 2 2
[1] FALSE
D348V7, 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
D348V8, binary
                cls
clus               0   1
  MSH6 MUTATED    31   8
  MSH6 WILD-TYPE 286  40
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH6 MUTATED     31    8
  MSH6 WILD-TYPE  286   40
                               clus
vv                              MSH6 MUTATED MSH6 WILD-TYPE
  COLON ADENOCARCINOMA                    31            286
  COLON MUCINOUS ADENOCARCINOMA            8             40
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MSH6 MUTATED    23   1   0   4
  MSH6 WILD-TYPE 234   1  22  17
D348V9, multiclass
    clus
vv   MSH6 MUTATED MSH6 WILD-TYPE
  R0           23            234
  R1            1              1
  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"
D348V10, 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
D348V11, 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(349) Variable = CTNNB1 MUTATION ANALYSIS
D349V1, survival
                  sevent
clus2                0   1
  CTNNB1 MUTATED    52  18
  CTNNB1 WILD-TYPE 230  55
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              70              285 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              18               55 
$`CTNNB1 MUTATED`
TCGA-A6-2678 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-3496 
       42.28        29.19        33.53        22.06        20.12         1.02 
TCGA-AA-3510 TCGA-AA-3534 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       63.98        29.00        61.02        78.08         6.05         6.97 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3831 TCGA-AA-A00N TCGA-AA-A00U TCGA-AA-A01K 
        5.03        85.05        17.98         4.01        17.03        31.00 
TCGA-AD-6901 TCGA-AD-6964 TCGA-AU-3779 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-AZ-6598 
       22.42        10.88        14.50        58.39        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-6717 TCGA-CA-6718 
        6.77       100.01         5.23         1.94         0.33         0.10 
TCGA-CK-4952 TCGA-CK-5916 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 
       15.62        21.14        23.05        20.02        25.02        13.02 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6168 
       22.03        30.08        16.01        14.04        29.03        12.99 
TCGA-CM-6171 TCGA-CM-6675 TCGA-D5-5540 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 
       14.04        13.05        13.51         1.32        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-DM-A0XF TCGA-DM-A1D4 
        4.80        17.13        16.14        15.58        38.20        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1DB TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6854 
       49.91        13.32        44.32        13.45        35.87         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6303 TCGA-G4-6315 TCGA-G4-6323 TCGA-G4-6586 
       35.41        19.43        65.85        36.72        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

$`CTNNB1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2683 
       43.76        46.65        43.76        42.90        24.33        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 
       31.63        30.44        23.61        22.09        32.71        27.09 
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 
       22.52         8.38        25.08        25.18        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 
       24.69        24.39        23.87        19.66        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        3.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 
       19.07         0.00        19.07        34.03        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       13.94        19.99        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       19.00        36.00        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3833 
       35.05        33.04         0.99        25.02         1.02        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        14.99        21.99        34.98        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        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       27.42         0.20        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 
       22.36        62.79        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 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 
        1.35        17.56       102.44        40.34        49.08        51.32 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4746 TCGA-CM-5341 
       21.99         2.93         2.01       124.27        37.02        29.06 
TCGA-CM-5348 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       22.98        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 
       15.02        12.00        16.04        21.99        14.99        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-D5-5541 
       10.06        12.03        45.40        12.26        19.59        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6920 
       20.19        18.25        43.27        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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA 
       24.43       130.65        12.59       140.38         7.50       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 
       60.79       117.07        98.24         8.61        13.38         6.18 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      107.67        74.56        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 
       45.11        36.00        22.09 

  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
             0.1              0.0 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
          100.01           140.38 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
           20.07            20.28 
[1] "0.1 - 100.0 (20.1)" "0.0 - 140.4 (20.3)"
[1] "hr=" "1.2"
D349V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CTNNB1 MUTATED        11        1        7        29         2         0
  CTNNB1 WILD-TYPE      53        0       18        80         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CTNNB1 MUTATED           3          1          8          3        4
  CTNNB1 WILD-TYPE        16          9         33         28       31
                  vv
clus               STAGE IVA STAGE IVB
  CTNNB1 MUTATED           1         1
  CTNNB1 WILD-TYPE        12         0
D349V3, multiclass
            clus
vv           CTNNB1 MUTATED CTNNB1 WILD-TYPE
  STAGE I                11               53
  STAGE IA                1                0
  STAGE II                7               18
  STAGE IIA              29               80
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               3               16
  STAGE IIIA              1                9
  STAGE IIIB              8               33
  STAGE IIIC              3               28
  STAGE IV                4               31
  STAGE IVA               1               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
  CTNNB1 MUTATED     3   9  52   8
  CTNNB1 WILD-TYPE   6  59 196  33
D349V4, multiclass
    clus
vv   CTNNB1 MUTATED CTNNB1 WILD-TYPE
  T1              3                6
  T2              9               59
  T3             52              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   9
  CTNNB1 WILD-TYPE 167  69  57
D349V5, multiclass
    clus
vv   CTNNB1 MUTATED CTNNB1 WILD-TYPE
  N0             53              167
  N1             11               69
  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"
D349V6, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED    57   6
  CTNNB1 WILD-TYPE 226  42
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED     57    6
  CTNNB1 WILD-TYPE  226   42
   clus
vv  CTNNB1 MUTATED CTNNB1 WILD-TYPE
  0             57              226
  1              6               42
[1] 2 2
[1] FALSE
D349V7, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED    31  42
  CTNNB1 WILD-TYPE 139 155
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED     31   42
  CTNNB1 WILD-TYPE  139  155
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  FEMALE             31              139
  MALE               42              155
[1] 2 2
[1] FALSE
D349V8, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED    65   8
  CTNNB1 WILD-TYPE 252  40
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED     65    8
  CTNNB1 WILD-TYPE  252   40
                               clus
vv                              CTNNB1 MUTATED CTNNB1 WILD-TYPE
  COLON ADENOCARCINOMA                      65              252
  COLON MUCINOUS ADENOCARCINOMA              8               40
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CTNNB1 MUTATED    49   0   2   7
  CTNNB1 WILD-TYPE 208   2  20  14
D349V9, multiclass
    clus
vv   CTNNB1 MUTATED CTNNB1 WILD-TYPE
  R0             49              208
  R1              0                2
  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"
D349V10, 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                           6    51
  CTNNB1 WILD-TYPE                        13   125
D349V11, multiclass
                                  clus
vv                                 CTNNB1 MUTATED CTNNB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     6               13
  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(350) Variable = GPR112 MUTATION ANALYSIS
D350V1, survival
                  sevent
clus2                0   1
  GPR112 MUTATED    22   8
  GPR112 WILD-TYPE 260  65
  GPR112 MUTATED GPR112 WILD-TYPE 
              30              325 
  GPR112 MUTATED GPR112 WILD-TYPE 
               8               65 
$`GPR112 MUTATED`
TCGA-A6-2672 TCGA-A6-2678 TCGA-A6-3809 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3510 
       46.65        42.28        32.75        22.06        19.66        63.98 
TCGA-AA-3555 TCGA-AA-3678 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3950 TCGA-AA-3977 
       29.95        47.01        26.99        10.06        24.00        25.02 
TCGA-AA-A00N TCGA-AA-A02J TCGA-AD-6889 TCGA-AD-6890 TCGA-AZ-4315 TCGA-AZ-5407 
        4.01         5.03        56.55         0.79        58.39        61.41 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-5349 TCGA-CM-5864 
      100.01        29.56         0.33         0.10        30.08        15.02 
TCGA-CM-6161 TCGA-CM-6169 TCGA-CM-6678 TCGA-DM-A285 TCGA-DM-A28F TCGA-G4-6303 
       15.02        13.02        11.01         6.12        35.97        65.85 

$`GPR112 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2683 TCGA-A6-3807 
       43.76        43.76        42.90        24.33        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        36.53        14.53        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 
       29.19        33.53        23.61        22.09        32.71        27.09 
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 
       22.52         8.38        25.08        25.18        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 
       24.69        24.39        23.87        20.12        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        3.02         1.02        35.01         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        17.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 
        5.03        85.05        19.04        19.04        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       51.98        39.98         2.01        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6605 TCGA-AZ-6606 
       62.79        49.41         6.77        12.10         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07         0.26         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 
        0.53        35.41        19.43       107.67        74.56        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  GPR112 MUTATED GPR112 WILD-TYPE 
             0.1              0.0 
  GPR112 MUTATED GPR112 WILD-TYPE 
          100.01           140.38 
  GPR112 MUTATED GPR112 WILD-TYPE 
          26.005           19.990 
[1] "0.1 - 100.0 (26.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.1"
D350V2, 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       23        99         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPR112 MUTATED           2          0          3          1        3
  GPR112 WILD-TYPE        17         10         38         30       32
                  vv
clus               STAGE IVA STAGE IVB
  GPR112 MUTATED           1         0
  GPR112 WILD-TYPE        12         1
D350V3, multiclass
            clus
vv           GPR112 MUTATED GPR112 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA              10               99
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               2               17
  STAGE IIIA              0               10
  STAGE IIIB              3               38
  STAGE IIIC              1               30
  STAGE IV                3               32
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  63 229  37
D350V4, multiclass
    clus
vv   GPR112 MUTATED GPR112 WILD-TYPE
  T1              2                7
  T2              5               63
  T3             19              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
  GPR112 MUTATED    20   8   2
  GPR112 WILD-TYPE 200  72  64
D350V5, multiclass
    clus
vv   GPR112 MUTATED GPR112 WILD-TYPE
  N0             20              200
  N1              8               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"
D350V6, binary
                  cls
clus                 0   1
  GPR112 MUTATED    22   4
  GPR112 WILD-TYPE 261  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR112 MUTATED     22    4
  GPR112 WILD-TYPE  261   44
   clus
vv  GPR112 MUTATED GPR112 WILD-TYPE
  0             22              261
  1              4               44
[1] 2 2
[1] FALSE
D350V7, 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
D350V8, binary
                  cls
clus                 0   1
  GPR112 MUTATED    23   7
  GPR112 WILD-TYPE 294  41
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR112 MUTATED     23    7
  GPR112 WILD-TYPE  294   41
                               clus
vv                              GPR112 MUTATED GPR112 WILD-TYPE
  COLON ADENOCARCINOMA                      23              294
  COLON MUCINOUS ADENOCARCINOMA              7               41
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  GPR112 MUTATED    19   0   1   2
  GPR112 WILD-TYPE 238   2  21  19
D350V9, multiclass
    clus
vv   GPR112 MUTATED GPR112 WILD-TYPE
  R0             19              238
  R1              0                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"
D350V10, 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
D350V11, 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(351) Variable = SLC11A2 MUTATION ANALYSIS
D351V1, survival
                   sevent
clus2                 0   1
  SLC11A2 MUTATED     6   1
  SLC11A2 WILD-TYPE 276  72
  SLC11A2 MUTATED SLC11A2 WILD-TYPE 
                7               348 
  SLC11A2 MUTATED SLC11A2 WILD-TYPE 
                1                72 
$`SLC11A2 MUTATED`
TCGA-AA-3949 TCGA-AA-3950 TCGA-AD-6895 TCGA-AD-6964 TCGA-CM-6171 TCGA-D5-6928 
       26.01        24.00         0.72        10.88        14.04        11.64 
TCGA-G4-6586 
       35.80 

$`SLC11A2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3952 
       31.00         2.01        12.99        24.00        33.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       56.55         0.79         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        26.17        91.79        46.75        52.80 

  SLC11A2 MUTATED SLC11A2 WILD-TYPE 
             0.72              0.00 
  SLC11A2 MUTATED SLC11A2 WILD-TYPE 
            35.80            140.38 
  SLC11A2 MUTATED SLC11A2 WILD-TYPE 
           14.040            20.235 
[1] "0.7 - 35.8 (14.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1"  
D351V2, 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       25       105         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC11A2 MUTATED           0          0          1          0        0
  SLC11A2 WILD-TYPE        19         10         40         31       35
                   vv
clus                STAGE IVA STAGE IVB
  SLC11A2 MUTATED           0         0
  SLC11A2 WILD-TYPE        13         1
D351V3, multiclass
            clus
vv           SLC11A2 MUTATED SLC11A2 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                4               105
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC11A2 MUTATED     0   1   6   1
  SLC11A2 WILD-TYPE   9  67 242  40
D351V4, multiclass
    clus
vv   SLC11A2 MUTATED SLC11A2 WILD-TYPE
  T1               0                 9
  T2               1                67
  T3               6               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
  SLC11A2 MUTATED     5   2   1
  SLC11A2 WILD-TYPE 215  78  65
D351V5, multiclass
    clus
vv   SLC11A2 MUTATED SLC11A2 WILD-TYPE
  N0               5               215
  N1               2                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"
D351V6, binary
                   cls
clus                  0   1
  SLC11A2 MUTATED     6   0
  SLC11A2 WILD-TYPE 277  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC11A2 MUTATED      6    0
  SLC11A2 WILD-TYPE  277   48
   clus
vv  SLC11A2 MUTATED SLC11A2 WILD-TYPE
  0               6               277
  1               0                48
[1] 2 2
[1] FALSE
D351V7, 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
D351V8, binary
                   cls
clus                  0   1
  SLC11A2 MUTATED     5   3
  SLC11A2 WILD-TYPE 312  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC11A2 MUTATED      5    3
  SLC11A2 WILD-TYPE  312   45
                               clus
vv                              SLC11A2 MUTATED SLC11A2 WILD-TYPE
  COLON ADENOCARCINOMA                        5               312
  COLON MUCINOUS ADENOCARCINOMA               3                45
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SLC11A2 MUTATED     6   0   0   0
  SLC11A2 WILD-TYPE 251   2  22  21
D351V9, multiclass
    clus
vv   SLC11A2 MUTATED SLC11A2 WILD-TYPE
  R0               6               251
  R1               0                 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"
D351V10, 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
D351V11, 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(352) Variable = CYP4X1 MUTATION ANALYSIS
D352V1, survival
                  sevent
clus2                0   1
  CYP4X1 MUTATED     4   1
  CYP4X1 WILD-TYPE 278  72
  CYP4X1 MUTATED CYP4X1 WILD-TYPE 
               5              350 
  CYP4X1 MUTATED CYP4X1 WILD-TYPE 
               1               72 
$`CYP4X1 MUTATED`
TCGA-AZ-5407 TCGA-CA-6717 TCGA-CK-4947 TCGA-F4-6809 TCGA-G4-6309 
       61.41         0.33        17.56        13.25        51.75 

$`CYP4X1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 
        3.29         0.07         0.26         0.10         1.35       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       33.67         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  CYP4X1 MUTATED CYP4X1 WILD-TYPE 
            0.33             0.00 
  CYP4X1 MUTATED CYP4X1 WILD-TYPE 
           61.41           140.38 
  CYP4X1 MUTATED CYP4X1 WILD-TYPE 
          17.560           20.235 
[1] "0.3 - 61.4 (17.6)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.3"
D352V2, 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       25       108         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CYP4X1 MUTATED           0          0          1          0        0
  CYP4X1 WILD-TYPE        19         10         40         31       35
                  vv
clus               STAGE IVA STAGE IVB
  CYP4X1 MUTATED           2         0
  CYP4X1 WILD-TYPE        11         1
D352V3, multiclass
            clus
vv           CYP4X1 MUTATED CYP4X1 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               1              108
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               2               11
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  68 245  40
D352V4, multiclass
    clus
vv   CYP4X1 MUTATED CYP4X1 WILD-TYPE
  T1              1                8
  T2              0               68
  T3              3              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
  CYP4X1 MUTATED     2   3   0
  CYP4X1 WILD-TYPE 218  77  66
D352V5, multiclass
    clus
vv   CYP4X1 MUTATED CYP4X1 WILD-TYPE
  N0              2              218
  N1              3               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"
D352V6, binary
                  cls
clus                 0   1
  CYP4X1 MUTATED     4   1
  CYP4X1 WILD-TYPE 279  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP4X1 MUTATED      4    1
  CYP4X1 WILD-TYPE  279   47
   clus
vv  CYP4X1 MUTATED CYP4X1 WILD-TYPE
  0              4              279
  1              1               47
[1] 2 2
[1] FALSE
D352V7, 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
D352V8, binary
                  cls
clus                 0   1
  CYP4X1 MUTATED     4   1
  CYP4X1 WILD-TYPE 313  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP4X1 MUTATED      4    1
  CYP4X1 WILD-TYPE  313   47
                               clus
vv                              CYP4X1 MUTATED CYP4X1 WILD-TYPE
  COLON ADENOCARCINOMA                       4              313
  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 255   2  22  19
D352V9, multiclass
    clus
vv   CYP4X1 MUTATED CYP4X1 WILD-TYPE
  R0              2              255
  R1              0                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"
D352V10, 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
D352V11, 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(353) Variable = NUP160 MUTATION ANALYSIS
D353V1, survival
                  sevent
clus2                0   1
  NUP160 MUTATED     8   2
  NUP160 WILD-TYPE 274  71
  NUP160 MUTATED NUP160 WILD-TYPE 
              10              345 
  NUP160 MUTATED NUP160 WILD-TYPE 
               2               71 
$`NUP160 MUTATED`
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-A00J TCGA-CM-4743 TCGA-D5-6537 TCGA-D5-6923 
       25.02        27.02        18.05        23.05         4.80        12.43 
TCGA-D5-6930 TCGA-DM-A1DA TCGA-G4-6309 TCGA-G4-6323 
        1.51         7.50        51.75        13.78 

$`NUP160 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 
       18.25         1.32        43.27        15.12        17.85        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         7.53        12.39        10.13 
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-A1DB 
       92.75        49.91        13.32        12.59       140.38        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       45.11        36.72        36.00        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  NUP160 MUTATED NUP160 WILD-TYPE 
            1.51             0.00 
  NUP160 MUTATED NUP160 WILD-TYPE 
           51.75           140.38 
  NUP160 MUTATED NUP160 WILD-TYPE 
          15.915           20.280 
[1] "1.5 - 51.8 (15.9)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.2"
D353V2, 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       24       107         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NUP160 MUTATED           0          0          3          1        0
  NUP160 WILD-TYPE        19         10         38         30       35
                  vv
clus               STAGE IVA STAGE IVB
  NUP160 MUTATED           0         0
  NUP160 WILD-TYPE        13         1
D353V3, multiclass
            clus
vv           NUP160 MUTATED NUP160 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                1                0
  STAGE II                1               24
  STAGE IIA               2              107
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              3               38
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  NUP160 MUTATED     0   3   5   2
  NUP160 WILD-TYPE   9  65 243  39
D353V4, multiclass
    clus
vv   NUP160 MUTATED NUP160 WILD-TYPE
  T1              0                9
  T2              3               65
  T3              5              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
  NUP160 MUTATED     7   3   1
  NUP160 WILD-TYPE 213  77  65
D353V5, multiclass
    clus
vv   NUP160 MUTATED NUP160 WILD-TYPE
  N0              7              213
  N1              3               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"
D353V6, binary
                  cls
clus                 0   1
  NUP160 MUTATED     8   0
  NUP160 WILD-TYPE 275  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUP160 MUTATED      8    0
  NUP160 WILD-TYPE  275   48
   clus
vv  NUP160 MUTATED NUP160 WILD-TYPE
  0              8              275
  1              0               48
[1] 2 2
[1] FALSE
D353V7, 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
D353V8, binary
                  cls
clus                 0   1
  NUP160 MUTATED     9   2
  NUP160 WILD-TYPE 308  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUP160 MUTATED      9    2
  NUP160 WILD-TYPE  308   46
                               clus
vv                              NUP160 MUTATED NUP160 WILD-TYPE
  COLON ADENOCARCINOMA                       9              308
  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 249   2  22  21
D353V9, multiclass
    clus
vv   NUP160 MUTATED NUP160 WILD-TYPE
  R0              8              249
  R1              0                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"
D353V10, 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
D353V11, 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(354) Variable = TRPM7 MUTATION ANALYSIS
D354V1, survival
                 sevent
clus2               0   1
  TRPM7 MUTATED    21   6
  TRPM7 WILD-TYPE 261  67
  TRPM7 MUTATED TRPM7 WILD-TYPE 
             27             328 
  TRPM7 MUTATED TRPM7 WILD-TYPE 
              6              67 
$`TRPM7 MUTATED`
TCGA-A6-5660 TCGA-A6-5666 TCGA-A6-6649 TCGA-A6-6653 TCGA-AA-3672 TCGA-AA-3947 
       29.19        32.71        24.16        24.39         0.92        33.01 
TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01V TCGA-AD-5900 TCGA-AD-6964 
       25.02         4.01        34.98        35.01         0.07        10.88 
TCGA-AY-6196 TCGA-AZ-4681 TCGA-AZ-6600 TCGA-AZ-6607 TCGA-CA-6717 TCGA-CA-6718 
        0.20        83.80        12.10         3.19         0.33         0.10 
TCGA-CK-4952 TCGA-D5-5538 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6928 TCGA-DM-A1D4 
       15.62        12.26        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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       21.76        24.69        23.87        20.12        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        7.04         3.02         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 
       18.05        31.00         2.01        12.99        24.00        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        15.75        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        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 
        6.77       100.01        29.56         5.23        11.74         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 
        1.35        17.56       102.44        40.34        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6537 
       11.51        20.19        18.25         1.32        15.12         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20       130.65        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
        7.50       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       35.97        60.79        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  TRPM7 MUTATED TRPM7 WILD-TYPE 
           0.07            0.00 
  TRPM7 MUTATED TRPM7 WILD-TYPE 
         135.65          140.38 
  TRPM7 MUTATED TRPM7 WILD-TYPE 
         24.160          20.155 
[1] "0.1 - 135.7 (24.2)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1"  
D354V2, 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       25       100         5         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TRPM7 MUTATED           2          0          3          3        2         0
  TRPM7 WILD-TYPE        17         10         38         28       33        13
                 vv
clus              STAGE IVB
  TRPM7 MUTATED           0
  TRPM7 WILD-TYPE         1
D354V3, multiclass
            clus
vv           TRPM7 MUTATED TRPM7 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              9             100
  STAGE IIB              3               5
  STAGE IIC              1               0
  STAGE III              2              17
  STAGE IIIA             0              10
  STAGE IIIB             3              38
  STAGE IIIC             3              28
  STAGE IV               2              33
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TRPM7 MUTATED     0   4  16   8
  TRPM7 WILD-TYPE   9  64 232  33
D354V4, multiclass
    clus
vv   TRPM7 MUTATED TRPM7 WILD-TYPE
  T1             0               9
  T2             4              64
  T3            16             232
  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  75  60
D354V5, multiclass
    clus
vv   TRPM7 MUTATED TRPM7 WILD-TYPE
  N0            17             203
  N1             5              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"
D354V6, binary
                 cls
clus                0   1
  TRPM7 MUTATED    22   2
  TRPM7 WILD-TYPE 261  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPM7 MUTATED     22    2
  TRPM7 WILD-TYPE  261   46
   clus
vv  TRPM7 MUTATED TRPM7 WILD-TYPE
  0            22             261
  1             2              46
[1] 2 2
[1] FALSE
D354V7, 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
D354V8, binary
                 cls
clus                0   1
  TRPM7 MUTATED    20   8
  TRPM7 WILD-TYPE 297  40
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPM7 MUTATED     20    8
  TRPM7 WILD-TYPE  297   40
                               clus
vv                              TRPM7 MUTATED TRPM7 WILD-TYPE
  COLON ADENOCARCINOMA                     20             297
  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 244   2  22  18
D354V9, multiclass
    clus
vv   TRPM7 MUTATED TRPM7 WILD-TYPE
  R0            13             244
  R1             0               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"
D354V10, 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
D354V11, 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(355) Variable = MFN1 MUTATION ANALYSIS
D355V1, survival
                sevent
clus2              0   1
  MFN1 MUTATED     9   4
  MFN1 WILD-TYPE 273  69
  MFN1 MUTATED MFN1 WILD-TYPE 
            13            342 
  MFN1 MUTATED MFN1 WILD-TYPE 
             4             69 
$`MFN1 MUTATED`
TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-3516 TCGA-AD-6895 TCGA-AZ-6601 TCGA-CA-6715 
       22.06        20.12        13.02         0.72       100.01         0.07 
TCGA-CK-5916 TCGA-D5-6532 TCGA-D5-6922 TCGA-D5-6930 TCGA-DM-A1DA TCGA-F4-6808 
       21.14        18.25        10.13         1.51         7.50        33.67 
TCGA-G4-6299 
       74.56 

$`MFN1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.06         3.25         3.29         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       13.51        11.51        20.19         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        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-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       12.59       140.38        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 
        1.55        16.31        29.59        16.24        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.41        19.43       107.67        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  MFN1 MUTATED MFN1 WILD-TYPE 
          0.07           0.00 
  MFN1 MUTATED MFN1 WILD-TYPE 
        100.01         140.38 
  MFN1 MUTATED MFN1 WILD-TYPE 
         18.25          20.63 
[1] "0.1 - 100.0 (18.2)" "0.0 - 140.4 (20.6)"
[1] "hr=" "1.5"
D355V2, 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       24       105         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MFN1 MUTATED           1          1          1          2        0         0
  MFN1 WILD-TYPE        18          9         40         29       35        13
                vv
clus             STAGE IVB
  MFN1 MUTATED           0
  MFN1 WILD-TYPE         1
D355V3, multiclass
            clus
vv           MFN1 MUTATED MFN1 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             4            105
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            1              9
  STAGE IIIB            1             40
  STAGE IIIC            2             29
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MFN1 MUTATED     2   0  11   0
  MFN1 WILD-TYPE   7  68 237  41
D355V4, multiclass
    clus
vv   MFN1 MUTATED MFN1 WILD-TYPE
  T1            2              7
  T2            0             68
  T3           11            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
  MFN1 MUTATED     7   3   3
  MFN1 WILD-TYPE 213  77  63
D355V5, multiclass
    clus
vv   MFN1 MUTATED MFN1 WILD-TYPE
  N0            7            213
  N1            3             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"
D355V6, binary
                cls
clus               0   1
  MFN1 MUTATED    11   0
  MFN1 WILD-TYPE 272  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  MFN1 MUTATED     11    0
  MFN1 WILD-TYPE  272   48
   clus
vv  MFN1 MUTATED MFN1 WILD-TYPE
  0           11            272
  1            0             48
[1] 2 2
[1] FALSE
D355V7, 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
D355V8, binary
                cls
clus               0   1
  MFN1 MUTATED    10   3
  MFN1 WILD-TYPE 307  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  MFN1 MUTATED     10    3
  MFN1 WILD-TYPE  307   45
                               clus
vv                              MFN1 MUTATED MFN1 WILD-TYPE
  COLON ADENOCARCINOMA                    10            307
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MFN1 MUTATED     6   0   0   2
  MFN1 WILD-TYPE 251   2  22  19
D355V9, multiclass
    clus
vv   MFN1 MUTATED MFN1 WILD-TYPE
  R0            6            251
  R1            0              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"
D355V10, 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
D355V11, 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(356) Variable = RPS6KA3 MUTATION ANALYSIS
D356V1, survival
                   sevent
clus2                 0   1
  RPS6KA3 MUTATED    11   2
  RPS6KA3 WILD-TYPE 271  71
  RPS6KA3 MUTATED RPS6KA3 WILD-TYPE 
               13               342 
  RPS6KA3 MUTATED RPS6KA3 WILD-TYPE 
                2                71 
$`RPS6KA3 MUTATED`
TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3662 TCGA-AA-3854 TCGA-AA-3877 TCGA-AA-3950 
        3.02        63.98         6.05        36.03        31.00        24.00 
TCGA-AA-A010 TCGA-AZ-6598 TCGA-CK-4952 TCGA-CM-6680 TCGA-D5-6539 TCGA-D5-7000 
       34.98        49.41        15.62        12.03        12.49        10.26 
TCGA-DM-A28E 
      119.93 

$`RPS6KA3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
        0.00        33.07         0.00        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      102.44        40.34        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        16.14        15.58         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 
        1.51        12.00        11.38       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-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 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  RPS6KA3 MUTATED RPS6KA3 WILD-TYPE 
             3.02              0.00 
  RPS6KA3 MUTATED RPS6KA3 WILD-TYPE 
           119.93            140.38 
  RPS6KA3 MUTATED RPS6KA3 WILD-TYPE 
           24.000            20.155 
[1] "3.0 - 119.9 (24.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.7"
D356V2, 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       22       107         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RPS6KA3 MUTATED           1          1          1          0        1
  RPS6KA3 WILD-TYPE        18          9         40         31       34
                   vv
clus                STAGE IVA STAGE IVB
  RPS6KA3 MUTATED           0         0
  RPS6KA3 WILD-TYPE        13         1
D356V3, multiclass
            clus
vv           RPS6KA3 MUTATED RPS6KA3 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 3                22
  STAGE IIA                2               107
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               1                 9
  STAGE IIIB               1                40
  STAGE IIIC               0                31
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  RPS6KA3 MUTATED     1   2   7   3
  RPS6KA3 WILD-TYPE   8  66 241  38
D356V4, multiclass
    clus
vv   RPS6KA3 MUTATED RPS6KA3 WILD-TYPE
  T1               1                 8
  T2               2                66
  T3               7               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
  RPS6KA3 MUTATED    10   0   3
  RPS6KA3 WILD-TYPE 210  80  63
D356V5, multiclass
    clus
vv   RPS6KA3 MUTATED RPS6KA3 WILD-TYPE
  N0              10               210
  N1               0                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"
D356V6, binary
                   cls
clus                  0   1
  RPS6KA3 MUTATED    11   1
  RPS6KA3 WILD-TYPE 272  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPS6KA3 MUTATED     11    1
  RPS6KA3 WILD-TYPE  272   47
   clus
vv  RPS6KA3 MUTATED RPS6KA3 WILD-TYPE
  0              11               272
  1               1                47
[1] 2 2
[1] FALSE
D356V7, 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
D356V8, binary
                   cls
clus                  0   1
  RPS6KA3 MUTATED     8   5
  RPS6KA3 WILD-TYPE 309  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPS6KA3 MUTATED      8    5
  RPS6KA3 WILD-TYPE  309   43
                               clus
vv                              RPS6KA3 MUTATED RPS6KA3 WILD-TYPE
  COLON ADENOCARCINOMA                        8               309
  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 248   2  21  20
D356V9, multiclass
    clus
vv   RPS6KA3 MUTATED RPS6KA3 WILD-TYPE
  R0               9               248
  R1               0                 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"
D356V10, 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
D356V11, 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(357) Variable = FUT10 MUTATION ANALYSIS
D357V1, survival
                 sevent
clus2               0   1
  FUT10 MUTATED     5   0
  FUT10 WILD-TYPE 277  73
  FUT10 MUTATED FUT10 WILD-TYPE 
              5             350 
  FUT10 MUTATED FUT10 WILD-TYPE 
              0              73 
$`FUT10 MUTATED`
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-6649 TCGA-AD-6963 TCGA-G4-6586 
       33.53        23.61        24.16        27.42        35.80 

$`FUT10 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5664 TCGA-A6-5665 
       32.91        31.63        30.44        29.19        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  FUT10 MUTATED FUT10 WILD-TYPE 
          23.61            0.00 
  FUT10 MUTATED FUT10 WILD-TYPE 
          35.80          140.38 
  FUT10 MUTATED FUT10 WILD-TYPE 
         27.420          20.005 
[1] "23.6 - 35.8 (27.4)" "0.0 - 140.4 (20.0)"
[1] "hr="     "9200000"
D357V2, 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       25       106         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        19         10         40         31       35        12
                 vv
clus              STAGE IVB
  FUT10 MUTATED           0
  FUT10 WILD-TYPE         1
D357V3, multiclass
            clus
vv           FUT10 MUTATED FUT10 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              3             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  68 242  41
D357V4, multiclass
    clus
vv   FUT10 MUTATED FUT10 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             6             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
  FUT10 MUTATED     4   1   1
  FUT10 WILD-TYPE 216  79  65
D357V5, multiclass
    clus
vv   FUT10 MUTATED FUT10 WILD-TYPE
  N0             4             216
  N1             1              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"
D357V6, binary
                 cls
clus                0   1
  FUT10 MUTATED     4   1
  FUT10 WILD-TYPE 279  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FUT10 MUTATED      4    1
  FUT10 WILD-TYPE  279   47
   clus
vv  FUT10 MUTATED FUT10 WILD-TYPE
  0             4             279
  1             1              47
[1] 2 2
[1] FALSE
D357V7, 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
D357V8, binary
                 cls
clus                0   1
  FUT10 MUTATED     6   0
  FUT10 WILD-TYPE 311  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FUT10 MUTATED      6    0
  FUT10 WILD-TYPE  311   48
                               clus
vv                              FUT10 MUTATED FUT10 WILD-TYPE
  COLON ADENOCARCINOMA                      6             311
  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 254   2  22  21
D357V9, multiclass
    clus
vv   FUT10 MUTATED FUT10 WILD-TYPE
  R0             3             254
  R1             0               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"
D357V10, 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
D357V11, 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(358) Variable = ARHGAP32 MUTATION ANALYSIS
D358V1, survival
                    sevent
clus2                  0   1
  ARHGAP32 MUTATED    18   3
  ARHGAP32 WILD-TYPE 264  70
  ARHGAP32 MUTATED ARHGAP32 WILD-TYPE 
                21                334 
  ARHGAP32 MUTATED ARHGAP32 WILD-TYPE 
                 3                 70 
$`ARHGAP32 MUTATED`
TCGA-A6-3809 TCGA-A6-5661 TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3697 TCGA-AA-3713 
       32.75        33.53        22.06         3.02        85.05        19.04 
TCGA-AA-3815 TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-4682 TCGA-CK-6751 TCGA-CM-5341 
       33.04         4.01        34.98        22.36       124.27        29.06 
TCGA-CM-6674 TCGA-D5-5539 TCGA-D5-6532 TCGA-D5-6541 TCGA-D5-6923 TCGA-DM-A0X9 
       12.95        19.59        18.25        15.58        12.43       119.70 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6588 
       36.00        13.78        26.17 

$`ARHGAP32 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       31.63        30.44        29.19        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 
        5.98        37.05        19.00        36.00         5.03        26.99 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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-D5-5540 
       11.01        10.06        12.03        45.40        12.26        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       11.51        20.19         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        16.14         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-A0XD TCGA-DM-A0XF 
        1.51        12.00        11.38        10.26        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 
       44.68        55.04        51.75        45.11        36.72        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        91.79        46.75        52.80 

  ARHGAP32 MUTATED ARHGAP32 WILD-TYPE 
              3.02               0.00 
  ARHGAP32 MUTATED ARHGAP32 WILD-TYPE 
            124.27             140.38 
  ARHGAP32 MUTATED ARHGAP32 WILD-TYPE 
             22.36              20.07 
[1] "3.0 - 124.3 (22.4)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.8"
D358V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ARHGAP32 MUTATED         2        1        2         8         3         0
  ARHGAP32 WILD-TYPE      62        0       23       101         5         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARHGAP32 MUTATED           1          2          0          1        1
  ARHGAP32 WILD-TYPE        18          8         41         30       34
                    vv
clus                 STAGE IVA STAGE IVB
  ARHGAP32 MUTATED           1         0
  ARHGAP32 WILD-TYPE        12         1
D358V3, multiclass
            clus
vv           ARHGAP32 MUTATED ARHGAP32 WILD-TYPE
  STAGE I                   2                 62
  STAGE IA                  1                  0
  STAGE II                  2                 23
  STAGE IIA                 8                101
  STAGE IIB                 3                  5
  STAGE IIC                 0                  1
  STAGE III                 1                 18
  STAGE IIIA                2                  8
  STAGE IIIB                0                 41
  STAGE IIIC                1                 30
  STAGE IV                  1                 34
  STAGE IVA                 1                 12
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of 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  14   4
  ARHGAP32 WILD-TYPE   9  65 234  37
D358V4, multiclass
    clus
vv   ARHGAP32 MUTATED ARHGAP32 WILD-TYPE
  T1                0                  9
  T2                3                 65
  T3               14                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
  ARHGAP32 MUTATED    19   2   1
  ARHGAP32 WILD-TYPE 201  78  65
D358V5, multiclass
    clus
vv   ARHGAP32 MUTATED ARHGAP32 WILD-TYPE
  N0               19                201
  N1                2                 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"
D358V6, binary
                    cls
clus                   0   1
  ARHGAP32 MUTATED    17   2
  ARHGAP32 WILD-TYPE 266  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP32 MUTATED     17    2
  ARHGAP32 WILD-TYPE  266   46
   clus
vv  ARHGAP32 MUTATED ARHGAP32 WILD-TYPE
  0               17                266
  1                2                 46
[1] 2 2
[1] FALSE
D358V7, binary
                    cls
clus                   0   1
  ARHGAP32 MUTATED    12  10
  ARHGAP32 WILD-TYPE 158 187
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP32 MUTATED     12   10
  ARHGAP32 WILD-TYPE  158  187
        clus
vv       ARHGAP32 MUTATED ARHGAP32 WILD-TYPE
  FEMALE               12                158
  MALE                 10                187
[1] 2 2
[1] FALSE
D358V8, binary
                    cls
clus                   0   1
  ARHGAP32 MUTATED    18   4
  ARHGAP32 WILD-TYPE 299  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP32 MUTATED     18    4
  ARHGAP32 WILD-TYPE  299   44
                               clus
vv                              ARHGAP32 MUTATED ARHGAP32 WILD-TYPE
  COLON ADENOCARCINOMA                        18                299
  COLON MUCINOUS ADENOCARCINOMA                4                 44
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  ARHGAP32 MUTATED    19   0   1   1
  ARHGAP32 WILD-TYPE 238   2  21  20
D358V9, multiclass
    clus
vv   ARHGAP32 MUTATED ARHGAP32 WILD-TYPE
  R0               19                238
  R1                0                  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"
D358V10, 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
D358V11, 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(359) Variable = CNIH4 MUTATION ANALYSIS
D359V1, survival
                 sevent
clus2               0   1
  CNIH4 MUTATED     6   0
  CNIH4 WILD-TYPE 276  73
  CNIH4 MUTATED CNIH4 WILD-TYPE 
              6             349 
  CNIH4 MUTATED CNIH4 WILD-TYPE 
              0              73 
$`CNIH4 MUTATED`
TCGA-A6-6142 TCGA-CM-5344 TCGA-D5-7000 TCGA-F4-6807 TCGA-F4-6808 TCGA-G4-6299 
       25.08        22.03        10.26        16.24        33.67        74.56 

$`CNIH4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6809 
        6.18        35.87         1.55        16.31        29.59        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 
        0.53        35.41        19.43       107.67        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  CNIH4 MUTATED CNIH4 WILD-TYPE 
          10.26            0.00 
  CNIH4 MUTATED CNIH4 WILD-TYPE 
          74.56          140.38 
  CNIH4 MUTATED CNIH4 WILD-TYPE 
         23.555          20.120 
[1] "10.3 - 74.6 (23.6)" "0.0 - 140.4 (20.1)"
[1] "hr="     "9200000"
D359V2, 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       25       109         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        19         10         40         29       35        12
                 vv
clus              STAGE IVB
  CNIH4 MUTATED           0
  CNIH4 WILD-TYPE         1
D359V3, multiclass
            clus
vv           CNIH4 MUTATED CNIH4 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              0             109
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             2              29
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 244  41
D359V4, multiclass
    clus
vv   CNIH4 MUTATED CNIH4 WILD-TYPE
  T1             1               8
  T2             1              67
  T3             4             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
  CNIH4 MUTATED     2   2   2
  CNIH4 WILD-TYPE 218  78  64
D359V5, multiclass
    clus
vv   CNIH4 MUTATED CNIH4 WILD-TYPE
  N0             2             218
  N1             2              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
  CNIH4 MUTATED     5   1
  CNIH4 WILD-TYPE 278  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNIH4 MUTATED      5    1
  CNIH4 WILD-TYPE  278   47
   clus
vv  CNIH4 MUTATED CNIH4 WILD-TYPE
  0             5             278
  1             1              47
[1] 2 2
[1] FALSE
D359V7, 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
D359V8, binary
                 cls
clus                0   1
  CNIH4 MUTATED     5   1
  CNIH4 WILD-TYPE 312  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNIH4 MUTATED      5    1
  CNIH4 WILD-TYPE  312   47
                               clus
vv                              CNIH4 MUTATED CNIH4 WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  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 252   2  22  21
D359V9, multiclass
    clus
vv   CNIH4 MUTATED CNIH4 WILD-TYPE
  R0             5             252
  R1             0               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"
D359V10, 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
D359V11, 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(360) Variable = MET MUTATION ANALYSIS
D360V1, survival
               sevent
clus2             0   1
  MET MUTATED    30  11
  MET WILD-TYPE 252  62
  MET MUTATED MET WILD-TYPE 
           41           314 
  MET MUTATED MET WILD-TYPE 
           11            62 
$`MET MUTATED`
TCGA-A6-4105 TCGA-A6-5666 TCGA-A6-6141 TCGA-AA-3662 TCGA-AA-3713 TCGA-AA-3950 
       14.53        32.71         8.38         6.05        19.04        24.00 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A02K TCGA-AD-6889 TCGA-AD-6890 TCGA-AU-3779 
        4.01        34.98        14.01        56.55         0.79        14.50 
TCGA-AY-6197 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-CA-6715 TCGA-CA-6718 
       21.44        49.41        12.10        29.56         0.07         0.10 
TCGA-CA-6719 TCGA-CK-4952 TCGA-CM-4743 TCGA-CM-5341 TCGA-CM-5864 TCGA-CM-6167 
        1.35        15.62        23.05        29.06        15.02        14.99 
TCGA-CM-6170 TCGA-CM-6674 TCGA-CM-6675 TCGA-D5-6533 TCGA-D5-6924 TCGA-DM-A1D8 
       15.02        12.95        13.05         1.32        14.30        12.59 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A285 TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 
        7.50        44.32         6.12       117.07         8.61        13.38 
TCGA-G4-6293 TCGA-G4-6304 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6628 
      107.67        53.62        45.11        22.09        52.80 

$`MET WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       22.06        27.09        22.52        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
       39.98         2.01         5.03         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       18.05        40.96         0.07        21.37         4.21         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 
        5.79        22.42        27.42        10.88         0.20        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        15.75         0.20        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
        6.77       100.01         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 
        2.24         3.06         3.25         3.29         0.26         0.33 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       102.44        40.34        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14         2.93         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        16.01 
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-6168 TCGA-CM-6169 
       14.04        29.03        16.04        21.99        12.99        13.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       14.04        11.01        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        13.51        11.51 
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-D5-6926 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 
        1.51        12.00        11.38        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-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-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-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       60.79        98.24        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 
       35.41        19.43        74.56        65.85        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       51.75        36.72        36.00        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 
       91.79        46.75 

  MET MUTATED MET WILD-TYPE 
         0.07          0.00 
  MET MUTATED MET WILD-TYPE 
       117.07        140.38 
  MET MUTATED MET WILD-TYPE 
       14.990        21.075 
[1] "0.1 - 117.1 (15.0)" "0.0 - 140.4 (21.1)"
[1] "hr=" "1.4"
D360V2, 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       24        96         5         0
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MET MUTATED           3          1          5          3        5         0
  MET WILD-TYPE        16          9         36         28       30        13
               vv
clus            STAGE IVB
  MET MUTATED           1
  MET WILD-TYPE         0
D360V3, multiclass
            clus
vv           MET MUTATED MET WILD-TYPE
  STAGE I              3            61
  STAGE IA             0             1
  STAGE II             1            24
  STAGE IIA           13            96
  STAGE IIB            3             5
  STAGE IIC            1             0
  STAGE III            3            16
  STAGE IIIA           1             9
  STAGE IIIB           5            36
  STAGE IIIC           3            28
  STAGE IV             5            30
  STAGE IVA            0            13
  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  62 222  32
D360V4, multiclass
    clus
vv   MET MUTATED MET WILD-TYPE
  T1           1             8
  T2           6            62
  T3          26           222
  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  71  57
D360V5, multiclass
    clus
vv   MET MUTATED MET WILD-TYPE
  N0          24           196
  N1           9            71
  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"
D360V6, binary
               cls
clus              0   1
  MET MUTATED    30   6
  MET WILD-TYPE 253  42
[1] "tbl2"
               cls
clus            [,1] [,2]
  MET MUTATED     30    6
  MET WILD-TYPE  253   42
   clus
vv  MET MUTATED MET WILD-TYPE
  0          30           253
  1           6            42
[1] 2 2
[1] FALSE
D360V7, 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
D360V8, binary
               cls
clus              0   1
  MET MUTATED    38   4
  MET WILD-TYPE 279  44
[1] "tbl2"
               cls
clus            [,1] [,2]
  MET MUTATED     38    4
  MET WILD-TYPE  279   44
                               clus
vv                              MET MUTATED MET WILD-TYPE
  COLON ADENOCARCINOMA                   38           279
  COLON MUCINOUS ADENOCARCINOMA           4            44
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  MET MUTATED    22   0   3   4
  MET WILD-TYPE 235   2  19  17
D360V9, multiclass
    clus
vv   MET MUTATED MET WILD-TYPE
  R0          22           235
  R1           0             2
  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"
D360V10, 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
D360V11, 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(361) Variable = ERBB3 MUTATION ANALYSIS
D361V1, survival
                 sevent
clus2               0   1
  ERBB3 MUTATED    23   1
  ERBB3 WILD-TYPE 259  72
  ERBB3 MUTATED ERBB3 WILD-TYPE 
             24             331 
  ERBB3 MUTATED ERBB3 WILD-TYPE 
              1              72 
$`ERBB3 MUTATED`
TCGA-A6-5657 TCGA-AA-3519 TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3819 
       31.63         9.07         0.92        19.04        19.04        25.02 
TCGA-AA-3864 TCGA-AA-3950 TCGA-AA-3976 TCGA-AA-A00A TCGA-AA-A00R TCGA-AA-A010 
       53.00        24.00        26.01        38.04         0.99        34.98 
TCGA-AD-6890 TCGA-AY-6197 TCGA-CA-5254 TCGA-CK-4947 TCGA-CM-4746 TCGA-CM-5348 
        0.79        21.44         2.24        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        19.43        53.62 

$`ERBB3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        1.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       85.05        26.99        10.06        35.05        33.04         0.99 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E 
       19.07         7.96        27.02        13.94        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
       42.02        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21        56.55         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        15.75         0.20        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19         1.94         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.33         0.10         1.35       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       29.06        22.03        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 
       13.51        11.51        20.19        18.25         1.32        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        7.53        12.39        10.13        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44        13.41         1.51        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        35.41       107.67        74.56        65.85 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  ERBB3 MUTATED ERBB3 WILD-TYPE 
           0.79            0.00 
  ERBB3 MUTATED ERBB3 WILD-TYPE 
          53.62          140.38 
  ERBB3 MUTATED ERBB3 WILD-TYPE 
          22.21           20.12 
[1] "0.8 - 53.6 (22.2)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "4.6"
D361V2, 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       22       101         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ERBB3 MUTATED           2          1          2          1        2         1
  ERBB3 WILD-TYPE        17          9         39         30       33        12
                 vv
clus              STAGE IVB
  ERBB3 MUTATED           0
  ERBB3 WILD-TYPE         1
D361V3, multiclass
            clus
vv           ERBB3 MUTATED ERBB3 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              8             101
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             1               9
  STAGE IIIB             2              39
  STAGE IIIC             1              30
  STAGE IV               2              33
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  64 232  36
D361V4, multiclass
    clus
vv   ERBB3 MUTATED ERBB3 WILD-TYPE
  T1             1               8
  T2             4              64
  T3            16             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
  ERBB3 MUTATED    18   6   2
  ERBB3 WILD-TYPE 202  74  64
D361V5, multiclass
    clus
vv   ERBB3 MUTATED ERBB3 WILD-TYPE
  N0            18             202
  N1             6              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"
D361V6, binary
                 cls
clus                0   1
  ERBB3 MUTATED    22   2
  ERBB3 WILD-TYPE 261  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB3 MUTATED     22    2
  ERBB3 WILD-TYPE  261   46
   clus
vv  ERBB3 MUTATED ERBB3 WILD-TYPE
  0            22             261
  1             2              46
[1] 2 2
[1] FALSE
D361V7, 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
D361V8, binary
                 cls
clus                0   1
  ERBB3 MUTATED    22   4
  ERBB3 WILD-TYPE 295  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB3 MUTATED     22    4
  ERBB3 WILD-TYPE  295   44
                               clus
vv                              ERBB3 MUTATED ERBB3 WILD-TYPE
  COLON ADENOCARCINOMA                     22             295
  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 236   2  20  19
D361V9, multiclass
    clus
vv   ERBB3 MUTATED ERBB3 WILD-TYPE
  R0            21             236
  R1             0               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"
D361V10, 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
D361V11, 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(362) Variable = GOLGB1 MUTATION ANALYSIS
D362V1, survival
                  sevent
clus2                0   1
  GOLGB1 MUTATED    30   7
  GOLGB1 WILD-TYPE 252  66
  GOLGB1 MUTATED GOLGB1 WILD-TYPE 
              37              318 
  GOLGB1 MUTATED GOLGB1 WILD-TYPE 
               7               66 
$`GOLGB1 MUTATED`
TCGA-A6-5659 TCGA-A6-6141 TCGA-A6-6780 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3555 
       30.44         8.38        20.12        35.01        63.98        29.95 
TCGA-AA-3561 TCGA-AA-3710 TCGA-AA-3864 TCGA-AA-3977 TCGA-AA-A00J TCGA-AA-A00N 
       13.94        26.99        53.00        25.02        18.05         4.01 
TCGA-AA-A010 TCGA-AD-6901 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6606 TCGA-CA-6716 
       34.98        22.42        58.39        49.41        11.74         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4746 TCGA-CM-6162 TCGA-CM-6170 TCGA-CM-6680 
        0.33         0.10        37.02        12.00        15.02        12.03 
TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6927 
       17.85        17.13        16.14        15.58         7.53         9.44 
TCGA-DM-A0XF TCGA-DM-A282 TCGA-F4-6570 TCGA-F4-6809 TCGA-G4-6307 TCGA-G4-6317 
       38.20       139.17         6.18        13.25        55.04        36.00 
TCGA-G4-6588 
       26.17 

$`GOLGB1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 
       24.16        21.76        24.69        24.39        23.87        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3511 TCGA-AA-3514 
       20.28         7.04         3.02         1.02         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 
       33.99        21.01        13.02        24.00        17.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       20.98        19.99        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 
        4.21        56.55         0.79         0.72         5.79        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
      100.01        29.56         5.23         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4947 
        3.06         3.25         3.29         0.07         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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 
       16.01        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 
       12.00        11.38        10.26       119.70        24.43       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       135.65         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       33.67         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        51.75        45.11        36.72 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        52.80 

  GOLGB1 MUTATED GOLGB1 WILD-TYPE 
             0.1              0.0 
  GOLGB1 MUTATED GOLGB1 WILD-TYPE 
          139.17           140.38 
  GOLGB1 MUTATED GOLGB1 WILD-TYPE 
           18.05            20.63 
[1] "0.1 - 139.2 (18.1)" "0.0 - 140.4 (20.6)"
[1] "hr=" "1.1"
D362V2, 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       22        93         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GOLGB1 MUTATED           0          0          5          2        1
  GOLGB1 WILD-TYPE        19         10         36         29       34
                  vv
clus               STAGE IVA STAGE IVB
  GOLGB1 MUTATED           1         0
  GOLGB1 WILD-TYPE        12         1
D362V3, multiclass
            clus
vv           GOLGB1 MUTATED GOLGB1 WILD-TYPE
  STAGE I                 6               58
  STAGE IA                0                1
  STAGE II                3               22
  STAGE IIA              16               93
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              5               36
  STAGE IIIC              2               29
  STAGE IV                1               34
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  61 221  37
D362V4, multiclass
    clus
vv   GOLGB1 MUTATED GOLGB1 WILD-TYPE
  T1              0                9
  T2              7               61
  T3             27              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
  GOLGB1 MUTATED    29   4   5
  GOLGB1 WILD-TYPE 191  76  61
D362V5, multiclass
    clus
vv   GOLGB1 MUTATED GOLGB1 WILD-TYPE
  N0             29              191
  N1              4               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"
D362V6, binary
                  cls
clus                 0   1
  GOLGB1 MUTATED    31   2
  GOLGB1 WILD-TYPE 252  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GOLGB1 MUTATED     31    2
  GOLGB1 WILD-TYPE  252   46
   clus
vv  GOLGB1 MUTATED GOLGB1 WILD-TYPE
  0             31              252
  1              2               46
[1] 2 2
[1] FALSE
D362V7, 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
D362V8, binary
                  cls
clus                 0   1
  GOLGB1 MUTATED    30   8
  GOLGB1 WILD-TYPE 287  40
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GOLGB1 MUTATED     30    8
  GOLGB1 WILD-TYPE  287   40
                               clus
vv                              GOLGB1 MUTATED GOLGB1 WILD-TYPE
  COLON ADENOCARCINOMA                      30              287
  COLON MUCINOUS ADENOCARCINOMA              8               40
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  GOLGB1 MUTATED    27   0   0   3
  GOLGB1 WILD-TYPE 230   2  22  18
D362V9, multiclass
    clus
vv   GOLGB1 MUTATED GOLGB1 WILD-TYPE
  R0             27              230
  R1              0                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"
D362V10, 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
D362V11, 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(363) Variable = BRAF MUTATION ANALYSIS
D363V1, survival
                sevent
clus2              0   1
  BRAF MUTATED    71  21
  BRAF WILD-TYPE 211  52
  BRAF MUTATED BRAF WILD-TYPE 
            92            263 
  BRAF MUTATED BRAF WILD-TYPE 
            21             52 
$`BRAF MUTATED`
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-3809 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5664 
       46.65        42.90        32.75        31.63        33.53        22.09 
TCGA-A6-5665 TCGA-A6-6649 TCGA-A6-6653 TCGA-AA-3492 TCGA-AA-3516 TCGA-AA-3525 
       22.06        24.16        24.39         3.02        13.02         8.05 
TCGA-AA-3543 TCGA-AA-3664 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3815 TCGA-AA-3821 
        0.99        54.02        19.04        19.04        33.04         1.02 
TCGA-AA-3833 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3966 
       15.95        31.00        33.01        26.01        24.00         2.01 
TCGA-AA-A00D TCGA-AA-A00J TCGA-AA-A01D TCGA-AA-A01P TCGA-AD-5900 TCGA-AD-6889 
       19.00        18.05        10.98        38.07         0.07        56.55 
TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 TCGA-AU-6004 TCGA-AY-6196 TCGA-AZ-5407 
        0.72        27.42        10.88        27.09         0.20        61.41 
TCGA-AZ-6598 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-CA-5796 TCGA-CA-6717 TCGA-CA-6718 
       49.41        29.56        11.74         3.25         0.33         0.10 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
       17.56        40.34        15.62        51.32        21.99         2.93 
TCGA-CM-4744 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5864 
       20.02        22.98        30.08        16.01        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       17.03        12.00        12.99        13.02        15.02        14.04 
TCGA-CM-6674 TCGA-CM-6675 TCGA-D5-5538 TCGA-D5-6529 TCGA-D5-6534 TCGA-D5-6535 
       12.95        13.05        12.26        20.19        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6928 TCGA-D5-6930 TCGA-DM-A0XD 
       17.85        12.49        16.14        11.64         1.51        24.43 
TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1DA TCGA-DM-A1HB 
       38.20        92.75        49.91        13.32         7.50       135.65 
TCGA-DM-A285 TCGA-DM-A28C TCGA-F4-6460 TCGA-F4-6570 TCGA-G4-6299 TCGA-G4-6303 
        6.12        81.37        13.38         6.18        74.56        65.85 
TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       45.11        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

$`BRAF WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       43.76        43.76        24.33        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 
       33.34        36.53        14.53        32.91        30.44        29.19 
TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       23.61        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       25.18        21.76        24.69        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
        1.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
       36.03        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01        12.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
        6.97         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
        5.03        85.05        26.99        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       25.02        17.98        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       12.99        24.00         2.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L 
       13.94        38.04        30.02        34.03        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        34.98        15.02        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        21.37         4.21         0.79         5.79        22.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        14.50        16.31         0.95        15.75        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6607 
       62.79         6.77        12.10       100.01         5.23         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        1.94         2.24         3.06         3.29         0.07         0.26 
TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 
        1.35       102.44        49.08        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        13.51        11.51 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6541 TCGA-D5-6898 
       18.25         1.32         4.80        17.13        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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        13.45 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6304 
       13.25         0.53        35.41        19.43       107.67        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        36.72        36.00 

  BRAF MUTATED BRAF WILD-TYPE 
          0.07           0.00 
  BRAF MUTATED BRAF WILD-TYPE 
        135.65         140.38 
  BRAF MUTATED BRAF WILD-TYPE 
         19.04          20.98 
[1] "0.1 - 135.7 (19.0)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.1"
D363V2, 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       20        76         4         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BRAF MUTATED           5          2         14          6        5         2
  BRAF WILD-TYPE        14          8         27         25       30        11
                vv
clus             STAGE IVB
  BRAF MUTATED           1
  BRAF WILD-TYPE         0
D363V3, multiclass
            clus
vv           BRAF MUTATED BRAF WILD-TYPE
  STAGE I              14             50
  STAGE IA              1              0
  STAGE II              5             20
  STAGE IIA            33             76
  STAGE IIB             4              4
  STAGE IIC             0              1
  STAGE III             5             14
  STAGE IIIA            2              8
  STAGE IIIB           14             27
  STAGE IIIC            6             25
  STAGE IV              5             30
  STAGE IVA             2             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  54 182  28
D363V4, multiclass
    clus
vv   BRAF MUTATED BRAF WILD-TYPE
  T1            2              7
  T2           14             54
  T3           66            182
  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  58  52
D363V5, multiclass
    clus
vv   BRAF MUTATED BRAF WILD-TYPE
  N0           60            160
  N1           22             58
  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"
D363V6, binary
                cls
clus               0   1
  BRAF MUTATED    74   7
  BRAF WILD-TYPE 209  41
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED     74    7
  BRAF WILD-TYPE  209   41
   clus
vv  BRAF MUTATED BRAF WILD-TYPE
  0           74            209
  1            7             41
[1] 2 2
[1] FALSE
D363V7, 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
D363V8, binary
                cls
clus               0   1
  BRAF MUTATED    71  25
  BRAF WILD-TYPE 246  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED     71   25
  BRAF WILD-TYPE  246   23
                               clus
vv                              BRAF MUTATED BRAF WILD-TYPE
  COLON ADENOCARCINOMA                    71            246
  COLON MUCINOUS ADENOCARCINOMA           25             23
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  BRAF MUTATED    62   1   2   9
  BRAF WILD-TYPE 195   1  20  12
D363V9, multiclass
    clus
vv   BRAF MUTATED BRAF WILD-TYPE
  R0           62            195
  R1            1              1
  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"
D363V10, 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
D363V11, 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(364) Variable = HLA-A MUTATION ANALYSIS
D364V1, survival
                 sevent
clus2               0   1
  HLA-A MUTATED    15   1
  HLA-A WILD-TYPE 267  72
  HLA-A MUTATED HLA-A WILD-TYPE 
             16             339 
  HLA-A MUTATED HLA-A WILD-TYPE 
              1              72 
$`HLA-A MUTATED`
TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3713 TCGA-AA-3815 TCGA-AA-3861 
       22.06        19.66         3.02        19.04        33.04        30.05 
TCGA-AA-3977 TCGA-AD-6889 TCGA-AZ-4315 TCGA-CA-6718 TCGA-CK-5913 TCGA-CM-4743 
       25.02        56.55        58.39         0.10        51.32        23.05 
TCGA-D5-6541 TCGA-D5-6931 TCGA-G4-6304 TCGA-G4-6586 
       15.58        12.00        53.62        35.80 

$`HLA-A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.12        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       85.05        26.99        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        4.21         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.33         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 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-D5-6932 
        9.04         9.44        11.64        13.41         1.51        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      107.67        74.56        65.85        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 
       45.11        36.72        36.00        22.09        13.78        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  HLA-A MUTATED HLA-A WILD-TYPE 
            0.1             0.0 
  HLA-A MUTATED HLA-A WILD-TYPE 
          58.39          140.38 
  HLA-A MUTATED HLA-A WILD-TYPE 
         24.035          20.020 
[1] "0.1 - 58.4 (24.0)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "3.9"
D364V2, 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       24        99         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HLA-A MUTATED           0          0          0          2        1         0
  HLA-A WILD-TYPE        19         10         41         29       34        13
                 vv
clus              STAGE IVB
  HLA-A MUTATED           0
  HLA-A WILD-TYPE         1
D364V3, multiclass
            clus
vv           HLA-A MUTATED HLA-A WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA             10              99
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             2              29
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HLA-A MUTATED     0   1  12   3
  HLA-A WILD-TYPE   9  67 236  38
D364V4, multiclass
    clus
vv   HLA-A MUTATED HLA-A WILD-TYPE
  T1             0               9
  T2             1              67
  T3            12             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
  HLA-A MUTATED    14   1   1
  HLA-A WILD-TYPE 206  79  65
D364V5, multiclass
    clus
vv   HLA-A MUTATED HLA-A WILD-TYPE
  N0            14             206
  N1             1              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"
D364V6, binary
                 cls
clus                0   1
  HLA-A MUTATED    12   1
  HLA-A WILD-TYPE 271  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED     12    1
  HLA-A WILD-TYPE  271   47
   clus
vv  HLA-A MUTATED HLA-A WILD-TYPE
  0            12             271
  1             1              47
[1] 2 2
[1] FALSE
D364V7, binary
                 cls
clus                0   1
  HLA-A MUTATED     6  10
  HLA-A WILD-TYPE 164 187
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED      6   10
  HLA-A WILD-TYPE  164  187
        clus
vv       HLA-A MUTATED HLA-A WILD-TYPE
  FEMALE             6             164
  MALE              10             187
[1] 2 2
[1] FALSE
D364V8, binary
                 cls
clus                0   1
  HLA-A MUTATED    15   1
  HLA-A WILD-TYPE 302  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED     15    1
  HLA-A WILD-TYPE  302   47
                               clus
vv                              HLA-A MUTATED HLA-A WILD-TYPE
  COLON ADENOCARCINOMA                     15             302
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  HLA-A MUTATED    11   0   1   2
  HLA-A WILD-TYPE 246   2  21  19
D364V9, multiclass
    clus
vv   HLA-A MUTATED HLA-A WILD-TYPE
  R0            11             246
  R1             0               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"
D364V10, 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
D364V11, 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(365) Variable = C6ORF89 MUTATION ANALYSIS
D365V1, survival
                   sevent
clus2                 0   1
  C6ORF89 MUTATED     3   2
  C6ORF89 WILD-TYPE 279  71
  C6ORF89 MUTATED C6ORF89 WILD-TYPE 
                5               350 
  C6ORF89 MUTATED C6ORF89 WILD-TYPE 
                2                71 
$`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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       15.75        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  C6ORF89 MUTATED C6ORF89 WILD-TYPE 
              0.2               0.0 
  C6ORF89 MUTATED C6ORF89 WILD-TYPE 
            25.02            140.38 
  C6ORF89 MUTATED C6ORF89 WILD-TYPE 
            11.01             20.63 
[1] "0.2 - 25.0 (11.0)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "3.7"
D365V2, 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       25       108         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C6ORF89 MUTATED           1          0          0          1        0
  C6ORF89 WILD-TYPE        18         10         41         30       35
                   vv
clus                STAGE IVA STAGE IVB
  C6ORF89 MUTATED           2         0
  C6ORF89 WILD-TYPE        11         1
D365V3, multiclass
            clus
vv           C6ORF89 MUTATED C6ORF89 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                1               108
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               1                30
  STAGE IV                 0                35
  STAGE IVA                2                11
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 244  40
D365V4, multiclass
    clus
vv   C6ORF89 MUTATED C6ORF89 WILD-TYPE
  T1               0                 9
  T2               1                67
  T3               4               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
  C6ORF89 MUTATED     2   2   2
  C6ORF89 WILD-TYPE 218  78  64
D365V5, multiclass
    clus
vv   C6ORF89 MUTATED C6ORF89 WILD-TYPE
  N0               2               218
  N1               2                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"
D365V6, binary
                   cls
clus                  0   1
  C6ORF89 MUTATED     2   2
  C6ORF89 WILD-TYPE 281  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C6ORF89 MUTATED      2    2
  C6ORF89 WILD-TYPE  281   46
   clus
vv  C6ORF89 MUTATED C6ORF89 WILD-TYPE
  0               2               281
  1               2                46
[1] 2 2
[1] FALSE
D365V7, 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
D365V8, binary
                   cls
clus                  0   1
  C6ORF89 MUTATED     5   1
  C6ORF89 WILD-TYPE 312  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C6ORF89 MUTATED      5    1
  C6ORF89 WILD-TYPE  312   47
                               clus
vv                              C6ORF89 MUTATED C6ORF89 WILD-TYPE
  COLON ADENOCARCINOMA                        5               312
  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 252   2  22  21
D365V9, multiclass
    clus
vv   C6ORF89 MUTATED C6ORF89 WILD-TYPE
  R0               5               252
  R1               0                 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"
D365V10, 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
D365V11, 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(366) Variable = VPS13B MUTATION ANALYSIS
D366V1, survival
                  sevent
clus2                0   1
  VPS13B MUTATED    40  10
  VPS13B WILD-TYPE 242  63
  VPS13B MUTATED VPS13B WILD-TYPE 
              50              305 
  VPS13B MUTATED VPS13B WILD-TYPE 
              10               63 
$`VPS13B MUTATED`
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3496 
       29.19        33.53        24.39        19.66         3.02         1.02 
TCGA-AA-3516 TCGA-AA-3529 TCGA-AA-3555 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3713 
       13.02         0.00        29.95        14.01         0.92        19.04 
TCGA-AA-3715 TCGA-AA-3864 TCGA-AA-3956 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-A00N 
       19.04        53.00        34.03        25.02        27.02         4.01 
TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-6964 TCGA-AY-4071 TCGA-AY-6197 TCGA-AZ-4315 
       34.98        35.01        10.88         0.95        21.44        58.39 
TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       62.79        49.41        12.10         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-5913 TCGA-CM-4746 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-6162 
        1.35        51.32        37.02        30.08        16.01        12.00 
TCGA-CM-6164 TCGA-CM-6171 TCGA-CM-6674 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6535 
       29.03        14.04        12.95        19.59        11.51        15.12 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-6931 TCGA-F4-6805 
       16.14        15.58         9.44         1.51        12.00        16.31 
TCGA-G4-6293 TCGA-G4-6628 
      107.67        52.80 

$`VPS13B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       32.91        31.63        30.44        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 
       24.16        21.76        24.69        23.87        20.12        20.28 
TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        7.04        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
       19.07        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        2.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       34.06        26.01        24.00        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6196 
        0.20        14.50        27.09        16.31        15.75         0.20 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 
       17.82         1.41         5.13        83.80        22.36        61.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
       17.56       102.44        40.34        15.62        49.08        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        12.26        13.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        17.85         4.80        17.13        12.49 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
        1.55        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.41        19.43        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       13.78        35.80        26.17        91.79        46.75 

  VPS13B MUTATED VPS13B WILD-TYPE 
               0                0 
  VPS13B MUTATED VPS13B WILD-TYPE 
          107.67           140.38 
  VPS13B MUTATED VPS13B WILD-TYPE 
          16.225           21.140 
[1] "0.0 - 107.7 (16.2)" "0.0 - 140.4 (21.1)"
[1] "hr=" "1.1"
D366V2, 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       18        91         5         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  VPS13B MUTATED           4          1          3          4        2
  VPS13B WILD-TYPE        15          9         38         27       33
                  vv
clus               STAGE IVA STAGE IVB
  VPS13B MUTATED           0         0
  VPS13B WILD-TYPE        13         1
D366V3, multiclass
            clus
vv           VPS13B MUTATED VPS13B WILD-TYPE
  STAGE I                 8               56
  STAGE IA                0                1
  STAGE II                7               18
  STAGE IIA              18               91
  STAGE IIB               3                5
  STAGE IIC               0                1
  STAGE III               4               15
  STAGE IIIA              1                9
  STAGE IIIB              3               38
  STAGE IIIC              4               27
  STAGE IV                2               33
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  VPS13B MUTATED     1   8  35   8
  VPS13B WILD-TYPE   8  60 213  33
D366V4, multiclass
    clus
vv   VPS13B MUTATED VPS13B WILD-TYPE
  T1              1                8
  T2              8               60
  T3             35              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
  VPS13B MUTATED    38   8   6
  VPS13B WILD-TYPE 182  72  60
D366V5, multiclass
    clus
vv   VPS13B MUTATED VPS13B WILD-TYPE
  N0             38              182
  N1              8               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"
D366V6, binary
                  cls
clus                 0   1
  VPS13B MUTATED    40   2
  VPS13B WILD-TYPE 243  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VPS13B MUTATED     40    2
  VPS13B WILD-TYPE  243   46
   clus
vv  VPS13B MUTATED VPS13B WILD-TYPE
  0             40              243
  1              2               46
[1] 2 2
[1] FALSE
D366V7, 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
D366V8, binary
                  cls
clus                 0   1
  VPS13B MUTATED    41  10
  VPS13B WILD-TYPE 276  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VPS13B MUTATED     41   10
  VPS13B WILD-TYPE  276   38
                               clus
vv                              VPS13B MUTATED VPS13B WILD-TYPE
  COLON ADENOCARCINOMA                      41              276
  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 222   2  21  14
D366V9, multiclass
    clus
vv   VPS13B MUTATED VPS13B WILD-TYPE
  R0             35              222
  R1              0                2
  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"
D366V10, 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
D366V11, 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(367) Variable = C6ORF170 MUTATION ANALYSIS
D367V1, survival
                    sevent
clus2                  0   1
  C6ORF170 MUTATED    13   5
  C6ORF170 WILD-TYPE 269  68
  C6ORF170 MUTATED C6ORF170 WILD-TYPE 
                18                337 
  C6ORF170 MUTATED C6ORF170 WILD-TYPE 
                 5                 68 
$`C6ORF170 MUTATED`
TCGA-A6-6142 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3977 
       25.08        63.98         6.97        26.99        19.04        25.02 
TCGA-AA-A010 TCGA-AD-6901 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CA-6718 
       34.98        22.42        58.39        49.41         0.33         0.10 
TCGA-CM-5864 TCGA-CM-6162 TCGA-D5-6898 TCGA-DM-A28C TCGA-DM-A28F TCGA-F4-6704 
       15.02        12.00         7.53        81.37        35.97         1.55 

$`C6ORF170 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       35.01         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       85.05        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 
        4.21        56.55         0.79         0.72         5.79        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
      135.65       139.17         6.12       119.93        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  C6ORF170 MUTATED C6ORF170 WILD-TYPE 
               0.1                0.0 
  C6ORF170 MUTATED C6ORF170 WILD-TYPE 
             81.37             140.38 
  C6ORF170 MUTATED C6ORF170 WILD-TYPE 
             23.72              20.12 
[1] "0.1 - 81.4 (23.7)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.3"
D367V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C6ORF170 MUTATED         2        0        4         6         1         0
  C6ORF170 WILD-TYPE      62        1       21       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        19         10         39         30       35
                    vv
clus                 STAGE IVA STAGE IVB
  C6ORF170 MUTATED           1         0
  C6ORF170 WILD-TYPE        12         1
D367V3, multiclass
            clus
vv           C6ORF170 MUTATED C6ORF170 WILD-TYPE
  STAGE I                   2                 62
  STAGE IA                  0                  1
  STAGE II                  4                 21
  STAGE IIA                 6                103
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                0                 10
  STAGE IIIB                2                 39
  STAGE IIIC                1                 30
  STAGE IV                  0                 35
  STAGE IVA                 1                 12
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of 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  14   2
  C6ORF170 WILD-TYPE   9  65 234  39
D367V4, multiclass
    clus
vv   C6ORF170 MUTATED C6ORF170 WILD-TYPE
  T1                0                  9
  T2                3                 65
  T3               14                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
  C6ORF170 MUTATED    15   3   1
  C6ORF170 WILD-TYPE 205  77  65
D367V5, multiclass
    clus
vv   C6ORF170 MUTATED C6ORF170 WILD-TYPE
  N0               15                205
  N1                3                 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"
D367V6, binary
                    cls
clus                   0   1
  C6ORF170 MUTATED    14   1
  C6ORF170 WILD-TYPE 269  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF170 MUTATED     14    1
  C6ORF170 WILD-TYPE  269   47
   clus
vv  C6ORF170 MUTATED C6ORF170 WILD-TYPE
  0               14                269
  1                1                 47
[1] 2 2
[1] FALSE
D367V7, binary
                    cls
clus                   0   1
  C6ORF170 MUTATED     7  12
  C6ORF170 WILD-TYPE 163 185
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF170 MUTATED      7   12
  C6ORF170 WILD-TYPE  163  185
        clus
vv       C6ORF170 MUTATED C6ORF170 WILD-TYPE
  FEMALE                7                163
  MALE                 12                185
[1] 2 2
[1] FALSE
D367V8, binary
                    cls
clus                   0   1
  C6ORF170 MUTATED    16   3
  C6ORF170 WILD-TYPE 301  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF170 MUTATED     16    3
  C6ORF170 WILD-TYPE  301   45
                               clus
vv                              C6ORF170 MUTATED C6ORF170 WILD-TYPE
  COLON ADENOCARCINOMA                        16                301
  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 246   2  22  19
D367V9, multiclass
    clus
vv   C6ORF170 MUTATED C6ORF170 WILD-TYPE
  R0               11                246
  R1                0                  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"
D367V10, 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     9
  C6ORF170 WILD-TYPE                        19   167
D367V11, 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                                           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(368) Variable = RAB6C MUTATION ANALYSIS
D368V1, survival
                 sevent
clus2               0   1
  RAB6C MUTATED     4   1
  RAB6C WILD-TYPE 278  72
  RAB6C MUTATED RAB6C WILD-TYPE 
              5             350 
  RAB6C MUTATED RAB6C WILD-TYPE 
              1              72 
$`RAB6C MUTATED`
TCGA-AA-3660 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4952 TCGA-D5-5537 
       78.08         0.33         0.10        15.62        45.40 

$`RAB6C WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        61.02         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07         0.26         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       40.34        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  RAB6C MUTATED RAB6C WILD-TYPE 
            0.1             0.0 
  RAB6C MUTATED RAB6C WILD-TYPE 
          78.08          140.38 
  RAB6C MUTATED RAB6C WILD-TYPE 
         15.620          20.235 
[1] "0.1 - 78.1 (15.6)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D368V2, 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       24       106         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RAB6C MUTATED           1          0          0          0        0         0
  RAB6C WILD-TYPE        18         10         41         31       35        13
                 vv
clus              STAGE IVB
  RAB6C MUTATED           0
  RAB6C WILD-TYPE         1
D368V3, multiclass
            clus
vv           RAB6C MUTATED RAB6C WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              3             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RAB6C MUTATED     0   0   4   1
  RAB6C WILD-TYPE   9  68 244  40
D368V4, multiclass
    clus
vv   RAB6C MUTATED RAB6C WILD-TYPE
  T1             0               9
  T2             0              68
  T3             4             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
  RAB6C MUTATED     3   0   2
  RAB6C WILD-TYPE 217  80  64
D368V5, multiclass
    clus
vv   RAB6C MUTATED RAB6C WILD-TYPE
  N0             3             217
  N1             0              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"
D368V6, binary
                 cls
clus                0   1
  RAB6C MUTATED     4   0
  RAB6C WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB6C MUTATED      4    0
  RAB6C WILD-TYPE  279   48
   clus
vv  RAB6C MUTATED RAB6C WILD-TYPE
  0             4             279
  1             0              48
[1] 2 2
[1] FALSE
D368V7, 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
D368V8, binary
                 cls
clus                0   1
  RAB6C MUTATED     3   2
  RAB6C WILD-TYPE 314  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB6C MUTATED      3    2
  RAB6C WILD-TYPE  314   46
                               clus
vv                              RAB6C MUTATED RAB6C WILD-TYPE
  COLON ADENOCARCINOMA                      3             314
  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 256   2  22  17
D368V9, multiclass
    clus
vv   RAB6C MUTATED RAB6C WILD-TYPE
  R0             1             256
  R1             0               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"
D368V10, 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
D368V11, 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(369) Variable = ZNF708 MUTATION ANALYSIS
D369V1, survival
                  sevent
clus2                0   1
  ZNF708 MUTATED     6   3
  ZNF708 WILD-TYPE 276  70
  ZNF708 MUTATED ZNF708 WILD-TYPE 
               9              346 
  ZNF708 MUTATED ZNF708 WILD-TYPE 
               3               70 
$`ZNF708 MUTATED`
TCGA-A6-5666 TCGA-AA-3713 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6964 TCGA-AY-5543 
       32.71        19.04         4.01        34.98        10.88        15.75 
TCGA-CA-6718 TCGA-D5-6928 TCGA-DM-A28G 
        0.10        11.64        60.79 

$`ZNF708 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
        0.72         5.79        22.42        27.42         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-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-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.33         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       35.97       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  ZNF708 MUTATED ZNF708 WILD-TYPE 
             0.1              0.0 
  ZNF708 MUTATED ZNF708 WILD-TYPE 
           60.79           140.38 
  ZNF708 MUTATED ZNF708 WILD-TYPE 
           15.75            20.63 
[1] "0.1 - 60.8 (15.8)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "2"  
D369V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF708 MUTATED         0        0        0         4         2         1
  ZNF708 WILD-TYPE      64        1       25       105         6         0
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF708 MUTATED           0          0          0          0        1
  ZNF708 WILD-TYPE        19         10         41         31       34
                  vv
clus               STAGE IVA STAGE IVB
  ZNF708 MUTATED           1         0
  ZNF708 WILD-TYPE        12         1
D369V3, multiclass
            clus
vv           ZNF708 MUTATED ZNF708 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               4              105
  STAGE IIB               2                6
  STAGE IIC               1                0
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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   0   6   4
  ZNF708 WILD-TYPE   9  68 242  37
D369V4, multiclass
    clus
vv   ZNF708 MUTATED ZNF708 WILD-TYPE
  T1              0                9
  T2              0               68
  T3              6              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     8   1   1
  ZNF708 WILD-TYPE 212  79  65
D369V5, multiclass
    clus
vv   ZNF708 MUTATED ZNF708 WILD-TYPE
  N0              8              212
  N1              1               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"
D369V6, binary
                  cls
clus                 0   1
  ZNF708 MUTATED     7   2
  ZNF708 WILD-TYPE 276  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF708 MUTATED      7    2
  ZNF708 WILD-TYPE  276   46
   clus
vv  ZNF708 MUTATED ZNF708 WILD-TYPE
  0              7              276
  1              2               46
[1] 2 2
[1] FALSE
D369V7, binary
                  cls
clus                 0   1
  ZNF708 MUTATED     3   7
  ZNF708 WILD-TYPE 167 190
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF708 MUTATED      3    7
  ZNF708 WILD-TYPE  167  190
        clus
vv       ZNF708 MUTATED ZNF708 WILD-TYPE
  FEMALE              3              167
  MALE                7              190
[1] 2 2
[1] FALSE
D369V8, binary
                  cls
clus                 0   1
  ZNF708 MUTATED     8   2
  ZNF708 WILD-TYPE 309  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF708 MUTATED      8    2
  ZNF708 WILD-TYPE  309   46
                               clus
vv                              ZNF708 MUTATED ZNF708 WILD-TYPE
  COLON ADENOCARCINOMA                       8              309
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF708 MUTATED     5   0   1   1
  ZNF708 WILD-TYPE 252   2  21  20
D369V9, multiclass
    clus
vv   ZNF708 MUTATED ZNF708 WILD-TYPE
  R0              5              252
  R1              0                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"
D369V10, 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     4
  ZNF708 WILD-TYPE                        18   172
D369V11, 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                                         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(370) Variable = CHML MUTATION ANALYSIS
D370V1, survival
                sevent
clus2              0   1
  CHML MUTATED    16   4
  CHML WILD-TYPE 266  69
  CHML MUTATED CHML WILD-TYPE 
            20            335 
  CHML MUTATED CHML WILD-TYPE 
             4             69 
$`CHML MUTATED`
TCGA-A6-3809 TCGA-A6-6138 TCGA-A6-6141 TCGA-AA-3492 TCGA-AA-3525 TCGA-AA-3662 
       32.75        22.52         8.38         3.02         8.05         6.05 
TCGA-AA-3672 TCGA-AA-3947 TCGA-AD-6964 TCGA-AU-6004 TCGA-AZ-6601 TCGA-CM-5348 
        0.92        33.01        10.88        27.09       100.01        22.98 
TCGA-CM-6162 TCGA-D5-5537 TCGA-D5-6923 TCGA-D5-6928 TCGA-D5-6929 TCGA-F4-6460 
       12.00        45.40        12.43        11.64        13.41        13.38 
TCGA-G4-6323 TCGA-G4-6625 
       13.78        91.79 

$`CHML WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       22.06        32.71        27.09        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       37.05        36.03        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       78.08         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.20        14.50        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6628 
       22.09        35.80        26.17        46.75        52.80 

  CHML MUTATED CHML WILD-TYPE 
          0.92           0.00 
  CHML MUTATED CHML WILD-TYPE 
        100.01         140.38 
  CHML MUTATED CHML WILD-TYPE 
        13.395         20.980 
[1] "0.9 - 100.0 (13.4)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1"  
D370V2, 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       23       105         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        18         10         37         31       33        13
                vv
clus             STAGE IVB
  CHML MUTATED           0
  CHML WILD-TYPE         1
D370V3, multiclass
            clus
vv           CHML MUTATED CHML WILD-TYPE
  STAGE I               3             61
  STAGE IA              1              0
  STAGE II              2             23
  STAGE IIA             4            105
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            4             37
  STAGE IIIC            0             31
  STAGE IV              2             33
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CHML MUTATED     0   3  12   4
  CHML WILD-TYPE   9  65 236  37
D370V4, multiclass
    clus
vv   CHML MUTATED CHML WILD-TYPE
  T1            0              9
  T2            3             65
  T3           12            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
  CHML MUTATED    11   6   3
  CHML WILD-TYPE 209  74  63
D370V5, multiclass
    clus
vv   CHML MUTATED CHML WILD-TYPE
  N0           11            209
  N1            6             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"
D370V6, binary
                cls
clus               0   1
  CHML MUTATED    15   2
  CHML WILD-TYPE 268  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHML MUTATED     15    2
  CHML WILD-TYPE  268   46
   clus
vv  CHML MUTATED CHML WILD-TYPE
  0           15            268
  1            2             46
[1] 2 2
[1] FALSE
D370V7, 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
D370V8, binary
                cls
clus               0   1
  CHML MUTATED    16   4
  CHML WILD-TYPE 301  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHML MUTATED     16    4
  CHML WILD-TYPE  301   44
                               clus
vv                              CHML MUTATED CHML WILD-TYPE
  COLON ADENOCARCINOMA                    16            301
  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 243   2  21  20
D370V9, multiclass
    clus
vv   CHML MUTATED CHML WILD-TYPE
  R0           14            243
  R1            0              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"
D370V10, 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
D370V11, 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(371) Variable = PHF3 MUTATION ANALYSIS
D371V1, survival
                sevent
clus2              0   1
  PHF3 MUTATED    18   2
  PHF3 WILD-TYPE 264  71
  PHF3 MUTATED PHF3 WILD-TYPE 
            20            335 
  PHF3 MUTATED PHF3 WILD-TYPE 
             2             71 
$`PHF3 MUTATED`
TCGA-A6-5660 TCGA-A6-6142 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3710 TCGA-AA-3947 
       29.19        25.08        19.66        63.98        26.99        33.01 
TCGA-AA-3966 TCGA-AA-A00A TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-5900 TCGA-AU-6004 
        2.01        38.04         4.01        34.98         0.07        27.09 
TCGA-AY-6197 TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4948 TCGA-CM-6169 
       21.44         3.29         0.33         0.10       102.44        13.02 
TCGA-D5-6541 TCGA-DM-A28F 
       15.58        35.97 

$`PHF3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6648 
       22.06        32.71        27.09        22.52         8.38        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 
       18.05        31.00         2.01        12.99        24.00        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        15.75         0.20        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 
        0.07         0.26         1.35        17.56        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
      119.93        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  PHF3 MUTATED PHF3 WILD-TYPE 
          0.07           0.00 
  PHF3 MUTATED PHF3 WILD-TYPE 
        102.44         140.38 
  PHF3 MUTATED PHF3 WILD-TYPE 
         23.26          20.12 
[1] "0.1 - 102.4 (23.3)" "0.0 - 140.4 (20.1)"
[1] "hr=" "2"  
D371V2, 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       23       100         5         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PHF3 MUTATED           1          1          1          2        1         1
  PHF3 WILD-TYPE        18          9         40         29       34        12
                vv
clus             STAGE IVB
  PHF3 MUTATED           0
  PHF3 WILD-TYPE         1
D371V3, multiclass
            clus
vv           PHF3 MUTATED PHF3 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             9            100
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            1              9
  STAGE IIIB            1             40
  STAGE IIIC            2             29
  STAGE IV              1             34
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 232  36
D371V4, multiclass
    clus
vv   PHF3 MUTATED PHF3 WILD-TYPE
  T1            0              9
  T2            2             66
  T3           16            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
  PHF3 MUTATED    16   4   3
  PHF3 WILD-TYPE 204  76  63
D371V5, multiclass
    clus
vv   PHF3 MUTATED PHF3 WILD-TYPE
  N0           16            204
  N1            4             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"
D371V6, binary
                cls
clus               0   1
  PHF3 MUTATED    18   2
  PHF3 WILD-TYPE 265  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  PHF3 MUTATED     18    2
  PHF3 WILD-TYPE  265   46
   clus
vv  PHF3 MUTATED PHF3 WILD-TYPE
  0           18            265
  1            2             46
[1] 2 2
[1] FALSE
D371V7, 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
D371V8, binary
                cls
clus               0   1
  PHF3 MUTATED    17   6
  PHF3 WILD-TYPE 300  42
[1] "tbl2"
                cls
clus             [,1] [,2]
  PHF3 MUTATED     17    6
  PHF3 WILD-TYPE  300   42
                               clus
vv                              PHF3 MUTATED PHF3 WILD-TYPE
  COLON ADENOCARCINOMA                    17            300
  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 241   2  21  19
D371V9, multiclass
    clus
vv   PHF3 MUTATED PHF3 WILD-TYPE
  R0           16            241
  R1            0              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"
D371V10, 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
D371V11, 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(372) Variable = STAB2 MUTATION ANALYSIS
D372V1, survival
                 sevent
clus2               0   1
  STAB2 MUTATED    27   4
  STAB2 WILD-TYPE 255  69
  STAB2 MUTATED STAB2 WILD-TYPE 
             31             324 
  STAB2 MUTATED STAB2 WILD-TYPE 
              4              69 
$`STAB2 MUTATED`
TCGA-A6-2672 TCGA-A6-3809 TCGA-A6-6141 TCGA-A6-6653 TCGA-A6-6780 TCGA-AA-3492 
       46.65        32.75         8.38        24.39        20.12         3.02 
TCGA-AA-3510 TCGA-AA-3554 TCGA-AA-3845 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3947 
       63.98        17.95         0.00        31.07        53.00        33.01 
TCGA-AA-3949 TCGA-AA-3977 TCGA-AA-A00K TCGA-AA-A010 TCGA-AA-A01T TCGA-AZ-4315 
       26.01        25.02        18.05        34.98        33.04        58.39 
TCGA-AZ-6600 TCGA-CA-5797 TCGA-CA-6717 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6679 
       12.10         3.29         0.33        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        35.87 
TCGA-G4-6323 
       13.78 

$`STAB2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       34.65        33.34        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       32.71        27.09        22.52        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 
       21.76        24.69        23.87        19.66        20.28         7.04 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02        14.93        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3950 
       18.05        31.00         2.01        12.99        24.00        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X 
       38.07         1.02        35.01         1.02        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41        49.41         6.77       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6168 
       15.02        12.00        14.04        29.03        16.04        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.08        11.01        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       43.27        15.12         4.80        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       10.26       119.70        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 
      117.07         8.61        13.38        13.45         6.18         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        35.80        26.17        91.79        46.75        52.80 

  STAB2 MUTATED STAB2 WILD-TYPE 
              0               0 
  STAB2 MUTATED STAB2 WILD-TYPE 
         135.65          140.38 
  STAB2 MUTATED STAB2 WILD-TYPE 
         24.390          20.005 
[1] "0.0 - 135.7 (24.4)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.9"
D372V2, 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       22        96         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        18         10         37         30       34        13
                 vv
clus              STAGE IVB
  STAB2 MUTATED           0
  STAB2 WILD-TYPE         1
D372V3, multiclass
            clus
vv           STAB2 MUTATED STAB2 WILD-TYPE
  STAGE I                4              60
  STAGE IA               1               0
  STAGE II               3              22
  STAGE IIA             13              96
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             4              37
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  STAB2 MUTATED     0   5  22   4
  STAB2 WILD-TYPE   9  63 226  37
D372V4, multiclass
    clus
vv   STAB2 MUTATED STAB2 WILD-TYPE
  T1             0               9
  T2             5              63
  T3            22             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
  STAB2 MUTATED    25   5   2
  STAB2 WILD-TYPE 195  75  64
D372V5, multiclass
    clus
vv   STAB2 MUTATED STAB2 WILD-TYPE
  N0            25             195
  N1             5              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"
D372V6, binary
                 cls
clus                0   1
  STAB2 MUTATED    27   1
  STAB2 WILD-TYPE 256  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAB2 MUTATED     27    1
  STAB2 WILD-TYPE  256   47
   clus
vv  STAB2 MUTATED STAB2 WILD-TYPE
  0            27             256
  1             1              47
[1] 2 2
[1] FALSE
D372V7, 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
D372V8, binary
                 cls
clus                0   1
  STAB2 MUTATED    26   6
  STAB2 WILD-TYPE 291  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAB2 MUTATED     26    6
  STAB2 WILD-TYPE  291   42
                               clus
vv                              STAB2 MUTATED STAB2 WILD-TYPE
  COLON ADENOCARCINOMA                     26             291
  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 235   2  22  19
D372V9, multiclass
    clus
vv   STAB2 MUTATED STAB2 WILD-TYPE
  R0            22             235
  R1             0               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"
D372V10, 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
D372V11, 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(373) Variable = TRRAP MUTATION ANALYSIS
D373V1, survival
                 sevent
clus2               0   1
  TRRAP MUTATED    34  10
  TRRAP WILD-TYPE 248  63
  TRRAP MUTATED TRRAP WILD-TYPE 
             44             311 
  TRRAP MUTATED TRRAP WILD-TYPE 
             10              63 
$`TRRAP MUTATED`
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-6138 
       42.90        42.28        31.63        29.19        23.61        22.52 
TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3552 TCGA-AA-3663 
       19.66         3.02         1.02        63.98        13.02         6.97 
TCGA-AA-3672 TCGA-AA-3678 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3815 
        0.92        47.01        26.99        19.04        10.06        33.04 
TCGA-AA-A00A TCGA-AA-A010 TCGA-AA-A01P TCGA-AA-A01R TCGA-AD-6901 TCGA-AZ-4315 
       38.04        34.98        38.07        35.01        22.42        58.39 
TCGA-AZ-4681 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4952 
       83.80        61.41         6.77         0.10        17.56        15.62 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CM-4752 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-6171 
       51.32        21.14        13.02        16.01        15.02        14.04 
TCGA-D5-5539 TCGA-D5-6535 TCGA-DM-A1D4 TCGA-DM-A1HA TCGA-F4-6808 TCGA-G4-6306 
       19.59        15.12        92.75       131.51        33.67        44.68 
TCGA-G4-6586 TCGA-G4-6628 
       35.80        52.80 

$`TRRAP WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2683 TCGA-A6-3807 
       43.76        46.65        43.76        24.33        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5659 
       33.34        32.75        36.53        14.53        32.91        30.44 
TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 
       33.53        22.09        22.06        32.71        27.09         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3511 
       23.87        20.12        20.28         7.04        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       14.01        33.99        21.01        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       78.08         6.05        54.02         2.01        14.01        50.04 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        85.05        19.04        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       13.94        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        0.72         5.79        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         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-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 
        0.26         0.33         1.35       102.44        40.34        49.08 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99         2.93         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-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 
       10.26       119.70        24.43        38.20       130.65        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB 
       13.32        12.59       140.38         7.50        44.32       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 
       35.87         1.55        16.31        29.59        16.24        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        26.17        91.79        46.75 

  TRRAP MUTATED TRRAP WILD-TYPE 
            0.1             0.0 
  TRRAP MUTATED TRRAP WILD-TYPE 
         131.51          140.38 
  TRRAP MUTATED TRRAP WILD-TYPE 
          25.30           19.99 
[1] "0.1 - 131.5 (25.3)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.1"
D373V2, 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       19        95         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TRRAP MUTATED           6          1          3          4        0         2
  TRRAP WILD-TYPE        13          9         38         27       35        11
                 vv
clus              STAGE IVB
  TRRAP MUTATED           0
  TRRAP WILD-TYPE         1
D373V3, multiclass
            clus
vv           TRRAP MUTATED TRRAP WILD-TYPE
  STAGE I                8              56
  STAGE IA               0               1
  STAGE II               6              19
  STAGE IIA             14              95
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              6              13
  STAGE IIIA             1               9
  STAGE IIIB             3              38
  STAGE IIIC             4              27
  STAGE IV               0              35
  STAGE IVA              2              11
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  31   7
  TRRAP WILD-TYPE   6  61 217  34
D373V4, multiclass
    clus
vv   TRRAP MUTATED TRRAP WILD-TYPE
  T1             3               6
  T2             7              61
  T3            31             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    32   9   7
  TRRAP WILD-TYPE 188  71  59
D373V5, multiclass
    clus
vv   TRRAP MUTATED TRRAP WILD-TYPE
  N0            32             188
  N1             9              71
  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"
D373V6, binary
                 cls
clus                0   1
  TRRAP MUTATED    40   1
  TRRAP WILD-TYPE 243  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRRAP MUTATED     40    1
  TRRAP WILD-TYPE  243   47
   clus
vv  TRRAP MUTATED TRRAP WILD-TYPE
  0            40             243
  1             1              47
[1] 2 2
[1] FALSE
D373V7, binary
                 cls
clus                0   1
  TRRAP MUTATED    25  23
  TRRAP WILD-TYPE 145 174
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRRAP MUTATED     25   23
  TRRAP WILD-TYPE  145  174
        clus
vv       TRRAP MUTATED TRRAP WILD-TYPE
  FEMALE            25             145
  MALE              23             174
[1] 2 2
[1] FALSE
D373V8, binary
                 cls
clus                0   1
  TRRAP MUTATED    44   4
  TRRAP WILD-TYPE 273  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRRAP MUTATED     44    4
  TRRAP WILD-TYPE  273   44
                               clus
vv                              TRRAP MUTATED TRRAP WILD-TYPE
  COLON ADENOCARCINOMA                     44             273
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TRRAP MUTATED    32   0   0   8
  TRRAP WILD-TYPE 225   2  22  13
D373V9, multiclass
    clus
vv   TRRAP MUTATED TRRAP WILD-TYPE
  R0            32             225
  R1             0               2
  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"
D373V10, 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    27
  TRRAP WILD-TYPE                        16   149
D373V11, 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                                       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(374) Variable = PRKAA2 MUTATION ANALYSIS
D374V1, survival
                  sevent
clus2                0   1
  PRKAA2 MUTATED     7   4
  PRKAA2 WILD-TYPE 275  69
  PRKAA2 MUTATED PRKAA2 WILD-TYPE 
              11              344 
  PRKAA2 MUTATED PRKAA2 WILD-TYPE 
               4               69 
$`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         0.33        12.95         6.18 

$`PRKAA2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       23.87        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       15.95        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
        7.96        27.02        13.94        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       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        13.38        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  PRKAA2 MUTATED PRKAA2 WILD-TYPE 
            0.33             0.00 
  PRKAA2 MUTATED PRKAA2 WILD-TYPE 
           58.39           140.38 
  PRKAA2 MUTATED PRKAA2 WILD-TYPE 
          20.120           20.235 
[1] "0.3 - 58.4 (20.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2"  
D374V2, 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       23       101         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PRKAA2 MUTATED           0          0          0          0        0
  PRKAA2 WILD-TYPE        19         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  PRKAA2 MUTATED           0         0
  PRKAA2 WILD-TYPE        13         1
D374V3, multiclass
            clus
vv           PRKAA2 MUTATED PRKAA2 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               8              101
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PRKAA2 MUTATED     0   1  10   1
  PRKAA2 WILD-TYPE   9  67 238  40
D374V4, multiclass
    clus
vv   PRKAA2 MUTATED PRKAA2 WILD-TYPE
  T1              0                9
  T2              1               67
  T3             10              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
  PRKAA2 MUTATED    12   0   0
  PRKAA2 WILD-TYPE 208  80  66
D374V5, multiclass
    clus
vv   PRKAA2 MUTATED PRKAA2 WILD-TYPE
  N0             12              208
  N1              0               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"
D374V6, binary
                  cls
clus                 0   1
  PRKAA2 MUTATED    10   0
  PRKAA2 WILD-TYPE 273  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRKAA2 MUTATED     10    0
  PRKAA2 WILD-TYPE  273   48
   clus
vv  PRKAA2 MUTATED PRKAA2 WILD-TYPE
  0             10              273
  1              0               48
[1] 2 2
[1] FALSE
D374V7, 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
D374V8, binary
                  cls
clus                 0   1
  PRKAA2 MUTATED     8   4
  PRKAA2 WILD-TYPE 309  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRKAA2 MUTATED      8    4
  PRKAA2 WILD-TYPE  309   44
                               clus
vv                              PRKAA2 MUTATED PRKAA2 WILD-TYPE
  COLON ADENOCARCINOMA                       8              309
  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 248   2  22  20
D374V9, multiclass
    clus
vv   PRKAA2 MUTATED PRKAA2 WILD-TYPE
  R0              9              248
  R1              0                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"
D374V10, 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
D374V11, 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(375) Variable = KLRC3 MUTATION ANALYSIS
D375V1, survival
                 sevent
clus2               0   1
  KLRC3 MUTATED     5   2
  KLRC3 WILD-TYPE 277  71
  KLRC3 MUTATED KLRC3 WILD-TYPE 
              7             348 
  KLRC3 MUTATED KLRC3 WILD-TYPE 
              2              71 
$`KLRC3 MUTATED`
TCGA-AA-3510 TCGA-AA-3715 TCGA-AA-3845 TCGA-D5-6931 TCGA-DM-A28K TCGA-F4-6704 
       63.98        19.04         0.00        12.00        98.24         1.55 
TCGA-G4-6309 
       51.75 

$`KLRC3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02        14.93        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
      117.07         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  KLRC3 MUTATED KLRC3 WILD-TYPE 
              0               0 
  KLRC3 MUTATED KLRC3 WILD-TYPE 
          98.24          140.38 
  KLRC3 MUTATED KLRC3 WILD-TYPE 
         19.040          20.235 
[1] "0.0 - 98.2 (19.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1"  
D375V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KLRC3 MUTATED         0        0        2         2         0         0
  KLRC3 WILD-TYPE      64        1       23       107         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        19         10         40         29       35        13
                 vv
clus              STAGE IVB
  KLRC3 MUTATED           0
  KLRC3 WILD-TYPE         1
D375V3, multiclass
            clus
vv           KLRC3 MUTATED KLRC3 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              2             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             2              29
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KLRC3 MUTATED     0   0   6   1
  KLRC3 WILD-TYPE   9  68 242  40
D375V4, multiclass
    clus
vv   KLRC3 MUTATED KLRC3 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             6             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
  KLRC3 MUTATED     4   1   2
  KLRC3 WILD-TYPE 216  79  64
D375V5, multiclass
    clus
vv   KLRC3 MUTATED KLRC3 WILD-TYPE
  N0             4             216
  N1             1              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"
D375V6, binary
                 cls
clus                0   1
  KLRC3 MUTATED     6   0
  KLRC3 WILD-TYPE 277  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLRC3 MUTATED      6    0
  KLRC3 WILD-TYPE  277   48
   clus
vv  KLRC3 MUTATED KLRC3 WILD-TYPE
  0             6             277
  1             0              48
[1] 2 2
[1] FALSE
D375V7, binary
                 cls
clus                0   1
  KLRC3 MUTATED     2   5
  KLRC3 WILD-TYPE 168 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLRC3 MUTATED      2    5
  KLRC3 WILD-TYPE  168  192
        clus
vv       KLRC3 MUTATED KLRC3 WILD-TYPE
  FEMALE             2             168
  MALE               5             192
[1] 2 2
[1] FALSE
D375V8, binary
                 cls
clus                0   1
  KLRC3 MUTATED     5   2
  KLRC3 WILD-TYPE 312  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLRC3 MUTATED      5    2
  KLRC3 WILD-TYPE  312   46
                               clus
vv                              KLRC3 MUTATED KLRC3 WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  KLRC3 MUTATED     6   0   0   0
  KLRC3 WILD-TYPE 251   2  22  21
D375V9, multiclass
    clus
vv   KLRC3 MUTATED KLRC3 WILD-TYPE
  R0             6             251
  R1             0               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"
D375V10, 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
D375V11, 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(376) Variable = FLG2 MUTATION ANALYSIS
D376V1, survival
                sevent
clus2              0   1
  FLG2 MUTATED    21   6
  FLG2 WILD-TYPE 261  67
  FLG2 MUTATED FLG2 WILD-TYPE 
            27            328 
  FLG2 MUTATED FLG2 WILD-TYPE 
             6             67 
$`FLG2 MUTATED`
TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3525 TCGA-AA-3532 TCGA-AA-3663 TCGA-AA-3710 
        1.02        63.98         8.05        29.00         6.97        26.99 
TCGA-AA-3837 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3986 TCGA-AA-A00N 
       38.99        31.00         2.01        33.01        19.07         4.01 
TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6606 TCGA-CA-6717 TCGA-CA-6718 
       27.09        58.39        49.41        11.74         0.33         0.10 
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        13.51        20.19 
TCGA-DM-A1D4 TCGA-F4-6570 TCGA-G4-6309 
       92.75         6.18        51.75 

$`FLG2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 
        9.07        24.03        37.05        36.03        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       19.07        34.03        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.05        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 
       37.05        19.00        36.00         5.03        85.05        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
        1.02        17.98        15.95        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3939 
       17.03        24.03        27.02        29.98        18.05        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       26.01        25.02        24.00        27.02        27.02         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13        83.80        22.36        62.79        61.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10       100.01        29.56         5.23         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       12.95        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 
       45.40        12.26        19.59        11.51        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.38        13.45        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  FLG2 MUTATED FLG2 WILD-TYPE 
           0.1            0.0 
  FLG2 MUTATED FLG2 WILD-TYPE 
         92.75         140.38 
  FLG2 MUTATED FLG2 WILD-TYPE 
         20.19          20.20 
[1] "0.1 - 92.8 (20.2)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1"  
D376V2, 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       21        97         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        19         10         39         30       33        12
                vv
clus             STAGE IVB
  FLG2 MUTATED           1
  FLG2 WILD-TYPE         0
D376V3, multiclass
            clus
vv           FLG2 MUTATED FLG2 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              4             21
  STAGE IIA            12             97
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            2             39
  STAGE IIIC            1             30
  STAGE IV              2             33
  STAGE IVA             1             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
  FLG2 MUTATED     1   2  21   4
  FLG2 WILD-TYPE   8  66 227  37
D376V4, multiclass
    clus
vv   FLG2 MUTATED FLG2 WILD-TYPE
  T1            1              8
  T2            2             66
  T3           21            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
  FLG2 MUTATED    21   3   4
  FLG2 WILD-TYPE 199  77  62
D376V5, multiclass
    clus
vv   FLG2 MUTATED FLG2 WILD-TYPE
  N0           21            199
  N1            3             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"
D376V6, binary
                cls
clus               0   1
  FLG2 MUTATED    22   4
  FLG2 WILD-TYPE 261  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLG2 MUTATED     22    4
  FLG2 WILD-TYPE  261   44
   clus
vv  FLG2 MUTATED FLG2 WILD-TYPE
  0           22            261
  1            4             44
[1] 2 2
[1] FALSE
D376V7, 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
D376V8, binary
                cls
clus               0   1
  FLG2 MUTATED    23   5
  FLG2 WILD-TYPE 294  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLG2 MUTATED     23    5
  FLG2 WILD-TYPE  294   43
                               clus
vv                              FLG2 MUTATED FLG2 WILD-TYPE
  COLON ADENOCARCINOMA                    23            294
  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 236   2  21  18
D376V9, multiclass
    clus
vv   FLG2 MUTATED FLG2 WILD-TYPE
  R0           21            236
  R1            0              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"
D376V10, 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
D376V11, 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(377) Variable = PPP1R3A MUTATION ANALYSIS
D377V1, survival
                   sevent
clus2                 0   1
  PPP1R3A MUTATED    23   7
  PPP1R3A WILD-TYPE 259  66
  PPP1R3A MUTATED PPP1R3A WILD-TYPE 
               30               325 
  PPP1R3A MUTATED PPP1R3A WILD-TYPE 
                7                66 
$`PPP1R3A MUTATED`
TCGA-A6-6648 TCGA-A6-6652 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3655 TCGA-AA-3660 
       25.18        24.69         3.02        63.98        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3848 TCGA-AA-3852 TCGA-AA-3977 
        6.05         0.92        19.04        10.06         0.00        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q TCGA-AD-6963 TCGA-AD-6964 TCGA-AZ-4315 
        4.01        34.98         1.02        27.42        10.88        58.39 
TCGA-AZ-6608 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-5861 TCGA-CM-6163 TCGA-CM-6675 
        1.94         0.33         0.10        15.02        14.04        13.05 
TCGA-D5-5540 TCGA-D5-6538 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A28K TCGA-F4-6703 
       13.51        17.13        44.32       131.51        98.24        35.87 

$`PPP1R3A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.08        24.16        21.76        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       19.66        20.28         7.04         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 
       38.99        37.02        14.93         0.00        17.03         0.00 
TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
       33.07        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 
        0.79         0.72         5.79        22.42         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07         0.26         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       12.00        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 
       13.02        15.02        14.04        11.01        12.95        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       19.59        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85         4.80        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HB 
       49.91        13.32        12.59       140.38         7.50       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 
      117.07         8.61        13.38        13.45         6.18         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  PPP1R3A MUTATED PPP1R3A WILD-TYPE 
                0                 0 
  PPP1R3A MUTATED PPP1R3A WILD-TYPE 
           131.51            140.38 
  PPP1R3A MUTATED PPP1R3A WILD-TYPE 
           16.075            20.980 
[1] "0.0 - 131.5 (16.1)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.1"
D377V2, 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       20        99         5         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PPP1R3A MUTATED           1          1          1          2        2
  PPP1R3A WILD-TYPE        18          9         40         29       33
                   vv
clus                STAGE IVA STAGE IVB
  PPP1R3A MUTATED           2         1
  PPP1R3A WILD-TYPE        11         0
D377V3, multiclass
            clus
vv           PPP1R3A MUTATED PPP1R3A WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 5                20
  STAGE IIA               10                99
  STAGE IIB                3                 5
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               1                 9
  STAGE IIIB               1                40
  STAGE IIIC               2                29
  STAGE IV                 2                33
  STAGE IVA                2                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
  PPP1R3A MUTATED     1   2  24   5
  PPP1R3A WILD-TYPE   8  66 224  36
D377V4, multiclass
    clus
vv   PPP1R3A MUTATED PPP1R3A WILD-TYPE
  T1               1                 8
  T2               2                66
  T3              24               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
  PPP1R3A MUTATED    24   2   6
  PPP1R3A WILD-TYPE 196  78  60
D377V5, multiclass
    clus
vv   PPP1R3A MUTATED PPP1R3A WILD-TYPE
  N0              24               196
  N1               2                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"
D377V6, binary
                   cls
clus                  0   1
  PPP1R3A MUTATED    23   5
  PPP1R3A WILD-TYPE 260  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP1R3A MUTATED     23    5
  PPP1R3A WILD-TYPE  260   43
   clus
vv  PPP1R3A MUTATED PPP1R3A WILD-TYPE
  0              23               260
  1               5                43
[1] 2 2
[1] FALSE
D377V7, 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
D377V8, binary
                   cls
clus                  0   1
  PPP1R3A MUTATED    28   4
  PPP1R3A WILD-TYPE 289  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP1R3A MUTATED     28    4
  PPP1R3A WILD-TYPE  289   44
                               clus
vv                              PPP1R3A MUTATED PPP1R3A WILD-TYPE
  COLON ADENOCARCINOMA                       28               289
  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 239   2  20  18
D377V9, multiclass
    clus
vv   PPP1R3A MUTATED PPP1R3A WILD-TYPE
  R0              18               239
  R1               0                 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"
D377V10, 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
D377V11, 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(378) Variable = GTF3C3 MUTATION ANALYSIS
D378V1, survival
                  sevent
clus2                0   1
  GTF3C3 MUTATED    11   4
  GTF3C3 WILD-TYPE 271  69
  GTF3C3 MUTATED GTF3C3 WILD-TYPE 
              15              340 
  GTF3C3 MUTATED GTF3C3 WILD-TYPE 
               4               69 
$`GTF3C3 MUTATED`
TCGA-A6-5661 TCGA-AA-3496 TCGA-AA-3977 TCGA-AA-A010 TCGA-AD-6964 TCGA-AZ-4315 
       33.53         1.02        25.02        34.98        10.88        58.39 
TCGA-AZ-6598 TCGA-CA-6715 TCGA-CA-6717 TCGA-CM-6163 TCGA-CM-6674 TCGA-DM-A0XD 
       49.41         0.07         0.33        14.04        12.95        24.43 
TCGA-DM-A1D6 TCGA-F4-6807 TCGA-G4-6628 
       49.91        16.24        52.80 

$`GTF3C3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
        0.72         5.79        22.42        27.42         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        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-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       29.59        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       35.80        26.17        91.79        46.75 

  GTF3C3 MUTATED GTF3C3 WILD-TYPE 
            0.07             0.00 
  GTF3C3 MUTATED GTF3C3 WILD-TYPE 
           58.39           140.38 
  GTF3C3 MUTATED GTF3C3 WILD-TYPE 
          24.430           20.155 
[1] "0.1 - 58.4 (24.4)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.3"
D378V2, 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       23       103         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GTF3C3 MUTATED           0          0          1          1        0
  GTF3C3 WILD-TYPE        19         10         40         30       35
                  vv
clus               STAGE IVA STAGE IVB
  GTF3C3 MUTATED           0         0
  GTF3C3 WILD-TYPE        13         1
D378V3, multiclass
            clus
vv           GTF3C3 MUTATED GTF3C3 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               6              103
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GTF3C3 MUTATED     1   2  10   2
  GTF3C3 WILD-TYPE   8  66 238  39
D378V4, multiclass
    clus
vv   GTF3C3 MUTATED GTF3C3 WILD-TYPE
  T1              1                8
  T2              2               66
  T3             10              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
  GTF3C3 MUTATED    12   1   2
  GTF3C3 WILD-TYPE 208  79  64
D378V5, multiclass
    clus
vv   GTF3C3 MUTATED GTF3C3 WILD-TYPE
  N0             12              208
  N1              1               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"
D378V6, binary
                  cls
clus                 0   1
  GTF3C3 MUTATED    12   0
  GTF3C3 WILD-TYPE 271  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF3C3 MUTATED     12    0
  GTF3C3 WILD-TYPE  271   48
   clus
vv  GTF3C3 MUTATED GTF3C3 WILD-TYPE
  0             12              271
  1              0               48
[1] 2 2
[1] FALSE
D378V7, 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
D378V8, binary
                  cls
clus                 0   1
  GTF3C3 MUTATED    13   2
  GTF3C3 WILD-TYPE 304  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF3C3 MUTATED     13    2
  GTF3C3 WILD-TYPE  304   46
                               clus
vv                              GTF3C3 MUTATED GTF3C3 WILD-TYPE
  COLON ADENOCARCINOMA                      13              304
  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 249   2  22  19
D378V9, multiclass
    clus
vv   GTF3C3 MUTATED GTF3C3 WILD-TYPE
  R0              8              249
  R1              0                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"
D378V10, 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
D378V11, 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(379) Variable = DDX5 MUTATION ANALYSIS
D379V1, survival
                sevent
clus2              0   1
  DDX5 MUTATED     8   1
  DDX5 WILD-TYPE 274  72
  DDX5 MUTATED DDX5 WILD-TYPE 
             9            346 
  DDX5 MUTATED DDX5 WILD-TYPE 
             1             72 
$`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         0.33        20.02 
TCGA-D5-6533 TCGA-G4-6304 TCGA-G4-6323 
        1.32        53.62        13.78 

$`DDX5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 
       19.59        13.51        11.51        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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 
       19.43       107.67        74.56        65.85        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 
       51.75        45.11        36.72        36.00        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  DDX5 MUTATED DDX5 WILD-TYPE 
          0.33           0.00 
  DDX5 MUTATED DDX5 WILD-TYPE 
         53.62         140.38 
  DDX5 MUTATED DDX5 WILD-TYPE 
         6.050         20.995 
[1] "0.3 - 53.6 (6.0)"   "0.0 - 140.4 (21.0)"
[1] "hr=" "1.1"
D379V2, 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       25       107         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DDX5 MUTATED           0          0          1          0        2         0
  DDX5 WILD-TYPE        19         10         40         31       33        13
                vv
clus             STAGE IVB
  DDX5 MUTATED           0
  DDX5 WILD-TYPE         1
D379V3, multiclass
            clus
vv           DDX5 MUTATED DDX5 WILD-TYPE
  STAGE I               1             63
  STAGE IA              1              0
  STAGE II              0             25
  STAGE IIA             2            107
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              2             33
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  DDX5 MUTATED     0   1   3   4
  DDX5 WILD-TYPE   9  67 245  37
D379V4, multiclass
    clus
vv   DDX5 MUTATED DDX5 WILD-TYPE
  T1            0              9
  T2            1             67
  T3            3            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
  DDX5 MUTATED     8   0   1
  DDX5 WILD-TYPE 212  80  65
D379V5, multiclass
    clus
vv   DDX5 MUTATED DDX5 WILD-TYPE
  N0            8            212
  N1            0             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"
D379V6, binary
                cls
clus               0   1
  DDX5 MUTATED     6   2
  DDX5 WILD-TYPE 277  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDX5 MUTATED      6    2
  DDX5 WILD-TYPE  277   46
   clus
vv  DDX5 MUTATED DDX5 WILD-TYPE
  0            6            277
  1            2             46
[1] 2 2
[1] FALSE
D379V7, 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
D379V8, binary
                cls
clus               0   1
  DDX5 MUTATED     6   3
  DDX5 WILD-TYPE 311  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDX5 MUTATED      6    3
  DDX5 WILD-TYPE  311   45
                               clus
vv                              DDX5 MUTATED DDX5 WILD-TYPE
  COLON ADENOCARCINOMA                     6            311
  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 252   2  20  20
D379V9, multiclass
    clus
vv   DDX5 MUTATED DDX5 WILD-TYPE
  R0            5            252
  R1            0              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"
D379V10, 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
D379V11, 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(380) Variable = RELN MUTATION ANALYSIS
D380V1, survival
                sevent
clus2              0   1
  RELN MUTATED    48  14
  RELN WILD-TYPE 234  59
  RELN MUTATED RELN WILD-TYPE 
            62            293 
  RELN MUTATED RELN WILD-TYPE 
            14             59 
$`RELN MUTATED`
TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6141 
       34.65        32.75        33.53        22.06        32.71         8.38 
TCGA-A6-6652 TCGA-AA-3516 TCGA-AA-3525 TCGA-AA-3532 TCGA-AA-3555 TCGA-AA-3664 
       24.69        13.02         8.05        29.00        29.95        54.02 
TCGA-AA-3672 TCGA-AA-3680 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3818 TCGA-AA-3837 
        0.92        11.01        19.04        19.04         0.99        38.99 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 
       33.01        26.01        24.00        25.02         4.01        34.98 
TCGA-AD-6889 TCGA-AD-6901 TCGA-AD-6964 TCGA-AY-6196 TCGA-AZ-4315 TCGA-AZ-5407 
       56.55        22.42        10.88         0.20        58.39        61.41 
TCGA-AZ-6601 TCGA-CA-5796 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4743 TCGA-CM-4744 
      100.01         3.25         0.33         0.10        23.05        20.02 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6674 
       22.98        30.08         5.03        15.02        17.03        12.95 
TCGA-CM-6675 TCGA-D5-6532 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6923 
       13.05        18.25         4.80        12.49        15.58        12.43 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1DA 
       11.64        13.41         1.51        38.20        92.75         7.50 
TCGA-DM-A1DB TCGA-DM-A28E TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6586 
       44.32       119.93        55.04        51.75        45.11        35.80 
TCGA-G4-6588 TCGA-G4-6628 
       26.17        52.80 

$`RELN WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       16.57        33.34        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-6137 TCGA-A6-6138 
       30.44        29.19        23.61        22.09        27.09        22.52 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 
        9.07        24.03        37.05        36.03        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       19.07        34.03        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       78.08         6.05         6.97         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       47.01        15.02         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.03        85.05        26.99        10.06        35.05        33.04 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3844 
       25.02         1.02        17.98        15.95        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3952 TCGA-AA-3955 
       31.00         2.01        12.99        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 
       21.37         4.21         0.79         0.72         5.79        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       62.79        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5797 
       11.74         3.19         1.94         2.24         3.06         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07         0.26         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
        2.01       124.27        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 
       22.03        16.01        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-6676 TCGA-CM-6677 
       13.02        15.02        14.04        11.01        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       13.51        11.51        20.19         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.85        17.13        16.14         7.53        12.39        10.13 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       14.30         9.04         9.44        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
      119.70        24.43       130.65        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
      140.38       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6315 
      107.67        74.56        65.85        53.62        44.68        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        91.79        46.75 

  RELN MUTATED RELN WILD-TYPE 
           0.1            0.0 
  RELN MUTATED RELN WILD-TYPE 
        119.93         140.38 
  RELN MUTATED RELN WILD-TYPE 
         22.70          19.99 
[1] "0.1 - 119.9 (22.7)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1"  
D380V2, 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       22        83         3         0
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RELN MUTATED           2          1          7          4        4         3
  RELN WILD-TYPE        17          9         34         27       31        10
                vv
clus             STAGE IVB
  RELN MUTATED           1
  RELN WILD-TYPE         0
D380V3, multiclass
            clus
vv           RELN MUTATED RELN WILD-TYPE
  STAGE I               5             59
  STAGE IA              0              1
  STAGE II              3             22
  STAGE IIA            26             83
  STAGE IIB             5              3
  STAGE IIC             1              0
  STAGE III             2             17
  STAGE IIIA            1              9
  STAGE IIIB            7             34
  STAGE IIIC            4             27
  STAGE IV              4             31
  STAGE IVA             3             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
  RELN MUTATED     1   5  50   9
  RELN WILD-TYPE   8  63 198  32
D380V4, multiclass
    clus
vv   RELN MUTATED RELN WILD-TYPE
  T1            1              8
  T2            5             63
  T3           50            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
  RELN MUTATED    45  11   9
  RELN WILD-TYPE 175  69  57
D380V5, multiclass
    clus
vv   RELN MUTATED RELN WILD-TYPE
  N0           45            175
  N1           11             69
  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"
D380V6, binary
                cls
clus               0   1
  RELN MUTATED    51   8
  RELN WILD-TYPE 232  40
[1] "tbl2"
                cls
clus             [,1] [,2]
  RELN MUTATED     51    8
  RELN WILD-TYPE  232   40
   clus
vv  RELN MUTATED RELN WILD-TYPE
  0           51            232
  1            8             40
[1] 2 2
[1] FALSE
D380V7, 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
D380V8, binary
                cls
clus               0   1
  RELN MUTATED    51  14
  RELN WILD-TYPE 266  34
[1] "tbl2"
                cls
clus             [,1] [,2]
  RELN MUTATED     51   14
  RELN WILD-TYPE  266   34
                               clus
vv                              RELN MUTATED RELN WILD-TYPE
  COLON ADENOCARCINOMA                    51            266
  COLON MUCINOUS ADENOCARCINOMA           14             34
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RELN MUTATED    44   0   3   3
  RELN WILD-TYPE 213   2  19  18
D380V9, multiclass
    clus
vv   RELN MUTATED RELN WILD-TYPE
  R0           44            213
  R1            0              2
  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"
D380V10, 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
D380V11, 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(381) Variable = USP25 MUTATION ANALYSIS
D381V1, survival
                 sevent
clus2               0   1
  USP25 MUTATED    17   2
  USP25 WILD-TYPE 265  71
  USP25 MUTATED USP25 WILD-TYPE 
             19             336 
  USP25 MUTATED USP25 WILD-TYPE 
              2              71 
$`USP25 MUTATED`
TCGA-A6-5656 TCGA-A6-6654 TCGA-AA-3977 TCGA-AA-A00N TCGA-AD-6889 TCGA-AD-6895 
       32.91        23.87        25.02         4.01        56.55         0.72 
TCGA-AU-3779 TCGA-AZ-4315 TCGA-AZ-6603 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6719 
       14.50        58.39        29.56         0.07         0.33         1.35 
TCGA-CK-6751 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-6164 TCGA-CM-6172 TCGA-D5-6540 
      124.27        22.98        16.01        29.03        11.01        16.14 
TCGA-D5-6920 
       12.39 

$`USP25 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 
       40.96         0.07        21.37         4.21         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10       100.01         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 
        1.94         2.24         3.06         3.25         3.29         0.26 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        0.10        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 
       51.32        21.99        21.14         2.93         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-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-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-6674 TCGA-CM-6675 
       12.99        13.02        15.02        14.04        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       12.49        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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  USP25 MUTATED USP25 WILD-TYPE 
           0.07            0.00 
  USP25 MUTATED USP25 WILD-TYPE 
         124.27          140.38 
  USP25 MUTATED USP25 WILD-TYPE 
         16.140          20.235 
[1] "0.1 - 124.3 (16.1)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.9"
D381V2, 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       25       101         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  USP25 MUTATED           0          0          4          0        0         0
  USP25 WILD-TYPE        19         10         37         31       35        13
                 vv
clus              STAGE IVB
  USP25 MUTATED           0
  USP25 WILD-TYPE         1
D381V3, multiclass
            clus
vv           USP25 MUTATED USP25 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              8             101
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             4              37
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  USP25 MUTATED     0   5  13   1
  USP25 WILD-TYPE   9  63 235  40
D381V4, multiclass
    clus
vv   USP25 MUTATED USP25 WILD-TYPE
  T1             0               9
  T2             5              63
  T3            13             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
  USP25 MUTATED    13   6   0
  USP25 WILD-TYPE 207  74  66
D381V5, multiclass
    clus
vv   USP25 MUTATED USP25 WILD-TYPE
  N0            13             207
  N1             6              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"
D381V6, binary
                 cls
clus                0   1
  USP25 MUTATED    15   0
  USP25 WILD-TYPE 268  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP25 MUTATED     15    0
  USP25 WILD-TYPE  268   48
   clus
vv  USP25 MUTATED USP25 WILD-TYPE
  0            15             268
  1             0              48
[1] 2 2
[1] FALSE
D381V7, 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
D381V8, binary
                 cls
clus                0   1
  USP25 MUTATED    15   4
  USP25 WILD-TYPE 302  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP25 MUTATED     15    4
  USP25 WILD-TYPE  302   44
                               clus
vv                              USP25 MUTATED USP25 WILD-TYPE
  COLON ADENOCARCINOMA                     15             302
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  USP25 MUTATED     9   0   0   4
  USP25 WILD-TYPE 248   2  22  17
D381V9, multiclass
    clus
vv   USP25 MUTATED USP25 WILD-TYPE
  R0             9             248
  R1             0               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"
D381V10, 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
D381V11, 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(382) Variable = CLVS2 MUTATION ANALYSIS
D382V1, survival
                 sevent
clus2               0   1
  CLVS2 MUTATED     7   0
  CLVS2 WILD-TYPE 275  73
  CLVS2 MUTATED CLVS2 WILD-TYPE 
              7             348 
  CLVS2 MUTATED CLVS2 WILD-TYPE 
              0              73 
$`CLVS2 MUTATED`
TCGA-AA-3713 TCGA-AA-3864 TCGA-AD-6889 TCGA-CM-5348 TCGA-D5-6532 TCGA-D5-6533 
       19.04        53.00        56.55        22.98        18.25         1.32 
TCGA-D5-6540 
       16.14 

$`CLVS2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  CLVS2 MUTATED CLVS2 WILD-TYPE 
           1.32            0.00 
  CLVS2 MUTATED CLVS2 WILD-TYPE 
          56.55          140.38 
  CLVS2 MUTATED CLVS2 WILD-TYPE 
         19.040          20.235 
[1] "1.3 - 56.5 (19.0)"  "0.0 - 140.4 (20.2)"
[1] "hr="     "9300000"
D382V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CLVS2 MUTATED         2        0        1         2         0         0
  CLVS2 WILD-TYPE      62        1       24       107         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CLVS2 MUTATED           0          0          2          0        1         0
  CLVS2 WILD-TYPE        19         10         39         31       34        13
                 vv
clus              STAGE IVB
  CLVS2 MUTATED           0
  CLVS2 WILD-TYPE         1
D382V3, multiclass
            clus
vv           CLVS2 MUTATED CLVS2 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              2             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CLVS2 MUTATED     0   2   5   1
  CLVS2 WILD-TYPE   9  66 243  40
D382V4, multiclass
    clus
vv   CLVS2 MUTATED CLVS2 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             5             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     7   1   0
  CLVS2 WILD-TYPE 213  79  66
D382V5, multiclass
    clus
vv   CLVS2 MUTATED CLVS2 WILD-TYPE
  N0             7             213
  N1             1              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"
D382V6, binary
                 cls
clus                0   1
  CLVS2 MUTATED     6   1
  CLVS2 WILD-TYPE 277  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLVS2 MUTATED      6    1
  CLVS2 WILD-TYPE  277   47
   clus
vv  CLVS2 MUTATED CLVS2 WILD-TYPE
  0             6             277
  1             1              47
[1] 2 2
[1] FALSE
D382V7, binary
                 cls
clus                0   1
  CLVS2 MUTATED     1   7
  CLVS2 WILD-TYPE 169 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLVS2 MUTATED      1    7
  CLVS2 WILD-TYPE  169  190
        clus
vv       CLVS2 MUTATED CLVS2 WILD-TYPE
  FEMALE             1             169
  MALE               7             190
[1] 2 2
[1] FALSE
D382V8, binary
                 cls
clus                0   1
  CLVS2 MUTATED     7   1
  CLVS2 WILD-TYPE 310  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLVS2 MUTATED      7    1
  CLVS2 WILD-TYPE  310   47
                               clus
vv                              CLVS2 MUTATED CLVS2 WILD-TYPE
  COLON ADENOCARCINOMA                      7             310
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CLVS2 MUTATED     5   0   1   1
  CLVS2 WILD-TYPE 252   2  21  20
D382V9, multiclass
    clus
vv   CLVS2 MUTATED CLVS2 WILD-TYPE
  R0             5             252
  R1             0               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"
D382V10, 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
D382V11, 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(383) Variable = MYO3B MUTATION ANALYSIS
D383V1, survival
                 sevent
clus2               0   1
  MYO3B MUTATED    24   6
  MYO3B WILD-TYPE 258  67
  MYO3B MUTATED MYO3B WILD-TYPE 
             30             325 
  MYO3B MUTATED MYO3B WILD-TYPE 
              6              67 
$`MYO3B MUTATED`
TCGA-A6-2671 TCGA-A6-6141 TCGA-A6-6781 TCGA-AA-3662 TCGA-AA-3697 TCGA-AA-3713 
       43.76         8.38        19.66         6.05        85.05        19.04 
TCGA-AA-3845 TCGA-AA-A00N TCGA-AD-6964 TCGA-AU-3779 TCGA-AY-5543 TCGA-AZ-4315 
        0.00         4.01        10.88        14.50        15.75        58.39 
TCGA-AZ-6607 TCGA-CA-6717 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4752 TCGA-CM-5860 
        3.19         0.33       124.27        23.05        13.02        16.01 
TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6674 TCGA-CM-6676 TCGA-D5-6532 TCGA-D5-6927 
       21.99        13.02        12.95        11.08        18.25         9.44 
TCGA-D5-6931 TCGA-F4-6570 TCGA-F4-6856 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6586 
       12.00         6.18        19.43        36.72        22.09        35.80 

$`MYO3B WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 
        5.98        37.05        19.00        36.00         5.03        26.99 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 
        0.20        27.09        16.31         0.95         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       21.14         2.93         2.01        20.02        37.02        25.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-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-6170 TCGA-CM-6171 
       29.03        16.04        14.99        12.99        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       11.01        13.05        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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         1.51 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.38        13.45        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 
       16.24        33.67        13.25         0.53        35.41       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       45.11        36.00        13.78        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  MYO3B MUTATED MYO3B WILD-TYPE 
              0               0 
  MYO3B MUTATED MYO3B WILD-TYPE 
         124.27          140.38 
  MYO3B MUTATED MYO3B WILD-TYPE 
         15.125          21.370 
[1] "0.0 - 124.3 (15.1)" "0.0 - 140.4 (21.4)"
[1] "hr=" "1.1"
D383V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MYO3B MUTATED         4        0        0        14         1         0
  MYO3B WILD-TYPE      60        1       25        95         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MYO3B MUTATED           3          0          0          2        5         1
  MYO3B WILD-TYPE        16         10         41         29       30        12
                 vv
clus              STAGE IVB
  MYO3B MUTATED           0
  MYO3B WILD-TYPE         1
D383V3, multiclass
            clus
vv           MYO3B MUTATED MYO3B WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA             14              95
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              3              16
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             2              29
  STAGE IV               5              30
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  63 228  35
D383V4, multiclass
    clus
vv   MYO3B MUTATED MYO3B WILD-TYPE
  T1             0               9
  T2             5              63
  T3            20             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
  MYO3B MUTATED    21   4   6
  MYO3B WILD-TYPE 199  76  60
D383V5, multiclass
    clus
vv   MYO3B MUTATED MYO3B WILD-TYPE
  N0            21             199
  N1             4              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"
D383V6, binary
                 cls
clus                0   1
  MYO3B MUTATED    21   6
  MYO3B WILD-TYPE 262  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYO3B MUTATED     21    6
  MYO3B WILD-TYPE  262   42
   clus
vv  MYO3B MUTATED MYO3B WILD-TYPE
  0            21             262
  1             6              42
[1] 2 2
[1] FALSE
D383V7, 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
D383V8, binary
                 cls
clus                0   1
  MYO3B MUTATED    26   5
  MYO3B WILD-TYPE 291  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYO3B MUTATED     26    5
  MYO3B WILD-TYPE  291   43
                               clus
vv                              MYO3B MUTATED MYO3B WILD-TYPE
  COLON ADENOCARCINOMA                     26             291
  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 233   2  20  19
D383V9, multiclass
    clus
vv   MYO3B MUTATED MYO3B WILD-TYPE
  R0            24             233
  R1             0               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"
D383V10, 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
D383V11, 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(384) Variable = CNTNAP5 MUTATION ANALYSIS
D384V1, survival
                   sevent
clus2                 0   1
  CNTNAP5 MUTATED    30   9
  CNTNAP5 WILD-TYPE 252  64
  CNTNAP5 MUTATED CNTNAP5 WILD-TYPE 
               39               316 
  CNTNAP5 MUTATED CNTNAP5 WILD-TYPE 
                9                64 
$`CNTNAP5 MUTATED`
TCGA-A6-2671 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6654 TCGA-A6-6780 
       43.76        33.53        22.06         8.38        23.87        20.12 
TCGA-AA-3660 TCGA-AA-3947 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R 
       78.08        33.01        25.02         4.01        34.98        35.01 
TCGA-AA-A01Z TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6901 TCGA-AD-6964 TCGA-AU-6004 
       37.02         0.07        56.55        22.42        10.88        27.09 
TCGA-AZ-4315 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6608 TCGA-CA-6716 TCGA-CA-6717 
       58.39        62.79        49.41         1.94         0.26         0.33 
TCGA-CA-6718 TCGA-CK-5914 TCGA-CM-4746 TCGA-CM-5341 TCGA-CM-6166 TCGA-D5-6532 
        0.10        21.99        37.02        29.06        21.99        18.25 
TCGA-D5-6930 TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-F4-6569 TCGA-F4-6570 TCGA-G4-6309 
        1.51       130.65        49.91        13.45         6.18        51.75 
TCGA-G4-6315 TCGA-G4-6323 TCGA-G4-6628 
       36.72        13.78        52.80 

$`CNTNAP5 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       31.63        30.44        29.19        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 
       27.09        22.52        25.08        25.18        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.69        24.39        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        61.02         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 
        1.02         1.02        33.04        35.01        26.01        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37         4.21 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
        0.79         0.72         5.79        27.42         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6599 
        1.41         5.13        83.80        22.36        61.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6719 
        2.24         3.06         3.25         3.29         0.07         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         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 
       12.26        19.59        13.51        11.51        20.19         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6703 
       60.79       117.07        98.24         8.61        13.38        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 
       53.62        44.68        55.04        45.11        36.00        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       35.80        26.17        91.79        46.75 

  CNTNAP5 MUTATED CNTNAP5 WILD-TYPE 
             0.07              0.00 
  CNTNAP5 MUTATED CNTNAP5 WILD-TYPE 
           130.65            140.38 
  CNTNAP5 MUTATED CNTNAP5 WILD-TYPE 
            25.02             19.51 
[1] "0.1 - 130.7 (25.0)" "0.0 - 140.4 (19.5)"
[1] "hr=" "1"  
D384V2, 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       21        94         5         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CNTNAP5 MUTATED           1          2          3          0        2
  CNTNAP5 WILD-TYPE        18          8         38         31       33
                   vv
clus                STAGE IVA STAGE IVB
  CNTNAP5 MUTATED           0         0
  CNTNAP5 WILD-TYPE        13         1
D384V3, multiclass
            clus
vv           CNTNAP5 MUTATED CNTNAP5 WILD-TYPE
  STAGE I                  6                58
  STAGE IA                 1                 0
  STAGE II                 4                21
  STAGE IIA               15                94
  STAGE IIB                3                 5
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               2                 8
  STAGE IIIB               3                38
  STAGE IIIC               0                31
  STAGE IV                 2                33
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CNTNAP5 MUTATED     0   9  26   4
  CNTNAP5 WILD-TYPE   9  59 222  37
D384V4, multiclass
    clus
vv   CNTNAP5 MUTATED CNTNAP5 WILD-TYPE
  T1               0                 9
  T2               9                59
  T3              26               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
  CNTNAP5 MUTATED    31   6   3
  CNTNAP5 WILD-TYPE 189  74  63
D384V5, multiclass
    clus
vv   CNTNAP5 MUTATED CNTNAP5 WILD-TYPE
  N0              31               189
  N1               6                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"
D384V6, binary
                   cls
clus                  0   1
  CNTNAP5 MUTATED    29   2
  CNTNAP5 WILD-TYPE 254  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CNTNAP5 MUTATED     29    2
  CNTNAP5 WILD-TYPE  254   46
   clus
vv  CNTNAP5 MUTATED CNTNAP5 WILD-TYPE
  0              29               254
  1               2                46
[1] 2 2
[1] FALSE
D384V7, 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
D384V8, binary
                   cls
clus                  0   1
  CNTNAP5 MUTATED    32   8
  CNTNAP5 WILD-TYPE 285  40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CNTNAP5 MUTATED     32    8
  CNTNAP5 WILD-TYPE  285   40
                               clus
vv                              CNTNAP5 MUTATED CNTNAP5 WILD-TYPE
  COLON ADENOCARCINOMA                       32               285
  COLON MUCINOUS ADENOCARCINOMA               8                40
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  CNTNAP5 MUTATED    24   0   0   4
  CNTNAP5 WILD-TYPE 233   2  22  17
D384V9, multiclass
    clus
vv   CNTNAP5 MUTATED CNTNAP5 WILD-TYPE
  R0              24               233
  R1               0                 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"
D384V10, 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
D384V11, 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(385) Variable = TAT MUTATION ANALYSIS
D385V1, survival
               sevent
clus2             0   1
  TAT MUTATED    11   2
  TAT WILD-TYPE 271  71
  TAT MUTATED TAT WILD-TYPE 
           13           342 
  TAT MUTATED TAT WILD-TYPE 
            2            71 
$`TAT MUTATED`
TCGA-AA-3713 TCGA-AA-3950 TCGA-AA-3977 TCGA-AA-A00R TCGA-AZ-6598 TCGA-AZ-6601 
       19.04        24.00        25.02         0.99        49.41       100.01 
TCGA-CA-6718 TCGA-CK-4950 TCGA-CM-5348 TCGA-CM-6161 TCGA-D5-7000 TCGA-G4-6304 
        0.10        40.34        22.98        15.02        10.26        53.62 
TCGA-G4-6588 
       26.17 

$`TAT WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       27.02        42.02        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       22.36        62.79        61.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.33         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       102.44        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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 
       16.01        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        52.80 

  TAT MUTATED TAT WILD-TYPE 
          0.1           0.0 
  TAT MUTATED TAT WILD-TYPE 
       100.01        140.38 
  TAT MUTATED TAT WILD-TYPE 
        24.00         20.07 
[1] "0.1 - 100.0 (24.0)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.6"
D385V2, 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       23       105         7         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TAT MUTATED           0          1          1          0        1         0
  TAT WILD-TYPE        19          9         40         31       34        13
               vv
clus            STAGE IVB
  TAT MUTATED           0
  TAT WILD-TYPE         1
D385V3, multiclass
            clus
vv           TAT MUTATED TAT WILD-TYPE
  STAGE I              3            61
  STAGE IA             0             1
  STAGE II             2            23
  STAGE IIA            4           105
  STAGE IIB            1             7
  STAGE IIC            0             1
  STAGE III            0            19
  STAGE IIIA           1             9
  STAGE IIIB           1            40
  STAGE IIIC           0            31
  STAGE IV             1            34
  STAGE IVA            0            13
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  TAT MUTATED     0   4   9   1
  TAT WILD-TYPE   9  64 239  40
D385V4, multiclass
    clus
vv   TAT MUTATED TAT WILD-TYPE
  T1           0             9
  T2           4            64
  T3           9           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
  TAT MUTATED    12   2   0
  TAT WILD-TYPE 208  78  66
D385V5, multiclass
    clus
vv   TAT MUTATED TAT WILD-TYPE
  N0          12           208
  N1           2            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
  TAT MUTATED    11   1
  TAT WILD-TYPE 272  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  TAT MUTATED     11    1
  TAT WILD-TYPE  272   47
   clus
vv  TAT MUTATED TAT WILD-TYPE
  0          11           272
  1           1            47
[1] 2 2
[1] FALSE
D385V7, 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
D385V8, binary
               cls
clus              0   1
  TAT MUTATED    12   2
  TAT WILD-TYPE 305  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  TAT MUTATED     12    2
  TAT WILD-TYPE  305   46
                               clus
vv                              TAT MUTATED TAT WILD-TYPE
  COLON ADENOCARCINOMA                   12           305
  COLON MUCINOUS ADENOCARCINOMA           2            46
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  TAT MUTATED     8   1   1   1
  TAT WILD-TYPE 249   1  21  20
D385V9, multiclass
    clus
vv   TAT MUTATED TAT WILD-TYPE
  R0           8           249
  R1           1             1
  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"
D385V10, 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
D385V11, 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(386) Variable = MUC17 MUTATION ANALYSIS
D386V1, survival
                 sevent
clus2               0   1
  MUC17 MUTATED    37   7
  MUC17 WILD-TYPE 245  66
  MUC17 MUTATED MUC17 WILD-TYPE 
             44             311 
  MUC17 MUTATED MUC17 WILD-TYPE 
              7              66 
$`MUC17 MUTATED`
TCGA-A6-2672 TCGA-A6-3807 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6649 TCGA-A6-6781 
       46.65        34.65        33.53        22.06        24.16        19.66 
TCGA-A6-6782 TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3660 TCGA-AA-3696 TCGA-AA-3697 
       20.28        63.98        13.02        78.08         5.03        85.05 
TCGA-AA-3713 TCGA-AA-3815 TCGA-AA-3864 TCGA-AA-3950 TCGA-AA-3977 TCGA-AA-3980 
       19.04        33.04        53.00        24.00        25.02        27.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01I TCGA-AA-A029 TCGA-AD-6889 TCGA-AD-6895 
        4.01        34.98        31.00        51.98        56.55         0.72 
TCGA-AD-6899 TCGA-AZ-4315 TCGA-AZ-4681 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-CA-6716 
        5.79        58.39        83.80        61.41        12.10         0.26 
TCGA-CK-5916 TCGA-CM-6161 TCGA-CM-6674 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6922 
       21.14        15.02        12.95        17.13        16.14        10.13 
TCGA-D5-6928 TCGA-D5-6929 TCGA-DM-A28H TCGA-DM-A28K TCGA-G4-6321 TCGA-G4-6586 
       11.64        13.41       117.07        98.24        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6626 
       26.17        46.75 

$`MUC17 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       33.34        32.75        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 
       30.44        29.19        23.61        22.09        32.71        27.09 
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 
       22.52         8.38        25.08        25.18        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       24.39        23.87        20.12         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       35.01         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3710 TCGA-AA-3715 
        5.98        37.05        19.00        36.00        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       26.01        24.00        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A02F TCGA-AA-A02H 
       35.01        26.01        37.02        39.06        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6901 
       40.96         0.07        21.37         4.21         0.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         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-6601 
        5.13        22.36        62.79        49.41         6.77       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99         2.93         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        16.01        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-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 
        4.80        12.49        15.58         7.53        12.39        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
       14.30         9.04         9.44         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       35.97        60.79         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6628 
       36.72        36.00        13.78        91.79        52.80 

  MUC17 MUTATED MUC17 WILD-TYPE 
           0.26            0.00 
  MUC17 MUTATED MUC17 WILD-TYPE 
         117.07          140.38 
  MUC17 MUTATED MUC17 WILD-TYPE 
          24.59           19.43 
[1] "0.3 - 117.1 (24.6)" "0.0 - 140.4 (19.4)"
[1] "hr=" "1.8"
D386V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MUC17 MUTATED         6        0        4        15         4         0
  MUC17 WILD-TYPE      58        1       21        94         4         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MUC17 MUTATED           3          1          3          4        4         0
  MUC17 WILD-TYPE        16          9         38         27       31        13
                 vv
clus              STAGE IVB
  MUC17 MUTATED           0
  MUC17 WILD-TYPE         1
D386V3, multiclass
            clus
vv           MUC17 MUTATED MUC17 WILD-TYPE
  STAGE I                6              58
  STAGE IA               0               1
  STAGE II               4              21
  STAGE IIA             15              94
  STAGE IIB              4               4
  STAGE IIC              0               1
  STAGE III              3              16
  STAGE IIIA             1               9
  STAGE IIIB             3              38
  STAGE IIIC             4              27
  STAGE IV               4              31
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MUC17 MUTATED     2   6  31   7
  MUC17 WILD-TYPE   7  62 217  34
D386V4, multiclass
    clus
vv   MUC17 MUTATED MUC17 WILD-TYPE
  T1             2               7
  T2             6              62
  T3            31             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
  MUC17 MUTATED    32   9   5
  MUC17 WILD-TYPE 188  71  61
D386V5, multiclass
    clus
vv   MUC17 MUTATED MUC17 WILD-TYPE
  N0            32             188
  N1             9              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"
D386V6, binary
                 cls
clus                0   1
  MUC17 MUTATED    35   4
  MUC17 WILD-TYPE 248  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC17 MUTATED     35    4
  MUC17 WILD-TYPE  248   44
   clus
vv  MUC17 MUTATED MUC17 WILD-TYPE
  0            35             248
  1             4              44
[1] 2 2
[1] FALSE
D386V7, 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
D386V8, binary
                 cls
clus                0   1
  MUC17 MUTATED    38   8
  MUC17 WILD-TYPE 279  40
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC17 MUTATED     38    8
  MUC17 WILD-TYPE  279   40
                               clus
vv                              MUC17 MUTATED MUC17 WILD-TYPE
  COLON ADENOCARCINOMA                     38             279
  COLON MUCINOUS ADENOCARCINOMA             8              40
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MUC17 MUTATED    29   0   2   3
  MUC17 WILD-TYPE 228   2  20  18
D386V9, multiclass
    clus
vv   MUC17 MUTATED MUC17 WILD-TYPE
  R0            29             228
  R1             0               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"
D386V10, 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
D386V11, 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(387) Variable = ATG2B MUTATION ANALYSIS
D387V1, survival
                 sevent
clus2               0   1
  ATG2B MUTATED    10   4
  ATG2B WILD-TYPE 272  69
  ATG2B MUTATED ATG2B WILD-TYPE 
             14             341 
  ATG2B MUTATED ATG2B WILD-TYPE 
              4              69 
$`ATG2B MUTATED`
TCGA-A6-6780 TCGA-AA-3492 TCGA-AA-3663 TCGA-AA-3681 TCGA-AA-3811 TCGA-AA-3819 
       20.12         3.02         6.97         5.98        10.06        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-6608 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-5861 
        4.01        34.98         1.94         0.33         0.10        15.02 
TCGA-CM-6171 TCGA-G4-6628 
       14.04        52.80 

$`ATG2B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       23.87        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
       11.01        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        19.04        35.05        33.04         0.99 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.26         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       13.78        35.80        26.17        91.79        46.75 

  ATG2B MUTATED ATG2B WILD-TYPE 
            0.1             0.0 
  ATG2B MUTATED ATG2B WILD-TYPE 
          52.80          140.38 
  ATG2B MUTATED ATG2B WILD-TYPE 
          8.515          21.010 
[1] "0.1 - 52.8 (8.5)"   "0.0 - 140.4 (21.0)"
[1] "hr=" "2.4"
D387V2, 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       23       103         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        17          9         41         31       35        13
                 vv
clus              STAGE IVB
  ATG2B MUTATED           0
  ATG2B WILD-TYPE         1
D387V3, multiclass
            clus
vv           ATG2B MUTATED ATG2B WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              6             103
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             1               9
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ATG2B MUTATED     0   3  10   2
  ATG2B WILD-TYPE   9  65 238  39
D387V4, multiclass
    clus
vv   ATG2B MUTATED ATG2B WILD-TYPE
  T1             0               9
  T2             3              65
  T3            10             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
  ATG2B MUTATED    12   2   1
  ATG2B WILD-TYPE 208  78  65
D387V5, multiclass
    clus
vv   ATG2B MUTATED ATG2B WILD-TYPE
  N0            12             208
  N1             2              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"
D387V6, binary
                 cls
clus                0   1
  ATG2B MUTATED    14   0
  ATG2B WILD-TYPE 269  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATG2B MUTATED     14    0
  ATG2B WILD-TYPE  269   48
   clus
vv  ATG2B MUTATED ATG2B WILD-TYPE
  0            14             269
  1             0              48
[1] 2 2
[1] FALSE
D387V7, 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
D387V8, binary
                 cls
clus                0   1
  ATG2B MUTATED    12   3
  ATG2B WILD-TYPE 305  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATG2B MUTATED     12    3
  ATG2B WILD-TYPE  305   45
                               clus
vv                              ATG2B MUTATED ATG2B WILD-TYPE
  COLON ADENOCARCINOMA                     12             305
  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 246   2  22  19
D387V9, multiclass
    clus
vv   ATG2B MUTATED ATG2B WILD-TYPE
  R0            11             246
  R1             0               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"
D387V10, 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
D387V11, 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(388) Variable = NTRK3 MUTATION ANALYSIS
D388V1, survival
                 sevent
clus2               0   1
  NTRK3 MUTATED    20   3
  NTRK3 WILD-TYPE 262  70
  NTRK3 MUTATED NTRK3 WILD-TYPE 
             23             332 
  NTRK3 MUTATED NTRK3 WILD-TYPE 
              3              70 
$`NTRK3 MUTATED`
TCGA-A6-5657 TCGA-A6-6781 TCGA-AA-3664 TCGA-AA-3713 TCGA-AA-3815 TCGA-AA-3833 
       31.63        19.66        54.02        19.04        33.04        15.95 
TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-A010 TCGA-AD-5900 TCGA-AZ-4682 TCGA-AZ-6599 
       31.00        24.00        34.98         0.07        22.36         6.77 
TCGA-CA-6718 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-6161 TCGA-CM-6166 
        0.10        30.08        16.01        15.02        15.02        21.99 
TCGA-D5-6931 TCGA-DM-A1D9 TCGA-G4-6303 TCGA-G4-6315 TCGA-G4-6586 
       12.00       140.38        65.85        36.72        35.80 

$`NTRK3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       85.05        26.99        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
       25.02         1.02        17.98        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41        49.41        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.33         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        49.91        13.32        12.59         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      107.67        74.56        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 
       45.11        36.00        22.09        13.78        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  NTRK3 MUTATED NTRK3 WILD-TYPE 
           0.07            0.00 
  NTRK3 MUTATED NTRK3 WILD-TYPE 
         140.38          139.17 
  NTRK3 MUTATED NTRK3 WILD-TYPE 
          22.36           20.07 
[1] "0.1 - 140.4 (22.4)" "0.0 - 139.2 (20.1)"
[1] "hr=" "1.7"
D388V2, 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       23       100         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        19         10         40         29       32        11
                 vv
clus              STAGE IVB
  NTRK3 MUTATED           0
  NTRK3 WILD-TYPE         1
D388V3, multiclass
            clus
vv           NTRK3 MUTATED NTRK3 WILD-TYPE
  STAGE I                5              59
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              9             100
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             2              29
  STAGE IV               3              32
  STAGE IVA              2              11
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  64 233  36
D388V4, multiclass
    clus
vv   NTRK3 MUTATED NTRK3 WILD-TYPE
  T1             1               8
  T2             4              64
  T3            15             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
  NTRK3 MUTATED    19   5   1
  NTRK3 WILD-TYPE 201  75  65
D388V5, multiclass
    clus
vv   NTRK3 MUTATED NTRK3 WILD-TYPE
  N0            19             201
  N1             5              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"
D388V6, binary
                 cls
clus                0   1
  NTRK3 MUTATED    17   5
  NTRK3 WILD-TYPE 266  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTRK3 MUTATED     17    5
  NTRK3 WILD-TYPE  266   43
   clus
vv  NTRK3 MUTATED NTRK3 WILD-TYPE
  0            17             266
  1             5              43
[1] 2 2
[1] FALSE
D388V7, 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
D388V8, binary
                 cls
clus                0   1
  NTRK3 MUTATED    22   3
  NTRK3 WILD-TYPE 295  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTRK3 MUTATED     22    3
  NTRK3 WILD-TYPE  295   45
                               clus
vv                              NTRK3 MUTATED NTRK3 WILD-TYPE
  COLON ADENOCARCINOMA                     22             295
  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 236   2  21  20
D388V9, multiclass
    clus
vv   NTRK3 MUTATED NTRK3 WILD-TYPE
  R0            21             236
  R1             0               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"
D388V10, 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
D388V11, 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(389) Variable = KRT14 MUTATION ANALYSIS
D389V1, survival
                 sevent
clus2               0   1
  KRT14 MUTATED     5   3
  KRT14 WILD-TYPE 277  70
  KRT14 MUTATED KRT14 WILD-TYPE 
              8             347 
  KRT14 MUTATED KRT14 WILD-TYPE 
              3              70 
$`KRT14 MUTATED`
TCGA-A6-5665 TCGA-AA-3662 TCGA-AD-6964 TCGA-AZ-4682 TCGA-AZ-6599 TCGA-CM-6674 
       22.06         6.05        10.88        22.36         6.77        12.95 
TCGA-DM-A28E TCGA-G4-6588 
      119.93        26.17 

$`KRT14 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       19.99        13.94        19.99        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 
       83.80        62.79        61.41        49.41        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
       81.37        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        91.79        46.75        52.80 

  KRT14 MUTATED KRT14 WILD-TYPE 
           6.05            0.00 
  KRT14 MUTATED KRT14 WILD-TYPE 
         119.93          140.38 
  KRT14 MUTATED KRT14 WILD-TYPE 
         17.505          20.190 
[1] "6.0 - 119.9 (17.5)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.8"
D389V2, 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       25       105         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        19         10         41         31       34        12
                 vv
clus              STAGE IVB
  KRT14 MUTATED           0
  KRT14 WILD-TYPE         1
D389V3, multiclass
            clus
vv           KRT14 MUTATED KRT14 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              4             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 243  39
D389V4, multiclass
    clus
vv   KRT14 MUTATED KRT14 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             5             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
  KRT14 MUTATED     6   0   2
  KRT14 WILD-TYPE 214  80  64
D389V5, multiclass
    clus
vv   KRT14 MUTATED KRT14 WILD-TYPE
  N0             6             214
  N1             0              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"
D389V6, binary
                 cls
clus                0   1
  KRT14 MUTATED     4   2
  KRT14 WILD-TYPE 279  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT14 MUTATED      4    2
  KRT14 WILD-TYPE  279   46
   clus
vv  KRT14 MUTATED KRT14 WILD-TYPE
  0             4             279
  1             2              46
[1] 2 2
[1] FALSE
D389V7, 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
D389V8, binary
                 cls
clus                0   1
  KRT14 MUTATED     8   0
  KRT14 WILD-TYPE 309  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT14 MUTATED      8    0
  KRT14 WILD-TYPE  309   48
                               clus
vv                              KRT14 MUTATED KRT14 WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  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 253   2  21  21
D389V9, multiclass
    clus
vv   KRT14 MUTATED KRT14 WILD-TYPE
  R0             4             253
  R1             0               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"
D389V10, 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
D389V11, 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(390) Variable = SMG1 MUTATION ANALYSIS
D390V1, survival
                sevent
clus2              0   1
  SMG1 MUTATED    19   6
  SMG1 WILD-TYPE 263  67
  SMG1 MUTATED SMG1 WILD-TYPE 
            25            330 
  SMG1 MUTATED SMG1 WILD-TYPE 
             6             67 
$`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        15.75        49.41 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CM-4746 
        0.33         0.10        17.56       102.44        40.34        37.02 
TCGA-CM-5344 TCGA-CM-5348 TCGA-D5-5538 TCGA-DM-A0XF TCGA-DM-A28G TCGA-F4-6460 
       22.03        22.98        12.26        38.20        60.79        13.38 
TCGA-G4-6626 
       46.75 

$`SMG1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       23.87        20.12        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 
       33.04         0.99        25.02         1.02        17.98        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 
       18.05        31.00         2.01        12.99        24.00        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07         1.02         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-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-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4952 
        3.25         3.29         0.07         0.26         1.35        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        16.01        15.02         5.03        15.02        15.02 
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        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        24.43       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H 
      139.17         6.12        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        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       22.09        13.78        35.80        26.17        91.79        52.80 

  SMG1 MUTATED SMG1 WILD-TYPE 
           0.1            0.0 
  SMG1 MUTATED SMG1 WILD-TYPE 
        102.44         140.38 
  SMG1 MUTATED SMG1 WILD-TYPE 
         22.98          20.07 
[1] "0.1 - 102.4 (23.0)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.1"
D390V2, 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       21       104         5         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SMG1 MUTATED           1          2          4          2        0         2
  SMG1 WILD-TYPE        18          8         37         29       35        11
                vv
clus             STAGE IVB
  SMG1 MUTATED           0
  SMG1 WILD-TYPE         1
D390V3, multiclass
            clus
vv           SMG1 MUTATED SMG1 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              4             21
  STAGE IIA             5            104
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            2              8
  STAGE IIIB            4             37
  STAGE IIIC            2             29
  STAGE IV              0             35
  STAGE IVA             2             11
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 230  36
D390V4, multiclass
    clus
vv   SMG1 MUTATED SMG1 WILD-TYPE
  T1            0              9
  T2            2             66
  T3           18            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
  SMG1 MUTATED    14   9   2
  SMG1 WILD-TYPE 206  71  64
D390V5, multiclass
    clus
vv   SMG1 MUTATED SMG1 WILD-TYPE
  N0           14            206
  N1            9             71
  N2            2             64
[1] 3 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
  SMG1 MUTATED    22   1
  SMG1 WILD-TYPE 261  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMG1 MUTATED     22    1
  SMG1 WILD-TYPE  261   47
   clus
vv  SMG1 MUTATED SMG1 WILD-TYPE
  0           22            261
  1            1             47
[1] 2 2
[1] FALSE
D390V7, 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
D390V8, binary
                cls
clus               0   1
  SMG1 MUTATED    19   6
  SMG1 WILD-TYPE 298  42
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMG1 MUTATED     19    6
  SMG1 WILD-TYPE  298   42
                               clus
vv                              SMG1 MUTATED SMG1 WILD-TYPE
  COLON ADENOCARCINOMA                    19            298
  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 239   1  22  18
D390V9, multiclass
    clus
vv   SMG1 MUTATED SMG1 WILD-TYPE
  R0           18            239
  R1            1              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"
D390V10, 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
D390V11, 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(391) Variable = ODZ1 MUTATION ANALYSIS
D391V1, survival
                sevent
clus2              0   1
  ODZ1 MUTATED    48  11
  ODZ1 WILD-TYPE 234  62
  ODZ1 MUTATED ODZ1 WILD-TYPE 
            59            296 
  ODZ1 MUTATED ODZ1 WILD-TYPE 
            11             62 
$`ODZ1 MUTATED`
TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-6652 TCGA-AA-3502 TCGA-AA-3516 TCGA-AA-3553 
       31.63        33.53        24.69        35.01        13.02        24.00 
TCGA-AA-3555 TCGA-AA-3560 TCGA-AA-3662 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       29.95        19.99         6.05        19.04        19.04        10.06 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3837 TCGA-AA-3845 TCGA-AA-3947 
       33.04         0.99         1.02        38.99         0.00        33.01 
TCGA-AA-3980 TCGA-AA-A00Q TCGA-AA-A01P TCGA-AA-A03F TCGA-AD-6889 TCGA-AU-3779 
       27.02        42.02        38.07        18.05        56.55        14.50 
TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4681 TCGA-CA-6717 
        0.95         0.20        17.82        58.39        83.80         0.33 
TCGA-CA-6718 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-6747 TCGA-CM-5344 
        0.10        40.34        15.62        51.32         2.93        22.03 
TCGA-CM-5861 TCGA-CM-6161 TCGA-CM-6167 TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6678 
       15.02        15.02        14.99        12.95        11.08        11.01 
TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6931 TCGA-D5-6932 
       12.26        13.51        16.14        15.58        12.00        11.38 
TCGA-DM-A1D8 TCGA-DM-A1DB TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6808 TCGA-G4-6293 
       12.59        44.32         6.18        35.87        33.67       107.67 
TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       53.62        55.04        13.78        35.80        26.17 

$`ODZ1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       32.91        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       24.16        21.76        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
        1.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 
       33.99        21.01        13.02        17.95        23.01        20.98 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 
       85.05        26.99        35.05        25.02        17.98        15.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02        14.93        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 
       18.05        31.00         2.01        12.99        24.00        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       24.00        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04         4.01        27.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37         4.21         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 
        5.79        22.42        27.42        10.88         0.20        27.09 
TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
       16.31        15.75        21.44         1.41         5.13        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07         0.26         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 
       17.56       102.44        49.08        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-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 
       29.06        22.98        30.08        16.01         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-6675 TCGA-CM-6676 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 
       13.05        11.08        10.06        12.03        45.40        19.59 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6920 
       17.85         4.80        17.13        12.49         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-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       13.41         1.51        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        92.75        49.91        13.32       140.38         7.50 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 
       13.45         1.55        16.31        29.59        16.24        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 
        0.53        35.41        19.43        74.56        65.85        44.68 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6625 
       51.75        45.11        36.72        36.00        22.09        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  ODZ1 MUTATED ODZ1 WILD-TYPE 
             0              0 
  ODZ1 MUTATED ODZ1 WILD-TYPE 
        107.67         140.38 
  ODZ1 MUTATED ODZ1 WILD-TYPE 
        18.050         20.995 
[1] "0.0 - 107.7 (18.1)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.1"
D391V2, 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       24        83         5         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ODZ1 MUTATED           6          1          6          4        2         2
  ODZ1 WILD-TYPE        13          9         35         27       33        11
                vv
clus             STAGE IVB
  ODZ1 MUTATED           0
  ODZ1 WILD-TYPE         1
D391V3, multiclass
            clus
vv           ODZ1 MUTATED ODZ1 WILD-TYPE
  STAGE I               8             56
  STAGE IA              1              0
  STAGE II              1             24
  STAGE IIA            26             83
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             6             13
  STAGE IIIA            1              9
  STAGE IIIB            6             35
  STAGE IIIC            4             27
  STAGE IV              2             33
  STAGE IVA             2             11
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  62 204  33
D391V4, multiclass
    clus
vv   ODZ1 MUTATED ODZ1 WILD-TYPE
  T1            2              7
  T2            6             62
  T3           44            204
  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  69  57
D391V5, multiclass
    clus
vv   ODZ1 MUTATED ODZ1 WILD-TYPE
  N0           41            179
  N1           11             69
  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
  ODZ1 MUTATED    50   4
  ODZ1 WILD-TYPE 233  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  ODZ1 MUTATED     50    4
  ODZ1 WILD-TYPE  233   44
   clus
vv  ODZ1 MUTATED ODZ1 WILD-TYPE
  0           50            233
  1            4             44
[1] 2 2
[1] FALSE
D391V7, 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
D391V8, binary
                cls
clus               0   1
  ODZ1 MUTATED    50  10
  ODZ1 WILD-TYPE 267  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  ODZ1 MUTATED     50   10
  ODZ1 WILD-TYPE  267   38
                               clus
vv                              ODZ1 MUTATED ODZ1 WILD-TYPE
  COLON ADENOCARCINOMA                    50            267
  COLON MUCINOUS ADENOCARCINOMA           10             38
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ODZ1 MUTATED    46   1   2   6
  ODZ1 WILD-TYPE 211   1  20  15
D391V9, multiclass
    clus
vv   ODZ1 MUTATED ODZ1 WILD-TYPE
  R0           46            211
  R1            1              1
  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"
D391V10, 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
D391V11, 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(392) Variable = JAK2 MUTATION ANALYSIS
D392V1, survival
                sevent
clus2              0   1
  JAK2 MUTATED    31   7
  JAK2 WILD-TYPE 251  66
  JAK2 MUTATED JAK2 WILD-TYPE 
            38            317 
  JAK2 MUTATED JAK2 WILD-TYPE 
             7             66 
$`JAK2 MUTATED`
TCGA-A6-5662 TCGA-A6-5666 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3713 TCGA-AA-3815 
       23.61        32.71        78.08         6.05        19.04        33.04 
TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A02K TCGA-AU-6004 
       24.00         2.01         4.01        34.98        14.01        27.09 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AZ-4616 TCGA-AZ-6598 TCGA-AZ-6606 TCGA-CA-6717 
       15.75         0.20         5.13        49.41        11.74         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CM-4746 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5868 
        0.10         1.35        37.02        16.01         5.03        17.03 
TCGA-CM-6161 TCGA-CM-6169 TCGA-CM-6170 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6541 
       15.02        13.02        15.02        18.25         1.32        15.58 
TCGA-D5-6929 TCGA-DM-A0XD TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6807 TCGA-G4-6293 
       13.41        24.43        13.45         1.55        16.24       107.67 
TCGA-G4-6309 TCGA-G4-6625 
       51.75        91.79 

$`JAK2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        33.53        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        19.99        61.02         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       26.99        19.04        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       16.31         0.95        21.44        17.82        58.39         1.41 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
      100.01        29.56         5.23         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CK-4947 
        3.06         3.25         3.29         0.07         0.26        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        12.26        19.59        13.51        11.51 
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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38        10.26       119.70        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 
        6.18        35.87        16.31        29.59        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        35.41        19.43        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        46.75        52.80 

  JAK2 MUTATED JAK2 WILD-TYPE 
           0.1            0.0 
  JAK2 MUTATED JAK2 WILD-TYPE 
        107.67         140.38 
  JAK2 MUTATED JAK2 WILD-TYPE 
        15.665         21.370 
[1] "0.1 - 107.7 (15.7)" "0.0 - 140.4 (21.4)"
[1] "hr=" "1"  
D392V2, 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       23        96         5         0
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  JAK2 MUTATED           1          0          2          3        6         4
  JAK2 WILD-TYPE        18         10         39         28       29         9
                vv
clus             STAGE IVB
  JAK2 MUTATED           0
  JAK2 WILD-TYPE         1
D392V3, multiclass
            clus
vv           JAK2 MUTATED JAK2 WILD-TYPE
  STAGE I               5             59
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA            13             96
  STAGE IIB             3              5
  STAGE IIC             1              0
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            2             39
  STAGE IIIC            3             28
  STAGE IV              6             29
  STAGE IVA             4              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
  JAK2 MUTATED     0   5  26   9
  JAK2 WILD-TYPE   9  63 222  32
D392V4, multiclass
    clus
vv   JAK2 MUTATED JAK2 WILD-TYPE
  T1            0              9
  T2            5             63
  T3           26            222
  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  74  58
D392V5, multiclass
    clus
vv   JAK2 MUTATED JAK2 WILD-TYPE
  N0           26            194
  N1            6             74
  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"
D392V6, binary
                cls
clus               0   1
  JAK2 MUTATED    26  10
  JAK2 WILD-TYPE 257  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  JAK2 MUTATED     26   10
  JAK2 WILD-TYPE  257   38
   clus
vv  JAK2 MUTATED JAK2 WILD-TYPE
  0           26            257
  1           10             38
[1] 2 2
[1] FALSE
D392V7, 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
D392V8, binary
                cls
clus               0   1
  JAK2 MUTATED    34   6
  JAK2 WILD-TYPE 283  42
[1] "tbl2"
                cls
clus             [,1] [,2]
  JAK2 MUTATED     34    6
  JAK2 WILD-TYPE  283   42
                               clus
vv                              JAK2 MUTATED JAK2 WILD-TYPE
  COLON ADENOCARCINOMA                    34            283
  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 231   2  19  17
D392V9, multiclass
    clus
vv   JAK2 MUTATED JAK2 WILD-TYPE
  R0           26            231
  R1            0              2
  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"
D392V10, 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
D392V11, 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(393) Variable = ADAM18 MUTATION ANALYSIS
D393V1, survival
                  sevent
clus2                0   1
  ADAM18 MUTATED    14   4
  ADAM18 WILD-TYPE 268  69
  ADAM18 MUTATED ADAM18 WILD-TYPE 
              18              337 
  ADAM18 MUTATED ADAM18 WILD-TYPE 
               4               69 
$`ADAM18 MUTATED`
TCGA-A6-5661 TCGA-A6-6137 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 
       33.53        27.09        19.04        19.04        35.05        33.04 
TCGA-AA-3845 TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-5913 
        0.00        34.98        58.39        49.41         0.33        51.32 
TCGA-CM-6168 TCGA-CM-6172 TCGA-D5-5541 TCGA-D5-6540 TCGA-DM-A1DB TCGA-G4-6307 
       12.99        11.01        11.51        16.14        44.32        55.04 

$`ADAM18 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3818 TCGA-AA-3819 
        5.03        85.05        26.99        10.06         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       14.04        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        13.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       12.59       140.38         7.50       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  ADAM18 MUTATED ADAM18 WILD-TYPE 
               0                0 
  ADAM18 MUTATED ADAM18 WILD-TYPE 
           58.39           140.38 
  ADAM18 MUTATED ADAM18 WILD-TYPE 
          30.065           20.120 
[1] "0.0 - 58.4 (30.1)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1"  
D393V2, 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       23       100         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ADAM18 MUTATED           0          0          4          0        1
  ADAM18 WILD-TYPE        19         10         37         31       34
                  vv
clus               STAGE IVA STAGE IVB
  ADAM18 MUTATED           0         0
  ADAM18 WILD-TYPE        13         1
D393V3, multiclass
            clus
vv           ADAM18 MUTATED ADAM18 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               9              100
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              4               37
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ADAM18 MUTATED     0   1  16   1
  ADAM18 WILD-TYPE   9  67 232  40
D393V4, multiclass
    clus
vv   ADAM18 MUTATED ADAM18 WILD-TYPE
  T1              0                9
  T2              1               67
  T3             16              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
  ADAM18 MUTATED    14   4   0
  ADAM18 WILD-TYPE 206  76  66
D393V5, multiclass
    clus
vv   ADAM18 MUTATED ADAM18 WILD-TYPE
  N0             14              206
  N1              4               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"
D393V6, binary
                  cls
clus                 0   1
  ADAM18 MUTATED    15   1
  ADAM18 WILD-TYPE 268  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM18 MUTATED     15    1
  ADAM18 WILD-TYPE  268   47
   clus
vv  ADAM18 MUTATED ADAM18 WILD-TYPE
  0             15              268
  1              1               47
[1] 2 2
[1] FALSE
D393V7, 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
D393V8, binary
                  cls
clus                 0   1
  ADAM18 MUTATED    16   2
  ADAM18 WILD-TYPE 301  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM18 MUTATED     16    2
  ADAM18 WILD-TYPE  301   46
                               clus
vv                              ADAM18 MUTATED ADAM18 WILD-TYPE
  COLON ADENOCARCINOMA                      16              301
  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 245   2  21  19
D393V9, multiclass
    clus
vv   ADAM18 MUTATED ADAM18 WILD-TYPE
  R0             12              245
  R1              0                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"
D393V10, 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
D393V11, 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(394) Variable = PTPN11 MUTATION ANALYSIS
D394V1, survival
                  sevent
clus2                0   1
  PTPN11 MUTATED    20   8
  PTPN11 WILD-TYPE 262  65
  PTPN11 MUTATED PTPN11 WILD-TYPE 
              28              327 
  PTPN11 MUTATED PTPN11 WILD-TYPE 
               8               65 
$`PTPN11 MUTATED`
TCGA-AA-3555 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3697 TCGA-AA-3977 TCGA-AD-6964 
       29.95        61.02        78.08        85.05        25.02        10.88 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CA-6718 TCGA-CK-5914 
       49.41         6.77       100.01         1.94         0.10        21.99 
TCGA-CK-6747 TCGA-CM-5862 TCGA-CM-6675 TCGA-CM-6676 TCGA-D5-6534 TCGA-D5-6535 
        2.93         5.03        13.05        11.08        43.27        15.12 
TCGA-D5-6538 TCGA-DM-A0X9 TCGA-DM-A1HA TCGA-DM-A28F TCGA-G4-6299 TCGA-G4-6303 
       17.13       119.70       131.51        35.97        74.56        65.85 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6588 
       44.68        55.04        45.11        26.17 

$`PTPN11 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        17.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        13.94        19.99         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       61.41        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 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.33         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       49.08        51.32        21.14         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        16.01        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-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       11.01        12.95        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 
       18.25         1.32        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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38        10.26        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G 
      135.65       139.17         6.12        81.37       119.93        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6304 
       13.25         0.53        35.41        19.43       107.67        53.62 
TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       51.75        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  PTPN11 MUTATED PTPN11 WILD-TYPE 
             0.1              0.0 
  PTPN11 MUTATED PTPN11 WILD-TYPE 
          131.51           140.38 
  PTPN11 MUTATED PTPN11 WILD-TYPE 
           32.96            19.99 
[1] "0.1 - 131.5 (33.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.2"
D394V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PTPN11 MUTATED         3        0        4         7         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           2          1          6          2        1
  PTPN11 WILD-TYPE        17          9         35         29       34
                  vv
clus               STAGE IVA STAGE IVB
  PTPN11 MUTATED           1         1
  PTPN11 WILD-TYPE        12         0
D394V3, multiclass
            clus
vv           PTPN11 MUTATED PTPN11 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                4               21
  STAGE IIA               7              102
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               2               17
  STAGE IIIA              1                9
  STAGE IIIB              6               35
  STAGE IIIC              2               29
  STAGE IV                1               34
  STAGE IVA               1               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
  PTPN11 MUTATED     0   6  23   1
  PTPN11 WILD-TYPE   9  62 225  40
D394V4, multiclass
    clus
vv   PTPN11 MUTATED PTPN11 WILD-TYPE
  T1              0                9
  T2              6               62
  T3             23              225
  T4              1               40
[1] 4 2
[1] TRUE
[1] "dimension 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  72  60
D394V5, multiclass
    clus
vv   PTPN11 MUTATED PTPN11 WILD-TYPE
  N0             16              204
  N1              8               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"
D394V6, binary
                  cls
clus                 0   1
  PTPN11 MUTATED    19   3
  PTPN11 WILD-TYPE 264  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN11 MUTATED     19    3
  PTPN11 WILD-TYPE  264   45
   clus
vv  PTPN11 MUTATED PTPN11 WILD-TYPE
  0             19              264
  1              3               45
[1] 2 2
[1] FALSE
D394V7, 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
D394V8, binary
                  cls
clus                 0   1
  PTPN11 MUTATED    28   2
  PTPN11 WILD-TYPE 289  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN11 MUTATED     28    2
  PTPN11 WILD-TYPE  289   46
                               clus
vv                              PTPN11 MUTATED PTPN11 WILD-TYPE
  COLON ADENOCARCINOMA                      28              289
  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 241   2  22  16
D394V9, multiclass
    clus
vv   PTPN11 MUTATED PTPN11 WILD-TYPE
  R0             16              241
  R1              0                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"
D394V10, 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
D394V11, 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(395) Variable = EGFR MUTATION ANALYSIS
D395V1, survival
                sevent
clus2              0   1
  EGFR MUTATED    52  20
  EGFR WILD-TYPE 230  53
  EGFR MUTATED EGFR WILD-TYPE 
            72            283 
  EGFR MUTATED EGFR WILD-TYPE 
            20             53 
$`EGFR MUTATED`
TCGA-A6-3809 TCGA-A6-5660 TCGA-AA-3502 TCGA-AA-3518 TCGA-AA-3542 TCGA-AA-3663 
       32.75        29.19        35.01         1.02        12.99         6.97 
TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3982 TCGA-AA-A00E 
       85.05        10.06         2.01        21.99        27.02        30.02 
TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A01R TCGA-AA-A02K TCGA-AD-5900 TCGA-AD-6901 
        4.01         0.99        35.01        14.01         0.07        22.42 
TCGA-AD-6964 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6196 TCGA-AZ-5403 
       10.88        14.50        27.09        15.75         0.20        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6608 TCGA-CA-6717 TCGA-CK-5914 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-5344 
        1.94         0.33        21.99         2.01       124.27        22.03 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-6162 TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 
       16.01         5.03        12.00        21.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6680 TCGA-D5-5539 TCGA-D5-5540 
       15.02        11.08        11.08        12.03        19.59        13.51 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        17.85         4.80        17.13        12.49 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6928 TCGA-DM-A1D8 TCGA-DM-A1DB TCGA-DM-A1HB 
        7.53        12.39        11.64        12.59        44.32       135.65 
TCGA-DM-A285 TCGA-DM-A28F TCGA-F4-6460 TCGA-F4-6808 TCGA-F4-6809 TCGA-G4-6299 
        6.12        35.97        13.38        33.67        13.25        74.56 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6588 
       65.85        44.68        55.04        36.72        36.00        26.17 

$`EGFR WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3510 
       19.66        20.28         7.04         3.02         1.02        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 
        6.97         1.02        13.02        38.99         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 
       34.03        29.00        29.00        26.01         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       78.08         6.05        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       20.98        34.03        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3986 TCGA-AA-3989 
       26.01        25.02        24.00        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J 
       27.02        13.94        38.04        19.00        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W 
       18.05        38.04        27.02        42.02        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 
        5.79        27.42         0.20        16.31         0.95        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        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         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 
      102.44        40.34        15.62        49.08        51.32        21.14 
TCGA-CK-6747 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        2.93        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 
       29.06        22.98        30.08        15.02        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-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6678 TCGA-CM-6679 
       14.04        11.01        12.95        13.05        11.01        10.06 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6535 
       45.40        12.26        11.51        20.19        18.25        15.12 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       16.14        15.58        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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-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-A1HA TCGA-DM-A282 TCGA-DM-A28C 
       13.32       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-F4-6569 
      119.93        60.79       117.07        98.24         8.61        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6304 TCGA-G4-6309 
        0.53        35.41        19.43       107.67        53.62        51.75 
TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       45.11        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 
       52.80 

  EGFR MUTATED EGFR WILD-TYPE 
          0.07           0.00 
  EGFR MUTATED EGFR WILD-TYPE 
        135.65         140.38 
  EGFR MUTATED EGFR WILD-TYPE 
        15.385         21.140 
[1] "0.1 - 135.7 (15.4)" "0.0 - 140.4 (21.1)"
[1] "hr=" "1.5"
D395V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EGFR MUTATED        14        0        4        17         2         0
  EGFR WILD-TYPE      50        1       21        92         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EGFR MUTATED           4          3         12          5        6         3
  EGFR WILD-TYPE        15          7         29         26       29        10
                vv
clus             STAGE IVB
  EGFR MUTATED           0
  EGFR WILD-TYPE         1
D395V3, multiclass
            clus
vv           EGFR MUTATED EGFR WILD-TYPE
  STAGE I              14             50
  STAGE IA              0              1
  STAGE II              4             21
  STAGE IIA            17             92
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             4             15
  STAGE IIIA            3              7
  STAGE IIIB           12             29
  STAGE IIIC            5             26
  STAGE IV              6             29
  STAGE IVA             3             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
  EGFR MUTATED     2  15  51   6
  EGFR WILD-TYPE   7  53 197  35
D395V4, multiclass
    clus
vv   EGFR MUTATED EGFR WILD-TYPE
  T1            2              7
  T2           15             53
  T3           51            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    41  20  13
  EGFR WILD-TYPE 179  60  53
D395V5, multiclass
    clus
vv   EGFR MUTATED EGFR WILD-TYPE
  N0           41            179
  N1           20             60
  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"
D395V6, binary
                cls
clus               0   1
  EGFR MUTATED    51   9
  EGFR WILD-TYPE 232  39
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGFR MUTATED     51    9
  EGFR WILD-TYPE  232   39
   clus
vv  EGFR MUTATED EGFR WILD-TYPE
  0           51            232
  1            9             39
[1] 2 2
[1] FALSE
D395V7, binary
                cls
clus               0   1
  EGFR MUTATED    37  37
  EGFR WILD-TYPE 133 160
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGFR MUTATED     37   37
  EGFR WILD-TYPE  133  160
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  FEMALE           37            133
  MALE             37            160
[1] 2 2
[1] FALSE
D395V8, binary
                cls
clus               0   1
  EGFR MUTATED    60  14
  EGFR WILD-TYPE 257  34
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGFR MUTATED     60   14
  EGFR WILD-TYPE  257   34
                               clus
vv                              EGFR MUTATED EGFR WILD-TYPE
  COLON ADENOCARCINOMA                    60            257
  COLON MUCINOUS ADENOCARCINOMA           14             34
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  EGFR MUTATED    50   0   1   5
  EGFR WILD-TYPE 207   2  21  16
D395V9, multiclass
    clus
vv   EGFR MUTATED EGFR WILD-TYPE
  R0           50            207
  R1            0              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"
D395V10, 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    53
  EGFR WILD-TYPE                        14   123
D395V11, 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                                      53            123
[1] 4 2
[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 = EZH2 MUTATION ANALYSIS
D396V1, survival
                sevent
clus2              0   1
  EZH2 MUTATED    33  10
  EZH2 WILD-TYPE 249  63
  EZH2 MUTATED EZH2 WILD-TYPE 
            43            312 
  EZH2 MUTATED EZH2 WILD-TYPE 
            10             63 
$`EZH2 MUTATED`
TCGA-A6-2676 TCGA-A6-3809 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6141 
       42.90        32.75        29.19        33.53        22.06         8.38 
TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3672 
       24.39        19.66        63.98         6.05         6.97         0.92 
TCGA-AA-3713 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6964 TCGA-AY-6196 TCGA-AY-6197 
       19.04         4.01        34.98        10.88         0.20        21.44 
TCGA-AZ-6599 TCGA-AZ-6608 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-5344 TCGA-CM-5863 
        6.77         1.94         0.33         0.10        22.03        15.02 
TCGA-CM-5864 TCGA-D5-5540 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6540 
       15.02        13.51        15.12        17.85         4.80        16.14 
TCGA-D5-6541 TCGA-D5-6920 TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A28F TCGA-F4-6808 
       15.58        12.39        44.32       135.65        35.97        33.67 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6317 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 
       65.85        44.68        36.00        35.80        26.17        46.75 
TCGA-G4-6628 
       52.80 

$`EZH2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       34.65        33.34        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       30.44        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       19.99        61.02        78.08        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 
       14.50        27.09        16.31         0.95        15.75        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41        49.41        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07         0.26         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
        5.03        17.03        15.02        12.00        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6538 
       11.51        20.19        18.25         1.32        43.27        17.13 
TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       12.49         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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38         7.50       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
      139.17         6.12        81.37       119.93        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 
        1.55        16.31        29.59        16.24        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6307 
       35.41        19.43       107.67        74.56        53.62        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 
       51.75        45.11        36.72        22.09        13.78        91.79 

  EZH2 MUTATED EZH2 WILD-TYPE 
           0.1            0.0 
  EZH2 MUTATED EZH2 WILD-TYPE 
        135.65         140.38 
  EZH2 MUTATED EZH2 WILD-TYPE 
        19.660         20.235 
[1] "0.1 - 135.7 (19.7)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D396V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EZH2 MUTATED         6        0        2        15         4         0
  EZH2 WILD-TYPE      58        1       23        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        17          9         35         27       32        13
                vv
clus             STAGE IVB
  EZH2 MUTATED           0
  EZH2 WILD-TYPE         1
D396V3, multiclass
            clus
vv           EZH2 MUTATED EZH2 WILD-TYPE
  STAGE I               6             58
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA            15             94
  STAGE IIB             4              4
  STAGE IIC             0              1
  STAGE III             2             17
  STAGE IIIA            1              9
  STAGE IIIB            6             35
  STAGE IIIC            4             27
  STAGE IV              3             32
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  EZH2 MUTATED     1   7  29   7
  EZH2 WILD-TYPE   8  61 219  34
D396V4, multiclass
    clus
vv   EZH2 MUTATED EZH2 WILD-TYPE
  T1            1              8
  T2            7             61
  T3           29            219
  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  70  60
D396V5, multiclass
    clus
vv   EZH2 MUTATED EZH2 WILD-TYPE
  N0           28            192
  N1           10             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"
D396V6, binary
                cls
clus               0   1
  EZH2 MUTATED    33   3
  EZH2 WILD-TYPE 250  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  EZH2 MUTATED     33    3
  EZH2 WILD-TYPE  250   45
   clus
vv  EZH2 MUTATED EZH2 WILD-TYPE
  0           33            250
  1            3             45
[1] 2 2
[1] FALSE
D396V7, 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
D396V8, binary
                cls
clus               0   1
  EZH2 MUTATED    37   7
  EZH2 WILD-TYPE 280  41
[1] "tbl2"
                cls
clus             [,1] [,2]
  EZH2 MUTATED     37    7
  EZH2 WILD-TYPE  280   41
                               clus
vv                              EZH2 MUTATED EZH2 WILD-TYPE
  COLON ADENOCARCINOMA                    37            280
  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 227   2  20  18
D396V9, multiclass
    clus
vv   EZH2 MUTATED EZH2 WILD-TYPE
  R0           30            227
  R1            0              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"
D396V10, 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
D396V11, 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(397) Variable = EP300 MUTATION ANALYSIS
D397V1, survival
                 sevent
clus2               0   1
  EP300 MUTATED    32   3
  EP300 WILD-TYPE 250  70
  EP300 MUTATED EP300 WILD-TYPE 
             35             320 
  EP300 MUTATED EP300 WILD-TYPE 
              3              70 
$`EP300 MUTATED`
TCGA-A6-5659 TCGA-A6-6141 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3554 
       30.44         8.38        24.39        20.12        19.66        17.95 
TCGA-AA-3555 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3715 TCGA-AA-3864 TCGA-AA-3877 
       29.95        61.02         6.05        19.04        53.00        31.00 
TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01G TCGA-AD-6889 
       18.05         4.01         0.99        34.98        12.00        56.55 
TCGA-AU-6004 TCGA-AY-6386 TCGA-CA-5796 TCGA-CA-6717 TCGA-CK-5913 TCGA-CM-4743 
       27.09        17.82         3.25         0.33        51.32        23.05 
TCGA-CM-4752 TCGA-CM-5868 TCGA-CM-6162 TCGA-D5-5540 TCGA-D5-6539 TCGA-D5-6920 
       13.02        17.03        12.00        13.51        12.49        12.39 
TCGA-D5-6931 TCGA-DM-A1D0 TCGA-DM-A1DA TCGA-G4-6323 TCGA-G4-6628 
       12.00       130.65         7.50        13.78        52.80 

$`EP300 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 
       24.16        21.76        24.69        23.87        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        3.02         1.02        35.01        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3558 
       33.99        21.01        13.02        24.00        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       19.99        13.94        19.99        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       38.04        27.02        42.02        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       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        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37         4.21         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5797 TCGA-CA-6715 
        3.19         1.94         2.24         3.06         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        21.99        21.14         2.93         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        16.01        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        12.26        19.59        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 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         1.51 
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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       45.11        36.72        36.00        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 
       91.79        46.75 

  EP300 MUTATED EP300 WILD-TYPE 
           0.33            0.00 
  EP300 MUTATED EP300 WILD-TYPE 
         130.65          140.38 
  EP300 MUTATED EP300 WILD-TYPE 
         17.950          21.075 
[1] "0.3 - 130.7 (17.9)" "0.0 - 140.4 (21.1)"
[1] "hr=" "2.5"
D397V2, 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       22        94         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EP300 MUTATED           0          1          3          3        1         1
  EP300 WILD-TYPE        19          9         38         28       34        12
                 vv
clus              STAGE IVB
  EP300 MUTATED           0
  EP300 WILD-TYPE         1
D397V3, multiclass
            clus
vv           EP300 MUTATED EP300 WILD-TYPE
  STAGE I                6              58
  STAGE IA               1               0
  STAGE II               3              22
  STAGE IIA             15              94
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             3              38
  STAGE IIIC             3              28
  STAGE IV               1              34
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  63 226  34
D397V4, multiclass
    clus
vv   EP300 MUTATED EP300 WILD-TYPE
  T1             1               8
  T2             5              63
  T3            22             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
  EP300 MUTATED    28   5   3
  EP300 WILD-TYPE 192  75  63
D397V5, multiclass
    clus
vv   EP300 MUTATED EP300 WILD-TYPE
  N0            28             192
  N1             5              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"
D397V6, binary
                 cls
clus                0   1
  EP300 MUTATED    30   2
  EP300 WILD-TYPE 253  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED     30    2
  EP300 WILD-TYPE  253   46
   clus
vv  EP300 MUTATED EP300 WILD-TYPE
  0            30             253
  1             2              46
[1] 2 2
[1] FALSE
D397V7, 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
D397V8, binary
                 cls
clus                0   1
  EP300 MUTATED    26  10
  EP300 WILD-TYPE 291  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED     26   10
  EP300 WILD-TYPE  291   38
                               clus
vv                              EP300 MUTATED EP300 WILD-TYPE
  COLON ADENOCARCINOMA                     26             291
  COLON MUCINOUS ADENOCARCINOMA            10              38
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  EP300 MUTATED    27   0   1   2
  EP300 WILD-TYPE 230   2  21  19
D397V9, multiclass
    clus
vv   EP300 MUTATED EP300 WILD-TYPE
  R0            27             230
  R1             0               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"
D397V10, 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
D397V11, 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(398) Variable = OSBPL11 MUTATION ANALYSIS
D398V1, survival
                   sevent
clus2                 0   1
  OSBPL11 MUTATED     8   8
  OSBPL11 WILD-TYPE 274  65
  OSBPL11 MUTATED OSBPL11 WILD-TYPE 
               16               339 
  OSBPL11 MUTATED OSBPL11 WILD-TYPE 
                8                65 
$`OSBPL11 MUTATED`
TCGA-AA-3554 TCGA-AA-3662 TCGA-AA-3715 TCGA-AA-3966 TCGA-AA-A00A TCGA-AA-A00N 
       17.95         6.05        19.04         2.01        38.04         4.01 
TCGA-AD-6964 TCGA-AY-6196 TCGA-CA-6717 TCGA-D5-5537 TCGA-DM-A0XD TCGA-F4-6570 
       10.88         0.20         0.33        45.40        24.43         6.18 
TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6626 
      107.67        65.85        44.68        46.75 

$`OSBPL11 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       19.99        13.94        19.99        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
        7.96        27.02        13.94        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        15.75        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        13.38        13.45        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 
       35.41        19.43        74.56        53.62        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       26.17        91.79        52.80 

  OSBPL11 MUTATED OSBPL11 WILD-TYPE 
              0.2               0.0 
  OSBPL11 MUTATED OSBPL11 WILD-TYPE 
           107.67            140.38 
  OSBPL11 MUTATED OSBPL11 WILD-TYPE 
           18.495            20.280 
[1] "0.2 - 107.7 (18.5)" "0.0 - 140.4 (20.3)"
[1] "hr=" "2.4"
D398V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OSBPL11 MUTATED         0        0        1         9         1         0
  OSBPL11 WILD-TYPE      64        1       24       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        18         10         41         30       33
                   vv
clus                STAGE IVA STAGE IVB
  OSBPL11 MUTATED           0         0
  OSBPL11 WILD-TYPE        13         1
D398V3, multiclass
            clus
vv           OSBPL11 MUTATED OSBPL11 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                9               100
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               1                30
  STAGE IV                 2                33
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  OSBPL11 MUTATED     0   1  12   3
  OSBPL11 WILD-TYPE   9  67 236  38
D398V4, multiclass
    clus
vv   OSBPL11 MUTATED OSBPL11 WILD-TYPE
  T1               0                 9
  T2               1                67
  T3              12               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
  OSBPL11 MUTATED    10   2   4
  OSBPL11 WILD-TYPE 210  78  62
D398V5, multiclass
    clus
vv   OSBPL11 MUTATED OSBPL11 WILD-TYPE
  N0              10               210
  N1               2                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"
D398V6, binary
                   cls
clus                  0   1
  OSBPL11 MUTATED    11   2
  OSBPL11 WILD-TYPE 272  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  OSBPL11 MUTATED     11    2
  OSBPL11 WILD-TYPE  272   46
   clus
vv  OSBPL11 MUTATED OSBPL11 WILD-TYPE
  0              11               272
  1               2                46
[1] 2 2
[1] FALSE
D398V7, 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
D398V8, binary
                   cls
clus                  0   1
  OSBPL11 MUTATED    12   4
  OSBPL11 WILD-TYPE 305  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  OSBPL11 MUTATED     12    4
  OSBPL11 WILD-TYPE  305   44
                               clus
vv                              OSBPL11 MUTATED OSBPL11 WILD-TYPE
  COLON ADENOCARCINOMA                       12               305
  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 247   2  21  19
D398V9, multiclass
    clus
vv   OSBPL11 MUTATED OSBPL11 WILD-TYPE
  R0              10               247
  R1               0                 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"
D398V10, 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
D398V11, 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(399) Variable = FBN2 MUTATION ANALYSIS
D399V1, survival
                sevent
clus2              0   1
  FBN2 MUTATED    31  10
  FBN2 WILD-TYPE 251  63
  FBN2 MUTATED FBN2 WILD-TYPE 
            41            314 
  FBN2 MUTATED FBN2 WILD-TYPE 
            10             63 
$`FBN2 MUTATED`
TCGA-A6-3809 TCGA-A6-4105 TCGA-A6-5665 TCGA-A6-6649 TCGA-A6-6653 TCGA-AA-3510 
       32.75        14.53        22.06        24.16        24.39        63.98 
TCGA-AA-3516 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3864 TCGA-AA-3947 
       13.02         0.99        13.02        17.95        53.00        33.01 
TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01G TCGA-AA-A01Q 
        2.01        25.02         4.01        34.98        12.00         1.02 
TCGA-AA-A01V TCGA-AA-A03F TCGA-AD-5900 TCGA-AY-4071 TCGA-AY-6196 TCGA-AZ-4315 
       35.01        18.05         0.07         0.95         0.20        58.39 
TCGA-AZ-6601 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5914 TCGA-CK-6751 TCGA-CM-6169 
      100.01         0.33         0.10        21.99       124.27        13.02 
TCGA-CM-6674 TCGA-D5-6898 TCGA-D5-6928 TCGA-DM-A0XF TCGA-DM-A28F TCGA-F4-6460 
       12.95         7.53        11.64        38.20        35.97        13.38 
TCGA-F4-6570 TCGA-F4-6704 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6588 
        6.18         1.55        36.72        22.09        26.17 

$`FBN2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 
       16.57        34.65        33.34        36.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       30.44        29.19        33.53        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 
       27.09        22.52         8.38        25.08        25.18        21.76 
TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 
       24.69        23.87        20.12        19.66        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02         1.02        35.01         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 
       26.01        12.99        14.01        33.99        21.01        24.00 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 
       18.05        31.00         2.01        12.99        24.00        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-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-A024 
       35.01         1.02        33.04        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-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-6548 TCGA-AD-6888 TCGA-AD-6889 
       41.00        39.98        40.96        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6197 
        0.20        14.50        27.09        16.31        15.75        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07         0.26         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 
       40.34        15.62        49.08        51.32        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        14.04        11.01        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58        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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        24.43       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
      139.17         6.12        81.37       119.93        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 
       98.24         8.61        13.45        35.87        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       51.75        45.11        36.00        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  FBN2 MUTATED FBN2 WILD-TYPE 
          0.07           0.00 
  FBN2 MUTATED FBN2 WILD-TYPE 
        124.27         140.38 
  FBN2 MUTATED FBN2 WILD-TYPE 
         17.95          20.63 
[1] "0.1 - 124.3 (17.9)" "0.0 - 140.4 (20.6)"
[1] "hr=" "1.4"
D399V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FBN2 MUTATED         7        0        4        14         4         0
  FBN2 WILD-TYPE      57        1       21        95         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        16         10         37         27       34        13
                vv
clus             STAGE IVB
  FBN2 MUTATED           0
  FBN2 WILD-TYPE         1
D399V3, multiclass
            clus
vv           FBN2 MUTATED FBN2 WILD-TYPE
  STAGE I               7             57
  STAGE IA              0              1
  STAGE II              4             21
  STAGE IIA            14             95
  STAGE IIB             4              4
  STAGE IIC             0              1
  STAGE III             3             16
  STAGE IIIA            0             10
  STAGE IIIB            4             37
  STAGE IIIC            4             27
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  FBN2 MUTATED     1   8  29   4
  FBN2 WILD-TYPE   8  60 219  37
D399V4, multiclass
    clus
vv   FBN2 MUTATED FBN2 WILD-TYPE
  T1            1              8
  T2            8             60
  T3           29            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    30   6   6
  FBN2 WILD-TYPE 190  74  60
D399V5, multiclass
    clus
vv   FBN2 MUTATED FBN2 WILD-TYPE
  N0           30            190
  N1            6             74
  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"
D399V6, binary
                cls
clus               0   1
  FBN2 MUTATED    33   1
  FBN2 WILD-TYPE 250  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  FBN2 MUTATED     33    1
  FBN2 WILD-TYPE  250   47
   clus
vv  FBN2 MUTATED FBN2 WILD-TYPE
  0           33            250
  1            1             47
[1] 2 2
[1] FALSE
D399V7, binary
                cls
clus               0   1
  FBN2 MUTATED    18  24
  FBN2 WILD-TYPE 152 173
[1] "tbl2"
                cls
clus             [,1] [,2]
  FBN2 MUTATED     18   24
  FBN2 WILD-TYPE  152  173
        clus
vv       FBN2 MUTATED FBN2 WILD-TYPE
  FEMALE           18            152
  MALE             24            173
[1] 2 2
[1] FALSE
D399V8, binary
                cls
clus               0   1
  FBN2 MUTATED    26  15
  FBN2 WILD-TYPE 291  33
[1] "tbl2"
                cls
clus             [,1] [,2]
  FBN2 MUTATED     26   15
  FBN2 WILD-TYPE  291   33
                               clus
vv                              FBN2 MUTATED FBN2 WILD-TYPE
  COLON ADENOCARCINOMA                    26            291
  COLON MUCINOUS ADENOCARCINOMA           15             33
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  FBN2 MUTATED    29   0   0   4
  FBN2 WILD-TYPE 228   2  22  17
D399V9, multiclass
    clus
vv   FBN2 MUTATED FBN2 WILD-TYPE
  R0           29            228
  R1            0              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"
D399V10, 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
D399V11, 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(400) Variable = DKK2 MUTATION ANALYSIS
D400V1, survival
                sevent
clus2              0   1
  DKK2 MUTATED    19   4
  DKK2 WILD-TYPE 263  69
  DKK2 MUTATED DKK2 WILD-TYPE 
            23            332 
  DKK2 MUTATED DKK2 WILD-TYPE 
             4             69 
$`DKK2 MUTATED`
TCGA-A6-2676 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-6782 TCGA-AA-3554 TCGA-AA-3672 
       42.90        30.44        33.53        20.28        17.95         0.92 
TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3971 TCGA-AD-6964 TCGA-AY-5543 TCGA-AY-6196 
       85.05        19.04        16.08        10.88        15.75         0.20 
TCGA-AZ-4315 TCGA-CK-4952 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6930 TCGA-D5-6932 
       58.39        15.62        15.58         7.53         1.51        11.38 
TCGA-F4-6805 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6588 TCGA-G4-6626 
       16.31        51.75        45.11        26.17        46.75 

$`DKK2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       31.63        29.19        23.61        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        7.04         3.02         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3555 
       14.01        33.99        21.01        13.02        24.00        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       19.00        36.00         5.03        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03         2.01        21.99        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 
       14.50        27.09        16.31         0.95        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       102.44        40.34        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6920 
       17.85         4.80        17.13        12.49        16.14        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-D5-7000 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-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       55.04        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6628 
       91.79        52.80 

  DKK2 MUTATED DKK2 WILD-TYPE 
           0.2            0.0 
  DKK2 MUTATED DKK2 WILD-TYPE 
         85.05         140.38 
  DKK2 MUTATED DKK2 WILD-TYPE 
         17.95          20.98 
[1] "0.2 - 85.0 (17.9)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.2"
D400V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DKK2 MUTATED         2        0        1         9         2         0
  DKK2 WILD-TYPE      62        1       24       100         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DKK2 MUTATED           4          0          2          1        0         1
  DKK2 WILD-TYPE        15         10         39         30       35        12
                vv
clus             STAGE IVB
  DKK2 MUTATED           0
  DKK2 WILD-TYPE         1
D400V3, multiclass
            clus
vv           DKK2 MUTATED DKK2 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             9            100
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             4             15
  STAGE IIIA            0             10
  STAGE IIIB            2             39
  STAGE IIIC            1             30
  STAGE IV              0             35
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 231  37
D400V4, multiclass
    clus
vv   DKK2 MUTATED DKK2 WILD-TYPE
  T1            0              9
  T2            2             66
  T3           17            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
  DKK2 MUTATED    15   5   3
  DKK2 WILD-TYPE 205  75  63
D400V5, multiclass
    clus
vv   DKK2 MUTATED DKK2 WILD-TYPE
  N0           15            205
  N1            5             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"
D400V6, binary
                cls
clus               0   1
  DKK2 MUTATED    19   1
  DKK2 WILD-TYPE 264  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  DKK2 MUTATED     19    1
  DKK2 WILD-TYPE  264   47
   clus
vv  DKK2 MUTATED DKK2 WILD-TYPE
  0           19            264
  1            1             47
[1] 2 2
[1] FALSE
D400V7, 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
D400V8, binary
                cls
clus               0   1
  DKK2 MUTATED    20   3
  DKK2 WILD-TYPE 297  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  DKK2 MUTATED     20    3
  DKK2 WILD-TYPE  297   45
                               clus
vv                              DKK2 MUTATED DKK2 WILD-TYPE
  COLON ADENOCARCINOMA                    20            297
  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 237   2  22  20
D400V9, multiclass
    clus
vv   DKK2 MUTATED DKK2 WILD-TYPE
  R0           20            237
  R1            0              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"
D400V10, 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
D400V11, 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(401) Variable = KIAA1409 MUTATION ANALYSIS
D401V1, survival
                    sevent
clus2                  0   1
  KIAA1409 MUTATED    31   7
  KIAA1409 WILD-TYPE 251  66
  KIAA1409 MUTATED KIAA1409 WILD-TYPE 
                38                317 
  KIAA1409 MUTATED KIAA1409 WILD-TYPE 
                 7                 66 
$`KIAA1409 MUTATED`
TCGA-A6-2672 TCGA-A6-5659 TCGA-A6-5662 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3510 
       46.65        30.44        23.61         3.02         1.02        63.98 
TCGA-AA-3525 TCGA-AA-3556 TCGA-AA-3660 TCGA-AA-3672 TCGA-AA-3680 TCGA-AA-3713 
        8.05        23.01        78.08         0.92        11.01        19.04 
TCGA-AA-3811 TCGA-AA-3815 TCGA-AA-3845 TCGA-AA-3864 TCGA-AA-3977 TCGA-AA-A00J 
       10.06        33.04         0.00        53.00        25.02        18.05 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-5900 TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-6600 
        4.01        34.98         0.07        27.09        58.39        12.10 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4952 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6676 
        0.33         0.10        15.62        12.00        29.03        11.08 
TCGA-CM-6680 TCGA-D5-6536 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       12.03        17.85         9.04        11.64         1.51        12.00 
TCGA-DM-A1D7 TCGA-G4-6304 
       13.32        53.62 

$`KIAA1409 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       31.63        29.19        33.53        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
       20.28         7.04        35.01         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        17.95        29.95        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 
        2.01        14.01        50.04        47.01        15.02         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       19.04        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02        14.93        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.20        14.50        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41        49.41         6.77       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07         0.26         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      102.44        40.34        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        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-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.01        10.06        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 
        7.53        12.39        10.13        12.43        14.30         9.44 
TCGA-D5-6929 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       13.41        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        92.75        49.91        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 
       19.43       107.67        74.56        65.85        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  KIAA1409 MUTATED KIAA1409 WILD-TYPE 
                 0                  0 
  KIAA1409 MUTATED KIAA1409 WILD-TYPE 
             78.08             140.38 
  KIAA1409 MUTATED KIAA1409 WILD-TYPE 
             12.71              21.14 
[1] "0.0 - 78.1 (12.7)"  "0.0 - 140.4 (21.1)"
[1] "hr=" "1.1"
D401V2, 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       20        99         5         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1409 MUTATED           3          1          5          1        4
  KIAA1409 WILD-TYPE        16          9         36         30       31
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA1409 MUTATED           1         0
  KIAA1409 WILD-TYPE        12         1
D401V3, multiclass
            clus
vv           KIAA1409 MUTATED KIAA1409 WILD-TYPE
  STAGE I                   5                 59
  STAGE IA                  0                  1
  STAGE II                  5                 20
  STAGE IIA                10                 99
  STAGE IIB                 3                  5
  STAGE IIC                 0                  1
  STAGE III                 3                 16
  STAGE IIIA                1                  9
  STAGE IIIB                5                 36
  STAGE IIIC                1                 30
  STAGE IV                  4                 31
  STAGE IVA                 1                 12
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of 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  62 224  32
D401V4, multiclass
    clus
vv   KIAA1409 MUTATED KIAA1409 WILD-TYPE
  T1                0                  9
  T2                6                 62
  T3               24                224
  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  73  59
D401V5, multiclass
    clus
vv   KIAA1409 MUTATED KIAA1409 WILD-TYPE
  N0               25                195
  N1                7                 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"
D401V6, binary
                    cls
clus                   0   1
  KIAA1409 MUTATED    32   5
  KIAA1409 WILD-TYPE 251  43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1409 MUTATED     32    5
  KIAA1409 WILD-TYPE  251   43
   clus
vv  KIAA1409 MUTATED KIAA1409 WILD-TYPE
  0               32                251
  1                5                 43
[1] 2 2
[1] FALSE
D401V7, 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
D401V8, binary
                    cls
clus                   0   1
  KIAA1409 MUTATED    30   8
  KIAA1409 WILD-TYPE 287  40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1409 MUTATED     30    8
  KIAA1409 WILD-TYPE  287   40
                               clus
vv                              KIAA1409 MUTATED KIAA1409 WILD-TYPE
  COLON ADENOCARCINOMA                        30                287
  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 228   2  19  18
D401V9, multiclass
    clus
vv   KIAA1409 MUTATED KIAA1409 WILD-TYPE
  R0               29                228
  R1                0                  2
  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"
D401V10, 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
D401V11, 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(402) Variable = SPANXN2 MUTATION ANALYSIS
D402V1, survival
                   sevent
clus2                 0   1
  SPANXN2 MUTATED     8   0
  SPANXN2 WILD-TYPE 274  73
  SPANXN2 MUTATED SPANXN2 WILD-TYPE 
                8               347 
  SPANXN2 MUTATED SPANXN2 WILD-TYPE 
                0                73 
$`SPANXN2 MUTATED`
TCGA-A6-6781 TCGA-AA-3815 TCGA-AA-3950 TCGA-AA-3977 TCGA-AZ-4315 TCGA-D5-6535 
       19.66        33.04        24.00        25.02        58.39        15.12 
TCGA-G4-6307 TCGA-G4-6309 
       55.04        51.75 

$`SPANXN2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       44.68        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  SPANXN2 MUTATED SPANXN2 WILD-TYPE 
            15.12              0.00 
  SPANXN2 MUTATED SPANXN2 WILD-TYPE 
            58.39            140.38 
  SPANXN2 MUTATED SPANXN2 WILD-TYPE 
            29.03             20.02 
[1] "15.1 - 58.4 (29.0)" "0.0 - 140.4 (20.0)"
[1] "hr="     "2.6e+07"
D402V2, 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       25       106         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SPANXN2 MUTATED           0          0          3          1        0
  SPANXN2 WILD-TYPE        19         10         38         30       35
                   vv
clus                STAGE IVA STAGE IVB
  SPANXN2 MUTATED           0         0
  SPANXN2 WILD-TYPE        13         1
D402V3, multiclass
            clus
vv           SPANXN2 MUTATED SPANXN2 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                3               106
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               3                38
  STAGE IIIC               1                30
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SPANXN2 MUTATED     0   1   6   1
  SPANXN2 WILD-TYPE   9  67 242  40
D402V4, multiclass
    clus
vv   SPANXN2 MUTATED SPANXN2 WILD-TYPE
  T1               0                 9
  T2               1                67
  T3               6               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
  SPANXN2 MUTATED     4   4   0
  SPANXN2 WILD-TYPE 216  76  66
D402V5, multiclass
    clus
vv   SPANXN2 MUTATED SPANXN2 WILD-TYPE
  N0               4               216
  N1               4                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"
D402V6, binary
                   cls
clus                  0   1
  SPANXN2 MUTATED     5   0
  SPANXN2 WILD-TYPE 278  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPANXN2 MUTATED      5    0
  SPANXN2 WILD-TYPE  278   48
   clus
vv  SPANXN2 MUTATED SPANXN2 WILD-TYPE
  0               5               278
  1               0                48
[1] 2 2
[1] FALSE
D402V7, 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
D402V8, binary
                   cls
clus                  0   1
  SPANXN2 MUTATED     6   2
  SPANXN2 WILD-TYPE 311  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPANXN2 MUTATED      6    2
  SPANXN2 WILD-TYPE  311   46
                               clus
vv                              SPANXN2 MUTATED SPANXN2 WILD-TYPE
  COLON ADENOCARCINOMA                        6               311
  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 251   2  22  20
D402V9, multiclass
    clus
vv   SPANXN2 MUTATED SPANXN2 WILD-TYPE
  R0               6               251
  R1               0                 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"
D402V10, 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
D402V11, 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(403) Variable = GRM7 MUTATION ANALYSIS
D403V1, survival
                sevent
clus2              0   1
  GRM7 MUTATED    18   4
  GRM7 WILD-TYPE 264  69
  GRM7 MUTATED GRM7 WILD-TYPE 
            22            333 
  GRM7 MUTATED GRM7 WILD-TYPE 
             4             69 
$`GRM7 MUTATED`
TCGA-A6-3809 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6652 TCGA-AA-3662 
       32.75        33.53        22.06         8.38        24.69         6.05 
TCGA-AA-3680 TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3947 TCGA-AA-A00N TCGA-AA-A02W 
       11.01        85.05        14.93        33.01         4.01        41.00 
TCGA-AU-6004 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CK-5913 TCGA-CM-6165 
       27.09         6.77       100.01         0.33        51.32        16.04 
TCGA-CM-6171 TCGA-F4-6807 TCGA-G4-6309 TCGA-G4-6628 
       14.04        16.24        51.75        52.80 

$`GRM7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       31.63        30.44        29.19        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 
       27.09        22.52        25.08        25.18        24.16        21.76 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 
       24.39        23.87        20.12        19.66        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        3.02         1.02        35.01        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       78.08         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       50.04        47.01        15.02         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
       14.01         0.92        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       49.41        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       29.59        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       26.17        91.79        46.75 

  GRM7 MUTATED GRM7 WILD-TYPE 
          0.33           0.00 
  GRM7 MUTATED GRM7 WILD-TYPE 
        100.01         140.38 
  GRM7 MUTATED GRM7 WILD-TYPE 
        23.375         20.120 
[1] "0.3 - 100.0 (23.4)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.4"
D403V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GRM7 MUTATED         6        0        1         8         3         0
  GRM7 WILD-TYPE      58        1       24       101         5         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GRM7 MUTATED           1          0          1          2        2         1
  GRM7 WILD-TYPE        18         10         40         29       33        12
                vv
clus             STAGE IVB
  GRM7 MUTATED           0
  GRM7 WILD-TYPE         1
D403V3, multiclass
            clus
vv           GRM7 MUTATED GRM7 WILD-TYPE
  STAGE I               6             58
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             8            101
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            2             29
  STAGE IV              2             33
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  62 234  36
D403V4, multiclass
    clus
vv   GRM7 MUTATED GRM7 WILD-TYPE
  T1            0              9
  T2            6             62
  T3           14            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
  GRM7 MUTATED    20   1   4
  GRM7 WILD-TYPE 200  79  62
D403V5, multiclass
    clus
vv   GRM7 MUTATED GRM7 WILD-TYPE
  N0           20            200
  N1            1             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"
D403V6, binary
                cls
clus               0   1
  GRM7 MUTATED    19   3
  GRM7 WILD-TYPE 264  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRM7 MUTATED     19    3
  GRM7 WILD-TYPE  264   45
   clus
vv  GRM7 MUTATED GRM7 WILD-TYPE
  0           19            264
  1            3             45
[1] 2 2
[1] FALSE
D403V7, 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
D403V8, binary
                cls
clus               0   1
  GRM7 MUTATED    21   4
  GRM7 WILD-TYPE 296  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRM7 MUTATED     21    4
  GRM7 WILD-TYPE  296   44
                               clus
vv                              GRM7 MUTATED GRM7 WILD-TYPE
  COLON ADENOCARCINOMA                    21            296
  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 241   2  20  18
D403V9, multiclass
    clus
vv   GRM7 MUTATED GRM7 WILD-TYPE
  R0           16            241
  R1            0              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"
D403V10, 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
D403V11, 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(404) Variable = EPHA3 MUTATION ANALYSIS
D404V1, survival
                 sevent
clus2               0   1
  EPHA3 MUTATED    42  12
  EPHA3 WILD-TYPE 240  61
  EPHA3 MUTATED EPHA3 WILD-TYPE 
             54             301 
  EPHA3 MUTATED EPHA3 WILD-TYPE 
             12              61 
$`EPHA3 MUTATED`
TCGA-A6-5660 TCGA-A6-5661 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3516 
       29.19        33.53         3.02        35.01        63.98        13.02 
TCGA-AA-3544 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3688 TCGA-AA-3713 TCGA-AA-3811 
       14.01        13.94        61.02        19.00        19.04        10.06 
TCGA-AA-3833 TCGA-AA-3845 TCGA-AA-3861 TCGA-AA-3869 TCGA-AA-3949 TCGA-AA-3950 
       15.95         0.00        30.05        27.02        26.01        24.00 
TCGA-AA-3966 TCGA-AA-A00E TCGA-AA-A010 TCGA-AD-6889 TCGA-AD-6899 TCGA-AD-6965 
        2.01        30.02        34.98        56.55         5.79         0.20 
TCGA-AU-6004 TCGA-AY-5543 TCGA-AZ-5403 TCGA-AZ-6600 TCGA-CA-6717 TCGA-CK-4952 
       27.09        15.75        62.79        12.10         0.33        15.62 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CM-5344 TCGA-CM-6162 TCGA-CM-6171 TCGA-CM-6674 
       51.32        21.14        22.03        12.00        14.04        12.95 
TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-6533 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6926 
       12.03        12.26         1.32        16.14        15.58         9.04 
TCGA-D5-6928 TCGA-D5-6930 TCGA-DM-A1D0 TCGA-DM-A1D7 TCGA-DM-A1HB TCGA-DM-A28G 
       11.64         1.51       130.65        13.32       135.65        60.79 
TCGA-F4-6460 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6626 
       13.38        44.68        51.75        22.09        26.17        46.75 

$`EPHA3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       32.91        31.63        30.44        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3511 TCGA-AA-3514 
       19.66        20.28         7.04         1.02         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01        12.99         0.99        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        19.99        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
       11.01         5.98        37.05        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       26.99        19.04        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
        1.02        17.98        38.99        37.02        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        53.00        17.03        24.03 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       33.01         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37         4.21         0.79 
TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AU-3779 TCGA-AY-4070 
        0.72        22.42        27.42        10.88        14.50        16.31 
TCGA-AY-4071 TCGA-AY-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-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13        83.80        22.36        61.41        49.41         6.77 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 
        0.10         1.35        17.56       102.44        40.34        49.08 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99         2.93         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 
       16.01        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-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-D5-5539 TCGA-D5-5540 
       11.08        11.01        10.06        45.40        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       11.51        20.19        18.25        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-D5-6927 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 
       12.43        14.30         9.44        13.41        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-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K 
        6.12        81.37       119.93        35.97       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 
       19.43       107.67        74.56        65.85        53.62        55.04 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       45.11        36.72        36.00        13.78        35.80        91.79 
TCGA-G4-6628 
       52.80 

  EPHA3 MUTATED EPHA3 WILD-TYPE 
              0               0 
  EPHA3 MUTATED EPHA3 WILD-TYPE 
         135.65          140.38 
  EPHA3 MUTATED EPHA3 WILD-TYPE 
          17.57           20.98 
[1] "0.0 - 135.7 (17.6)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1"  
D404V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EPHA3 MUTATED         6        0        4        22         2         0
  EPHA3 WILD-TYPE      58        1       21        87         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EPHA3 MUTATED           4          1          9          2        4         1
  EPHA3 WILD-TYPE        15          9         32         29       31        12
                 vv
clus              STAGE IVB
  EPHA3 MUTATED           0
  EPHA3 WILD-TYPE         1
D404V3, multiclass
            clus
vv           EPHA3 MUTATED EPHA3 WILD-TYPE
  STAGE I                6              58
  STAGE IA               0               1
  STAGE II               4              21
  STAGE IIA             22              87
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              4              15
  STAGE IIIA             1               9
  STAGE IIIB             9              32
  STAGE IIIC             2              29
  STAGE IV               4              31
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  39   9
  EPHA3 WILD-TYPE   8  61 209  32
D404V4, multiclass
    clus
vv   EPHA3 MUTATED EPHA3 WILD-TYPE
  T1             1               8
  T2             7              61
  T3            39             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  12   8
  EPHA3 WILD-TYPE 184  68  58
D404V5, multiclass
    clus
vv   EPHA3 MUTATED EPHA3 WILD-TYPE
  N0            36             184
  N1            12              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"
D404V6, binary
                 cls
clus                0   1
  EPHA3 MUTATED    45   5
  EPHA3 WILD-TYPE 238  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA3 MUTATED     45    5
  EPHA3 WILD-TYPE  238   43
   clus
vv  EPHA3 MUTATED EPHA3 WILD-TYPE
  0            45             238
  1             5              43
[1] 2 2
[1] FALSE
D404V7, binary
                 cls
clus                0   1
  EPHA3 MUTATED    28  28
  EPHA3 WILD-TYPE 142 169
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA3 MUTATED     28   28
  EPHA3 WILD-TYPE  142  169
        clus
vv       EPHA3 MUTATED EPHA3 WILD-TYPE
  FEMALE            28             142
  MALE              28             169
[1] 2 2
[1] FALSE
D404V8, binary
                 cls
clus                0   1
  EPHA3 MUTATED    45  11
  EPHA3 WILD-TYPE 272  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA3 MUTATED     45   11
  EPHA3 WILD-TYPE  272   37
                               clus
vv                              EPHA3 MUTATED EPHA3 WILD-TYPE
  COLON ADENOCARCINOMA                     45             272
  COLON MUCINOUS ADENOCARCINOMA            11              37
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  EPHA3 MUTATED    36   0   3   5
  EPHA3 WILD-TYPE 221   2  19  16
D404V9, multiclass
    clus
vv   EPHA3 MUTATED EPHA3 WILD-TYPE
  R0            36             221
  R1             0               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"
D404V10, 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    29
  EPHA3 WILD-TYPE                        14   147
D404V11, 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                                       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(405) Variable = KIT MUTATION ANALYSIS
D405V1, survival
               sevent
clus2             0   1
  KIT MUTATED    75  17
  KIT WILD-TYPE 207  56
  KIT MUTATED KIT WILD-TYPE 
           92           263 
  KIT MUTATED KIT WILD-TYPE 
           17            56 
$`KIT MUTATED`
TCGA-A6-3809 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5665 
       32.75        31.63        30.44        29.19        33.53        22.06 
TCGA-A6-5666 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6781 
       32.71         8.38        25.18        24.69        23.87        19.66 
TCGA-AA-3492 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-A00N 
        3.02        61.02         6.05        85.05        19.04         4.01 
TCGA-AA-A010 TCGA-AA-A024 TCGA-AD-5900 TCGA-AD-6890 TCGA-AD-6899 TCGA-AU-3779 
       34.98        39.06         0.07         0.79         5.79        14.50 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-5403 TCGA-AZ-5407 
        0.20        21.44        17.82        58.39        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 
       49.41       100.01         5.23         3.29         0.26         0.33 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       17.56       102.44        15.62        51.32        21.99        21.14 
TCGA-CK-6748 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5868 
        2.01        13.02        22.03        30.08         5.03        17.03 
TCGA-CM-6161 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6170 TCGA-CM-6171 
       15.02        29.03        16.04        14.99        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-D5-5538 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       11.01        12.95        12.26        11.51        20.19        18.25 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6927 TCGA-D5-6929 
        4.80        17.13        16.14        15.58         9.44        13.41 
TCGA-D5-6930 TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA 
        1.51       130.65        49.91        13.32       140.38         7.50 
TCGA-DM-A1HA TCGA-DM-A28C TCGA-DM-A28E TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
      131.51        81.37       119.93         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6808 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6304 TCGA-G4-6307 
        6.18        33.67        19.43       107.67        53.62        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 
       35.80        26.17 

$`KIT WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6649 
       23.61        22.09        27.09        22.52        25.08        24.16 
TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       21.76        24.39        20.12        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       19.99        13.94        19.99        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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        35.01        26.01        37.02        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37         4.21        56.55 
TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 
        0.72        22.42        27.42        10.88         0.20        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       16.31         0.95        15.75         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 
       22.36         6.77        12.10        29.56        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6718 
        1.94         2.24         3.06         3.25         0.07         0.10 
TCGA-CA-6719 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
        1.35        40.34        49.08         2.93       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5860 
       20.02        37.02        25.02        29.06        22.98        16.01 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6166 
       15.02        15.02        15.02        12.00        14.04        21.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       12.99        13.02        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6533 
       10.06        12.03        45.40        19.59        13.51         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6920 
       43.27        15.12        17.85        12.49         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6931 
       10.13        12.43        14.30         9.04        11.64        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 
       11.38        10.26       119.70        24.43        38.20        92.75 
TCGA-DM-A1D8 TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28F 
       12.59        44.32       135.65       139.17         6.12        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       60.79       117.07        98.24        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6299 
       29.59        16.24        13.25         0.53        35.41        74.56 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       65.85        44.68        91.79        46.75        52.80 

  KIT MUTATED KIT WILD-TYPE 
         0.07          0.00 
  KIT MUTATED KIT WILD-TYPE 
       140.38        139.17 
  KIT MUTATED KIT WILD-TYPE 
       19.545        20.980 
[1] "0.1 - 140.4 (19.5)" "0.0 - 139.2 (21.0)"
[1] "hr=" "1.4"
D405V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIT MUTATED        12        1        6        30         4         1
  KIT WILD-TYPE      52        0       19        79         4         0
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KIT MUTATED           5          1         16          8        6         5
  KIT WILD-TYPE        14          9         25         23       29         8
               vv
clus            STAGE IVB
  KIT MUTATED           0
  KIT WILD-TYPE         1
D405V3, multiclass
            clus
vv           KIT MUTATED KIT WILD-TYPE
  STAGE I             12            52
  STAGE IA             1             0
  STAGE II             6            19
  STAGE IIA           30            79
  STAGE IIB            4             4
  STAGE IIC            1             0
  STAGE III            5            14
  STAGE IIIA           1             9
  STAGE IIIB          16            25
  STAGE IIIC           8            23
  STAGE IV             6            29
  STAGE IVA            5             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  58 180  28
D405V4, multiclass
    clus
vv   KIT MUTATED KIT WILD-TYPE
  T1           4             5
  T2          10            58
  T3          68           180
  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  55  54
D405V5, multiclass
    clus
vv   KIT MUTATED KIT WILD-TYPE
  N0          59           161
  N1          25            55
  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"
D405V6, binary
               cls
clus              0   1
  KIT MUTATED    71  10
  KIT WILD-TYPE 212  38
[1] "tbl2"
               cls
clus            [,1] [,2]
  KIT MUTATED     71   10
  KIT WILD-TYPE  212   38
   clus
vv  KIT MUTATED KIT WILD-TYPE
  0          71           212
  1          10            38
[1] 2 2
[1] FALSE
D405V7, 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
D405V8, binary
               cls
clus              0   1
  KIT MUTATED    82  14
  KIT WILD-TYPE 235  34
[1] "tbl2"
               cls
clus            [,1] [,2]
  KIT MUTATED     82   14
  KIT WILD-TYPE  235   34
                               clus
vv                              KIT MUTATED KIT WILD-TYPE
  COLON ADENOCARCINOMA                   82           235
  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 194   2  19  12
D405V9, multiclass
    clus
vv   KIT MUTATED KIT WILD-TYPE
  R0          63           194
  R1           0             2
  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"
D405V10, 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
D405V11, 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(406) Variable = GRM8 MUTATION ANALYSIS
D406V1, survival
                sevent
clus2              0   1
  GRM8 MUTATED    14   6
  GRM8 WILD-TYPE 268  67
  GRM8 MUTATED GRM8 WILD-TYPE 
            20            335 
  GRM8 MUTATED GRM8 WILD-TYPE 
             6             67 
$`GRM8 MUTATED`
TCGA-A6-5661 TCGA-A6-5665 TCGA-AA-3489 TCGA-AA-3715 TCGA-AA-3977 TCGA-AA-A00N 
       33.53        22.06         7.04        19.04        25.02         4.01 
TCGA-AA-A010 TCGA-AY-6196 TCGA-AZ-4315 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-CA-6717 
       34.98         0.20        58.39        62.79        49.41         0.33 
TCGA-CA-6718 TCGA-CM-5860 TCGA-CM-6677 TCGA-D5-6927 TCGA-F4-6805 TCGA-F4-6856 
        0.10        16.01        11.08         9.44        16.31        19.43 
TCGA-G4-6303 TCGA-G4-6309 
       65.85        51.75 

$`GRM8 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        15.75        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       83.80        22.36        61.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07         0.26         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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-6678 TCGA-CM-6679 
       11.01        12.95        13.05        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       35.87         1.55        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 
        0.53        35.41       107.67        74.56        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  GRM8 MUTATED GRM8 WILD-TYPE 
           0.1            0.0 
  GRM8 MUTATED GRM8 WILD-TYPE 
         65.85         140.38 
  GRM8 MUTATED GRM8 WILD-TYPE 
        19.235         20.280 
[1] "0.1 - 65.8 (19.2)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.4"
D406V2, 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       21       100         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        19         10         40         30       34        13
                vv
clus             STAGE IVB
  GRM8 MUTATED           0
  GRM8 WILD-TYPE         1
D406V3, multiclass
            clus
vv           GRM8 MUTATED GRM8 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              4             21
  STAGE IIA             9            100
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            1             30
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GRM8 MUTATED     0   2  16   3
  GRM8 WILD-TYPE   9  66 232  38
D406V4, multiclass
    clus
vv   GRM8 MUTATED GRM8 WILD-TYPE
  T1            0              9
  T2            2             66
  T3           16            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
  GRM8 MUTATED    18   2   1
  GRM8 WILD-TYPE 202  78  65
D406V5, multiclass
    clus
vv   GRM8 MUTATED GRM8 WILD-TYPE
  N0           18            202
  N1            2             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"
D406V6, binary
                cls
clus               0   1
  GRM8 MUTATED    15   1
  GRM8 WILD-TYPE 268  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRM8 MUTATED     15    1
  GRM8 WILD-TYPE  268   47
   clus
vv  GRM8 MUTATED GRM8 WILD-TYPE
  0           15            268
  1            1             47
[1] 2 2
[1] FALSE
D406V7, 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
D406V8, binary
                cls
clus               0   1
  GRM8 MUTATED    17   4
  GRM8 WILD-TYPE 300  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRM8 MUTATED     17    4
  GRM8 WILD-TYPE  300   44
                               clus
vv                              GRM8 MUTATED GRM8 WILD-TYPE
  COLON ADENOCARCINOMA                    17            300
  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 242   2  22  18
D406V9, multiclass
    clus
vv   GRM8 MUTATED GRM8 WILD-TYPE
  R0           15            242
  R1            0              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"
D406V10, 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
D406V11, 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(407) Variable = APOB MUTATION ANALYSIS
D407V1, survival
                sevent
clus2              0   1
  APOB MUTATED    44   7
  APOB WILD-TYPE 238  66
  APOB MUTATED APOB WILD-TYPE 
            51            304 
  APOB MUTATED APOB WILD-TYPE 
             7             66 
$`APOB MUTATED`
TCGA-A6-2672 TCGA-A6-3809 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5665 TCGA-AA-3489 
       46.65        32.75        29.19        23.61        22.06         7.04 
TCGA-AA-3525 TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3710 TCGA-AA-3713 
        8.05        21.01        29.95        23.01        26.99        19.04 
TCGA-AA-3950 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A00U TCGA-AA-A010 TCGA-AA-A01P 
       24.00        18.05         4.01        17.03        34.98        38.07 
TCGA-AA-A01Q TCGA-AA-A02F TCGA-AD-6964 TCGA-AU-6004 TCGA-AY-6196 TCGA-AZ-4315 
        1.02        39.98        10.88        27.09         0.20        58.39 
TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6607 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 
       62.79        49.41         3.19         3.29         0.26         0.33 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-5913 TCGA-CK-5914 TCGA-CM-4743 TCGA-CM-5348 
        1.35        17.56        51.32        21.99        23.05        22.98 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-6168 TCGA-D5-5538 TCGA-D5-5541 TCGA-D5-6538 
       16.01        15.02        12.99        12.26        11.51        17.13 
TCGA-D5-6927 TCGA-D5-6931 TCGA-DM-A0X9 TCGA-DM-A1D0 TCGA-F4-6460 TCGA-F4-6854 
        9.44        12.00       119.70       130.65        13.38         0.53 
TCGA-F4-6855 TCGA-G4-6586 TCGA-G4-6628 
       35.41        35.80        52.80 

$`APOB WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       34.65        33.34        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       30.44        33.53        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 
        8.38        25.08        25.18        24.16        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3492 
       24.39        23.87        20.12        19.66        20.28         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 
       26.01        12.99         0.99        14.01        33.99        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       24.00        17.95        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       27.02        42.02         0.99        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01R 
       10.98        32.02        12.00        31.00        31.00        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       51.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        14.50        16.31         0.95        15.75        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 
       17.82         1.41         5.13        83.80        22.36        61.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6718 
        1.94         2.24         3.06         3.25         0.07         0.10 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5916 TCGA-CK-6747 
      102.44        40.34        15.62        49.08        21.14         2.93 
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-5862 TCGA-CM-5863 TCGA-CM-5864 
       29.06        22.03        30.08         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00        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-D5-5539 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6532 
       12.03        45.40        19.59        13.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 
        1.32        43.27        15.12        17.85         4.80        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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         1.51        11.38 
TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       10.26        24.43        38.20        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
      117.07        98.24         8.61        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       13.78        26.17        91.79        46.75 

  APOB MUTATED APOB WILD-TYPE 
           0.2            0.0 
  APOB MUTATED APOB WILD-TYPE 
        130.65         140.38 
  APOB MUTATED APOB WILD-TYPE 
        21.010         20.155 
[1] "0.2 - 130.7 (21.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.6"
D407V2, 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       20        88         4         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  APOB MUTATED           1          0         10          3        3         2
  APOB WILD-TYPE        18         10         31         28       32        11
                vv
clus             STAGE IVB
  APOB MUTATED           0
  APOB WILD-TYPE         1
D407V3, multiclass
            clus
vv           APOB MUTATED APOB WILD-TYPE
  STAGE I               4             60
  STAGE IA              0              1
  STAGE II              5             20
  STAGE IIA            21             88
  STAGE IIB             4              4
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB           10             31
  STAGE IIIC            3             28
  STAGE IV              3             32
  STAGE IVA             2             11
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  64 208  31
D407V4, multiclass
    clus
vv   APOB MUTATED APOB WILD-TYPE
  T1            0              9
  T2            4             64
  T3           40            208
  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  68  59
D407V5, multiclass
    clus
vv   APOB MUTATED APOB WILD-TYPE
  N0           35            185
  N1           12             68
  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"
D407V6, binary
                cls
clus               0   1
  APOB MUTATED    43   4
  APOB WILD-TYPE 240  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  APOB MUTATED     43    4
  APOB WILD-TYPE  240   44
   clus
vv  APOB MUTATED APOB WILD-TYPE
  0           43            240
  1            4             44
[1] 2 2
[1] FALSE
D407V7, 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
D407V8, binary
                cls
clus               0   1
  APOB MUTATED    46   7
  APOB WILD-TYPE 271  41
[1] "tbl2"
                cls
clus             [,1] [,2]
  APOB MUTATED     46    7
  APOB WILD-TYPE  271   41
                               clus
vv                              APOB MUTATED APOB WILD-TYPE
  COLON ADENOCARCINOMA                    46            271
  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 220   2  20  14
D407V9, multiclass
    clus
vv   APOB MUTATED APOB WILD-TYPE
  R0           37            220
  R1            0              2
  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"
D407V10, 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
D407V11, 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(408) Variable = PIK3CA MUTATION ANALYSIS
D408V1, survival
                  sevent
clus2                0   1
  PIK3CA MUTATED   135  38
  PIK3CA WILD-TYPE 147  35
  PIK3CA MUTATED PIK3CA WILD-TYPE 
             173              182 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              38               35 
$`PIK3CA MUTATED`
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        14.53        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6141 
       29.19        33.53        23.61        22.06        32.71         8.38 
TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 
       24.16        24.69        23.87        20.12        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3655 
        3.02         1.02        35.01        63.98         6.97        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3673 TCGA-AA-3696 TCGA-AA-3697 
       78.08         6.05         6.97        50.04         5.03        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3837 
       19.04        19.04        35.05        33.04         0.99        38.99 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
       10.06         0.00         0.00        30.05        53.00        17.03 
TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3956 TCGA-AA-3977 
       31.00        12.99        33.01        24.00        34.03        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01V TCGA-AA-A02O 
        4.01        34.98        31.00        31.00        35.01         0.92 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6890 
       39.98        18.05        40.96         0.07        21.37         0.79 
TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4616 TCGA-AZ-4682 
       15.75        21.44        17.82        58.39         5.13        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6606 
       62.79        61.41        49.41         6.77       100.01        11.74 
TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        1.94         3.06         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 
      102.44        40.34        15.62        49.08        21.99        21.14 
TCGA-CK-6747 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5344 
        2.93        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        16.01        15.02         5.03        15.02        15.02 
TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 
       12.00        29.03        21.99        12.99        13.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5538 
       11.01        12.95        11.08        11.01        12.03        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 
       19.59        13.51        11.51        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-A285 TCGA-DM-A28C 
      140.38        44.32       131.51       135.65         6.12        81.37 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       35.97        60.79       117.07         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        6.18        35.87        16.31        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        45.11        36.72        36.00 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        52.80 

$`PIK3CA WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-5664 TCGA-A6-6137 TCGA-A6-6138 
       16.57        34.65        36.53        22.09        27.09        22.52 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3514 
       25.08        25.18        21.76        24.39        19.66         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3664 
       23.01        20.98        19.99        13.94        19.99        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01         0.92        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3710 TCGA-AA-3811 
        5.98        37.05        19.00        36.00        26.99        10.06 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3844 
       25.02         1.02        17.98        15.95        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        17.03        33.07        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       31.07        31.07        24.03        27.02        29.98        18.05 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3966 
        2.01        24.00        26.01         2.01        20.98         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01X 
       38.07         1.02        35.01         1.02        33.04        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02W TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6901 
       14.01        41.00         4.21        56.55         0.72        22.42 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AZ-4323 TCGA-AZ-4681 TCGA-AZ-6600 
       16.31         0.95         0.20         1.41        83.80        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5796 TCGA-CA-5797 
       29.56         5.23         3.19         2.24         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CK-5913 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
        0.07         0.26        51.32         2.01       124.27        20.02 
TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6165 
       29.06        22.98        15.02        17.03        14.04        16.04 
TCGA-CM-6167 TCGA-CM-6170 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6679 TCGA-D5-5537 
       14.99        15.02        13.05        11.08        10.06        45.40 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6539 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6928 
        1.32        15.12        12.49        10.13        14.30        11.64 
TCGA-D5-6930 TCGA-D5-6932 TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1DA 
        1.51        11.38       130.65        92.75        49.91         7.50 
TCGA-DM-A282 TCGA-DM-A28E TCGA-DM-A28K TCGA-F4-6704 TCGA-F4-6806 TCGA-G4-6309 
      139.17       119.93        98.24         1.55        29.59        51.75 
TCGA-G4-6321 TCGA-G4-6626 
       22.09        46.75 

  PIK3CA MUTATED PIK3CA WILD-TYPE 
               0                0 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
          140.38           139.17 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
           20.19            20.50 
[1] "0.0 - 140.4 (20.2)" "0.0 - 139.2 (20.5)"
[1] "hr=" "1"  
D408V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PIK3CA MUTATED        31        1       15        56         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           5          5         19         11        9
  PIK3CA WILD-TYPE        14          5         22         20       26
                  vv
clus               STAGE IVA STAGE IVB
  PIK3CA MUTATED           9         0
  PIK3CA WILD-TYPE         4         1
D408V3, multiclass
            clus
vv           PIK3CA MUTATED PIK3CA WILD-TYPE
  STAGE I                31               33
  STAGE IA                1                0
  STAGE II               15               10
  STAGE IIA              56               53
  STAGE IIB               7                1
  STAGE IIC               1                0
  STAGE III               5               14
  STAGE IIIA              5                5
  STAGE IIIB             19               22
  STAGE IIIC             11               20
  STAGE IV                9               26
  STAGE IVA               9                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  38 129  21
D408V4, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  T1              5                4
  T2             30               38
  T3            119              129
  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  47  42
D408V5, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  N0            118              102
  N1             33               47
  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"
D408V6, binary
                  cls
clus                 0   1
  PIK3CA MUTATED   137  17
  PIK3CA WILD-TYPE 146  31
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED    137   17
  PIK3CA WILD-TYPE  146   31
   clus
vv  PIK3CA MUTATED PIK3CA WILD-TYPE
  0            137              146
  1             17               31
[1] 2 2
[1] FALSE
D408V7, 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
D408V8, binary
                  cls
clus                 0   1
  PIK3CA MUTATED   154  21
  PIK3CA WILD-TYPE 163  27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED    154   21
  PIK3CA WILD-TYPE  163   27
                               clus
vv                              PIK3CA MUTATED PIK3CA WILD-TYPE
  COLON ADENOCARCINOMA                     154              163
  COLON MUCINOUS ADENOCARCINOMA             21               27
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PIK3CA MUTATED   121   1   3  11
  PIK3CA WILD-TYPE 136   1  19  10
D408V9, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  R0            121              136
  R1              1                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"
D408V10, 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
D408V11, 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(409) Variable = MYH1 MUTATION ANALYSIS
D409V1, survival
                sevent
clus2              0   1
  MYH1 MUTATED    24   6
  MYH1 WILD-TYPE 258  67
  MYH1 MUTATED MYH1 WILD-TYPE 
            30            325 
  MYH1 MUTATED MYH1 WILD-TYPE 
             6             67 
$`MYH1 MUTATED`
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5666 TCGA-AA-3492 TCGA-AA-3966 
       30.44        29.19        33.53        32.71         3.02         2.01 
TCGA-AA-3977 TCGA-AA-A00J TCGA-AA-A010 TCGA-AD-6889 TCGA-AD-6890 TCGA-AZ-4315 
       25.02        18.05        34.98        56.55         0.79        58.39 
TCGA-AZ-6601 TCGA-AZ-6605 TCGA-CA-6717 TCGA-CK-4948 TCGA-CK-5913 TCGA-CM-4743 
      100.01         5.23         0.33       102.44        51.32        23.05 
TCGA-CM-5863 TCGA-CM-6162 TCGA-CM-6167 TCGA-CM-6676 TCGA-D5-6535 TCGA-D5-6922 
       15.02        12.00        14.99        11.08        15.12        10.13 
TCGA-D5-6923 TCGA-DM-A1D8 TCGA-DM-A28F TCGA-G4-6306 TCGA-G4-6586 TCGA-G4-6626 
       12.43        12.59        35.97        44.68        35.80        46.75 

$`MYH1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 
       32.91        31.63        23.61        22.09        22.06        27.09 
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 
       22.52         8.38        25.08        25.18        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        7.04         1.02        35.01        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       26.01        24.00         2.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       18.05        40.96         0.07        21.37         4.21         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6606 
       61.41        49.41         6.77        12.10        29.56        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 
        0.07         0.26         0.10         1.35        17.56        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        21.99        21.14         2.93         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        16.01        15.02         5.03 
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-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-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        43.27        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6924 
       12.49        16.14        15.58         7.53        12.39        14.30 
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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        49.91        13.32       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        53.62        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        26.17        91.79 
TCGA-G4-6628 
       52.80 

  MYH1 MUTATED MYH1 WILD-TYPE 
          0.33           0.00 
  MYH1 MUTATED MYH1 WILD-TYPE 
        102.44         140.38 
  MYH1 MUTATED MYH1 WILD-TYPE 
        24.035         20.120 
[1] "0.3 - 102.4 (24.0)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.2"
D409V2, 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       23        98         7         0
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MYH1 MUTATED           0          2          6          2        0         0
  MYH1 WILD-TYPE        19          8         35         29       35        13
                vv
clus             STAGE IVB
  MYH1 MUTATED           0
  MYH1 WILD-TYPE         1
D409V3, multiclass
            clus
vv           MYH1 MUTATED MYH1 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA            11             98
  STAGE IIB             1              7
  STAGE IIC             1              0
  STAGE III             0             19
  STAGE IIIA            2              8
  STAGE IIIB            6             35
  STAGE IIIC            2             29
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MYH1 MUTATED     1   5  21   4
  MYH1 WILD-TYPE   8  63 227  37
D409V4, multiclass
    clus
vv   MYH1 MUTATED MYH1 WILD-TYPE
  T1            1              8
  T2            5             63
  T3           21            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    20   9   2
  MYH1 WILD-TYPE 200  71  64
D409V5, multiclass
    clus
vv   MYH1 MUTATED MYH1 WILD-TYPE
  N0           20            200
  N1            9             71
  N2            2             64
[1] 3 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
  MYH1 MUTATED    26   0
  MYH1 WILD-TYPE 257  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYH1 MUTATED     26    0
  MYH1 WILD-TYPE  257   48
   clus
vv  MYH1 MUTATED MYH1 WILD-TYPE
  0           26            257
  1            0             48
[1] 2 2
[1] FALSE
D409V7, binary
                cls
clus               0   1
  MYH1 MUTATED    13  18
  MYH1 WILD-TYPE 157 179
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYH1 MUTATED     13   18
  MYH1 WILD-TYPE  157  179
        clus
vv       MYH1 MUTATED MYH1 WILD-TYPE
  FEMALE           13            157
  MALE             18            179
[1] 2 2
[1] FALSE
D409V8, binary
                cls
clus               0   1
  MYH1 MUTATED    26   5
  MYH1 WILD-TYPE 291  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYH1 MUTATED     26    5
  MYH1 WILD-TYPE  291   43
                               clus
vv                              MYH1 MUTATED MYH1 WILD-TYPE
  COLON ADENOCARCINOMA                    26            291
  COLON MUCINOUS ADENOCARCINOMA            5             43
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MYH1 MUTATED    18   0   0   3
  MYH1 WILD-TYPE 239   2  22  18
D409V9, multiclass
    clus
vv   MYH1 MUTATED MYH1 WILD-TYPE
  R0           18            239
  R1            0              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"
D409V10, 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
D409V11, 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(410) Variable = TAF1 MUTATION ANALYSIS
D410V1, survival
                sevent
clus2              0   1
  TAF1 MUTATED    16   6
  TAF1 WILD-TYPE 266  67
  TAF1 MUTATED TAF1 WILD-TYPE 
            22            333 
  TAF1 MUTATED TAF1 WILD-TYPE 
             6             67 
$`TAF1 MUTATED`
TCGA-A6-2683 TCGA-A6-5657 TCGA-A6-5665 TCGA-AA-3697 TCGA-AA-3864 TCGA-AA-3977 
       16.57        31.63        22.06        85.05        53.00        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A03F TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 
        4.01        34.98        18.05        58.39         0.33         0.10 
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        51.75 

$`TAF1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       30.44        29.19        33.53        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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-5863 TCGA-CM-5864 
       22.03        22.98        16.01        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-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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-D5-6929 TCGA-D5-6930 
       12.43        14.30         9.04         9.44        13.41         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        11.38        10.26       119.70        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB 
       92.75        49.91        13.32        12.59       140.38        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28F 
      131.51       135.65       139.17         6.12        81.37        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       74.56        65.85        53.62        44.68        55.04        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  TAF1 MUTATED TAF1 WILD-TYPE 
           0.1            0.0 
  TAF1 MUTATED TAF1 WILD-TYPE 
        119.93         140.38 
  TAF1 MUTATED TAF1 WILD-TYPE 
        22.025         20.120 
[1] "0.1 - 119.9 (22.0)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.2"
D410V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TAF1 MUTATED         2        0        1         8         2         0
  TAF1 WILD-TYPE      62        1       24       101         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TAF1 MUTATED           2          1          2          1        1         1
  TAF1 WILD-TYPE        17          9         39         30       34        12
                vv
clus             STAGE IVB
  TAF1 MUTATED           0
  TAF1 WILD-TYPE         1
D410V3, multiclass
            clus
vv           TAF1 MUTATED TAF1 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             8            101
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             2             17
  STAGE IIIA            1              9
  STAGE IIIB            2             39
  STAGE IIIC            1             30
  STAGE IV              1             34
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  65 232  38
D410V4, multiclass
    clus
vv   TAF1 MUTATED TAF1 WILD-TYPE
  T1            0              9
  T2            3             65
  T3           16            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
  TAF1 MUTATED    16   4   2
  TAF1 WILD-TYPE 204  76  64
D410V5, multiclass
    clus
vv   TAF1 MUTATED TAF1 WILD-TYPE
  N0           16            204
  N1            4             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"
D410V6, binary
                cls
clus               0   1
  TAF1 MUTATED    19   2
  TAF1 WILD-TYPE 264  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF1 MUTATED     19    2
  TAF1 WILD-TYPE  264   46
   clus
vv  TAF1 MUTATED TAF1 WILD-TYPE
  0           19            264
  1            2             46
[1] 2 2
[1] FALSE
D410V7, 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
D410V8, binary
                cls
clus               0   1
  TAF1 MUTATED    18   4
  TAF1 WILD-TYPE 299  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF1 MUTATED     18    4
  TAF1 WILD-TYPE  299   44
                               clus
vv                              TAF1 MUTATED TAF1 WILD-TYPE
  COLON ADENOCARCINOMA                    18            299
  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 241   2  22  19
D410V9, multiclass
    clus
vv   TAF1 MUTATED TAF1 WILD-TYPE
  R0           16            241
  R1            0              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"
D410V10, 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
D410V11, 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(411) Variable = ANKRD30A MUTATION ANALYSIS
D411V1, survival
                    sevent
clus2                  0   1
  ANKRD30A MUTATED    22   5
  ANKRD30A WILD-TYPE 260  68
  ANKRD30A MUTATED ANKRD30A WILD-TYPE 
                27                328 
  ANKRD30A MUTATED ANKRD30A WILD-TYPE 
                 5                 68 
$`ANKRD30A MUTATED`
TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-AA-3660 
       14.53        32.91        22.52         8.38        25.08        78.08 
TCGA-AA-3977 TCGA-AA-A010 TCGA-AA-A01Z TCGA-AD-5900 TCGA-AU-3779 TCGA-AZ-4315 
       25.02        34.98        37.02         0.07        14.50        58.39 
TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-6751 TCGA-CM-5862 TCGA-CM-6164 
        0.07         0.33         0.10       124.27         5.03        29.03 
TCGA-CM-6168 TCGA-D5-5537 TCGA-D5-6931 TCGA-DM-A28E TCGA-DM-A28F TCGA-F4-6703 
       12.99        45.40        12.00       119.93        35.97        35.87 
TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6588 
       65.85        55.04        26.17 

$`ANKRD30A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5657 
       16.57        34.65        33.34        32.75        36.53        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 
       32.71        27.09        25.18        24.16        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 
       24.39        23.87        20.12        19.66        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        3.02         1.02        35.01        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       33.04        35.01        26.01        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.25         3.29         0.26         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93         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        16.01 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28H 
      135.65       139.17         6.12        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        13.38        13.45         6.18         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 
       35.41        19.43       107.67        74.56        53.62        44.68 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        91.79        46.75        52.80 

  ANKRD30A MUTATED ANKRD30A WILD-TYPE 
              0.07               0.00 
  ANKRD30A MUTATED ANKRD30A WILD-TYPE 
            124.27             140.38 
  ANKRD30A MUTATED ANKRD30A WILD-TYPE 
             26.17              19.99 
[1] "0.1 - 124.3 (26.2)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.4"
D411V2, 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       23        97         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANKRD30A MUTATED           1          0          3          1        1
  ANKRD30A WILD-TYPE        18         10         38         30       34
                    vv
clus                 STAGE IVA STAGE IVB
  ANKRD30A MUTATED           2         0
  ANKRD30A WILD-TYPE        11         1
D411V3, multiclass
            clus
vv           ANKRD30A MUTATED ANKRD30A WILD-TYPE
  STAGE I                   4                 60
  STAGE IA                  0                  1
  STAGE II                  2                 23
  STAGE IIA                12                 97
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 1                 18
  STAGE IIIA                0                 10
  STAGE IIIB                3                 38
  STAGE IIIC                1                 30
  STAGE IV                  1                 34
  STAGE IVA                 2                 11
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of 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  63 227  39
D411V4, multiclass
    clus
vv   ANKRD30A MUTATED ANKRD30A WILD-TYPE
  T1                0                  9
  T2                5                 63
  T3               21                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
  ANKRD30A MUTATED    19   6   3
  ANKRD30A WILD-TYPE 201  74  63
D411V5, multiclass
    clus
vv   ANKRD30A MUTATED ANKRD30A WILD-TYPE
  N0               19                201
  N1                6                 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"
D411V6, binary
                    cls
clus                   0   1
  ANKRD30A MUTATED    21   3
  ANKRD30A WILD-TYPE 262  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ANKRD30A MUTATED     21    3
  ANKRD30A WILD-TYPE  262   45
   clus
vv  ANKRD30A MUTATED ANKRD30A WILD-TYPE
  0               21                262
  1                3                 45
[1] 2 2
[1] FALSE
D411V7, 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
D411V8, binary
                    cls
clus                   0   1
  ANKRD30A MUTATED    25   3
  ANKRD30A WILD-TYPE 292  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ANKRD30A MUTATED     25    3
  ANKRD30A WILD-TYPE  292   45
                               clus
vv                              ANKRD30A MUTATED ANKRD30A WILD-TYPE
  COLON ADENOCARCINOMA                        25                292
  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 242   2  22  16
D411V9, multiclass
    clus
vv   ANKRD30A MUTATED ANKRD30A WILD-TYPE
  R0               15                242
  R1                0                  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"
D411V10, 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
D411V11, 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(412) Variable = AIFM1 MUTATION ANALYSIS
D412V1, survival
                 sevent
clus2               0   1
  AIFM1 MUTATED    10   1
  AIFM1 WILD-TYPE 272  72
  AIFM1 MUTATED AIFM1 WILD-TYPE 
             11             344 
  AIFM1 MUTATED AIFM1 WILD-TYPE 
              1              72 
$`AIFM1 MUTATED`
TCGA-A6-5659 TCGA-AA-A00J TCGA-AD-6895 TCGA-CA-6718 TCGA-CM-5348 TCGA-CM-5862 
       30.44        18.05         0.72         0.10        22.98         5.03 
TCGA-CM-5863 TCGA-D5-6931 TCGA-DM-A1HB TCGA-G4-6315 TCGA-G4-6321 
       15.02        12.00       135.65        36.72        22.09 

$`AIFM1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.33         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       45.11        36.00        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  AIFM1 MUTATED AIFM1 WILD-TYPE 
            0.1             0.0 
  AIFM1 MUTATED AIFM1 WILD-TYPE 
         135.65          140.38 
  AIFM1 MUTATED AIFM1 WILD-TYPE 
         18.050          20.235 
[1] "0.1 - 135.7 (18.1)" "0.0 - 140.4 (20.2)"
[1] "hr=" "2.2"
D412V2, 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       25       108         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AIFM1 MUTATED           1          0          4          1        1         1
  AIFM1 WILD-TYPE        18         10         37         30       34        12
                 vv
clus              STAGE IVB
  AIFM1 MUTATED           0
  AIFM1 WILD-TYPE         1
D412V3, multiclass
            clus
vv           AIFM1 MUTATED AIFM1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              1             108
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             4              37
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 241  39
D412V4, multiclass
    clus
vv   AIFM1 MUTATED AIFM1 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             7             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
  AIFM1 MUTATED     2   8   1
  AIFM1 WILD-TYPE 218  72  65
D412V5, multiclass
    clus
vv   AIFM1 MUTATED AIFM1 WILD-TYPE
  N0             2             218
  N1             8              72
  N2             1              65
[1] 3 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
  AIFM1 MUTATED     7   2
  AIFM1 WILD-TYPE 276  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AIFM1 MUTATED      7    2
  AIFM1 WILD-TYPE  276   46
   clus
vv  AIFM1 MUTATED AIFM1 WILD-TYPE
  0             7             276
  1             2              46
[1] 2 2
[1] FALSE
D412V7, 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
D412V8, binary
                 cls
clus                0   1
  AIFM1 MUTATED     9   2
  AIFM1 WILD-TYPE 308  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AIFM1 MUTATED      9    2
  AIFM1 WILD-TYPE  308   46
                               clus
vv                              AIFM1 MUTATED AIFM1 WILD-TYPE
  COLON ADENOCARCINOMA                      9             308
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  AIFM1 MUTATED     8   0   0   1
  AIFM1 WILD-TYPE 249   2  22  20
D412V9, multiclass
    clus
vv   AIFM1 MUTATED AIFM1 WILD-TYPE
  R0             8             249
  R1             0               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"
D412V10, 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
D412V11, 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(413) Variable = PTPRD MUTATION ANALYSIS
D413V1, survival
                 sevent
clus2               0   1
  PTPRD MUTATED    25   6
  PTPRD WILD-TYPE 257  67
  PTPRD MUTATED PTPRD WILD-TYPE 
             31             324 
  PTPRD MUTATED PTPRD WILD-TYPE 
              6              67 
$`PTPRD MUTATED`
TCGA-A6-2677 TCGA-A6-5659 TCGA-A6-5660 TCGA-AA-3660 TCGA-AA-3811 TCGA-AA-3947 
       24.33        30.44        29.19        78.08        10.06        33.01 
TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01P TCGA-AY-6196 
        2.01        25.02         4.01        34.98        38.07         0.20 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-CA-6717 TCGA-CK-5912 TCGA-CK-5913 TCGA-CM-4743 
       62.79        61.41         0.33        49.08        51.32        23.05 
TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5860 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6171 
       13.02        22.03        16.01        12.00        14.04        14.04 
TCGA-CM-6674 TCGA-D5-5539 TCGA-D5-5540 TCGA-DM-A28E TCGA-DM-A28K TCGA-G4-6304 
       12.95        19.59        13.51       119.93        98.24        53.62 
TCGA-G4-6588 
       26.17 

$`PTPRD WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        42.90        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       31.63        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        19.04        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 
       18.05        31.00         2.01        12.99        24.00        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       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        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        15.75        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-6598 
       58.39         1.41         5.13        83.80        22.36        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       40.34        15.62        21.99        21.14         2.93         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        12.26        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G 
      135.65       139.17         6.12        81.37        35.97        60.79 
TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
      117.07         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        52.80 

  PTPRD MUTATED PTPRD WILD-TYPE 
            0.2             0.0 
  PTPRD MUTATED PTPRD WILD-TYPE 
         119.93          140.38 
  PTPRD MUTATED PTPRD WILD-TYPE 
         24.330          20.005 
[1] "0.2 - 119.9 (24.3)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.4"
D413V2, 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       23        97         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        17          9         39         28       35        13
                 vv
clus              STAGE IVB
  PTPRD MUTATED           0
  PTPRD WILD-TYPE         1
D413V3, multiclass
            clus
vv           PTPRD MUTATED PTPRD WILD-TYPE
  STAGE I                5              59
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA             12              97
  STAGE IIB              4               4
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             1               9
  STAGE IIIB             2              39
  STAGE IIIC             3              28
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PTPRD MUTATED     2   4  22   4
  PTPRD WILD-TYPE   7  64 226  37
D413V4, multiclass
    clus
vv   PTPRD MUTATED PTPRD WILD-TYPE
  T1             2               7
  T2             4              64
  T3            22             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
  PTPRD MUTATED    24   4   4
  PTPRD WILD-TYPE 196  76  62
D413V5, multiclass
    clus
vv   PTPRD MUTATED PTPRD WILD-TYPE
  N0            24             196
  N1             4              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"
D413V6, binary
                 cls
clus                0   1
  PTPRD MUTATED    27   0
  PTPRD WILD-TYPE 256  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRD MUTATED     27    0
  PTPRD WILD-TYPE  256   48
   clus
vv  PTPRD MUTATED PTPRD WILD-TYPE
  0            27             256
  1             0              48
[1] 2 2
[1] FALSE
D413V7, 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
D413V8, binary
                 cls
clus                0   1
  PTPRD MUTATED    24   8
  PTPRD WILD-TYPE 293  40
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRD MUTATED     24    8
  PTPRD WILD-TYPE  293   40
                               clus
vv                              PTPRD MUTATED PTPRD WILD-TYPE
  COLON ADENOCARCINOMA                     24             293
  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 235   2  22  18
D413V9, multiclass
    clus
vv   PTPRD MUTATED PTPRD WILD-TYPE
  R0            22             235
  R1             0               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"
D413V10, 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
D413V11, 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(414) Variable = CSMD3 MUTATION ANALYSIS
D414V1, survival
                 sevent
clus2               0   1
  CSMD3 MUTATED    67  17
  CSMD3 WILD-TYPE 215  56
  CSMD3 MUTATED CSMD3 WILD-TYPE 
             84             271 
  CSMD3 MUTATED CSMD3 WILD-TYPE 
             17              56 
$`CSMD3 MUTATED`
TCGA-A6-2676 TCGA-A6-3809 TCGA-A6-5660 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6653 
       42.90        32.75        29.19        27.09         8.38        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3511 
       23.87        20.12        19.66         3.02        63.98         6.97 
TCGA-AA-3516 TCGA-AA-3525 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3660 TCGA-AA-3692 
       13.02         8.05        17.95        29.95        78.08        36.00 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3821 TCGA-AA-3861 TCGA-AA-3950 
       85.05        19.04        19.04         1.02        30.05        24.00 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-A00E TCGA-AA-A00J 
        2.01        21.99        13.05        25.02        30.02        18.05 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q TCGA-AA-A01Z TCGA-AD-6889 TCGA-AD-6895 
        4.01        34.98         1.02        37.02        56.55         0.72 
TCGA-AY-5543 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 
       15.75        58.39        61.41         6.77       100.01        29.56 
TCGA-CA-5254 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        2.24         3.29         0.07         0.26         0.33         0.10 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-5916 TCGA-CM-4744 TCGA-CM-4752 TCGA-CM-5348 
       17.56       102.44        21.14        20.02        13.02        22.98 
TCGA-CM-5860 TCGA-CM-6167 TCGA-CM-6171 TCGA-CM-6674 TCGA-D5-6533 TCGA-D5-6535 
       16.01        14.99        14.04        12.95         1.32        15.12 
TCGA-D5-6540 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D0 
       16.14        11.64        13.41        10.26       119.70       130.65 
TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A285 TCGA-DM-A28H TCGA-DM-A28K 
       12.59         7.50        44.32         6.12       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6807 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6303 TCGA-G4-6304 
        8.61        16.24        35.41        19.43        65.85        53.62 
TCGA-G4-6307 TCGA-G4-6317 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6628 
       55.04        36.00        35.80        26.17        46.75        52.80 

$`CSMD3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       34.65        33.34        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       30.44        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 
       22.52        25.08        25.18        24.16        21.76        24.69 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3514 TCGA-AA-3517 
       20.28         7.04         1.02        35.01         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 
        1.02         9.07        24.03        37.05        36.03        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       24.00        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
       37.05        19.00         5.03        26.99        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       33.04         0.99        25.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3972 
       26.01         2.01        20.98        34.03        16.08        50.99 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F 
        7.96        27.02        13.94        38.04        19.00        34.03 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       35.01        26.01        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 
       40.96         0.07        21.37         4.21         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 
        5.13        83.80        22.36        62.79        49.41        12.10 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19         1.94         3.06         3.25 
TCGA-CA-6719 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
        1.35        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 
        2.93         2.01       124.27        23.05        37.02        25.02 
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-6162 TCGA-CM-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-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       18.25        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-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0XD 
        9.04         9.44         1.51        12.00        11.38        24.43 
TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1HA 
       38.20        92.75        49.91        13.32       140.38       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      135.65       139.17        81.37       119.93        35.97        60.79 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-G4-6293 TCGA-G4-6299 
       29.59        33.67        13.25         0.53       107.67        74.56 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 
       44.68        51.75        45.11        36.72        22.09        13.78 
TCGA-G4-6625 
       91.79 

  CSMD3 MUTATED CSMD3 WILD-TYPE 
           0.07            0.00 
  CSMD3 MUTATED CSMD3 WILD-TYPE 
         130.65          140.38 
  CSMD3 MUTATED CSMD3 WILD-TYPE 
          19.84           20.98 
[1] "0.1 - 130.7 (19.8)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.2"
D414V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CSMD3 MUTATED        12        0        9        28         5         0
  CSMD3 WILD-TYPE      52        1       16        81         3         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CSMD3 MUTATED           2          1         10          7        6         2
  CSMD3 WILD-TYPE        17          9         31         24       29        11
                 vv
clus              STAGE IVB
  CSMD3 MUTATED           0
  CSMD3 WILD-TYPE         1
D414V3, multiclass
            clus
vv           CSMD3 MUTATED CSMD3 WILD-TYPE
  STAGE I               12              52
  STAGE IA               0               1
  STAGE II               9              16
  STAGE IIA             28              81
  STAGE IIB              5               3
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             1               9
  STAGE IIIB            10              31
  STAGE IIIC             7              24
  STAGE IV               6              29
  STAGE IVA              2              11
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  56 188  29
D414V4, multiclass
    clus
vv   CSMD3 MUTATED CSMD3 WILD-TYPE
  T1             2               7
  T2            12              56
  T3            60             188
  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  62  56
D414V5, multiclass
    clus
vv   CSMD3 MUTATED CSMD3 WILD-TYPE
  N0            58             162
  N1            18              62
  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"
D414V6, binary
                 cls
clus                0   1
  CSMD3 MUTATED    70   7
  CSMD3 WILD-TYPE 213  41
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CSMD3 MUTATED     70    7
  CSMD3 WILD-TYPE  213   41
   clus
vv  CSMD3 MUTATED CSMD3 WILD-TYPE
  0            70             213
  1             7              41
[1] 2 2
[1] FALSE
D414V7, 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
D414V8, binary
                 cls
clus                0   1
  CSMD3 MUTATED    68  18
  CSMD3 WILD-TYPE 249  30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CSMD3 MUTATED     68   18
  CSMD3 WILD-TYPE  249   30
                               clus
vv                              CSMD3 MUTATED CSMD3 WILD-TYPE
  COLON ADENOCARCINOMA                     68             249
  COLON MUCINOUS ADENOCARCINOMA            18              30
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CSMD3 MUTATED    52   0   3   8
  CSMD3 WILD-TYPE 205   2  19  13
D414V9, multiclass
    clus
vv   CSMD3 MUTATED CSMD3 WILD-TYPE
  R0            52             205
  R1             0               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"
D414V10, 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
D414V11, 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(415) Variable = USH2A MUTATION ANALYSIS
D415V1, survival
                 sevent
clus2               0   1
  USH2A MUTATED    59  13
  USH2A WILD-TYPE 223  60
  USH2A MUTATED USH2A WILD-TYPE 
             72             283 
  USH2A MUTATED USH2A WILD-TYPE 
             13              60 
$`USH2A MUTATED`
TCGA-A6-5660 TCGA-A6-6141 TCGA-A6-6649 TCGA-A6-6654 TCGA-A6-6781 TCGA-AA-3489 
       29.19         8.38        24.16        23.87        19.66         7.04 
TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3560 
        3.02        63.98         6.97         8.05        19.07        19.99 
TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3710 TCGA-AA-3715 
       61.02         6.05         6.97         0.92        26.99        19.04 
TCGA-AA-3821 TCGA-AA-3846 TCGA-AA-3855 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3877 
        1.02        17.03        32.05        30.05        53.00        31.00 
TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A004 TCGA-AA-A00N TCGA-AA-A00R 
        2.01         2.01        25.02        13.94         4.01         0.99 
TCGA-AA-A00U TCGA-AA-A010 TCGA-AA-A01Q TCGA-AA-A02H TCGA-AD-6895 TCGA-AD-6964 
       17.03        34.98         1.02         2.01         0.72        10.88 
TCGA-AY-6196 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6607 TCGA-CA-6717 
        0.20        58.39        61.41        12.10         3.19         0.33 
TCGA-CA-6718 TCGA-CK-4952 TCGA-CK-5916 TCGA-CK-6751 TCGA-CM-4746 TCGA-CM-5349 
        0.10        15.62        21.14       124.27        37.02        30.08 
TCGA-CM-5861 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6164 TCGA-CM-6171 TCGA-D5-5538 
       15.02        15.02        15.02        29.03        14.04        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       19.59        13.51        15.12        17.85         4.80        17.13 
TCGA-D5-6541 TCGA-DM-A1D8 TCGA-DM-A1HB TCGA-DM-A282 TCGA-F4-6570 TCGA-F4-6704 
       15.58        12.59       135.65       139.17         6.18         1.55 
TCGA-F4-6807 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6315 TCGA-G4-6586 TCGA-G4-6628 
       16.24        35.41       107.67        36.72        35.80        52.80 

$`USH2A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3496 
       21.76        24.69        24.39        20.12        20.28         1.02 
TCGA-AA-3502 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       35.01         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       24.03        37.05        36.03         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3664 
       23.01        20.98        13.94        19.99        78.08        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 
       10.06         0.00        33.07         0.00        36.03         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        31.07        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       24.00        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       19.07         7.96        27.02        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        15.75        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13        83.80        22.36        62.79        49.41         6.77 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 
      100.01        29.56         5.23        11.74         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07         0.26         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       102.44        40.34        49.08        51.32        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 
        2.93         2.01        23.05        20.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 
       29.06        22.03        22.98        16.01         5.03        15.02 
TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       17.03        12.00        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-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6539 
       11.51        20.19        18.25         1.32        43.27        12.49 
TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       16.14         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        49.91        13.32       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      131.51         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      117.07        98.24         8.61        13.38        13.45        35.87 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 
       16.31        29.59        33.67        13.25         0.53        19.43 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 
       45.11        36.00        22.09        13.78        26.17        91.79 
TCGA-G4-6626 
       46.75 

  USH2A MUTATED USH2A WILD-TYPE 
            0.1             0.0 
  USH2A MUTATED USH2A WILD-TYPE 
         139.17          140.38 
  USH2A MUTATED USH2A WILD-TYPE 
          15.93           21.99 
[1] "0.1 - 139.2 (15.9)" "0.0 - 140.4 (22.0)"
[1] "hr=" "1.1"
D415V2, 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       16        89         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  USH2A MUTATED           4          1          9          7        5         0
  USH2A WILD-TYPE        15          9         32         24       30        13
                 vv
clus              STAGE IVB
  USH2A MUTATED           0
  USH2A WILD-TYPE         1
D415V3, multiclass
            clus
vv           USH2A MUTATED USH2A WILD-TYPE
  STAGE I               13              51
  STAGE IA               0               1
  STAGE II               9              16
  STAGE IIA             20              89
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              4              15
  STAGE IIIA             1               9
  STAGE IIIB             9              32
  STAGE IIIC             7              24
  STAGE IV               5              30
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  USH2A MUTATED     3  11  51   9
  USH2A WILD-TYPE   6  57 197  32
D415V4, multiclass
    clus
vv   USH2A MUTATED USH2A WILD-TYPE
  T1             3               6
  T2            11              57
  T3            51             197
  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  64  53
D415V5, multiclass
    clus
vv   USH2A MUTATED USH2A WILD-TYPE
  N0            45             175
  N1            16              64
  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"
D415V6, binary
                 cls
clus                0   1
  USH2A MUTATED    59   5
  USH2A WILD-TYPE 224  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USH2A MUTATED     59    5
  USH2A WILD-TYPE  224   43
   clus
vv  USH2A MUTATED USH2A WILD-TYPE
  0            59             224
  1             5              43
[1] 2 2
[1] FALSE
D415V7, 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
D415V8, binary
                 cls
clus                0   1
  USH2A MUTATED    63  11
  USH2A WILD-TYPE 254  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USH2A MUTATED     63   11
  USH2A WILD-TYPE  254   37
                               clus
vv                              USH2A MUTATED USH2A WILD-TYPE
  COLON ADENOCARCINOMA                     63             254
  COLON MUCINOUS ADENOCARCINOMA            11              37
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  USH2A MUTATED    52   0   2   6
  USH2A WILD-TYPE 205   2  20  15
D415V9, multiclass
    clus
vv   USH2A MUTATED USH2A WILD-TYPE
  R0            52             205
  R1             0               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"
D415V10, 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
D415V11, 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(416) Variable = SP4 MUTATION ANALYSIS
D416V1, survival
               sevent
clus2             0   1
  SP4 MUTATED     8   4
  SP4 WILD-TYPE 274  69
  SP4 MUTATED SP4 WILD-TYPE 
           12           343 
  SP4 MUTATED SP4 WILD-TYPE 
            4            69 
$`SP4 MUTATED`
TCGA-AA-3966 TCGA-AA-A010 TCGA-AA-A01Q TCGA-AD-6964 TCGA-AU-6004 TCGA-AY-6386 
        2.01        34.98         1.02        10.88        27.09        17.82 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-CK-4950 TCGA-D5-5540 TCGA-D5-6541 TCGA-DM-A1DB 
       49.41        12.10        40.34        13.51        15.58        44.32 

$`SP4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        15.75         0.20        21.44 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       61.41         6.77       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      102.44        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        16.14         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  SP4 MUTATED SP4 WILD-TYPE 
         1.02          0.00 
  SP4 MUTATED SP4 WILD-TYPE 
        49.41        140.38 
  SP4 MUTATED SP4 WILD-TYPE 
        16.70         20.28 
[1] "1.0 - 49.4 (16.7)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.9"
D416V2, 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       23       105         7         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SP4 MUTATED           0          1          1          0        1         0
  SP4 WILD-TYPE        19          9         40         31       34        13
               vv
clus            STAGE IVB
  SP4 MUTATED           0
  SP4 WILD-TYPE         1
D416V3, multiclass
            clus
vv           SP4 MUTATED SP4 WILD-TYPE
  STAGE I              1            63
  STAGE IA             0             1
  STAGE II             2            23
  STAGE IIA            4           105
  STAGE IIB            1             7
  STAGE IIC            0             1
  STAGE III            0            19
  STAGE IIIA           1             9
  STAGE IIIB           1            40
  STAGE IIIC           0            31
  STAGE IV             1            34
  STAGE IVA            0            13
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  SP4 MUTATED     0   1   8   3
  SP4 WILD-TYPE   9  67 240  38
D416V4, multiclass
    clus
vv   SP4 MUTATED SP4 WILD-TYPE
  T1           0             9
  T2           1            67
  T3           8           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
  SP4 MUTATED     8   3   1
  SP4 WILD-TYPE 212  77  65
D416V5, multiclass
    clus
vv   SP4 MUTATED SP4 WILD-TYPE
  N0           8           212
  N1           3            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"
D416V6, binary
               cls
clus              0   1
  SP4 MUTATED     9   1
  SP4 WILD-TYPE 274  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  SP4 MUTATED      9    1
  SP4 WILD-TYPE  274   47
   clus
vv  SP4 MUTATED SP4 WILD-TYPE
  0           9           274
  1           1            47
[1] 2 2
[1] FALSE
D416V7, 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
D416V8, binary
               cls
clus              0   1
  SP4 MUTATED    11   1
  SP4 WILD-TYPE 306  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  SP4 MUTATED     11    1
  SP4 WILD-TYPE  306   47
                               clus
vv                              SP4 MUTATED SP4 WILD-TYPE
  COLON ADENOCARCINOMA                   11           306
  COLON MUCINOUS ADENOCARCINOMA           1            47
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  SP4 MUTATED     6   1   0   0
  SP4 WILD-TYPE 251   1  22  21
D416V9, multiclass
    clus
vv   SP4 MUTATED SP4 WILD-TYPE
  R0           6           251
  R1           1             1
  R2           0            22
  RX           0            21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D416V10, 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
D416V11, 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(417) Variable = PLEKHA6 MUTATION ANALYSIS
D417V1, survival
                   sevent
clus2                 0   1
  PLEKHA6 MUTATED    15   2
  PLEKHA6 WILD-TYPE 267  71
  PLEKHA6 MUTATED PLEKHA6 WILD-TYPE 
               17               338 
  PLEKHA6 MUTATED PLEKHA6 WILD-TYPE 
                2                71 
$`PLEKHA6 MUTATED`
TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 
       24.39        19.66         6.97         0.92        19.04        19.04 
TCGA-AA-3815 TCGA-AA-3821 TCGA-AA-3966 TCGA-AD-6889 TCGA-AU-6004 TCGA-AY-6197 
       33.04         1.02         2.01        56.55        27.09        21.44 
TCGA-AZ-6598 TCGA-CM-5861 TCGA-D5-6540 TCGA-D5-6928 TCGA-F4-6856 
       49.41        15.02        16.14        11.64        19.43 

$`PLEKHA6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 
       26.99        10.06        35.05         0.99        25.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37         4.21         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       14.50        16.31         0.95        15.75         0.20        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        35.41       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  PLEKHA6 MUTATED PLEKHA6 WILD-TYPE 
             0.92              0.00 
  PLEKHA6 MUTATED PLEKHA6 WILD-TYPE 
            56.55            140.38 
  PLEKHA6 MUTATED PLEKHA6 WILD-TYPE 
            19.04             20.98 
[1] "0.9 - 56.5 (19.0)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.5"
D417V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PLEKHA6 MUTATED         5        0        3         7         0         0
  PLEKHA6 WILD-TYPE      59        1       22       102         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLEKHA6 MUTATED           1          0          0          1        1
  PLEKHA6 WILD-TYPE        18         10         41         30       34
                   vv
clus                STAGE IVA STAGE IVB
  PLEKHA6 MUTATED           0         0
  PLEKHA6 WILD-TYPE        13         1
D417V3, multiclass
            clus
vv           PLEKHA6 MUTATED PLEKHA6 WILD-TYPE
  STAGE I                  5                59
  STAGE IA                 0                 1
  STAGE II                 3                22
  STAGE IIA                7               102
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               1                30
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PLEKHA6 MUTATED     0   5  12   1
  PLEKHA6 WILD-TYPE   9  63 236  40
D417V4, multiclass
    clus
vv   PLEKHA6 MUTATED PLEKHA6 WILD-TYPE
  T1               0                 9
  T2               5                63
  T3              12               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    16   2   0
  PLEKHA6 WILD-TYPE 204  78  66
D417V5, multiclass
    clus
vv   PLEKHA6 MUTATED PLEKHA6 WILD-TYPE
  N0              16               204
  N1               2                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"
D417V6, binary
                   cls
clus                  0   1
  PLEKHA6 MUTATED    14   1
  PLEKHA6 WILD-TYPE 269  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHA6 MUTATED     14    1
  PLEKHA6 WILD-TYPE  269   47
   clus
vv  PLEKHA6 MUTATED PLEKHA6 WILD-TYPE
  0              14               269
  1               1                47
[1] 2 2
[1] FALSE
D417V7, binary
                   cls
clus                  0   1
  PLEKHA6 MUTATED     8  10
  PLEKHA6 WILD-TYPE 162 187
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHA6 MUTATED      8   10
  PLEKHA6 WILD-TYPE  162  187
        clus
vv       PLEKHA6 MUTATED PLEKHA6 WILD-TYPE
  FEMALE               8               162
  MALE                10               187
[1] 2 2
[1] FALSE
D417V8, binary
                   cls
clus                  0   1
  PLEKHA6 MUTATED    12   6
  PLEKHA6 WILD-TYPE 305  42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHA6 MUTATED     12    6
  PLEKHA6 WILD-TYPE  305   42
                               clus
vv                              PLEKHA6 MUTATED PLEKHA6 WILD-TYPE
  COLON ADENOCARCINOMA                       12               305
  COLON MUCINOUS ADENOCARCINOMA               6                42
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  PLEKHA6 MUTATED    13   0   1   0
  PLEKHA6 WILD-TYPE 244   2  21  21
D417V9, multiclass
    clus
vv   PLEKHA6 MUTATED PLEKHA6 WILD-TYPE
  R0              13               244
  R1               0                 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"
D417V10, 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
D417V11, 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(418) Variable = ZBTB7C MUTATION ANALYSIS
D418V1, survival
                  sevent
clus2                0   1
  ZBTB7C MUTATED     9   4
  ZBTB7C WILD-TYPE 273  69
  ZBTB7C MUTATED ZBTB7C WILD-TYPE 
              13              342 
  ZBTB7C MUTATED ZBTB7C WILD-TYPE 
               4               69 
$`ZBTB7C MUTATED`
TCGA-AA-3492 TCGA-AA-3663 TCGA-AA-3710 TCGA-AA-3852 TCGA-AA-3864 TCGA-AA-3966 
        3.02         6.97        26.99         0.00        53.00         2.01 
TCGA-AD-6889 TCGA-AU-6004 TCGA-CK-5913 TCGA-CM-6161 TCGA-DM-A28G TCGA-F4-6459 
       56.55        27.09        51.32        15.02        60.79         8.61 
TCGA-G4-6309 
       51.75 

$`ZBTB7C WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
        0.00        33.07        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       26.01        24.00         2.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 
      102.44        40.34        15.62        49.08        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H 
      139.17         6.12        81.37       119.93        35.97       117.07 
TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       98.24        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  ZBTB7C MUTATED ZBTB7C WILD-TYPE 
               0                0 
  ZBTB7C MUTATED ZBTB7C WILD-TYPE 
           60.79           140.38 
  ZBTB7C MUTATED ZBTB7C WILD-TYPE 
          26.990           20.155 
[1] "0.0 - 60.8 (27.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.3"
D418V2, 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       22       103         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZBTB7C MUTATED           0          0          2          0        1
  ZBTB7C WILD-TYPE        19         10         39         31       34
                  vv
clus               STAGE IVA STAGE IVB
  ZBTB7C MUTATED           0         0
  ZBTB7C WILD-TYPE        13         1
D418V3, multiclass
            clus
vv           ZBTB7C MUTATED ZBTB7C WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                3               22
  STAGE IIA               6              103
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZBTB7C MUTATED     0   2  11   1
  ZBTB7C WILD-TYPE   9  66 237  40
D418V4, multiclass
    clus
vv   ZBTB7C MUTATED ZBTB7C WILD-TYPE
  T1              0                9
  T2              2               66
  T3             11              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
  ZBTB7C MUTATED    11   1   2
  ZBTB7C WILD-TYPE 209  79  64
D418V5, multiclass
    clus
vv   ZBTB7C MUTATED ZBTB7C WILD-TYPE
  N0             11              209
  N1              1               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"
D418V6, binary
                  cls
clus                 0   1
  ZBTB7C MUTATED    12   1
  ZBTB7C WILD-TYPE 271  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB7C MUTATED     12    1
  ZBTB7C WILD-TYPE  271   47
   clus
vv  ZBTB7C MUTATED ZBTB7C WILD-TYPE
  0             12              271
  1              1               47
[1] 2 2
[1] FALSE
D418V7, 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
D418V8, binary
                  cls
clus                 0   1
  ZBTB7C MUTATED    12   2
  ZBTB7C WILD-TYPE 305  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB7C MUTATED     12    2
  ZBTB7C WILD-TYPE  305   46
                               clus
vv                              ZBTB7C MUTATED ZBTB7C WILD-TYPE
  COLON ADENOCARCINOMA                      12              305
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZBTB7C MUTATED     9   0   1   1
  ZBTB7C WILD-TYPE 248   2  21  20
D418V9, multiclass
    clus
vv   ZBTB7C MUTATED ZBTB7C WILD-TYPE
  R0              9              248
  R1              0                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"
D418V10, 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
D418V11, 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(419) Variable = VCX2 MUTATION ANALYSIS
D419V1, survival
                sevent
clus2              0   1
  VCX2 MUTATED     5   1
  VCX2 WILD-TYPE 277  72
  VCX2 MUTATED VCX2 WILD-TYPE 
             6            349 
  VCX2 MUTATED VCX2 WILD-TYPE 
             1             72 
$`VCX2 MUTATED`
TCGA-A6-5656 TCGA-A6-5657 TCGA-D5-6932 TCGA-DM-A1D7 TCGA-F4-6460 TCGA-G4-6586 
       32.91        31.63        11.38        13.32        13.38        35.80 

$`VCX2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
      117.07        98.24         8.61        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  VCX2 MUTATED VCX2 WILD-TYPE 
         11.38           0.00 
  VCX2 MUTATED VCX2 WILD-TYPE 
         35.80         140.38 
  VCX2 MUTATED VCX2 WILD-TYPE 
        22.505         20.190 
[1] "11.4 - 35.8 (22.5)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1"  
D419V2, 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       25       106         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        18         10         39         31       35        13
                vv
clus             STAGE IVB
  VCX2 MUTATED           0
  VCX2 WILD-TYPE         1
D419V3, multiclass
            clus
vv           VCX2 MUTATED VCX2 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             3            106
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            2             39
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  VCX2 MUTATED     0   1   6   0
  VCX2 WILD-TYPE   9  67 242  41
D419V4, multiclass
    clus
vv   VCX2 MUTATED VCX2 WILD-TYPE
  T1            0              9
  T2            1             67
  T3            6            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
  VCX2 MUTATED     4   2   1
  VCX2 WILD-TYPE 216  78  65
D419V5, multiclass
    clus
vv   VCX2 MUTATED VCX2 WILD-TYPE
  N0            4            216
  N1            2             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"
D419V6, binary
                cls
clus               0   1
  VCX2 MUTATED     7   0
  VCX2 WILD-TYPE 276  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  VCX2 MUTATED      7    0
  VCX2 WILD-TYPE  276   48
   clus
vv  VCX2 MUTATED VCX2 WILD-TYPE
  0            7            276
  1            0             48
[1] 2 2
[1] FALSE
D419V7, 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
D419V8, binary
                cls
clus               0   1
  VCX2 MUTATED     7   0
  VCX2 WILD-TYPE 310  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  VCX2 MUTATED      7    0
  VCX2 WILD-TYPE  310   48
                               clus
vv                              VCX2 MUTATED VCX2 WILD-TYPE
  COLON ADENOCARCINOMA                     7            310
  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 252   2  22  21
D419V9, multiclass
    clus
vv   VCX2 MUTATED VCX2 WILD-TYPE
  R0            5            252
  R1            0              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"
D419V10, 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
D419V11, 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(420) Variable = PAXIP1 MUTATION ANALYSIS
D420V1, survival
                  sevent
clus2                0   1
  PAXIP1 MUTATED    10   6
  PAXIP1 WILD-TYPE 272  67
  PAXIP1 MUTATED PAXIP1 WILD-TYPE 
              16              339 
  PAXIP1 MUTATED PAXIP1 WILD-TYPE 
               6               67 
$`PAXIP1 MUTATED`
TCGA-A6-6141 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3811 TCGA-AA-3877 TCGA-AA-3977 
        8.38        20.12        19.66        10.06        31.00        25.02 
TCGA-AA-A00N TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-6601 TCGA-AZ-6607 TCGA-CK-4952 
        4.01         4.21        10.88       100.01         3.19        15.62 
TCGA-CM-6674 TCGA-D5-5539 TCGA-D5-6533 TCGA-DM-A1D4 
       12.95        19.59         1.32        92.75 

$`PAXIP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        19.04        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 
       12.10        29.56         5.23        11.74         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 
        0.10         1.35        17.56       102.44        40.34        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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-D5-5540 
       11.01        10.06        12.03        45.40        12.26        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       11.51        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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        24.43        38.20       130.65        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  PAXIP1 MUTATED PAXIP1 WILD-TYPE 
            1.32             0.00 
  PAXIP1 MUTATED PAXIP1 WILD-TYPE 
          100.01           140.38 
  PAXIP1 MUTATED PAXIP1 WILD-TYPE 
          14.285           21.010 
[1] "1.3 - 100.0 (14.3)" "0.0 - 140.4 (21.0)"
[1] "hr=" "2"  
D420V2, 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       24       105         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PAXIP1 MUTATED           2          1          2          1        1
  PAXIP1 WILD-TYPE        17          9         39         30       34
                  vv
clus               STAGE IVA STAGE IVB
  PAXIP1 MUTATED           0         0
  PAXIP1 WILD-TYPE        13         1
D420V3, multiclass
            clus
vv           PAXIP1 MUTATED PAXIP1 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               4              105
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               2               17
  STAGE IIIA              1                9
  STAGE IIIB              2               39
  STAGE IIIC              1               30
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PAXIP1 MUTATED     1   2   7   6
  PAXIP1 WILD-TYPE   8  66 241  35
D420V4, multiclass
    clus
vv   PAXIP1 MUTATED PAXIP1 WILD-TYPE
  T1              1                8
  T2              2               66
  T3              7              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   2   4
  PAXIP1 WILD-TYPE 211  78  62
D420V5, multiclass
    clus
vv   PAXIP1 MUTATED PAXIP1 WILD-TYPE
  N0              9              211
  N1              2               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"
D420V6, binary
                  cls
clus                 0   1
  PAXIP1 MUTATED    11   1
  PAXIP1 WILD-TYPE 272  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PAXIP1 MUTATED     11    1
  PAXIP1 WILD-TYPE  272   47
   clus
vv  PAXIP1 MUTATED PAXIP1 WILD-TYPE
  0             11              272
  1              1               47
[1] 2 2
[1] FALSE
D420V7, 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
D420V8, binary
                  cls
clus                 0   1
  PAXIP1 MUTATED    10   6
  PAXIP1 WILD-TYPE 307  42
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PAXIP1 MUTATED     10    6
  PAXIP1 WILD-TYPE  307   42
                               clus
vv                              PAXIP1 MUTATED PAXIP1 WILD-TYPE
  COLON ADENOCARCINOMA                      10              307
  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 249   2  22  20
D420V9, multiclass
    clus
vv   PAXIP1 MUTATED PAXIP1 WILD-TYPE
  R0              8              249
  R1              0                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"
D420V10, 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
D420V11, 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(421) Variable = AGBL2 MUTATION ANALYSIS
D421V1, survival
                 sevent
clus2               0   1
  AGBL2 MUTATED    10   2
  AGBL2 WILD-TYPE 272  71
  AGBL2 MUTATED AGBL2 WILD-TYPE 
             12             343 
  AGBL2 MUTATED AGBL2 WILD-TYPE 
              2              71 
$`AGBL2 MUTATED`
TCGA-A6-4105 TCGA-A6-5665 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-A00K TCGA-AA-A00N 
       14.53        22.06         6.05         6.97        18.05         4.01 
TCGA-AA-A010 TCGA-AD-5900 TCGA-AZ-4315 TCGA-CK-4948 TCGA-CM-5861 TCGA-G4-6315 
       34.98         0.07        58.39       102.44        15.02        36.72 

$`AGBL2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       13.94        19.99        61.02        78.08        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 
        0.26         0.33         0.10         1.35        17.56        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 
       53.62        44.68        55.04        51.75        45.11        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  AGBL2 MUTATED AGBL2 WILD-TYPE 
           0.07            0.00 
  AGBL2 MUTATED AGBL2 WILD-TYPE 
         102.44          140.38 
  AGBL2 MUTATED AGBL2 WILD-TYPE 
         16.535          20.280 
[1] "0.1 - 102.4 (16.5)" "0.0 - 140.4 (20.3)"
[1] "hr=" "1.3"
D421V2, 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       24       103         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AGBL2 MUTATED           0          1          0          0        2         0
  AGBL2 WILD-TYPE        19          9         41         31       33        13
                 vv
clus              STAGE IVB
  AGBL2 MUTATED           0
  AGBL2 WILD-TYPE         1
D421V3, multiclass
            clus
vv           AGBL2 MUTATED AGBL2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              6             103
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               2              33
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  AGBL2 MUTATED     0   1   9   4
  AGBL2 WILD-TYPE   9  67 239  37
D421V4, multiclass
    clus
vv   AGBL2 MUTATED AGBL2 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             9             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
  AGBL2 MUTATED    11   2   1
  AGBL2 WILD-TYPE 209  78  65
D421V5, multiclass
    clus
vv   AGBL2 MUTATED AGBL2 WILD-TYPE
  N0            11             209
  N1             2              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"
D421V6, binary
                 cls
clus                0   1
  AGBL2 MUTATED    10   2
  AGBL2 WILD-TYPE 273  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGBL2 MUTATED     10    2
  AGBL2 WILD-TYPE  273   46
   clus
vv  AGBL2 MUTATED AGBL2 WILD-TYPE
  0            10             273
  1             2              46
[1] 2 2
[1] FALSE
D421V7, 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
D421V8, binary
                 cls
clus                0   1
  AGBL2 MUTATED    12   2
  AGBL2 WILD-TYPE 305  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGBL2 MUTATED     12    2
  AGBL2 WILD-TYPE  305   46
                               clus
vv                              AGBL2 MUTATED AGBL2 WILD-TYPE
  COLON ADENOCARCINOMA                     12             305
  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 246   2  21  20
D421V9, multiclass
    clus
vv   AGBL2 MUTATED AGBL2 WILD-TYPE
  R0            11             246
  R1             0               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"
D421V10, 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
D421V11, 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(422) Variable = KAT2B MUTATION ANALYSIS
D422V1, survival
                 sevent
clus2               0   1
  KAT2B MUTATED    12   2
  KAT2B WILD-TYPE 270  71
  KAT2B MUTATED KAT2B WILD-TYPE 
             14             341 
  KAT2B MUTATED KAT2B WILD-TYPE 
              2              71 
$`KAT2B MUTATED`
TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3950 TCGA-AA-3977 TCGA-AA-A00N TCGA-AD-5900 
       22.06        19.66        24.00        25.02         4.01         0.07 
TCGA-AU-6004 TCGA-AZ-4315 TCGA-CA-5254 TCGA-CK-5916 TCGA-CM-6171 TCGA-DM-A1HB 
       27.09        58.39         2.24        21.14        14.04       135.65 
TCGA-DM-A28H TCGA-G4-6304 
      117.07        53.62 

$`KAT2B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19         1.94         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
       40.34        15.62        49.08        51.32        21.99         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-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 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 
       19.43       107.67        74.56        65.85        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  KAT2B MUTATED KAT2B WILD-TYPE 
           0.07            0.00 
  KAT2B MUTATED KAT2B WILD-TYPE 
         135.65          140.38 
  KAT2B MUTATED KAT2B WILD-TYPE 
          23.03           20.02 
[1] "0.1 - 135.7 (23.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "2"  
D422V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KAT2B MUTATED         4        0        0         4         3         0
  KAT2B WILD-TYPE      60        1       25       105         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KAT2B MUTATED           0          0          1          2        0         0
  KAT2B WILD-TYPE        19         10         40         29       35        13
                 vv
clus              STAGE IVB
  KAT2B MUTATED           0
  KAT2B WILD-TYPE         1
D422V3, multiclass
            clus
vv           KAT2B MUTATED KAT2B WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              4             105
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             2              29
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KAT2B MUTATED     1   4   6   4
  KAT2B WILD-TYPE   8  64 242  37
D422V4, multiclass
    clus
vv   KAT2B MUTATED KAT2B WILD-TYPE
  T1             1               8
  T2             4              64
  T3             6             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
  KAT2B MUTATED    12   2   1
  KAT2B WILD-TYPE 208  78  65
D422V5, multiclass
    clus
vv   KAT2B MUTATED KAT2B WILD-TYPE
  N0            12             208
  N1             2              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"
D422V6, binary
                 cls
clus                0   1
  KAT2B MUTATED    11   0
  KAT2B WILD-TYPE 272  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KAT2B MUTATED     11    0
  KAT2B WILD-TYPE  272   48
   clus
vv  KAT2B MUTATED KAT2B WILD-TYPE
  0            11             272
  1             0              48
[1] 2 2
[1] FALSE
D422V7, binary
                 cls
clus                0   1
  KAT2B MUTATED     8   7
  KAT2B WILD-TYPE 162 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KAT2B MUTATED      8    7
  KAT2B WILD-TYPE  162  190
        clus
vv       KAT2B MUTATED KAT2B WILD-TYPE
  FEMALE             8             162
  MALE               7             190
[1] 2 2
[1] FALSE
D422V8, binary
                 cls
clus                0   1
  KAT2B MUTATED    11   4
  KAT2B WILD-TYPE 306  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KAT2B MUTATED     11    4
  KAT2B WILD-TYPE  306   44
                               clus
vv                              KAT2B MUTATED KAT2B WILD-TYPE
  COLON ADENOCARCINOMA                     11             306
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  KAT2B MUTATED     9   0   0   3
  KAT2B WILD-TYPE 248   2  22  18
D422V9, multiclass
    clus
vv   KAT2B MUTATED KAT2B WILD-TYPE
  R0             9             248
  R1             0               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"
D422V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KAT2B MUTATED                                  0     1
  KAT2B WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KAT2B MUTATED                           0    11
  KAT2B WILD-TYPE                        19   165
D422V11, multiclass
                                  clus
vv                                 KAT2B MUTATED KAT2B 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(423) Variable = RIF1 MUTATION ANALYSIS
D423V1, survival
                sevent
clus2              0   1
  RIF1 MUTATED    29   5
  RIF1 WILD-TYPE 253  68
  RIF1 MUTATED RIF1 WILD-TYPE 
            34            321 
  RIF1 MUTATED RIF1 WILD-TYPE 
             5             68 
$`RIF1 MUTATED`
TCGA-A6-2672 TCGA-A6-3807 TCGA-A6-5665 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3510 
       46.65        34.65        22.06        20.12        19.66        63.98 
TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3815 TCGA-AA-3821 
       61.02         6.05        19.04        19.04        33.04         1.02 
TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01P TCGA-AY-5543 TCGA-AY-6196 
       18.05         4.01        34.98        38.07        15.75         0.20 
TCGA-AZ-4315 TCGA-AZ-6603 TCGA-CA-5797 TCGA-CA-6718 TCGA-CK-4952 TCGA-CM-5868 
       58.39        29.56         3.29         0.10        15.62        17.03 
TCGA-CM-6167 TCGA-D5-6533 TCGA-D5-6541 TCGA-D5-6927 TCGA-F4-6570 TCGA-F4-6808 
       14.99         1.32        15.58         9.44         6.18        33.67 
TCGA-G4-6293 TCGA-G4-6304 TCGA-G4-6321 TCGA-G4-6628 
      107.67        53.62        22.09        52.80 

$`RIF1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       33.34        32.75        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       30.44        29.19        33.53        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 
       21.76        24.69        24.39        23.87        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        3.02         1.02        35.01         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3663 
       20.98        19.99        13.94        19.99        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
        5.03        85.05        26.99        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
       25.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 
       14.50        27.09        16.31         0.95        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10       100.01         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 
        3.19         1.94         2.24         3.06         3.25         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.33         1.35        17.56       102.44        40.34 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        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-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 
       13.51        11.51        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-D5-6928 
       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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       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        13.38        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 
        1.55        16.31        29.59        16.24        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 
       35.41        19.43        74.56        65.85        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 
       51.75        45.11        36.72        36.00        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       26.17        91.79        46.75 

  RIF1 MUTATED RIF1 WILD-TYPE 
           0.1            0.0 
  RIF1 MUTATED RIF1 WILD-TYPE 
        107.67         140.38 
  RIF1 MUTATED RIF1 WILD-TYPE 
         19.35          20.98 
[1] "0.1 - 107.7 (19.4)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.5"
D423V2, 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       22       100         5         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RIF1 MUTATED           5          0          3          4        2         2
  RIF1 WILD-TYPE        14         10         38         27       33        11
                vv
clus             STAGE IVB
  RIF1 MUTATED           0
  RIF1 WILD-TYPE         1
D423V3, multiclass
            clus
vv           RIF1 MUTATED RIF1 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              3             22
  STAGE IIA             9            100
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             5             14
  STAGE IIIA            0             10
  STAGE IIIB            3             38
  STAGE IIIC            4             27
  STAGE IV              2             33
  STAGE IVA             2             11
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  64 227  32
D423V4, multiclass
    clus
vv   RIF1 MUTATED RIF1 WILD-TYPE
  T1            1              8
  T2            4             64
  T3           21            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
  RIF1 MUTATED    20   9   6
  RIF1 WILD-TYPE 200  71  60
D423V5, multiclass
    clus
vv   RIF1 MUTATED RIF1 WILD-TYPE
  N0           20            200
  N1            9             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"
D423V6, binary
                cls
clus               0   1
  RIF1 MUTATED    26   4
  RIF1 WILD-TYPE 257  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  RIF1 MUTATED     26    4
  RIF1 WILD-TYPE  257   44
   clus
vv  RIF1 MUTATED RIF1 WILD-TYPE
  0           26            257
  1            4             44
[1] 2 2
[1] FALSE
D423V7, 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
D423V8, binary
                cls
clus               0   1
  RIF1 MUTATED    28   7
  RIF1 WILD-TYPE 289  41
[1] "tbl2"
                cls
clus             [,1] [,2]
  RIF1 MUTATED     28    7
  RIF1 WILD-TYPE  289   41
                               clus
vv                              RIF1 MUTATED RIF1 WILD-TYPE
  COLON ADENOCARCINOMA                    28            289
  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 228   2  20  19
D423V9, multiclass
    clus
vv   RIF1 MUTATED RIF1 WILD-TYPE
  R0           29            228
  R1            0              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"
D423V10, 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
D423V11, 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(424) Variable = KDM5C MUTATION ANALYSIS
D424V1, survival
                 sevent
clus2               0   1
  KDM5C MUTATED    16   4
  KDM5C WILD-TYPE 266  69
  KDM5C MUTATED KDM5C WILD-TYPE 
             20             335 
  KDM5C MUTATED KDM5C WILD-TYPE 
              4              69 
$`KDM5C MUTATED`
TCGA-A6-2672 TCGA-A6-2676 TCGA-AA-3516 TCGA-AA-3555 TCGA-AA-3697 TCGA-AA-3710 
       46.65        42.90        13.02        29.95        85.05        26.99 
TCGA-AA-3947 TCGA-AA-3977 TCGA-AA-3979 TCGA-CM-4752 TCGA-CM-5348 TCGA-CM-5861 
       33.01        25.02        24.00        13.02        22.98        15.02 
TCGA-CM-5863 TCGA-CM-5868 TCGA-D5-7000 TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-F4-6809 
       15.02        17.03        10.26       130.65        92.75        13.25 
TCGA-G4-6293 TCGA-G4-6304 
      107.67        53.62 

$`KDM5C WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       43.76        43.76        24.33        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       33.34        32.75        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3713 
        5.98        37.05        19.00        36.00         5.03        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3980 TCGA-AA-3982 
       50.99        13.05        34.06        26.01        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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-5862 
       25.02        29.06        22.03        30.08        16.01         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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
      119.70        24.43        38.20        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 
        1.55        16.31        29.59        16.24        33.67         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 
       35.41        19.43        74.56        65.85        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  KDM5C MUTATED KDM5C WILD-TYPE 
          10.26            0.00 
  KDM5C MUTATED KDM5C WILD-TYPE 
         130.65          140.38 
  KDM5C MUTATED KDM5C WILD-TYPE 
         26.005          19.990 
[1] "10.3 - 130.7 (26.0)" "0.0 - 140.4 (20.0)" 
[1] "hr=" "1.6"
D424V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KDM5C MUTATED         1        0        0         7         4         0
  KDM5C WILD-TYPE      63        1       25       102         4         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KDM5C MUTATED           3          0          3          0        0         2
  KDM5C WILD-TYPE        16         10         38         31       35        11
                 vv
clus              STAGE IVB
  KDM5C MUTATED           0
  KDM5C WILD-TYPE         1
D424V3, multiclass
            clus
vv           KDM5C MUTATED KDM5C WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              7             102
  STAGE IIB              4               4
  STAGE IIC              0               1
  STAGE III              3              16
  STAGE IIIA             0              10
  STAGE IIIB             3              38
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              2              11
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 234  36
D424V4, multiclass
    clus
vv   KDM5C MUTATED KDM5C WILD-TYPE
  T1             0               9
  T2             2              66
  T3            14             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
  KDM5C MUTATED    14   6   1
  KDM5C WILD-TYPE 206  74  65
D424V5, multiclass
    clus
vv   KDM5C MUTATED KDM5C WILD-TYPE
  N0            14             206
  N1             6              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"
D424V6, binary
                 cls
clus                0   1
  KDM5C MUTATED    17   2
  KDM5C WILD-TYPE 266  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM5C MUTATED     17    2
  KDM5C WILD-TYPE  266   46
   clus
vv  KDM5C MUTATED KDM5C WILD-TYPE
  0            17             266
  1             2              46
[1] 2 2
[1] FALSE
D424V7, 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
D424V8, binary
                 cls
clus                0   1
  KDM5C MUTATED    16   5
  KDM5C WILD-TYPE 301  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM5C MUTATED     16    5
  KDM5C WILD-TYPE  301   43
                               clus
vv                              KDM5C MUTATED KDM5C WILD-TYPE
  COLON ADENOCARCINOMA                     16             301
  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 241   2  22  20
D424V9, multiclass
    clus
vv   KDM5C MUTATED KDM5C WILD-TYPE
  R0            16             241
  R1             0               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"
D424V10, 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
D424V11, 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(425) Variable = IL12RB2 MUTATION ANALYSIS
D425V1, survival
                   sevent
clus2                 0   1
  IL12RB2 MUTATED    10   3
  IL12RB2 WILD-TYPE 272  70
  IL12RB2 MUTATED IL12RB2 WILD-TYPE 
               13               342 
  IL12RB2 MUTATED IL12RB2 WILD-TYPE 
                3                70 
$`IL12RB2 MUTATED`
TCGA-AA-3525 TCGA-AA-3811 TCGA-AA-A010 TCGA-AA-A01I TCGA-AD-6889 TCGA-AU-6004 
        8.05        10.06        34.98        31.00        56.55        27.09 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4950 TCGA-CK-5916 TCGA-D5-5538 TCGA-DM-A28C 
        0.33         0.10        40.34        21.14        12.26        81.37 
TCGA-G4-6588 
       26.17 

$`IL12RB2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K 
       21.99        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        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37         4.21         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07         0.26         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
      102.44        15.62        49.08        51.32        21.99         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
        6.12       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        52.80 

  IL12RB2 MUTATED IL12RB2 WILD-TYPE 
              0.1               0.0 
  IL12RB2 MUTATED IL12RB2 WILD-TYPE 
            81.37            140.38 
  IL12RB2 MUTATED IL12RB2 WILD-TYPE 
            26.17             20.07 
[1] "0.1 - 81.4 (26.2)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.1"
D425V2, 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       25       103         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IL12RB2 MUTATED           1          1          2          0        0
  IL12RB2 WILD-TYPE        18          9         39         31       35
                   vv
clus                STAGE IVA STAGE IVB
  IL12RB2 MUTATED           0         0
  IL12RB2 WILD-TYPE        13         1
D425V3, multiclass
            clus
vv           IL12RB2 MUTATED IL12RB2 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                6               103
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               1                 9
  STAGE IIIB               2                39
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  IL12RB2 MUTATED     1   2  10   1
  IL12RB2 WILD-TYPE   8  66 238  40
D425V4, multiclass
    clus
vv   IL12RB2 MUTATED IL12RB2 WILD-TYPE
  T1               1                 8
  T2               2                66
  T3              10               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
  IL12RB2 MUTATED    10   3   1
  IL12RB2 WILD-TYPE 210  77  65
D425V5, multiclass
    clus
vv   IL12RB2 MUTATED IL12RB2 WILD-TYPE
  N0              10               210
  N1               3                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"
D425V6, binary
                   cls
clus                  0   1
  IL12RB2 MUTATED    14   0
  IL12RB2 WILD-TYPE 269  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  IL12RB2 MUTATED     14    0
  IL12RB2 WILD-TYPE  269   48
   clus
vv  IL12RB2 MUTATED IL12RB2 WILD-TYPE
  0              14               269
  1               0                48
[1] 2 2
[1] FALSE
D425V7, 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
D425V8, binary
                   cls
clus                  0   1
  IL12RB2 MUTATED    13   1
  IL12RB2 WILD-TYPE 304  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  IL12RB2 MUTATED     13    1
  IL12RB2 WILD-TYPE  304   47
                               clus
vv                              IL12RB2 MUTATED IL12RB2 WILD-TYPE
  COLON ADENOCARCINOMA                       13               304
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  IL12RB2 MUTATED     8   1   0   3
  IL12RB2 WILD-TYPE 249   1  22  18
D425V9, multiclass
    clus
vv   IL12RB2 MUTATED IL12RB2 WILD-TYPE
  R0               8               249
  R1               1                 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"
D425V10, 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
D425V11, 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(426) Variable = SFRS18 MUTATION ANALYSIS
D426V1, survival
                  sevent
clus2                0   1
  SFRS18 MUTATED    10   1
  SFRS18 WILD-TYPE 272  72
  SFRS18 MUTATED SFRS18 WILD-TYPE 
              11              344 
  SFRS18 MUTATED SFRS18 WILD-TYPE 
               1               72 
$`SFRS18 MUTATED`
TCGA-A6-5661 TCGA-AA-3947 TCGA-AA-A00E TCGA-AA-A010 TCGA-AD-5900 TCGA-AD-6889 
       33.53        33.01        30.02        34.98         0.07        56.55 
TCGA-AD-6895 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-5913 
        0.72        58.39        49.41         0.33        51.32 

$`SFRS18 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        21.37         4.21         0.79         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13        83.80        22.36        62.79        61.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  SFRS18 MUTATED SFRS18 WILD-TYPE 
            0.07             0.00 
  SFRS18 MUTATED SFRS18 WILD-TYPE 
           58.39           140.38 
  SFRS18 MUTATED SFRS18 WILD-TYPE 
          33.530           20.005 
[1] "0.1 - 58.4 (33.5)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "2.8"
D426V2, 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       24       102         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SFRS18 MUTATED           0          0          0          0        0
  SFRS18 WILD-TYPE        19         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  SFRS18 MUTATED           0         0
  SFRS18 WILD-TYPE        13         1
D426V3, multiclass
            clus
vv           SFRS18 MUTATED SFRS18 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               7              102
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SFRS18 MUTATED     0   1   9   2
  SFRS18 WILD-TYPE   9  67 239  39
D426V4, multiclass
    clus
vv   SFRS18 MUTATED SFRS18 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              9              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
  SFRS18 MUTATED    11   1   0
  SFRS18 WILD-TYPE 209  79  66
D426V5, multiclass
    clus
vv   SFRS18 MUTATED SFRS18 WILD-TYPE
  N0             11              209
  N1              1               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"
D426V6, binary
                  cls
clus                 0   1
  SFRS18 MUTATED     8   0
  SFRS18 WILD-TYPE 275  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SFRS18 MUTATED      8    0
  SFRS18 WILD-TYPE  275   48
   clus
vv  SFRS18 MUTATED SFRS18 WILD-TYPE
  0              8              275
  1              0               48
[1] 2 2
[1] FALSE
D426V7, 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
D426V8, binary
                  cls
clus                 0   1
  SFRS18 MUTATED     9   3
  SFRS18 WILD-TYPE 308  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SFRS18 MUTATED      9    3
  SFRS18 WILD-TYPE  308   45
                               clus
vv                              SFRS18 MUTATED SFRS18 WILD-TYPE
  COLON ADENOCARCINOMA                       9              308
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SFRS18 MUTATED     7   0   0   2
  SFRS18 WILD-TYPE 250   2  22  19
D426V9, multiclass
    clus
vv   SFRS18 MUTATED SFRS18 WILD-TYPE
  R0              7              250
  R1              0                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"
D426V10, 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
D426V11, 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(427) Variable = ALDH2 MUTATION ANALYSIS
D427V1, survival
                 sevent
clus2               0   1
  ALDH2 MUTATED     8   2
  ALDH2 WILD-TYPE 274  71
  ALDH2 MUTATED ALDH2 WILD-TYPE 
             10             345 
  ALDH2 MUTATED ALDH2 WILD-TYPE 
              2              71 
$`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        15.75 
TCGA-AZ-6598 TCGA-CA-5797 TCGA-D5-6928 TCGA-G4-6304 
       49.41         3.29        11.64        53.62 

$`ALDH2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        0.72         5.79        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-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-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  ALDH2 MUTATED ALDH2 WILD-TYPE 
           1.02            0.00 
  ALDH2 MUTATED ALDH2 WILD-TYPE 
          53.62          140.38 
  ALDH2 MUTATED ALDH2 WILD-TYPE 
          16.90           20.28 
[1] "1.0 - 53.6 (16.9)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.1"
D427V2, 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       22       106         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        19         10         40         31       35        12
                 vv
clus              STAGE IVB
  ALDH2 MUTATED           0
  ALDH2 WILD-TYPE         1
D427V3, multiclass
            clus
vv           ALDH2 MUTATED ALDH2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              3             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 241  38
D427V4, multiclass
    clus
vv   ALDH2 MUTATED ALDH2 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             7             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
  ALDH2 MUTATED     9   2   0
  ALDH2 WILD-TYPE 211  78  66
D427V5, multiclass
    clus
vv   ALDH2 MUTATED ALDH2 WILD-TYPE
  N0             9             211
  N1             2              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"
D427V6, binary
                 cls
clus                0   1
  ALDH2 MUTATED     8   1
  ALDH2 WILD-TYPE 275  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALDH2 MUTATED      8    1
  ALDH2 WILD-TYPE  275   47
   clus
vv  ALDH2 MUTATED ALDH2 WILD-TYPE
  0             8             275
  1             1              47
[1] 2 2
[1] FALSE
D427V7, 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
D427V8, binary
                 cls
clus                0   1
  ALDH2 MUTATED     9   2
  ALDH2 WILD-TYPE 308  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALDH2 MUTATED      9    2
  ALDH2 WILD-TYPE  308   46
                               clus
vv                              ALDH2 MUTATED ALDH2 WILD-TYPE
  COLON ADENOCARCINOMA                      9             308
  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 248   2  22  21
D427V9, multiclass
    clus
vv   ALDH2 MUTATED ALDH2 WILD-TYPE
  R0             9             248
  R1             0               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"
D427V10, 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
D427V11, 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(428) Variable = MDH1 MUTATION ANALYSIS
D428V1, survival
                sevent
clus2              0   1
  MDH1 MUTATED     6   2
  MDH1 WILD-TYPE 276  71
  MDH1 MUTATED MDH1 WILD-TYPE 
             8            347 
  MDH1 MUTATED MDH1 WILD-TYPE 
             2             71 
$`MDH1 MUTATED`
TCGA-AA-3845 TCGA-AY-5543 TCGA-AZ-4315 TCGA-AZ-4616 TCGA-CA-6717 TCGA-CM-5860 
        0.00        15.75        58.39         5.13         0.33        16.01 
TCGA-CM-6676 TCGA-D5-6532 
       11.08        18.25 

$`MDH1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4681 
        0.95         0.20        21.44        17.82         1.41        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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-6677 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       13.51        11.51        20.19         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  MDH1 MUTATED MDH1 WILD-TYPE 
             0              0 
  MDH1 MUTATED MDH1 WILD-TYPE 
         58.39         140.38 
  MDH1 MUTATED MDH1 WILD-TYPE 
        13.415         20.980 
[1] "0.0 - 58.4 (13.4)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.8"
D428V2, 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       25       104         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        19         10         41         31       34        12
                vv
clus             STAGE IVB
  MDH1 MUTATED           0
  MDH1 WILD-TYPE         1
D428V3, multiclass
            clus
vv           MDH1 MUTATED MDH1 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             5            104
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 241  41
D428V4, multiclass
    clus
vv   MDH1 MUTATED MDH1 WILD-TYPE
  T1            0              9
  T2            1             67
  T3            7            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
  MDH1 MUTATED     6   1   1
  MDH1 WILD-TYPE 214  79  65
D428V5, multiclass
    clus
vv   MDH1 MUTATED MDH1 WILD-TYPE
  N0            6            214
  N1            1             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"
D428V6, binary
                cls
clus               0   1
  MDH1 MUTATED     6   2
  MDH1 WILD-TYPE 277  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  MDH1 MUTATED      6    2
  MDH1 WILD-TYPE  277   46
   clus
vv  MDH1 MUTATED MDH1 WILD-TYPE
  0            6            277
  1            2             46
[1] 2 2
[1] FALSE
D428V7, 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
D428V8, binary
                cls
clus               0   1
  MDH1 MUTATED     7   1
  MDH1 WILD-TYPE 310  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  MDH1 MUTATED      7    1
  MDH1 WILD-TYPE  310   47
                               clus
vv                              MDH1 MUTATED MDH1 WILD-TYPE
  COLON ADENOCARCINOMA                     7            310
  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 251   2  22  20
D428V9, multiclass
    clus
vv   MDH1 MUTATED MDH1 WILD-TYPE
  R0            6            251
  R1            0              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"
D428V10, 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
D428V11, 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(429) Variable = CYLC1 MUTATION ANALYSIS
D429V1, survival
                 sevent
clus2               0   1
  CYLC1 MUTATED    21   6
  CYLC1 WILD-TYPE 261  67
  CYLC1 MUTATED CYLC1 WILD-TYPE 
             27             328 
  CYLC1 MUTATED CYLC1 WILD-TYPE 
              6              67 
$`CYLC1 MUTATED`
TCGA-A6-3809 TCGA-A6-5665 TCGA-A6-6653 TCGA-AA-3511 TCGA-AA-A00J TCGA-AA-A010 
       32.75        22.06        24.39         6.97        18.05        34.98 
TCGA-AA-A01P TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6899 TCGA-AZ-4315 TCGA-AZ-4616 
       38.07        21.37        56.55         5.79        58.39         5.13 
TCGA-CA-6717 TCGA-CM-5860 TCGA-CM-6167 TCGA-D5-5537 TCGA-D5-5540 TCGA-D5-6929 
        0.33        16.01        14.99        45.40        13.51        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        16.31       107.67        74.56 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6588 
       36.72        36.00        26.17 

$`CYLC1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       24.16        21.76        24.69        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6888 
       41.00        39.98        18.05        40.96         0.07         4.21 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         0.72        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       21.44        17.82         1.41        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       21.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.03        12.26        19.59        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       13.45        35.87         1.55        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6303 TCGA-G4-6304 
       13.25         0.53        35.41        19.43        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6323 
       44.68        55.04        51.75        45.11        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        91.79        46.75        52.80 

  CYLC1 MUTATED CYLC1 WILD-TYPE 
           0.33            0.00 
  CYLC1 MUTATED CYLC1 WILD-TYPE 
         119.93          140.38 
  CYLC1 MUTATED CYLC1 WILD-TYPE 
          22.06           20.07 
[1] "0.3 - 119.9 (22.1)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.1"
D429V2, 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       24        98         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CYLC1 MUTATED           2          0          1          5        3         0
  CYLC1 WILD-TYPE        17         10         40         26       32        13
                 vv
clus              STAGE IVB
  CYLC1 MUTATED           0
  CYLC1 WILD-TYPE         1
D429V3, multiclass
            clus
vv           CYLC1 MUTATED CYLC1 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA             11              98
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             5              26
  STAGE IV               3              32
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CYLC1 MUTATED     0   2  20   6
  CYLC1 WILD-TYPE   9  66 228  35
D429V4, multiclass
    clus
vv   CYLC1 MUTATED CYLC1 WILD-TYPE
  T1             0               9
  T2             2              66
  T3            20             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
  CYLC1 MUTATED    16   5   7
  CYLC1 WILD-TYPE 204  75  59
D429V5, multiclass
    clus
vv   CYLC1 MUTATED CYLC1 WILD-TYPE
  N0            16             204
  N1             5              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"
D429V6, binary
                 cls
clus                0   1
  CYLC1 MUTATED    21   3
  CYLC1 WILD-TYPE 262  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CYLC1 MUTATED     21    3
  CYLC1 WILD-TYPE  262   45
   clus
vv  CYLC1 MUTATED CYLC1 WILD-TYPE
  0            21             262
  1             3              45
[1] 2 2
[1] FALSE
D429V7, binary
                 cls
clus                0   1
  CYLC1 MUTATED    16  12
  CYLC1 WILD-TYPE 154 185
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CYLC1 MUTATED     16   12
  CYLC1 WILD-TYPE  154  185
        clus
vv       CYLC1 MUTATED CYLC1 WILD-TYPE
  FEMALE            16             154
  MALE              12             185
[1] 2 2
[1] FALSE
D429V8, binary
                 cls
clus                0   1
  CYLC1 MUTATED    24   4
  CYLC1 WILD-TYPE 293  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CYLC1 MUTATED     24    4
  CYLC1 WILD-TYPE  293   44
                               clus
vv                              CYLC1 MUTATED CYLC1 WILD-TYPE
  COLON ADENOCARCINOMA                     24             293
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CYLC1 MUTATED    19   0   0   3
  CYLC1 WILD-TYPE 238   2  22  18
D429V9, multiclass
    clus
vv   CYLC1 MUTATED CYLC1 WILD-TYPE
  R0            19             238
  R1             0               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"
D429V10, 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
D429V11, 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(430) Variable = KCNS3 MUTATION ANALYSIS
D430V1, survival
                 sevent
clus2               0   1
  KCNS3 MUTATED    16   3
  KCNS3 WILD-TYPE 266  70
  KCNS3 MUTATED KCNS3 WILD-TYPE 
             19             336 
  KCNS3 MUTATED KCNS3 WILD-TYPE 
              3              70 
$`KCNS3 MUTATED`
TCGA-A6-3809 TCGA-A6-6780 TCGA-AA-3496 TCGA-AA-3812 TCGA-AA-A010 TCGA-AD-5900 
       32.75        20.12         1.02        35.05        34.98         0.07 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-CM-4746 TCGA-CM-4752 
       15.75        21.44        49.41         6.77        37.02        13.02 
TCGA-CM-5864 TCGA-CM-6678 TCGA-D5-5540 TCGA-D5-6533 TCGA-DM-A28C TCGA-G4-6299 
       15.02        11.01        13.51         1.32        81.37        74.56 
TCGA-G4-6628 
       52.80 

$`KCNS3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         3.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3815 
       85.05        26.99        19.04        19.04        10.06        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 
        5.13        83.80        22.36        62.79        61.41        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        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        12.26        19.59        11.51 
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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
      139.17         6.12       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 
        0.53        35.41        19.43       107.67        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 

  KCNS3 MUTATED KCNS3 WILD-TYPE 
           0.07            0.00 
  KCNS3 MUTATED KCNS3 WILD-TYPE 
          81.37          140.38 
  KCNS3 MUTATED KCNS3 WILD-TYPE 
         20.120          20.235 
[1] "0.1 - 81.4 (20.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.4"
D430V2, 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       23       103         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KCNS3 MUTATED           0          0          1          1        0         2
  KCNS3 WILD-TYPE        19         10         40         30       35        11
                 vv
clus              STAGE IVB
  KCNS3 MUTATED           0
  KCNS3 WILD-TYPE         1
D430V3, multiclass
            clus
vv           KCNS3 MUTATED KCNS3 WILD-TYPE
  STAGE I                5              59
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              6             103
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              2              11
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  63 238  37
D430V4, multiclass
    clus
vv   KCNS3 MUTATED KCNS3 WILD-TYPE
  T1             0               9
  T2             5              63
  T3            10             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
  KCNS3 MUTATED    16   2   1
  KCNS3 WILD-TYPE 204  78  65
D430V5, multiclass
    clus
vv   KCNS3 MUTATED KCNS3 WILD-TYPE
  N0            16             204
  N1             2              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"
D430V6, binary
                 cls
clus                0   1
  KCNS3 MUTATED    12   2
  KCNS3 WILD-TYPE 271  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNS3 MUTATED     12    2
  KCNS3 WILD-TYPE  271   46
   clus
vv  KCNS3 MUTATED KCNS3 WILD-TYPE
  0            12             271
  1             2              46
[1] 2 2
[1] FALSE
D430V7, 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
D430V8, binary
                 cls
clus                0   1
  KCNS3 MUTATED    16   3
  KCNS3 WILD-TYPE 301  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNS3 MUTATED     16    3
  KCNS3 WILD-TYPE  301   45
                               clus
vv                              KCNS3 MUTATED KCNS3 WILD-TYPE
  COLON ADENOCARCINOMA                     16             301
  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 242   2  22  21
D430V9, multiclass
    clus
vv   KCNS3 MUTATED KCNS3 WILD-TYPE
  R0            15             242
  R1             0               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"
D430V10, 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
D430V11, 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(431) Variable = SOX7 MUTATION ANALYSIS
D431V1, survival
                sevent
clus2              0   1
  SOX7 MUTATED     9   2
  SOX7 WILD-TYPE 273  71
  SOX7 MUTATED SOX7 WILD-TYPE 
            11            344 
  SOX7 MUTATED SOX7 WILD-TYPE 
             2             71 
$`SOX7 MUTATED`
TCGA-A6-6780 TCGA-AA-3672 TCGA-AA-3815 TCGA-AA-3947 TCGA-AA-A010 TCGA-AY-6197 
       20.12         0.92        33.04        33.01        34.98        21.44 
TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CM-6171 TCGA-DM-A1D7 
       58.39        49.41         0.33        14.04        13.32 

$`SOX7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       27.09        16.31         0.95        15.75         0.20        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 
       24.43        38.20       130.65        92.75        49.91        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  SOX7 MUTATED SOX7 WILD-TYPE 
          0.33           0.00 
  SOX7 MUTATED SOX7 WILD-TYPE 
         58.39         140.38 
  SOX7 MUTATED SOX7 WILD-TYPE 
        21.440         20.105 
[1] "0.3 - 58.4 (21.4)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.1"
D431V2, 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       24       103         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        18         10         41         31       35        13
                vv
clus             STAGE IVB
  SOX7 MUTATED           0
  SOX7 WILD-TYPE         1
D431V3, multiclass
            clus
vv           SOX7 MUTATED SOX7 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             6            103
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SOX7 MUTATED     0   1   8   2
  SOX7 WILD-TYPE   9  67 240  39
D431V4, multiclass
    clus
vv   SOX7 MUTATED SOX7 WILD-TYPE
  T1            0              9
  T2            1             67
  T3            8            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
  SOX7 MUTATED    10   1   0
  SOX7 WILD-TYPE 210  79  66
D431V5, multiclass
    clus
vv   SOX7 MUTATED SOX7 WILD-TYPE
  N0           10            210
  N1            1             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
  SOX7 MUTATED     8   0
  SOX7 WILD-TYPE 275  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOX7 MUTATED      8    0
  SOX7 WILD-TYPE  275   48
   clus
vv  SOX7 MUTATED SOX7 WILD-TYPE
  0            8            275
  1            0             48
[1] 2 2
[1] FALSE
D431V7, 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
D431V8, binary
                cls
clus               0   1
  SOX7 MUTATED     8   3
  SOX7 WILD-TYPE 309  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOX7 MUTATED      8    3
  SOX7 WILD-TYPE  309   45
                               clus
vv                              SOX7 MUTATED SOX7 WILD-TYPE
  COLON ADENOCARCINOMA                     8            309
  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 250   2  22  20
D431V9, multiclass
    clus
vv   SOX7 MUTATED SOX7 WILD-TYPE
  R0            7            250
  R1            0              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"
D431V10, 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
D431V11, 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(432) Variable = OVCH1 MUTATION ANALYSIS
D432V1, survival
                 sevent
clus2               0   1
  OVCH1 MUTATED    14   7
  OVCH1 WILD-TYPE 268  66
  OVCH1 MUTATED OVCH1 WILD-TYPE 
             21             334 
  OVCH1 MUTATED OVCH1 WILD-TYPE 
              7              66 
$`OVCH1 MUTATED`
TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3680 TCGA-AA-3710 TCGA-AA-3977 
       20.12        19.66         3.02        11.01        26.99        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6901 TCGA-AU-3779 TCGA-CA-5796 TCGA-CA-6717 
        4.01        34.98        22.42        14.50         3.25         0.33 
TCGA-CM-5864 TCGA-CM-6164 TCGA-CM-6171 TCGA-D5-6923 TCGA-DM-A1DB TCGA-DM-A1HB 
       15.02        29.03        14.04        12.43        44.32       135.65 
TCGA-F4-6570 TCGA-G4-6303 TCGA-G4-6588 
        6.18        65.85        26.17 

$`OVCH1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       23.87        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         0.72         5.79        27.42        10.88 
TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.20        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        2.24         3.06         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
       12.59       140.38         7.50       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-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        13.38        13.45        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       19.43       107.67        74.56        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        91.79        46.75        52.80 

  OVCH1 MUTATED OVCH1 WILD-TYPE 
           0.33            0.00 
  OVCH1 MUTATED OVCH1 WILD-TYPE 
         135.65          140.38 
  OVCH1 MUTATED OVCH1 WILD-TYPE 
          19.66           20.63 
[1] "0.3 - 135.7 (19.7)" "0.0 - 140.4 (20.6)"
[1] "hr=" "1.8"
D432V2, 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       24        99         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        19         10         40         30       33        13
                 vv
clus              STAGE IVB
  OVCH1 MUTATED           0
  OVCH1 WILD-TYPE         1
D432V3, multiclass
            clus
vv           OVCH1 MUTATED OVCH1 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA             10              99
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             1              30
  STAGE IV               2              33
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OVCH1 MUTATED     0   4  14   4
  OVCH1 WILD-TYPE   9  64 234  37
D432V4, multiclass
    clus
vv   OVCH1 MUTATED OVCH1 WILD-TYPE
  T1             0               9
  T2             4              64
  T3            14             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
  OVCH1 MUTATED    18   3   1
  OVCH1 WILD-TYPE 202  77  65
D432V5, multiclass
    clus
vv   OVCH1 MUTATED OVCH1 WILD-TYPE
  N0            18             202
  N1             3              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"
D432V6, binary
                 cls
clus                0   1
  OVCH1 MUTATED    16   2
  OVCH1 WILD-TYPE 267  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OVCH1 MUTATED     16    2
  OVCH1 WILD-TYPE  267   46
   clus
vv  OVCH1 MUTATED OVCH1 WILD-TYPE
  0            16             267
  1             2              46
[1] 2 2
[1] FALSE
D432V7, 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
D432V8, binary
                 cls
clus                0   1
  OVCH1 MUTATED    17   5
  OVCH1 WILD-TYPE 300  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OVCH1 MUTATED     17    5
  OVCH1 WILD-TYPE  300   43
                               clus
vv                              OVCH1 MUTATED OVCH1 WILD-TYPE
  COLON ADENOCARCINOMA                     17             300
  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 242   2  21  20
D432V9, multiclass
    clus
vv   OVCH1 MUTATED OVCH1 WILD-TYPE
  R0            15             242
  R1             0               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"
D432V10, 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
D432V11, 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(433) Variable = SLC7A10 MUTATION ANALYSIS
D433V1, survival
                   sevent
clus2                 0   1
  SLC7A10 MUTATED     6   2
  SLC7A10 WILD-TYPE 276  71
  SLC7A10 MUTATED SLC7A10 WILD-TYPE 
                8               347 
  SLC7A10 MUTATED SLC7A10 WILD-TYPE 
                2                71 
$`SLC7A10 MUTATED`
TCGA-AA-3664 TCGA-AA-3715 TCGA-AA-3947 TCGA-AD-6889 TCGA-AU-6004 TCGA-AZ-6598 
       54.02        19.04        33.01        56.55        27.09        49.41 
TCGA-CM-6674 TCGA-D5-6928 
       12.95        11.64 

$`SLC7A10 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05         6.97         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37         4.21         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  SLC7A10 MUTATED SLC7A10 WILD-TYPE 
            11.64              0.00 
  SLC7A10 MUTATED SLC7A10 WILD-TYPE 
            56.55            140.38 
  SLC7A10 MUTATED SLC7A10 WILD-TYPE 
            30.05             20.12 
[1] "11.6 - 56.5 (30.0)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.1"
D433V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC7A10 MUTATED         1        0        3         3         2         0
  SLC7A10 WILD-TYPE      63        1       22       106         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC7A10 MUTATED           0          0          0          0        0
  SLC7A10 WILD-TYPE        19         10         41         31       35
                   vv
clus                STAGE IVA STAGE IVB
  SLC7A10 MUTATED           0         0
  SLC7A10 WILD-TYPE        13         1
D433V3, multiclass
            clus
vv           SLC7A10 MUTATED SLC7A10 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 3                22
  STAGE IIA                3               106
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC7A10 MUTATED     0   1   6   2
  SLC7A10 WILD-TYPE   9  67 242  39
D433V4, multiclass
    clus
vv   SLC7A10 MUTATED SLC7A10 WILD-TYPE
  T1               0                 9
  T2               1                67
  T3               6               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
  SLC7A10 MUTATED     9   0   0
  SLC7A10 WILD-TYPE 211  80  66
D433V5, multiclass
    clus
vv   SLC7A10 MUTATED SLC7A10 WILD-TYPE
  N0               9               211
  N1               0                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"
D433V6, binary
                   cls
clus                  0   1
  SLC7A10 MUTATED     7   0
  SLC7A10 WILD-TYPE 276  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC7A10 MUTATED      7    0
  SLC7A10 WILD-TYPE  276   48
   clus
vv  SLC7A10 MUTATED SLC7A10 WILD-TYPE
  0               7               276
  1               0                48
[1] 2 2
[1] FALSE
D433V7, binary
                   cls
clus                  0   1
  SLC7A10 MUTATED     5   4
  SLC7A10 WILD-TYPE 165 193
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC7A10 MUTATED      5    4
  SLC7A10 WILD-TYPE  165  193
        clus
vv       SLC7A10 MUTATED SLC7A10 WILD-TYPE
  FEMALE               5               165
  MALE                 4               193
[1] 2 2
[1] FALSE
D433V8, binary
                   cls
clus                  0   1
  SLC7A10 MUTATED     7   2
  SLC7A10 WILD-TYPE 310  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC7A10 MUTATED      7    2
  SLC7A10 WILD-TYPE  310   46
                               clus
vv                              SLC7A10 MUTATED SLC7A10 WILD-TYPE
  COLON ADENOCARCINOMA                        7               310
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SLC7A10 MUTATED     6   0   0   1
  SLC7A10 WILD-TYPE 251   2  22  20
D433V9, multiclass
    clus
vv   SLC7A10 MUTATED SLC7A10 WILD-TYPE
  R0               6               251
  R1               0                 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"
D433V10, 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
D433V11, 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(434) Variable = TMEM37 MUTATION ANALYSIS
D434V1, survival
                  sevent
clus2                0   1
  TMEM37 MUTATED     7   1
  TMEM37 WILD-TYPE 275  72
  TMEM37 MUTATED TMEM37 WILD-TYPE 
               8              347 
  TMEM37 MUTATED TMEM37 WILD-TYPE 
               1               72 
$`TMEM37 MUTATED`
TCGA-A6-3809 TCGA-A6-6141 TCGA-AA-A01R TCGA-AD-6895 TCGA-AZ-6607 TCGA-CA-5796 
       32.75         8.38        35.01         0.72         3.19         3.25 
TCGA-CA-5797 TCGA-CK-4947 
        3.29        17.56 

$`TMEM37 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 
      100.01        29.56         5.23        11.74         1.94         2.24 
TCGA-CA-5255 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.06         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  TMEM37 MUTATED TMEM37 WILD-TYPE 
            0.72             0.00 
  TMEM37 MUTATED TMEM37 WILD-TYPE 
           35.01           140.38 
  TMEM37 MUTATED TMEM37 WILD-TYPE 
           5.835           20.980 
[1] "0.7 - 35.0 (5.8)"   "0.0 - 140.4 (21.0)"
[1] "hr=" "1.2"
D434V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TMEM37 MUTATED         0        0        0         3         1         0
  TMEM37 WILD-TYPE      64        1       25       106         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM37 MUTATED           1          0          0          0        1
  TMEM37 WILD-TYPE        18         10         41         31       34
                  vv
clus               STAGE IVA STAGE IVB
  TMEM37 MUTATED           1         0
  TMEM37 WILD-TYPE        12         1
D434V3, multiclass
            clus
vv           TMEM37 MUTATED TMEM37 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               3              106
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TMEM37 MUTATED     0   0   5   3
  TMEM37 WILD-TYPE   9  68 243  38
D434V4, multiclass
    clus
vv   TMEM37 MUTATED TMEM37 WILD-TYPE
  T1              0                9
  T2              0               68
  T3              5              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
  TMEM37 MUTATED     4   2   2
  TMEM37 WILD-TYPE 216  78  64
D434V5, multiclass
    clus
vv   TMEM37 MUTATED TMEM37 WILD-TYPE
  N0              4              216
  N1              2               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"
D434V6, binary
                  cls
clus                 0   1
  TMEM37 MUTATED     6   1
  TMEM37 WILD-TYPE 277  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM37 MUTATED      6    1
  TMEM37 WILD-TYPE  277   47
   clus
vv  TMEM37 MUTATED TMEM37 WILD-TYPE
  0              6              277
  1              1               47
[1] 2 2
[1] FALSE
D434V7, binary
                  cls
clus                 0   1
  TMEM37 MUTATED     3   5
  TMEM37 WILD-TYPE 167 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM37 MUTATED      3    5
  TMEM37 WILD-TYPE  167  192
        clus
vv       TMEM37 MUTATED TMEM37 WILD-TYPE
  FEMALE              3              167
  MALE                5              192
[1] 2 2
[1] FALSE
D434V8, binary
                  cls
clus                 0   1
  TMEM37 MUTATED     5   3
  TMEM37 WILD-TYPE 312  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM37 MUTATED      5    3
  TMEM37 WILD-TYPE  312   45
                               clus
vv                              TMEM37 MUTATED TMEM37 WILD-TYPE
  COLON ADENOCARCINOMA                       5              312
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TMEM37 MUTATED     4   0   0   1
  TMEM37 WILD-TYPE 253   2  22  20
D434V9, multiclass
    clus
vv   TMEM37 MUTATED TMEM37 WILD-TYPE
  R0              4              253
  R1              0                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"
D434V10, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TMEM37 MUTATED                                  0     2
  TMEM37 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TMEM37 MUTATED                           1     4
  TMEM37 WILD-TYPE                        18   172
D434V11, multiclass
                                  clus
vv                                 TMEM37 MUTATED TMEM37 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(435) Variable = TMEM169 MUTATION ANALYSIS
D435V1, survival
                   sevent
clus2                 0   1
  TMEM169 MUTATED     6   7
  TMEM169 WILD-TYPE 276  66
  TMEM169 MUTATED TMEM169 WILD-TYPE 
               13               342 
  TMEM169 MUTATED TMEM169 WILD-TYPE 
                7                66 
$`TMEM169 MUTATED`
TCGA-A6-4105 TCGA-AA-3489 TCGA-AA-3510 TCGA-AA-3713 TCGA-AD-6889 TCGA-CK-5916 
       14.53         7.04        63.98        19.04        56.55        21.14 
TCGA-CK-6751 TCGA-D5-6529 TCGA-D5-6539 TCGA-DM-A1D7 TCGA-DM-A28F TCGA-F4-6570 
      124.27        20.19        12.49        13.32        35.97         6.18 
TCGA-G4-6303 
       65.85 

$`TMEM169 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37         4.21         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 
       49.08        51.32        21.99         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       13.51        11.51        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
      139.17         6.12        81.37       119.93        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        13.38        13.45        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 
       35.41        19.43       107.67        74.56        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  TMEM169 MUTATED TMEM169 WILD-TYPE 
             6.18              0.00 
  TMEM169 MUTATED TMEM169 WILD-TYPE 
           124.27            140.38 
  TMEM169 MUTATED TMEM169 WILD-TYPE 
            20.19             20.20 
[1] "6.2 - 124.3 (20.2)" "0.0 - 140.4 (20.2)"
[1] "hr=" "2"  
D435V2, 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       23       104         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM169 MUTATED           0          1          1          0        2
  TMEM169 WILD-TYPE        19          9         40         31       33
                   vv
clus                STAGE IVA STAGE IVB
  TMEM169 MUTATED           0         0
  TMEM169 WILD-TYPE        13         1
D435V3, multiclass
            clus
vv           TMEM169 MUTATED TMEM169 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 2                23
  STAGE IIA                5               104
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               1                 9
  STAGE IIIB               1                40
  STAGE IIIC               0                31
  STAGE IV                 2                33
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TMEM169 MUTATED     1   1  11   0
  TMEM169 WILD-TYPE   8  67 237  41
D435V4, multiclass
    clus
vv   TMEM169 MUTATED TMEM169 WILD-TYPE
  T1               1                 8
  T2               1                67
  T3              11               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
  TMEM169 MUTATED    11   2   0
  TMEM169 WILD-TYPE 209  78  66
D435V5, multiclass
    clus
vv   TMEM169 MUTATED TMEM169 WILD-TYPE
  N0              11               209
  N1               2                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"
D435V6, binary
                   cls
clus                  0   1
  TMEM169 MUTATED    10   2
  TMEM169 WILD-TYPE 273  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM169 MUTATED     10    2
  TMEM169 WILD-TYPE  273   46
   clus
vv  TMEM169 MUTATED TMEM169 WILD-TYPE
  0              10               273
  1               2                46
[1] 2 2
[1] FALSE
D435V7, 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
D435V8, binary
                   cls
clus                  0   1
  TMEM169 MUTATED    12   1
  TMEM169 WILD-TYPE 305  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM169 MUTATED     12    1
  TMEM169 WILD-TYPE  305   47
                               clus
vv                              TMEM169 MUTATED TMEM169 WILD-TYPE
  COLON ADENOCARCINOMA                       12               305
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  TMEM169 MUTATED     6   0   1   2
  TMEM169 WILD-TYPE 251   2  21  19
D435V9, multiclass
    clus
vv   TMEM169 MUTATED TMEM169 WILD-TYPE
  R0               6               251
  R1               0                 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"
D435V10, 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
D435V11, 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(436) Variable = RBL2 MUTATION ANALYSIS
D436V1, survival
                sevent
clus2              0   1
  RBL2 MUTATED    18   2
  RBL2 WILD-TYPE 264  71
  RBL2 MUTATED RBL2 WILD-TYPE 
            20            335 
  RBL2 MUTATED RBL2 WILD-TYPE 
             2             71 
$`RBL2 MUTATED`
TCGA-A6-3809 TCGA-A6-5665 TCGA-AA-3554 TCGA-AA-3558 TCGA-AA-3811 TCGA-AA-3864 
       32.75        22.06        17.95        20.98        10.06        53.00 
TCGA-AA-3977 TCGA-AA-A010 TCGA-AA-A01Q TCGA-AD-5900 TCGA-AD-6895 TCGA-AZ-4315 
       25.02        34.98         1.02         0.07         0.72        58.39 
TCGA-AZ-6605 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-5861 TCGA-CM-5864 TCGA-CM-6169 
        5.23         0.33         0.10        15.02        15.02        13.02 
TCGA-D5-5538 TCGA-G4-6588 
       12.26        26.17 

$`RBL2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       24.00        29.95        23.01        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        19.04        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37         4.21        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07         0.26         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01         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 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        91.79        46.75        52.80 

  RBL2 MUTATED RBL2 WILD-TYPE 
          0.07           0.00 
  RBL2 MUTATED RBL2 WILD-TYPE 
         58.39         140.38 
  RBL2 MUTATED RBL2 WILD-TYPE 
         15.02          20.98 
[1] "0.1 - 58.4 (15.0)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.5"
D436V2, 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       22       101         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RBL2 MUTATED           1          0          2          0        0         0
  RBL2 WILD-TYPE        18         10         39         31       35        13
                vv
clus             STAGE IVB
  RBL2 MUTATED           0
  RBL2 WILD-TYPE         1
D436V3, multiclass
            clus
vv           RBL2 MUTATED RBL2 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              3             22
  STAGE IIA             8            101
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            2             39
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RBL2 MUTATED     0   4  13   4
  RBL2 WILD-TYPE   9  64 235  37
D436V4, multiclass
    clus
vv   RBL2 MUTATED RBL2 WILD-TYPE
  T1            0              9
  T2            4             64
  T3           13            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
  RBL2 MUTATED    17   3   1
  RBL2 WILD-TYPE 203  77  65
D436V5, multiclass
    clus
vv   RBL2 MUTATED RBL2 WILD-TYPE
  N0           17            203
  N1            3             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"
D436V6, binary
                cls
clus               0   1
  RBL2 MUTATED    18   0
  RBL2 WILD-TYPE 265  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBL2 MUTATED     18    0
  RBL2 WILD-TYPE  265   48
   clus
vv  RBL2 MUTATED RBL2 WILD-TYPE
  0           18            265
  1            0             48
[1] 2 2
[1] FALSE
D436V7, 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
D436V8, binary
                cls
clus               0   1
  RBL2 MUTATED    18   3
  RBL2 WILD-TYPE 299  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBL2 MUTATED     18    3
  RBL2 WILD-TYPE  299   45
                               clus
vv                              RBL2 MUTATED RBL2 WILD-TYPE
  COLON ADENOCARCINOMA                    18            299
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RBL2 MUTATED    15   0   1   2
  RBL2 WILD-TYPE 242   2  21  19
D436V9, multiclass
    clus
vv   RBL2 MUTATED RBL2 WILD-TYPE
  R0           15            242
  R1            0              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"
D436V10, 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
D436V11, 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(437) Variable = DDX17 MUTATION ANALYSIS
D437V1, survival
                 sevent
clus2               0   1
  DDX17 MUTATED     7   5
  DDX17 WILD-TYPE 275  68
  DDX17 MUTATED DDX17 WILD-TYPE 
             12             343 
  DDX17 MUTATED DDX17 WILD-TYPE 
              5              68 
$`DDX17 MUTATED`
TCGA-A6-2676 TCGA-AA-3715 TCGA-AA-3852 TCGA-AA-3949 TCGA-AA-A00N TCGA-AA-A01Q 
       42.90        19.04         0.00        26.01         4.01         1.02 
TCGA-AD-6889 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CM-4746 TCGA-CM-6674 TCGA-G4-6628 
       56.55        49.41         0.33        37.02        12.95        52.80 

$`DDX17 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       10.06         0.00        33.07        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        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        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        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        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 
       46.75 

  DDX17 MUTATED DDX17 WILD-TYPE 
              0               0 
  DDX17 MUTATED DDX17 WILD-TYPE 
          56.55          140.38 
  DDX17 MUTATED DDX17 WILD-TYPE 
         22.525          20.190 
[1] "0.0 - 56.5 (22.5)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2.1"
D437V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DDX17 MUTATED         2        0        3         4         2         0
  DDX17 WILD-TYPE      62        1       22       105         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DDX17 MUTATED           0          0          1          0        0         0
  DDX17 WILD-TYPE        19         10         40         31       35        13
                 vv
clus              STAGE IVB
  DDX17 MUTATED           0
  DDX17 WILD-TYPE         1
D437V3, multiclass
            clus
vv           DDX17 MUTATED DDX17 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              4             105
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DDX17 MUTATED     0   2   8   2
  DDX17 WILD-TYPE   9  66 240  39
D437V4, multiclass
    clus
vv   DDX17 MUTATED DDX17 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             8             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
  DDX17 MUTATED    11   1   0
  DDX17 WILD-TYPE 209  79  66
D437V5, multiclass
    clus
vv   DDX17 MUTATED DDX17 WILD-TYPE
  N0            11             209
  N1             1              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"
D437V6, binary
                 cls
clus                0   1
  DDX17 MUTATED    11   0
  DDX17 WILD-TYPE 272  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX17 MUTATED     11    0
  DDX17 WILD-TYPE  272   48
   clus
vv  DDX17 MUTATED DDX17 WILD-TYPE
  0            11             272
  1             0              48
[1] 2 2
[1] FALSE
D437V7, binary
                 cls
clus                0   1
  DDX17 MUTATED     4   8
  DDX17 WILD-TYPE 166 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX17 MUTATED      4    8
  DDX17 WILD-TYPE  166  189
        clus
vv       DDX17 MUTATED DDX17 WILD-TYPE
  FEMALE             4             166
  MALE               8             189
[1] 2 2
[1] FALSE
D437V8, binary
                 cls
clus                0   1
  DDX17 MUTATED     8   4
  DDX17 WILD-TYPE 309  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX17 MUTATED      8    4
  DDX17 WILD-TYPE  309   44
                               clus
vv                              DDX17 MUTATED DDX17 WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DDX17 MUTATED     9   0   0   1
  DDX17 WILD-TYPE 248   2  22  20
D437V9, multiclass
    clus
vv   DDX17 MUTATED DDX17 WILD-TYPE
  R0             9             248
  R1             0               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"
D437V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DDX17 MUTATED                                  0     2
  DDX17 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DDX17 MUTATED                           1     4
  DDX17 WILD-TYPE                        18   172
D437V11, multiclass
                                  clus
vv                                 DDX17 MUTATED DDX17 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(438) Variable = DDX3X MUTATION ANALYSIS
D438V1, survival
                 sevent
clus2               0   1
  DDX3X MUTATED     6   3
  DDX3X WILD-TYPE 276  70
  DDX3X MUTATED DDX3X WILD-TYPE 
              9             346 
  DDX3X MUTATED DDX3X WILD-TYPE 
              3              70 
$`DDX3X MUTATED`
TCGA-AA-3492 TCGA-AA-3662 TCGA-AA-A010 TCGA-AD-6964 TCGA-AU-6004 TCGA-CA-6717 
        3.02         6.05        34.98        10.88        27.09         0.33 
TCGA-CK-4950 TCGA-CM-5344 TCGA-G4-6626 
       40.34        22.03        46.75 

$`DDX3X WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       19.99        13.94        19.99        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
        1.35        17.56       102.44        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       35.80        26.17        91.79        52.80 

  DDX3X MUTATED DDX3X WILD-TYPE 
           0.33            0.00 
  DDX3X MUTATED DDX3X WILD-TYPE 
          46.75          140.38 
  DDX3X MUTATED DDX3X WILD-TYPE 
         22.030          20.155 
[1] "0.3 - 46.8 (22.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2.1"
D438V2, 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       24       106         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DDX3X MUTATED           0          1          1          0        1         0
  DDX3X WILD-TYPE        19          9         40         31       34        13
                 vv
clus              STAGE IVB
  DDX3X MUTATED           0
  DDX3X WILD-TYPE         1
D438V3, multiclass
            clus
vv           DDX3X MUTATED DDX3X WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              3             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DDX3X MUTATED     0   1   6   3
  DDX3X WILD-TYPE   9  67 242  38
D438V4, multiclass
    clus
vv   DDX3X MUTATED DDX3X WILD-TYPE
  T1             0               9
  T2             1              67
  T3             6             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
  DDX3X MUTATED     6   2   2
  DDX3X WILD-TYPE 214  78  64
D438V5, multiclass
    clus
vv   DDX3X MUTATED DDX3X WILD-TYPE
  N0             6             214
  N1             2              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"
D438V6, binary
                 cls
clus                0   1
  DDX3X MUTATED     8   1
  DDX3X WILD-TYPE 275  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX3X MUTATED      8    1
  DDX3X WILD-TYPE  275   47
   clus
vv  DDX3X MUTATED DDX3X WILD-TYPE
  0             8             275
  1             1              47
[1] 2 2
[1] FALSE
D438V7, 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
D438V8, binary
                 cls
clus                0   1
  DDX3X MUTATED     9   1
  DDX3X WILD-TYPE 308  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX3X MUTATED      9    1
  DDX3X WILD-TYPE  308   47
                               clus
vv                              DDX3X MUTATED DDX3X WILD-TYPE
  COLON ADENOCARCINOMA                      9             308
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DDX3X MUTATED     6   1   1   1
  DDX3X WILD-TYPE 251   1  21  20
D438V9, multiclass
    clus
vv   DDX3X MUTATED DDX3X WILD-TYPE
  R0             6             251
  R1             1               1
  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"
D438V10, 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
D438V11, 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(439) Variable = HSD17B11 MUTATION ANALYSIS
D439V1, survival
                    sevent
clus2                  0   1
  HSD17B11 MUTATED     4   0
  HSD17B11 WILD-TYPE 278  73
  HSD17B11 MUTATED HSD17B11 WILD-TYPE 
                 4                351 
  HSD17B11 MUTATED HSD17B11 WILD-TYPE 
                 0                 73 
$`HSD17B11 MUTATED`
TCGA-CK-4952 TCGA-CM-5868 TCGA-D5-6529 TCGA-F4-6808 
       15.62        17.03        20.19        33.67 

$`HSD17B11 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 
        1.35        17.56       102.44        40.34        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       11.51        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  HSD17B11 MUTATED HSD17B11 WILD-TYPE 
             15.62               0.00 
  HSD17B11 MUTATED HSD17B11 WILD-TYPE 
             33.67             140.38 
  HSD17B11 MUTATED HSD17B11 WILD-TYPE 
             18.61              20.28 
[1] "15.6 - 33.7 (18.6)" "0.0 - 140.4 (20.3)"
[1] "hr="     "3300000"
D439V2, 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       25       108         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HSD17B11 MUTATED           1          0          0          0        0
  HSD17B11 WILD-TYPE        18         10         41         31       35
                    vv
clus                 STAGE IVA STAGE IVB
  HSD17B11 MUTATED           1         0
  HSD17B11 WILD-TYPE        12         1
D439V3, multiclass
            clus
vv           HSD17B11 MUTATED HSD17B11 WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  0                 25
  STAGE IIA                 1                108
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 1                 18
  STAGE IIIA                0                 10
  STAGE IIIB                0                 41
  STAGE IIIC                0                 31
  STAGE IV                  0                 35
  STAGE IVA                 1                 12
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of 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  68 247  39
D439V4, multiclass
    clus
vv   HSD17B11 MUTATED HSD17B11 WILD-TYPE
  T1                1                  8
  T2                0                 68
  T3                1                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
  HSD17B11 MUTATED     2   1   1
  HSD17B11 WILD-TYPE 218  79  65
D439V5, multiclass
    clus
vv   HSD17B11 MUTATED HSD17B11 WILD-TYPE
  N0                2                218
  N1                1                 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"
D439V6, binary
                    cls
clus                   0   1
  HSD17B11 MUTATED     3   1
  HSD17B11 WILD-TYPE 280  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HSD17B11 MUTATED      3    1
  HSD17B11 WILD-TYPE  280   47
   clus
vv  HSD17B11 MUTATED HSD17B11 WILD-TYPE
  0                3                280
  1                1                 47
[1] 2 2
[1] FALSE
D439V7, 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
D439V8, binary
                    cls
clus                   0   1
  HSD17B11 MUTATED     3   1
  HSD17B11 WILD-TYPE 314  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HSD17B11 MUTATED      3    1
  HSD17B11 WILD-TYPE  314   47
                               clus
vv                              HSD17B11 MUTATED HSD17B11 WILD-TYPE
  COLON ADENOCARCINOMA                         3                314
  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 254   2  22  20
D439V9, multiclass
    clus
vv   HSD17B11 MUTATED HSD17B11 WILD-TYPE
  R0                3                254
  R1                0                  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"
D439V10, 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
D439V11, 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(440) Variable = HDAC1 MUTATION ANALYSIS
D440V1, survival
                 sevent
clus2               0   1
  HDAC1 MUTATED     4   1
  HDAC1 WILD-TYPE 278  72
  HDAC1 MUTATED HDAC1 WILD-TYPE 
              5             350 
  HDAC1 MUTATED HDAC1 WILD-TYPE 
              1              72 
$`HDAC1 MUTATED`
TCGA-A6-5661 TCGA-A6-6780 TCGA-AA-A01Q TCGA-AA-A02K TCGA-D5-6535 
       33.53        20.12         1.02        14.01        15.12 

$`HDAC1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        43.27        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  HDAC1 MUTATED HDAC1 WILD-TYPE 
           1.02            0.00 
  HDAC1 MUTATED HDAC1 WILD-TYPE 
          33.53          140.38 
  HDAC1 MUTATED HDAC1 WILD-TYPE 
          15.12           20.63 
[1] "1.0 - 33.5 (15.1)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "1.5"
D440V2, 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       24       107         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        19         10         40         31       34        13
                 vv
clus              STAGE IVB
  HDAC1 MUTATED           0
  HDAC1 WILD-TYPE         1
D440V3, multiclass
            clus
vv           HDAC1 MUTATED HDAC1 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              2             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HDAC1 MUTATED     0   0   4   1
  HDAC1 WILD-TYPE   9  68 244  40
D440V4, multiclass
    clus
vv   HDAC1 MUTATED HDAC1 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             4             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
  HDAC1 MUTATED     3   1   1
  HDAC1 WILD-TYPE 217  79  65
D440V5, multiclass
    clus
vv   HDAC1 MUTATED HDAC1 WILD-TYPE
  N0             3             217
  N1             1              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"
D440V6, binary
                 cls
clus                0   1
  HDAC1 MUTATED     2   1
  HDAC1 WILD-TYPE 281  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HDAC1 MUTATED      2    1
  HDAC1 WILD-TYPE  281   47
   clus
vv  HDAC1 MUTATED HDAC1 WILD-TYPE
  0             2             281
  1             1              47
[1] 2 2
[1] FALSE
D440V7, 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
D440V8, binary
                 cls
clus                0   1
  HDAC1 MUTATED     4   1
  HDAC1 WILD-TYPE 313  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HDAC1 MUTATED      4    1
  HDAC1 WILD-TYPE  313   47
                               clus
vv                              HDAC1 MUTATED HDAC1 WILD-TYPE
  COLON ADENOCARCINOMA                      4             313
  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 255   2  21  20
D440V9, multiclass
    clus
vv   HDAC1 MUTATED HDAC1 WILD-TYPE
  R0             2             255
  R1             0               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"
D440V10, 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
D440V11, 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(441) Variable = ENSA MUTATION ANALYSIS
D441V1, survival
                sevent
clus2              0   1
  ENSA MUTATED     3   2
  ENSA WILD-TYPE 279  71
  ENSA MUTATED ENSA WILD-TYPE 
             5            350 
  ENSA MUTATED ENSA WILD-TYPE 
             2             71 
$`ENSA MUTATED`
TCGA-AA-3492 TCGA-CA-6718 TCGA-D5-5537 TCGA-D5-6532 TCGA-G4-6309 
        3.02         0.10        45.40        18.25        51.75 

$`ENSA WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.33         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  ENSA MUTATED ENSA WILD-TYPE 
           0.1            0.0 
  ENSA MUTATED ENSA WILD-TYPE 
         51.75         140.38 
  ENSA MUTATED ENSA WILD-TYPE 
        18.250         20.235 
[1] "0.1 - 51.8 (18.2)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.9"
D441V2, 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       24       106         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        19         10         40         31       35        13
                vv
clus             STAGE IVB
  ENSA MUTATED           0
  ENSA WILD-TYPE         1
D441V3, multiclass
            clus
vv           ENSA MUTATED ENSA WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             3            106
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ENSA MUTATED     0   0   5   0
  ENSA WILD-TYPE   9  68 243  41
D441V4, multiclass
    clus
vv   ENSA MUTATED ENSA WILD-TYPE
  T1            0              9
  T2            0             68
  T3            5            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
  ENSA MUTATED     3   1   1
  ENSA WILD-TYPE 217  79  65
D441V5, multiclass
    clus
vv   ENSA MUTATED ENSA WILD-TYPE
  N0            3            217
  N1            1             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"
D441V6, binary
                cls
clus               0   1
  ENSA MUTATED     4   0
  ENSA WILD-TYPE 279  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  ENSA MUTATED      4    0
  ENSA WILD-TYPE  279   48
   clus
vv  ENSA MUTATED ENSA WILD-TYPE
  0            4            279
  1            0             48
[1] 2 2
[1] FALSE
D441V7, 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
D441V8, binary
                cls
clus               0   1
  ENSA MUTATED     5   0
  ENSA WILD-TYPE 312  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  ENSA MUTATED      5    0
  ENSA WILD-TYPE  312   48
                               clus
vv                              ENSA MUTATED ENSA WILD-TYPE
  COLON ADENOCARCINOMA                     5            312
  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 254   2  22  19
D441V9, multiclass
    clus
vv   ENSA MUTATED ENSA WILD-TYPE
  R0            3            254
  R1            0              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"
D441V10, 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
D441V11, 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(442) Variable = TNPO1 MUTATION ANALYSIS
D442V1, survival
                 sevent
clus2               0   1
  TNPO1 MUTATED    13   2
  TNPO1 WILD-TYPE 269  71
  TNPO1 MUTATED TNPO1 WILD-TYPE 
             15             340 
  TNPO1 MUTATED TNPO1 WILD-TYPE 
              2              71 
$`TNPO1 MUTATED`
TCGA-A6-3809 TCGA-A6-6141 TCGA-AA-3510 TCGA-AA-3518 TCGA-AA-3966 TCGA-AA-3977 
       32.75         8.38        63.98         1.02         2.01        25.02 
TCGA-AA-A010 TCGA-AU-6004 TCGA-AZ-6598 TCGA-CK-5914 TCGA-CK-5916 TCGA-CM-6678 
       34.98        27.09        49.41        21.99        21.14        11.01 
TCGA-D5-6929 TCGA-G4-6323 TCGA-G4-6586 
       13.41        13.78        35.80 

$`TNPO1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 
        6.97         1.02        13.02        38.99         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13        83.80        22.36        62.79        61.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-6747 TCGA-CK-6748 
       40.34        15.62        49.08        51.32         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  TNPO1 MUTATED TNPO1 WILD-TYPE 
           1.02            0.00 
  TNPO1 MUTATED TNPO1 WILD-TYPE 
          63.98          140.38 
  TNPO1 MUTATED TNPO1 WILD-TYPE 
          21.99           20.07 
[1] "1.0 - 64.0 (22.0)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.5"
D442V2, 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       23       104         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        19         10         40         31       34        12
                 vv
clus              STAGE IVB
  TNPO1 MUTATED           0
  TNPO1 WILD-TYPE         1
D442V3, multiclass
            clus
vv           TNPO1 MUTATED TNPO1 WILD-TYPE
  STAGE I                2              62
  STAGE IA               1               0
  STAGE II               2              23
  STAGE IIA              5             104
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 239  38
D442V4, multiclass
    clus
vv   TNPO1 MUTATED TNPO1 WILD-TYPE
  T1             1               8
  T2             2              66
  T3             9             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
  TNPO1 MUTATED    13   3   0
  TNPO1 WILD-TYPE 207  77  66
D442V5, multiclass
    clus
vv   TNPO1 MUTATED TNPO1 WILD-TYPE
  N0            13             207
  N1             3              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"
D442V6, binary
                 cls
clus                0   1
  TNPO1 MUTATED    10   2
  TNPO1 WILD-TYPE 273  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TNPO1 MUTATED     10    2
  TNPO1 WILD-TYPE  273   46
   clus
vv  TNPO1 MUTATED TNPO1 WILD-TYPE
  0            10             273
  1             2              46
[1] 2 2
[1] FALSE
D442V7, 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
D442V8, binary
                 cls
clus                0   1
  TNPO1 MUTATED    14   2
  TNPO1 WILD-TYPE 303  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TNPO1 MUTATED     14    2
  TNPO1 WILD-TYPE  303   46
                               clus
vv                              TNPO1 MUTATED TNPO1 WILD-TYPE
  COLON ADENOCARCINOMA                     14             303
  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 247   2  22  19
D442V9, multiclass
    clus
vv   TNPO1 MUTATED TNPO1 WILD-TYPE
  R0            10             247
  R1             0               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"
D442V10, 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
D442V11, 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(443) Variable = KIAA1804 MUTATION ANALYSIS
D443V1, survival
                    sevent
clus2                  0   1
  KIAA1804 MUTATED    13   3
  KIAA1804 WILD-TYPE 269  70
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                16                339 
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                 3                 70 
$`KIAA1804 MUTATED`
TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3845 
       22.06        63.98        29.95         0.92        19.00         0.00 
TCGA-AA-3966 TCGA-AA-A010 TCGA-AD-6964 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CM-4744 
        2.01        34.98        10.88        49.41         0.33        20.02 
TCGA-CM-5861 TCGA-D5-6538 TCGA-G4-6317 TCGA-G4-6628 
       15.02        17.13        36.00        52.80 

$`KIAA1804 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
        5.98        37.05        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       14.93        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85         4.80        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       51.75        45.11        36.72        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       26.17        91.79        46.75 

  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                 0                  0 
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
             63.98             140.38 
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
             19.51              20.28 
[1] "0.0 - 64.0 (19.5)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1"  
D443V2, 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       23       103         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1804 MUTATED           1          0          1          1        1
  KIAA1804 WILD-TYPE        18         10         40         30       34
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA1804 MUTATED           0         0
  KIAA1804 WILD-TYPE        13         1
D443V3, multiclass
            clus
vv           KIAA1804 MUTATED KIAA1804 WILD-TYPE
  STAGE I                   2                 62
  STAGE IA                  0                  1
  STAGE II                  2                 23
  STAGE IIA                 6                103
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 1                 18
  STAGE IIIA                0                 10
  STAGE IIIB                1                 40
  STAGE IIIC                1                 30
  STAGE IV                  1                 34
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA1804 MUTATED     0   2  12   2
  KIAA1804 WILD-TYPE   9  66 236  39
D443V4, multiclass
    clus
vv   KIAA1804 MUTATED KIAA1804 WILD-TYPE
  T1                0                  9
  T2                2                 66
  T3               12                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
  KIAA1804 MUTATED    11   2   3
  KIAA1804 WILD-TYPE 209  78  63
D443V5, multiclass
    clus
vv   KIAA1804 MUTATED KIAA1804 WILD-TYPE
  N0               11                209
  N1                2                 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"
D443V6, binary
                    cls
clus                   0   1
  KIAA1804 MUTATED    12   1
  KIAA1804 WILD-TYPE 271  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1804 MUTATED     12    1
  KIAA1804 WILD-TYPE  271   47
   clus
vv  KIAA1804 MUTATED KIAA1804 WILD-TYPE
  0               12                271
  1                1                 47
[1] 2 2
[1] FALSE
D443V7, 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
D443V8, binary
                    cls
clus                   0   1
  KIAA1804 MUTATED    13   3
  KIAA1804 WILD-TYPE 304  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1804 MUTATED     13    3
  KIAA1804 WILD-TYPE  304   45
                               clus
vv                              KIAA1804 MUTATED KIAA1804 WILD-TYPE
  COLON ADENOCARCINOMA                        13                304
  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 246   2  21  20
D443V9, multiclass
    clus
vv   KIAA1804 MUTATED KIAA1804 WILD-TYPE
  R0               11                246
  R1                0                  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"
D443V10, 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
D443V11, 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(444) Variable = PARP12 MUTATION ANALYSIS
D444V1, survival
                  sevent
clus2                0   1
  PARP12 MUTATED     9   1
  PARP12 WILD-TYPE 273  72
  PARP12 MUTATED PARP12 WILD-TYPE 
              10              345 
  PARP12 MUTATED PARP12 WILD-TYPE 
               1               72 
$`PARP12 MUTATED`
TCGA-A6-6780 TCGA-AA-3660 TCGA-AA-3685 TCGA-AA-3950 TCGA-AA-3966 TCGA-AZ-6598 
       20.12        78.08        37.05        24.00         2.01        49.41 
TCGA-CK-4947 TCGA-F4-6460 TCGA-G4-6321 TCGA-G4-6628 
       17.56        13.38        22.09        52.80 

$`PARP12 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        61.02         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       15.02        11.01         5.98        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01         2.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        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        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
        1.35       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 
       51.75        45.11        36.72        36.00        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       26.17        91.79        46.75 

  PARP12 MUTATED PARP12 WILD-TYPE 
            2.01             0.00 
  PARP12 MUTATED PARP12 WILD-TYPE 
           78.08           140.38 
  PARP12 MUTATED PARP12 WILD-TYPE 
          23.045           20.020 
[1] "2.0 - 78.1 (23.0)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "2.7"
D444V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PARP12 MUTATED         1        0        3         3         0         0
  PARP12 WILD-TYPE      63        1       22       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PARP12 MUTATED           1          0          1          0        0
  PARP12 WILD-TYPE        18         10         40         31       35
                  vv
clus               STAGE IVA STAGE IVB
  PARP12 MUTATED           1         0
  PARP12 WILD-TYPE        12         1
D444V3, multiclass
            clus
vv           PARP12 MUTATED PARP12 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                3               22
  STAGE IIA               3              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PARP12 MUTATED     0   2   7   1
  PARP12 WILD-TYPE   9  66 241  40
D444V4, multiclass
    clus
vv   PARP12 MUTATED PARP12 WILD-TYPE
  T1              0                9
  T2              2               66
  T3              7              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
  PARP12 MUTATED     7   3   0
  PARP12 WILD-TYPE 213  77  66
D444V5, multiclass
    clus
vv   PARP12 MUTATED PARP12 WILD-TYPE
  N0              7              213
  N1              3               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"
D444V6, binary
                  cls
clus                 0   1
  PARP12 MUTATED     7   0
  PARP12 WILD-TYPE 276  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PARP12 MUTATED      7    0
  PARP12 WILD-TYPE  276   48
   clus
vv  PARP12 MUTATED PARP12 WILD-TYPE
  0              7              276
  1              0               48
[1] 2 2
[1] FALSE
D444V7, binary
                  cls
clus                 0   1
  PARP12 MUTATED     7   3
  PARP12 WILD-TYPE 163 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PARP12 MUTATED      7    3
  PARP12 WILD-TYPE  163  194
        clus
vv       PARP12 MUTATED PARP12 WILD-TYPE
  FEMALE              7              163
  MALE                3              194
[1] 2 2
[1] FALSE
D444V8, binary
                  cls
clus                 0   1
  PARP12 MUTATED     7   3
  PARP12 WILD-TYPE 310  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PARP12 MUTATED      7    3
  PARP12 WILD-TYPE  310   45
                               clus
vv                              PARP12 MUTATED PARP12 WILD-TYPE
  COLON ADENOCARCINOMA                       7              310
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PARP12 MUTATED     6   0   0   1
  PARP12 WILD-TYPE 251   2  22  20
D444V9, multiclass
    clus
vv   PARP12 MUTATED PARP12 WILD-TYPE
  R0              6              251
  R1              0                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"
D444V10, 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
D444V11, 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(445) Variable = SCLT1 MUTATION ANALYSIS
D445V1, survival
                 sevent
clus2               0   1
  SCLT1 MUTATED    13   4
  SCLT1 WILD-TYPE 269  69
  SCLT1 MUTATED SCLT1 WILD-TYPE 
             17             338 
  SCLT1 MUTATED SCLT1 WILD-TYPE 
              4              69 
$`SCLT1 MUTATED`
TCGA-A6-6782 TCGA-AA-3496 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3845 TCGA-AA-3864 
       20.28         1.02         6.97         0.92         0.00        53.00 
TCGA-AA-A010 TCGA-AA-A01Q TCGA-AD-6889 TCGA-AZ-4315 TCGA-AZ-6601 TCGA-CA-6717 
       34.98         1.02        56.55        58.39       100.01         0.33 
TCGA-DM-A0XD TCGA-DM-A28F TCGA-G4-6299 TCGA-G4-6307 TCGA-G4-6588 
       24.43        35.97        74.56        55.04        26.17 

$`SCLT1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       23.87        20.12        19.66         7.04         3.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02        14.93        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        11.38        10.26       119.70        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
      119.93        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 
      107.67        65.85        53.62        44.68        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  SCLT1 MUTATED SCLT1 WILD-TYPE 
              0               0 
  SCLT1 MUTATED SCLT1 WILD-TYPE 
         100.01          140.38 
  SCLT1 MUTATED SCLT1 WILD-TYPE 
         26.170          20.005 
[1] "0.0 - 100.0 (26.2)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.1"
D445V2, 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       20       103         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        18         10         39         30       35        13
                 vv
clus              STAGE IVB
  SCLT1 MUTATED           0
  SCLT1 WILD-TYPE         1
D445V3, multiclass
            clus
vv           SCLT1 MUTATED SCLT1 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               5              20
  STAGE IIA              6             103
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SCLT1 MUTATED     0   0  15   3
  SCLT1 WILD-TYPE   9  68 233  38
D445V4, multiclass
    clus
vv   SCLT1 MUTATED SCLT1 WILD-TYPE
  T1             0               9
  T2             0              68
  T3            15             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
  SCLT1 MUTATED    14   3   1
  SCLT1 WILD-TYPE 206  77  65
D445V5, multiclass
    clus
vv   SCLT1 MUTATED SCLT1 WILD-TYPE
  N0            14             206
  N1             3              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"
D445V6, binary
                 cls
clus                0   1
  SCLT1 MUTATED    16   0
  SCLT1 WILD-TYPE 267  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCLT1 MUTATED     16    0
  SCLT1 WILD-TYPE  267   48
   clus
vv  SCLT1 MUTATED SCLT1 WILD-TYPE
  0            16             267
  1             0              48
[1] 2 2
[1] FALSE
D445V7, 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
D445V8, binary
                 cls
clus                0   1
  SCLT1 MUTATED    17   1
  SCLT1 WILD-TYPE 300  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCLT1 MUTATED     17    1
  SCLT1 WILD-TYPE  300   47
                               clus
vv                              SCLT1 MUTATED SCLT1 WILD-TYPE
  COLON ADENOCARCINOMA                     17             300
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SCLT1 MUTATED    11   0   0   2
  SCLT1 WILD-TYPE 246   2  22  19
D445V9, multiclass
    clus
vv   SCLT1 MUTATED SCLT1 WILD-TYPE
  R0            11             246
  R1             0               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"
D445V10, 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
D445V11, 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(446) Variable = ATAD2B MUTATION ANALYSIS
D446V1, survival
                  sevent
clus2                0   1
  ATAD2B MUTATED    12   3
  ATAD2B WILD-TYPE 270  70
  ATAD2B MUTATED ATAD2B WILD-TYPE 
              15              340 
  ATAD2B MUTATED ATAD2B WILD-TYPE 
               3               70 
$`ATAD2B MUTATED`
TCGA-A6-3809 TCGA-A6-5665 TCGA-A6-6782 TCGA-AA-3977 TCGA-AA-A010 TCGA-AA-A01K 
       32.75        22.06        20.28        25.02        34.98        31.00 
TCGA-AD-5900 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-6717 TCGA-CM-5348 
        0.07       100.01         5.23         3.19         0.33        22.98 
TCGA-CM-6171 TCGA-D5-6930 TCGA-DM-A1D9 
       14.04         1.51       140.38 

$`ATAD2B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        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        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6608 
       49.41         6.77        12.10        29.56        11.74         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32        12.59         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  ATAD2B MUTATED ATAD2B WILD-TYPE 
            0.07             0.00 
  ATAD2B MUTATED ATAD2B WILD-TYPE 
          140.38           139.17 
  ATAD2B MUTATED ATAD2B WILD-TYPE 
           22.06            20.07 
[1] "0.1 - 140.4 (22.1)" "0.0 - 139.2 (20.1)"
[1] "hr=" "1.1"
D446V2, 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       24       105         5         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATAD2B MUTATED           0          0          2          1        1
  ATAD2B WILD-TYPE        19         10         39         30       34
                  vv
clus               STAGE IVA STAGE IVB
  ATAD2B MUTATED           0         0
  ATAD2B WILD-TYPE        13         1
D446V3, multiclass
            clus
vv           ATAD2B MUTATED ATAD2B WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               4              105
  STAGE IIB               3                5
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              1               30
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ATAD2B MUTATED     0   3   7   5
  ATAD2B WILD-TYPE   9  65 241  36
D446V4, multiclass
    clus
vv   ATAD2B MUTATED ATAD2B WILD-TYPE
  T1              0                9
  T2              3               65
  T3              7              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
  ATAD2B MUTATED    11   2   2
  ATAD2B WILD-TYPE 209  78  64
D446V5, multiclass
    clus
vv   ATAD2B MUTATED ATAD2B WILD-TYPE
  N0             11              209
  N1              2               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"
D446V6, binary
                  cls
clus                 0   1
  ATAD2B MUTATED    11   1
  ATAD2B WILD-TYPE 272  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATAD2B MUTATED     11    1
  ATAD2B WILD-TYPE  272   47
   clus
vv  ATAD2B MUTATED ATAD2B WILD-TYPE
  0             11              272
  1              1               47
[1] 2 2
[1] FALSE
D446V7, 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
D446V8, binary
                  cls
clus                 0   1
  ATAD2B MUTATED    11   4
  ATAD2B WILD-TYPE 306  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATAD2B MUTATED     11    4
  ATAD2B WILD-TYPE  306   44
                               clus
vv                              ATAD2B MUTATED ATAD2B WILD-TYPE
  COLON ADENOCARCINOMA                      11              306
  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 249   2  22  20
D446V9, multiclass
    clus
vv   ATAD2B MUTATED ATAD2B WILD-TYPE
  R0              8              249
  R1              0                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"
D446V10, 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
D446V11, 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(447) Variable = CCDC160 MUTATION ANALYSIS
D447V1, survival
                   sevent
clus2                 0   1
  CCDC160 MUTATED     8   0
  CCDC160 WILD-TYPE 274  73
  CCDC160 MUTATED CCDC160 WILD-TYPE 
                8               347 
  CCDC160 MUTATED CCDC160 WILD-TYPE 
                0                73 
$`CCDC160 MUTATED`
TCGA-A6-6653 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-A010 TCGA-CK-6751 TCGA-G4-6586 
       24.39         0.92        19.00        34.98       124.27        35.80 
TCGA-G4-6588 TCGA-G4-6628 
       26.17        52.80 

$`CCDC160 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 
       15.02        11.01         5.98        37.05        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        91.79        46.75 

  CCDC160 MUTATED CCDC160 WILD-TYPE 
             0.92              0.00 
  CCDC160 MUTATED CCDC160 WILD-TYPE 
           124.27            140.38 
  CCDC160 MUTATED CCDC160 WILD-TYPE 
           30.575            20.020 
[1] "0.9 - 124.3 (30.6)" "0.0 - 140.4 (20.0)"
[1] "hr="     "2.6e+07"
D447V2, 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       24       106         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC160 MUTATED           1          0          0          0        1
  CCDC160 WILD-TYPE        18         10         41         31       34
                   vv
clus                STAGE IVA STAGE IVB
  CCDC160 MUTATED           0         0
  CCDC160 WILD-TYPE        13         1
D447V3, multiclass
            clus
vv           CCDC160 MUTATED CCDC160 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                3               106
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               0                31
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CCDC160 MUTATED     0   3   5   2
  CCDC160 WILD-TYPE   9  65 243  39
D447V4, multiclass
    clus
vv   CCDC160 MUTATED CCDC160 WILD-TYPE
  T1               0                 9
  T2               3                65
  T3               5               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
  CCDC160 MUTATED     8   2   0
  CCDC160 WILD-TYPE 212  78  66
D447V5, multiclass
    clus
vv   CCDC160 MUTATED CCDC160 WILD-TYPE
  N0               8               212
  N1               2                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"
D447V6, binary
                   cls
clus                  0   1
  CCDC160 MUTATED     8   1
  CCDC160 WILD-TYPE 275  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC160 MUTATED      8    1
  CCDC160 WILD-TYPE  275   47
   clus
vv  CCDC160 MUTATED CCDC160 WILD-TYPE
  0               8               275
  1               1                47
[1] 2 2
[1] FALSE
D447V7, 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
D447V8, binary
                   cls
clus                  0   1
  CCDC160 MUTATED     9   1
  CCDC160 WILD-TYPE 308  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC160 MUTATED      9    1
  CCDC160 WILD-TYPE  308   47
                               clus
vv                              CCDC160 MUTATED CCDC160 WILD-TYPE
  COLON ADENOCARCINOMA                        9               308
  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 250   2  21  20
D447V9, multiclass
    clus
vv   CCDC160 MUTATED CCDC160 WILD-TYPE
  R0               7               250
  R1               0                 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"
D447V10, 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
D447V11, 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(448) Variable = ATAD5 MUTATION ANALYSIS
D448V1, survival
                 sevent
clus2               0   1
  ATAD5 MUTATED    16   4
  ATAD5 WILD-TYPE 266  69
  ATAD5 MUTATED ATAD5 WILD-TYPE 
             20             335 
  ATAD5 MUTATED ATAD5 WILD-TYPE 
              4              69 
$`ATAD5 MUTATED`
TCGA-A6-5661 TCGA-AA-3555 TCGA-AA-3663 TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-3966 
       33.53        29.95         6.97        53.00        33.01         2.01 
TCGA-AA-A010 TCGA-AA-A01P TCGA-AD-6889 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-CA-6717 
       34.98        38.07        56.55        61.41        49.41         0.33 
TCGA-CA-6718 TCGA-F4-6570 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6309 TCGA-G4-6588 
        0.10         6.18         0.53        19.43        51.75        26.17 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

$`ATAD5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        17.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       26.01        24.00         2.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       83.80        22.36        62.79         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07         0.26         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.38        13.45        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 
       16.24        33.67        13.25        35.41       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        91.79 

  ATAD5 MUTATED ATAD5 WILD-TYPE 
            0.1             0.0 
  ATAD5 MUTATED ATAD5 WILD-TYPE 
          61.41          140.38 
  ATAD5 MUTATED ATAD5 WILD-TYPE 
          33.27           19.99 
[1] "0.1 - 61.4 (33.3)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1.3"
D448V2, 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       22        98         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        18         10         40         31       35        13
                 vv
clus              STAGE IVB
  ATAD5 MUTATED           0
  ATAD5 WILD-TYPE         1
D448V3, multiclass
            clus
vv           ATAD5 MUTATED ATAD5 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA             11              98
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ATAD5 MUTATED     1   2  16   2
  ATAD5 WILD-TYPE   8  66 232  39
D448V4, multiclass
    clus
vv   ATAD5 MUTATED ATAD5 WILD-TYPE
  T1             1               8
  T2             2              66
  T3            16             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
  ATAD5 MUTATED    19   2   0
  ATAD5 WILD-TYPE 201  78  66
D448V5, multiclass
    clus
vv   ATAD5 MUTATED ATAD5 WILD-TYPE
  N0            19             201
  N1             2              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"
D448V6, binary
                 cls
clus                0   1
  ATAD5 MUTATED    20   0
  ATAD5 WILD-TYPE 263  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATAD5 MUTATED     20    0
  ATAD5 WILD-TYPE  263   48
   clus
vv  ATAD5 MUTATED ATAD5 WILD-TYPE
  0            20             263
  1             0              48
[1] 2 2
[1] FALSE
D448V7, 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
D448V8, binary
                 cls
clus                0   1
  ATAD5 MUTATED    16   5
  ATAD5 WILD-TYPE 301  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATAD5 MUTATED     16    5
  ATAD5 WILD-TYPE  301   43
                               clus
vv                              ATAD5 MUTATED ATAD5 WILD-TYPE
  COLON ADENOCARCINOMA                     16             301
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ATAD5 MUTATED    15   0   0   2
  ATAD5 WILD-TYPE 242   2  22  19
D448V9, multiclass
    clus
vv   ATAD5 MUTATED ATAD5 WILD-TYPE
  R0            15             242
  R1             0               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"
D448V10, 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
D448V11, 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(449) Variable = PI4K2B MUTATION ANALYSIS
D449V1, survival
                  sevent
clus2                0   1
  PI4K2B MUTATED     8   1
  PI4K2B WILD-TYPE 274  72
  PI4K2B MUTATED PI4K2B WILD-TYPE 
               9              346 
  PI4K2B MUTATED PI4K2B WILD-TYPE 
               1               72 
$`PI4K2B MUTATED`
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-6648 TCGA-AA-A00J TCGA-AY-6196 TCGA-AZ-6608 
       32.91        30.44        25.18        18.05         0.20         1.94 
TCGA-CA-6717 TCGA-CK-5913 TCGA-DM-A1HA 
        0.33        51.32       131.51 

$`PI4K2B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6649 
       32.71        27.09        22.52         8.38        25.08        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        15.75        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
       17.56       102.44        40.34        15.62        49.08        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  PI4K2B MUTATED PI4K2B WILD-TYPE 
             0.2              0.0 
  PI4K2B MUTATED PI4K2B WILD-TYPE 
          131.51           140.38 
  PI4K2B MUTATED PI4K2B WILD-TYPE 
          25.180           20.155 
[1] "0.2 - 131.5 (25.2)" "0.0 - 140.4 (20.2)"
[1] "hr=" "2.2"
D449V2, 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       25       107         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PI4K2B MUTATED           1          1          1          2        0
  PI4K2B WILD-TYPE        18          9         40         29       35
                  vv
clus               STAGE IVA STAGE IVB
  PI4K2B MUTATED           1         0
  PI4K2B WILD-TYPE        12         1
D449V3, multiclass
            clus
vv           PI4K2B MUTATED PI4K2B WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               2              107
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              1                9
  STAGE IIIB              1               40
  STAGE IIIC              2               29
  STAGE IV                0               35
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  65 242  40
D449V4, multiclass
    clus
vv   PI4K2B MUTATED PI4K2B WILD-TYPE
  T1              0                9
  T2              3               65
  T3              6              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
  PI4K2B MUTATED     5   2   3
  PI4K2B WILD-TYPE 215  78  63
D449V5, multiclass
    clus
vv   PI4K2B MUTATED PI4K2B WILD-TYPE
  N0              5              215
  N1              2               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"
D449V6, binary
                  cls
clus                 0   1
  PI4K2B MUTATED     7   1
  PI4K2B WILD-TYPE 276  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PI4K2B MUTATED      7    1
  PI4K2B WILD-TYPE  276   47
   clus
vv  PI4K2B MUTATED PI4K2B WILD-TYPE
  0              7              276
  1              1               47
[1] 2 2
[1] FALSE
D449V7, 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
D449V8, binary
                  cls
clus                 0   1
  PI4K2B MUTATED     7   3
  PI4K2B WILD-TYPE 310  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PI4K2B MUTATED      7    3
  PI4K2B WILD-TYPE  310   45
                               clus
vv                              PI4K2B MUTATED PI4K2B WILD-TYPE
  COLON ADENOCARCINOMA                       7              310
  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 253   2  22  19
D449V9, multiclass
    clus
vv   PI4K2B MUTATED PI4K2B WILD-TYPE
  R0              4              253
  R1              0                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"
D449V10, 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
D449V11, 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(450) Variable = FGFR3 MUTATION ANALYSIS
D450V1, survival
                 sevent
clus2               0   1
  FGFR3 MUTATED    18   4
  FGFR3 WILD-TYPE 264  69
  FGFR3 MUTATED FGFR3 WILD-TYPE 
             22             333 
  FGFR3 MUTATED FGFR3 WILD-TYPE 
              4              69 
$`FGFR3 MUTATED`
TCGA-A6-5665 TCGA-AA-3939 TCGA-AA-A01R TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6963 
       22.06        12.99        35.01        56.55         0.72        27.42 
TCGA-AD-6964 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-CA-6719 TCGA-CM-5860 
       10.88        58.39        49.41         6.77         1.35        16.01 
TCGA-CM-6162 TCGA-CM-6167 TCGA-D5-6534 TCGA-D5-6540 TCGA-D5-6541 TCGA-DM-A1D7 
       12.00        14.99        43.27        16.14        15.58        13.32 
TCGA-F4-6703 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6310 
       35.87        19.43       107.67        45.11 

$`FGFR3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37         4.21         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
        5.79        22.42         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 
        5.13        83.80        22.36        62.79        61.41        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.33         0.10        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 
       11.51        20.19        18.25         1.32        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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20       130.65        92.75        49.91        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 
        8.61        13.38        13.45         6.18         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  FGFR3 MUTATED FGFR3 WILD-TYPE 
           0.72            0.00 
  FGFR3 MUTATED FGFR3 WILD-TYPE 
         107.67          140.38 
  FGFR3 MUTATED FGFR3 WILD-TYPE 
         17.785          20.280 
[1] "0.7 - 107.7 (17.8)" "0.0 - 140.4 (20.3)"
[1] "hr=" "1.3"
D450V2, 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       24        99         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FGFR3 MUTATED           2          0          2          1        0         0
  FGFR3 WILD-TYPE        17         10         39         30       35        13
                 vv
clus              STAGE IVB
  FGFR3 MUTATED           0
  FGFR3 WILD-TYPE         1
D450V3, multiclass
            clus
vv           FGFR3 MUTATED FGFR3 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA             10              99
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FGFR3 MUTATED     0   3  18   1
  FGFR3 WILD-TYPE   9  65 230  40
D450V4, multiclass
    clus
vv   FGFR3 MUTATED FGFR3 WILD-TYPE
  T1             0               9
  T2             3              65
  T3            18             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
  FGFR3 MUTATED    15   4   3
  FGFR3 WILD-TYPE 205  76  63
D450V5, multiclass
    clus
vv   FGFR3 MUTATED FGFR3 WILD-TYPE
  N0            15             205
  N1             4              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"
D450V6, binary
                 cls
clus                0   1
  FGFR3 MUTATED    17   0
  FGFR3 WILD-TYPE 266  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGFR3 MUTATED     17    0
  FGFR3 WILD-TYPE  266   48
   clus
vv  FGFR3 MUTATED FGFR3 WILD-TYPE
  0            17             266
  1             0              48
[1] 2 2
[1] FALSE
D450V7, 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
D450V8, binary
                 cls
clus                0   1
  FGFR3 MUTATED    17   5
  FGFR3 WILD-TYPE 300  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGFR3 MUTATED     17    5
  FGFR3 WILD-TYPE  300   43
                               clus
vv                              FGFR3 MUTATED FGFR3 WILD-TYPE
  COLON ADENOCARCINOMA                     17             300
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  FGFR3 MUTATED    14   0   0   1
  FGFR3 WILD-TYPE 243   2  22  20
D450V9, multiclass
    clus
vv   FGFR3 MUTATED FGFR3 WILD-TYPE
  R0            14             243
  R1             0               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"
D450V10, 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
D450V11, 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(451) Variable = EEA1 MUTATION ANALYSIS
D451V1, survival
                sevent
clus2              0   1
  EEA1 MUTATED    10   3
  EEA1 WILD-TYPE 272  70
  EEA1 MUTATED EEA1 WILD-TYPE 
            13            342 
  EEA1 MUTATED EEA1 WILD-TYPE 
             3             70 
$`EEA1 MUTATED`
TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3947 TCGA-AA-A010 
       22.06        63.98        19.04        19.04        33.01        34.98 
TCGA-AZ-4315 TCGA-CA-6717 TCGA-CM-4746 TCGA-D5-6927 TCGA-DM-A1DA TCGA-F4-6570 
       58.39         0.33        37.02         9.44         7.50         6.18 
TCGA-F4-6856 
       19.43 

$`EEA1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.03        85.05        26.99        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       12.59       140.38        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        13.38        13.45        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.41       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  EEA1 MUTATED EEA1 WILD-TYPE 
          0.33           0.00 
  EEA1 MUTATED EEA1 WILD-TYPE 
         63.98         140.38 
  EEA1 MUTATED EEA1 WILD-TYPE 
        19.430         20.235 
[1] "0.3 - 64.0 (19.4)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D451V2, 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       23       104         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        19         10         41         30       34        13
                vv
clus             STAGE IVB
  EEA1 MUTATED           0
  EEA1 WILD-TYPE         1
D451V3, multiclass
            clus
vv           EEA1 MUTATED EEA1 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             5            104
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            1             30
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  EEA1 MUTATED     0   2   9   2
  EEA1 WILD-TYPE   9  66 239  39
D451V4, multiclass
    clus
vv   EEA1 MUTATED EEA1 WILD-TYPE
  T1            0              9
  T2            2             66
  T3            9            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
  EEA1 MUTATED    12   0   1
  EEA1 WILD-TYPE 208  80  65
D451V5, multiclass
    clus
vv   EEA1 MUTATED EEA1 WILD-TYPE
  N0           12            208
  N1            0             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"
D451V6, binary
                cls
clus               0   1
  EEA1 MUTATED    12   1
  EEA1 WILD-TYPE 271  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  EEA1 MUTATED     12    1
  EEA1 WILD-TYPE  271   47
   clus
vv  EEA1 MUTATED EEA1 WILD-TYPE
  0           12            271
  1            1             47
[1] 2 2
[1] FALSE
D451V7, 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
D451V8, binary
                cls
clus               0   1
  EEA1 MUTATED    10   3
  EEA1 WILD-TYPE 307  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  EEA1 MUTATED     10    3
  EEA1 WILD-TYPE  307   45
                               clus
vv                              EEA1 MUTATED EEA1 WILD-TYPE
  COLON ADENOCARCINOMA                    10            307
  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 247   2  21  20
D451V9, multiclass
    clus
vv   EEA1 MUTATED EEA1 WILD-TYPE
  R0           10            247
  R1            0              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"
D451V10, 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
D451V11, 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(452) Variable = NCOA7 MUTATION ANALYSIS
D452V1, survival
                 sevent
clus2               0   1
  NCOA7 MUTATED    14   1
  NCOA7 WILD-TYPE 268  72
  NCOA7 MUTATED NCOA7 WILD-TYPE 
             15             340 
  NCOA7 MUTATED NCOA7 WILD-TYPE 
              1              72 
$`NCOA7 MUTATED`
TCGA-A6-6653 TCGA-A6-6654 TCGA-AA-3496 TCGA-AA-3518 TCGA-AA-3655 TCGA-AA-3966 
       24.39        23.87         1.02         1.02        61.02         2.01 
TCGA-AA-A00J TCGA-AD-5900 TCGA-AU-6004 TCGA-AZ-4616 TCGA-CM-5861 TCGA-CM-6170 
       18.05         0.07        27.09         5.13        15.02        15.02 
TCGA-CM-6171 TCGA-D5-6928 TCGA-G4-6317 
       14.04        11.64        36.00 

$`NCOA7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6780 
       25.08        25.18        24.16        21.76        24.69        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         3.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 
        6.97         1.02        13.02        38.99         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       26.01        24.00         2.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4681 
        0.20        21.44        17.82        58.39         1.41        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       51.75        45.11        36.72        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  NCOA7 MUTATED NCOA7 WILD-TYPE 
           0.07            0.00 
  NCOA7 MUTATED NCOA7 WILD-TYPE 
          61.02          140.38 
  NCOA7 MUTATED NCOA7 WILD-TYPE 
          15.02           20.98 
[1] "0.1 - 61.0 (15.0)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "2.2"
D452V2, 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       23       105         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        19         10         39         30       34        13
                 vv
clus              STAGE IVB
  NCOA7 MUTATED           0
  NCOA7 WILD-TYPE         1
D452V3, multiclass
            clus
vv           NCOA7 MUTATED NCOA7 WILD-TYPE
  STAGE I                5              59
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              4             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NCOA7 MUTATED     0   5   9   1
  NCOA7 WILD-TYPE   9  63 239  40
D452V4, multiclass
    clus
vv   NCOA7 MUTATED NCOA7 WILD-TYPE
  T1             0               9
  T2             5              63
  T3             9             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
  NCOA7 MUTATED    11   2   2
  NCOA7 WILD-TYPE 209  78  64
D452V5, multiclass
    clus
vv   NCOA7 MUTATED NCOA7 WILD-TYPE
  N0            11             209
  N1             2              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"
D452V6, binary
                 cls
clus                0   1
  NCOA7 MUTATED    12   1
  NCOA7 WILD-TYPE 271  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA7 MUTATED     12    1
  NCOA7 WILD-TYPE  271   47
   clus
vv  NCOA7 MUTATED NCOA7 WILD-TYPE
  0            12             271
  1             1              47
[1] 2 2
[1] FALSE
D452V7, 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
D452V8, binary
                 cls
clus                0   1
  NCOA7 MUTATED    11   4
  NCOA7 WILD-TYPE 306  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA7 MUTATED     11    4
  NCOA7 WILD-TYPE  306   44
                               clus
vv                              NCOA7 MUTATED NCOA7 WILD-TYPE
  COLON ADENOCARCINOMA                     11             306
  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 246   2  22  21
D452V9, multiclass
    clus
vv   NCOA7 MUTATED NCOA7 WILD-TYPE
  R0            11             246
  R1             0               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"
D452V10, 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
D452V11, 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(453) Variable = EML4 MUTATION ANALYSIS
D453V1, survival
                sevent
clus2              0   1
  EML4 MUTATED     8   1
  EML4 WILD-TYPE 274  72
  EML4 MUTATED EML4 WILD-TYPE 
             9            346 
  EML4 MUTATED EML4 WILD-TYPE 
             1             72 
$`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         0.33 
TCGA-D5-6540 TCGA-DM-A0X9 TCGA-F4-6459 
       16.14       119.70         8.61 

$`EML4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.20        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38        10.26        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 
       35.97        60.79       117.07        98.24        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  EML4 MUTATED EML4 WILD-TYPE 
          0.33           0.00 
  EML4 MUTATED EML4 WILD-TYPE 
        119.70         140.38 
  EML4 MUTATED EML4 WILD-TYPE 
        24.000         20.155 
[1] "0.3 - 119.7 (24.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "2.8"
D453V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EML4 MUTATED         1        0        0         6         0         0
  EML4 WILD-TYPE      63        1       25       103         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EML4 MUTATED           1          0          1          0        0         0
  EML4 WILD-TYPE        18         10         40         31       35        13
                vv
clus             STAGE IVB
  EML4 MUTATED           0
  EML4 WILD-TYPE         1
D453V3, multiclass
            clus
vv           EML4 MUTATED EML4 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             6            103
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  EML4 MUTATED     0   2   8   0
  EML4 WILD-TYPE   9  66 240  41
D453V4, multiclass
    clus
vv   EML4 MUTATED EML4 WILD-TYPE
  T1            0              9
  T2            2             66
  T3            8            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
  EML4 MUTATED     9   0   1
  EML4 WILD-TYPE 211  80  65
D453V5, multiclass
    clus
vv   EML4 MUTATED EML4 WILD-TYPE
  N0            9            211
  N1            0             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"
D453V6, binary
                cls
clus               0   1
  EML4 MUTATED     9   0
  EML4 WILD-TYPE 274  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  EML4 MUTATED      9    0
  EML4 WILD-TYPE  274   48
   clus
vv  EML4 MUTATED EML4 WILD-TYPE
  0            9            274
  1            0             48
[1] 2 2
[1] FALSE
D453V7, 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
D453V8, binary
                cls
clus               0   1
  EML4 MUTATED     7   3
  EML4 WILD-TYPE 310  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  EML4 MUTATED      7    3
  EML4 WILD-TYPE  310   45
                               clus
vv                              EML4 MUTATED EML4 WILD-TYPE
  COLON ADENOCARCINOMA                     7            310
  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 250   2  22  20
D453V9, multiclass
    clus
vv   EML4 MUTATED EML4 WILD-TYPE
  R0            7            250
  R1            0              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"
D453V10, 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
D453V11, 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(454) Variable = RBPJ MUTATION ANALYSIS
D454V1, survival
                sevent
clus2              0   1
  RBPJ MUTATED    11   3
  RBPJ WILD-TYPE 271  70
  RBPJ MUTATED RBPJ WILD-TYPE 
            14            341 
  RBPJ MUTATED RBPJ WILD-TYPE 
             3             70 
$`RBPJ MUTATED`
TCGA-A6-6141 TCGA-A6-6782 TCGA-AA-3815 TCGA-AA-A00Q TCGA-AD-5900 TCGA-AD-6889 
        8.38        20.28        33.04        42.02         0.07        56.55 
TCGA-AY-6197 TCGA-CA-6716 TCGA-CA-6717 TCGA-CM-5860 TCGA-CM-6674 TCGA-D5-6537 
       21.44         0.26         0.33        16.01        12.95         4.80 
TCGA-G4-6303 TCGA-G4-6626 
       65.85        46.75 

$`RBPJ WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       27.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       40.96        21.37         4.21         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        15.75         0.20        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        15.12        17.85        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 
       35.41        19.43       107.67        74.56        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        52.80 

  RBPJ MUTATED RBPJ WILD-TYPE 
          0.07           0.00 
  RBPJ MUTATED RBPJ WILD-TYPE 
         65.85         140.38 
  RBPJ MUTATED RBPJ WILD-TYPE 
        18.145         20.190 
[1] "0.1 - 65.8 (18.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D454V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RBPJ MUTATED         1        0        0         9         1         0
  RBPJ WILD-TYPE      63        1       25       100         7         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        19         10         39         31       34        13
                vv
clus             STAGE IVB
  RBPJ MUTATED           0
  RBPJ WILD-TYPE         1
D454V3, multiclass
            clus
vv           RBPJ MUTATED RBPJ WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             9            100
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            2             39
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RBPJ MUTATED     0   1  11   2
  RBPJ WILD-TYPE   9  67 237  39
D454V4, multiclass
    clus
vv   RBPJ MUTATED RBPJ WILD-TYPE
  T1            0              9
  T2            1             67
  T3           11            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
  RBPJ MUTATED    11   3   0
  RBPJ WILD-TYPE 209  77  66
D454V5, multiclass
    clus
vv   RBPJ MUTATED RBPJ WILD-TYPE
  N0           11            209
  N1            3             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
  RBPJ MUTATED     9   1
  RBPJ WILD-TYPE 274  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBPJ MUTATED      9    1
  RBPJ WILD-TYPE  274   47
   clus
vv  RBPJ MUTATED RBPJ WILD-TYPE
  0            9            274
  1            1             47
[1] 2 2
[1] FALSE
D454V7, binary
                cls
clus               0   1
  RBPJ MUTATED     3  11
  RBPJ WILD-TYPE 167 186
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBPJ MUTATED      3   11
  RBPJ WILD-TYPE  167  186
        clus
vv       RBPJ MUTATED RBPJ WILD-TYPE
  FEMALE            3            167
  MALE             11            186
[1] 2 2
[1] FALSE
D454V8, binary
                cls
clus               0   1
  RBPJ MUTATED    12   2
  RBPJ WILD-TYPE 305  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBPJ MUTATED     12    2
  RBPJ WILD-TYPE  305   46
                               clus
vv                              RBPJ MUTATED RBPJ WILD-TYPE
  COLON ADENOCARCINOMA                    12            305
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RBPJ MUTATED     9   0   0   2
  RBPJ WILD-TYPE 248   2  22  19
D454V9, multiclass
    clus
vv   RBPJ MUTATED RBPJ WILD-TYPE
  R0            9            248
  R1            0              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"
D454V10, 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     8
  RBPJ WILD-TYPE                        18   168
D454V11, 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                                       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(455) Variable = KDM2B MUTATION ANALYSIS
D455V1, survival
                 sevent
clus2               0   1
  KDM2B MUTATED    14   4
  KDM2B WILD-TYPE 268  69
  KDM2B MUTATED KDM2B WILD-TYPE 
             18             337 
  KDM2B MUTATED KDM2B WILD-TYPE 
              4              69 
$`KDM2B MUTATED`
TCGA-A6-3809 TCGA-A6-5665 TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3663 
       32.75        22.06        24.39        19.66         3.02         6.97 
TCGA-AA-3672 TCGA-AA-3697 TCGA-AA-3815 TCGA-AA-3848 TCGA-AA-3877 TCGA-AY-4070 
        0.92        85.05        33.04        10.06        31.00        16.31 
TCGA-AZ-6598 TCGA-CK-5913 TCGA-CM-5868 TCGA-CM-6162 TCGA-G4-6586 TCGA-G4-6588 
       49.41        51.32        17.03        12.00        35.80        26.17 

$`KDM2B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 
       24.16        21.76        24.69        23.87        20.12        20.28 
TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        7.04         1.02        35.01        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       78.08         6.05        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 
       38.99        37.02        14.93         0.00        17.03         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       27.09         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
       17.56       102.44        40.34        15.62        49.08        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 
       36.72        36.00        22.09        13.78        91.79        46.75 
TCGA-G4-6628 
       52.80 

  KDM2B MUTATED KDM2B WILD-TYPE 
           0.92            0.00 
  KDM2B MUTATED KDM2B WILD-TYPE 
          85.05          140.38 
  KDM2B MUTATED KDM2B WILD-TYPE 
         23.225          20.120 
[1] "0.9 - 85.0 (23.2)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.1"
D455V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KDM2B MUTATED         3        0        3         5         2         0
  KDM2B WILD-TYPE      61        1       22       104         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KDM2B MUTATED           2          0          1          3        0         1
  KDM2B WILD-TYPE        17         10         40         28       35        12
                 vv
clus              STAGE IVB
  KDM2B MUTATED           0
  KDM2B WILD-TYPE         1
D455V3, multiclass
            clus
vv           KDM2B MUTATED KDM2B WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              5             104
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             3              28
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 235  37
D455V4, multiclass
    clus
vv   KDM2B MUTATED KDM2B WILD-TYPE
  T1             1               8
  T2             2              66
  T3            13             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
  KDM2B MUTATED    14   4   2
  KDM2B WILD-TYPE 206  76  64
D455V5, multiclass
    clus
vv   KDM2B MUTATED KDM2B WILD-TYPE
  N0            14             206
  N1             4              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"
D455V6, binary
                 cls
clus                0   1
  KDM2B MUTATED    14   1
  KDM2B WILD-TYPE 269  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM2B MUTATED     14    1
  KDM2B WILD-TYPE  269   47
   clus
vv  KDM2B MUTATED KDM2B WILD-TYPE
  0            14             269
  1             1              47
[1] 2 2
[1] FALSE
D455V7, 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
D455V8, binary
                 cls
clus                0   1
  KDM2B MUTATED    16   4
  KDM2B WILD-TYPE 301  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM2B MUTATED     16    4
  KDM2B WILD-TYPE  301   44
                               clus
vv                              KDM2B MUTATED KDM2B WILD-TYPE
  COLON ADENOCARCINOMA                     16             301
  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 243   1  22  18
D455V9, multiclass
    clus
vv   KDM2B MUTATED KDM2B WILD-TYPE
  R0            14             243
  R1             1               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"
D455V10, 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
D455V11, 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(456) Variable = RTP3 MUTATION ANALYSIS
D456V1, survival
                sevent
clus2              0   1
  RTP3 MUTATED     2   3
  RTP3 WILD-TYPE 280  70
  RTP3 MUTATED RTP3 WILD-TYPE 
             5            350 
  RTP3 MUTATED RTP3 WILD-TYPE 
             3             70 
$`RTP3 MUTATED`
TCGA-AZ-6598 TCGA-AZ-6603 TCGA-AZ-6608 TCGA-CK-4948 TCGA-D5-6532 
       49.41        29.56         1.94       102.44        18.25 

$`RTP3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 
       61.41         6.77        12.10       100.01         5.23        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 
        0.26         0.33         0.10         1.35        17.56        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  RTP3 MUTATED RTP3 WILD-TYPE 
          1.94           0.00 
  RTP3 MUTATED RTP3 WILD-TYPE 
        102.44         140.38 
  RTP3 MUTATED RTP3 WILD-TYPE 
        29.560         20.155 
[1] "1.9 - 102.4 (29.6)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.9"
D456V2, 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       24       108         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RTP3 MUTATED           0          2          0          0        0         0
  RTP3 WILD-TYPE        19          8         41         31       35        13
                vv
clus             STAGE IVB
  RTP3 MUTATED           0
  RTP3 WILD-TYPE         1
D456V3, multiclass
            clus
vv           RTP3 MUTATED RTP3 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             1            108
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            2              8
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RTP3 MUTATED     0   2   3   0
  RTP3 WILD-TYPE   9  66 245  41
D456V4, multiclass
    clus
vv   RTP3 MUTATED RTP3 WILD-TYPE
  T1            0              9
  T2            2             66
  T3            3            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
  RTP3 MUTATED     2   3   0
  RTP3 WILD-TYPE 218  77  66
D456V5, multiclass
    clus
vv   RTP3 MUTATED RTP3 WILD-TYPE
  N0            2            218
  N1            3             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"
D456V6, binary
                cls
clus               0   1
  RTP3 MUTATED     3   0
  RTP3 WILD-TYPE 280  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  RTP3 MUTATED      3    0
  RTP3 WILD-TYPE  280   48
   clus
vv  RTP3 MUTATED RTP3 WILD-TYPE
  0            3            280
  1            0             48
[1] 2 2
[1] FALSE
D456V7, 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
D456V8, binary
                cls
clus               0   1
  RTP3 MUTATED     5   0
  RTP3 WILD-TYPE 312  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  RTP3 MUTATED      5    0
  RTP3 WILD-TYPE  312   48
                               clus
vv                              RTP3 MUTATED RTP3 WILD-TYPE
  COLON ADENOCARCINOMA                     5            312
  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 255   2  22  21
D456V9, multiclass
[1] "Remove cluster labels:" "RTP3 MUTATED"          
clus
  RTP3 MUTATED RTP3 WILD-TYPE 
             2            300 
    TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810     TCGA-A6-5657 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-A6-5659     TCGA-A6-5661     TCGA-A6-5665     TCGA-A6-6781 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3489     TCGA-AA-3492     TCGA-AA-3496     TCGA-AA-3502 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3510     TCGA-AA-3511     TCGA-AA-3514     TCGA-AA-3517 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3518     TCGA-AA-3519     TCGA-AA-3520     TCGA-AA-3521 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3522     TCGA-AA-3524     TCGA-AA-3525     TCGA-AA-3526 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3527     TCGA-AA-3529     TCGA-AA-3530     TCGA-AA-3531 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3532     TCGA-AA-3534     TCGA-AA-3538     TCGA-AA-3542 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3543     TCGA-AA-3544     TCGA-AA-3548     TCGA-AA-3549 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3552     TCGA-AA-3553     TCGA-AA-3554     TCGA-AA-3555 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3556     TCGA-AA-3558     TCGA-AA-3560     TCGA-AA-3561 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3562     TCGA-AA-3655     TCGA-AA-3660     TCGA-AA-3662 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3663     TCGA-AA-3664     TCGA-AA-3666     TCGA-AA-3667 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3672     TCGA-AA-3673     TCGA-AA-3678     TCGA-AA-3679 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3680     TCGA-AA-3681     TCGA-AA-3684     TCGA-AA-3685 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3688     TCGA-AA-3692     TCGA-AA-3693     TCGA-AA-3695 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3696     TCGA-AA-3697     TCGA-AA-3710     TCGA-AA-3712 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3713     TCGA-AA-3715     TCGA-AA-3811     TCGA-AA-3812 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3814     TCGA-AA-3815     TCGA-AA-3818     TCGA-AA-3819 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3821     TCGA-AA-3831     TCGA-AA-3833     TCGA-AA-3837 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3842     TCGA-AA-3844     TCGA-AA-3845     TCGA-AA-3846 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3848     TCGA-AA-3850     TCGA-AA-3851     TCGA-AA-3852 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3854     TCGA-AA-3855     TCGA-AA-3856     TCGA-AA-3858 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3860     TCGA-AA-3861     TCGA-AA-3864     TCGA-AA-3866 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3867     TCGA-AA-3869     TCGA-AA-3870     TCGA-AA-3872 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3875     TCGA-AA-3877     TCGA-AA-3930     TCGA-AA-3939 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3941     TCGA-AA-3947     TCGA-AA-3949     TCGA-AA-3950 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3952     TCGA-AA-3955     TCGA-AA-3956     TCGA-AA-3968 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3971     TCGA-AA-3972     TCGA-AA-3973     TCGA-AA-3975 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3976     TCGA-AA-3979     TCGA-AA-3984     TCGA-AA-3986 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3989     TCGA-AA-3994     TCGA-AA-A004     TCGA-AA-A00A 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-A00D     TCGA-AA-A00E     TCGA-AA-A00F     TCGA-AA-A00J 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-A00K     TCGA-AA-A00L     TCGA-AA-A00N     TCGA-AA-A00O 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-A00Q     TCGA-AA-A00R     TCGA-AA-A00U     TCGA-AA-A00W 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-A00Z     TCGA-AA-A010     TCGA-AA-A017     TCGA-AA-A01D 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-A01F     TCGA-AA-A01G     TCGA-AA-A01I     TCGA-AA-A01K 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-A01P     TCGA-AA-A01Q     TCGA-AA-A01R     TCGA-AA-A01S 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-A01T     TCGA-AA-A01V     TCGA-AA-A01X     TCGA-AA-A01Z 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-A022     TCGA-AA-A024     TCGA-AA-A029     TCGA-AA-A02F 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-A02H     TCGA-AA-A02J     TCGA-AA-A02K     TCGA-AA-A02O 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-A02W     TCGA-AA-A02Y     TCGA-AA-A03F     TCGA-AA-A03J 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AD-5900     TCGA-AD-6548     TCGA-AD-6888     TCGA-AU-3779 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AU-6004     TCGA-AY-4070     TCGA-AY-4071     TCGA-AY-5543 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AY-6196     TCGA-AY-6197     TCGA-AY-6386     TCGA-AZ-4315 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AZ-4681     TCGA-AZ-4682     TCGA-CA-5254     TCGA-CA-5255 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-CA-5796     TCGA-CA-5797     TCGA-CA-6715     TCGA-CA-6716 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-CA-6717     TCGA-CA-6718     TCGA-CA-6719     TCGA-CK-4947 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-CK-4950     TCGA-CK-4952     TCGA-CK-5912     TCGA-CK-5913 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-CK-5914     TCGA-CK-5915     TCGA-CK-5916     TCGA-CK-6746 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-CK-6747     TCGA-CK-6748     TCGA-CK-6751     TCGA-CM-4743 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-CM-4744     TCGA-CM-4746     TCGA-CM-4747     TCGA-CM-4752 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-CM-5341     TCGA-CM-5344     TCGA-CM-5348     TCGA-CM-5349 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-CM-5860     TCGA-CM-5861     TCGA-CM-5862     TCGA-CM-5863 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-CM-5864     TCGA-CM-5868     TCGA-CM-6161     TCGA-CM-6162 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-CM-6163     TCGA-CM-6164     TCGA-CM-6165     TCGA-CM-6166 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-CM-6167     TCGA-CM-6168     TCGA-CM-6169     TCGA-CM-6170 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-CM-6171     TCGA-CM-6172     TCGA-CM-6674     TCGA-CM-6675 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-CM-6676     TCGA-CM-6677     TCGA-CM-6678     TCGA-CM-6679 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-CM-6680     TCGA-D5-5537     TCGA-D5-5538     TCGA-D5-5539 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-D5-5540     TCGA-D5-5541     TCGA-D5-6529     TCGA-D5-6533 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-D5-6534     TCGA-D5-6535     TCGA-D5-6536     TCGA-D5-6537 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-D5-6538     TCGA-D5-6539     TCGA-D5-6540     TCGA-D5-6541 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-D5-6898     TCGA-D5-6920     TCGA-D5-6922     TCGA-D5-6923 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-D5-6924     TCGA-D5-6926     TCGA-D5-6927     TCGA-D5-6928 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-D5-6929     TCGA-D5-6930     TCGA-D5-6931     TCGA-D5-6932 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-D5-7000     TCGA-F4-6459     TCGA-F4-6460     TCGA-F4-6569 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-F4-6570     TCGA-F4-6703     TCGA-F4-6704     TCGA-F4-6805 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-F4-6806     TCGA-F4-6807     TCGA-F4-6808     TCGA-F4-6809 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-F4-6854     TCGA-F4-6855     TCGA-F4-6856     TCGA-G4-6293 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-G4-6299     TCGA-G4-6303     TCGA-G4-6304     TCGA-G4-6306 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-G4-6307     TCGA-G4-6309     TCGA-G4-6310     TCGA-G4-6315 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-G4-6317     TCGA-G4-6321     TCGA-G4-6323     TCGA-G4-6586 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-G4-6588     TCGA-G4-6625     TCGA-G4-6626     TCGA-G4-6628 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
D456V10, 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
D456V11, 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(457) Variable = DDX23 MUTATION ANALYSIS
D457V1, survival
                 sevent
clus2               0   1
  DDX23 MUTATED    14   3
  DDX23 WILD-TYPE 268  70
  DDX23 MUTATED DDX23 WILD-TYPE 
             17             338 
  DDX23 MUTATED DDX23 WILD-TYPE 
              3              70 
$`DDX23 MUTATED`
TCGA-A6-6781 TCGA-AA-3660 TCGA-AA-3713 TCGA-AA-3815 TCGA-AA-A004 TCGA-AA-A00N 
       19.66        78.08        19.04        33.04        13.94         4.01 
TCGA-AA-A00R TCGA-AD-6548 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 
        0.99        21.37        21.44        58.39        49.41         0.33 
TCGA-CK-4952 TCGA-CM-5349 TCGA-DM-A1D4 TCGA-F4-6854 TCGA-G4-6315 
       15.62        30.08        92.75         0.53        36.72 

$`DDX23 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        61.02         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
        7.96        27.02        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U 
       18.05        18.05        38.04        27.02        42.02        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6888 
       41.00        39.98        18.05        40.96         0.07         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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-4681 
       15.75         0.20        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 
        1.35        17.56       102.44        40.34        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 
       10.26       119.70        24.43        38.20       130.65        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       33.67        13.25        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  DDX23 MUTATED DDX23 WILD-TYPE 
           0.33            0.00 
  DDX23 MUTATED DDX23 WILD-TYPE 
          92.75          140.38 
  DDX23 MUTATED DDX23 WILD-TYPE 
         21.370          20.155 
[1] "0.3 - 92.8 (21.4)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.3"
D457V2, 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       23       100         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DDX23 MUTATED           1          0          0          1        2         0
  DDX23 WILD-TYPE        18         10         41         30       33        13
                 vv
clus              STAGE IVB
  DDX23 MUTATED           0
  DDX23 WILD-TYPE         1
D457V3, multiclass
            clus
vv           DDX23 MUTATED DDX23 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              9             100
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               2              33
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DDX23 MUTATED     0   2  13   3
  DDX23 WILD-TYPE   9  66 235  38
D457V4, multiclass
    clus
vv   DDX23 MUTATED DDX23 WILD-TYPE
  T1             0               9
  T2             2              66
  T3            13             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
  DDX23 MUTATED    15   2   1
  DDX23 WILD-TYPE 205  78  65
D457V5, multiclass
    clus
vv   DDX23 MUTATED DDX23 WILD-TYPE
  N0            15             205
  N1             2              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"
D457V6, binary
                 cls
clus                0   1
  DDX23 MUTATED    13   2
  DDX23 WILD-TYPE 270  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX23 MUTATED     13    2
  DDX23 WILD-TYPE  270   46
   clus
vv  DDX23 MUTATED DDX23 WILD-TYPE
  0            13             270
  1             2              46
[1] 2 2
[1] FALSE
D457V7, 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
D457V8, binary
                 cls
clus                0   1
  DDX23 MUTATED    14   4
  DDX23 WILD-TYPE 303  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX23 MUTATED     14    4
  DDX23 WILD-TYPE  303   44
                               clus
vv                              DDX23 MUTATED DDX23 WILD-TYPE
  COLON ADENOCARCINOMA                     14             303
  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 244   2  21  19
D457V9, multiclass
    clus
vv   DDX23 MUTATED DDX23 WILD-TYPE
  R0            13             244
  R1             0               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"
D457V10, 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
D457V11, 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(458) Variable = LNX2 MUTATION ANALYSIS
D458V1, survival
                sevent
clus2              0   1
  LNX2 MUTATED    12   4
  LNX2 WILD-TYPE 270  69
  LNX2 MUTATED LNX2 WILD-TYPE 
            16            339 
  LNX2 MUTATED LNX2 WILD-TYPE 
             4             69 
$`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         0.10        22.98        21.99 
TCGA-D5-5541 TCGA-D5-6533 TCGA-D5-6930 TCGA-DM-A1D4 
       11.51         1.32         1.51        92.75 

$`LNX2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       35.05        33.04        25.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U 
       18.05        18.05        38.04        27.02        42.02        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.33         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 
       19.59        13.51        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-A1D6 TCGA-DM-A1D7 
      119.70        24.43        38.20       130.65        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  LNX2 MUTATED LNX2 WILD-TYPE 
           0.1            0.0 
  LNX2 MUTATED LNX2 WILD-TYPE 
         92.75         140.38 
  LNX2 MUTATED LNX2 WILD-TYPE 
        10.785         20.280 
[1] "0.1 - 92.8 (10.8)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.8"
D458V2, 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       25       104         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LNX2 MUTATED           2          0          4          0        0         0
  LNX2 WILD-TYPE        17         10         37         31       35        13
                vv
clus             STAGE IVB
  LNX2 MUTATED           0
  LNX2 WILD-TYPE         1
D458V3, multiclass
            clus
vv           LNX2 MUTATED LNX2 WILD-TYPE
  STAGE I               4             60
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             5            104
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             2             17
  STAGE IIIA            0             10
  STAGE IIIB            4             37
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  LNX2 MUTATED     0   4  10   2
  LNX2 WILD-TYPE   9  64 238  39
D458V4, multiclass
    clus
vv   LNX2 MUTATED LNX2 WILD-TYPE
  T1            0              9
  T2            4             64
  T3           10            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
  LNX2 MUTATED    11   3   2
  LNX2 WILD-TYPE 209  77  64
D458V5, multiclass
    clus
vv   LNX2 MUTATED LNX2 WILD-TYPE
  N0           11            209
  N1            3             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"
D458V6, binary
                cls
clus               0   1
  LNX2 MUTATED    16   0
  LNX2 WILD-TYPE 267  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  LNX2 MUTATED     16    0
  LNX2 WILD-TYPE  267   48
   clus
vv  LNX2 MUTATED LNX2 WILD-TYPE
  0           16            267
  1            0             48
[1] 2 2
[1] FALSE
D458V7, 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
D458V8, binary
                cls
clus               0   1
  LNX2 MUTATED    11   5
  LNX2 WILD-TYPE 306  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  LNX2 MUTATED     11    5
  LNX2 WILD-TYPE  306   43
                               clus
vv                              LNX2 MUTATED LNX2 WILD-TYPE
  COLON ADENOCARCINOMA                    11            306
  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 243   2  22  20
D458V9, multiclass
    clus
vv   LNX2 MUTATED LNX2 WILD-TYPE
  R0           14            243
  R1            0              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"
D458V10, 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
D458V11, 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(459) Variable = MARK1 MUTATION ANALYSIS
D459V1, survival
                 sevent
clus2               0   1
  MARK1 MUTATED    19   4
  MARK1 WILD-TYPE 263  69
  MARK1 MUTATED MARK1 WILD-TYPE 
             23             332 
  MARK1 MUTATED MARK1 WILD-TYPE 
              4              69 
$`MARK1 MUTATED`
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3710 
       31.63        30.44        22.06        63.98        29.95        26.99 
TCGA-AA-3821 TCGA-AA-3977 TCGA-AA-A024 TCGA-AU-3779 TCGA-AZ-4315 TCGA-AZ-4681 
        1.02        25.02        39.06        14.50        58.39        83.80 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-CA-6717 TCGA-CK-4947 TCGA-CM-4747 TCGA-CM-6166 
        6.77        12.10         0.33        17.56        25.02        21.99 
TCGA-D5-5537 TCGA-D5-6539 TCGA-D5-6923 TCGA-DM-A28H TCGA-G4-6299 
       45.40        12.49        12.43       117.07        74.56 

$`MARK1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       32.91        29.19        33.53        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 
       37.05        19.00        36.00         5.03        85.05        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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        35.01        26.01        37.02        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.20        27.09        16.31         0.95        15.75         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-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       61.41        49.41       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 
        0.07         0.26         0.10         1.35       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-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-D5-5538 TCGA-D5-5539 
       11.08        11.01        10.06        12.03        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 
       13.25         0.53        35.41        19.43       107.67        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  MARK1 MUTATED MARK1 WILD-TYPE 
           0.33            0.00 
  MARK1 MUTATED MARK1 WILD-TYPE 
         117.07          140.38 
  MARK1 MUTATED MARK1 WILD-TYPE 
          25.02           19.99 
[1] "0.3 - 117.1 (25.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.6"
D459V2, 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       23       100         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MARK1 MUTATED           0          1          1          2        1         2
  MARK1 WILD-TYPE        19          9         40         29       34        11
                 vv
clus              STAGE IVB
  MARK1 MUTATED           0
  MARK1 WILD-TYPE         1
D459V3, multiclass
            clus
vv           MARK1 MUTATED MARK1 WILD-TYPE
  STAGE I                5              59
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              9             100
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             1              40
  STAGE IIIC             2              29
  STAGE IV               1              34
  STAGE IVA              2              11
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  15   3
  MARK1 WILD-TYPE   9  62 233  38
D459V4, multiclass
    clus
vv   MARK1 MUTATED MARK1 WILD-TYPE
  T1             0               9
  T2             6              62
  T3            15             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   4   3
  MARK1 WILD-TYPE 203  76  63
D459V5, multiclass
    clus
vv   MARK1 MUTATED MARK1 WILD-TYPE
  N0            17             203
  N1             4              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"
D459V6, binary
                 cls
clus                0   1
  MARK1 MUTATED    19   2
  MARK1 WILD-TYPE 264  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MARK1 MUTATED     19    2
  MARK1 WILD-TYPE  264   46
   clus
vv  MARK1 MUTATED MARK1 WILD-TYPE
  0            19             264
  1             2              46
[1] 2 2
[1] FALSE
D459V7, binary
                 cls
clus                0   1
  MARK1 MUTATED    10  14
  MARK1 WILD-TYPE 160 183
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MARK1 MUTATED     10   14
  MARK1 WILD-TYPE  160  183
        clus
vv       MARK1 MUTATED MARK1 WILD-TYPE
  FEMALE            10             160
  MALE              14             183
[1] 2 2
[1] FALSE
D459V8, binary
                 cls
clus                0   1
  MARK1 MUTATED    20   4
  MARK1 WILD-TYPE 297  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MARK1 MUTATED     20    4
  MARK1 WILD-TYPE  297   44
                               clus
vv                              MARK1 MUTATED MARK1 WILD-TYPE
  COLON ADENOCARCINOMA                     20             297
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MARK1 MUTATED    17   0   0   3
  MARK1 WILD-TYPE 240   2  22  18
D459V9, multiclass
    clus
vv   MARK1 MUTATED MARK1 WILD-TYPE
  R0            17             240
  R1             0               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"
D459V10, 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                           2    14
  MARK1 WILD-TYPE                        17   162
D459V11, multiclass
                                  clus
vv                                 MARK1 MUTATED MARK1 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(460) Variable = OVGP1 MUTATION ANALYSIS
D460V1, survival
                 sevent
clus2               0   1
  OVGP1 MUTATED    13   1
  OVGP1 WILD-TYPE 269  72
  OVGP1 MUTATED OVGP1 WILD-TYPE 
             14             341 
  OVGP1 MUTATED OVGP1 WILD-TYPE 
              1              72 
$`OVGP1 MUTATED`
TCGA-A6-5666 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3864 TCGA-AA-A00A TCGA-AD-5900 
       32.71        63.98         6.97        53.00        38.04         0.07 
TCGA-AD-6889 TCGA-AD-6899 TCGA-AU-3779 TCGA-AY-6386 TCGA-AZ-4681 TCGA-CM-6163 
       56.55         5.79        14.50        17.82        83.80        14.04 
TCGA-CM-6679 TCGA-D5-6536 
       10.06        17.85 

$`OVGP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
        7.96        27.02        13.94        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 
       21.37         4.21         0.79         0.72        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        27.09        16.31         0.95        15.75 
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-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-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-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.01        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  OVGP1 MUTATED OVGP1 WILD-TYPE 
           0.07            0.00 
  OVGP1 MUTATED OVGP1 WILD-TYPE 
          83.80          140.38 
  OVGP1 MUTATED OVGP1 WILD-TYPE 
         17.835          20.280 
[1] "0.1 - 83.8 (17.8)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "3.6"
D460V2, 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       22       103         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        19         10         40         30       35        13
                 vv
clus              STAGE IVB
  OVGP1 MUTATED           0
  OVGP1 WILD-TYPE         1
D460V3, multiclass
            clus
vv           OVGP1 MUTATED OVGP1 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              6             103
  STAGE IIB              0               8
  STAGE IIC              1               0
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OVGP1 MUTATED     1   1  10   2
  OVGP1 WILD-TYPE   8  67 238  39
D460V4, multiclass
    clus
vv   OVGP1 MUTATED OVGP1 WILD-TYPE
  T1             1               8
  T2             1              67
  T3            10             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
  OVGP1 MUTATED    12   1   1
  OVGP1 WILD-TYPE 208  79  65
D460V5, multiclass
    clus
vv   OVGP1 MUTATED OVGP1 WILD-TYPE
  N0            12             208
  N1             1              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"
D460V6, binary
                 cls
clus                0   1
  OVGP1 MUTATED    12   0
  OVGP1 WILD-TYPE 271  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OVGP1 MUTATED     12    0
  OVGP1 WILD-TYPE  271   48
   clus
vv  OVGP1 MUTATED OVGP1 WILD-TYPE
  0            12             271
  1             0              48
[1] 2 2
[1] FALSE
D460V7, 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
D460V8, binary
                 cls
clus                0   1
  OVGP1 MUTATED    12   2
  OVGP1 WILD-TYPE 305  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OVGP1 MUTATED     12    2
  OVGP1 WILD-TYPE  305   46
                               clus
vv                              OVGP1 MUTATED OVGP1 WILD-TYPE
  COLON ADENOCARCINOMA                     12             305
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  OVGP1 MUTATED    11   0   0   0
  OVGP1 WILD-TYPE 246   2  22  21
D460V9, multiclass
    clus
vv   OVGP1 MUTATED OVGP1 WILD-TYPE
  R0            11             246
  R1             0               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"
D460V10, 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
D460V11, 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(461) Variable = ARMC9 MUTATION ANALYSIS
D461V1, survival
                 sevent
clus2               0   1
  ARMC9 MUTATED     5   3
  ARMC9 WILD-TYPE 277  70
  ARMC9 MUTATED ARMC9 WILD-TYPE 
              8             347 
  ARMC9 MUTATED ARMC9 WILD-TYPE 
              3              70 
$`ARMC9 MUTATED`
TCGA-AA-3555 TCGA-AA-3663 TCGA-AA-A00N TCGA-CK-4952 TCGA-CK-5916 TCGA-DM-A1D9 
       29.95         6.97         4.01        15.62        21.14       140.38 
TCGA-F4-6856 TCGA-G4-6303 
       19.43        65.85 

$`ARMC9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        17.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       40.34        49.08        51.32        21.99         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       35.41       107.67        74.56        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  ARMC9 MUTATED ARMC9 WILD-TYPE 
           4.01            0.00 
  ARMC9 MUTATED ARMC9 WILD-TYPE 
         140.38          139.17 
  ARMC9 MUTATED ARMC9 WILD-TYPE 
         20.285          20.190 
[1] "4.0 - 140.4 (20.3)" "0.0 - 139.2 (20.2)"
[1] "hr=" "1.4"
D461V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ARMC9 MUTATED         2        0        1         2         1         0
  ARMC9 WILD-TYPE      62        1       24       107         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ARMC9 MUTATED           1          0          0          0        1         0
  ARMC9 WILD-TYPE        18         10         41         31       34        13
                 vv
clus              STAGE IVB
  ARMC9 MUTATED           0
  ARMC9 WILD-TYPE         1
D461V3, multiclass
            clus
vv           ARMC9 MUTATED ARMC9 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              2             107
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ARMC9 MUTATED     1   1   4   2
  ARMC9 WILD-TYPE   8  67 244  39
D461V4, multiclass
    clus
vv   ARMC9 MUTATED ARMC9 WILD-TYPE
  T1             1               8
  T2             1              67
  T3             4             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
  ARMC9 MUTATED     6   1   1
  ARMC9 WILD-TYPE 214  79  65
D461V5, multiclass
    clus
vv   ARMC9 MUTATED ARMC9 WILD-TYPE
  N0             6             214
  N1             1              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"
D461V6, binary
                 cls
clus                0   1
  ARMC9 MUTATED     7   1
  ARMC9 WILD-TYPE 276  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARMC9 MUTATED      7    1
  ARMC9 WILD-TYPE  276   47
   clus
vv  ARMC9 MUTATED ARMC9 WILD-TYPE
  0             7             276
  1             1              47
[1] 2 2
[1] FALSE
D461V7, binary
                 cls
clus                0   1
  ARMC9 MUTATED     5   3
  ARMC9 WILD-TYPE 165 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARMC9 MUTATED      5    3
  ARMC9 WILD-TYPE  165  194
        clus
vv       ARMC9 MUTATED ARMC9 WILD-TYPE
  FEMALE             5             165
  MALE               3             194
[1] 2 2
[1] FALSE
D461V8, binary
                 cls
clus                0   1
  ARMC9 MUTATED     4   4
  ARMC9 WILD-TYPE 313  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARMC9 MUTATED      4    4
  ARMC9 WILD-TYPE  313   44
                               clus
vv                              ARMC9 MUTATED ARMC9 WILD-TYPE
  COLON ADENOCARCINOMA                      4             313
  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 252   2  22  19
D461V9, multiclass
    clus
vv   ARMC9 MUTATED ARMC9 WILD-TYPE
  R0             5             252
  R1             0               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"
D461V10, 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     5
  ARMC9 WILD-TYPE                        19   171
D461V11, 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                                        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(462) Variable = NUDCD1 MUTATION ANALYSIS
D462V1, survival
                  sevent
clus2                0   1
  NUDCD1 MUTATED     6   2
  NUDCD1 WILD-TYPE 276  71
  NUDCD1 MUTATED NUDCD1 WILD-TYPE 
               8              347 
  NUDCD1 MUTATED NUDCD1 WILD-TYPE 
               2               71 
$`NUDCD1 MUTATED`
TCGA-A6-6654 TCGA-AA-3710 TCGA-AA-A00N TCGA-CM-5868 TCGA-D5-6536 TCGA-DM-A1D8 
       23.87        26.99         4.01        17.03        17.85        12.59 
TCGA-DM-A1HB TCGA-G4-6588 
      135.65        26.17 

$`NUDCD1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        43.27        15.12         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        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-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        91.79        46.75        52.80 

  NUDCD1 MUTATED NUDCD1 WILD-TYPE 
            4.01             0.00 
  NUDCD1 MUTATED NUDCD1 WILD-TYPE 
          135.65           140.38 
  NUDCD1 MUTATED NUDCD1 WILD-TYPE 
           20.86            20.19 
[1] "4.0 - 135.7 (20.9)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D462V2, 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       25       105         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NUDCD1 MUTATED           0          0          2          0        0
  NUDCD1 WILD-TYPE        19         10         39         31       35
                  vv
clus               STAGE IVA STAGE IVB
  NUDCD1 MUTATED           1         0
  NUDCD1 WILD-TYPE        12         1
D462V3, multiclass
            clus
vv           NUDCD1 MUTATED NUDCD1 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               4              105
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  68 241  39
D462V4, multiclass
    clus
vv   NUDCD1 MUTATED NUDCD1 WILD-TYPE
  T1              0                9
  T2              0               68
  T3              7              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
  NUDCD1 MUTATED     5   4   0
  NUDCD1 WILD-TYPE 215  76  66
D462V5, multiclass
    clus
vv   NUDCD1 MUTATED NUDCD1 WILD-TYPE
  N0              5              215
  N1              4               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"
D462V6, binary
                  cls
clus                 0   1
  NUDCD1 MUTATED     7   1
  NUDCD1 WILD-TYPE 276  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDCD1 MUTATED      7    1
  NUDCD1 WILD-TYPE  276   47
   clus
vv  NUDCD1 MUTATED NUDCD1 WILD-TYPE
  0              7              276
  1              1               47
[1] 2 2
[1] FALSE
D462V7, 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
D462V8, binary
                  cls
clus                 0   1
  NUDCD1 MUTATED     8   1
  NUDCD1 WILD-TYPE 309  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDCD1 MUTATED      8    1
  NUDCD1 WILD-TYPE  309   47
                               clus
vv                              NUDCD1 MUTATED NUDCD1 WILD-TYPE
  COLON ADENOCARCINOMA                       8              309
  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 251   2  22  21
D462V9, multiclass
    clus
vv   NUDCD1 MUTATED NUDCD1 WILD-TYPE
  R0              6              251
  R1              0                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"
D462V10, 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
D462V11, 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(463) Variable = ALG2 MUTATION ANALYSIS
D463V1, survival
                sevent
clus2              0   1
  ALG2 MUTATED     5   3
  ALG2 WILD-TYPE 277  70
  ALG2 MUTATED ALG2 WILD-TYPE 
             8            347 
  ALG2 MUTATED ALG2 WILD-TYPE 
             3             70 
$`ALG2 MUTATED`
TCGA-AA-3518 TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-CM-5349 
        1.02         4.01        34.98        62.79        61.41        30.08 
TCGA-D5-6537 TCGA-G4-6588 
        4.80        26.17 

$`ALG2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       38.99         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       83.80        22.36        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12        17.85        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        91.79        46.75        52.80 

  ALG2 MUTATED ALG2 WILD-TYPE 
          1.02           0.00 
  ALG2 MUTATED ALG2 WILD-TYPE 
         62.79         140.38 
  ALG2 MUTATED ALG2 WILD-TYPE 
        28.125         20.120 
[1] "1.0 - 62.8 (28.1)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.7"
D463V2, 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       24       106         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        19         10         40         31       35        13
                vv
clus             STAGE IVB
  ALG2 MUTATED           0
  ALG2 WILD-TYPE         1
D463V3, multiclass
            clus
vv           ALG2 MUTATED ALG2 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             3            106
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ALG2 MUTATED     1   0   5   2
  ALG2 WILD-TYPE   8  68 243  39
D463V4, multiclass
    clus
vv   ALG2 MUTATED ALG2 WILD-TYPE
  T1            1              8
  T2            0             68
  T3            5            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
  ALG2 MUTATED     7   1   0
  ALG2 WILD-TYPE 213  79  66
D463V5, multiclass
    clus
vv   ALG2 MUTATED ALG2 WILD-TYPE
  N0            7            213
  N1            1             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"
D463V6, binary
                cls
clus               0   1
  ALG2 MUTATED     6   0
  ALG2 WILD-TYPE 277  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  ALG2 MUTATED      6    0
  ALG2 WILD-TYPE  277   48
   clus
vv  ALG2 MUTATED ALG2 WILD-TYPE
  0            6            277
  1            0             48
[1] 2 2
[1] FALSE
D463V7, 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
D463V8, binary
                cls
clus               0   1
  ALG2 MUTATED     7   1
  ALG2 WILD-TYPE 310  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  ALG2 MUTATED      7    1
  ALG2 WILD-TYPE  310   47
                               clus
vv                              ALG2 MUTATED ALG2 WILD-TYPE
  COLON ADENOCARCINOMA                     7            310
  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 251   2  22  21
D463V9, multiclass
    clus
vv   ALG2 MUTATED ALG2 WILD-TYPE
  R0            6            251
  R1            0              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"
D463V10, 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
D463V11, 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(464) Variable = ZNF449 MUTATION ANALYSIS
D464V1, survival
                  sevent
clus2                0   1
  ZNF449 MUTATED    10   0
  ZNF449 WILD-TYPE 272  73
  ZNF449 MUTATED ZNF449 WILD-TYPE 
              10              345 
  ZNF449 MUTATED ZNF449 WILD-TYPE 
               0               73 
$`ZNF449 MUTATED`
TCGA-A6-5661 TCGA-A6-5665 TCGA-AA-3663 TCGA-AA-A01Q TCGA-AD-5900 TCGA-AU-6004 
       33.53        22.06         6.97         1.02         0.07        27.09 
TCGA-CA-6716 TCGA-D5-6931 TCGA-F4-6805 TCGA-G4-6588 
        0.26        12.00        16.31        26.17 

$`ZNF449 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6807 
       13.45         6.18        35.87         1.55        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  ZNF449 MUTATED ZNF449 WILD-TYPE 
            0.07             0.00 
  ZNF449 MUTATED ZNF449 WILD-TYPE 
           33.53           140.38 
  ZNF449 MUTATED ZNF449 WILD-TYPE 
          14.155           20.280 
[1] "0.1 - 33.5 (14.2)"  "0.0 - 140.4 (20.3)"
[1] "hr="     "9200000"
D464V2, 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       23       104         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF449 MUTATED           0          0          0          1        0
  ZNF449 WILD-TYPE        19         10         41         30       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF449 MUTATED           0         0
  ZNF449 WILD-TYPE        13         1
D464V3, multiclass
            clus
vv           ZNF449 MUTATED ZNF449 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               5              104
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF449 MUTATED     0   2   7   1
  ZNF449 WILD-TYPE   9  66 241  40
D464V4, multiclass
    clus
vv   ZNF449 MUTATED ZNF449 WILD-TYPE
  T1              0                9
  T2              2               66
  T3              7              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
  ZNF449 MUTATED     9   0   1
  ZNF449 WILD-TYPE 211  80  65
D464V5, multiclass
    clus
vv   ZNF449 MUTATED ZNF449 WILD-TYPE
  N0              9              211
  N1              0               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"
D464V6, binary
                  cls
clus                 0   1
  ZNF449 MUTATED     9   0
  ZNF449 WILD-TYPE 274  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF449 MUTATED      9    0
  ZNF449 WILD-TYPE  274   48
   clus
vv  ZNF449 MUTATED ZNF449 WILD-TYPE
  0              9              274
  1              0               48
[1] 2 2
[1] FALSE
D464V7, 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
D464V8, binary
                  cls
clus                 0   1
  ZNF449 MUTATED     9   1
  ZNF449 WILD-TYPE 308  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF449 MUTATED      9    1
  ZNF449 WILD-TYPE  308   47
                               clus
vv                              ZNF449 MUTATED ZNF449 WILD-TYPE
  COLON ADENOCARCINOMA                       9              308
  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 248   2  22  20
D464V9, multiclass
    clus
vv   ZNF449 MUTATED ZNF449 WILD-TYPE
  R0              9              248
  R1              0                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"
D464V10, 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
D464V11, 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(465) Variable = MAP9 MUTATION ANALYSIS
D465V1, survival
                sevent
clus2              0   1
  MAP9 MUTATED    13   3
  MAP9 WILD-TYPE 269  70
  MAP9 MUTATED MAP9 WILD-TYPE 
            16            339 
  MAP9 MUTATED MAP9 WILD-TYPE 
             3             70 
$`MAP9 MUTATED`
TCGA-A6-5665 TCGA-AA-3662 TCGA-AA-3837 TCGA-AA-3845 TCGA-AA-3977 TCGA-AU-6004 
       22.06         6.05        38.99         0.00        25.02        27.09 
TCGA-AZ-6598 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5913 TCGA-CM-4743 TCGA-CM-5348 
       49.41         0.33         0.10        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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       19.99        13.94        19.99        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       15.95        37.02        14.93        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07         0.26         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       40.34        15.62        49.08        21.99        21.14         2.93 
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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       43.27        15.12        17.85        12.49        16.14        15.58 
TCGA-D5-6898 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-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  MAP9 MUTATED MAP9 WILD-TYPE 
             0              0 
  MAP9 MUTATED MAP9 WILD-TYPE 
         51.32         140.38 
  MAP9 MUTATED MAP9 WILD-TYPE 
        19.595         20.190 
[1] "0.0 - 51.3 (19.6)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D465V2, 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       24       102         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        19          9         38         31       33        13
                vv
clus             STAGE IVB
  MAP9 MUTATED           0
  MAP9 WILD-TYPE         1
D465V3, multiclass
            clus
vv           MAP9 MUTATED MAP9 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             7            102
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            1              9
  STAGE IIIB            3             38
  STAGE IIIC            0             31
  STAGE IV              2             33
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MAP9 MUTATED     0   2  13   1
  MAP9 WILD-TYPE   9  66 235  40
D465V4, multiclass
    clus
vv   MAP9 MUTATED MAP9 WILD-TYPE
  T1            0              9
  T2            2             66
  T3           13            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
  MAP9 MUTATED    10   4   2
  MAP9 WILD-TYPE 210  76  64
D465V5, multiclass
    clus
vv   MAP9 MUTATED MAP9 WILD-TYPE
  N0           10            210
  N1            4             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"
D465V6, binary
                cls
clus               0   1
  MAP9 MUTATED    10   2
  MAP9 WILD-TYPE 273  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAP9 MUTATED     10    2
  MAP9 WILD-TYPE  273   46
   clus
vv  MAP9 MUTATED MAP9 WILD-TYPE
  0           10            273
  1            2             46
[1] 2 2
[1] FALSE
D465V7, 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
D465V8, binary
                cls
clus               0   1
  MAP9 MUTATED    14   2
  MAP9 WILD-TYPE 303  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAP9 MUTATED     14    2
  MAP9 WILD-TYPE  303   46
                               clus
vv                              MAP9 MUTATED MAP9 WILD-TYPE
  COLON ADENOCARCINOMA                    14            303
  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 247   2  21  18
D465V9, multiclass
    clus
vv   MAP9 MUTATED MAP9 WILD-TYPE
  R0           10            247
  R1            0              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"
D465V10, 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
D465V11, 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(466) Variable = IRAK3 MUTATION ANALYSIS
D466V1, survival
                 sevent
clus2               0   1
  IRAK3 MUTATED     6   2
  IRAK3 WILD-TYPE 276  71
  IRAK3 MUTATED IRAK3 WILD-TYPE 
              8             347 
  IRAK3 MUTATED IRAK3 WILD-TYPE 
              2              71 
$`IRAK3 MUTATED`
TCGA-AA-3492 TCGA-AA-A00N TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-D5-6535 
        3.02         4.01        58.39         0.33         0.10        15.12 
TCGA-D5-6540 TCGA-G4-6309 
       16.14        51.75 

$`IRAK3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.26         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        17.85         4.80        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  IRAK3 MUTATED IRAK3 WILD-TYPE 
            0.1             0.0 
  IRAK3 MUTATED IRAK3 WILD-TYPE 
          58.39          140.38 
  IRAK3 MUTATED IRAK3 WILD-TYPE 
          9.565          20.980 
[1] "0.1 - 58.4 (9.6)"   "0.0 - 140.4 (21.0)"
[1] "hr=" "1.5"
D466V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IRAK3 MUTATED         2        0        1         3         1         0
  IRAK3 WILD-TYPE      62        1       24       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        19         10         39         31       35        13
                 vv
clus              STAGE IVB
  IRAK3 MUTATED           0
  IRAK3 WILD-TYPE         1
D466V3, multiclass
            clus
vv           IRAK3 MUTATED IRAK3 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              3             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  IRAK3 MUTATED     0   2   6   1
  IRAK3 WILD-TYPE   9  66 242  40
D466V4, multiclass
    clus
vv   IRAK3 MUTATED IRAK3 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             6             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
  IRAK3 MUTATED     7   2   0
  IRAK3 WILD-TYPE 213  78  66
D466V5, multiclass
    clus
vv   IRAK3 MUTATED IRAK3 WILD-TYPE
  N0             7             213
  N1             2              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"
D466V6, binary
                 cls
clus                0   1
  IRAK3 MUTATED     7   0
  IRAK3 WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IRAK3 MUTATED      7    0
  IRAK3 WILD-TYPE  276   48
   clus
vv  IRAK3 MUTATED IRAK3 WILD-TYPE
  0             7             276
  1             0              48
[1] 2 2
[1] FALSE
D466V7, binary
                 cls
clus                0   1
  IRAK3 MUTATED     3   6
  IRAK3 WILD-TYPE 167 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IRAK3 MUTATED      3    6
  IRAK3 WILD-TYPE  167  191
        clus
vv       IRAK3 MUTATED IRAK3 WILD-TYPE
  FEMALE             3             167
  MALE               6             191
[1] 2 2
[1] FALSE
D466V8, binary
                 cls
clus                0   1
  IRAK3 MUTATED     6   3
  IRAK3 WILD-TYPE 311  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IRAK3 MUTATED      6    3
  IRAK3 WILD-TYPE  311   45
                               clus
vv                              IRAK3 MUTATED IRAK3 WILD-TYPE
  COLON ADENOCARCINOMA                      6             311
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  IRAK3 MUTATED     5   0   0   4
  IRAK3 WILD-TYPE 252   2  22  17
D466V9, multiclass
    clus
vv   IRAK3 MUTATED IRAK3 WILD-TYPE
  R0             5             252
  R1             0               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"
D466V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IRAK3 MUTATED                                  0     2
  IRAK3 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  IRAK3 MUTATED                           1     4
  IRAK3 WILD-TYPE                        18   172
D466V11, multiclass
                                  clus
vv                                 IRAK3 MUTATED IRAK3 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(467) Variable = PTPRK MUTATION ANALYSIS
D467V1, survival
                 sevent
clus2               0   1
  PTPRK MUTATED    28   4
  PTPRK WILD-TYPE 254  69
  PTPRK MUTATED PTPRK WILD-TYPE 
             32             323 
  PTPRK MUTATED PTPRK WILD-TYPE 
              4              69 
$`PTPRK MUTATED`
TCGA-A6-3809 TCGA-A6-5665 TCGA-A6-6141 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3663 
       32.75        22.06         8.38        63.98        29.95         6.97 
TCGA-AA-3715 TCGA-AA-3815 TCGA-AA-3867 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3977 
       19.04        33.04        24.03        33.01        24.00        25.02 
TCGA-AA-A00N TCGA-AA-A01R TCGA-AA-A01V TCGA-AD-6895 TCGA-AU-6004 TCGA-AY-6197 
        4.01        35.01        35.01         0.72        27.09        21.44 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CM-4743 TCGA-CM-5349 TCGA-CM-6165 TCGA-CM-6674 
       15.62        51.32        23.05        30.08        16.04        12.95 
TCGA-D5-6532 TCGA-DM-A0XD TCGA-DM-A1D8 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6304 
       18.25        24.43        12.59         0.53        19.43        53.62 
TCGA-G4-6310 TCGA-G4-6588 
       45.11        26.17 

$`PTPRK WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       32.71        27.09        22.52        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       78.08         6.05        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        26.01         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       33.04        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       14.50        16.31         0.95        15.75         0.20        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5914 
        1.35        17.56       102.44        40.34        49.08        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14         2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-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-6675 TCGA-CM-6676 
       13.02        15.02        14.04        11.01        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 
       19.59        13.51        11.51        20.19         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38        10.26       119.70        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       33.67        13.25        35.41       107.67        74.56        65.85 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        51.75        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        91.79        46.75        52.80 

  PTPRK MUTATED PTPRK WILD-TYPE 
           0.53            0.00 
  PTPRK MUTATED PTPRK WILD-TYPE 
          63.98          140.38 
  PTPRK MUTATED PTPRK WILD-TYPE 
         24.015          19.990 
[1] "0.5 - 64.0 (24.0)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1.6"
D467V2, 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       22        94         4         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PTPRK MUTATED           2          0          1          0        2         0
  PTPRK WILD-TYPE        17         10         40         31       33        13
                 vv
clus              STAGE IVB
  PTPRK MUTATED           0
  PTPRK WILD-TYPE         1
D467V3, multiclass
            clus
vv           PTPRK MUTATED PTPRK WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA             15              94
  STAGE IIB              4               4
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               2              33
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PTPRK MUTATED     0   4  23   6
  PTPRK WILD-TYPE   9  64 225  35
D467V4, multiclass
    clus
vv   PTPRK MUTATED PTPRK WILD-TYPE
  T1             0               9
  T2             4              64
  T3            23             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
  PTPRK MUTATED    26   3   4
  PTPRK WILD-TYPE 194  77  62
D467V5, multiclass
    clus
vv   PTPRK MUTATED PTPRK WILD-TYPE
  N0            26             194
  N1             3              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"
D467V6, binary
                 cls
clus                0   1
  PTPRK MUTATED    26   2
  PTPRK WILD-TYPE 257  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRK MUTATED     26    2
  PTPRK WILD-TYPE  257   46
   clus
vv  PTPRK MUTATED PTPRK WILD-TYPE
  0            26             257
  1             2              46
[1] 2 2
[1] FALSE
D467V7, 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
D467V8, binary
                 cls
clus                0   1
  PTPRK MUTATED    24   9
  PTPRK WILD-TYPE 293  39
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRK MUTATED     24    9
  PTPRK WILD-TYPE  293   39
                               clus
vv                              PTPRK MUTATED PTPRK WILD-TYPE
  COLON ADENOCARCINOMA                     24             293
  COLON MUCINOUS ADENOCARCINOMA             9              39
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PTPRK MUTATED    24   0   2   2
  PTPRK WILD-TYPE 233   2  20  19
D467V9, multiclass
    clus
vv   PTPRK MUTATED PTPRK WILD-TYPE
  R0            24             233
  R1             0               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"
D467V10, 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
D467V11, 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(468) Variable = SCLY MUTATION ANALYSIS
D468V1, survival
                sevent
clus2              0   1
  SCLY MUTATED     7   3
  SCLY WILD-TYPE 275  70
  SCLY MUTATED SCLY WILD-TYPE 
            10            345 
  SCLY MUTATED SCLY WILD-TYPE 
             3             70 
$`SCLY MUTATED`
TCGA-A6-3809 TCGA-AA-3877 TCGA-AZ-6598 TCGA-CK-5916 TCGA-CM-5349 TCGA-CM-5861 
       32.75        31.00        49.41        21.14        30.08        15.02 
TCGA-CM-5864 TCGA-D5-6930 TCGA-DM-A28F TCGA-F4-6703 
       15.02         1.51        35.97        35.87 

$`SCLY WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13        83.80        22.36        62.79        61.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
       40.34        15.62        49.08        51.32        21.99         2.93 
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        16.01         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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  SCLY MUTATED SCLY WILD-TYPE 
          1.51           0.00 
  SCLY MUTATED SCLY WILD-TYPE 
         49.41         140.38 
  SCLY MUTATED SCLY WILD-TYPE 
         30.54          20.02 
[1] "1.5 - 49.4 (30.5)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1.5"
D468V2, 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       24       105         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SCLY MUTATED           0          0          1          0        0         0
  SCLY WILD-TYPE        19         10         40         31       35        13
                vv
clus             STAGE IVB
  SCLY MUTATED           0
  SCLY WILD-TYPE         1
D468V3, multiclass
            clus
vv           SCLY MUTATED SCLY WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             4            105
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SCLY MUTATED     2   1   6   1
  SCLY WILD-TYPE   7  67 242  40
D468V4, multiclass
    clus
vv   SCLY MUTATED SCLY WILD-TYPE
  T1            2              7
  T2            1             67
  T3            6            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
  SCLY MUTATED     9   1   0
  SCLY WILD-TYPE 211  79  66
D468V5, multiclass
    clus
vv   SCLY MUTATED SCLY WILD-TYPE
  N0            9            211
  N1            1             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"
D468V6, binary
                cls
clus               0   1
  SCLY MUTATED     9   0
  SCLY WILD-TYPE 274  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  SCLY MUTATED      9    0
  SCLY WILD-TYPE  274   48
   clus
vv  SCLY MUTATED SCLY WILD-TYPE
  0            9            274
  1            0             48
[1] 2 2
[1] FALSE
D468V7, binary
                cls
clus               0   1
  SCLY MUTATED     6   4
  SCLY WILD-TYPE 164 193
[1] "tbl2"
                cls
clus             [,1] [,2]
  SCLY MUTATED      6    4
  SCLY WILD-TYPE  164  193
        clus
vv       SCLY MUTATED SCLY WILD-TYPE
  FEMALE            6            164
  MALE              4            193
[1] 2 2
[1] FALSE
D468V8, binary
                cls
clus               0   1
  SCLY MUTATED     7   3
  SCLY WILD-TYPE 310  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  SCLY MUTATED      7    3
  SCLY WILD-TYPE  310   45
                               clus
vv                              SCLY MUTATED SCLY WILD-TYPE
  COLON ADENOCARCINOMA                     7            310
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SCLY MUTATED     7   0   0   1
  SCLY WILD-TYPE 250   2  22  20
D468V9, multiclass
    clus
vv   SCLY MUTATED SCLY WILD-TYPE
  R0            7            250
  R1            0              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"
D468V10, 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
D468V11, 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(469) Variable = RBAK MUTATION ANALYSIS
D469V1, survival
                sevent
clus2              0   1
  RBAK MUTATED    15   2
  RBAK WILD-TYPE 267  71
  RBAK MUTATED RBAK WILD-TYPE 
            17            338 
  RBAK MUTATED RBAK WILD-TYPE 
             2             71 
$`RBAK MUTATED`
TCGA-AA-3525 TCGA-AA-3660 TCGA-AA-3939 TCGA-AA-A010 TCGA-AZ-4315 TCGA-CA-6717 
        8.05        78.08        12.99        34.98        58.39         0.33 
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       107.67        53.62 

$`RBAK WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        61.02         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 
        1.35        17.56       102.44        40.34        49.08        51.32 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 
       21.99         2.93         2.01        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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64        13.41         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 
       16.24        33.67         0.53        35.41        19.43        74.56 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  RBAK MUTATED RBAK WILD-TYPE 
          0.33           0.00 
  RBAK MUTATED RBAK WILD-TYPE 
        131.51         140.38 
  RBAK MUTATED RBAK WILD-TYPE 
        29.030         20.005 
[1] "0.3 - 131.5 (29.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "3"  
D469V2, 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       24       103         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RBAK MUTATED           2          0          1          1        0         1
  RBAK WILD-TYPE        17         10         40         30       35        12
                vv
clus             STAGE IVB
  RBAK MUTATED           0
  RBAK WILD-TYPE         1
D469V3, multiclass
            clus
vv           RBAK MUTATED RBAK WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             6            103
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             2             17
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            1             30
  STAGE IV              0             35
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 237  38
D469V4, multiclass
    clus
vv   RBAK MUTATED RBAK WILD-TYPE
  T1            1              8
  T2            2             66
  T3           11            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
  RBAK MUTATED    12   3   2
  RBAK WILD-TYPE 208  77  64
D469V5, multiclass
    clus
vv   RBAK MUTATED RBAK WILD-TYPE
  N0           12            208
  N1            3             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"
D469V6, binary
                cls
clus               0   1
  RBAK MUTATED    15   1
  RBAK WILD-TYPE 268  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBAK MUTATED     15    1
  RBAK WILD-TYPE  268   47
   clus
vv  RBAK MUTATED RBAK WILD-TYPE
  0           15            268
  1            1             47
[1] 2 2
[1] FALSE
D469V7, 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
D469V8, binary
                cls
clus               0   1
  RBAK MUTATED    14   3
  RBAK WILD-TYPE 303  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBAK MUTATED     14    3
  RBAK WILD-TYPE  303   45
                               clus
vv                              RBAK MUTATED RBAK WILD-TYPE
  COLON ADENOCARCINOMA                    14            303
  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 245   2  22  17
D469V9, multiclass
    clus
vv   RBAK MUTATED RBAK WILD-TYPE
  R0           12            245
  R1            0              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"
D469V10, 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
D469V11, 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(470) Variable = ERBB2 MUTATION ANALYSIS
D470V1, survival
                 sevent
clus2               0   1
  ERBB2 MUTATED    20   7
  ERBB2 WILD-TYPE 262  66
  ERBB2 MUTATED ERBB2 WILD-TYPE 
             27             328 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
              7              66 
$`ERBB2 MUTATED`
TCGA-A6-4105 TCGA-A6-6138 TCGA-AA-3502 TCGA-AA-3660 TCGA-AA-3864 TCGA-AA-3869 
       14.53        22.52        35.01        78.08        53.00        27.02 
TCGA-AA-3947 TCGA-AA-3977 TCGA-AA-3994 TCGA-AD-6888 TCGA-AY-5543 TCGA-AZ-6599 
       33.01        25.02        27.02         4.21        15.75         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-CK-4947 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-6162 
       12.10       100.01        17.56        30.08        16.01        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 
       35.41        65.85        55.04 

$`ERBB2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3510 
       19.66        20.28         7.04         3.02         1.02        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3875 
       31.07        30.05        17.03        24.03        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       27.02        19.07         7.96        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96         0.07        21.37        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-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-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       62.79        61.41        49.41        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 
        0.07         0.26         0.33         0.10         1.35       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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-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-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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       11.51        20.19         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 
       19.43       107.67        74.56        53.62        44.68        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  ERBB2 MUTATED ERBB2 WILD-TYPE 
           4.21            0.00 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
         100.01          140.38 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
         22.520          20.155 
[1] "4.2 - 100.0 (22.5)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D470V2, 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       22       103         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ERBB2 MUTATED           0          1          4          1        3         2
  ERBB2 WILD-TYPE        19          9         37         30       32        11
                 vv
clus              STAGE IVB
  ERBB2 MUTATED           1
  ERBB2 WILD-TYPE         0
D470V3, multiclass
            clus
vv           ERBB2 MUTATED ERBB2 WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              6             103
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             4              37
  STAGE IIIC             1              30
  STAGE IV               3              32
  STAGE IVA              2              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   6  17   4
  ERBB2 WILD-TYPE   9  62 231  37
D470V4, multiclass
    clus
vv   ERBB2 MUTATED ERBB2 WILD-TYPE
  T1             0               9
  T2             6              62
  T3            17             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   7   3
  ERBB2 WILD-TYPE 204  73  63
D470V5, multiclass
    clus
vv   ERBB2 MUTATED ERBB2 WILD-TYPE
  N0            16             204
  N1             7              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"
D470V6, binary
                 cls
clus                0   1
  ERBB2 MUTATED    20   5
  ERBB2 WILD-TYPE 263  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED     20    5
  ERBB2 WILD-TYPE  263   43
   clus
vv  ERBB2 MUTATED ERBB2 WILD-TYPE
  0            20             263
  1             5              43
[1] 2 2
[1] FALSE
D470V7, 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
D470V8, binary
                 cls
clus                0   1
  ERBB2 MUTATED    23   4
  ERBB2 WILD-TYPE 294  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED     23    4
  ERBB2 WILD-TYPE  294   44
                               clus
vv                              ERBB2 MUTATED ERBB2 WILD-TYPE
  COLON ADENOCARCINOMA                     23             294
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ERBB2 MUTATED    18   0   1   1
  ERBB2 WILD-TYPE 239   2  21  20
D470V9, multiclass
    clus
vv   ERBB2 MUTATED ERBB2 WILD-TYPE
  R0            18             239
  R1             0               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"
D470V10, 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
D470V11, 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(471) Variable = ALX4 MUTATION ANALYSIS
D471V1, survival
                sevent
clus2              0   1
  ALX4 MUTATED     9   2
  ALX4 WILD-TYPE 273  71
  ALX4 MUTATED ALX4 WILD-TYPE 
            11            344 
  ALX4 MUTATED ALX4 WILD-TYPE 
             2             71 
$`ALX4 MUTATED`
TCGA-A6-6653 TCGA-AA-3713 TCGA-AA-3949 TCGA-AY-6197 TCGA-AZ-6598 TCGA-AZ-6601 
       24.39        19.04        26.01        21.44        49.41       100.01 
TCGA-CM-5861 TCGA-CM-6170 TCGA-D5-6540 TCGA-D5-6927 TCGA-G4-6588 
       15.02        15.02        16.14         9.44        26.17 

$`ALX4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       22.36        62.79        61.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  ALX4 MUTATED ALX4 WILD-TYPE 
          9.44           0.00 
  ALX4 MUTATED ALX4 WILD-TYPE 
        100.01         140.38 
  ALX4 MUTATED ALX4 WILD-TYPE 
        21.440         20.155 
[1] "9.4 - 100.0 (21.4)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.4"
D471V2, 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       23       105         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        19         10         40         31       34        13
                vv
clus             STAGE IVB
  ALX4 MUTATED           0
  ALX4 WILD-TYPE         1
D471V3, multiclass
            clus
vv           ALX4 MUTATED ALX4 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             4            105
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ALX4 MUTATED     0   3   8   0
  ALX4 WILD-TYPE   9  65 240  41
D471V4, multiclass
    clus
vv   ALX4 MUTATED ALX4 WILD-TYPE
  T1            0              9
  T2            3             65
  T3            8            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
  ALX4 MUTATED    10   1   0
  ALX4 WILD-TYPE 210  79  66
D471V5, multiclass
    clus
vv   ALX4 MUTATED ALX4 WILD-TYPE
  N0           10            210
  N1            1             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"
D471V6, binary
                cls
clus               0   1
  ALX4 MUTATED     8   1
  ALX4 WILD-TYPE 275  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  ALX4 MUTATED      8    1
  ALX4 WILD-TYPE  275   47
   clus
vv  ALX4 MUTATED ALX4 WILD-TYPE
  0            8            275
  1            1             47
[1] 2 2
[1] FALSE
D471V7, 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
D471V8, binary
                cls
clus               0   1
  ALX4 MUTATED     9   2
  ALX4 WILD-TYPE 308  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  ALX4 MUTATED      9    2
  ALX4 WILD-TYPE  308   46
                               clus
vv                              ALX4 MUTATED ALX4 WILD-TYPE
  COLON ADENOCARCINOMA                     9            308
  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 250   2  21  21
D471V9, multiclass
    clus
vv   ALX4 MUTATED ALX4 WILD-TYPE
  R0            7            250
  R1            0              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"
D471V10, 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
D471V11, 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(472) Variable = MEPE MUTATION ANALYSIS
D472V1, survival
                sevent
clus2              0   1
  MEPE MUTATED    12   3
  MEPE WILD-TYPE 270  70
  MEPE MUTATED MEPE WILD-TYPE 
            15            340 
  MEPE MUTATED MEPE WILD-TYPE 
             3             70 
$`MEPE MUTATED`
TCGA-A6-5665 TCGA-A6-6141 TCGA-AA-3555 TCGA-AA-3697 TCGA-AA-A00N TCGA-AA-A01P 
       22.06         8.38        29.95        85.05         4.01        38.07 
TCGA-AD-6889 TCGA-AU-6004 TCGA-AZ-6605 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-5868 
       56.55        27.09         5.23         0.33         0.10        17.03 
TCGA-D5-6924 TCGA-D5-6930 TCGA-F4-6703 
       14.30         1.51        35.87 

$`MEPE WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.09        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        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        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10       100.01        29.56        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.26         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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-D5-6926 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-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45         6.18         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  MEPE MUTATED MEPE WILD-TYPE 
           0.1            0.0 
  MEPE MUTATED MEPE WILD-TYPE 
         85.05         140.38 
  MEPE MUTATED MEPE WILD-TYPE 
        17.030         20.235 
[1] "0.1 - 85.0 (17.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D472V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MEPE MUTATED         1        0        0         9         1         0
  MEPE WILD-TYPE      63        1       25       100         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MEPE MUTATED           2          0          1          0        0         1
  MEPE WILD-TYPE        17         10         40         31       35        12
                vv
clus             STAGE IVB
  MEPE MUTATED           0
  MEPE WILD-TYPE         1
D472V3, multiclass
            clus
vv           MEPE MUTATED MEPE WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             9            100
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             2             17
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 237  38
D472V4, multiclass
    clus
vv   MEPE MUTATED MEPE WILD-TYPE
  T1            0              9
  T2            1             67
  T3           11            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
  MEPE MUTATED    12   3   0
  MEPE WILD-TYPE 208  77  66
D472V5, multiclass
    clus
vv   MEPE MUTATED MEPE WILD-TYPE
  N0           12            208
  N1            3             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"
D472V6, binary
                cls
clus               0   1
  MEPE MUTATED    14   1
  MEPE WILD-TYPE 269  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  MEPE MUTATED     14    1
  MEPE WILD-TYPE  269   47
   clus
vv  MEPE MUTATED MEPE WILD-TYPE
  0           14            269
  1            1             47
[1] 2 2
[1] FALSE
D472V7, 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
D472V8, binary
                cls
clus               0   1
  MEPE MUTATED    11   4
  MEPE WILD-TYPE 306  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  MEPE MUTATED     11    4
  MEPE WILD-TYPE  306   44
                               clus
vv                              MEPE MUTATED MEPE WILD-TYPE
  COLON ADENOCARCINOMA                    11            306
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MEPE MUTATED    10   0   0   2
  MEPE WILD-TYPE 247   2  22  19
D472V9, multiclass
    clus
vv   MEPE MUTATED MEPE WILD-TYPE
  R0           10            247
  R1            0              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"
D472V10, 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
D472V11, 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(473) Variable = ADNP2 MUTATION ANALYSIS
D473V1, survival
                 sevent
clus2               0   1
  ADNP2 MUTATED    12   3
  ADNP2 WILD-TYPE 270  70
  ADNP2 MUTATED ADNP2 WILD-TYPE 
             15             340 
  ADNP2 MUTATED ADNP2 WILD-TYPE 
              3              70 
$`ADNP2 MUTATED`
TCGA-A6-5665 TCGA-A6-6141 TCGA-AA-3510 TCGA-AA-3710 TCGA-AA-A01Q TCGA-AA-A02O 
       22.06         8.38        63.98        26.99         1.02         0.92 
TCGA-AY-6197 TCGA-CK-4947 TCGA-D5-6535 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1HB 
       21.44        17.56        15.12        92.75        49.91       135.65 
TCGA-F4-6570 TCGA-G4-6293 TCGA-G4-6628 
        6.18       107.67        52.80 

$`ADNP2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.09        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       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        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
       14.01        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        15.75         0.20        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 
       11.51        20.19        18.25         1.32        43.27        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        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-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        13.38        13.45        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       19.43        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       35.80        26.17        91.79        46.75 

  ADNP2 MUTATED ADNP2 WILD-TYPE 
           0.92            0.00 
  ADNP2 MUTATED ADNP2 WILD-TYPE 
         135.65          140.38 
  ADNP2 MUTATED ADNP2 WILD-TYPE 
          22.06           20.07 
[1] "0.9 - 135.7 (22.1)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.7"
D473V2, 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       22       102         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ADNP2 MUTATED           1          0          2          0        0         1
  ADNP2 WILD-TYPE        18         10         39         31       35        12
                 vv
clus              STAGE IVB
  ADNP2 MUTATED           0
  ADNP2 WILD-TYPE         1
D473V3, multiclass
            clus
vv           ADNP2 MUTATED ADNP2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              7             102
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 235  40
D473V4, multiclass
    clus
vv   ADNP2 MUTATED ADNP2 WILD-TYPE
  T1             0               9
  T2             1              67
  T3            13             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
  ADNP2 MUTATED    11   4   0
  ADNP2 WILD-TYPE 209  76  66
D473V5, multiclass
    clus
vv   ADNP2 MUTATED ADNP2 WILD-TYPE
  N0            11             209
  N1             4              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"
D473V6, binary
                 cls
clus                0   1
  ADNP2 MUTATED    13   0
  ADNP2 WILD-TYPE 270  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADNP2 MUTATED     13    0
  ADNP2 WILD-TYPE  270   48
   clus
vv  ADNP2 MUTATED ADNP2 WILD-TYPE
  0            13             270
  1             0              48
[1] 2 2
[1] FALSE
D473V7, 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
D473V8, binary
                 cls
clus                0   1
  ADNP2 MUTATED    14   1
  ADNP2 WILD-TYPE 303  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADNP2 MUTATED     14    1
  ADNP2 WILD-TYPE  303   47
                               clus
vv                              ADNP2 MUTATED ADNP2 WILD-TYPE
  COLON ADENOCARCINOMA                     14             303
  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 248   2  22  19
D473V9, multiclass
    clus
vv   ADNP2 MUTATED ADNP2 WILD-TYPE
  R0             9             248
  R1             0               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"
D473V10, 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
D473V11, 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(474) Variable = SLC33A1 MUTATION ANALYSIS
D474V1, survival
                   sevent
clus2                 0   1
  SLC33A1 MUTATED     6   2
  SLC33A1 WILD-TYPE 276  71
  SLC33A1 MUTATED SLC33A1 WILD-TYPE 
                8               347 
  SLC33A1 MUTATED SLC33A1 WILD-TYPE 
                2                71 
$`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        36.72 

$`SLC33A1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 
        1.32        43.27        15.12         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        51.75        45.11        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  SLC33A1 MUTATED SLC33A1 WILD-TYPE 
             6.77              0.00 
  SLC33A1 MUTATED SLC33A1 WILD-TYPE 
           124.27            140.38 
  SLC33A1 MUTATED SLC33A1 WILD-TYPE 
           20.135            20.190 
[1] "6.8 - 124.3 (20.1)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D474V2, 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       25       106         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC33A1 MUTATED           0          1          1          0        1
  SLC33A1 WILD-TYPE        19          9         40         31       34
                   vv
clus                STAGE IVA STAGE IVB
  SLC33A1 MUTATED           0         0
  SLC33A1 WILD-TYPE        13         1
D474V3, multiclass
            clus
vv           SLC33A1 MUTATED SLC33A1 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                3               106
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               1                 9
  STAGE IIIB               1                40
  STAGE IIIC               0                31
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC33A1 MUTATED     0   2   7   0
  SLC33A1 WILD-TYPE   9  66 241  41
D474V4, multiclass
    clus
vv   SLC33A1 MUTATED SLC33A1 WILD-TYPE
  T1               0                 9
  T2               2                66
  T3               7               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
  SLC33A1 MUTATED     7   1   1
  SLC33A1 WILD-TYPE 213  79  65
D474V5, multiclass
    clus
vv   SLC33A1 MUTATED SLC33A1 WILD-TYPE
  N0               7               213
  N1               1                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"
D474V6, binary
                   cls
clus                  0   1
  SLC33A1 MUTATED     5   1
  SLC33A1 WILD-TYPE 278  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC33A1 MUTATED      5    1
  SLC33A1 WILD-TYPE  278   47
   clus
vv  SLC33A1 MUTATED SLC33A1 WILD-TYPE
  0               5               278
  1               1                47
[1] 2 2
[1] FALSE
D474V7, 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
D474V8, binary
                   cls
clus                  0   1
  SLC33A1 MUTATED     8   1
  SLC33A1 WILD-TYPE 309  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC33A1 MUTATED      8    1
  SLC33A1 WILD-TYPE  309   47
                               clus
vv                              SLC33A1 MUTATED SLC33A1 WILD-TYPE
  COLON ADENOCARCINOMA                        8               309
  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 251   2  22  20
D474V9, multiclass
    clus
vv   SLC33A1 MUTATED SLC33A1 WILD-TYPE
  R0               6               251
  R1               0                 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"
D474V10, 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
D474V11, 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(475) Variable = ABCB4 MUTATION ANALYSIS
D475V1, survival
                 sevent
clus2               0   1
  ABCB4 MUTATED    18   3
  ABCB4 WILD-TYPE 264  70
  ABCB4 MUTATED ABCB4 WILD-TYPE 
             21             334 
  ABCB4 MUTATED ABCB4 WILD-TYPE 
              3              70 
$`ABCB4 MUTATED`
TCGA-A6-5666 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3525 TCGA-AA-3680 TCGA-AA-3811 
       32.71        19.66        63.98         8.05        11.01        10.06 
TCGA-AA-A004 TCGA-AA-A00R TCGA-AA-A010 TCGA-AD-5900 TCGA-AD-6889 TCGA-AU-3779 
       13.94         0.99        34.98         0.07        56.55        14.50 
TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4746 TCGA-D5-6540 
       58.39        49.41         0.33         0.10        37.02        16.14 
TCGA-D5-6541 TCGA-D5-6928 TCGA-D5-6930 
       15.58        11.64         1.51 

$`ABCB4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       24.03        37.05        36.03        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 
       14.01         0.92        50.04        47.01        15.02         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        19.04        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W 
       38.04         4.01        27.02        42.02        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       18.05        40.96        21.37         4.21         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 
        5.79        22.42        27.42        10.88         0.20        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07         0.26         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       12.49         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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  ABCB4 MUTATED ABCB4 WILD-TYPE 
           0.07            0.00 
  ABCB4 MUTATED ABCB4 WILD-TYPE 
          63.98          140.38 
  ABCB4 MUTATED ABCB4 WILD-TYPE 
         14.500          20.995 
[1] "0.1 - 64.0 (14.5)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.3"
D475V2, 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       22       100         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        18         10         40         30       34        13
                 vv
clus              STAGE IVB
  ABCB4 MUTATED           0
  ABCB4 WILD-TYPE         1
D475V3, multiclass
            clus
vv           ABCB4 MUTATED ABCB4 WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              9             100
  STAGE IIB              1               7
  STAGE IIC              1               0
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ABCB4 MUTATED     0   4  13   5
  ABCB4 WILD-TYPE   9  64 235  36
D475V4, multiclass
    clus
vv   ABCB4 MUTATED ABCB4 WILD-TYPE
  T1             0               9
  T2             4              64
  T3            13             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
  ABCB4 MUTATED    18   2   2
  ABCB4 WILD-TYPE 202  78  64
D475V5, multiclass
    clus
vv   ABCB4 MUTATED ABCB4 WILD-TYPE
  N0            18             202
  N1             2              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"
D475V6, binary
                 cls
clus                0   1
  ABCB4 MUTATED    18   1
  ABCB4 WILD-TYPE 265  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCB4 MUTATED     18    1
  ABCB4 WILD-TYPE  265   47
   clus
vv  ABCB4 MUTATED ABCB4 WILD-TYPE
  0            18             265
  1             1              47
[1] 2 2
[1] FALSE
D475V7, 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
D475V8, binary
                 cls
clus                0   1
  ABCB4 MUTATED    16   6
  ABCB4 WILD-TYPE 301  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCB4 MUTATED     16    6
  ABCB4 WILD-TYPE  301   42
                               clus
vv                              ABCB4 MUTATED ABCB4 WILD-TYPE
  COLON ADENOCARCINOMA                     16             301
  COLON MUCINOUS ADENOCARCINOMA             6              42
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ABCB4 MUTATED    16   0   1   2
  ABCB4 WILD-TYPE 241   2  21  19
D475V9, multiclass
    clus
vv   ABCB4 MUTATED ABCB4 WILD-TYPE
  R0            16             241
  R1             0               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"
D475V10, 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
D475V11, 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(476) Variable = KLC4 MUTATION ANALYSIS
D476V1, survival
                sevent
clus2              0   1
  KLC4 MUTATED    12   2
  KLC4 WILD-TYPE 270  71
  KLC4 MUTATED KLC4 WILD-TYPE 
            14            341 
  KLC4 MUTATED KLC4 WILD-TYPE 
             2             71 
$`KLC4 MUTATED`
TCGA-A6-2676 TCGA-AA-3518 TCGA-AA-3713 TCGA-AA-3845 TCGA-AA-3860 TCGA-AA-3864 
       42.90         1.02        19.04         0.00        31.07        53.00 
TCGA-CA-6718 TCGA-CK-5913 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-6166 TCGA-CM-6677 
        0.10        51.32        23.05        37.02        21.99        11.08 
TCGA-D5-5539 TCGA-F4-6460 
       19.59        13.38 

$`KLC4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       38.99        37.02        14.93        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.33         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
       17.56       102.44        40.34        15.62        49.08        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4747 
       21.14         2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         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-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  KLC4 MUTATED KLC4 WILD-TYPE 
             0              0 
  KLC4 MUTATED KLC4 WILD-TYPE 
         53.00         140.38 
  KLC4 MUTATED KLC4 WILD-TYPE 
         20.79          20.19 
[1] "0.0 - 53.0 (20.8)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.4"
D476V2, 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       24       103         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        19          9         39         31       33        13
                vv
clus             STAGE IVB
  KLC4 MUTATED           0
  KLC4 WILD-TYPE         1
D476V3, multiclass
            clus
vv           KLC4 MUTATED KLC4 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             6            103
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            1              9
  STAGE IIIB            2             39
  STAGE IIIC            0             31
  STAGE IV              2             33
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  KLC4 MUTATED     0   3  12   1
  KLC4 WILD-TYPE   9  65 236  40
D476V4, multiclass
    clus
vv   KLC4 MUTATED KLC4 WILD-TYPE
  T1            0              9
  T2            3             65
  T3           12            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
  KLC4 MUTATED    12   3   1
  KLC4 WILD-TYPE 208  77  65
D476V5, multiclass
    clus
vv   KLC4 MUTATED KLC4 WILD-TYPE
  N0           12            208
  N1            3             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"
D476V6, binary
                cls
clus               0   1
  KLC4 MUTATED    12   2
  KLC4 WILD-TYPE 271  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLC4 MUTATED     12    2
  KLC4 WILD-TYPE  271   46
   clus
vv  KLC4 MUTATED KLC4 WILD-TYPE
  0           12            271
  1            2             46
[1] 2 2
[1] FALSE
D476V7, 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
D476V8, binary
                cls
clus               0   1
  KLC4 MUTATED    15   1
  KLC4 WILD-TYPE 302  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLC4 MUTATED     15    1
  KLC4 WILD-TYPE  302   47
                               clus
vv                              KLC4 MUTATED KLC4 WILD-TYPE
  COLON ADENOCARCINOMA                    15            302
  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 246   2  20  18
D476V9, multiclass
    clus
vv   KLC4 MUTATED KLC4 WILD-TYPE
  R0           11            246
  R1            0              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"
D476V10, 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
D476V11, 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(477) Variable = RPA3 MUTATION ANALYSIS
D477V1, survival
                sevent
clus2              0   1
  RPA3 MUTATED     4   0
  RPA3 WILD-TYPE 278  73
  RPA3 MUTATED RPA3 WILD-TYPE 
             4            351 
  RPA3 MUTATED RPA3 WILD-TYPE 
             0             73 
$`RPA3 MUTATED`
TCGA-AA-3496 TCGA-AA-3511 TCGA-CM-6676 TCGA-G4-6309 
        1.02         6.97        11.08        51.75 

$`RPA3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       74.56        65.85        53.62        44.68        55.04        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  RPA3 MUTATED RPA3 WILD-TYPE 
          1.02           0.00 
  RPA3 MUTATED RPA3 WILD-TYPE 
         51.75         140.38 
  RPA3 MUTATED RPA3 WILD-TYPE 
         9.025         20.280 
[1] "1.0 - 51.8 (9.0)"   "0.0 - 140.4 (20.3)"
[1] "hr="     "3300000"
D477V2, 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       23       109         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        19         10         40         31       35        13
                vv
clus             STAGE IVB
  RPA3 MUTATED           0
  RPA3 WILD-TYPE         1
D477V3, multiclass
            clus
vv           RPA3 MUTATED RPA3 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             0            109
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RPA3 MUTATED     0   1   2   1
  RPA3 WILD-TYPE   9  67 246  40
D477V4, multiclass
    clus
vv   RPA3 MUTATED RPA3 WILD-TYPE
  T1            0              9
  T2            1             67
  T3            2            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
  RPA3 MUTATED     3   1   0
  RPA3 WILD-TYPE 217  79  66
D477V5, multiclass
    clus
vv   RPA3 MUTATED RPA3 WILD-TYPE
  N0            3            217
  N1            1             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"
D477V6, binary
                cls
clus               0   1
  RPA3 MUTATED     4   0
  RPA3 WILD-TYPE 279  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPA3 MUTATED      4    0
  RPA3 WILD-TYPE  279   48
   clus
vv  RPA3 MUTATED RPA3 WILD-TYPE
  0            4            279
  1            0             48
[1] 2 2
[1] FALSE
D477V7, 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
D477V8, binary
                cls
clus               0   1
  RPA3 MUTATED     4   0
  RPA3 WILD-TYPE 313  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPA3 MUTATED      4    0
  RPA3 WILD-TYPE  313   48
                               clus
vv                              RPA3 MUTATED RPA3 WILD-TYPE
  COLON ADENOCARCINOMA                     4            313
  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 253   2  22  21
D477V9, multiclass
    clus
vv   RPA3 MUTATED RPA3 WILD-TYPE
  R0            4            253
  R1            0              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"
D477V10, 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
D477V11, multiclass
[1] "Remove cluster labels:" "RPA3 MUTATED"          
clus
  RPA3 MUTATED RPA3 WILD-TYPE 
             2            204 
    TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810     TCGA-A6-4105 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-A6-5656     TCGA-A6-5657     TCGA-A6-5659     TCGA-A6-5660 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-A6-5661     TCGA-A6-5662     TCGA-A6-5664     TCGA-A6-5665 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-A6-5666     TCGA-A6-6137     TCGA-A6-6138     TCGA-A6-6141 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-A6-6142     TCGA-A6-6648     TCGA-A6-6649     TCGA-A6-6651 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-A6-6652     TCGA-A6-6653     TCGA-A6-6654     TCGA-A6-6780 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-A6-6781     TCGA-A6-6782     TCGA-AD-5900     TCGA-AD-6548 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-AD-6888     TCGA-AD-6889     TCGA-AD-6890     TCGA-AD-6895 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-AD-6899     TCGA-AD-6901     TCGA-AD-6963     TCGA-AD-6964 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-AD-6965     TCGA-AU-3779     TCGA-AU-6004     TCGA-AY-4070 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-AY-4071     TCGA-AY-5543     TCGA-AY-6196     TCGA-AY-6197 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-AY-6386     TCGA-AZ-4315     TCGA-AZ-4323     TCGA-AZ-4616 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-AZ-4681     TCGA-AZ-4682     TCGA-AZ-5403     TCGA-AZ-5407 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-AZ-6598     TCGA-AZ-6599     TCGA-AZ-6600     TCGA-AZ-6601 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-AZ-6603     TCGA-AZ-6605     TCGA-AZ-6606     TCGA-AZ-6607 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-AZ-6608     TCGA-CA-5254     TCGA-CA-5255     TCGA-CA-5796 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-CA-5797     TCGA-CA-6715     TCGA-CA-6716     TCGA-CA-6717 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-CA-6718     TCGA-CA-6719     TCGA-CK-4947     TCGA-CK-4948 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-CK-4950     TCGA-CK-4952     TCGA-CK-5912     TCGA-CK-5913 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-CK-5914     TCGA-CK-5915     TCGA-CK-5916     TCGA-CK-6746 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-CK-6747     TCGA-CK-6748     TCGA-CK-6751     TCGA-CM-4743 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-CM-4744     TCGA-CM-4746     TCGA-CM-4747     TCGA-CM-4752 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-CM-5341     TCGA-CM-5344     TCGA-CM-5348     TCGA-CM-5349 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-CM-5860     TCGA-CM-5861     TCGA-CM-5862     TCGA-CM-5863 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-CM-5864     TCGA-CM-5868     TCGA-CM-6161     TCGA-CM-6162 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-CM-6163     TCGA-CM-6164     TCGA-CM-6165     TCGA-CM-6166 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-CM-6167     TCGA-CM-6168     TCGA-CM-6169     TCGA-CM-6170 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-CM-6171     TCGA-CM-6172     TCGA-CM-6674     TCGA-CM-6675 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-CM-6677     TCGA-CM-6678     TCGA-CM-6679     TCGA-CM-6680 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-D5-5537     TCGA-D5-5538     TCGA-D5-5539     TCGA-D5-5540 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-D5-5541     TCGA-D5-6529     TCGA-D5-6532     TCGA-D5-6533 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-D5-6534     TCGA-D5-6535     TCGA-D5-6536     TCGA-D5-6537 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-D5-6538     TCGA-D5-6539     TCGA-D5-6540     TCGA-D5-6541 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-D5-6898     TCGA-D5-6920     TCGA-D5-6922     TCGA-D5-6923 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-D5-6924     TCGA-D5-6926     TCGA-D5-6927     TCGA-D5-6928 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-D5-6929     TCGA-D5-6930     TCGA-D5-6931     TCGA-D5-6932 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-D5-7000     TCGA-DM-A0X9     TCGA-DM-A0XD     TCGA-DM-A0XF 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-DM-A1D0     TCGA-DM-A1D4     TCGA-DM-A1D6     TCGA-DM-A1D7 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-DM-A1D8     TCGA-DM-A1D9     TCGA-DM-A1DA     TCGA-DM-A1DB 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-DM-A1HA     TCGA-DM-A1HB     TCGA-DM-A282     TCGA-DM-A285 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-DM-A28C     TCGA-DM-A28E     TCGA-DM-A28F     TCGA-DM-A28G 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-DM-A28H     TCGA-DM-A28K     TCGA-F4-6459     TCGA-F4-6460 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-F4-6569     TCGA-F4-6570     TCGA-F4-6703     TCGA-F4-6704 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-F4-6805     TCGA-F4-6806     TCGA-F4-6807     TCGA-F4-6808 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-F4-6809     TCGA-F4-6854     TCGA-F4-6855     TCGA-F4-6856 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-G4-6293     TCGA-G4-6299     TCGA-G4-6303     TCGA-G4-6304 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-G4-6306     TCGA-G4-6307     TCGA-G4-6310     TCGA-G4-6315 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-G4-6317     TCGA-G4-6321     TCGA-G4-6323     TCGA-G4-6586 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-G4-6588     TCGA-G4-6625     TCGA-G4-6626     TCGA-G4-6628 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 

Clustering(478) Variable = RBBP7 MUTATION ANALYSIS
D478V1, survival
                 sevent
clus2               0   1
  RBBP7 MUTATED    12   3
  RBBP7 WILD-TYPE 270  70
  RBBP7 MUTATED RBBP7 WILD-TYPE 
             15             340 
  RBBP7 MUTATED RBBP7 WILD-TYPE 
              3              70 
$`RBBP7 MUTATED`
TCGA-A6-2671 TCGA-AA-3662 TCGA-AA-3864 TCGA-AA-3941 TCGA-AA-A00N TCGA-AA-A010 
       43.76         6.05        53.00        24.00         4.01        34.98 
TCGA-AA-A01Q TCGA-AD-5900 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CK-5916 TCGA-CM-5344 
        1.02         0.07        58.39         0.33        21.14        22.03 
TCGA-CM-5861 TCGA-CM-6171 TCGA-D5-5538 
       15.02        14.04        12.26 

$`RBBP7 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       19.99        13.94        19.99        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        51.32        21.99         2.93         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-5862 TCGA-CM-5863 
       29.06        22.98        30.08        16.01         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  RBBP7 MUTATED RBBP7 WILD-TYPE 
           0.07            0.00 
  RBBP7 MUTATED RBBP7 WILD-TYPE 
          58.39          140.38 
  RBBP7 MUTATED RBBP7 WILD-TYPE 
         15.020          20.235 
[1] "0.1 - 58.4 (15.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D478V2, 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       23       106         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        19         10         39         31       33        12
                 vv
clus              STAGE IVB
  RBBP7 MUTATED           0
  RBBP7 WILD-TYPE         1
D478V3, multiclass
            clus
vv           RBBP7 MUTATED RBBP7 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              3             106
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               2              33
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 240  37
D478V4, multiclass
    clus
vv   RBBP7 MUTATED RBBP7 WILD-TYPE
  T1             1               8
  T2             2              66
  T3             8             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
  RBBP7 MUTATED    10   3   2
  RBBP7 WILD-TYPE 210  77  64
D478V5, multiclass
    clus
vv   RBBP7 MUTATED RBBP7 WILD-TYPE
  N0            10             210
  N1             3              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"
D478V6, binary
                 cls
clus                0   1
  RBBP7 MUTATED    11   3
  RBBP7 WILD-TYPE 272  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBBP7 MUTATED     11    3
  RBBP7 WILD-TYPE  272   45
   clus
vv  RBBP7 MUTATED RBBP7 WILD-TYPE
  0            11             272
  1             3              45
[1] 2 2
[1] FALSE
D478V7, 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
D478V8, binary
                 cls
clus                0   1
  RBBP7 MUTATED    12   3
  RBBP7 WILD-TYPE 305  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBBP7 MUTATED     12    3
  RBBP7 WILD-TYPE  305   45
                               clus
vv                              RBBP7 MUTATED RBBP7 WILD-TYPE
  COLON ADENOCARCINOMA                     12             305
  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 245   2  21  19
D478V9, multiclass
    clus
vv   RBBP7 MUTATED RBBP7 WILD-TYPE
  R0            12             245
  R1             0               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"
D478V10, 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
D478V11, 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(479) Variable = SYT1 MUTATION ANALYSIS
D479V1, survival
                sevent
clus2              0   1
  SYT1 MUTATED    12   1
  SYT1 WILD-TYPE 270  72
  SYT1 MUTATED SYT1 WILD-TYPE 
            13            342 
  SYT1 MUTATED SYT1 WILD-TYPE 
             1             72 
$`SYT1 MUTATED`
TCGA-A6-5660 TCGA-AA-3510 TCGA-AA-3697 TCGA-AA-A010 TCGA-CA-6717 TCGA-CK-6751 
       29.19        63.98        85.05        34.98         0.33       124.27 
TCGA-CM-4743 TCGA-CM-5861 TCGA-CM-6680 TCGA-D5-6529 TCGA-G4-6323 TCGA-G4-6586 
       23.05        15.02        12.03        20.19        13.78        35.80 
TCGA-G4-6626 
       46.75 

$`SYT1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       36.72        36.00        22.09        26.17        91.79        52.80 

  SYT1 MUTATED SYT1 WILD-TYPE 
          0.33           0.00 
  SYT1 MUTATED SYT1 WILD-TYPE 
        124.27         140.38 
  SYT1 MUTATED SYT1 WILD-TYPE 
        29.190         20.005 
[1] "0.3 - 124.3 (29.2)" "0.0 - 140.4 (20.0)"
[1] "hr=" "4"  
D479V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SYT1 MUTATED         1        1        1         6         1         0
  SYT1 WILD-TYPE      63        0       24       103         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SYT1 MUTATED           1          0          1          1        0         0
  SYT1 WILD-TYPE        18         10         40         30       35        13
                vv
clus             STAGE IVB
  SYT1 MUTATED           0
  SYT1 WILD-TYPE         1
D479V3, multiclass
            clus
vv           SYT1 MUTATED SYT1 WILD-TYPE
  STAGE I               1             63
  STAGE IA              1              0
  STAGE II              1             24
  STAGE IIA             6            103
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            1             30
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SYT1 MUTATED     0   1  10   1
  SYT1 WILD-TYPE   9  67 238  40
D479V4, multiclass
    clus
vv   SYT1 MUTATED SYT1 WILD-TYPE
  T1            0              9
  T2            1             67
  T3           10            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
  SYT1 MUTATED    11   0   2
  SYT1 WILD-TYPE 209  80  64
D479V5, multiclass
    clus
vv   SYT1 MUTATED SYT1 WILD-TYPE
  N0           11            209
  N1            0             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"
D479V6, binary
                cls
clus               0   1
  SYT1 MUTATED    11   0
  SYT1 WILD-TYPE 272  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  SYT1 MUTATED     11    0
  SYT1 WILD-TYPE  272   48
   clus
vv  SYT1 MUTATED SYT1 WILD-TYPE
  0           11            272
  1            0             48
[1] 2 2
[1] FALSE
D479V7, 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
D479V8, binary
                cls
clus               0   1
  SYT1 MUTATED    11   2
  SYT1 WILD-TYPE 306  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  SYT1 MUTATED     11    2
  SYT1 WILD-TYPE  306   46
                               clus
vv                              SYT1 MUTATED SYT1 WILD-TYPE
  COLON ADENOCARCINOMA                    11            306
  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 247   2  22  19
D479V9, multiclass
    clus
vv   SYT1 MUTATED SYT1 WILD-TYPE
  R0           10            247
  R1            0              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"
D479V10, 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
D479V11, 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(480) Variable = STRADB MUTATION ANALYSIS
D480V1, survival
                  sevent
clus2                0   1
  STRADB MUTATED     3   2
  STRADB WILD-TYPE 279  71
  STRADB MUTATED STRADB WILD-TYPE 
               5              350 
  STRADB MUTATED STRADB WILD-TYPE 
               2               71 
$`STRADB MUTATED`
TCGA-AA-3492 TCGA-AA-3713 TCGA-AD-6964 TCGA-AY-6196 TCGA-DM-A28H 
        3.02        19.04        10.88         0.20       117.07 

$`STRADB WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  STRADB MUTATED STRADB WILD-TYPE 
             0.2              0.0 
  STRADB MUTATED STRADB WILD-TYPE 
          117.07           140.38 
  STRADB MUTATED STRADB WILD-TYPE 
           10.88            20.63 
[1] "0.2 - 117.1 (10.9)" "0.0 - 140.4 (20.6)"
[1] "hr=" "1.8"
D480V2, 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       24       109         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  STRADB MUTATED           0          0          0          2        1
  STRADB WILD-TYPE        19         10         41         29       34
                  vv
clus               STAGE IVA STAGE IVB
  STRADB MUTATED           0         0
  STRADB WILD-TYPE        13         1
D480V3, multiclass
            clus
vv           STRADB MUTATED STRADB WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               0              109
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              2               29
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  STRADB MUTATED     0   0   4   1
  STRADB WILD-TYPE   9  68 244  40
D480V4, multiclass
    clus
vv   STRADB MUTATED STRADB WILD-TYPE
  T1              0                9
  T2              0               68
  T3              4              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
  STRADB MUTATED     2   0   3
  STRADB WILD-TYPE 218  80  63
D480V5, multiclass
    clus
vv   STRADB MUTATED STRADB WILD-TYPE
  N0              2              218
  N1              0               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"
D480V6, binary
                  cls
clus                 0   1
  STRADB MUTATED     2   1
  STRADB WILD-TYPE 281  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STRADB MUTATED      2    1
  STRADB WILD-TYPE  281   47
   clus
vv  STRADB MUTATED STRADB WILD-TYPE
  0              2              281
  1              1               47
[1] 2 2
[1] FALSE
D480V7, 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
D480V8, binary
                  cls
clus                 0   1
  STRADB MUTATED     4   1
  STRADB WILD-TYPE 313  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STRADB MUTATED      4    1
  STRADB WILD-TYPE  313   47
                               clus
vv                              STRADB MUTATED STRADB WILD-TYPE
  COLON ADENOCARCINOMA                       4              313
  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 255   2  21  21
D480V9, multiclass
    clus
vv   STRADB MUTATED STRADB WILD-TYPE
  R0              2              255
  R1              0                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"
D480V10, 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
D480V11, 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(481) Variable = C9ORF131 MUTATION ANALYSIS
D481V1, survival
                    sevent
clus2                  0   1
  C9ORF131 MUTATED     9   2
  C9ORF131 WILD-TYPE 273  71
  C9ORF131 MUTATED C9ORF131 WILD-TYPE 
                11                344 
  C9ORF131 MUTATED C9ORF131 WILD-TYPE 
                 2                 71 
$`C9ORF131 MUTATED`
TCGA-A6-5665 TCGA-AA-3555 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6895 TCGA-AU-6004 
       22.06        29.95         4.01        34.98         0.72        27.09 
TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-5913 TCGA-D5-6540 TCGA-G4-6628 
       49.41         0.33        51.32        16.14        52.80 

$`C9ORF131 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        17.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 
      102.44        40.34        15.62        49.08        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 
       91.79        46.75 

  C9ORF131 MUTATED C9ORF131 WILD-TYPE 
              0.33               0.00 
  C9ORF131 MUTATED C9ORF131 WILD-TYPE 
             52.80             140.38 
  C9ORF131 MUTATED C9ORF131 WILD-TYPE 
             27.09              20.07 
[1] "0.3 - 52.8 (27.1)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.2"
D481V2, 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       24       104         5         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C9ORF131 MUTATED           0          0          0          0        0
  C9ORF131 WILD-TYPE        19         10         41         31       35
                    vv
clus                 STAGE IVA STAGE IVB
  C9ORF131 MUTATED           0         0
  C9ORF131 WILD-TYPE        13         1
D481V3, multiclass
            clus
vv           C9ORF131 MUTATED C9ORF131 WILD-TYPE
  STAGE I                   3                 61
  STAGE IA                  0                  1
  STAGE II                  1                 24
  STAGE IIA                 5                104
  STAGE IIB                 3                  5
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                0                 10
  STAGE IIIB                0                 41
  STAGE IIIC                0                 31
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C9ORF131 MUTATED     0   3   7   3
  C9ORF131 WILD-TYPE   9  65 241  38
D481V4, multiclass
    clus
vv   C9ORF131 MUTATED C9ORF131 WILD-TYPE
  T1                0                  9
  T2                3                 65
  T3                7                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
  C9ORF131 MUTATED    12   1   0
  C9ORF131 WILD-TYPE 208  79  66
D481V5, multiclass
    clus
vv   C9ORF131 MUTATED C9ORF131 WILD-TYPE
  N0               12                208
  N1                1                 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"
D481V6, binary
                    cls
clus                   0   1
  C9ORF131 MUTATED     9   0
  C9ORF131 WILD-TYPE 274  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF131 MUTATED      9    0
  C9ORF131 WILD-TYPE  274   48
   clus
vv  C9ORF131 MUTATED C9ORF131 WILD-TYPE
  0                9                274
  1                0                 48
[1] 2 2
[1] FALSE
D481V7, 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
D481V8, binary
                    cls
clus                   0   1
  C9ORF131 MUTATED     9   4
  C9ORF131 WILD-TYPE 308  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF131 MUTATED      9    4
  C9ORF131 WILD-TYPE  308   44
                               clus
vv                              C9ORF131 MUTATED C9ORF131 WILD-TYPE
  COLON ADENOCARCINOMA                         9                308
  COLON MUCINOUS ADENOCARCINOMA                4                 44
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C9ORF131 MUTATED     8   0   0   3
  C9ORF131 WILD-TYPE 249   2  22  18
D481V9, multiclass
    clus
vv   C9ORF131 MUTATED C9ORF131 WILD-TYPE
  R0                8                249
  R1                0                  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"
D481V10, 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
D481V11, 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(482) Variable = ENPP1 MUTATION ANALYSIS
D482V1, survival
                 sevent
clus2               0   1
  ENPP1 MUTATED     9   4
  ENPP1 WILD-TYPE 273  69
  ENPP1 MUTATED ENPP1 WILD-TYPE 
             13             342 
  ENPP1 MUTATED ENPP1 WILD-TYPE 
              4              69 
$`ENPP1 MUTATED`
TCGA-AA-3848 TCGA-AA-A00N TCGA-AZ-4315 TCGA-AZ-6601 TCGA-CA-5254 TCGA-CA-6717 
       10.06         4.01        58.39       100.01         2.24         0.33 
TCGA-CM-5861 TCGA-CM-6172 TCGA-D5-5541 TCGA-D5-6538 TCGA-F4-6570 TCGA-G4-6306 
       15.02        11.01        11.51        17.13         6.18        44.68 
TCGA-G4-6588 
       26.17 

$`ENPP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
        0.00        17.03         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59        13.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        12.49        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       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        13.38        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        52.80 

  ENPP1 MUTATED ENPP1 WILD-TYPE 
           0.33            0.00 
  ENPP1 MUTATED ENPP1 WILD-TYPE 
         100.01          140.38 
  ENPP1 MUTATED ENPP1 WILD-TYPE 
          11.51           20.98 
[1] "0.3 - 100.0 (11.5)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.6"
D482V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ENPP1 MUTATED         0        0        1         8         1         0
  ENPP1 WILD-TYPE      64        1       24       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        19         10         38         30       35        13
                 vv
clus              STAGE IVB
  ENPP1 MUTATED           0
  ENPP1 WILD-TYPE         1
D482V3, multiclass
            clus
vv           ENPP1 MUTATED ENPP1 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              8             101
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             3              38
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ENPP1 MUTATED     0   1  12   1
  ENPP1 WILD-TYPE   9  67 236  40
D482V4, multiclass
    clus
vv   ENPP1 MUTATED ENPP1 WILD-TYPE
  T1             0               9
  T2             1              67
  T3            12             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
  ENPP1 MUTATED    10   2   2
  ENPP1 WILD-TYPE 210  78  64
D482V5, multiclass
    clus
vv   ENPP1 MUTATED ENPP1 WILD-TYPE
  N0            10             210
  N1             2              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
  ENPP1 MUTATED    14   0
  ENPP1 WILD-TYPE 269  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ENPP1 MUTATED     14    0
  ENPP1 WILD-TYPE  269   48
   clus
vv  ENPP1 MUTATED ENPP1 WILD-TYPE
  0            14             269
  1             0              48
[1] 2 2
[1] FALSE
D482V7, 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
D482V8, binary
                 cls
clus                0   1
  ENPP1 MUTATED    12   2
  ENPP1 WILD-TYPE 305  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ENPP1 MUTATED     12    2
  ENPP1 WILD-TYPE  305   46
                               clus
vv                              ENPP1 MUTATED ENPP1 WILD-TYPE
  COLON ADENOCARCINOMA                     12             305
  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 246   2  22  19
D482V9, multiclass
    clus
vv   ENPP1 MUTATED ENPP1 WILD-TYPE
  R0            11             246
  R1             0               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"
D482V10, 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
D482V11, 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(483) Variable = NRK MUTATION ANALYSIS
D483V1, survival
               sevent
clus2             0   1
  NRK MUTATED    18   3
  NRK WILD-TYPE 264  70
  NRK MUTATED NRK WILD-TYPE 
           21           334 
  NRK MUTATED NRK WILD-TYPE 
            3            70 
$`NRK MUTATED`
TCGA-A6-5661 TCGA-A6-5666 TCGA-A6-6654 TCGA-AA-3496 TCGA-AA-3511 TCGA-AA-3663 
       33.53        32.71        23.87         1.02         6.97         6.97 
TCGA-AA-3672 TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A010 
        0.92         5.03        10.06         2.01        25.02        34.98 
TCGA-AU-6004 TCGA-AZ-6600 TCGA-CA-6717 TCGA-CK-4950 TCGA-CK-5913 TCGA-CM-5860 
       27.09        12.10         0.33        40.34        51.32        16.01 
TCGA-CM-5861 TCGA-CM-6171 TCGA-D5-6931 
       15.02        14.04        12.00 

$`NRK WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       24.16        21.76        24.69        24.39        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 
       20.28         7.04         3.02        35.01        63.98         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       78.08         6.05        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
       36.00        85.05        26.99        19.04        19.04        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        21.99        21.14         2.93         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-6164 
       15.02        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  NRK MUTATED NRK WILD-TYPE 
         0.33          0.00 
  NRK MUTATED NRK WILD-TYPE 
        51.32        140.38 
  NRK MUTATED NRK WILD-TYPE 
        14.04         20.98 
[1] "0.3 - 51.3 (14.0)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1"  
D483V2, 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       22       102         7         0
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NRK MUTATED           2          1          1          1        2         0
  NRK WILD-TYPE        17          9         40         30       33        13
               vv
clus            STAGE IVB
  NRK MUTATED           0
  NRK WILD-TYPE         1
D483V3, multiclass
            clus
vv           NRK MUTATED NRK WILD-TYPE
  STAGE I              3            61
  STAGE IA             0             1
  STAGE II             3            22
  STAGE IIA            7           102
  STAGE IIB            1             7
  STAGE IIC            1             0
  STAGE III            2            17
  STAGE IIIA           1             9
  STAGE IIIB           1            40
  STAGE IIIC           1            30
  STAGE IV             2            33
  STAGE IVA            0            13
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  NRK MUTATED     0   4  14   5
  NRK WILD-TYPE   9  64 234  36
D483V4, multiclass
    clus
vv   NRK MUTATED NRK WILD-TYPE
  T1           0             9
  T2           4            64
  T3          14           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
  NRK MUTATED    16   5   2
  NRK WILD-TYPE 204  75  64
D483V5, multiclass
    clus
vv   NRK MUTATED NRK WILD-TYPE
  N0          16           204
  N1           5            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"
D483V6, binary
               cls
clus              0   1
  NRK MUTATED    18   2
  NRK WILD-TYPE 265  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  NRK MUTATED     18    2
  NRK WILD-TYPE  265   46
   clus
vv  NRK MUTATED NRK WILD-TYPE
  0          18           265
  1           2            46
[1] 2 2
[1] FALSE
D483V7, 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
D483V8, binary
               cls
clus              0   1
  NRK MUTATED    21   2
  NRK WILD-TYPE 296  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  NRK MUTATED     21    2
  NRK WILD-TYPE  296   46
                               clus
vv                              NRK MUTATED NRK WILD-TYPE
  COLON ADENOCARCINOMA                   21           296
  COLON MUCINOUS ADENOCARCINOMA           2            46
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  NRK MUTATED    13   1   1   3
  NRK WILD-TYPE 244   1  21  18
D483V9, multiclass
    clus
vv   NRK MUTATED NRK WILD-TYPE
  R0          13           244
  R1           1             1
  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"
D483V10, 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
D483V11, 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(484) Variable = ERCC3 MUTATION ANALYSIS
D484V1, survival
                 sevent
clus2               0   1
  ERCC3 MUTATED    11   5
  ERCC3 WILD-TYPE 271  68
  ERCC3 MUTATED ERCC3 WILD-TYPE 
             16             339 
  ERCC3 MUTATED ERCC3 WILD-TYPE 
              5              68 
$`ERCC3 MUTATED`
TCGA-A6-5657 TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3516 TCGA-AA-3815 TCGA-AA-3845 
       31.63        22.06         3.02        13.02        33.04         0.00 
TCGA-AA-A010 TCGA-AA-A01K TCGA-AZ-6605 TCGA-CA-6717 TCGA-CK-4950 TCGA-CM-5348 
       34.98        31.00         5.23         0.33        40.34        22.98 
TCGA-D5-6920 TCGA-D5-6930 TCGA-DM-A1D9 TCGA-F4-6570 
       12.39         1.51       140.38         6.18 

$`ERCC3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        6.97         1.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       14.93        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10       100.01        29.56        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 
        0.26         0.10         1.35        17.56       102.44        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       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-D5-6931 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-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32        12.59         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  ERCC3 MUTATED ERCC3 WILD-TYPE 
              0               0 
  ERCC3 MUTATED ERCC3 WILD-TYPE 
         140.38          139.17 
  ERCC3 MUTATED ERCC3 WILD-TYPE 
          17.54           20.19 
[1] "0.0 - 140.4 (17.5)" "0.0 - 139.2 (20.2)"
[1] "hr=" "1.9"
D484V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ERCC3 MUTATED         0        0        1         9         2         0
  ERCC3 WILD-TYPE      64        1       24       100         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ERCC3 MUTATED           1          1          3          1        0         0
  ERCC3 WILD-TYPE        18          9         38         30       35        13
                 vv
clus              STAGE IVB
  ERCC3 MUTATED           0
  ERCC3 WILD-TYPE         1
D484V3, multiclass
            clus
vv           ERCC3 MUTATED ERCC3 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              9             100
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             1               9
  STAGE IIIB             3              38
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ERCC3 MUTATED     0   0  15   3
  ERCC3 WILD-TYPE   9  68 233  38
D484V4, multiclass
    clus
vv   ERCC3 MUTATED ERCC3 WILD-TYPE
  T1             0               9
  T2             0              68
  T3            15             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    12   4   2
  ERCC3 WILD-TYPE 208  76  64
D484V5, multiclass
    clus
vv   ERCC3 MUTATED ERCC3 WILD-TYPE
  N0            12             208
  N1             4              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"
D484V6, binary
                 cls
clus                0   1
  ERCC3 MUTATED    17   0
  ERCC3 WILD-TYPE 266  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC3 MUTATED     17    0
  ERCC3 WILD-TYPE  266   48
   clus
vv  ERCC3 MUTATED ERCC3 WILD-TYPE
  0            17             266
  1             0              48
[1] 2 2
[1] FALSE
D484V7, binary
                 cls
clus                0   1
  ERCC3 MUTATED    13   5
  ERCC3 WILD-TYPE 157 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC3 MUTATED     13    5
  ERCC3 WILD-TYPE  157  192
        clus
vv       ERCC3 MUTATED ERCC3 WILD-TYPE
  FEMALE            13             157
  MALE               5             192
[1] 2 2
[1] FALSE
D484V8, binary
                 cls
clus                0   1
  ERCC3 MUTATED    15   3
  ERCC3 WILD-TYPE 302  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC3 MUTATED     15    3
  ERCC3 WILD-TYPE  302   45
                               clus
vv                              ERCC3 MUTATED ERCC3 WILD-TYPE
  COLON ADENOCARCINOMA                     15             302
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ERCC3 MUTATED    12   1   0   2
  ERCC3 WILD-TYPE 245   1  22  19
D484V9, multiclass
    clus
vv   ERCC3 MUTATED ERCC3 WILD-TYPE
  R0            12             245
  R1             1               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"
D484V10, 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     8
  ERCC3 WILD-TYPE                        17   168
D484V11, 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                                        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 = GABPA MUTATION ANALYSIS
D485V1, survival
                 sevent
clus2               0   1
  GABPA MUTATED     9   2
  GABPA WILD-TYPE 273  71
  GABPA MUTATED GABPA WILD-TYPE 
             11             344 
  GABPA MUTATED GABPA WILD-TYPE 
              2              71 
$`GABPA MUTATED`
TCGA-A6-6142 TCGA-AA-3672 TCGA-AA-3950 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6889 
       25.08         0.92        24.00         4.01        34.98        56.55 
TCGA-AD-6895 TCGA-CM-6161 TCGA-D5-6533 TCGA-DM-A0XD TCGA-G4-6588 
        0.72        15.02         1.32        24.43        26.17 

$`GABPA WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
        0.07        21.37         4.21         0.79         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       11.51        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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  GABPA MUTATED GABPA WILD-TYPE 
           0.72            0.00 
  GABPA MUTATED GABPA WILD-TYPE 
          56.55          140.38 
  GABPA MUTATED GABPA WILD-TYPE 
         24.000          20.155 
[1] "0.7 - 56.5 (24.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D485V2, 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       25       105         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        18         10         40         31       35        12
                 vv
clus              STAGE IVB
  GABPA MUTATED           0
  GABPA WILD-TYPE         1
D485V3, multiclass
            clus
vv           GABPA MUTATED GABPA WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              4             105
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 241  38
D485V4, multiclass
    clus
vv   GABPA MUTATED GABPA WILD-TYPE
  T1             0               9
  T2             1              67
  T3             7             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
  GABPA MUTATED     8   3   0
  GABPA WILD-TYPE 212  77  66
D485V5, multiclass
    clus
vv   GABPA MUTATED GABPA WILD-TYPE
  N0             8             212
  N1             3              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"
D485V6, binary
                 cls
clus                0   1
  GABPA MUTATED     9   1
  GABPA WILD-TYPE 274  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GABPA MUTATED      9    1
  GABPA WILD-TYPE  274   47
   clus
vv  GABPA MUTATED GABPA WILD-TYPE
  0             9             274
  1             1              47
[1] 2 2
[1] FALSE
D485V7, 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
D485V8, binary
                 cls
clus                0   1
  GABPA MUTATED     9   2
  GABPA WILD-TYPE 308  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GABPA MUTATED      9    2
  GABPA WILD-TYPE  308   46
                               clus
vv                              GABPA MUTATED GABPA WILD-TYPE
  COLON ADENOCARCINOMA                      9             308
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  GABPA MUTATED     7   0   0   0
  GABPA WILD-TYPE 250   2  22  21
D485V9, multiclass
    clus
vv   GABPA MUTATED GABPA WILD-TYPE
  R0             7             250
  R1             0               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"
D485V10, 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
D485V11, 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(486) Variable = CLIP4 MUTATION ANALYSIS
D486V1, survival
                 sevent
clus2               0   1
  CLIP4 MUTATED     8   5
  CLIP4 WILD-TYPE 274  68
  CLIP4 MUTATED CLIP4 WILD-TYPE 
             13             342 
  CLIP4 MUTATED CLIP4 WILD-TYPE 
              5              68 
$`CLIP4 MUTATED`
TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3662 TCGA-AA-3815 TCGA-AA-3977 TCGA-AA-A00N 
       63.98        29.95         6.05        33.04        25.02         4.01 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6964 TCGA-AY-6386 TCGA-AZ-6598 TCGA-CM-6677 
       18.05        40.96        10.88        17.82        49.41        11.08 
TCGA-DM-A1D4 
       92.75 

$`CLIP4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        17.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
        0.92        41.00        39.98         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  CLIP4 MUTATED CLIP4 WILD-TYPE 
           4.01            0.00 
  CLIP4 MUTATED CLIP4 WILD-TYPE 
          92.75          140.38 
  CLIP4 MUTATED CLIP4 WILD-TYPE 
         25.020          20.155 
[1] "4.0 - 92.8 (25.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.6"
D486V2, 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       23       104         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        18         10         40         31       34        13
                 vv
clus              STAGE IVB
  CLIP4 MUTATED           0
  CLIP4 WILD-TYPE         1
D486V3, multiclass
            clus
vv           CLIP4 MUTATED CLIP4 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              5             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CLIP4 MUTATED     0   2   9   3
  CLIP4 WILD-TYPE   9  66 239  38
D486V4, multiclass
    clus
vv   CLIP4 MUTATED CLIP4 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             9             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
  CLIP4 MUTATED    10   1   3
  CLIP4 WILD-TYPE 210  79  63
D486V5, multiclass
    clus
vv   CLIP4 MUTATED CLIP4 WILD-TYPE
  N0            10             210
  N1             1              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"
D486V6, binary
                 cls
clus                0   1
  CLIP4 MUTATED    10   1
  CLIP4 WILD-TYPE 273  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLIP4 MUTATED     10    1
  CLIP4 WILD-TYPE  273   47
   clus
vv  CLIP4 MUTATED CLIP4 WILD-TYPE
  0            10             273
  1             1              47
[1] 2 2
[1] FALSE
D486V7, 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
D486V8, binary
                 cls
clus                0   1
  CLIP4 MUTATED    11   3
  CLIP4 WILD-TYPE 306  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLIP4 MUTATED     11    3
  CLIP4 WILD-TYPE  306   45
                               clus
vv                              CLIP4 MUTATED CLIP4 WILD-TYPE
  COLON ADENOCARCINOMA                     11             306
  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 248   2  21  21
D486V9, multiclass
    clus
vv   CLIP4 MUTATED CLIP4 WILD-TYPE
  R0             9             248
  R1             0               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"
D486V10, 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
D486V11, 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(487) Variable = PLA2G4E MUTATION ANALYSIS
D487V1, survival
                   sevent
clus2                 0   1
  PLA2G4E MUTATED     7   2
  PLA2G4E WILD-TYPE 275  71
  PLA2G4E MUTATED PLA2G4E WILD-TYPE 
                9               346 
  PLA2G4E MUTATED PLA2G4E WILD-TYPE 
                2                71 
$`PLA2G4E MUTATED`
TCGA-A6-6780 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3697 TCGA-AU-6004 TCGA-AZ-6598 
       20.12        61.02         6.05        85.05        27.09        49.41 
TCGA-CA-6717 TCGA-CK-5916 TCGA-G4-6588 
        0.33        21.14        26.17 

$`PLA2G4E WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       19.99        13.94        19.99        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        91.79        46.75        52.80 

  PLA2G4E MUTATED PLA2G4E WILD-TYPE 
             0.33              0.00 
  PLA2G4E MUTATED PLA2G4E WILD-TYPE 
            85.05            140.38 
  PLA2G4E MUTATED PLA2G4E WILD-TYPE 
           26.170            20.005 
[1] "0.3 - 85.0 (26.2)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1.2"
D487V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PLA2G4E MUTATED         2        0        2         3         0         0
  PLA2G4E WILD-TYPE      62        1       23       106         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLA2G4E MUTATED           2          0          0          0        1
  PLA2G4E WILD-TYPE        17         10         41         31       34
                   vv
clus                STAGE IVA STAGE IVB
  PLA2G4E MUTATED           0         0
  PLA2G4E WILD-TYPE        13         1
D487V3, multiclass
            clus
vv           PLA2G4E MUTATED PLA2G4E WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 2                23
  STAGE IIA                3               106
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                2                17
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               0                31
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PLA2G4E MUTATED     1   1   7   1
  PLA2G4E WILD-TYPE   8  67 241  40
D487V4, multiclass
    clus
vv   PLA2G4E MUTATED PLA2G4E WILD-TYPE
  T1               1                 8
  T2               1                67
  T3               7               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
  PLA2G4E MUTATED     8   0   2
  PLA2G4E WILD-TYPE 212  80  64
D487V5, multiclass
    clus
vv   PLA2G4E MUTATED PLA2G4E WILD-TYPE
  N0               8               212
  N1               0                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"
D487V6, binary
                   cls
clus                  0   1
  PLA2G4E MUTATED     7   1
  PLA2G4E WILD-TYPE 276  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLA2G4E MUTATED      7    1
  PLA2G4E WILD-TYPE  276   47
   clus
vv  PLA2G4E MUTATED PLA2G4E WILD-TYPE
  0               7               276
  1               1                47
[1] 2 2
[1] FALSE
D487V7, 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
D487V8, binary
                   cls
clus                  0   1
  PLA2G4E MUTATED     8   2
  PLA2G4E WILD-TYPE 309  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLA2G4E MUTATED      8    2
  PLA2G4E WILD-TYPE  309   46
                               clus
vv                              PLA2G4E MUTATED PLA2G4E WILD-TYPE
  COLON ADENOCARCINOMA                        8               309
  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 252   2  21  19
D487V9, multiclass
    clus
vv   PLA2G4E MUTATED PLA2G4E WILD-TYPE
  R0               5               252
  R1               0                 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"
D487V10, 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
D487V11, 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(488) Variable = CHUK MUTATION ANALYSIS
D488V1, survival
                sevent
clus2              0   1
  CHUK MUTATED    16   5
  CHUK WILD-TYPE 266  68
  CHUK MUTATED CHUK WILD-TYPE 
            21            334 
  CHUK MUTATED CHUK WILD-TYPE 
             5             68 
$`CHUK MUTATED`
TCGA-A6-5659 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3662 TCGA-AA-A00A TCGA-AA-A010 
       30.44        63.98        29.95         6.05        38.04        34.98 
TCGA-AA-A02K TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6607 TCGA-CA-6718 
       14.01        61.41        49.41         6.77         3.19         0.10 
TCGA-CA-6719 TCGA-CM-4743 TCGA-CM-5349 TCGA-CM-6161 TCGA-CM-6677 TCGA-D5-6534 
        1.35        23.05        30.08        15.02        11.08        43.27 
TCGA-DM-A1D8 TCGA-F4-6856 TCGA-G4-6304 
       12.59        19.43        53.62 

$`CHUK WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
        7.96        27.02        13.94        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       39.06        51.98        39.98         2.01         5.03         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6600 
        1.41         5.13        83.80        22.36        62.79        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 
      100.01        29.56         5.23        11.74         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
       21.99        21.14         2.93         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 
       16.01        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-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       13.05        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        92.75        49.91        13.32       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      107.67        74.56        65.85        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  CHUK MUTATED CHUK WILD-TYPE 
           0.1            0.0 
  CHUK MUTATED CHUK WILD-TYPE 
         63.98         140.38 
  CHUK MUTATED CHUK WILD-TYPE 
        23.050         20.155 
[1] "0.1 - 64.0 (23.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D488V2, 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       23       101         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        19         10         41         31       32        13
                vv
clus             STAGE IVB
  CHUK MUTATED           0
  CHUK WILD-TYPE         1
D488V3, multiclass
            clus
vv           CHUK MUTATED CHUK WILD-TYPE
  STAGE I               5             59
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             8            101
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              3             32
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CHUK MUTATED     1   4  11   5
  CHUK WILD-TYPE   8  64 237  36
D488V4, multiclass
    clus
vv   CHUK MUTATED CHUK WILD-TYPE
  T1            1              8
  T2            4             64
  T3           11            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
  CHUK MUTATED    17   1   3
  CHUK WILD-TYPE 203  79  63
D488V5, multiclass
    clus
vv   CHUK MUTATED CHUK WILD-TYPE
  N0           17            203
  N1            1             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"
D488V6, binary
                cls
clus               0   1
  CHUK MUTATED    15   3
  CHUK WILD-TYPE 268  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHUK MUTATED     15    3
  CHUK WILD-TYPE  268   45
   clus
vv  CHUK MUTATED CHUK WILD-TYPE
  0           15            268
  1            3             45
[1] 2 2
[1] FALSE
D488V7, 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
D488V8, binary
                cls
clus               0   1
  CHUK MUTATED    18   3
  CHUK WILD-TYPE 299  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHUK MUTATED     18    3
  CHUK WILD-TYPE  299   45
                               clus
vv                              CHUK MUTATED CHUK WILD-TYPE
  COLON ADENOCARCINOMA                    18            299
  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 245   2  20  19
D488V9, multiclass
    clus
vv   CHUK MUTATED CHUK WILD-TYPE
  R0           12            245
  R1            0              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"
D488V10, 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
D488V11, 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(489) Variable = IDH2 MUTATION ANALYSIS
D489V1, survival
                sevent
clus2              0   1
  IDH2 MUTATED    12   1
  IDH2 WILD-TYPE 270  72
  IDH2 MUTATED IDH2 WILD-TYPE 
            13            342 
  IDH2 MUTATED IDH2 WILD-TYPE 
             1             72 
$`IDH2 MUTATED`
TCGA-A6-5661 TCGA-AA-3556 TCGA-AA-3672 TCGA-AA-3715 TCGA-AA-3833 TCGA-AA-A01Z 
       33.53        23.01         0.92        19.04        15.95        37.02 
TCGA-AD-6889 TCGA-AY-6196 TCGA-CK-4948 TCGA-CM-6164 TCGA-CM-6170 TCGA-D5-6535 
       56.55         0.20       102.44        29.03        15.02        15.12 
TCGA-G4-6307 
       55.04 

$`IDH2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        17.95        29.95        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 
        0.99        25.02         1.02        17.98        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        15.75        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  IDH2 MUTATED IDH2 WILD-TYPE 
           0.2            0.0 
  IDH2 MUTATED IDH2 WILD-TYPE 
        102.44         140.38 
  IDH2 MUTATED IDH2 WILD-TYPE 
        23.010         20.155 
[1] "0.2 - 102.4 (23.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "3.3"
D489V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IDH2 MUTATED         2        0        3         4         1         0
  IDH2 WILD-TYPE      62        1       22       105         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IDH2 MUTATED           1          1          2          1        1         0
  IDH2 WILD-TYPE        18          9         39         30       34        13
                vv
clus             STAGE IVB
  IDH2 MUTATED           0
  IDH2 WILD-TYPE         1
D489V3, multiclass
            clus
vv           IDH2 MUTATED IDH2 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              3             22
  STAGE IIA             4            105
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            1              9
  STAGE IIIB            2             39
  STAGE IIIC            1             30
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  IDH2 MUTATED     0   2  11   3
  IDH2 WILD-TYPE   9  66 237  38
D489V4, multiclass
    clus
vv   IDH2 MUTATED IDH2 WILD-TYPE
  T1            0              9
  T2            2             66
  T3           11            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    10   5   1
  IDH2 WILD-TYPE 210  75  65
D489V5, multiclass
    clus
vv   IDH2 MUTATED IDH2 WILD-TYPE
  N0           10            210
  N1            5             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"
D489V6, binary
                cls
clus               0   1
  IDH2 MUTATED    12   1
  IDH2 WILD-TYPE 271  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH2 MUTATED     12    1
  IDH2 WILD-TYPE  271   47
   clus
vv  IDH2 MUTATED IDH2 WILD-TYPE
  0           12            271
  1            1             47
[1] 2 2
[1] FALSE
D489V7, binary
                cls
clus               0   1
  IDH2 MUTATED    11   5
  IDH2 WILD-TYPE 159 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH2 MUTATED     11    5
  IDH2 WILD-TYPE  159  192
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  FEMALE           11            159
  MALE              5            192
[1] 2 2
[1] FALSE
D489V8, binary
                cls
clus               0   1
  IDH2 MUTATED    14   1
  IDH2 WILD-TYPE 303  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH2 MUTATED     14    1
  IDH2 WILD-TYPE  303   47
                               clus
vv                              IDH2 MUTATED IDH2 WILD-TYPE
  COLON ADENOCARCINOMA                    14            303
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  IDH2 MUTATED    12   0   1   2
  IDH2 WILD-TYPE 245   2  21  19
D489V9, multiclass
    clus
vv   IDH2 MUTATED IDH2 WILD-TYPE
  R0           12            245
  R1            0              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"
D489V10, 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
D489V11, 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(490) Variable = TET3 MUTATION ANALYSIS
D490V1, survival
                sevent
clus2              0   1
  TET3 MUTATED    16   2
  TET3 WILD-TYPE 266  71
  TET3 MUTATED TET3 WILD-TYPE 
            18            337 
  TET3 MUTATED TET3 WILD-TYPE 
             2             71 
$`TET3 MUTATED`
TCGA-A6-6653 TCGA-AA-3663 TCGA-AA-3673 TCGA-AA-3713 TCGA-AA-3846 TCGA-AA-3864 
       24.39         6.97        50.04        19.04        17.03        53.00 
TCGA-AA-3950 TCGA-AD-6889 TCGA-CA-6715 TCGA-CA-6718 TCGA-CK-5913 TCGA-CM-4743 
       24.00        56.55         0.07         0.10        51.32        23.05 
TCGA-CM-4746 TCGA-CM-6171 TCGA-D5-6533 TCGA-DM-A1D4 TCGA-F4-6570 TCGA-G4-6321 
       37.02        14.04         1.32        92.75         6.18        22.09 

$`TET3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01         0.92        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02        14.93         0.00        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        4.21         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.33         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       11.51        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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        24.43        38.20       130.65        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      117.07        98.24         8.61        13.38        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  TET3 MUTATED TET3 WILD-TYPE 
          0.07           0.00 
  TET3 MUTATED TET3 WILD-TYPE 
         92.75         140.38 
  TET3 MUTATED TET3 WILD-TYPE 
         22.57          20.12 
[1] "0.1 - 92.8 (22.6)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "2.2"
D490V2, 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       21       101         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TET3 MUTATED           1          0          2          0        1         0
  TET3 WILD-TYPE        18         10         39         31       34        13
                vv
clus             STAGE IVB
  TET3 MUTATED           0
  TET3 WILD-TYPE         1
D490V3, multiclass
            clus
vv           TET3 MUTATED TET3 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              4             21
  STAGE IIA             8            101
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            2             39
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TET3 MUTATED     0   4  13   3
  TET3 WILD-TYPE   9  64 235  38
D490V4, multiclass
    clus
vv   TET3 MUTATED TET3 WILD-TYPE
  T1            0              9
  T2            4             64
  T3           13            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
  TET3 MUTATED    18   2   0
  TET3 WILD-TYPE 202  78  66
D490V5, multiclass
    clus
vv   TET3 MUTATED TET3 WILD-TYPE
  N0           18            202
  N1            2             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"
D490V6, binary
                cls
clus               0   1
  TET3 MUTATED    16   1
  TET3 WILD-TYPE 267  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  TET3 MUTATED     16    1
  TET3 WILD-TYPE  267   47
   clus
vv  TET3 MUTATED TET3 WILD-TYPE
  0           16            267
  1            1             47
[1] 2 2
[1] FALSE
D490V7, 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
D490V8, binary
                cls
clus               0   1
  TET3 MUTATED    19   1
  TET3 WILD-TYPE 298  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  TET3 MUTATED     19    1
  TET3 WILD-TYPE  298   47
                               clus
vv                              TET3 MUTATED TET3 WILD-TYPE
  COLON ADENOCARCINOMA                    19            298
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TET3 MUTATED    12   0   1   4
  TET3 WILD-TYPE 245   2  21  17
D490V9, multiclass
    clus
vv   TET3 MUTATED TET3 WILD-TYPE
  R0           12            245
  R1            0              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"
D490V10, 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
D490V11, 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(491) Variable = SCAI MUTATION ANALYSIS
D491V1, survival
                sevent
clus2              0   1
  SCAI MUTATED    12   2
  SCAI WILD-TYPE 270  71
  SCAI MUTATED SCAI WILD-TYPE 
            14            341 
  SCAI MUTATED SCAI WILD-TYPE 
             2             71 
$`SCAI MUTATED`
TCGA-A6-5666 TCGA-AA-3950 TCGA-AA-A01R TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-5403 
       32.71        24.00        35.01         4.21         0.72        62.79 
TCGA-CA-6717 TCGA-CK-5913 TCGA-D5-6541 TCGA-D5-6927 TCGA-DM-A1HB TCGA-DM-A285 
        0.33        51.32        15.58         9.44       135.65         6.12 
TCGA-DM-A28H TCGA-DM-A28K 
      117.07        98.24 

$`SCAI WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96         0.07        21.37        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
       17.56       102.44        40.34        15.62        49.08        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        16.14         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        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        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  SCAI MUTATED SCAI WILD-TYPE 
          0.33           0.00 
  SCAI MUTATED SCAI WILD-TYPE 
        135.65         140.38 
  SCAI MUTATED SCAI WILD-TYPE 
        28.355         20.120 
[1] "0.3 - 135.7 (28.4)" "0.0 - 140.4 (20.1)"
[1] "hr=" "2.3"
D491V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SCAI MUTATED         0        0        1         7         0         1
  SCAI WILD-TYPE      64        1       24       102         8         0
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SCAI MUTATED           1          0          2          1        1         0
  SCAI WILD-TYPE        18         10         39         30       34        13
                vv
clus             STAGE IVB
  SCAI MUTATED           0
  SCAI WILD-TYPE         1
D491V3, multiclass
            clus
vv           SCAI MUTATED SCAI WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             7            102
  STAGE IIB             0              8
  STAGE IIC             1              0
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            2             39
  STAGE IIIC            1             30
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SCAI MUTATED     0   1  13   1
  SCAI WILD-TYPE   9  67 235  40
D491V4, multiclass
    clus
vv   SCAI MUTATED SCAI WILD-TYPE
  T1            0              9
  T2            1             67
  T3           13            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
  SCAI MUTATED     9   2   3
  SCAI WILD-TYPE 211  78  63
D491V5, multiclass
    clus
vv   SCAI MUTATED SCAI WILD-TYPE
  N0            9            211
  N1            2             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"
D491V6, binary
                cls
clus               0   1
  SCAI MUTATED    11   1
  SCAI WILD-TYPE 272  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  SCAI MUTATED     11    1
  SCAI WILD-TYPE  272   47
   clus
vv  SCAI MUTATED SCAI WILD-TYPE
  0           11            272
  1            1             47
[1] 2 2
[1] FALSE
D491V7, binary
                cls
clus               0   1
  SCAI MUTATED     4  11
  SCAI WILD-TYPE 166 186
[1] "tbl2"
                cls
clus             [,1] [,2]
  SCAI MUTATED      4   11
  SCAI WILD-TYPE  166  186
        clus
vv       SCAI MUTATED SCAI WILD-TYPE
  FEMALE            4            166
  MALE             11            186
[1] 2 2
[1] FALSE
D491V8, binary
                cls
clus               0   1
  SCAI MUTATED    10   5
  SCAI WILD-TYPE 307  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  SCAI MUTATED     10    5
  SCAI WILD-TYPE  307   43
                               clus
vv                              SCAI MUTATED SCAI WILD-TYPE
  COLON ADENOCARCINOMA                    10            307
  COLON MUCINOUS ADENOCARCINOMA            5             43
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SCAI MUTATED     6   0   0   2
  SCAI WILD-TYPE 251   2  22  19
D491V9, multiclass
    clus
vv   SCAI MUTATED SCAI WILD-TYPE
  R0            6            251
  R1            0              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"
D491V10, 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    11
  SCAI WILD-TYPE                        19   165
D491V11, 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                                      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(492) Variable = EIF2AK4 MUTATION ANALYSIS
D492V1, survival
                   sevent
clus2                 0   1
  EIF2AK4 MUTATED    16   2
  EIF2AK4 WILD-TYPE 266  71
  EIF2AK4 MUTATED EIF2AK4 WILD-TYPE 
               18               337 
  EIF2AK4 MUTATED EIF2AK4 WILD-TYPE 
                2                71 
$`EIF2AK4 MUTATED`
TCGA-A6-3809 TCGA-A6-5661 TCGA-A6-6780 TCGA-AA-3681 TCGA-AA-3815 TCGA-AA-3864 
       32.75        33.53        20.12         5.98        33.04        53.00 
TCGA-AA-3977 TCGA-AA-A024 TCGA-AD-6895 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CM-5349 
       25.02        39.06         0.72       100.01         0.33        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        19.43 

$`EIF2AK4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 
       24.16        21.76        24.69        24.39        23.87        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
       11.01        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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        35.01        26.01        37.02        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6164 TCGA-CM-6165 
       15.02        15.02        17.03        15.02        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 
       21.99        14.99        12.99        15.02        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        35.41       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  EIF2AK4 MUTATED EIF2AK4 WILD-TYPE 
             0.33              0.00 
  EIF2AK4 MUTATED EIF2AK4 WILD-TYPE 
           100.01            140.38 
  EIF2AK4 MUTATED EIF2AK4 WILD-TYPE 
            22.57             20.19 
[1] "0.3 - 100.0 (22.6)" "0.0 - 140.4 (20.2)"
[1] "hr=" "2"  
D492V2, 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       22       102         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EIF2AK4 MUTATED           1          0          1          0        0
  EIF2AK4 WILD-TYPE        18         10         40         31       35
                   vv
clus                STAGE IVA STAGE IVB
  EIF2AK4 MUTATED           0         0
  EIF2AK4 WILD-TYPE        13         1
D492V3, multiclass
            clus
vv           EIF2AK4 MUTATED EIF2AK4 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 3                22
  STAGE IIA                7               102
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  EIF2AK4 MUTATED     1   3  13   1
  EIF2AK4 WILD-TYPE   8  65 235  40
D492V4, multiclass
    clus
vv   EIF2AK4 MUTATED EIF2AK4 WILD-TYPE
  T1               1                 8
  T2               3                65
  T3              13               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
  EIF2AK4 MUTATED    15   3   0
  EIF2AK4 WILD-TYPE 205  77  66
D492V5, multiclass
    clus
vv   EIF2AK4 MUTATED EIF2AK4 WILD-TYPE
  N0              15               205
  N1               3                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"
D492V6, binary
                   cls
clus                  0   1
  EIF2AK4 MUTATED    15   0
  EIF2AK4 WILD-TYPE 268  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EIF2AK4 MUTATED     15    0
  EIF2AK4 WILD-TYPE  268   48
   clus
vv  EIF2AK4 MUTATED EIF2AK4 WILD-TYPE
  0              15               268
  1               0                48
[1] 2 2
[1] FALSE
D492V7, 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
D492V8, binary
                   cls
clus                  0   1
  EIF2AK4 MUTATED    11   7
  EIF2AK4 WILD-TYPE 306  41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EIF2AK4 MUTATED     11    7
  EIF2AK4 WILD-TYPE  306   41
                               clus
vv                              EIF2AK4 MUTATED EIF2AK4 WILD-TYPE
  COLON ADENOCARCINOMA                       11               306
  COLON MUCINOUS ADENOCARCINOMA               7                41
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  EIF2AK4 MUTATED    13   0   0   1
  EIF2AK4 WILD-TYPE 244   2  22  20
D492V9, multiclass
    clus
vv   EIF2AK4 MUTATED EIF2AK4 WILD-TYPE
  R0              13               244
  R1               0                 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"
D492V10, 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
D492V11, 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(493) Variable = UGT3A2 MUTATION ANALYSIS
D493V1, survival
                  sevent
clus2                0   1
  UGT3A2 MUTATED    15   3
  UGT3A2 WILD-TYPE 267  70
  UGT3A2 MUTATED UGT3A2 WILD-TYPE 
              18              337 
  UGT3A2 MUTATED UGT3A2 WILD-TYPE 
               3               70 
$`UGT3A2 MUTATED`
TCGA-A6-5661 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3977 TCGA-AA-3982 
       33.53         3.02        63.98        29.95        25.02        27.02 
TCGA-AA-A010 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CK-5913 TCGA-CK-5916 TCGA-CM-4743 
       34.98       100.01         0.33        51.32        21.14        23.05 
TCGA-CM-6674 TCGA-D5-6533 TCGA-D5-6536 TCGA-D5-6920 TCGA-G4-6307 TCGA-G4-6586 
       12.95         1.32        17.85        12.39        55.04        35.80 

$`UGT3A2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       26.01        24.00        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       40.34        15.62        49.08        21.99         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 
       13.51        11.51        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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  UGT3A2 MUTATED UGT3A2 WILD-TYPE 
            0.33             0.00 
  UGT3A2 MUTATED UGT3A2 WILD-TYPE 
          100.01           140.38 
  UGT3A2 MUTATED UGT3A2 WILD-TYPE 
           26.02            19.99 
[1] "0.3 - 100.0 (26.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.5"
D493V2, 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       22       100         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  UGT3A2 MUTATED           0          0          3          0        0
  UGT3A2 WILD-TYPE        19         10         38         31       35
                  vv
clus               STAGE IVA STAGE IVB
  UGT3A2 MUTATED           0         0
  UGT3A2 WILD-TYPE        13         1
D493V3, multiclass
            clus
vv           UGT3A2 MUTATED UGT3A2 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                3               22
  STAGE IIA               9              100
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              3               38
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  UGT3A2 MUTATED     1   1  14   2
  UGT3A2 WILD-TYPE   8  67 234  39
D493V4, multiclass
    clus
vv   UGT3A2 MUTATED UGT3A2 WILD-TYPE
  T1              1                8
  T2              1               67
  T3             14              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
  UGT3A2 MUTATED    16   2   0
  UGT3A2 WILD-TYPE 204  78  66
D493V5, multiclass
    clus
vv   UGT3A2 MUTATED UGT3A2 WILD-TYPE
  N0             16              204
  N1              2               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"
D493V6, binary
                  cls
clus                 0   1
  UGT3A2 MUTATED    16   0
  UGT3A2 WILD-TYPE 267  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT3A2 MUTATED     16    0
  UGT3A2 WILD-TYPE  267   48
   clus
vv  UGT3A2 MUTATED UGT3A2 WILD-TYPE
  0             16              267
  1              0               48
[1] 2 2
[1] FALSE
D493V7, 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
D493V8, binary
                  cls
clus                 0   1
  UGT3A2 MUTATED    16   2
  UGT3A2 WILD-TYPE 301  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT3A2 MUTATED     16    2
  UGT3A2 WILD-TYPE  301   46
                               clus
vv                              UGT3A2 MUTATED UGT3A2 WILD-TYPE
  COLON ADENOCARCINOMA                      16              301
  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 245   2  22  18
D493V9, multiclass
    clus
vv   UGT3A2 MUTATED UGT3A2 WILD-TYPE
  R0             12              245
  R1              0                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"
D493V10, 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
D493V11, 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(494) Variable = UGT1A7 MUTATION ANALYSIS
D494V1, survival
                  sevent
clus2                0   1
  UGT1A7 MUTATED     6   2
  UGT1A7 WILD-TYPE 276  71
  UGT1A7 MUTATED UGT1A7 WILD-TYPE 
               8              347 
  UGT1A7 MUTATED UGT1A7 WILD-TYPE 
               2               71 
$`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        61.41         0.07        16.14 
TCGA-D5-6930 TCGA-DM-A1D8 
        1.51        12.59 

$`UGT1A7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 
        2.24         3.06         3.25         3.29         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         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-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        49.91        13.32       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  UGT1A7 MUTATED UGT1A7 WILD-TYPE 
            0.07             0.00 
  UGT1A7 MUTATED UGT1A7 WILD-TYPE 
           61.41           140.38 
  UGT1A7 MUTATED UGT1A7 WILD-TYPE 
          14.365           20.280 
[1] "0.1 - 61.4 (14.4)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.3"
D494V2, 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       25       107         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  UGT1A7 MUTATED           0          0          1          0        0
  UGT1A7 WILD-TYPE        19         10         40         31       35
                  vv
clus               STAGE IVA STAGE IVB
  UGT1A7 MUTATED           0         0
  UGT1A7 WILD-TYPE        13         1
D494V3, multiclass
            clus
vv           UGT1A7 MUTATED UGT1A7 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               2              107
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  UGT1A7 MUTATED     1   1   4   2
  UGT1A7 WILD-TYPE   8  67 244  39
D494V4, multiclass
    clus
vv   UGT1A7 MUTATED UGT1A7 WILD-TYPE
  T1              1                8
  T2              1               67
  T3              4              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
  UGT1A7 MUTATED     6   2   0
  UGT1A7 WILD-TYPE 214  78  66
D494V5, multiclass
    clus
vv   UGT1A7 MUTATED UGT1A7 WILD-TYPE
  N0              6              214
  N1              2               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"
D494V6, binary
                  cls
clus                 0   1
  UGT1A7 MUTATED     7   0
  UGT1A7 WILD-TYPE 276  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT1A7 MUTATED      7    0
  UGT1A7 WILD-TYPE  276   48
   clus
vv  UGT1A7 MUTATED UGT1A7 WILD-TYPE
  0              7              276
  1              0               48
[1] 2 2
[1] FALSE
D494V7, 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
D494V8, binary
                  cls
clus                 0   1
  UGT1A7 MUTATED     5   3
  UGT1A7 WILD-TYPE 312  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT1A7 MUTATED      5    3
  UGT1A7 WILD-TYPE  312   45
                               clus
vv                              UGT1A7 MUTATED UGT1A7 WILD-TYPE
  COLON ADENOCARCINOMA                       5              312
  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 252   2  22  20
D494V9, multiclass
    clus
vv   UGT1A7 MUTATED UGT1A7 WILD-TYPE
  R0              5              252
  R1              0                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"
D494V10, 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
D494V11, 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(495) Variable = NOS3 MUTATION ANALYSIS
D495V1, survival
                sevent
clus2              0   1
  NOS3 MUTATED    16   3
  NOS3 WILD-TYPE 266  70
  NOS3 MUTATED NOS3 WILD-TYPE 
            19            336 
  NOS3 MUTATED NOS3 WILD-TYPE 
             3             70 
$`NOS3 MUTATED`
TCGA-A6-6141 TCGA-A6-6781 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3976 TCGA-AA-3977 
        8.38        19.66         6.05         6.97        26.01        25.02 
TCGA-AD-6889 TCGA-AY-6197 TCGA-AZ-6598 TCGA-CA-5254 TCGA-CA-6717 TCGA-CK-5916 
       56.55        21.44        49.41         2.24         0.33        21.14 
TCGA-CM-4746 TCGA-CM-5861 TCGA-CM-6674 TCGA-D5-6535 TCGA-F4-6570 TCGA-F4-6856 
       37.02        15.02        12.95        15.12         6.18        19.43 
TCGA-G4-6307 
       55.04 

$`NOS3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       13.94        19.99        61.02        78.08        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        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        15.75         0.20        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13        83.80        22.36        62.79        61.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        1.94         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32        21.99         2.93         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-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        16.01         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 
       20.19        18.25         1.32        43.27        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       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        13.38        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        35.41       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  NOS3 MUTATED NOS3 WILD-TYPE 
          0.33           0.00 
  NOS3 MUTATED NOS3 WILD-TYPE 
         56.55         140.38 
  NOS3 MUTATED NOS3 WILD-TYPE 
         19.43          20.63 
[1] "0.3 - 56.5 (19.4)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "1.2"
D495V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NOS3 MUTATED         3        0        2         8         0         0
  NOS3 WILD-TYPE      61        1       23       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        19          9         39         30       34        13
                vv
clus             STAGE IVB
  NOS3 MUTATED           0
  NOS3 WILD-TYPE         1
D495V3, multiclass
            clus
vv           NOS3 MUTATED NOS3 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             8            101
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            1              9
  STAGE IIIB            2             39
  STAGE IIIC            1             30
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NOS3 MUTATED     1   4  12   2
  NOS3 WILD-TYPE   8  64 236  39
D495V4, multiclass
    clus
vv   NOS3 MUTATED NOS3 WILD-TYPE
  T1            1              8
  T2            4             64
  T3           12            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
  NOS3 MUTATED    14   4   1
  NOS3 WILD-TYPE 206  76  65
D495V5, multiclass
    clus
vv   NOS3 MUTATED NOS3 WILD-TYPE
  N0           14            206
  N1            4             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"
D495V6, binary
                cls
clus               0   1
  NOS3 MUTATED    13   1
  NOS3 WILD-TYPE 270  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOS3 MUTATED     13    1
  NOS3 WILD-TYPE  270   47
   clus
vv  NOS3 MUTATED NOS3 WILD-TYPE
  0           13            270
  1            1             47
[1] 2 2
[1] FALSE
D495V7, binary
                cls
clus               0   1
  NOS3 MUTATED     8  11
  NOS3 WILD-TYPE 162 186
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOS3 MUTATED      8   11
  NOS3 WILD-TYPE  162  186
        clus
vv       NOS3 MUTATED NOS3 WILD-TYPE
  FEMALE            8            162
  MALE             11            186
[1] 2 2
[1] FALSE
D495V8, binary
                cls
clus               0   1
  NOS3 MUTATED    16   3
  NOS3 WILD-TYPE 301  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOS3 MUTATED     16    3
  NOS3 WILD-TYPE  301   45
                               clus
vv                              NOS3 MUTATED NOS3 WILD-TYPE
  COLON ADENOCARCINOMA                    16            301
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  NOS3 MUTATED    10   0   1   4
  NOS3 WILD-TYPE 247   2  21  17
D495V9, multiclass
    clus
vv   NOS3 MUTATED NOS3 WILD-TYPE
  R0           10            247
  R1            0              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"
D495V10, 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                           2    10
  NOS3 WILD-TYPE                        17   166
D495V11, multiclass
                                  clus
vv                                 NOS3 MUTATED NOS3 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(496) Variable = GPR75 MUTATION ANALYSIS
D496V1, survival
                 sevent
clus2               0   1
  GPR75 MUTATED     6   2
  GPR75 WILD-TYPE 276  71
  GPR75 MUTATED GPR75 WILD-TYPE 
              8             347 
  GPR75 MUTATED GPR75 WILD-TYPE 
              2              71 
$`GPR75 MUTATED`
TCGA-AA-3811 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-6162 
       10.06        49.41         0.33        30.08        15.02        12.00 
TCGA-G4-6306 TCGA-G4-6588 
       44.68        26.17 

$`GPR75 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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        16.01 
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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        91.79        46.75        52.80 

  GPR75 MUTATED GPR75 WILD-TYPE 
           0.33            0.00 
  GPR75 MUTATED GPR75 WILD-TYPE 
          49.41          140.38 
  GPR75 MUTATED GPR75 WILD-TYPE 
         20.595          20.190 
[1] "0.3 - 49.4 (20.6)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.3"
D496V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GPR75 MUTATED         0        0        1         5         0         0
  GPR75 WILD-TYPE      64        1       24       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        18         10         40         31       35        13
                 vv
clus              STAGE IVB
  GPR75 MUTATED           0
  GPR75 WILD-TYPE         1
D496V3, multiclass
            clus
vv           GPR75 MUTATED GPR75 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              5             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GPR75 MUTATED     0   1   7   0
  GPR75 WILD-TYPE   9  67 241  41
D496V4, multiclass
    clus
vv   GPR75 MUTATED GPR75 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             7             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
  GPR75 MUTATED     6   1   1
  GPR75 WILD-TYPE 214  79  65
D496V5, multiclass
    clus
vv   GPR75 MUTATED GPR75 WILD-TYPE
  N0             6             214
  N1             1              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"
D496V6, binary
                 cls
clus                0   1
  GPR75 MUTATED     7   0
  GPR75 WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR75 MUTATED      7    0
  GPR75 WILD-TYPE  276   48
   clus
vv  GPR75 MUTATED GPR75 WILD-TYPE
  0             7             276
  1             0              48
[1] 2 2
[1] FALSE
D496V7, 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
D496V8, binary
                 cls
clus                0   1
  GPR75 MUTATED     6   2
  GPR75 WILD-TYPE 311  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR75 MUTATED      6    2
  GPR75 WILD-TYPE  311   46
                               clus
vv                              GPR75 MUTATED GPR75 WILD-TYPE
  COLON ADENOCARCINOMA                      6             311
  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 251   2  22  20
D496V9, multiclass
    clus
vv   GPR75 MUTATED GPR75 WILD-TYPE
  R0             6             251
  R1             0               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"
D496V10, 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
D496V11, 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(497) Variable = FRS3 MUTATION ANALYSIS
D497V1, survival
                sevent
clus2              0   1
  FRS3 MUTATED     8   2
  FRS3 WILD-TYPE 274  71
  FRS3 MUTATED FRS3 WILD-TYPE 
            10            345 
  FRS3 MUTATED FRS3 WILD-TYPE 
             2             71 
$`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         0.33 
TCGA-CM-5349 TCGA-D5-6930 TCGA-DM-A1D9 TCGA-DM-A28K 
       30.08         1.51       140.38        98.24 

$`FRS3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01        63.98         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
       39.98         2.01         5.03         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32        12.59         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79       117.07         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  FRS3 MUTATED FRS3 WILD-TYPE 
          0.33           0.00 
  FRS3 MUTATED FRS3 WILD-TYPE 
        140.38         139.17 
  FRS3 MUTATED FRS3 WILD-TYPE 
        32.545         20.120 
[1] "0.3 - 140.4 (32.5)" "0.0 - 139.2 (20.1)"
[1] "hr=" "1.6"
D497V2, 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       23       103         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        18         10         41         31       34        13
                vv
clus             STAGE IVB
  FRS3 MUTATED           0
  FRS3 WILD-TYPE         1
D497V3, multiclass
            clus
vv           FRS3 MUTATED FRS3 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             6            103
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  FRS3 MUTATED     0   0   8   2
  FRS3 WILD-TYPE   9  68 240  39
D497V4, multiclass
    clus
vv   FRS3 MUTATED FRS3 WILD-TYPE
  T1            0              9
  T2            0             68
  T3            8            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
  FRS3 MUTATED     8   0   2
  FRS3 WILD-TYPE 212  80  64
D497V5, multiclass
    clus
vv   FRS3 MUTATED FRS3 WILD-TYPE
  N0            8            212
  N1            0             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"
D497V6, binary
                cls
clus               0   1
  FRS3 MUTATED     8   1
  FRS3 WILD-TYPE 275  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  FRS3 MUTATED      8    1
  FRS3 WILD-TYPE  275   47
   clus
vv  FRS3 MUTATED FRS3 WILD-TYPE
  0            8            275
  1            1             47
[1] 2 2
[1] FALSE
D497V7, 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
D497V8, binary
                cls
clus               0   1
  FRS3 MUTATED     6   4
  FRS3 WILD-TYPE 311  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  FRS3 MUTATED      6    4
  FRS3 WILD-TYPE  311   44
                               clus
vv                              FRS3 MUTATED FRS3 WILD-TYPE
  COLON ADENOCARCINOMA                     6            311
  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 252   2  21  20
D497V9, multiclass
    clus
vv   FRS3 MUTATED FRS3 WILD-TYPE
  R0            5            252
  R1            0              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"
D497V10, 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
D497V11, 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(498) Variable = CDC42BPA MUTATION ANALYSIS
D498V1, survival
                    sevent
clus2                  0   1
  CDC42BPA MUTATED    19  10
  CDC42BPA WILD-TYPE 263  63
  CDC42BPA MUTATED CDC42BPA WILD-TYPE 
                29                326 
  CDC42BPA MUTATED CDC42BPA WILD-TYPE 
                10                 63 
$`CDC42BPA MUTATED`
TCGA-A6-2672 TCGA-A6-4105 TCGA-A6-5657 TCGA-A6-5661 TCGA-AA-3492 TCGA-AA-3516 
       46.65        14.53        31.63        33.53         3.02        13.02 
TCGA-AA-3655 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3864 TCGA-AA-3950 
       61.02        85.05        26.99        19.04        53.00        24.00 
TCGA-AA-3977 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A02J TCGA-AD-6888 TCGA-AD-6889 
       25.02        18.05         4.01         5.03         4.21        56.55 
TCGA-AZ-4315 TCGA-AZ-4616 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CM-5349 TCGA-DM-A1DB 
       58.39         5.13       100.01         0.33        30.08        44.32 
TCGA-DM-A28G TCGA-F4-6703 TCGA-F4-6856 TCGA-G4-6588 TCGA-G4-6626 
       60.79        35.87        19.43        26.17        46.75 

$`CDC42BPA WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5659 
       34.65        33.34        32.75        36.53        32.91        30.44 
TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 
       29.19        23.61        22.09        22.06        32.71        27.09 
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 
       22.52         8.38        25.08        25.18        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        7.04         1.02        35.01        63.98         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       36.00         5.03        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        2.01        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       40.96         0.07        21.37         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        1.41        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-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-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.38        13.45         6.18         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 
       16.24        33.67        13.25         0.53        35.41       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6628 
       91.79        52.80 

  CDC42BPA MUTATED CDC42BPA WILD-TYPE 
              0.33               0.00 
  CDC42BPA MUTATED CDC42BPA WILD-TYPE 
            100.01             140.38 
  CDC42BPA MUTATED CDC42BPA WILD-TYPE 
             26.99              19.99 
[1] "0.3 - 100.0 (27.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.4"
D498V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CDC42BPA MUTATED         1        0        4        13         1         0
  CDC42BPA WILD-TYPE      63        1       21        96         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CDC42BPA MUTATED           2          0          4          0        3
  CDC42BPA WILD-TYPE        17         10         37         31       32
                    vv
clus                 STAGE IVA STAGE IVB
  CDC42BPA MUTATED           0         0
  CDC42BPA WILD-TYPE        13         1
D498V3, multiclass
            clus
vv           CDC42BPA MUTATED CDC42BPA WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  4                 21
  STAGE IIA                13                 96
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 2                 17
  STAGE IIIA                0                 10
  STAGE IIIB                4                 37
  STAGE IIIC                0                 31
  STAGE IV                  3                 32
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  CDC42BPA MUTATED     0   3  24   2
  CDC42BPA WILD-TYPE   9  65 224  39
D498V4, multiclass
    clus
vv   CDC42BPA MUTATED CDC42BPA WILD-TYPE
  T1                0                  9
  T2                3                 65
  T3               24                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   3   2
  CDC42BPA WILD-TYPE 197  77  64
D498V5, multiclass
    clus
vv   CDC42BPA MUTATED CDC42BPA WILD-TYPE
  N0               23                197
  N1                3                 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"
D498V6, binary
                    cls
clus                   0   1
  CDC42BPA MUTATED    25   3
  CDC42BPA WILD-TYPE 258  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CDC42BPA MUTATED     25    3
  CDC42BPA WILD-TYPE  258   45
   clus
vv  CDC42BPA MUTATED CDC42BPA WILD-TYPE
  0               25                258
  1                3                 45
[1] 2 2
[1] FALSE
D498V7, 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
D498V8, binary
                    cls
clus                   0   1
  CDC42BPA MUTATED    23   6
  CDC42BPA WILD-TYPE 294  42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CDC42BPA MUTATED     23    6
  CDC42BPA WILD-TYPE  294   42
                               clus
vv                              CDC42BPA MUTATED CDC42BPA WILD-TYPE
  COLON ADENOCARCINOMA                        23                294
  COLON MUCINOUS ADENOCARCINOMA                6                 42
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  CDC42BPA MUTATED    18   0   2   1
  CDC42BPA WILD-TYPE 239   2  20  20
D498V9, multiclass
    clus
vv   CDC42BPA MUTATED CDC42BPA WILD-TYPE
  R0               18                239
  R1                0                  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"
D498V10, 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
D498V11, 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(499) Variable = KIAA0195 MUTATION ANALYSIS
D499V1, survival
                    sevent
clus2                  0   1
  KIAA0195 MUTATED    14   2
  KIAA0195 WILD-TYPE 268  71
  KIAA0195 MUTATED KIAA0195 WILD-TYPE 
                16                339 
  KIAA0195 MUTATED KIAA0195 WILD-TYPE 
                 2                 71 
$`KIAA0195 MUTATED`
TCGA-AA-3672 TCGA-AA-A00W TCGA-AA-A01K TCGA-AD-5900 TCGA-AD-6895 TCGA-AD-6964 
        0.92        14.99        31.00         0.07         0.72        10.88 
TCGA-AY-6197 TCGA-CK-5916 TCGA-CM-4743 TCGA-CM-5861 TCGA-CM-6674 TCGA-D5-6540 
       21.44        21.14        23.05        15.02        12.95        16.14 
TCGA-DM-A1HB TCGA-F4-6808 TCGA-G4-6304 TCGA-G4-6588 
      135.65        33.67        53.62        26.17 

$`KIAA0195 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
        6.05         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37         4.21        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        15.75         0.20        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.99         2.93         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 
       16.01         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       29.59        16.24        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      107.67        74.56        65.85        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  KIAA0195 MUTATED KIAA0195 WILD-TYPE 
              0.07               0.00 
  KIAA0195 MUTATED KIAA0195 WILD-TYPE 
            135.65             140.38 
  KIAA0195 MUTATED KIAA0195 WILD-TYPE 
             18.64              20.19 
[1] "0.1 - 135.7 (18.6)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.6"
D499V2, 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       24       104         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0195 MUTATED           1          0          1          1        0
  KIAA0195 WILD-TYPE        18         10         40         30       35
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA0195 MUTATED           0         0
  KIAA0195 WILD-TYPE        13         1
D499V3, multiclass
            clus
vv           KIAA0195 MUTATED KIAA0195 WILD-TYPE
  STAGE I                   5                 59
  STAGE IA                  0                  1
  STAGE II                  1                 24
  STAGE IIA                 5                104
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 1                 18
  STAGE IIIA                0                 10
  STAGE IIIB                1                 40
  STAGE IIIC                1                 30
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA0195 MUTATED     3   2   9   3
  KIAA0195 WILD-TYPE   6  66 239  38
D499V4, multiclass
    clus
vv   KIAA0195 MUTATED KIAA0195 WILD-TYPE
  T1                3                  6
  T2                2                 66
  T3                9                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
  KIAA0195 MUTATED    12   3   2
  KIAA0195 WILD-TYPE 208  77  64
D499V5, multiclass
    clus
vv   KIAA0195 MUTATED KIAA0195 WILD-TYPE
  N0               12                208
  N1                3                 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"
D499V6, binary
                    cls
clus                   0   1
  KIAA0195 MUTATED    13   0
  KIAA0195 WILD-TYPE 270  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0195 MUTATED     13    0
  KIAA0195 WILD-TYPE  270   48
   clus
vv  KIAA0195 MUTATED KIAA0195 WILD-TYPE
  0               13                270
  1                0                 48
[1] 2 2
[1] FALSE
D499V7, 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
D499V8, binary
                    cls
clus                   0   1
  KIAA0195 MUTATED    15   2
  KIAA0195 WILD-TYPE 302  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0195 MUTATED     15    2
  KIAA0195 WILD-TYPE  302   46
                               clus
vv                              KIAA0195 MUTATED KIAA0195 WILD-TYPE
  COLON ADENOCARCINOMA                        15                302
  COLON MUCINOUS ADENOCARCINOMA                2                 46
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  KIAA0195 MUTATED    13   0   0   1
  KIAA0195 WILD-TYPE 244   2  22  20
D499V9, multiclass
    clus
vv   KIAA0195 MUTATED KIAA0195 WILD-TYPE
  R0               13                244
  R1                0                  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"
D499V10, 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
D499V11, 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(500) Variable = INPP1 MUTATION ANALYSIS
D500V1, survival
                 sevent
clus2               0   1
  INPP1 MUTATED     4   2
  INPP1 WILD-TYPE 278  71
  INPP1 MUTATED INPP1 WILD-TYPE 
              6             349 
  INPP1 MUTATED INPP1 WILD-TYPE 
              2              71 
$`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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
       40.34        15.62        49.08        51.32        21.99         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       12.00        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        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        13.38        13.45        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  INPP1 MUTATED INPP1 WILD-TYPE 
           6.18            0.00 
  INPP1 MUTATED INPP1 WILD-TYPE 
          85.05          140.38 
  INPP1 MUTATED INPP1 WILD-TYPE 
         19.085          20.190 
[1] "6.2 - 85.0 (19.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.4"
D500V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  INPP1 MUTATED         4        0        0         1         1         0
  INPP1 WILD-TYPE      60        1       25       108         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  INPP1 MUTATED           1          0          0          0        0         0
  INPP1 WILD-TYPE        18         10         41         31       35        13
                 vv
clus              STAGE IVB
  INPP1 MUTATED           0
  INPP1 WILD-TYPE         1
D500V3, multiclass
            clus
vv           INPP1 MUTATED INPP1 WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              1             108
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  INPP1 MUTATED     2   2   2   1
  INPP1 WILD-TYPE   7  66 246  40
D500V4, multiclass
    clus
vv   INPP1 MUTATED INPP1 WILD-TYPE
  T1             2               7
  T2             2              66
  T3             2             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
  INPP1 MUTATED     7   0   0
  INPP1 WILD-TYPE 213  80  66
D500V5, multiclass
    clus
vv   INPP1 MUTATED INPP1 WILD-TYPE
  N0             7             213
  N1             0              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"
D500V6, binary
                 cls
clus                0   1
  INPP1 MUTATED     6   0
  INPP1 WILD-TYPE 277  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INPP1 MUTATED      6    0
  INPP1 WILD-TYPE  277   48
   clus
vv  INPP1 MUTATED INPP1 WILD-TYPE
  0             6             277
  1             0              48
[1] 2 2
[1] FALSE
D500V7, 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
D500V8, binary
                 cls
clus                0   1
  INPP1 MUTATED     7   0
  INPP1 WILD-TYPE 310  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INPP1 MUTATED      7    0
  INPP1 WILD-TYPE  310   48
                               clus
vv                              INPP1 MUTATED INPP1 WILD-TYPE
  COLON ADENOCARCINOMA                      7             310
  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 252   2  22  19
D500V9, multiclass
    clus
vv   INPP1 MUTATED INPP1 WILD-TYPE
  R0             5             252
  R1             0               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"
D500V10, 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
D500V11, 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(501) Variable = N4BP2 MUTATION ANALYSIS
D501V1, survival
                 sevent
clus2               0   1
  N4BP2 MUTATED    18   5
  N4BP2 WILD-TYPE 264  68
  N4BP2 MUTATED N4BP2 WILD-TYPE 
             23             332 
  N4BP2 MUTATED N4BP2 WILD-TYPE 
              5              68 
$`N4BP2 MUTATED`
TCGA-A6-2676 TCGA-A6-3809 TCGA-A6-5666 TCGA-A6-6648 TCGA-A6-6651 TCGA-AA-3819 
       42.90        32.75        32.71        25.18        21.76        25.02 
TCGA-AA-A00E TCGA-AA-A010 TCGA-AD-5900 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 
       30.02        34.98         0.07        58.39        49.41         0.33 
TCGA-CA-6718 TCGA-CK-5916 TCGA-CK-6747 TCGA-CM-6162 TCGA-CM-6171 TCGA-CM-6675 
        0.10        21.14         2.93        12.00        14.04        13.05 
TCGA-D5-5537 TCGA-D5-6538 TCGA-DM-A28C TCGA-F4-6704 TCGA-G4-6588 
       45.40        17.13        81.37         1.55        26.17 

$`N4BP2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       34.65        33.34        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6652 
       27.09        22.52         8.38        25.08        24.16        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 
       24.39        23.87        20.12        19.66        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        3.02         1.02        35.01        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        19.00        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07         0.26         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        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 
       16.01        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85         4.80        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28E TCGA-DM-A28F 
      131.51       135.65       139.17         6.12       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18        35.87        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  N4BP2 MUTATED N4BP2 WILD-TYPE 
           0.07            0.00 
  N4BP2 MUTATED N4BP2 WILD-TYPE 
          81.37          140.38 
  N4BP2 MUTATED N4BP2 WILD-TYPE 
         25.020          20.005 
[1] "0.1 - 81.4 (25.0)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1.1"
D501V2, 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       24        99         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        19         10         38         30       35        12
                 vv
clus              STAGE IVB
  N4BP2 MUTATED           1
  N4BP2 WILD-TYPE         0
D501V3, multiclass
            clus
vv           N4BP2 MUTATED N4BP2 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA             10              99
  STAGE IIB              3               5
  STAGE IIC              1               0
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             3              38
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              1              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
  N4BP2 MUTATED     1   2  17   4
  N4BP2 WILD-TYPE   8  66 231  37
D501V4, multiclass
    clus
vv   N4BP2 MUTATED N4BP2 WILD-TYPE
  T1             1               8
  T2             2              66
  T3            17             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
  N4BP2 MUTATED    18   2   4
  N4BP2 WILD-TYPE 202  78  62
D501V5, multiclass
    clus
vv   N4BP2 MUTATED N4BP2 WILD-TYPE
  N0            18             202
  N1             2              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"
D501V6, binary
                 cls
clus                0   1
  N4BP2 MUTATED    16   2
  N4BP2 WILD-TYPE 267  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  N4BP2 MUTATED     16    2
  N4BP2 WILD-TYPE  267   46
   clus
vv  N4BP2 MUTATED N4BP2 WILD-TYPE
  0            16             267
  1             2              46
[1] 2 2
[1] FALSE
D501V7, 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
D501V8, binary
                 cls
clus                0   1
  N4BP2 MUTATED    19   5
  N4BP2 WILD-TYPE 298  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  N4BP2 MUTATED     19    5
  N4BP2 WILD-TYPE  298   43
                               clus
vv                              N4BP2 MUTATED N4BP2 WILD-TYPE
  COLON ADENOCARCINOMA                     19             298
  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 243   2  22  16
D501V9, multiclass
    clus
vv   N4BP2 MUTATED N4BP2 WILD-TYPE
  R0            14             243
  R1             0               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"
D501V10, 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
D501V11, 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(502) Variable = CDKL2 MUTATION ANALYSIS
D502V1, survival
                 sevent
clus2               0   1
  CDKL2 MUTATED     9   1
  CDKL2 WILD-TYPE 273  72
  CDKL2 MUTATED CDKL2 WILD-TYPE 
             10             345 
  CDKL2 MUTATED CDKL2 WILD-TYPE 
              1              72 
$`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        15.75         0.33 
TCGA-CK-5913 TCGA-CM-6167 TCGA-CM-6172 TCGA-DM-A28G 
       51.32        14.99        11.01        60.79 

$`CDKL2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       38.99         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-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-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-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-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  CDKL2 MUTATED CDKL2 WILD-TYPE 
           0.33            0.00 
  CDKL2 MUTATED CDKL2 WILD-TYPE 
          60.79          140.38 
  CDKL2 MUTATED CDKL2 WILD-TYPE 
          15.37           20.98 
[1] "0.3 - 60.8 (15.4)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.9"
D502V2, 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       24       104         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        19         10         39         30       35        12
                 vv
clus              STAGE IVB
  CDKL2 MUTATED           0
  CDKL2 WILD-TYPE         1
D502V3, multiclass
            clus
vv           CDKL2 MUTATED CDKL2 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              5             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  68 239  39
D502V4, multiclass
    clus
vv   CDKL2 MUTATED CDKL2 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             9             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
  CDKL2 MUTATED     7   3   1
  CDKL2 WILD-TYPE 213  77  65
D502V5, multiclass
    clus
vv   CDKL2 MUTATED CDKL2 WILD-TYPE
  N0             7             213
  N1             3              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"
D502V6, binary
                 cls
clus                0   1
  CDKL2 MUTATED     9   1
  CDKL2 WILD-TYPE 274  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDKL2 MUTATED      9    1
  CDKL2 WILD-TYPE  274   47
   clus
vv  CDKL2 MUTATED CDKL2 WILD-TYPE
  0             9             274
  1             1              47
[1] 2 2
[1] FALSE
D502V7, 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
D502V8, binary
                 cls
clus                0   1
  CDKL2 MUTATED     9   2
  CDKL2 WILD-TYPE 308  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDKL2 MUTATED      9    2
  CDKL2 WILD-TYPE  308   46
                               clus
vv                              CDKL2 MUTATED CDKL2 WILD-TYPE
  COLON ADENOCARCINOMA                      9             308
  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 249   2  22  19
D502V9, multiclass
    clus
vv   CDKL2 MUTATED CDKL2 WILD-TYPE
  R0             8             249
  R1             0               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"
D502V10, 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
D502V11, 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(503) Variable = EXOC4 MUTATION ANALYSIS
D503V1, survival
                 sevent
clus2               0   1
  EXOC4 MUTATED    14   3
  EXOC4 WILD-TYPE 268  70
  EXOC4 MUTATED EXOC4 WILD-TYPE 
             17             338 
  EXOC4 MUTATED EXOC4 WILD-TYPE 
              3              70 
$`EXOC4 MUTATED`
TCGA-A6-5661 TCGA-A6-6141 TCGA-A6-6780 TCGA-AA-3713 TCGA-AA-3845 TCGA-AA-3854 
       33.53         8.38        20.12        19.04         0.00        36.03 
TCGA-AA-3864 TCGA-AD-6895 TCGA-AZ-4315 TCGA-AZ-6599 TCGA-CK-4948 TCGA-D5-6540 
       53.00         0.72        58.39         6.77       102.44        16.14 
TCGA-D5-6924 TCGA-DM-A0X9 TCGA-DM-A1DA TCGA-DM-A1HB TCGA-G4-6628 
       14.30       119.70         7.50       135.65        52.80 

$`EXOC4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 
       24.16        21.76        24.69        24.39        23.87        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02        14.93        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
        0.00        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        4.21        56.55         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41        49.41        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 
        0.33         0.10         1.35        17.56        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38        10.26        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 
       91.79        46.75 

  EXOC4 MUTATED EXOC4 WILD-TYPE 
              0               0 
  EXOC4 MUTATED EXOC4 WILD-TYPE 
         135.65          140.38 
  EXOC4 MUTATED EXOC4 WILD-TYPE 
         20.120          20.235 
[1] "0.0 - 135.7 (20.1)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.8"
D503V2, 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       24       102         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EXOC4 MUTATED           1          1          1          1        1         0
  EXOC4 WILD-TYPE        18          9         40         30       34        13
                 vv
clus              STAGE IVB
  EXOC4 MUTATED           0
  EXOC4 WILD-TYPE         1
D503V3, multiclass
            clus
vv           EXOC4 MUTATED EXOC4 WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              7             102
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             1               9
  STAGE IIIB             1              40
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EXOC4 MUTATED     0   4  14   0
  EXOC4 WILD-TYPE   9  64 234  41
D503V4, multiclass
    clus
vv   EXOC4 MUTATED EXOC4 WILD-TYPE
  T1             0               9
  T2             4              64
  T3            14             234
  T4             0              41
[1] 4 2
[1] TRUE
[1] "dimension 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  77  64
D503V5, multiclass
    clus
vv   EXOC4 MUTATED EXOC4 WILD-TYPE
  N0            13             207
  N1             3              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"
D503V6, binary
                 cls
clus                0   1
  EXOC4 MUTATED    14   1
  EXOC4 WILD-TYPE 269  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EXOC4 MUTATED     14    1
  EXOC4 WILD-TYPE  269   47
   clus
vv  EXOC4 MUTATED EXOC4 WILD-TYPE
  0            14             269
  1             1              47
[1] 2 2
[1] FALSE
D503V7, 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
D503V8, binary
                 cls
clus                0   1
  EXOC4 MUTATED    15   3
  EXOC4 WILD-TYPE 302  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EXOC4 MUTATED     15    3
  EXOC4 WILD-TYPE  302   45
                               clus
vv                              EXOC4 MUTATED EXOC4 WILD-TYPE
  COLON ADENOCARCINOMA                     15             302
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  EXOC4 MUTATED    10   0   1   0
  EXOC4 WILD-TYPE 247   2  21  21
D503V9, multiclass
    clus
vv   EXOC4 MUTATED EXOC4 WILD-TYPE
  R0            10             247
  R1             0               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"
D503V10, 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
D503V11, 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(504) Variable = C5ORF22 MUTATION ANALYSIS
D504V1, survival
                   sevent
clus2                 0   1
  C5ORF22 MUTATED     7   3
  C5ORF22 WILD-TYPE 275  70
  C5ORF22 MUTATED C5ORF22 WILD-TYPE 
               10               345 
  C5ORF22 MUTATED C5ORF22 WILD-TYPE 
                3                70 
$`C5ORF22 MUTATED`
TCGA-A6-5661 TCGA-AA-3655 TCGA-AA-3672 TCGA-AA-3850 TCGA-CK-5912 TCGA-DM-A1D4 
       33.53        61.02         0.92         0.00        49.08        92.75 
TCGA-F4-6805 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6588 
       16.31        51.75        36.72        26.17 

$`C5ORF22 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
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         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20       130.65        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       55.04        45.11        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  C5ORF22 MUTATED C5ORF22 WILD-TYPE 
                0                 0 
  C5ORF22 MUTATED C5ORF22 WILD-TYPE 
            92.75            140.38 
  C5ORF22 MUTATED C5ORF22 WILD-TYPE 
           35.125            20.020 
[1] "0.0 - 92.8 (35.1)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1"  
D504V2, 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       24       105         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C5ORF22 MUTATED           1          0          1          0        1
  C5ORF22 WILD-TYPE        18         10         40         31       34
                   vv
clus                STAGE IVA STAGE IVB
  C5ORF22 MUTATED           0         0
  C5ORF22 WILD-TYPE        13         1
D504V3, multiclass
            clus
vv           C5ORF22 MUTATED C5ORF22 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                4               105
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               0                31
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C5ORF22 MUTATED     0   3   8   0
  C5ORF22 WILD-TYPE   9  65 240  41
D504V4, multiclass
    clus
vv   C5ORF22 MUTATED C5ORF22 WILD-TYPE
  T1               0                 9
  T2               3                65
  T3               8               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
  C5ORF22 MUTATED     8   3   0
  C5ORF22 WILD-TYPE 212  77  66
D504V5, multiclass
    clus
vv   C5ORF22 MUTATED C5ORF22 WILD-TYPE
  N0               8               212
  N1               3                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"
D504V6, binary
                   cls
clus                  0   1
  C5ORF22 MUTATED     8   1
  C5ORF22 WILD-TYPE 275  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF22 MUTATED      8    1
  C5ORF22 WILD-TYPE  275   47
   clus
vv  C5ORF22 MUTATED C5ORF22 WILD-TYPE
  0               8               275
  1               1                47
[1] 2 2
[1] FALSE
D504V7, 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
D504V8, binary
                   cls
clus                  0   1
  C5ORF22 MUTATED    11   0
  C5ORF22 WILD-TYPE 306  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF22 MUTATED     11    0
  C5ORF22 WILD-TYPE  306   48
                               clus
vv                              C5ORF22 MUTATED C5ORF22 WILD-TYPE
  COLON ADENOCARCINOMA                       11               306
  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 249   2  22  19
D504V9, multiclass
    clus
vv   C5ORF22 MUTATED C5ORF22 WILD-TYPE
  R0               8               249
  R1               0                 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"
D504V10, 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
D504V11, 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(505) Variable = MMP12 MUTATION ANALYSIS
D505V1, survival
                 sevent
clus2               0   1
  MMP12 MUTATED     6   2
  MMP12 WILD-TYPE 276  71
  MMP12 MUTATED MMP12 WILD-TYPE 
              8             347 
  MMP12 MUTATED MMP12 WILD-TYPE 
              2              71 
$`MMP12 MUTATED`
TCGA-AA-3715 TCGA-AA-3977 TCGA-AD-6889 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CM-4743 
       19.04        25.02        56.55        58.39        49.41        23.05 
TCGA-CM-6162 TCGA-D5-6540 
       12.00        16.14 

$`MMP12 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  MMP12 MUTATED MMP12 WILD-TYPE 
             12               0 
  MMP12 MUTATED MMP12 WILD-TYPE 
          58.39          140.38 
  MMP12 MUTATED MMP12 WILD-TYPE 
         24.035          20.120 
[1] "12.0 - 58.4 (24.0)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.1"
D505V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MMP12 MUTATED         1        0        2         3         0         0
  MMP12 WILD-TYPE      63        1       23       106         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MMP12 MUTATED           0          0          1          0        0         0
  MMP12 WILD-TYPE        19         10         40         31       35        13
                 vv
clus              STAGE IVB
  MMP12 MUTATED           0
  MMP12 WILD-TYPE         1
D505V3, multiclass
            clus
vv           MMP12 MUTATED MMP12 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              3             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MMP12 MUTATED     0   2   6   0
  MMP12 WILD-TYPE   9  66 242  41
D505V4, multiclass
    clus
vv   MMP12 MUTATED MMP12 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             6             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
  MMP12 MUTATED     7   1   0
  MMP12 WILD-TYPE 213  79  66
D505V5, multiclass
    clus
vv   MMP12 MUTATED MMP12 WILD-TYPE
  N0             7             213
  N1             1              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"
D505V6, binary
                 cls
clus                0   1
  MMP12 MUTATED     6   0
  MMP12 WILD-TYPE 277  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP12 MUTATED      6    0
  MMP12 WILD-TYPE  277   48
   clus
vv  MMP12 MUTATED MMP12 WILD-TYPE
  0             6             277
  1             0              48
[1] 2 2
[1] FALSE
D505V7, binary
                 cls
clus                0   1
  MMP12 MUTATED     2   6
  MMP12 WILD-TYPE 168 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP12 MUTATED      2    6
  MMP12 WILD-TYPE  168  191
        clus
vv       MMP12 MUTATED MMP12 WILD-TYPE
  FEMALE             2             168
  MALE               6             191
[1] 2 2
[1] FALSE
D505V8, binary
                 cls
clus                0   1
  MMP12 MUTATED     6   2
  MMP12 WILD-TYPE 311  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP12 MUTATED      6    2
  MMP12 WILD-TYPE  311   46
                               clus
vv                              MMP12 MUTATED MMP12 WILD-TYPE
  COLON ADENOCARCINOMA                      6             311
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MMP12 MUTATED     5   0   0   0
  MMP12 WILD-TYPE 252   2  22  21
D505V9, multiclass
    clus
vv   MMP12 MUTATED MMP12 WILD-TYPE
  R0             5             252
  R1             0               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"
D505V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MMP12 MUTATED                                  0     1
  MMP12 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MMP12 MUTATED                           0     5
  MMP12 WILD-TYPE                        19   171
D505V11, multiclass
                                  clus
vv                                 MMP12 MUTATED MMP12 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(506) Variable = PAK3 MUTATION ANALYSIS
D506V1, survival
                sevent
clus2              0   1
  PAK3 MUTATED    16   1
  PAK3 WILD-TYPE 266  72
  PAK3 MUTATED PAK3 WILD-TYPE 
            17            338 
  PAK3 MUTATED PAK3 WILD-TYPE 
             1             72 
$`PAK3 MUTATED`
TCGA-A6-2676 TCGA-AA-3510 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3681 TCGA-AA-3977 
       42.90        63.98        61.02         6.97         5.98        25.02 
TCGA-CA-6718 TCGA-CM-6164 TCGA-CM-6171 TCGA-CM-6676 TCGA-D5-6536 TCGA-D5-6541 
        0.10        29.03        14.04        11.08        17.85        15.58 
TCGA-DM-A1HB TCGA-DM-A28K TCGA-F4-6569 TCGA-G4-6586 TCGA-G4-6625 
      135.65        98.24        13.45        35.80        91.79 

$`PAK3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       13.94        19.99        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.33         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        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-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        43.27        15.12         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 
      119.93        35.97        60.79       117.07         8.61        13.38 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 
       45.11        36.72        36.00        22.09        13.78        26.17 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  PAK3 MUTATED PAK3 WILD-TYPE 
           0.1            0.0 
  PAK3 MUTATED PAK3 WILD-TYPE 
        135.65         140.38 
  PAK3 MUTATED PAK3 WILD-TYPE 
        25.020         20.155 
[1] "0.1 - 135.7 (25.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "5.4"
D506V2, 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       22       102         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        18         10         40         31       35        13
                vv
clus             STAGE IVB
  PAK3 MUTATED           0
  PAK3 WILD-TYPE         1
D506V3, multiclass
            clus
vv           PAK3 MUTATED PAK3 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              3             22
  STAGE IIA             7            102
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PAK3 MUTATED     0   4  12   1
  PAK3 WILD-TYPE   9  64 236  40
D506V4, multiclass
    clus
vv   PAK3 MUTATED PAK3 WILD-TYPE
  T1            0              9
  T2            4             64
  T3           12            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
  PAK3 MUTATED    15   2   0
  PAK3 WILD-TYPE 205  78  66
D506V5, multiclass
    clus
vv   PAK3 MUTATED PAK3 WILD-TYPE
  N0           15            205
  N1            2             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"
D506V6, binary
                cls
clus               0   1
  PAK3 MUTATED    16   0
  PAK3 WILD-TYPE 267  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK3 MUTATED     16    0
  PAK3 WILD-TYPE  267   48
   clus
vv  PAK3 MUTATED PAK3 WILD-TYPE
  0           16            267
  1            0             48
[1] 2 2
[1] FALSE
D506V7, 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
D506V8, binary
                cls
clus               0   1
  PAK3 MUTATED    16   1
  PAK3 WILD-TYPE 301  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK3 MUTATED     16    1
  PAK3 WILD-TYPE  301   47
                               clus
vv                              PAK3 MUTATED PAK3 WILD-TYPE
  COLON ADENOCARCINOMA                    16            301
  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 244   2  22  20
D506V9, multiclass
    clus
vv   PAK3 MUTATED PAK3 WILD-TYPE
  R0           13            244
  R1            0              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"
D506V10, 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
D506V11, 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(507) Variable = ZFC3H1 MUTATION ANALYSIS
D507V1, survival
                  sevent
clus2                0   1
  ZFC3H1 MUTATED    13   5
  ZFC3H1 WILD-TYPE 269  68
  ZFC3H1 MUTATED ZFC3H1 WILD-TYPE 
              18              337 
  ZFC3H1 MUTATED ZFC3H1 WILD-TYPE 
               5               68 
$`ZFC3H1 MUTATED`
TCGA-A6-5661 TCGA-A6-5665 TCGA-AA-3663 TCGA-AA-3715 TCGA-AA-3815 TCGA-AA-3864 
       33.53        22.06         6.97        19.04        33.04        53.00 
TCGA-AA-3875 TCGA-AA-3950 TCGA-AA-3975 TCGA-AA-A010 TCGA-AY-6386 TCGA-AZ-6598 
       18.05        24.00        34.06        34.98        17.82        49.41 
TCGA-AZ-6600 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5912 TCGA-CK-5916 TCGA-D5-6927 
       12.10         0.33         0.10        49.08        21.14         9.44 

$`ZFC3H1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       85.05        26.99        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3877 
       30.05        17.03        24.03        27.02        29.98        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       62.79        61.41         6.77       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07         0.26         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       40.34        15.62        51.32        21.99         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  ZFC3H1 MUTATED ZFC3H1 WILD-TYPE 
             0.1              0.0 
  ZFC3H1 MUTATED ZFC3H1 WILD-TYPE 
           53.00           140.38 
  ZFC3H1 MUTATED ZFC3H1 WILD-TYPE 
           21.60            20.12 
[1] "0.1 - 53.0 (21.6)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.5"
D507V2, 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       21       102         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZFC3H1 MUTATED           0          0          1          0        1
  ZFC3H1 WILD-TYPE        19         10         40         31       34
                  vv
clus               STAGE IVA STAGE IVB
  ZFC3H1 MUTATED           0         0
  ZFC3H1 WILD-TYPE        13         1
D507V3, multiclass
            clus
vv           ZFC3H1 MUTATED ZFC3H1 WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                4               21
  STAGE IIA               7              102
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZFC3H1 MUTATED     2   2  12   3
  ZFC3H1 WILD-TYPE   7  66 236  38
D507V4, multiclass
    clus
vv   ZFC3H1 MUTATED ZFC3H1 WILD-TYPE
  T1              2                7
  T2              2               66
  T3             12              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
  ZFC3H1 MUTATED    17   2   0
  ZFC3H1 WILD-TYPE 203  78  66
D507V5, multiclass
    clus
vv   ZFC3H1 MUTATED ZFC3H1 WILD-TYPE
  N0             17              203
  N1              2               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"
D507V6, binary
                  cls
clus                 0   1
  ZFC3H1 MUTATED    15   1
  ZFC3H1 WILD-TYPE 268  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZFC3H1 MUTATED     15    1
  ZFC3H1 WILD-TYPE  268   47
   clus
vv  ZFC3H1 MUTATED ZFC3H1 WILD-TYPE
  0             15              268
  1              1               47
[1] 2 2
[1] FALSE
D507V7, 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
D507V8, binary
                  cls
clus                 0   1
  ZFC3H1 MUTATED    17   2
  ZFC3H1 WILD-TYPE 300  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZFC3H1 MUTATED     17    2
  ZFC3H1 WILD-TYPE  300   46
                               clus
vv                              ZFC3H1 MUTATED ZFC3H1 WILD-TYPE
  COLON ADENOCARCINOMA                      17              300
  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 245   2  22  16
D507V9, multiclass
    clus
vv   ZFC3H1 MUTATED ZFC3H1 WILD-TYPE
  R0             12              245
  R1              0                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"
D507V10, 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
D507V11, 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(508) Variable = ZNF547 MUTATION ANALYSIS
D508V1, survival
                  sevent
clus2                0   1
  ZNF547 MUTATED     7   1
  ZNF547 WILD-TYPE 275  72
  ZNF547 MUTATED ZNF547 WILD-TYPE 
               8              347 
  ZNF547 MUTATED ZNF547 WILD-TYPE 
               1               72 
$`ZNF547 MUTATED`
TCGA-AA-3697 TCGA-AU-6004 TCGA-AZ-6608 TCGA-CA-6717 TCGA-CM-4744 TCGA-CM-6168 
       85.05        27.09         1.94         0.33        20.02        12.99 
TCGA-DM-A1D9 TCGA-G4-6588 
      140.38        26.17 

$`ZNF547 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA 
      130.65        92.75        49.91        13.32        12.59         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        91.79        46.75        52.80 

  ZNF547 MUTATED ZNF547 WILD-TYPE 
            0.33             0.00 
  ZNF547 MUTATED ZNF547 WILD-TYPE 
          140.38           139.17 
  ZNF547 MUTATED ZNF547 WILD-TYPE 
          23.095           20.190 
[1] "0.3 - 140.4 (23.1)" "0.0 - 139.2 (20.2)"
[1] "hr=" "2.2"
D508V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF547 MUTATED         2        0        0         4         0         0
  ZNF547 WILD-TYPE      62        1       25       105         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF547 MUTATED           1          1          0          0        0
  ZNF547 WILD-TYPE        18          9         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF547 MUTATED           0         0
  ZNF547 WILD-TYPE        13         1
D508V3, multiclass
            clus
vv           ZNF547 MUTATED ZNF547 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               4              105
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              1                9
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF547 MUTATED     0   3   5   0
  ZNF547 WILD-TYPE   9  65 243  41
D508V4, multiclass
    clus
vv   ZNF547 MUTATED ZNF547 WILD-TYPE
  T1              0                9
  T2              3               65
  T3              5              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
  ZNF547 MUTATED     7   1   0
  ZNF547 WILD-TYPE 213  79  66
D508V5, multiclass
    clus
vv   ZNF547 MUTATED ZNF547 WILD-TYPE
  N0              7              213
  N1              1               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"
D508V6, binary
                  cls
clus                 0   1
  ZNF547 MUTATED     8   0
  ZNF547 WILD-TYPE 275  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF547 MUTATED      8    0
  ZNF547 WILD-TYPE  275   48
   clus
vv  ZNF547 MUTATED ZNF547 WILD-TYPE
  0              8              275
  1              0               48
[1] 2 2
[1] FALSE
D508V7, 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
D508V8, binary
                  cls
clus                 0   1
  ZNF547 MUTATED     7   1
  ZNF547 WILD-TYPE 310  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF547 MUTATED      7    1
  ZNF547 WILD-TYPE  310   47
                               clus
vv                              ZNF547 MUTATED ZNF547 WILD-TYPE
  COLON ADENOCARCINOMA                       7              310
  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 252   2  22  20
D508V9, multiclass
    clus
vv   ZNF547 MUTATED ZNF547 WILD-TYPE
  R0              5              252
  R1              0                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"
D508V10, 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
D508V11, 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(509) Variable = RUFY1 MUTATION ANALYSIS
D509V1, survival
                 sevent
clus2               0   1
  RUFY1 MUTATED    12   1
  RUFY1 WILD-TYPE 270  72
  RUFY1 MUTATED RUFY1 WILD-TYPE 
             13             342 
  RUFY1 MUTATED RUFY1 WILD-TYPE 
              1              72 
$`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         2.24        12.49        16.14        12.00        44.32 
TCGA-G4-6309 
       51.75 

$`RUFY1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.09        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        19.99         6.05        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19         1.94         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.85         4.80        17.13        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         1.51        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  RUFY1 MUTATED RUFY1 WILD-TYPE 
           2.24            0.00 
  RUFY1 MUTATED RUFY1 WILD-TYPE 
          78.08          140.38 
  RUFY1 MUTATED RUFY1 WILD-TYPE 
         22.060          20.155 
[1] "2.2 - 78.1 (22.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "3.6"
D509V2, 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       22       105         8         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RUFY1 MUTATED           0          1          2          1        0         0
  RUFY1 WILD-TYPE        19          9         39         30       35        13
                 vv
clus              STAGE IVB
  RUFY1 MUTATED           0
  RUFY1 WILD-TYPE         1
D509V3, multiclass
            clus
vv           RUFY1 MUTATED RUFY1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              4             105
  STAGE IIB              0               8
  STAGE IIC              1               0
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             2              39
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RUFY1 MUTATED     0   1  10   2
  RUFY1 WILD-TYPE   9  67 238  39
D509V4, multiclass
    clus
vv   RUFY1 MUTATED RUFY1 WILD-TYPE
  T1             0               9
  T2             1              67
  T3            10             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
  RUFY1 MUTATED    10   2   1
  RUFY1 WILD-TYPE 210  78  65
D509V5, multiclass
    clus
vv   RUFY1 MUTATED RUFY1 WILD-TYPE
  N0            10             210
  N1             2              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"
D509V6, binary
                 cls
clus                0   1
  RUFY1 MUTATED    13   0
  RUFY1 WILD-TYPE 270  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUFY1 MUTATED     13    0
  RUFY1 WILD-TYPE  270   48
   clus
vv  RUFY1 MUTATED RUFY1 WILD-TYPE
  0            13             270
  1             0              48
[1] 2 2
[1] FALSE
D509V7, 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
D509V8, binary
                 cls
clus                0   1
  RUFY1 MUTATED    12   1
  RUFY1 WILD-TYPE 305  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUFY1 MUTATED     12    1
  RUFY1 WILD-TYPE  305   47
                               clus
vv                              RUFY1 MUTATED RUFY1 WILD-TYPE
  COLON ADENOCARCINOMA                     12             305
  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 247   2  22  20
D509V9, multiclass
    clus
vv   RUFY1 MUTATED RUFY1 WILD-TYPE
  R0            10             247
  R1             0               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"
D509V10, 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
D509V11, 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(510) Variable = THRAP3 MUTATION ANALYSIS
D510V1, survival
                  sevent
clus2                0   1
  THRAP3 MUTATED     8   3
  THRAP3 WILD-TYPE 274  70
  THRAP3 MUTATED THRAP3 WILD-TYPE 
              11              344 
  THRAP3 MUTATED THRAP3 WILD-TYPE 
               3               70 
$`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 
        0.33        23.05        16.14        14.30        35.87 

$`THRAP3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 
       10.06        35.05         0.99        25.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       38.99        37.02        14.93        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  THRAP3 MUTATED THRAP3 WILD-TYPE 
               0                0 
  THRAP3 MUTATED THRAP3 WILD-TYPE 
           35.87           140.38 
  THRAP3 MUTATED THRAP3 WILD-TYPE 
           14.30            20.98 
[1] "0.0 - 35.9 (14.3)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "2.6"
D510V2, 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       24       103         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  THRAP3 MUTATED           0          0          1          0        0
  THRAP3 WILD-TYPE        19         10         40         31       35
                  vv
clus               STAGE IVA STAGE IVB
  THRAP3 MUTATED           0         0
  THRAP3 WILD-TYPE        13         1
D510V3, multiclass
            clus
vv           THRAP3 MUTATED THRAP3 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               6              103
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  THRAP3 MUTATED     0   2   8   1
  THRAP3 WILD-TYPE   9  66 240  40
D510V4, multiclass
    clus
vv   THRAP3 MUTATED THRAP3 WILD-TYPE
  T1              0                9
  T2              2               66
  T3              8              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
  THRAP3 MUTATED    10   1   0
  THRAP3 WILD-TYPE 210  79  66
D510V5, multiclass
    clus
vv   THRAP3 MUTATED THRAP3 WILD-TYPE
  N0             10              210
  N1              1               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"
D510V6, binary
                  cls
clus                 0   1
  THRAP3 MUTATED    11   0
  THRAP3 WILD-TYPE 272  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THRAP3 MUTATED     11    0
  THRAP3 WILD-TYPE  272   48
   clus
vv  THRAP3 MUTATED THRAP3 WILD-TYPE
  0             11              272
  1              0               48
[1] 2 2
[1] FALSE
D510V7, 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
D510V8, binary
                  cls
clus                 0   1
  THRAP3 MUTATED     7   4
  THRAP3 WILD-TYPE 310  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THRAP3 MUTATED      7    4
  THRAP3 WILD-TYPE  310   44
                               clus
vv                              THRAP3 MUTATED THRAP3 WILD-TYPE
  COLON ADENOCARCINOMA                       7              310
  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 247   2  22  20
D510V9, multiclass
    clus
vv   THRAP3 MUTATED THRAP3 WILD-TYPE
  R0             10              247
  R1              0                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"
D510V10, 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
D510V11, 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(511) Variable = FAHD2A MUTATION ANALYSIS
D511V1, survival
                  sevent
clus2                0   1
  FAHD2A MUTATED     5   1
  FAHD2A WILD-TYPE 277  72
  FAHD2A MUTATED FAHD2A WILD-TYPE 
               6              349 
  FAHD2A MUTATED FAHD2A WILD-TYPE 
               1               72 
$`FAHD2A MUTATED`
TCGA-A6-5665 TCGA-A6-6653 TCGA-AA-3950 TCGA-CK-5916 TCGA-D5-6533 TCGA-G4-6586 
       22.06        24.39        24.00        21.14         1.32        35.80 

$`FAHD2A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
       40.34        15.62        49.08        51.32        21.99         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  FAHD2A MUTATED FAHD2A WILD-TYPE 
            1.32             0.00 
  FAHD2A MUTATED FAHD2A WILD-TYPE 
           35.80           140.38 
  FAHD2A MUTATED FAHD2A WILD-TYPE 
           23.03            20.02 
[1] "1.3 - 35.8 (23.0)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1.1"
D511V2, 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       25       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAHD2A MUTATED           0          0          1          0        0
  FAHD2A WILD-TYPE        19         10         40         31       35
                  vv
clus               STAGE IVA STAGE IVB
  FAHD2A MUTATED           0         0
  FAHD2A WILD-TYPE        13         1
D511V3, multiclass
            clus
vv           FAHD2A MUTATED FAHD2A WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               3              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FAHD2A MUTATED     1   1   3   1
  FAHD2A WILD-TYPE   8  67 245  40
D511V4, multiclass
    clus
vv   FAHD2A MUTATED FAHD2A WILD-TYPE
  T1              1                8
  T2              1               67
  T3              3              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
  FAHD2A MUTATED     6   0   0
  FAHD2A WILD-TYPE 214  80  66
D511V5, multiclass
    clus
vv   FAHD2A MUTATED FAHD2A WILD-TYPE
  N0              6              214
  N1              0               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"
D511V6, binary
                  cls
clus                 0   1
  FAHD2A MUTATED     6   0
  FAHD2A WILD-TYPE 277  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAHD2A MUTATED      6    0
  FAHD2A WILD-TYPE  277   48
   clus
vv  FAHD2A MUTATED FAHD2A WILD-TYPE
  0              6              277
  1              0               48
[1] 2 2
[1] FALSE
D511V7, 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
D511V8, binary
                  cls
clus                 0   1
  FAHD2A MUTATED     5   1
  FAHD2A WILD-TYPE 312  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAHD2A MUTATED      5    1
  FAHD2A WILD-TYPE  312   47
                               clus
vv                              FAHD2A MUTATED FAHD2A WILD-TYPE
  COLON ADENOCARCINOMA                       5              312
  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 253   2  22  20
D511V9, multiclass
    clus
vv   FAHD2A MUTATED FAHD2A WILD-TYPE
  R0              4              253
  R1              0                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"
D511V10, 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
D511V11, 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(512) Variable = ARFIP1 MUTATION ANALYSIS
D512V1, survival
                  sevent
clus2                0   1
  ARFIP1 MUTATED    10   2
  ARFIP1 WILD-TYPE 272  71
  ARFIP1 MUTATED ARFIP1 WILD-TYPE 
              12              343 
  ARFIP1 MUTATED ARFIP1 WILD-TYPE 
               2               71 
$`ARFIP1 MUTATED`
TCGA-A6-5657 TCGA-AA-3518 TCGA-AA-3558 TCGA-AA-3975 TCGA-AA-A00N TCGA-AA-A01P 
       31.63         1.02        20.98        34.06         4.01        38.07 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4743 TCGA-G4-6588 
       17.82        58.39         0.33         0.10        23.05        26.17 

$`ARFIP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        29.95        23.01        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        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        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4323 
       16.31         0.95        15.75         0.20        21.44         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07         0.26         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 
       52.80 

  ARFIP1 MUTATED ARFIP1 WILD-TYPE 
             0.1              0.0 
  ARFIP1 MUTATED ARFIP1 WILD-TYPE 
           58.39           140.38 
  ARFIP1 MUTATED ARFIP1 WILD-TYPE 
          22.015           20.120 
[1] "0.1 - 58.4 (22.0)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1"  
D512V2, 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       25       103         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARFIP1 MUTATED           1          0          2          0        0
  ARFIP1 WILD-TYPE        18         10         39         31       35
                  vv
clus               STAGE IVA STAGE IVB
  ARFIP1 MUTATED           0         0
  ARFIP1 WILD-TYPE        13         1
D512V3, multiclass
            clus
vv           ARFIP1 MUTATED ARFIP1 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               6              103
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ARFIP1 MUTATED     0   2   9   1
  ARFIP1 WILD-TYPE   9  66 239  40
D512V4, multiclass
    clus
vv   ARFIP1 MUTATED ARFIP1 WILD-TYPE
  T1              0                9
  T2              2               66
  T3              9              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
  ARFIP1 MUTATED     9   3   0
  ARFIP1 WILD-TYPE 211  77  66
D512V5, multiclass
    clus
vv   ARFIP1 MUTATED ARFIP1 WILD-TYPE
  N0              9              211
  N1              3               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"
D512V6, binary
                  cls
clus                 0   1
  ARFIP1 MUTATED    12   0
  ARFIP1 WILD-TYPE 271  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARFIP1 MUTATED     12    0
  ARFIP1 WILD-TYPE  271   48
   clus
vv  ARFIP1 MUTATED ARFIP1 WILD-TYPE
  0             12              271
  1              0               48
[1] 2 2
[1] FALSE
D512V7, 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
D512V8, binary
                  cls
clus                 0   1
  ARFIP1 MUTATED    10   2
  ARFIP1 WILD-TYPE 307  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARFIP1 MUTATED     10    2
  ARFIP1 WILD-TYPE  307   46
                               clus
vv                              ARFIP1 MUTATED ARFIP1 WILD-TYPE
  COLON ADENOCARCINOMA                      10              307
  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 248   2  21  19
D512V9, multiclass
    clus
vv   ARFIP1 MUTATED ARFIP1 WILD-TYPE
  R0              9              248
  R1              0                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"
D512V10, 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
D512V11, 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(513) Variable = HM13 MUTATION ANALYSIS
D513V1, survival
                sevent
clus2              0   1
  HM13 MUTATED     4   1
  HM13 WILD-TYPE 278  72
  HM13 MUTATED HM13 WILD-TYPE 
             5            350 
  HM13 MUTATED HM13 WILD-TYPE 
             1             72 
$`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        35.87 

$`HM13 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        17.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       15.12         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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79       117.07        98.24        13.38        13.45         6.18 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  HM13 MUTATED HM13 WILD-TYPE 
          8.61           0.00 
  HM13 MUTATED HM13 WILD-TYPE 
         35.87         140.38 
  HM13 MUTATED HM13 WILD-TYPE 
        17.850         20.235 
[1] "8.6 - 35.9 (17.9)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.3"
D513V2, 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       25       106         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HM13 MUTATED           0          1          1          0        0         0
  HM13 WILD-TYPE        19          9         40         31       35        13
                vv
clus             STAGE IVB
  HM13 MUTATED           0
  HM13 WILD-TYPE         1
D513V3, multiclass
            clus
vv           HM13 MUTATED HM13 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             3            106
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            1              9
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  HM13 MUTATED     0   0   5   0
  HM13 WILD-TYPE   9  68 243  41
D513V4, multiclass
    clus
vv   HM13 MUTATED HM13 WILD-TYPE
  T1            0              9
  T2            0             68
  T3            5            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
  HM13 MUTATED     4   0   1
  HM13 WILD-TYPE 216  80  65
D513V5, multiclass
    clus
vv   HM13 MUTATED HM13 WILD-TYPE
  N0            4            216
  N1            0             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"
D513V6, binary
                cls
clus               0   1
  HM13 MUTATED     5   0
  HM13 WILD-TYPE 278  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  HM13 MUTATED      5    0
  HM13 WILD-TYPE  278   48
   clus
vv  HM13 MUTATED HM13 WILD-TYPE
  0            5            278
  1            0             48
[1] 2 2
[1] FALSE
D513V7, 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
D513V8, binary
                cls
clus               0   1
  HM13 MUTATED     4   1
  HM13 WILD-TYPE 313  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  HM13 MUTATED      4    1
  HM13 WILD-TYPE  313   47
                               clus
vv                              HM13 MUTATED HM13 WILD-TYPE
  COLON ADENOCARCINOMA                     4            313
  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 252   2  22  21
D513V9, multiclass
    clus
vv   HM13 MUTATED HM13 WILD-TYPE
  R0            5            252
  R1            0              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"
D513V10, 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
D513V11, 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(514) Variable = WBP11 MUTATION ANALYSIS
D514V1, survival
                 sevent
clus2               0   1
  WBP11 MUTATED     6   1
  WBP11 WILD-TYPE 276  72
  WBP11 MUTATED WBP11 WILD-TYPE 
              7             348 
  WBP11 MUTATED WBP11 WILD-TYPE 
              1              72 
$`WBP11 MUTATED`
TCGA-A6-5665 TCGA-AA-3713 TCGA-CK-4950 TCGA-D5-6540 TCGA-D5-6541 TCGA-DM-A28G 
       22.06        19.04        40.34        16.14        15.58        60.79 
TCGA-G4-6309 
       51.75 

$`WBP11 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      102.44        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
        4.80        17.13        12.49         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K 
        6.12        81.37       119.93        35.97       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  WBP11 MUTATED WBP11 WILD-TYPE 
          15.58            0.00 
  WBP11 MUTATED WBP11 WILD-TYPE 
          60.79          140.38 
  WBP11 MUTATED WBP11 WILD-TYPE 
         22.060          20.155 
[1] "15.6 - 60.8 (22.1)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.9"
D514V2, 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       25       105         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  WBP11 MUTATED           0          1          1          0        1         0
  WBP11 WILD-TYPE        19          9         40         31       34        13
                 vv
clus              STAGE IVB
  WBP11 MUTATED           0
  WBP11 WILD-TYPE         1
D514V3, multiclass
            clus
vv           WBP11 MUTATED WBP11 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              4             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  WBP11 MUTATED     0   1   7   0
  WBP11 WILD-TYPE   9  67 241  41
D514V4, multiclass
    clus
vv   WBP11 MUTATED WBP11 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             7             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
  WBP11 MUTATED     6   2   0
  WBP11 WILD-TYPE 214  78  66
D514V5, multiclass
    clus
vv   WBP11 MUTATED WBP11 WILD-TYPE
  N0             6             214
  N1             2              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"
D514V6, binary
                 cls
clus                0   1
  WBP11 MUTATED     7   1
  WBP11 WILD-TYPE 276  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WBP11 MUTATED      7    1
  WBP11 WILD-TYPE  276   47
   clus
vv  WBP11 MUTATED WBP11 WILD-TYPE
  0             7             276
  1             1              47
[1] 2 2
[1] FALSE
D514V7, 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
D514V8, binary
                 cls
clus                0   1
  WBP11 MUTATED     7   1
  WBP11 WILD-TYPE 310  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WBP11 MUTATED      7    1
  WBP11 WILD-TYPE  310   47
                               clus
vv                              WBP11 MUTATED WBP11 WILD-TYPE
  COLON ADENOCARCINOMA                      7             310
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  WBP11 MUTATED     5   1   1   0
  WBP11 WILD-TYPE 252   1  21  21
D514V9, multiclass
    clus
vv   WBP11 MUTATED WBP11 WILD-TYPE
  R0             5             252
  R1             1               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"
D514V10, 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
D514V11, 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(515) Variable = RCSD1 MUTATION ANALYSIS
D515V1, survival
                 sevent
clus2               0   1
  RCSD1 MUTATED    10   4
  RCSD1 WILD-TYPE 272  69
  RCSD1 MUTATED RCSD1 WILD-TYPE 
             14             341 
  RCSD1 MUTATED RCSD1 WILD-TYPE 
              4              69 
$`RCSD1 MUTATED`
TCGA-A6-2672 TCGA-AA-3542 TCGA-AA-3713 TCGA-AA-A00J TCGA-AD-6899 TCGA-AU-6004 
       46.65        12.99        19.04        18.05         5.79        27.09 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-5913 TCGA-CK-5914 
       49.41        12.10         0.10         1.35        51.32        21.99 
TCGA-D5-6930 TCGA-G4-6303 
        1.51        65.85 

$`RCSD1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       26.01         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        0.72        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       61.41         6.77       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07         0.26         0.33        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        49.08        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       19.43       107.67        74.56        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  RCSD1 MUTATED RCSD1 WILD-TYPE 
            0.1             0.0 
  RCSD1 MUTATED RCSD1 WILD-TYPE 
          65.85          140.38 
  RCSD1 MUTATED RCSD1 WILD-TYPE 
         18.545          20.280 
[1] "0.1 - 65.8 (18.5)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.4"
D515V2, 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       24       105         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        19         10         38         29       32        13
                 vv
clus              STAGE IVB
  RCSD1 MUTATED           0
  RCSD1 WILD-TYPE         1
D515V3, multiclass
            clus
vv           RCSD1 MUTATED RCSD1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              4             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             3              38
  STAGE IIIC             2              29
  STAGE IV               3              32
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RCSD1 MUTATED     0   1  10   3
  RCSD1 WILD-TYPE   9  67 238  38
D515V4, multiclass
    clus
vv   RCSD1 MUTATED RCSD1 WILD-TYPE
  T1             0               9
  T2             1              67
  T3            10             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
  RCSD1 MUTATED     7   5   2
  RCSD1 WILD-TYPE 213  75  64
D515V5, multiclass
    clus
vv   RCSD1 MUTATED RCSD1 WILD-TYPE
  N0             7             213
  N1             5              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"
D515V6, binary
                 cls
clus                0   1
  RCSD1 MUTATED     7   3
  RCSD1 WILD-TYPE 276  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RCSD1 MUTATED      7    3
  RCSD1 WILD-TYPE  276   45
   clus
vv  RCSD1 MUTATED RCSD1 WILD-TYPE
  0             7             276
  1             3              45
[1] 2 2
[1] FALSE
D515V7, 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
D515V8, binary
                 cls
clus                0   1
  RCSD1 MUTATED    11   3
  RCSD1 WILD-TYPE 306  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RCSD1 MUTATED     11    3
  RCSD1 WILD-TYPE  306   45
                               clus
vv                              RCSD1 MUTATED RCSD1 WILD-TYPE
  COLON ADENOCARCINOMA                     11             306
  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 251   2  21  17
D515V9, multiclass
    clus
vv   RCSD1 MUTATED RCSD1 WILD-TYPE
  R0             6             251
  R1             0               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"
D515V10, 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
D515V11, 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(516) Variable = EAPP MUTATION ANALYSIS
D516V1, survival
                sevent
clus2              0   1
  EAPP MUTATED     1   2
  EAPP WILD-TYPE 281  71
  EAPP MUTATED EAPP WILD-TYPE 
             3            352 
  EAPP MUTATED EAPP WILD-TYPE 
             2             71 
$`EAPP MUTATED`
TCGA-A6-4105 TCGA-AA-A03F TCGA-D5-6535 
       14.53        18.05        15.12 

$`EAPP WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 
       11.51        20.19        18.25         1.32        43.27        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  EAPP MUTATED EAPP WILD-TYPE 
         14.53           0.00 
  EAPP MUTATED EAPP WILD-TYPE 
         18.05         140.38 
  EAPP MUTATED EAPP WILD-TYPE 
         15.12          20.63 
[1] "14.5 - 18.1 (15.1)" "0.0 - 140.4 (20.6)"
[1] "hr=" "4.6"
D516V2, 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       25       108         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        17         10         40         31       35        13
                vv
clus             STAGE IVB
  EAPP MUTATED           0
  EAPP WILD-TYPE         1
D516V3, multiclass
            clus
vv           EAPP MUTATED EAPP WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             1            108
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             2             17
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  EAPP MUTATED     0   0   4   0
  EAPP WILD-TYPE   9  68 244  41
D516V4, multiclass
    clus
vv   EAPP MUTATED EAPP WILD-TYPE
  T1            0              9
  T2            0             68
  T3            4            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
  EAPP MUTATED     1   1   2
  EAPP WILD-TYPE 219  79  64
D516V5, multiclass
    clus
vv   EAPP MUTATED EAPP WILD-TYPE
  N0            1            219
  N1            1             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"
D516V6, binary
                cls
clus               0   1
  EAPP MUTATED     3   0
  EAPP WILD-TYPE 280  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  EAPP MUTATED      3    0
  EAPP WILD-TYPE  280   48
   clus
vv  EAPP MUTATED EAPP WILD-TYPE
  0            3            280
  1            0             48
[1] 2 2
[1] FALSE
D516V7, 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
D516V8, binary
                cls
clus               0   1
  EAPP MUTATED     3   1
  EAPP WILD-TYPE 314  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  EAPP MUTATED      3    1
  EAPP WILD-TYPE  314   47
                               clus
vv                              EAPP MUTATED EAPP WILD-TYPE
  COLON ADENOCARCINOMA                     3            314
  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 255   2  22  20
D516V9, multiclass
    clus
vv   EAPP MUTATED EAPP WILD-TYPE
  R0            2            255
  R1            0              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"
D516V10, 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
D516V11, multiclass
[1] "Remove cluster labels:" "EAPP MUTATED"          
clus
  EAPP MUTATED EAPP WILD-TYPE 
             2            204 
    TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810     TCGA-A6-5656 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-A6-5657     TCGA-A6-5659     TCGA-A6-5660     TCGA-A6-5661 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-A6-5662     TCGA-A6-5664     TCGA-A6-5665     TCGA-A6-5666 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-A6-6137     TCGA-A6-6138     TCGA-A6-6141     TCGA-A6-6142 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-A6-6648     TCGA-A6-6649     TCGA-A6-6651     TCGA-A6-6652 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-A6-6653     TCGA-A6-6654     TCGA-A6-6780     TCGA-A6-6781 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-A6-6782     TCGA-AD-5900     TCGA-AD-6548     TCGA-AD-6888 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-AD-6889     TCGA-AD-6890     TCGA-AD-6895     TCGA-AD-6899 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-AD-6901     TCGA-AD-6963     TCGA-AD-6964     TCGA-AD-6965 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-AU-3779     TCGA-AU-6004     TCGA-AY-4070     TCGA-AY-4071 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-AY-5543     TCGA-AY-6196     TCGA-AY-6197     TCGA-AY-6386 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-AZ-4315     TCGA-AZ-4323     TCGA-AZ-4616     TCGA-AZ-4681 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-AZ-4682     TCGA-AZ-5403     TCGA-AZ-5407     TCGA-AZ-6598 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-AZ-6599     TCGA-AZ-6600     TCGA-AZ-6601     TCGA-AZ-6603 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-AZ-6605     TCGA-AZ-6606     TCGA-AZ-6607     TCGA-AZ-6608 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-CA-5254     TCGA-CA-5255     TCGA-CA-5796     TCGA-CA-5797 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-CA-6715     TCGA-CA-6716     TCGA-CA-6717     TCGA-CA-6718 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-CA-6719     TCGA-CK-4947     TCGA-CK-4948     TCGA-CK-4950 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-CK-4952     TCGA-CK-5912     TCGA-CK-5913     TCGA-CK-5914 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-CK-5915     TCGA-CK-5916     TCGA-CK-6746     TCGA-CK-6747 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-CK-6748     TCGA-CK-6751     TCGA-CM-4743     TCGA-CM-4744 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-CM-4746     TCGA-CM-4747     TCGA-CM-4752     TCGA-CM-5341 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-CM-5344     TCGA-CM-5348     TCGA-CM-5349     TCGA-CM-5860 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-CM-5861     TCGA-CM-5862     TCGA-CM-5863     TCGA-CM-5864 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-CM-5868     TCGA-CM-6161     TCGA-CM-6162     TCGA-CM-6163 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-CM-6164     TCGA-CM-6165     TCGA-CM-6166     TCGA-CM-6167 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-CM-6168     TCGA-CM-6169     TCGA-CM-6170     TCGA-CM-6171 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-CM-6172     TCGA-CM-6674     TCGA-CM-6675     TCGA-CM-6676 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-CM-6677     TCGA-CM-6678     TCGA-CM-6679     TCGA-CM-6680 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-D5-5537     TCGA-D5-5538     TCGA-D5-5539     TCGA-D5-5540 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-D5-5541     TCGA-D5-6529     TCGA-D5-6532     TCGA-D5-6533 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-D5-6534     TCGA-D5-6536     TCGA-D5-6537     TCGA-D5-6538 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-D5-6539     TCGA-D5-6540     TCGA-D5-6541     TCGA-D5-6898 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-D5-6920     TCGA-D5-6922     TCGA-D5-6923     TCGA-D5-6924 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-D5-6926     TCGA-D5-6927     TCGA-D5-6928     TCGA-D5-6929 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-D5-6930     TCGA-D5-6931     TCGA-D5-6932     TCGA-D5-7000 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-DM-A0X9     TCGA-DM-A0XD     TCGA-DM-A0XF     TCGA-DM-A1D0 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-DM-A1D4     TCGA-DM-A1D6     TCGA-DM-A1D7     TCGA-DM-A1D8 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-DM-A1D9     TCGA-DM-A1DA     TCGA-DM-A1DB     TCGA-DM-A1HA 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-DM-A1HB     TCGA-DM-A282     TCGA-DM-A285     TCGA-DM-A28C 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-DM-A28E     TCGA-DM-A28F     TCGA-DM-A28G     TCGA-DM-A28H 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-DM-A28K     TCGA-F4-6459     TCGA-F4-6460     TCGA-F4-6569 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-F4-6570     TCGA-F4-6703     TCGA-F4-6704     TCGA-F4-6805 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-F4-6806     TCGA-F4-6807     TCGA-F4-6808     TCGA-F4-6809 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-F4-6854     TCGA-F4-6855     TCGA-F4-6856     TCGA-G4-6293 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-G4-6299     TCGA-G4-6303     TCGA-G4-6304     TCGA-G4-6306 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-G4-6307     TCGA-G4-6309     TCGA-G4-6310     TCGA-G4-6315 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-G4-6317     TCGA-G4-6321     TCGA-G4-6323     TCGA-G4-6586 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-G4-6588     TCGA-G4-6625     TCGA-G4-6626     TCGA-G4-6628 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 

Clustering(517) Variable = NLK MUTATION ANALYSIS
D517V1, survival
               sevent
clus2             0   1
  NLK MUTATED    11   0
  NLK WILD-TYPE 271  73
  NLK MUTATED NLK WILD-TYPE 
           11           344 
  NLK MUTATED NLK WILD-TYPE 
            0            73 
$`NLK MUTATED`
TCGA-A6-3807 TCGA-A6-5661 TCGA-AA-3662 TCGA-AA-3663 TCGA-AU-6004 TCGA-CK-6747 
       34.65        33.53         6.05         6.97        27.09         2.93 
TCGA-CM-5349 TCGA-D5-5539 TCGA-F4-6805 TCGA-G4-6307 TCGA-G4-6309 
       30.08        19.59        16.31        55.04        51.75 

$`NLK WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       13.94        19.99        61.02        78.08        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 
       49.08        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-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6807 
       13.45         6.18        35.87         1.55        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6310 TCGA-G4-6315 
       74.56        65.85        53.62        44.68        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  NLK MUTATED NLK WILD-TYPE 
         2.93          0.00 
  NLK MUTATED NLK WILD-TYPE 
        55.04        140.38 
  NLK MUTATED NLK WILD-TYPE 
       27.090        20.155 
[1] "2.9 - 55.0 (27.1)"  "0.0 - 140.4 (20.2)"
[1] "hr="     "2.6e+07"
D517V2, 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       24       105         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        19          9         39         30       34        13
               vv
clus            STAGE IVB
  NLK MUTATED           0
  NLK WILD-TYPE         1
D517V3, multiclass
            clus
vv           NLK MUTATED NLK WILD-TYPE
  STAGE I              1            63
  STAGE IA             0             1
  STAGE II             1            24
  STAGE IIA            4           105
  STAGE IIB            0             8
  STAGE IIC            0             1
  STAGE III            0            19
  STAGE IIIA           1             9
  STAGE IIIB           2            39
  STAGE IIIC           1            30
  STAGE IV             1            34
  STAGE IVA            0            13
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  NLK MUTATED     0   1   9   1
  NLK WILD-TYPE   9  67 239  40
D517V4, multiclass
    clus
vv   NLK MUTATED NLK WILD-TYPE
  T1           0             9
  T2           1            67
  T3           9           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
  NLK MUTATED     6   3   2
  NLK WILD-TYPE 214  77  64
D517V5, multiclass
    clus
vv   NLK MUTATED NLK WILD-TYPE
  N0           6           214
  N1           3            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"
D517V6, binary
               cls
clus              0   1
  NLK MUTATED     9   1
  NLK WILD-TYPE 274  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  NLK MUTATED      9    1
  NLK WILD-TYPE  274   47
   clus
vv  NLK MUTATED NLK WILD-TYPE
  0           9           274
  1           1            47
[1] 2 2
[1] FALSE
D517V7, 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
D517V8, binary
               cls
clus              0   1
  NLK MUTATED    10   1
  NLK WILD-TYPE 307  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  NLK MUTATED     10    1
  NLK WILD-TYPE  307   47
                               clus
vv                              NLK MUTATED NLK WILD-TYPE
  COLON ADENOCARCINOMA                   10           307
  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 248   2  21  20
D517V9, multiclass
    clus
vv   NLK MUTATED NLK WILD-TYPE
  R0           9           248
  R1           0             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"
D517V10, 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
D517V11, 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(518) Variable = HERC5 MUTATION ANALYSIS
D518V1, survival
                 sevent
clus2               0   1
  HERC5 MUTATED    15   3
  HERC5 WILD-TYPE 267  70
  HERC5 MUTATED HERC5 WILD-TYPE 
             18             337 
  HERC5 MUTATED HERC5 WILD-TYPE 
              3              70 
$`HERC5 MUTATED`
TCGA-A6-5659 TCGA-A6-6649 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3713 TCGA-AA-3715 
       30.44        24.16        63.98        29.95        19.04        19.04 
TCGA-AA-3848 TCGA-AA-3982 TCGA-AA-A010 TCGA-AD-6965 TCGA-AZ-4315 TCGA-CK-5914 
       10.06        27.02        34.98         0.20        58.39        21.99 
TCGA-CM-6675 TCGA-D5-6926 TCGA-DM-A1D4 TCGA-F4-6854 TCGA-G4-6307 TCGA-G4-6586 
       13.05         9.04        92.75         0.53        55.04        35.80 

$`HERC5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.18        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       26.99        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
        0.00        17.03         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 
       10.26       119.70        24.43        38.20       130.65        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       33.67        13.25        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  HERC5 MUTATED HERC5 WILD-TYPE 
            0.2             0.0 
  HERC5 MUTATED HERC5 WILD-TYPE 
          92.75          140.38 
  HERC5 MUTATED HERC5 WILD-TYPE 
          25.59           20.02 
[1] "0.2 - 92.8 (25.6)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1.5"
D518V2, 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       23       104         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HERC5 MUTATED           0          1          4          1        1         0
  HERC5 WILD-TYPE        19          9         37         30       34        13
                 vv
clus              STAGE IVB
  HERC5 MUTATED           1
  HERC5 WILD-TYPE         0
D518V3, multiclass
            clus
vv           HERC5 MUTATED HERC5 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              5             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             4              37
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              0              13
  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  67 234  38
D518V4, multiclass
    clus
vv   HERC5 MUTATED HERC5 WILD-TYPE
  T1             0               9
  T2             1              67
  T3            14             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
  HERC5 MUTATED    10   5   3
  HERC5 WILD-TYPE 210  75  63
D518V5, multiclass
    clus
vv   HERC5 MUTATED HERC5 WILD-TYPE
  N0            10             210
  N1             5              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"
D518V6, binary
                 cls
clus                0   1
  HERC5 MUTATED    14   2
  HERC5 WILD-TYPE 269  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HERC5 MUTATED     14    2
  HERC5 WILD-TYPE  269   46
   clus
vv  HERC5 MUTATED HERC5 WILD-TYPE
  0            14             269
  1             2              46
[1] 2 2
[1] FALSE
D518V7, 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
D518V8, binary
                 cls
clus                0   1
  HERC5 MUTATED    17   1
  HERC5 WILD-TYPE 300  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HERC5 MUTATED     17    1
  HERC5 WILD-TYPE  300   47
                               clus
vv                              HERC5 MUTATED HERC5 WILD-TYPE
  COLON ADENOCARCINOMA                     17             300
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  HERC5 MUTATED    12   0   1   1
  HERC5 WILD-TYPE 245   2  21  20
D518V9, multiclass
    clus
vv   HERC5 MUTATED HERC5 WILD-TYPE
  R0            12             245
  R1             0               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"
D518V10, 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
D518V11, 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(519) Variable = POLM MUTATION ANALYSIS
D519V1, survival
                sevent
clus2              0   1
  POLM MUTATED     9   1
  POLM WILD-TYPE 273  72
  POLM MUTATED POLM WILD-TYPE 
            10            345 
  POLM MUTATED POLM WILD-TYPE 
             1             72 
$`POLM MUTATED`
TCGA-A6-6781 TCGA-AA-3672 TCGA-AZ-4682 TCGA-CK-5913 TCGA-CM-5861 TCGA-D5-6535 
       19.66         0.92        22.36        51.32        15.02        15.12 
TCGA-D5-6927 TCGA-D5-6930 TCGA-DM-A1HB TCGA-G4-6293 
        9.44         1.51       135.65       107.67 

$`POLM WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13        83.80        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       40.34        15.62        49.08        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 
       33.67        13.25         0.53        35.41        19.43        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  POLM MUTATED POLM WILD-TYPE 
          0.92           0.00 
  POLM MUTATED POLM WILD-TYPE 
        135.65         140.38 
  POLM MUTATED POLM WILD-TYPE 
         17.39          20.28 
[1] "0.9 - 135.7 (17.4)" "0.0 - 140.4 (20.3)"
[1] "hr=" "3"  
D519V2, 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       25       105         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        17         10         39         30       35        12
                vv
clus             STAGE IVB
  POLM MUTATED           0
  POLM WILD-TYPE         1
D519V3, multiclass
            clus
vv           POLM MUTATED POLM WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             4            105
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             2             17
  STAGE IIIA            0             10
  STAGE IIIB            2             39
  STAGE IIIC            1             30
  STAGE IV              0             35
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  68 239  39
D519V4, multiclass
    clus
vv   POLM MUTATED POLM WILD-TYPE
  T1            0              9
  T2            0             68
  T3            9            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
  POLM MUTATED     6   5   0
  POLM WILD-TYPE 214  75  66
D519V5, multiclass
    clus
vv   POLM MUTATED POLM WILD-TYPE
  N0            6            214
  N1            5             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"
D519V6, binary
                cls
clus               0   1
  POLM MUTATED     6   1
  POLM WILD-TYPE 277  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  POLM MUTATED      6    1
  POLM WILD-TYPE  277   47
   clus
vv  POLM MUTATED POLM WILD-TYPE
  0            6            277
  1            1             47
[1] 2 2
[1] FALSE
D519V7, 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
D519V8, binary
                cls
clus               0   1
  POLM MUTATED     9   2
  POLM WILD-TYPE 308  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  POLM MUTATED      9    2
  POLM WILD-TYPE  308   46
                               clus
vv                              POLM MUTATED POLM WILD-TYPE
  COLON ADENOCARCINOMA                     9            308
  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 250   2  22  18
D519V9, multiclass
    clus
vv   POLM MUTATED POLM WILD-TYPE
  R0            7            250
  R1            0              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"
D519V10, 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
D519V11, 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(520) Variable = CYP1B1 MUTATION ANALYSIS
D520V1, survival
                  sevent
clus2                0   1
  CYP1B1 MUTATED     8   2
  CYP1B1 WILD-TYPE 274  71
  CYP1B1 MUTATED CYP1B1 WILD-TYPE 
              10              345 
  CYP1B1 MUTATED CYP1B1 WILD-TYPE 
               2               71 
$`CYP1B1 MUTATED`
TCGA-A6-5665 TCGA-A6-6654 TCGA-AA-3715 TCGA-AA-3861 TCGA-CA-6717 TCGA-CM-5348 
       22.06        23.87        19.04        30.05         0.33        22.98 
TCGA-D5-6533 TCGA-G4-6303 TCGA-G4-6586 TCGA-G4-6588 
        1.32        65.85        35.80        26.17 

$`CYP1B1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 
       19.59        13.51        11.51        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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       19.43       107.67        74.56        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  CYP1B1 MUTATED CYP1B1 WILD-TYPE 
            0.33             0.00 
  CYP1B1 MUTATED CYP1B1 WILD-TYPE 
           65.85           140.38 
  CYP1B1 MUTATED CYP1B1 WILD-TYPE 
          23.425           20.020 
[1] "0.3 - 65.8 (23.4)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1"  
D520V2, 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       24       103         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CYP1B1 MUTATED           0          0          3          0        1
  CYP1B1 WILD-TYPE        19         10         38         31       34
                  vv
clus               STAGE IVA STAGE IVB
  CYP1B1 MUTATED           0         0
  CYP1B1 WILD-TYPE        13         1
D520V3, multiclass
            clus
vv           CYP1B1 MUTATED CYP1B1 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               6              103
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              3               38
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CYP1B1 MUTATED     0   0  10   1
  CYP1B1 WILD-TYPE   9  68 238  40
D520V4, multiclass
    clus
vv   CYP1B1 MUTATED CYP1B1 WILD-TYPE
  T1              0                9
  T2              0               68
  T3             10              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
  CYP1B1 MUTATED     8   3   0
  CYP1B1 WILD-TYPE 212  77  66
D520V5, multiclass
    clus
vv   CYP1B1 MUTATED CYP1B1 WILD-TYPE
  N0              8              212
  N1              3               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"
D520V6, binary
                  cls
clus                 0   1
  CYP1B1 MUTATED    10   1
  CYP1B1 WILD-TYPE 273  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP1B1 MUTATED     10    1
  CYP1B1 WILD-TYPE  273   47
   clus
vv  CYP1B1 MUTATED CYP1B1 WILD-TYPE
  0             10              273
  1              1               47
[1] 2 2
[1] FALSE
D520V7, 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
D520V8, binary
                  cls
clus                 0   1
  CYP1B1 MUTATED    10   1
  CYP1B1 WILD-TYPE 307  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP1B1 MUTATED     10    1
  CYP1B1 WILD-TYPE  307   47
                               clus
vv                              CYP1B1 MUTATED CYP1B1 WILD-TYPE
  COLON ADENOCARCINOMA                      10              307
  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 248   2  22  20
D520V9, multiclass
    clus
vv   CYP1B1 MUTATED CYP1B1 WILD-TYPE
  R0              9              248
  R1              0                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"
D520V10, 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
D520V11, 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(521) Variable = PNPLA8 MUTATION ANALYSIS
D521V1, survival
                  sevent
clus2                0   1
  PNPLA8 MUTATED    14   4
  PNPLA8 WILD-TYPE 268  69
  PNPLA8 MUTATED PNPLA8 WILD-TYPE 
              18              337 
  PNPLA8 MUTATED PNPLA8 WILD-TYPE 
               4               69 
$`PNPLA8 MUTATED`
TCGA-A6-3809 TCGA-A6-6653 TCGA-AA-3710 TCGA-AA-3977 TCGA-AA-A00N TCGA-AD-6895 
       32.75        24.39        26.99        25.02         4.01         0.72 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-6717 TCGA-CA-6718 
       17.82        58.39         3.19         1.94         0.33         0.10 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5916 TCGA-CK-6747 TCGA-CM-5344 TCGA-CM-6161 
      102.44        40.34        21.14         2.93        22.03        15.02 

$`PNPLA8 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
        0.07        21.37         4.21        56.55         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4323 
       16.31         0.95        15.75         0.20        21.44         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
        1.35        17.56        15.62        49.08        51.32        21.99 
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        16.01        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  PNPLA8 MUTATED PNPLA8 WILD-TYPE 
             0.1              0.0 
  PNPLA8 MUTATED PNPLA8 WILD-TYPE 
          102.44           140.38 
  PNPLA8 MUTATED PNPLA8 WILD-TYPE 
           19.48            20.19 
[1] "0.1 - 102.4 (19.5)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.3"
D521V2, 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       25       104         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PNPLA8 MUTATED           0          3          2          0        1
  PNPLA8 WILD-TYPE        19          7         39         31       34
                  vv
clus               STAGE IVA STAGE IVB
  PNPLA8 MUTATED           0         0
  PNPLA8 WILD-TYPE        13         1
D521V3, multiclass
            clus
vv           PNPLA8 MUTATED PNPLA8 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               5              104
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              3                7
  STAGE IIIB              2               39
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PNPLA8 MUTATED     1   4  10   3
  PNPLA8 WILD-TYPE   8  64 238  38
D521V4, multiclass
    clus
vv   PNPLA8 MUTATED PNPLA8 WILD-TYPE
  T1              1                8
  T2              4               64
  T3             10              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
  PNPLA8 MUTATED    11   6   1
  PNPLA8 WILD-TYPE 209  74  65
D521V5, multiclass
    clus
vv   PNPLA8 MUTATED PNPLA8 WILD-TYPE
  N0             11              209
  N1              6               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"
D521V6, binary
                  cls
clus                 0   1
  PNPLA8 MUTATED    14   1
  PNPLA8 WILD-TYPE 269  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PNPLA8 MUTATED     14    1
  PNPLA8 WILD-TYPE  269   47
   clus
vv  PNPLA8 MUTATED PNPLA8 WILD-TYPE
  0             14              269
  1              1               47
[1] 2 2
[1] FALSE
D521V7, 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
D521V8, binary
                  cls
clus                 0   1
  PNPLA8 MUTATED    15   3
  PNPLA8 WILD-TYPE 302  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PNPLA8 MUTATED     15    3
  PNPLA8 WILD-TYPE  302   45
                               clus
vv                              PNPLA8 MUTATED PNPLA8 WILD-TYPE
  COLON ADENOCARCINOMA                      15              302
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PNPLA8 MUTATED     8   1   0   4
  PNPLA8 WILD-TYPE 249   1  22  17
D521V9, multiclass
    clus
vv   PNPLA8 MUTATED PNPLA8 WILD-TYPE
  R0              8              249
  R1              1                1
  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"
D521V10, 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
D521V11, 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(522) Variable = DOCK5 MUTATION ANALYSIS
D522V1, survival
                 sevent
clus2               0   1
  DOCK5 MUTATED    20   6
  DOCK5 WILD-TYPE 262  67
  DOCK5 MUTATED DOCK5 WILD-TYPE 
             26             329 
  DOCK5 MUTATED DOCK5 WILD-TYPE 
              6              67 
$`DOCK5 MUTATED`
TCGA-A6-5660 TCGA-A6-6780 TCGA-AA-3555 TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 
       29.19        20.12        29.95         0.92        19.04        19.04 
TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3950 TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00N 
       53.00        31.00        24.00        30.02        18.05         4.01 
TCGA-AA-A010 TCGA-AD-5900 TCGA-AD-6964 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6599 
       34.98         0.07        10.88        21.44        58.39         6.77 
TCGA-AZ-6601 TCGA-CA-6717 TCGA-CM-5861 TCGA-CM-6161 TCGA-DM-A0XF TCGA-F4-6856 
      100.01         0.33        15.02        15.02        38.20        19.43 
TCGA-G4-6304 TCGA-G4-6628 
       53.62        52.80 

$`DOCK5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       26.99        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
        0.20        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       62.79        61.41        49.41        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01         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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 
        0.53        35.41       107.67        74.56        65.85        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       13.78        35.80        26.17        91.79        46.75 

  DOCK5 MUTATED DOCK5 WILD-TYPE 
           0.07            0.00 
  DOCK5 MUTATED DOCK5 WILD-TYPE 
         100.01          140.38 
  DOCK5 MUTATED DOCK5 WILD-TYPE 
          20.78           20.19 
[1] "0.1 - 100.0 (20.8)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1"  
D522V2, 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       22       101         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        18         10         40         29       34        13
                 vv
clus              STAGE IVB
  DOCK5 MUTATED           0
  DOCK5 WILD-TYPE         1
D522V3, multiclass
            clus
vv           DOCK5 MUTATED DOCK5 WILD-TYPE
  STAGE I                6              58
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              8             101
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             2              29
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DOCK5 MUTATED     1   5  15   5
  DOCK5 WILD-TYPE   8  63 233  36
D522V4, multiclass
    clus
vv   DOCK5 MUTATED DOCK5 WILD-TYPE
  T1             1               8
  T2             5              63
  T3            15             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
  DOCK5 MUTATED    21   2   3
  DOCK5 WILD-TYPE 199  78  63
D522V5, multiclass
    clus
vv   DOCK5 MUTATED DOCK5 WILD-TYPE
  N0            21             199
  N1             2              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"
D522V6, binary
                 cls
clus                0   1
  DOCK5 MUTATED    20   1
  DOCK5 WILD-TYPE 263  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK5 MUTATED     20    1
  DOCK5 WILD-TYPE  263   47
   clus
vv  DOCK5 MUTATED DOCK5 WILD-TYPE
  0            20             263
  1             1              47
[1] 2 2
[1] FALSE
D522V7, 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
D522V8, binary
                 cls
clus                0   1
  DOCK5 MUTATED    16  10
  DOCK5 WILD-TYPE 301  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK5 MUTATED     16   10
  DOCK5 WILD-TYPE  301   38
                               clus
vv                              DOCK5 MUTATED DOCK5 WILD-TYPE
  COLON ADENOCARCINOMA                     16             301
  COLON MUCINOUS ADENOCARCINOMA            10              38
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DOCK5 MUTATED    18   0   1   1
  DOCK5 WILD-TYPE 239   2  21  20
D522V9, multiclass
    clus
vv   DOCK5 MUTATED DOCK5 WILD-TYPE
  R0            18             239
  R1             0               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"
D522V10, 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
D522V11, 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(523) Variable = CUL2 MUTATION ANALYSIS
D523V1, survival
                sevent
clus2              0   1
  CUL2 MUTATED    12   1
  CUL2 WILD-TYPE 270  72
  CUL2 MUTATED CUL2 WILD-TYPE 
            13            342 
  CUL2 MUTATED CUL2 WILD-TYPE 
             1             72 
$`CUL2 MUTATED`
TCGA-AA-3555 TCGA-AA-3966 TCGA-AA-A010 TCGA-AA-A01Q TCGA-AD-6889 TCGA-AZ-4315 
       29.95         2.01        34.98         1.02        56.55        58.39 
TCGA-AZ-6598 TCGA-CA-6717 TCGA-CM-4743 TCGA-D5-6532 TCGA-D5-6538 TCGA-D5-6928 
       49.41         0.33        23.05        18.25        17.13        11.64 
TCGA-G4-6628 
       52.80 

$`CUL2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        17.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37         4.21         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14         2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 

  CUL2 MUTATED CUL2 WILD-TYPE 
          0.33           0.00 
  CUL2 MUTATED CUL2 WILD-TYPE 
         58.39         140.38 
  CUL2 MUTATED CUL2 WILD-TYPE 
        23.050         20.155 
[1] "0.3 - 58.4 (23.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "3.1"
D523V2, 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       23       101         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        19         10         40         31       35        13
                vv
clus             STAGE IVB
  CUL2 MUTATED           0
  CUL2 WILD-TYPE         1
D523V3, multiclass
            clus
vv           CUL2 MUTATED CUL2 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             8            101
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CUL2 MUTATED     0   1  11   2
  CUL2 WILD-TYPE   9  67 237  39
D523V4, multiclass
    clus
vv   CUL2 MUTATED CUL2 WILD-TYPE
  T1            0              9
  T2            1             67
  T3           11            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
  CUL2 MUTATED    13   0   1
  CUL2 WILD-TYPE 207  80  65
D523V5, multiclass
    clus
vv   CUL2 MUTATED CUL2 WILD-TYPE
  N0           13            207
  N1            0             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"
D523V6, binary
                cls
clus               0   1
  CUL2 MUTATED    12   0
  CUL2 WILD-TYPE 271  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL2 MUTATED     12    0
  CUL2 WILD-TYPE  271   48
   clus
vv  CUL2 MUTATED CUL2 WILD-TYPE
  0           12            271
  1            0             48
[1] 2 2
[1] FALSE
D523V7, 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
D523V8, binary
                cls
clus               0   1
  CUL2 MUTATED    10   4
  CUL2 WILD-TYPE 307  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL2 MUTATED     10    4
  CUL2 WILD-TYPE  307   44
                               clus
vv                              CUL2 MUTATED CUL2 WILD-TYPE
  COLON ADENOCARCINOMA                    10            307
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CUL2 MUTATED     9   0   0   2
  CUL2 WILD-TYPE 248   2  22  19
D523V9, multiclass
    clus
vv   CUL2 MUTATED CUL2 WILD-TYPE
  R0            9            248
  R1            0              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"
D523V10, 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
D523V11, 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(524) Variable = MTMR8 MUTATION ANALYSIS
D524V1, survival
                 sevent
clus2               0   1
  MTMR8 MUTATED     8   3
  MTMR8 WILD-TYPE 274  70
  MTMR8 MUTATED MTMR8 WILD-TYPE 
             11             344 
  MTMR8 MUTATED MTMR8 WILD-TYPE 
              3              70 
$`MTMR8 MUTATED`
TCGA-A6-5665 TCGA-AA-3710 TCGA-AA-3947 TCGA-AA-A01D TCGA-AU-3779 TCGA-AZ-5403 
       22.06        26.99        33.01        10.98        14.50        62.79 
TCGA-AZ-6603 TCGA-CM-5344 TCGA-CM-6163 TCGA-D5-6541 TCGA-G4-6586 
       29.56        22.03        14.04        15.58        35.80 

$`MTMR8 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       34.98        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        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 
       61.41        49.41         6.77        12.10       100.01         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02        12.00        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        16.14         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  MTMR8 MUTATED MTMR8 WILD-TYPE 
          10.98            0.00 
  MTMR8 MUTATED MTMR8 WILD-TYPE 
          62.79          140.38 
  MTMR8 MUTATED MTMR8 WILD-TYPE 
          22.06           20.07 
[1] "11.0 - 62.8 (22.1)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.3"
D524V2, 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       24       104         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        19         10         40         30       35        13
                 vv
clus              STAGE IVB
  MTMR8 MUTATED           0
  MTMR8 WILD-TYPE         1
D524V3, multiclass
            clus
vv           MTMR8 MUTATED MTMR8 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              5             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MTMR8 MUTATED     1   1   8   1
  MTMR8 WILD-TYPE   8  67 240  40
D524V4, multiclass
    clus
vv   MTMR8 MUTATED MTMR8 WILD-TYPE
  T1             1               8
  T2             1              67
  T3             8             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
  MTMR8 MUTATED     8   2   1
  MTMR8 WILD-TYPE 212  78  65
D524V5, multiclass
    clus
vv   MTMR8 MUTATED MTMR8 WILD-TYPE
  N0             8             212
  N1             2              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"
D524V6, binary
                 cls
clus                0   1
  MTMR8 MUTATED     9   0
  MTMR8 WILD-TYPE 274  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTMR8 MUTATED      9    0
  MTMR8 WILD-TYPE  274   48
   clus
vv  MTMR8 MUTATED MTMR8 WILD-TYPE
  0             9             274
  1             0              48
[1] 2 2
[1] FALSE
D524V7, 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
D524V8, binary
                 cls
clus                0   1
  MTMR8 MUTATED     9   2
  MTMR8 WILD-TYPE 308  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTMR8 MUTATED      9    2
  MTMR8 WILD-TYPE  308   46
                               clus
vv                              MTMR8 MUTATED MTMR8 WILD-TYPE
  COLON ADENOCARCINOMA                      9             308
  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 248   2  22  21
D524V9, multiclass
    clus
vv   MTMR8 MUTATED MTMR8 WILD-TYPE
  R0             9             248
  R1             0               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"
D524V10, 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
D524V11, 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(525) Variable = CREBBP MUTATION ANALYSIS
D525V1, survival
                  sevent
clus2                0   1
  CREBBP MUTATED    47  10
  CREBBP WILD-TYPE 235  63
  CREBBP MUTATED CREBBP WILD-TYPE 
              57              298 
  CREBBP MUTATED CREBBP WILD-TYPE 
              10               63 
$`CREBBP MUTATED`
TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3525 TCGA-AA-3662 
       22.06        63.98        13.02         1.02         8.05         6.05 
TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3815 TCGA-AA-3818 
        0.92        19.04        19.04        10.06        33.04         0.99 
TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3966 TCGA-AA-3973 TCGA-AA-A00E 
       53.00        31.00        33.01         2.01        13.05        30.02 
TCGA-AA-A010 TCGA-AA-A029 TCGA-AD-5900 TCGA-AD-6963 TCGA-AU-3779 TCGA-AU-6004 
       34.98        51.98         0.07        27.42        14.50        27.09 
TCGA-AY-5543 TCGA-AZ-4315 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CK-4948 
       15.75        58.39         6.77       100.01         0.33       102.44 
TCGA-CM-4743 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-6164 TCGA-CM-6168 
       23.05        22.03        30.08        15.02        29.03        12.99 
TCGA-CM-6171 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-6535 TCGA-D5-6540 
       14.04        12.03        45.40        12.26        15.12        16.14 
TCGA-D5-6923 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A28H 
       12.43        13.32        12.59         7.50       131.51       117.07 
TCGA-F4-6460 TCGA-F4-6808 TCGA-G4-6293 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6586 
       13.38        33.67       107.67        53.62        55.04        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       26.17        91.79        52.80 

$`CREBBP WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 
       35.01         6.97         1.02        38.99         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       37.05        36.03        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       78.08         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3819 
       36.00         5.03        85.05        26.99        35.05        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3975 TCGA-AA-3976 
       34.03        21.99        16.08        50.99        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J 
       27.02        13.94        38.04        19.00        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        10.88         0.20 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        0.10         1.35        17.56        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         2.01       124.27 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 
       20.02        37.02        25.02        13.02        29.06        22.98 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       16.01         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 
       12.00        14.04        16.04        21.99        14.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       11.01        10.06        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        43.27        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 
       12.49        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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 
       92.75        49.91       140.38        44.32       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K 
        6.12        81.37       119.93        35.97        60.79        98.24 
TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       29.59        16.24        13.25         0.53        35.41        19.43 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       74.56        65.85        44.68        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6626 
       36.00        22.09        13.78        46.75 

  CREBBP MUTATED CREBBP WILD-TYPE 
            0.07             0.00 
  CREBBP MUTATED CREBBP WILD-TYPE 
          131.51           140.38 
  CREBBP MUTATED CREBBP WILD-TYPE 
          22.030           20.155 
[1] "0.1 - 131.5 (22.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.6"
D525V2, 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       19        89         4         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CREBBP MUTATED           4          1          7          3        3
  CREBBP WILD-TYPE        15          9         34         28       32
                  vv
clus               STAGE IVA STAGE IVB
  CREBBP MUTATED           1         0
  CREBBP WILD-TYPE        12         1
D525V3, multiclass
            clus
vv           CREBBP MUTATED CREBBP WILD-TYPE
  STAGE I                 9               55
  STAGE IA                0                1
  STAGE II                6               19
  STAGE IIA              20               89
  STAGE IIB               4                4
  STAGE IIC               0                1
  STAGE III               4               15
  STAGE IIIA              1                9
  STAGE IIIB              7               34
  STAGE IIIC              3               28
  STAGE IV                3               32
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  61 204  34
D525V4, multiclass
    clus
vv   CREBBP MUTATED CREBBP WILD-TYPE
  T1              2                7
  T2              7               61
  T3             44              204
  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  68  58
D525V5, multiclass
    clus
vv   CREBBP MUTATED CREBBP WILD-TYPE
  N0             40              180
  N1             12               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"
D525V6, binary
                  cls
clus                 0   1
  CREBBP MUTATED    49   4
  CREBBP WILD-TYPE 234  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CREBBP MUTATED     49    4
  CREBBP WILD-TYPE  234   44
   clus
vv  CREBBP MUTATED CREBBP WILD-TYPE
  0             49              234
  1              4               44
[1] 2 2
[1] FALSE
D525V7, 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
D525V8, binary
                  cls
clus                 0   1
  CREBBP MUTATED    53   7
  CREBBP WILD-TYPE 264  41
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CREBBP MUTATED     53    7
  CREBBP WILD-TYPE  264   41
                               clus
vv                              CREBBP MUTATED CREBBP WILD-TYPE
  COLON ADENOCARCINOMA                      53              264
  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 214   2  19  17
D525V9, multiclass
    clus
vv   CREBBP MUTATED CREBBP WILD-TYPE
  R0             43              214
  R1              0                2
  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"
D525V10, 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
D525V11, 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(526) Variable = ETF1 MUTATION ANALYSIS
D526V1, survival
                sevent
clus2              0   1
  ETF1 MUTATED     9   1
  ETF1 WILD-TYPE 273  72
  ETF1 MUTATED ETF1 WILD-TYPE 
            10            345 
  ETF1 MUTATED ETF1 WILD-TYPE 
             1             72 
$`ETF1 MUTATED`
TCGA-A6-5665 TCGA-A6-6654 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3966 TCGA-CA-5797 
       22.06        23.87         6.97         0.92         2.01         3.29 
TCGA-CA-6716 TCGA-CM-6168 TCGA-F4-6809 TCGA-G4-6586 
        0.26        12.99        13.25        35.80 

$`ETF1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.06         3.25         0.07         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       16.24        33.67         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 
       45.11        36.72        36.00        22.09        13.78        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  ETF1 MUTATED ETF1 WILD-TYPE 
          0.26           0.00 
  ETF1 MUTATED ETF1 WILD-TYPE 
         35.80         140.38 
  ETF1 MUTATED ETF1 WILD-TYPE 
          9.98          20.98 
[1] "0.3 - 35.8 (10.0)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1"  
D526V2, 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       24       103         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        18         10         40         31       35        12
                vv
clus             STAGE IVB
  ETF1 MUTATED           0
  ETF1 WILD-TYPE         1
D526V3, multiclass
            clus
vv           ETF1 MUTATED ETF1 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             6            103
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  68 238  41
D526V4, multiclass
    clus
vv   ETF1 MUTATED ETF1 WILD-TYPE
  T1            0              9
  T2            0             68
  T3           10            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
  ETF1 MUTATED     7   3   0
  ETF1 WILD-TYPE 213  77  66
D526V5, multiclass
    clus
vv   ETF1 MUTATED ETF1 WILD-TYPE
  N0            7            213
  N1            3             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"
D526V6, binary
                cls
clus               0   1
  ETF1 MUTATED     9   1
  ETF1 WILD-TYPE 274  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  ETF1 MUTATED      9    1
  ETF1 WILD-TYPE  274   47
   clus
vv  ETF1 MUTATED ETF1 WILD-TYPE
  0            9            274
  1            1             47
[1] 2 2
[1] FALSE
D526V7, 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
D526V8, binary
                cls
clus               0   1
  ETF1 MUTATED     9   1
  ETF1 WILD-TYPE 308  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  ETF1 MUTATED      9    1
  ETF1 WILD-TYPE  308   47
                               clus
vv                              ETF1 MUTATED ETF1 WILD-TYPE
  COLON ADENOCARCINOMA                     9            308
  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 250   2  22  20
D526V9, multiclass
    clus
vv   ETF1 MUTATED ETF1 WILD-TYPE
  R0            7            250
  R1            0              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"
D526V10, 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
D526V11, 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(527) Variable = RBM12 MUTATION ANALYSIS
D527V1, survival
                 sevent
clus2               0   1
  RBM12 MUTATED    10   2
  RBM12 WILD-TYPE 272  71
  RBM12 MUTATED RBM12 WILD-TYPE 
             12             343 
  RBM12 MUTATED RBM12 WILD-TYPE 
              2              71 
$`RBM12 MUTATED`
TCGA-A6-6651 TCGA-AA-3529 TCGA-AA-3663 TCGA-AA-3713 TCGA-AA-3949 TCGA-AD-5900 
       21.76         0.00         6.97        19.04        26.01         0.07 
TCGA-AZ-4315 TCGA-AZ-6599 TCGA-CM-6171 TCGA-DM-A28K TCGA-G4-6315 TCGA-G4-6625 
       58.39         6.77        14.04        98.24        36.72        91.79 

$`RBM12 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        24.16        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
       19.07        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79       117.07         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        26.17        46.75 
TCGA-G4-6628 
       52.80 

  RBM12 MUTATED RBM12 WILD-TYPE 
              0               0 
  RBM12 MUTATED RBM12 WILD-TYPE 
          98.24          140.38 
  RBM12 MUTATED RBM12 WILD-TYPE 
          20.40           20.19 
[1] "0.0 - 98.2 (20.4)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.5"
D527V2, 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       24       106         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        19         10         39         30       33        13
                 vv
clus              STAGE IVB
  RBM12 MUTATED           0
  RBM12 WILD-TYPE         1
D527V3, multiclass
            clus
vv           RBM12 MUTATED RBM12 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              3             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             1              30
  STAGE IV               2              33
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RBM12 MUTATED     0   3   9   0
  RBM12 WILD-TYPE   9  65 239  41
D527V4, multiclass
    clus
vv   RBM12 MUTATED RBM12 WILD-TYPE
  T1             0               9
  T2             3              65
  T3             9             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
  RBM12 MUTATED     8   3   1
  RBM12 WILD-TYPE 212  77  65
D527V5, multiclass
    clus
vv   RBM12 MUTATED RBM12 WILD-TYPE
  N0             8             212
  N1             3              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"
D527V6, binary
                 cls
clus                0   1
  RBM12 MUTATED     7   2
  RBM12 WILD-TYPE 276  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM12 MUTATED      7    2
  RBM12 WILD-TYPE  276   46
   clus
vv  RBM12 MUTATED RBM12 WILD-TYPE
  0             7             276
  1             2              46
[1] 2 2
[1] FALSE
D527V7, 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
D527V8, binary
                 cls
clus                0   1
  RBM12 MUTATED     9   3
  RBM12 WILD-TYPE 308  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM12 MUTATED      9    3
  RBM12 WILD-TYPE  308   45
                               clus
vv                              RBM12 MUTATED RBM12 WILD-TYPE
  COLON ADENOCARCINOMA                      9             308
  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 249   2  21  21
D527V9, multiclass
    clus
vv   RBM12 MUTATED RBM12 WILD-TYPE
  R0             8             249
  R1             0               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"
D527V10, 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
D527V11, 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(528) Variable = HORMAD1 MUTATION ANALYSIS
D528V1, survival
                   sevent
clus2                 0   1
  HORMAD1 MUTATED    10   4
  HORMAD1 WILD-TYPE 272  69
  HORMAD1 MUTATED HORMAD1 WILD-TYPE 
               14               341 
  HORMAD1 MUTATED HORMAD1 WILD-TYPE 
                4                69 
$`HORMAD1 MUTATED`
TCGA-A6-6653 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6895 TCGA-AZ-6607 
       24.39        25.02         4.01        34.98         0.72         3.19 
TCGA-CK-4950 TCGA-DM-A1D0 TCGA-DM-A1HA TCGA-DM-A28F TCGA-F4-6570 TCGA-F4-6806 
       40.34       130.65       131.51        35.97         6.18        29.59 
TCGA-G4-6309 TCGA-G4-6628 
       51.75        52.80 

$`HORMAD1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
        1.35        17.56       102.44        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 
       11.38        10.26       119.70        24.43        38.20        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G 
      135.65       139.17         6.12        81.37       119.93        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      117.07        98.24         8.61        13.38        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
        1.55        16.31        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       13.78        35.80        26.17        91.79        46.75 

  HORMAD1 MUTATED HORMAD1 WILD-TYPE 
             0.72              0.00 
  HORMAD1 MUTATED HORMAD1 WILD-TYPE 
           131.51            140.38 
  HORMAD1 MUTATED HORMAD1 WILD-TYPE 
           32.285            19.990 
[1] "0.7 - 131.5 (32.3)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1"  
D528V2, 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       25       107         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HORMAD1 MUTATED           0          1          2          1        1
  HORMAD1 WILD-TYPE        19          9         39         30       34
                   vv
clus                STAGE IVA STAGE IVB
  HORMAD1 MUTATED           0         0
  HORMAD1 WILD-TYPE        13         1
D528V3, multiclass
            clus
vv           HORMAD1 MUTATED HORMAD1 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                2               107
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               1                 9
  STAGE IIIB               2                39
  STAGE IIIC               1                30
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  HORMAD1 MUTATED     0   4   7   3
  HORMAD1 WILD-TYPE   9  64 241  38
D528V4, multiclass
    clus
vv   HORMAD1 MUTATED HORMAD1 WILD-TYPE
  T1               0                 9
  T2               4                64
  T3               7               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
  HORMAD1 MUTATED     8   4   2
  HORMAD1 WILD-TYPE 212  76  64
D528V5, multiclass
    clus
vv   HORMAD1 MUTATED HORMAD1 WILD-TYPE
  N0               8               212
  N1               4                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"
D528V6, binary
                   cls
clus                  0   1
  HORMAD1 MUTATED    11   1
  HORMAD1 WILD-TYPE 272  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HORMAD1 MUTATED     11    1
  HORMAD1 WILD-TYPE  272   47
   clus
vv  HORMAD1 MUTATED HORMAD1 WILD-TYPE
  0              11               272
  1               1                47
[1] 2 2
[1] FALSE
D528V7, binary
                   cls
clus                  0   1
  HORMAD1 MUTATED     6   8
  HORMAD1 WILD-TYPE 164 189
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HORMAD1 MUTATED      6    8
  HORMAD1 WILD-TYPE  164  189
        clus
vv       HORMAD1 MUTATED HORMAD1 WILD-TYPE
  FEMALE               6               164
  MALE                 8               189
[1] 2 2
[1] FALSE
D528V8, binary
                   cls
clus                  0   1
  HORMAD1 MUTATED    13   1
  HORMAD1 WILD-TYPE 304  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HORMAD1 MUTATED     13    1
  HORMAD1 WILD-TYPE  304   47
                               clus
vv                              HORMAD1 MUTATED HORMAD1 WILD-TYPE
  COLON ADENOCARCINOMA                       13               304
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  HORMAD1 MUTATED     6   1   0   0
  HORMAD1 WILD-TYPE 251   1  22  21
D528V9, multiclass
    clus
vv   HORMAD1 MUTATED HORMAD1 WILD-TYPE
  R0               6               251
  R1               1                 1
  R2               0                22
  RX               0                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D528V10, 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
D528V11, 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(529) Variable = LRRC39 MUTATION ANALYSIS
D529V1, survival
                  sevent
clus2                0   1
  LRRC39 MUTATED     7   1
  LRRC39 WILD-TYPE 275  72
  LRRC39 MUTATED LRRC39 WILD-TYPE 
               8              347 
  LRRC39 MUTATED LRRC39 WILD-TYPE 
               1               72 
$`LRRC39 MUTATED`
TCGA-A6-5662 TCGA-AA-3811 TCGA-AA-3977 TCGA-AU-6004 TCGA-CA-6717 TCGA-CM-4743 
       23.61        10.06        25.02        27.09         0.33        23.05 
TCGA-D5-6540 TCGA-G4-6628 
       16.14        52.80 

$`LRRC39 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        33.53        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.20        14.50        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       13.78        35.80        26.17        91.79        46.75 

  LRRC39 MUTATED LRRC39 WILD-TYPE 
            0.33             0.00 
  LRRC39 MUTATED LRRC39 WILD-TYPE 
           52.80           140.38 
  LRRC39 MUTATED LRRC39 WILD-TYPE 
           23.33            20.12 
[1] "0.3 - 52.8 (23.3)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.5"
D529V2, 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       25       107         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LRRC39 MUTATED           1          0          0          0        0
  LRRC39 WILD-TYPE        18         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  LRRC39 MUTATED           1         0
  LRRC39 WILD-TYPE        12         1
D529V3, multiclass
            clus
vv           LRRC39 MUTATED LRRC39 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               2              107
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  64 244  41
D529V4, multiclass
    clus
vv   LRRC39 MUTATED LRRC39 WILD-TYPE
  T1              0                9
  T2              4               64
  T3              4              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
  LRRC39 MUTATED     6   0   2
  LRRC39 WILD-TYPE 214  80  64
D529V5, multiclass
    clus
vv   LRRC39 MUTATED LRRC39 WILD-TYPE
  N0              6              214
  N1              0               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"
D529V6, binary
                  cls
clus                 0   1
  LRRC39 MUTATED     6   1
  LRRC39 WILD-TYPE 277  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRC39 MUTATED      6    1
  LRRC39 WILD-TYPE  277   47
   clus
vv  LRRC39 MUTATED LRRC39 WILD-TYPE
  0              6              277
  1              1               47
[1] 2 2
[1] FALSE
D529V7, 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
D529V8, binary
                  cls
clus                 0   1
  LRRC39 MUTATED     6   2
  LRRC39 WILD-TYPE 311  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRC39 MUTATED      6    2
  LRRC39 WILD-TYPE  311   46
                               clus
vv                              LRRC39 MUTATED LRRC39 WILD-TYPE
  COLON ADENOCARCINOMA                       6              311
  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 252   2  22  20
D529V9, multiclass
    clus
vv   LRRC39 MUTATED LRRC39 WILD-TYPE
  R0              5              252
  R1              0                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"
D529V10, 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
D529V11, 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(530) Variable = PLK2 MUTATION ANALYSIS
D530V1, survival
                sevent
clus2              0   1
  PLK2 MUTATED     3   2
  PLK2 WILD-TYPE 279  71
  PLK2 MUTATED PLK2 WILD-TYPE 
             5            350 
  PLK2 MUTATED PLK2 WILD-TYPE 
             2             71 
$`PLK2 MUTATED`
TCGA-AA-3516 TCGA-D5-6541 TCGA-DM-A1HB TCGA-DM-A28C TCGA-G4-6588 
       13.02        15.58       135.65        81.37        26.17 

$`PLK2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        1.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      131.51       139.17         6.12       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  PLK2 MUTATED PLK2 WILD-TYPE 
         13.02           0.00 
  PLK2 MUTATED PLK2 WILD-TYPE 
        135.65         140.38 
  PLK2 MUTATED PLK2 WILD-TYPE 
        26.170         20.155 
[1] "13.0 - 135.7 (26.2)" "0.0 - 140.4 (20.2)" 
[1] "hr=" "1"  
D530V2, 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       25       105         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        18         10         40         31       35        13
                vv
clus             STAGE IVB
  PLK2 MUTATED           0
  PLK2 WILD-TYPE         1
D530V3, multiclass
            clus
vv           PLK2 MUTATED PLK2 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             4            105
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PLK2 MUTATED     0   0   6   0
  PLK2 WILD-TYPE   9  68 242  41
D530V4, multiclass
    clus
vv   PLK2 MUTATED PLK2 WILD-TYPE
  T1            0              9
  T2            0             68
  T3            6            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
  PLK2 MUTATED     4   1   1
  PLK2 WILD-TYPE 216  79  65
D530V5, multiclass
    clus
vv   PLK2 MUTATED PLK2 WILD-TYPE
  N0            4            216
  N1            1             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"
D530V6, binary
                cls
clus               0   1
  PLK2 MUTATED     6   0
  PLK2 WILD-TYPE 277  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLK2 MUTATED      6    0
  PLK2 WILD-TYPE  277   48
   clus
vv  PLK2 MUTATED PLK2 WILD-TYPE
  0            6            277
  1            0             48
[1] 2 2
[1] FALSE
D530V7, 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
D530V8, binary
                cls
clus               0   1
  PLK2 MUTATED     5   1
  PLK2 WILD-TYPE 312  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLK2 MUTATED      5    1
  PLK2 WILD-TYPE  312   47
                               clus
vv                              PLK2 MUTATED PLK2 WILD-TYPE
  COLON ADENOCARCINOMA                     5            312
  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 254   2  22  21
D530V9, multiclass
    clus
vv   PLK2 MUTATED PLK2 WILD-TYPE
  R0            3            254
  R1            0              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"
D530V10, 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
D530V11, 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(531) Variable = ERGIC1 MUTATION ANALYSIS
D531V1, survival
                  sevent
clus2                0   1
  ERGIC1 MUTATED     4   0
  ERGIC1 WILD-TYPE 278  73
  ERGIC1 MUTATED ERGIC1 WILD-TYPE 
               4              351 
  ERGIC1 MUTATED ERGIC1 WILD-TYPE 
               0               73 
$`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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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-6678 TCGA-CM-6679 
       14.04        11.01        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        16.14         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  ERGIC1 MUTATED ERGIC1 WILD-TYPE 
           11.08             0.00 
  ERGIC1 MUTATED ERGIC1 WILD-TYPE 
           29.19           140.38 
  ERGIC1 MUTATED ERGIC1 WILD-TYPE 
          14.315           20.280 
[1] "11.1 - 29.2 (14.3)" "0.0 - 140.4 (20.3)"
[1] "hr="     "3300000"
D531V2, 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       25       107         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ERGIC1 MUTATED           0          0          0          1        0
  ERGIC1 WILD-TYPE        19         10         41         30       35
                  vv
clus               STAGE IVA STAGE IVB
  ERGIC1 MUTATED           0         1
  ERGIC1 WILD-TYPE        13         0
D531V3, multiclass
            clus
vv           ERGIC1 MUTATED ERGIC1 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               2              107
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  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  68 244  41
D531V4, multiclass
    clus
vv   ERGIC1 MUTATED ERGIC1 WILD-TYPE
  T1              0                9
  T2              0               68
  T3              4              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
  ERGIC1 MUTATED     2   0   2
  ERGIC1 WILD-TYPE 218  80  64
D531V5, multiclass
    clus
vv   ERGIC1 MUTATED ERGIC1 WILD-TYPE
  N0              2              218
  N1              0               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"
D531V6, binary
                  cls
clus                 0   1
  ERGIC1 MUTATED     3   1
  ERGIC1 WILD-TYPE 280  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ERGIC1 MUTATED      3    1
  ERGIC1 WILD-TYPE  280   47
   clus
vv  ERGIC1 MUTATED ERGIC1 WILD-TYPE
  0              3              280
  1              1               47
[1] 2 2
[1] FALSE
D531V7, 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
D531V8, binary
                  cls
clus                 0   1
  ERGIC1 MUTATED     4   0
  ERGIC1 WILD-TYPE 313  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ERGIC1 MUTATED      4    0
  ERGIC1 WILD-TYPE  313   48
                               clus
vv                              ERGIC1 MUTATED ERGIC1 WILD-TYPE
  COLON ADENOCARCINOMA                       4              313
  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 254   2  22  21
D531V9, multiclass
    clus
vv   ERGIC1 MUTATED ERGIC1 WILD-TYPE
  R0              3              254
  R1              0                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"
D531V10, 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
D531V11, 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(532) Variable = OLR1 MUTATION ANALYSIS
D532V1, survival
                sevent
clus2              0   1
  OLR1 MUTATED     8   1
  OLR1 WILD-TYPE 274  72
  OLR1 MUTATED OLR1 WILD-TYPE 
             9            346 
  OLR1 MUTATED OLR1 WILD-TYPE 
             1             72 
$`OLR1 MUTATED`
TCGA-A6-5665 TCGA-A6-6649 TCGA-AA-A01R TCGA-AD-5900 TCGA-CM-4752 TCGA-D5-5539 
       22.06        24.16        35.01         0.07        13.02        19.59 
TCGA-DM-A1D7 TCGA-DM-A1HA TCGA-G4-6307 
       13.32       131.51        55.04 

$`OLR1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.18        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-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-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 
      107.67        74.56        65.85        53.62        44.68        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  OLR1 MUTATED OLR1 WILD-TYPE 
          0.07           0.00 
  OLR1 MUTATED OLR1 WILD-TYPE 
        131.51         140.38 
  OLR1 MUTATED OLR1 WILD-TYPE 
        22.060         20.155 
[1] "0.1 - 131.5 (22.1)" "0.0 - 140.4 (20.2)"
[1] "hr=" "2.3"
D532V2, 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       25       106         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        18          9         39         30       35        13
                vv
clus             STAGE IVB
  OLR1 MUTATED           0
  OLR1 WILD-TYPE         1
D532V3, multiclass
            clus
vv           OLR1 MUTATED OLR1 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             3            106
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            1              9
  STAGE IIIB            2             39
  STAGE IIIC            1             30
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  OLR1 MUTATED     0   1   8   0
  OLR1 WILD-TYPE   9  67 240  41
D532V4, multiclass
    clus
vv   OLR1 MUTATED OLR1 WILD-TYPE
  T1            0              9
  T2            1             67
  T3            8            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
  OLR1 MUTATED     4   3   2
  OLR1 WILD-TYPE 216  77  64
D532V5, multiclass
    clus
vv   OLR1 MUTATED OLR1 WILD-TYPE
  N0            4            216
  N1            3             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"
D532V6, binary
                cls
clus               0   1
  OLR1 MUTATED     8   0
  OLR1 WILD-TYPE 275  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  OLR1 MUTATED      8    0
  OLR1 WILD-TYPE  275   48
   clus
vv  OLR1 MUTATED OLR1 WILD-TYPE
  0            8            275
  1            0             48
[1] 2 2
[1] FALSE
D532V7, 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
D532V8, binary
                cls
clus               0   1
  OLR1 MUTATED     6   3
  OLR1 WILD-TYPE 311  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  OLR1 MUTATED      6    3
  OLR1 WILD-TYPE  311   45
                               clus
vv                              OLR1 MUTATED OLR1 WILD-TYPE
  COLON ADENOCARCINOMA                     6            311
  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 251   2  22  21
D532V9, multiclass
    clus
vv   OLR1 MUTATED OLR1 WILD-TYPE
  R0            6            251
  R1            0              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"
D532V10, 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
D532V11, 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(533) Variable = OR5B2 MUTATION ANALYSIS
D533V1, survival
                 sevent
clus2               0   1
  OR5B2 MUTATED     9   2
  OR5B2 WILD-TYPE 273  71
  OR5B2 MUTATED OR5B2 WILD-TYPE 
             11             344 
  OR5B2 MUTATED OR5B2 WILD-TYPE 
              2              71 
$`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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         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         1.51        12.00        11.38        10.26        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  OR5B2 MUTATED OR5B2 WILD-TYPE 
            0.2             0.0 
  OR5B2 MUTATED OR5B2 WILD-TYPE 
         119.70          140.38 
  OR5B2 MUTATED OR5B2 WILD-TYPE 
          21.99           20.07 
[1] "0.2 - 119.7 (22.0)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.4"
D533V2, 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       24       106         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        18         10         39         30       35        13
                 vv
clus              STAGE IVB
  OR5B2 MUTATED           0
  OR5B2 WILD-TYPE         1
D533V3, multiclass
            clus
vv           OR5B2 MUTATED OR5B2 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              3             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR5B2 MUTATED     0   3   7   2
  OR5B2 WILD-TYPE   9  65 241  39
D533V4, multiclass
    clus
vv   OR5B2 MUTATED OR5B2 WILD-TYPE
  T1             0               9
  T2             3              65
  T3             7             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
  OR5B2 MUTATED     8   2   2
  OR5B2 WILD-TYPE 212  78  64
D533V5, multiclass
    clus
vv   OR5B2 MUTATED OR5B2 WILD-TYPE
  N0             8             212
  N1             2              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"
D533V6, binary
                 cls
clus                0   1
  OR5B2 MUTATED     8   0
  OR5B2 WILD-TYPE 275  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5B2 MUTATED      8    0
  OR5B2 WILD-TYPE  275   48
   clus
vv  OR5B2 MUTATED OR5B2 WILD-TYPE
  0             8             275
  1             0              48
[1] 2 2
[1] FALSE
D533V7, 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
D533V8, binary
                 cls
clus                0   1
  OR5B2 MUTATED    11   1
  OR5B2 WILD-TYPE 306  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5B2 MUTATED     11    1
  OR5B2 WILD-TYPE  306   47
                               clus
vv                              OR5B2 MUTATED OR5B2 WILD-TYPE
  COLON ADENOCARCINOMA                     11             306
  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 248   2  22  21
D533V9, multiclass
    clus
vv   OR5B2 MUTATED OR5B2 WILD-TYPE
  R0             9             248
  R1             0               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"
D533V10, 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
D533V11, 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(534) Variable = GCNT2 MUTATION ANALYSIS
D534V1, survival
                 sevent
clus2               0   1
  GCNT2 MUTATED    19   2
  GCNT2 WILD-TYPE 263  71
  GCNT2 MUTATED GCNT2 WILD-TYPE 
             21             334 
  GCNT2 MUTATED GCNT2 WILD-TYPE 
              2              71 
$`GCNT2 MUTATED`
TCGA-A6-2674 TCGA-A6-5659 TCGA-AA-3510 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3977 
       43.76        30.44        63.98        31.00        33.01        25.02 
TCGA-AA-A00D TCGA-AA-A010 TCGA-AA-A03J TCGA-AD-6889 TCGA-AD-6964 TCGA-AZ-4315 
       19.00        34.98        40.96        56.55        10.88        58.39 
TCGA-CA-6715 TCGA-CK-4950 TCGA-D5-5538 TCGA-D5-6538 TCGA-D5-6927 TCGA-DM-A28F 
        0.07        40.34        12.26        17.13         9.44        35.97 
TCGA-DM-A28K TCGA-G4-6586 TCGA-G4-6588 
       98.24        35.80        26.17 

$`GCNT2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       27.02        29.98        18.05         2.01        12.99        24.00 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       39.98        18.05         0.07        21.37         4.21         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
        0.72         5.79        22.42        27.42         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       102.44        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 
        6.12        81.37       119.93        60.79       117.07         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        91.79        46.75        52.80 

  GCNT2 MUTATED GCNT2 WILD-TYPE 
           0.07            0.00 
  GCNT2 MUTATED GCNT2 WILD-TYPE 
          98.24          140.38 
  GCNT2 MUTATED GCNT2 WILD-TYPE 
         33.010          19.825 
[1] "0.1 - 98.2 (33.0)"  "0.0 - 140.4 (19.8)"
[1] "hr=" "2.9"
D534V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GCNT2 MUTATED         4        0        1         7         2         0
  GCNT2 WILD-TYPE      60        1       24       102         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GCNT2 MUTATED           0          1          4          0        1         0
  GCNT2 WILD-TYPE        19          9         37         31       34        13
                 vv
clus              STAGE IVB
  GCNT2 MUTATED           0
  GCNT2 WILD-TYPE         1
D534V3, multiclass
            clus
vv           GCNT2 MUTATED GCNT2 WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              7             102
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             4              37
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GCNT2 MUTATED     1   4  14   3
  GCNT2 WILD-TYPE   8  64 234  38
D534V4, multiclass
    clus
vv   GCNT2 MUTATED GCNT2 WILD-TYPE
  T1             1               8
  T2             4              64
  T3            14             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
  GCNT2 MUTATED    15   4   3
  GCNT2 WILD-TYPE 205  76  63
D534V5, multiclass
    clus
vv   GCNT2 MUTATED GCNT2 WILD-TYPE
  N0            15             205
  N1             4              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"
D534V6, binary
                 cls
clus                0   1
  GCNT2 MUTATED    19   1
  GCNT2 WILD-TYPE 264  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GCNT2 MUTATED     19    1
  GCNT2 WILD-TYPE  264   47
   clus
vv  GCNT2 MUTATED GCNT2 WILD-TYPE
  0            19             264
  1             1              47
[1] 2 2
[1] FALSE
D534V7, binary
                 cls
clus                0   1
  GCNT2 MUTATED    10  12
  GCNT2 WILD-TYPE 160 185
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GCNT2 MUTATED     10   12
  GCNT2 WILD-TYPE  160  185
        clus
vv       GCNT2 MUTATED GCNT2 WILD-TYPE
  FEMALE            10             160
  MALE              12             185
[1] 2 2
[1] FALSE
D534V8, binary
                 cls
clus                0   1
  GCNT2 MUTATED    18   4
  GCNT2 WILD-TYPE 299  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GCNT2 MUTATED     18    4
  GCNT2 WILD-TYPE  299   44
                               clus
vv                              GCNT2 MUTATED GCNT2 WILD-TYPE
  COLON ADENOCARCINOMA                     18             299
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  GCNT2 MUTATED    15   1   0   1
  GCNT2 WILD-TYPE 242   1  22  20
D534V9, multiclass
    clus
vv   GCNT2 MUTATED GCNT2 WILD-TYPE
  R0            15             242
  R1             1               1
  R2             0              22
  RX             1              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D534V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GCNT2 MUTATED                                  0     2
  GCNT2 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GCNT2 MUTATED                           1    11
  GCNT2 WILD-TYPE                        18   165
D534V11, multiclass
                                  clus
vv                                 GCNT2 MUTATED GCNT2 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(535) Variable = SKIV2L MUTATION ANALYSIS
D535V1, survival
                  sevent
clus2                0   1
  SKIV2L MUTATED     8   4
  SKIV2L WILD-TYPE 274  69
  SKIV2L MUTATED SKIV2L WILD-TYPE 
              12              343 
  SKIV2L MUTATED SKIV2L WILD-TYPE 
               4               69 
$`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       107.67        65.85 

$`SKIV2L WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.12        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        6.97        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32        12.59       140.38        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6304 
       13.25         0.53        35.41        19.43        74.56        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  SKIV2L MUTATED SKIV2L WILD-TYPE 
            1.02             0.00 
  SKIV2L MUTATED SKIV2L WILD-TYPE 
          107.67           140.38 
  SKIV2L MUTATED SKIV2L WILD-TYPE 
           23.34            20.19 
[1] "1.0 - 107.7 (23.3)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.3"
D535V2, 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       23       108         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SKIV2L MUTATED           1          0          2          2        2
  SKIV2L WILD-TYPE        18         10         39         29       33
                  vv
clus               STAGE IVA STAGE IVB
  SKIV2L MUTATED           0         0
  SKIV2L WILD-TYPE        13         1
D535V3, multiclass
            clus
vv           SKIV2L MUTATED SKIV2L WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               1              108
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              2               29
  STAGE IV                2               33
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SKIV2L MUTATED     0   1   8   3
  SKIV2L WILD-TYPE   9  67 240  38
D535V4, multiclass
    clus
vv   SKIV2L MUTATED SKIV2L WILD-TYPE
  T1              0                9
  T2              1               67
  T3              8              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
  SKIV2L MUTATED     5   6   1
  SKIV2L WILD-TYPE 215  74  65
D535V5, multiclass
    clus
vv   SKIV2L MUTATED SKIV2L WILD-TYPE
  N0              5              215
  N1              6               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"
D535V6, binary
                  cls
clus                 0   1
  SKIV2L MUTATED     9   2
  SKIV2L WILD-TYPE 274  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SKIV2L MUTATED      9    2
  SKIV2L WILD-TYPE  274   46
   clus
vv  SKIV2L MUTATED SKIV2L WILD-TYPE
  0              9              274
  1              2               46
[1] 2 2
[1] FALSE
D535V7, 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
D535V8, binary
                  cls
clus                 0   1
  SKIV2L MUTATED    10   2
  SKIV2L WILD-TYPE 307  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SKIV2L MUTATED     10    2
  SKIV2L WILD-TYPE  307   46
                               clus
vv                              SKIV2L MUTATED SKIV2L WILD-TYPE
  COLON ADENOCARCINOMA                      10              307
  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 247   2  22  21
D535V9, multiclass
    clus
vv   SKIV2L MUTATED SKIV2L WILD-TYPE
  R0             10              247
  R1              0                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"
D535V10, 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
D535V11, 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(536) Variable = LAMC1 MUTATION ANALYSIS
D536V1, survival
                 sevent
clus2               0   1
  LAMC1 MUTATED    16   5
  LAMC1 WILD-TYPE 266  68
  LAMC1 MUTATED LAMC1 WILD-TYPE 
             21             334 
  LAMC1 MUTATED LAMC1 WILD-TYPE 
              5              68 
$`LAMC1 MUTATED`
TCGA-A6-4105 TCGA-A6-5660 TCGA-AA-3510 TCGA-AA-3715 TCGA-AA-3864 TCGA-AA-3977 
       14.53        29.19        63.98        19.04        53.00        25.02 
TCGA-AA-A00E TCGA-AA-A00U TCGA-AA-A010 TCGA-AA-A017 TCGA-AY-6197 TCGA-AZ-4315 
       30.02        17.03        34.98        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 
        1.51        13.32         6.18 

$`LAMC1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        19.00        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00W 
       38.04         4.01        27.02        42.02         0.99        14.99 
TCGA-AA-A00Z TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       21.99        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 
       61.41        49.41         6.77        12.10       100.01         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 
       16.01        15.02         5.03        15.02        17.03        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 
       12.49        16.14        15.58         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-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        49.91        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  LAMC1 MUTATED LAMC1 WILD-TYPE 
           1.51            0.00 
  LAMC1 MUTATED LAMC1 WILD-TYPE 
          63.98          140.38 
  LAMC1 MUTATED LAMC1 WILD-TYPE 
         21.440          20.155 
[1] "1.5 - 64.0 (21.4)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D536V2, 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       22        99         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        19         10         38         30       35        13
                 vv
clus              STAGE IVB
  LAMC1 MUTATED           0
  LAMC1 WILD-TYPE         1
D536V3, multiclass
            clus
vv           LAMC1 MUTATED LAMC1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA             10              99
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             3              38
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LAMC1 MUTATED     0   3  17   1
  LAMC1 WILD-TYPE   9  65 231  40
D536V4, multiclass
    clus
vv   LAMC1 MUTATED LAMC1 WILD-TYPE
  T1             0               9
  T2             3              65
  T3            17             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
  LAMC1 MUTATED    16   4   1
  LAMC1 WILD-TYPE 204  76  65
D536V5, multiclass
    clus
vv   LAMC1 MUTATED LAMC1 WILD-TYPE
  N0            16             204
  N1             4              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"
D536V6, binary
                 cls
clus                0   1
  LAMC1 MUTATED    18   0
  LAMC1 WILD-TYPE 265  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LAMC1 MUTATED     18    0
  LAMC1 WILD-TYPE  265   48
   clus
vv  LAMC1 MUTATED LAMC1 WILD-TYPE
  0            18             265
  1             0              48
[1] 2 2
[1] FALSE
D536V7, 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
D536V8, binary
                 cls
clus                0   1
  LAMC1 MUTATED    19   2
  LAMC1 WILD-TYPE 298  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LAMC1 MUTATED     19    2
  LAMC1 WILD-TYPE  298   46
                               clus
vv                              LAMC1 MUTATED LAMC1 WILD-TYPE
  COLON ADENOCARCINOMA                     19             298
  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 241   2  22  21
D536V9, multiclass
    clus
vv   LAMC1 MUTATED LAMC1 WILD-TYPE
  R0            16             241
  R1             0               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"
D536V10, 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
D536V11, 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(537) Variable = THAP9 MUTATION ANALYSIS
D537V1, survival
                 sevent
clus2               0   1
  THAP9 MUTATED     9   3
  THAP9 WILD-TYPE 273  70
  THAP9 MUTATED THAP9 WILD-TYPE 
             12             343 
  THAP9 MUTATED THAP9 WILD-TYPE 
              3              70 
$`THAP9 MUTATED`
TCGA-A6-5666 TCGA-AA-3713 TCGA-AA-3848 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-A00N 
       32.71        19.04        10.06        31.00        33.01         4.01 
TCGA-AA-A010 TCGA-AA-A01Q TCGA-AY-6386 TCGA-AZ-5407 TCGA-D5-6929 TCGA-DM-A1DA 
       34.98         1.02        17.82        61.41        13.41         7.50 

$`THAP9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       27.02        29.98        18.05         2.01        12.99        24.00 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
      140.38        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  THAP9 MUTATED THAP9 WILD-TYPE 
           1.02            0.00 
  THAP9 MUTATED THAP9 WILD-TYPE 
          61.41          140.38 
  THAP9 MUTATED THAP9 WILD-TYPE 
          18.43           20.28 
[1] "1.0 - 61.4 (18.4)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.5"
D537V2, 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       24       109         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        19         10         40         29       33        13
                 vv
clus              STAGE IVB
  THAP9 MUTATED           0
  THAP9 WILD-TYPE         1
D537V3, multiclass
            clus
vv           THAP9 MUTATED THAP9 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              0             109
  STAGE IIB              3               5
  STAGE IIC              1               0
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             2              29
  STAGE IV               2              33
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  THAP9 MUTATED     2   0   6   4
  THAP9 WILD-TYPE   7  68 242  37
D537V4, multiclass
    clus
vv   THAP9 MUTATED THAP9 WILD-TYPE
  T1             2               7
  T2             0              68
  T3             6             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
  THAP9 MUTATED     8   2   2
  THAP9 WILD-TYPE 212  78  64
D537V5, multiclass
    clus
vv   THAP9 MUTATED THAP9 WILD-TYPE
  N0             8             212
  N1             2              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"
D537V6, binary
                 cls
clus                0   1
  THAP9 MUTATED    10   2
  THAP9 WILD-TYPE 273  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THAP9 MUTATED     10    2
  THAP9 WILD-TYPE  273   46
   clus
vv  THAP9 MUTATED THAP9 WILD-TYPE
  0            10             273
  1             2              46
[1] 2 2
[1] FALSE
D537V7, 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
D537V8, binary
                 cls
clus                0   1
  THAP9 MUTATED     9   3
  THAP9 WILD-TYPE 308  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THAP9 MUTATED      9    3
  THAP9 WILD-TYPE  308   45
                               clus
vv                              THAP9 MUTATED THAP9 WILD-TYPE
  COLON ADENOCARCINOMA                      9             308
  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 249   2  21  21
D537V9, multiclass
    clus
vv   THAP9 MUTATED THAP9 WILD-TYPE
  R0             8             249
  R1             0               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"
D537V10, 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
D537V11, 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(538) Variable = LPCAT3 MUTATION ANALYSIS
D538V1, survival
                  sevent
clus2                0   1
  LPCAT3 MUTATED     4   1
  LPCAT3 WILD-TYPE 278  72
  LPCAT3 MUTATED LPCAT3 WILD-TYPE 
               5              350 
  LPCAT3 MUTATED LPCAT3 WILD-TYPE 
               1               72 
$`LPCAT3 MUTATED`
TCGA-AA-3542 TCGA-AA-A01Q TCGA-AZ-6598 TCGA-D5-6536 TCGA-G4-6628 
       12.99         1.02        49.41        17.85        52.80 

$`LPCAT3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13        83.80        22.36        62.79        61.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 
       20.19        18.25         1.32        43.27        15.12         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 
       91.79        46.75 

  LPCAT3 MUTATED LPCAT3 WILD-TYPE 
            1.02             0.00 
  LPCAT3 MUTATED LPCAT3 WILD-TYPE 
           52.80           140.38 
  LPCAT3 MUTATED LPCAT3 WILD-TYPE 
          17.850           20.235 
[1] "1.0 - 52.8 (17.9)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D538V2, 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       23       108         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LPCAT3 MUTATED           0          0          0          1        0
  LPCAT3 WILD-TYPE        19         10         41         30       35
                  vv
clus               STAGE IVA STAGE IVB
  LPCAT3 MUTATED           0         0
  LPCAT3 WILD-TYPE        13         1
D538V3, multiclass
            clus
vv           LPCAT3 MUTATED LPCAT3 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               1              108
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  LPCAT3 MUTATED     0   1   4   0
  LPCAT3 WILD-TYPE   9  67 244  41
D538V4, multiclass
    clus
vv   LPCAT3 MUTATED LPCAT3 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              4              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
  LPCAT3 MUTATED     4   0   1
  LPCAT3 WILD-TYPE 216  80  65
D538V5, multiclass
    clus
vv   LPCAT3 MUTATED LPCAT3 WILD-TYPE
  N0              4              216
  N1              0               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"
D538V6, binary
                  cls
clus                 0   1
  LPCAT3 MUTATED     4   0
  LPCAT3 WILD-TYPE 279  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LPCAT3 MUTATED      4    0
  LPCAT3 WILD-TYPE  279   48
   clus
vv  LPCAT3 MUTATED LPCAT3 WILD-TYPE
  0              4              279
  1              0               48
[1] 2 2
[1] FALSE
D538V7, 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
D538V8, binary
                  cls
clus                 0   1
  LPCAT3 MUTATED     5   0
  LPCAT3 WILD-TYPE 312  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LPCAT3 MUTATED      5    0
  LPCAT3 WILD-TYPE  312   48
                               clus
vv                              LPCAT3 MUTATED LPCAT3 WILD-TYPE
  COLON ADENOCARCINOMA                       5              312
  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 253   2  22  21
D538V9, multiclass
    clus
vv   LPCAT3 MUTATED LPCAT3 WILD-TYPE
  R0              4              253
  R1              0                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"
D538V10, 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
D538V11, 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(539) Variable = SLC22A9 MUTATION ANALYSIS
D539V1, survival
                   sevent
clus2                 0   1
  SLC22A9 MUTATED     8   0
  SLC22A9 WILD-TYPE 274  73
  SLC22A9 MUTATED SLC22A9 WILD-TYPE 
                8               347 
  SLC22A9 MUTATED SLC22A9 WILD-TYPE 
                0                73 
$`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         0.33 
TCGA-CK-5913 TCGA-D5-6541 
       51.32        15.58 

$`SLC22A9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        15.75        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  SLC22A9 MUTATED SLC22A9 WILD-TYPE 
              0.2               0.0 
  SLC22A9 MUTATED SLC22A9 WILD-TYPE 
            51.32            140.38 
  SLC22A9 MUTATED SLC22A9 WILD-TYPE 
            17.62             20.28 
[1] "0.2 - 51.3 (17.6)"  "0.0 - 140.4 (20.3)"
[1] "hr="     "9200000"
D539V2, 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       24       105         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC22A9 MUTATED           0          0          0          2        0
  SLC22A9 WILD-TYPE        19         10         41         29       35
                   vv
clus                STAGE IVA STAGE IVB
  SLC22A9 MUTATED           1         0
  SLC22A9 WILD-TYPE        12         1
D539V3, multiclass
            clus
vv           SLC22A9 MUTATED SLC22A9 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                4               105
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               2                29
  STAGE IV                 0                35
  STAGE IVA                1                12
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 242  39
D539V4, multiclass
    clus
vv   SLC22A9 MUTATED SLC22A9 WILD-TYPE
  T1               0                 9
  T2               1                67
  T3               6               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
  SLC22A9 MUTATED     6   2   1
  SLC22A9 WILD-TYPE 214  78  65
D539V5, multiclass
    clus
vv   SLC22A9 MUTATED SLC22A9 WILD-TYPE
  N0               6               214
  N1               2                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
  SLC22A9 MUTATED     4   1
  SLC22A9 WILD-TYPE 279  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC22A9 MUTATED      4    1
  SLC22A9 WILD-TYPE  279   47
   clus
vv  SLC22A9 MUTATED SLC22A9 WILD-TYPE
  0               4               279
  1               1                47
[1] 2 2
[1] FALSE
D539V7, 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
D539V8, binary
                   cls
clus                  0   1
  SLC22A9 MUTATED     6   3
  SLC22A9 WILD-TYPE 311  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC22A9 MUTATED      6    3
  SLC22A9 WILD-TYPE  311   45
                               clus
vv                              SLC22A9 MUTATED SLC22A9 WILD-TYPE
  COLON ADENOCARCINOMA                        6               311
  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 252   2  22  19
D539V9, multiclass
    clus
vv   SLC22A9 MUTATED SLC22A9 WILD-TYPE
  R0               5               252
  R1               0                 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"
D539V10, 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
D539V11, 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(540) Variable = RAB38 MUTATION ANALYSIS
D540V1, survival
                 sevent
clus2               0   1
  RAB38 MUTATED     2   3
  RAB38 WILD-TYPE 280  70
  RAB38 MUTATED RAB38 WILD-TYPE 
              5             350 
  RAB38 MUTATED RAB38 WILD-TYPE 
              3              70 
$`RAB38 MUTATED`
TCGA-A6-2676 TCGA-A6-5665 TCGA-AD-6890 TCGA-AZ-6598 TCGA-CM-5862 
       42.90        22.06         0.79        49.41         5.03 

$`RAB38 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  RAB38 MUTATED RAB38 WILD-TYPE 
           0.79            0.00 
  RAB38 MUTATED RAB38 WILD-TYPE 
          49.41          140.38 
  RAB38 MUTATED RAB38 WILD-TYPE 
         22.060          20.155 
[1] "0.8 - 49.4 (22.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "3.1"
D540V2, 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       24       108         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        19         10         41         31       35        12
                 vv
clus              STAGE IVB
  RAB38 MUTATED           0
  RAB38 WILD-TYPE         1
D540V3, multiclass
            clus
vv           RAB38 MUTATED RAB38 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              1             108
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  68 245  40
D540V4, multiclass
    clus
vv   RAB38 MUTATED RAB38 WILD-TYPE
  T1             1               8
  T2             0              68
  T3             3             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
  RAB38 MUTATED     4   1   0
  RAB38 WILD-TYPE 216  79  66
D540V5, multiclass
    clus
vv   RAB38 MUTATED RAB38 WILD-TYPE
  N0             4             216
  N1             1              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"
D540V6, binary
                 cls
clus                0   1
  RAB38 MUTATED     2   1
  RAB38 WILD-TYPE 281  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB38 MUTATED      2    1
  RAB38 WILD-TYPE  281   47
   clus
vv  RAB38 MUTATED RAB38 WILD-TYPE
  0             2             281
  1             1              47
[1] 2 2
[1] FALSE
D540V7, 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
D540V8, binary
                 cls
clus                0   1
  RAB38 MUTATED     5   0
  RAB38 WILD-TYPE 312  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB38 MUTATED      5    0
  RAB38 WILD-TYPE  312   48
                               clus
vv                              RAB38 MUTATED RAB38 WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  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 254   2  22  21
D540V9, multiclass
    clus
vv   RAB38 MUTATED RAB38 WILD-TYPE
  R0             3             254
  R1             0               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"
D540V10, 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
D540V11, 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(541) Variable = ENPEP MUTATION ANALYSIS
D541V1, survival
                 sevent
clus2               0   1
  ENPEP MUTATED    13   8
  ENPEP WILD-TYPE 269  65
  ENPEP MUTATED ENPEP WILD-TYPE 
             21             334 
  ENPEP MUTATED ENPEP WILD-TYPE 
              8              65 
$`ENPEP MUTATED`
TCGA-A6-2672 TCGA-A6-5661 TCGA-A6-6141 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3516 
       46.65        33.53         8.38         3.02        63.98        13.02 
TCGA-AA-3664 TCGA-AA-3977 TCGA-AA-A00U TCGA-AA-A010 TCGA-AD-6890 TCGA-AD-6964 
       54.02        25.02        17.03        34.98         0.79        10.88 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-CA-5796 TCGA-CA-6717 TCGA-D5-5538 
        6.77        12.10       100.01         3.25         0.33        12.26 
TCGA-D5-6536 TCGA-DM-A1D7 TCGA-F4-6809 
       17.85        13.32        13.25 

$`ENPEP WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       32.71        27.09        22.52        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 
       20.28         7.04         1.02        35.01         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05         6.97         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A00Z 
        4.01        27.02        42.02         0.99        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 
       40.96         0.07        21.37         4.21        56.55         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       61.41        49.41        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        1.94         2.24         3.06         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        49.91        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       16.24        33.67         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  ENPEP MUTATED ENPEP WILD-TYPE 
           0.33            0.00 
  ENPEP MUTATED ENPEP WILD-TYPE 
         100.01          140.38 
  ENPEP MUTATED ENPEP WILD-TYPE 
         13.250          20.995 
[1] "0.3 - 100.0 (13.2)" "0.0 - 140.4 (21.0)"
[1] "hr=" "2"  
D541V2, 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       21       103         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        18         10         38         31       34        12
                 vv
clus              STAGE IVB
  ENPEP MUTATED           0
  ENPEP WILD-TYPE         1
D541V3, multiclass
            clus
vv           ENPEP MUTATED ENPEP WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               4              21
  STAGE IIA              6             103
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             3              38
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 233  38
D541V4, multiclass
    clus
vv   ENPEP MUTATED ENPEP WILD-TYPE
  T1             1               8
  T2             2              66
  T3            15             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
  ENPEP MUTATED    14   5   2
  ENPEP WILD-TYPE 206  75  64
D541V5, multiclass
    clus
vv   ENPEP MUTATED ENPEP WILD-TYPE
  N0            14             206
  N1             5              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"
D541V6, binary
                 cls
clus                0   1
  ENPEP MUTATED    15   2
  ENPEP WILD-TYPE 268  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ENPEP MUTATED     15    2
  ENPEP WILD-TYPE  268   46
   clus
vv  ENPEP MUTATED ENPEP WILD-TYPE
  0            15             268
  1             2              46
[1] 2 2
[1] FALSE
D541V7, 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
D541V8, binary
                 cls
clus                0   1
  ENPEP MUTATED    18   3
  ENPEP WILD-TYPE 299  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ENPEP MUTATED     18    3
  ENPEP WILD-TYPE  299   45
                               clus
vv                              ENPEP MUTATED ENPEP WILD-TYPE
  COLON ADENOCARCINOMA                     18             299
  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 246   2  22  20
D541V9, multiclass
    clus
vv   ENPEP MUTATED ENPEP WILD-TYPE
  R0            11             246
  R1             0               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"
D541V10, 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
D541V11, 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(542) Variable = AGFG1 MUTATION ANALYSIS
D542V1, survival
                 sevent
clus2               0   1
  AGFG1 MUTATED     9   3
  AGFG1 WILD-TYPE 273  70
  AGFG1 MUTATED AGFG1 WILD-TYPE 
             12             343 
  AGFG1 MUTATED AGFG1 WILD-TYPE 
              3              70 
$`AGFG1 MUTATED`
TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3968 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6895 
       22.06        63.98        21.99         4.01        34.98         0.72 
TCGA-AY-6196 TCGA-AZ-4682 TCGA-AZ-6598 TCGA-CA-6718 TCGA-CM-5349 TCGA-DM-A0X9 
        0.20        22.36        49.41         0.10        30.08       119.70 

$`AGFG1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03         2.01        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
        0.07        21.37         4.21        56.55         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        15.75        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        1.41         5.13        83.80        62.79        61.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.33         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  AGFG1 MUTATED AGFG1 WILD-TYPE 
            0.1             0.0 
  AGFG1 MUTATED AGFG1 WILD-TYPE 
         119.70          140.38 
  AGFG1 MUTATED AGFG1 WILD-TYPE 
          22.21           20.02 
[1] "0.1 - 119.7 (22.2)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.1"
D542V2, 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       22       105         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AGFG1 MUTATED           1          0          0          1        0         1
  AGFG1 WILD-TYPE        18         10         41         30       35        12
                 vv
clus              STAGE IVB
  AGFG1 MUTATED           0
  AGFG1 WILD-TYPE         1
D542V3, multiclass
            clus
vv           AGFG1 MUTATED AGFG1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              4             105
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 237  38
D542V4, multiclass
    clus
vv   AGFG1 MUTATED AGFG1 WILD-TYPE
  T1             0               9
  T2             1              67
  T3            11             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
  AGFG1 MUTATED    12   1   2
  AGFG1 WILD-TYPE 208  79  64
D542V5, multiclass
    clus
vv   AGFG1 MUTATED AGFG1 WILD-TYPE
  N0            12             208
  N1             1              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"
D542V6, binary
                 cls
clus                0   1
  AGFG1 MUTATED    10   1
  AGFG1 WILD-TYPE 273  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGFG1 MUTATED     10    1
  AGFG1 WILD-TYPE  273   47
   clus
vv  AGFG1 MUTATED AGFG1 WILD-TYPE
  0            10             273
  1             1              47
[1] 2 2
[1] FALSE
D542V7, 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
D542V8, binary
                 cls
clus                0   1
  AGFG1 MUTATED    13   2
  AGFG1 WILD-TYPE 304  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGFG1 MUTATED     13    2
  AGFG1 WILD-TYPE  304   46
                               clus
vv                              AGFG1 MUTATED AGFG1 WILD-TYPE
  COLON ADENOCARCINOMA                     13             304
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  AGFG1 MUTATED    10   0   0   2
  AGFG1 WILD-TYPE 247   2  22  19
D542V9, multiclass
    clus
vv   AGFG1 MUTATED AGFG1 WILD-TYPE
  R0            10             247
  R1             0               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"
D542V10, 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
D542V11, 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(543) Variable = KDM3B MUTATION ANALYSIS
D543V1, survival
                 sevent
clus2               0   1
  KDM3B MUTATED    27   3
  KDM3B WILD-TYPE 255  70
  KDM3B MUTATED KDM3B WILD-TYPE 
             30             325 
  KDM3B MUTATED KDM3B WILD-TYPE 
              3              70 
$`KDM3B MUTATED`
TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3555 TCGA-AA-3672 
       33.53        22.06        19.66        20.28        29.95         0.92 
TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A010 TCGA-AA-A01Q TCGA-AD-6895 
       24.00         2.01        25.02        34.98         1.02         0.72 
TCGA-AD-6963 TCGA-AY-6196 TCGA-AZ-6598 TCGA-AZ-6605 TCGA-CA-6717 TCGA-CA-6719 
       27.42         0.20        49.41         5.23         0.33         1.35 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-6163 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6676 
       29.06        22.03        14.04        12.99        14.04        11.08 
TCGA-D5-6923 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A28H TCGA-F4-6703 TCGA-G4-6321 
       12.43        12.59       140.38       117.07        35.87        22.09 

$`KDM3B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        7.04         3.02         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       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        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
        0.07        21.37         4.21        56.55         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        15.75        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13        83.80        22.36        62.79        61.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10       100.01        29.56        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        0.10        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02        12.00        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       14.99        13.02        15.02        11.01        12.95        13.05 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       92.75        49.91        13.32         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  KDM3B MUTATED KDM3B WILD-TYPE 
            0.2             0.0 
  KDM3B MUTATED KDM3B WILD-TYPE 
         140.38          139.17 
  KDM3B MUTATED KDM3B WILD-TYPE 
          19.97           20.19 
[1] "0.2 - 140.4 (20.0)" "0.0 - 139.2 (20.2)"
[1] "hr=" "1.9"
D543V2, 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       23        97         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KDM3B MUTATED           2          1          2          3        0         0
  KDM3B WILD-TYPE        17          9         39         28       35        13
                 vv
clus              STAGE IVB
  KDM3B MUTATED           0
  KDM3B WILD-TYPE         1
D543V3, multiclass
            clus
vv           KDM3B MUTATED KDM3B WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA             12              97
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             1               9
  STAGE IIIB             2              39
  STAGE IIIC             3              28
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KDM3B MUTATED     1   6  21   4
  KDM3B WILD-TYPE   8  62 227  37
D543V4, multiclass
    clus
vv   KDM3B MUTATED KDM3B WILD-TYPE
  T1             1               8
  T2             6              62
  T3            21             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
  KDM3B MUTATED    22   8   2
  KDM3B WILD-TYPE 198  72  64
D543V5, multiclass
    clus
vv   KDM3B MUTATED KDM3B WILD-TYPE
  N0            22             198
  N1             8              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"
D543V6, binary
                 cls
clus                0   1
  KDM3B MUTATED    23   0
  KDM3B WILD-TYPE 260  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM3B MUTATED     23    0
  KDM3B WILD-TYPE  260   48
   clus
vv  KDM3B MUTATED KDM3B WILD-TYPE
  0            23             260
  1             0              48
[1] 2 2
[1] FALSE
D543V7, 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
D543V8, binary
                 cls
clus                0   1
  KDM3B MUTATED    26   6
  KDM3B WILD-TYPE 291  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM3B MUTATED     26    6
  KDM3B WILD-TYPE  291   42
                               clus
vv                              KDM3B MUTATED KDM3B WILD-TYPE
  COLON ADENOCARCINOMA                     26             291
  COLON MUCINOUS ADENOCARCINOMA             6              42
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  KDM3B MUTATED    20   0   0   2
  KDM3B WILD-TYPE 237   2  22  19
D543V9, multiclass
    clus
vv   KDM3B MUTATED KDM3B WILD-TYPE
  R0            20             237
  R1             0               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"
D543V10, 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
D543V11, 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(544) Variable = GAB1 MUTATION ANALYSIS
D544V1, survival
                sevent
clus2              0   1
  GAB1 MUTATED     8   6
  GAB1 WILD-TYPE 274  67
  GAB1 MUTATED GAB1 WILD-TYPE 
            14            341 
  GAB1 MUTATED GAB1 WILD-TYPE 
             6             67 
$`GAB1 MUTATED`
TCGA-A6-2676 TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3715 TCGA-AA-3854 TCGA-AA-A00N 
       42.90        22.06         3.02        19.04        36.03         4.01 
TCGA-AA-A010 TCGA-AD-6889 TCGA-AZ-6605 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-6679 
       34.98        56.55         5.23        30.08        16.01        10.06 
TCGA-DM-A28C TCGA-G4-6588 
       81.37        26.17 

$`GAB1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
       33.07         0.00        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        4.21         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10       100.01        29.56        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        91.79        46.75        52.80 

  GAB1 MUTATED GAB1 WILD-TYPE 
          3.02           0.00 
  GAB1 MUTATED GAB1 WILD-TYPE 
         81.37         140.38 
  GAB1 MUTATED GAB1 WILD-TYPE 
        24.115         20.120 
[1] "3.0 - 81.4 (24.1)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "2.1"
D544V2, 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       23       101         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        19         10         40         31       35        13
                vv
clus             STAGE IVB
  GAB1 MUTATED           0
  GAB1 WILD-TYPE         1
D544V3, multiclass
            clus
vv           GAB1 MUTATED GAB1 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             8            101
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GAB1 MUTATED     0   1  10   4
  GAB1 WILD-TYPE   9  67 238  37
D544V4, multiclass
    clus
vv   GAB1 MUTATED GAB1 WILD-TYPE
  T1            0              9
  T2            1             67
  T3           10            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
  GAB1 MUTATED    14   1   0
  GAB1 WILD-TYPE 206  79  66
D544V5, multiclass
    clus
vv   GAB1 MUTATED GAB1 WILD-TYPE
  N0           14            206
  N1            1             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"
D544V6, binary
                cls
clus               0   1
  GAB1 MUTATED    15   0
  GAB1 WILD-TYPE 268  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAB1 MUTATED     15    0
  GAB1 WILD-TYPE  268   48
   clus
vv  GAB1 MUTATED GAB1 WILD-TYPE
  0           15            268
  1            0             48
[1] 2 2
[1] FALSE
D544V7, 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
D544V8, binary
                cls
clus               0   1
  GAB1 MUTATED    13   2
  GAB1 WILD-TYPE 304  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAB1 MUTATED     13    2
  GAB1 WILD-TYPE  304   46
                               clus
vv                              GAB1 MUTATED GAB1 WILD-TYPE
  COLON ADENOCARCINOMA                    13            304
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  GAB1 MUTATED    12   0   0   0
  GAB1 WILD-TYPE 245   2  22  21
D544V9, multiclass
    clus
vv   GAB1 MUTATED GAB1 WILD-TYPE
  R0           12            245
  R1            0              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"
D544V10, 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
D544V11, 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(545) Variable = ADK MUTATION ANALYSIS
D545V1, survival
               sevent
clus2             0   1
  ADK MUTATED     7   0
  ADK WILD-TYPE 275  73
  ADK MUTATED ADK WILD-TYPE 
            7           348 
  ADK MUTATED ADK WILD-TYPE 
            0            73 
$`ADK MUTATED`
TCGA-AA-A010 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-CA-5254 TCGA-CM-5349 
       34.98        21.44        17.82        58.39         2.24        30.08 
TCGA-G4-6588 
       26.17 

$`ADK WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.95        15.75         0.20         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        52.80 

  ADK MUTATED ADK WILD-TYPE 
         2.24          0.00 
  ADK MUTATED ADK WILD-TYPE 
        58.39        140.38 
  ADK MUTATED ADK WILD-TYPE 
        26.17         20.07 
[1] "2.2 - 58.4 (26.2)"  "0.0 - 140.4 (20.1)"
[1] "hr="     "9200000"
D545V2, 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       25       104         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        19         10         40         31       35        13
               vv
clus            STAGE IVB
  ADK MUTATED           0
  ADK WILD-TYPE         1
D545V3, multiclass
            clus
vv           ADK MUTATED ADK WILD-TYPE
  STAGE I              0            64
  STAGE IA             0             1
  STAGE II             0            25
  STAGE IIA            5           104
  STAGE IIB            1             7
  STAGE IIC            0             1
  STAGE III            0            19
  STAGE IIIA           0            10
  STAGE IIIB           1            40
  STAGE IIIC           0            31
  STAGE IV             0            35
  STAGE IVA            0            13
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  ADK MUTATED     0   0   6   1
  ADK WILD-TYPE   9  68 242  40
D545V4, multiclass
    clus
vv   ADK MUTATED ADK WILD-TYPE
  T1           0             9
  T2           0            68
  T3           6           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
  ADK MUTATED     6   1   0
  ADK WILD-TYPE 214  79  66
D545V5, multiclass
    clus
vv   ADK MUTATED ADK WILD-TYPE
  N0           6           214
  N1           1            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"
D545V6, binary
               cls
clus              0   1
  ADK MUTATED     6   0
  ADK WILD-TYPE 277  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  ADK MUTATED      6    0
  ADK WILD-TYPE  277   48
   clus
vv  ADK MUTATED ADK WILD-TYPE
  0           6           277
  1           0            48
[1] 2 2
[1] FALSE
D545V7, 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
D545V8, binary
               cls
clus              0   1
  ADK MUTATED     7   0
  ADK WILD-TYPE 310  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  ADK MUTATED      7    0
  ADK WILD-TYPE  310   48
                               clus
vv                              ADK MUTATED ADK WILD-TYPE
  COLON ADENOCARCINOMA                    7           310
  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 251   2  22  20
D545V9, multiclass
    clus
vv   ADK MUTATED ADK WILD-TYPE
  R0           6           251
  R1           0             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"
D545V10, 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
D545V11, 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(546) Variable = TXNDC17 MUTATION ANALYSIS
D546V1, survival
                   sevent
clus2                 0   1
  TXNDC17 MUTATED     5   0
  TXNDC17 WILD-TYPE 277  73
  TXNDC17 MUTATED TXNDC17 WILD-TYPE 
                5               350 
  TXNDC17 MUTATED TXNDC17 WILD-TYPE 
                0                73 
$`TXNDC17 MUTATED`
TCGA-A6-5665 TCGA-AA-3663 TCGA-CM-5861 TCGA-D5-6533 TCGA-D5-6923 
       22.06         6.97        15.02         1.32        12.43 

$`TXNDC17 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  TXNDC17 MUTATED TXNDC17 WILD-TYPE 
             1.32              0.00 
  TXNDC17 MUTATED TXNDC17 WILD-TYPE 
            22.06            140.38 
  TXNDC17 MUTATED TXNDC17 WILD-TYPE 
            12.43             20.63 
[1] "1.3 - 22.1 (12.4)"  "0.0 - 140.4 (20.6)"
[1] "hr="     "3300000"
D546V2, 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       24       107         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TXNDC17 MUTATED           0          0          1          0        0
  TXNDC17 WILD-TYPE        19         10         40         31       35
                   vv
clus                STAGE IVA STAGE IVB
  TXNDC17 MUTATED           0         0
  TXNDC17 WILD-TYPE        13         1
D546V3, multiclass
            clus
vv           TXNDC17 MUTATED TXNDC17 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                2               107
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TXNDC17 MUTATED     0   1   3   1
  TXNDC17 WILD-TYPE   9  67 245  40
D546V4, multiclass
    clus
vv   TXNDC17 MUTATED TXNDC17 WILD-TYPE
  T1               0                 9
  T2               1                67
  T3               3               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
  TXNDC17 MUTATED     5   0   0
  TXNDC17 WILD-TYPE 215  80  66
D546V5, multiclass
    clus
vv   TXNDC17 MUTATED TXNDC17 WILD-TYPE
  N0               5               215
  N1               0                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
  TXNDC17 MUTATED     5   0
  TXNDC17 WILD-TYPE 278  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TXNDC17 MUTATED      5    0
  TXNDC17 WILD-TYPE  278   48
   clus
vv  TXNDC17 MUTATED TXNDC17 WILD-TYPE
  0               5               278
  1               0                48
[1] 2 2
[1] FALSE
D546V7, 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
D546V8, binary
                   cls
clus                  0   1
  TXNDC17 MUTATED     5   0
  TXNDC17 WILD-TYPE 312  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TXNDC17 MUTATED      5    0
  TXNDC17 WILD-TYPE  312   48
                               clus
vv                              TXNDC17 MUTATED TXNDC17 WILD-TYPE
  COLON ADENOCARCINOMA                        5               312
  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 252   2  22  21
D546V9, multiclass
    clus
vv   TXNDC17 MUTATED TXNDC17 WILD-TYPE
  R0               5               252
  R1               0                 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"
D546V10, 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
D546V11, 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(547) Variable = BRE MUTATION ANALYSIS
D547V1, survival
               sevent
clus2             0   1
  BRE MUTATED     6   5
  BRE WILD-TYPE 276  68
  BRE MUTATED BRE WILD-TYPE 
           11           344 
  BRE MUTATED BRE WILD-TYPE 
            5            68 
$`BRE MUTATED`
TCGA-A6-2676 TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3815 TCGA-AA-3845 TCGA-AZ-6598 
       42.90        22.06         3.02        33.04         0.00        49.41 
TCGA-AZ-6606 TCGA-CM-4746 TCGA-CM-4752 TCGA-CM-6677 TCGA-G4-6293 
       11.74        37.02        13.02        11.08       107.67 

$`BRE WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02        14.93        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        35.41        19.43        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  BRE MUTATED BRE WILD-TYPE 
            0             0 
  BRE MUTATED BRE WILD-TYPE 
       107.67        140.38 
  BRE MUTATED BRE WILD-TYPE 
       22.060        20.155 
[1] "0.0 - 107.7 (22.1)" "0.0 - 140.4 (20.2)"
[1] "hr=" "2"  
D547V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BRE MUTATED         1        0        2         5         1         0
  BRE WILD-TYPE      63        1       23       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        18         10         41         31       34        13
               vv
clus            STAGE IVB
  BRE MUTATED           0
  BRE WILD-TYPE         1
D547V3, multiclass
            clus
vv           BRE MUTATED BRE WILD-TYPE
  STAGE I              1            63
  STAGE IA             0             1
  STAGE II             2            23
  STAGE IIA            5           104
  STAGE IIB            1             7
  STAGE IIC            0             1
  STAGE III            1            18
  STAGE IIIA           0            10
  STAGE IIIB           0            41
  STAGE IIIC           0            31
  STAGE IV             1            34
  STAGE IVA            0            13
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  BRE MUTATED     0   1   8   2
  BRE WILD-TYPE   9  67 240  39
D547V4, multiclass
    clus
vv   BRE MUTATED BRE WILD-TYPE
  T1           0             9
  T2           1            67
  T3           8           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
  BRE MUTATED     9   1   1
  BRE WILD-TYPE 211  79  65
D547V5, multiclass
    clus
vv   BRE MUTATED BRE WILD-TYPE
  N0           9           211
  N1           1            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"
D547V6, binary
               cls
clus              0   1
  BRE MUTATED     9   1
  BRE WILD-TYPE 274  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  BRE MUTATED      9    1
  BRE WILD-TYPE  274   47
   clus
vv  BRE MUTATED BRE WILD-TYPE
  0           9           274
  1           1            47
[1] 2 2
[1] FALSE
D547V7, binary
               cls
clus              0   1
  BRE MUTATED     8   3
  BRE WILD-TYPE 162 194
[1] "tbl2"
               cls
clus            [,1] [,2]
  BRE MUTATED      8    3
  BRE WILD-TYPE  162  194
        clus
vv       BRE MUTATED BRE WILD-TYPE
  FEMALE           8           162
  MALE             3           194
[1] 2 2
[1] FALSE
D547V8, binary
               cls
clus              0   1
  BRE MUTATED    11   0
  BRE WILD-TYPE 306  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  BRE MUTATED     11    0
  BRE WILD-TYPE  306   48
                               clus
vv                              BRE MUTATED BRE WILD-TYPE
  COLON ADENOCARCINOMA                   11           306
  COLON MUCINOUS ADENOCARCINOMA           0            48
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  BRE MUTATED     9   0   0   0
  BRE WILD-TYPE 248   2  22  21
D547V9, multiclass
    clus
vv   BRE MUTATED BRE WILD-TYPE
  R0           9           248
  R1           0             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"
D547V10, 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
D547V11, 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(548) Variable = AMOT MUTATION ANALYSIS
D548V1, survival
                sevent
clus2              0   1
  AMOT MUTATED     7   4
  AMOT WILD-TYPE 275  69
  AMOT MUTATED AMOT WILD-TYPE 
            11            344 
  AMOT MUTATED AMOT WILD-TYPE 
             4             69 
$`AMOT MUTATED`
TCGA-A6-2676 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3713 TCGA-AA-A00R TCGA-AA-A01P 
       42.90        19.66         3.02        19.04         0.99        38.07 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CM-6162 TCGA-DM-A1D8 
       21.44        58.39         0.33        12.00        12.59 

$`AMOT WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.12        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
       42.02        17.03        14.99        21.99        34.98        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        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        15.75         0.20        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  AMOT MUTATED AMOT WILD-TYPE 
          0.33           0.00 
  AMOT MUTATED AMOT WILD-TYPE 
         58.39         140.38 
  AMOT MUTATED AMOT WILD-TYPE 
         19.04          20.63 
[1] "0.3 - 58.4 (19.0)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "2.3"
D548V2, 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       24       106         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        18         10         40         30       34        13
                vv
clus             STAGE IVB
  AMOT MUTATED           0
  AMOT WILD-TYPE         1
D548V3, multiclass
            clus
vv           AMOT MUTATED AMOT WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             3            106
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            1             30
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  AMOT MUTATED     0   2   8   3
  AMOT WILD-TYPE   9  66 240  38
D548V4, multiclass
    clus
vv   AMOT MUTATED AMOT WILD-TYPE
  T1            0              9
  T2            2             66
  T3            8            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
  AMOT MUTATED     9   4   0
  AMOT WILD-TYPE 211  76  66
D548V5, multiclass
    clus
vv   AMOT MUTATED AMOT WILD-TYPE
  N0            9            211
  N1            4             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"
D548V6, binary
                cls
clus               0   1
  AMOT MUTATED     7   1
  AMOT WILD-TYPE 276  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  AMOT MUTATED      7    1
  AMOT WILD-TYPE  276   47
   clus
vv  AMOT MUTATED AMOT WILD-TYPE
  0            7            276
  1            1             47
[1] 2 2
[1] FALSE
D548V7, 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
D548V8, binary
                cls
clus               0   1
  AMOT MUTATED    10   3
  AMOT WILD-TYPE 307  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  AMOT MUTATED     10    3
  AMOT WILD-TYPE  307   45
                               clus
vv                              AMOT MUTATED AMOT WILD-TYPE
  COLON ADENOCARCINOMA                    10            307
  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 249   2  21  18
D548V9, multiclass
    clus
vv   AMOT MUTATED AMOT WILD-TYPE
  R0            8            249
  R1            0              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"
D548V10, 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
D548V11, 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(549) Variable = HFE2 MUTATION ANALYSIS
D549V1, survival
                sevent
clus2              0   1
  HFE2 MUTATED     5   1
  HFE2 WILD-TYPE 277  72
  HFE2 MUTATED HFE2 WILD-TYPE 
             6            349 
  HFE2 MUTATED HFE2 WILD-TYPE 
             1             72 
$`HFE2 MUTATED`
TCGA-AA-3815 TCGA-AA-A03J TCGA-AZ-6601 TCGA-CK-5914 TCGA-G4-6306 TCGA-G4-6315 
       33.04        40.96       100.01        21.99        44.68        36.72 

$`HFE2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 
       40.34        15.62        49.08        51.32        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 
       65.85        53.62        55.04        51.75        45.11        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  HFE2 MUTATED HFE2 WILD-TYPE 
         21.99           0.00 
  HFE2 MUTATED HFE2 WILD-TYPE 
        100.01         140.38 
  HFE2 MUTATED HFE2 WILD-TYPE 
         38.84          19.99 
[1] "22.0 - 100.0 (38.8)" "0.0 - 140.4 (20.0)" 
[1] "hr=" "2.1"
D549V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HFE2 MUTATED         2        0        2         2         0         0
  HFE2 WILD-TYPE      62        1       23       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        19         10         40         31       34        13
                vv
clus             STAGE IVB
  HFE2 MUTATED           0
  HFE2 WILD-TYPE         1
D549V3, multiclass
            clus
vv           HFE2 MUTATED HFE2 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             2            107
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  HFE2 MUTATED     0   3   4   1
  HFE2 WILD-TYPE   9  65 244  40
D549V4, multiclass
    clus
vv   HFE2 MUTATED HFE2 WILD-TYPE
  T1            0              9
  T2            3             65
  T3            4            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
  HFE2 MUTATED     6   2   0
  HFE2 WILD-TYPE 214  78  66
D549V5, multiclass
    clus
vv   HFE2 MUTATED HFE2 WILD-TYPE
  N0            6            214
  N1            2             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"
D549V6, binary
                cls
clus               0   1
  HFE2 MUTATED     5   1
  HFE2 WILD-TYPE 278  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  HFE2 MUTATED      5    1
  HFE2 WILD-TYPE  278   47
   clus
vv  HFE2 MUTATED HFE2 WILD-TYPE
  0            5            278
  1            1             47
[1] 2 2
[1] FALSE
D549V7, 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
D549V8, binary
                cls
clus               0   1
  HFE2 MUTATED     8   0
  HFE2 WILD-TYPE 309  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  HFE2 MUTATED      8    0
  HFE2 WILD-TYPE  309   48
                               clus
vv                              HFE2 MUTATED HFE2 WILD-TYPE
  COLON ADENOCARCINOMA                     8            309
  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 252   2  22  19
D549V9, multiclass
    clus
vv   HFE2 MUTATED HFE2 WILD-TYPE
  R0            5            252
  R1            0              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"
D549V10, 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
D549V11, 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(550) Variable = SPCS2 MUTATION ANALYSIS
D550V1, survival
                 sevent
clus2               0   1
  SPCS2 MUTATED     3   2
  SPCS2 WILD-TYPE 279  71
  SPCS2 MUTATED SPCS2 WILD-TYPE 
              5             350 
  SPCS2 MUTATED SPCS2 WILD-TYPE 
              2              71 
$`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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14         2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
      139.17         6.12       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  SPCS2 MUTATED SPCS2 WILD-TYPE 
           1.94            0.00 
  SPCS2 MUTATED SPCS2 WILD-TYPE 
         124.27          140.38 
  SPCS2 MUTATED SPCS2 WILD-TYPE 
         81.370          20.155 
[1] "1.9 - 124.3 (81.4)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D550V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SPCS2 MUTATED         2        0        0         1         0         0
  SPCS2 WILD-TYPE      62        1       25       108         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SPCS2 MUTATED           1          1          0          0        0         0
  SPCS2 WILD-TYPE        18          9         41         31       35        13
                 vv
clus              STAGE IVB
  SPCS2 MUTATED           0
  SPCS2 WILD-TYPE         1
D550V3, multiclass
            clus
vv           SPCS2 MUTATED SPCS2 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              1             108
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             1               9
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SPCS2 MUTATED     0   3   2   0
  SPCS2 WILD-TYPE   9  65 246  41
D550V4, multiclass
    clus
vv   SPCS2 MUTATED SPCS2 WILD-TYPE
  T1             0               9
  T2             3              65
  T3             2             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
  SPCS2 MUTATED     4   1   0
  SPCS2 WILD-TYPE 216  79  66
D550V5, multiclass
    clus
vv   SPCS2 MUTATED SPCS2 WILD-TYPE
  N0             4             216
  N1             1              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"
D550V6, binary
                 cls
clus                0   1
  SPCS2 MUTATED     4   0
  SPCS2 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPCS2 MUTATED      4    0
  SPCS2 WILD-TYPE  279   48
   clus
vv  SPCS2 MUTATED SPCS2 WILD-TYPE
  0             4             279
  1             0              48
[1] 2 2
[1] FALSE
D550V7, 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
D550V8, binary
                 cls
clus                0   1
  SPCS2 MUTATED     4   1
  SPCS2 WILD-TYPE 313  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPCS2 MUTATED      4    1
  SPCS2 WILD-TYPE  313   47
                               clus
vv                              SPCS2 MUTATED SPCS2 WILD-TYPE
  COLON ADENOCARCINOMA                      4             313
  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 255   2  22  20
D550V9, multiclass
    clus
vv   SPCS2 MUTATED SPCS2 WILD-TYPE
  R0             2             255
  R1             0               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"
D550V10, 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
D550V11, 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(551) Variable = GPR22 MUTATION ANALYSIS
D551V1, survival
                 sevent
clus2               0   1
  GPR22 MUTATED     6   3
  GPR22 WILD-TYPE 276  70
  GPR22 MUTATED GPR22 WILD-TYPE 
              9             346 
  GPR22 MUTATED GPR22 WILD-TYPE 
              3              70 
$`GPR22 MUTATED`
TCGA-AA-3492 TCGA-AA-3713 TCGA-AA-3833 TCGA-AA-A00N TCGA-AU-6004 TCGA-CA-6717 
        3.02        19.04        15.95         4.01        27.09         0.33 
TCGA-CK-5916 TCGA-F4-6856 TCGA-G4-6306 
       21.14        19.43        44.68 

$`GPR22 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 
      107.67        74.56        65.85        53.62        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  GPR22 MUTATED GPR22 WILD-TYPE 
           0.33            0.00 
  GPR22 MUTATED GPR22 WILD-TYPE 
          44.68          140.38 
  GPR22 MUTATED GPR22 WILD-TYPE 
          19.04           20.63 
[1] "0.3 - 44.7 (19.0)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "2.4"
D551V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GPR22 MUTATED         3        0        1         3         1         0
  GPR22 WILD-TYPE      61        1       24       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        19         10         41         31       34        13
                 vv
clus              STAGE IVB
  GPR22 MUTATED           0
  GPR22 WILD-TYPE         1
D551V3, multiclass
            clus
vv           GPR22 MUTATED GPR22 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              3             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GPR22 MUTATED     1   3   4   1
  GPR22 WILD-TYPE   8  65 244  40
D551V4, multiclass
    clus
vv   GPR22 MUTATED GPR22 WILD-TYPE
  T1             1               8
  T2             3              65
  T3             4             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
  GPR22 MUTATED     9   0   0
  GPR22 WILD-TYPE 211  80  66
D551V5, multiclass
    clus
vv   GPR22 MUTATED GPR22 WILD-TYPE
  N0             9             211
  N1             0              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"
D551V6, binary
                 cls
clus                0   1
  GPR22 MUTATED     8   1
  GPR22 WILD-TYPE 275  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR22 MUTATED      8    1
  GPR22 WILD-TYPE  275   47
   clus
vv  GPR22 MUTATED GPR22 WILD-TYPE
  0             8             275
  1             1              47
[1] 2 2
[1] FALSE
D551V7, 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
D551V8, binary
                 cls
clus                0   1
  GPR22 MUTATED     6   3
  GPR22 WILD-TYPE 311  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR22 MUTATED      6    3
  GPR22 WILD-TYPE  311   45
                               clus
vv                              GPR22 MUTATED GPR22 WILD-TYPE
  COLON ADENOCARCINOMA                      6             311
  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 251   2  21  19
D551V9, multiclass
    clus
vv   GPR22 MUTATED GPR22 WILD-TYPE
  R0             6             251
  R1             0               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"
D551V10, 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
D551V11, 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(552) Variable = GPR115 MUTATION ANALYSIS
D552V1, survival
                  sevent
clus2                0   1
  GPR115 MUTATED    12   6
  GPR115 WILD-TYPE 270  67
  GPR115 MUTATED GPR115 WILD-TYPE 
              18              337 
  GPR115 MUTATED GPR115 WILD-TYPE 
               6               67 
$`GPR115 MUTATED`
TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-5666 TCGA-AA-3510 TCGA-AA-3713 TCGA-AA-3715 
       33.53        22.06        32.71        63.98        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3815 TCGA-AD-6964 TCGA-AZ-4315 TCGA-AZ-6603 TCGA-CA-6717 
       10.06        33.04        10.88        58.39        29.56         0.33 
TCGA-CK-5916 TCGA-CM-5341 TCGA-DM-A1DA TCGA-DM-A28H TCGA-G4-6306 TCGA-G4-6321 
       21.14        29.06         7.50       117.07        44.68        22.09 

$`GPR115 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       26.99        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
      100.01         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  GPR115 MUTATED GPR115 WILD-TYPE 
            0.33             0.00 
  GPR115 MUTATED GPR115 WILD-TYPE 
          117.07           140.38 
  GPR115 MUTATED GPR115 WILD-TYPE 
          25.575           19.990 
[1] "0.3 - 117.1 (25.6)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.4"
D552V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GPR115 MUTATED         1        0        2         6         0         1
  GPR115 WILD-TYPE      63        1       23       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        17          9         41         29       34
                  vv
clus               STAGE IVA STAGE IVB
  GPR115 MUTATED           0         0
  GPR115 WILD-TYPE        13         1
D552V3, multiclass
            clus
vv           GPR115 MUTATED GPR115 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               6              103
  STAGE IIB               0                8
  STAGE IIC               1                0
  STAGE III               2               17
  STAGE IIIA              1                9
  STAGE IIIB              0               41
  STAGE IIIC              2               29
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GPR115 MUTATED     1   4  11   2
  GPR115 WILD-TYPE   8  64 237  39
D552V4, multiclass
    clus
vv   GPR115 MUTATED GPR115 WILD-TYPE
  T1              1                8
  T2              4               64
  T3             11              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
  GPR115 MUTATED    11   3   4
  GPR115 WILD-TYPE 209  77  62
D552V5, multiclass
    clus
vv   GPR115 MUTATED GPR115 WILD-TYPE
  N0             11              209
  N1              3               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"
D552V6, binary
                  cls
clus                 0   1
  GPR115 MUTATED    14   1
  GPR115 WILD-TYPE 269  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR115 MUTATED     14    1
  GPR115 WILD-TYPE  269   47
   clus
vv  GPR115 MUTATED GPR115 WILD-TYPE
  0             14              269
  1              1               47
[1] 2 2
[1] FALSE
D552V7, 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
D552V8, binary
                  cls
clus                 0   1
  GPR115 MUTATED    17   1
  GPR115 WILD-TYPE 300  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR115 MUTATED     17    1
  GPR115 WILD-TYPE  300   47
                               clus
vv                              GPR115 MUTATED GPR115 WILD-TYPE
  COLON ADENOCARCINOMA                      17              300
  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 247   2  21  19
D552V9, multiclass
    clus
vv   GPR115 MUTATED GPR115 WILD-TYPE
  R0             10              247
  R1              0                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"
D552V10, 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
D552V11, 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(553) Variable = KIAA0319L MUTATION ANALYSIS
D553V1, survival
                     sevent
clus2                   0   1
  KIAA0319L MUTATED    15   4
  KIAA0319L WILD-TYPE 267  69
  KIAA0319L MUTATED KIAA0319L WILD-TYPE 
                 19                 336 
  KIAA0319L MUTATED KIAA0319L WILD-TYPE 
                  4                  69 
$`KIAA0319L MUTATED`
TCGA-A6-2676 TCGA-A6-5659 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3819 TCGA-AA-3877 
       42.90        30.44        19.66         3.02        25.02        31.00 
TCGA-AA-3977 TCGA-AA-A010 TCGA-AA-A01Q TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 
       25.02        34.98         1.02        58.39        49.41         0.33 
TCGA-CK-4947 TCGA-CM-4746 TCGA-D5-6927 TCGA-DM-A1HB TCGA-F4-6570 TCGA-G4-6307 
       17.56        37.02         9.44       135.65         6.18        55.04 
TCGA-G4-6588 
       26.17 

$`KIAA0319L WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
        0.99         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
        1.35       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      117.07        98.24         8.61        13.38        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        52.80 

  KIAA0319L MUTATED KIAA0319L WILD-TYPE 
               0.33                0.00 
  KIAA0319L MUTATED KIAA0319L WILD-TYPE 
             135.65              140.38 
  KIAA0319L MUTATED KIAA0319L WILD-TYPE 
             26.170              20.005 
[1] "0.3 - 135.7 (26.2)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.1"
D553V2, 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       22       103         6         1
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0319L MUTATED           0          0          2          1        0
  KIAA0319L WILD-TYPE        19         10         39         30       35
                     vv
clus                  STAGE IVA STAGE IVB
  KIAA0319L MUTATED           1         0
  KIAA0319L WILD-TYPE        12         1
D553V3, multiclass
            clus
vv           KIAA0319L MUTATED KIAA0319L WILD-TYPE
  STAGE I                    3                  61
  STAGE IA                   0                   1
  STAGE II                   3                  22
  STAGE IIA                  6                 103
  STAGE IIB                  2                   6
  STAGE IIC                  0                   1
  STAGE III                  0                  19
  STAGE IIIA                 0                  10
  STAGE IIIB                 2                  39
  STAGE IIIC                 1                  30
  STAGE IV                   0                  35
  STAGE IVA                  1                  12
  STAGE IVB                  0                   1
[1] 13  2
[1] TRUE
[1] "dimension of 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  65 237  37
D553V4, multiclass
    clus
vv   KIAA0319L MUTATED KIAA0319L WILD-TYPE
  T1                 1                   8
  T2                 3                  65
  T3                11                 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
  KIAA0319L MUTATED    15   4   0
  KIAA0319L WILD-TYPE 205  76  66
D553V5, multiclass
    clus
vv   KIAA0319L MUTATED KIAA0319L WILD-TYPE
  N0                15                 205
  N1                 4                  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"
D553V6, binary
                     cls
clus                    0   1
  KIAA0319L MUTATED    16   0
  KIAA0319L WILD-TYPE 267  48
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KIAA0319L MUTATED     16    0
  KIAA0319L WILD-TYPE  267   48
   clus
vv  KIAA0319L MUTATED KIAA0319L WILD-TYPE
  0                16                 267
  1                 0                  48
[1] 2 2
[1] FALSE
D553V7, 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
D553V8, binary
                     cls
clus                    0   1
  KIAA0319L MUTATED    16   3
  KIAA0319L WILD-TYPE 301  45
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KIAA0319L MUTATED     16    3
  KIAA0319L WILD-TYPE  301   45
                               clus
vv                              KIAA0319L MUTATED KIAA0319L WILD-TYPE
  COLON ADENOCARCINOMA                         16                 301
  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 243   2  22  19
D553V9, multiclass
    clus
vv   KIAA0319L MUTATED KIAA0319L WILD-TYPE
  R0                14                 243
  R1                 0                   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"
D553V10, 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
D553V11, 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(554) Variable = ZKSCAN2 MUTATION ANALYSIS
D554V1, survival
                   sevent
clus2                 0   1
  ZKSCAN2 MUTATED    11   2
  ZKSCAN2 WILD-TYPE 271  71
  ZKSCAN2 MUTATED ZKSCAN2 WILD-TYPE 
               13               342 
  ZKSCAN2 MUTATED ZKSCAN2 WILD-TYPE 
                2                71 
$`ZKSCAN2 MUTATED`
TCGA-AA-3492 TCGA-AA-3821 TCGA-AA-3941 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00N 
        3.02         1.02        24.00         2.01        25.02         4.01 
TCGA-AD-6965 TCGA-AZ-4315 TCGA-CK-4947 TCGA-CM-5349 TCGA-CM-6676 TCGA-D5-6928 
        0.20        58.39        17.56        30.08        11.08        11.64 
TCGA-G4-6306 
       44.68 

$`ZKSCAN2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 
       10.06        35.05        33.04         0.99        25.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        10.88        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 
        0.07         0.26         0.33         0.10         1.35       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  ZKSCAN2 MUTATED ZKSCAN2 WILD-TYPE 
              0.2               0.0 
  ZKSCAN2 MUTATED ZKSCAN2 WILD-TYPE 
            58.39            140.38 
  ZKSCAN2 MUTATED ZKSCAN2 WILD-TYPE 
            11.64             20.63 
[1] "0.2 - 58.4 (11.6)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "1"  
D554V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZKSCAN2 MUTATED         2        0        1         5         1         0
  ZKSCAN2 WILD-TYPE      62        1       24       104         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZKSCAN2 MUTATED           0          0          0          0        0
  ZKSCAN2 WILD-TYPE        19         10         41         31       35
                   vv
clus                STAGE IVA STAGE IVB
  ZKSCAN2 MUTATED           2         0
  ZKSCAN2 WILD-TYPE        11         1
D554V3, multiclass
            clus
vv           ZKSCAN2 MUTATED ZKSCAN2 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                5               104
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                2                11
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of 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  64 243  37
D554V4, multiclass
    clus
vv   ZKSCAN2 MUTATED ZKSCAN2 WILD-TYPE
  T1               0                 9
  T2               4                64
  T3               5               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
  ZKSCAN2 MUTATED    10   2   1
  ZKSCAN2 WILD-TYPE 210  78  65
D554V5, multiclass
    clus
vv   ZKSCAN2 MUTATED ZKSCAN2 WILD-TYPE
  N0              10               210
  N1               2                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"
D554V6, binary
                   cls
clus                  0   1
  ZKSCAN2 MUTATED    10   1
  ZKSCAN2 WILD-TYPE 273  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZKSCAN2 MUTATED     10    1
  ZKSCAN2 WILD-TYPE  273   47
   clus
vv  ZKSCAN2 MUTATED ZKSCAN2 WILD-TYPE
  0              10               273
  1               1                47
[1] 2 2
[1] FALSE
D554V7, 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
D554V8, binary
                   cls
clus                  0   1
  ZKSCAN2 MUTATED     9   4
  ZKSCAN2 WILD-TYPE 308  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZKSCAN2 MUTATED      9    4
  ZKSCAN2 WILD-TYPE  308   44
                               clus
vv                              ZKSCAN2 MUTATED ZKSCAN2 WILD-TYPE
  COLON ADENOCARCINOMA                        9               308
  COLON MUCINOUS ADENOCARCINOMA               4                44
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ZKSCAN2 MUTATED     9   0   0   1
  ZKSCAN2 WILD-TYPE 248   2  22  20
D554V9, multiclass
    clus
vv   ZKSCAN2 MUTATED ZKSCAN2 WILD-TYPE
  R0               9               248
  R1               0                 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"
D554V10, 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
D554V11, 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(555) Variable = PNP MUTATION ANALYSIS
D555V1, survival
               sevent
clus2             0   1
  PNP MUTATED     0   3
  PNP WILD-TYPE 282  70
  PNP MUTATED PNP WILD-TYPE 
            3           352 
  PNP MUTATED PNP WILD-TYPE 
            3            70 
$`PNP MUTATED`
TCGA-AA-3492 TCGA-AA-3845 TCGA-AZ-6598 
        3.02         0.00        49.41 

$`PNP WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
       17.98        15.95        38.99        37.02        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13        83.80        22.36        62.79        61.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  PNP MUTATED PNP WILD-TYPE 
            0             0 
  PNP MUTATED PNP WILD-TYPE 
        49.41        140.38 
  PNP MUTATED PNP WILD-TYPE 
        3.020        20.235 
[1] "0.0 - 49.4 (3.0)"   "0.0 - 140.4 (20.2)"
[1] "hr=" "6.5"
D555V2, 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       23       108         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        19         10         41         31       35        13
               vv
clus            STAGE IVB
  PNP MUTATED           0
  PNP WILD-TYPE         1
D555V3, multiclass
            clus
vv           PNP MUTATED PNP WILD-TYPE
  STAGE I              1            63
  STAGE IA             0             1
  STAGE II             2            23
  STAGE IIA            1           108
  STAGE IIB            0             8
  STAGE IIC            0             1
  STAGE III            0            19
  STAGE IIIA           0            10
  STAGE IIIB           0            41
  STAGE IIIC           0            31
  STAGE IV             0            35
  STAGE IVA            0            13
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  PNP MUTATED     0   1   3   0
  PNP WILD-TYPE   9  67 245  41
D555V4, multiclass
    clus
vv   PNP MUTATED PNP WILD-TYPE
  T1           0             9
  T2           1            67
  T3           3           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
  PNP MUTATED     4   0   0
  PNP WILD-TYPE 216  80  66
D555V5, multiclass
    clus
vv   PNP MUTATED PNP WILD-TYPE
  N0           4           216
  N1           0            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"
D555V6, binary
               cls
clus              0   1
  PNP MUTATED     2   0
  PNP WILD-TYPE 281  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  PNP MUTATED      2    0
  PNP WILD-TYPE  281   48
   clus
vv  PNP MUTATED PNP WILD-TYPE
  0           2           281
  1           0            48
[1] 2 2
[1] FALSE
D555V7, 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
D555V8, binary
               cls
clus              0   1
  PNP MUTATED     4   0
  PNP WILD-TYPE 313  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  PNP MUTATED      4    0
  PNP WILD-TYPE  313   48
                               clus
vv                              PNP MUTATED PNP WILD-TYPE
  COLON ADENOCARCINOMA                    4           313
  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 255   2  22  20
D555V9, multiclass
    clus
vv   PNP MUTATED PNP WILD-TYPE
  R0           2           255
  R1           0             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"
D555V10, 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
D555V11, multiclass
[1] "Remove cluster labels:" "PNP MUTATED"           
clus
  PNP MUTATED PNP WILD-TYPE 
            2           204 
   TCGA-A6-2671    TCGA-A6-2672    TCGA-A6-2674    TCGA-A6-2676    TCGA-A6-2677 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-A6-2678    TCGA-A6-2683    TCGA-A6-3807    TCGA-A6-3808    TCGA-A6-3809 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-A6-3810    TCGA-A6-4105    TCGA-A6-5656    TCGA-A6-5657    TCGA-A6-5659 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-A6-5660    TCGA-A6-5661    TCGA-A6-5662    TCGA-A6-5664    TCGA-A6-5665 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-A6-5666    TCGA-A6-6137    TCGA-A6-6138    TCGA-A6-6141    TCGA-A6-6142 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-A6-6648    TCGA-A6-6649    TCGA-A6-6651    TCGA-A6-6652    TCGA-A6-6653 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-A6-6654    TCGA-A6-6780    TCGA-A6-6781    TCGA-A6-6782    TCGA-AD-5900 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-AD-6548    TCGA-AD-6888    TCGA-AD-6889    TCGA-AD-6890    TCGA-AD-6895 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-AD-6899    TCGA-AD-6901    TCGA-AD-6963    TCGA-AD-6964    TCGA-AD-6965 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-AU-3779    TCGA-AU-6004    TCGA-AY-4070    TCGA-AY-4071    TCGA-AY-5543 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-AY-6196    TCGA-AY-6197    TCGA-AY-6386    TCGA-AZ-4315    TCGA-AZ-4323 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-AZ-4616    TCGA-AZ-4681    TCGA-AZ-4682    TCGA-AZ-5403    TCGA-AZ-5407 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-AZ-6599    TCGA-AZ-6600    TCGA-AZ-6601    TCGA-AZ-6603    TCGA-AZ-6605 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-AZ-6606    TCGA-AZ-6607    TCGA-AZ-6608    TCGA-CA-5254    TCGA-CA-5255 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-CA-5796    TCGA-CA-5797    TCGA-CA-6715    TCGA-CA-6716    TCGA-CA-6717 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-CA-6718    TCGA-CA-6719    TCGA-CK-4947    TCGA-CK-4948    TCGA-CK-4950 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-CK-4952    TCGA-CK-5912    TCGA-CK-5913    TCGA-CK-5914    TCGA-CK-5916 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-CK-6746    TCGA-CK-6747    TCGA-CK-6748    TCGA-CK-6751    TCGA-CM-4743 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-CM-4744    TCGA-CM-4746    TCGA-CM-4747    TCGA-CM-4752    TCGA-CM-5341 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-CM-5344    TCGA-CM-5348    TCGA-CM-5349    TCGA-CM-5860    TCGA-CM-5861 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-CM-5862    TCGA-CM-5863    TCGA-CM-5864    TCGA-CM-5868    TCGA-CM-6161 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-CM-6162    TCGA-CM-6163    TCGA-CM-6164    TCGA-CM-6165    TCGA-CM-6166 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-CM-6167    TCGA-CM-6168    TCGA-CM-6169    TCGA-CM-6170    TCGA-CM-6171 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-CM-6172    TCGA-CM-6674    TCGA-CM-6675    TCGA-CM-6676    TCGA-CM-6677 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-CM-6678    TCGA-CM-6679    TCGA-CM-6680    TCGA-D5-5537    TCGA-D5-5538 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-D5-5539    TCGA-D5-5540    TCGA-D5-5541    TCGA-D5-6529    TCGA-D5-6532 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-D5-6533    TCGA-D5-6534    TCGA-D5-6535    TCGA-D5-6536    TCGA-D5-6537 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-D5-6538    TCGA-D5-6539    TCGA-D5-6540    TCGA-D5-6541    TCGA-D5-6898 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-D5-6920    TCGA-D5-6922    TCGA-D5-6923    TCGA-D5-6924    TCGA-D5-6926 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-D5-6927    TCGA-D5-6928    TCGA-D5-6929    TCGA-D5-6930    TCGA-D5-6931 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-D5-6932    TCGA-D5-7000    TCGA-DM-A0X9    TCGA-DM-A0XD    TCGA-DM-A0XF 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-DM-A1D0    TCGA-DM-A1D4    TCGA-DM-A1D6    TCGA-DM-A1D7    TCGA-DM-A1D8 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-DM-A1D9    TCGA-DM-A1DA    TCGA-DM-A1DB    TCGA-DM-A1HA    TCGA-DM-A1HB 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-DM-A282    TCGA-DM-A285    TCGA-DM-A28C    TCGA-DM-A28E    TCGA-DM-A28F 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-DM-A28G    TCGA-DM-A28H    TCGA-DM-A28K    TCGA-F4-6459    TCGA-F4-6460 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-F4-6569    TCGA-F4-6570    TCGA-F4-6703    TCGA-F4-6704    TCGA-F4-6805 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-F4-6806    TCGA-F4-6807    TCGA-F4-6808    TCGA-F4-6809    TCGA-F4-6854 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-F4-6855    TCGA-F4-6856    TCGA-G4-6293    TCGA-G4-6299    TCGA-G4-6303 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-G4-6304    TCGA-G4-6306    TCGA-G4-6307    TCGA-G4-6309    TCGA-G4-6310 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-G4-6315    TCGA-G4-6317    TCGA-G4-6321    TCGA-G4-6323    TCGA-G4-6586 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-G4-6588    TCGA-G4-6625    TCGA-G4-6626    TCGA-G4-6628 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 

Clustering(556) Variable = DSG1 MUTATION ANALYSIS
D556V1, survival
                sevent
clus2              0   1
  DSG1 MUTATED    17   1
  DSG1 WILD-TYPE 265  72
  DSG1 MUTATED DSG1 WILD-TYPE 
            18            337 
  DSG1 MUTATED DSG1 WILD-TYPE 
             1             72 
$`DSG1 MUTATED`
TCGA-AA-3510 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-A00N TCGA-AA-A010 
       63.98        26.01        24.00         2.01         4.01        34.98 
TCGA-AA-A01F TCGA-AA-A01R TCGA-AU-6004 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 
       32.02        35.01        27.09        58.39         0.33         0.10 
TCGA-CM-6169 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6931 TCGA-G4-6307 TCGA-G4-6586 
       13.02        12.49        15.58        12.00        55.04        35.80 

$`DSG1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3952 TCGA-AA-3955 
        2.01        12.99        24.00        33.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S 
       12.00        31.00        31.00        38.07         1.02         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6898 
       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         1.51        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  DSG1 MUTATED DSG1 WILD-TYPE 
           0.1            0.0 
  DSG1 MUTATED DSG1 WILD-TYPE 
         63.98         140.38 
  DSG1 MUTATED DSG1 WILD-TYPE 
        25.005         20.120 
[1] "0.1 - 64.0 (25.0)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "3.7"
D556V2, 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       24       101         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DSG1 MUTATED           1          1          3          1        0         0
  DSG1 WILD-TYPE        18          9         38         30       35        13
                vv
clus             STAGE IVB
  DSG1 MUTATED           0
  DSG1 WILD-TYPE         1
D556V3, multiclass
            clus
vv           DSG1 MUTATED DSG1 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             8            101
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            1              9
  STAGE IIIB            3             38
  STAGE IIIC            1             30
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  DSG1 MUTATED     0   1  14   3
  DSG1 WILD-TYPE   9  67 234  38
D556V4, multiclass
    clus
vv   DSG1 MUTATED DSG1 WILD-TYPE
  T1            0              9
  T2            1             67
  T3           14            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
  DSG1 MUTATED    13   3   2
  DSG1 WILD-TYPE 207  77  64
D556V5, multiclass
    clus
vv   DSG1 MUTATED DSG1 WILD-TYPE
  N0           13            207
  N1            3             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"
D556V6, binary
                cls
clus               0   1
  DSG1 MUTATED    18   0
  DSG1 WILD-TYPE 265  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSG1 MUTATED     18    0
  DSG1 WILD-TYPE  265   48
   clus
vv  DSG1 MUTATED DSG1 WILD-TYPE
  0           18            265
  1            0             48
[1] 2 2
[1] FALSE
D556V7, 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
D556V8, binary
                cls
clus               0   1
  DSG1 MUTATED    12   6
  DSG1 WILD-TYPE 305  42
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSG1 MUTATED     12    6
  DSG1 WILD-TYPE  305   42
                               clus
vv                              DSG1 MUTATED DSG1 WILD-TYPE
  COLON ADENOCARCINOMA                    12            305
  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 242   2  22  19
D556V9, multiclass
    clus
vv   DSG1 MUTATED DSG1 WILD-TYPE
  R0           15            242
  R1            0              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"
D556V10, 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
D556V11, 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(557) Variable = ENTPD4 MUTATION ANALYSIS
D557V1, survival
                  sevent
clus2                0   1
  ENTPD4 MUTATED    13   3
  ENTPD4 WILD-TYPE 269  70
  ENTPD4 MUTATED ENTPD4 WILD-TYPE 
              16              339 
  ENTPD4 MUTATED ENTPD4 WILD-TYPE 
               3               70 
$`ENTPD4 MUTATED`
TCGA-A6-6649 TCGA-AA-3489 TCGA-AA-3715 TCGA-AA-3949 TCGA-AA-A010 TCGA-AA-A01P 
       24.16         7.04        19.04        26.01        34.98        38.07 
TCGA-AD-6889 TCGA-AD-6895 TCGA-CM-6170 TCGA-D5-6929 TCGA-D5-6930 TCGA-DM-A1HB 
       56.55         0.72        15.02        13.41         1.51       135.65 
TCGA-F4-6856 TCGA-G4-6315 TCGA-G4-6588 TCGA-G4-6628 
       19.43        36.72        26.17        52.80 

$`ENTPD4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        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        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       21.37         4.21         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.41       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        51.75        45.11        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       35.80        91.79        46.75 

  ENTPD4 MUTATED ENTPD4 WILD-TYPE 
            0.72             0.00 
  ENTPD4 MUTATED ENTPD4 WILD-TYPE 
          135.65           140.38 
  ENTPD4 MUTATED ENTPD4 WILD-TYPE 
          25.085           20.120 
[1] "0.7 - 135.7 (25.1)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.3"
D557V2, 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       22       106         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ENTPD4 MUTATED           1          0          3          0        2
  ENTPD4 WILD-TYPE        18         10         38         31       33
                  vv
clus               STAGE IVA STAGE IVB
  ENTPD4 MUTATED           0         0
  ENTPD4 WILD-TYPE        13         1
D557V3, multiclass
            clus
vv           ENTPD4 MUTATED ENTPD4 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                3               22
  STAGE IIA               3              106
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              3               38
  STAGE IIIC              0               31
  STAGE IV                2               33
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ENTPD4 MUTATED     0   3  12   2
  ENTPD4 WILD-TYPE   9  65 236  39
D557V4, multiclass
    clus
vv   ENTPD4 MUTATED ENTPD4 WILD-TYPE
  T1              0                9
  T2              3               65
  T3             12              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
  ENTPD4 MUTATED    10   7   0
  ENTPD4 WILD-TYPE 210  73  66
D557V5, multiclass
    clus
vv   ENTPD4 MUTATED ENTPD4 WILD-TYPE
  N0             10              210
  N1              7               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"
D557V6, binary
                  cls
clus                 0   1
  ENTPD4 MUTATED    14   2
  ENTPD4 WILD-TYPE 269  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ENTPD4 MUTATED     14    2
  ENTPD4 WILD-TYPE  269   46
   clus
vv  ENTPD4 MUTATED ENTPD4 WILD-TYPE
  0             14              269
  1              2               46
[1] 2 2
[1] FALSE
D557V7, 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
D557V8, binary
                  cls
clus                 0   1
  ENTPD4 MUTATED    14   3
  ENTPD4 WILD-TYPE 303  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ENTPD4 MUTATED     14    3
  ENTPD4 WILD-TYPE  303   45
                               clus
vv                              ENTPD4 MUTATED ENTPD4 WILD-TYPE
  COLON ADENOCARCINOMA                      14              303
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ENTPD4 MUTATED    13   0   0   0
  ENTPD4 WILD-TYPE 244   2  22  21
D557V9, multiclass
    clus
vv   ENTPD4 MUTATED ENTPD4 WILD-TYPE
  R0             13              244
  R1              0                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"
D557V10, 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
D557V11, 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(558) Variable = ATP6V1D MUTATION ANALYSIS
D558V1, survival
                   sevent
clus2                 0   1
  ATP6V1D MUTATED     4   1
  ATP6V1D WILD-TYPE 278  72
  ATP6V1D MUTATED ATP6V1D WILD-TYPE 
                5               350 
  ATP6V1D MUTATED ATP6V1D WILD-TYPE 
                1                72 
$`ATP6V1D MUTATED`
TCGA-A6-5660 TCGA-AA-3713 TCGA-AZ-6600 TCGA-CK-5914 TCGA-CM-6164 
       29.19        19.04        12.10        21.99        29.03 

$`ATP6V1D WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 
       40.34        15.62        49.08        51.32        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  ATP6V1D MUTATED ATP6V1D WILD-TYPE 
             12.1               0.0 
  ATP6V1D MUTATED ATP6V1D WILD-TYPE 
            29.19            140.38 
  ATP6V1D MUTATED ATP6V1D WILD-TYPE 
           21.990            20.155 
[1] "12.1 - 29.2 (22.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D558V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATP6V1D MUTATED         0        0        0         1         0         0
  ATP6V1D WILD-TYPE      64        1       25       108         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP6V1D MUTATED           0          0          1          1        2
  ATP6V1D WILD-TYPE        19         10         40         30       33
                   vv
clus                STAGE IVA STAGE IVB
  ATP6V1D MUTATED           0         0
  ATP6V1D WILD-TYPE        13         1
D558V3, multiclass
            clus
vv           ATP6V1D MUTATED ATP6V1D WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                1               108
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               1                30
  STAGE IV                 2                33
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ATP6V1D MUTATED     0   0   4   1
  ATP6V1D WILD-TYPE   9  68 244  40
D558V4, multiclass
    clus
vv   ATP6V1D MUTATED ATP6V1D WILD-TYPE
  T1               0                 9
  T2               0                68
  T3               4               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
  ATP6V1D MUTATED     2   2   1
  ATP6V1D WILD-TYPE 218  78  65
D558V5, multiclass
    clus
vv   ATP6V1D MUTATED ATP6V1D WILD-TYPE
  N0               2               218
  N1               2                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"
D558V6, binary
                   cls
clus                  0   1
  ATP6V1D MUTATED     2   2
  ATP6V1D WILD-TYPE 281  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ATP6V1D MUTATED      2    2
  ATP6V1D WILD-TYPE  281   46
   clus
vv  ATP6V1D MUTATED ATP6V1D WILD-TYPE
  0               2               281
  1               2                46
[1] 2 2
[1] FALSE
D558V7, binary
                   cls
clus                  0   1
  ATP6V1D MUTATED     1   4
  ATP6V1D WILD-TYPE 169 193
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ATP6V1D MUTATED      1    4
  ATP6V1D WILD-TYPE  169  193
        clus
vv       ATP6V1D MUTATED ATP6V1D WILD-TYPE
  FEMALE               1               169
  MALE                 4               193
[1] 2 2
[1] FALSE
D558V8, binary
                   cls
clus                  0   1
  ATP6V1D MUTATED     5   0
  ATP6V1D WILD-TYPE 312  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ATP6V1D MUTATED      5    0
  ATP6V1D WILD-TYPE  312   48
                               clus
vv                              ATP6V1D MUTATED ATP6V1D WILD-TYPE
  COLON ADENOCARCINOMA                        5               312
  COLON MUCINOUS ADENOCARCINOMA               0                48
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ATP6V1D MUTATED     1   0   1   1
  ATP6V1D WILD-TYPE 256   2  21  20
D558V9, multiclass
    clus
vv   ATP6V1D MUTATED ATP6V1D WILD-TYPE
  R0               1               256
  R1               0                 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"
D558V10, 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     2
  ATP6V1D WILD-TYPE                        17   174
D558V11, 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                                          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(559) Variable = ACTL8 MUTATION ANALYSIS
D559V1, survival
                 sevent
clus2               0   1
  ACTL8 MUTATED     6   2
  ACTL8 WILD-TYPE 276  71
  ACTL8 MUTATED ACTL8 WILD-TYPE 
              8             347 
  ACTL8 MUTATED ACTL8 WILD-TYPE 
              2              71 
$`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        40.34 
TCGA-CM-6676 TCGA-G4-6323 
       11.08        13.78 

$`ACTL8 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       17.03        24.03        27.02        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 
       56.55         0.79         0.72         5.79        22.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 
       22.36        62.79        61.41        49.41         6.77       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 
        0.10         1.35        17.56       102.44        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  ACTL8 MUTATED ACTL8 WILD-TYPE 
          11.08            0.00 
  ACTL8 MUTATED ACTL8 WILD-TYPE 
          40.34          140.38 
  ACTL8 MUTATED ACTL8 WILD-TYPE 
          20.24           20.19 
[1] "11.1 - 40.3 (20.2)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.4"
D559V2, 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       24       107         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ACTL8 MUTATED           0          1          0          0        2         0
  ACTL8 WILD-TYPE        19          9         41         31       33        13
                 vv
clus              STAGE IVB
  ACTL8 MUTATED           0
  ACTL8 WILD-TYPE         1
D559V3, multiclass
            clus
vv           ACTL8 MUTATED ACTL8 WILD-TYPE
  STAGE I                1              63
  STAGE IA               1               0
  STAGE II               1              24
  STAGE IIA              2             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               2              33
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ACTL8 MUTATED     0   1   6   1
  ACTL8 WILD-TYPE   9  67 242  40
D559V4, multiclass
    clus
vv   ACTL8 MUTATED ACTL8 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             6             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
  ACTL8 MUTATED     6   2   1
  ACTL8 WILD-TYPE 214  78  65
D559V5, multiclass
    clus
vv   ACTL8 MUTATED ACTL8 WILD-TYPE
  N0             6             214
  N1             2              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"
D559V6, binary
                 cls
clus                0   1
  ACTL8 MUTATED     4   2
  ACTL8 WILD-TYPE 279  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACTL8 MUTATED      4    2
  ACTL8 WILD-TYPE  279   46
   clus
vv  ACTL8 MUTATED ACTL8 WILD-TYPE
  0             4             279
  1             2              46
[1] 2 2
[1] FALSE
D559V7, 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
D559V8, binary
                 cls
clus                0   1
  ACTL8 MUTATED     9   0
  ACTL8 WILD-TYPE 308  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACTL8 MUTATED      9    0
  ACTL8 WILD-TYPE  308   48
                               clus
vv                              ACTL8 MUTATED ACTL8 WILD-TYPE
  COLON ADENOCARCINOMA                      9             308
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ACTL8 MUTATED     6   1   0   0
  ACTL8 WILD-TYPE 251   1  22  21
D559V9, multiclass
    clus
vv   ACTL8 MUTATED ACTL8 WILD-TYPE
  R0             6             251
  R1             1               1
  R2             0              22
  RX             0              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D559V10, 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
D559V11, 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(560) Variable = MMP13 MUTATION ANALYSIS
D560V1, survival
                 sevent
clus2               0   1
  MMP13 MUTATED     9   4
  MMP13 WILD-TYPE 273  69
  MMP13 MUTATED MMP13 WILD-TYPE 
             13             342 
  MMP13 MUTATED MMP13 WILD-TYPE 
              4              69 
$`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         2.24         0.33 
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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
       51.32        21.99         2.93         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        16.01        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-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       45.40        12.26        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
        6.12        81.37       119.93        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        13.38        13.45        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  MMP13 MUTATED MMP13 WILD-TYPE 
           0.33            0.00 
  MMP13 MUTATED MMP13 WILD-TYPE 
          49.41          140.38 
  MMP13 MUTATED MMP13 WILD-TYPE 
         21.140          20.155 
[1] "0.3 - 49.4 (21.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.9"
D560V2, 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       24       104         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        19          9         37         31       35        13
                 vv
clus              STAGE IVB
  MMP13 MUTATED           0
  MMP13 WILD-TYPE         1
D560V3, multiclass
            clus
vv           MMP13 MUTATED MMP13 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              5             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             4              37
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MMP13 MUTATED     1   0  11   1
  MMP13 WILD-TYPE   8  68 237  40
D560V4, multiclass
    clus
vv   MMP13 MUTATED MMP13 WILD-TYPE
  T1             1               8
  T2             0              68
  T3            11             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
  MMP13 MUTATED     8   4   1
  MMP13 WILD-TYPE 212  76  65
D560V5, multiclass
    clus
vv   MMP13 MUTATED MMP13 WILD-TYPE
  N0             8             212
  N1             4              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"
D560V6, binary
                 cls
clus                0   1
  MMP13 MUTATED    12   0
  MMP13 WILD-TYPE 271  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP13 MUTATED     12    0
  MMP13 WILD-TYPE  271   48
   clus
vv  MMP13 MUTATED MMP13 WILD-TYPE
  0            12             271
  1             0              48
[1] 2 2
[1] FALSE
D560V7, 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
D560V8, binary
                 cls
clus                0   1
  MMP13 MUTATED    10   3
  MMP13 WILD-TYPE 307  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP13 MUTATED     10    3
  MMP13 WILD-TYPE  307   45
                               clus
vv                              MMP13 MUTATED MMP13 WILD-TYPE
  COLON ADENOCARCINOMA                     10             307
  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 250   2  22  18
D560V9, multiclass
    clus
vv   MMP13 MUTATED MMP13 WILD-TYPE
  R0             7             250
  R1             0               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"
D560V10, 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
D560V11, 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(561) Variable = SPAST MUTATION ANALYSIS
D561V1, survival
                 sevent
clus2               0   1
  SPAST MUTATED     5   3
  SPAST WILD-TYPE 277  70
  SPAST MUTATED SPAST WILD-TYPE 
              8             347 
  SPAST MUTATED SPAST WILD-TYPE 
              3              70 
$`SPAST MUTATED`
TCGA-AA-3715 TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-3977 TCGA-AZ-4315 TCGA-AZ-6601 
       19.04        53.00        33.01        25.02        58.39       100.01 
TCGA-AZ-6603 TCGA-CA-6718 
       29.56         0.10 

$`SPAST WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6605 
       62.79        61.41        49.41         6.77        12.10         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.33         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  SPAST MUTATED SPAST WILD-TYPE 
            0.1             0.0 
  SPAST MUTATED SPAST WILD-TYPE 
         100.01          140.38 
  SPAST MUTATED SPAST WILD-TYPE 
         31.285          20.020 
[1] "0.1 - 100.0 (31.3)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.2"
D561V2, 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       22       107         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SPAST MUTATED           0          0          0          0        0         0
  SPAST WILD-TYPE        19         10         41         31       35        13
                 vv
clus              STAGE IVB
  SPAST MUTATED           0
  SPAST WILD-TYPE         1
D561V3, multiclass
            clus
vv           SPAST MUTATED SPAST WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              2             107
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SPAST MUTATED     0   2   5   1
  SPAST WILD-TYPE   9  66 243  40
D561V4, multiclass
    clus
vv   SPAST MUTATED SPAST WILD-TYPE
  T1             0               9
  T2             2              66
  T3             5             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   1   0
  SPAST WILD-TYPE 213  79  66
D561V5, multiclass
    clus
vv   SPAST MUTATED SPAST WILD-TYPE
  N0             7             213
  N1             1              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
  SPAST MUTATED     6   0
  SPAST WILD-TYPE 277  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPAST MUTATED      6    0
  SPAST WILD-TYPE  277   48
   clus
vv  SPAST MUTATED SPAST WILD-TYPE
  0             6             277
  1             0              48
[1] 2 2
[1] FALSE
D561V7, binary
                 cls
clus                0   1
  SPAST MUTATED     2   6
  SPAST WILD-TYPE 168 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPAST MUTATED      2    6
  SPAST WILD-TYPE  168  191
        clus
vv       SPAST MUTATED SPAST WILD-TYPE
  FEMALE             2             168
  MALE               6             191
[1] 2 2
[1] FALSE
D561V8, binary
                 cls
clus                0   1
  SPAST MUTATED     7   1
  SPAST WILD-TYPE 310  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPAST MUTATED      7    1
  SPAST WILD-TYPE  310   47
                               clus
vv                              SPAST MUTATED SPAST WILD-TYPE
  COLON ADENOCARCINOMA                      7             310
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SPAST MUTATED     4   0   0   1
  SPAST WILD-TYPE 253   2  22  20
D561V9, multiclass
    clus
vv   SPAST MUTATED SPAST WILD-TYPE
  R0             4             253
  R1             0               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"
D561V10, 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                           0     3
  SPAST WILD-TYPE                        19   173
D561V11, multiclass
                                  clus
vv                                 SPAST MUTATED SPAST 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(562) Variable = ZNF518B MUTATION ANALYSIS
D562V1, survival
                   sevent
clus2                 0   1
  ZNF518B MUTATED     8   1
  ZNF518B WILD-TYPE 274  72
  ZNF518B MUTATED ZNF518B WILD-TYPE 
                9               346 
  ZNF518B MUTATED ZNF518B WILD-TYPE 
                1                72 
$`ZNF518B MUTATED`
TCGA-A6-6781 TCGA-AD-6889 TCGA-AD-6901 TCGA-CA-6717 TCGA-CM-6163 TCGA-CM-6171 
       19.66        56.55        22.42         0.33        14.04        14.04 
TCGA-CM-6172 TCGA-D5-6929 TCGA-G4-6306 
       11.01        13.41        44.68 

$`ZNF518B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 
        4.21         0.79         0.72         5.79        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-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-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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 
      107.67        74.56        65.85        53.62        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  ZNF518B MUTATED ZNF518B WILD-TYPE 
             0.33              0.00 
  ZNF518B MUTATED ZNF518B WILD-TYPE 
            56.55            140.38 
  ZNF518B MUTATED ZNF518B WILD-TYPE 
            14.04             20.63 
[1] "0.3 - 56.5 (14.0)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "1.7"
D562V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF518B MUTATED         3        0        0         3         0         0
  ZNF518B WILD-TYPE      61        1       25       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        19         10         40         30       34
                   vv
clus                STAGE IVA STAGE IVB
  ZNF518B MUTATED           0         0
  ZNF518B WILD-TYPE        13         1
D562V3, multiclass
            clus
vv           ZNF518B MUTATED ZNF518B WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                3               106
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               1                30
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ZNF518B MUTATED     1   3   5   1
  ZNF518B WILD-TYPE   8  65 243  40
D562V4, multiclass
    clus
vv   ZNF518B MUTATED ZNF518B WILD-TYPE
  T1               1                 8
  T2               3                65
  T3               5               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
  ZNF518B MUTATED     7   3   0
  ZNF518B WILD-TYPE 213  77  66
D562V5, multiclass
    clus
vv   ZNF518B MUTATED ZNF518B WILD-TYPE
  N0               7               213
  N1               3                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"
D562V6, binary
                   cls
clus                  0   1
  ZNF518B MUTATED     6   1
  ZNF518B WILD-TYPE 277  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF518B MUTATED      6    1
  ZNF518B WILD-TYPE  277   47
   clus
vv  ZNF518B MUTATED ZNF518B WILD-TYPE
  0               6               277
  1               1                47
[1] 2 2
[1] FALSE
D562V7, 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
D562V8, binary
                   cls
clus                  0   1
  ZNF518B MUTATED     8   2
  ZNF518B WILD-TYPE 309  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF518B MUTATED      8    2
  ZNF518B WILD-TYPE  309   46
                               clus
vv                              ZNF518B MUTATED ZNF518B WILD-TYPE
  COLON ADENOCARCINOMA                        8               309
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ZNF518B MUTATED     6   0   0   2
  ZNF518B WILD-TYPE 251   2  22  19
D562V9, multiclass
    clus
vv   ZNF518B MUTATED ZNF518B WILD-TYPE
  R0               6               251
  R1               0                 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"
D562V10, 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
D562V11, 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(563) Variable = DSG4 MUTATION ANALYSIS
D563V1, survival
                sevent
clus2              0   1
  DSG4 MUTATED    20   1
  DSG4 WILD-TYPE 262  72
  DSG4 MUTATED DSG4 WILD-TYPE 
            21            334 
  DSG4 MUTATED DSG4 WILD-TYPE 
             1             72 
$`DSG4 MUTATED`
TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3660 TCGA-AA-3672 
       20.12        19.66        63.98        29.95        78.08         0.92 
TCGA-AA-3864 TCGA-AA-3950 TCGA-AA-A00J TCGA-AY-6196 TCGA-AY-6386 TCGA-CA-6718 
       53.00        24.00        18.05         0.20        17.82         0.10 
TCGA-CK-4950 TCGA-D5-6533 TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6929 TCGA-DM-A282 
       40.34         1.32        16.14        12.39        13.41       139.17 
TCGA-F4-6570 TCGA-F4-6703 TCGA-G4-6321 
        6.18        35.87        22.09 

$`DSG4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       23.87        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
        1.35        17.56       102.44        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 
       13.51        11.51        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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A285 
      140.38         7.50        44.32       131.51       135.65         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
        8.61        13.38        13.45         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 
       51.75        45.11        36.72        36.00        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  DSG4 MUTATED DSG4 WILD-TYPE 
           0.1            0.0 
  DSG4 MUTATED DSG4 WILD-TYPE 
        139.17         140.38 
  DSG4 MUTATED DSG4 WILD-TYPE 
         19.66          20.63 
[1] "0.1 - 139.2 (19.7)" "0.0 - 140.4 (20.6)"
[1] "hr=" "4.9"
D563V2, 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       22       101         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DSG4 MUTATED           2          1          3          2        1         0
  DSG4 WILD-TYPE        17          9         38         29       34        13
                vv
clus             STAGE IVB
  DSG4 MUTATED           0
  DSG4 WILD-TYPE         1
D563V3, multiclass
            clus
vv           DSG4 MUTATED DSG4 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              3             22
  STAGE IIA             8            101
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             2             17
  STAGE IIIA            1              9
  STAGE IIIB            3             38
  STAGE IIIC            2             29
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  DSG4 MUTATED     0   2  16   3
  DSG4 WILD-TYPE   9  66 232  38
D563V4, multiclass
    clus
vv   DSG4 MUTATED DSG4 WILD-TYPE
  T1            0              9
  T2            2             66
  T3           16            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
  DSG4 MUTATED    13   7   1
  DSG4 WILD-TYPE 207  73  65
D563V5, multiclass
    clus
vv   DSG4 MUTATED DSG4 WILD-TYPE
  N0           13            207
  N1            7             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"
D563V6, binary
                cls
clus               0   1
  DSG4 MUTATED    16   1
  DSG4 WILD-TYPE 267  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSG4 MUTATED     16    1
  DSG4 WILD-TYPE  267   47
   clus
vv  DSG4 MUTATED DSG4 WILD-TYPE
  0           16            267
  1            1             47
[1] 2 2
[1] FALSE
D563V7, 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
D563V8, binary
                cls
clus               0   1
  DSG4 MUTATED    14   7
  DSG4 WILD-TYPE 303  41
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSG4 MUTATED     14    7
  DSG4 WILD-TYPE  303   41
                               clus
vv                              DSG4 MUTATED DSG4 WILD-TYPE
  COLON ADENOCARCINOMA                    14            303
  COLON MUCINOUS ADENOCARCINOMA            7             41
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  DSG4 MUTATED    17   1   0   1
  DSG4 WILD-TYPE 240   1  22  20
D563V9, multiclass
    clus
vv   DSG4 MUTATED DSG4 WILD-TYPE
  R0           17            240
  R1            1              1
  R2            0             22
  RX            1             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D563V10, 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
D563V11, 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(564) Variable = NOVA1 MUTATION ANALYSIS
D564V1, survival
                 sevent
clus2               0   1
  NOVA1 MUTATED     8   5
  NOVA1 WILD-TYPE 274  68
  NOVA1 MUTATED NOVA1 WILD-TYPE 
             13             342 
  NOVA1 MUTATED NOVA1 WILD-TYPE 
              5              68 
$`NOVA1 MUTATED`
TCGA-A6-2677 TCGA-A6-3810 TCGA-A6-6781 TCGA-AA-3710 TCGA-AA-3877 TCGA-AA-A010 
       24.33        36.53        19.66        26.99        31.00        34.98 
TCGA-AD-5900 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-CK-5916 TCGA-D5-6540 TCGA-G4-6303 
        0.07        49.41         6.77        21.14        16.14        65.85 
TCGA-G4-6310 
       45.11 

$`NOVA1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        42.90        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       34.65        33.34        32.75        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
       40.34        15.62        49.08        51.32        21.99         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 
        0.53        35.41        19.43       107.67        74.56        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        51.75        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  NOVA1 MUTATED NOVA1 WILD-TYPE 
           0.07            0.00 
  NOVA1 MUTATED NOVA1 WILD-TYPE 
          65.85          140.38 
  NOVA1 MUTATED NOVA1 WILD-TYPE 
         26.990          20.005 
[1] "0.1 - 65.8 (27.0)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1.7"
D564V2, 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       24       107         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        19         10         40         29       34        13
                 vv
clus              STAGE IVB
  NOVA1 MUTATED           0
  NOVA1 WILD-TYPE         1
D564V3, multiclass
            clus
vv           NOVA1 MUTATED NOVA1 WILD-TYPE
  STAGE I                5              59
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              2             107
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             2              29
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NOVA1 MUTATED     2   3   6   3
  NOVA1 WILD-TYPE   7  65 242  38
D564V4, multiclass
    clus
vv   NOVA1 MUTATED NOVA1 WILD-TYPE
  T1             2               7
  T2             3              65
  T3             6             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
  NOVA1 MUTATED    10   3   1
  NOVA1 WILD-TYPE 210  77  65
D564V5, multiclass
    clus
vv   NOVA1 MUTATED NOVA1 WILD-TYPE
  N0            10             210
  N1             3              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"
D564V6, binary
                 cls
clus                0   1
  NOVA1 MUTATED     8   1
  NOVA1 WILD-TYPE 275  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NOVA1 MUTATED      8    1
  NOVA1 WILD-TYPE  275   47
   clus
vv  NOVA1 MUTATED NOVA1 WILD-TYPE
  0             8             275
  1             1              47
[1] 2 2
[1] FALSE
D564V7, 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
D564V8, binary
                 cls
clus                0   1
  NOVA1 MUTATED    10   4
  NOVA1 WILD-TYPE 307  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NOVA1 MUTATED     10    4
  NOVA1 WILD-TYPE  307   44
                               clus
vv                              NOVA1 MUTATED NOVA1 WILD-TYPE
  COLON ADENOCARCINOMA                     10             307
  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 247   2  22  19
D564V9, multiclass
    clus
vv   NOVA1 MUTATED NOVA1 WILD-TYPE
  R0            10             247
  R1             0               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"
D564V10, 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
D564V11, 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(565) Variable = OR6C75 MUTATION ANALYSIS
D565V1, survival
                  sevent
clus2                0   1
  OR6C75 MUTATED     6   1
  OR6C75 WILD-TYPE 276  72
  OR6C75 MUTATED OR6C75 WILD-TYPE 
               7              348 
  OR6C75 MUTATED OR6C75 WILD-TYPE 
               1               72 
$`OR6C75 MUTATED`
TCGA-AA-3710 TCGA-AA-3977 TCGA-AZ-4315 TCGA-AZ-6601 TCGA-CA-5255 TCGA-CM-6170 
       26.99        25.02        58.39       100.01         3.06        15.02 
TCGA-D5-6932 
       11.38 

$`OR6C75 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        2.24         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  OR6C75 MUTATED OR6C75 WILD-TYPE 
            3.06             0.00 
  OR6C75 MUTATED OR6C75 WILD-TYPE 
          100.01           140.38 
  OR6C75 MUTATED OR6C75 WILD-TYPE 
          25.020           20.155 
[1] "3.1 - 100.0 (25.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "2"  
D565V2, 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       24       105         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR6C75 MUTATED           0          0          0          0        0
  OR6C75 WILD-TYPE        19         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  OR6C75 MUTATED           0         0
  OR6C75 WILD-TYPE        13         1
D565V3, multiclass
            clus
vv           OR6C75 MUTATED OR6C75 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               4              105
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  OR6C75 MUTATED     0   2   5   0
  OR6C75 WILD-TYPE   9  66 243  41
D565V4, multiclass
    clus
vv   OR6C75 MUTATED OR6C75 WILD-TYPE
  T1              0                9
  T2              2               66
  T3              5              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
  OR6C75 MUTATED     7   0   0
  OR6C75 WILD-TYPE 213  80  66
D565V5, multiclass
    clus
vv   OR6C75 MUTATED OR6C75 WILD-TYPE
  N0              7              213
  N1              0               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"
D565V6, binary
                  cls
clus                 0   1
  OR6C75 MUTATED     6   0
  OR6C75 WILD-TYPE 277  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR6C75 MUTATED      6    0
  OR6C75 WILD-TYPE  277   48
   clus
vv  OR6C75 MUTATED OR6C75 WILD-TYPE
  0              6              277
  1              0               48
[1] 2 2
[1] FALSE
D565V7, 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
D565V8, binary
                  cls
clus                 0   1
  OR6C75 MUTATED     7   0
  OR6C75 WILD-TYPE 310  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR6C75 MUTATED      7    0
  OR6C75 WILD-TYPE  310   48
                               clus
vv                              OR6C75 MUTATED OR6C75 WILD-TYPE
  COLON ADENOCARCINOMA                       7              310
  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 253   2  22  20
D565V9, multiclass
    clus
vv   OR6C75 MUTATED OR6C75 WILD-TYPE
  R0              4              253
  R1              0                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"
D565V10, 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
D565V11, 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(566) Variable = CYP2C18 MUTATION ANALYSIS
D566V1, survival
                   sevent
clus2                 0   1
  CYP2C18 MUTATED     4   1
  CYP2C18 WILD-TYPE 278  72
  CYP2C18 MUTATED CYP2C18 WILD-TYPE 
                5               350 
  CYP2C18 MUTATED CYP2C18 WILD-TYPE 
                1                72 
$`CYP2C18 MUTATED`
TCGA-AD-6889 TCGA-AZ-5403 TCGA-CM-5860 TCGA-F4-6856 TCGA-G4-6310 
       56.55        62.79        16.01        19.43        45.11 

$`CYP2C18 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        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        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 
        1.41         5.13        83.80        22.36        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 
       33.67        13.25         0.53        35.41       107.67        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        51.75        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  CYP2C18 MUTATED CYP2C18 WILD-TYPE 
            16.01              0.00 
  CYP2C18 MUTATED CYP2C18 WILD-TYPE 
            62.79            140.38 
  CYP2C18 MUTATED CYP2C18 WILD-TYPE 
           45.110            20.155 
[1] "16.0 - 62.8 (45.1)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.7"
D566V2, 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       24       107         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CYP2C18 MUTATED           0          0          1          0        0
  CYP2C18 WILD-TYPE        19         10         40         31       35
                   vv
clus                STAGE IVA STAGE IVB
  CYP2C18 MUTATED           0         0
  CYP2C18 WILD-TYPE        13         1
D566V3, multiclass
            clus
vv           CYP2C18 MUTATED CYP2C18 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                2               107
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CYP2C18 MUTATED     0   1   4   0
  CYP2C18 WILD-TYPE   9  67 244  41
D566V4, multiclass
    clus
vv   CYP2C18 MUTATED CYP2C18 WILD-TYPE
  T1               0                 9
  T2               1                67
  T3               4               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
  CYP2C18 MUTATED     4   1   0
  CYP2C18 WILD-TYPE 216  79  66
D566V5, multiclass
    clus
vv   CYP2C18 MUTATED CYP2C18 WILD-TYPE
  N0               4               216
  N1               1                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"
D566V6, binary
                   cls
clus                  0   1
  CYP2C18 MUTATED     4   0
  CYP2C18 WILD-TYPE 279  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP2C18 MUTATED      4    0
  CYP2C18 WILD-TYPE  279   48
   clus
vv  CYP2C18 MUTATED CYP2C18 WILD-TYPE
  0               4               279
  1               0                48
[1] 2 2
[1] FALSE
D566V7, 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
D566V8, binary
                   cls
clus                  0   1
  CYP2C18 MUTATED     4   1
  CYP2C18 WILD-TYPE 313  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP2C18 MUTATED      4    1
  CYP2C18 WILD-TYPE  313   47
                               clus
vv                              CYP2C18 MUTATED CYP2C18 WILD-TYPE
  COLON ADENOCARCINOMA                        4               313
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  CYP2C18 MUTATED     3   0   0   0
  CYP2C18 WILD-TYPE 254   2  22  21
D566V9, multiclass
    clus
vv   CYP2C18 MUTATED CYP2C18 WILD-TYPE
  R0               3               254
  R1               0                 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"
D566V10, 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
D566V11, 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(567) Variable = NCR3 MUTATION ANALYSIS
D567V1, survival
                sevent
clus2              0   1
  NCR3 MUTATED     4   1
  NCR3 WILD-TYPE 278  72
  NCR3 MUTATED NCR3 WILD-TYPE 
             5            350 
  NCR3 MUTATED NCR3 WILD-TYPE 
             1             72 
$`NCR3 MUTATED`
TCGA-AA-3864 TCGA-AZ-6598 TCGA-CK-4952 TCGA-D5-6931 TCGA-G4-6293 
       53.00        49.41        15.62        12.00       107.67 

$`NCR3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      102.44        40.34        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        35.41        19.43        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  NCR3 MUTATED NCR3 WILD-TYPE 
            12              0 
  NCR3 MUTATED NCR3 WILD-TYPE 
        107.67         140.38 
  NCR3 MUTATED NCR3 WILD-TYPE 
        49.410         20.155 
[1] "12.0 - 107.7 (49.4)" "0.0 - 140.4 (20.2)" 
[1] "hr=" "2"  
D567V2, 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       23       109         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NCR3 MUTATED           2          0          0          1        0         0
  NCR3 WILD-TYPE        17         10         41         30       35        13
                vv
clus             STAGE IVB
  NCR3 MUTATED           0
  NCR3 WILD-TYPE         1
D567V3, multiclass
            clus
vv           NCR3 MUTATED NCR3 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             0            109
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             2             17
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            1             30
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NCR3 MUTATED     0   0   3   3
  NCR3 WILD-TYPE   9  68 245  38
D567V4, multiclass
    clus
vv   NCR3 MUTATED NCR3 WILD-TYPE
  T1            0              9
  T2            0             68
  T3            3            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
  NCR3 MUTATED     3   1   2
  NCR3 WILD-TYPE 217  79  64
D567V5, multiclass
    clus
vv   NCR3 MUTATED NCR3 WILD-TYPE
  N0            3            217
  N1            1             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"
D567V6, binary
                cls
clus               0   1
  NCR3 MUTATED     4   0
  NCR3 WILD-TYPE 279  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  NCR3 MUTATED      4    0
  NCR3 WILD-TYPE  279   48
   clus
vv  NCR3 MUTATED NCR3 WILD-TYPE
  0            4            279
  1            0             48
[1] 2 2
[1] FALSE
D567V7, binary
                cls
clus               0   1
  NCR3 MUTATED     4   2
  NCR3 WILD-TYPE 166 195
[1] "tbl2"
                cls
clus             [,1] [,2]
  NCR3 MUTATED      4    2
  NCR3 WILD-TYPE  166  195
        clus
vv       NCR3 MUTATED NCR3 WILD-TYPE
  FEMALE            4            166
  MALE              2            195
[1] 2 2
[1] FALSE
D567V8, binary
                cls
clus               0   1
  NCR3 MUTATED     5   1
  NCR3 WILD-TYPE 312  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  NCR3 MUTATED      5    1
  NCR3 WILD-TYPE  312   47
                               clus
vv                              NCR3 MUTATED NCR3 WILD-TYPE
  COLON ADENOCARCINOMA                     5            312
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  NCR3 MUTATED     3   0   0   2
  NCR3 WILD-TYPE 254   2  22  19
D567V9, multiclass
    clus
vv   NCR3 MUTATED NCR3 WILD-TYPE
  R0            3            254
  R1            0              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"
D567V10, 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     5
  NCR3 WILD-TYPE                        19   171
D567V11, 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                                       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(568) Variable = IQSEC2 MUTATION ANALYSIS
D568V1, survival
                  sevent
clus2                0   1
  IQSEC2 MUTATED    14   1
  IQSEC2 WILD-TYPE 268  72
  IQSEC2 MUTATED IQSEC2 WILD-TYPE 
              15              340 
  IQSEC2 MUTATED IQSEC2 WILD-TYPE 
               1               72 
$`IQSEC2 MUTATED`
TCGA-A6-5665 TCGA-AA-3560 TCGA-AA-3662 TCGA-AA-3821 TCGA-AA-3877 TCGA-AA-3947 
       22.06        19.99         6.05         1.02        31.00        33.01 
TCGA-AY-5543 TCGA-AZ-6598 TCGA-CK-5913 TCGA-CM-4743 TCGA-CM-6171 TCGA-D5-6535 
       15.75        49.41        51.32        23.05        14.04        15.12 
TCGA-DM-A1HB TCGA-F4-6856 TCGA-G4-6588 
      135.65        19.43        26.17 

$`IQSEC2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       33.04         0.99        25.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 
       29.98        18.05         2.01        12.99        24.00        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 
      102.44        40.34        15.62        49.08        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        91.79        46.75        52.80 

  IQSEC2 MUTATED IQSEC2 WILD-TYPE 
            1.02             0.00 
  IQSEC2 MUTATED IQSEC2 WILD-TYPE 
          135.65           140.38 
  IQSEC2 MUTATED IQSEC2 WILD-TYPE 
          22.060           20.155 
[1] "1.0 - 135.7 (22.1)" "0.0 - 140.4 (20.2)"
[1] "hr=" "3.7"
D568V2, 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       24       105         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IQSEC2 MUTATED           0          0          2          1        1
  IQSEC2 WILD-TYPE        19         10         39         30       34
                  vv
clus               STAGE IVA STAGE IVB
  IQSEC2 MUTATED           1         0
  IQSEC2 WILD-TYPE        12         1
D568V3, multiclass
            clus
vv           IQSEC2 MUTATED IQSEC2 WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               4              105
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              1               30
  STAGE IV                1               34
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  65 239  38
D568V4, multiclass
    clus
vv   IQSEC2 MUTATED IQSEC2 WILD-TYPE
  T1              1                8
  T2              3               65
  T3              9              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
  IQSEC2 MUTATED    11   3   2
  IQSEC2 WILD-TYPE 209  77  64
D568V5, multiclass
    clus
vv   IQSEC2 MUTATED IQSEC2 WILD-TYPE
  N0             11              209
  N1              3               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"
D568V6, binary
                  cls
clus                 0   1
  IQSEC2 MUTATED    10   2
  IQSEC2 WILD-TYPE 273  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IQSEC2 MUTATED     10    2
  IQSEC2 WILD-TYPE  273   46
   clus
vv  IQSEC2 MUTATED IQSEC2 WILD-TYPE
  0             10              273
  1              2               46
[1] 2 2
[1] FALSE
D568V7, 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
D568V8, binary
                  cls
clus                 0   1
  IQSEC2 MUTATED    12   4
  IQSEC2 WILD-TYPE 305  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IQSEC2 MUTATED     12    4
  IQSEC2 WILD-TYPE  305   44
                               clus
vv                              IQSEC2 MUTATED IQSEC2 WILD-TYPE
  COLON ADENOCARCINOMA                      12              305
  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 247   2  21  18
D568V9, multiclass
    clus
vv   IQSEC2 MUTATED IQSEC2 WILD-TYPE
  R0             10              247
  R1              0                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"
D568V10, 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
D568V11, 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(569) Variable = DBN1 MUTATION ANALYSIS
D569V1, survival
                sevent
clus2              0   1
  DBN1 MUTATED     7   3
  DBN1 WILD-TYPE 275  70
  DBN1 MUTATED DBN1 WILD-TYPE 
            10            345 
  DBN1 MUTATED DBN1 WILD-TYPE 
             3             70 
$`DBN1 MUTATED`
TCGA-A6-5662 TCGA-AA-3713 TCGA-AA-3950 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-D5-6533 
       23.61        19.04        24.00        49.41        12.10         1.32 
TCGA-D5-6540 TCGA-D5-6924 TCGA-D5-7000 TCGA-F4-6570 
       16.14        14.30        10.26         6.18 

$`DBN1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        33.53        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 
       83.80        22.36        62.79        61.41         6.77       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        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-D5-6926 
       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         1.51        12.00        11.38 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  DBN1 MUTATED DBN1 WILD-TYPE 
          1.32           0.00 
  DBN1 MUTATED DBN1 WILD-TYPE 
         49.41         140.38 
  DBN1 MUTATED DBN1 WILD-TYPE 
         15.22          20.98 
[1] "1.3 - 49.4 (15.2)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.9"
D569V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DBN1 MUTATED         2        0        1         3         0         0
  DBN1 WILD-TYPE      62        1       24       106         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DBN1 MUTATED           0          0          1          0        2         1
  DBN1 WILD-TYPE        19         10         40         31       33        12
                vv
clus             STAGE IVB
  DBN1 MUTATED           0
  DBN1 WILD-TYPE         1
D569V3, multiclass
            clus
vv           DBN1 MUTATED DBN1 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             3            106
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              2             33
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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   6   2
  DBN1 WILD-TYPE   9  66 242  39
D569V4, multiclass
    clus
vv   DBN1 MUTATED DBN1 WILD-TYPE
  T1            0              9
  T2            2             66
  T3            6            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
  DBN1 MUTATED     8   1   1
  DBN1 WILD-TYPE 212  79  65
D569V5, multiclass
    clus
vv   DBN1 MUTATED DBN1 WILD-TYPE
  N0            8            212
  N1            1             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"
D569V6, binary
                cls
clus               0   1
  DBN1 MUTATED     6   3
  DBN1 WILD-TYPE 277  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  DBN1 MUTATED      6    3
  DBN1 WILD-TYPE  277   45
   clus
vv  DBN1 MUTATED DBN1 WILD-TYPE
  0            6            277
  1            3             45
[1] 2 2
[1] FALSE
D569V7, binary
                cls
clus               0   1
  DBN1 MUTATED     5   5
  DBN1 WILD-TYPE 165 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  DBN1 MUTATED      5    5
  DBN1 WILD-TYPE  165  192
        clus
vv       DBN1 MUTATED DBN1 WILD-TYPE
  FEMALE            5            165
  MALE              5            192
[1] 2 2
[1] FALSE
D569V8, binary
                cls
clus               0   1
  DBN1 MUTATED     7   3
  DBN1 WILD-TYPE 310  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  DBN1 MUTATED      7    3
  DBN1 WILD-TYPE  310   45
                               clus
vv                              DBN1 MUTATED DBN1 WILD-TYPE
  COLON ADENOCARCINOMA                     7            310
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  DBN1 MUTATED     6   0   1   0
  DBN1 WILD-TYPE 251   2  21  21
D569V9, multiclass
    clus
vv   DBN1 MUTATED DBN1 WILD-TYPE
  R0            6            251
  R1            0              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"
D569V10, 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     7
  DBN1 WILD-TYPE                        18   169
D569V11, 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                                       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(570) Variable = TJP1 MUTATION ANALYSIS
D570V1, survival
                sevent
clus2              0   1
  TJP1 MUTATED    13   5
  TJP1 WILD-TYPE 269  68
  TJP1 MUTATED TJP1 WILD-TYPE 
            18            337 
  TJP1 MUTATED TJP1 WILD-TYPE 
             5             68 
$`TJP1 MUTATED`
TCGA-A6-5666 TCGA-AA-3492 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3715 TCGA-AA-3864 
       32.71         3.02        78.08         6.97        19.04        53.00 
TCGA-AA-3977 TCGA-AA-A00N TCGA-AD-6895 TCGA-AY-6196 TCGA-AZ-5403 TCGA-CA-6718 
       25.02         4.01         0.72         0.20        62.79         0.10 
TCGA-D5-5539 TCGA-D5-6538 TCGA-D5-6928 TCGA-DM-A1D6 TCGA-DM-A1HB TCGA-G4-6588 
       19.59        17.13        11.64        49.91       135.65        26.17 

$`TJP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       13.94        19.99        61.02         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85         4.80        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 
      119.70        24.43        38.20       130.65        92.75        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 
       52.80 

  TJP1 MUTATED TJP1 WILD-TYPE 
           0.1            0.0 
  TJP1 MUTATED TJP1 WILD-TYPE 
        135.65         140.38 
  TJP1 MUTATED TJP1 WILD-TYPE 
        19.315         20.280 
[1] "0.1 - 135.7 (19.3)" "0.0 - 140.4 (20.3)"
[1] "hr=" "1.2"
D570V2, 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       19       105         7         0
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TJP1 MUTATED           0          1          2          1        0         0
  TJP1 WILD-TYPE        19          9         39         30       35        13
                vv
clus             STAGE IVB
  TJP1 MUTATED           0
  TJP1 WILD-TYPE         1
D570V3, multiclass
            clus
vv           TJP1 MUTATED TJP1 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              6             19
  STAGE IIA             4            105
  STAGE IIB             1              7
  STAGE IIC             1              0
  STAGE III             0             19
  STAGE IIIA            1              9
  STAGE IIIB            2             39
  STAGE IIIC            1             30
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TJP1 MUTATED     0   1  15   2
  TJP1 WILD-TYPE   9  67 233  39
D570V4, multiclass
    clus
vv   TJP1 MUTATED TJP1 WILD-TYPE
  T1            0              9
  T2            1             67
  T3           15            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
  TJP1 MUTATED    13   3   2
  TJP1 WILD-TYPE 207  77  64
D570V5, multiclass
    clus
vv   TJP1 MUTATED TJP1 WILD-TYPE
  N0           13            207
  N1            3             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"
D570V6, binary
                cls
clus               0   1
  TJP1 MUTATED    14   0
  TJP1 WILD-TYPE 269  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  TJP1 MUTATED     14    0
  TJP1 WILD-TYPE  269   48
   clus
vv  TJP1 MUTATED TJP1 WILD-TYPE
  0           14            269
  1            0             48
[1] 2 2
[1] FALSE
D570V7, 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
D570V8, binary
                cls
clus               0   1
  TJP1 MUTATED    13   5
  TJP1 WILD-TYPE 304  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  TJP1 MUTATED     13    5
  TJP1 WILD-TYPE  304   43
                               clus
vv                              TJP1 MUTATED TJP1 WILD-TYPE
  COLON ADENOCARCINOMA                    13            304
  COLON MUCINOUS ADENOCARCINOMA            5             43
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TJP1 MUTATED    11   0   0   1
  TJP1 WILD-TYPE 246   2  22  20
D570V9, multiclass
    clus
vv   TJP1 MUTATED TJP1 WILD-TYPE
  R0           11            246
  R1            0              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"
D570V10, 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
D570V11, 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(571) Variable = ACTL6A MUTATION ANALYSIS
D571V1, survival
                  sevent
clus2                0   1
  ACTL6A MUTATED     4   2
  ACTL6A WILD-TYPE 278  71
  ACTL6A MUTATED ACTL6A WILD-TYPE 
               6              349 
  ACTL6A MUTATED ACTL6A WILD-TYPE 
               2               71 
$`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-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32        21.99         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  ACTL6A MUTATED ACTL6A WILD-TYPE 
            4.01             0.00 
  ACTL6A MUTATED ACTL6A WILD-TYPE 
           46.65           140.38 
  ACTL6A MUTATED ACTL6A WILD-TYPE 
          27.075           20.120 
[1] "4.0 - 46.6 (27.1)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.7"
D571V2, 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       25       108         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ACTL6A MUTATED           0          0          1          1        0
  ACTL6A WILD-TYPE        19         10         40         30       35
                  vv
clus               STAGE IVA STAGE IVB
  ACTL6A MUTATED           0         0
  ACTL6A WILD-TYPE        13         1
D571V3, multiclass
            clus
vv           ACTL6A MUTATED ACTL6A WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               1              108
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ACTL6A MUTATED     1   0   2   3
  ACTL6A WILD-TYPE   8  68 246  38
D571V4, multiclass
    clus
vv   ACTL6A MUTATED ACTL6A WILD-TYPE
  T1              1                8
  T2              0               68
  T3              2              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
  ACTL6A MUTATED     4   2   0
  ACTL6A WILD-TYPE 216  78  66
D571V5, multiclass
    clus
vv   ACTL6A MUTATED ACTL6A WILD-TYPE
  N0              4              216
  N1              2               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"
D571V6, binary
                  cls
clus                 0   1
  ACTL6A MUTATED     5   0
  ACTL6A WILD-TYPE 278  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACTL6A MUTATED      5    0
  ACTL6A WILD-TYPE  278   48
   clus
vv  ACTL6A MUTATED ACTL6A WILD-TYPE
  0              5              278
  1              0               48
[1] 2 2
[1] FALSE
D571V7, 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
D571V8, binary
                  cls
clus                 0   1
  ACTL6A MUTATED     3   3
  ACTL6A WILD-TYPE 314  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACTL6A MUTATED      3    3
  ACTL6A WILD-TYPE  314   45
                               clus
vv                              ACTL6A MUTATED ACTL6A WILD-TYPE
  COLON ADENOCARCINOMA                       3              314
  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 252   2  22  20
D571V9, multiclass
    clus
vv   ACTL6A MUTATED ACTL6A WILD-TYPE
  R0              5              252
  R1              0                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"
D571V10, 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
D571V11, 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(572) Variable = WT1 MUTATION ANALYSIS
D572V1, survival
               sevent
clus2             0   1
  WT1 MUTATED    21   5
  WT1 WILD-TYPE 261  68
  WT1 MUTATED WT1 WILD-TYPE 
           26           329 
  WT1 MUTATED WT1 WILD-TYPE 
            5            68 
$`WT1 MUTATED`
TCGA-A6-2672 TCGA-A6-5657 TCGA-A6-5662 TCGA-AA-3544 TCGA-AA-3662 TCGA-AA-3715 
       46.65        31.63        23.61        14.01         6.05        19.04 
TCGA-AA-3930 TCGA-AD-6895 TCGA-AY-6197 TCGA-AZ-4323 TCGA-AZ-6600 TCGA-AZ-6601 
        2.01         0.72        21.44         1.41        12.10       100.01 
TCGA-CA-6717 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5914 TCGA-CM-4743 
        0.33        17.56       102.44        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        12.26        18.25        12.43 
TCGA-F4-6806 TCGA-G4-6306 
       29.59        44.68 

$`WT1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       30.44        29.19        33.53        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
        0.99        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       31.00        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        4.21        56.55         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4616 TCGA-AZ-4681 
       15.75         0.20        17.82        58.39         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6603 
       22.36        62.79        61.41        49.41         6.77        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       40.34        49.08        51.32        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        12.00        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-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       12.03        45.40        19.59        13.51        11.51        20.19 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       16.31        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 
       19.43       107.67        74.56        65.85        53.62        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  WT1 MUTATED WT1 WILD-TYPE 
         0.33          0.00 
  WT1 MUTATED WT1 WILD-TYPE 
       102.44        140.38 
  WT1 MUTATED WT1 WILD-TYPE 
        16.59         20.98 
[1] "0.3 - 102.4 (16.6)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1"  
D572V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  WT1 MUTATED         5        0        2         5         0         0
  WT1 WILD-TYPE      59        1       23       104         8         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  WT1 MUTATED           1          1          4          0        4         2
  WT1 WILD-TYPE        18          9         37         31       31        11
               vv
clus            STAGE IVB
  WT1 MUTATED           1
  WT1 WILD-TYPE         0
D572V3, multiclass
            clus
vv           WT1 MUTATED WT1 WILD-TYPE
  STAGE I              5            59
  STAGE IA             0             1
  STAGE II             2            23
  STAGE IIA            5           104
  STAGE IIB            0             8
  STAGE IIC            0             1
  STAGE III            1            18
  STAGE IIIA           1             9
  STAGE IIIB           4            37
  STAGE IIIC           0            31
  STAGE IV             4            31
  STAGE IVA            2            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  62 233  36
D572V4, multiclass
    clus
vv   WT1 MUTATED WT1 WILD-TYPE
  T1           0             9
  T2           6            62
  T3          15           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
  WT1 MUTATED    12   8   6
  WT1 WILD-TYPE 208  72  60
D572V5, multiclass
    clus
vv   WT1 MUTATED WT1 WILD-TYPE
  N0          12           208
  N1           8            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"
D572V6, binary
               cls
clus              0   1
  WT1 MUTATED    17   6
  WT1 WILD-TYPE 266  42
[1] "tbl2"
               cls
clus            [,1] [,2]
  WT1 MUTATED     17    6
  WT1 WILD-TYPE  266   42
   clus
vv  WT1 MUTATED WT1 WILD-TYPE
  0          17           266
  1           6            42
[1] 2 2
[1] FALSE
D572V7, 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
D572V8, binary
               cls
clus              0   1
  WT1 MUTATED    24   2
  WT1 WILD-TYPE 293  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  WT1 MUTATED     24    2
  WT1 WILD-TYPE  293   46
                               clus
vv                              WT1 MUTATED WT1 WILD-TYPE
  COLON ADENOCARCINOMA                   24           293
  COLON MUCINOUS ADENOCARCINOMA           2            46
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  WT1 MUTATED    15   0   2   4
  WT1 WILD-TYPE 242   2  20  17
D572V9, multiclass
    clus
vv   WT1 MUTATED WT1 WILD-TYPE
  R0          15           242
  R1           0             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"
D572V10, 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
D572V11, 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(573) Variable = ADAMTS4 MUTATION ANALYSIS
D573V1, survival
                   sevent
clus2                 0   1
  ADAMTS4 MUTATED    11   3
  ADAMTS4 WILD-TYPE 271  70
  ADAMTS4 MUTATED ADAMTS4 WILD-TYPE 
               14               341 
  ADAMTS4 MUTATED ADAMTS4 WILD-TYPE 
                3                70 
$`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        19.43 

$`ADAMTS4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 
       24.16        21.76        24.69        24.39        23.87        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 
        1.35        17.56       102.44        40.34        49.08        51.32 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.99         2.93         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 
       16.01         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 
        1.32        43.27        15.12        17.85         4.80        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        11.38        10.26       119.70        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  ADAMTS4 MUTATED ADAMTS4 WILD-TYPE 
            14.04              0.00 
  ADAMTS4 MUTATED ADAMTS4 WILD-TYPE 
            78.08            140.38 
  ADAMTS4 MUTATED ADAMTS4 WILD-TYPE 
            21.60             20.02 
[1] "14.0 - 78.1 (21.6)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1"  
D573V2, 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       23       103         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ADAMTS4 MUTATED           1          0          1          0        0
  ADAMTS4 WILD-TYPE        18         10         40         31       35
                   vv
clus                STAGE IVA STAGE IVB
  ADAMTS4 MUTATED           0         0
  ADAMTS4 WILD-TYPE        13         1
D573V3, multiclass
            clus
vv           ADAMTS4 MUTATED ADAMTS4 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 2                23
  STAGE IIA                6               103
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ADAMTS4 MUTATED     1   2   9   2
  ADAMTS4 WILD-TYPE   8  66 239  39
D573V4, multiclass
    clus
vv   ADAMTS4 MUTATED ADAMTS4 WILD-TYPE
  T1               1                 8
  T2               2                66
  T3               9               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
  ADAMTS4 MUTATED    12   0   2
  ADAMTS4 WILD-TYPE 208  80  64
D573V5, multiclass
    clus
vv   ADAMTS4 MUTATED ADAMTS4 WILD-TYPE
  N0              12               208
  N1               0                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"
D573V6, binary
                   cls
clus                  0   1
  ADAMTS4 MUTATED    12   0
  ADAMTS4 WILD-TYPE 271  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ADAMTS4 MUTATED     12    0
  ADAMTS4 WILD-TYPE  271   48
   clus
vv  ADAMTS4 MUTATED ADAMTS4 WILD-TYPE
  0              12               271
  1               0                48
[1] 2 2
[1] FALSE
D573V7, 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
D573V8, binary
                   cls
clus                  0   1
  ADAMTS4 MUTATED    11   3
  ADAMTS4 WILD-TYPE 306  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ADAMTS4 MUTATED     11    3
  ADAMTS4 WILD-TYPE  306   45
                               clus
vv                              ADAMTS4 MUTATED ADAMTS4 WILD-TYPE
  COLON ADENOCARCINOMA                       11               306
  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 248   2  22  19
D573V9, multiclass
    clus
vv   ADAMTS4 MUTATED ADAMTS4 WILD-TYPE
  R0               9               248
  R1               0                 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"
D573V10, 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
D573V11, 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(574) Variable = JMJD1C MUTATION ANALYSIS
D574V1, survival
                  sevent
clus2                0   1
  JMJD1C MUTATED    22   1
  JMJD1C WILD-TYPE 260  72
  JMJD1C MUTATED JMJD1C WILD-TYPE 
              23              332 
  JMJD1C MUTATED JMJD1C WILD-TYPE 
               1               72 
$`JMJD1C MUTATED`
TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3672 TCGA-AA-3866 TCGA-AA-3949 TCGA-AA-3977 
       19.66        63.98         0.92        17.03        26.01        25.02 
TCGA-AA-A010 TCGA-AA-A01K TCGA-AD-6964 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       34.98        31.00        10.88        21.44        17.82        58.39 
TCGA-CA-6717 TCGA-CK-4952 TCGA-CM-4744 TCGA-CM-6169 TCGA-CM-6674 TCGA-CM-6678 
        0.33        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       107.67        13.78 

$`JMJD1C WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        53.00        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
        0.20         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       102.44        40.34        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 
       21.14         2.93         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 
       16.01        15.02         5.03        15.02        15.02        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-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.08        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12        17.85         4.80        12.49        16.14 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 
       33.67        13.25         0.53        35.41        19.43        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.72        36.00        22.09        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  JMJD1C MUTATED JMJD1C WILD-TYPE 
            0.33             0.00 
  JMJD1C MUTATED JMJD1C WILD-TYPE 
          107.67           140.38 
  JMJD1C MUTATED JMJD1C WILD-TYPE 
          17.130           20.995 
[1] "0.3 - 107.7 (17.1)" "0.0 - 140.4 (21.0)"
[1] "hr=" "4.9"
D574V2, 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       24       101         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  JMJD1C MUTATED           3          0          3          2        0
  JMJD1C WILD-TYPE        16         10         38         29       35
                  vv
clus               STAGE IVA STAGE IVB
  JMJD1C MUTATED           1         0
  JMJD1C WILD-TYPE        12         1
D574V3, multiclass
            clus
vv           JMJD1C MUTATED JMJD1C WILD-TYPE
  STAGE I                 2               62
  STAGE IA                1                0
  STAGE II                1               24
  STAGE IIA               8              101
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               3               16
  STAGE IIIA              0               10
  STAGE IIIB              3               38
  STAGE IIIC              2               29
  STAGE IV                0               35
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  65 233  36
D574V4, multiclass
    clus
vv   JMJD1C MUTATED JMJD1C WILD-TYPE
  T1              0                9
  T2              3               65
  T3             15              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
  JMJD1C MUTATED    14   6   4
  JMJD1C WILD-TYPE 206  74  62
D574V5, multiclass
    clus
vv   JMJD1C MUTATED JMJD1C WILD-TYPE
  N0             14              206
  N1              6               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"
D574V6, binary
                  cls
clus                 0   1
  JMJD1C MUTATED    18   1
  JMJD1C WILD-TYPE 265  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  JMJD1C MUTATED     18    1
  JMJD1C WILD-TYPE  265   47
   clus
vv  JMJD1C MUTATED JMJD1C WILD-TYPE
  0             18              265
  1              1               47
[1] 2 2
[1] FALSE
D574V7, 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
D574V8, binary
                  cls
clus                 0   1
  JMJD1C MUTATED    19   5
  JMJD1C WILD-TYPE 298  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  JMJD1C MUTATED     19    5
  JMJD1C WILD-TYPE  298   43
                               clus
vv                              JMJD1C MUTATED JMJD1C WILD-TYPE
  COLON ADENOCARCINOMA                      19              298
  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 237   2  22  19
D574V9, multiclass
    clus
vv   JMJD1C MUTATED JMJD1C WILD-TYPE
  R0             20              237
  R1              0                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"
D574V10, 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
D574V11, 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(575) Variable = ERBB2IP MUTATION ANALYSIS
D575V1, survival
                   sevent
clus2                 0   1
  ERBB2IP MUTATED    13   1
  ERBB2IP WILD-TYPE 269  72
  ERBB2IP MUTATED ERBB2IP WILD-TYPE 
               14               341 
  ERBB2IP MUTATED ERBB2IP WILD-TYPE 
                1                72 
$`ERBB2IP MUTATED`
TCGA-A6-6142 TCGA-AA-3510 TCGA-AA-3655 TCGA-AA-3864 TCGA-AA-3977 TCGA-AA-A00N 
       25.08        63.98        61.02        53.00        25.02         4.01 
TCGA-AA-A010 TCGA-AU-6004 TCGA-CA-6717 TCGA-CM-6674 TCGA-CM-6677 TCGA-DM-A1HA 
       34.98        27.09         0.33        12.95        11.08       131.51 
TCGA-F4-6856 TCGA-G4-6628 
       19.43        52.80 

$`ERBB2IP WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.41       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       13.78        35.80        26.17        91.79        46.75 

  ERBB2IP MUTATED ERBB2IP WILD-TYPE 
             0.33              0.00 
  ERBB2IP MUTATED ERBB2IP WILD-TYPE 
           131.51            140.38 
  ERBB2IP MUTATED ERBB2IP WILD-TYPE 
           26.085            20.020 
[1] "0.3 - 131.5 (26.1)" "0.0 - 140.4 (20.0)"
[1] "hr=" "4.3"
D575V2, 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       22       106         5         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ERBB2IP MUTATED           0          0          0          1        0
  ERBB2IP WILD-TYPE        19         10         41         30       35
                   vv
clus                STAGE IVA STAGE IVB
  ERBB2IP MUTATED           1         0
  ERBB2IP WILD-TYPE        12         1
D575V3, multiclass
            clus
vv           ERBB2IP MUTATED ERBB2IP WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 3                22
  STAGE IIA                3               106
  STAGE IIB                3                 5
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               1                30
  STAGE IV                 0                35
  STAGE IVA                1                12
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of 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  64 240  38
D575V4, multiclass
    clus
vv   ERBB2IP MUTATED ERBB2IP WILD-TYPE
  T1               0                 9
  T2               4                64
  T3               8               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
  ERBB2IP MUTATED    13   1   1
  ERBB2IP WILD-TYPE 207  79  65
D575V5, multiclass
    clus
vv   ERBB2IP MUTATED ERBB2IP WILD-TYPE
  N0              13               207
  N1               1                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"
D575V6, binary
                   cls
clus                  0   1
  ERBB2IP MUTATED    12   1
  ERBB2IP WILD-TYPE 271  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ERBB2IP MUTATED     12    1
  ERBB2IP WILD-TYPE  271   47
   clus
vv  ERBB2IP MUTATED ERBB2IP WILD-TYPE
  0              12               271
  1               1                47
[1] 2 2
[1] FALSE
D575V7, 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
D575V8, binary
                   cls
clus                  0   1
  ERBB2IP MUTATED    12   3
  ERBB2IP WILD-TYPE 305  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ERBB2IP MUTATED     12    3
  ERBB2IP WILD-TYPE  305   45
                               clus
vv                              ERBB2IP MUTATED ERBB2IP WILD-TYPE
  COLON ADENOCARCINOMA                       12               305
  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 247   2  22  19
D575V9, multiclass
    clus
vv   ERBB2IP MUTATED ERBB2IP WILD-TYPE
  R0              10               247
  R1               0                 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"
D575V10, 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
D575V11, 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(576) Variable = ING2 MUTATION ANALYSIS
D576V1, survival
                sevent
clus2              0   1
  ING2 MUTATED     6   0
  ING2 WILD-TYPE 276  73
  ING2 MUTATED ING2 WILD-TYPE 
             6            349 
  ING2 MUTATED ING2 WILD-TYPE 
             0             73 
$`ING2 MUTATED`
TCGA-AA-3663 TCGA-AD-5900 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-F4-6703 TCGA-G4-6586 
        6.97         0.07        58.39        61.41        35.87        35.80 

$`ING2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  ING2 MUTATED ING2 WILD-TYPE 
          0.07           0.00 
  ING2 MUTATED ING2 WILD-TYPE 
         61.41         140.38 
  ING2 MUTATED ING2 WILD-TYPE 
        35.835         20.120 
[1] "0.1 - 61.4 (35.8)"  "0.0 - 140.4 (20.1)"
[1] "hr="     "9300000"
D576V2, 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       24       106         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        19         10         41         31       35        13
                vv
clus             STAGE IVB
  ING2 MUTATED           0
  ING2 WILD-TYPE         1
D576V3, multiclass
            clus
vv           ING2 MUTATED ING2 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             3            106
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ING2 MUTATED     1   1   4   0
  ING2 WILD-TYPE   8  67 244  41
D576V4, multiclass
    clus
vv   ING2 MUTATED ING2 WILD-TYPE
  T1            1              8
  T2            1             67
  T3            4            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
  ING2 MUTATED     6   0   0
  ING2 WILD-TYPE 214  80  66
D576V5, multiclass
    clus
vv   ING2 MUTATED ING2 WILD-TYPE
  N0            6            214
  N1            0             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"
D576V6, binary
                cls
clus               0   1
  ING2 MUTATED     5   0
  ING2 WILD-TYPE 278  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  ING2 MUTATED      5    0
  ING2 WILD-TYPE  278   48
   clus
vv  ING2 MUTATED ING2 WILD-TYPE
  0            5            278
  1            0             48
[1] 2 2
[1] FALSE
D576V7, 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
D576V8, binary
                cls
clus               0   1
  ING2 MUTATED     5   1
  ING2 WILD-TYPE 312  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  ING2 MUTATED      5    1
  ING2 WILD-TYPE  312   47
                               clus
vv                              ING2 MUTATED ING2 WILD-TYPE
  COLON ADENOCARCINOMA                     5            312
  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 252   2  22  21
D576V9, multiclass
    clus
vv   ING2 MUTATED ING2 WILD-TYPE
  R0            5            252
  R1            0              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"
D576V10, 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
D576V11, 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(577) Variable = OR4M2 MUTATION ANALYSIS
D577V1, survival
                 sevent
clus2               0   1
  OR4M2 MUTATED    10   3
  OR4M2 WILD-TYPE 272  70
  OR4M2 MUTATED OR4M2 WILD-TYPE 
             13             342 
  OR4M2 MUTATED OR4M2 WILD-TYPE 
              3              70 
$`OR4M2 MUTATED`
TCGA-A6-5665 TCGA-A6-6653 TCGA-AA-3715 TCGA-AA-3864 TCGA-AA-A010 TCGA-AU-6004 
       22.06        24.39        19.04        53.00        34.98        27.09 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5913 TCGA-D5-6927 
       49.41         6.77         0.33         0.10        51.32         9.44 
TCGA-D5-6930 
        1.51 

$`OR4M2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       61.41        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07         0.26         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  OR4M2 MUTATED OR4M2 WILD-TYPE 
            0.1             0.0 
  OR4M2 MUTATED OR4M2 WILD-TYPE 
          53.00          140.38 
  OR4M2 MUTATED OR4M2 WILD-TYPE 
         22.060          20.155 
[1] "0.1 - 53.0 (22.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D577V2, 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       22       103         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        19         10         41         31       35        13
                 vv
clus              STAGE IVB
  OR4M2 MUTATED           0
  OR4M2 WILD-TYPE         1
D577V3, multiclass
            clus
vv           OR4M2 MUTATED OR4M2 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              6             103
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR4M2 MUTATED     0   3   9   2
  OR4M2 WILD-TYPE   9  65 239  39
D577V4, multiclass
    clus
vv   OR4M2 MUTATED OR4M2 WILD-TYPE
  T1             0               9
  T2             3              65
  T3             9             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
  OR4M2 MUTATED    14   0   0
  OR4M2 WILD-TYPE 206  80  66
D577V5, multiclass
    clus
vv   OR4M2 MUTATED OR4M2 WILD-TYPE
  N0            14             206
  N1             0              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"
D577V6, binary
                 cls
clus                0   1
  OR4M2 MUTATED    10   0
  OR4M2 WILD-TYPE 273  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4M2 MUTATED     10    0
  OR4M2 WILD-TYPE  273   48
   clus
vv  OR4M2 MUTATED OR4M2 WILD-TYPE
  0            10             273
  1             0              48
[1] 2 2
[1] FALSE
D577V7, 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
D577V8, binary
                 cls
clus                0   1
  OR4M2 MUTATED    12   2
  OR4M2 WILD-TYPE 305  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4M2 MUTATED     12    2
  OR4M2 WILD-TYPE  305   46
                               clus
vv                              OR4M2 MUTATED OR4M2 WILD-TYPE
  COLON ADENOCARCINOMA                     12             305
  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 250   2  22  17
D577V9, multiclass
    clus
vv   OR4M2 MUTATED OR4M2 WILD-TYPE
  R0             7             250
  R1             0               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"
D577V10, 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
D577V11, 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(578) Variable = ARHGEF10 MUTATION ANALYSIS
D578V1, survival
                    sevent
clus2                  0   1
  ARHGEF10 MUTATED    21   2
  ARHGEF10 WILD-TYPE 261  71
  ARHGEF10 MUTATED ARHGEF10 WILD-TYPE 
                23                332 
  ARHGEF10 MUTATED ARHGEF10 WILD-TYPE 
                 2                 71 
$`ARHGEF10 MUTATED`
TCGA-A6-6141 TCGA-A6-6780 TCGA-AA-3496 TCGA-AA-3518 TCGA-AA-3672 TCGA-AA-3710 
        8.38        20.12         1.02         1.02         0.92        26.99 
TCGA-AA-3713 TCGA-AA-3864 TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A01P 
       19.04        53.00        24.00         2.01        25.02        38.07 
TCGA-AD-5900 TCGA-AZ-4315 TCGA-AZ-6603 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4743 
        0.07        58.39        29.56         0.33         0.10        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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         3.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 
        6.97         1.02        13.02        38.99         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3715 
       37.05        19.00        36.00         5.03        85.05        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        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        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10       100.01         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.26         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       15.02        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
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-D5-6929 
       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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  ARHGEF10 MUTATED ARHGEF10 WILD-TYPE 
              0.07               0.00 
  ARHGEF10 MUTATED ARHGEF10 WILD-TYPE 
             58.39             140.38 
  ARHGEF10 MUTATED ARHGEF10 WILD-TYPE 
            15.580             20.995 
[1] "0.1 - 58.4 (15.6)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.7"
D578V2, 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       23        96         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARHGEF10 MUTATED           2          0          1          0        1
  ARHGEF10 WILD-TYPE        17         10         40         31       34
                    vv
clus                 STAGE IVA STAGE IVB
  ARHGEF10 MUTATED           0         0
  ARHGEF10 WILD-TYPE        13         1
D578V3, multiclass
            clus
vv           ARHGEF10 MUTATED ARHGEF10 WILD-TYPE
  STAGE I                   2                 62
  STAGE IA                  0                  1
  STAGE II                  2                 23
  STAGE IIA                13                 96
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 2                 17
  STAGE IIIA                0                 10
  STAGE IIIB                1                 40
  STAGE IIIC                0                 31
  STAGE IV                  1                 34
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  ARHGEF10 MUTATED     0   4  19   0
  ARHGEF10 WILD-TYPE   9  64 229  41
D578V4, multiclass
    clus
vv   ARHGEF10 MUTATED ARHGEF10 WILD-TYPE
  T1                0                  9
  T2                4                 64
  T3               19                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
  ARHGEF10 MUTATED    19   4   0
  ARHGEF10 WILD-TYPE 201  76  66
D578V5, multiclass
    clus
vv   ARHGEF10 MUTATED ARHGEF10 WILD-TYPE
  N0               19                201
  N1                4                 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"
D578V6, binary
                    cls
clus                   0   1
  ARHGEF10 MUTATED    18   1
  ARHGEF10 WILD-TYPE 265  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGEF10 MUTATED     18    1
  ARHGEF10 WILD-TYPE  265   47
   clus
vv  ARHGEF10 MUTATED ARHGEF10 WILD-TYPE
  0               18                265
  1                1                 47
[1] 2 2
[1] FALSE
D578V7, 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
D578V8, binary
                    cls
clus                   0   1
  ARHGEF10 MUTATED    17   6
  ARHGEF10 WILD-TYPE 300  42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGEF10 MUTATED     17    6
  ARHGEF10 WILD-TYPE  300   42
                               clus
vv                              ARHGEF10 MUTATED ARHGEF10 WILD-TYPE
  COLON ADENOCARCINOMA                        17                300
  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 242   2  21  19
D578V9, multiclass
    clus
vv   ARHGEF10 MUTATED ARHGEF10 WILD-TYPE
  R0               15                242
  R1                0                  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"
D578V10, 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
D578V11, 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(579) Variable = MUC7 MUTATION ANALYSIS
D579V1, survival
                sevent
clus2              0   1
  MUC7 MUTATED     6   3
  MUC7 WILD-TYPE 276  70
  MUC7 MUTATED MUC7 WILD-TYPE 
             9            346 
  MUC7 MUTATED MUC7 WILD-TYPE 
             3             70 
$`MUC7 MUTATED`
TCGA-A6-6141 TCGA-AA-3715 TCGA-AY-6196 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-AZ-6603 
        8.38        19.04         0.20        58.39        61.41        29.56 
TCGA-D5-6536 TCGA-DM-A1DA TCGA-G4-6309 
       17.85         7.50        51.75 

$`MUC7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       15.75        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        49.41         6.77        12.10       100.01 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB 
       92.75        49.91        13.32        12.59       140.38        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  MUC7 MUTATED MUC7 WILD-TYPE 
           0.2            0.0 
  MUC7 MUTATED MUC7 WILD-TYPE 
         61.41         140.38 
  MUC7 MUTATED MUC7 WILD-TYPE 
        19.040         20.235 
[1] "0.2 - 61.4 (19.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.4"
D579V2, 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       24       106         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        19         10         40         29       35        13
                vv
clus             STAGE IVB
  MUC7 MUTATED           0
  MUC7 WILD-TYPE         1
D579V3, multiclass
            clus
vv           MUC7 MUTATED MUC7 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             3            106
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            2             29
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MUC7 MUTATED     1   1   7   0
  MUC7 WILD-TYPE   8  67 241  41
D579V4, multiclass
    clus
vv   MUC7 MUTATED MUC7 WILD-TYPE
  T1            1              8
  T2            1             67
  T3            7            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
  MUC7 MUTATED     5   2   2
  MUC7 WILD-TYPE 215  78  64
D579V5, multiclass
    clus
vv   MUC7 MUTATED MUC7 WILD-TYPE
  N0            5            215
  N1            2             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"
D579V6, binary
                cls
clus               0   1
  MUC7 MUTATED     7   0
  MUC7 WILD-TYPE 276  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC7 MUTATED      7    0
  MUC7 WILD-TYPE  276   48
   clus
vv  MUC7 MUTATED MUC7 WILD-TYPE
  0            7            276
  1            0             48
[1] 2 2
[1] FALSE
D579V7, 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
D579V8, binary
                cls
clus               0   1
  MUC7 MUTATED     8   1
  MUC7 WILD-TYPE 309  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC7 MUTATED      8    1
  MUC7 WILD-TYPE  309   47
                               clus
vv                              MUC7 MUTATED MUC7 WILD-TYPE
  COLON ADENOCARCINOMA                     8            309
  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 252   2  22  21
D579V9, multiclass
    clus
vv   MUC7 MUTATED MUC7 WILD-TYPE
  R0            5            252
  R1            0              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"
D579V10, 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
D579V11, 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(580) Variable = EIF2B5 MUTATION ANALYSIS
D580V1, survival
                  sevent
clus2                0   1
  EIF2B5 MUTATED    11   3
  EIF2B5 WILD-TYPE 271  70
  EIF2B5 MUTATED EIF2B5 WILD-TYPE 
              14              341 
  EIF2B5 MUTATED EIF2B5 WILD-TYPE 
               3               70 
$`EIF2B5 MUTATED`
TCGA-AA-3525 TCGA-AA-3542 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-A00J TCGA-AA-A010 
        8.05        12.99        19.04        10.06        18.05        34.98 
TCGA-AY-5543 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-CM-6170 TCGA-CM-6675 
       15.75        58.39        49.41        12.10        15.02        13.05 
TCGA-D5-6536 TCGA-G4-6307 
       17.85        55.04 

$`EIF2B5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       26.01         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 
        5.03        85.05        26.99        19.04        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13        83.80        22.36        62.79        61.41         6.77 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  EIF2B5 MUTATED EIF2B5 WILD-TYPE 
            8.05             0.00 
  EIF2B5 MUTATED EIF2B5 WILD-TYPE 
           58.39           140.38 
  EIF2B5 MUTATED EIF2B5 WILD-TYPE 
           16.80            20.98 
[1] "8.1 - 58.4 (16.8)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1"  
D580V2, 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       24       107         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EIF2B5 MUTATED           1          0          3          1        2
  EIF2B5 WILD-TYPE        18         10         38         30       33
                  vv
clus               STAGE IVA STAGE IVB
  EIF2B5 MUTATED           1         1
  EIF2B5 WILD-TYPE        12         0
D580V3, multiclass
            clus
vv           EIF2B5 MUTATED EIF2B5 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               2              107
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              3               38
  STAGE IIIC              1               30
  STAGE IV                2               33
  STAGE IVA               1               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
  EIF2B5 MUTATED     0   1  10   3
  EIF2B5 WILD-TYPE   9  67 238  38
D580V4, multiclass
    clus
vv   EIF2B5 MUTATED EIF2B5 WILD-TYPE
  T1              0                9
  T2              1               67
  T3             10              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
  EIF2B5 MUTATED     6   5   3
  EIF2B5 WILD-TYPE 214  75  63
D580V5, multiclass
    clus
vv   EIF2B5 MUTATED EIF2B5 WILD-TYPE
  N0              6              214
  N1              5               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"
D580V6, binary
                  cls
clus                 0   1
  EIF2B5 MUTATED     9   4
  EIF2B5 WILD-TYPE 274  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF2B5 MUTATED      9    4
  EIF2B5 WILD-TYPE  274   44
   clus
vv  EIF2B5 MUTATED EIF2B5 WILD-TYPE
  0              9              274
  1              4               44
[1] 2 2
[1] FALSE
D580V7, binary
                  cls
clus                 0   1
  EIF2B5 MUTATED     6   8
  EIF2B5 WILD-TYPE 164 189
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF2B5 MUTATED      6    8
  EIF2B5 WILD-TYPE  164  189
        clus
vv       EIF2B5 MUTATED EIF2B5 WILD-TYPE
  FEMALE              6              164
  MALE                8              189
[1] 2 2
[1] FALSE
D580V8, binary
                  cls
clus                 0   1
  EIF2B5 MUTATED    13   1
  EIF2B5 WILD-TYPE 304  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF2B5 MUTATED     13    1
  EIF2B5 WILD-TYPE  304   47
                               clus
vv                              EIF2B5 MUTATED EIF2B5 WILD-TYPE
  COLON ADENOCARCINOMA                      13              304
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  EIF2B5 MUTATED    11   0   1   0
  EIF2B5 WILD-TYPE 246   2  21  21
D580V9, multiclass
    clus
vv   EIF2B5 MUTATED EIF2B5 WILD-TYPE
  R0             11              246
  R1              0                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"
D580V10, 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     5
  EIF2B5 WILD-TYPE                        16   171
D580V11, 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                                         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(581) Variable = LMTK3 MUTATION ANALYSIS
D581V1, survival
                 sevent
clus2               0   1
  LMTK3 MUTATED    10   5
  LMTK3 WILD-TYPE 272  68
  LMTK3 MUTATED LMTK3 WILD-TYPE 
             15             340 
  LMTK3 MUTATED LMTK3 WILD-TYPE 
              5              68 
$`LMTK3 MUTATED`
TCGA-AD-6889 TCGA-AD-6899 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-6716 TCGA-CA-6717 
       56.55         5.79        49.41       100.01         0.26         0.33 
TCGA-CM-6168 TCGA-CM-6171 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6930 TCGA-F4-6459 
       12.99        14.04        15.12         4.80         1.51         8.61 
TCGA-F4-6856 TCGA-G4-6304 TCGA-G4-6628 
       19.43        53.62        52.80 

$`LMTK3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 
       21.37         4.21         0.79         0.72        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13        83.80        22.36        62.79        61.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6718 
        2.24         3.06         3.25         3.29         0.07         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 
       11.51        20.19        18.25         1.32        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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       98.24        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 
       35.41       107.67        74.56        65.85        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       35.80        26.17        91.79        46.75 

  LMTK3 MUTATED LMTK3 WILD-TYPE 
           0.26            0.00 
  LMTK3 MUTATED LMTK3 WILD-TYPE 
         100.01          140.38 
  LMTK3 MUTATED LMTK3 WILD-TYPE 
          14.04           20.98 
[1] "0.3 - 100.0 (14.0)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.5"
D581V2, 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       23       104         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        19         10         38         30       35        13
                 vv
clus              STAGE IVB
  LMTK3 MUTATED           0
  LMTK3 WILD-TYPE         1
D581V3, multiclass
            clus
vv           LMTK3 MUTATED LMTK3 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              5             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             3              38
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LMTK3 MUTATED     0   3  10   2
  LMTK3 WILD-TYPE   9  65 238  39
D581V4, multiclass
    clus
vv   LMTK3 MUTATED LMTK3 WILD-TYPE
  T1             0               9
  T2             3              65
  T3            10             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
  LMTK3 MUTATED    11   2   2
  LMTK3 WILD-TYPE 209  78  64
D581V5, multiclass
    clus
vv   LMTK3 MUTATED LMTK3 WILD-TYPE
  N0            11             209
  N1             2              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"
D581V6, binary
                 cls
clus                0   1
  LMTK3 MUTATED    11   0
  LMTK3 WILD-TYPE 272  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LMTK3 MUTATED     11    0
  LMTK3 WILD-TYPE  272   48
   clus
vv  LMTK3 MUTATED LMTK3 WILD-TYPE
  0            11             272
  1             0              48
[1] 2 2
[1] FALSE
D581V7, 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
D581V8, binary
                 cls
clus                0   1
  LMTK3 MUTATED    11   4
  LMTK3 WILD-TYPE 306  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LMTK3 MUTATED     11    4
  LMTK3 WILD-TYPE  306   44
                               clus
vv                              LMTK3 MUTATED LMTK3 WILD-TYPE
  COLON ADENOCARCINOMA                     11             306
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  LMTK3 MUTATED     8   0   0   3
  LMTK3 WILD-TYPE 249   2  22  18
D581V9, multiclass
    clus
vv   LMTK3 MUTATED LMTK3 WILD-TYPE
  R0             8             249
  R1             0               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"
D581V10, 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
D581V11, 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(582) Variable = MAPK9 MUTATION ANALYSIS
D582V1, survival
                 sevent
clus2               0   1
  MAPK9 MUTATED     7   2
  MAPK9 WILD-TYPE 275  71
  MAPK9 MUTATED MAPK9 WILD-TYPE 
              9             346 
  MAPK9 MUTATED MAPK9 WILD-TYPE 
              2              71 
$`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         0.10        12.99 
TCGA-D5-6929 TCGA-F4-6570 TCGA-G4-6306 
       13.41         6.18        44.68 

$`MAPK9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       51.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.33         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.38        13.45        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 
      107.67        74.56        65.85        53.62        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  MAPK9 MUTATED MAPK9 WILD-TYPE 
            0.1             0.0 
  MAPK9 MUTATED MAPK9 WILD-TYPE 
          49.41          140.38 
  MAPK9 MUTATED MAPK9 WILD-TYPE 
         17.820          20.235 
[1] "0.1 - 49.4 (17.8)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D582V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MAPK9 MUTATED         0        0        1         5         1         0
  MAPK9 WILD-TYPE      64        1       24       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        19         10         40         31       33        13
                 vv
clus              STAGE IVB
  MAPK9 MUTATED           0
  MAPK9 WILD-TYPE         1
D582V3, multiclass
            clus
vv           MAPK9 MUTATED MAPK9 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              5             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               2              33
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MAPK9 MUTATED     0   1   8   1
  MAPK9 WILD-TYPE   9  67 240  40
D582V4, multiclass
    clus
vv   MAPK9 MUTATED MAPK9 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             8             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
  MAPK9 MUTATED     7   3   0
  MAPK9 WILD-TYPE 213  77  66
D582V5, multiclass
    clus
vv   MAPK9 MUTATED MAPK9 WILD-TYPE
  N0             7             213
  N1             3              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"
D582V6, binary
                 cls
clus                0   1
  MAPK9 MUTATED     7   2
  MAPK9 WILD-TYPE 276  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAPK9 MUTATED      7    2
  MAPK9 WILD-TYPE  276   46
   clus
vv  MAPK9 MUTATED MAPK9 WILD-TYPE
  0             7             276
  1             2              46
[1] 2 2
[1] FALSE
D582V7, 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
D582V8, binary
                 cls
clus                0   1
  MAPK9 MUTATED    10   0
  MAPK9 WILD-TYPE 307  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAPK9 MUTATED     10    0
  MAPK9 WILD-TYPE  307   48
                               clus
vv                              MAPK9 MUTATED MAPK9 WILD-TYPE
  COLON ADENOCARCINOMA                     10             307
  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 250   2  21  20
D582V9, multiclass
    clus
vv   MAPK9 MUTATED MAPK9 WILD-TYPE
  R0             7             250
  R1             0               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"
D582V10, 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
D582V11, 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(583) Variable = LBP MUTATION ANALYSIS
D583V1, survival
               sevent
clus2             0   1
  LBP MUTATED     6   0
  LBP WILD-TYPE 276  73
  LBP MUTATED LBP WILD-TYPE 
            6           349 
  LBP MUTATED LBP WILD-TYPE 
            0            73 
$`LBP MUTATED`
TCGA-AA-3660 TCGA-AD-5900 TCGA-CK-5913 TCGA-F4-6856 TCGA-G4-6306 TCGA-G4-6307 
       78.08         0.07        51.32        19.43        44.68        55.04 

$`LBP WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        61.02         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 
      102.44        40.34        15.62        49.08        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 
       33.67        13.25         0.53        35.41       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       65.85        53.62        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  LBP MUTATED LBP WILD-TYPE 
         0.07          0.00 
  LBP MUTATED LBP WILD-TYPE 
        78.08        140.38 
  LBP MUTATED LBP WILD-TYPE 
        48.00         20.12 
[1] "0.1 - 78.1 (48.0)"  "0.0 - 140.4 (20.1)"
[1] "hr="     "2.6e+07"
D583V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LBP MUTATED         2        0        1         2         0         0
  LBP WILD-TYPE      62        1       24       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        19         10         40         31       34        13
               vv
clus            STAGE IVB
  LBP MUTATED           0
  LBP WILD-TYPE         1
D583V3, multiclass
            clus
vv           LBP MUTATED LBP WILD-TYPE
  STAGE I              2            62
  STAGE IA             0             1
  STAGE II             1            24
  STAGE IIA            2           107
  STAGE IIB            0             8
  STAGE IIC            0             1
  STAGE III            0            19
  STAGE IIIA           0            10
  STAGE IIIB           1            40
  STAGE IIIC           0            31
  STAGE IV             1            34
  STAGE IVA            0            13
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  LBP MUTATED     0   3   3   1
  LBP WILD-TYPE   9  65 245  40
D583V4, multiclass
    clus
vv   LBP MUTATED LBP WILD-TYPE
  T1           0             9
  T2           3            65
  T3           3           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
  LBP MUTATED     5   1   1
  LBP WILD-TYPE 215  79  65
D583V5, multiclass
    clus
vv   LBP MUTATED LBP WILD-TYPE
  N0           5           215
  N1           1            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"
D583V6, binary
               cls
clus              0   1
  LBP MUTATED     4   1
  LBP WILD-TYPE 279  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  LBP MUTATED      4    1
  LBP WILD-TYPE  279   47
   clus
vv  LBP MUTATED LBP WILD-TYPE
  0           4           279
  1           1            47
[1] 2 2
[1] FALSE
D583V7, 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
D583V8, binary
               cls
clus              0   1
  LBP MUTATED     5   2
  LBP WILD-TYPE 312  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  LBP MUTATED      5    2
  LBP WILD-TYPE  312   46
                               clus
vv                              LBP MUTATED LBP WILD-TYPE
  COLON ADENOCARCINOMA                    5           312
  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 252   2  21  20
D583V9, multiclass
    clus
vv   LBP MUTATED LBP WILD-TYPE
  R0           5           252
  R1           0             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"
D583V10, 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
D583V11, 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(584) Variable = PIK3C2G MUTATION ANALYSIS
D584V1, survival
                   sevent
clus2                 0   1
  PIK3C2G MUTATED    17   2
  PIK3C2G WILD-TYPE 265  71
  PIK3C2G MUTATED PIK3C2G WILD-TYPE 
               19               336 
  PIK3C2G MUTATED PIK3C2G WILD-TYPE 
                2                71 
$`PIK3C2G MUTATED`
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3977 TCGA-AA-A010 TCGA-AD-6895 TCGA-AZ-6599 
       25.02         1.02        25.02        34.98         0.72         6.77 
TCGA-CA-6717 TCGA-CM-5349 TCGA-CM-6161 TCGA-CM-6674 TCGA-D5-6534 TCGA-DM-A1HB 
        0.33        30.08        15.02        12.95        43.27       135.65 
TCGA-DM-A28C TCGA-F4-6856 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6317 
       81.37        19.43        53.62        44.68        51.75        36.00 
TCGA-G4-6586 
       35.80 

$`PIK3C2G WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3831 
       19.04        10.06        35.05        33.04         0.99        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41        49.41        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
      107.67        74.56        65.85        55.04        45.11        36.72 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        26.17        91.79        46.75        52.80 

  PIK3C2G MUTATED PIK3C2G WILD-TYPE 
             0.33              0.00 
  PIK3C2G MUTATED PIK3C2G WILD-TYPE 
           135.65            140.38 
  PIK3C2G MUTATED PIK3C2G WILD-TYPE 
           30.080            20.005 
[1] "0.3 - 135.7 (30.1)" "0.0 - 140.4 (20.0)"
[1] "hr=" "2.6"
D584V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PIK3C2G MUTATED         4        0        0         9         2         0
  PIK3C2G WILD-TYPE      60        1       25       100         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PIK3C2G MUTATED           0          0          2          1        0
  PIK3C2G WILD-TYPE        19         10         39         30       35
                   vv
clus                STAGE IVA STAGE IVB
  PIK3C2G MUTATED           0         0
  PIK3C2G WILD-TYPE        13         1
D584V3, multiclass
            clus
vv           PIK3C2G MUTATED PIK3C2G WILD-TYPE
  STAGE I                  4                60
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                9               100
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               2                39
  STAGE IIIC               1                30
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PIK3C2G MUTATED     0   6  12   2
  PIK3C2G WILD-TYPE   9  62 236  39
D584V4, multiclass
    clus
vv   PIK3C2G MUTATED PIK3C2G WILD-TYPE
  T1               0                 9
  T2               6                62
  T3              12               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
  PIK3C2G MUTATED    16   3   1
  PIK3C2G WILD-TYPE 204  77  65
D584V5, multiclass
    clus
vv   PIK3C2G MUTATED PIK3C2G WILD-TYPE
  N0              16               204
  N1               3                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"
D584V6, binary
                   cls
clus                  0   1
  PIK3C2G MUTATED    16   0
  PIK3C2G WILD-TYPE 267  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PIK3C2G MUTATED     16    0
  PIK3C2G WILD-TYPE  267   48
   clus
vv  PIK3C2G MUTATED PIK3C2G WILD-TYPE
  0              16               267
  1               0                48
[1] 2 2
[1] FALSE
D584V7, 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
D584V8, binary
                   cls
clus                  0   1
  PIK3C2G MUTATED    16   4
  PIK3C2G WILD-TYPE 301  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PIK3C2G MUTATED     16    4
  PIK3C2G WILD-TYPE  301   44
                               clus
vv                              PIK3C2G MUTATED PIK3C2G WILD-TYPE
  COLON ADENOCARCINOMA                       16               301
  COLON MUCINOUS ADENOCARCINOMA               4                44
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  PIK3C2G MUTATED    14   0   0   1
  PIK3C2G WILD-TYPE 243   2  22  20
D584V9, multiclass
    clus
vv   PIK3C2G MUTATED PIK3C2G WILD-TYPE
  R0              14               243
  R1               0                 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"
D584V10, 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
D584V11, 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(585) Variable = FAM160B1 MUTATION ANALYSIS
D585V1, survival
                    sevent
clus2                  0   1
  FAM160B1 MUTATED     5   0
  FAM160B1 WILD-TYPE 277  73
  FAM160B1 MUTATED FAM160B1 WILD-TYPE 
                 5                350 
  FAM160B1 MUTATED FAM160B1 WILD-TYPE 
                 0                 73 
$`FAM160B1 MUTATED`
TCGA-A6-6780 TCGA-AA-3713 TCGA-CK-4950 TCGA-CM-4746 TCGA-CM-6161 
       20.12        19.04        40.34        37.02        15.02 

$`FAM160B1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      102.44        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 
        2.93         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        16.01 
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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  FAM160B1 MUTATED FAM160B1 WILD-TYPE 
             15.02               0.00 
  FAM160B1 MUTATED FAM160B1 WILD-TYPE 
             40.34             140.38 
  FAM160B1 MUTATED FAM160B1 WILD-TYPE 
            20.120             20.235 
[1] "15.0 - 40.3 (20.1)" "0.0 - 140.4 (20.2)"
[1] "hr="     "9100000"
D585V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FAM160B1 MUTATED         2        0        1         2         0         0
  FAM160B1 WILD-TYPE      62        1       24       107         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM160B1 MUTATED           0          1          0          0        1
  FAM160B1 WILD-TYPE        19          9         41         31       34
                    vv
clus                 STAGE IVA STAGE IVB
  FAM160B1 MUTATED           0         0
  FAM160B1 WILD-TYPE        13         1
D585V3, multiclass
            clus
vv           FAM160B1 MUTATED FAM160B1 WILD-TYPE
  STAGE I                   2                 62
  STAGE IA                  0                  1
  STAGE II                  1                 24
  STAGE IIA                 2                107
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                1                  9
  STAGE IIIB                0                 41
  STAGE IIIC                0                 31
  STAGE IV                  1                 34
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  FAM160B1 MUTATED     0   2   4   1
  FAM160B1 WILD-TYPE   9  66 244  40
D585V4, multiclass
    clus
vv   FAM160B1 MUTATED FAM160B1 WILD-TYPE
  T1                0                  9
  T2                2                 66
  T3                4                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
  FAM160B1 MUTATED     6   1   0
  FAM160B1 WILD-TYPE 214  79  66
D585V5, multiclass
    clus
vv   FAM160B1 MUTATED FAM160B1 WILD-TYPE
  N0                6                214
  N1                1                 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"
D585V6, binary
                    cls
clus                   0   1
  FAM160B1 MUTATED     5   1
  FAM160B1 WILD-TYPE 278  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  FAM160B1 MUTATED      5    1
  FAM160B1 WILD-TYPE  278   47
   clus
vv  FAM160B1 MUTATED FAM160B1 WILD-TYPE
  0                5                278
  1                1                 47
[1] 2 2
[1] FALSE
D585V7, binary
                    cls
clus                   0   1
  FAM160B1 MUTATED     4   3
  FAM160B1 WILD-TYPE 166 194
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  FAM160B1 MUTATED      4    3
  FAM160B1 WILD-TYPE  166  194
        clus
vv       FAM160B1 MUTATED FAM160B1 WILD-TYPE
  FEMALE                4                166
  MALE                  3                194
[1] 2 2
[1] FALSE
D585V8, binary
                    cls
clus                   0   1
  FAM160B1 MUTATED     6   1
  FAM160B1 WILD-TYPE 311  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  FAM160B1 MUTATED      6    1
  FAM160B1 WILD-TYPE  311   47
                               clus
vv                              FAM160B1 MUTATED FAM160B1 WILD-TYPE
  COLON ADENOCARCINOMA                         6                311
  COLON MUCINOUS ADENOCARCINOMA                1                 47
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  FAM160B1 MUTATED     4   1   1   0
  FAM160B1 WILD-TYPE 253   1  21  21
D585V9, multiclass
    clus
vv   FAM160B1 MUTATED FAM160B1 WILD-TYPE
  R0                4                253
  R1                1                  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"
D585V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM160B1 MUTATED                                  0     0
  FAM160B1 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  FAM160B1 MUTATED                           2     2
  FAM160B1 WILD-TYPE                        17   174
D585V11, multiclass
                                  clus
vv                                 FAM160B1 MUTATED FAM160B1 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(586) Variable = NCOA6 MUTATION ANALYSIS
D586V1, survival
                 sevent
clus2               0   1
  NCOA6 MUTATED    19   5
  NCOA6 WILD-TYPE 263  68
  NCOA6 MUTATED NCOA6 WILD-TYPE 
             24             331 
  NCOA6 MUTATED NCOA6 WILD-TYPE 
              5              68 
$`NCOA6 MUTATED`
TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3525 TCGA-AA-3663 TCGA-AA-3715 TCGA-AA-3966 
       19.66        63.98         8.05         6.97        19.04         2.01 
TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-6607 TCGA-CA-6716 TCGA-CA-6717 
       25.02         4.01        34.98         3.19         0.26         0.33 
TCGA-CA-6718 TCGA-CK-5913 TCGA-CM-5344 TCGA-CM-6679 TCGA-D5-5538 TCGA-D5-6927 
        0.10        51.32        22.03        10.06        12.26         9.44 
TCGA-DM-A1DB TCGA-F4-6570 TCGA-G4-6299 TCGA-G4-6307 TCGA-G4-6588 TCGA-G4-6628 
       44.32         6.18        74.56        55.04        26.17        52.80 

$`NCOA6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 
        9.07        24.03        37.05        36.03        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       26.01        24.00         2.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 
       12.10       100.01        29.56         5.23        11.74         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6719 
        2.24         3.06         3.25         3.29         0.07         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
       17.56       102.44        40.34        15.62        49.08        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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 
       16.01        15.02         5.03        15.02        15.02        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-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       45.40        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.38        13.45        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 
      107.67        65.85        53.62        44.68        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 
       46.75 

  NCOA6 MUTATED NCOA6 WILD-TYPE 
            0.1             0.0 
  NCOA6 MUTATED NCOA6 WILD-TYPE 
          74.56          140.38 
  NCOA6 MUTATED NCOA6 WILD-TYPE 
          15.65           20.98 
[1] "0.1 - 74.6 (15.6)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.1"
D586V2, 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       22        99         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        19         10         37         29       34        13
                 vv
clus              STAGE IVB
  NCOA6 MUTATED           0
  NCOA6 WILD-TYPE         1
D586V3, multiclass
            clus
vv           NCOA6 MUTATED NCOA6 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA             10              99
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             4              37
  STAGE IIIC             2              29
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NCOA6 MUTATED     0   2  18   4
  NCOA6 WILD-TYPE   9  66 230  37
D586V4, multiclass
    clus
vv   NCOA6 MUTATED NCOA6 WILD-TYPE
  T1             0               9
  T2             2              66
  T3            18             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
  NCOA6 MUTATED    17   5   2
  NCOA6 WILD-TYPE 203  75  64
D586V5, multiclass
    clus
vv   NCOA6 MUTATED NCOA6 WILD-TYPE
  N0            17             203
  N1             5              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"
D586V6, binary
                 cls
clus                0   1
  NCOA6 MUTATED    20   1
  NCOA6 WILD-TYPE 263  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA6 MUTATED     20    1
  NCOA6 WILD-TYPE  263   47
   clus
vv  NCOA6 MUTATED NCOA6 WILD-TYPE
  0            20             263
  1             1              47
[1] 2 2
[1] FALSE
D586V7, 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
D586V8, binary
                 cls
clus                0   1
  NCOA6 MUTATED    20   4
  NCOA6 WILD-TYPE 297  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA6 MUTATED     20    4
  NCOA6 WILD-TYPE  297   44
                               clus
vv                              NCOA6 MUTATED NCOA6 WILD-TYPE
  COLON ADENOCARCINOMA                     20             297
  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 241   2  22  17
D586V9, multiclass
    clus
vv   NCOA6 MUTATED NCOA6 WILD-TYPE
  R0            16             241
  R1             0               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"
D586V10, 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
D586V11, 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(587) Variable = FUBP3 MUTATION ANALYSIS
D587V1, survival
                 sevent
clus2               0   1
  FUBP3 MUTATED     8   1
  FUBP3 WILD-TYPE 274  72
  FUBP3 MUTATED FUBP3 WILD-TYPE 
              9             346 
  FUBP3 MUTATED FUBP3 WILD-TYPE 
              1              72 
$`FUBP3 MUTATED`
TCGA-AA-3663 TCGA-AA-3950 TCGA-AA-A010 TCGA-AD-5900 TCGA-AD-6895 TCGA-AZ-4315 
        6.97        24.00        34.98         0.07         0.72        58.39 
TCGA-CM-6162 TCGA-F4-6570 TCGA-F4-6856 
       12.00         6.18        19.43 

$`FUBP3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37         4.21        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.38        13.45        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 
       16.24        33.67        13.25         0.53        35.41       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  FUBP3 MUTATED FUBP3 WILD-TYPE 
           0.07            0.00 
  FUBP3 MUTATED FUBP3 WILD-TYPE 
          58.39          140.38 
  FUBP3 MUTATED FUBP3 WILD-TYPE 
          12.00           20.63 
[1] "0.1 - 58.4 (12.0)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "1.3"
D587V2, 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       24       106         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FUBP3 MUTATED           0          0          1          0        0         0
  FUBP3 WILD-TYPE        19         10         40         31       35        13
                 vv
clus              STAGE IVB
  FUBP3 MUTATED           0
  FUBP3 WILD-TYPE         1
D587V3, multiclass
            clus
vv           FUBP3 MUTATED FUBP3 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              3             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FUBP3 MUTATED     0   2   6   1
  FUBP3 WILD-TYPE   9  66 242  40
D587V4, multiclass
    clus
vv   FUBP3 MUTATED FUBP3 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             6             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
  FUBP3 MUTATED     7   2   0
  FUBP3 WILD-TYPE 213  78  66
D587V5, multiclass
    clus
vv   FUBP3 MUTATED FUBP3 WILD-TYPE
  N0             7             213
  N1             2              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"
D587V6, binary
                 cls
clus                0   1
  FUBP3 MUTATED     7   0
  FUBP3 WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FUBP3 MUTATED      7    0
  FUBP3 WILD-TYPE  276   48
   clus
vv  FUBP3 MUTATED FUBP3 WILD-TYPE
  0             7             276
  1             0              48
[1] 2 2
[1] FALSE
D587V7, 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
D587V8, binary
                 cls
clus                0   1
  FUBP3 MUTATED     5   4
  FUBP3 WILD-TYPE 312  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FUBP3 MUTATED      5    4
  FUBP3 WILD-TYPE  312   44
                               clus
vv                              FUBP3 MUTATED FUBP3 WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  FUBP3 MUTATED     8   0   0   0
  FUBP3 WILD-TYPE 249   2  22  21
D587V9, multiclass
    clus
vv   FUBP3 MUTATED FUBP3 WILD-TYPE
  R0             8             249
  R1             0               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"
D587V10, 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
D587V11, 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(588) Variable = YSK4 MUTATION ANALYSIS
D588V1, survival
                sevent
clus2              0   1
  YSK4 MUTATED    21   5
  YSK4 WILD-TYPE 261  68
  YSK4 MUTATED YSK4 WILD-TYPE 
            26            329 
  YSK4 MUTATED YSK4 WILD-TYPE 
             5             68 
$`YSK4 MUTATED`
TCGA-A6-6138 TCGA-A6-6653 TCGA-AA-3516 TCGA-AA-3555 TCGA-AA-3697 TCGA-AA-3713 
       22.52        24.39        13.02        29.95        85.05        19.04 
TCGA-AA-3715 TCGA-AA-3833 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6895 
       19.04        15.95        25.02         4.01        34.98         0.72 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4752 
       15.75        21.44        58.39         0.33         0.10        13.02 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6537 TCGA-D5-6540 TCGA-DM-A1D9 TCGA-DM-A28E 
       20.19        18.25         4.80        16.14       140.38       119.93 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

$`YSK4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        32.71        27.09         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 
        5.98        37.05        19.00        36.00         5.03        26.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       17.98        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
        0.07        21.37         4.21        56.55         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       16.31         0.95         0.20        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.26         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       19.59        13.51        11.51         1.32        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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       12.59         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
        6.12        81.37        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       22.09        13.78        35.80        26.17        91.79 

  YSK4 MUTATED YSK4 WILD-TYPE 
           0.1            0.0 
  YSK4 MUTATED YSK4 WILD-TYPE 
        140.38         139.17 
  YSK4 MUTATED YSK4 WILD-TYPE 
        19.615         20.280 
[1] "0.1 - 140.4 (19.6)" "0.0 - 139.2 (20.3)"
[1] "hr=" "1.3"
D588V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  YSK4 MUTATED         4        0        1        12         2         0
  YSK4 WILD-TYPE      60        1       24        97         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  YSK4 MUTATED           2          0          1          0        1         1
  YSK4 WILD-TYPE        17         10         40         31       34        12
                vv
clus             STAGE IVB
  YSK4 MUTATED           0
  YSK4 WILD-TYPE         1
D588V3, multiclass
            clus
vv           YSK4 MUTATED YSK4 WILD-TYPE
  STAGE I               4             60
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA            12             97
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             2             17
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  63 229  39
D588V4, multiclass
    clus
vv   YSK4 MUTATED YSK4 WILD-TYPE
  T1            0              9
  T2            5             63
  T3           19            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
  YSK4 MUTATED    22   3   1
  YSK4 WILD-TYPE 198  77  65
D588V5, multiclass
    clus
vv   YSK4 MUTATED YSK4 WILD-TYPE
  N0           22            198
  N1            3             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"
D588V6, binary
                cls
clus               0   1
  YSK4 MUTATED    20   2
  YSK4 WILD-TYPE 263  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  YSK4 MUTATED     20    2
  YSK4 WILD-TYPE  263   46
   clus
vv  YSK4 MUTATED YSK4 WILD-TYPE
  0           20            263
  1            2             46
[1] 2 2
[1] FALSE
D588V7, 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
D588V8, binary
                cls
clus               0   1
  YSK4 MUTATED    21   5
  YSK4 WILD-TYPE 296  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  YSK4 MUTATED     21    5
  YSK4 WILD-TYPE  296   43
                               clus
vv                              YSK4 MUTATED YSK4 WILD-TYPE
  COLON ADENOCARCINOMA                    21            296
  COLON MUCINOUS ADENOCARCINOMA            5             43
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  YSK4 MUTATED    16   0   1   2
  YSK4 WILD-TYPE 241   2  21  19
D588V9, multiclass
    clus
vv   YSK4 MUTATED YSK4 WILD-TYPE
  R0           16            241
  R1            0              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"
D588V10, 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
D588V11, 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(589) Variable = CCAR1 MUTATION ANALYSIS
D589V1, survival
                 sevent
clus2               0   1
  CCAR1 MUTATED    14   3
  CCAR1 WILD-TYPE 268  70
  CCAR1 MUTATED CCAR1 WILD-TYPE 
             17             338 
  CCAR1 MUTATED CCAR1 WILD-TYPE 
              3              70 
$`CCAR1 MUTATED`
TCGA-A6-5665 TCGA-A6-6651 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3855 TCGA-AA-3966 
       22.06        21.76        19.66        63.98        32.05         2.01 
TCGA-AA-A00J TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6719 TCGA-CM-6162 TCGA-CM-6680 
       18.05        58.39        49.41         1.35        12.00        12.03 
TCGA-D5-6929 TCGA-DM-A1D4 TCGA-G4-6304 TCGA-G4-6626 TCGA-G4-6628 
       13.41        92.75        53.62        46.75        52.80 

$`CCAR1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
       33.07         0.00        36.03         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       26.01        24.00         2.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13        83.80        22.36        62.79        61.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.33         0.10        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      107.67        74.56        65.85        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 
       26.17        91.79 

  CCAR1 MUTATED CCAR1 WILD-TYPE 
           1.35            0.00 
  CCAR1 MUTATED CCAR1 WILD-TYPE 
          92.75          140.38 
  CCAR1 MUTATED CCAR1 WILD-TYPE 
          22.06           20.07 
[1] "1.4 - 92.8 (22.1)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.7"
D589V2, 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       23       102         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        19         10         37         30       34        13
                 vv
clus              STAGE IVB
  CCAR1 MUTATED           0
  CCAR1 WILD-TYPE         1
D589V3, multiclass
            clus
vv           CCAR1 MUTATED CCAR1 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              7             102
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             4              37
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CCAR1 MUTATED     0   2  13   3
  CCAR1 WILD-TYPE   9  66 235  38
D589V4, multiclass
    clus
vv   CCAR1 MUTATED CCAR1 WILD-TYPE
  T1             0               9
  T2             2              66
  T3            13             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
  CCAR1 MUTATED    12   5   1
  CCAR1 WILD-TYPE 208  75  65
D589V5, multiclass
    clus
vv   CCAR1 MUTATED CCAR1 WILD-TYPE
  N0            12             208
  N1             5              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"
D589V6, binary
                 cls
clus                0   1
  CCAR1 MUTATED    14   1
  CCAR1 WILD-TYPE 269  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCAR1 MUTATED     14    1
  CCAR1 WILD-TYPE  269   47
   clus
vv  CCAR1 MUTATED CCAR1 WILD-TYPE
  0            14             269
  1             1              47
[1] 2 2
[1] FALSE
D589V7, 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
D589V8, binary
                 cls
clus                0   1
  CCAR1 MUTATED    14   4
  CCAR1 WILD-TYPE 303  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCAR1 MUTATED     14    4
  CCAR1 WILD-TYPE  303   44
                               clus
vv                              CCAR1 MUTATED CCAR1 WILD-TYPE
  COLON ADENOCARCINOMA                     14             303
  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 244   2  22  20
D589V9, multiclass
    clus
vv   CCAR1 MUTATED CCAR1 WILD-TYPE
  R0            13             244
  R1             0               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"
D589V10, 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
D589V11, 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(590) Variable = HRSP12 MUTATION ANALYSIS
D590V1, survival
                  sevent
clus2                0   1
  HRSP12 MUTATED     5   1
  HRSP12 WILD-TYPE 277  72
  HRSP12 MUTATED HRSP12 WILD-TYPE 
               6              349 
  HRSP12 MUTATED HRSP12 WILD-TYPE 
               1               72 
$`HRSP12 MUTATED`
TCGA-AA-3510 TCGA-AA-3662 TCGA-AA-3947 TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-6598 
       63.98         6.05        33.01        34.98        58.39        49.41 

$`HRSP12 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       19.99        13.94        19.99        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  HRSP12 MUTATED HRSP12 WILD-TYPE 
            6.05             0.00 
  HRSP12 MUTATED HRSP12 WILD-TYPE 
           63.98           140.38 
  HRSP12 MUTATED HRSP12 WILD-TYPE 
          42.195           20.020 
[1] "6.0 - 64.0 (42.2)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "2"  
D590V2, 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       23       108         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HRSP12 MUTATED           0          0          0          0        1
  HRSP12 WILD-TYPE        19         10         41         31       34
                  vv
clus               STAGE IVA STAGE IVB
  HRSP12 MUTATED           0         0
  HRSP12 WILD-TYPE        13         1
D590V3, multiclass
            clus
vv           HRSP12 MUTATED HRSP12 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               1              108
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  HRSP12 MUTATED     0   0   3   3
  HRSP12 WILD-TYPE   9  68 245  38
D590V4, multiclass
    clus
vv   HRSP12 MUTATED HRSP12 WILD-TYPE
  T1              0                9
  T2              0               68
  T3              3              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
  HRSP12 MUTATED     5   0   1
  HRSP12 WILD-TYPE 215  80  65
D590V5, multiclass
    clus
vv   HRSP12 MUTATED HRSP12 WILD-TYPE
  N0              5              215
  N1              0               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
  HRSP12 MUTATED     4   1
  HRSP12 WILD-TYPE 279  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HRSP12 MUTATED      4    1
  HRSP12 WILD-TYPE  279   47
   clus
vv  HRSP12 MUTATED HRSP12 WILD-TYPE
  0              4              279
  1              1               47
[1] 2 2
[1] FALSE
D590V7, 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
D590V8, binary
                  cls
clus                 0   1
  HRSP12 MUTATED     5   1
  HRSP12 WILD-TYPE 312  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HRSP12 MUTATED      5    1
  HRSP12 WILD-TYPE  312   47
                               clus
vv                              HRSP12 MUTATED HRSP12 WILD-TYPE
  COLON ADENOCARCINOMA                       5              312
  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 253   2  21  21
D590V9, multiclass
    clus
vv   HRSP12 MUTATED HRSP12 WILD-TYPE
  R0              4              253
  R1              0                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"
D590V10, 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
D590V11, multiclass
[1] "Remove cluster labels:" "HRSP12 MUTATED"        
clus
  HRSP12 MUTATED HRSP12 WILD-TYPE 
               2              204 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-4105 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-A6-5661       TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5665 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-A6-5666       TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-A6-6142       TCGA-A6-6648       TCGA-A6-6649       TCGA-A6-6651 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-A6-6652       TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-A6-6781       TCGA-A6-6782       TCGA-AD-5900       TCGA-AD-6548 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-AD-6888       TCGA-AD-6889       TCGA-AD-6890       TCGA-AD-6895 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-AD-6899       TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6964 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-AD-6965       TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-AY-4071       TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-AY-6386       TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4681 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-AZ-4682       TCGA-AZ-5403       TCGA-AZ-5407       TCGA-AZ-6599 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-AZ-6600       TCGA-AZ-6601       TCGA-AZ-6603       TCGA-AZ-6605 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-AZ-6606       TCGA-AZ-6607       TCGA-AZ-6608       TCGA-CA-5254 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-CA-5255       TCGA-CA-5796       TCGA-CA-5797       TCGA-CA-6715 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-CA-6716       TCGA-CA-6717       TCGA-CA-6718       TCGA-CA-6719 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-CK-4947       TCGA-CK-4948       TCGA-CK-4950       TCGA-CK-4952 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-CK-5912       TCGA-CK-5913       TCGA-CK-5914       TCGA-CK-5915 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-CK-5916       TCGA-CK-6746       TCGA-CK-6747       TCGA-CK-6748 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-CK-6751       TCGA-CM-4743       TCGA-CM-4744       TCGA-CM-4746 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341       TCGA-CM-5344 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860       TCGA-CM-5861 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864       TCGA-CM-5868 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163       TCGA-CM-6164 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167       TCGA-CM-6168 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171       TCGA-CM-6172 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676       TCGA-CM-6677 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680       TCGA-D5-5537 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540       TCGA-D5-5541 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533       TCGA-D5-6534 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537       TCGA-D5-6538 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541       TCGA-D5-6898 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923       TCGA-D5-6924 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928       TCGA-D5-6929 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932       TCGA-D5-7000 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-DM-A0X9       TCGA-DM-A0XD       TCGA-DM-A0XF       TCGA-DM-A1D0 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-DM-A1D4       TCGA-DM-A1D6       TCGA-DM-A1D7       TCGA-DM-A1D8 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-DM-A1D9       TCGA-DM-A1DA       TCGA-DM-A1DB       TCGA-DM-A1HA 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-DM-A1HB       TCGA-DM-A282       TCGA-DM-A285       TCGA-DM-A28C 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-DM-A28E       TCGA-DM-A28F       TCGA-DM-A28G       TCGA-DM-A28H 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-DM-A28K       TCGA-F4-6459       TCGA-F4-6460       TCGA-F4-6569 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704       TCGA-F4-6805 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808       TCGA-F4-6809 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856       TCGA-G4-6293 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304       TCGA-G4-6306 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310       TCGA-G4-6315 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323       TCGA-G4-6586 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 

Clustering(591) Variable = MCCC1 MUTATION ANALYSIS
D591V1, survival
                 sevent
clus2               0   1
  MCCC1 MUTATED    13   3
  MCCC1 WILD-TYPE 269  70
  MCCC1 MUTATED MCCC1 WILD-TYPE 
             16             339 
  MCCC1 MUTATED MCCC1 WILD-TYPE 
              3              70 
$`MCCC1 MUTATED`
TCGA-A6-2676 TCGA-A6-6652 TCGA-AA-3555 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3877 
       42.90        24.69        29.95        78.08        54.02        31.00 
TCGA-AA-A00E TCGA-AA-A010 TCGA-AD-6890 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6608 
       30.02        34.98         0.79        58.39        49.41         1.94 
TCGA-CM-4743 TCGA-G4-6293 TCGA-G4-6304 TCGA-G4-6307 
       23.05       107.67        53.62        55.04 

$`MCCC1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 
       19.99        61.02         6.05         6.97         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        19.00        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 
       19.43        74.56        65.85        44.68        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  MCCC1 MUTATED MCCC1 WILD-TYPE 
           0.79            0.00 
  MCCC1 MUTATED MCCC1 WILD-TYPE 
         107.67          140.38 
  MCCC1 MUTATED MCCC1 WILD-TYPE 
          38.94           19.59 
[1] "0.8 - 107.7 (38.9)" "0.0 - 140.4 (19.6)"
[1] "hr=" "1.8"
D591V2, 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       21       105         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        18          9         40         31       35        12
                 vv
clus              STAGE IVB
  MCCC1 MUTATED           0
  MCCC1 WILD-TYPE         1
D591V3, multiclass
            clus
vv           MCCC1 MUTATED MCCC1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               4              21
  STAGE IIA              4             105
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             1               9
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 238  37
D591V4, multiclass
    clus
vv   MCCC1 MUTATED MCCC1 WILD-TYPE
  T1             2               7
  T2             1              67
  T3            10             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
  MCCC1 MUTATED    14   3   0
  MCCC1 WILD-TYPE 206  77  66
D591V5, multiclass
    clus
vv   MCCC1 MUTATED MCCC1 WILD-TYPE
  N0            14             206
  N1             3              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"
D591V6, binary
                 cls
clus                0   1
  MCCC1 MUTATED    14   1
  MCCC1 WILD-TYPE 269  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MCCC1 MUTATED     14    1
  MCCC1 WILD-TYPE  269   47
   clus
vv  MCCC1 MUTATED MCCC1 WILD-TYPE
  0            14             269
  1             1              47
[1] 2 2
[1] FALSE
D591V7, 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
D591V8, binary
                 cls
clus                0   1
  MCCC1 MUTATED    15   2
  MCCC1 WILD-TYPE 302  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MCCC1 MUTATED     15    2
  MCCC1 WILD-TYPE  302   46
                               clus
vv                              MCCC1 MUTATED MCCC1 WILD-TYPE
  COLON ADENOCARCINOMA                     15             302
  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 244   2  22  21
D591V9, multiclass
    clus
vv   MCCC1 MUTATED MCCC1 WILD-TYPE
  R0            13             244
  R1             0               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"
D591V10, 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
D591V11, 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(592) Variable = PCDH12 MUTATION ANALYSIS
D592V1, survival
                  sevent
clus2                0   1
  PCDH12 MUTATED    15   2
  PCDH12 WILD-TYPE 267  71
  PCDH12 MUTATED PCDH12 WILD-TYPE 
              17              338 
  PCDH12 MUTATED PCDH12 WILD-TYPE 
               2               71 
$`PCDH12 MUTATED`
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5665 TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3821 
       33.53        23.61        22.06         0.92        19.04         1.02 
TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-A010 TCGA-AD-6964 TCGA-AZ-6598 TCGA-CA-6715 
       53.00        31.00        34.98        10.88        49.41         0.07 
TCGA-CA-6717 TCGA-CK-5913 TCGA-CM-6171 TCGA-D5-6927 TCGA-D5-6928 
        0.33        51.32        14.04         9.44        11.64 

$`PCDH12 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5664 TCGA-A6-5666 
       32.91        31.63        30.44        29.19        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
       25.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.06         3.25         3.29         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
       17.56       102.44        40.34        15.62        49.08        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 
       12.39        10.13        12.43        14.30         9.04        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  PCDH12 MUTATED PCDH12 WILD-TYPE 
            0.07             0.00 
  PCDH12 MUTATED PCDH12 WILD-TYPE 
           53.00           140.38 
  PCDH12 MUTATED PCDH12 WILD-TYPE 
          19.040           20.235 
[1] "0.1 - 53.0 (19.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.5"
D592V2, 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       23       103         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PCDH12 MUTATED           1          0          1          0        1
  PCDH12 WILD-TYPE        18         10         40         31       34
                  vv
clus               STAGE IVA STAGE IVB
  PCDH12 MUTATED           1         0
  PCDH12 WILD-TYPE        12         1
D592V3, multiclass
            clus
vv           PCDH12 MUTATED PCDH12 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               6              103
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 236  39
D592V4, multiclass
    clus
vv   PCDH12 MUTATED PCDH12 WILD-TYPE
  T1              1                8
  T2              2               66
  T3             12              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
  PCDH12 MUTATED    13   2   2
  PCDH12 WILD-TYPE 207  78  64
D592V5, multiclass
    clus
vv   PCDH12 MUTATED PCDH12 WILD-TYPE
  N0             13              207
  N1              2               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"
D592V6, binary
                  cls
clus                 0   1
  PCDH12 MUTATED    12   2
  PCDH12 WILD-TYPE 271  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH12 MUTATED     12    2
  PCDH12 WILD-TYPE  271   46
   clus
vv  PCDH12 MUTATED PCDH12 WILD-TYPE
  0             12              271
  1              2               46
[1] 2 2
[1] FALSE
D592V7, 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
D592V8, binary
                  cls
clus                 0   1
  PCDH12 MUTATED    13   4
  PCDH12 WILD-TYPE 304  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH12 MUTATED     13    4
  PCDH12 WILD-TYPE  304   44
                               clus
vv                              PCDH12 MUTATED PCDH12 WILD-TYPE
  COLON ADENOCARCINOMA                      13              304
  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 247   2  21  18
D592V9, multiclass
    clus
vv   PCDH12 MUTATED PCDH12 WILD-TYPE
  R0             10              247
  R1              0                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"
D592V10, 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
D592V11, 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(593) Variable = CCR2 MUTATION ANALYSIS
D593V1, survival
                sevent
clus2              0   1
  CCR2 MUTATED     7   0
  CCR2 WILD-TYPE 275  73
  CCR2 MUTATED CCR2 WILD-TYPE 
             7            348 
  CCR2 MUTATED CCR2 WILD-TYPE 
             0             73 
$`CCR2 MUTATED`
TCGA-A6-5666 TCGA-A6-6781 TCGA-AD-6548 TCGA-CA-6717 TCGA-CK-4950 TCGA-D5-5541 
       32.71        19.66        21.37         0.33        40.34        11.51 
TCGA-D5-6540 
       16.14 

$`CCR2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96         0.07         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 
        0.26         0.10         1.35        17.56       102.44        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  CCR2 MUTATED CCR2 WILD-TYPE 
          0.33           0.00 
  CCR2 MUTATED CCR2 WILD-TYPE 
         40.34         140.38 
  CCR2 MUTATED CCR2 WILD-TYPE 
        19.660         20.235 
[1] "0.3 - 40.3 (19.7)"  "0.0 - 140.4 (20.2)"
[1] "hr="     "9200000"
D593V2, 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       25       108         8         0
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CCR2 MUTATED           0          1          1          1        0         0
  CCR2 WILD-TYPE        19          9         40         30       35        13
                vv
clus             STAGE IVB
  CCR2 MUTATED           0
  CCR2 WILD-TYPE         1
D593V3, multiclass
            clus
vv           CCR2 MUTATED CCR2 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             1            108
  STAGE IIB             0              8
  STAGE IIC             1              0
  STAGE III             0             19
  STAGE IIIA            1              9
  STAGE IIIB            1             40
  STAGE IIIC            1             30
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CCR2 MUTATED     0   2   3   2
  CCR2 WILD-TYPE   9  66 245  39
D593V4, multiclass
    clus
vv   CCR2 MUTATED CCR2 WILD-TYPE
  T1            0              9
  T2            2             66
  T3            3            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
  CCR2 MUTATED     4   3   0
  CCR2 WILD-TYPE 216  77  66
D593V5, multiclass
    clus
vv   CCR2 MUTATED CCR2 WILD-TYPE
  N0            4            216
  N1            3             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"
D593V6, binary
                cls
clus               0   1
  CCR2 MUTATED     6   0
  CCR2 WILD-TYPE 277  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCR2 MUTATED      6    0
  CCR2 WILD-TYPE  277   48
   clus
vv  CCR2 MUTATED CCR2 WILD-TYPE
  0            6            277
  1            0             48
[1] 2 2
[1] FALSE
D593V7, 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
D593V8, binary
                cls
clus               0   1
  CCR2 MUTATED     4   3
  CCR2 WILD-TYPE 313  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCR2 MUTATED      4    3
  CCR2 WILD-TYPE  313   45
                               clus
vv                              CCR2 MUTATED CCR2 WILD-TYPE
  COLON ADENOCARCINOMA                     4            313
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CCR2 MUTATED     4   1   0   1
  CCR2 WILD-TYPE 253   1  22  20
D593V9, multiclass
    clus
vv   CCR2 MUTATED CCR2 WILD-TYPE
  R0            4            253
  R1            1              1
  R2            0             22
  RX            1             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D593V10, 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
D593V11, 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(594) Variable = G3BP2 MUTATION ANALYSIS
D594V1, survival
                 sevent
clus2               0   1
  G3BP2 MUTATED     7   2
  G3BP2 WILD-TYPE 275  71
  G3BP2 MUTATED G3BP2 WILD-TYPE 
              9             346 
  G3BP2 MUTATED G3BP2 WILD-TYPE 
              2              71 
$`G3BP2 MUTATED`
TCGA-A6-5661 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6548 TCGA-CA-6717 TCGA-D5-6536 
       33.53         4.01        34.98        21.37         0.33        17.85 
TCGA-D5-6540 TCGA-DM-A0XD TCGA-G4-6628 
       16.14        24.43        52.80 

$`G3BP2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96         0.07         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        15.12         4.80        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38        10.26       119.70        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       35.80        26.17        91.79        46.75 

  G3BP2 MUTATED G3BP2 WILD-TYPE 
           0.33            0.00 
  G3BP2 MUTATED G3BP2 WILD-TYPE 
          52.80          140.38 
  G3BP2 MUTATED G3BP2 WILD-TYPE 
         21.370          20.155 
[1] "0.3 - 52.8 (21.4)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D594V2, 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       25       105         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        19         10         41         31       35        13
                 vv
clus              STAGE IVB
  G3BP2 MUTATED           0
  G3BP2 WILD-TYPE         1
D594V3, multiclass
            clus
vv           G3BP2 MUTATED G3BP2 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              4             105
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  G3BP2 MUTATED     0   3   4   2
  G3BP2 WILD-TYPE   9  65 244  39
D594V4, multiclass
    clus
vv   G3BP2 MUTATED G3BP2 WILD-TYPE
  T1             0               9
  T2             3              65
  T3             4             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
  G3BP2 MUTATED     9   0   0
  G3BP2 WILD-TYPE 211  80  66
D594V5, multiclass
    clus
vv   G3BP2 MUTATED G3BP2 WILD-TYPE
  N0             9             211
  N1             0              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"
D594V6, binary
                 cls
clus                0   1
  G3BP2 MUTATED     9   0
  G3BP2 WILD-TYPE 274  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  G3BP2 MUTATED      9    0
  G3BP2 WILD-TYPE  274   48
   clus
vv  G3BP2 MUTATED G3BP2 WILD-TYPE
  0             9             274
  1             0              48
[1] 2 2
[1] FALSE
D594V7, 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
D594V8, binary
                 cls
clus                0   1
  G3BP2 MUTATED     6   3
  G3BP2 WILD-TYPE 311  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  G3BP2 MUTATED      6    3
  G3BP2 WILD-TYPE  311   45
                               clus
vv                              G3BP2 MUTATED G3BP2 WILD-TYPE
  COLON ADENOCARCINOMA                      6             311
  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 250   2  22  20
D594V9, multiclass
    clus
vv   G3BP2 MUTATED G3BP2 WILD-TYPE
  R0             7             250
  R1             0               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"
D594V10, 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
D594V11, 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(595) Variable = MOV10L1 MUTATION ANALYSIS
D595V1, survival
                   sevent
clus2                 0   1
  MOV10L1 MUTATED    12   3
  MOV10L1 WILD-TYPE 270  70
  MOV10L1 MUTATED MOV10L1 WILD-TYPE 
               15               340 
  MOV10L1 MUTATED MOV10L1 WILD-TYPE 
                3                70 
$`MOV10L1 MUTATED`
TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-5661 TCGA-AA-3672 TCGA-AA-3947 TCGA-AA-3977 
       34.65        32.75        33.53         0.92        33.01        25.02 
TCGA-AA-A00N TCGA-AU-6004 TCGA-CM-5860 TCGA-CM-6172 TCGA-D5-6532 TCGA-D5-6537 
        4.01        27.09        16.01        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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       16.57        33.34        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       30.44        29.19        23.61        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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-6674 
       14.99        12.99        13.02        15.02        14.04        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        15.12        17.85        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6898 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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38        10.26       119.70        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 
      107.67        74.56        65.85        53.62        44.68        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  MOV10L1 MUTATED MOV10L1 WILD-TYPE 
             0.92              0.00 
  MOV10L1 MUTATED MOV10L1 WILD-TYPE 
            55.04            140.38 
  MOV10L1 MUTATED MOV10L1 WILD-TYPE 
           24.430            20.155 
[1] "0.9 - 55.0 (24.4)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D595V2, 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       25       104         5         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MOV10L1 MUTATED           1          0          3          1        0
  MOV10L1 WILD-TYPE        18         10         38         30       35
                   vv
clus                STAGE IVA STAGE IVB
  MOV10L1 MUTATED           0         0
  MOV10L1 WILD-TYPE        13         1
D595V3, multiclass
            clus
vv           MOV10L1 MUTATED MOV10L1 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                5               104
  STAGE IIB                3                 5
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               0                10
  STAGE IIIB               3                38
  STAGE IIIC               1                30
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  MOV10L1 MUTATED     0   2  10   3
  MOV10L1 WILD-TYPE   9  66 238  38
D595V4, multiclass
    clus
vv   MOV10L1 MUTATED MOV10L1 WILD-TYPE
  T1               0                 9
  T2               2                66
  T3              10               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
  MOV10L1 MUTATED    10   4   1
  MOV10L1 WILD-TYPE 210  76  65
D595V5, multiclass
    clus
vv   MOV10L1 MUTATED MOV10L1 WILD-TYPE
  N0              10               210
  N1               4                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"
D595V6, binary
                   cls
clus                  0   1
  MOV10L1 MUTATED    13   0
  MOV10L1 WILD-TYPE 270  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MOV10L1 MUTATED     13    0
  MOV10L1 WILD-TYPE  270   48
   clus
vv  MOV10L1 MUTATED MOV10L1 WILD-TYPE
  0              13               270
  1               0                48
[1] 2 2
[1] FALSE
D595V7, 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
D595V8, binary
                   cls
clus                  0   1
  MOV10L1 MUTATED    12   3
  MOV10L1 WILD-TYPE 305  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MOV10L1 MUTATED     12    3
  MOV10L1 WILD-TYPE  305   45
                               clus
vv                              MOV10L1 MUTATED MOV10L1 WILD-TYPE
  COLON ADENOCARCINOMA                       12               305
  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 244   2  22  21
D595V9, multiclass
    clus
vv   MOV10L1 MUTATED MOV10L1 WILD-TYPE
  R0              13               244
  R1               0                 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"
D595V10, 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
D595V11, 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(596) Variable = MRAS MUTATION ANALYSIS
D596V1, survival
                sevent
clus2              0   1
  MRAS MUTATED     3   1
  MRAS WILD-TYPE 279  72
  MRAS MUTATED MRAS WILD-TYPE 
             4            351 
  MRAS MUTATED MRAS WILD-TYPE 
             1             72 
$`MRAS MUTATED`
TCGA-A6-2676 TCGA-CM-5344 TCGA-CM-6161 TCGA-DM-A1HB 
       42.90        22.03        15.02       135.65 

$`MRAS WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  MRAS MUTATED MRAS WILD-TYPE 
         15.02           0.00 
  MRAS MUTATED MRAS WILD-TYPE 
        135.65         140.38 
  MRAS MUTATED MRAS WILD-TYPE 
        32.465         20.120 
[1] "15.0 - 135.7 (32.5)" "0.0 - 140.4 (20.1)" 
[1] "hr=" "1.4"
D596V2, 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       25       109         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        19         10         39         31       35        13
                vv
clus             STAGE IVB
  MRAS MUTATED           0
  MRAS WILD-TYPE         1
D596V3, multiclass
            clus
vv           MRAS MUTATED MRAS WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             0            109
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            2             39
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MRAS MUTATED     0   1   2   1
  MRAS WILD-TYPE   9  67 246  40
D596V4, multiclass
    clus
vv   MRAS MUTATED MRAS WILD-TYPE
  T1            0              9
  T2            1             67
  T3            2            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
  MRAS MUTATED     2   2   0
  MRAS WILD-TYPE 218  78  66
D596V5, multiclass
    clus
vv   MRAS MUTATED MRAS WILD-TYPE
  N0            2            218
  N1            2             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"
D596V6, binary
                cls
clus               0   1
  MRAS MUTATED     4   0
  MRAS WILD-TYPE 279  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  MRAS MUTATED      4    0
  MRAS WILD-TYPE  279   48
   clus
vv  MRAS MUTATED MRAS WILD-TYPE
  0            4            279
  1            0             48
[1] 2 2
[1] FALSE
D596V7, 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
D596V8, binary
                cls
clus               0   1
  MRAS MUTATED     4   0
  MRAS WILD-TYPE 313  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  MRAS MUTATED      4    0
  MRAS WILD-TYPE  313   48
                               clus
vv                              MRAS MUTATED MRAS WILD-TYPE
  COLON ADENOCARCINOMA                     4            313
  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 254   2  22  21
D596V9, multiclass
    clus
vv   MRAS MUTATED MRAS WILD-TYPE
  R0            3            254
  R1            0              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"
D596V10, 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
D596V11, 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(597) Variable = KIFAP3 MUTATION ANALYSIS
D597V1, survival
                  sevent
clus2                0   1
  KIFAP3 MUTATED     8   0
  KIFAP3 WILD-TYPE 274  73
  KIFAP3 MUTATED KIFAP3 WILD-TYPE 
               8              347 
  KIFAP3 MUTATED KIFAP3 WILD-TYPE 
               0               73 
$`KIFAP3 MUTATED`
TCGA-AA-3663 TCGA-AA-3713 TCGA-AA-3815 TCGA-AA-A00A TCGA-AU-6004 TCGA-CA-6717 
        6.97        19.04        33.04        38.04        27.09         0.33 
TCGA-CM-4746 TCGA-D5-6540 
       37.02        16.14 

$`KIFAP3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E 
       19.07         7.96        27.02        13.94        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  KIFAP3 MUTATED KIFAP3 WILD-TYPE 
            0.33             0.00 
  KIFAP3 MUTATED KIFAP3 WILD-TYPE 
           38.04           140.38 
  KIFAP3 MUTATED KIFAP3 WILD-TYPE 
          23.065           20.190 
[1] "0.3 - 38.0 (23.1)"  "0.0 - 140.4 (20.2)"
[1] "hr="     "9200000"
D597V2, 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       23       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIFAP3 MUTATED           0          0          0          0        1
  KIFAP3 WILD-TYPE        19         10         41         31       34
                  vv
clus               STAGE IVA STAGE IVB
  KIFAP3 MUTATED           0         0
  KIFAP3 WILD-TYPE        13         1
D597V3, multiclass
            clus
vv           KIFAP3 MUTATED KIFAP3 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               3              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  KIFAP3 MUTATED     0   3   5   1
  KIFAP3 WILD-TYPE   9  65 243  40
D597V4, multiclass
    clus
vv   KIFAP3 MUTATED KIFAP3 WILD-TYPE
  T1              0                9
  T2              3               65
  T3              5              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
  KIFAP3 MUTATED     9   0   0
  KIFAP3 WILD-TYPE 211  80  66
D597V5, multiclass
    clus
vv   KIFAP3 MUTATED KIFAP3 WILD-TYPE
  N0              9              211
  N1              0               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"
D597V6, binary
                  cls
clus                 0   1
  KIFAP3 MUTATED     8   1
  KIFAP3 WILD-TYPE 275  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIFAP3 MUTATED      8    1
  KIFAP3 WILD-TYPE  275   47
   clus
vv  KIFAP3 MUTATED KIFAP3 WILD-TYPE
  0              8              275
  1              1               47
[1] 2 2
[1] FALSE
D597V7, 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
D597V8, binary
                  cls
clus                 0   1
  KIFAP3 MUTATED     7   2
  KIFAP3 WILD-TYPE 310  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIFAP3 MUTATED      7    2
  KIFAP3 WILD-TYPE  310   46
                               clus
vv                              KIFAP3 MUTATED KIFAP3 WILD-TYPE
  COLON ADENOCARCINOMA                       7              310
  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 250   2  21  20
D597V9, multiclass
    clus
vv   KIFAP3 MUTATED KIFAP3 WILD-TYPE
  R0              7              250
  R1              0                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"
D597V10, 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
D597V11, 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(598) Variable = BCL9L MUTATION ANALYSIS
D598V1, survival
                 sevent
clus2               0   1
  BCL9L MUTATED    17   2
  BCL9L WILD-TYPE 265  71
  BCL9L MUTATED BCL9L WILD-TYPE 
             19             336 
  BCL9L MUTATED BCL9L WILD-TYPE 
              2              71 
$`BCL9L MUTATED`
TCGA-A6-6781 TCGA-AA-3663 TCGA-AA-3713 TCGA-AA-3833 TCGA-AA-3866 TCGA-AA-3870 
       19.66         6.97        19.04        15.95        17.03        29.98 
TCGA-AA-3972 TCGA-AA-A01R TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6964 TCGA-AU-6004 
       50.99        35.01         0.79         0.72        10.88        27.09 
TCGA-AZ-4315 TCGA-AZ-6601 TCGA-CM-6161 TCGA-D5-6536 TCGA-DM-A1HB TCGA-F4-6856 
       58.39       100.01        15.02        17.85       135.65        19.43 
TCGA-G4-6304 
       53.62 

$`BCL9L WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 
       33.04         0.99        25.02         1.02        17.98        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        24.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       16.08        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       56.55         5.79        22.42        27.42         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 
       20.19        18.25         1.32        43.27        15.12         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 
        0.53        35.41       107.67        74.56        65.85        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  BCL9L MUTATED BCL9L WILD-TYPE 
           0.72            0.00 
  BCL9L MUTATED BCL9L WILD-TYPE 
         135.65          140.38 
  BCL9L MUTATED BCL9L WILD-TYPE 
          19.43           20.63 
[1] "0.7 - 135.7 (19.4)" "0.0 - 140.4 (20.6)"
[1] "hr=" "2.6"
D598V2, 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       23       106         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BCL9L MUTATED           1          0          1          1        3         0
  BCL9L WILD-TYPE        18         10         40         30       32        13
                 vv
clus              STAGE IVB
  BCL9L MUTATED           0
  BCL9L WILD-TYPE         1
D598V3, multiclass
            clus
vv           BCL9L MUTATED BCL9L WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              3             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             1              30
  STAGE IV               3              32
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  BCL9L MUTATED     1   4  11   3
  BCL9L WILD-TYPE   8  64 237  38
D598V4, multiclass
    clus
vv   BCL9L MUTATED BCL9L WILD-TYPE
  T1             1               8
  T2             4              64
  T3            11             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
  BCL9L MUTATED    12   4   3
  BCL9L WILD-TYPE 208  76  63
D598V5, multiclass
    clus
vv   BCL9L MUTATED BCL9L WILD-TYPE
  N0            12             208
  N1             4              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"
D598V6, binary
                 cls
clus                0   1
  BCL9L MUTATED    12   3
  BCL9L WILD-TYPE 271  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BCL9L MUTATED     12    3
  BCL9L WILD-TYPE  271   45
   clus
vv  BCL9L MUTATED BCL9L WILD-TYPE
  0            12             271
  1             3              45
[1] 2 2
[1] FALSE
D598V7, 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
D598V8, binary
                 cls
clus                0   1
  BCL9L MUTATED    16   3
  BCL9L WILD-TYPE 301  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BCL9L MUTATED     16    3
  BCL9L WILD-TYPE  301   45
                               clus
vv                              BCL9L MUTATED BCL9L WILD-TYPE
  COLON ADENOCARCINOMA                     16             301
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  BCL9L MUTATED    12   0   2   0
  BCL9L WILD-TYPE 245   2  20  21
D598V9, multiclass
    clus
vv   BCL9L MUTATED BCL9L WILD-TYPE
  R0            12             245
  R1             0               2
  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"
D598V10, 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
D598V11, 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(599) Variable = EFHC1 MUTATION ANALYSIS
D599V1, survival
                 sevent
clus2               0   1
  EFHC1 MUTATED     9   0
  EFHC1 WILD-TYPE 273  73
  EFHC1 MUTATED EFHC1 WILD-TYPE 
              9             346 
  EFHC1 MUTATED EFHC1 WILD-TYPE 
              0              73 
$`EFHC1 MUTATED`
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3977 TCGA-AA-A010 TCGA-AU-6004 TCGA-CA-6718 
       20.98        34.03        25.02        34.98        27.09         0.10 
TCGA-CA-6719 TCGA-CM-6163 TCGA-G4-6628 
        1.35        14.04        52.80 

$`EFHC1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       24.00         2.01         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02        12.00        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       35.80        26.17        91.79        46.75 

  EFHC1 MUTATED EFHC1 WILD-TYPE 
            0.1             0.0 
  EFHC1 MUTATED EFHC1 WILD-TYPE 
          52.80          140.38 
  EFHC1 MUTATED EFHC1 WILD-TYPE 
          25.02           20.07 
[1] "0.1 - 52.8 (25.0)"  "0.0 - 140.4 (20.1)"
[1] "hr="     "9300000"
D599V2, 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       25       106         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        18         10         40         31       35        13
                 vv
clus              STAGE IVB
  EFHC1 MUTATED           0
  EFHC1 WILD-TYPE         1
D599V3, multiclass
            clus
vv           EFHC1 MUTATED EFHC1 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              3             106
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EFHC1 MUTATED     1   4   4   2
  EFHC1 WILD-TYPE   8  64 244  39
D599V4, multiclass
    clus
vv   EFHC1 MUTATED EFHC1 WILD-TYPE
  T1             1               8
  T2             4              64
  T3             4             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
  EFHC1 MUTATED     9   0   2
  EFHC1 WILD-TYPE 211  80  64
D599V5, multiclass
    clus
vv   EFHC1 MUTATED EFHC1 WILD-TYPE
  N0             9             211
  N1             0              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"
D599V6, binary
                 cls
clus                0   1
  EFHC1 MUTATED     9   0
  EFHC1 WILD-TYPE 274  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHC1 MUTATED      9    0
  EFHC1 WILD-TYPE  274   48
   clus
vv  EFHC1 MUTATED EFHC1 WILD-TYPE
  0             9             274
  1             0              48
[1] 2 2
[1] FALSE
D599V7, 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
D599V8, binary
                 cls
clus                0   1
  EFHC1 MUTATED    11   0
  EFHC1 WILD-TYPE 306  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHC1 MUTATED     11    0
  EFHC1 WILD-TYPE  306   48
                               clus
vv                              EFHC1 MUTATED EFHC1 WILD-TYPE
  COLON ADENOCARCINOMA                     11             306
  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 250   2  22  18
D599V9, multiclass
    clus
vv   EFHC1 MUTATED EFHC1 WILD-TYPE
  R0             7             250
  R1             0               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"
D599V10, 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
D599V11, 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(600) Variable = RAB40C MUTATION ANALYSIS
D600V1, survival
                  sevent
clus2                0   1
  RAB40C MUTATED     5   2
  RAB40C WILD-TYPE 277  71
  RAB40C MUTATED RAB40C WILD-TYPE 
               7              348 
  RAB40C MUTATED RAB40C WILD-TYPE 
               2               71 
$`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 
       19.43 

$`RAB40C WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       23.87        20.12        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.20        14.50        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.41       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  RAB40C MUTATED RAB40C WILD-TYPE 
            3.02             0.00 
  RAB40C MUTATED RAB40C WILD-TYPE 
           49.41           140.38 
  RAB40C MUTATED RAB40C WILD-TYPE 
          27.090           20.155 
[1] "3.0 - 49.4 (27.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.4"
D600V2, 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       23       108         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RAB40C MUTATED           0          0          0          1        0
  RAB40C WILD-TYPE        19         10         41         30       35
                  vv
clus               STAGE IVA STAGE IVB
  RAB40C MUTATED           0         0
  RAB40C WILD-TYPE        13         1
D600V3, multiclass
            clus
vv           RAB40C MUTATED RAB40C WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               1              108
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  RAB40C MUTATED     0   3   3   2
  RAB40C WILD-TYPE   9  65 245  39
D600V4, multiclass
    clus
vv   RAB40C MUTATED RAB40C WILD-TYPE
  T1              0                9
  T2              3               65
  T3              3              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
  RAB40C MUTATED     7   1   0
  RAB40C WILD-TYPE 213  79  66
D600V5, multiclass
    clus
vv   RAB40C MUTATED RAB40C WILD-TYPE
  N0              7              213
  N1              1               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
  RAB40C MUTATED     5   0
  RAB40C WILD-TYPE 278  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RAB40C MUTATED      5    0
  RAB40C WILD-TYPE  278   48
   clus
vv  RAB40C MUTATED RAB40C WILD-TYPE
  0              5              278
  1              0               48
[1] 2 2
[1] FALSE
D600V7, 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
D600V8, binary
                  cls
clus                 0   1
  RAB40C MUTATED     6   2
  RAB40C WILD-TYPE 311  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RAB40C MUTATED      6    2
  RAB40C WILD-TYPE  311   46
                               clus
vv                              RAB40C MUTATED RAB40C WILD-TYPE
  COLON ADENOCARCINOMA                       6              311
  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 251   2  22  20
D600V9, multiclass
    clus
vv   RAB40C MUTATED RAB40C WILD-TYPE
  R0              6              251
  R1              0                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"
D600V10, 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
D600V11, 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(601) Variable = CIC MUTATION ANALYSIS
D601V1, survival
               sevent
clus2             0   1
  CIC MUTATED    20   3
  CIC WILD-TYPE 262  70
  CIC MUTATED CIC WILD-TYPE 
           23           332 
  CIC MUTATED CIC WILD-TYPE 
            3            70 
$`CIC MUTATED`
TCGA-A6-5665 TCGA-AA-3715 TCGA-AA-3877 TCGA-AA-3966 TCGA-AA-A01R TCGA-AD-6889 
       22.06        19.04        31.00         2.01        35.01        56.55 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6601 TCGA-CA-6718 TCGA-CK-5913 TCGA-CK-5914 
       21.44        58.39       100.01         0.10        51.32        21.99 
TCGA-CM-4743 TCGA-CM-6163 TCGA-CM-6171 TCGA-CM-6674 TCGA-D5-6928 TCGA-DM-A1HB 
       23.05        14.04        14.04        12.95        11.64       135.65 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 
       65.85        53.62        35.80        26.17        52.80 

$`CIC WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        18.05         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       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        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37         4.21         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        15.75         0.20        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.33         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        49.08        21.14         2.93         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        16.01        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-6172 
       21.99        14.99        12.99        13.02        15.02        11.01 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6306 TCGA-G4-6307 
       35.41        19.43       107.67        74.56        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6625 TCGA-G4-6626 
       91.79        46.75 

  CIC MUTATED CIC WILD-TYPE 
          0.1           0.0 
  CIC MUTATED CIC WILD-TYPE 
       135.65        140.38 
  CIC MUTATED CIC WILD-TYPE 
       26.170        19.825 
[1] "0.1 - 135.7 (26.2)" "0.0 - 140.4 (19.8)"
[1] "hr=" "2.4"
D601V2, 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       23        97         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        18         10         39         31       34        13
               vv
clus            STAGE IVB
  CIC MUTATED           0
  CIC WILD-TYPE         1
D601V3, multiclass
            clus
vv           CIC MUTATED CIC WILD-TYPE
  STAGE I              4            60
  STAGE IA             0             1
  STAGE II             2            23
  STAGE IIA           12            97
  STAGE IIB            1             7
  STAGE IIC            0             1
  STAGE III            1            18
  STAGE IIIA           0            10
  STAGE IIIB           2            39
  STAGE IIIC           0            31
  STAGE IV             1            34
  STAGE IVA            0            13
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  CIC MUTATED     2   2  18   1
  CIC WILD-TYPE   7  66 230  40
D601V4, multiclass
    clus
vv   CIC MUTATED CIC WILD-TYPE
  T1           2             7
  T2           2            66
  T3          18           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
  CIC MUTATED    19   3   1
  CIC WILD-TYPE 201  77  65
D601V5, multiclass
    clus
vv   CIC MUTATED CIC WILD-TYPE
  N0          19           201
  N1           3            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"
D601V6, binary
               cls
clus              0   1
  CIC MUTATED    19   1
  CIC WILD-TYPE 264  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  CIC MUTATED     19    1
  CIC WILD-TYPE  264   47
   clus
vv  CIC MUTATED CIC WILD-TYPE
  0          19           264
  1           1            47
[1] 2 2
[1] FALSE
D601V7, 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
D601V8, binary
               cls
clus              0   1
  CIC MUTATED    19   4
  CIC WILD-TYPE 298  44
[1] "tbl2"
               cls
clus            [,1] [,2]
  CIC MUTATED     19    4
  CIC WILD-TYPE  298   44
                               clus
vv                              CIC MUTATED CIC WILD-TYPE
  COLON ADENOCARCINOMA                   19           298
  COLON MUCINOUS ADENOCARCINOMA           4            44
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  CIC MUTATED    16   0   0   3
  CIC WILD-TYPE 241   2  22  18
D601V9, multiclass
    clus
vv   CIC MUTATED CIC WILD-TYPE
  R0          16           241
  R1           0             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"
D601V10, 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
D601V11, 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(602) Variable = TNFAIP3 MUTATION ANALYSIS
D602V1, survival
                   sevent
clus2                 0   1
  TNFAIP3 MUTATED    31   3
  TNFAIP3 WILD-TYPE 251  70
  TNFAIP3 MUTATED TNFAIP3 WILD-TYPE 
               34               321 
  TNFAIP3 MUTATED TNFAIP3 WILD-TYPE 
                3                70 
$`TNFAIP3 MUTATED`
TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6138 TCGA-AA-3510 TCGA-AA-3713 TCGA-AA-3811 
       33.53        22.06        22.52        63.98        19.04        10.06 
TCGA-AA-3950 TCGA-AA-3975 TCGA-AD-6895 TCGA-AU-3779 TCGA-AZ-4315 TCGA-AZ-5407 
       24.00        34.06         0.72        14.50        58.39        61.41 
TCGA-AZ-6599 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5914 
        6.77         0.33         0.10        40.34        15.62        21.99 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-6169 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       23.05        20.02        13.02        15.12        17.85         4.80 
TCGA-D5-6541 TCGA-D5-6929 TCGA-DM-A1HB TCGA-DM-A28K TCGA-G4-6293 TCGA-G4-6299 
       15.58        13.41       135.65        98.24       107.67        74.56 
TCGA-G4-6315 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6628 
       36.72        13.78        35.80        52.80 

$`TNFAIP3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       32.71        27.09         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       26.99        19.04        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.20        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       62.79        49.41        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07         0.26         1.35        17.56       102.44 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32        21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6538 TCGA-D5-6539 
       20.19        18.25         1.32        43.27        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-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44        11.64         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79       117.07         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6303 TCGA-G4-6304 
       13.25         0.53        35.41        19.43        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        51.75        45.11        36.00        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       26.17        91.79        46.75 

  TNFAIP3 MUTATED TNFAIP3 WILD-TYPE 
              0.1               0.0 
  TNFAIP3 MUTATED TNFAIP3 WILD-TYPE 
           135.65            140.38 
  TNFAIP3 MUTATED TNFAIP3 WILD-TYPE 
           22.025            20.120 
[1] "0.1 - 135.7 (22.0)" "0.0 - 140.4 (20.1)"
[1] "hr=" "3.2"
D602V2, 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       24        96         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TNFAIP3 MUTATED           3          1          4          1        3
  TNFAIP3 WILD-TYPE        16          9         37         30       32
                   vv
clus                STAGE IVA STAGE IVB
  TNFAIP3 MUTATED           0         0
  TNFAIP3 WILD-TYPE        13         1
D602V3, multiclass
            clus
vv           TNFAIP3 MUTATED TNFAIP3 WILD-TYPE
  STAGE I                  6                58
  STAGE IA                 1                 0
  STAGE II                 1                24
  STAGE IIA               13                96
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                3                16
  STAGE IIIA               1                 9
  STAGE IIIB               4                37
  STAGE IIIC               1                30
  STAGE IV                 3                32
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TNFAIP3 MUTATED     1   5  26   1
  TNFAIP3 WILD-TYPE   8  63 222  40
D602V4, multiclass
    clus
vv   TNFAIP3 MUTATED TNFAIP3 WILD-TYPE
  T1               1                 8
  T2               5                63
  T3              26               222
  T4               1                40
[1] 4 2
[1] TRUE
[1] "dimension 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  71  63
D602V5, multiclass
    clus
vv   TNFAIP3 MUTATED TNFAIP3 WILD-TYPE
  N0              22               198
  N1               9                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"
D602V6, binary
                   cls
clus                  0   1
  TNFAIP3 MUTATED    25   3
  TNFAIP3 WILD-TYPE 258  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFAIP3 MUTATED     25    3
  TNFAIP3 WILD-TYPE  258   45
   clus
vv  TNFAIP3 MUTATED TNFAIP3 WILD-TYPE
  0              25               258
  1               3                45
[1] 2 2
[1] FALSE
D602V7, 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
D602V8, binary
                   cls
clus                  0   1
  TNFAIP3 MUTATED    30   4
  TNFAIP3 WILD-TYPE 287  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFAIP3 MUTATED     30    4
  TNFAIP3 WILD-TYPE  287   44
                               clus
vv                              TNFAIP3 MUTATED TNFAIP3 WILD-TYPE
  COLON ADENOCARCINOMA                       30               287
  COLON MUCINOUS ADENOCARCINOMA               4                44
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  TNFAIP3 MUTATED    21   1   1   5
  TNFAIP3 WILD-TYPE 236   1  21  16
D602V9, multiclass
    clus
vv   TNFAIP3 MUTATED TNFAIP3 WILD-TYPE
  R0              21               236
  R1               1                 1
  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"
D602V10, 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
D602V11, 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(603) Variable = MCART1 MUTATION ANALYSIS
D603V1, survival
                  sevent
clus2                0   1
  MCART1 MUTATED    11   1
  MCART1 WILD-TYPE 271  72
  MCART1 MUTATED MCART1 WILD-TYPE 
              12              343 
  MCART1 MUTATED MCART1 WILD-TYPE 
               1               72 
$`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        40.34 
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        51.75 

$`MCART1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        18.05         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 
        0.10         1.35        17.56       102.44        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       12.59         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  MCART1 MUTATED MCART1 WILD-TYPE 
            7.04             0.00 
  MCART1 MUTATED MCART1 WILD-TYPE 
          140.38           139.17 
  MCART1 MUTATED MCART1 WILD-TYPE 
          35.275           19.990 
[1] "7.0 - 140.4 (35.3)" "0.0 - 139.2 (20.0)"
[1] "hr=" "4.4"
D603V2, 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       24       105         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MCART1 MUTATED           0          1          2          0        0
  MCART1 WILD-TYPE        19          9         39         31       35
                  vv
clus               STAGE IVA STAGE IVB
  MCART1 MUTATED           0         0
  MCART1 WILD-TYPE        13         1
D603V3, multiclass
            clus
vv           MCART1 MUTATED MCART1 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               4              105
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              1                9
  STAGE IIIB              2               39
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MCART1 MUTATED     1   2   8   1
  MCART1 WILD-TYPE   8  66 240  40
D603V4, multiclass
    clus
vv   MCART1 MUTATED MCART1 WILD-TYPE
  T1              1                8
  T2              2               66
  T3              8              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
  MCART1 MUTATED     9   3   0
  MCART1 WILD-TYPE 211  77  66
D603V5, multiclass
    clus
vv   MCART1 MUTATED MCART1 WILD-TYPE
  N0              9              211
  N1              3               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"
D603V6, binary
                  cls
clus                 0   1
  MCART1 MUTATED    12   0
  MCART1 WILD-TYPE 271  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MCART1 MUTATED     12    0
  MCART1 WILD-TYPE  271   48
   clus
vv  MCART1 MUTATED MCART1 WILD-TYPE
  0             12              271
  1              0               48
[1] 2 2
[1] FALSE
D603V7, 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
D603V8, binary
                  cls
clus                 0   1
  MCART1 MUTATED     9   3
  MCART1 WILD-TYPE 308  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MCART1 MUTATED      9    3
  MCART1 WILD-TYPE  308   45
                               clus
vv                              MCART1 MUTATED MCART1 WILD-TYPE
  COLON ADENOCARCINOMA                       9              308
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  MCART1 MUTATED     9   1   0   0
  MCART1 WILD-TYPE 248   1  22  21
D603V9, multiclass
    clus
vv   MCART1 MUTATED MCART1 WILD-TYPE
  R0              9              248
  R1              1                1
  R2              0               22
  RX              0               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D603V10, 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
D603V11, 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(604) Variable = MYH3 MUTATION ANALYSIS
D604V1, survival
                sevent
clus2              0   1
  MYH3 MUTATED    21   8
  MYH3 WILD-TYPE 261  65
  MYH3 MUTATED MYH3 WILD-TYPE 
            29            326 
  MYH3 MUTATED MYH3 WILD-TYPE 
             8             65 
$`MYH3 MUTATED`
TCGA-AA-3516 TCGA-AA-3555 TCGA-AA-3662 TCGA-AA-3950 TCGA-AA-A00N TCGA-AD-6889 
       13.02        29.95         6.05        24.00         4.01        56.55 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4315 TCGA-AZ-4616 TCGA-AZ-6600 TCGA-AZ-6601 
        0.72        10.88        58.39         5.13        12.10       100.01 
TCGA-AZ-6606 TCGA-CA-6717 TCGA-CK-4947 TCGA-CK-6751 TCGA-CM-4747 TCGA-CM-6169 
       11.74         0.33        17.56       124.27        25.02        13.02 
TCGA-CM-6172 TCGA-CM-6674 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6539 
       11.01        12.95        20.19         1.32        15.12        12.49 
TCGA-DM-A28G TCGA-F4-6808 TCGA-G4-6306 TCGA-G4-6321 TCGA-G4-6586 
       60.79        33.67        44.68        22.09        35.80 

$`MYH3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        1.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        17.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
        0.07        21.37         4.21         0.79         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4681 
       15.75         0.20        21.44        17.82         1.41        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6603 
       22.36        62.79        61.41        49.41         6.77        29.56 
TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 
        3.29         0.07         0.26         0.10         1.35       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4752 
        2.93         2.01        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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       15.02        14.04        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       11.51        18.25        43.27        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
       81.37       119.93        35.97       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       29.59        16.24        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 
      107.67        74.56        65.85        53.62        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 
       45.11        36.72        36.00        13.78        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  MYH3 MUTATED MYH3 WILD-TYPE 
          0.33           0.00 
  MYH3 MUTATED MYH3 WILD-TYPE 
        124.27         140.38 
  MYH3 MUTATED MYH3 WILD-TYPE 
         15.12          20.98 
[1] "0.3 - 124.3 (15.1)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.3"
D604V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MYH3 MUTATED         3        0        2        12         1         0
  MYH3 WILD-TYPE      61        1       23        97         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MYH3 MUTATED           2          1          3          0        4         2
  MYH3 WILD-TYPE        17          9         38         31       31        11
                vv
clus             STAGE IVB
  MYH3 MUTATED           0
  MYH3 WILD-TYPE         1
D604V3, multiclass
            clus
vv           MYH3 MUTATED MYH3 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA            12             97
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             2             17
  STAGE IIIA            1              9
  STAGE IIIB            3             38
  STAGE IIIC            0             31
  STAGE IV              4             31
  STAGE IVA             2             11
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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   9
  MYH3 WILD-TYPE   8  64 230  32
D604V4, multiclass
    clus
vv   MYH3 MUTATED MYH3 WILD-TYPE
  T1            1              8
  T2            4             64
  T3           18            230
  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
  MYH3 MUTATED    20   7   5
  MYH3 WILD-TYPE 200  73  61
D604V5, multiclass
    clus
vv   MYH3 MUTATED MYH3 WILD-TYPE
  N0           20            200
  N1            7             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"
D604V6, binary
                cls
clus               0   1
  MYH3 MUTATED    21   5
  MYH3 WILD-TYPE 262  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYH3 MUTATED     21    5
  MYH3 WILD-TYPE  262   43
   clus
vv  MYH3 MUTATED MYH3 WILD-TYPE
  0           21            262
  1            5             43
[1] 2 2
[1] FALSE
D604V7, binary
                cls
clus               0   1
  MYH3 MUTATED    16  16
  MYH3 WILD-TYPE 154 181
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYH3 MUTATED     16   16
  MYH3 WILD-TYPE  154  181
        clus
vv       MYH3 MUTATED MYH3 WILD-TYPE
  FEMALE           16            154
  MALE             16            181
[1] 2 2
[1] FALSE
D604V8, binary
                cls
clus               0   1
  MYH3 MUTATED    26   6
  MYH3 WILD-TYPE 291  42
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYH3 MUTATED     26    6
  MYH3 WILD-TYPE  291   42
                               clus
vv                              MYH3 MUTATED MYH3 WILD-TYPE
  COLON ADENOCARCINOMA                    26            291
  COLON MUCINOUS ADENOCARCINOMA            6             42
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MYH3 MUTATED    17   0   1   5
  MYH3 WILD-TYPE 240   2  21  16
D604V9, multiclass
    clus
vv   MYH3 MUTATED MYH3 WILD-TYPE
  R0           17            240
  R1            0              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"
D604V10, 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    21
  MYH3 WILD-TYPE                        17   155
D604V11, 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                                      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(605) Variable = DENND4A MUTATION ANALYSIS
D605V1, survival
                   sevent
clus2                 0   1
  DENND4A MUTATED    18   4
  DENND4A WILD-TYPE 264  69
  DENND4A MUTATED DENND4A WILD-TYPE 
               22               333 
  DENND4A MUTATED DENND4A WILD-TYPE 
                4                69 
$`DENND4A MUTATED`
TCGA-A6-5657 TCGA-A6-5665 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3715 TCGA-AA-3864 
       31.63        22.06         6.97         0.92        19.04        53.00 
TCGA-AA-3947 TCGA-AA-3966 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6889 TCGA-AY-6196 
       33.01         2.01         4.01        34.98        56.55         0.20 
TCGA-AZ-4315 TCGA-AZ-6605 TCGA-CK-5914 TCGA-CK-6747 TCGA-CM-5864 TCGA-CM-6171 
       58.39         5.23        21.99         2.93        15.02        14.04 
TCGA-D5-5539 TCGA-DM-A1HB TCGA-G4-6303 TCGA-G4-6586 
       19.59       135.65        65.85        35.80 

$`DENND4A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37         4.21         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        15.75        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 
       49.41         6.77        12.10       100.01        29.56        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 
      102.44        40.34        15.62        49.08        51.32        21.14 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        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        16.01 
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        12.26 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      107.67        74.56        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 
       45.11        36.72        36.00        22.09        13.78        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  DENND4A MUTATED DENND4A WILD-TYPE 
              0.2               0.0 
  DENND4A MUTATED DENND4A WILD-TYPE 
           135.65            140.38 
  DENND4A MUTATED DENND4A WILD-TYPE 
            20.79             20.19 
[1] "0.2 - 135.7 (20.8)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D605V2, 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       22       102         5         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DENND4A MUTATED           1          1          4          1        1
  DENND4A WILD-TYPE        18          9         37         30       34
                   vv
clus                STAGE IVA STAGE IVB
  DENND4A MUTATED           0         0
  DENND4A WILD-TYPE        13         1
D605V3, multiclass
            clus
vv           DENND4A MUTATED DENND4A WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 3                22
  STAGE IIA                7               102
  STAGE IIB                3                 5
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               1                 9
  STAGE IIIB               4                37
  STAGE IIIC               1                30
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  DENND4A MUTATED     0   2  17   4
  DENND4A WILD-TYPE   9  66 231  37
D605V4, multiclass
    clus
vv   DENND4A MUTATED DENND4A WILD-TYPE
  T1               0                 9
  T2               2                66
  T3              17               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
  DENND4A MUTATED    15   7   1
  DENND4A WILD-TYPE 205  73  65
D605V5, multiclass
    clus
vv   DENND4A MUTATED DENND4A WILD-TYPE
  N0              15               205
  N1               7                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"
D605V6, binary
                   cls
clus                  0   1
  DENND4A MUTATED    19   1
  DENND4A WILD-TYPE 264  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DENND4A MUTATED     19    1
  DENND4A WILD-TYPE  264   47
   clus
vv  DENND4A MUTATED DENND4A WILD-TYPE
  0              19               264
  1               1                47
[1] 2 2
[1] FALSE
D605V7, binary
                   cls
clus                  0   1
  DENND4A MUTATED    10  13
  DENND4A WILD-TYPE 160 184
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DENND4A MUTATED     10   13
  DENND4A WILD-TYPE  160  184
        clus
vv       DENND4A MUTATED DENND4A WILD-TYPE
  FEMALE              10               160
  MALE                13               184
[1] 2 2
[1] FALSE
D605V8, binary
                   cls
clus                  0   1
  DENND4A MUTATED    18   5
  DENND4A WILD-TYPE 299  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DENND4A MUTATED     18    5
  DENND4A WILD-TYPE  299   43
                               clus
vv                              DENND4A MUTATED DENND4A WILD-TYPE
  COLON ADENOCARCINOMA                       18               299
  COLON MUCINOUS ADENOCARCINOMA               5                43
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  DENND4A MUTATED    17   0   0   2
  DENND4A WILD-TYPE 240   2  22  19
D605V9, multiclass
    clus
vv   DENND4A MUTATED DENND4A WILD-TYPE
  R0              17               240
  R1               0                 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"
D605V10, 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    12
  DENND4A WILD-TYPE                        18   164
D605V11, 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                                         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(606) Variable = SERPINA9 MUTATION ANALYSIS
D606V1, survival
                    sevent
clus2                  0   1
  SERPINA9 MUTATED     7   2
  SERPINA9 WILD-TYPE 275  71
  SERPINA9 MUTATED SERPINA9 WILD-TYPE 
                 9                346 
  SERPINA9 MUTATED SERPINA9 WILD-TYPE 
                 2                 71 
$`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         0.10        23.05        22.03 
TCGA-CM-5348 TCGA-CM-6675 TCGA-D5-6923 
       22.98        13.05        12.43 

$`SERPINA9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 
        4.21        56.55         0.79         0.72         5.79        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13        83.80        22.36        62.79        61.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.33         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       29.06        30.08        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  SERPINA9 MUTATED SERPINA9 WILD-TYPE 
               0.1                0.0 
  SERPINA9 MUTATED SERPINA9 WILD-TYPE 
             49.41             140.38 
  SERPINA9 MUTATED SERPINA9 WILD-TYPE 
             22.42              20.07 
[1] "0.1 - 49.4 (22.4)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.2"
D606V2, 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       24       107         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SERPINA9 MUTATED           1          0          3          0        0
  SERPINA9 WILD-TYPE        18         10         38         31       35
                    vv
clus                 STAGE IVA STAGE IVB
  SERPINA9 MUTATED           0         1
  SERPINA9 WILD-TYPE        13         0
D606V3, multiclass
            clus
vv           SERPINA9 MUTATED SERPINA9 WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  1                 24
  STAGE IIA                 2                107
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 1                 18
  STAGE IIIA                0                 10
  STAGE IIIB                3                 38
  STAGE IIIC                0                 31
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  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  67 239  41
D606V4, multiclass
    clus
vv   SERPINA9 MUTATED SERPINA9 WILD-TYPE
  T1                0                  9
  T2                1                 67
  T3                9                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
  SERPINA9 MUTATED     5   3   2
  SERPINA9 WILD-TYPE 215  77  64
D606V5, multiclass
    clus
vv   SERPINA9 MUTATED SERPINA9 WILD-TYPE
  N0                5                215
  N1                3                 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"
D606V6, binary
                    cls
clus                   0   1
  SERPINA9 MUTATED     7   1
  SERPINA9 WILD-TYPE 276  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINA9 MUTATED      7    1
  SERPINA9 WILD-TYPE  276   47
   clus
vv  SERPINA9 MUTATED SERPINA9 WILD-TYPE
  0                7                276
  1                1                 47
[1] 2 2
[1] FALSE
D606V7, 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
D606V8, binary
                    cls
clus                   0   1
  SERPINA9 MUTATED    10   0
  SERPINA9 WILD-TYPE 307  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINA9 MUTATED     10    0
  SERPINA9 WILD-TYPE  307   48
                               clus
vv                              SERPINA9 MUTATED SERPINA9 WILD-TYPE
  COLON ADENOCARCINOMA                        10                307
  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 250   2  22  20
D606V9, multiclass
    clus
vv   SERPINA9 MUTATED SERPINA9 WILD-TYPE
  R0                7                250
  R1                0                  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"
D606V10, 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
D606V11, 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(607) Variable = RNF111 MUTATION ANALYSIS
D607V1, survival
                  sevent
clus2                0   1
  RNF111 MUTATED    11   2
  RNF111 WILD-TYPE 271  71
  RNF111 MUTATED RNF111 WILD-TYPE 
              13              342 
  RNF111 MUTATED RNF111 WILD-TYPE 
               2               71 
$`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         0.33         0.10        15.02        18.25 
TCGA-G4-6626 
       46.75 

$`RNF111 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       85.05        19.04        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U 
       18.05        38.04         4.01        27.02        42.02        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07         0.26         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       22.09        13.78        35.80        26.17        91.79        52.80 

  RNF111 MUTATED RNF111 WILD-TYPE 
               0                0 
  RNF111 MUTATED RNF111 WILD-TYPE 
           58.39           140.38 
  RNF111 MUTATED RNF111 WILD-TYPE 
           19.66            20.63 
[1] "0.0 - 58.4 (19.7)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "1.1"
D607V2, 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       25        99         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RNF111 MUTATED           1          0          0          1        0
  RNF111 WILD-TYPE        18         10         41         30       35
                  vv
clus               STAGE IVA STAGE IVB
  RNF111 MUTATED           0         0
  RNF111 WILD-TYPE        13         1
D607V3, multiclass
            clus
vv           RNF111 MUTATED RNF111 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA              10               99
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  RNF111 MUTATED     0   1  11   2
  RNF111 WILD-TYPE   9  67 237  39
D607V4, multiclass
    clus
vv   RNF111 MUTATED RNF111 WILD-TYPE
  T1              0                9
  T2              1               67
  T3             11              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
  RNF111 MUTATED    12   1   1
  RNF111 WILD-TYPE 208  79  65
D607V5, multiclass
    clus
vv   RNF111 MUTATED RNF111 WILD-TYPE
  N0             12              208
  N1              1               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"
D607V6, binary
                  cls
clus                 0   1
  RNF111 MUTATED    12   0
  RNF111 WILD-TYPE 271  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF111 MUTATED     12    0
  RNF111 WILD-TYPE  271   48
   clus
vv  RNF111 MUTATED RNF111 WILD-TYPE
  0             12              271
  1              0               48
[1] 2 2
[1] FALSE
D607V7, 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
D607V8, binary
                  cls
clus                 0   1
  RNF111 MUTATED     9   5
  RNF111 WILD-TYPE 308  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF111 MUTATED      9    5
  RNF111 WILD-TYPE  308   43
                               clus
vv                              RNF111 MUTATED RNF111 WILD-TYPE
  COLON ADENOCARCINOMA                       9              308
  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 246   2  22  19
D607V9, multiclass
    clus
vv   RNF111 MUTATED RNF111 WILD-TYPE
  R0             11              246
  R1              0                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"
D607V10, 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
D607V11, 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(608) Variable = SP110 MUTATION ANALYSIS
D608V1, survival
                 sevent
clus2               0   1
  SP110 MUTATED     8   2
  SP110 WILD-TYPE 274  71
  SP110 MUTATED SP110 WILD-TYPE 
             10             345 
  SP110 MUTATED SP110 WILD-TYPE 
              2              71 
$`SP110 MUTATED`
TCGA-AA-3710 TCGA-AD-6899 TCGA-AU-3779 TCGA-CM-5861 TCGA-CM-6166 TCGA-CM-6172 
       26.99         5.79        14.50        15.02        21.99        11.01 
TCGA-CM-6676 TCGA-D5-6539 TCGA-D5-6930 TCGA-DM-A1DA 
       11.08        12.49         1.51         7.50 

$`SP110 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 
        4.21        56.55         0.79         0.72        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01         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-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-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  SP110 MUTATED SP110 WILD-TYPE 
           1.51            0.00 
  SP110 MUTATED SP110 WILD-TYPE 
          26.99          140.38 
  SP110 MUTATED SP110 WILD-TYPE 
         11.785          20.980 
[1] "1.5 - 27.0 (11.8)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.7"
D608V2, 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       25       105         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SP110 MUTATED           0          1          1          2        0         0
  SP110 WILD-TYPE        19          9         40         29       35        13
                 vv
clus              STAGE IVB
  SP110 MUTATED           0
  SP110 WILD-TYPE         1
D608V3, multiclass
            clus
vv           SP110 MUTATED SP110 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              4             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             1              40
  STAGE IIIC             2              29
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SP110 MUTATED     0   2   7   1
  SP110 WILD-TYPE   9  66 241  40
D608V4, multiclass
    clus
vv   SP110 MUTATED SP110 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             7             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
  SP110 MUTATED     7   1   2
  SP110 WILD-TYPE 213  79  64
D608V5, multiclass
    clus
vv   SP110 MUTATED SP110 WILD-TYPE
  N0             7             213
  N1             1              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"
D608V6, binary
                 cls
clus                0   1
  SP110 MUTATED     9   0
  SP110 WILD-TYPE 274  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SP110 MUTATED      9    0
  SP110 WILD-TYPE  274   48
   clus
vv  SP110 MUTATED SP110 WILD-TYPE
  0             9             274
  1             0              48
[1] 2 2
[1] FALSE
D608V7, 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
D608V8, binary
                 cls
clus                0   1
  SP110 MUTATED     8   2
  SP110 WILD-TYPE 309  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SP110 MUTATED      8    2
  SP110 WILD-TYPE  309   46
                               clus
vv                              SP110 MUTATED SP110 WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  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 249   2  22  21
D608V9, multiclass
    clus
vv   SP110 MUTATED SP110 WILD-TYPE
  R0             8             249
  R1             0               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"
D608V10, 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
D608V11, 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(609) Variable = FIGNL1 MUTATION ANALYSIS
D609V1, survival
                  sevent
clus2                0   1
  FIGNL1 MUTATED    14   1
  FIGNL1 WILD-TYPE 268  72
  FIGNL1 MUTATED FIGNL1 WILD-TYPE 
              15              340 
  FIGNL1 MUTATED FIGNL1 WILD-TYPE 
               1               72 
$`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         0.33        15.62        30.08       119.70       135.65 
TCGA-F4-6703 TCGA-G4-6293 TCGA-G4-6303 
       35.87       107.67        65.85 

$`FIGNL1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5664 TCGA-A6-5665 
       32.91        31.63        30.44        29.19        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 
        6.97         1.02        13.02        38.99         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      102.44        40.34        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 
        8.61        13.38        13.45         6.18         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       19.43        74.56        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  FIGNL1 MUTATED FIGNL1 WILD-TYPE 
            0.33             0.00 
  FIGNL1 MUTATED FIGNL1 WILD-TYPE 
          135.65           140.38 
  FIGNL1 MUTATED FIGNL1 WILD-TYPE 
           34.98            19.99 
[1] "0.3 - 135.7 (35.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "6"  
D609V2, 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       24       101         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FIGNL1 MUTATED           2          0          2          0        1
  FIGNL1 WILD-TYPE        17         10         39         31       34
                  vv
clus               STAGE IVA STAGE IVB
  FIGNL1 MUTATED           1         0
  FIGNL1 WILD-TYPE        12         1
D609V3, multiclass
            clus
vv           FIGNL1 MUTATED FIGNL1 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               8              101
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               2               17
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  68 235  38
D609V4, multiclass
    clus
vv   FIGNL1 MUTATED FIGNL1 WILD-TYPE
  T1              0                9
  T2              0               68
  T3             13              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
  FIGNL1 MUTATED    10   4   2
  FIGNL1 WILD-TYPE 210  76  64
D609V5, multiclass
    clus
vv   FIGNL1 MUTATED FIGNL1 WILD-TYPE
  N0             10              210
  N1              4               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"
D609V6, binary
                  cls
clus                 0   1
  FIGNL1 MUTATED    14   2
  FIGNL1 WILD-TYPE 269  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FIGNL1 MUTATED     14    2
  FIGNL1 WILD-TYPE  269   46
   clus
vv  FIGNL1 MUTATED FIGNL1 WILD-TYPE
  0             14              269
  1              2               46
[1] 2 2
[1] FALSE
D609V7, 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
D609V8, binary
                  cls
clus                 0   1
  FIGNL1 MUTATED    13   3
  FIGNL1 WILD-TYPE 304  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FIGNL1 MUTATED     13    3
  FIGNL1 WILD-TYPE  304   45
                               clus
vv                              FIGNL1 MUTATED FIGNL1 WILD-TYPE
  COLON ADENOCARCINOMA                      13              304
  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 246   2  22  19
D609V9, multiclass
    clus
vv   FIGNL1 MUTATED FIGNL1 WILD-TYPE
  R0             11              246
  R1              0                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"
D609V10, 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
D609V11, 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(610) Variable = WDR66 MUTATION ANALYSIS
D610V1, survival
                 sevent
clus2               0   1
  WDR66 MUTATED    15   3
  WDR66 WILD-TYPE 267  70
  WDR66 MUTATED WDR66 WILD-TYPE 
             18             337 
  WDR66 MUTATED WDR66 WILD-TYPE 
              3              70 
$`WDR66 MUTATED`
TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3710 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3977 
       63.98         6.97        26.99        31.07        30.05        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6964 TCGA-AY-6196 TCGA-CA-6717 TCGA-CA-6718 
        4.01        34.98        10.88         0.20         0.33         0.10 
TCGA-CM-6162 TCGA-D5-6930 TCGA-DM-A282 TCGA-F4-6459 TCGA-F4-6808 TCGA-G4-6586 
       12.00         1.51       139.17         8.61        33.67        35.80 

$`WDR66 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       135.65         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79       117.07        98.24        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 
       35.87         1.55        16.31        29.59        16.24        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  WDR66 MUTATED WDR66 WILD-TYPE 
            0.1             0.0 
  WDR66 MUTATED WDR66 WILD-TYPE 
         139.17          140.38 
  WDR66 MUTATED WDR66 WILD-TYPE 
          18.51           20.19 
[1] "0.1 - 139.2 (18.5)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D610V2, 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       23       101         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        19         10         38         30       35        13
                 vv
clus              STAGE IVB
  WDR66 MUTATED           0
  WDR66 WILD-TYPE         1
D610V3, multiclass
            clus
vv           WDR66 MUTATED WDR66 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              8             101
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             3              38
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  WDR66 MUTATED     1   1  14   3
  WDR66 WILD-TYPE   8  67 234  38
D610V4, multiclass
    clus
vv   WDR66 MUTATED WDR66 WILD-TYPE
  T1             1               8
  T2             1              67
  T3            14             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
  WDR66 MUTATED    14   2   3
  WDR66 WILD-TYPE 206  78  63
D610V5, multiclass
    clus
vv   WDR66 MUTATED WDR66 WILD-TYPE
  N0            14             206
  N1             2              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"
D610V6, binary
                 cls
clus                0   1
  WDR66 MUTATED    16   0
  WDR66 WILD-TYPE 267  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR66 MUTATED     16    0
  WDR66 WILD-TYPE  267   48
   clus
vv  WDR66 MUTATED WDR66 WILD-TYPE
  0            16             267
  1             0              48
[1] 2 2
[1] FALSE
D610V7, 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
D610V8, binary
                 cls
clus                0   1
  WDR66 MUTATED    14   5
  WDR66 WILD-TYPE 303  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR66 MUTATED     14    5
  WDR66 WILD-TYPE  303   43
                               clus
vv                              WDR66 MUTATED WDR66 WILD-TYPE
  COLON ADENOCARCINOMA                     14             303
  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 243   2  22  19
D610V9, multiclass
    clus
vv   WDR66 MUTATED WDR66 WILD-TYPE
  R0            14             243
  R1             0               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"
D610V10, 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
D610V11, 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(611) Variable = POLD3 MUTATION ANALYSIS
D611V1, survival
                 sevent
clus2               0   1
  POLD3 MUTATED    10   1
  POLD3 WILD-TYPE 272  72
  POLD3 MUTATED POLD3 WILD-TYPE 
             11             344 
  POLD3 MUTATED POLD3 WILD-TYPE 
              1              72 
$`POLD3 MUTATED`
TCGA-A6-6141 TCGA-A6-6781 TCGA-AA-3518 TCGA-AA-3672 TCGA-AZ-4315 TCGA-D5-6540 
        8.38        19.66         1.02         0.92        58.39        16.14 
TCGA-D5-6931 TCGA-DM-A1D4 TCGA-F4-6856 TCGA-G4-6588 TCGA-G4-6628 
       12.00        92.75        19.43        26.17        52.80 

$`POLD3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 
       63.98         6.97         1.02        13.02        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         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         1.51 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 
       16.24        33.67        13.25         0.53        35.41       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 
       91.79        46.75 

  POLD3 MUTATED POLD3 WILD-TYPE 
           0.92            0.00 
  POLD3 MUTATED POLD3 WILD-TYPE 
          92.75          140.38 
  POLD3 MUTATED POLD3 WILD-TYPE 
          19.43           20.63 
[1] "0.9 - 92.8 (19.4)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "2.6"
D611V2, 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       25       104         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        18         10         41         29       35        13
                 vv
clus              STAGE IVB
  POLD3 MUTATED           0
  POLD3 WILD-TYPE         1
D611V3, multiclass
            clus
vv           POLD3 MUTATED POLD3 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              5             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             2              29
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  POLD3 MUTATED     0   3   6   2
  POLD3 WILD-TYPE   9  65 242  39
D611V4, multiclass
    clus
vv   POLD3 MUTATED POLD3 WILD-TYPE
  T1             0               9
  T2             3              65
  T3             6             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
  POLD3 MUTATED     8   2   1
  POLD3 WILD-TYPE 212  78  65
D611V5, multiclass
    clus
vv   POLD3 MUTATED POLD3 WILD-TYPE
  N0             8             212
  N1             2              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"
D611V6, binary
                 cls
clus                0   1
  POLD3 MUTATED    10   0
  POLD3 WILD-TYPE 273  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POLD3 MUTATED     10    0
  POLD3 WILD-TYPE  273   48
   clus
vv  POLD3 MUTATED POLD3 WILD-TYPE
  0            10             273
  1             0              48
[1] 2 2
[1] FALSE
D611V7, 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
D611V8, binary
                 cls
clus                0   1
  POLD3 MUTATED     8   3
  POLD3 WILD-TYPE 309  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POLD3 MUTATED      8    3
  POLD3 WILD-TYPE  309   45
                               clus
vv                              POLD3 MUTATED POLD3 WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  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 248   2  22  21
D611V9, multiclass
    clus
vv   POLD3 MUTATED POLD3 WILD-TYPE
  R0             9             248
  R1             0               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"
D611V10, 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
D611V11, 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(612) Variable = LEF1 MUTATION ANALYSIS
D612V1, survival
                sevent
clus2              0   1
  LEF1 MUTATED     7   1
  LEF1 WILD-TYPE 275  72
  LEF1 MUTATED LEF1 WILD-TYPE 
             8            347 
  LEF1 MUTATED LEF1 WILD-TYPE 
             1             72 
$`LEF1 MUTATED`
TCGA-AA-3510 TCGA-AA-3553 TCGA-AA-3811 TCGA-AA-3815 TCGA-AA-3994 TCGA-AD-5900 
       63.98        24.00        10.06        33.04        27.02         0.07 
TCGA-CA-6717 TCGA-G4-6586 
        0.33        35.80 

$`LEF1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        19.04        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
        7.96        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        26.17        91.79        46.75        52.80 

  LEF1 MUTATED LEF1 WILD-TYPE 
          0.07           0.00 
  LEF1 MUTATED LEF1 WILD-TYPE 
         63.98         140.38 
  LEF1 MUTATED LEF1 WILD-TYPE 
         25.51          20.12 
[1] "0.1 - 64.0 (25.5)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.5"
D612V2, 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       24       105         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        18         10         40         31       35        13
                vv
clus             STAGE IVB
  LEF1 MUTATED           0
  LEF1 WILD-TYPE         1
D612V3, multiclass
            clus
vv           LEF1 MUTATED LEF1 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             4            105
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  LEF1 MUTATED     0   2   7   0
  LEF1 WILD-TYPE   9  66 241  41
D612V4, multiclass
    clus
vv   LEF1 MUTATED LEF1 WILD-TYPE
  T1            0              9
  T2            2             66
  T3            7            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
  LEF1 MUTATED     7   1   1
  LEF1 WILD-TYPE 213  79  65
D612V5, multiclass
    clus
vv   LEF1 MUTATED LEF1 WILD-TYPE
  N0            7            213
  N1            1             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"
D612V6, binary
                cls
clus               0   1
  LEF1 MUTATED     8   0
  LEF1 WILD-TYPE 275  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  LEF1 MUTATED      8    0
  LEF1 WILD-TYPE  275   48
   clus
vv  LEF1 MUTATED LEF1 WILD-TYPE
  0            8            275
  1            0             48
[1] 2 2
[1] FALSE
D612V7, 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
D612V8, binary
                cls
clus               0   1
  LEF1 MUTATED     6   3
  LEF1 WILD-TYPE 311  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  LEF1 MUTATED      6    3
  LEF1 WILD-TYPE  311   45
                               clus
vv                              LEF1 MUTATED LEF1 WILD-TYPE
  COLON ADENOCARCINOMA                     6            311
  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 249   2  22  20
D612V9, multiclass
    clus
vv   LEF1 MUTATED LEF1 WILD-TYPE
  R0            8            249
  R1            0              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"
D612V10, 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
D612V11, 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(613) Variable = BCHE MUTATION ANALYSIS
D613V1, survival
                sevent
clus2              0   1
  BCHE MUTATED    18   6
  BCHE WILD-TYPE 264  67
  BCHE MUTATED BCHE WILD-TYPE 
            24            331 
  BCHE MUTATED BCHE WILD-TYPE 
             6             67 
$`BCHE MUTATED`
TCGA-AA-3492 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3544 TCGA-AA-3811 TCGA-AA-3815 
        3.02        13.02        38.99        14.01        10.06        33.04 
TCGA-AA-3977 TCGA-AA-A00E TCGA-AA-A01V TCGA-AD-6889 TCGA-AD-6964 TCGA-AU-6004 
       25.02        30.02        35.01        56.55        10.88        27.09 
TCGA-AZ-4315 TCGA-CA-5796 TCGA-CA-6717 TCGA-CK-4952 TCGA-CK-6748 TCGA-CM-5860 
       58.39         3.25         0.33        15.62         2.01        16.01 
TCGA-CM-5861 TCGA-D5-6533 TCGA-D5-6927 TCGA-D5-6930 TCGA-DM-A0XF TCGA-G4-6303 
       15.02         1.32         9.44         1.51        38.20        65.85 

$`BCHE WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3519 
       35.01        63.98         6.97         1.02         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
        0.99        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       26.99        19.04        19.04        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       33.04        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37         4.21         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
        0.72         5.79        22.42        27.42         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5797 
       11.74         3.19         1.94         2.24         3.06         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       40.34        49.08        51.32        21.99        21.14         2.93 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        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-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 
       13.51        11.51        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-D5-6928 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-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 
        0.53        35.41        19.43       107.67        74.56        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  BCHE MUTATED BCHE WILD-TYPE 
          0.33           0.00 
  BCHE MUTATED BCHE WILD-TYPE 
         65.85         140.38 
  BCHE MUTATED BCHE WILD-TYPE 
         15.32          20.98 
[1] "0.3 - 65.8 (15.3)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.4"
D613V2, 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       24        98         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BCHE MUTATED           4          0          1          1        2         0
  BCHE WILD-TYPE        15         10         40         30       33        13
                vv
clus             STAGE IVB
  BCHE MUTATED           0
  BCHE WILD-TYPE         1
D613V3, multiclass
            clus
vv           BCHE MUTATED BCHE WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA            11             98
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             4             15
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            1             30
  STAGE IV              2             33
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  BCHE MUTATED     0   4  18   3
  BCHE WILD-TYPE   9  64 230  38
D613V4, multiclass
    clus
vv   BCHE MUTATED BCHE WILD-TYPE
  T1            0              9
  T2            4             64
  T3           18            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
  BCHE MUTATED    17   2   6
  BCHE WILD-TYPE 203  78  60
D613V5, multiclass
    clus
vv   BCHE MUTATED BCHE WILD-TYPE
  N0           17            203
  N1            2             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"
D613V6, binary
                cls
clus               0   1
  BCHE MUTATED    21   2
  BCHE WILD-TYPE 262  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCHE MUTATED     21    2
  BCHE WILD-TYPE  262   46
   clus
vv  BCHE MUTATED BCHE WILD-TYPE
  0           21            262
  1            2             46
[1] 2 2
[1] FALSE
D613V7, 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
D613V8, binary
                cls
clus               0   1
  BCHE MUTATED    18   7
  BCHE WILD-TYPE 299  41
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCHE MUTATED     18    7
  BCHE WILD-TYPE  299   41
                               clus
vv                              BCHE MUTATED BCHE WILD-TYPE
  COLON ADENOCARCINOMA                    18            299
  COLON MUCINOUS ADENOCARCINOMA            7             41
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  BCHE MUTATED    17   0   0   3
  BCHE WILD-TYPE 240   2  22  18
D613V9, multiclass
    clus
vv   BCHE MUTATED BCHE WILD-TYPE
  R0           17            240
  R1            0              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"
D613V10, 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
D613V11, 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(614) Variable = MRE11A MUTATION ANALYSIS
D614V1, survival
                  sevent
clus2                0   1
  MRE11A MUTATED     9   2
  MRE11A WILD-TYPE 273  71
  MRE11A MUTATED MRE11A WILD-TYPE 
              11              344 
  MRE11A MUTATED MRE11A WILD-TYPE 
               2               71 
$`MRE11A MUTATED`
TCGA-A6-6141 TCGA-AA-A00N TCGA-CA-6717 TCGA-CM-4743 TCGA-CM-5861 TCGA-CM-6161 
        8.38         4.01         0.33        23.05        15.02        15.02 
TCGA-CM-6677 TCGA-D5-6534 TCGA-DM-A0XD TCGA-F4-6856 TCGA-G4-6588 
       11.08        43.27        24.43        19.43        26.17 

$`MRE11A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93         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        16.01 
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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 
       13.51        11.51        20.19        18.25         1.32        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       10.26       119.70        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 
       33.67        13.25         0.53        35.41       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  MRE11A MUTATED MRE11A WILD-TYPE 
            0.33             0.00 
  MRE11A MUTATED MRE11A WILD-TYPE 
           43.27           140.38 
  MRE11A MUTATED MRE11A WILD-TYPE 
           15.02            20.63 
[1] "0.3 - 43.3 (15.0)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "1.3"
D614V2, 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       25       101         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MRE11A MUTATED           0          0          0          0        0
  MRE11A WILD-TYPE        19         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  MRE11A MUTATED           0         0
  MRE11A WILD-TYPE        13         1
D614V3, multiclass
            clus
vv           MRE11A MUTATED MRE11A WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               8              101
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MRE11A MUTATED     0   2   8   2
  MRE11A WILD-TYPE   9  66 240  39
D614V4, multiclass
    clus
vv   MRE11A MUTATED MRE11A WILD-TYPE
  T1              0                9
  T2              2               66
  T3              8              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
  MRE11A MUTATED    12   0   0
  MRE11A WILD-TYPE 208  80  66
D614V5, multiclass
    clus
vv   MRE11A MUTATED MRE11A WILD-TYPE
  N0             12              208
  N1              0               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"
D614V6, binary
                  cls
clus                 0   1
  MRE11A MUTATED    11   0
  MRE11A WILD-TYPE 272  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRE11A MUTATED     11    0
  MRE11A WILD-TYPE  272   48
   clus
vv  MRE11A MUTATED MRE11A WILD-TYPE
  0             11              272
  1              0               48
[1] 2 2
[1] FALSE
D614V7, 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
D614V8, binary
                  cls
clus                 0   1
  MRE11A MUTATED     8   4
  MRE11A WILD-TYPE 309  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRE11A MUTATED      8    4
  MRE11A WILD-TYPE  309   44
                               clus
vv                              MRE11A MUTATED MRE11A WILD-TYPE
  COLON ADENOCARCINOMA                       8              309
  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 249   2  22  19
D614V9, multiclass
    clus
vv   MRE11A MUTATED MRE11A WILD-TYPE
  R0              8              249
  R1              0                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"
D614V10, 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
D614V11, 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(615) Variable = ITPR1 MUTATION ANALYSIS
D615V1, survival
                 sevent
clus2               0   1
  ITPR1 MUTATED    26   9
  ITPR1 WILD-TYPE 256  64
  ITPR1 MUTATED ITPR1 WILD-TYPE 
             35             320 
  ITPR1 MUTATED ITPR1 WILD-TYPE 
              9              64 
$`ITPR1 MUTATED`
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3510 
       32.91        31.63        33.53        22.06        19.66        63.98 
TCGA-AA-3664 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3815 TCGA-AA-3833 TCGA-AA-3845 
       54.02        85.05        19.04        33.04        15.95         0.00 
TCGA-AA-3864 TCGA-AA-3994 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A02Y TCGA-AD-6895 
       53.00        27.02         4.01        34.98        39.98         0.72 
TCGA-AZ-4315 TCGA-AZ-4682 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CA-6718 
       58.39        22.36        49.41       100.01         0.33         0.10 
TCGA-CK-5913 TCGA-CM-5861 TCGA-CM-6171 TCGA-D5-6533 TCGA-D5-6536 TCGA-DM-A1DB 
       51.32        15.02        14.04         1.32        17.85        44.32 
TCGA-DM-A28F TCGA-F4-6570 TCGA-F4-6703 TCGA-G4-6309 TCGA-G4-6628 
       35.97         6.18        35.87        51.75        52.80 

$`ITPR1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 
       30.44        29.19        23.61        22.09        32.71        27.09 
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 
       22.52         8.38        25.08        25.18        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 
       24.69        24.39        23.87        20.12        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        3.02         1.02        35.01         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05         6.97         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
       36.00         5.03        26.99        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 
        0.99        25.02         1.02        17.98        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       14.93        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        27.02        19.07         7.96        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A03F TCGA-AA-A03J 
        5.03        14.01         0.92        41.00        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
        0.07        21.37         4.21        56.55         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        1.41         5.13        83.80        62.79        61.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-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-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.38        13.45         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       74.56        65.85        53.62        44.68        55.04        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 
       91.79        46.75 

  ITPR1 MUTATED ITPR1 WILD-TYPE 
              0               0 
  ITPR1 MUTATED ITPR1 WILD-TYPE 
         100.01          140.38 
  ITPR1 MUTATED ITPR1 WILD-TYPE 
          32.91           19.79 
[1] "0.0 - 100.0 (32.9)" "0.0 - 140.4 (19.8)"
[1] "hr=" "1"  
D615V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ITPR1 MUTATED         4        0        6        14         2         0
  ITPR1 WILD-TYPE      60        1       19        95         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ITPR1 MUTATED           2          0          5          1        1         1
  ITPR1 WILD-TYPE        17         10         36         30       34        12
                 vv
clus              STAGE IVB
  ITPR1 MUTATED           0
  ITPR1 WILD-TYPE         1
D615V3, multiclass
            clus
vv           ITPR1 MUTATED ITPR1 WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               6              19
  STAGE IIA             14              95
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             0              10
  STAGE IIIB             5              36
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  64 219  37
D615V4, multiclass
    clus
vv   ITPR1 MUTATED ITPR1 WILD-TYPE
  T1             0               9
  T2             4              64
  T3            29             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
  ITPR1 MUTATED    29   6   2
  ITPR1 WILD-TYPE 191  74  64
D615V5, multiclass
    clus
vv   ITPR1 MUTATED ITPR1 WILD-TYPE
  N0            29             191
  N1             6              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"
D615V6, binary
                 cls
clus                0   1
  ITPR1 MUTATED    31   2
  ITPR1 WILD-TYPE 252  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITPR1 MUTATED     31    2
  ITPR1 WILD-TYPE  252   46
   clus
vv  ITPR1 MUTATED ITPR1 WILD-TYPE
  0            31             252
  1             2              46
[1] 2 2
[1] FALSE
D615V7, 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
D615V8, binary
                 cls
clus                0   1
  ITPR1 MUTATED    33   4
  ITPR1 WILD-TYPE 284  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITPR1 MUTATED     33    4
  ITPR1 WILD-TYPE  284   44
                               clus
vv                              ITPR1 MUTATED ITPR1 WILD-TYPE
  COLON ADENOCARCINOMA                     33             284
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ITPR1 MUTATED    27   0   1   3
  ITPR1 WILD-TYPE 230   2  21  18
D615V9, multiclass
    clus
vv   ITPR1 MUTATED ITPR1 WILD-TYPE
  R0            27             230
  R1             0               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"
D615V10, 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
D615V11, 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(616) Variable = NOX5 MUTATION ANALYSIS
D616V1, survival
                sevent
clus2              0   1
  NOX5 MUTATED     5   0
  NOX5 WILD-TYPE 277  73
  NOX5 MUTATED NOX5 WILD-TYPE 
             5            350 
  NOX5 MUTATED NOX5 WILD-TYPE 
             0             73 
$`NOX5 MUTATED`
TCGA-A6-6781 TCGA-AA-3713 TCGA-AA-3966 TCGA-CA-6717 TCGA-D5-6930 
       19.66        19.04         2.01         0.33         1.51 

$`NOX5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  NOX5 MUTATED NOX5 WILD-TYPE 
          0.33           0.00 
  NOX5 MUTATED NOX5 WILD-TYPE 
         19.66         140.38 
  NOX5 MUTATED NOX5 WILD-TYPE 
          2.01          20.98 
[1] "0.3 - 19.7 (2.0)"   "0.0 - 140.4 (21.0)"
[1] "hr="     "3300000"
D616V2, 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       25       106         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        19         10         41         30       34        13
                vv
clus             STAGE IVB
  NOX5 MUTATED           0
  NOX5 WILD-TYPE         1
D616V3, multiclass
            clus
vv           NOX5 MUTATED NOX5 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             3            106
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            1             30
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NOX5 MUTATED     0   0   4   1
  NOX5 WILD-TYPE   9  68 244  40
D616V4, multiclass
    clus
vv   NOX5 MUTATED NOX5 WILD-TYPE
  T1            0              9
  T2            0             68
  T3            4            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
  NOX5 MUTATED     4   1   0
  NOX5 WILD-TYPE 216  79  66
D616V5, multiclass
    clus
vv   NOX5 MUTATED NOX5 WILD-TYPE
  N0            4            216
  N1            1             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"
D616V6, binary
                cls
clus               0   1
  NOX5 MUTATED     3   1
  NOX5 WILD-TYPE 280  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOX5 MUTATED      3    1
  NOX5 WILD-TYPE  280   47
   clus
vv  NOX5 MUTATED NOX5 WILD-TYPE
  0            3            280
  1            1             47
[1] 2 2
[1] FALSE
D616V7, 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
D616V8, binary
                cls
clus               0   1
  NOX5 MUTATED     1   4
  NOX5 WILD-TYPE 316  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOX5 MUTATED      1    4
  NOX5 WILD-TYPE  316   44
                               clus
vv                              NOX5 MUTATED NOX5 WILD-TYPE
  COLON ADENOCARCINOMA                     1            316
  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 255   2  21  20
D616V9, multiclass
    clus
vv   NOX5 MUTATED NOX5 WILD-TYPE
  R0            2            255
  R1            0              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"
D616V10, 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
D616V11, 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(617) Variable = FAS MUTATION ANALYSIS
D617V1, survival
               sevent
clus2             0   1
  FAS MUTATED     6   1
  FAS WILD-TYPE 276  72
  FAS MUTATED FAS WILD-TYPE 
            7           348 
  FAS MUTATED FAS WILD-TYPE 
            1            72 
$`FAS MUTATED`
TCGA-A6-6780 TCGA-AD-6889 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CK-4947 TCGA-CM-5862 
       20.12        56.55        58.39         0.33        17.56         5.03 
TCGA-D5-6927 
        9.44 

$`FAS WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        4.21         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.26         0.10         1.35       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  FAS MUTATED FAS WILD-TYPE 
         0.33          0.00 
  FAS MUTATED FAS WILD-TYPE 
        58.39        140.38 
  FAS MUTATED FAS WILD-TYPE 
        17.56         20.63 
[1] "0.3 - 58.4 (17.6)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "1.4"
D617V2, 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       25       104         8         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FAS MUTATED           0          0          0          0        0         2
  FAS WILD-TYPE        19         10         41         31       35        11
               vv
clus            STAGE IVB
  FAS MUTATED           0
  FAS WILD-TYPE         1
D617V3, multiclass
            clus
vv           FAS MUTATED FAS WILD-TYPE
  STAGE I              0            64
  STAGE IA             0             1
  STAGE II             0            25
  STAGE IIA            5           104
  STAGE IIB            0             8
  STAGE IIC            0             1
  STAGE III            0            19
  STAGE IIIA           0            10
  STAGE IIIB           0            41
  STAGE IIIC           0            31
  STAGE IV             0            35
  STAGE IVA            2            11
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of 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  68 242  40
D617V4, multiclass
    clus
vv   FAS MUTATED FAS WILD-TYPE
  T1           0             9
  T2           0            68
  T3           6           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
  FAS MUTATED     5   2   0
  FAS WILD-TYPE 215  78  66
D617V5, multiclass
    clus
vv   FAS MUTATED FAS WILD-TYPE
  N0           5           215
  N1           2            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
  FAS MUTATED     5   1
  FAS WILD-TYPE 278  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  FAS MUTATED      5    1
  FAS WILD-TYPE  278   47
   clus
vv  FAS MUTATED FAS WILD-TYPE
  0           5           278
  1           1            47
[1] 2 2
[1] FALSE
D617V7, 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
D617V8, binary
               cls
clus              0   1
  FAS MUTATED     5   2
  FAS WILD-TYPE 312  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  FAS MUTATED      5    2
  FAS WILD-TYPE  312   46
                               clus
vv                              FAS MUTATED FAS WILD-TYPE
  COLON ADENOCARCINOMA                    5           312
  COLON MUCINOUS ADENOCARCINOMA           2            46
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  FAS MUTATED     3   0   0   2
  FAS WILD-TYPE 254   2  22  19
D617V9, multiclass
    clus
vv   FAS MUTATED FAS WILD-TYPE
  R0           3           254
  R1           0             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"
D617V10, 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
D617V11, 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(618) Variable = OR2V2 MUTATION ANALYSIS
D618V1, survival
                 sevent
clus2               0   1
  OR2V2 MUTATED     4   2
  OR2V2 WILD-TYPE 278  71
  OR2V2 MUTATED OR2V2 WILD-TYPE 
              6             349 
  OR2V2 MUTATED OR2V2 WILD-TYPE 
              2              71 
$`OR2V2 MUTATED`
TCGA-A6-3809 TCGA-A6-5661 TCGA-A6-6142 TCGA-A6-6648 TCGA-AZ-6598 TCGA-F4-6809 
       32.75        33.53        25.08        25.18        49.41        13.25 

$`OR2V2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6649 TCGA-A6-6651 
       32.71        27.09        22.52         8.38        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        7.04         3.02         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 
        1.55        16.31        29.59        16.24        33.67         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  OR2V2 MUTATED OR2V2 WILD-TYPE 
          13.25            0.00 
  OR2V2 MUTATED OR2V2 WILD-TYPE 
          49.41          140.38 
  OR2V2 MUTATED OR2V2 WILD-TYPE 
         28.965          20.020 
[1] "13.2 - 49.4 (29.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.4"
D618V2, 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       24       108         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        19         10         41         31       35        10
                 vv
clus              STAGE IVB
  OR2V2 MUTATED           0
  OR2V2 WILD-TYPE         1
D618V3, multiclass
            clus
vv           OR2V2 MUTATED OR2V2 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              1             108
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              3              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
  OR2V2 MUTATED     0   0   5   1
  OR2V2 WILD-TYPE   9  68 243  40
D618V4, multiclass
    clus
vv   OR2V2 MUTATED OR2V2 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             5             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
  OR2V2 MUTATED     4   2   0
  OR2V2 WILD-TYPE 216  78  66
D618V5, multiclass
    clus
vv   OR2V2 MUTATED OR2V2 WILD-TYPE
  N0             4             216
  N1             2              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"
D618V6, binary
                 cls
clus                0   1
  OR2V2 MUTATED     2   3
  OR2V2 WILD-TYPE 281  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2V2 MUTATED      2    3
  OR2V2 WILD-TYPE  281   45
   clus
vv  OR2V2 MUTATED OR2V2 WILD-TYPE
  0             2             281
  1             3              45
[1] 2 2
[1] FALSE
D618V7, 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
D618V8, binary
                 cls
clus                0   1
  OR2V2 MUTATED     5   1
  OR2V2 WILD-TYPE 312  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2V2 MUTATED      5    1
  OR2V2 WILD-TYPE  312   47
                               clus
vv                              OR2V2 MUTATED OR2V2 WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  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 254   2  22  21
D618V9, multiclass
    clus
vv   OR2V2 MUTATED OR2V2 WILD-TYPE
  R0             3             254
  R1             0               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"
D618V10, 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
D618V11, 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(619) Variable = IGF2R MUTATION ANALYSIS
D619V1, survival
                 sevent
clus2               0   1
  IGF2R MUTATED    28   5
  IGF2R WILD-TYPE 254  68
  IGF2R MUTATED IGF2R WILD-TYPE 
             33             322 
  IGF2R MUTATED IGF2R WILD-TYPE 
              5              68 
$`IGF2R MUTATED`
TCGA-A6-3809 TCGA-A6-6780 TCGA-AA-3492 TCGA-AA-3516 TCGA-AA-3525 TCGA-AA-3543 
       32.75        20.12         3.02        13.02         8.05         0.99 
TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3679 TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-A00A 
        6.97         0.92        15.02        53.00        33.01        38.04 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-6889 TCGA-AZ-4315 TCGA-AZ-5407 
        4.01        34.98        35.01        56.55        58.39        61.41 
TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4952 TCGA-CM-4746 
       49.41       100.01         0.33         0.10        15.62        37.02 
TCGA-D5-6540 TCGA-D5-6928 TCGA-D5-6930 TCGA-DM-A28H TCGA-DM-A28K TCGA-G4-6306 
       16.14        11.64         1.51       117.07        98.24        44.68 
TCGA-G4-6307 TCGA-G4-6317 TCGA-G4-6588 
       55.04        36.00        26.17 

$`IGF2R WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        6.97         1.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       37.05        36.03        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
       29.00        29.00        26.01        12.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.05        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       27.02        13.94        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37         4.21         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       62.79         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07         0.26         1.35        17.56       102.44        40.34 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       60.79         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 
       53.62        51.75        45.11        36.72        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        91.79        46.75        52.80 

  IGF2R MUTATED IGF2R WILD-TYPE 
            0.1             0.0 
  IGF2R MUTATED IGF2R WILD-TYPE 
         117.07          140.38 
  IGF2R MUTATED IGF2R WILD-TYPE 
         32.750          20.005 
[1] "0.1 - 117.1 (32.8)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.8"
D619V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IGF2R MUTATED         4        0        5        12         5         0
  IGF2R WILD-TYPE      60        1       20        97         3         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IGF2R MUTATED           4          0          2          2        1         0
  IGF2R WILD-TYPE        15         10         39         29       34        13
                 vv
clus              STAGE IVB
  IGF2R MUTATED           0
  IGF2R WILD-TYPE         1
D619V3, multiclass
            clus
vv           IGF2R MUTATED IGF2R WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               5              20
  STAGE IIA             12              97
  STAGE IIB              5               3
  STAGE IIC              0               1
  STAGE III              4              15
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             2              29
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  IGF2R MUTATED     1   4  24   6
  IGF2R WILD-TYPE   8  64 224  35
D619V4, multiclass
    clus
vv   IGF2R MUTATED IGF2R WILD-TYPE
  T1             1               8
  T2             4              64
  T3            24             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
  IGF2R MUTATED    26   3   6
  IGF2R WILD-TYPE 194  77  60
D619V5, multiclass
    clus
vv   IGF2R MUTATED IGF2R WILD-TYPE
  N0            26             194
  N1             3              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"
D619V6, binary
                 cls
clus                0   1
  IGF2R MUTATED    30   1
  IGF2R WILD-TYPE 253  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGF2R MUTATED     30    1
  IGF2R WILD-TYPE  253   47
   clus
vv  IGF2R MUTATED IGF2R WILD-TYPE
  0            30             253
  1             1              47
[1] 2 2
[1] FALSE
D619V7, binary
                 cls
clus                0   1
  IGF2R MUTATED    14  21
  IGF2R WILD-TYPE 156 176
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGF2R MUTATED     14   21
  IGF2R WILD-TYPE  156  176
        clus
vv       IGF2R MUTATED IGF2R WILD-TYPE
  FEMALE            14             156
  MALE              21             176
[1] 2 2
[1] FALSE
D619V8, binary
                 cls
clus                0   1
  IGF2R MUTATED    22  13
  IGF2R WILD-TYPE 295  35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGF2R MUTATED     22   13
  IGF2R WILD-TYPE  295   35
                               clus
vv                              IGF2R MUTATED IGF2R WILD-TYPE
  COLON ADENOCARCINOMA                     22             295
  COLON MUCINOUS ADENOCARCINOMA            13              35
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  IGF2R MUTATED    22   0   1   4
  IGF2R WILD-TYPE 235   2  21  17
D619V9, multiclass
    clus
vv   IGF2R MUTATED IGF2R WILD-TYPE
  R0            22             235
  R1             0               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"
D619V10, 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    17
  IGF2R WILD-TYPE                        18   159
D619V11, 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                                       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(620) Variable = ZNF180 MUTATION ANALYSIS
D620V1, survival
                  sevent
clus2                0   1
  ZNF180 MUTATED    10   3
  ZNF180 WILD-TYPE 272  70
  ZNF180 MUTATED ZNF180 WILD-TYPE 
              13              342 
  ZNF180 MUTATED ZNF180 WILD-TYPE 
               3               70 
$`ZNF180 MUTATED`
TCGA-A6-3809 TCGA-AA-3510 TCGA-AA-3660 TCGA-AA-3713 TCGA-AA-3864 TCGA-AA-3866 
       32.75        63.98        78.08        19.04        53.00        17.03 
TCGA-AA-3977 TCGA-AA-A00N TCGA-AY-6197 TCGA-AZ-6600 TCGA-CA-6717 TCGA-CM-5348 
       25.02         4.01        21.44        12.10         0.33        22.98 
TCGA-D5-6537 
        4.80 

$`ZNF180 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       31.07        30.05        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12        17.85        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  ZNF180 MUTATED ZNF180 WILD-TYPE 
            0.33             0.00 
  ZNF180 MUTATED ZNF180 WILD-TYPE 
           78.08           140.38 
  ZNF180 MUTATED ZNF180 WILD-TYPE 
          21.440           20.155 
[1] "0.3 - 78.1 (21.4)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1"  
D620V2, 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       22       106         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF180 MUTATED           0          0          2          0        2
  ZNF180 WILD-TYPE        19         10         39         31       33
                  vv
clus               STAGE IVA STAGE IVB
  ZNF180 MUTATED           0         0
  ZNF180 WILD-TYPE        13         1
D620V3, multiclass
            clus
vv           ZNF180 MUTATED ZNF180 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                3               22
  STAGE IIA               3              106
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              0               31
  STAGE IV                2               33
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF180 MUTATED     0   2   9   3
  ZNF180 WILD-TYPE   9  66 239  38
D620V4, multiclass
    clus
vv   ZNF180 MUTATED ZNF180 WILD-TYPE
  T1              0                9
  T2              2               66
  T3              9              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
  ZNF180 MUTATED    11   3   0
  ZNF180 WILD-TYPE 209  77  66
D620V5, multiclass
    clus
vv   ZNF180 MUTATED ZNF180 WILD-TYPE
  N0             11              209
  N1              3               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"
D620V6, binary
                  cls
clus                 0   1
  ZNF180 MUTATED     9   2
  ZNF180 WILD-TYPE 274  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF180 MUTATED      9    2
  ZNF180 WILD-TYPE  274   46
   clus
vv  ZNF180 MUTATED ZNF180 WILD-TYPE
  0              9              274
  1              2               46
[1] 2 2
[1] FALSE
D620V7, 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
D620V8, binary
                  cls
clus                 0   1
  ZNF180 MUTATED    11   3
  ZNF180 WILD-TYPE 306  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF180 MUTATED     11    3
  ZNF180 WILD-TYPE  306   45
                               clus
vv                              ZNF180 MUTATED ZNF180 WILD-TYPE
  COLON ADENOCARCINOMA                      11              306
  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 247   2  21  20
D620V9, multiclass
    clus
vv   ZNF180 MUTATED ZNF180 WILD-TYPE
  R0             10              247
  R1              0                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"
D620V10, 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
D620V11, 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(621) Variable = ULK1 MUTATION ANALYSIS
D621V1, survival
                sevent
clus2              0   1
  ULK1 MUTATED     6   3
  ULK1 WILD-TYPE 276  70
  ULK1 MUTATED ULK1 WILD-TYPE 
             9            346 
  ULK1 MUTATED ULK1 WILD-TYPE 
             3             70 
$`ULK1 MUTATED`
TCGA-A6-6780 TCGA-AY-6197 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-CM-5349 
       20.12        21.44        62.79        49.41         6.77        30.08 
TCGA-D5-6928 TCGA-G4-6586 TCGA-G4-6588 
       11.64        35.80        26.17 

$`ULK1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        15.75         0.20        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6601 
        5.13        83.80        22.36        61.41        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        91.79        46.75        52.80 

  ULK1 MUTATED ULK1 WILD-TYPE 
          6.77           0.00 
  ULK1 MUTATED ULK1 WILD-TYPE 
         62.79         140.38 
  ULK1 MUTATED ULK1 WILD-TYPE 
        26.170         20.005 
[1] "6.8 - 62.8 (26.2)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1.4"
D621V2, 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       23       103         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        19         10         41         31       35        13
                vv
clus             STAGE IVB
  ULK1 MUTATED           0
  ULK1 WILD-TYPE         1
D621V3, multiclass
            clus
vv           ULK1 MUTATED ULK1 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             6            103
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ULK1 MUTATED     0   1   8   1
  ULK1 WILD-TYPE   9  67 240  40
D621V4, multiclass
    clus
vv   ULK1 MUTATED ULK1 WILD-TYPE
  T1            0              9
  T2            1             67
  T3            8            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
  ULK1 MUTATED    10   0   0
  ULK1 WILD-TYPE 210  80  66
D621V5, multiclass
    clus
vv   ULK1 MUTATED ULK1 WILD-TYPE
  N0           10            210
  N1            0             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"
D621V6, binary
                cls
clus               0   1
  ULK1 MUTATED     4   0
  ULK1 WILD-TYPE 279  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  ULK1 MUTATED      4    0
  ULK1 WILD-TYPE  279   48
   clus
vv  ULK1 MUTATED ULK1 WILD-TYPE
  0            4            279
  1            0             48
[1] 2 2
[1] FALSE
D621V7, 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
D621V8, binary
                cls
clus               0   1
  ULK1 MUTATED     8   2
  ULK1 WILD-TYPE 309  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  ULK1 MUTATED      8    2
  ULK1 WILD-TYPE  309   46
                               clus
vv                              ULK1 MUTATED ULK1 WILD-TYPE
  COLON ADENOCARCINOMA                     8            309
  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 252   2  22  20
D621V9, multiclass
    clus
vv   ULK1 MUTATED ULK1 WILD-TYPE
  R0            5            252
  R1            0              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"
D621V10, 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
D621V11, 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(622) Variable = FAM163B MUTATION ANALYSIS
D622V1, survival
                   sevent
clus2                 0   1
  FAM163B MUTATED     2   2
  FAM163B WILD-TYPE 280  71
  FAM163B MUTATED FAM163B WILD-TYPE 
                4               351 
  FAM163B MUTATED FAM163B WILD-TYPE 
                2                71 
$`FAM163B MUTATED`
TCGA-A6-5661 TCGA-AA-3855 TCGA-AZ-6601 TCGA-DM-A28C 
       33.53        32.05       100.01        81.37 

$`FAM163B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      135.65       139.17         6.12       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  FAM163B MUTATED FAM163B WILD-TYPE 
            32.05              0.00 
  FAM163B MUTATED FAM163B WILD-TYPE 
           100.01            140.38 
  FAM163B MUTATED FAM163B WILD-TYPE 
            57.45             20.02 
[1] "32.0 - 100.0 (57.5)" "0.0 - 140.4 (20.0)" 
[1] "hr=" "1.1"
D622V2, 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       24       107         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM163B MUTATED           0          0          0          0        0
  FAM163B WILD-TYPE        19         10         41         31       35
                   vv
clus                STAGE IVA STAGE IVB
  FAM163B MUTATED           0         0
  FAM163B WILD-TYPE        13         1
D622V3, multiclass
            clus
vv           FAM163B MUTATED FAM163B WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                2               107
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  FAM163B MUTATED     0   1   3   0
  FAM163B WILD-TYPE   9  67 245  41
D622V4, multiclass
    clus
vv   FAM163B MUTATED FAM163B WILD-TYPE
  T1               0                 9
  T2               1                67
  T3               3               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
  FAM163B MUTATED     4   0   0
  FAM163B WILD-TYPE 216  80  66
D622V5, multiclass
    clus
vv   FAM163B MUTATED FAM163B WILD-TYPE
  N0               4               216
  N1               0                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"
D622V6, binary
                   cls
clus                  0   1
  FAM163B MUTATED     4   0
  FAM163B WILD-TYPE 279  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM163B MUTATED      4    0
  FAM163B WILD-TYPE  279   48
   clus
vv  FAM163B MUTATED FAM163B WILD-TYPE
  0               4               279
  1               0                48
[1] 2 2
[1] FALSE
D622V7, 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
D622V8, binary
                   cls
clus                  0   1
  FAM163B MUTATED     4   0
  FAM163B WILD-TYPE 313  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM163B MUTATED      4    0
  FAM163B WILD-TYPE  313   48
                               clus
vv                              FAM163B MUTATED FAM163B WILD-TYPE
  COLON ADENOCARCINOMA                        4               313
  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 255   2  22  21
D622V9, multiclass
[1] "Remove cluster labels:" "FAM163B MUTATED"       
clus
  FAM163B MUTATED FAM163B WILD-TYPE 
                2               300 
       TCGA-A6-2671        TCGA-A6-2672        TCGA-A6-2674        TCGA-A6-2676 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-A6-2677        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-3496        TCGA-AA-3502        TCGA-AA-3510 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-3511        TCGA-AA-3514        TCGA-AA-3517        TCGA-AA-3518 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-3519        TCGA-AA-3520        TCGA-AA-3521        TCGA-AA-3522 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-3524        TCGA-AA-3525        TCGA-AA-3526        TCGA-AA-3527 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-3529        TCGA-AA-3530        TCGA-AA-3531        TCGA-AA-3532 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-3534        TCGA-AA-3538        TCGA-AA-3542        TCGA-AA-3543 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-3544        TCGA-AA-3548        TCGA-AA-3549        TCGA-AA-3552 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-3553        TCGA-AA-3554        TCGA-AA-3555        TCGA-AA-3556 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-3558        TCGA-AA-3560        TCGA-AA-3561        TCGA-AA-3562 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-3655        TCGA-AA-3660        TCGA-AA-3662        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-3672 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-3673        TCGA-AA-3678        TCGA-AA-3679        TCGA-AA-3680 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-3681        TCGA-AA-3684        TCGA-AA-3685        TCGA-AA-3688 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-3692        TCGA-AA-3693        TCGA-AA-3695        TCGA-AA-3696 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-3697        TCGA-AA-3710        TCGA-AA-3712        TCGA-AA-3713 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-3715        TCGA-AA-3811        TCGA-AA-3812        TCGA-AA-3814 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-3815        TCGA-AA-3818        TCGA-AA-3819        TCGA-AA-3821 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-3831        TCGA-AA-3833        TCGA-AA-3837        TCGA-AA-3842 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-3844        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-3860        TCGA-AA-3861 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-3864        TCGA-AA-3866        TCGA-AA-3867        TCGA-AA-3869 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-3870        TCGA-AA-3872        TCGA-AA-3875        TCGA-AA-3877 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-3930        TCGA-AA-3939        TCGA-AA-3941        TCGA-AA-3947 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-3949        TCGA-AA-3950        TCGA-AA-3952        TCGA-AA-3955 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-3956        TCGA-AA-3968        TCGA-AA-3971        TCGA-AA-3972 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-3973        TCGA-AA-3975        TCGA-AA-3976        TCGA-AA-3979 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-3984        TCGA-AA-3986        TCGA-AA-3989        TCGA-AA-3994 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-A004        TCGA-AA-A00A        TCGA-AA-A00D        TCGA-AA-A00E 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-A00F        TCGA-AA-A00J        TCGA-AA-A00K        TCGA-AA-A00L 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-A00N        TCGA-AA-A00O        TCGA-AA-A00Q        TCGA-AA-A00R 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-A00U        TCGA-AA-A00W        TCGA-AA-A00Z        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-A024 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-A029        TCGA-AA-A02F        TCGA-AA-A02H        TCGA-AA-A02J 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-A02K        TCGA-AA-A02O        TCGA-AA-A02W        TCGA-AA-A02Y 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AA-A03F        TCGA-AA-A03J        TCGA-AD-5900        TCGA-AD-6548 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AD-6888        TCGA-AU-3779        TCGA-AU-6004        TCGA-AY-4070 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AY-4071        TCGA-AY-5543        TCGA-AY-6196        TCGA-AY-6197 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-AY-6386        TCGA-AZ-4315        TCGA-AZ-4681        TCGA-AZ-4682 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-CA-5254        TCGA-CA-5255        TCGA-CA-5796        TCGA-CA-5797 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-CA-6715        TCGA-CA-6716        TCGA-CA-6717        TCGA-CA-6718 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-CA-6719        TCGA-CK-4947        TCGA-CK-4948        TCGA-CK-4950 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-CK-4952        TCGA-CK-5912        TCGA-CK-5913        TCGA-CK-5914 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-CK-5915        TCGA-CK-5916        TCGA-CK-6746        TCGA-CK-6747 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-CK-6748        TCGA-CK-6751        TCGA-CM-4743        TCGA-CM-4744 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-CM-4746        TCGA-CM-4747        TCGA-CM-4752        TCGA-CM-5341 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-CM-5344        TCGA-CM-5348        TCGA-CM-5349        TCGA-CM-5860 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-CM-5861        TCGA-CM-5862        TCGA-CM-5863        TCGA-CM-5864 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-CM-5868        TCGA-CM-6161        TCGA-CM-6162        TCGA-CM-6163 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-CM-6164        TCGA-CM-6165        TCGA-CM-6166        TCGA-CM-6167 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-CM-6168        TCGA-CM-6169        TCGA-CM-6170        TCGA-CM-6171 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-CM-6172        TCGA-CM-6674        TCGA-CM-6675        TCGA-CM-6676 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-CM-6677        TCGA-CM-6678        TCGA-CM-6679        TCGA-CM-6680 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-D5-5537        TCGA-D5-5538        TCGA-D5-5539        TCGA-D5-5540 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-D5-5541        TCGA-D5-6529        TCGA-D5-6532        TCGA-D5-6533 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-D5-6534        TCGA-D5-6535        TCGA-D5-6536        TCGA-D5-6537 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-D5-6538        TCGA-D5-6539        TCGA-D5-6540        TCGA-D5-6541 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-D5-6898        TCGA-D5-6920        TCGA-D5-6922        TCGA-D5-6923 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-D5-6924        TCGA-D5-6926        TCGA-D5-6927        TCGA-D5-6928 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-D5-6929        TCGA-D5-6930        TCGA-D5-6931        TCGA-D5-6932 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-D5-7000        TCGA-F4-6459        TCGA-F4-6460        TCGA-F4-6569 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-F4-6570        TCGA-F4-6703        TCGA-F4-6704        TCGA-F4-6805 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-F4-6806        TCGA-F4-6807        TCGA-F4-6808        TCGA-F4-6809 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-F4-6854        TCGA-F4-6855        TCGA-F4-6856        TCGA-G4-6293 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-G4-6299        TCGA-G4-6303        TCGA-G4-6304        TCGA-G4-6306 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-G4-6307        TCGA-G4-6309        TCGA-G4-6310        TCGA-G4-6315 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-G4-6317        TCGA-G4-6321        TCGA-G4-6323        TCGA-G4-6586 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
       TCGA-G4-6588        TCGA-G4-6625        TCGA-G4-6626        TCGA-G4-6628 
"FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" "FAM163B WILD-TYPE" 
D622V10, 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
D622V11, 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(623) Variable = PHF21A MUTATION ANALYSIS
D623V1, survival
                  sevent
clus2                0   1
  PHF21A MUTATED     8   3
  PHF21A WILD-TYPE 274  70
  PHF21A MUTATED PHF21A WILD-TYPE 
              11              344 
  PHF21A MUTATED PHF21A WILD-TYPE 
               3               70 
$`PHF21A MUTATED`
TCGA-AA-3492 TCGA-AA-3525 TCGA-AA-3672 TCGA-AA-3947 TCGA-AA-3949 TCGA-AD-6964 
        3.02         8.05         0.92        33.01        26.01        10.88 
TCGA-AZ-4681 TCGA-CK-5916 TCGA-D5-6930 TCGA-G4-6304 TCGA-G4-6588 
       83.80        21.14         1.51        53.62        26.17 

$`PHF21A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 
        1.02         9.07        24.03        37.05        36.03        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         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        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  PHF21A MUTATED PHF21A WILD-TYPE 
            0.92             0.00 
  PHF21A MUTATED PHF21A WILD-TYPE 
           83.80           140.38 
  PHF21A MUTATED PHF21A WILD-TYPE 
          21.140           20.155 
[1] "0.9 - 83.8 (21.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.4"
D623V2, 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       24       106         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PHF21A MUTATED           1          0          2          0        0
  PHF21A WILD-TYPE        18         10         39         31       35
                  vv
clus               STAGE IVA STAGE IVB
  PHF21A MUTATED           0         0
  PHF21A WILD-TYPE        13         1
D623V3, multiclass
            clus
vv           PHF21A MUTATED PHF21A WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               3              106
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PHF21A MUTATED     1   0   7   3
  PHF21A WILD-TYPE   8  68 241  38
D623V4, multiclass
    clus
vv   PHF21A MUTATED PHF21A WILD-TYPE
  T1              1                8
  T2              0               68
  T3              7              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
  PHF21A MUTATED     7   3   1
  PHF21A WILD-TYPE 213  77  65
D623V5, multiclass
    clus
vv   PHF21A MUTATED PHF21A WILD-TYPE
  N0              7              213
  N1              3               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"
D623V6, binary
                  cls
clus                 0   1
  PHF21A MUTATED    10   0
  PHF21A WILD-TYPE 273  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PHF21A MUTATED     10    0
  PHF21A WILD-TYPE  273   48
   clus
vv  PHF21A MUTATED PHF21A WILD-TYPE
  0             10              273
  1              0               48
[1] 2 2
[1] FALSE
D623V7, 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
D623V8, binary
                  cls
clus                 0   1
  PHF21A MUTATED     8   3
  PHF21A WILD-TYPE 309  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PHF21A MUTATED      8    3
  PHF21A WILD-TYPE  309   45
                               clus
vv                              PHF21A MUTATED PHF21A WILD-TYPE
  COLON ADENOCARCINOMA                       8              309
  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 248   2  22  20
D623V9, multiclass
    clus
vv   PHF21A MUTATED PHF21A WILD-TYPE
  R0              9              248
  R1              0                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"
D623V10, 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
D623V11, 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(624) Variable = NFASC MUTATION ANALYSIS
D624V1, survival
                 sevent
clus2               0   1
  NFASC MUTATED    28   3
  NFASC WILD-TYPE 254  70
  NFASC MUTATED NFASC WILD-TYPE 
             31             324 
  NFASC MUTATED NFASC WILD-TYPE 
              3              70 
$`NFASC MUTATED`
TCGA-A6-6653 TCGA-A6-6780 TCGA-AA-3543 TCGA-AA-3660 TCGA-AA-3697 TCGA-AA-3713 
       24.39        20.12         0.99        78.08        85.05        19.04 
TCGA-AA-3815 TCGA-AA-3844 TCGA-AA-3866 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3966 
       33.04        14.93        17.03        33.01        26.01         2.01 
TCGA-AA-3982 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R TCGA-AY-6197 
       27.02        18.05         4.01        34.98        35.01        21.44 
TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4743 TCGA-CM-5341 TCGA-CM-6162 
       58.39         0.33         0.10        23.05        29.06        12.00 
TCGA-D5-6533 TCGA-D5-6930 TCGA-DM-A1D4 TCGA-DM-A1HB TCGA-DM-A28C TCGA-DM-A28H 
        1.32         1.51        92.75       135.65        81.37       117.07 
TCGA-F4-6704 
        1.55 

$`NFASC WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
       12.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 
        5.98        37.05        19.00        36.00         5.03        26.99 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 
       17.98        15.95        38.99        37.02         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        53.00        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       24.00        24.00         2.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       24.00        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       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        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       27.09        16.31         0.95        15.75         0.20        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07         0.26         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93         2.01       124.27        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       13.02        22.03        22.98        30.08        16.01        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 
       19.59        13.51        11.51        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-A282 TCGA-DM-A285 TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K 
      139.17         6.12       119.93        35.97        60.79        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 
        8.61        13.38        13.45         6.18        35.87        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  NFASC MUTATED NFASC WILD-TYPE 
            0.1             0.0 
  NFASC MUTATED NFASC WILD-TYPE 
         135.65          140.38 
  NFASC MUTATED NFASC WILD-TYPE 
         23.050          20.005 
[1] "0.1 - 135.7 (23.1)" "0.0 - 140.4 (20.0)"
[1] "hr=" "2.9"
D624V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NFASC MUTATED         3        0        1        12         3         0
  NFASC WILD-TYPE      61        1       24        97         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NFASC MUTATED           2          1          6          3        1         0
  NFASC WILD-TYPE        17          9         35         28       34        13
                 vv
clus              STAGE IVB
  NFASC MUTATED           0
  NFASC WILD-TYPE         1
D624V3, multiclass
            clus
vv           NFASC MUTATED NFASC WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA             12              97
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             1               9
  STAGE IIIB             6              35
  STAGE IIIC             3              28
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NFASC MUTATED     0   4  23   5
  NFASC WILD-TYPE   9  64 225  36
D624V4, multiclass
    clus
vv   NFASC MUTATED NFASC WILD-TYPE
  T1             0               9
  T2             4              64
  T3            23             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
  NFASC MUTATED    22   6   4
  NFASC WILD-TYPE 198  74  62
D624V5, multiclass
    clus
vv   NFASC MUTATED NFASC WILD-TYPE
  N0            22             198
  N1             6              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"
D624V6, binary
                 cls
clus                0   1
  NFASC MUTATED    28   1
  NFASC WILD-TYPE 255  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFASC MUTATED     28    1
  NFASC WILD-TYPE  255   47
   clus
vv  NFASC MUTATED NFASC WILD-TYPE
  0            28             255
  1             1              47
[1] 2 2
[1] FALSE
D624V7, 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
D624V8, binary
                 cls
clus                0   1
  NFASC MUTATED    20  12
  NFASC WILD-TYPE 297  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFASC MUTATED     20   12
  NFASC WILD-TYPE  297   36
                               clus
vv                              NFASC MUTATED NFASC WILD-TYPE
  COLON ADENOCARCINOMA                     20             297
  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 236   2  21  19
D624V9, multiclass
    clus
vv   NFASC MUTATED NFASC WILD-TYPE
  R0            21             236
  R1             0               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"
D624V10, 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
D624V11, 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(625) Variable = DDX59 MUTATION ANALYSIS
D625V1, survival
                 sevent
clus2               0   1
  DDX59 MUTATED    10   1
  DDX59 WILD-TYPE 272  72
  DDX59 MUTATED DDX59 WILD-TYPE 
             11             344 
  DDX59 MUTATED DDX59 WILD-TYPE 
              1              72 
$`DDX59 MUTATED`
TCGA-A6-5665 TCGA-AA-3510 TCGA-AD-6895 TCGA-AZ-4315 TCGA-AZ-6600 TCGA-CA-6717 
       22.06        63.98         0.72        58.39        12.10         0.33 
TCGA-CK-4947 TCGA-D5-6540 TCGA-D5-6930 TCGA-G4-6306 TCGA-G4-6586 
       17.56        16.14         1.51        44.68        35.80 

$`DDX59 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 
       22.36        62.79        61.41        49.41         6.77       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
        1.35       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        53.62        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  DDX59 MUTATED DDX59 WILD-TYPE 
           0.33            0.00 
  DDX59 MUTATED DDX59 WILD-TYPE 
          63.98          140.38 
  DDX59 MUTATED DDX59 WILD-TYPE 
         17.560          20.235 
[1] "0.3 - 64.0 (17.6)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2.3"
D625V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DDX59 MUTATED         1        0        1         6         0         0
  DDX59 WILD-TYPE      63        1       24       103         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DDX59 MUTATED           0          0          0          0        1         1
  DDX59 WILD-TYPE        19         10         41         31       34        12
                 vv
clus              STAGE IVB
  DDX59 MUTATED           0
  DDX59 WILD-TYPE         1
D625V3, multiclass
            clus
vv           DDX59 MUTATED DDX59 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              6             103
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 241  39
D625V4, multiclass
    clus
vv   DDX59 MUTATED DDX59 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             7             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
  DDX59 MUTATED     8   3   0
  DDX59 WILD-TYPE 212  77  66
D625V5, multiclass
    clus
vv   DDX59 MUTATED DDX59 WILD-TYPE
  N0             8             212
  N1             3              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"
D625V6, binary
                 cls
clus                0   1
  DDX59 MUTATED     9   1
  DDX59 WILD-TYPE 274  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX59 MUTATED      9    1
  DDX59 WILD-TYPE  274   47
   clus
vv  DDX59 MUTATED DDX59 WILD-TYPE
  0             9             274
  1             1              47
[1] 2 2
[1] FALSE
D625V7, 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
D625V8, binary
                 cls
clus                0   1
  DDX59 MUTATED     8   3
  DDX59 WILD-TYPE 309  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX59 MUTATED      8    3
  DDX59 WILD-TYPE  309   45
                               clus
vv                              DDX59 MUTATED DDX59 WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DDX59 MUTATED     7   0   0   2
  DDX59 WILD-TYPE 250   2  22  19
D625V9, multiclass
    clus
vv   DDX59 MUTATED DDX59 WILD-TYPE
  R0             7             250
  R1             0               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"
D625V10, 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
D625V11, 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(626) Variable = PTPRC MUTATION ANALYSIS
D626V1, survival
                 sevent
clus2               0   1
  PTPRC MUTATED    21   3
  PTPRC WILD-TYPE 261  70
  PTPRC MUTATED PTPRC WILD-TYPE 
             24             331 
  PTPRC MUTATED PTPRC WILD-TYPE 
              3              70 
$`PTPRC MUTATED`
TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-6142 TCGA-A6-6780 TCGA-AA-3510 TCGA-AA-3660 
       31.63        33.53        25.08        20.12        63.98        78.08 
TCGA-AA-3710 TCGA-AA-3845 TCGA-AA-3877 TCGA-AA-3956 TCGA-AA-3977 TCGA-AA-A00J 
       26.99         0.00        31.00        34.03        25.02        18.05 
TCGA-AA-A010 TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6901 TCGA-AZ-4315 TCGA-CA-6717 
       34.98         0.07        56.55        22.42        58.39         0.33 
TCGA-CA-6718 TCGA-CM-5860 TCGA-DM-A1HB TCGA-F4-6460 TCGA-F4-6570 TCGA-G4-6628 
        0.10        16.01       135.65        13.38         6.18        52.80 

$`PTPRC WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       32.91        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 
       32.71        27.09        22.52         8.38        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 
       21.76        24.69        24.39        23.87        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 
        7.04         3.02         1.02        35.01         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
       17.98        15.95        38.99        37.02        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        18.05         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37         4.21 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         0.72         5.79        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07         0.26         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6703 
       60.79       117.07        98.24         8.61        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 
       46.75 

  PTPRC MUTATED PTPRC WILD-TYPE 
              0               0 
  PTPRC MUTATED PTPRC WILD-TYPE 
         135.65          140.38 
  PTPRC MUTATED PTPRC WILD-TYPE 
         26.035          19.990 
[1] "0.0 - 135.7 (26.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "2.1"
D626V2, 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       22        98         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        19         10         37         31       35        12
                 vv
clus              STAGE IVB
  PTPRC MUTATED           0
  PTPRC WILD-TYPE         1
D626V3, multiclass
            clus
vv           PTPRC MUTATED PTPRC WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA             11              98
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             4              37
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  65 230  38
D626V4, multiclass
    clus
vv   PTPRC MUTATED PTPRC WILD-TYPE
  T1             1               8
  T2             3              65
  T3            18             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
  PTPRC MUTATED    20   5   0
  PTPRC WILD-TYPE 200  75  66
D626V5, multiclass
    clus
vv   PTPRC MUTATED PTPRC WILD-TYPE
  N0            20             200
  N1             5              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"
D626V6, binary
                 cls
clus                0   1
  PTPRC MUTATED    20   1
  PTPRC WILD-TYPE 263  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRC MUTATED     20    1
  PTPRC WILD-TYPE  263   47
   clus
vv  PTPRC MUTATED PTPRC WILD-TYPE
  0            20             263
  1             1              47
[1] 2 2
[1] FALSE
D626V7, 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
D626V8, binary
                 cls
clus                0   1
  PTPRC MUTATED    20   5
  PTPRC WILD-TYPE 297  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRC MUTATED     20    5
  PTPRC WILD-TYPE  297   43
                               clus
vv                              PTPRC MUTATED PTPRC WILD-TYPE
  COLON ADENOCARCINOMA                     20             297
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PTPRC MUTATED    17   0   0   2
  PTPRC WILD-TYPE 240   2  22  19
D626V9, multiclass
    clus
vv   PTPRC MUTATED PTPRC WILD-TYPE
  R0            17             240
  R1             0               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"
D626V10, 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
D626V11, 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(627) Variable = EFEMP1 MUTATION ANALYSIS
D627V1, survival
                  sevent
clus2                0   1
  EFEMP1 MUTATED    17   3
  EFEMP1 WILD-TYPE 265  70
  EFEMP1 MUTATED EFEMP1 WILD-TYPE 
              20              335 
  EFEMP1 MUTATED EFEMP1 WILD-TYPE 
               3               70 
$`EFEMP1 MUTATED`
TCGA-AA-3672 TCGA-AA-3844 TCGA-AA-3950 TCGA-AD-6965 TCGA-AZ-6601 TCGA-CA-6718 
        0.92        14.93        24.00         0.20       100.01         0.10 
TCGA-CK-5916 TCGA-CM-4752 TCGA-CM-5860 TCGA-CM-5863 TCGA-CM-6168 TCGA-CM-6172 
       21.14        13.02        16.01        15.02        12.99        11.01 
TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6529 TCGA-DM-A1D9 TCGA-DM-A1HB TCGA-DM-A28C 
       12.26        13.51        20.19       140.38       135.65        81.37 
TCGA-F4-6569 TCGA-F4-6807 
       13.45        16.24 

$`EFEMP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
        6.05         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 
       17.98        15.95        38.99        37.02         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99         2.93         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-5861 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       30.08        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-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        14.04        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 
       11.08        11.01        10.06        12.03        45.40        19.59 
TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       11.51        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-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-A282 
       13.32        12.59         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
        6.12       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        13.38         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       29.59        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  EFEMP1 MUTATED EFEMP1 WILD-TYPE 
             0.1              0.0 
  EFEMP1 MUTATED EFEMP1 WILD-TYPE 
          140.38           139.17 
  EFEMP1 MUTATED EFEMP1 WILD-TYPE 
          14.975           21.010 
[1] "0.1 - 140.4 (15.0)" "0.0 - 139.2 (21.0)"
[1] "hr=" "1.7"
D627V2, 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       24       100         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EFEMP1 MUTATED           1          0          4          2        0
  EFEMP1 WILD-TYPE        18         10         37         29       35
                  vv
clus               STAGE IVA STAGE IVB
  EFEMP1 MUTATED           0         0
  EFEMP1 WILD-TYPE        13         1
D627V3, multiclass
            clus
vv           EFEMP1 MUTATED EFEMP1 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               9              100
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              4               37
  STAGE IIIC              2               29
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  EFEMP1 MUTATED     1   1  17   1
  EFEMP1 WILD-TYPE   8  67 231  40
D627V4, multiclass
    clus
vv   EFEMP1 MUTATED EFEMP1 WILD-TYPE
  T1              1                8
  T2              1               67
  T3             17              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
  EFEMP1 MUTATED    12   5   3
  EFEMP1 WILD-TYPE 208  75  63
D627V5, multiclass
    clus
vv   EFEMP1 MUTATED EFEMP1 WILD-TYPE
  N0             12              208
  N1              5               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"
D627V6, binary
                  cls
clus                 0   1
  EFEMP1 MUTATED    19   0
  EFEMP1 WILD-TYPE 264  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EFEMP1 MUTATED     19    0
  EFEMP1 WILD-TYPE  264   48
   clus
vv  EFEMP1 MUTATED EFEMP1 WILD-TYPE
  0             19              264
  1              0               48
[1] 2 2
[1] FALSE
D627V7, 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
D627V8, binary
                  cls
clus                 0   1
  EFEMP1 MUTATED    18   2
  EFEMP1 WILD-TYPE 299  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EFEMP1 MUTATED     18    2
  EFEMP1 WILD-TYPE  299   46
                               clus
vv                              EFEMP1 MUTATED EFEMP1 WILD-TYPE
  COLON ADENOCARCINOMA                      18              299
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  EFEMP1 MUTATED    13   0   0   2
  EFEMP1 WILD-TYPE 244   2  22  19
D627V9, multiclass
    clus
vv   EFEMP1 MUTATED EFEMP1 WILD-TYPE
  R0             13              244
  R1              0                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"
D627V10, 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
D627V11, 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(628) Variable = KCTD16 MUTATION ANALYSIS
D628V1, survival
                  sevent
clus2                0   1
  KCTD16 MUTATED     6   6
  KCTD16 WILD-TYPE 276  67
  KCTD16 MUTATED KCTD16 WILD-TYPE 
              12              343 
  KCTD16 MUTATED KCTD16 WILD-TYPE 
               6               67 
$`KCTD16 MUTATED`
TCGA-A6-2676 TCGA-AA-3549 TCGA-AA-3697 TCGA-AD-6964 TCGA-AZ-6601 TCGA-AZ-6605 
       42.90        21.01        85.05        10.88       100.01         5.23 
TCGA-CM-5864 TCGA-DM-A1D4 TCGA-DM-A1DA TCGA-DM-A28K TCGA-F4-6460 TCGA-G4-6306 
       15.02        92.75         7.50        98.24        13.38        44.68 

$`KCTD16 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 
       26.01        12.99         0.99        14.01        33.99        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
       29.56        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-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-A1DB TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       60.79       117.07         8.61        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  KCTD16 MUTATED KCTD16 WILD-TYPE 
            5.23             0.00 
  KCTD16 MUTATED KCTD16 WILD-TYPE 
          100.01           140.38 
  KCTD16 MUTATED KCTD16 WILD-TYPE 
          31.955           20.120 
[1] "5.2 - 100.0 (32.0)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.5"
D628V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KCTD16 MUTATED         2        0        1         3         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           1          0          2          1        0
  KCTD16 WILD-TYPE        18         10         39         30       35
                  vv
clus               STAGE IVA STAGE IVB
  KCTD16 MUTATED           0         0
  KCTD16 WILD-TYPE        13         1
D628V3, multiclass
            clus
vv           KCTD16 MUTATED KCTD16 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               3              106
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  KCTD16 MUTATED     0   3   6   3
  KCTD16 WILD-TYPE   9  65 242  38
D628V4, multiclass
    clus
vv   KCTD16 MUTATED KCTD16 WILD-TYPE
  T1              0                9
  T2              3               65
  T3              6              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
  KCTD16 MUTATED     8   2   2
  KCTD16 WILD-TYPE 212  78  64
D628V5, multiclass
    clus
vv   KCTD16 MUTATED KCTD16 WILD-TYPE
  N0              8              212
  N1              2               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"
D628V6, binary
                  cls
clus                 0   1
  KCTD16 MUTATED    11   0
  KCTD16 WILD-TYPE 272  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCTD16 MUTATED     11    0
  KCTD16 WILD-TYPE  272   48
   clus
vv  KCTD16 MUTATED KCTD16 WILD-TYPE
  0             11              272
  1              0               48
[1] 2 2
[1] FALSE
D628V7, 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
D628V8, binary
                  cls
clus                 0   1
  KCTD16 MUTATED    11   1
  KCTD16 WILD-TYPE 306  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCTD16 MUTATED     11    1
  KCTD16 WILD-TYPE  306   47
                               clus
vv                              KCTD16 MUTATED KCTD16 WILD-TYPE
  COLON ADENOCARCINOMA                      11              306
  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 251   2  22  21
D628V9, multiclass
    clus
vv   KCTD16 MUTATED KCTD16 WILD-TYPE
  R0              6              251
  R1              0                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"
D628V10, 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
D628V11, 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(629) Variable = HNRNPH3 MUTATION ANALYSIS
D629V1, survival
                   sevent
clus2                 0   1
  HNRNPH3 MUTATED     6   3
  HNRNPH3 WILD-TYPE 276  70
  HNRNPH3 MUTATED HNRNPH3 WILD-TYPE 
                9               346 
  HNRNPH3 MUTATED HNRNPH3 WILD-TYPE 
                3                70 
$`HNRNPH3 MUTATED`
TCGA-AA-3956 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-CK-4952 TCGA-CM-5348 TCGA-CM-5861 
       34.03        49.41         6.77        15.62        22.98        15.02 
TCGA-CM-6171 TCGA-D5-6537 TCGA-G4-6293 
       14.04         4.80       107.67 

$`HNRNPH3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        20.98         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       40.34        49.08        51.32        21.99        21.14         2.93 
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-5862 
       13.02        29.06        22.03        30.08        16.01         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  HNRNPH3 MUTATED HNRNPH3 WILD-TYPE 
              4.8               0.0 
  HNRNPH3 MUTATED HNRNPH3 WILD-TYPE 
           107.67            140.38 
  HNRNPH3 MUTATED HNRNPH3 WILD-TYPE 
           15.620            20.235 
[1] "4.8 - 107.7 (15.6)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.4"
D629V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HNRNPH3 MUTATED         2        0        1         2         0         0
  HNRNPH3 WILD-TYPE      62        1       24       107         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HNRNPH3 MUTATED           2          0          2          0        0
  HNRNPH3 WILD-TYPE        17         10         39         31       35
                   vv
clus                STAGE IVA STAGE IVB
  HNRNPH3 MUTATED           0         0
  HNRNPH3 WILD-TYPE        13         1
D629V3, multiclass
            clus
vv           HNRNPH3 MUTATED HNRNPH3 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                2               107
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                2                17
  STAGE IIIA               0                10
  STAGE IIIB               2                39
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  HNRNPH3 MUTATED     0   2   6   1
  HNRNPH3 WILD-TYPE   9  66 242  40
D629V4, multiclass
    clus
vv   HNRNPH3 MUTATED HNRNPH3 WILD-TYPE
  T1               0                 9
  T2               2                66
  T3               6               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
  HNRNPH3 MUTATED     5   3   1
  HNRNPH3 WILD-TYPE 215  77  65
D629V5, multiclass
    clus
vv   HNRNPH3 MUTATED HNRNPH3 WILD-TYPE
  N0               5               215
  N1               3                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"
D629V6, binary
                   cls
clus                  0   1
  HNRNPH3 MUTATED     6   0
  HNRNPH3 WILD-TYPE 277  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HNRNPH3 MUTATED      6    0
  HNRNPH3 WILD-TYPE  277   48
   clus
vv  HNRNPH3 MUTATED HNRNPH3 WILD-TYPE
  0               6               277
  1               0                48
[1] 2 2
[1] FALSE
D629V7, binary
                   cls
clus                  0   1
  HNRNPH3 MUTATED     5   4
  HNRNPH3 WILD-TYPE 165 193
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HNRNPH3 MUTATED      5    4
  HNRNPH3 WILD-TYPE  165  193
        clus
vv       HNRNPH3 MUTATED HNRNPH3 WILD-TYPE
  FEMALE               5               165
  MALE                 4               193
[1] 2 2
[1] FALSE
D629V8, binary
                   cls
clus                  0   1
  HNRNPH3 MUTATED     8   1
  HNRNPH3 WILD-TYPE 309  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HNRNPH3 MUTATED      8    1
  HNRNPH3 WILD-TYPE  309   47
                               clus
vv                              HNRNPH3 MUTATED HNRNPH3 WILD-TYPE
  COLON ADENOCARCINOMA                        8               309
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  HNRNPH3 MUTATED     6   0   0   1
  HNRNPH3 WILD-TYPE 251   2  22  20
D629V9, multiclass
    clus
vv   HNRNPH3 MUTATED HNRNPH3 WILD-TYPE
  R0               6               251
  R1               0                 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"
D629V10, 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     8
  HNRNPH3 WILD-TYPE                        19   168
D629V11, 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                                          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(630) Variable = OAS1 MUTATION ANALYSIS
D630V1, survival
                sevent
clus2              0   1
  OAS1 MUTATED     5   2
  OAS1 WILD-TYPE 277  71
  OAS1 MUTATED OAS1 WILD-TYPE 
             7            348 
  OAS1 MUTATED OAS1 WILD-TYPE 
             2             71 
$`OAS1 MUTATED`
TCGA-AA-3660 TCGA-AA-3845 TCGA-AA-3950 TCGA-AZ-4315 TCGA-D5-6534 TCGA-DM-A285 
       78.08         0.00        24.00        58.39        43.27         6.12 
TCGA-G4-6307 
       55.04 

$`OAS1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        61.02         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
       17.98        15.95        38.99        37.02        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  OAS1 MUTATED OAS1 WILD-TYPE 
             0              0 
  OAS1 MUTATED OAS1 WILD-TYPE 
         78.08         140.38 
  OAS1 MUTATED OAS1 WILD-TYPE 
         43.27          20.07 
[1] "0.0 - 78.1 (43.3)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.1"
D630V2, 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       24       104         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        19         10         40         31       34        13
                vv
clus             STAGE IVB
  OAS1 MUTATED           0
  OAS1 WILD-TYPE         1
D630V3, multiclass
            clus
vv           OAS1 MUTATED OAS1 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             5            104
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  OAS1 MUTATED     0   0   8   0
  OAS1 WILD-TYPE   9  68 240  41
D630V4, multiclass
    clus
vv   OAS1 MUTATED OAS1 WILD-TYPE
  T1            0              9
  T2            0             68
  T3            8            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
  OAS1 MUTATED     6   1   1
  OAS1 WILD-TYPE 214  79  65
D630V5, multiclass
    clus
vv   OAS1 MUTATED OAS1 WILD-TYPE
  N0            6            214
  N1            1             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"
D630V6, binary
                cls
clus               0   1
  OAS1 MUTATED     7   1
  OAS1 WILD-TYPE 276  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  OAS1 MUTATED      7    1
  OAS1 WILD-TYPE  276   47
   clus
vv  OAS1 MUTATED OAS1 WILD-TYPE
  0            7            276
  1            1             47
[1] 2 2
[1] FALSE
D630V7, 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
D630V8, binary
                cls
clus               0   1
  OAS1 MUTATED     5   3
  OAS1 WILD-TYPE 312  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  OAS1 MUTATED      5    3
  OAS1 WILD-TYPE  312   45
                               clus
vv                              OAS1 MUTATED OAS1 WILD-TYPE
  COLON ADENOCARCINOMA                     5            312
  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 250   2  22  21
D630V9, multiclass
    clus
vv   OAS1 MUTATED OAS1 WILD-TYPE
  R0            7            250
  R1            0              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"
D630V10, 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
D630V11, 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(631) Variable = OTX2 MUTATION ANALYSIS
D631V1, survival
                sevent
clus2              0   1
  OTX2 MUTATED     4   1
  OTX2 WILD-TYPE 278  72
  OTX2 MUTATED OTX2 WILD-TYPE 
             5            350 
  OTX2 MUTATED OTX2 WILD-TYPE 
             1             72 
$`OTX2 MUTATED`
TCGA-A6-6780 TCGA-AA-3492 TCGA-AA-3697 TCGA-AD-6889 TCGA-D5-6540 
       20.12         3.02        85.05        56.55        16.14 

$`OTX2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       23.87        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37         4.21         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  OTX2 MUTATED OTX2 WILD-TYPE 
          3.02           0.00 
  OTX2 MUTATED OTX2 WILD-TYPE 
         85.05         140.38 
  OTX2 MUTATED OTX2 WILD-TYPE 
        20.120         20.235 
[1] "3.0 - 85.0 (20.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.5"
D631V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OTX2 MUTATED         1        0        1         3         0         0
  OTX2 WILD-TYPE      63        1       24       106         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OTX2 MUTATED           1          0          0          0        0         0
  OTX2 WILD-TYPE        18         10         41         31       35        13
                vv
clus             STAGE IVB
  OTX2 MUTATED           0
  OTX2 WILD-TYPE         1
D631V3, multiclass
            clus
vv           OTX2 MUTATED OTX2 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             3            106
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  OTX2 MUTATED     0   1   5   0
  OTX2 WILD-TYPE   9  67 243  41
D631V4, multiclass
    clus
vv   OTX2 MUTATED OTX2 WILD-TYPE
  T1            0              9
  T2            1             67
  T3            5            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
  OTX2 MUTATED     6   0   0
  OTX2 WILD-TYPE 214  80  66
D631V5, multiclass
    clus
vv   OTX2 MUTATED OTX2 WILD-TYPE
  N0            6            214
  N1            0             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"
D631V6, binary
                cls
clus               0   1
  OTX2 MUTATED     5   0
  OTX2 WILD-TYPE 278  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  OTX2 MUTATED      5    0
  OTX2 WILD-TYPE  278   48
   clus
vv  OTX2 MUTATED OTX2 WILD-TYPE
  0            5            278
  1            0             48
[1] 2 2
[1] FALSE
D631V7, 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
D631V8, binary
                cls
clus               0   1
  OTX2 MUTATED     4   2
  OTX2 WILD-TYPE 313  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  OTX2 MUTATED      4    2
  OTX2 WILD-TYPE  313   46
                               clus
vv                              OTX2 MUTATED OTX2 WILD-TYPE
  COLON ADENOCARCINOMA                     4            313
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  OTX2 MUTATED     4   0   0   0
  OTX2 WILD-TYPE 253   2  22  21
D631V9, multiclass
    clus
vv   OTX2 MUTATED OTX2 WILD-TYPE
  R0            4            253
  R1            0              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"
D631V10, 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
D631V11, 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(632) Variable = PAAF1 MUTATION ANALYSIS
D632V1, survival
                 sevent
clus2               0   1
  PAAF1 MUTATED     4   1
  PAAF1 WILD-TYPE 278  72
  PAAF1 MUTATED PAAF1 WILD-TYPE 
              5             350 
  PAAF1 MUTATED PAAF1 WILD-TYPE 
              1              72 
$`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        36.72 

$`PAAF1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10       100.01         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      135.65         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  PAAF1 MUTATED PAAF1 WILD-TYPE 
          29.56            0.00 
  PAAF1 MUTATED PAAF1 WILD-TYPE 
         139.17          140.38 
  PAAF1 MUTATED PAAF1 WILD-TYPE 
         36.720          20.005 
[1] "29.6 - 139.2 (36.7)" "0.0 - 140.4 (20.0)" 
[1] "hr=" "2"  
D632V2, 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       25       106         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        19         10         41         31       34        13
                 vv
clus              STAGE IVB
  PAAF1 MUTATED           0
  PAAF1 WILD-TYPE         1
D632V3, multiclass
            clus
vv           PAAF1 MUTATED PAAF1 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              3             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PAAF1 MUTATED     0   1   4   0
  PAAF1 WILD-TYPE   9  67 244  41
D632V4, multiclass
    clus
vv   PAAF1 MUTATED PAAF1 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             4             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
  PAAF1 MUTATED     3   2   0
  PAAF1 WILD-TYPE 217  78  66
D632V5, multiclass
    clus
vv   PAAF1 MUTATED PAAF1 WILD-TYPE
  N0             3             217
  N1             2              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"
D632V6, binary
                 cls
clus                0   1
  PAAF1 MUTATED     3   1
  PAAF1 WILD-TYPE 280  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAAF1 MUTATED      3    1
  PAAF1 WILD-TYPE  280   47
   clus
vv  PAAF1 MUTATED PAAF1 WILD-TYPE
  0             3             280
  1             1              47
[1] 2 2
[1] FALSE
D632V7, 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
D632V8, binary
                 cls
clus                0   1
  PAAF1 MUTATED     5   0
  PAAF1 WILD-TYPE 312  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAAF1 MUTATED      5    0
  PAAF1 WILD-TYPE  312   48
                               clus
vv                              PAAF1 MUTATED PAAF1 WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  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 254   2  22  21
D632V9, multiclass
    clus
vv   PAAF1 MUTATED PAAF1 WILD-TYPE
  R0             3             254
  R1             0               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"
D632V10, 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
D632V11, 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(633) Variable = AGTR2 MUTATION ANALYSIS
D633V1, survival
                 sevent
clus2               0   1
  AGTR2 MUTATED    10   5
  AGTR2 WILD-TYPE 272  68
  AGTR2 MUTATED AGTR2 WILD-TYPE 
             15             340 
  AGTR2 MUTATED AGTR2 WILD-TYPE 
              5              68 
$`AGTR2 MUTATED`
TCGA-A6-3809 TCGA-A6-5666 TCGA-AA-3821 TCGA-AA-3989 TCGA-AA-A00N TCGA-AA-A017 
       32.75        32.71         1.02         7.96         4.01        15.02 
TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6899 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CM-6171 
       56.55         0.72         5.79       100.01         0.33        14.04 
TCGA-D5-6539 TCGA-DM-A285 TCGA-G4-6323 
       12.49         6.12        13.78 

$`AGTR2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 
       35.05        33.04         0.99        25.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       19.07        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        34.98        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       21.37         4.21         0.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 
       43.27        15.12        17.85         4.80        17.13        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        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        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 
       51.75        45.11        36.72        36.00        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  AGTR2 MUTATED AGTR2 WILD-TYPE 
           0.33            0.00 
  AGTR2 MUTATED AGTR2 WILD-TYPE 
         100.01          140.38 
  AGTR2 MUTATED AGTR2 WILD-TYPE 
         12.490          20.995 
[1] "0.3 - 100.0 (12.5)" "0.0 - 140.4 (21.0)"
[1] "hr=" "2"  
D633V2, 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       24       106         6         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AGTR2 MUTATED           0          1          0          1        2         0
  AGTR2 WILD-TYPE        19          9         41         30       33        13
                 vv
clus              STAGE IVB
  AGTR2 MUTATED           0
  AGTR2 WILD-TYPE         1
D633V3, multiclass
            clus
vv           AGTR2 MUTATED AGTR2 WILD-TYPE
  STAGE I                2              62
  STAGE IA               1               0
  STAGE II               1              24
  STAGE IIA              3             106
  STAGE IIB              2               6
  STAGE IIC              1               0
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               2              33
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  AGTR2 MUTATED     0   2   8   4
  AGTR2 WILD-TYPE   9  66 240  37
D633V4, multiclass
    clus
vv   AGTR2 MUTATED AGTR2 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             8             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
  AGTR2 MUTATED    11   1   3
  AGTR2 WILD-TYPE 209  79  63
D633V5, multiclass
    clus
vv   AGTR2 MUTATED AGTR2 WILD-TYPE
  N0            11             209
  N1             1              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"
D633V6, binary
                 cls
clus                0   1
  AGTR2 MUTATED    10   2
  AGTR2 WILD-TYPE 273  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGTR2 MUTATED     10    2
  AGTR2 WILD-TYPE  273   46
   clus
vv  AGTR2 MUTATED AGTR2 WILD-TYPE
  0            10             273
  1             2              46
[1] 2 2
[1] FALSE
D633V7, 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
D633V8, binary
                 cls
clus                0   1
  AGTR2 MUTATED     9   6
  AGTR2 WILD-TYPE 308  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGTR2 MUTATED      9    6
  AGTR2 WILD-TYPE  308   42
                               clus
vv                              AGTR2 MUTATED AGTR2 WILD-TYPE
  COLON ADENOCARCINOMA                      9             308
  COLON MUCINOUS ADENOCARCINOMA             6              42
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  AGTR2 MUTATED     7   0   1   1
  AGTR2 WILD-TYPE 250   2  21  20
D633V9, multiclass
    clus
vv   AGTR2 MUTATED AGTR2 WILD-TYPE
  R0             7             250
  R1             0               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"
D633V10, 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
D633V11, 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(634) Variable = GAB2 MUTATION ANALYSIS
D634V1, survival
                sevent
clus2              0   1
  GAB2 MUTATED     9   0
  GAB2 WILD-TYPE 273  73
  GAB2 MUTATED GAB2 WILD-TYPE 
             9            346 
  GAB2 MUTATED GAB2 WILD-TYPE 
             0             73 
$`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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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        16.01 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       135.65         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 
      107.67        74.56        65.85        53.62        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  GAB2 MUTATED GAB2 WILD-TYPE 
          1.02           0.00 
  GAB2 MUTATED GAB2 WILD-TYPE 
        139.17         140.38 
  GAB2 MUTATED GAB2 WILD-TYPE 
         15.02          20.63 
[1] "1.0 - 139.2 (15.0)" "0.0 - 140.4 (20.6)"
[1] "hr="     "2.5e+07"
D634V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GAB2 MUTATED         1        0        1         6         0         0
  GAB2 WILD-TYPE      63        1       24       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        19         10         41         30       35        13
                vv
clus             STAGE IVB
  GAB2 MUTATED           0
  GAB2 WILD-TYPE         1
D634V3, multiclass
            clus
vv           GAB2 MUTATED GAB2 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             6            103
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            1             30
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GAB2 MUTATED     0   2   6   1
  GAB2 WILD-TYPE   9  66 242  40
D634V4, multiclass
    clus
vv   GAB2 MUTATED GAB2 WILD-TYPE
  T1            0              9
  T2            2             66
  T3            6            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
  GAB2 MUTATED     8   1   0
  GAB2 WILD-TYPE 212  79  66
D634V5, multiclass
    clus
vv   GAB2 MUTATED GAB2 WILD-TYPE
  N0            8            212
  N1            1             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"
D634V6, binary
                cls
clus               0   1
  GAB2 MUTATED     8   0
  GAB2 WILD-TYPE 275  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAB2 MUTATED      8    0
  GAB2 WILD-TYPE  275   48
   clus
vv  GAB2 MUTATED GAB2 WILD-TYPE
  0            8            275
  1            0             48
[1] 2 2
[1] FALSE
D634V7, 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
D634V8, binary
                cls
clus               0   1
  GAB2 MUTATED     8   1
  GAB2 WILD-TYPE 309  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAB2 MUTATED      8    1
  GAB2 WILD-TYPE  309   47
                               clus
vv                              GAB2 MUTATED GAB2 WILD-TYPE
  COLON ADENOCARCINOMA                     8            309
  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 249   2  22  21
D634V9, multiclass
    clus
vv   GAB2 MUTATED GAB2 WILD-TYPE
  R0            8            249
  R1            0              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"
D634V10, 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
D634V11, 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(635) Variable = SMTN MUTATION ANALYSIS
D635V1, survival
                sevent
clus2              0   1
  SMTN MUTATED    10   3
  SMTN WILD-TYPE 272  70
  SMTN MUTATED SMTN WILD-TYPE 
            13            342 
  SMTN MUTATED SMTN WILD-TYPE 
             3             70 
$`SMTN MUTATED`
TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3845 TCGA-AA-A00A TCGA-AD-6964 TCGA-AU-6004 
       22.06         3.02         0.00        38.04        10.88        27.09 
TCGA-CM-6674 TCGA-D5-6920 TCGA-D5-6928 TCGA-D5-6930 TCGA-G4-6304 TCGA-G4-6588 
       12.95        12.39        11.64         1.51        53.62        26.17 
TCGA-G4-6628 
       52.80 

$`SMTN WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02        14.93        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E 
       19.07         7.96        27.02        13.94        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
        0.72         5.79        22.42        27.42         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58         7.53        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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 

  SMTN MUTATED SMTN WILD-TYPE 
             0              0 
  SMTN MUTATED SMTN WILD-TYPE 
         53.62         140.38 
  SMTN MUTATED SMTN WILD-TYPE 
        12.950         20.235 
[1] "0.0 - 53.6 (12.9)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.3"
D635V2, 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       23       101         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        19         10         41         31       35        13
                vv
clus             STAGE IVB
  SMTN MUTATED           0
  SMTN WILD-TYPE         1
D635V3, multiclass
            clus
vv           SMTN MUTATED SMTN WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             8            101
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SMTN MUTATED     0   2   9   3
  SMTN WILD-TYPE   9  66 239  38
D635V4, multiclass
    clus
vv   SMTN MUTATED SMTN WILD-TYPE
  T1            0              9
  T2            2             66
  T3            9            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
  SMTN MUTATED    13   0   1
  SMTN WILD-TYPE 207  80  65
D635V5, multiclass
    clus
vv   SMTN MUTATED SMTN WILD-TYPE
  N0           13            207
  N1            0             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"
D635V6, binary
                cls
clus               0   1
  SMTN MUTATED    13   0
  SMTN WILD-TYPE 270  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMTN MUTATED     13    0
  SMTN WILD-TYPE  270   48
   clus
vv  SMTN MUTATED SMTN WILD-TYPE
  0           13            270
  1            0             48
[1] 2 2
[1] FALSE
D635V7, 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
D635V8, binary
                cls
clus               0   1
  SMTN MUTATED    12   2
  SMTN WILD-TYPE 305  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMTN MUTATED     12    2
  SMTN WILD-TYPE  305   46
                               clus
vv                              SMTN MUTATED SMTN WILD-TYPE
  COLON ADENOCARCINOMA                    12            305
  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 244   2  22  21
D635V9, multiclass
    clus
vv   SMTN MUTATED SMTN WILD-TYPE
  R0           13            244
  R1            0              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"
D635V10, 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
D635V11, 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(636) Variable = ERBB4 MUTATION ANALYSIS
D636V1, survival
                 sevent
clus2               0   1
  ERBB4 MUTATED    32  12
  ERBB4 WILD-TYPE 250  61
  ERBB4 MUTATED ERBB4 WILD-TYPE 
             44             311 
  ERBB4 MUTATED ERBB4 WILD-TYPE 
             12              61 
$`ERBB4 MUTATED`
TCGA-A6-2672 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6649 TCGA-AA-3510 TCGA-AA-3713 
       46.65        22.06        27.09        24.16        63.98        19.04 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3850 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3875 
       33.04         0.99         0.00        30.05        53.00        18.05 
TCGA-AA-3947 TCGA-AA-3966 TCGA-AA-3982 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q 
       33.01         2.01        27.02         4.01        34.98         1.02 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AY-4071 TCGA-AZ-4616 TCGA-AZ-6601 TCGA-AZ-6608 
        0.72         5.79         0.95         5.13       100.01         1.94 
TCGA-CA-6717 TCGA-CK-4948 TCGA-CM-4743 TCGA-CM-5861 TCGA-CM-6163 TCGA-CM-6167 
        0.33       102.44        23.05        15.02        14.04        14.99 
TCGA-CM-6170 TCGA-CM-6172 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6541 TCGA-D5-6898 
       15.02        11.01        12.26        13.51        15.58         7.53 
TCGA-D5-6928 TCGA-D5-6932 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A285 TCGA-F4-6459 
       11.64        11.38         7.50        44.32         6.12         8.61 
TCGA-F4-6703 TCGA-G4-6588 
       35.87        26.17 

$`ERBB4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 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-A6-6138 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-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 
        7.04         3.02         1.02        35.01         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       19.04        10.06        35.05        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       10.06        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        31.07        17.03        24.03        27.02        29.98 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6963 
       21.37         4.21        56.55         0.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 
       10.88         0.20        14.50        27.09        16.31        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4681 
        0.20        21.44        17.82        58.39         1.41        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        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         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14         2.93         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 
       16.01         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 
       12.00        29.03        16.04        21.99        12.99        13.02 
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-D5-5541 TCGA-D5-6529 
       10.06        12.03        45.40        19.59        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       17.13        12.49        16.14        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         1.51        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A1HB 
       49.91        13.32        12.59       140.38       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-F4-6704 TCGA-F4-6805 
       98.24        13.38        13.45         6.18         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        91.79        46.75        52.80 

  ERBB4 MUTATED ERBB4 WILD-TYPE 
              0               0 
  ERBB4 MUTATED ERBB4 WILD-TYPE 
         102.44          140.38 
  ERBB4 MUTATED ERBB4 WILD-TYPE 
         15.005          21.140 
[1] "0.0 - 102.4 (15.0)" "0.0 - 140.4 (21.1)"
[1] "hr=" "1.6"
D636V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ERBB4 MUTATED         6        0        4        17         4         0
  ERBB4 WILD-TYPE      58        1       21        92         4         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ERBB4 MUTATED           0          2          7          3        3         0
  ERBB4 WILD-TYPE        19          8         34         28       32        13
                 vv
clus              STAGE IVB
  ERBB4 MUTATED           0
  ERBB4 WILD-TYPE         1
D636V3, multiclass
            clus
vv           ERBB4 MUTATED ERBB4 WILD-TYPE
  STAGE I                6              58
  STAGE IA               0               1
  STAGE II               4              21
  STAGE IIA             17              92
  STAGE IIB              4               4
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             2               8
  STAGE IIIB             7              34
  STAGE IIIC             3              28
  STAGE IV               3              32
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ERBB4 MUTATED     3   4  35   5
  ERBB4 WILD-TYPE   6  64 213  36
D636V4, multiclass
    clus
vv   ERBB4 MUTATED ERBB4 WILD-TYPE
  T1             3               6
  T2             4              64
  T3            35             213
  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    32   9   6
  ERBB4 WILD-TYPE 188  71  60
D636V5, multiclass
    clus
vv   ERBB4 MUTATED ERBB4 WILD-TYPE
  N0            32             188
  N1             9              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"
D636V6, binary
                 cls
clus                0   1
  ERBB4 MUTATED    40   3
  ERBB4 WILD-TYPE 243  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB4 MUTATED     40    3
  ERBB4 WILD-TYPE  243   45
   clus
vv  ERBB4 MUTATED ERBB4 WILD-TYPE
  0            40             243
  1             3              45
[1] 2 2
[1] FALSE
D636V7, binary
                 cls
clus                0   1
  ERBB4 MUTATED    26  21
  ERBB4 WILD-TYPE 144 176
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB4 MUTATED     26   21
  ERBB4 WILD-TYPE  144  176
        clus
vv       ERBB4 MUTATED ERBB4 WILD-TYPE
  FEMALE            26             144
  MALE              21             176
[1] 2 2
[1] FALSE
D636V8, binary
                 cls
clus                0   1
  ERBB4 MUTATED    39   7
  ERBB4 WILD-TYPE 278  41
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB4 MUTATED     39    7
  ERBB4 WILD-TYPE  278   41
                               clus
vv                              ERBB4 MUTATED ERBB4 WILD-TYPE
  COLON ADENOCARCINOMA                     39             278
  COLON MUCINOUS ADENOCARCINOMA             7              41
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ERBB4 MUTATED    32   0   1   2
  ERBB4 WILD-TYPE 225   2  21  19
D636V9, multiclass
    clus
vv   ERBB4 MUTATED ERBB4 WILD-TYPE
  R0            32             225
  R1             0               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"
D636V10, 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                           1    29
  ERBB4 WILD-TYPE                        18   147
D636V11, multiclass
                                  clus
vv                                 ERBB4 MUTATED ERBB4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    1              18
  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(637) Variable = POMGNT1 MUTATION ANALYSIS
D637V1, survival
                   sevent
clus2                 0   1
  POMGNT1 MUTATED     6   2
  POMGNT1 WILD-TYPE 276  71
  POMGNT1 MUTATED POMGNT1 WILD-TYPE 
                8               347 
  POMGNT1 MUTATED POMGNT1 WILD-TYPE 
                2                71 
$`POMGNT1 MUTATED`
TCGA-AA-3715 TCGA-AA-3966 TCGA-CM-4743 TCGA-CM-5349 TCGA-D5-6537 TCGA-D5-6540 
       19.04         2.01        23.05        30.08         4.80        16.14 
TCGA-D5-6930 TCGA-G4-6588 
        1.51        26.17 

$`POMGNT1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14         2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 
       18.25         1.32        43.27        15.12        17.85        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         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-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        91.79        46.75        52.80 

  POMGNT1 MUTATED POMGNT1 WILD-TYPE 
             1.51              0.00 
  POMGNT1 MUTATED POMGNT1 WILD-TYPE 
            30.08            140.38 
  POMGNT1 MUTATED POMGNT1 WILD-TYPE 
            17.59             20.28 
[1] "1.5 - 30.1 (17.6)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "2"  
D637V2, 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       24       104         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  POMGNT1 MUTATED           0          0          1          0        0
  POMGNT1 WILD-TYPE        19         10         40         31       35
                   vv
clus                STAGE IVA STAGE IVB
  POMGNT1 MUTATED           0         0
  POMGNT1 WILD-TYPE        13         1
D637V3, multiclass
            clus
vv           POMGNT1 MUTATED POMGNT1 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                5               104
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  POMGNT1 MUTATED     0   1   7   0
  POMGNT1 WILD-TYPE   9  67 241  41
D637V4, multiclass
    clus
vv   POMGNT1 MUTATED POMGNT1 WILD-TYPE
  T1               0                 9
  T2               1                67
  T3               7               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
  POMGNT1 MUTATED     7   1   0
  POMGNT1 WILD-TYPE 213  79  66
D637V5, multiclass
    clus
vv   POMGNT1 MUTATED POMGNT1 WILD-TYPE
  N0               7               213
  N1               1                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"
D637V6, binary
                   cls
clus                  0   1
  POMGNT1 MUTATED     7   0
  POMGNT1 WILD-TYPE 276  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  POMGNT1 MUTATED      7    0
  POMGNT1 WILD-TYPE  276   48
   clus
vv  POMGNT1 MUTATED POMGNT1 WILD-TYPE
  0               7               276
  1               0                48
[1] 2 2
[1] FALSE
D637V7, 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
D637V8, binary
                   cls
clus                  0   1
  POMGNT1 MUTATED     5   3
  POMGNT1 WILD-TYPE 312  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  POMGNT1 MUTATED      5    3
  POMGNT1 WILD-TYPE  312   45
                               clus
vv                              POMGNT1 MUTATED POMGNT1 WILD-TYPE
  COLON ADENOCARCINOMA                        5               312
  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 250   2  22  21
D637V9, multiclass
    clus
vv   POMGNT1 MUTATED POMGNT1 WILD-TYPE
  R0               7               250
  R1               0                 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"
D637V10, 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
D637V11, 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(638) Variable = DHX35 MUTATION ANALYSIS
D638V1, survival
                 sevent
clus2               0   1
  DHX35 MUTATED     7   3
  DHX35 WILD-TYPE 275  70
  DHX35 MUTATED DHX35 WILD-TYPE 
             10             345 
  DHX35 MUTATED DHX35 WILD-TYPE 
              3              70 
$`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        16.01        14.04        36.72 

$`DHX35 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       62.79        61.41         6.77       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       45.11        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  DHX35 MUTATED DHX35 WILD-TYPE 
           1.02            0.00 
  DHX35 MUTATED DHX35 WILD-TYPE 
          58.39          140.38 
  DHX35 MUTATED DHX35 WILD-TYPE 
          24.77           20.19 
[1] "1.0 - 58.4 (24.8)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.4"
D638V2, 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       24       104         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        19         10         41         31       32        13
                 vv
clus              STAGE IVB
  DHX35 MUTATED           0
  DHX35 WILD-TYPE         1
D638V3, multiclass
            clus
vv           DHX35 MUTATED DHX35 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              5             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               3              32
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DHX35 MUTATED     0   1   7   3
  DHX35 WILD-TYPE   9  67 241  38
D638V4, multiclass
    clus
vv   DHX35 MUTATED DHX35 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             7             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
  DHX35 MUTATED     8   2   1
  DHX35 WILD-TYPE 212  78  65
D638V5, multiclass
    clus
vv   DHX35 MUTATED DHX35 WILD-TYPE
  N0             8             212
  N1             2              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"
D638V6, binary
                 cls
clus                0   1
  DHX35 MUTATED     7   3
  DHX35 WILD-TYPE 276  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX35 MUTATED      7    3
  DHX35 WILD-TYPE  276   45
   clus
vv  DHX35 MUTATED DHX35 WILD-TYPE
  0             7             276
  1             3              45
[1] 2 2
[1] FALSE
D638V7, 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
D638V8, binary
                 cls
clus                0   1
  DHX35 MUTATED    11   0
  DHX35 WILD-TYPE 306  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX35 MUTATED     11    0
  DHX35 WILD-TYPE  306   48
                               clus
vv                              DHX35 MUTATED DHX35 WILD-TYPE
  COLON ADENOCARCINOMA                     11             306
  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 249   2  21  21
D638V9, multiclass
    clus
vv   DHX35 MUTATED DHX35 WILD-TYPE
  R0             8             249
  R1             0               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"
D638V10, 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
D638V11, 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(639) Variable = PLEK MUTATION ANALYSIS
D639V1, survival
                sevent
clus2              0   1
  PLEK MUTATED    11   1
  PLEK WILD-TYPE 271  72
  PLEK MUTATED PLEK WILD-TYPE 
            12            343 
  PLEK MUTATED PLEK WILD-TYPE 
             1             72 
$`PLEK MUTATED`
TCGA-A6-6653 TCGA-AA-3518 TCGA-AA-3555 TCGA-AA-3662 TCGA-AA-3815 TCGA-AA-A00N 
       24.39         1.02        29.95         6.05        33.04         4.01 
TCGA-AA-A010 TCGA-AD-5900 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CK-5914 TCGA-D5-6931 
       34.98         0.07        58.39         0.33        21.99        12.00 

$`PLEK WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        51.32        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  PLEK MUTATED PLEK WILD-TYPE 
          0.07           0.00 
  PLEK MUTATED PLEK WILD-TYPE 
         58.39         140.38 
  PLEK MUTATED PLEK WILD-TYPE 
        16.995         20.190 
[1] "0.1 - 58.4 (17.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.8"
D639V2, 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       25       104         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        19         10         40         30       34        13
                vv
clus             STAGE IVB
  PLEK MUTATED           0
  PLEK WILD-TYPE         1
D639V3, multiclass
            clus
vv           PLEK MUTATED PLEK WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             5            104
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            1             30
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PLEK MUTATED     0   2   6   4
  PLEK WILD-TYPE   9  66 242  37
D639V4, multiclass
    clus
vv   PLEK MUTATED PLEK WILD-TYPE
  T1            0              9
  T2            2             66
  T3            6            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
  PLEK MUTATED     9   1   2
  PLEK WILD-TYPE 211  79  64
D639V5, multiclass
    clus
vv   PLEK MUTATED PLEK WILD-TYPE
  N0            9            211
  N1            1             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"
D639V6, binary
                cls
clus               0   1
  PLEK MUTATED     9   1
  PLEK WILD-TYPE 274  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLEK MUTATED      9    1
  PLEK WILD-TYPE  274   47
   clus
vv  PLEK MUTATED PLEK WILD-TYPE
  0            9            274
  1            1             47
[1] 2 2
[1] FALSE
D639V7, 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
D639V8, binary
                cls
clus               0   1
  PLEK MUTATED     8   4
  PLEK WILD-TYPE 309  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLEK MUTATED      8    4
  PLEK WILD-TYPE  309   44
                               clus
vv                              PLEK MUTATED PLEK WILD-TYPE
  COLON ADENOCARCINOMA                     8            309
  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 249   2  21  19
D639V9, multiclass
    clus
vv   PLEK MUTATED PLEK WILD-TYPE
  R0            8            249
  R1            0              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"
D639V10, 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
D639V11, 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(640) Variable = BMPR1A MUTATION ANALYSIS
D640V1, survival
                  sevent
clus2                0   1
  BMPR1A MUTATED    16   2
  BMPR1A WILD-TYPE 266  71
  BMPR1A MUTATED BMPR1A WILD-TYPE 
              18              337 
  BMPR1A MUTATED BMPR1A WILD-TYPE 
               2               71 
$`BMPR1A MUTATED`
TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3833 TCGA-AA-3950 TCGA-AA-3966 
       63.98         6.97        54.02        15.95        24.00         2.01 
TCGA-AA-A00J TCGA-AD-6964 TCGA-AY-6386 TCGA-AZ-6601 TCGA-CM-4743 TCGA-CM-5344 
       18.05        10.88        17.82       100.01        23.05        22.03 
TCGA-CM-6162 TCGA-D5-6539 TCGA-DM-A1D9 TCGA-DM-A28K TCGA-F4-6704 TCGA-G4-6317 
       12.00        12.49       140.38        98.24         1.55        36.00 

$`BMPR1A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 
       33.04         0.99        25.02         1.02        17.98        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       33.01        26.01         2.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       15.75         0.20        21.44        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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-5860 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.98        30.08        16.01        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32        12.59         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79       117.07         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       35.87        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  BMPR1A MUTATED BMPR1A WILD-TYPE 
            1.55             0.00 
  BMPR1A MUTATED BMPR1A WILD-TYPE 
          140.38           139.17 
  BMPR1A MUTATED BMPR1A WILD-TYPE 
           20.04            20.19 
[1] "1.6 - 140.4 (20.0)" "0.0 - 139.2 (20.2)"
[1] "hr=" "2.7"
D640V2, 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       21       103         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BMPR1A MUTATED           0          1          4          2        0
  BMPR1A WILD-TYPE        19          9         37         29       35
                  vv
clus               STAGE IVA STAGE IVB
  BMPR1A MUTATED           0         0
  BMPR1A WILD-TYPE        13         1
D640V3, multiclass
            clus
vv           BMPR1A MUTATED BMPR1A WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                4               21
  STAGE IIA               6              103
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              1                9
  STAGE IIIB              4               37
  STAGE IIIC              2               29
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  BMPR1A MUTATED     0   0  16   2
  BMPR1A WILD-TYPE   9  68 232  39
D640V4, multiclass
    clus
vv   BMPR1A MUTATED BMPR1A WILD-TYPE
  T1              0                9
  T2              0               68
  T3             16              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
  BMPR1A MUTATED    11   4   3
  BMPR1A WILD-TYPE 209  76  63
D640V5, multiclass
    clus
vv   BMPR1A MUTATED BMPR1A WILD-TYPE
  N0             11              209
  N1              4               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"
D640V6, binary
                  cls
clus                 0   1
  BMPR1A MUTATED    15   0
  BMPR1A WILD-TYPE 268  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BMPR1A MUTATED     15    0
  BMPR1A WILD-TYPE  268   48
   clus
vv  BMPR1A MUTATED BMPR1A WILD-TYPE
  0             15              268
  1              0               48
[1] 2 2
[1] FALSE
D640V7, 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
D640V8, binary
                  cls
clus                 0   1
  BMPR1A MUTATED    12   6
  BMPR1A WILD-TYPE 305  42
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BMPR1A MUTATED     12    6
  BMPR1A WILD-TYPE  305   42
                               clus
vv                              BMPR1A MUTATED BMPR1A WILD-TYPE
  COLON ADENOCARCINOMA                      12              305
  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 244   2  22  21
D640V9, multiclass
    clus
vv   BMPR1A MUTATED BMPR1A WILD-TYPE
  R0             13              244
  R1              0                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"
D640V10, 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
D640V11, 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(641) Variable = RING1 MUTATION ANALYSIS
D641V1, survival
                 sevent
clus2               0   1
  RING1 MUTATED     8   0
  RING1 WILD-TYPE 274  73
  RING1 MUTATED RING1 WILD-TYPE 
              8             347 
  RING1 MUTATED RING1 WILD-TYPE 
              0              73 
$`RING1 MUTATED`
TCGA-A6-6141 TCGA-AA-3713 TCGA-AZ-4315 TCGA-CM-4743 TCGA-CM-6171 TCGA-D5-6930 
        8.38        19.04        58.39        23.05        14.04         1.51 
TCGA-DM-A1HA TCGA-G4-6586 
      131.51        35.80 

$`RING1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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-A285 TCGA-DM-A28C 
        7.50        44.32       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        26.17        91.79        46.75        52.80 

  RING1 MUTATED RING1 WILD-TYPE 
           1.51            0.00 
  RING1 MUTATED RING1 WILD-TYPE 
         131.51          140.38 
  RING1 MUTATED RING1 WILD-TYPE 
         21.045          20.190 
[1] "1.5 - 131.5 (21.0)" "0.0 - 140.4 (20.2)"
[1] "hr="     "2.6e+07"
D641V2, 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       25       103         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        19         10         41         30       34        13
                 vv
clus              STAGE IVB
  RING1 MUTATED           0
  RING1 WILD-TYPE         1
D641V3, multiclass
            clus
vv           RING1 MUTATED RING1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              6             103
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RING1 MUTATED     0   1   8   1
  RING1 WILD-TYPE   9  67 240  40
D641V4, multiclass
    clus
vv   RING1 MUTATED RING1 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             8             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
  RING1 MUTATED     9   0   1
  RING1 WILD-TYPE 211  80  65
D641V5, multiclass
    clus
vv   RING1 MUTATED RING1 WILD-TYPE
  N0             9             211
  N1             0              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"
D641V6, binary
                 cls
clus                0   1
  RING1 MUTATED     8   1
  RING1 WILD-TYPE 275  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RING1 MUTATED      8    1
  RING1 WILD-TYPE  275   47
   clus
vv  RING1 MUTATED RING1 WILD-TYPE
  0             8             275
  1             1              47
[1] 2 2
[1] FALSE
D641V7, 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
D641V8, binary
                 cls
clus                0   1
  RING1 MUTATED     9   1
  RING1 WILD-TYPE 308  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RING1 MUTATED      9    1
  RING1 WILD-TYPE  308   47
                               clus
vv                              RING1 MUTATED RING1 WILD-TYPE
  COLON ADENOCARCINOMA                      9             308
  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 251   2  21  20
D641V9, multiclass
    clus
vv   RING1 MUTATED RING1 WILD-TYPE
  R0             6             251
  R1             0               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"
D641V10, 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
D641V11, 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(642) Variable = C17ORF47 MUTATION ANALYSIS
D642V1, survival
                    sevent
clus2                  0   1
  C17ORF47 MUTATED     4   1
  C17ORF47 WILD-TYPE 278  72
  C17ORF47 MUTATED C17ORF47 WILD-TYPE 
                 5                350 
  C17ORF47 MUTATED C17ORF47 WILD-TYPE 
                 1                 72 
$`C17ORF47 MUTATED`
TCGA-A6-5666 TCGA-A6-6649 TCGA-AA-A010 TCGA-CA-6717 TCGA-CM-5862 
       32.71        24.16        34.98         0.33         5.03 

$`C17ORF47 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.18        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  C17ORF47 MUTATED C17ORF47 WILD-TYPE 
              0.33               0.00 
  C17ORF47 MUTATED C17ORF47 WILD-TYPE 
             34.98             140.38 
  C17ORF47 MUTATED C17ORF47 WILD-TYPE 
            24.160             20.155 
[1] "0.3 - 35.0 (24.2)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.5"
D642V2, 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       25       108         7         0
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C17ORF47 MUTATED           0          0          1          0        0
  C17ORF47 WILD-TYPE        19         10         40         31       35
                    vv
clus                 STAGE IVA STAGE IVB
  C17ORF47 MUTATED           1         0
  C17ORF47 WILD-TYPE        12         1
D642V3, multiclass
            clus
vv           C17ORF47 MUTATED C17ORF47 WILD-TYPE
  STAGE I                   0                 64
  STAGE IA                  0                  1
  STAGE II                  0                 25
  STAGE IIA                 1                108
  STAGE IIB                 1                  7
  STAGE IIC                 1                  0
  STAGE III                 0                 19
  STAGE IIIA                0                 10
  STAGE IIIB                1                 40
  STAGE IIIC                0                 31
  STAGE IV                  0                 35
  STAGE IVA                 1                 12
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of 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  68 245  39
D642V4, multiclass
    clus
vv   C17ORF47 MUTATED C17ORF47 WILD-TYPE
  T1                0                  9
  T2                0                 68
  T3                3                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
  C17ORF47 MUTATED     3   2   0
  C17ORF47 WILD-TYPE 217  78  66
D642V5, multiclass
    clus
vv   C17ORF47 MUTATED C17ORF47 WILD-TYPE
  N0                3                217
  N1                2                 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"
D642V6, binary
                    cls
clus                   0   1
  C17ORF47 MUTATED     4   1
  C17ORF47 WILD-TYPE 279  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C17ORF47 MUTATED      4    1
  C17ORF47 WILD-TYPE  279   47
   clus
vv  C17ORF47 MUTATED C17ORF47 WILD-TYPE
  0                4                279
  1                1                 47
[1] 2 2
[1] FALSE
D642V7, 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
D642V8, binary
                    cls
clus                   0   1
  C17ORF47 MUTATED     4   1
  C17ORF47 WILD-TYPE 313  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C17ORF47 MUTATED      4    1
  C17ORF47 WILD-TYPE  313   47
                               clus
vv                              C17ORF47 MUTATED C17ORF47 WILD-TYPE
  COLON ADENOCARCINOMA                         4                313
  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 255   2  22  20
D642V9, multiclass
    clus
vv   C17ORF47 MUTATED C17ORF47 WILD-TYPE
  R0                2                255
  R1                0                  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"
D642V10, 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
D642V11, 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(643) Variable = PALLD MUTATION ANALYSIS
D643V1, survival
                 sevent
clus2               0   1
  PALLD MUTATED     7   2
  PALLD WILD-TYPE 275  71
  PALLD MUTATED PALLD WILD-TYPE 
              9             346 
  PALLD MUTATED PALLD WILD-TYPE 
              2              71 
$`PALLD MUTATED`
TCGA-AA-3660 TCGA-AA-3680 TCGA-AA-3966 TCGA-AU-6004 TCGA-AZ-6601 TCGA-CM-4747 
       78.08        11.01         2.01        27.09       100.01        25.02 
TCGA-D5-6533 TCGA-DM-A1HB TCGA-G4-6588 
        1.32       135.65        26.17 

$`PALLD WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        61.02         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       47.01        15.02         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.20        14.50        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 
       19.59        13.51        11.51        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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        91.79        46.75        52.80 

  PALLD MUTATED PALLD WILD-TYPE 
           1.32            0.00 
  PALLD MUTATED PALLD WILD-TYPE 
         135.65          140.38 
  PALLD MUTATED PALLD WILD-TYPE 
          26.17           20.07 
[1] "1.3 - 135.7 (26.2)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.5"
D643V2, 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       23       107         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PALLD MUTATED           0          0          2          0        1         1
  PALLD WILD-TYPE        19         10         39         31       34        12
                 vv
clus              STAGE IVB
  PALLD MUTATED           0
  PALLD WILD-TYPE         1
D643V3, multiclass
            clus
vv           PALLD MUTATED PALLD WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              2             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 243  38
D643V4, multiclass
    clus
vv   PALLD MUTATED PALLD WILD-TYPE
  T1             0               9
  T2             1              67
  T3             5             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
  PALLD MUTATED     6   2   1
  PALLD WILD-TYPE 214  78  65
D643V5, multiclass
    clus
vv   PALLD MUTATED PALLD WILD-TYPE
  N0             6             214
  N1             2              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"
D643V6, binary
                 cls
clus                0   1
  PALLD MUTATED     7   2
  PALLD WILD-TYPE 276  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PALLD MUTATED      7    2
  PALLD WILD-TYPE  276   46
   clus
vv  PALLD MUTATED PALLD WILD-TYPE
  0             7             276
  1             2              46
[1] 2 2
[1] FALSE
D643V7, 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
D643V8, binary
                 cls
clus                0   1
  PALLD MUTATED     8   1
  PALLD WILD-TYPE 309  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PALLD MUTATED      8    1
  PALLD WILD-TYPE  309   47
                               clus
vv                              PALLD MUTATED PALLD WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  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 252   2  21  21
D643V9, multiclass
    clus
vv   PALLD MUTATED PALLD WILD-TYPE
  R0             5             252
  R1             0               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"
D643V10, 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
D643V11, 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(644) Variable = AFM MUTATION ANALYSIS
D644V1, survival
               sevent
clus2             0   1
  AFM MUTATED    11   2
  AFM WILD-TYPE 271  71
  AFM MUTATED AFM WILD-TYPE 
           13           342 
  AFM MUTATED AFM WILD-TYPE 
            2            71 
$`AFM MUTATED`
TCGA-A6-3809 TCGA-AA-3518 TCGA-AA-3713 TCGA-AA-A010 TCGA-AA-A01Q TCGA-AD-6965 
       32.75         1.02        19.04        34.98         1.02         0.20 
TCGA-AZ-6599 TCGA-CA-6718 TCGA-CM-5861 TCGA-D5-6923 TCGA-DM-A1DB TCGA-DM-A1HA 
        6.77         0.10        15.02        12.43        44.32       131.51 
TCGA-G4-6310 
       45.11 

$`AFM WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       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        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        10.88        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41        49.41        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.33         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-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-A285 
       12.59       140.38         7.50       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        51.75        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  AFM MUTATED AFM WILD-TYPE 
          0.1           0.0 
  AFM MUTATED AFM WILD-TYPE 
       131.51        140.38 
  AFM MUTATED AFM WILD-TYPE 
        15.02         20.63 
[1] "0.1 - 131.5 (15.0)" "0.0 - 140.4 (20.6)"
[1] "hr=" "1.3"
D644V2, 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       24       105         6         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AFM MUTATED           0          0          1          1        1         0
  AFM WILD-TYPE        19         10         40         30       34        13
               vv
clus            STAGE IVB
  AFM MUTATED           0
  AFM WILD-TYPE         1
D644V3, multiclass
            clus
vv           AFM MUTATED AFM WILD-TYPE
  STAGE I              2            62
  STAGE IA             0             1
  STAGE II             1            24
  STAGE IIA            4           105
  STAGE IIB            2             6
  STAGE IIC            0             1
  STAGE III            0            19
  STAGE IIIA           0            10
  STAGE IIIB           1            40
  STAGE IIIC           1            30
  STAGE IV             1            34
  STAGE IVA            0            13
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  AFM MUTATED     0   2   8   3
  AFM WILD-TYPE   9  66 240  38
D644V4, multiclass
    clus
vv   AFM MUTATED AFM WILD-TYPE
  T1           0             9
  T2           2            66
  T3           8           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
  AFM MUTATED    10   1   2
  AFM WILD-TYPE 210  79  64
D644V5, multiclass
    clus
vv   AFM MUTATED AFM WILD-TYPE
  N0          10           210
  N1           1            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"
D644V6, binary
               cls
clus              0   1
  AFM MUTATED    10   1
  AFM WILD-TYPE 273  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  AFM MUTATED     10    1
  AFM WILD-TYPE  273   47
   clus
vv  AFM MUTATED AFM WILD-TYPE
  0          10           273
  1           1            47
[1] 2 2
[1] FALSE
D644V7, 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
D644V8, binary
               cls
clus              0   1
  AFM MUTATED    12   1
  AFM WILD-TYPE 305  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  AFM MUTATED     12    1
  AFM WILD-TYPE  305   47
                               clus
vv                              AFM MUTATED AFM WILD-TYPE
  COLON ADENOCARCINOMA                   12           305
  COLON MUCINOUS ADENOCARCINOMA           1            47
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  AFM MUTATED     7   0   1   1
  AFM WILD-TYPE 250   2  21  20
D644V9, multiclass
    clus
vv   AFM MUTATED AFM WILD-TYPE
  R0           7           250
  R1           0             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"
D644V10, 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
D644V11, 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(645) Variable = C1ORF168 MUTATION ANALYSIS
D645V1, survival
                    sevent
clus2                  0   1
  C1ORF168 MUTATED    11   3
  C1ORF168 WILD-TYPE 271  70
  C1ORF168 MUTATED C1ORF168 WILD-TYPE 
                14                341 
  C1ORF168 MUTATED C1ORF168 WILD-TYPE 
                 3                 70 
$`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        61.41 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5916 TCGA-CM-4746 TCGA-D5-6923 TCGA-DM-A28H 
        0.33         0.10        21.14        37.02        12.43       117.07 
TCGA-F4-6570 TCGA-G4-6304 
        6.18        53.62 

$`C1ORF168 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        32.71        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07         0.26         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K 
        6.12        81.37       119.93        35.97        60.79        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        13.38        13.45        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 
       19.43       107.67        74.56        65.85        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  C1ORF168 MUTATED C1ORF168 WILD-TYPE 
               0.1                0.0 
  C1ORF168 MUTATED C1ORF168 WILD-TYPE 
            117.07             140.38 
  C1ORF168 MUTATED C1ORF168 WILD-TYPE 
            26.005             20.020 
[1] "0.1 - 117.1 (26.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.1"
D645V2, 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       25       105         5         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C1ORF168 MUTATED           0          0          1          1        0
  C1ORF168 WILD-TYPE        19         10         40         30       35
                    vv
clus                 STAGE IVA STAGE IVB
  C1ORF168 MUTATED           0         0
  C1ORF168 WILD-TYPE        13         1
D645V3, multiclass
            clus
vv           C1ORF168 MUTATED C1ORF168 WILD-TYPE
  STAGE I                   4                 60
  STAGE IA                  0                  1
  STAGE II                  0                 25
  STAGE IIA                 4                105
  STAGE IIB                 3                  5
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                0                 10
  STAGE IIIB                1                 40
  STAGE IIIC                1                 30
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C1ORF168 MUTATED     2   3   6   3
  C1ORF168 WILD-TYPE   7  65 242  38
D645V4, multiclass
    clus
vv   C1ORF168 MUTATED C1ORF168 WILD-TYPE
  T1                2                  7
  T2                3                 65
  T3                6                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
  C1ORF168 MUTATED    12   1   1
  C1ORF168 WILD-TYPE 208  79  65
D645V5, multiclass
    clus
vv   C1ORF168 MUTATED C1ORF168 WILD-TYPE
  N0               12                208
  N1                1                 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"
D645V6, binary
                    cls
clus                   0   1
  C1ORF168 MUTATED    13   0
  C1ORF168 WILD-TYPE 270  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF168 MUTATED     13    0
  C1ORF168 WILD-TYPE  270   48
   clus
vv  C1ORF168 MUTATED C1ORF168 WILD-TYPE
  0               13                270
  1                0                 48
[1] 2 2
[1] FALSE
D645V7, 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
D645V8, binary
                    cls
clus                   0   1
  C1ORF168 MUTATED    12   2
  C1ORF168 WILD-TYPE 305  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF168 MUTATED     12    2
  C1ORF168 WILD-TYPE  305   46
                               clus
vv                              C1ORF168 MUTATED C1ORF168 WILD-TYPE
  COLON ADENOCARCINOMA                        12                305
  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 250   2  22  18
D645V9, multiclass
    clus
vv   C1ORF168 MUTATED C1ORF168 WILD-TYPE
  R0                7                250
  R1                0                  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"
D645V10, 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
D645V11, 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(646) Variable = ZC3H13 MUTATION ANALYSIS
D646V1, survival
                  sevent
clus2                0   1
  ZC3H13 MUTATED    27   7
  ZC3H13 WILD-TYPE 255  66
  ZC3H13 MUTATED ZC3H13 WILD-TYPE 
              34              321 
  ZC3H13 MUTATED ZC3H13 WILD-TYPE 
               7               66 
$`ZC3H13 MUTATED`
TCGA-A6-2677 TCGA-A6-5661 TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3525 
       24.33        33.53        22.06        63.98        13.02         8.05 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3713 TCGA-AA-3815 TCGA-AA-3864 
       17.95        29.95        23.01        19.04        33.04        53.00 
TCGA-AA-3947 TCGA-AA-3956 TCGA-AA-3977 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A00R 
       33.01        34.03        25.02        18.05         4.01         0.99 
TCGA-AA-A010 TCGA-AA-A01F TCGA-AA-A01Q TCGA-AA-A01R TCGA-AZ-4315 TCGA-CA-6717 
       34.98        32.02         1.02        35.01        58.39         0.33 
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 
       13.45         6.18        53.62        46.75 

$`ZC3H13 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        42.90        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       31.63        30.44        29.19        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
        1.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
       36.03        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       21.01        13.02        24.00        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       85.05        26.99        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        38.04        27.02        42.02 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01G 
       17.03        14.99        21.99        15.02        10.98        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        31.00        38.07         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
        8.61        13.38        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      107.67        74.56        65.85        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       26.17        91.79        52.80 

  ZC3H13 MUTATED ZC3H13 WILD-TYPE 
            0.33             0.00 
  ZC3H13 MUTATED ZC3H13 WILD-TYPE 
           98.24           140.38 
  ZC3H13 MUTATED ZC3H13 WILD-TYPE 
          24.675           19.990 
[1] "0.3 - 98.2 (24.7)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1.1"
D646V2, 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       22        98         4         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZC3H13 MUTATED           2          3          3          2        1
  ZC3H13 WILD-TYPE        17          7         38         29       34
                  vv
clus               STAGE IVA STAGE IVB
  ZC3H13 MUTATED           0         0
  ZC3H13 WILD-TYPE        13         1
D646V3, multiclass
            clus
vv           ZC3H13 MUTATED ZC3H13 WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                3               22
  STAGE IIA              11               98
  STAGE IIB               4                4
  STAGE IIC               0                1
  STAGE III               2               17
  STAGE IIIA              3                7
  STAGE IIIB              3               38
  STAGE IIIC              2               29
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZC3H13 MUTATED     1   5  23   5
  ZC3H13 WILD-TYPE   8  63 225  36
D646V4, multiclass
    clus
vv   ZC3H13 MUTATED ZC3H13 WILD-TYPE
  T1              1                8
  T2              5               63
  T3             23              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
  ZC3H13 MUTATED    24   6   4
  ZC3H13 WILD-TYPE 196  74  62
D646V5, multiclass
    clus
vv   ZC3H13 MUTATED ZC3H13 WILD-TYPE
  N0             24              196
  N1              6               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"
D646V6, binary
                  cls
clus                 0   1
  ZC3H13 MUTATED    32   1
  ZC3H13 WILD-TYPE 251  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZC3H13 MUTATED     32    1
  ZC3H13 WILD-TYPE  251   47
   clus
vv  ZC3H13 MUTATED ZC3H13 WILD-TYPE
  0             32              251
  1              1               47
[1] 2 2
[1] FALSE
D646V7, 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
D646V8, binary
                  cls
clus                 0   1
  ZC3H13 MUTATED    23  10
  ZC3H13 WILD-TYPE 294  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZC3H13 MUTATED     23   10
  ZC3H13 WILD-TYPE  294   38
                               clus
vv                              ZC3H13 MUTATED ZC3H13 WILD-TYPE
  COLON ADENOCARCINOMA                      23              294
  COLON MUCINOUS ADENOCARCINOMA             10               38
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZC3H13 MUTATED    27   0   1   2
  ZC3H13 WILD-TYPE 230   2  21  19
D646V9, multiclass
    clus
vv   ZC3H13 MUTATED ZC3H13 WILD-TYPE
  R0             27              230
  R1              0                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"
D646V10, 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
D646V11, 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(647) Variable = HUWE1 MUTATION ANALYSIS
D647V1, survival
                 sevent
clus2               0   1
  HUWE1 MUTATED    32   9
  HUWE1 WILD-TYPE 250  64
  HUWE1 MUTATED HUWE1 WILD-TYPE 
             41             314 
  HUWE1 MUTATED HUWE1 WILD-TYPE 
              9              64 
$`HUWE1 MUTATED`
TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-3555 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       22.06        20.12        29.95        78.08         6.05         6.97 
TCGA-AA-3713 TCGA-AA-3818 TCGA-AA-3837 TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3941 
       19.04         0.99        38.99        36.03        53.00        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-A010 TCGA-AA-A01P 
       33.01        26.01        24.00         2.01        34.98        38.07 
TCGA-AA-A01Q TCGA-AA-A02F TCGA-AD-6895 TCGA-AD-6964 TCGA-AU-3779 TCGA-AU-6004 
        1.02        39.98         0.72        10.88        14.50        27.09 
TCGA-AZ-4315 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6603 TCGA-CM-4752 TCGA-CM-6162 
       58.39        62.79        49.41        29.56        13.02        12.00 
TCGA-CM-6164 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6674 TCGA-D5-6540 TCGA-D5-6541 
       29.03        14.99        13.02        12.95        16.14        15.58 
TCGA-DM-A1DA TCGA-DM-A1HB TCGA-F4-6459 TCGA-F4-6570 TCGA-F4-6703 
        7.50       135.65         8.61         6.18        35.87 

$`HUWE1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       19.99        61.02        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05        33.04        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       15.95        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
        0.00        33.07         0.00        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3955 
       18.05        31.00         2.01        12.99         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01R 
       10.98        32.02        12.00        31.00        31.00        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       51.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       56.55         0.79         5.79        22.42        27.42         0.20 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6599 
        1.41         5.13        83.80        22.36        61.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10       100.01         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        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-6168 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       16.04        21.99        12.99        15.02        14.04        11.01 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       17.13        12.49         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 
       35.97        60.79       117.07        98.24        13.38        13.45 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  HUWE1 MUTATED HUWE1 WILD-TYPE 
           0.72            0.00 
  HUWE1 MUTATED HUWE1 WILD-TYPE 
         135.65          140.38 
  HUWE1 MUTATED HUWE1 WILD-TYPE 
         22.060          20.105 
[1] "0.7 - 135.7 (22.1)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.1"
D647V2, 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       19        93         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HUWE1 MUTATED           1          0          4          2        3         1
  HUWE1 WILD-TYPE        18         10         37         29       32        12
                 vv
clus              STAGE IVB
  HUWE1 MUTATED           0
  HUWE1 WILD-TYPE         1
D647V3, multiclass
            clus
vv           HUWE1 MUTATED HUWE1 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               6              19
  STAGE IIA             16              93
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             4              37
  STAGE IIIC             2              29
  STAGE IV               3              32
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  64 216  35
D647V4, multiclass
    clus
vv   HUWE1 MUTATED HUWE1 WILD-TYPE
  T1             0               9
  T2             4              64
  T3            32             216
  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  72  61
D647V5, multiclass
    clus
vv   HUWE1 MUTATED HUWE1 WILD-TYPE
  N0            29             191
  N1             8              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"
D647V6, binary
                 cls
clus                0   1
  HUWE1 MUTATED    31   4
  HUWE1 WILD-TYPE 252  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HUWE1 MUTATED     31    4
  HUWE1 WILD-TYPE  252   44
   clus
vv  HUWE1 MUTATED HUWE1 WILD-TYPE
  0            31             252
  1             4              44
[1] 2 2
[1] FALSE
D647V7, 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
D647V8, binary
                 cls
clus                0   1
  HUWE1 MUTATED    32  10
  HUWE1 WILD-TYPE 285  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HUWE1 MUTATED     32   10
  HUWE1 WILD-TYPE  285   38
                               clus
vv                              HUWE1 MUTATED HUWE1 WILD-TYPE
  COLON ADENOCARCINOMA                     32             285
  COLON MUCINOUS ADENOCARCINOMA            10              38
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  HUWE1 MUTATED    29   0   3   1
  HUWE1 WILD-TYPE 228   2  19  20
D647V9, multiclass
    clus
vv   HUWE1 MUTATED HUWE1 WILD-TYPE
  R0            29             228
  R1             0               2
  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"
D647V10, 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
D647V11, 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(648) Variable = SLC26A8 MUTATION ANALYSIS
D648V1, survival
                   sevent
clus2                 0   1
  SLC26A8 MUTATED    10   4
  SLC26A8 WILD-TYPE 272  69
  SLC26A8 MUTATED SLC26A8 WILD-TYPE 
               14               341 
  SLC26A8 MUTATED SLC26A8 WILD-TYPE 
                4                69 
$`SLC26A8 MUTATED`
TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-A010 TCGA-AA-A01D 
       22.06        19.66         3.02        63.98        34.98        10.98 
TCGA-CA-6717 TCGA-CM-4743 TCGA-D5-6537 TCGA-D5-6924 TCGA-DM-A1HB TCGA-DM-A28F 
        0.33        23.05         4.80        14.30       135.65        35.97 
TCGA-G4-6588 TCGA-G4-6628 
       26.17        52.80 

$`SLC26A8 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.12        20.28         7.04         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85        17.13        12.49        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
        6.12        81.37       119.93        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        91.79        46.75 

  SLC26A8 MUTATED SLC26A8 WILD-TYPE 
             0.33              0.00 
  SLC26A8 MUTATED SLC26A8 WILD-TYPE 
           135.65            140.38 
  SLC26A8 MUTATED SLC26A8 WILD-TYPE 
           22.555            20.120 
[1] "0.3 - 135.7 (22.6)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.2"
D648V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC26A8 MUTATED         1        0        2         6         1         0
  SLC26A8 WILD-TYPE      63        1       23       103         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC26A8 MUTATED           0          0          3          2        0
  SLC26A8 WILD-TYPE        19         10         38         29       35
                   vv
clus                STAGE IVA STAGE IVB
  SLC26A8 MUTATED           0         0
  SLC26A8 WILD-TYPE        13         1
D648V3, multiclass
            clus
vv           SLC26A8 MUTATED SLC26A8 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 2                23
  STAGE IIA                6               103
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               3                38
  STAGE IIIC               2                29
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC26A8 MUTATED     0   1  12   2
  SLC26A8 WILD-TYPE   9  67 236  39
D648V4, multiclass
    clus
vv   SLC26A8 MUTATED SLC26A8 WILD-TYPE
  T1               0                 9
  T2               1                67
  T3              12               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    10   4   1
  SLC26A8 WILD-TYPE 210  76  65
D648V5, multiclass
    clus
vv   SLC26A8 MUTATED SLC26A8 WILD-TYPE
  N0              10               210
  N1               4                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"
D648V6, binary
                   cls
clus                  0   1
  SLC26A8 MUTATED    13   0
  SLC26A8 WILD-TYPE 270  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC26A8 MUTATED     13    0
  SLC26A8 WILD-TYPE  270   48
   clus
vv  SLC26A8 MUTATED SLC26A8 WILD-TYPE
  0              13               270
  1               0                48
[1] 2 2
[1] FALSE
D648V7, binary
                   cls
clus                  0   1
  SLC26A8 MUTATED     6   9
  SLC26A8 WILD-TYPE 164 188
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC26A8 MUTATED      6    9
  SLC26A8 WILD-TYPE  164  188
        clus
vv       SLC26A8 MUTATED SLC26A8 WILD-TYPE
  FEMALE               6               164
  MALE                 9               188
[1] 2 2
[1] FALSE
D648V8, binary
                   cls
clus                  0   1
  SLC26A8 MUTATED    12   3
  SLC26A8 WILD-TYPE 305  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC26A8 MUTATED     12    3
  SLC26A8 WILD-TYPE  305   45
                               clus
vv                              SLC26A8 MUTATED SLC26A8 WILD-TYPE
  COLON ADENOCARCINOMA                       12               305
  COLON MUCINOUS ADENOCARCINOMA               3                45
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SLC26A8 MUTATED    12   0   0   1
  SLC26A8 WILD-TYPE 245   2  22  20
D648V9, multiclass
    clus
vv   SLC26A8 MUTATED SLC26A8 WILD-TYPE
  R0              12               245
  R1               0                 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"
D648V10, 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
D648V11, 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(649) Variable = OR4E2 MUTATION ANALYSIS
D649V1, survival
                 sevent
clus2               0   1
  OR4E2 MUTATED     4   0
  OR4E2 WILD-TYPE 278  73
  OR4E2 MUTATED OR4E2 WILD-TYPE 
              4             351 
  OR4E2 MUTATED OR4E2 WILD-TYPE 
              0              73 
$`OR4E2 MUTATED`
TCGA-A6-5665 TCGA-AA-3510 TCGA-CM-6675 TCGA-G4-6586 
       22.06        63.98        13.05        35.80 

$`OR4E2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 
       45.11        36.72        36.00        22.09        13.78        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  OR4E2 MUTATED OR4E2 WILD-TYPE 
          13.05            0.00 
  OR4E2 MUTATED OR4E2 WILD-TYPE 
          63.98          140.38 
  OR4E2 MUTATED OR4E2 WILD-TYPE 
          28.93           20.12 
[1] "13.1 - 64.0 (28.9)" "0.0 - 140.4 (20.1)"
[1] "hr="     "9100000"
D649V2, 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       24       107         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        19         10         41         31       35        13
                 vv
clus              STAGE IVB
  OR4E2 MUTATED           1
  OR4E2 WILD-TYPE         0
D649V3, multiclass
            clus
vv           OR4E2 MUTATED OR4E2 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              2             107
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  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  68 244  40
D649V4, multiclass
    clus
vv   OR4E2 MUTATED OR4E2 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             4             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
  OR4E2 MUTATED     4   0   1
  OR4E2 WILD-TYPE 216  80  65
D649V5, multiclass
    clus
vv   OR4E2 MUTATED OR4E2 WILD-TYPE
  N0             4             216
  N1             0              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"
D649V6, binary
                 cls
clus                0   1
  OR4E2 MUTATED     3   1
  OR4E2 WILD-TYPE 280  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4E2 MUTATED      3    1
  OR4E2 WILD-TYPE  280   47
   clus
vv  OR4E2 MUTATED OR4E2 WILD-TYPE
  0             3             280
  1             1              47
[1] 2 2
[1] FALSE
D649V7, 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
D649V8, binary
                 cls
clus                0   1
  OR4E2 MUTATED     5   0
  OR4E2 WILD-TYPE 312  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4E2 MUTATED      5    0
  OR4E2 WILD-TYPE  312   48
                               clus
vv                              OR4E2 MUTATED OR4E2 WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  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 253   2  22  20
D649V9, multiclass
    clus
vv   OR4E2 MUTATED OR4E2 WILD-TYPE
  R0             4             253
  R1             0               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"
D649V10, 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
D649V11, 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(650) Variable = ARHGAP25 MUTATION ANALYSIS
D650V1, survival
                    sevent
clus2                  0   1
  ARHGAP25 MUTATED     9   1
  ARHGAP25 WILD-TYPE 273  72
  ARHGAP25 MUTATED ARHGAP25 WILD-TYPE 
                10                345 
  ARHGAP25 MUTATED ARHGAP25 WILD-TYPE 
                 1                 72 
$`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         0.33 
TCGA-D5-6533 TCGA-D5-6536 TCGA-D5-6922 TCGA-DM-A0XF 
        1.32        17.85        10.13        38.20 

$`ARHGAP25 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        61.02         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.20        14.50        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 
       19.59        13.51        11.51        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-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        24.43       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  ARHGAP25 MUTATED ARHGAP25 WILD-TYPE 
              0.33               0.00 
  ARHGAP25 MUTATED ARHGAP25 WILD-TYPE 
             78.08             140.38 
  ARHGAP25 MUTATED ARHGAP25 WILD-TYPE 
             30.05              20.12 
[1] "0.3 - 78.1 (30.0)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "2.3"
D650V2, 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       24       106         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARHGAP25 MUTATED           1          1          1          1        0
  ARHGAP25 WILD-TYPE        18          9         40         30       35
                    vv
clus                 STAGE IVA STAGE IVB
  ARHGAP25 MUTATED           0         0
  ARHGAP25 WILD-TYPE        13         1
D650V3, multiclass
            clus
vv           ARHGAP25 MUTATED ARHGAP25 WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  1                 24
  STAGE IIA                 3                106
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 1                 18
  STAGE IIIA                1                  9
  STAGE IIIB                1                 40
  STAGE IIIC                1                 30
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  ARHGAP25 MUTATED     0   1   7   2
  ARHGAP25 WILD-TYPE   9  67 241  39
D650V4, multiclass
    clus
vv   ARHGAP25 MUTATED ARHGAP25 WILD-TYPE
  T1                0                  9
  T2                1                 67
  T3                7                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
  ARHGAP25 MUTATED     7   1   2
  ARHGAP25 WILD-TYPE 213  79  64
D650V5, multiclass
    clus
vv   ARHGAP25 MUTATED ARHGAP25 WILD-TYPE
  N0                7                213
  N1                1                 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"
D650V6, binary
                    cls
clus                   0   1
  ARHGAP25 MUTATED    10   0
  ARHGAP25 WILD-TYPE 273  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP25 MUTATED     10    0
  ARHGAP25 WILD-TYPE  273   48
   clus
vv  ARHGAP25 MUTATED ARHGAP25 WILD-TYPE
  0               10                273
  1                0                 48
[1] 2 2
[1] FALSE
D650V7, 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
D650V8, binary
                    cls
clus                   0   1
  ARHGAP25 MUTATED     6   4
  ARHGAP25 WILD-TYPE 311  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP25 MUTATED      6    4
  ARHGAP25 WILD-TYPE  311   44
                               clus
vv                              ARHGAP25 MUTATED ARHGAP25 WILD-TYPE
  COLON ADENOCARCINOMA                         6                311
  COLON MUCINOUS ADENOCARCINOMA                4                 44
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  ARHGAP25 MUTATED     8   0   0   1
  ARHGAP25 WILD-TYPE 249   2  22  20
D650V9, multiclass
    clus
vv   ARHGAP25 MUTATED ARHGAP25 WILD-TYPE
  R0                8                249
  R1                0                  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"
D650V10, 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
D650V11, 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(651) Variable = FLT3 MUTATION ANALYSIS
D651V1, survival
                sevent
clus2              0   1
  FLT3 MUTATED    18   5
  FLT3 WILD-TYPE 264  68
  FLT3 MUTATED FLT3 WILD-TYPE 
            23            332 
  FLT3 MUTATED FLT3 WILD-TYPE 
             5             68 
$`FLT3 MUTATED`
TCGA-A6-5656 TCGA-A6-5666 TCGA-A6-6141 TCGA-AA-3864 TCGA-AA-3950 TCGA-AA-A010 
       32.91        32.71         8.38        53.00        24.00        34.98 
TCGA-AA-A02K TCGA-AD-6899 TCGA-AU-6004 TCGA-AY-5543 TCGA-AZ-6608 TCGA-CA-6717 
       14.01         5.79        27.09        15.75         1.94         0.33 
TCGA-CM-5860 TCGA-CM-5864 TCGA-CM-6171 TCGA-D5-6537 TCGA-D5-6922 TCGA-D5-6923 
       16.01        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       107.67        36.72        13.78 

$`FLT3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       22.06        27.09        22.52        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       39.06        51.98        39.98         2.01         5.03         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 
        4.21        56.55         0.79         0.72        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 
       10.88         0.20        14.50        16.31         0.95         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
      100.01        29.56         5.23        11.74         3.19         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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-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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        49.91        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       45.11        36.00        22.09        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  FLT3 MUTATED FLT3 WILD-TYPE 
          0.33           0.00 
  FLT3 MUTATED FLT3 WILD-TYPE 
        107.67         140.38 
  FLT3 MUTATED FLT3 WILD-TYPE 
        14.040         20.995 
[1] "0.3 - 107.7 (14.0)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.2"
D651V2, 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       24       102         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        18          8         40         30       33        12
                vv
clus             STAGE IVB
  FLT3 MUTATED           0
  FLT3 WILD-TYPE         1
D651V3, multiclass
            clus
vv           FLT3 MUTATED FLT3 WILD-TYPE
  STAGE I               5             59
  STAGE IA              1              0
  STAGE II              1             24
  STAGE IIA             7            102
  STAGE IIB             1              7
  STAGE IIC             1              0
  STAGE III             1             18
  STAGE IIIA            2              8
  STAGE IIIB            1             40
  STAGE IIIC            1             30
  STAGE IV              2             33
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  62 235  37
D651V4, multiclass
    clus
vv   FLT3 MUTATED FLT3 WILD-TYPE
  T1            0              9
  T2            6             62
  T3           13            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
  FLT3 MUTATED    16   6   2
  FLT3 WILD-TYPE 204  74  64
D651V5, multiclass
    clus
vv   FLT3 MUTATED FLT3 WILD-TYPE
  N0           16            204
  N1            6             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"
D651V6, binary
                cls
clus               0   1
  FLT3 MUTATED    18   3
  FLT3 WILD-TYPE 265  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLT3 MUTATED     18    3
  FLT3 WILD-TYPE  265   45
   clus
vv  FLT3 MUTATED FLT3 WILD-TYPE
  0           18            265
  1            3             45
[1] 2 2
[1] FALSE
D651V7, 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
D651V8, binary
                cls
clus               0   1
  FLT3 MUTATED    21   3
  FLT3 WILD-TYPE 296  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLT3 MUTATED     21    3
  FLT3 WILD-TYPE  296   45
                               clus
vv                              FLT3 MUTATED FLT3 WILD-TYPE
  COLON ADENOCARCINOMA                    21            296
  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 241   2  21  20
D651V9, multiclass
    clus
vv   FLT3 MUTATED FLT3 WILD-TYPE
  R0           16            241
  R1            0              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"
D651V10, 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
D651V11, 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(652) Variable = CPZ MUTATION ANALYSIS
D652V1, survival
               sevent
clus2             0   1
  CPZ MUTATED    10   4
  CPZ WILD-TYPE 272  69
  CPZ MUTATED CPZ WILD-TYPE 
           14           341 
  CPZ MUTATED CPZ WILD-TYPE 
            4            69 
$`CPZ MUTATED`
TCGA-A6-2676 TCGA-A6-5657 TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-A010 TCGA-AZ-4315 
       42.90        31.63        22.06        20.12        34.98        58.39 
TCGA-AZ-6598 TCGA-AZ-6606 TCGA-CK-5916 TCGA-CM-4743 TCGA-CM-6162 TCGA-D5-6928 
       49.41        11.74        21.14        23.05        12.00        11.64 
TCGA-F4-6856 TCGA-G4-6586 
       19.43        35.80 

$`CPZ WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       30.44        29.19        33.53        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 
       21.76        24.69        24.39        23.87        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        7.04         3.02         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.41       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        26.17        91.79        46.75        52.80 

  CPZ MUTATED CPZ WILD-TYPE 
        11.64          0.00 
  CPZ MUTATED CPZ WILD-TYPE 
        58.39        140.38 
  CPZ MUTATED CPZ WILD-TYPE 
       22.555        19.990 
[1] "11.6 - 58.4 (22.6)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.3"
D652V2, 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       24       102         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        19         10         39         31       34        13
               vv
clus            STAGE IVB
  CPZ MUTATED           0
  CPZ WILD-TYPE         1
D652V3, multiclass
            clus
vv           CPZ MUTATED CPZ WILD-TYPE
  STAGE I              2            62
  STAGE IA             0             1
  STAGE II             1            24
  STAGE IIA            7           102
  STAGE IIB            2             6
  STAGE IIC            0             1
  STAGE III            0            19
  STAGE IIIA           0            10
  STAGE IIIB           2            39
  STAGE IIIC           0            31
  STAGE IV             1            34
  STAGE IVA            0            13
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  CPZ MUTATED     1   1  10   3
  CPZ WILD-TYPE   8  67 238  38
D652V4, multiclass
    clus
vv   CPZ MUTATED CPZ WILD-TYPE
  T1           1             8
  T2           1            67
  T3          10           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
  CPZ MUTATED    12   2   1
  CPZ WILD-TYPE 208  78  65
D652V5, multiclass
    clus
vv   CPZ MUTATED CPZ WILD-TYPE
  N0          12           208
  N1           2            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"
D652V6, binary
               cls
clus              0   1
  CPZ MUTATED    12   1
  CPZ WILD-TYPE 271  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  CPZ MUTATED     12    1
  CPZ WILD-TYPE  271   47
   clus
vv  CPZ MUTATED CPZ WILD-TYPE
  0          12           271
  1           1            47
[1] 2 2
[1] FALSE
D652V7, 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
D652V8, binary
               cls
clus              0   1
  CPZ MUTATED    11   4
  CPZ WILD-TYPE 306  44
[1] "tbl2"
               cls
clus            [,1] [,2]
  CPZ MUTATED     11    4
  CPZ WILD-TYPE  306   44
                               clus
vv                              CPZ MUTATED CPZ WILD-TYPE
  COLON ADENOCARCINOMA                   11           306
  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 246   2  22  20
D652V9, multiclass
    clus
vv   CPZ MUTATED CPZ WILD-TYPE
  R0          11           246
  R1           0             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"
D652V10, 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
D652V11, 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(653) Variable = CD3D MUTATION ANALYSIS
D653V1, survival
                sevent
clus2              0   1
  CD3D MUTATED     2   2
  CD3D WILD-TYPE 280  71
  CD3D MUTATED CD3D WILD-TYPE 
             4            351 
  CD3D MUTATED CD3D WILD-TYPE 
             2             71 
$`CD3D MUTATED`
TCGA-A6-5657 TCGA-AA-A00N TCGA-AZ-6608 TCGA-CA-5254 
       31.63         4.01         1.94         2.24 

$`CD3D WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        3.19         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  CD3D MUTATED CD3D WILD-TYPE 
          1.94           0.00 
  CD3D MUTATED CD3D WILD-TYPE 
         31.63         140.38 
  CD3D MUTATED CD3D WILD-TYPE 
         3.125         20.280 
[1] "1.9 - 31.6 (3.1)"   "0.0 - 140.4 (20.3)"
[1] "hr=" "6.5"
D653V2, 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       25       108         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        19          9         40         31       35        13
                vv
clus             STAGE IVB
  CD3D MUTATED           0
  CD3D WILD-TYPE         1
D653V3, multiclass
            clus
vv           CD3D MUTATED CD3D WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             1            108
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            1              9
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CD3D MUTATED     0   1   2   1
  CD3D WILD-TYPE   9  67 246  40
D653V4, multiclass
    clus
vv   CD3D MUTATED CD3D WILD-TYPE
  T1            0              9
  T2            1             67
  T3            2            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
  CD3D MUTATED     2   2   0
  CD3D WILD-TYPE 218  78  66
D653V5, multiclass
    clus
vv   CD3D MUTATED CD3D WILD-TYPE
  N0            2            218
  N1            2             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"
D653V6, binary
                cls
clus               0   1
  CD3D MUTATED     4   0
  CD3D WILD-TYPE 279  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD3D MUTATED      4    0
  CD3D WILD-TYPE  279   48
   clus
vv  CD3D MUTATED CD3D WILD-TYPE
  0            4            279
  1            0             48
[1] 2 2
[1] FALSE
D653V7, 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
D653V8, binary
                cls
clus               0   1
  CD3D MUTATED     3   1
  CD3D WILD-TYPE 314  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD3D MUTATED      3    1
  CD3D WILD-TYPE  314   47
                               clus
vv                              CD3D MUTATED CD3D WILD-TYPE
  COLON ADENOCARCINOMA                     3            314
  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 255   2  22  20
D653V9, multiclass
    clus
vv   CD3D MUTATED CD3D WILD-TYPE
  R0            2            255
  R1            0              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"
D653V10, 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
D653V11, 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(654) Variable = OR2T33 MUTATION ANALYSIS
D654V1, survival
                  sevent
clus2                0   1
  OR2T33 MUTATED    11   4
  OR2T33 WILD-TYPE 271  69
  OR2T33 MUTATED OR2T33 WILD-TYPE 
              15              340 
  OR2T33 MUTATED OR2T33 WILD-TYPE 
               4               69 
$`OR2T33 MUTATED`
TCGA-A6-6780 TCGA-AA-3492 TCGA-AA-3662 TCGA-AA-3715 TCGA-AA-3977 TCGA-AA-A010 
       20.12         3.02         6.05        19.04        25.02        34.98 
TCGA-AA-A03J TCGA-AZ-4315 TCGA-AZ-6600 TCGA-CA-6717 TCGA-CM-5349 TCGA-CM-6168 
       40.96        58.39        12.10         0.33        30.08        12.99 
TCGA-D5-6532 TCGA-DM-A1DB TCGA-G4-6625 
       18.25        44.32        91.79 

$`OR2T33 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       23.87        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 
        0.92        41.00        39.98        18.05         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 
       19.59        13.51        11.51        20.19         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        46.75        52.80 

  OR2T33 MUTATED OR2T33 WILD-TYPE 
            0.33             0.00 
  OR2T33 MUTATED OR2T33 WILD-TYPE 
           91.79           140.38 
  OR2T33 MUTATED OR2T33 WILD-TYPE 
          20.120           20.235 
[1] "0.3 - 91.8 (20.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D654V2, 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       23       100         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR2T33 MUTATED           0          0          0          0        2
  OR2T33 WILD-TYPE        19         10         41         31       33
                  vv
clus               STAGE IVA STAGE IVB
  OR2T33 MUTATED           0         0
  OR2T33 WILD-TYPE        13         1
D654V3, multiclass
            clus
vv           OR2T33 MUTATED OR2T33 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               9              100
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                2               33
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  OR2T33 MUTATED     0   2  11   3
  OR2T33 WILD-TYPE   9  66 237  38
D654V4, multiclass
    clus
vv   OR2T33 MUTATED OR2T33 WILD-TYPE
  T1              0                9
  T2              2               66
  T3             11              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
  OR2T33 MUTATED    14   1   1
  OR2T33 WILD-TYPE 206  79  65
D654V5, multiclass
    clus
vv   OR2T33 MUTATED OR2T33 WILD-TYPE
  N0             14              206
  N1              1               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"
D654V6, binary
                  cls
clus                 0   1
  OR2T33 MUTATED    12   2
  OR2T33 WILD-TYPE 271  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR2T33 MUTATED     12    2
  OR2T33 WILD-TYPE  271   46
   clus
vv  OR2T33 MUTATED OR2T33 WILD-TYPE
  0             12              271
  1              2               46
[1] 2 2
[1] FALSE
D654V7, 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
D654V8, binary
                  cls
clus                 0   1
  OR2T33 MUTATED    14   2
  OR2T33 WILD-TYPE 303  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR2T33 MUTATED     14    2
  OR2T33 WILD-TYPE  303   46
                               clus
vv                              OR2T33 MUTATED OR2T33 WILD-TYPE
  COLON ADENOCARCINOMA                      14              303
  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 247   2  21  20
D654V9, multiclass
    clus
vv   OR2T33 MUTATED OR2T33 WILD-TYPE
  R0             10              247
  R1              0                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"
D654V10, 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
D654V11, 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(655) Variable = PTPN3 MUTATION ANALYSIS
D655V1, survival
                 sevent
clus2               0   1
  PTPN3 MUTATED    12   2
  PTPN3 WILD-TYPE 270  71
  PTPN3 MUTATED PTPN3 WILD-TYPE 
             14             341 
  PTPN3 MUTATED PTPN3 WILD-TYPE 
              2              71 
$`PTPN3 MUTATED`
TCGA-AA-3542 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-5900 TCGA-AU-3779 
       12.99        18.05         4.01        34.98         0.07        14.50 
TCGA-AY-6197 TCGA-AZ-6598 TCGA-CK-5914 TCGA-CM-6162 TCGA-CM-6166 TCGA-CM-6171 
       21.44        49.41        21.99        12.00        21.99        14.04 
TCGA-D5-6539 TCGA-G4-6315 
       12.49        36.72 

$`PTPN3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 
        5.79        22.42        27.42        10.88         0.20        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        15.75         0.20        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 
      102.44        40.34        15.62        49.08        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         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-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 
       43.27        15.12        17.85         4.80        17.13        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        51.75        45.11        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  PTPN3 MUTATED PTPN3 WILD-TYPE 
           0.07            0.00 
  PTPN3 MUTATED PTPN3 WILD-TYPE 
          49.41          140.38 
  PTPN3 MUTATED PTPN3 WILD-TYPE 
         16.275          20.280 
[1] "0.1 - 49.4 (16.3)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.1"
D655V2, 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       24       106         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PTPN3 MUTATED           0          1          3          1        1         0
  PTPN3 WILD-TYPE        19          9         38         30       34        13
                 vv
clus              STAGE IVB
  PTPN3 MUTATED           0
  PTPN3 WILD-TYPE         1
D655V3, multiclass
            clus
vv           PTPN3 MUTATED PTPN3 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              3             106
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             3              38
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PTPN3 MUTATED     0   3   9   3
  PTPN3 WILD-TYPE   9  65 239  38
D655V4, multiclass
    clus
vv   PTPN3 MUTATED PTPN3 WILD-TYPE
  T1             0               9
  T2             3              65
  T3             9             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
  PTPN3 MUTATED    10   4   1
  PTPN3 WILD-TYPE 210  76  65
D655V5, multiclass
    clus
vv   PTPN3 MUTATED PTPN3 WILD-TYPE
  N0            10             210
  N1             4              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"
D655V6, binary
                 cls
clus                0   1
  PTPN3 MUTATED    10   1
  PTPN3 WILD-TYPE 273  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPN3 MUTATED     10    1
  PTPN3 WILD-TYPE  273   47
   clus
vv  PTPN3 MUTATED PTPN3 WILD-TYPE
  0            10             273
  1             1              47
[1] 2 2
[1] FALSE
D655V7, 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
D655V8, binary
                 cls
clus                0   1
  PTPN3 MUTATED    11   4
  PTPN3 WILD-TYPE 306  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPN3 MUTATED     11    4
  PTPN3 WILD-TYPE  306   44
                               clus
vv                              PTPN3 MUTATED PTPN3 WILD-TYPE
  COLON ADENOCARCINOMA                     11             306
  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 244   2  22  20
D655V9, multiclass
    clus
vv   PTPN3 MUTATED PTPN3 WILD-TYPE
  R0            13             244
  R1             0               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"
D655V10, 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
D655V11, 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(656) Variable = ACVR2A MUTATION ANALYSIS
D656V1, survival
                  sevent
clus2                0   1
  ACVR2A MUTATED    12   4
  ACVR2A WILD-TYPE 270  69
  ACVR2A MUTATED ACVR2A WILD-TYPE 
              16              339 
  ACVR2A MUTATED ACVR2A WILD-TYPE 
               4               69 
$`ACVR2A MUTATED`
TCGA-A6-2672 TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3710 TCGA-AA-A010 
       46.65        22.06         3.02        63.98        26.99        34.98 
TCGA-AA-A01V TCGA-AA-A02F TCGA-AD-6901 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-CA-6717 
       35.01        39.98        22.42        61.41        49.41         0.33 
TCGA-CA-6718 TCGA-CK-6751 TCGA-CM-6677 TCGA-DM-A1DA 
        0.10       124.27        11.08         7.50 

$`ACVR2A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       19.66        20.28         7.04         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
       35.01         1.02        33.04        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       51.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         0.72         5.79        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       83.80        22.36        62.79         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07         0.26         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32        12.59       140.38        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  ACVR2A MUTATED ACVR2A WILD-TYPE 
             0.1              0.0 
  ACVR2A MUTATED ACVR2A WILD-TYPE 
          124.27           140.38 
  ACVR2A MUTATED ACVR2A WILD-TYPE 
          30.985           19.990 
[1] "0.1 - 124.3 (31.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.1"
D656V2, 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       22       103         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ACVR2A MUTATED           0          0          1          1        1
  ACVR2A WILD-TYPE        19         10         40         30       34
                  vv
clus               STAGE IVA STAGE IVB
  ACVR2A MUTATED           0         0
  ACVR2A WILD-TYPE        13         1
D656V3, multiclass
            clus
vv           ACVR2A MUTATED ACVR2A WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                3               22
  STAGE IIA               6              103
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              1               30
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ACVR2A MUTATED     1   2  13   1
  ACVR2A WILD-TYPE   8  66 235  40
D656V4, multiclass
    clus
vv   ACVR2A MUTATED ACVR2A WILD-TYPE
  T1              1                8
  T2              2               66
  T3             13              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
  ACVR2A MUTATED    14   2   1
  ACVR2A WILD-TYPE 206  78  65
D656V5, multiclass
    clus
vv   ACVR2A MUTATED ACVR2A WILD-TYPE
  N0             14              206
  N1              2               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"
D656V6, binary
                  cls
clus                 0   1
  ACVR2A MUTATED    13   1
  ACVR2A WILD-TYPE 270  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACVR2A MUTATED     13    1
  ACVR2A WILD-TYPE  270   47
   clus
vv  ACVR2A MUTATED ACVR2A WILD-TYPE
  0             13              270
  1              1               47
[1] 2 2
[1] FALSE
D656V7, 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
D656V8, binary
                  cls
clus                 0   1
  ACVR2A MUTATED    15   2
  ACVR2A WILD-TYPE 302  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACVR2A MUTATED     15    2
  ACVR2A WILD-TYPE  302   46
                               clus
vv                              ACVR2A MUTATED ACVR2A WILD-TYPE
  COLON ADENOCARCINOMA                      15              302
  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 248   2  21  18
D656V9, multiclass
    clus
vv   ACVR2A MUTATED ACVR2A WILD-TYPE
  R0              9              248
  R1              0                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"
D656V10, 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
D656V11, 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(657) Variable = MAP7D1 MUTATION ANALYSIS
D657V1, survival
                  sevent
clus2                0   1
  MAP7D1 MUTATED    12   2
  MAP7D1 WILD-TYPE 270  71
  MAP7D1 MUTATED MAP7D1 WILD-TYPE 
              14              341 
  MAP7D1 MUTATED MAP7D1 WILD-TYPE 
               2               71 
$`MAP7D1 MUTATED`
TCGA-A6-6781 TCGA-AA-A00N TCGA-AD-5900 TCGA-AU-6004 TCGA-CA-6719 TCGA-CK-5913 
       19.66         4.01         0.07        27.09         1.35        51.32 
TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-6162 TCGA-D5-6930 TCGA-DM-A1D8 TCGA-G4-6309 
       30.08        15.02        12.00         1.51        12.59        51.75 
TCGA-G4-6586 TCGA-G4-6628 
       35.80        52.80 

$`MAP7D1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.20        14.50        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.33         0.10        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        21.99        21.14         2.93         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        16.01         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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        26.17        91.79        46.75 

  MAP7D1 MUTATED MAP7D1 WILD-TYPE 
            0.07             0.00 
  MAP7D1 MUTATED MAP7D1 WILD-TYPE 
           52.80           140.38 
  MAP7D1 MUTATED MAP7D1 WILD-TYPE 
           17.34            20.28 
[1] "0.1 - 52.8 (17.3)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.4"
D657V2, 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       25       103         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAP7D1 MUTATED           0          0          2          1        0
  MAP7D1 WILD-TYPE        19         10         39         30       35
                  vv
clus               STAGE IVA STAGE IVB
  MAP7D1 MUTATED           0         0
  MAP7D1 WILD-TYPE        13         1
D657V3, multiclass
            clus
vv           MAP7D1 MUTATED MAP7D1 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               6              103
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MAP7D1 MUTATED     0   3   9   3
  MAP7D1 WILD-TYPE   9  65 239  38
D657V4, multiclass
    clus
vv   MAP7D1 MUTATED MAP7D1 WILD-TYPE
  T1              0                9
  T2              3               65
  T3              9              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
  MAP7D1 MUTATED    11   4   0
  MAP7D1 WILD-TYPE 209  76  66
D657V5, multiclass
    clus
vv   MAP7D1 MUTATED MAP7D1 WILD-TYPE
  N0             11              209
  N1              4               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"
D657V6, binary
                  cls
clus                 0   1
  MAP7D1 MUTATED    10   0
  MAP7D1 WILD-TYPE 273  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP7D1 MUTATED     10    0
  MAP7D1 WILD-TYPE  273   48
   clus
vv  MAP7D1 MUTATED MAP7D1 WILD-TYPE
  0             10              273
  1              0               48
[1] 2 2
[1] FALSE
D657V7, 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
D657V8, binary
                  cls
clus                 0   1
  MAP7D1 MUTATED    10   5
  MAP7D1 WILD-TYPE 307  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP7D1 MUTATED     10    5
  MAP7D1 WILD-TYPE  307   43
                               clus
vv                              MAP7D1 MUTATED MAP7D1 WILD-TYPE
  COLON ADENOCARCINOMA                      10              307
  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 246   2  22  18
D657V9, multiclass
    clus
vv   MAP7D1 MUTATED MAP7D1 WILD-TYPE
  R0             11              246
  R1              0                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"
D657V10, 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
D657V11, 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(658) Variable = KRT19 MUTATION ANALYSIS
D658V1, survival
                 sevent
clus2               0   1
  KRT19 MUTATED     3   1
  KRT19 WILD-TYPE 279  72
  KRT19 MUTATED KRT19 WILD-TYPE 
              4             351 
  KRT19 MUTATED KRT19 WILD-TYPE 
              1              72 
$`KRT19 MUTATED`
TCGA-AA-3672 TCGA-AA-A010 TCGA-AZ-6598 TCGA-CM-4743 
        0.92        34.98        49.41        23.05 

$`KRT19 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
        6.05         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13        83.80        22.36        62.79        61.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  KRT19 MUTATED KRT19 WILD-TYPE 
           0.92            0.00 
  KRT19 MUTATED KRT19 WILD-TYPE 
          49.41          140.38 
  KRT19 MUTATED KRT19 WILD-TYPE 
         29.015          20.120 
[1] "0.9 - 49.4 (29.0)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.2"
D658V2, 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       24       108         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        18         10         41         31       35        13
                 vv
clus              STAGE IVB
  KRT19 MUTATED           0
  KRT19 WILD-TYPE         1
D658V3, multiclass
            clus
vv           KRT19 MUTATED KRT19 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              1             108
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KRT19 MUTATED     0   0   3   1
  KRT19 WILD-TYPE   9  68 245  40
D658V4, multiclass
    clus
vv   KRT19 MUTATED KRT19 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             3             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
  KRT19 MUTATED     3   1   0
  KRT19 WILD-TYPE 217  79  66
D658V5, multiclass
    clus
vv   KRT19 MUTATED KRT19 WILD-TYPE
  N0             3             217
  N1             1              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"
D658V6, binary
                 cls
clus                0   1
  KRT19 MUTATED     3   0
  KRT19 WILD-TYPE 280  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT19 MUTATED      3    0
  KRT19 WILD-TYPE  280   48
   clus
vv  KRT19 MUTATED KRT19 WILD-TYPE
  0             3             280
  1             0              48
[1] 2 2
[1] FALSE
D658V7, 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
D658V8, binary
                 cls
clus                0   1
  KRT19 MUTATED     4   0
  KRT19 WILD-TYPE 313  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT19 MUTATED      4    0
  KRT19 WILD-TYPE  313   48
                               clus
vv                              KRT19 MUTATED KRT19 WILD-TYPE
  COLON ADENOCARCINOMA                      4             313
  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 254   2  22  21
D658V9, multiclass
    clus
vv   KRT19 MUTATED KRT19 WILD-TYPE
  R0             3             254
  R1             0               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"
D658V10, 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
D658V11, multiclass
[1] "Remove cluster labels:" "KRT19 MUTATED"         
clus
  KRT19 MUTATED KRT19 WILD-TYPE 
              2             204 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-4105 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-A6-5656      TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5660 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-A6-5661      TCGA-A6-5662      TCGA-A6-5664      TCGA-A6-5665 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-A6-5666      TCGA-A6-6137      TCGA-A6-6138      TCGA-A6-6141 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-A6-6142      TCGA-A6-6648      TCGA-A6-6649      TCGA-A6-6651 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-A6-6652      TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-A6-6781      TCGA-A6-6782      TCGA-AD-5900      TCGA-AD-6548 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-AD-6888      TCGA-AD-6889      TCGA-AD-6890      TCGA-AD-6895 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-AD-6899      TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6964 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-AD-6965      TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-AY-4071      TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-AY-6386      TCGA-AZ-4315      TCGA-AZ-4323      TCGA-AZ-4616 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-AZ-4681      TCGA-AZ-4682      TCGA-AZ-5403      TCGA-AZ-5407 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-AZ-6599      TCGA-AZ-6600      TCGA-AZ-6601      TCGA-AZ-6603 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-AZ-6605      TCGA-AZ-6606      TCGA-AZ-6607      TCGA-AZ-6608 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-CA-5254      TCGA-CA-5255      TCGA-CA-5796      TCGA-CA-5797 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-CA-6715      TCGA-CA-6716      TCGA-CA-6717      TCGA-CA-6718 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-CA-6719      TCGA-CK-4947      TCGA-CK-4948      TCGA-CK-4950 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-CK-4952      TCGA-CK-5912      TCGA-CK-5913      TCGA-CK-5914 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-CK-5915      TCGA-CK-5916      TCGA-CK-6746      TCGA-CK-6747 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-CK-6748      TCGA-CK-6751      TCGA-CM-4744      TCGA-CM-4746 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-CM-4747      TCGA-CM-4752      TCGA-CM-5341      TCGA-CM-5344 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-CM-5348      TCGA-CM-5349      TCGA-CM-5860      TCGA-CM-5861 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-CM-5862      TCGA-CM-5863      TCGA-CM-5864      TCGA-CM-5868 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-CM-6161      TCGA-CM-6162      TCGA-CM-6163      TCGA-CM-6164 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-CM-6165      TCGA-CM-6166      TCGA-CM-6167      TCGA-CM-6168 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-CM-6169      TCGA-CM-6170      TCGA-CM-6171      TCGA-CM-6172 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-CM-6674      TCGA-CM-6675      TCGA-CM-6676      TCGA-CM-6677 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-CM-6678      TCGA-CM-6679      TCGA-CM-6680      TCGA-D5-5537 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-D5-5538      TCGA-D5-5539      TCGA-D5-5540      TCGA-D5-5541 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-D5-6529      TCGA-D5-6532      TCGA-D5-6533      TCGA-D5-6534 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-D5-6535      TCGA-D5-6536      TCGA-D5-6537      TCGA-D5-6538 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-D5-6539      TCGA-D5-6540      TCGA-D5-6541      TCGA-D5-6898 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923      TCGA-D5-6924 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-D5-6926      TCGA-D5-6927      TCGA-D5-6928      TCGA-D5-6929 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-D5-6930      TCGA-D5-6931      TCGA-D5-6932      TCGA-D5-7000 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-DM-A0X9      TCGA-DM-A0XD      TCGA-DM-A0XF      TCGA-DM-A1D0 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-DM-A1D4      TCGA-DM-A1D6      TCGA-DM-A1D7      TCGA-DM-A1D8 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-DM-A1D9      TCGA-DM-A1DA      TCGA-DM-A1DB      TCGA-DM-A1HA 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-DM-A1HB      TCGA-DM-A282      TCGA-DM-A285      TCGA-DM-A28C 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-DM-A28E      TCGA-DM-A28F      TCGA-DM-A28G      TCGA-DM-A28H 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-DM-A28K      TCGA-F4-6459      TCGA-F4-6460      TCGA-F4-6569 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704      TCGA-F4-6805 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808      TCGA-F4-6809 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856      TCGA-G4-6293 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304      TCGA-G4-6306 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310      TCGA-G4-6315 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323      TCGA-G4-6586 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-G4-6588      TCGA-G4-6625      TCGA-G4-6626      TCGA-G4-6628 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 

Clustering(659) Variable = HIST1H1E MUTATION ANALYSIS
D659V1, survival
                    sevent
clus2                  0   1
  HIST1H1E MUTATED     5   1
  HIST1H1E WILD-TYPE 277  72
  HIST1H1E MUTATED HIST1H1E WILD-TYPE 
                 6                349 
  HIST1H1E MUTATED HIST1H1E WILD-TYPE 
                 1                 72 
$`HIST1H1E MUTATED`
TCGA-A6-5665 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CM-4746 TCGA-CM-5861 TCGA-CM-6169 
       22.06        49.41         0.33        37.02        15.02        13.02 

$`HIST1H1E WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 
        2.93         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        16.01 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  HIST1H1E MUTATED HIST1H1E WILD-TYPE 
              0.33               0.00 
  HIST1H1E MUTATED HIST1H1E WILD-TYPE 
             49.41             140.38 
  HIST1H1E MUTATED HIST1H1E WILD-TYPE 
             18.54              20.19 
[1] "0.3 - 49.4 (18.5)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D659V2, 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       24       105         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HIST1H1E MUTATED           0          0          0          0        0
  HIST1H1E WILD-TYPE        19         10         41         31       35
                    vv
clus                 STAGE IVA STAGE IVB
  HIST1H1E MUTATED           0         0
  HIST1H1E WILD-TYPE        13         1
D659V3, multiclass
            clus
vv           HIST1H1E MUTATED HIST1H1E WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  1                 24
  STAGE IIA                 4                105
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                0                 10
  STAGE IIIB                0                 41
  STAGE IIIC                0                 31
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  HIST1H1E MUTATED     0   1   5   0
  HIST1H1E WILD-TYPE   9  67 243  41
D659V4, multiclass
    clus
vv   HIST1H1E MUTATED HIST1H1E WILD-TYPE
  T1                0                  9
  T2                1                 67
  T3                5                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
  HIST1H1E MUTATED     6   0   0
  HIST1H1E WILD-TYPE 214  80  66
D659V5, multiclass
    clus
vv   HIST1H1E MUTATED HIST1H1E WILD-TYPE
  N0                6                214
  N1                0                 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"
D659V6, binary
                    cls
clus                   0   1
  HIST1H1E MUTATED     5   0
  HIST1H1E WILD-TYPE 278  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1E MUTATED      5    0
  HIST1H1E WILD-TYPE  278   48
   clus
vv  HIST1H1E MUTATED HIST1H1E WILD-TYPE
  0                5                278
  1                0                 48
[1] 2 2
[1] FALSE
D659V7, 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
D659V8, binary
                    cls
clus                   0   1
  HIST1H1E MUTATED     5   1
  HIST1H1E WILD-TYPE 312  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1E MUTATED      5    1
  HIST1H1E WILD-TYPE  312   47
                               clus
vv                              HIST1H1E MUTATED HIST1H1E WILD-TYPE
  COLON ADENOCARCINOMA                         5                312
  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 253   2  22  20
D659V9, multiclass
    clus
vv   HIST1H1E MUTATED HIST1H1E WILD-TYPE
  R0                4                253
  R1                0                  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"
D659V10, 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
D659V11, 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(660) Variable = CETN3 MUTATION ANALYSIS
D660V1, survival
                 sevent
clus2               0   1
  CETN3 MUTATED     6   0
  CETN3 WILD-TYPE 276  73
  CETN3 MUTATED CETN3 WILD-TYPE 
              6             349 
  CETN3 MUTATED CETN3 WILD-TYPE 
              0              73 
$`CETN3 MUTATED`
TCGA-A6-6781 TCGA-CA-6717 TCGA-CM-6162 TCGA-CM-6171 TCGA-G4-6586 TCGA-G4-6628 
       19.66         0.33        12.00        14.04        35.80        52.80 

$`CETN3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        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-6674 
       14.99        12.99        13.02        15.02        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        26.17        91.79 
TCGA-G4-6626 
       46.75 

  CETN3 MUTATED CETN3 WILD-TYPE 
           0.33            0.00 
  CETN3 MUTATED CETN3 WILD-TYPE 
          52.80          140.38 
  CETN3 MUTATED CETN3 WILD-TYPE 
          16.85           20.28 
[1] "0.3 - 52.8 (16.9)"  "0.0 - 140.4 (20.3)"
[1] "hr="     "9100000"
D660V2, 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       25       107         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        19         10         40         30       35        13
                 vv
clus              STAGE IVB
  CETN3 MUTATED           0
  CETN3 WILD-TYPE         1
D660V3, multiclass
            clus
vv           CETN3 MUTATED CETN3 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              2             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CETN3 MUTATED     0   2   3   1
  CETN3 WILD-TYPE   9  66 245  40
D660V4, multiclass
    clus
vv   CETN3 MUTATED CETN3 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             3             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
  CETN3 MUTATED     4   2   0
  CETN3 WILD-TYPE 216  78  66
D660V5, multiclass
    clus
vv   CETN3 MUTATED CETN3 WILD-TYPE
  N0             4             216
  N1             2              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"
D660V6, binary
                 cls
clus                0   1
  CETN3 MUTATED     5   0
  CETN3 WILD-TYPE 278  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CETN3 MUTATED      5    0
  CETN3 WILD-TYPE  278   48
   clus
vv  CETN3 MUTATED CETN3 WILD-TYPE
  0             5             278
  1             0              48
[1] 2 2
[1] FALSE
D660V7, 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
D660V8, binary
                 cls
clus                0   1
  CETN3 MUTATED     3   3
  CETN3 WILD-TYPE 314  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CETN3 MUTATED      3    3
  CETN3 WILD-TYPE  314   45
                               clus
vv                              CETN3 MUTATED CETN3 WILD-TYPE
  COLON ADENOCARCINOMA                      3             314
  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 252   2  22  20
D660V9, multiclass
    clus
vv   CETN3 MUTATED CETN3 WILD-TYPE
  R0             5             252
  R1             0               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"
D660V10, 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
D660V11, 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(661) Variable = FGFR1 MUTATION ANALYSIS
D661V1, survival
                 sevent
clus2               0   1
  FGFR1 MUTATED    13   2
  FGFR1 WILD-TYPE 269  71
  FGFR1 MUTATED FGFR1 WILD-TYPE 
             15             340 
  FGFR1 MUTATED FGFR1 WILD-TYPE 
              2              71 
$`FGFR1 MUTATED`
TCGA-AA-3510 TCGA-AA-3715 TCGA-AZ-4681 TCGA-CA-6717 TCGA-CK-4950 TCGA-CM-4744 
       63.98        19.04        83.80         0.33        40.34        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        29.59 
TCGA-G4-6303 TCGA-G4-6309 TCGA-G4-6315 
       65.85        51.75        36.72 

$`FGFR1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         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        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 
        0.26         0.10         1.35        17.56       102.44        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       11.01        10.06        45.40        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
      117.07         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
        1.55        16.31        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 
       35.41        19.43       107.67        74.56        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       55.04        45.11        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  FGFR1 MUTATED FGFR1 WILD-TYPE 
           0.33            0.00 
  FGFR1 MUTATED FGFR1 WILD-TYPE 
         135.65          140.38 
  FGFR1 MUTATED FGFR1 WILD-TYPE 
         36.720          20.055 
[1] "0.3 - 135.7 (36.7)" "0.0 - 140.4 (20.1)"
[1] "hr=" "2.8"
D661V2, 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       23       105         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FGFR1 MUTATED           1          1          3          1        2         0
  FGFR1 WILD-TYPE        18          9         38         30       33        13
                 vv
clus              STAGE IVB
  FGFR1 MUTATED           0
  FGFR1 WILD-TYPE         1
D661V3, multiclass
            clus
vv           FGFR1 MUTATED FGFR1 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              4             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             1               9
  STAGE IIIB             3              38
  STAGE IIIC             1              30
  STAGE IV               2              33
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FGFR1 MUTATED     0   3  13   1
  FGFR1 WILD-TYPE   9  65 235  40
D661V4, multiclass
    clus
vv   FGFR1 MUTATED FGFR1 WILD-TYPE
  T1             0               9
  T2             3              65
  T3            13             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
  FGFR1 MUTATED     9   5   3
  FGFR1 WILD-TYPE 211  75  63
D661V5, multiclass
    clus
vv   FGFR1 MUTATED FGFR1 WILD-TYPE
  N0             9             211
  N1             5              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"
D661V6, binary
                 cls
clus                0   1
  FGFR1 MUTATED    15   2
  FGFR1 WILD-TYPE 268  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGFR1 MUTATED     15    2
  FGFR1 WILD-TYPE  268   46
   clus
vv  FGFR1 MUTATED FGFR1 WILD-TYPE
  0            15             268
  1             2              46
[1] 2 2
[1] FALSE
D661V7, 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
D661V8, binary
                 cls
clus                0   1
  FGFR1 MUTATED    15   2
  FGFR1 WILD-TYPE 302  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGFR1 MUTATED     15    2
  FGFR1 WILD-TYPE  302   46
                               clus
vv                              FGFR1 MUTATED FGFR1 WILD-TYPE
  COLON ADENOCARCINOMA                     15             302
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  FGFR1 MUTATED    13   1   0   1
  FGFR1 WILD-TYPE 244   1  22  20
D661V9, multiclass
    clus
vv   FGFR1 MUTATED FGFR1 WILD-TYPE
  R0            13             244
  R1             1               1
  R2             0              22
  RX             1              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D661V10, 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
D661V11, 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(662) Variable = PCSK5 MUTATION ANALYSIS
D662V1, survival
                 sevent
clus2               0   1
  PCSK5 MUTATED    15   2
  PCSK5 WILD-TYPE 267  71
  PCSK5 MUTATED PCSK5 WILD-TYPE 
             17             338 
  PCSK5 MUTATED PCSK5 WILD-TYPE 
              2              71 
$`PCSK5 MUTATED`
TCGA-A6-6142 TCGA-A6-6653 TCGA-AA-3518 TCGA-AA-3866 TCGA-AA-3947 TCGA-AA-A010 
       25.08        24.39         1.02        17.03        33.01        34.98 
TCGA-AA-A03F TCGA-AD-6964 TCGA-AY-5543 TCGA-CA-6717 TCGA-CM-6163 TCGA-D5-6532 
       18.05        10.88        15.75         0.33        14.04        18.25 
TCGA-D5-6928 TCGA-D5-6930 TCGA-DM-A1HB TCGA-DM-A282 TCGA-G4-6588 
       11.64         1.51       135.65       139.17        26.17 

$`PCSK5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 
       63.98         6.97         1.02        13.02        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        53.00        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
        0.92        41.00        39.98        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       12.00        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 
       12.26        19.59        13.51        11.51        20.19         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      131.51         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  PCSK5 MUTATED PCSK5 WILD-TYPE 
           0.33            0.00 
  PCSK5 MUTATED PCSK5 WILD-TYPE 
         139.17          140.38 
  PCSK5 MUTATED PCSK5 WILD-TYPE 
          18.05           20.63 
[1] "0.3 - 139.2 (18.1)" "0.0 - 140.4 (20.6)"
[1] "hr=" "1.9"
D662V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PCSK5 MUTATED         3        0        0         7         2         0
  PCSK5 WILD-TYPE      61        1       25       102         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PCSK5 MUTATED           1          0          1          0        0         2
  PCSK5 WILD-TYPE        18         10         40         31       35        11
                 vv
clus              STAGE IVB
  PCSK5 MUTATED           0
  PCSK5 WILD-TYPE         1
D662V3, multiclass
            clus
vv           PCSK5 MUTATED PCSK5 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              7             102
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              2              11
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  11   3
  PCSK5 WILD-TYPE   8  66 237  38
D662V4, multiclass
    clus
vv   PCSK5 MUTATED PCSK5 WILD-TYPE
  T1             1               8
  T2             2              66
  T3            11             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
  PCSK5 MUTATED    12   3   2
  PCSK5 WILD-TYPE 208  77  64
D662V5, multiclass
    clus
vv   PCSK5 MUTATED PCSK5 WILD-TYPE
  N0            12             208
  N1             3              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"
D662V6, binary
                 cls
clus                0   1
  PCSK5 MUTATED    14   2
  PCSK5 WILD-TYPE 269  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCSK5 MUTATED     14    2
  PCSK5 WILD-TYPE  269   46
   clus
vv  PCSK5 MUTATED PCSK5 WILD-TYPE
  0            14             269
  1             2              46
[1] 2 2
[1] FALSE
D662V7, binary
                 cls
clus                0   1
  PCSK5 MUTATED     9   8
  PCSK5 WILD-TYPE 161 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCSK5 MUTATED      9    8
  PCSK5 WILD-TYPE  161  189
        clus
vv       PCSK5 MUTATED PCSK5 WILD-TYPE
  FEMALE             9             161
  MALE               8             189
[1] 2 2
[1] FALSE
D662V8, binary
                 cls
clus                0   1
  PCSK5 MUTATED    12   5
  PCSK5 WILD-TYPE 305  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCSK5 MUTATED     12    5
  PCSK5 WILD-TYPE  305   43
                               clus
vv                              PCSK5 MUTATED PCSK5 WILD-TYPE
  COLON ADENOCARCINOMA                     12             305
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PCSK5 MUTATED    11   0   0   1
  PCSK5 WILD-TYPE 246   2  22  20
D662V9, multiclass
    clus
vv   PCSK5 MUTATED PCSK5 WILD-TYPE
  R0            11             246
  R1             0               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"
D662V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PCSK5 MUTATED                                  0     1
  PCSK5 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PCSK5 MUTATED                           1    10
  PCSK5 WILD-TYPE                        18   166
D662V11, multiclass
                                  clus
vv                                 PCSK5 MUTATED PCSK5 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(663) Variable = GRB14 MUTATION ANALYSIS
D663V1, survival
                 sevent
clus2               0   1
  GRB14 MUTATED     5   3
  GRB14 WILD-TYPE 277  70
  GRB14 MUTATED GRB14 WILD-TYPE 
              8             347 
  GRB14 MUTATED GRB14 WILD-TYPE 
              3              70 
$`GRB14 MUTATED`
TCGA-AA-3516 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3949 TCGA-AZ-6599 TCGA-CM-6163 
       13.02        26.99        19.04        26.01         6.77        14.04 
TCGA-D5-6536 TCGA-DM-A1D6 
       17.85        49.91 

$`GRB14 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        1.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       36.00         5.03        85.05        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41        49.41        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  GRB14 MUTATED GRB14 WILD-TYPE 
           6.77            0.00 
  GRB14 MUTATED GRB14 WILD-TYPE 
          49.91          140.38 
  GRB14 MUTATED GRB14 WILD-TYPE 
         18.445          20.280 
[1] "6.8 - 49.9 (18.4)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "2"  
D663V2, 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       25       105         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        18         10         40         31       34        13
                 vv
clus              STAGE IVB
  GRB14 MUTATED           0
  GRB14 WILD-TYPE         1
D663V3, multiclass
            clus
vv           GRB14 MUTATED GRB14 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              4             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GRB14 MUTATED     1   1   7   0
  GRB14 WILD-TYPE   8  67 241  41
D663V4, multiclass
    clus
vv   GRB14 MUTATED GRB14 WILD-TYPE
  T1             1               8
  T2             1              67
  T3             7             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
  GRB14 MUTATED     7   1   1
  GRB14 WILD-TYPE 213  79  65
D663V5, multiclass
    clus
vv   GRB14 MUTATED GRB14 WILD-TYPE
  N0             7             213
  N1             1              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"
D663V6, binary
                 cls
clus                0   1
  GRB14 MUTATED     7   1
  GRB14 WILD-TYPE 276  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GRB14 MUTATED      7    1
  GRB14 WILD-TYPE  276   47
   clus
vv  GRB14 MUTATED GRB14 WILD-TYPE
  0             7             276
  1             1              47
[1] 2 2
[1] FALSE
D663V7, 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
D663V8, binary
                 cls
clus                0   1
  GRB14 MUTATED     6   3
  GRB14 WILD-TYPE 311  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GRB14 MUTATED      6    3
  GRB14 WILD-TYPE  311   45
                               clus
vv                              GRB14 MUTATED GRB14 WILD-TYPE
  COLON ADENOCARCINOMA                      6             311
  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 252   2  21  21
D663V9, multiclass
    clus
vv   GRB14 MUTATED GRB14 WILD-TYPE
  R0             5             252
  R1             0               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"
D663V10, 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
D663V11, 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(664) Variable = RANBP1 MUTATION ANALYSIS
D664V1, survival
                  sevent
clus2                0   1
  RANBP1 MUTATED     6   0
  RANBP1 WILD-TYPE 276  73
  RANBP1 MUTATED RANBP1 WILD-TYPE 
               6              349 
  RANBP1 MUTATED RANBP1 WILD-TYPE 
               0               73 
$`RANBP1 MUTATED`
TCGA-A6-5665 TCGA-AZ-4315 TCGA-CM-5860 TCGA-F4-6460 TCGA-F4-6856 TCGA-G4-6588 
       22.06        58.39        16.01        13.38        19.43        26.17 

$`RANBP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 
       60.79       117.07        98.24         8.61        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        35.41       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 
       52.80 

  RANBP1 MUTATED RANBP1 WILD-TYPE 
           13.38             0.00 
  RANBP1 MUTATED RANBP1 WILD-TYPE 
           58.39           140.38 
  RANBP1 MUTATED RANBP1 WILD-TYPE 
          20.745           20.190 
[1] "13.4 - 58.4 (20.7)" "0.0 - 140.4 (20.2)"
[1] "hr="     "9200000"
D664V2, 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       25       105         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RANBP1 MUTATED           0          0          1          0        0
  RANBP1 WILD-TYPE        19         10         40         31       35
                  vv
clus               STAGE IVA STAGE IVB
  RANBP1 MUTATED           0         0
  RANBP1 WILD-TYPE        13         1
D664V3, multiclass
            clus
vv           RANBP1 MUTATED RANBP1 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               4              105
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  RANBP1 MUTATED     0   1   5   0
  RANBP1 WILD-TYPE   9  67 243  41
D664V4, multiclass
    clus
vv   RANBP1 MUTATED RANBP1 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              5              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
  RANBP1 MUTATED     5   1   0
  RANBP1 WILD-TYPE 215  79  66
D664V5, multiclass
    clus
vv   RANBP1 MUTATED RANBP1 WILD-TYPE
  N0              5              215
  N1              1               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"
D664V6, binary
                  cls
clus                 0   1
  RANBP1 MUTATED     6   0
  RANBP1 WILD-TYPE 277  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RANBP1 MUTATED      6    0
  RANBP1 WILD-TYPE  277   48
   clus
vv  RANBP1 MUTATED RANBP1 WILD-TYPE
  0              6              277
  1              0               48
[1] 2 2
[1] FALSE
D664V7, 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
D664V8, binary
                  cls
clus                 0   1
  RANBP1 MUTATED     5   1
  RANBP1 WILD-TYPE 312  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RANBP1 MUTATED      5    1
  RANBP1 WILD-TYPE  312   47
                               clus
vv                              RANBP1 MUTATED RANBP1 WILD-TYPE
  COLON ADENOCARCINOMA                       5              312
  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 251   2  22  21
D664V9, multiclass
    clus
vv   RANBP1 MUTATED RANBP1 WILD-TYPE
  R0              6              251
  R1              0                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"
D664V10, 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
D664V11, 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(665) Variable = C19ORF66 MUTATION ANALYSIS
D665V1, survival
                    sevent
clus2                  0   1
  C19ORF66 MUTATED     4   0
  C19ORF66 WILD-TYPE 278  73
  C19ORF66 MUTATED C19ORF66 WILD-TYPE 
                 4                351 
  C19ORF66 MUTATED C19ORF66 WILD-TYPE 
                 0                 73 
$`C19ORF66 MUTATED`
TCGA-AA-3663 TCGA-AA-3713 TCGA-AA-3949 TCGA-D5-6540 
        6.97        19.04        26.01        16.14 

$`C19ORF66 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  C19ORF66 MUTATED C19ORF66 WILD-TYPE 
              6.97               0.00 
  C19ORF66 MUTATED C19ORF66 WILD-TYPE 
             26.01             140.38 
  C19ORF66 MUTATED C19ORF66 WILD-TYPE 
             17.59              20.28 
[1] "7.0 - 26.0 (17.6)"  "0.0 - 140.4 (20.3)"
[1] "hr="     "3300000"
D665V2, 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       24       109         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C19ORF66 MUTATED           0          0          1          0        1
  C19ORF66 WILD-TYPE        19         10         40         31       34
                    vv
clus                 STAGE IVA STAGE IVB
  C19ORF66 MUTATED           0         0
  C19ORF66 WILD-TYPE        13         1
D665V3, multiclass
            clus
vv           C19ORF66 MUTATED C19ORF66 WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  1                 24
  STAGE IIA                 0                109
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                0                 10
  STAGE IIIB                1                 40
  STAGE IIIC                0                 31
  STAGE IV                  1                 34
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C19ORF66 MUTATED     0   1   3   0
  C19ORF66 WILD-TYPE   9  67 245  41
D665V4, multiclass
    clus
vv   C19ORF66 MUTATED C19ORF66 WILD-TYPE
  T1                0                  9
  T2                1                 67
  T3                3                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
  C19ORF66 MUTATED     3   1   0
  C19ORF66 WILD-TYPE 217  79  66
D665V5, multiclass
    clus
vv   C19ORF66 MUTATED C19ORF66 WILD-TYPE
  N0                3                217
  N1                1                 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"
D665V6, binary
                    cls
clus                   0   1
  C19ORF66 MUTATED     3   1
  C19ORF66 WILD-TYPE 280  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF66 MUTATED      3    1
  C19ORF66 WILD-TYPE  280   47
   clus
vv  C19ORF66 MUTATED C19ORF66 WILD-TYPE
  0                3                280
  1                1                 47
[1] 2 2
[1] FALSE
D665V7, 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
D665V8, binary
                    cls
clus                   0   1
  C19ORF66 MUTATED     2   2
  C19ORF66 WILD-TYPE 315  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF66 MUTATED      2    2
  C19ORF66 WILD-TYPE  315   46
                               clus
vv                              C19ORF66 MUTATED C19ORF66 WILD-TYPE
  COLON ADENOCARCINOMA                         2                315
  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 254   2  21  21
D665V9, multiclass
    clus
vv   C19ORF66 MUTATED C19ORF66 WILD-TYPE
  R0                3                254
  R1                0                  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"
D665V10, 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
D665V11, multiclass
[1] "Remove cluster labels:" "C19ORF66 MUTATED"      
clus
  C19ORF66 MUTATED C19ORF66 WILD-TYPE 
                 1                205 
        TCGA-A6-2671         TCGA-A6-2672         TCGA-A6-2674 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-A6-2676         TCGA-A6-2677         TCGA-A6-2678 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-A6-2683         TCGA-A6-3807         TCGA-A6-3808 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-A6-3809         TCGA-A6-3810         TCGA-A6-4105 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-A6-5656         TCGA-A6-5657         TCGA-A6-5659 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-A6-5660         TCGA-A6-5661         TCGA-A6-5662 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-A6-5664         TCGA-A6-5665         TCGA-A6-5666 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-A6-6137         TCGA-A6-6138         TCGA-A6-6141 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-A6-6142         TCGA-A6-6648         TCGA-A6-6649 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-A6-6651         TCGA-A6-6652         TCGA-A6-6653 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-A6-6654         TCGA-A6-6780         TCGA-A6-6781 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-A6-6782         TCGA-AD-5900         TCGA-AD-6548 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-AD-6888         TCGA-AD-6889         TCGA-AD-6890 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-AD-6895         TCGA-AD-6899         TCGA-AD-6901 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-AD-6963         TCGA-AD-6964         TCGA-AD-6965 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-AU-3779         TCGA-AU-6004         TCGA-AY-4070 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-AY-4071         TCGA-AY-5543         TCGA-AY-6196 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-AY-6197         TCGA-AY-6386         TCGA-AZ-4315 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-AZ-4323         TCGA-AZ-4616         TCGA-AZ-4681 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-AZ-4682         TCGA-AZ-5403         TCGA-AZ-5407 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-AZ-6598         TCGA-AZ-6599         TCGA-AZ-6600 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-AZ-6601         TCGA-AZ-6603         TCGA-AZ-6605 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-AZ-6606         TCGA-AZ-6607         TCGA-AZ-6608 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CA-5254         TCGA-CA-5255         TCGA-CA-5796 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CA-5797         TCGA-CA-6715         TCGA-CA-6716 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CA-6717         TCGA-CA-6718         TCGA-CA-6719 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CK-4947         TCGA-CK-4948         TCGA-CK-4950 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CK-4952         TCGA-CK-5912         TCGA-CK-5913 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CK-5914         TCGA-CK-5915         TCGA-CK-5916 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CK-6746         TCGA-CK-6747         TCGA-CK-6748 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CK-6751         TCGA-CM-4743         TCGA-CM-4744 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CM-4746         TCGA-CM-4747         TCGA-CM-4752 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CM-5341         TCGA-CM-5344         TCGA-CM-5348 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CM-5349         TCGA-CM-5860         TCGA-CM-5861 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CM-5862         TCGA-CM-5863         TCGA-CM-5864 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CM-5868         TCGA-CM-6161         TCGA-CM-6162 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CM-6163         TCGA-CM-6164         TCGA-CM-6165 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CM-6166         TCGA-CM-6167         TCGA-CM-6168 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CM-6169         TCGA-CM-6170         TCGA-CM-6171 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CM-6172         TCGA-CM-6674         TCGA-CM-6675 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CM-6676         TCGA-CM-6677         TCGA-CM-6678 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CM-6679         TCGA-CM-6680         TCGA-D5-5537 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-D5-5538         TCGA-D5-5539         TCGA-D5-5540 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-D5-5541         TCGA-D5-6529         TCGA-D5-6532 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-D5-6533         TCGA-D5-6534         TCGA-D5-6535 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-D5-6536         TCGA-D5-6537         TCGA-D5-6538 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-D5-6539         TCGA-D5-6541         TCGA-D5-6898 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-D5-6920         TCGA-D5-6922         TCGA-D5-6923 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-D5-6924         TCGA-D5-6926         TCGA-D5-6927 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-D5-6928         TCGA-D5-6929         TCGA-D5-6930 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-D5-6931         TCGA-D5-6932         TCGA-D5-7000 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-DM-A0X9         TCGA-DM-A0XD         TCGA-DM-A0XF 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-DM-A1D0         TCGA-DM-A1D4         TCGA-DM-A1D6 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-DM-A1D7         TCGA-DM-A1D8         TCGA-DM-A1D9 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-DM-A1DA         TCGA-DM-A1DB         TCGA-DM-A1HA 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-DM-A1HB         TCGA-DM-A282         TCGA-DM-A285 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-DM-A28C         TCGA-DM-A28E         TCGA-DM-A28F 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-DM-A28G         TCGA-DM-A28H         TCGA-DM-A28K 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-F4-6459         TCGA-F4-6460         TCGA-F4-6569 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-F4-6570         TCGA-F4-6703         TCGA-F4-6704 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-F4-6805         TCGA-F4-6806         TCGA-F4-6807 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-F4-6808         TCGA-F4-6809         TCGA-F4-6854 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-F4-6855         TCGA-F4-6856         TCGA-G4-6293 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-G4-6299         TCGA-G4-6303         TCGA-G4-6304 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-G4-6306         TCGA-G4-6307         TCGA-G4-6309 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-G4-6310         TCGA-G4-6315         TCGA-G4-6317 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-G4-6321         TCGA-G4-6323         TCGA-G4-6586 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-G4-6588         TCGA-G4-6625         TCGA-G4-6626 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-G4-6628 
"C19ORF66 WILD-TYPE" 

Clustering(666) Variable = SLC22A3 MUTATION ANALYSIS
D666V1, survival
                   sevent
clus2                 0   1
  SLC22A3 MUTATED    10   2
  SLC22A3 WILD-TYPE 272  71
  SLC22A3 MUTATED SLC22A3 WILD-TYPE 
               12               343 
  SLC22A3 MUTATED SLC22A3 WILD-TYPE 
                2                71 
$`SLC22A3 MUTATED`
TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3877 TCGA-AA-A010 TCGA-AD-6889 TCGA-AU-6004 
       19.66        63.98        31.00        34.98        56.55        27.09 
TCGA-AY-6386 TCGA-CK-4948 TCGA-CM-6168 TCGA-F4-6570 TCGA-F4-6806 TCGA-G4-6626 
       17.82       102.44        12.99         6.18        29.59        46.75 

$`SLC22A3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        18.05         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37         4.21         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 
       16.31         0.95        15.75         0.20        21.44        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       35.87         1.55        16.31        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6628 
       52.80 

  SLC22A3 MUTATED SLC22A3 WILD-TYPE 
             6.18              0.00 
  SLC22A3 MUTATED SLC22A3 WILD-TYPE 
           102.44            140.38 
  SLC22A3 MUTATED SLC22A3 WILD-TYPE 
           30.295            20.020 
[1] "6.2 - 102.4 (30.3)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.8"
D666V2, 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       24       105         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC22A3 MUTATED           0          1          1          1        0
  SLC22A3 WILD-TYPE        19          9         40         30       35
                   vv
clus                STAGE IVA STAGE IVB
  SLC22A3 MUTATED           0         0
  SLC22A3 WILD-TYPE        13         1
D666V3, multiclass
            clus
vv           SLC22A3 MUTATED SLC22A3 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                4               105
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               1                 9
  STAGE IIIB               1                40
  STAGE IIIC               1                30
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC22A3 MUTATED     1   2   7   2
  SLC22A3 WILD-TYPE   8  66 241  39
D666V4, multiclass
    clus
vv   SLC22A3 MUTATED SLC22A3 WILD-TYPE
  T1               1                 8
  T2               2                66
  T3               7               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
  SLC22A3 MUTATED     9   3   0
  SLC22A3 WILD-TYPE 211  77  66
D666V5, multiclass
    clus
vv   SLC22A3 MUTATED SLC22A3 WILD-TYPE
  N0               9               211
  N1               3                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"
D666V6, binary
                   cls
clus                  0   1
  SLC22A3 MUTATED    11   0
  SLC22A3 WILD-TYPE 272  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC22A3 MUTATED     11    0
  SLC22A3 WILD-TYPE  272   48
   clus
vv  SLC22A3 MUTATED SLC22A3 WILD-TYPE
  0              11               272
  1               0                48
[1] 2 2
[1] FALSE
D666V7, 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
D666V8, binary
                   cls
clus                  0   1
  SLC22A3 MUTATED    10   2
  SLC22A3 WILD-TYPE 307  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC22A3 MUTATED     10    2
  SLC22A3 WILD-TYPE  307   46
                               clus
vv                              SLC22A3 MUTATED SLC22A3 WILD-TYPE
  COLON ADENOCARCINOMA                       10               307
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SLC22A3 MUTATED    11   0   0   0
  SLC22A3 WILD-TYPE 246   2  22  21
D666V9, multiclass
    clus
vv   SLC22A3 MUTATED SLC22A3 WILD-TYPE
  R0              11               246
  R1               0                 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"
D666V10, 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
D666V11, 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(667) Variable = OR7C1 MUTATION ANALYSIS
D667V1, survival
                 sevent
clus2               0   1
  OR7C1 MUTATED     5   4
  OR7C1 WILD-TYPE 277  69
  OR7C1 MUTATED OR7C1 WILD-TYPE 
              9             346 
  OR7C1 MUTATED OR7C1 WILD-TYPE 
              4              69 
$`OR7C1 MUTATED`
TCGA-AA-3492 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3821 TCGA-AA-3864 TCGA-AA-3982 
        3.02        13.02         1.02         1.02        53.00        27.02 
TCGA-AD-5900 TCGA-AY-4071 TCGA-AZ-6603 
        0.07         0.95        29.56 

$`OR7C1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 
       35.01        63.98         6.97         1.02        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       33.04         0.99        25.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       25.02        24.00        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10       100.01         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  OR7C1 MUTATED OR7C1 WILD-TYPE 
           0.07            0.00 
  OR7C1 MUTATED OR7C1 WILD-TYPE 
          53.00          140.38 
  OR7C1 MUTATED OR7C1 WILD-TYPE 
           3.02           20.63 
[1] "0.1 - 53.0 (3.0)"   "0.0 - 140.4 (20.6)"
[1] "hr=" "3.8"
D667V2, 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       23       108         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        18         10         40         31       35        13
                 vv
clus              STAGE IVB
  OR7C1 MUTATED           0
  OR7C1 WILD-TYPE         1
D667V3, multiclass
            clus
vv           OR7C1 MUTATED OR7C1 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              1             108
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR7C1 MUTATED     1   3   5   0
  OR7C1 WILD-TYPE   8  65 243  41
D667V4, multiclass
    clus
vv   OR7C1 MUTATED OR7C1 WILD-TYPE
  T1             1               8
  T2             3              65
  T3             5             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
  OR7C1 MUTATED     6   2   1
  OR7C1 WILD-TYPE 214  78  65
D667V5, multiclass
    clus
vv   OR7C1 MUTATED OR7C1 WILD-TYPE
  N0             6             214
  N1             2              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"
D667V6, binary
                 cls
clus                0   1
  OR7C1 MUTATED     6   0
  OR7C1 WILD-TYPE 277  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR7C1 MUTATED      6    0
  OR7C1 WILD-TYPE  277   48
   clus
vv  OR7C1 MUTATED OR7C1 WILD-TYPE
  0             6             277
  1             0              48
[1] 2 2
[1] FALSE
D667V7, 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
D667V8, binary
                 cls
clus                0   1
  OR7C1 MUTATED     5   3
  OR7C1 WILD-TYPE 312  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR7C1 MUTATED      5    3
  OR7C1 WILD-TYPE  312   45
                               clus
vv                              OR7C1 MUTATED OR7C1 WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  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 251   2  22  21
D667V9, multiclass
    clus
vv   OR7C1 MUTATED OR7C1 WILD-TYPE
  R0             6             251
  R1             0               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"
D667V10, 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
D667V11, 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(668) Variable = ZNF473 MUTATION ANALYSIS
D668V1, survival
                  sevent
clus2                0   1
  ZNF473 MUTATED    11   2
  ZNF473 WILD-TYPE 271  71
  ZNF473 MUTATED ZNF473 WILD-TYPE 
              13              342 
  ZNF473 MUTATED ZNF473 WILD-TYPE 
               2               71 
$`ZNF473 MUTATED`
TCGA-A6-2676 TCGA-A6-6141 TCGA-AA-3949 TCGA-AA-3975 TCGA-AA-A00N TCGA-CA-6718 
       42.90         8.38        26.01        34.06         4.01         0.10 
TCGA-CK-4950 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5864 TCGA-CM-6678 TCGA-D5-5540 
       40.34        30.08        16.01        15.02        11.01        13.51 
TCGA-G4-6588 
       26.17 

$`ZNF473 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
        1.35        17.56       102.44        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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 
       12.26        19.59        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        52.80 

  ZNF473 MUTATED ZNF473 WILD-TYPE 
             0.1              0.0 
  ZNF473 MUTATED ZNF473 WILD-TYPE 
           42.90           140.38 
  ZNF473 MUTATED ZNF473 WILD-TYPE 
          16.010           20.235 
[1] "0.1 - 42.9 (16.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D668V2, 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       25       102         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF473 MUTATED           0          1          1          0        0
  ZNF473 WILD-TYPE        19          9         40         31       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF473 MUTATED           1         0
  ZNF473 WILD-TYPE        12         1
D668V3, multiclass
            clus
vv           ZNF473 MUTATED ZNF473 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               7              102
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              1                9
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 239  38
D668V4, multiclass
    clus
vv   ZNF473 MUTATED ZNF473 WILD-TYPE
  T1              0                9
  T2              2               66
  T3              9              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
  ZNF473 MUTATED    11   3   0
  ZNF473 WILD-TYPE 209  77  66
D668V5, multiclass
    clus
vv   ZNF473 MUTATED ZNF473 WILD-TYPE
  N0             11              209
  N1              3               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"
D668V6, binary
                  cls
clus                 0   1
  ZNF473 MUTATED    13   1
  ZNF473 WILD-TYPE 270  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF473 MUTATED     13    1
  ZNF473 WILD-TYPE  270   47
   clus
vv  ZNF473 MUTATED ZNF473 WILD-TYPE
  0             13              270
  1              1               47
[1] 2 2
[1] FALSE
D668V7, 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
D668V8, binary
                  cls
clus                 0   1
  ZNF473 MUTATED    12   2
  ZNF473 WILD-TYPE 305  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF473 MUTATED     12    2
  ZNF473 WILD-TYPE  305   46
                               clus
vv                              ZNF473 MUTATED ZNF473 WILD-TYPE
  COLON ADENOCARCINOMA                      12              305
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF473 MUTATED    11   1   0   1
  ZNF473 WILD-TYPE 246   1  22  20
D668V9, multiclass
    clus
vv   ZNF473 MUTATED ZNF473 WILD-TYPE
  R0             11              246
  R1              1                1
  R2              0               22
  RX              1               20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D668V10, 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
D668V11, 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(669) Variable = RBM19 MUTATION ANALYSIS
D669V1, survival
                 sevent
clus2               0   1
  RBM19 MUTATED    14   7
  RBM19 WILD-TYPE 268  66
  RBM19 MUTATED RBM19 WILD-TYPE 
             21             334 
  RBM19 MUTATED RBM19 WILD-TYPE 
              7              66 
$`RBM19 MUTATED`
TCGA-A6-5660 TCGA-AA-3492 TCGA-AA-3516 TCGA-AA-3672 TCGA-AA-3947 TCGA-AA-3977 
       29.19         3.02        13.02         0.92        33.01        25.02 
TCGA-AA-A00J TCGA-AA-A00N TCGA-AD-6964 TCGA-AU-3779 TCGA-AZ-4315 TCGA-AZ-6601 
       18.05         4.01        10.88        14.50        58.39       100.01 
TCGA-CK-5916 TCGA-CM-5860 TCGA-CM-6161 TCGA-CM-6162 TCGA-D5-5539 TCGA-D5-6537 
       21.14        16.01        15.02        12.00        19.59         4.80 
TCGA-G4-6299 TCGA-G4-6310 TCGA-G4-6317 
       74.56        45.11        36.00 

$`RBM19 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.20        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        61.41        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99         2.93         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        12.26        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        15.12        17.85        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.41        19.43       107.67        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       55.04        51.75        36.72        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  RBM19 MUTATED RBM19 WILD-TYPE 
           0.92            0.00 
  RBM19 MUTATED RBM19 WILD-TYPE 
         100.01          140.38 
  RBM19 MUTATED RBM19 WILD-TYPE 
          18.05           20.63 
[1] "0.9 - 100.0 (18.1)" "0.0 - 140.4 (20.6)"
[1] "hr=" "1.6"
D669V2, 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       23       106         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        17          9         37         28       35        13
                 vv
clus              STAGE IVB
  RBM19 MUTATED           0
  RBM19 WILD-TYPE         1
D669V3, multiclass
            clus
vv           RBM19 MUTATED RBM19 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              3             106
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             1               9
  STAGE IIIB             4              37
  STAGE IIIC             3              28
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RBM19 MUTATED     1   2  14   4
  RBM19 WILD-TYPE   8  66 234  37
D669V4, multiclass
    clus
vv   RBM19 MUTATED RBM19 WILD-TYPE
  T1             1               8
  T2             2              66
  T3            14             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
  RBM19 MUTATED    10   6   5
  RBM19 WILD-TYPE 210  74  61
D669V5, multiclass
    clus
vv   RBM19 MUTATED RBM19 WILD-TYPE
  N0            10             210
  N1             6              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"
D669V6, binary
                 cls
clus                0   1
  RBM19 MUTATED    17   0
  RBM19 WILD-TYPE 266  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM19 MUTATED     17    0
  RBM19 WILD-TYPE  266   48
   clus
vv  RBM19 MUTATED RBM19 WILD-TYPE
  0            17             266
  1             0              48
[1] 2 2
[1] FALSE
D669V7, 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
D669V8, binary
                 cls
clus                0   1
  RBM19 MUTATED    15   6
  RBM19 WILD-TYPE 302  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM19 MUTATED     15    6
  RBM19 WILD-TYPE  302   42
                               clus
vv                              RBM19 MUTATED RBM19 WILD-TYPE
  COLON ADENOCARCINOMA                     15             302
  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 242   2  22  20
D669V9, multiclass
    clus
vv   RBM19 MUTATED RBM19 WILD-TYPE
  R0            15             242
  R1             0               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"
D669V10, 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
D669V11, 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(670) Variable = CTCF MUTATION ANALYSIS
D670V1, survival
                sevent
clus2              0   1
  CTCF MUTATED    14   3
  CTCF WILD-TYPE 268  70
  CTCF MUTATED CTCF WILD-TYPE 
            17            338 
  CTCF MUTATED CTCF WILD-TYPE 
             3             70 
$`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         2.24        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        51.75 

$`CTCF WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       43.76        43.76        24.33        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       33.34        32.75        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       30.44        29.19        33.53        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 
        6.97         1.02        13.02        38.99         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       14.93        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        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-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 
        7.53        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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  CTCF MUTATED CTCF WILD-TYPE 
             0              0 
  CTCF MUTATED CTCF WILD-TYPE 
         51.75         140.38 
  CTCF MUTATED CTCF WILD-TYPE 
        19.000         20.235 
[1] "0.0 - 51.8 (19.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1"  
D670V2, 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       25       101         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        19         10         38         31       34        13
                vv
clus             STAGE IVB
  CTCF MUTATED           0
  CTCF WILD-TYPE         1
D670V3, multiclass
            clus
vv           CTCF MUTATED CTCF WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             8            101
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            3             38
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CTCF MUTATED     0   3  11   3
  CTCF WILD-TYPE   9  65 237  38
D670V4, multiclass
    clus
vv   CTCF MUTATED CTCF WILD-TYPE
  T1            0              9
  T2            3             65
  T3           11            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
  CTCF MUTATED    13   4   0
  CTCF WILD-TYPE 207  76  66
D670V5, multiclass
    clus
vv   CTCF MUTATED CTCF WILD-TYPE
  N0           13            207
  N1            4             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"
D670V6, binary
                cls
clus               0   1
  CTCF MUTATED    15   1
  CTCF WILD-TYPE 268  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTCF MUTATED     15    1
  CTCF WILD-TYPE  268   47
   clus
vv  CTCF MUTATED CTCF WILD-TYPE
  0           15            268
  1            1             47
[1] 2 2
[1] FALSE
D670V7, 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
D670V8, binary
                cls
clus               0   1
  CTCF MUTATED    17   0
  CTCF WILD-TYPE 300  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTCF MUTATED     17    0
  CTCF WILD-TYPE  300   48
                               clus
vv                              CTCF MUTATED CTCF WILD-TYPE
  COLON ADENOCARCINOMA                    17            300
  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 242   2  22  20
D670V9, multiclass
    clus
vv   CTCF MUTATED CTCF WILD-TYPE
  R0           15            242
  R1            0              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"
D670V10, 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
D670V11, 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(671) Variable = OR2Y1 MUTATION ANALYSIS
D671V1, survival
                 sevent
clus2               0   1
  OR2Y1 MUTATED     6   1
  OR2Y1 WILD-TYPE 276  72
  OR2Y1 MUTATED OR2Y1 WILD-TYPE 
              7             348 
  OR2Y1 MUTATED OR2Y1 WILD-TYPE 
              1              72 
$`OR2Y1 MUTATED`
TCGA-A6-6653 TCGA-AA-A00N TCGA-CA-5254 TCGA-CM-6166 TCGA-D5-6540 TCGA-G4-6586 
       24.39         4.01         2.24        21.99        16.14        35.80 
TCGA-G4-6588 
       26.17 

$`OR2Y1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19         1.94         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       36.00        22.09        13.78        91.79        46.75        52.80 

  OR2Y1 MUTATED OR2Y1 WILD-TYPE 
           2.24            0.00 
  OR2Y1 MUTATED OR2Y1 WILD-TYPE 
          35.80          140.38 
  OR2Y1 MUTATED OR2Y1 WILD-TYPE 
         21.990          20.155 
[1] "2.2 - 35.8 (22.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1"  
D671V2, 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       25       106         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        19         10         41         31       35        13
                 vv
clus              STAGE IVB
  OR2Y1 MUTATED           0
  OR2Y1 WILD-TYPE         1
D671V3, multiclass
            clus
vv           OR2Y1 MUTATED OR2Y1 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              3             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR2Y1 MUTATED     0   3   3   1
  OR2Y1 WILD-TYPE   9  65 245  40
D671V4, multiclass
    clus
vv   OR2Y1 MUTATED OR2Y1 WILD-TYPE
  T1             0               9
  T2             3              65
  T3             3             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
  OR2Y1 MUTATED     7   0   0
  OR2Y1 WILD-TYPE 213  80  66
D671V5, multiclass
    clus
vv   OR2Y1 MUTATED OR2Y1 WILD-TYPE
  N0             7             213
  N1             0              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"
D671V6, binary
                 cls
clus                0   1
  OR2Y1 MUTATED     7   0
  OR2Y1 WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2Y1 MUTATED      7    0
  OR2Y1 WILD-TYPE  276   48
   clus
vv  OR2Y1 MUTATED OR2Y1 WILD-TYPE
  0             7             276
  1             0              48
[1] 2 2
[1] FALSE
D671V7, 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
D671V8, binary
                 cls
clus                0   1
  OR2Y1 MUTATED     5   2
  OR2Y1 WILD-TYPE 312  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2Y1 MUTATED      5    2
  OR2Y1 WILD-TYPE  312   46
                               clus
vv                              OR2Y1 MUTATED OR2Y1 WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  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 252   2  22  20
D671V9, multiclass
    clus
vv   OR2Y1 MUTATED OR2Y1 WILD-TYPE
  R0             5             252
  R1             0               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"
D671V10, 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
D671V11, 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(672) Variable = DNAJC16 MUTATION ANALYSIS
D672V1, survival
                   sevent
clus2                 0   1
  DNAJC16 MUTATED     7   2
  DNAJC16 WILD-TYPE 275  71
  DNAJC16 MUTATED DNAJC16 WILD-TYPE 
                9               346 
  DNAJC16 MUTATED DNAJC16 WILD-TYPE 
                2                71 
$`DNAJC16 MUTATED`
TCGA-A6-3809 TCGA-AA-3553 TCGA-AA-3663 TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-5407 
       32.75        24.00         6.97        34.98        58.39        61.41 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-G4-6628 
       12.10       100.01        52.80 

$`DNAJC16 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       62.79        49.41         6.77        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       35.80        26.17        91.79        46.75 

  DNAJC16 MUTATED DNAJC16 WILD-TYPE 
             6.97              0.00 
  DNAJC16 MUTATED DNAJC16 WILD-TYPE 
           100.01            140.38 
  DNAJC16 MUTATED DNAJC16 WILD-TYPE 
           34.980            20.005 
[1] "7.0 - 100.0 (35.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.6"
D672V2, 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       23       108         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DNAJC16 MUTATED           0          0          0          0        1
  DNAJC16 WILD-TYPE        19         10         41         31       34
                   vv
clus                STAGE IVA STAGE IVB
  DNAJC16 MUTATED           0         0
  DNAJC16 WILD-TYPE        13         1
D672V3, multiclass
            clus
vv           DNAJC16 MUTATED DNAJC16 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 2                23
  STAGE IIA                1               108
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               0                31
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  DNAJC16 MUTATED     1   2   3   3
  DNAJC16 WILD-TYPE   8  66 245  38
D672V4, multiclass
    clus
vv   DNAJC16 MUTATED DNAJC16 WILD-TYPE
  T1               1                 8
  T2               2                66
  T3               3               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
  DNAJC16 MUTATED     8   1   0
  DNAJC16 WILD-TYPE 212  79  66
D672V5, multiclass
    clus
vv   DNAJC16 MUTATED DNAJC16 WILD-TYPE
  N0               8               212
  N1               1                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"
D672V6, binary
                   cls
clus                  0   1
  DNAJC16 MUTATED     8   1
  DNAJC16 WILD-TYPE 275  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DNAJC16 MUTATED      8    1
  DNAJC16 WILD-TYPE  275   47
   clus
vv  DNAJC16 MUTATED DNAJC16 WILD-TYPE
  0               8               275
  1               1                47
[1] 2 2
[1] FALSE
D672V7, 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
D672V8, binary
                   cls
clus                  0   1
  DNAJC16 MUTATED     8   1
  DNAJC16 WILD-TYPE 309  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DNAJC16 MUTATED      8    1
  DNAJC16 WILD-TYPE  309   47
                               clus
vv                              DNAJC16 MUTATED DNAJC16 WILD-TYPE
  COLON ADENOCARCINOMA                        8               309
  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 251   2  22  21
D672V9, multiclass
    clus
vv   DNAJC16 MUTATED DNAJC16 WILD-TYPE
  R0               6               251
  R1               0                 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"
D672V10, 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
D672V11, 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(673) Variable = ARMCX5 MUTATION ANALYSIS
D673V1, survival
                  sevent
clus2                0   1
  ARMCX5 MUTATED     5   2
  ARMCX5 WILD-TYPE 277  71
  ARMCX5 MUTATED ARMCX5 WILD-TYPE 
               7              348 
  ARMCX5 MUTATED ARMCX5 WILD-TYPE 
               2               71 
$`ARMCX5 MUTATED`
TCGA-A6-2672 TCGA-AA-3660 TCGA-AA-3815 TCGA-AA-A00N TCGA-AZ-6598 TCGA-CM-5860 
       46.65        78.08        33.04         4.01        49.41        16.01 
TCGA-G4-6588 
       26.17 

$`ARMCX5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        61.02         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        52.80 

  ARMCX5 MUTATED ARMCX5 WILD-TYPE 
            4.01             0.00 
  ARMCX5 MUTATED ARMCX5 WILD-TYPE 
           78.08           140.38 
  ARMCX5 MUTATED ARMCX5 WILD-TYPE 
           33.04            20.07 
[1] "4.0 - 78.1 (33.0)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1"  
D673V2, 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       23       106         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARMCX5 MUTATED           0          0          1          0        1
  ARMCX5 WILD-TYPE        19         10         40         31       34
                  vv
clus               STAGE IVA STAGE IVB
  ARMCX5 MUTATED           0         0
  ARMCX5 WILD-TYPE        13         1
D673V3, multiclass
            clus
vv           ARMCX5 MUTATED ARMCX5 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               3              106
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ARMCX5 MUTATED     0   0   7   1
  ARMCX5 WILD-TYPE   9  68 241  40
D673V4, multiclass
    clus
vv   ARMCX5 MUTATED ARMCX5 WILD-TYPE
  T1              0                9
  T2              0               68
  T3              7              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
  ARMCX5 MUTATED     6   1   1
  ARMCX5 WILD-TYPE 214  79  65
D673V5, multiclass
    clus
vv   ARMCX5 MUTATED ARMCX5 WILD-TYPE
  N0              6              214
  N1              1               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"
D673V6, binary
                  cls
clus                 0   1
  ARMCX5 MUTATED     6   1
  ARMCX5 WILD-TYPE 277  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARMCX5 MUTATED      6    1
  ARMCX5 WILD-TYPE  277   47
   clus
vv  ARMCX5 MUTATED ARMCX5 WILD-TYPE
  0              6              277
  1              1               47
[1] 2 2
[1] FALSE
D673V7, 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
D673V8, binary
                  cls
clus                 0   1
  ARMCX5 MUTATED     7   1
  ARMCX5 WILD-TYPE 310  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARMCX5 MUTATED      7    1
  ARMCX5 WILD-TYPE  310   47
                               clus
vv                              ARMCX5 MUTATED ARMCX5 WILD-TYPE
  COLON ADENOCARCINOMA                       7              310
  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 251   2  21  21
D673V9, multiclass
    clus
vv   ARMCX5 MUTATED ARMCX5 WILD-TYPE
  R0              6              251
  R1              0                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"
D673V10, 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
D673V11, 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(674) Variable = GGT5 MUTATION ANALYSIS
D674V1, survival
                sevent
clus2              0   1
  GGT5 MUTATED    10   3
  GGT5 WILD-TYPE 272  70
  GGT5 MUTATED GGT5 WILD-TYPE 
            13            342 
  GGT5 MUTATED GGT5 WILD-TYPE 
             3             70 
$`GGT5 MUTATED`
TCGA-AA-3697 TCGA-AA-A00E TCGA-AD-6889 TCGA-AD-6964 TCGA-AZ-4315 TCGA-AZ-6598 
       85.05        30.02        56.55        10.88        58.39        49.41 
TCGA-AZ-6601 TCGA-CM-4743 TCGA-CM-5861 TCGA-CM-6168 TCGA-CM-6169 TCGA-D5-6535 
      100.01        23.05        15.02        12.99        13.02        15.12 
TCGA-G4-6304 
       53.62 

$`GGT5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       62.79        61.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
       21.99        21.14         2.93         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        16.01         5.03        15.02        15.02        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-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-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 
       35.41        19.43       107.67        74.56        65.85        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  GGT5 MUTATED GGT5 WILD-TYPE 
         10.88           0.00 
  GGT5 MUTATED GGT5 WILD-TYPE 
        100.01         140.38 
  GGT5 MUTATED GGT5 WILD-TYPE 
         30.02          20.07 
[1] "10.9 - 100.0 (30.0)" "0.0 - 140.4 (20.1)" 
[1] "hr=" "1.5"
D674V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GGT5 MUTATED         0        0        3         7         1         0
  GGT5 WILD-TYPE      64        1       22       102         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GGT5 MUTATED           1          0          1          0        0         0
  GGT5 WILD-TYPE        18         10         40         31       35        13
                vv
clus             STAGE IVB
  GGT5 MUTATED           0
  GGT5 WILD-TYPE         1
D674V3, multiclass
            clus
vv           GGT5 MUTATED GGT5 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              3             22
  STAGE IIA             7            102
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GGT5 MUTATED     0   0  11   3
  GGT5 WILD-TYPE   9  68 237  38
D674V4, multiclass
    clus
vv   GGT5 MUTATED GGT5 WILD-TYPE
  T1            0              9
  T2            0             68
  T3           11            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
  GGT5 MUTATED    12   1   1
  GGT5 WILD-TYPE 208  79  65
D674V5, multiclass
    clus
vv   GGT5 MUTATED GGT5 WILD-TYPE
  N0           12            208
  N1            1             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"
D674V6, binary
                cls
clus               0   1
  GGT5 MUTATED    11   0
  GGT5 WILD-TYPE 272  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  GGT5 MUTATED     11    0
  GGT5 WILD-TYPE  272   48
   clus
vv  GGT5 MUTATED GGT5 WILD-TYPE
  0           11            272
  1            0             48
[1] 2 2
[1] FALSE
D674V7, 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
D674V8, binary
                cls
clus               0   1
  GGT5 MUTATED    14   0
  GGT5 WILD-TYPE 303  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  GGT5 MUTATED     14    0
  GGT5 WILD-TYPE  303   48
                               clus
vv                              GGT5 MUTATED GGT5 WILD-TYPE
  COLON ADENOCARCINOMA                    14            303
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  GGT5 MUTATED     9   0   0   1
  GGT5 WILD-TYPE 248   2  22  20
D674V9, multiclass
    clus
vv   GGT5 MUTATED GGT5 WILD-TYPE
  R0            9            248
  R1            0              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"
D674V10, 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
D674V11, 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(675) Variable = MTDH MUTATION ANALYSIS
D675V1, survival
                sevent
clus2              0   1
  MTDH MUTATED    10   1
  MTDH WILD-TYPE 272  72
  MTDH MUTATED MTDH WILD-TYPE 
            11            344 
  MTDH MUTATED MTDH WILD-TYPE 
             1             72 
$`MTDH MUTATED`
TCGA-A6-2676 TCGA-AA-3511 TCGA-AA-3979 TCGA-AA-A010 TCGA-AD-6889 TCGA-AD-6895 
       42.90         6.97        24.00        34.98        56.55         0.72 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4950 TCGA-CM-4744 TCGA-G4-6310 
        0.33         0.10        40.34        20.02        45.11 

$`MTDH WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        25.02        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 
       40.96         0.07        21.37         4.21         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07         0.26         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      102.44        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        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        51.75        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  MTDH MUTATED MTDH WILD-TYPE 
           0.1            0.0 
  MTDH MUTATED MTDH WILD-TYPE 
         56.55         140.38 
  MTDH MUTATED MTDH WILD-TYPE 
        24.000         20.155 
[1] "0.1 - 56.5 (24.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2.1"
D675V2, 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       24       105         5         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MTDH MUTATED           0          1          1          0        0         0
  MTDH WILD-TYPE        19          9         40         31       35        13
                vv
clus             STAGE IVB
  MTDH MUTATED           0
  MTDH WILD-TYPE         1
D675V3, multiclass
            clus
vv           MTDH MUTATED MTDH WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             4            105
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            1              9
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MTDH MUTATED     0   1   7   4
  MTDH WILD-TYPE   9  67 241  37
D675V4, multiclass
    clus
vv   MTDH MUTATED MTDH WILD-TYPE
  T1            0              9
  T2            1             67
  T3            7            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
  MTDH MUTATED     9   3   0
  MTDH WILD-TYPE 211  77  66
D675V5, multiclass
    clus
vv   MTDH MUTATED MTDH WILD-TYPE
  N0            9            211
  N1            3             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"
D675V6, binary
                cls
clus               0   1
  MTDH MUTATED    10   0
  MTDH WILD-TYPE 273  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTDH MUTATED     10    0
  MTDH WILD-TYPE  273   48
   clus
vv  MTDH MUTATED MTDH WILD-TYPE
  0           10            273
  1            0             48
[1] 2 2
[1] FALSE
D675V7, 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
D675V8, binary
                cls
clus               0   1
  MTDH MUTATED    11   1
  MTDH WILD-TYPE 306  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTDH MUTATED     11    1
  MTDH WILD-TYPE  306   47
                               clus
vv                              MTDH MUTATED MTDH WILD-TYPE
  COLON ADENOCARCINOMA                    11            306
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MTDH MUTATED     6   1   0   3
  MTDH WILD-TYPE 251   1  22  18
D675V9, multiclass
    clus
vv   MTDH MUTATED MTDH WILD-TYPE
  R0            6            251
  R1            1              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"
D675V10, 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
D675V11, 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(676) Variable = CAMSAP1L1 MUTATION ANALYSIS
D676V1, survival
                     sevent
clus2                   0   1
  CAMSAP1L1 MUTATED    18   3
  CAMSAP1L1 WILD-TYPE 264  70
  CAMSAP1L1 MUTATED CAMSAP1L1 WILD-TYPE 
                 21                 334 
  CAMSAP1L1 MUTATED CAMSAP1L1 WILD-TYPE 
                  3                  70 
$`CAMSAP1L1 MUTATED`
TCGA-A6-3809 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5664 TCGA-AA-3496 TCGA-AA-3715 
       32.75        30.44        33.53        22.09         1.02        19.04 
TCGA-AA-3815 TCGA-AA-3877 TCGA-AU-6004 TCGA-AY-6196 TCGA-AZ-4315 TCGA-AZ-6599 
       33.04        31.00        27.09         0.20        58.39         6.77 
TCGA-CA-6717 TCGA-CM-6162 TCGA-D5-6927 TCGA-D5-6930 TCGA-F4-6570 TCGA-G4-6304 
        0.33        12.00         9.44         1.51         6.18        53.62 
TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6586 
       51.75        36.72        35.80 

$`CAMSAP1L1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 
       31.63        29.19        23.61        22.06        32.71        27.09 
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 
       22.52         8.38        25.08        25.18        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        7.04         3.02        35.01        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        15.75 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41        49.41        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       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        13.38        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       44.68        55.04        45.11        36.00        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  CAMSAP1L1 MUTATED CAMSAP1L1 WILD-TYPE 
                0.2                 0.0 
  CAMSAP1L1 MUTATED CAMSAP1L1 WILD-TYPE 
              58.39              140.38 
  CAMSAP1L1 MUTATED CAMSAP1L1 WILD-TYPE 
              27.09               20.07 
[1] "0.2 - 58.4 (27.1)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.3"
D676V2, 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       23       101         6         1
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CAMSAP1L1 MUTATED           0          0          2          2        1
  CAMSAP1L1 WILD-TYPE        19         10         39         29       34
                     vv
clus                  STAGE IVA STAGE IVB
  CAMSAP1L1 MUTATED           0         0
  CAMSAP1L1 WILD-TYPE        13         1
D676V3, multiclass
            clus
vv           CAMSAP1L1 MUTATED CAMSAP1L1 WILD-TYPE
  STAGE I                    4                  60
  STAGE IA                   0                   1
  STAGE II                   2                  23
  STAGE IIA                  8                 101
  STAGE IIB                  2                   6
  STAGE IIC                  0                   1
  STAGE III                  0                  19
  STAGE IIIA                 0                  10
  STAGE IIIB                 2                  39
  STAGE IIIC                 2                  29
  STAGE IV                   1                  34
  STAGE IVA                  0                  13
  STAGE IVB                  0                   1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2  T3  T4
  CAMSAP1L1 MUTATED     1   3  14   3
  CAMSAP1L1 WILD-TYPE   8  65 234  38
D676V4, multiclass
    clus
vv   CAMSAP1L1 MUTATED CAMSAP1L1 WILD-TYPE
  T1                 1                   8
  T2                 3                  65
  T3                14                 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
  CAMSAP1L1 MUTATED    16   3   2
  CAMSAP1L1 WILD-TYPE 204  77  64
D676V5, multiclass
    clus
vv   CAMSAP1L1 MUTATED CAMSAP1L1 WILD-TYPE
  N0                16                 204
  N1                 3                  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"
D676V6, binary
                     cls
clus                    0   1
  CAMSAP1L1 MUTATED    17   1
  CAMSAP1L1 WILD-TYPE 266  47
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  CAMSAP1L1 MUTATED     17    1
  CAMSAP1L1 WILD-TYPE  266   47
   clus
vv  CAMSAP1L1 MUTATED CAMSAP1L1 WILD-TYPE
  0                17                 266
  1                 1                  47
[1] 2 2
[1] FALSE
D676V7, 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
D676V8, binary
                     cls
clus                    0   1
  CAMSAP1L1 MUTATED    15   6
  CAMSAP1L1 WILD-TYPE 302  42
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  CAMSAP1L1 MUTATED     15    6
  CAMSAP1L1 WILD-TYPE  302   42
                               clus
vv                              CAMSAP1L1 MUTATED CAMSAP1L1 WILD-TYPE
  COLON ADENOCARCINOMA                         15                 302
  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 239   2  22  20
D676V9, multiclass
    clus
vv   CAMSAP1L1 MUTATED CAMSAP1L1 WILD-TYPE
  R0                18                 239
  R1                 0                   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"
D676V10, 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
D676V11, 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(677) Variable = LRRC37B MUTATION ANALYSIS
D677V1, survival
                   sevent
clus2                 0   1
  LRRC37B MUTATED     4   2
  LRRC37B WILD-TYPE 278  71
  LRRC37B MUTATED LRRC37B WILD-TYPE 
                6               349 
  LRRC37B MUTATED LRRC37B WILD-TYPE 
                2                71 
$`LRRC37B MUTATED`
TCGA-A6-4105 TCGA-AZ-6603 TCGA-CA-6717 TCGA-CK-4948 TCGA-D5-6932 TCGA-F4-6460 
       14.53        29.56         0.33       102.44        11.38        13.38 

$`LRRC37B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10       100.01         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 
        0.07         0.26         0.10         1.35        17.56        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  LRRC37B MUTATED LRRC37B WILD-TYPE 
             0.33              0.00 
  LRRC37B MUTATED LRRC37B WILD-TYPE 
           102.44            140.38 
  LRRC37B MUTATED LRRC37B WILD-TYPE 
           13.955            20.280 
[1] "0.3 - 102.4 (14.0)" "0.0 - 140.4 (20.3)"
[1] "hr=" "1.4"
D677V2, 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       25       106         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LRRC37B MUTATED           0          1          1          0        0
  LRRC37B WILD-TYPE        19          9         40         31       35
                   vv
clus                STAGE IVA STAGE IVB
  LRRC37B MUTATED           0         0
  LRRC37B WILD-TYPE        13         1
D677V3, multiclass
            clus
vv           LRRC37B MUTATED LRRC37B WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                3               106
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               1                 9
  STAGE IIIB               1                40
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  LRRC37B MUTATED     0   1   5   0
  LRRC37B WILD-TYPE   9  67 243  41
D677V4, multiclass
    clus
vv   LRRC37B MUTATED LRRC37B WILD-TYPE
  T1               0                 9
  T2               1                67
  T3               5               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
  LRRC37B MUTATED     3   3   0
  LRRC37B WILD-TYPE 217  77  66
D677V5, multiclass
    clus
vv   LRRC37B MUTATED LRRC37B WILD-TYPE
  N0               3               217
  N1               3                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"
D677V6, binary
                   cls
clus                  0   1
  LRRC37B MUTATED     5   0
  LRRC37B WILD-TYPE 278  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  LRRC37B MUTATED      5    0
  LRRC37B WILD-TYPE  278   48
   clus
vv  LRRC37B MUTATED LRRC37B WILD-TYPE
  0               5               278
  1               0                48
[1] 2 2
[1] FALSE
D677V7, 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
D677V8, binary
                   cls
clus                  0   1
  LRRC37B MUTATED     5   1
  LRRC37B WILD-TYPE 312  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  LRRC37B MUTATED      5    1
  LRRC37B WILD-TYPE  312   47
                               clus
vv                              LRRC37B MUTATED LRRC37B WILD-TYPE
  COLON ADENOCARCINOMA                        5               312
  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 254   2  22  20
D677V9, multiclass
    clus
vv   LRRC37B MUTATED LRRC37B WILD-TYPE
  R0               3               254
  R1               0                 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"
D677V10, 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
D677V11, 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(678) Variable = MARVELD2 MUTATION ANALYSIS
D678V1, survival
                    sevent
clus2                  0   1
  MARVELD2 MUTATED     8   2
  MARVELD2 WILD-TYPE 274  71
  MARVELD2 MUTATED MARVELD2 WILD-TYPE 
                10                345 
  MARVELD2 MUTATED MARVELD2 WILD-TYPE 
                 2                 71 
$`MARVELD2 MUTATED`
TCGA-A6-5661 TCGA-AA-3852 TCGA-AA-A00E TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-6601 
       33.53         0.00        30.02        27.09        58.39       100.01 
TCGA-CK-5913 TCGA-CM-4743 TCGA-F4-6856 TCGA-G4-6309 
       51.32        23.05        19.43        51.75 

$`MARVELD2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 
       17.03        10.06         0.00        33.07        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.20        14.50        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        61.41        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 
       16.24        33.67        13.25         0.53        35.41       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       74.56        65.85        53.62        44.68        55.04        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  MARVELD2 MUTATED MARVELD2 WILD-TYPE 
                 0                  0 
  MARVELD2 MUTATED MARVELD2 WILD-TYPE 
            100.01             140.38 
  MARVELD2 MUTATED MARVELD2 WILD-TYPE 
            31.775             19.990 
[1] "0.0 - 100.0 (31.8)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.6"
D678V2, 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       24       103         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MARVELD2 MUTATED           0          0          1          0        0
  MARVELD2 WILD-TYPE        19         10         40         31       35
                    vv
clus                 STAGE IVA STAGE IVB
  MARVELD2 MUTATED           0         0
  MARVELD2 WILD-TYPE        13         1
D678V3, multiclass
            clus
vv           MARVELD2 MUTATED MARVELD2 WILD-TYPE
  STAGE I                   2                 62
  STAGE IA                  0                  1
  STAGE II                  1                 24
  STAGE IIA                 6                103
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                0                 10
  STAGE IIIB                1                 40
  STAGE IIIC                0                 31
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  MARVELD2 MUTATED     0   2   8   0
  MARVELD2 WILD-TYPE   9  66 240  41
D678V4, multiclass
    clus
vv   MARVELD2 MUTATED MARVELD2 WILD-TYPE
  T1                0                  9
  T2                2                 66
  T3                8                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
  MARVELD2 MUTATED     9   1   0
  MARVELD2 WILD-TYPE 211  79  66
D678V5, multiclass
    clus
vv   MARVELD2 MUTATED MARVELD2 WILD-TYPE
  N0                9                211
  N1                1                 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"
D678V6, binary
                    cls
clus                   0   1
  MARVELD2 MUTATED     9   0
  MARVELD2 WILD-TYPE 274  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  MARVELD2 MUTATED      9    0
  MARVELD2 WILD-TYPE  274   48
   clus
vv  MARVELD2 MUTATED MARVELD2 WILD-TYPE
  0                9                274
  1                0                 48
[1] 2 2
[1] FALSE
D678V7, 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
D678V8, binary
                    cls
clus                   0   1
  MARVELD2 MUTATED     8   2
  MARVELD2 WILD-TYPE 309  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  MARVELD2 MUTATED      8    2
  MARVELD2 WILD-TYPE  309   46
                               clus
vv                              MARVELD2 MUTATED MARVELD2 WILD-TYPE
  COLON ADENOCARCINOMA                         8                309
  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 249   2  22  20
D678V9, multiclass
    clus
vv   MARVELD2 MUTATED MARVELD2 WILD-TYPE
  R0                8                249
  R1                0                  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"
D678V10, 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
D678V11, 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(679) Variable = PRKCD MUTATION ANALYSIS
D679V1, survival
                 sevent
clus2               0   1
  PRKCD MUTATED    12   0
  PRKCD WILD-TYPE 270  73
  PRKCD MUTATED PRKCD WILD-TYPE 
             12             343 
  PRKCD MUTATED PRKCD WILD-TYPE 
              0              73 
$`PRKCD MUTATED`
TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3710 TCGA-AA-3815 TCGA-AA-A01R 
       33.53        22.06        19.66        26.99        33.04        35.01 
TCGA-AD-5900 TCGA-CK-4947 TCGA-CM-6162 TCGA-D5-6541 TCGA-D5-6930 TCGA-D5-6931 
        0.07        17.56        12.00        15.58         1.51        12.00 

$`PRKCD WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       85.05        19.04        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        16.14         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-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       13.41        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  PRKCD MUTATED PRKCD WILD-TYPE 
           0.07            0.00 
  PRKCD MUTATED PRKCD WILD-TYPE 
          35.01          140.38 
  PRKCD MUTATED PRKCD WILD-TYPE 
          18.61           20.28 
[1] "0.1 - 35.0 (18.6)"  "0.0 - 140.4 (20.3)"
[1] "hr="     "9400000"
D679V2, 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       25       102         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PRKCD MUTATED           1          0          1          2        0         1
  PRKCD WILD-TYPE        18         10         40         29       35        12
                 vv
clus              STAGE IVB
  PRKCD MUTATED           0
  PRKCD WILD-TYPE         1
D679V3, multiclass
            clus
vv           PRKCD MUTATED PRKCD WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              7             102
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             2              29
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 239  38
D679V4, multiclass
    clus
vv   PRKCD MUTATED PRKCD WILD-TYPE
  T1             0               9
  T2             1              67
  T3             9             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
  PRKCD MUTATED     8   3   2
  PRKCD WILD-TYPE 212  77  64
D679V5, multiclass
    clus
vv   PRKCD MUTATED PRKCD WILD-TYPE
  N0             8             212
  N1             3              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"
D679V6, binary
                 cls
clus                0   1
  PRKCD MUTATED    11   0
  PRKCD WILD-TYPE 272  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCD MUTATED     11    0
  PRKCD WILD-TYPE  272   48
   clus
vv  PRKCD MUTATED PRKCD WILD-TYPE
  0            11             272
  1             0              48
[1] 2 2
[1] FALSE
D679V7, 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
D679V8, binary
                 cls
clus                0   1
  PRKCD MUTATED     8   5
  PRKCD WILD-TYPE 309  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCD MUTATED      8    5
  PRKCD WILD-TYPE  309   43
                               clus
vv                              PRKCD MUTATED PRKCD WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  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 245   2  22  20
D679V9, multiclass
    clus
vv   PRKCD MUTATED PRKCD WILD-TYPE
  R0            12             245
  R1             0               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"
D679V10, 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
D679V11, 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(680) Variable = ZNF658 MUTATION ANALYSIS
D680V1, survival
                  sevent
clus2                0   1
  ZNF658 MUTATED     4   5
  ZNF658 WILD-TYPE 278  68
  ZNF658 MUTATED ZNF658 WILD-TYPE 
               9              346 
  ZNF658 MUTATED ZNF658 WILD-TYPE 
               5               68 
$`ZNF658 MUTATED`
TCGA-A6-2677 TCGA-AA-3662 TCGA-AA-3715 TCGA-AA-3977 TCGA-AA-A00N TCGA-AZ-6598 
       24.33         6.05        19.04        25.02         4.01        49.41 
TCGA-CK-5912 TCGA-CM-5860 TCGA-D5-6928 
       49.08        16.01        11.64 

$`ZNF658 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        42.90        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       19.99        13.94        19.99        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 
        1.35        17.56       102.44        40.34        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         2.93         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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  ZNF658 MUTATED ZNF658 WILD-TYPE 
            4.01             0.00 
  ZNF658 MUTATED ZNF658 WILD-TYPE 
           49.41           140.38 
  ZNF658 MUTATED ZNF658 WILD-TYPE 
          19.040           20.235 
[1] "4.0 - 49.4 (19.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "3"  
D680V2, 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       23       106         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF658 MUTATED           0          0          0          1        1
  ZNF658 WILD-TYPE        19         10         41         30       34
                  vv
clus               STAGE IVA STAGE IVB
  ZNF658 MUTATED           0         0
  ZNF658 WILD-TYPE        13         1
D680V3, multiclass
            clus
vv           ZNF658 MUTATED ZNF658 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               3              106
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              1               30
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF658 MUTATED     0   2   6   2
  ZNF658 WILD-TYPE   9  66 242  39
D680V4, multiclass
    clus
vv   ZNF658 MUTATED ZNF658 WILD-TYPE
  T1              0                9
  T2              2               66
  T3              6              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
  ZNF658 MUTATED     8   0   2
  ZNF658 WILD-TYPE 212  80  64
D680V5, multiclass
    clus
vv   ZNF658 MUTATED ZNF658 WILD-TYPE
  N0              8              212
  N1              0               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"
D680V6, binary
                  cls
clus                 0   1
  ZNF658 MUTATED     6   1
  ZNF658 WILD-TYPE 277  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF658 MUTATED      6    1
  ZNF658 WILD-TYPE  277   47
   clus
vv  ZNF658 MUTATED ZNF658 WILD-TYPE
  0              6              277
  1              1               47
[1] 2 2
[1] FALSE
D680V7, 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
D680V8, binary
                  cls
clus                 0   1
  ZNF658 MUTATED     8   2
  ZNF658 WILD-TYPE 309  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF658 MUTATED      8    2
  ZNF658 WILD-TYPE  309   46
                               clus
vv                              ZNF658 MUTATED ZNF658 WILD-TYPE
  COLON ADENOCARCINOMA                       8              309
  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 251   2  21  20
D680V9, multiclass
    clus
vv   ZNF658 MUTATED ZNF658 WILD-TYPE
  R0              6              251
  R1              0                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"
D680V10, 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
D680V11, 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(681) Variable = SPEN MUTATION ANALYSIS
D681V1, survival
                sevent
clus2              0   1
  SPEN MUTATED    22   7
  SPEN WILD-TYPE 260  66
  SPEN MUTATED SPEN WILD-TYPE 
            29            326 
  SPEN MUTATED SPEN WILD-TYPE 
             7             66 
$`SPEN MUTATED`
TCGA-A6-3809 TCGA-A6-5661 TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3522 TCGA-AA-3543 
       32.75        33.53        22.06         3.02        37.05         0.99 
TCGA-AA-3672 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3949 TCGA-AA-3956 TCGA-AA-3977 
        0.92        26.99        10.06        26.01        34.03        25.02 
TCGA-AA-A00N TCGA-AD-5900 TCGA-AU-6004 TCGA-AY-5543 TCGA-AZ-4315 TCGA-AZ-6599 
        4.01         0.07        27.09        15.75        58.39         6.77 
TCGA-AZ-6603 TCGA-CK-5916 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-5868 TCGA-CM-6169 
       29.56        21.14        23.05        37.02        17.03        13.02 
TCGA-D5-5538 TCGA-D5-6541 TCGA-DM-A0XD TCGA-DM-A1HB TCGA-G4-6628 
       12.26        15.58        24.43       135.65        52.80 

$`SPEN WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       31.63        30.44        29.19        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
       29.00        29.00        26.01        12.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
        6.05         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
       36.00         5.03        85.05        19.04        19.04        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3966 
       24.00        33.01        24.00         2.01        20.98         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 
       10.88         0.20        14.50        16.31         0.95         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 
       62.79        61.41        49.41        12.10       100.01         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4747 
       21.99         2.93         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        16.01 
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 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       10.26       119.70        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 
       91.79        46.75 

  SPEN MUTATED SPEN WILD-TYPE 
          0.07           0.00 
  SPEN MUTATED SPEN WILD-TYPE 
        135.65         140.38 
  SPEN MUTATED SPEN WILD-TYPE 
        23.050         20.005 
[1] "0.1 - 135.7 (23.1)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.3"
D681V2, 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       24        98         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        17         10         38         31       35        11
                vv
clus             STAGE IVB
  SPEN MUTATED           0
  SPEN WILD-TYPE         1
D681V3, multiclass
            clus
vv           SPEN MUTATED SPEN WILD-TYPE
  STAGE I               7             57
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA            11             98
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             2             17
  STAGE IIIA            0             10
  STAGE IIIB            3             38
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             2             11
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  60 230  37
D681V4, multiclass
    clus
vv   SPEN MUTATED SPEN WILD-TYPE
  T1            1              8
  T2            8             60
  T3           18            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
  SPEN MUTATED    23   7   1
  SPEN WILD-TYPE 197  73  65
D681V5, multiclass
    clus
vv   SPEN MUTATED SPEN WILD-TYPE
  N0           23            197
  N1            7             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"
D681V6, binary
                cls
clus               0   1
  SPEN MUTATED    24   2
  SPEN WILD-TYPE 259  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  SPEN MUTATED     24    2
  SPEN WILD-TYPE  259   46
   clus
vv  SPEN MUTATED SPEN WILD-TYPE
  0           24            259
  1            2             46
[1] 2 2
[1] FALSE
D681V7, 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
D681V8, binary
                cls
clus               0   1
  SPEN MUTATED    26   5
  SPEN WILD-TYPE 291  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  SPEN MUTATED     26    5
  SPEN WILD-TYPE  291   43
                               clus
vv                              SPEN MUTATED SPEN WILD-TYPE
  COLON ADENOCARCINOMA                    26            291
  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 233   2  22  19
D681V9, multiclass
    clus
vv   SPEN MUTATED SPEN WILD-TYPE
  R0           24            233
  R1            0              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"
D681V10, 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
D681V11, 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(682) Variable = CAPRIN1 MUTATION ANALYSIS
D682V1, survival
                   sevent
clus2                 0   1
  CAPRIN1 MUTATED     8   3
  CAPRIN1 WILD-TYPE 274  70
  CAPRIN1 MUTATED CAPRIN1 WILD-TYPE 
               11               344 
  CAPRIN1 MUTATED CAPRIN1 WILD-TYPE 
                3                70 
$`CAPRIN1 MUTATED`
TCGA-A6-2672 TCGA-A6-3809 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3548 TCGA-AA-A01R 
       46.65        32.75         3.02         1.02        33.99        35.01 
TCGA-AD-6901 TCGA-CM-4746 TCGA-CM-6171 TCGA-D5-6540 TCGA-G4-6626 
       22.42        37.02        14.04        16.14        46.75 

$`CAPRIN1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       34.65        33.34        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       19.66        20.28         7.04        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       14.01        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 
       91.79        52.80 

  CAPRIN1 MUTATED CAPRIN1 WILD-TYPE 
             1.02              0.00 
  CAPRIN1 MUTATED CAPRIN1 WILD-TYPE 
            46.75            140.38 
  CAPRIN1 MUTATED CAPRIN1 WILD-TYPE 
            32.75             20.07 
[1] "1.0 - 46.8 (32.8)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.4"
D682V2, 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       23       108         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CAPRIN1 MUTATED           1          0          1          1        0
  CAPRIN1 WILD-TYPE        18         10         40         30       35
                   vv
clus                STAGE IVA STAGE IVB
  CAPRIN1 MUTATED           0         0
  CAPRIN1 WILD-TYPE        13         1
D682V3, multiclass
            clus
vv           CAPRIN1 MUTATED CAPRIN1 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 2                23
  STAGE IIA                1               108
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               1                30
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CAPRIN1 MUTATED     0   3   7   1
  CAPRIN1 WILD-TYPE   9  65 241  40
D682V4, multiclass
    clus
vv   CAPRIN1 MUTATED CAPRIN1 WILD-TYPE
  T1               0                 9
  T2               3                65
  T3               7               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
  CAPRIN1 MUTATED     8   1   2
  CAPRIN1 WILD-TYPE 212  79  64
D682V5, multiclass
    clus
vv   CAPRIN1 MUTATED CAPRIN1 WILD-TYPE
  N0               8               212
  N1               1                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"
D682V6, binary
                   cls
clus                  0   1
  CAPRIN1 MUTATED    10   0
  CAPRIN1 WILD-TYPE 273  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CAPRIN1 MUTATED     10    0
  CAPRIN1 WILD-TYPE  273   48
   clus
vv  CAPRIN1 MUTATED CAPRIN1 WILD-TYPE
  0              10               273
  1               0                48
[1] 2 2
[1] FALSE
D682V7, 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
D682V8, binary
                   cls
clus                  0   1
  CAPRIN1 MUTATED     8   3
  CAPRIN1 WILD-TYPE 309  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CAPRIN1 MUTATED      8    3
  CAPRIN1 WILD-TYPE  309   45
                               clus
vv                              CAPRIN1 MUTATED CAPRIN1 WILD-TYPE
  COLON ADENOCARCINOMA                        8               309
  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 247   2  22  21
D682V9, multiclass
    clus
vv   CAPRIN1 MUTATED CAPRIN1 WILD-TYPE
  R0              10               247
  R1               0                 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"
D682V10, 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
D682V11, 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(683) Variable = MFAP1 MUTATION ANALYSIS
D683V1, survival
                 sevent
clus2               0   1
  MFAP1 MUTATED     3   1
  MFAP1 WILD-TYPE 279  72
  MFAP1 MUTATED MFAP1 WILD-TYPE 
              4             351 
  MFAP1 MUTATED MFAP1 WILD-TYPE 
              1              72 
$`MFAP1 MUTATED`
TCGA-AZ-4315 TCGA-AZ-6599 TCGA-CK-4952 TCGA-CM-4743 
       58.39         6.77        15.62        23.05 

$`MFAP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      102.44        40.34        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  MFAP1 MUTATED MFAP1 WILD-TYPE 
           6.77            0.00 
  MFAP1 MUTATED MFAP1 WILD-TYPE 
          58.39          140.38 
  MFAP1 MUTATED MFAP1 WILD-TYPE 
         19.335          20.190 
[1] "6.8 - 58.4 (19.3)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D683V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MFAP1 MUTATED         1        0        0         2         0         0
  MFAP1 WILD-TYPE      63        1       25       107         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MFAP1 MUTATED           1          0          0          0        0         0
  MFAP1 WILD-TYPE        18         10         41         31       35        13
                 vv
clus              STAGE IVB
  MFAP1 MUTATED           0
  MFAP1 WILD-TYPE         1
D683V3, multiclass
            clus
vv           MFAP1 MUTATED MFAP1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              2             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MFAP1 MUTATED     0   1   2   1
  MFAP1 WILD-TYPE   9  67 246  40
D683V4, multiclass
    clus
vv   MFAP1 MUTATED MFAP1 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             2             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
  MFAP1 MUTATED     3   0   1
  MFAP1 WILD-TYPE 217  80  65
D683V5, multiclass
    clus
vv   MFAP1 MUTATED MFAP1 WILD-TYPE
  N0             3             217
  N1             0              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
  MFAP1 MUTATED     3   0
  MFAP1 WILD-TYPE 280  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MFAP1 MUTATED      3    0
  MFAP1 WILD-TYPE  280   48
   clus
vv  MFAP1 MUTATED MFAP1 WILD-TYPE
  0             3             280
  1             0              48
[1] 2 2
[1] FALSE
D683V7, binary
                 cls
clus                0   1
  MFAP1 MUTATED     1   3
  MFAP1 WILD-TYPE 169 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MFAP1 MUTATED      1    3
  MFAP1 WILD-TYPE  169  194
        clus
vv       MFAP1 MUTATED MFAP1 WILD-TYPE
  FEMALE             1             169
  MALE               3             194
[1] 2 2
[1] FALSE
D683V8, binary
                 cls
clus                0   1
  MFAP1 MUTATED     3   1
  MFAP1 WILD-TYPE 314  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MFAP1 MUTATED      3    1
  MFAP1 WILD-TYPE  314   47
                               clus
vv                              MFAP1 MUTATED MFAP1 WILD-TYPE
  COLON ADENOCARCINOMA                      3             314
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MFAP1 MUTATED     2   0   0   1
  MFAP1 WILD-TYPE 255   2  22  20
D683V9, multiclass
    clus
vv   MFAP1 MUTATED MFAP1 WILD-TYPE
  R0             2             255
  R1             0               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"
D683V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MFAP1 MUTATED                                  0     0
  MFAP1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MFAP1 MUTATED                           0     4
  MFAP1 WILD-TYPE                        19   172
D683V11, multiclass
                                  clus
vv                                 MFAP1 MUTATED MFAP1 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(684) Variable = ZCCHC6 MUTATION ANALYSIS
D684V1, survival
                  sevent
clus2                0   1
  ZCCHC6 MUTATED    15   3
  ZCCHC6 WILD-TYPE 267  70
  ZCCHC6 MUTATED ZCCHC6 WILD-TYPE 
              18              337 
  ZCCHC6 MUTATED ZCCHC6 WILD-TYPE 
               3               70 
$`ZCCHC6 MUTATED`
TCGA-AA-3516 TCGA-AA-3532 TCGA-AA-3663 TCGA-AA-3681 TCGA-AA-3821 TCGA-AA-3950 
       13.02        29.00         6.97         5.98         1.02        24.00 
TCGA-AA-A017 TCGA-AA-A02J TCGA-AD-6889 TCGA-AY-6197 TCGA-AZ-6598 TCGA-CA-6717 
       15.02         5.03        56.55        21.44        49.41         0.33 
TCGA-CK-4952 TCGA-CM-6680 TCGA-DM-A28K TCGA-G4-6309 TCGA-G4-6323 TCGA-G4-6628 
       15.62        12.03        98.24        51.75        13.78        52.80 

$`ZCCHC6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        1.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3538 
       19.07         0.00        19.07        34.03        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
       11.01        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
        0.99        25.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        34.98        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       51.98        39.98         2.01        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 
        1.35        17.56       102.44        40.34        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       35.97        60.79       117.07         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       74.56        65.85        53.62        44.68        55.04        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.72        36.00        22.09        35.80        26.17        91.79 
TCGA-G4-6626 
       46.75 

  ZCCHC6 MUTATED ZCCHC6 WILD-TYPE 
            0.33             0.00 
  ZCCHC6 MUTATED ZCCHC6 WILD-TYPE 
           98.24           140.38 
  ZCCHC6 MUTATED ZCCHC6 WILD-TYPE 
           15.32            20.28 
[1] "0.3 - 98.2 (15.3)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.4"
D684V2, 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       23       102         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZCCHC6 MUTATED           3          0          2          0        1
  ZCCHC6 WILD-TYPE        16         10         39         31       34
                  vv
clus               STAGE IVA STAGE IVB
  ZCCHC6 MUTATED           0         0
  ZCCHC6 WILD-TYPE        13         1
D684V3, multiclass
            clus
vv           ZCCHC6 MUTATED ZCCHC6 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                1                0
  STAGE II                2               23
  STAGE IIA               7              102
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               3               16
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZCCHC6 MUTATED     0   2  14   1
  ZCCHC6 WILD-TYPE   9  66 234  40
D684V4, multiclass
    clus
vv   ZCCHC6 MUTATED ZCCHC6 WILD-TYPE
  T1              0                9
  T2              2               66
  T3             14              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
  ZCCHC6 MUTATED    13   2   3
  ZCCHC6 WILD-TYPE 207  78  63
D684V5, multiclass
    clus
vv   ZCCHC6 MUTATED ZCCHC6 WILD-TYPE
  N0             13              207
  N1              2               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"
D684V6, binary
                  cls
clus                 0   1
  ZCCHC6 MUTATED    14   1
  ZCCHC6 WILD-TYPE 269  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZCCHC6 MUTATED     14    1
  ZCCHC6 WILD-TYPE  269   47
   clus
vv  ZCCHC6 MUTATED ZCCHC6 WILD-TYPE
  0             14              269
  1              1               47
[1] 2 2
[1] FALSE
D684V7, 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
D684V8, binary
                  cls
clus                 0   1
  ZCCHC6 MUTATED    12   6
  ZCCHC6 WILD-TYPE 305  42
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZCCHC6 MUTATED     12    6
  ZCCHC6 WILD-TYPE  305   42
                               clus
vv                              ZCCHC6 MUTATED ZCCHC6 WILD-TYPE
  COLON ADENOCARCINOMA                      12              305
  COLON MUCINOUS ADENOCARCINOMA              6               42
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZCCHC6 MUTATED    11   0   1   2
  ZCCHC6 WILD-TYPE 246   2  21  19
D684V9, multiclass
    clus
vv   ZCCHC6 MUTATED ZCCHC6 WILD-TYPE
  R0             11              246
  R1              0                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"
D684V10, 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
D684V11, 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(685) Variable = HIVEP2 MUTATION ANALYSIS
D685V1, survival
                  sevent
clus2                0   1
  HIVEP2 MUTATED    15   3
  HIVEP2 WILD-TYPE 267  70
  HIVEP2 MUTATED HIVEP2 WILD-TYPE 
              18              337 
  HIVEP2 MUTATED HIVEP2 WILD-TYPE 
               3               70 
$`HIVEP2 MUTATED`
TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3664 TCGA-AA-3710 TCGA-AA-3821 TCGA-AA-3877 
       19.66        63.98        54.02        26.99         1.02        31.00 
TCGA-AA-3950 TCGA-AD-6889 TCGA-AZ-6607 TCGA-CA-6717 TCGA-CM-4744 TCGA-CM-5344 
       24.00        56.55         3.19         0.33        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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
        0.99        25.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        4.21         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 
       29.06        22.98        30.08        16.01        15.02        15.02 
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-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.08        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6628 
       52.80 

  HIVEP2 MUTATED HIVEP2 WILD-TYPE 
            0.33             0.00 
  HIVEP2 MUTATED HIVEP2 WILD-TYPE 
          135.65           140.38 
  HIVEP2 MUTATED HIVEP2 WILD-TYPE 
          21.025           20.190 
[1] "0.3 - 135.7 (21.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.5"
D685V2, 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       23       102         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HIVEP2 MUTATED           0          0          2          1        1
  HIVEP2 WILD-TYPE        19         10         39         30       34
                  vv
clus               STAGE IVA STAGE IVB
  HIVEP2 MUTATED           2         0
  HIVEP2 WILD-TYPE        11         1
D685V3, multiclass
            clus
vv           HIVEP2 MUTATED HIVEP2 WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               7              102
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              1               30
  STAGE IV                1               34
  STAGE IVA               2               11
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  65 236  38
D685V4, multiclass
    clus
vv   HIVEP2 MUTATED HIVEP2 WILD-TYPE
  T1              1                8
  T2              3               65
  T3             12              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
  HIVEP2 MUTATED    13   5   1
  HIVEP2 WILD-TYPE 207  75  65
D685V5, multiclass
    clus
vv   HIVEP2 MUTATED HIVEP2 WILD-TYPE
  N0             13              207
  N1              5               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"
D685V6, binary
                  cls
clus                 0   1
  HIVEP2 MUTATED    15   3
  HIVEP2 WILD-TYPE 268  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HIVEP2 MUTATED     15    3
  HIVEP2 WILD-TYPE  268   45
   clus
vv  HIVEP2 MUTATED HIVEP2 WILD-TYPE
  0             15              268
  1              3               45
[1] 2 2
[1] FALSE
D685V7, 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
D685V8, binary
                  cls
clus                 0   1
  HIVEP2 MUTATED    14   5
  HIVEP2 WILD-TYPE 303  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HIVEP2 MUTATED     14    5
  HIVEP2 WILD-TYPE  303   43
                               clus
vv                              HIVEP2 MUTATED HIVEP2 WILD-TYPE
  COLON ADENOCARCINOMA                      14              303
  COLON MUCINOUS ADENOCARCINOMA              5               43
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  HIVEP2 MUTATED    15   0   0   1
  HIVEP2 WILD-TYPE 242   2  22  20
D685V9, multiclass
    clus
vv   HIVEP2 MUTATED HIVEP2 WILD-TYPE
  R0             15              242
  R1              0                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"
D685V10, 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
D685V11, 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(686) Variable = FER MUTATION ANALYSIS
D686V1, survival
               sevent
clus2             0   1
  FER MUTATED    12   2
  FER WILD-TYPE 270  71
  FER MUTATED FER WILD-TYPE 
           14           341 
  FER MUTATED FER WILD-TYPE 
            2            71 
$`FER MUTATED`
TCGA-AA-3867 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-A010 TCGA-AZ-4315 TCGA-CK-5914 
       24.03        33.01        24.00        34.98        58.39        21.99 
TCGA-CK-5916 TCGA-CM-5862 TCGA-CM-6172 TCGA-CM-6674 TCGA-D5-6930 TCGA-G4-6306 
       21.14         5.03        11.01        12.95         1.51        44.68 
TCGA-G4-6586 TCGA-G4-6628 
       35.80        52.80 

$`FER WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       53.00        17.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
        2.01        12.99        24.00        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       49.08        51.32         2.93         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        16.01        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-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        26.17        91.79        46.75 

  FER MUTATED FER WILD-TYPE 
         1.51          0.00 
  FER MUTATED FER WILD-TYPE 
        58.39        140.38 
  FER MUTATED FER WILD-TYPE 
       24.015        19.990 
[1] "1.5 - 58.4 (24.0)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1.5"
D686V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FER MUTATED         2        0        0         7         2         0
  FER WILD-TYPE      62        1       25       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        19         10         39         31       34        12
               vv
clus            STAGE IVB
  FER MUTATED           0
  FER WILD-TYPE         1
D686V3, multiclass
            clus
vv           FER MUTATED FER WILD-TYPE
  STAGE I              2            62
  STAGE IA             0             1
  STAGE II             0            25
  STAGE IIA            7           102
  STAGE IIB            2             6
  STAGE IIC            0             1
  STAGE III            0            19
  STAGE IIIA           0            10
  STAGE IIIB           2            39
  STAGE IIIC           0            31
  STAGE IV             1            34
  STAGE IVA            1            12
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 238  39
D686V4, multiclass
    clus
vv   FER MUTATED FER WILD-TYPE
  T1           1             8
  T2           2            66
  T3          10           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
  FER MUTATED    11   3   1
  FER WILD-TYPE 209  77  65
D686V5, multiclass
    clus
vv   FER MUTATED FER WILD-TYPE
  N0          11           209
  N1           3            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"
D686V6, binary
               cls
clus              0   1
  FER MUTATED    12   2
  FER WILD-TYPE 271  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  FER MUTATED     12    2
  FER WILD-TYPE  271   46
   clus
vv  FER MUTATED FER WILD-TYPE
  0          12           271
  1           2            46
[1] 2 2
[1] FALSE
D686V7, 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
D686V8, binary
               cls
clus              0   1
  FER MUTATED    12   3
  FER WILD-TYPE 305  45
[1] "tbl2"
               cls
clus            [,1] [,2]
  FER MUTATED     12    3
  FER WILD-TYPE  305   45
                               clus
vv                              FER MUTATED FER WILD-TYPE
  COLON ADENOCARCINOMA                   12           305
  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 245   2  21  19
D686V9, multiclass
    clus
vv   FER MUTATED FER WILD-TYPE
  R0          12           245
  R1           0             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"
D686V10, 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
D686V11, 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(687) Variable = PHF1 MUTATION ANALYSIS
D687V1, survival
                sevent
clus2              0   1
  PHF1 MUTATED     4   2
  PHF1 WILD-TYPE 278  71
  PHF1 MUTATED PHF1 WILD-TYPE 
             6            349 
  PHF1 MUTATED PHF1 WILD-TYPE 
             2             71 
$`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         0.33         6.18        36.72 

$`PHF1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13        83.80        22.36        62.79        61.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       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        13.38        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 
       53.62        44.68        55.04        51.75        45.11        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  PHF1 MUTATED PHF1 WILD-TYPE 
          0.33           0.00 
  PHF1 MUTATED PHF1 WILD-TYPE 
         49.41         140.38 
  PHF1 MUTATED PHF1 WILD-TYPE 
         20.86          20.19 
[1] "0.3 - 49.4 (20.9)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.8"
D687V2, 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       24       106         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        19         10         41         30       34        13
                vv
clus             STAGE IVB
  PHF1 MUTATED           0
  PHF1 WILD-TYPE         1
D687V3, multiclass
            clus
vv           PHF1 MUTATED PHF1 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             3            106
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            1             30
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PHF1 MUTATED     0   0   5   1
  PHF1 WILD-TYPE   9  68 243  40
D687V4, multiclass
    clus
vv   PHF1 MUTATED PHF1 WILD-TYPE
  T1            0              9
  T2            0             68
  T3            5            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
  PHF1 MUTATED     4   2   0
  PHF1 WILD-TYPE 216  78  66
D687V5, multiclass
    clus
vv   PHF1 MUTATED PHF1 WILD-TYPE
  N0            4            216
  N1            2             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"
D687V6, binary
                cls
clus               0   1
  PHF1 MUTATED     3   1
  PHF1 WILD-TYPE 280  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  PHF1 MUTATED      3    1
  PHF1 WILD-TYPE  280   47
   clus
vv  PHF1 MUTATED PHF1 WILD-TYPE
  0            3            280
  1            1             47
[1] 2 2
[1] FALSE
D687V7, 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
D687V8, binary
                cls
clus               0   1
  PHF1 MUTATED     4   2
  PHF1 WILD-TYPE 313  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  PHF1 MUTATED      4    2
  PHF1 WILD-TYPE  313   46
                               clus
vv                              PHF1 MUTATED PHF1 WILD-TYPE
  COLON ADENOCARCINOMA                     4            313
  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 253   2  22  20
D687V9, multiclass
    clus
vv   PHF1 MUTATED PHF1 WILD-TYPE
  R0            4            253
  R1            0              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"
D687V10, 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
D687V11, 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(688) Variable = ZNF799 MUTATION ANALYSIS
D688V1, survival
                  sevent
clus2                0   1
  ZNF799 MUTATED     5   1
  ZNF799 WILD-TYPE 277  72
  ZNF799 MUTATED ZNF799 WILD-TYPE 
               6              349 
  ZNF799 MUTATED ZNF799 WILD-TYPE 
               1               72 
$`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        61.41        18.25        44.32 

$`ZNF799 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  ZNF799 MUTATED ZNF799 WILD-TYPE 
            6.05             0.00 
  ZNF799 MUTATED ZNF799 WILD-TYPE 
           61.41           140.38 
  ZNF799 MUTATED ZNF799 WILD-TYPE 
           39.65            20.12 
[1] "6.0 - 61.4 (39.6)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.8"
D688V2, 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       25       106         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF799 MUTATED           0          0          0          0        1
  ZNF799 WILD-TYPE        19         10         41         31       34
                  vv
clus               STAGE IVA STAGE IVB
  ZNF799 MUTATED           0         0
  ZNF799 WILD-TYPE        13         1
D688V3, multiclass
            clus
vv           ZNF799 MUTATED ZNF799 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               3              106
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF799 MUTATED     1   0   3   2
  ZNF799 WILD-TYPE   8  68 245  39
D688V4, multiclass
    clus
vv   ZNF799 MUTATED ZNF799 WILD-TYPE
  T1              1                8
  T2              0               68
  T3              3              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
  ZNF799 MUTATED     5   0   1
  ZNF799 WILD-TYPE 215  80  65
D688V5, multiclass
    clus
vv   ZNF799 MUTATED ZNF799 WILD-TYPE
  N0              5              215
  N1              0               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"
D688V6, binary
                  cls
clus                 0   1
  ZNF799 MUTATED     5   1
  ZNF799 WILD-TYPE 278  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF799 MUTATED      5    1
  ZNF799 WILD-TYPE  278   47
   clus
vv  ZNF799 MUTATED ZNF799 WILD-TYPE
  0              5              278
  1              1               47
[1] 2 2
[1] FALSE
D688V7, 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
D688V8, binary
                  cls
clus                 0   1
  ZNF799 MUTATED     6   0
  ZNF799 WILD-TYPE 311  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF799 MUTATED      6    0
  ZNF799 WILD-TYPE  311   48
                               clus
vv                              ZNF799 MUTATED ZNF799 WILD-TYPE
  COLON ADENOCARCINOMA                       6              311
  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 254   2  21  21
D688V9, multiclass
    clus
vv   ZNF799 MUTATED ZNF799 WILD-TYPE
  R0              3              254
  R1              0                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"
D688V10, 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
D688V11, 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(689) Variable = CDK17 MUTATION ANALYSIS
D689V1, survival
                 sevent
clus2               0   1
  CDK17 MUTATED     7   3
  CDK17 WILD-TYPE 275  70
  CDK17 MUTATED CDK17 WILD-TYPE 
             10             345 
  CDK17 MUTATED CDK17 WILD-TYPE 
              3              70 
$`CDK17 MUTATED`
TCGA-AA-3994 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6963 TCGA-AZ-6598 TCGA-CA-6718 
       27.02         4.01        34.98        27.42        49.41         0.10 
TCGA-CK-4950 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6626 
       40.34        13.78        26.17        46.75 

$`CDK17 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 
       24.00        27.02        27.02        19.07         7.96        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
        1.35        17.56       102.44        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 
       35.80        91.79        52.80 

  CDK17 MUTATED CDK17 WILD-TYPE 
            0.1             0.0 
  CDK17 MUTATED CDK17 WILD-TYPE 
          49.41          140.38 
  CDK17 MUTATED CDK17 WILD-TYPE 
          27.22           20.02 
[1] "0.1 - 49.4 (27.2)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1.4"
D689V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CDK17 MUTATED         0        1        1         3         2         0
  CDK17 WILD-TYPE      64        0       24       106         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CDK17 MUTATED           0          1          1          0        0         0
  CDK17 WILD-TYPE        19          9         40         31       35        13
                 vv
clus              STAGE IVB
  CDK17 MUTATED           0
  CDK17 WILD-TYPE         1
D689V3, multiclass
            clus
vv           CDK17 MUTATED CDK17 WILD-TYPE
  STAGE I                0              64
  STAGE IA               1               0
  STAGE II               1              24
  STAGE IIA              3             106
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CDK17 MUTATED     0   0   7   2
  CDK17 WILD-TYPE   9  68 241  39
D689V4, multiclass
    clus
vv   CDK17 MUTATED CDK17 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             7             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
  CDK17 MUTATED     8   2   0
  CDK17 WILD-TYPE 212  78  66
D689V5, multiclass
    clus
vv   CDK17 MUTATED CDK17 WILD-TYPE
  N0             8             212
  N1             2              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"
D689V6, binary
                 cls
clus                0   1
  CDK17 MUTATED     7   0
  CDK17 WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK17 MUTATED      7    0
  CDK17 WILD-TYPE  276   48
   clus
vv  CDK17 MUTATED CDK17 WILD-TYPE
  0             7             276
  1             0              48
[1] 2 2
[1] FALSE
D689V7, binary
                 cls
clus                0   1
  CDK17 MUTATED     4   6
  CDK17 WILD-TYPE 166 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK17 MUTATED      4    6
  CDK17 WILD-TYPE  166  191
        clus
vv       CDK17 MUTATED CDK17 WILD-TYPE
  FEMALE             4             166
  MALE               6             191
[1] 2 2
[1] FALSE
D689V8, binary
                 cls
clus                0   1
  CDK17 MUTATED     8   2
  CDK17 WILD-TYPE 309  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK17 MUTATED      8    2
  CDK17 WILD-TYPE  309   46
                               clus
vv                              CDK17 MUTATED CDK17 WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CDK17 MUTATED     6   1   0   1
  CDK17 WILD-TYPE 251   1  22  20
D689V9, multiclass
    clus
vv   CDK17 MUTATED CDK17 WILD-TYPE
  R0             6             251
  R1             1               1
  R2             0              22
  RX             1              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D689V10, 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
D689V11, 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(690) Variable = FAM98B MUTATION ANALYSIS
D690V1, survival
                  sevent
clus2                0   1
  FAM98B MUTATED     4   0
  FAM98B WILD-TYPE 278  73
  FAM98B MUTATED FAM98B WILD-TYPE 
               4              351 
  FAM98B MUTATED FAM98B WILD-TYPE 
               0               73 
$`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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  FAM98B MUTATED FAM98B WILD-TYPE 
           12.43             0.00 
  FAM98B MUTATED FAM98B WILD-TYPE 
           25.02           140.38 
  FAM98B MUTATED FAM98B WILD-TYPE 
          15.255           20.280 
[1] "12.4 - 25.0 (15.3)" "0.0 - 140.4 (20.3)"
[1] "hr="     "3300000"
D690V2, 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       25       108         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM98B MUTATED           0          0          0          0        0
  FAM98B WILD-TYPE        19         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  FAM98B MUTATED           1         0
  FAM98B WILD-TYPE        12         1
D690V3, multiclass
            clus
vv           FAM98B MUTATED FAM98B WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               1              108
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 247  40
D690V4, multiclass
    clus
vv   FAM98B MUTATED FAM98B WILD-TYPE
  T1              0                9
  T2              2               66
  T3              1              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
  FAM98B MUTATED     3   1   0
  FAM98B WILD-TYPE 217  79  66
D690V5, multiclass
    clus
vv   FAM98B MUTATED FAM98B WILD-TYPE
  N0              3              217
  N1              1               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"
D690V6, binary
                  cls
clus                 0   1
  FAM98B MUTATED     3   0
  FAM98B WILD-TYPE 280  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM98B MUTATED      3    0
  FAM98B WILD-TYPE  280   48
   clus
vv  FAM98B MUTATED FAM98B WILD-TYPE
  0              3              280
  1              0               48
[1] 2 2
[1] FALSE
D690V7, 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
D690V8, binary
                  cls
clus                 0   1
  FAM98B MUTATED     4   0
  FAM98B WILD-TYPE 313  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM98B MUTATED      4    0
  FAM98B WILD-TYPE  313   48
                               clus
vv                              FAM98B MUTATED FAM98B WILD-TYPE
  COLON ADENOCARCINOMA                       4              313
  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 255   2  22  20
D690V9, multiclass
    clus
vv   FAM98B MUTATED FAM98B WILD-TYPE
  R0              2              255
  R1              0                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"
D690V10, 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
D690V11, 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(691) Variable = NCAPD3 MUTATION ANALYSIS
D691V1, survival
                  sevent
clus2                0   1
  NCAPD3 MUTATED    23   2
  NCAPD3 WILD-TYPE 259  71
  NCAPD3 MUTATED NCAPD3 WILD-TYPE 
              25              330 
  NCAPD3 MUTATED NCAPD3 WILD-TYPE 
               2               71 
$`NCAPD3 MUTATED`
TCGA-A6-3809 TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3655 
       32.75        22.06        63.98         1.02         1.02        61.02 
TCGA-AA-3713 TCGA-AA-3869 TCGA-AA-A010 TCGA-AD-6889 TCGA-AD-6963 TCGA-AD-6965 
       19.04        27.02        34.98        56.55        27.42         0.20 
TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4743 TCGA-CM-5861 TCGA-CM-6162 
       58.39         0.33         0.10        23.05        15.02        12.00 
TCGA-CM-6166 TCGA-CM-6170 TCGA-CM-6171 TCGA-D5-5541 TCGA-DM-A1D9 TCGA-F4-6570 
       21.99        15.02        14.04        11.51       140.38         6.18 
TCGA-G4-6586 
       35.80 

$`NCAPD3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
        6.97        13.02        38.99         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 
       23.01        20.98        19.99        13.94        19.99        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       17.03        24.03        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37         4.21         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 TCGA-AU-3779 TCGA-AU-6004 
        0.72         5.79        22.42        10.88        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07         0.26         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93         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        16.01 
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        12.26        19.59        13.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       12.59         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        13.38        13.45        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        26.17        91.79        46.75        52.80 

  NCAPD3 MUTATED NCAPD3 WILD-TYPE 
             0.1              0.0 
  NCAPD3 MUTATED NCAPD3 WILD-TYPE 
          140.38           139.17 
  NCAPD3 MUTATED NCAPD3 WILD-TYPE 
          21.990           20.155 
[1] "0.1 - 140.4 (22.0)" "0.0 - 139.2 (20.2)"
[1] "hr=" "2.8"
D691V2, 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       23        98         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NCAPD3 MUTATED           0          0          2          0        2
  NCAPD3 WILD-TYPE        19         10         39         31       33
                  vv
clus               STAGE IVA STAGE IVB
  NCAPD3 MUTATED           0         0
  NCAPD3 WILD-TYPE        13         1
D691V3, multiclass
            clus
vv           NCAPD3 MUTATED NCAPD3 WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA              11               98
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              0               31
  STAGE IV                2               33
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  NCAPD3 MUTATED     0   4  17   4
  NCAPD3 WILD-TYPE   9  64 231  37
D691V4, multiclass
    clus
vv   NCAPD3 MUTATED NCAPD3 WILD-TYPE
  T1              0                9
  T2              4               64
  T3             17              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
  NCAPD3 MUTATED    21   2   2
  NCAPD3 WILD-TYPE 199  78  64
D691V5, multiclass
    clus
vv   NCAPD3 MUTATED NCAPD3 WILD-TYPE
  N0             21              199
  N1              2               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"
D691V6, binary
                  cls
clus                 0   1
  NCAPD3 MUTATED    21   2
  NCAPD3 WILD-TYPE 262  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NCAPD3 MUTATED     21    2
  NCAPD3 WILD-TYPE  262   46
   clus
vv  NCAPD3 MUTATED NCAPD3 WILD-TYPE
  0             21              262
  1              2               46
[1] 2 2
[1] FALSE
D691V7, 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
D691V8, binary
                  cls
clus                 0   1
  NCAPD3 MUTATED    22   3
  NCAPD3 WILD-TYPE 295  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NCAPD3 MUTATED     22    3
  NCAPD3 WILD-TYPE  295   45
                               clus
vv                              NCAPD3 MUTATED NCAPD3 WILD-TYPE
  COLON ADENOCARCINOMA                      22              295
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  NCAPD3 MUTATED    17   0   2   2
  NCAPD3 WILD-TYPE 240   2  20  19
D691V9, multiclass
    clus
vv   NCAPD3 MUTATED NCAPD3 WILD-TYPE
  R0             17              240
  R1              0                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"
D691V10, 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
D691V11, 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(692) Variable = EYS MUTATION ANALYSIS
D692V1, survival
               sevent
clus2             0   1
  EYS MUTATED    37  10
  EYS WILD-TYPE 245  63
  EYS MUTATED EYS WILD-TYPE 
           47           308 
  EYS MUTATED EYS WILD-TYPE 
           10            63 
$`EYS MUTATED`
TCGA-A6-3809 TCGA-A6-5656 TCGA-A6-6141 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       32.75        32.91         8.38        20.28         7.04         1.02 
TCGA-AA-3511 TCGA-AA-3516 TCGA-AA-3815 TCGA-AA-3831 TCGA-AA-3861 TCGA-AA-3930 
        6.97        13.02        33.04        17.98        30.05         2.01 
TCGA-AA-3977 TCGA-AA-3994 TCGA-AA-A00N TCGA-AA-A01Q TCGA-AD-6889 TCGA-AD-6899 
       25.02        27.02         4.01         1.02        56.55         5.79 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 TCGA-CA-6717 
       27.42        10.88         0.20        21.44        58.39         0.33 
TCGA-CA-6718 TCGA-CK-5913 TCGA-CM-4743 TCGA-CM-4747 TCGA-CM-5348 TCGA-CM-5861 
        0.10        51.32        23.05        25.02        22.98        15.02 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-D5-6533 TCGA-D5-6540 TCGA-D5-6926 
       13.05        11.08        11.01         1.32        16.14         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6931 TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-DM-A28E 
        9.44        11.64        12.00        49.91         7.50       119.93 
TCGA-F4-6570 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6626 TCGA-G4-6628 
        6.18        53.62        44.68        46.75        52.80 

$`EYS WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5657 
       16.57        34.65        33.34        36.53        14.53        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       32.71        27.09        22.52        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-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-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3833 TCGA-AA-3837 
       35.05         0.99        25.02         1.02        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05        31.00        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        27.02        19.07         7.96        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-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        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37         4.21         0.79         0.72 
TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       22.42         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       15.75        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07         0.26         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
       17.56       102.44        40.34        15.62        49.08        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14         2.93         2.01       124.27        20.02        37.02 
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        16.01         5.03 
TCGA-CM-5863 TCGA-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-6677 TCGA-CM-6679 
       15.02        14.04        11.01        12.95        11.08        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        13.51        11.51 
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-D5-6922 
       17.13        12.49        15.58         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 
       12.43        14.30        13.41         1.51        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 
      119.70        24.43        38.20       130.65        92.75        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       12.59       140.38        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
        6.12        81.37        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        13.38        13.45        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6309 
       19.43       107.67        74.56        65.85        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 
       26.17        91.79 

  EYS MUTATED EYS WILD-TYPE 
          0.1           0.0 
  EYS MUTATED EYS WILD-TYPE 
       119.93        140.38 
  EYS MUTATED EYS WILD-TYPE 
       15.020        20.995 
[1] "0.1 - 119.9 (15.0)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.2"
D692V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EYS MUTATED         4        0        4        19         4         0
  EYS WILD-TYPE      60        1       21        90         4         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EYS MUTATED           1          1          3          4        1         2
  EYS WILD-TYPE        18          9         38         27       34        11
               vv
clus            STAGE IVB
  EYS MUTATED           1
  EYS WILD-TYPE         0
D692V3, multiclass
            clus
vv           EYS MUTATED EYS WILD-TYPE
  STAGE I              4            60
  STAGE IA             0             1
  STAGE II             4            21
  STAGE IIA           19            90
  STAGE IIB            4             4
  STAGE IIC            0             1
  STAGE III            1            18
  STAGE IIIA           1             9
  STAGE IIIB           3            38
  STAGE IIIC           4            27
  STAGE IV             1            34
  STAGE IVA            2            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   6  29  12
  EYS WILD-TYPE   9  62 219  29
D692V4, multiclass
    clus
vv   EYS MUTATED EYS WILD-TYPE
  T1           0             9
  T2           6            62
  T3          29           219
  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
  EYS MUTATED    34   5   8
  EYS WILD-TYPE 186  75  58
D692V5, multiclass
    clus
vv   EYS MUTATED EYS WILD-TYPE
  N0          34           186
  N1           5            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"
D692V6, binary
               cls
clus              0   1
  EYS MUTATED    35   4
  EYS WILD-TYPE 248  44
[1] "tbl2"
               cls
clus            [,1] [,2]
  EYS MUTATED     35    4
  EYS WILD-TYPE  248   44
   clus
vv  EYS MUTATED EYS WILD-TYPE
  0          35           248
  1           4            44
[1] 2 2
[1] FALSE
D692V7, binary
               cls
clus              0   1
  EYS MUTATED    13  34
  EYS WILD-TYPE 157 163
[1] "tbl2"
               cls
clus            [,1] [,2]
  EYS MUTATED     13   34
  EYS WILD-TYPE  157  163
        clus
vv       EYS MUTATED EYS WILD-TYPE
  FEMALE          13           157
  MALE            34           163
[1] 2 2
[1] FALSE
D692V8, binary
               cls
clus              0   1
  EYS MUTATED    37  10
  EYS WILD-TYPE 280  38
[1] "tbl2"
               cls
clus            [,1] [,2]
  EYS MUTATED     37   10
  EYS WILD-TYPE  280   38
                               clus
vv                              EYS MUTATED EYS WILD-TYPE
  COLON ADENOCARCINOMA                   37           280
  COLON MUCINOUS ADENOCARCINOMA          10            38
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  EYS MUTATED    31   0   1   3
  EYS WILD-TYPE 226   2  21  18
D692V9, multiclass
    clus
vv   EYS MUTATED EYS WILD-TYPE
  R0          31           226
  R1           0             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"
D692V10, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EYS MUTATED                                  0     3
  EYS WILD-TYPE                                1     7
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  EYS MUTATED                           2    30
  EYS WILD-TYPE                        17   146
D692V11, multiclass
                                  clus
vv                                 EYS MUTATED EYS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      3             7
  BLACK OR AFRICAN AMERICAN                  2            17
  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(693) Variable = NFATC3 MUTATION ANALYSIS
D693V1, survival
                  sevent
clus2                0   1
  NFATC3 MUTATED     9   1
  NFATC3 WILD-TYPE 273  72
  NFATC3 MUTATED NFATC3 WILD-TYPE 
              10              345 
  NFATC3 MUTATED NFATC3 WILD-TYPE 
               1               72 
$`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         0.26         0.33 
TCGA-CM-5868 TCGA-D5-6532 TCGA-D5-6540 TCGA-G4-6303 
       17.03        18.25        16.14        65.85 

$`NFATC3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6718 
        2.24         3.06         3.25         3.29         0.07         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       13.51        11.51        20.19         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  NFATC3 MUTATED NFATC3 WILD-TYPE 
            0.26             0.00 
  NFATC3 MUTATED NFATC3 WILD-TYPE 
           65.85           140.38 
  NFATC3 MUTATED NFATC3 WILD-TYPE 
           21.32            20.19 
[1] "0.3 - 65.8 (21.3)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2.3"
D693V2, 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       23       106         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NFATC3 MUTATED           0          0          0          0        2
  NFATC3 WILD-TYPE        19         10         41         31       33
                  vv
clus               STAGE IVA STAGE IVB
  NFATC3 MUTATED           1         0
  NFATC3 WILD-TYPE        12         1
D693V3, multiclass
            clus
vv           NFATC3 MUTATED NFATC3 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               3              106
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                2               33
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  65 243  37
D693V4, multiclass
    clus
vv   NFATC3 MUTATED NFATC3 WILD-TYPE
  T1              0                9
  T2              3               65
  T3              5              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
  NFATC3 MUTATED     9   3   0
  NFATC3 WILD-TYPE 211  77  66
D693V5, multiclass
    clus
vv   NFATC3 MUTATED NFATC3 WILD-TYPE
  N0              9              211
  N1              3               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"
D693V6, binary
                  cls
clus                 0   1
  NFATC3 MUTATED     9   3
  NFATC3 WILD-TYPE 274  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFATC3 MUTATED      9    3
  NFATC3 WILD-TYPE  274   45
   clus
vv  NFATC3 MUTATED NFATC3 WILD-TYPE
  0              9              274
  1              3               45
[1] 2 2
[1] FALSE
D693V7, 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
D693V8, binary
                  cls
clus                 0   1
  NFATC3 MUTATED    10   2
  NFATC3 WILD-TYPE 307  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFATC3 MUTATED     10    2
  NFATC3 WILD-TYPE  307   46
                               clus
vv                              NFATC3 MUTATED NFATC3 WILD-TYPE
  COLON ADENOCARCINOMA                      10              307
  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 249   2  21  19
D693V9, multiclass
    clus
vv   NFATC3 MUTATED NFATC3 WILD-TYPE
  R0              8              249
  R1              0                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"
D693V10, 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
D693V11, 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(694) Variable = ADAMTS19 MUTATION ANALYSIS
D694V1, survival
                    sevent
clus2                  0   1
  ADAMTS19 MUTATED    13   6
  ADAMTS19 WILD-TYPE 269  67
  ADAMTS19 MUTATED ADAMTS19 WILD-TYPE 
                19                336 
  ADAMTS19 MUTATED ADAMTS19 WILD-TYPE 
                 6                 67 
$`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 
      107.67 

$`ADAMTS19 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       19.00        30.02        34.03        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        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        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42        10.88         0.20        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       15.75         0.20        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41        49.41        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
       29.56        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19        18.25         1.32        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
        6.12        81.37       119.93        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.41        19.43        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  ADAMTS19 MUTATED ADAMTS19 WILD-TYPE 
              4.01               0.00 
  ADAMTS19 MUTATED ADAMTS19 WILD-TYPE 
            135.65             140.38 
  ADAMTS19 MUTATED ADAMTS19 WILD-TYPE 
             27.09              19.99 
[1] "4.0 - 135.7 (27.1)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.2"
D694V2, 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       25       102         5         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ADAMTS19 MUTATED           2          0          4          0        0
  ADAMTS19 WILD-TYPE        17         10         37         31       35
                    vv
clus                 STAGE IVA STAGE IVB
  ADAMTS19 MUTATED           1         0
  ADAMTS19 WILD-TYPE        12         1
D694V3, multiclass
            clus
vv           ADAMTS19 MUTATED ADAMTS19 WILD-TYPE
  STAGE I                   2                 62
  STAGE IA                  0                  1
  STAGE II                  0                 25
  STAGE IIA                 7                102
  STAGE IIB                 3                  5
  STAGE IIC                 0                  1
  STAGE III                 2                 17
  STAGE IIIA                0                 10
  STAGE IIIB                4                 37
  STAGE IIIC                0                 31
  STAGE IV                  0                 35
  STAGE IVA                 1                 12
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 237  35
D694V4, multiclass
    clus
vv   ADAMTS19 MUTATED ADAMTS19 WILD-TYPE
  T1                0                  9
  T2                2                 66
  T3               11                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
  ADAMTS19 MUTATED    12   7   0
  ADAMTS19 WILD-TYPE 208  73  66
D694V5, multiclass
    clus
vv   ADAMTS19 MUTATED ADAMTS19 WILD-TYPE
  N0               12                208
  N1                7                 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"
D694V6, binary
                    cls
clus                   0   1
  ADAMTS19 MUTATED    15   1
  ADAMTS19 WILD-TYPE 268  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ADAMTS19 MUTATED     15    1
  ADAMTS19 WILD-TYPE  268   47
   clus
vv  ADAMTS19 MUTATED ADAMTS19 WILD-TYPE
  0               15                268
  1                1                 47
[1] 2 2
[1] FALSE
D694V7, 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
D694V8, binary
                    cls
clus                   0   1
  ADAMTS19 MUTATED    15   4
  ADAMTS19 WILD-TYPE 302  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ADAMTS19 MUTATED     15    4
  ADAMTS19 WILD-TYPE  302   44
                               clus
vv                              ADAMTS19 MUTATED ADAMTS19 WILD-TYPE
  COLON ADENOCARCINOMA                        15                302
  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 243   2  22  21
D694V9, multiclass
    clus
vv   ADAMTS19 MUTATED ADAMTS19 WILD-TYPE
  R0               14                243
  R1                0                  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"
D694V10, 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
D694V11, 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(695) Variable = OR6A2 MUTATION ANALYSIS
D695V1, survival
                 sevent
clus2               0   1
  OR6A2 MUTATED     6   2
  OR6A2 WILD-TYPE 276  71
  OR6A2 MUTATED OR6A2 WILD-TYPE 
              8             347 
  OR6A2 MUTATED OR6A2 WILD-TYPE 
              2              71 
$`OR6A2 MUTATED`
TCGA-AA-3516 TCGA-AA-A00N TCGA-CA-6717 TCGA-CK-4948 TCGA-CM-5348 TCGA-CM-6168 
       13.02         4.01         0.33       102.44        22.98        12.99 
TCGA-D5-6541 TCGA-G4-6317 
       15.58        36.00 

$`OR6A2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        1.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 
        0.07         0.26         0.10         1.35        17.56        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 
       55.04        51.75        45.11        36.72        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  OR6A2 MUTATED OR6A2 WILD-TYPE 
           0.33            0.00 
  OR6A2 MUTATED OR6A2 WILD-TYPE 
         102.44          140.38 
  OR6A2 MUTATED OR6A2 WILD-TYPE 
          14.30           20.28 
[1] "0.3 - 102.4 (14.3)" "0.0 - 140.4 (20.3)"
[1] "hr=" "1.2"
D695V2, 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       25       106         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR6A2 MUTATED           1          1          1          1        0         0
  OR6A2 WILD-TYPE        18          9         40         30       35        13
                 vv
clus              STAGE IVB
  OR6A2 MUTATED           0
  OR6A2 WILD-TYPE         1
D695V3, multiclass
            clus
vv           OR6A2 MUTATED OR6A2 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              3             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             1               9
  STAGE IIIB             1              40
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR6A2 MUTATED     0   0   7   1
  OR6A2 WILD-TYPE   9  68 241  40
D695V4, multiclass
    clus
vv   OR6A2 MUTATED OR6A2 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             7             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
  OR6A2 MUTATED     4   2   2
  OR6A2 WILD-TYPE 216  78  64
D695V5, multiclass
    clus
vv   OR6A2 MUTATED OR6A2 WILD-TYPE
  N0             4             216
  N1             2              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"
D695V6, binary
                 cls
clus                0   1
  OR6A2 MUTATED     7   0
  OR6A2 WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR6A2 MUTATED      7    0
  OR6A2 WILD-TYPE  276   48
   clus
vv  OR6A2 MUTATED OR6A2 WILD-TYPE
  0             7             276
  1             0              48
[1] 2 2
[1] FALSE
D695V7, 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
D695V8, binary
                 cls
clus                0   1
  OR6A2 MUTATED     5   3
  OR6A2 WILD-TYPE 312  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR6A2 MUTATED      5    3
  OR6A2 WILD-TYPE  312   45
                               clus
vv                              OR6A2 MUTATED OR6A2 WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  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 251   2  22  20
D695V9, multiclass
    clus
vv   OR6A2 MUTATED OR6A2 WILD-TYPE
  R0             6             251
  R1             0               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"
D695V10, 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
D695V11, 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(696) Variable = FAM26E MUTATION ANALYSIS
D696V1, survival
                  sevent
clus2                0   1
  FAM26E MUTATED     5   0
  FAM26E WILD-TYPE 277  73
  FAM26E MUTATED FAM26E WILD-TYPE 
               5              350 
  FAM26E MUTATED FAM26E WILD-TYPE 
               0               73 
$`FAM26E MUTATED`
TCGA-A6-5661 TCGA-AA-3977 TCGA-AD-6889 TCGA-D5-6540 TCGA-F4-6856 
       33.53        25.02        56.55        16.14        19.43 

$`FAM26E WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        35.41       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  FAM26E MUTATED FAM26E WILD-TYPE 
           16.14             0.00 
  FAM26E MUTATED FAM26E WILD-TYPE 
           56.55           140.38 
  FAM26E MUTATED FAM26E WILD-TYPE 
          25.020           20.155 
[1] "16.1 - 56.5 (25.0)" "0.0 - 140.4 (20.2)"
[1] "hr="     "9100000"
D696V2, 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       25       107         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM26E MUTATED           0          0          0          0        0
  FAM26E WILD-TYPE        19         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  FAM26E MUTATED           0         0
  FAM26E WILD-TYPE        13         1
D696V3, multiclass
            clus
vv           FAM26E MUTATED FAM26E WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               2              107
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FAM26E MUTATED     0   3   2   0
  FAM26E WILD-TYPE   9  65 246  41
D696V4, multiclass
    clus
vv   FAM26E MUTATED FAM26E WILD-TYPE
  T1              0                9
  T2              3               65
  T3              2              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
  FAM26E MUTATED     5   0   0
  FAM26E WILD-TYPE 215  80  66
D696V5, multiclass
    clus
vv   FAM26E MUTATED FAM26E WILD-TYPE
  N0              5              215
  N1              0               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"
D696V6, binary
                  cls
clus                 0   1
  FAM26E MUTATED     4   0
  FAM26E WILD-TYPE 279  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM26E MUTATED      4    0
  FAM26E WILD-TYPE  279   48
   clus
vv  FAM26E MUTATED FAM26E WILD-TYPE
  0              4              279
  1              0               48
[1] 2 2
[1] FALSE
D696V7, 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
D696V8, binary
                  cls
clus                 0   1
  FAM26E MUTATED     3   2
  FAM26E WILD-TYPE 314  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM26E MUTATED      3    2
  FAM26E WILD-TYPE  314   46
                               clus
vv                              FAM26E MUTATED FAM26E WILD-TYPE
  COLON ADENOCARCINOMA                       3              314
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  FAM26E MUTATED     3   0   0   0
  FAM26E WILD-TYPE 254   2  22  21
D696V9, multiclass
    clus
vv   FAM26E MUTATED FAM26E WILD-TYPE
  R0              3              254
  R1              0                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"
D696V10, 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
D696V11, 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(697) Variable = AKAP9 MUTATION ANALYSIS
D697V1, survival
                 sevent
clus2               0   1
  AKAP9 MUTATED    31  10
  AKAP9 WILD-TYPE 251  63
  AKAP9 MUTATED AKAP9 WILD-TYPE 
             41             314 
  AKAP9 MUTATED AKAP9 WILD-TYPE 
             10              63 
$`AKAP9 MUTATED`
TCGA-A6-2676 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6142 TCGA-AA-3492 
       42.90        33.53        22.06        22.52        25.08         3.02 
TCGA-AA-3510 TCGA-AA-3532 TCGA-AA-3543 TCGA-AA-3555 TCGA-AA-3660 TCGA-AA-3672 
       63.98        29.00         0.99        29.95        78.08         0.92 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3864 TCGA-AA-3877 
       85.05        26.99        19.04        19.04        53.00        31.00 
TCGA-AA-3947 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6964 TCGA-AY-6197 TCGA-AZ-4315 
       33.01         4.01        34.98        10.88        21.44        58.39 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        6.77        12.10       100.01         0.26         0.33         0.10 
TCGA-CK-4947 TCGA-CM-4743 TCGA-CM-5861 TCGA-D5-6534 TCGA-D5-6923 TCGA-D5-6926 
       17.56        23.05        15.02        43.27        12.43         9.04 
TCGA-DM-A1DB TCGA-F4-6570 TCGA-G4-6310 TCGA-G4-6588 TCGA-G4-6628 
       44.32         6.18        45.11        26.17        52.80 

$`AKAP9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       31.63        30.44        29.19        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 
       27.09         8.38        25.18        24.16        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 
       24.39        23.87        20.12        19.66        20.28         7.04 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3538 
       19.07         0.00        19.07        34.03        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
       12.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       19.00        36.00         5.03        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       18.05         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       61.41        49.41        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
        1.35       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
       21.99        21.14         2.93         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        16.01         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19        18.25         1.32        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       10.13        14.30         9.44        11.64        13.41         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.38        13.45        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       51.75        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 
       91.79        46.75 

  AKAP9 MUTATED AKAP9 WILD-TYPE 
            0.1             0.0 
  AKAP9 MUTATED AKAP9 WILD-TYPE 
         100.01          140.38 
  AKAP9 MUTATED AKAP9 WILD-TYPE 
          23.05           19.99 
[1] "0.1 - 100.0 (23.1)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.1"
D697V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AKAP9 MUTATED         6        0        6        17         4         0
  AKAP9 WILD-TYPE      58        1       19        92         4         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AKAP9 MUTATED           2          1          1          0        3         2
  AKAP9 WILD-TYPE        17          9         40         31       32        11
                 vv
clus              STAGE IVB
  AKAP9 MUTATED           0
  AKAP9 WILD-TYPE         1
D697V3, multiclass
            clus
vv           AKAP9 MUTATED AKAP9 WILD-TYPE
  STAGE I                6              58
  STAGE IA               0               1
  STAGE II               6              19
  STAGE IIA             17              92
  STAGE IIB              4               4
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             1               9
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               3              32
  STAGE IVA              2              11
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  63 220  32
D697V4, multiclass
    clus
vv   AKAP9 MUTATED AKAP9 WILD-TYPE
  T1             1               8
  T2             5              63
  T3            28             220
  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  74  64
D697V5, multiclass
    clus
vv   AKAP9 MUTATED AKAP9 WILD-TYPE
  N0            35             185
  N1             6              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"
D697V6, binary
                 cls
clus                0   1
  AKAP9 MUTATED    36   4
  AKAP9 WILD-TYPE 247  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AKAP9 MUTATED     36    4
  AKAP9 WILD-TYPE  247   44
   clus
vv  AKAP9 MUTATED AKAP9 WILD-TYPE
  0            36             247
  1             4              44
[1] 2 2
[1] FALSE
D697V7, 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
D697V8, binary
                 cls
clus                0   1
  AKAP9 MUTATED    35   8
  AKAP9 WILD-TYPE 282  40
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AKAP9 MUTATED     35    8
  AKAP9 WILD-TYPE  282   40
                               clus
vv                              AKAP9 MUTATED AKAP9 WILD-TYPE
  COLON ADENOCARCINOMA                     35             282
  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 227   2  20  17
D697V9, multiclass
    clus
vv   AKAP9 MUTATED AKAP9 WILD-TYPE
  R0            30             227
  R1             0               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"
D697V10, 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
D697V11, 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(698) Variable = VAV3 MUTATION ANALYSIS
D698V1, survival
                sevent
clus2              0   1
  VAV3 MUTATED    21   2
  VAV3 WILD-TYPE 261  71
  VAV3 MUTATED VAV3 WILD-TYPE 
            23            332 
  VAV3 MUTATED VAV3 WILD-TYPE 
             2             71 
$`VAV3 MUTATED`
TCGA-A6-2672 TCGA-A6-6141 TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3867 TCGA-AA-3949 
       46.65         8.38         0.92        19.04        24.03        26.01 
TCGA-AA-A010 TCGA-AA-A01R TCGA-AZ-4315 TCGA-AZ-6603 TCGA-CA-6717 TCGA-CA-6718 
       34.98        35.01        58.39        29.56         0.33         0.10 
TCGA-CK-4947 TCGA-CM-4743 TCGA-CM-5868 TCGA-CM-6171 TCGA-CM-6677 TCGA-D5-5539 
       17.56        23.05        17.03        14.04        11.08        19.59 
TCGA-D5-6539 TCGA-D5-6540 TCGA-DM-A1DB TCGA-G4-6304 TCGA-G4-6321 
       12.49        16.14        44.32        53.62        22.09 

$`VAV3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        53.00        17.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10       100.01         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
        1.35       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
       21.99        21.14         2.93         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        16.01        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 
       12.26        13.51        11.51        20.19        18.25         1.32 
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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38         7.50       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.72        36.00        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  VAV3 MUTATED VAV3 WILD-TYPE 
           0.1            0.0 
  VAV3 MUTATED VAV3 WILD-TYPE 
         58.39         140.38 
  VAV3 MUTATED VAV3 WILD-TYPE 
        19.590         20.235 
[1] "0.1 - 58.4 (19.6)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2.2"
D698V2, 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       25       101         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  VAV3 MUTATED           3          2          2          0        2         2
  VAV3 WILD-TYPE        16          8         39         31       33        11
                vv
clus             STAGE IVB
  VAV3 MUTATED           0
  VAV3 WILD-TYPE         1
D698V3, multiclass
            clus
vv           VAV3 MUTATED VAV3 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             8            101
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             3             16
  STAGE IIIA            2              8
  STAGE IIIB            2             39
  STAGE IIIC            0             31
  STAGE IV              2             33
  STAGE IVA             2             11
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  64 232  37
D698V4, multiclass
    clus
vv   VAV3 MUTATED VAV3 WILD-TYPE
  T1            0              9
  T2            4             64
  T3           16            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
  VAV3 MUTATED    14   8   2
  VAV3 WILD-TYPE 206  72  64
D698V5, multiclass
    clus
vv   VAV3 MUTATED VAV3 WILD-TYPE
  N0           14            206
  N1            8             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"
D698V6, binary
                cls
clus               0   1
  VAV3 MUTATED    19   3
  VAV3 WILD-TYPE 264  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  VAV3 MUTATED     19    3
  VAV3 WILD-TYPE  264   45
   clus
vv  VAV3 MUTATED VAV3 WILD-TYPE
  0           19            264
  1            3             45
[1] 2 2
[1] FALSE
D698V7, 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
D698V8, binary
                cls
clus               0   1
  VAV3 MUTATED    19   5
  VAV3 WILD-TYPE 298  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  VAV3 MUTATED     19    5
  VAV3 WILD-TYPE  298   43
                               clus
vv                              VAV3 MUTATED VAV3 WILD-TYPE
  COLON ADENOCARCINOMA                    19            298
  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 241   2  20  18
D698V9, multiclass
    clus
vv   VAV3 MUTATED VAV3 WILD-TYPE
  R0           16            241
  R1            0              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"
D698V10, 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
D698V11, 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(699) Variable = C6ORF222 MUTATION ANALYSIS
D699V1, survival
                    sevent
clus2                  0   1
  C6ORF222 MUTATED     5   1
  C6ORF222 WILD-TYPE 277  72
  C6ORF222 MUTATED C6ORF222 WILD-TYPE 
                 6                349 
  C6ORF222 MUTATED C6ORF222 WILD-TYPE 
                 1                 72 
$`C6ORF222 MUTATED`
TCGA-A6-5665 TCGA-A6-6653 TCGA-AA-3663 TCGA-AA-3710 TCGA-AA-A00N TCGA-AA-A010 
       22.06        24.39         6.97        26.99         4.01        34.98 

$`C6ORF222 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  C6ORF222 MUTATED C6ORF222 WILD-TYPE 
              4.01               0.00 
  C6ORF222 MUTATED C6ORF222 WILD-TYPE 
             34.98             140.38 
  C6ORF222 MUTATED C6ORF222 WILD-TYPE 
            23.225             20.120 
[1] "4.0 - 35.0 (23.2)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.1"
D699V2, 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       24       107         6         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C6ORF222 MUTATED           0          0          0          0        0
  C6ORF222 WILD-TYPE        19         10         41         31       35
                    vv
clus                 STAGE IVA STAGE IVB
  C6ORF222 MUTATED           0         0
  C6ORF222 WILD-TYPE        13         1
D699V3, multiclass
            clus
vv           C6ORF222 MUTATED C6ORF222 WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  1                 24
  STAGE IIA                 2                107
  STAGE IIB                 2                  6
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                0                 10
  STAGE IIIB                0                 41
  STAGE IIIC                0                 31
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C6ORF222 MUTATED     0   1   3   2
  C6ORF222 WILD-TYPE   9  67 245  39
D699V4, multiclass
    clus
vv   C6ORF222 MUTATED C6ORF222 WILD-TYPE
  T1                0                  9
  T2                1                 67
  T3                3                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
  C6ORF222 MUTATED     6   0   0
  C6ORF222 WILD-TYPE 214  80  66
D699V5, multiclass
    clus
vv   C6ORF222 MUTATED C6ORF222 WILD-TYPE
  N0                6                214
  N1                0                 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"
D699V6, binary
                    cls
clus                   0   1
  C6ORF222 MUTATED     6   0
  C6ORF222 WILD-TYPE 277  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF222 MUTATED      6    0
  C6ORF222 WILD-TYPE  277   48
   clus
vv  C6ORF222 MUTATED C6ORF222 WILD-TYPE
  0                6                277
  1                0                 48
[1] 2 2
[1] FALSE
D699V7, 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
D699V8, binary
                    cls
clus                   0   1
  C6ORF222 MUTATED     5   1
  C6ORF222 WILD-TYPE 312  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF222 MUTATED      5    1
  C6ORF222 WILD-TYPE  312   47
                               clus
vv                              C6ORF222 MUTATED C6ORF222 WILD-TYPE
  COLON ADENOCARCINOMA                         5                312
  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 252   2  22  21
D699V9, multiclass
    clus
vv   C6ORF222 MUTATED C6ORF222 WILD-TYPE
  R0                5                252
  R1                0                  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"
D699V10, 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
D699V11, multiclass
[1] "Remove cluster labels:" "C6ORF222 MUTATED"      
clus
  C6ORF222 MUTATED C6ORF222 WILD-TYPE 
                 2                204 
        TCGA-A6-2671         TCGA-A6-2672         TCGA-A6-2674 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-A6-2676         TCGA-A6-2677         TCGA-A6-2678 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-A6-2683         TCGA-A6-3807         TCGA-A6-3808 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-A6-3809         TCGA-A6-3810         TCGA-A6-4105 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-A6-5656         TCGA-A6-5657         TCGA-A6-5659 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-A6-5660         TCGA-A6-5661         TCGA-A6-5662 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-A6-5664         TCGA-A6-5666         TCGA-A6-6137 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-A6-6138         TCGA-A6-6141         TCGA-A6-6142 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-A6-6648         TCGA-A6-6649         TCGA-A6-6651 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-A6-6652         TCGA-A6-6654         TCGA-A6-6780 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-A6-6781         TCGA-A6-6782         TCGA-AD-5900 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-AD-6548         TCGA-AD-6888         TCGA-AD-6889 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-AD-6890         TCGA-AD-6895         TCGA-AD-6899 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-AD-6901         TCGA-AD-6963         TCGA-AD-6964 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-AD-6965         TCGA-AU-3779         TCGA-AU-6004 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-AY-4070         TCGA-AY-4071         TCGA-AY-5543 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-AY-6196         TCGA-AY-6197         TCGA-AY-6386 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-AZ-4315         TCGA-AZ-4323         TCGA-AZ-4616 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-AZ-4681         TCGA-AZ-4682         TCGA-AZ-5403 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-AZ-5407         TCGA-AZ-6598         TCGA-AZ-6599 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-AZ-6600         TCGA-AZ-6601         TCGA-AZ-6603 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-AZ-6605         TCGA-AZ-6606         TCGA-AZ-6607 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-AZ-6608         TCGA-CA-5254         TCGA-CA-5255 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CA-5796         TCGA-CA-5797         TCGA-CA-6715 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CA-6716         TCGA-CA-6717         TCGA-CA-6718 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CA-6719         TCGA-CK-4947         TCGA-CK-4948 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CK-4950         TCGA-CK-4952         TCGA-CK-5912 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CK-5913         TCGA-CK-5914         TCGA-CK-5915 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CK-5916         TCGA-CK-6746         TCGA-CK-6747 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CK-6748         TCGA-CK-6751         TCGA-CM-4743 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CM-4744         TCGA-CM-4746         TCGA-CM-4747 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CM-4752         TCGA-CM-5341         TCGA-CM-5344 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CM-5348         TCGA-CM-5349         TCGA-CM-5860 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CM-5861         TCGA-CM-5862         TCGA-CM-5863 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CM-5864         TCGA-CM-5868         TCGA-CM-6161 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CM-6162         TCGA-CM-6163         TCGA-CM-6164 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CM-6165         TCGA-CM-6166         TCGA-CM-6167 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CM-6168         TCGA-CM-6169         TCGA-CM-6170 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CM-6171         TCGA-CM-6172         TCGA-CM-6674 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CM-6675         TCGA-CM-6676         TCGA-CM-6677 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CM-6678         TCGA-CM-6679         TCGA-CM-6680 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-D5-5537         TCGA-D5-5538         TCGA-D5-5539 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-D5-5540         TCGA-D5-5541         TCGA-D5-6529 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-D5-6532         TCGA-D5-6533         TCGA-D5-6534 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-D5-6535         TCGA-D5-6536         TCGA-D5-6537 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-D5-6538         TCGA-D5-6539         TCGA-D5-6540 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-D5-6541         TCGA-D5-6898         TCGA-D5-6920 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-D5-6922         TCGA-D5-6923         TCGA-D5-6924 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-D5-6926         TCGA-D5-6927         TCGA-D5-6928 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-D5-6929         TCGA-D5-6930         TCGA-D5-6931 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-D5-6932         TCGA-D5-7000         TCGA-DM-A0X9 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-DM-A0XD         TCGA-DM-A0XF         TCGA-DM-A1D0 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-DM-A1D4         TCGA-DM-A1D6         TCGA-DM-A1D7 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-DM-A1D8         TCGA-DM-A1D9         TCGA-DM-A1DA 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-DM-A1DB         TCGA-DM-A1HA         TCGA-DM-A1HB 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-DM-A282         TCGA-DM-A285         TCGA-DM-A28C 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-DM-A28E         TCGA-DM-A28F         TCGA-DM-A28G 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-DM-A28H         TCGA-DM-A28K         TCGA-F4-6459 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-F4-6460         TCGA-F4-6569         TCGA-F4-6570 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-F4-6703         TCGA-F4-6704         TCGA-F4-6805 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-F4-6806         TCGA-F4-6807         TCGA-F4-6808 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-F4-6809         TCGA-F4-6854         TCGA-F4-6855 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-F4-6856         TCGA-G4-6293         TCGA-G4-6299 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-G4-6303         TCGA-G4-6304         TCGA-G4-6306 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-G4-6307         TCGA-G4-6309         TCGA-G4-6310 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-G4-6315         TCGA-G4-6317         TCGA-G4-6321 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-G4-6323         TCGA-G4-6586         TCGA-G4-6588 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-G4-6625         TCGA-G4-6626         TCGA-G4-6628 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 

Clustering(700) Variable = LASS3 MUTATION ANALYSIS
D700V1, survival
                 sevent
clus2               0   1
  LASS3 MUTATED    13   1
  LASS3 WILD-TYPE 269  72
  LASS3 MUTATED LASS3 WILD-TYPE 
             14             341 
  LASS3 MUTATED LASS3 WILD-TYPE 
              1              72 
$`LASS3 MUTATED`
TCGA-AA-3510 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3977 
       63.98        54.02         0.92        26.99        19.04        25.02 
TCGA-AA-A010 TCGA-AA-A01I TCGA-AY-6386 TCGA-CM-5348 TCGA-D5-6533 TCGA-D5-6535 
       34.98        31.00        17.82        22.98         1.32        15.12 
TCGA-D5-6538 TCGA-F4-6459 
       17.13         8.61 

$`LASS3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        6.97         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       85.05        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 
       18.25        43.27        17.85         4.80        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 
      119.93        35.97        60.79       117.07        98.24        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  LASS3 MUTATED LASS3 WILD-TYPE 
           0.92            0.00 
  LASS3 MUTATED LASS3 WILD-TYPE 
          63.98          140.38 
  LASS3 MUTATED LASS3 WILD-TYPE 
          21.01           20.19 
[1] "0.9 - 64.0 (21.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2.8"
D700V2, 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       23       108         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LASS3 MUTATED           1          0          6          0        1         0
  LASS3 WILD-TYPE        18         10         35         31       34        13
                 vv
clus              STAGE IVB
  LASS3 MUTATED           0
  LASS3 WILD-TYPE         1
D700V3, multiclass
            clus
vv           LASS3 MUTATED LASS3 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              1             108
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             6              35
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LASS3 MUTATED     0   2  10   2
  LASS3 WILD-TYPE   9  66 238  39
D700V4, multiclass
    clus
vv   LASS3 MUTATED LASS3 WILD-TYPE
  T1             0               9
  T2             2              66
  T3            10             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
  LASS3 MUTATED     8   4   2
  LASS3 WILD-TYPE 212  76  64
D700V5, multiclass
    clus
vv   LASS3 MUTATED LASS3 WILD-TYPE
  N0             8             212
  N1             4              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"
D700V6, binary
                 cls
clus                0   1
  LASS3 MUTATED    11   1
  LASS3 WILD-TYPE 272  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LASS3 MUTATED     11    1
  LASS3 WILD-TYPE  272   47
   clus
vv  LASS3 MUTATED LASS3 WILD-TYPE
  0            11             272
  1             1              47
[1] 2 2
[1] FALSE
D700V7, 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
D700V8, binary
                 cls
clus                0   1
  LASS3 MUTATED    14   0
  LASS3 WILD-TYPE 303  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LASS3 MUTATED     14    0
  LASS3 WILD-TYPE  303   48
                               clus
vv                              LASS3 MUTATED LASS3 WILD-TYPE
  COLON ADENOCARCINOMA                     14             303
  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 246   2  21  20
D700V9, multiclass
    clus
vv   LASS3 MUTATED LASS3 WILD-TYPE
  R0            11             246
  R1             0               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"
D700V10, 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
D700V11, 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(701) Variable = PANK1 MUTATION ANALYSIS
D701V1, survival
                 sevent
clus2               0   1
  PANK1 MUTATED     6   1
  PANK1 WILD-TYPE 276  72
  PANK1 MUTATED PANK1 WILD-TYPE 
              7             348 
  PANK1 MUTATED PANK1 WILD-TYPE 
              1              72 
$`PANK1 MUTATED`
TCGA-A6-3809 TCGA-A6-5661 TCGA-A6-6653 TCGA-AA-3713 TCGA-AA-A00N TCGA-AA-A010 
       32.75        33.53        24.39        19.04         4.01        34.98 
TCGA-AZ-4315 
       58.39 

$`PANK1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       24.16        21.76        24.69        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  PANK1 MUTATED PANK1 WILD-TYPE 
           4.01            0.00 
  PANK1 MUTATED PANK1 WILD-TYPE 
          58.39          140.38 
  PANK1 MUTATED PANK1 WILD-TYPE 
          32.75           20.07 
[1] "4.0 - 58.4 (32.8)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.5"
D701V2, 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       25       107         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        19         10         41         31       34        13
                 vv
clus              STAGE IVB
  PANK1 MUTATED           0
  PANK1 WILD-TYPE         1
D701V3, multiclass
            clus
vv           PANK1 MUTATED PANK1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              2             107
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PANK1 MUTATED     0   1   3   3
  PANK1 WILD-TYPE   9  67 245  38
D701V4, multiclass
    clus
vv   PANK1 MUTATED PANK1 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             3             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
  PANK1 MUTATED     7   0   0
  PANK1 WILD-TYPE 213  80  66
D701V5, multiclass
    clus
vv   PANK1 MUTATED PANK1 WILD-TYPE
  N0             7             213
  N1             0              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"
D701V6, binary
                 cls
clus                0   1
  PANK1 MUTATED     6   1
  PANK1 WILD-TYPE 277  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PANK1 MUTATED      6    1
  PANK1 WILD-TYPE  277   47
   clus
vv  PANK1 MUTATED PANK1 WILD-TYPE
  0             6             277
  1             1              47
[1] 2 2
[1] FALSE
D701V7, 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
D701V8, binary
                 cls
clus                0   1
  PANK1 MUTATED     5   2
  PANK1 WILD-TYPE 312  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PANK1 MUTATED      5    2
  PANK1 WILD-TYPE  312   46
                               clus
vv                              PANK1 MUTATED PANK1 WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  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 252   2  21  21
D701V9, multiclass
    clus
vv   PANK1 MUTATED PANK1 WILD-TYPE
  R0             5             252
  R1             0               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"
D701V10, 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
D701V11, 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(702) Variable = TMTC4 MUTATION ANALYSIS
D702V1, survival
                 sevent
clus2               0   1
  TMTC4 MUTATED    11   2
  TMTC4 WILD-TYPE 271  71
  TMTC4 MUTATED TMTC4 WILD-TYPE 
             13             342 
  TMTC4 MUTATED TMTC4 WILD-TYPE 
              2              71 
$`TMTC4 MUTATED`
TCGA-A6-6138 TCGA-A6-6141 TCGA-AA-3542 TCGA-AA-3864 TCGA-AA-3950 TCGA-AD-6889 
       22.52         8.38        12.99        53.00        24.00        56.55 
TCGA-AU-6004 TCGA-AY-6386 TCGA-AZ-6601 TCGA-CM-5348 TCGA-CM-5860 TCGA-D5-5537 
       27.09        17.82       100.01        22.98        16.01        45.40 
TCGA-DM-A1D0 
      130.65 

$`TMTC4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6142 TCGA-A6-6648 
       22.09        22.06        32.71        27.09        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37         4.21         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 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-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  TMTC4 MUTATED TMTC4 WILD-TYPE 
           8.38            0.00 
  TMTC4 MUTATED TMTC4 WILD-TYPE 
         130.65          140.38 
  TMTC4 MUTATED TMTC4 WILD-TYPE 
         24.000          20.005 
[1] "8.4 - 130.7 (24.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "2.2"
D702V2, 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       23       103         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        19         10         39         30       35        13
                 vv
clus              STAGE IVB
  TMTC4 MUTATED           0
  TMTC4 WILD-TYPE         1
D702V3, multiclass
            clus
vv           TMTC4 MUTATED TMTC4 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              6             103
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TMTC4 MUTATED     0   2  11   0
  TMTC4 WILD-TYPE   9  66 237  41
D702V4, multiclass
    clus
vv   TMTC4 MUTATED TMTC4 WILD-TYPE
  T1             0               9
  T2             2              66
  T3            11             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
  TMTC4 MUTATED     9   2   2
  TMTC4 WILD-TYPE 211  78  64
D702V5, multiclass
    clus
vv   TMTC4 MUTATED TMTC4 WILD-TYPE
  N0             9             211
  N1             2              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"
D702V6, binary
                 cls
clus                0   1
  TMTC4 MUTATED    12   0
  TMTC4 WILD-TYPE 271  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMTC4 MUTATED     12    0
  TMTC4 WILD-TYPE  271   48
   clus
vv  TMTC4 MUTATED TMTC4 WILD-TYPE
  0            12             271
  1             0              48
[1] 2 2
[1] FALSE
D702V7, 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
D702V8, binary
                 cls
clus                0   1
  TMTC4 MUTATED    12   1
  TMTC4 WILD-TYPE 305  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMTC4 MUTATED     12    1
  TMTC4 WILD-TYPE  305   47
                               clus
vv                              TMTC4 MUTATED TMTC4 WILD-TYPE
  COLON ADENOCARCINOMA                     12             305
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TMTC4 MUTATED     7   0   0   1
  TMTC4 WILD-TYPE 250   2  22  20
D702V9, multiclass
    clus
vv   TMTC4 MUTATED TMTC4 WILD-TYPE
  R0             7             250
  R1             0               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"
D702V10, 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
D702V11, 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(703) Variable = ZNF721 MUTATION ANALYSIS
D703V1, survival
                  sevent
clus2                0   1
  ZNF721 MUTATED    11   3
  ZNF721 WILD-TYPE 271  70
  ZNF721 MUTATED ZNF721 WILD-TYPE 
              14              341 
  ZNF721 MUTATED ZNF721 WILD-TYPE 
               3               70 
$`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         0.33 
TCGA-CA-6718 TCGA-CM-5862 
        0.10         5.03 

$`ZNF721 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       85.05        19.04        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.20        14.50        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07         0.26         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  ZNF721 MUTATED ZNF721 WILD-TYPE 
             0.1              0.0 
  ZNF721 MUTATED ZNF721 WILD-TYPE 
           63.98           140.38 
  ZNF721 MUTATED ZNF721 WILD-TYPE 
          24.705           20.120 
[1] "0.1 - 64.0 (24.7)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.2"
D703V2, 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       24       102         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF721 MUTATED           1          0          0          0        0
  ZNF721 WILD-TYPE        18         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF721 MUTATED           1         0
  ZNF721 WILD-TYPE        12         1
D703V3, multiclass
            clus
vv           ZNF721 MUTATED ZNF721 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               7              102
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  65 238  39
D703V4, multiclass
    clus
vv   ZNF721 MUTATED ZNF721 WILD-TYPE
  T1              0                9
  T2              3               65
  T3             10              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
  ZNF721 MUTATED    13   1   1
  ZNF721 WILD-TYPE 207  79  65
D703V5, multiclass
    clus
vv   ZNF721 MUTATED ZNF721 WILD-TYPE
  N0             13              207
  N1              1               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"
D703V6, binary
                  cls
clus                 0   1
  ZNF721 MUTATED    13   1
  ZNF721 WILD-TYPE 270  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF721 MUTATED     13    1
  ZNF721 WILD-TYPE  270   47
   clus
vv  ZNF721 MUTATED ZNF721 WILD-TYPE
  0             13              270
  1              1               47
[1] 2 2
[1] FALSE
D703V7, 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
D703V8, binary
                  cls
clus                 0   1
  ZNF721 MUTATED    12   3
  ZNF721 WILD-TYPE 305  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF721 MUTATED     12    3
  ZNF721 WILD-TYPE  305   45
                               clus
vv                              ZNF721 MUTATED ZNF721 WILD-TYPE
  COLON ADENOCARCINOMA                      12              305
  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 247   2  22  19
D703V9, multiclass
    clus
vv   ZNF721 MUTATED ZNF721 WILD-TYPE
  R0             10              247
  R1              0                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"
D703V10, 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
D703V11, 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(704) Variable = MIA3 MUTATION ANALYSIS
D704V1, survival
                sevent
clus2              0   1
  MIA3 MUTATED    14   3
  MIA3 WILD-TYPE 268  70
  MIA3 MUTATED MIA3 WILD-TYPE 
            17            338 
  MIA3 MUTATED MIA3 WILD-TYPE 
             3             70 
$`MIA3 MUTATED`
TCGA-A6-6653 TCGA-AA-3510 TCGA-AA-3855 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3977 
       24.39        63.98        32.05         2.01        21.99        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CA-6718 
        4.01        34.98        58.39        49.41         0.33         0.10 
TCGA-CK-5916 TCGA-CM-5861 TCGA-DM-A0X9 TCGA-G4-6309 TCGA-G4-6586 
       21.14        15.02       119.70        51.75        35.80 

$`MIA3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 
       10.06         0.00        33.07         0.00        36.03         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       34.03        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99         2.93         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        16.01         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       10.26        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       74.56        65.85        53.62        44.68        55.04        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  MIA3 MUTATED MIA3 WILD-TYPE 
           0.1            0.0 
  MIA3 MUTATED MIA3 WILD-TYPE 
        119.70         140.38 
  MIA3 MUTATED MIA3 WILD-TYPE 
         25.02          19.99 
[1] "0.1 - 119.7 (25.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.5"
D704V2, 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       23       101         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        19         10         40         31       35        13
                vv
clus             STAGE IVB
  MIA3 MUTATED           0
  MIA3 WILD-TYPE         1
D704V3, multiclass
            clus
vv           MIA3 MUTATED MIA3 WILD-TYPE
  STAGE I               5             59
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             8            101
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MIA3 MUTATED     1   5  11   2
  MIA3 WILD-TYPE   8  63 237  39
D704V4, multiclass
    clus
vv   MIA3 MUTATED MIA3 WILD-TYPE
  T1            1              8
  T2            5             63
  T3           11            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
  MIA3 MUTATED    18   1   0
  MIA3 WILD-TYPE 202  79  66
D704V5, multiclass
    clus
vv   MIA3 MUTATED MIA3 WILD-TYPE
  N0           18            202
  N1            1             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
  MIA3 MUTATED    16   0
  MIA3 WILD-TYPE 267  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  MIA3 MUTATED     16    0
  MIA3 WILD-TYPE  267   48
   clus
vv  MIA3 MUTATED MIA3 WILD-TYPE
  0           16            267
  1            0             48
[1] 2 2
[1] FALSE
D704V7, 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
D704V8, binary
                cls
clus               0   1
  MIA3 MUTATED    16   3
  MIA3 WILD-TYPE 301  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  MIA3 MUTATED     16    3
  MIA3 WILD-TYPE  301   45
                               clus
vv                              MIA3 MUTATED MIA3 WILD-TYPE
  COLON ADENOCARCINOMA                    16            301
  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 247   2  22  17
D704V9, multiclass
    clus
vv   MIA3 MUTATED MIA3 WILD-TYPE
  R0           10            247
  R1            0              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"
D704V10, 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
D704V11, 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(705) Variable = OR8A1 MUTATION ANALYSIS
D705V1, survival
                 sevent
clus2               0   1
  OR8A1 MUTATED     4   0
  OR8A1 WILD-TYPE 278  73
  OR8A1 MUTATED OR8A1 WILD-TYPE 
              4             351 
  OR8A1 MUTATED OR8A1 WILD-TYPE 
              0              73 
$`OR8A1 MUTATED`
TCGA-D5-6534 TCGA-D5-6539 TCGA-DM-A1HB TCGA-G4-6315 
       43.27        12.49       135.65        36.72 

$`OR8A1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       45.11        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  OR8A1 MUTATED OR8A1 WILD-TYPE 
          12.49            0.00 
  OR8A1 MUTATED OR8A1 WILD-TYPE 
         135.65          140.38 
  OR8A1 MUTATED OR8A1 WILD-TYPE 
         39.995          20.120 
[1] "12.5 - 135.7 (40.0)" "0.0 - 140.4 (20.1)" 
[1] "hr="     "9300000"
D705V2, 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       25       108         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR8A1 MUTATED           0          1          1          0        1         0
  OR8A1 WILD-TYPE        19          9         40         31       34        13
                 vv
clus              STAGE IVB
  OR8A1 MUTATED           0
  OR8A1 WILD-TYPE         1
D705V3, multiclass
            clus
vv           OR8A1 MUTATED OR8A1 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              1             108
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR8A1 MUTATED     0   0   4   0
  OR8A1 WILD-TYPE   9  68 244  41
D705V4, multiclass
    clus
vv   OR8A1 MUTATED OR8A1 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             4             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
  OR8A1 MUTATED     2   2   0
  OR8A1 WILD-TYPE 218  78  66
D705V5, multiclass
    clus
vv   OR8A1 MUTATED OR8A1 WILD-TYPE
  N0             2             218
  N1             2              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"
D705V6, binary
                 cls
clus                0   1
  OR8A1 MUTATED     3   1
  OR8A1 WILD-TYPE 280  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR8A1 MUTATED      3    1
  OR8A1 WILD-TYPE  280   47
   clus
vv  OR8A1 MUTATED OR8A1 WILD-TYPE
  0             3             280
  1             1              47
[1] 2 2
[1] FALSE
D705V7, 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
D705V8, binary
                 cls
clus                0   1
  OR8A1 MUTATED     3   1
  OR8A1 WILD-TYPE 314  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR8A1 MUTATED      3    1
  OR8A1 WILD-TYPE  314   47
                               clus
vv                              OR8A1 MUTATED OR8A1 WILD-TYPE
  COLON ADENOCARCINOMA                      3             314
  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 254   2  22  21
D705V9, multiclass
    clus
vv   OR8A1 MUTATED OR8A1 WILD-TYPE
  R0             3             254
  R1             0               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"
D705V10, 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
D705V11, 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(706) Variable = METTL9 MUTATION ANALYSIS
D706V1, survival
                  sevent
clus2                0   1
  METTL9 MUTATED     4   0
  METTL9 WILD-TYPE 278  73
  METTL9 MUTATED METTL9 WILD-TYPE 
               4              351 
  METTL9 MUTATED METTL9 WILD-TYPE 
               0               73 
$`METTL9 MUTATED`
TCGA-AD-6963 TCGA-AU-6004 TCGA-CA-6717 TCGA-CM-5861 
       27.42        27.09         0.33        15.02 

$`METTL9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       22.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  METTL9 MUTATED METTL9 WILD-TYPE 
            0.33             0.00 
  METTL9 MUTATED METTL9 WILD-TYPE 
           27.42           140.38 
  METTL9 MUTATED METTL9 WILD-TYPE 
          21.055           20.190 
[1] "0.3 - 27.4 (21.1)"  "0.0 - 140.4 (20.2)"
[1] "hr="     "3300000"
D706V2, 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       25       107         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  METTL9 MUTATED           0          0          0          0        0
  METTL9 WILD-TYPE        19         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  METTL9 MUTATED           0         0
  METTL9 WILD-TYPE        13         1
D706V3, multiclass
            clus
vv           METTL9 MUTATED METTL9 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               2              107
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  METTL9 MUTATED     0   1   3   0
  METTL9 WILD-TYPE   9  67 245  41
D706V4, multiclass
    clus
vv   METTL9 MUTATED METTL9 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              3              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
  METTL9 MUTATED     4   0   0
  METTL9 WILD-TYPE 216  80  66
D706V5, multiclass
    clus
vv   METTL9 MUTATED METTL9 WILD-TYPE
  N0              4              216
  N1              0               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"
D706V6, binary
                  cls
clus                 0   1
  METTL9 MUTATED     3   0
  METTL9 WILD-TYPE 280  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  METTL9 MUTATED      3    0
  METTL9 WILD-TYPE  280   48
   clus
vv  METTL9 MUTATED METTL9 WILD-TYPE
  0              3              280
  1              0               48
[1] 2 2
[1] FALSE
D706V7, 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
D706V8, binary
                  cls
clus                 0   1
  METTL9 MUTATED     3   1
  METTL9 WILD-TYPE 314  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  METTL9 MUTATED      3    1
  METTL9 WILD-TYPE  314   47
                               clus
vv                              METTL9 MUTATED METTL9 WILD-TYPE
  COLON ADENOCARCINOMA                       3              314
  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 255   2  22  20
D706V9, multiclass
    clus
vv   METTL9 MUTATED METTL9 WILD-TYPE
  R0              2              255
  R1              0                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"
D706V10, 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
D706V11, 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(707) Variable = ZNF585A MUTATION ANALYSIS
D707V1, survival
                   sevent
clus2                 0   1
  ZNF585A MUTATED    11   4
  ZNF585A WILD-TYPE 271  69
  ZNF585A MUTATED ZNF585A WILD-TYPE 
               15               340 
  ZNF585A MUTATED ZNF585A WILD-TYPE 
                4                69 
$`ZNF585A MUTATED`
TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3525 TCGA-AA-3663 TCGA-AA-3713 
        1.02        63.98        13.02         8.05         6.97        19.04 
TCGA-AA-3715 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6895 TCGA-CA-6718 
       19.04        25.02         4.01        34.98         0.72         0.10 
TCGA-D5-6534 TCGA-G4-6293 TCGA-G4-6626 
       43.27       107.67        46.75 

$`ZNF585A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       35.01         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       24.03        37.05        36.03        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.05        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       19.43        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       35.80        26.17        91.79        52.80 

  ZNF585A MUTATED ZNF585A WILD-TYPE 
              0.1               0.0 
  ZNF585A MUTATED ZNF585A WILD-TYPE 
           107.67            140.38 
  ZNF585A MUTATED ZNF585A WILD-TYPE 
            19.04             20.63 
[1] "0.1 - 107.7 (19.0)" "0.0 - 140.4 (20.6)"
[1] "hr=" "1.3"
D707V2, 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       21       105         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF585A MUTATED           2          0          1          0        1
  ZNF585A WILD-TYPE        17         10         40         31       34
                   vv
clus                STAGE IVA STAGE IVB
  ZNF585A MUTATED           0         0
  ZNF585A WILD-TYPE        13         1
D707V3, multiclass
            clus
vv           ZNF585A MUTATED ZNF585A WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 4                21
  STAGE IIA                4               105
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                2                17
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               0                31
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ZNF585A MUTATED     0   1  13   2
  ZNF585A WILD-TYPE   9  67 235  39
D707V4, multiclass
    clus
vv   ZNF585A MUTATED ZNF585A WILD-TYPE
  T1               0                 9
  T2               1                67
  T3              13               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
  ZNF585A MUTATED    12   3   1
  ZNF585A WILD-TYPE 208  77  65
D707V5, multiclass
    clus
vv   ZNF585A MUTATED ZNF585A WILD-TYPE
  N0              12               208
  N1               3                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"
D707V6, binary
                   cls
clus                  0   1
  ZNF585A MUTATED    13   1
  ZNF585A WILD-TYPE 270  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF585A MUTATED     13    1
  ZNF585A WILD-TYPE  270   47
   clus
vv  ZNF585A MUTATED ZNF585A WILD-TYPE
  0              13               270
  1               1                47
[1] 2 2
[1] FALSE
D707V7, 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
D707V8, binary
                   cls
clus                  0   1
  ZNF585A MUTATED    13   3
  ZNF585A WILD-TYPE 304  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF585A MUTATED     13    3
  ZNF585A WILD-TYPE  304   45
                               clus
vv                              ZNF585A MUTATED ZNF585A WILD-TYPE
  COLON ADENOCARCINOMA                       13               304
  COLON MUCINOUS ADENOCARCINOMA               3                45
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ZNF585A MUTATED    11   0   1   1
  ZNF585A WILD-TYPE 246   2  21  20
D707V9, multiclass
    clus
vv   ZNF585A MUTATED ZNF585A WILD-TYPE
  R0              11               246
  R1               0                 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"
D707V10, 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
D707V11, 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(708) Variable = RAD51AP2 MUTATION ANALYSIS
D708V1, survival
                    sevent
clus2                  0   1
  RAD51AP2 MUTATED    13   2
  RAD51AP2 WILD-TYPE 269  71
  RAD51AP2 MUTATED RAD51AP2 WILD-TYPE 
                15                340 
  RAD51AP2 MUTATED RAD51AP2 WILD-TYPE 
                 2                 71 
$`RAD51AP2 MUTATED`
TCGA-A6-3809 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3713 TCGA-AA-3815 TCGA-AA-A00N 
       32.75        20.12        19.66        19.04        33.04         4.01 
TCGA-AA-A010 TCGA-AD-6895 TCGA-AY-6197 TCGA-AZ-4315 TCGA-D5-5537 TCGA-F4-6856 
       34.98         0.72        21.44        58.39        45.40        19.43 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 
       35.80        26.17        52.80 

$`RAD51AP2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       85.05        26.99        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        4.21        56.55         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       15.75         0.20        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        35.41       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        91.79        46.75 

  RAD51AP2 MUTATED RAD51AP2 WILD-TYPE 
              0.72               0.00 
  RAD51AP2 MUTATED RAD51AP2 WILD-TYPE 
             58.39             140.38 
  RAD51AP2 MUTATED RAD51AP2 WILD-TYPE 
            26.170             20.005 
[1] "0.7 - 58.4 (26.2)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1.7"
D708V2, 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       25       101         5         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RAD51AP2 MUTATED           0          0          0          1        1
  RAD51AP2 WILD-TYPE        19         10         41         30       34
                    vv
clus                 STAGE IVA STAGE IVB
  RAD51AP2 MUTATED           0         0
  RAD51AP2 WILD-TYPE        13         1
D708V3, multiclass
            clus
vv           RAD51AP2 MUTATED RAD51AP2 WILD-TYPE
  STAGE I                   2                 62
  STAGE IA                  0                  1
  STAGE II                  0                 25
  STAGE IIA                 8                101
  STAGE IIB                 3                  5
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                0                 10
  STAGE IIIB                0                 41
  STAGE IIIC                1                 30
  STAGE IV                  1                 34
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  RAD51AP2 MUTATED     0   2  10   4
  RAD51AP2 WILD-TYPE   9  66 238  37
D708V4, multiclass
    clus
vv   RAD51AP2 MUTATED RAD51AP2 WILD-TYPE
  T1                0                  9
  T2                2                 66
  T3               10                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
  RAD51AP2 MUTATED    13   2   1
  RAD51AP2 WILD-TYPE 207  78  65
D708V5, multiclass
    clus
vv   RAD51AP2 MUTATED RAD51AP2 WILD-TYPE
  N0               13                207
  N1                2                 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"
D708V6, binary
                    cls
clus                   0   1
  RAD51AP2 MUTATED    10   1
  RAD51AP2 WILD-TYPE 273  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  RAD51AP2 MUTATED     10    1
  RAD51AP2 WILD-TYPE  273   47
   clus
vv  RAD51AP2 MUTATED RAD51AP2 WILD-TYPE
  0               10                273
  1                1                 47
[1] 2 2
[1] FALSE
D708V7, 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
D708V8, binary
                    cls
clus                   0   1
  RAD51AP2 MUTATED    11   5
  RAD51AP2 WILD-TYPE 306  43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  RAD51AP2 MUTATED     11    5
  RAD51AP2 WILD-TYPE  306   43
                               clus
vv                              RAD51AP2 MUTATED RAD51AP2 WILD-TYPE
  COLON ADENOCARCINOMA                        11                306
  COLON MUCINOUS ADENOCARCINOMA                5                 43
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  RAD51AP2 MUTATED    12   0   1   1
  RAD51AP2 WILD-TYPE 245   2  21  20
D708V9, multiclass
    clus
vv   RAD51AP2 MUTATED RAD51AP2 WILD-TYPE
  R0               12                245
  R1                0                  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"
D708V10, 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
D708V11, 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(709) Variable = DNAH8 MUTATION ANALYSIS
D709V1, survival
                 sevent
clus2               0   1
  DNAH8 MUTATED    50   7
  DNAH8 WILD-TYPE 232  66
  DNAH8 MUTATED DNAH8 WILD-TYPE 
             57             298 
  DNAH8 MUTATED DNAH8 WILD-TYPE 
              7              66 
$`DNAH8 MUTATED`
TCGA-A6-2671 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5660 TCGA-A6-5664 
       43.76        32.75        36.53        14.53        29.19        22.09 
TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3672 
       22.06         8.38        24.39        19.66        63.98         0.92 
TCGA-AA-3713 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-3956 TCGA-AA-3966 
       19.04        30.05        53.00        33.01        34.03         2.01 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 
       34.06        25.02        30.02        18.05         4.01        34.98 
TCGA-AA-A01R TCGA-AD-6889 TCGA-AD-6964 TCGA-AU-3779 TCGA-AY-6197 TCGA-AZ-4315 
       35.01        56.55        10.88        14.50        21.44        58.39 
TCGA-AZ-4682 TCGA-AZ-6598 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       22.36        49.41         3.29         0.26         0.33         0.10 
TCGA-CK-4950 TCGA-CM-5344 TCGA-CM-6161 TCGA-CM-6168 TCGA-CM-6171 TCGA-D5-5538 
       40.34        22.03        15.02        12.99        14.04        12.26 
TCGA-D5-6539 TCGA-D5-6926 TCGA-D5-6932 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-F4-6570 
       12.49         9.04        11.38       140.38       131.51         6.18 
TCGA-F4-6703 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6856 TCGA-G4-6304 TCGA-G4-6306 
       35.87        16.24        33.67        19.43        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6588 TCGA-G4-6628 
       55.04        26.17        52.80 

$`DNAH8 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 
       34.65        33.34        32.91        31.63        30.44        33.53 
TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       23.61        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 
       24.16        21.76        24.69        23.87        20.12        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 
        7.04         3.02         1.02        35.01         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 
       32.05         0.99        31.07        31.07        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3968 
       24.00        26.01        24.00         2.01        20.98        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       16.08        50.99        13.05        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       19.00        34.03        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        4.21         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.20        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-5407 
       17.82         1.41         5.13        83.80        62.79        61.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 
        3.19         1.94         2.24         3.06         3.25         0.07 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
        1.35        17.56       102.44        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        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-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-6676 TCGA-CM-6677 TCGA-CM-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        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 
       43.27        15.12        17.85         4.80        17.13        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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-D5-7000 
        9.44        11.64        13.41         1.51        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-A1HB TCGA-DM-A282 
       13.32        12.59         7.50        44.32       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6805 
       98.24         8.61        13.38        13.45         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 
       29.59        13.25         0.53        35.41       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       65.85        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       13.78        35.80        91.79        46.75 

  DNAH8 MUTATED DNAH8 WILD-TYPE 
            0.1             0.0 
  DNAH8 MUTATED DNAH8 WILD-TYPE 
         140.38          139.17 
  DNAH8 MUTATED DNAH8 WILD-TYPE 
          22.36           19.79 
[1] "0.1 - 140.4 (22.4)" "0.0 - 139.2 (19.8)"
[1] "hr=" "2"  
D709V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DNAH8 MUTATED         7        0        3        24         6         0
  DNAH8 WILD-TYPE      57        1       22        85         2         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DNAH8 MUTATED           2          3          4          5        2         1
  DNAH8 WILD-TYPE        17          7         37         26       33        12
                 vv
clus              STAGE IVB
  DNAH8 MUTATED           0
  DNAH8 WILD-TYPE         1
D709V3, multiclass
            clus
vv           DNAH8 MUTATED DNAH8 WILD-TYPE
  STAGE I                7              57
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA             24              85
  STAGE IIB              6               2
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             3               7
  STAGE IIIB             4              37
  STAGE IIIC             5              26
  STAGE IV               2              33
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  60 209  30
D709V4, multiclass
    clus
vv   DNAH8 MUTATED DNAH8 WILD-TYPE
  T1             1               8
  T2             8              60
  T3            39             209
  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  72  59
D709V5, multiclass
    clus
vv   DNAH8 MUTATED DNAH8 WILD-TYPE
  N0            44             176
  N1             8              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"
D709V6, binary
                 cls
clus                0   1
  DNAH8 MUTATED    49   3
  DNAH8 WILD-TYPE 234  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH8 MUTATED     49    3
  DNAH8 WILD-TYPE  234   45
   clus
vv  DNAH8 MUTATED DNAH8 WILD-TYPE
  0            49             234
  1             3              45
[1] 2 2
[1] FALSE
D709V7, 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
D709V8, binary
                 cls
clus                0   1
  DNAH8 MUTATED    50   9
  DNAH8 WILD-TYPE 267  39
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH8 MUTATED     50    9
  DNAH8 WILD-TYPE  267   39
                               clus
vv                              DNAH8 MUTATED DNAH8 WILD-TYPE
  COLON ADENOCARCINOMA                     50             267
  COLON MUCINOUS ADENOCARCINOMA             9              39
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DNAH8 MUTATED    41   1   1   4
  DNAH8 WILD-TYPE 216   1  21  17
D709V9, multiclass
    clus
vv   DNAH8 MUTATED DNAH8 WILD-TYPE
  R0            41             216
  R1             1               1
  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"
D709V10, 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
D709V11, 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(710) Variable = CHM MUTATION ANALYSIS
D710V1, survival
               sevent
clus2             0   1
  CHM MUTATED     2   2
  CHM WILD-TYPE 280  71
  CHM MUTATED CHM WILD-TYPE 
            4           351 
  CHM MUTATED CHM WILD-TYPE 
            2            71 
$`CHM MUTATED`
TCGA-AZ-6600 TCGA-CM-5863 TCGA-CM-6678 TCGA-DM-A285 
       12.10        15.02        11.01         6.12 

$`CHM WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41        49.41         6.77       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  CHM MUTATED CHM WILD-TYPE 
         6.12          0.00 
  CHM MUTATED CHM WILD-TYPE 
        15.02        140.38 
  CHM MUTATED CHM WILD-TYPE 
       11.555        20.980 
[1] "6.1 - 15.0 (11.6)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "4.7"
D710V2, 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       25       109         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        19         10         40         31       33        12
               vv
clus            STAGE IVB
  CHM MUTATED           0
  CHM WILD-TYPE         1
D710V3, multiclass
            clus
vv           CHM MUTATED CHM WILD-TYPE
  STAGE I              0            64
  STAGE IA             0             1
  STAGE II             0            25
  STAGE IIA            0           109
  STAGE IIB            0             8
  STAGE IIC            0             1
  STAGE III            0            19
  STAGE IIIA           0            10
  STAGE IIIB           1            40
  STAGE IIIC           0            31
  STAGE IV             2            33
  STAGE IVA            1            12
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of 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  68 246  39
D710V4, multiclass
    clus
vv   CHM MUTATED CHM WILD-TYPE
  T1           0             9
  T2           0            68
  T3           2           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
  CHM MUTATED     0   3   1
  CHM WILD-TYPE 220  77  65
D710V5, multiclass
    clus
vv   CHM MUTATED CHM WILD-TYPE
  N0           0           220
  N1           3            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"
D710V6, binary
               cls
clus              0   1
  CHM MUTATED     1   3
  CHM WILD-TYPE 282  45
[1] "tbl2"
               cls
clus            [,1] [,2]
  CHM MUTATED      1    3
  CHM WILD-TYPE  282   45
   clus
vv  CHM MUTATED CHM WILD-TYPE
  0           1           282
  1           3            45
[1] 2 2
[1] FALSE
D710V7, 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
D710V8, binary
               cls
clus              0   1
  CHM MUTATED     2   2
  CHM WILD-TYPE 315  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  CHM MUTATED      2    2
  CHM WILD-TYPE  315   46
                               clus
vv                              CHM MUTATED CHM WILD-TYPE
  COLON ADENOCARCINOMA                    2           315
  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 255   2  22  21
D710V9, multiclass
[1] "Remove cluster labels:" "CHM MUTATED"           
clus
  CHM MUTATED CHM WILD-TYPE 
            2           300 
   TCGA-A6-2671    TCGA-A6-2672    TCGA-A6-2674    TCGA-A6-2676    TCGA-A6-2677 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-A6-2678    TCGA-A6-2683    TCGA-A6-3807    TCGA-A6-3808    TCGA-A6-3809 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-A6-3810    TCGA-A6-5657    TCGA-A6-5659    TCGA-A6-5661    TCGA-A6-5665 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-A6-6781    TCGA-AA-3489    TCGA-AA-3492    TCGA-AA-3496    TCGA-AA-3502 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-3510    TCGA-AA-3511    TCGA-AA-3514    TCGA-AA-3517    TCGA-AA-3518 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-3519    TCGA-AA-3520    TCGA-AA-3521    TCGA-AA-3522    TCGA-AA-3524 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-3525    TCGA-AA-3526    TCGA-AA-3527    TCGA-AA-3529    TCGA-AA-3530 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-3531    TCGA-AA-3532    TCGA-AA-3534    TCGA-AA-3538    TCGA-AA-3542 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-3543    TCGA-AA-3544    TCGA-AA-3548    TCGA-AA-3549    TCGA-AA-3552 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-3553    TCGA-AA-3554    TCGA-AA-3555    TCGA-AA-3556    TCGA-AA-3558 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-3560    TCGA-AA-3561    TCGA-AA-3562    TCGA-AA-3655    TCGA-AA-3660 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-3662    TCGA-AA-3663    TCGA-AA-3664    TCGA-AA-3666    TCGA-AA-3667 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-3672    TCGA-AA-3673    TCGA-AA-3678    TCGA-AA-3679    TCGA-AA-3680 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-3681    TCGA-AA-3684    TCGA-AA-3685    TCGA-AA-3688    TCGA-AA-3692 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-3693    TCGA-AA-3695    TCGA-AA-3696    TCGA-AA-3697    TCGA-AA-3710 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-3712    TCGA-AA-3713    TCGA-AA-3715    TCGA-AA-3811    TCGA-AA-3812 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-3814    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-3844 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-3845    TCGA-AA-3846    TCGA-AA-3848    TCGA-AA-3850    TCGA-AA-3851 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-3852    TCGA-AA-3854    TCGA-AA-3855    TCGA-AA-3856    TCGA-AA-3858 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-3860    TCGA-AA-3861    TCGA-AA-3864    TCGA-AA-3866    TCGA-AA-3867 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-3869    TCGA-AA-3870    TCGA-AA-3872    TCGA-AA-3875    TCGA-AA-3877 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-3930    TCGA-AA-3939    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-3950    TCGA-AA-3952    TCGA-AA-3955    TCGA-AA-3956    TCGA-AA-3968 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-3971    TCGA-AA-3972    TCGA-AA-3973    TCGA-AA-3975    TCGA-AA-3976 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-3979    TCGA-AA-3984    TCGA-AA-3986    TCGA-AA-3989    TCGA-AA-3994 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-A004    TCGA-AA-A00A    TCGA-AA-A00D    TCGA-AA-A00E    TCGA-AA-A00F 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-A00J    TCGA-AA-A00K    TCGA-AA-A00L    TCGA-AA-A00N    TCGA-AA-A00O 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-A00Q    TCGA-AA-A00R    TCGA-AA-A00U    TCGA-AA-A00W    TCGA-AA-A00Z 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-A010    TCGA-AA-A017    TCGA-AA-A01D    TCGA-AA-A01F    TCGA-AA-A01G 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-A01I    TCGA-AA-A01K    TCGA-AA-A01P    TCGA-AA-A01Q    TCGA-AA-A01R 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-A01S    TCGA-AA-A01T    TCGA-AA-A01V    TCGA-AA-A01X    TCGA-AA-A01Z 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-A022    TCGA-AA-A024    TCGA-AA-A029    TCGA-AA-A02F    TCGA-AA-A02H 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-A02J    TCGA-AA-A02K    TCGA-AA-A02O    TCGA-AA-A02W    TCGA-AA-A02Y 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AA-A03F    TCGA-AA-A03J    TCGA-AD-5900    TCGA-AD-6548    TCGA-AD-6888 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AU-3779    TCGA-AU-6004    TCGA-AY-4070    TCGA-AY-4071    TCGA-AY-5543 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-AY-6196    TCGA-AY-6197    TCGA-AY-6386    TCGA-AZ-4315    TCGA-AZ-4681 
"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-5912 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-CK-5913    TCGA-CK-5914    TCGA-CK-5915    TCGA-CK-5916    TCGA-CK-6746 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-CK-6747    TCGA-CK-6748    TCGA-CK-6751    TCGA-CM-4743    TCGA-CM-4744 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-CM-4746    TCGA-CM-4747    TCGA-CM-4752    TCGA-CM-5341    TCGA-CM-5344 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-CM-5348    TCGA-CM-5349    TCGA-CM-5860    TCGA-CM-5861    TCGA-CM-5862 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-CM-5864    TCGA-CM-5868    TCGA-CM-6161    TCGA-CM-6162    TCGA-CM-6163 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-CM-6164    TCGA-CM-6165    TCGA-CM-6166    TCGA-CM-6167    TCGA-CM-6168 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-CM-6169    TCGA-CM-6170    TCGA-CM-6171    TCGA-CM-6172    TCGA-CM-6674 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-CM-6675    TCGA-CM-6676    TCGA-CM-6677    TCGA-CM-6679    TCGA-CM-6680 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-D5-5537    TCGA-D5-5538    TCGA-D5-5539    TCGA-D5-5540    TCGA-D5-5541 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-D5-6529    TCGA-D5-6532    TCGA-D5-6533    TCGA-D5-6534    TCGA-D5-6535 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-D5-6536    TCGA-D5-6537    TCGA-D5-6538    TCGA-D5-6539    TCGA-D5-6540 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-D5-6541    TCGA-D5-6898    TCGA-D5-6920    TCGA-D5-6922    TCGA-D5-6923 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-D5-6924    TCGA-D5-6926    TCGA-D5-6927    TCGA-D5-6928    TCGA-D5-6929 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-D5-6930    TCGA-D5-6931    TCGA-D5-6932    TCGA-D5-7000    TCGA-F4-6459 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-F4-6460    TCGA-F4-6569    TCGA-F4-6570    TCGA-F4-6703    TCGA-F4-6704 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-F4-6805    TCGA-F4-6806    TCGA-F4-6807    TCGA-F4-6808    TCGA-F4-6809 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-F4-6854    TCGA-F4-6855    TCGA-F4-6856    TCGA-G4-6293    TCGA-G4-6299 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-G4-6303    TCGA-G4-6304    TCGA-G4-6306    TCGA-G4-6307    TCGA-G4-6309 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
   TCGA-G4-6310    TCGA-G4-6315    TCGA-G4-6317    TCGA-G4-6321    TCGA-G4-6323 
"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-G4-6626    TCGA-G4-6628 
"CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" "CHM WILD-TYPE" 
D710V10, 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
D710V11, 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(711) Variable = POLDIP3 MUTATION ANALYSIS
D711V1, survival
                   sevent
clus2                 0   1
  POLDIP3 MUTATED     3   2
  POLDIP3 WILD-TYPE 279  71
  POLDIP3 MUTATED POLDIP3 WILD-TYPE 
                5               350 
  POLDIP3 MUTATED POLDIP3 WILD-TYPE 
                2                71 
$`POLDIP3 MUTATED`
TCGA-AA-3811 TCGA-AA-3949 TCGA-AA-A01R TCGA-AD-6889 TCGA-F4-6570 
       10.06        26.01        35.01        56.55         6.18 

$`POLDIP3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37         4.21         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       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        13.38        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  POLDIP3 MUTATED POLDIP3 WILD-TYPE 
             6.18              0.00 
  POLDIP3 MUTATED POLDIP3 WILD-TYPE 
            56.55            140.38 
  POLDIP3 MUTATED POLDIP3 WILD-TYPE 
           26.010            20.155 
[1] "6.2 - 56.5 (26.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.9"
D711V2, 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       25       107         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  POLDIP3 MUTATED           2          0          1          0        0
  POLDIP3 WILD-TYPE        17         10         40         31       35
                   vv
clus                STAGE IVA STAGE IVB
  POLDIP3 MUTATED           0         0
  POLDIP3 WILD-TYPE        13         1
D711V3, multiclass
            clus
vv           POLDIP3 MUTATED POLDIP3 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                2               107
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                2                17
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  POLDIP3 MUTATED     0   0   5   0
  POLDIP3 WILD-TYPE   9  68 243  41
D711V4, multiclass
    clus
vv   POLDIP3 MUTATED POLDIP3 WILD-TYPE
  T1               0                 9
  T2               0                68
  T3               5               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
  POLDIP3 MUTATED     2   1   2
  POLDIP3 WILD-TYPE 218  79  64
D711V5, multiclass
    clus
vv   POLDIP3 MUTATED POLDIP3 WILD-TYPE
  N0               2               218
  N1               1                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"
D711V6, binary
                   cls
clus                  0   1
  POLDIP3 MUTATED     5   0
  POLDIP3 WILD-TYPE 278  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  POLDIP3 MUTATED      5    0
  POLDIP3 WILD-TYPE  278   48
   clus
vv  POLDIP3 MUTATED POLDIP3 WILD-TYPE
  0               5               278
  1               0                48
[1] 2 2
[1] FALSE
D711V7, 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
D711V8, binary
                   cls
clus                  0   1
  POLDIP3 MUTATED     3   2
  POLDIP3 WILD-TYPE 314  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  POLDIP3 MUTATED      3    2
  POLDIP3 WILD-TYPE  314   46
                               clus
vv                              POLDIP3 MUTATED POLDIP3 WILD-TYPE
  COLON ADENOCARCINOMA                        3               314
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  POLDIP3 MUTATED     4   0   0   0
  POLDIP3 WILD-TYPE 253   2  22  21
D711V9, multiclass
    clus
vv   POLDIP3 MUTATED POLDIP3 WILD-TYPE
  R0               4               253
  R1               0                 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"
D711V10, 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
D711V11, multiclass
[1] "Remove cluster labels:" "POLDIP3 MUTATED"       
clus
  POLDIP3 MUTATED POLDIP3 WILD-TYPE 
                2               204 
       TCGA-A6-2671        TCGA-A6-2672        TCGA-A6-2674        TCGA-A6-2676 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-A6-2677        TCGA-A6-2678        TCGA-A6-2683        TCGA-A6-3807 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-A6-3808        TCGA-A6-3809        TCGA-A6-3810        TCGA-A6-4105 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-A6-5656        TCGA-A6-5657        TCGA-A6-5659        TCGA-A6-5660 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-A6-5661        TCGA-A6-5662        TCGA-A6-5664        TCGA-A6-5665 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-A6-5666        TCGA-A6-6137        TCGA-A6-6138        TCGA-A6-6141 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-A6-6142        TCGA-A6-6648        TCGA-A6-6649        TCGA-A6-6651 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-A6-6652        TCGA-A6-6653        TCGA-A6-6654        TCGA-A6-6780 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-A6-6781        TCGA-A6-6782        TCGA-AD-5900        TCGA-AD-6548 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-AD-6888        TCGA-AD-6890        TCGA-AD-6895        TCGA-AD-6899 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-AD-6901        TCGA-AD-6963        TCGA-AD-6964        TCGA-AD-6965 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-AU-3779        TCGA-AU-6004        TCGA-AY-4070        TCGA-AY-4071 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-AY-5543        TCGA-AY-6196        TCGA-AY-6197        TCGA-AY-6386 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-AZ-4315        TCGA-AZ-4323        TCGA-AZ-4616        TCGA-AZ-4681 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-AZ-4682        TCGA-AZ-5403        TCGA-AZ-5407        TCGA-AZ-6598 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-AZ-6599        TCGA-AZ-6600        TCGA-AZ-6601        TCGA-AZ-6603 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-AZ-6605        TCGA-AZ-6606        TCGA-AZ-6607        TCGA-AZ-6608 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-CA-5254        TCGA-CA-5255        TCGA-CA-5796        TCGA-CA-5797 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-CA-6715        TCGA-CA-6716        TCGA-CA-6717        TCGA-CA-6718 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-CA-6719        TCGA-CK-4947        TCGA-CK-4948        TCGA-CK-4950 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-CK-4952        TCGA-CK-5912        TCGA-CK-5913        TCGA-CK-5914 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-CK-5915        TCGA-CK-5916        TCGA-CK-6746        TCGA-CK-6747 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-CK-6748        TCGA-CK-6751        TCGA-CM-4743        TCGA-CM-4744 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-CM-4746        TCGA-CM-4747        TCGA-CM-4752        TCGA-CM-5341 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-CM-5344        TCGA-CM-5348        TCGA-CM-5349        TCGA-CM-5860 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-CM-5861        TCGA-CM-5862        TCGA-CM-5863        TCGA-CM-5864 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-CM-5868        TCGA-CM-6161        TCGA-CM-6162        TCGA-CM-6163 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-CM-6164        TCGA-CM-6165        TCGA-CM-6166        TCGA-CM-6167 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-CM-6168        TCGA-CM-6169        TCGA-CM-6170        TCGA-CM-6171 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-CM-6172        TCGA-CM-6674        TCGA-CM-6675        TCGA-CM-6676 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-CM-6677        TCGA-CM-6678        TCGA-CM-6679        TCGA-CM-6680 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-D5-5537        TCGA-D5-5538        TCGA-D5-5539        TCGA-D5-5540 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-D5-5541        TCGA-D5-6529        TCGA-D5-6532        TCGA-D5-6533 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-D5-6534        TCGA-D5-6535        TCGA-D5-6536        TCGA-D5-6537 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-D5-6538        TCGA-D5-6539        TCGA-D5-6540        TCGA-D5-6541 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-D5-6898        TCGA-D5-6920        TCGA-D5-6922        TCGA-D5-6923 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-D5-6924        TCGA-D5-6926        TCGA-D5-6927        TCGA-D5-6928 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-D5-6929        TCGA-D5-6930        TCGA-D5-6931        TCGA-D5-6932 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-D5-7000        TCGA-DM-A0X9        TCGA-DM-A0XD        TCGA-DM-A0XF 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-DM-A1D0        TCGA-DM-A1D4        TCGA-DM-A1D6        TCGA-DM-A1D7 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-DM-A1D8        TCGA-DM-A1D9        TCGA-DM-A1DA        TCGA-DM-A1DB 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-DM-A1HA        TCGA-DM-A1HB        TCGA-DM-A282        TCGA-DM-A285 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-DM-A28C        TCGA-DM-A28E        TCGA-DM-A28F        TCGA-DM-A28G 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-DM-A28H        TCGA-DM-A28K        TCGA-F4-6459        TCGA-F4-6460 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-F4-6569        TCGA-F4-6703        TCGA-F4-6704        TCGA-F4-6805 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-F4-6806        TCGA-F4-6807        TCGA-F4-6808        TCGA-F4-6809 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-F4-6854        TCGA-F4-6855        TCGA-F4-6856        TCGA-G4-6293 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-G4-6299        TCGA-G4-6303        TCGA-G4-6304        TCGA-G4-6306 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-G4-6307        TCGA-G4-6309        TCGA-G4-6310        TCGA-G4-6315 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-G4-6317        TCGA-G4-6321        TCGA-G4-6323        TCGA-G4-6586 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-G4-6588        TCGA-G4-6625        TCGA-G4-6626        TCGA-G4-6628 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 

Clustering(712) Variable = ZNF384 MUTATION ANALYSIS
D712V1, survival
                  sevent
clus2                0   1
  ZNF384 MUTATED     8   1
  ZNF384 WILD-TYPE 274  72
  ZNF384 MUTATED ZNF384 WILD-TYPE 
               9              346 
  ZNF384 MUTATED ZNF384 WILD-TYPE 
               1               72 
$`ZNF384 MUTATED`
TCGA-AA-3815 TCGA-AD-6889 TCGA-AZ-4315 TCGA-AZ-5403 TCGA-CM-5864 TCGA-CM-6674 
       33.04        56.55        58.39        62.79        15.02        12.95 
TCGA-D5-5539 TCGA-D5-6540 TCGA-DM-A1HB 
       19.59        16.14       135.65 

$`ZNF384 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        4.21         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
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-6675 TCGA-CM-6676 
       13.02        15.02        14.04        11.01        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  ZNF384 MUTATED ZNF384 WILD-TYPE 
           12.95             0.00 
  ZNF384 MUTATED ZNF384 WILD-TYPE 
          135.65           140.38 
  ZNF384 MUTATED ZNF384 WILD-TYPE 
          33.040           20.155 
[1] "12.9 - 135.7 (33.0)" "0.0 - 140.4 (20.2)" 
[1] "hr=" "3.2"
D712V2, 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       24       105         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF384 MUTATED           0          1          1          0        0
  ZNF384 WILD-TYPE        19          9         40         31       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF384 MUTATED           0         0
  ZNF384 WILD-TYPE        13         1
D712V3, multiclass
            clus
vv           ZNF384 MUTATED ZNF384 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               4              105
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              1                9
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF384 MUTATED     0   2   7   0
  ZNF384 WILD-TYPE   9  66 241  41
D712V4, multiclass
    clus
vv   ZNF384 MUTATED ZNF384 WILD-TYPE
  T1              0                9
  T2              2               66
  T3              7              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
  ZNF384 MUTATED     7   2   0
  ZNF384 WILD-TYPE 213  78  66
D712V5, multiclass
    clus
vv   ZNF384 MUTATED ZNF384 WILD-TYPE
  N0              7              213
  N1              2               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"
D712V6, binary
                  cls
clus                 0   1
  ZNF384 MUTATED     8   0
  ZNF384 WILD-TYPE 275  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF384 MUTATED      8    0
  ZNF384 WILD-TYPE  275   48
   clus
vv  ZNF384 MUTATED ZNF384 WILD-TYPE
  0              8              275
  1              0               48
[1] 2 2
[1] FALSE
D712V7, 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
D712V8, binary
                  cls
clus                 0   1
  ZNF384 MUTATED     7   2
  ZNF384 WILD-TYPE 310  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF384 MUTATED      7    2
  ZNF384 WILD-TYPE  310   46
                               clus
vv                              ZNF384 MUTATED ZNF384 WILD-TYPE
  COLON ADENOCARCINOMA                       7              310
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF384 MUTATED     6   0   0   0
  ZNF384 WILD-TYPE 251   2  22  21
D712V9, multiclass
    clus
vv   ZNF384 MUTATED ZNF384 WILD-TYPE
  R0              6              251
  R1              0                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"
D712V10, 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
D712V11, 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(713) Variable = C20ORF177 MUTATION ANALYSIS
D713V1, survival
                     sevent
clus2                   0   1
  C20ORF177 MUTATED     8   1
  C20ORF177 WILD-TYPE 274  72
  C20ORF177 MUTATED C20ORF177 WILD-TYPE 
                  9                 346 
  C20ORF177 MUTATED C20ORF177 WILD-TYPE 
                  1                  72 
$`C20ORF177 MUTATED`
TCGA-AA-A00N TCGA-AA-A01R TCGA-CA-6718 TCGA-CA-6719 TCGA-CM-6171 TCGA-D5-6536 
        4.01        35.01         0.10         1.35        14.04        17.85 
TCGA-DM-A1D0 TCGA-F4-6704 TCGA-G4-6304 
      130.65         1.55        53.62 

$`C20ORF177 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07         0.26         0.33        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        15.12         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 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-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 
       13.38        13.45         6.18        35.87        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      107.67        74.56        65.85        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  C20ORF177 MUTATED C20ORF177 WILD-TYPE 
                0.1                 0.0 
  C20ORF177 MUTATED C20ORF177 WILD-TYPE 
             130.65              140.38 
  C20ORF177 MUTATED C20ORF177 WILD-TYPE 
              14.04               20.63 
[1] "0.1 - 130.7 (14.0)" "0.0 - 140.4 (20.6)"
[1] "hr=" "1.9"
D713V2, 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       25       105         6         1
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C20ORF177 MUTATED           1          0          0          1        0
  C20ORF177 WILD-TYPE        18         10         41         30       35
                     vv
clus                  STAGE IVA STAGE IVB
  C20ORF177 MUTATED           0         0
  C20ORF177 WILD-TYPE        13         1
D713V3, multiclass
            clus
vv           C20ORF177 MUTATED C20ORF177 WILD-TYPE
  STAGE I                    1                  63
  STAGE IA                   0                   1
  STAGE II                   0                  25
  STAGE IIA                  4                 105
  STAGE IIB                  2                   6
  STAGE IIC                  0                   1
  STAGE III                  1                  18
  STAGE IIIA                 0                  10
  STAGE IIIB                 0                  41
  STAGE IIIC                 1                  30
  STAGE IV                   0                  35
  STAGE IVA                  0                  13
  STAGE IVB                  0                   1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2  T3  T4
  C20ORF177 MUTATED     0   1   6   2
  C20ORF177 WILD-TYPE   9  67 242  39
D713V4, multiclass
    clus
vv   C20ORF177 MUTATED C20ORF177 WILD-TYPE
  T1                 0                   9
  T2                 1                  67
  T3                 6                 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
  C20ORF177 MUTATED     7   0   2
  C20ORF177 WILD-TYPE 213  80  64
D713V5, multiclass
    clus
vv   C20ORF177 MUTATED C20ORF177 WILD-TYPE
  N0                 7                 213
  N1                 0                  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"
D713V6, binary
                     cls
clus                    0   1
  C20ORF177 MUTATED     8   0
  C20ORF177 WILD-TYPE 275  48
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C20ORF177 MUTATED      8    0
  C20ORF177 WILD-TYPE  275   48
   clus
vv  C20ORF177 MUTATED C20ORF177 WILD-TYPE
  0                 8                 275
  1                 0                  48
[1] 2 2
[1] FALSE
D713V7, 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
D713V8, binary
                     cls
clus                    0   1
  C20ORF177 MUTATED     6   3
  C20ORF177 WILD-TYPE 311  45
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C20ORF177 MUTATED      6    3
  C20ORF177 WILD-TYPE  311   45
                               clus
vv                              C20ORF177 MUTATED C20ORF177 WILD-TYPE
  COLON ADENOCARCINOMA                          6                 311
  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 251   2  22  19
D713V9, multiclass
    clus
vv   C20ORF177 MUTATED C20ORF177 WILD-TYPE
  R0                 6                 251
  R1                 0                   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"
D713V10, 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
D713V11, 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(714) Variable = IFITM3 MUTATION ANALYSIS
D714V1, survival
                  sevent
clus2                0   1
  IFITM3 MUTATED     6   0
  IFITM3 WILD-TYPE 276  73
  IFITM3 MUTATED IFITM3 WILD-TYPE 
               6              349 
  IFITM3 MUTATED IFITM3 WILD-TYPE 
               0               73 
$`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        13.51        20.19        36.00 

$`IFITM3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        15.75         0.20        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         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-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        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-D5-6532 
       12.03        45.40        12.26        19.59        11.51        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  IFITM3 MUTATED IFITM3 WILD-TYPE 
           13.51             0.00 
  IFITM3 MUTATED IFITM3 WILD-TYPE 
           36.00           140.38 
  IFITM3 MUTATED IFITM3 WILD-TYPE 
          20.815           20.120 
[1] "13.5 - 36.0 (20.8)" "0.0 - 140.4 (20.1)"
[1] "hr="     "9200000"
D714V2, 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       25       104         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IFITM3 MUTATED           0          0          0          1        0
  IFITM3 WILD-TYPE        19         10         41         30       35
                  vv
clus               STAGE IVA STAGE IVB
  IFITM3 MUTATED           0         0
  IFITM3 WILD-TYPE        13         1
D714V3, multiclass
            clus
vv           IFITM3 MUTATED IFITM3 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               5              104
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  IFITM3 MUTATED     0   0   6   0
  IFITM3 WILD-TYPE   9  68 242  41
D714V4, multiclass
    clus
vv   IFITM3 MUTATED IFITM3 WILD-TYPE
  T1              0                9
  T2              0               68
  T3              6              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
  IFITM3 MUTATED     5   0   1
  IFITM3 WILD-TYPE 215  80  65
D714V5, multiclass
    clus
vv   IFITM3 MUTATED IFITM3 WILD-TYPE
  N0              5              215
  N1              0               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"
D714V6, binary
                  cls
clus                 0   1
  IFITM3 MUTATED     4   0
  IFITM3 WILD-TYPE 279  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFITM3 MUTATED      4    0
  IFITM3 WILD-TYPE  279   48
   clus
vv  IFITM3 MUTATED IFITM3 WILD-TYPE
  0              4              279
  1              0               48
[1] 2 2
[1] FALSE
D714V7, 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
D714V8, binary
                  cls
clus                 0   1
  IFITM3 MUTATED     6   0
  IFITM3 WILD-TYPE 311  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFITM3 MUTATED      6    0
  IFITM3 WILD-TYPE  311   48
                               clus
vv                              IFITM3 MUTATED IFITM3 WILD-TYPE
  COLON ADENOCARCINOMA                       6              311
  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 251   2  22  21
D714V9, multiclass
    clus
vv   IFITM3 MUTATED IFITM3 WILD-TYPE
  R0              6              251
  R1              0                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"
D714V10, 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
D714V11, 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(715) Variable = NIPA2 MUTATION ANALYSIS
D715V1, survival
                 sevent
clus2               0   1
  NIPA2 MUTATED     6   1
  NIPA2 WILD-TYPE 276  72
  NIPA2 MUTATED NIPA2 WILD-TYPE 
              7             348 
  NIPA2 MUTATED NIPA2 WILD-TYPE 
              1              72 
$`NIPA2 MUTATED`
TCGA-AA-3524 TCGA-AA-3663 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3977 TCGA-CM-4746 
       36.03         6.97        26.99        19.04        25.02        37.02 
TCGA-DM-A1HB 
      135.65 

$`NIPA2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 
       38.99         1.02         9.07        24.03        37.05         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.03        85.05        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  NIPA2 MUTATED NIPA2 WILD-TYPE 
           6.97            0.00 
  NIPA2 MUTATED NIPA2 WILD-TYPE 
         135.65          140.38 
  NIPA2 MUTATED NIPA2 WILD-TYPE 
          26.99           20.07 
[1] "7.0 - 135.7 (27.0)" "0.0 - 140.4 (20.1)"
[1] "hr=" "2"  
D715V2, 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       22       108         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        19         10         40         31       35        13
                 vv
clus              STAGE IVB
  NIPA2 MUTATED           0
  NIPA2 WILD-TYPE         1
D715V3, multiclass
            clus
vv           NIPA2 MUTATED NIPA2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              1             108
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NIPA2 MUTATED     0   2   5   0
  NIPA2 WILD-TYPE   9  66 243  41
D715V4, multiclass
    clus
vv   NIPA2 MUTATED NIPA2 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             5             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
  NIPA2 MUTATED     6   1   0
  NIPA2 WILD-TYPE 214  79  66
D715V5, multiclass
    clus
vv   NIPA2 MUTATED NIPA2 WILD-TYPE
  N0             6             214
  N1             1              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"
D715V6, binary
                 cls
clus                0   1
  NIPA2 MUTATED     6   0
  NIPA2 WILD-TYPE 277  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NIPA2 MUTATED      6    0
  NIPA2 WILD-TYPE  277   48
   clus
vv  NIPA2 MUTATED NIPA2 WILD-TYPE
  0             6             277
  1             0              48
[1] 2 2
[1] FALSE
D715V7, 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
D715V8, binary
                 cls
clus                0   1
  NIPA2 MUTATED     7   0
  NIPA2 WILD-TYPE 310  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NIPA2 MUTATED      7    0
  NIPA2 WILD-TYPE  310   48
                               clus
vv                              NIPA2 MUTATED NIPA2 WILD-TYPE
  COLON ADENOCARCINOMA                      7             310
  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 252   2  22  21
D715V9, multiclass
    clus
vv   NIPA2 MUTATED NIPA2 WILD-TYPE
  R0             5             252
  R1             0               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"
D715V10, 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
D715V11, multiclass
[1] "Remove cluster labels:" "NIPA2 MUTATED"         
clus
  NIPA2 MUTATED NIPA2 WILD-TYPE 
              2             204 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-4105 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-A6-5656      TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5660 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-A6-5661      TCGA-A6-5662      TCGA-A6-5664      TCGA-A6-5665 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-A6-5666      TCGA-A6-6137      TCGA-A6-6138      TCGA-A6-6141 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-A6-6142      TCGA-A6-6648      TCGA-A6-6649      TCGA-A6-6651 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-A6-6652      TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-A6-6781      TCGA-A6-6782      TCGA-AD-5900      TCGA-AD-6548 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-AD-6888      TCGA-AD-6889      TCGA-AD-6890      TCGA-AD-6895 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-AD-6899      TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6964 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-AD-6965      TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-AY-4071      TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-AY-6386      TCGA-AZ-4315      TCGA-AZ-4323      TCGA-AZ-4616 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-AZ-4681      TCGA-AZ-4682      TCGA-AZ-5403      TCGA-AZ-5407 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-AZ-6598      TCGA-AZ-6599      TCGA-AZ-6600      TCGA-AZ-6601 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-AZ-6603      TCGA-AZ-6605      TCGA-AZ-6606      TCGA-AZ-6607 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-AZ-6608      TCGA-CA-5254      TCGA-CA-5255      TCGA-CA-5796 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-CA-5797      TCGA-CA-6715      TCGA-CA-6716      TCGA-CA-6717 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-CA-6718      TCGA-CA-6719      TCGA-CK-4947      TCGA-CK-4948 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-CK-4950      TCGA-CK-4952      TCGA-CK-5912      TCGA-CK-5913 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-CK-5914      TCGA-CK-5915      TCGA-CK-5916      TCGA-CK-6746 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-CK-6747      TCGA-CK-6748      TCGA-CK-6751      TCGA-CM-4743 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-CM-4744      TCGA-CM-4747      TCGA-CM-4752      TCGA-CM-5341 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-CM-5344      TCGA-CM-5348      TCGA-CM-5349      TCGA-CM-5860 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-CM-5861      TCGA-CM-5862      TCGA-CM-5863      TCGA-CM-5864 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-CM-5868      TCGA-CM-6161      TCGA-CM-6162      TCGA-CM-6163 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-CM-6164      TCGA-CM-6165      TCGA-CM-6166      TCGA-CM-6167 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-CM-6168      TCGA-CM-6169      TCGA-CM-6170      TCGA-CM-6171 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-CM-6172      TCGA-CM-6674      TCGA-CM-6675      TCGA-CM-6676 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-CM-6677      TCGA-CM-6678      TCGA-CM-6679      TCGA-CM-6680 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-D5-5537      TCGA-D5-5538      TCGA-D5-5539      TCGA-D5-5540 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-D5-5541      TCGA-D5-6529      TCGA-D5-6532      TCGA-D5-6533 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-D5-6534      TCGA-D5-6535      TCGA-D5-6536      TCGA-D5-6537 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-D5-6538      TCGA-D5-6539      TCGA-D5-6540      TCGA-D5-6541 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-D5-6898      TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-D5-6924      TCGA-D5-6926      TCGA-D5-6927      TCGA-D5-6928 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-D5-6929      TCGA-D5-6930      TCGA-D5-6931      TCGA-D5-6932 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-D5-7000      TCGA-DM-A0X9      TCGA-DM-A0XD      TCGA-DM-A0XF 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-DM-A1D0      TCGA-DM-A1D4      TCGA-DM-A1D6      TCGA-DM-A1D7 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-DM-A1D8      TCGA-DM-A1D9      TCGA-DM-A1DA      TCGA-DM-A1DB 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-DM-A1HA      TCGA-DM-A282      TCGA-DM-A285      TCGA-DM-A28C 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-DM-A28E      TCGA-DM-A28F      TCGA-DM-A28G      TCGA-DM-A28H 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-DM-A28K      TCGA-F4-6459      TCGA-F4-6460      TCGA-F4-6569 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704      TCGA-F4-6805 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808      TCGA-F4-6809 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856      TCGA-G4-6293 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304      TCGA-G4-6306 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310      TCGA-G4-6315 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323      TCGA-G4-6586 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-G4-6588      TCGA-G4-6625      TCGA-G4-6626      TCGA-G4-6628 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 

Clustering(716) Variable = C14ORF39 MUTATION ANALYSIS
D716V1, survival
                    sevent
clus2                  0   1
  C14ORF39 MUTATED    11   1
  C14ORF39 WILD-TYPE 271  72
  C14ORF39 MUTATED C14ORF39 WILD-TYPE 
                12                343 
  C14ORF39 MUTATED C14ORF39 WILD-TYPE 
                 1                 72 
$`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        15.75        58.39 
TCGA-CA-6717 TCGA-CA-6718 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-6930 TCGA-DM-A28E 
        0.33         0.10        45.40        12.26         1.51       119.93 

$`C14ORF39 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 
        0.20        14.50        16.31         0.95         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07         0.26         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       10.06        12.03        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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-A285 TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
        6.12        81.37        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  C14ORF39 MUTATED C14ORF39 WILD-TYPE 
               0.1                0.0 
  C14ORF39 MUTATED C14ORF39 WILD-TYPE 
            119.93             140.38 
  C14ORF39 MUTATED C14ORF39 WILD-TYPE 
            26.055             20.120 
[1] "0.1 - 119.9 (26.1)" "0.0 - 140.4 (20.1)"
[1] "hr=" "3.2"
D716V2, 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       24       103         6         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C14ORF39 MUTATED           0          0          1          0        0
  C14ORF39 WILD-TYPE        19         10         40         31       35
                    vv
clus                 STAGE IVA STAGE IVB
  C14ORF39 MUTATED           1         0
  C14ORF39 WILD-TYPE        12         1
D716V3, multiclass
            clus
vv           C14ORF39 MUTATED C14ORF39 WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  1                 24
  STAGE IIA                 6                103
  STAGE IIB                 2                  6
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                0                 10
  STAGE IIIB                1                 40
  STAGE IIIC                0                 31
  STAGE IV                  0                 35
  STAGE IVA                 1                 12
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 239  39
D716V4, multiclass
    clus
vv   C14ORF39 MUTATED C14ORF39 WILD-TYPE
  T1                0                  9
  T2                2                 66
  T3                9                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
  C14ORF39 MUTATED    10   2   1
  C14ORF39 WILD-TYPE 210  78  65
D716V5, multiclass
    clus
vv   C14ORF39 MUTATED C14ORF39 WILD-TYPE
  N0               10                210
  N1                2                 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"
D716V6, binary
                    cls
clus                   0   1
  C14ORF39 MUTATED     9   1
  C14ORF39 WILD-TYPE 274  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF39 MUTATED      9    1
  C14ORF39 WILD-TYPE  274   47
   clus
vv  C14ORF39 MUTATED C14ORF39 WILD-TYPE
  0                9                274
  1                1                 47
[1] 2 2
[1] FALSE
D716V7, 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
D716V8, binary
                    cls
clus                   0   1
  C14ORF39 MUTATED    11   2
  C14ORF39 WILD-TYPE 306  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF39 MUTATED     11    2
  C14ORF39 WILD-TYPE  306   46
                               clus
vv                              C14ORF39 MUTATED C14ORF39 WILD-TYPE
  COLON ADENOCARCINOMA                        11                306
  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 250   2  22  17
D716V9, multiclass
    clus
vv   C14ORF39 MUTATED C14ORF39 WILD-TYPE
  R0                7                250
  R1                0                  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"
D716V10, 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
D716V11, 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(717) Variable = HNMT MUTATION ANALYSIS
D717V1, survival
                sevent
clus2              0   1
  HNMT MUTATED     9   1
  HNMT WILD-TYPE 273  72
  HNMT MUTATED HNMT WILD-TYPE 
            10            345 
  HNMT MUTATED HNMT WILD-TYPE 
             1             72 
$`HNMT MUTATED`
TCGA-A6-5665 TCGA-A6-6653 TCGA-AA-3710 TCGA-AA-3949 TCGA-AA-A010 TCGA-AD-6964 
       22.06        24.39        26.99        26.01        34.98        10.88 
TCGA-CK-4948 TCGA-D5-5538 TCGA-D5-6536 TCGA-DM-A1HB 
      102.44        12.26        17.85       135.65 

$`HNMT WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        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        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
        1.35        17.56        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  HNMT MUTATED HNMT WILD-TYPE 
         10.88           0.00 
  HNMT MUTATED HNMT WILD-TYPE 
        135.65         140.38 
  HNMT MUTATED HNMT WILD-TYPE 
         25.20          20.02 
[1] "10.9 - 135.7 (25.2)" "0.0 - 140.4 (20.0)" 
[1] "hr=" "3.1"
D717V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HNMT MUTATED         1        0        0         4         1         0
  HNMT WILD-TYPE      63        1       25       105         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HNMT MUTATED           0          1          3          0        0         0
  HNMT WILD-TYPE        19          9         38         31       35        13
                vv
clus             STAGE IVB
  HNMT MUTATED           0
  HNMT WILD-TYPE         1
D717V3, multiclass
            clus
vv           HNMT MUTATED HNMT WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             4            105
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            1              9
  STAGE IIIB            3             38
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  HNMT MUTATED     0   1   8   2
  HNMT WILD-TYPE   9  67 240  39
D717V4, multiclass
    clus
vv   HNMT MUTATED HNMT WILD-TYPE
  T1            0              9
  T2            1             67
  T3            8            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
  HNMT MUTATED     6   4   1
  HNMT WILD-TYPE 214  76  65
D717V5, multiclass
    clus
vv   HNMT MUTATED HNMT WILD-TYPE
  N0            6            214
  N1            4             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"
D717V6, binary
                cls
clus               0   1
  HNMT MUTATED    10   0
  HNMT WILD-TYPE 273  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  HNMT MUTATED     10    0
  HNMT WILD-TYPE  273   48
   clus
vv  HNMT MUTATED HNMT WILD-TYPE
  0           10            273
  1            0             48
[1] 2 2
[1] FALSE
D717V7, binary
                cls
clus               0   1
  HNMT MUTATED     7   4
  HNMT WILD-TYPE 163 193
[1] "tbl2"
                cls
clus             [,1] [,2]
  HNMT MUTATED      7    4
  HNMT WILD-TYPE  163  193
        clus
vv       HNMT MUTATED HNMT WILD-TYPE
  FEMALE            7            163
  MALE              4            193
[1] 2 2
[1] FALSE
D717V8, binary
                cls
clus               0   1
  HNMT MUTATED    10   1
  HNMT WILD-TYPE 307  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  HNMT MUTATED     10    1
  HNMT WILD-TYPE  307   47
                               clus
vv                              HNMT MUTATED HNMT WILD-TYPE
  COLON ADENOCARCINOMA                    10            307
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  HNMT MUTATED     8   0   0   0
  HNMT WILD-TYPE 249   2  22  21
D717V9, multiclass
    clus
vv   HNMT MUTATED HNMT WILD-TYPE
  R0            8            249
  R1            0              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"
D717V10, 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     7
  HNMT WILD-TYPE                        19   169
D717V11, 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                                       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(718) Variable = GMNN MUTATION ANALYSIS
D718V1, survival
                sevent
clus2              0   1
  GMNN MUTATED     3   0
  GMNN WILD-TYPE 279  73
  GMNN MUTATED GMNN WILD-TYPE 
             3            352 
  GMNN MUTATED GMNN WILD-TYPE 
             0             73 
$`GMNN MUTATED`
TCGA-AA-A010 TCGA-D5-5538 TCGA-D5-6538 
       34.98        12.26        17.13 

$`GMNN WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  GMNN MUTATED GMNN WILD-TYPE 
         12.26           0.00 
  GMNN MUTATED GMNN WILD-TYPE 
         34.98         140.38 
  GMNN MUTATED GMNN WILD-TYPE 
        17.130         20.235 
[1] "12.3 - 35.0 (17.1)" "0.0 - 140.4 (20.2)"
[1] "hr="     "3300000"
D718V2, 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       25       109         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        19         10         39         31       35        13
                vv
clus             STAGE IVB
  GMNN MUTATED           0
  GMNN WILD-TYPE         1
D718V3, multiclass
            clus
vv           GMNN MUTATED GMNN WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             0            109
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            2             39
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GMNN MUTATED     0   0   2   1
  GMNN WILD-TYPE   9  68 246  40
D718V4, multiclass
    clus
vv   GMNN MUTATED GMNN WILD-TYPE
  T1            0              9
  T2            0             68
  T3            2            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
  GMNN MUTATED     1   1   1
  GMNN WILD-TYPE 219  79  65
D718V5, multiclass
    clus
vv   GMNN MUTATED GMNN WILD-TYPE
  N0            1            219
  N1            1             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"
D718V6, binary
                cls
clus               0   1
  GMNN MUTATED     3   0
  GMNN WILD-TYPE 280  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  GMNN MUTATED      3    0
  GMNN WILD-TYPE  280   48
   clus
vv  GMNN MUTATED GMNN WILD-TYPE
  0            3            280
  1            0             48
[1] 2 2
[1] FALSE
D718V7, 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
D718V8, binary
                cls
clus               0   1
  GMNN MUTATED     3   0
  GMNN WILD-TYPE 314  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  GMNN MUTATED      3    0
  GMNN WILD-TYPE  314   48
                               clus
vv                              GMNN MUTATED GMNN WILD-TYPE
  COLON ADENOCARCINOMA                     3            314
  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 254   2  22  21
D718V9, multiclass
    clus
vv   GMNN MUTATED GMNN WILD-TYPE
  R0            3            254
  R1            0              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"
D718V10, 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
D718V11, multiclass
[1] "Remove cluster labels:" "GMNN MUTATED"          
clus
  GMNN MUTATED GMNN WILD-TYPE 
             2            204 
    TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810     TCGA-A6-4105 
"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-A6-6649     TCGA-A6-6651 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-A6-6652     TCGA-A6-6653     TCGA-A6-6654     TCGA-A6-6780 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-A6-6781     TCGA-A6-6782     TCGA-AD-5900     TCGA-AD-6548 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-AD-6888     TCGA-AD-6889     TCGA-AD-6890     TCGA-AD-6895 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-AD-6899     TCGA-AD-6901     TCGA-AD-6963     TCGA-AD-6964 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-AD-6965     TCGA-AU-3779     TCGA-AU-6004     TCGA-AY-4070 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-AY-4071     TCGA-AY-5543     TCGA-AY-6196     TCGA-AY-6197 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-AY-6386     TCGA-AZ-4315     TCGA-AZ-4323     TCGA-AZ-4616 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-AZ-4681     TCGA-AZ-4682     TCGA-AZ-5403     TCGA-AZ-5407 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-AZ-6598     TCGA-AZ-6599     TCGA-AZ-6600     TCGA-AZ-6601 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-AZ-6603     TCGA-AZ-6605     TCGA-AZ-6606     TCGA-AZ-6607 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-AZ-6608     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-5912     TCGA-CK-5913 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-CK-5914     TCGA-CK-5915     TCGA-CK-5916     TCGA-CK-6746 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-CK-6747     TCGA-CK-6748     TCGA-CK-6751     TCGA-CM-4743 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-CM-4744     TCGA-CM-4746     TCGA-CM-4747     TCGA-CM-4752 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-CM-5341     TCGA-CM-5344     TCGA-CM-5348     TCGA-CM-5349 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-CM-5860     TCGA-CM-5861     TCGA-CM-5862     TCGA-CM-5863 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-CM-5864     TCGA-CM-5868     TCGA-CM-6161     TCGA-CM-6162 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-CM-6163     TCGA-CM-6164     TCGA-CM-6165     TCGA-CM-6166 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-CM-6167     TCGA-CM-6168     TCGA-CM-6169     TCGA-CM-6170 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-CM-6171     TCGA-CM-6172     TCGA-CM-6674     TCGA-CM-6675 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-CM-6676     TCGA-CM-6677     TCGA-CM-6678     TCGA-CM-6679 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-CM-6680     TCGA-D5-5537     TCGA-D5-5539     TCGA-D5-5540 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-D5-5541     TCGA-D5-6529     TCGA-D5-6532     TCGA-D5-6533 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-D5-6534     TCGA-D5-6535     TCGA-D5-6536     TCGA-D5-6537 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-D5-6539     TCGA-D5-6540     TCGA-D5-6541     TCGA-D5-6898 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-D5-6920     TCGA-D5-6922     TCGA-D5-6923     TCGA-D5-6924 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-D5-6926     TCGA-D5-6927     TCGA-D5-6928     TCGA-D5-6929 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-D5-6930     TCGA-D5-6931     TCGA-D5-6932     TCGA-D5-7000 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-DM-A0X9     TCGA-DM-A0XD     TCGA-DM-A0XF     TCGA-DM-A1D0 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-DM-A1D4     TCGA-DM-A1D6     TCGA-DM-A1D7     TCGA-DM-A1D8 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-DM-A1D9     TCGA-DM-A1DA     TCGA-DM-A1DB     TCGA-DM-A1HA 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-DM-A1HB     TCGA-DM-A282     TCGA-DM-A285     TCGA-DM-A28C 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-DM-A28E     TCGA-DM-A28F     TCGA-DM-A28G     TCGA-DM-A28H 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-DM-A28K     TCGA-F4-6459     TCGA-F4-6460     TCGA-F4-6569 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-F4-6570     TCGA-F4-6703     TCGA-F4-6704     TCGA-F4-6805 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-F4-6806     TCGA-F4-6807     TCGA-F4-6808     TCGA-F4-6809 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-F4-6854     TCGA-F4-6855     TCGA-F4-6856     TCGA-G4-6293 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-G4-6299     TCGA-G4-6303     TCGA-G4-6304     TCGA-G4-6306 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-G4-6307     TCGA-G4-6309     TCGA-G4-6310     TCGA-G4-6315 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-G4-6317     TCGA-G4-6321     TCGA-G4-6323     TCGA-G4-6586 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 
    TCGA-G4-6588     TCGA-G4-6625     TCGA-G4-6626     TCGA-G4-6628 
"GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" "GMNN WILD-TYPE" 

Clustering(719) Variable = MACF1 MUTATION ANALYSIS
D719V1, survival
                 sevent
clus2               0   1
  MACF1 MUTATED    43  13
  MACF1 WILD-TYPE 239  60
  MACF1 MUTATED MACF1 WILD-TYPE 
             56             299 
  MACF1 MUTATED MACF1 WILD-TYPE 
             13              60 
$`MACF1 MUTATED`
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-5665 TCGA-A6-6653 TCGA-A6-6780 
       46.65        42.90        42.28        22.06        24.39        20.12 
TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3554 TCGA-AA-3662 TCGA-AA-3713 
        3.02        63.98        13.02        17.95         6.05        19.04 
TCGA-AA-3811 TCGA-AA-3815 TCGA-AA-3850 TCGA-AA-3864 TCGA-AA-3949 TCGA-AA-3966 
       10.06        33.04         0.00        53.00        26.01         2.01 
TCGA-AA-3977 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A00R 
       25.02        38.04        30.02        18.05         4.01         0.99 
TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-6895 TCGA-AD-6899 TCGA-AY-6197 TCGA-AZ-4315 
       34.98        35.01         0.72         5.79        21.44        58.39 
TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-CA-5796 TCGA-CA-6717 
       62.79        49.41        12.10       100.01         3.25         0.33 
TCGA-CK-4952 TCGA-CK-6751 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-6162 TCGA-CM-6165 
       15.62       124.27        15.02         5.03        12.00        16.04 
TCGA-CM-6171 TCGA-CM-6674 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6926 TCGA-D5-6927 
       14.04        12.95        15.12        17.85         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-F4-6570 TCGA-F4-6703 TCGA-G4-6315 TCGA-G4-6586 
       11.64         1.51         6.18        35.87        36.72        35.80 
TCGA-G4-6588 TCGA-G4-6628 
       26.17        52.80 

$`MACF1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        43.76        24.33        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       32.75        36.53        14.53        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 
       29.19        33.53        23.61        22.09        32.71        27.09 
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 
       22.52         8.38        25.08        25.18        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       24.69        23.87        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       35.01         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       19.04        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       10.06        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       33.01        24.00         2.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       19.00        34.03        18.05        38.04        27.02        42.02 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
       56.55         0.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 
       17.82         1.41         5.13        83.80        22.36        61.41 
TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
        6.77        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        2.24         3.06         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 
        1.35        17.56       102.44        40.34        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 
       21.99        21.14         2.93         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-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       30.08        16.01        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-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       15.02        11.01        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6537 
       11.51        20.19        18.25         1.32        43.27         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 
       10.13        12.43        14.30        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-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       13.45         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        91.79        46.75 

  MACF1 MUTATED MACF1 WILD-TYPE 
              0               0 
  MACF1 MUTATED MACF1 WILD-TYPE 
         124.27          140.38 
  MACF1 MUTATED MACF1 WILD-TYPE 
          18.00           20.98 
[1] "0.0 - 124.3 (18.0)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.2"
D719V2, 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       19        86         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MACF1 MUTATED           5          1          6          1        4         1
  MACF1 WILD-TYPE        14          9         35         30       31        12
                 vv
clus              STAGE IVB
  MACF1 MUTATED           0
  MACF1 WILD-TYPE         1
D719V3, multiclass
            clus
vv           MACF1 MUTATED MACF1 WILD-TYPE
  STAGE I                6              58
  STAGE IA               0               1
  STAGE II               6              19
  STAGE IIA             23              86
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              5              14
  STAGE IIIA             1               9
  STAGE IIIB             6              35
  STAGE IIIC             1              30
  STAGE IV               4              31
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  61 206  32
D719V4, multiclass
    clus
vv   MACF1 MUTATED MACF1 WILD-TYPE
  T1             0               9
  T2             7              61
  T3            42             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
  MACF1 MUTATED    40  11   7
  MACF1 WILD-TYPE 180  69  59
D719V5, multiclass
    clus
vv   MACF1 MUTATED MACF1 WILD-TYPE
  N0            40             180
  N1            11              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"
D719V6, binary
                 cls
clus                0   1
  MACF1 MUTATED    44   5
  MACF1 WILD-TYPE 239  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MACF1 MUTATED     44    5
  MACF1 WILD-TYPE  239   43
   clus
vv  MACF1 MUTATED MACF1 WILD-TYPE
  0            44             239
  1             5              43
[1] 2 2
[1] FALSE
D719V7, 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
D719V8, binary
                 cls
clus                0   1
  MACF1 MUTATED    43  15
  MACF1 WILD-TYPE 274  33
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MACF1 MUTATED     43   15
  MACF1 WILD-TYPE  274   33
                               clus
vv                              MACF1 MUTATED MACF1 WILD-TYPE
  COLON ADENOCARCINOMA                     43             274
  COLON MUCINOUS ADENOCARCINOMA            15              33
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MACF1 MUTATED    41   0   2   4
  MACF1 WILD-TYPE 216   2  20  17
D719V9, multiclass
    clus
vv   MACF1 MUTATED MACF1 WILD-TYPE
  R0            41             216
  R1             0               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"
D719V10, 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
D719V11, 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(720) Variable = UPF3A MUTATION ANALYSIS
D720V1, survival
                 sevent
clus2               0   1
  UPF3A MUTATED     8   1
  UPF3A WILD-TYPE 274  72
  UPF3A MUTATED UPF3A WILD-TYPE 
              9             346 
  UPF3A MUTATED UPF3A WILD-TYPE 
              1              72 
$`UPF3A MUTATED`
TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3663 TCGA-AA-3977 TCGA-AD-6889 
        3.02        63.98        29.95         6.97        25.02        56.55 
TCGA-AZ-4681 TCGA-CA-6718 TCGA-CK-5913 
       83.80         0.10        51.32 

$`UPF3A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37         4.21         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         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        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.33         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 
      102.44        40.34        15.62        49.08        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  UPF3A MUTATED UPF3A WILD-TYPE 
            0.1             0.0 
  UPF3A MUTATED UPF3A WILD-TYPE 
          83.80          140.38 
  UPF3A MUTATED UPF3A WILD-TYPE 
          29.95           20.07 
[1] "0.1 - 83.8 (29.9)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "2.8"
D720V2, 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       22       104         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        19         10         41         31       35        13
                 vv
clus              STAGE IVB
  UPF3A MUTATED           0
  UPF3A WILD-TYPE         1
D720V3, multiclass
            clus
vv           UPF3A MUTATED UPF3A WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              5             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  UPF3A MUTATED     0   1   8   0
  UPF3A WILD-TYPE   9  67 240  41
D720V4, multiclass
    clus
vv   UPF3A MUTATED UPF3A WILD-TYPE
  T1             0               9
  T2             1              67
  T3             8             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
  UPF3A MUTATED     9   0   0
  UPF3A WILD-TYPE 211  80  66
D720V5, multiclass
    clus
vv   UPF3A MUTATED UPF3A WILD-TYPE
  N0             9             211
  N1             0              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"
D720V6, binary
                 cls
clus                0   1
  UPF3A MUTATED     7   0
  UPF3A WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UPF3A MUTATED      7    0
  UPF3A WILD-TYPE  276   48
   clus
vv  UPF3A MUTATED UPF3A WILD-TYPE
  0             7             276
  1             0              48
[1] 2 2
[1] FALSE
D720V7, 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
D720V8, binary
                 cls
clus                0   1
  UPF3A MUTATED     8   1
  UPF3A WILD-TYPE 309  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UPF3A MUTATED      8    1
  UPF3A WILD-TYPE  309   47
                               clus
vv                              UPF3A MUTATED UPF3A WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  UPF3A MUTATED     5   0   0   2
  UPF3A WILD-TYPE 252   2  22  19
D720V9, multiclass
    clus
vv   UPF3A MUTATED UPF3A WILD-TYPE
  R0             5             252
  R1             0               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"
D720V10, 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
D720V11, 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(721) Variable = MAP7D3 MUTATION ANALYSIS
D721V1, survival
                  sevent
clus2                0   1
  MAP7D3 MUTATED    13   3
  MAP7D3 WILD-TYPE 269  70
  MAP7D3 MUTATED MAP7D3 WILD-TYPE 
              16              339 
  MAP7D3 MUTATED MAP7D3 WILD-TYPE 
               3               70 
$`MAP7D3 MUTATED`
TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3660 TCGA-AA-3710 TCGA-AA-3941 
       22.06         3.02        63.98        78.08        26.99        24.00 
TCGA-AA-A03J TCGA-AZ-4315 TCGA-AZ-4616 TCGA-CA-6717 TCGA-D5-6930 TCGA-DM-A28E 
       40.96        58.39         5.13         0.33         1.51       119.93 
TCGA-F4-6570 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
        6.18        35.80        26.17        91.79 

$`MAP7D3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 
       18.05        31.00         2.01        12.99        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 
        0.92        41.00        39.98        18.05         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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-A285 TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
        6.12        81.37        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        13.38        13.45        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6628 
       13.78        46.75        52.80 

  MAP7D3 MUTATED MAP7D3 WILD-TYPE 
            0.33             0.00 
  MAP7D3 MUTATED MAP7D3 WILD-TYPE 
          119.93           140.38 
  MAP7D3 MUTATED MAP7D3 WILD-TYPE 
           26.58            19.99 
[1] "0.3 - 119.9 (26.6)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.6"
D721V2, 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       22        98         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAP7D3 MUTATED           0          0          0          0        1
  MAP7D3 WILD-TYPE        19         10         41         31       34
                  vv
clus               STAGE IVA STAGE IVB
  MAP7D3 MUTATED           1         0
  MAP7D3 WILD-TYPE        12         1
D721V3, multiclass
            clus
vv           MAP7D3 MUTATED MAP7D3 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                3               22
  STAGE IIA              11               98
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 233  40
D721V4, multiclass
    clus
vv   MAP7D3 MUTATED MAP7D3 WILD-TYPE
  T1              0                9
  T2              1               67
  T3             15              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
  MAP7D3 MUTATED    15   1   1
  MAP7D3 WILD-TYPE 205  79  65
D721V5, multiclass
    clus
vv   MAP7D3 MUTATED MAP7D3 WILD-TYPE
  N0             15              205
  N1              1               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"
D721V6, binary
                  cls
clus                 0   1
  MAP7D3 MUTATED    15   2
  MAP7D3 WILD-TYPE 268  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP7D3 MUTATED     15    2
  MAP7D3 WILD-TYPE  268   46
   clus
vv  MAP7D3 MUTATED MAP7D3 WILD-TYPE
  0             15              268
  1              2               46
[1] 2 2
[1] FALSE
D721V7, 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
D721V8, binary
                  cls
clus                 0   1
  MAP7D3 MUTATED    15   2
  MAP7D3 WILD-TYPE 302  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP7D3 MUTATED     15    2
  MAP7D3 WILD-TYPE  302   46
                               clus
vv                              MAP7D3 MUTATED MAP7D3 WILD-TYPE
  COLON ADENOCARCINOMA                      15              302
  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 243   2  22  20
D721V9, multiclass
    clus
vv   MAP7D3 MUTATED MAP7D3 WILD-TYPE
  R0             14              243
  R1              0                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"
D721V10, 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
D721V11, 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(722) Variable = MIER1 MUTATION ANALYSIS
D722V1, survival
                 sevent
clus2               0   1
  MIER1 MUTATED     7   1
  MIER1 WILD-TYPE 275  72
  MIER1 MUTATED MIER1 WILD-TYPE 
              8             347 
  MIER1 MUTATED MIER1 WILD-TYPE 
              1              72 
$`MIER1 MUTATED`
TCGA-A6-5659 TCGA-A6-6781 TCGA-AA-3672 TCGA-AA-A010 TCGA-CA-6717 TCGA-DM-A28E 
       30.44        19.66         0.92        34.98         0.33       119.93 
TCGA-DM-A28F TCGA-G4-6588 
       35.97        26.17 

$`MIER1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
        6.12        81.37        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        91.79        46.75        52.80 

  MIER1 MUTATED MIER1 WILD-TYPE 
           0.33            0.00 
  MIER1 MUTATED MIER1 WILD-TYPE 
         119.93          140.38 
  MIER1 MUTATED MIER1 WILD-TYPE 
         28.305          20.120 
[1] "0.3 - 119.9 (28.3)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.9"
D722V2, 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       25       106         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MIER1 MUTATED           1          0          1          1        0         0
  MIER1 WILD-TYPE        18         10         40         30       35        13
                 vv
clus              STAGE IVB
  MIER1 MUTATED           0
  MIER1 WILD-TYPE         1
D722V3, multiclass
            clus
vv           MIER1 MUTATED MIER1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              3             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MIER1 MUTATED     0   1   5   2
  MIER1 WILD-TYPE   9  67 243  39
D722V4, multiclass
    clus
vv   MIER1 MUTATED MIER1 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             5             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
  MIER1 MUTATED     5   3   0
  MIER1 WILD-TYPE 215  77  66
D722V5, multiclass
    clus
vv   MIER1 MUTATED MIER1 WILD-TYPE
  N0             5             215
  N1             3              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"
D722V6, binary
                 cls
clus                0   1
  MIER1 MUTATED     7   0
  MIER1 WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MIER1 MUTATED      7    0
  MIER1 WILD-TYPE  276   48
   clus
vv  MIER1 MUTATED MIER1 WILD-TYPE
  0             7             276
  1             0              48
[1] 2 2
[1] FALSE
D722V7, binary
                 cls
clus                0   1
  MIER1 MUTATED     4   4
  MIER1 WILD-TYPE 166 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MIER1 MUTATED      4    4
  MIER1 WILD-TYPE  166  193
        clus
vv       MIER1 MUTATED MIER1 WILD-TYPE
  FEMALE             4             166
  MALE               4             193
[1] 2 2
[1] FALSE
D722V8, binary
                 cls
clus                0   1
  MIER1 MUTATED     6   2
  MIER1 WILD-TYPE 311  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MIER1 MUTATED      6    2
  MIER1 WILD-TYPE  311   46
                               clus
vv                              MIER1 MUTATED MIER1 WILD-TYPE
  COLON ADENOCARCINOMA                      6             311
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MIER1 MUTATED     5   0   0   1
  MIER1 WILD-TYPE 252   2  22  20
D722V9, multiclass
    clus
vv   MIER1 MUTATED MIER1 WILD-TYPE
  R0             5             252
  R1             0               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"
D722V10, 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     5
  MIER1 WILD-TYPE                        19   171
D722V11, 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                                        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(723) Variable = CNTFR MUTATION ANALYSIS
D723V1, survival
                 sevent
clus2               0   1
  CNTFR MUTATED     6   3
  CNTFR WILD-TYPE 276  70
  CNTFR MUTATED CNTFR WILD-TYPE 
              9             346 
  CNTFR MUTATED CNTFR WILD-TYPE 
              3              70 
$`CNTFR MUTATED`
TCGA-A6-6780 TCGA-AA-3673 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-6715 TCGA-CA-6717 
       20.12        50.04        49.41       100.01         0.07         0.33 
TCGA-CM-5862 TCGA-F4-6808 TCGA-G4-6586 
        5.03        33.67        35.80 

$`CNTFR WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3678 
        6.97        54.02         2.01        14.01         0.92        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13        83.80        22.36        62.79        61.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6718 
        2.24         3.06         3.25         3.29         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       29.59        16.24        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  CNTFR MUTATED CNTFR WILD-TYPE 
           0.07            0.00 
  CNTFR MUTATED CNTFR WILD-TYPE 
         100.01          140.38 
  CNTFR MUTATED CNTFR WILD-TYPE 
         33.670          20.105 
[1] "0.1 - 100.0 (33.7)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.3"
D723V2, 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       22       105         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        19         10         40         31       35        12
                 vv
clus              STAGE IVB
  CNTFR MUTATED           0
  CNTFR WILD-TYPE         1
D723V3, multiclass
            clus
vv           CNTFR MUTATED CNTFR WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              4             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  68 239  41
D723V4, multiclass
    clus
vv   CNTFR MUTATED CNTFR WILD-TYPE
  T1             1               8
  T2             0              68
  T3             9             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
  CNTFR MUTATED     8   2   0
  CNTFR WILD-TYPE 212  78  66
D723V5, multiclass
    clus
vv   CNTFR MUTATED CNTFR WILD-TYPE
  N0             8             212
  N1             2              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"
D723V6, binary
                 cls
clus                0   1
  CNTFR MUTATED     7   1
  CNTFR WILD-TYPE 276  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNTFR MUTATED      7    1
  CNTFR WILD-TYPE  276   47
   clus
vv  CNTFR MUTATED CNTFR WILD-TYPE
  0             7             276
  1             1              47
[1] 2 2
[1] FALSE
D723V7, 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
D723V8, binary
                 cls
clus                0   1
  CNTFR MUTATED     8   2
  CNTFR WILD-TYPE 309  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNTFR MUTATED      8    2
  CNTFR WILD-TYPE  309   46
                               clus
vv                              CNTFR MUTATED CNTFR WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  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 252   2  22  19
D723V9, multiclass
    clus
vv   CNTFR MUTATED CNTFR WILD-TYPE
  R0             5             252
  R1             0               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"
D723V10, 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
D723V11, 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(724) Variable = AHCTF1 MUTATION ANALYSIS
D724V1, survival
                  sevent
clus2                0   1
  AHCTF1 MUTATED    16   5
  AHCTF1 WILD-TYPE 266  68
  AHCTF1 MUTATED AHCTF1 WILD-TYPE 
              21              334 
  AHCTF1 MUTATED AHCTF1 WILD-TYPE 
               5               68 
$`AHCTF1 MUTATED`
TCGA-A6-6138 TCGA-A6-6653 TCGA-AA-3496 TCGA-AA-3518 TCGA-AA-3947 TCGA-AA-3956 
       22.52        24.39         1.02         1.02        33.01        34.03 
TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A010 TCGA-AA-A01I TCGA-AZ-4315 TCGA-AZ-5407 
        2.01        25.02        34.98        31.00        58.39        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-CA-6715 TCGA-CA-6717 TCGA-CK-6751 
       49.41         6.77        12.10         0.07         0.33       124.27 
TCGA-DM-A0XF TCGA-F4-6570 TCGA-G4-6628 
       38.20         6.18        52.80 

$`AHCTF1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        32.71        27.09         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         3.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 
        6.97         1.02        13.02        38.99         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3968 TCGA-AA-3971 
       26.01        24.00         2.01        20.98        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K 
       21.99        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        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       62.79       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 
        1.94         2.24         3.06         3.25         3.29         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 
       12.00        11.38        10.26       119.70        24.43       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.38        13.45        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       35.80        26.17        91.79        46.75 

  AHCTF1 MUTATED AHCTF1 WILD-TYPE 
            0.07             0.00 
  AHCTF1 MUTATED AHCTF1 WILD-TYPE 
          124.27           140.38 
  AHCTF1 MUTATED AHCTF1 WILD-TYPE 
          25.020           20.005 
[1] "0.1 - 124.3 (25.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.1"
D724V2, 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       23       103         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AHCTF1 MUTATED           0          0          1          1        1
  AHCTF1 WILD-TYPE        19         10         40         30       34
                  vv
clus               STAGE IVA STAGE IVB
  AHCTF1 MUTATED           0         0
  AHCTF1 WILD-TYPE        13         1
D724V3, multiclass
            clus
vv           AHCTF1 MUTATED AHCTF1 WILD-TYPE
  STAGE I                 7               57
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               6              103
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              1               30
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  AHCTF1 MUTATED     1   7  10   3
  AHCTF1 WILD-TYPE   8  61 238  38
D724V4, multiclass
    clus
vv   AHCTF1 MUTATED AHCTF1 WILD-TYPE
  T1              1                8
  T2              7               61
  T3             10              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
  AHCTF1 MUTATED    18   2   1
  AHCTF1 WILD-TYPE 202  78  65
D724V5, multiclass
    clus
vv   AHCTF1 MUTATED AHCTF1 WILD-TYPE
  N0             18              202
  N1              2               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"
D724V6, binary
                  cls
clus                 0   1
  AHCTF1 MUTATED    16   1
  AHCTF1 WILD-TYPE 267  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AHCTF1 MUTATED     16    1
  AHCTF1 WILD-TYPE  267   47
   clus
vv  AHCTF1 MUTATED AHCTF1 WILD-TYPE
  0             16              267
  1              1               47
[1] 2 2
[1] FALSE
D724V7, 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
D724V8, binary
                  cls
clus                 0   1
  AHCTF1 MUTATED    16   5
  AHCTF1 WILD-TYPE 301  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AHCTF1 MUTATED     16    5
  AHCTF1 WILD-TYPE  301   43
                               clus
vv                              AHCTF1 MUTATED AHCTF1 WILD-TYPE
  COLON ADENOCARCINOMA                      16              301
  COLON MUCINOUS ADENOCARCINOMA              5               43
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  AHCTF1 MUTATED     9   0   0   3
  AHCTF1 WILD-TYPE 248   2  22  18
D724V9, multiclass
    clus
vv   AHCTF1 MUTATED AHCTF1 WILD-TYPE
  R0              9              248
  R1              0                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"
D724V10, 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
D724V11, 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(725) Variable = CWF19L2 MUTATION ANALYSIS
D725V1, survival
                   sevent
clus2                 0   1
  CWF19L2 MUTATED    14   0
  CWF19L2 WILD-TYPE 268  73
  CWF19L2 MUTATED CWF19L2 WILD-TYPE 
               14               341 
  CWF19L2 MUTATED CWF19L2 WILD-TYPE 
                0                73 
$`CWF19L2 MUTATED`
TCGA-A6-5659 TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3543 TCGA-AA-3663 TCGA-AA-3977 
       30.44        24.39        19.66         0.99         6.97        25.02 
TCGA-AA-A00J TCGA-AA-A010 TCGA-AU-6004 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5913 
       18.05        34.98        27.09         0.33         0.10        51.32 
TCGA-CM-4743 TCGA-CM-5868 
       23.05        17.03 

$`CWF19L2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.05        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.26         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        21.99        21.14         2.93         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        16.01        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  CWF19L2 MUTATED CWF19L2 WILD-TYPE 
              0.1               0.0 
  CWF19L2 MUTATED CWF19L2 WILD-TYPE 
            51.32            140.38 
  CWF19L2 MUTATED CWF19L2 WILD-TYPE 
           21.355            20.190 
[1] "0.1 - 51.3 (21.4)"  "0.0 - 140.4 (20.2)"
[1] "hr="     "2.6e+07"
D725V2, 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       24       104         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CWF19L2 MUTATED           0          0          1          1        0
  CWF19L2 WILD-TYPE        19         10         40         30       35
                   vv
clus                STAGE IVA STAGE IVB
  CWF19L2 MUTATED           1         0
  CWF19L2 WILD-TYPE        12         1
D725V3, multiclass
            clus
vv           CWF19L2 MUTATED CWF19L2 WILD-TYPE
  STAGE I                  4                60
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                5               104
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               1                30
  STAGE IV                 0                35
  STAGE IVA                1                12
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of 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  63 242  37
D725V4, multiclass
    clus
vv   CWF19L2 MUTATED CWF19L2 WILD-TYPE
  T1               0                 9
  T2               5                63
  T3               6               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
  CWF19L2 MUTATED    12   3   0
  CWF19L2 WILD-TYPE 208  77  66
D725V5, multiclass
    clus
vv   CWF19L2 MUTATED CWF19L2 WILD-TYPE
  N0              12               208
  N1               3                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"
D725V6, binary
                   cls
clus                  0   1
  CWF19L2 MUTATED    11   1
  CWF19L2 WILD-TYPE 272  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CWF19L2 MUTATED     11    1
  CWF19L2 WILD-TYPE  272   47
   clus
vv  CWF19L2 MUTATED CWF19L2 WILD-TYPE
  0              11               272
  1               1                47
[1] 2 2
[1] FALSE
D725V7, 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
D725V8, binary
                   cls
clus                  0   1
  CWF19L2 MUTATED    11   4
  CWF19L2 WILD-TYPE 306  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CWF19L2 MUTATED     11    4
  CWF19L2 WILD-TYPE  306   44
                               clus
vv                              CWF19L2 MUTATED CWF19L2 WILD-TYPE
  COLON ADENOCARCINOMA                       11               306
  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 247   2  22  18
D725V9, multiclass
    clus
vv   CWF19L2 MUTATED CWF19L2 WILD-TYPE
  R0              10               247
  R1               0                 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"
D725V10, 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
D725V11, 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(726) Variable = ZP3 MUTATION ANALYSIS
D726V1, survival
               sevent
clus2             0   1
  ZP3 MUTATED     4   1
  ZP3 WILD-TYPE 278  72
  ZP3 MUTATED ZP3 WILD-TYPE 
            5           350 
  ZP3 MUTATED ZP3 WILD-TYPE 
            1            72 
$`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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3821 
       19.04        10.06        35.05        33.04         0.99         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10       100.01         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  ZP3 MUTATED ZP3 WILD-TYPE 
        13.02          0.00 
  ZP3 MUTATED ZP3 WILD-TYPE 
        34.98        140.38 
  ZP3 MUTATED ZP3 WILD-TYPE 
        25.02         20.07 
[1] "13.0 - 35.0 (25.0)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.1"
D726V2, 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       25       106         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        19         10         41         31       35        13
               vv
clus            STAGE IVB
  ZP3 MUTATED           0
  ZP3 WILD-TYPE         1
D726V3, multiclass
            clus
vv           ZP3 MUTATED ZP3 WILD-TYPE
  STAGE I              0            64
  STAGE IA             0             1
  STAGE II             0            25
  STAGE IIA            3           106
  STAGE IIB            2             6
  STAGE IIC            0             1
  STAGE III            0            19
  STAGE IIIA           0            10
  STAGE IIIB           0            41
  STAGE IIIC           0            31
  STAGE IV             0            35
  STAGE IVA            0            13
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  ZP3 MUTATED     0   1   3   2
  ZP3 WILD-TYPE   9  67 245  39
D726V4, multiclass
    clus
vv   ZP3 MUTATED ZP3 WILD-TYPE
  T1           0             9
  T2           1            67
  T3           3           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
  ZP3 MUTATED     5   1   0
  ZP3 WILD-TYPE 215  79  66
D726V5, multiclass
    clus
vv   ZP3 MUTATED ZP3 WILD-TYPE
  N0           5           215
  N1           1            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"
D726V6, binary
               cls
clus              0   1
  ZP3 MUTATED     3   0
  ZP3 WILD-TYPE 280  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  ZP3 MUTATED      3    0
  ZP3 WILD-TYPE  280   48
   clus
vv  ZP3 MUTATED ZP3 WILD-TYPE
  0           3           280
  1           0            48
[1] 2 2
[1] FALSE
D726V7, 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
D726V8, binary
               cls
clus              0   1
  ZP3 MUTATED     6   0
  ZP3 WILD-TYPE 311  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  ZP3 MUTATED      6    0
  ZP3 WILD-TYPE  311   48
                               clus
vv                              ZP3 MUTATED ZP3 WILD-TYPE
  COLON ADENOCARCINOMA                    6           311
  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 253   2  22  20
D726V9, multiclass
    clus
vv   ZP3 MUTATED ZP3 WILD-TYPE
  R0           4           253
  R1           0             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"
D726V10, 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
D726V11, 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(727) Variable = ACOT9 MUTATION ANALYSIS
D727V1, survival
                 sevent
clus2               0   1
  ACOT9 MUTATED     4   0
  ACOT9 WILD-TYPE 278  73
  ACOT9 MUTATED ACOT9 WILD-TYPE 
              4             351 
  ACOT9 MUTATED ACOT9 WILD-TYPE 
              0              73 
$`ACOT9 MUTATED`
TCGA-A6-5665 TCGA-AA-3697 TCGA-AA-3864 TCGA-CK-4948 
       22.06        85.05        53.00       102.44 

$`ACOT9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 
        0.26         0.33         0.10         1.35        17.56        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  ACOT9 MUTATED ACOT9 WILD-TYPE 
          22.06            0.00 
  ACOT9 MUTATED ACOT9 WILD-TYPE 
         102.44          140.38 
  ACOT9 MUTATED ACOT9 WILD-TYPE 
         69.025          20.020 
[1] "22.1 - 102.4 (69.0)" "0.0 - 140.4 (20.0)" 
[1] "hr="     "2.6e+07"
D727V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ACOT9 MUTATED         0        0        1         1         0         0
  ACOT9 WILD-TYPE      64        1       24       108         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ACOT9 MUTATED           1          1          0          0        0         0
  ACOT9 WILD-TYPE        18          9         41         31       35        13
                 vv
clus              STAGE IVB
  ACOT9 MUTATED           0
  ACOT9 WILD-TYPE         1
D727V3, multiclass
            clus
vv           ACOT9 MUTATED ACOT9 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              1             108
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             1               9
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ACOT9 MUTATED     0   0   4   0
  ACOT9 WILD-TYPE   9  68 244  41
D727V4, multiclass
    clus
vv   ACOT9 MUTATED ACOT9 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             4             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
  ACOT9 MUTATED     3   1   0
  ACOT9 WILD-TYPE 217  79  66
D727V5, multiclass
    clus
vv   ACOT9 MUTATED ACOT9 WILD-TYPE
  N0             3             217
  N1             1              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"
D727V6, binary
                 cls
clus                0   1
  ACOT9 MUTATED     4   0
  ACOT9 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACOT9 MUTATED      4    0
  ACOT9 WILD-TYPE  279   48
   clus
vv  ACOT9 MUTATED ACOT9 WILD-TYPE
  0             4             279
  1             0              48
[1] 2 2
[1] FALSE
D727V7, 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
D727V8, binary
                 cls
clus                0   1
  ACOT9 MUTATED     4   0
  ACOT9 WILD-TYPE 313  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACOT9 MUTATED      4    0
  ACOT9 WILD-TYPE  313   48
                               clus
vv                              ACOT9 MUTATED ACOT9 WILD-TYPE
  COLON ADENOCARCINOMA                      4             313
  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 253   2  22  21
D727V9, multiclass
    clus
vv   ACOT9 MUTATED ACOT9 WILD-TYPE
  R0             4             253
  R1             0               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"
D727V10, 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
D727V11, multiclass
[1] "Remove cluster labels:" "ACOT9 MUTATED"         
clus
  ACOT9 MUTATED ACOT9 WILD-TYPE 
              2             204 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-4105 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-A6-5656      TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5660 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-A6-5661      TCGA-A6-5662      TCGA-A6-5664      TCGA-A6-5666 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-A6-6137      TCGA-A6-6138      TCGA-A6-6141      TCGA-A6-6142 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-A6-6648      TCGA-A6-6649      TCGA-A6-6651      TCGA-A6-6652 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780      TCGA-A6-6781 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-A6-6782      TCGA-AD-5900      TCGA-AD-6548      TCGA-AD-6888 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-AD-6889      TCGA-AD-6890      TCGA-AD-6895      TCGA-AD-6899 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6964      TCGA-AD-6965 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070      TCGA-AY-4071 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197      TCGA-AY-6386 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-AZ-4315      TCGA-AZ-4323      TCGA-AZ-4616      TCGA-AZ-4681 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-AZ-4682      TCGA-AZ-5403      TCGA-AZ-5407      TCGA-AZ-6598 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-AZ-6599      TCGA-AZ-6600      TCGA-AZ-6601      TCGA-AZ-6603 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-AZ-6605      TCGA-AZ-6606      TCGA-AZ-6607      TCGA-AZ-6608 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-CA-5254      TCGA-CA-5255      TCGA-CA-5796      TCGA-CA-5797 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-CA-6715      TCGA-CA-6716      TCGA-CA-6717      TCGA-CA-6718 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-CA-6719      TCGA-CK-4947      TCGA-CK-4950      TCGA-CK-4952 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-CK-5912      TCGA-CK-5913      TCGA-CK-5914      TCGA-CK-5915 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-CK-5916      TCGA-CK-6746      TCGA-CK-6747      TCGA-CK-6748 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-CK-6751      TCGA-CM-4743      TCGA-CM-4744      TCGA-CM-4746 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-CM-4747      TCGA-CM-4752      TCGA-CM-5341      TCGA-CM-5344 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-CM-5348      TCGA-CM-5349      TCGA-CM-5860      TCGA-CM-5861 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-CM-5862      TCGA-CM-5863      TCGA-CM-5864      TCGA-CM-5868 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-CM-6161      TCGA-CM-6162      TCGA-CM-6163      TCGA-CM-6164 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-CM-6165      TCGA-CM-6166      TCGA-CM-6167      TCGA-CM-6168 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-CM-6169      TCGA-CM-6170      TCGA-CM-6171      TCGA-CM-6172 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-CM-6674      TCGA-CM-6675      TCGA-CM-6676      TCGA-CM-6677 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-CM-6678      TCGA-CM-6679      TCGA-CM-6680      TCGA-D5-5537 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-D5-5538      TCGA-D5-5539      TCGA-D5-5540      TCGA-D5-5541 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-D5-6529      TCGA-D5-6532      TCGA-D5-6533      TCGA-D5-6534 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-D5-6535      TCGA-D5-6536      TCGA-D5-6537      TCGA-D5-6538 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-D5-6539      TCGA-D5-6540      TCGA-D5-6541      TCGA-D5-6898 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923      TCGA-D5-6924 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-D5-6926      TCGA-D5-6927      TCGA-D5-6928      TCGA-D5-6929 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-D5-6930      TCGA-D5-6931      TCGA-D5-6932      TCGA-D5-7000 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-DM-A0X9      TCGA-DM-A0XD      TCGA-DM-A0XF      TCGA-DM-A1D0 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-DM-A1D4      TCGA-DM-A1D6      TCGA-DM-A1D7      TCGA-DM-A1D8 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-DM-A1D9      TCGA-DM-A1DA      TCGA-DM-A1DB      TCGA-DM-A1HA 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-DM-A1HB      TCGA-DM-A282      TCGA-DM-A285      TCGA-DM-A28C 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-DM-A28E      TCGA-DM-A28F      TCGA-DM-A28G      TCGA-DM-A28H 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-DM-A28K      TCGA-F4-6459      TCGA-F4-6460      TCGA-F4-6569 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704      TCGA-F4-6805 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808      TCGA-F4-6809 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856      TCGA-G4-6293 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304      TCGA-G4-6306 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310      TCGA-G4-6315 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323      TCGA-G4-6586 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-G4-6588      TCGA-G4-6625      TCGA-G4-6626      TCGA-G4-6628 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 

Clustering(728) Variable = PPIG MUTATION ANALYSIS
D728V1, survival
                sevent
clus2              0   1
  PPIG MUTATED    10   2
  PPIG WILD-TYPE 272  71
  PPIG MUTATED PPIG WILD-TYPE 
            12            343 
  PPIG MUTATED PPIG WILD-TYPE 
             2             71 
$`PPIG MUTATED`
TCGA-A6-6137 TCGA-AA-3525 TCGA-AA-3949 TCGA-AA-A00E TCGA-AA-A00N TCGA-AA-A010 
       27.09         8.05        26.01        30.02         4.01        34.98 
TCGA-AZ-4315 TCGA-AZ-6601 TCGA-D5-6540 TCGA-DM-A282 TCGA-G4-6309 TCGA-G4-6586 
       58.39       100.01        16.14       139.17        51.75        35.80 

$`PPIG WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        32.71        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 
        1.02         9.07        24.03        37.05        36.03        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      135.65         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  PPIG MUTATED PPIG WILD-TYPE 
          4.01           0.00 
  PPIG MUTATED PPIG WILD-TYPE 
        139.17         140.38 
  PPIG MUTATED PPIG WILD-TYPE 
         32.50          19.99 
[1] "4.0 - 139.2 (32.5)" "0.0 - 140.4 (20.0)"
[1] "hr=" "2"  
D728V2, 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       24       105         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        19         10         37         31       35        13
                vv
clus             STAGE IVB
  PPIG MUTATED           0
  PPIG WILD-TYPE         1
D728V3, multiclass
            clus
vv           PPIG MUTATED PPIG WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             4            105
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            4             37
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PPIG MUTATED     0   1   9   2
  PPIG WILD-TYPE   9  67 239  39
D728V4, multiclass
    clus
vv   PPIG MUTATED PPIG WILD-TYPE
  T1            0              9
  T2            1             67
  T3            9            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
  PPIG MUTATED     8   4   0
  PPIG WILD-TYPE 212  76  66
D728V5, multiclass
    clus
vv   PPIG MUTATED PPIG WILD-TYPE
  N0            8            212
  N1            4             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"
D728V6, binary
                cls
clus               0   1
  PPIG MUTATED    12   0
  PPIG WILD-TYPE 271  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  PPIG MUTATED     12    0
  PPIG WILD-TYPE  271   48
   clus
vv  PPIG MUTATED PPIG WILD-TYPE
  0           12            271
  1            0             48
[1] 2 2
[1] FALSE
D728V7, 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
D728V8, binary
                cls
clus               0   1
  PPIG MUTATED     9   3
  PPIG WILD-TYPE 308  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  PPIG MUTATED      9    3
  PPIG WILD-TYPE  308   45
                               clus
vv                              PPIG MUTATED PPIG WILD-TYPE
  COLON ADENOCARCINOMA                     9            308
  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 248   2  22  21
D728V9, multiclass
    clus
vv   PPIG MUTATED PPIG WILD-TYPE
  R0            9            248
  R1            0              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"
D728V10, 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
D728V11, 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(729) Variable = LEPRE1 MUTATION ANALYSIS
D729V1, survival
                  sevent
clus2                0   1
  LEPRE1 MUTATED     6   3
  LEPRE1 WILD-TYPE 276  70
  LEPRE1 MUTATED LEPRE1 WILD-TYPE 
               9              346 
  LEPRE1 MUTATED LEPRE1 WILD-TYPE 
               3               70 
$`LEPRE1 MUTATED`
TCGA-A6-6781 TCGA-AA-3713 TCGA-AY-6197 TCGA-AZ-6598 TCGA-CM-5861 TCGA-D5-6539 
       19.66        19.04        21.44        49.41        15.02        12.49 
TCGA-F4-6570 TCGA-F4-6809 TCGA-G4-6588 
        6.18        13.25        26.17 

$`LEPRE1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-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        13.38        13.45        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       29.59        16.24        33.67         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        91.79        46.75        52.80 

  LEPRE1 MUTATED LEPRE1 WILD-TYPE 
            6.18             0.00 
  LEPRE1 MUTATED LEPRE1 WILD-TYPE 
           49.41           140.38 
  LEPRE1 MUTATED LEPRE1 WILD-TYPE 
           19.04            20.63 
[1] "6.2 - 49.4 (19.0)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "1.9"
D729V2, 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       24       105         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LEPRE1 MUTATED           0          1          0          1        1
  LEPRE1 WILD-TYPE        19          9         41         30       34
                  vv
clus               STAGE IVA STAGE IVB
  LEPRE1 MUTATED           1         0
  LEPRE1 WILD-TYPE        12         1
D729V3, multiclass
            clus
vv           LEPRE1 MUTATED LEPRE1 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               4              105
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              1                9
  STAGE IIIB              0               41
  STAGE IIIC              1               30
  STAGE IV                1               34
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  68 240  40
D729V4, multiclass
    clus
vv   LEPRE1 MUTATED LEPRE1 WILD-TYPE
  T1              0                9
  T2              0               68
  T3              8              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
  LEPRE1 MUTATED     7   2   0
  LEPRE1 WILD-TYPE 213  78  66
D729V5, multiclass
    clus
vv   LEPRE1 MUTATED LEPRE1 WILD-TYPE
  N0              7              213
  N1              2               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"
D729V6, binary
                  cls
clus                 0   1
  LEPRE1 MUTATED     4   2
  LEPRE1 WILD-TYPE 279  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LEPRE1 MUTATED      4    2
  LEPRE1 WILD-TYPE  279   46
   clus
vv  LEPRE1 MUTATED LEPRE1 WILD-TYPE
  0              4              279
  1              2               46
[1] 2 2
[1] FALSE
D729V7, 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
D729V8, binary
                  cls
clus                 0   1
  LEPRE1 MUTATED     8   1
  LEPRE1 WILD-TYPE 309  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LEPRE1 MUTATED      8    1
  LEPRE1 WILD-TYPE  309   47
                               clus
vv                              LEPRE1 MUTATED LEPRE1 WILD-TYPE
  COLON ADENOCARCINOMA                       8              309
  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 250   2  21  21
D729V9, multiclass
    clus
vv   LEPRE1 MUTATED LEPRE1 WILD-TYPE
  R0              7              250
  R1              0                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"
D729V10, 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
D729V11, 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(730) Variable = OR4D2 MUTATION ANALYSIS
D730V1, survival
                 sevent
clus2               0   1
  OR4D2 MUTATED     3   1
  OR4D2 WILD-TYPE 279  72
  OR4D2 MUTATED OR4D2 WILD-TYPE 
              4             351 
  OR4D2 MUTATED OR4D2 WILD-TYPE 
              1              72 
$`OR4D2 MUTATED`
TCGA-A6-6653 TCGA-AA-3496 TCGA-AZ-6601 TCGA-G4-6588 
       24.39         1.02       100.01        26.17 

$`OR4D2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  OR4D2 MUTATED OR4D2 WILD-TYPE 
           1.02            0.00 
  OR4D2 MUTATED OR4D2 WILD-TYPE 
         100.01          140.38 
  OR4D2 MUTATED OR4D2 WILD-TYPE 
          25.28           20.12 
[1] "1.0 - 100.0 (25.3)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.2"
D730V2, 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       23       108         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        19         10         41         31       35        13
                 vv
clus              STAGE IVB
  OR4D2 MUTATED           0
  OR4D2 WILD-TYPE         1
D730V3, multiclass
            clus
vv           OR4D2 MUTATED OR4D2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              1             108
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR4D2 MUTATED     0   1   3   0
  OR4D2 WILD-TYPE   9  67 245  41
D730V4, multiclass
    clus
vv   OR4D2 MUTATED OR4D2 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             3             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
  OR4D2 MUTATED     4   0   0
  OR4D2 WILD-TYPE 216  80  66
D730V5, multiclass
    clus
vv   OR4D2 MUTATED OR4D2 WILD-TYPE
  N0             4             216
  N1             0              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"
D730V6, binary
                 cls
clus                0   1
  OR4D2 MUTATED     4   0
  OR4D2 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4D2 MUTATED      4    0
  OR4D2 WILD-TYPE  279   48
   clus
vv  OR4D2 MUTATED OR4D2 WILD-TYPE
  0             4             279
  1             0              48
[1] 2 2
[1] FALSE
D730V7, 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
D730V8, binary
                 cls
clus                0   1
  OR4D2 MUTATED     4   0
  OR4D2 WILD-TYPE 313  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4D2 MUTATED      4    0
  OR4D2 WILD-TYPE  313   48
                               clus
vv                              OR4D2 MUTATED OR4D2 WILD-TYPE
  COLON ADENOCARCINOMA                      4             313
  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 255   2  22  21
D730V9, multiclass
[1] "Remove cluster labels:" "OR4D2 MUTATED"         
clus
  OR4D2 MUTATED OR4D2 WILD-TYPE 
              2             300 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-5657 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-A6-5659      TCGA-A6-5661      TCGA-A6-5665      TCGA-A6-6781 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3489      TCGA-AA-3492      TCGA-AA-3502      TCGA-AA-3510 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3511      TCGA-AA-3514      TCGA-AA-3517      TCGA-AA-3518 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3519      TCGA-AA-3520      TCGA-AA-3521      TCGA-AA-3522 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3524      TCGA-AA-3525      TCGA-AA-3526      TCGA-AA-3527 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3529      TCGA-AA-3530      TCGA-AA-3531      TCGA-AA-3532 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3534      TCGA-AA-3538      TCGA-AA-3542      TCGA-AA-3543 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3544      TCGA-AA-3548      TCGA-AA-3549      TCGA-AA-3552 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3553      TCGA-AA-3554      TCGA-AA-3555      TCGA-AA-3556 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3558      TCGA-AA-3560      TCGA-AA-3561      TCGA-AA-3562 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3655      TCGA-AA-3660      TCGA-AA-3662      TCGA-AA-3663 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3664      TCGA-AA-3666      TCGA-AA-3667      TCGA-AA-3672 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3673      TCGA-AA-3678      TCGA-AA-3679      TCGA-AA-3680 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3681      TCGA-AA-3684      TCGA-AA-3685      TCGA-AA-3688 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3692      TCGA-AA-3693      TCGA-AA-3695      TCGA-AA-3696 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3697      TCGA-AA-3710      TCGA-AA-3712      TCGA-AA-3713 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3715      TCGA-AA-3811      TCGA-AA-3812      TCGA-AA-3814 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3815      TCGA-AA-3818      TCGA-AA-3819      TCGA-AA-3821 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3831      TCGA-AA-3833      TCGA-AA-3837      TCGA-AA-3842 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3844      TCGA-AA-3845      TCGA-AA-3846      TCGA-AA-3848 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3850      TCGA-AA-3851      TCGA-AA-3852      TCGA-AA-3854 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3855      TCGA-AA-3856      TCGA-AA-3858      TCGA-AA-3860 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3861      TCGA-AA-3864      TCGA-AA-3866      TCGA-AA-3867 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3869      TCGA-AA-3870      TCGA-AA-3872      TCGA-AA-3875 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3877      TCGA-AA-3930      TCGA-AA-3939      TCGA-AA-3941 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3947      TCGA-AA-3949      TCGA-AA-3950      TCGA-AA-3952 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3955      TCGA-AA-3956      TCGA-AA-3968      TCGA-AA-3971 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3972      TCGA-AA-3973      TCGA-AA-3975      TCGA-AA-3976 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3979      TCGA-AA-3984      TCGA-AA-3986      TCGA-AA-3989 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3994      TCGA-AA-A004      TCGA-AA-A00A      TCGA-AA-A00D 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-A00E      TCGA-AA-A00F      TCGA-AA-A00J      TCGA-AA-A00K 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-A00L      TCGA-AA-A00N      TCGA-AA-A00O      TCGA-AA-A00Q 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-A00R      TCGA-AA-A00U      TCGA-AA-A00W      TCGA-AA-A00Z 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-A010      TCGA-AA-A017      TCGA-AA-A01D      TCGA-AA-A01F 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-A01G      TCGA-AA-A01I      TCGA-AA-A01K      TCGA-AA-A01P 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-A01Q      TCGA-AA-A01R      TCGA-AA-A01S      TCGA-AA-A01T 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-A01V      TCGA-AA-A01X      TCGA-AA-A01Z      TCGA-AA-A022 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-A024      TCGA-AA-A029      TCGA-AA-A02F      TCGA-AA-A02H 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-A02J      TCGA-AA-A02K      TCGA-AA-A02O      TCGA-AA-A02W 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-A02Y      TCGA-AA-A03F      TCGA-AA-A03J      TCGA-AD-5900 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AD-6548      TCGA-AD-6888      TCGA-AU-3779      TCGA-AU-6004 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AY-4070      TCGA-AY-4071      TCGA-AY-5543      TCGA-AY-6196 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AY-6197      TCGA-AY-6386      TCGA-AZ-4315      TCGA-AZ-4681 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AZ-4682      TCGA-CA-5254      TCGA-CA-5255      TCGA-CA-5796 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-CA-5797      TCGA-CA-6715      TCGA-CA-6716      TCGA-CA-6717 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-CA-6718      TCGA-CA-6719      TCGA-CK-4947      TCGA-CK-4948 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-CK-4950      TCGA-CK-4952      TCGA-CK-5912      TCGA-CK-5913 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-CK-5914      TCGA-CK-5915      TCGA-CK-5916      TCGA-CK-6746 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-CK-6747      TCGA-CK-6748      TCGA-CK-6751      TCGA-CM-4743 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-CM-4744      TCGA-CM-4746      TCGA-CM-4747      TCGA-CM-4752 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-CM-5341      TCGA-CM-5344      TCGA-CM-5348      TCGA-CM-5349 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-CM-5860      TCGA-CM-5861      TCGA-CM-5862      TCGA-CM-5863 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-CM-5864      TCGA-CM-5868      TCGA-CM-6161      TCGA-CM-6162 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-CM-6163      TCGA-CM-6164      TCGA-CM-6165      TCGA-CM-6166 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-CM-6167      TCGA-CM-6168      TCGA-CM-6169      TCGA-CM-6170 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-CM-6171      TCGA-CM-6172      TCGA-CM-6674      TCGA-CM-6675 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-CM-6676      TCGA-CM-6677      TCGA-CM-6678      TCGA-CM-6679 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-CM-6680      TCGA-D5-5537      TCGA-D5-5538      TCGA-D5-5539 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-D5-5540      TCGA-D5-5541      TCGA-D5-6529      TCGA-D5-6532 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-D5-6533      TCGA-D5-6534      TCGA-D5-6535      TCGA-D5-6536 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-D5-6537      TCGA-D5-6538      TCGA-D5-6539      TCGA-D5-6540 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-D5-6541      TCGA-D5-6898      TCGA-D5-6920      TCGA-D5-6922 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-D5-6923      TCGA-D5-6924      TCGA-D5-6926      TCGA-D5-6927 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-D5-6928      TCGA-D5-6929      TCGA-D5-6930      TCGA-D5-6931 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-D5-6932      TCGA-D5-7000      TCGA-F4-6459      TCGA-F4-6460 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-F4-6805      TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-G4-6306      TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-G4-6586      TCGA-G4-6625      TCGA-G4-6626      TCGA-G4-6628 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
D730V10, 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
D730V11, 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(731) Variable = MRI1 MUTATION ANALYSIS
D731V1, survival
                sevent
clus2              0   1
  MRI1 MUTATED     5   1
  MRI1 WILD-TYPE 277  72
  MRI1 MUTATED MRI1 WILD-TYPE 
             6            349 
  MRI1 MUTATED MRI1 WILD-TYPE 
             1             72 
$`MRI1 MUTATED`
TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3516 TCGA-AA-3815 TCGA-AA-3877 TCGA-AD-6895 
       22.06        19.66        13.02        33.04        31.00         0.72 

$`MRI1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        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        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
        0.07        21.37         4.21        56.55         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  MRI1 MUTATED MRI1 WILD-TYPE 
          0.72           0.00 
  MRI1 MUTATED MRI1 WILD-TYPE 
         33.04         140.38 
  MRI1 MUTATED MRI1 WILD-TYPE 
         20.86          20.19 
[1] "0.7 - 33.0 (20.9)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D731V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MRI1 MUTATED         1        0        0         2         0         0
  MRI1 WILD-TYPE      63        1       25       107         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MRI1 MUTATED           1          0          0          1        0         0
  MRI1 WILD-TYPE        18         10         41         30       35        13
                vv
clus             STAGE IVB
  MRI1 MUTATED           0
  MRI1 WILD-TYPE         1
D731V3, multiclass
            clus
vv           MRI1 MUTATED MRI1 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             2            107
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            1             30
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MRI1 MUTATED     1   0   4   1
  MRI1 WILD-TYPE   8  68 244  40
D731V4, multiclass
    clus
vv   MRI1 MUTATED MRI1 WILD-TYPE
  T1            1              8
  T2            0             68
  T3            4            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
  MRI1 MUTATED     3   2   1
  MRI1 WILD-TYPE 217  78  65
D731V5, multiclass
    clus
vv   MRI1 MUTATED MRI1 WILD-TYPE
  N0            3            217
  N1            2             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"
D731V6, binary
                cls
clus               0   1
  MRI1 MUTATED     4   0
  MRI1 WILD-TYPE 279  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  MRI1 MUTATED      4    0
  MRI1 WILD-TYPE  279   48
   clus
vv  MRI1 MUTATED MRI1 WILD-TYPE
  0            4            279
  1            0             48
[1] 2 2
[1] FALSE
D731V7, binary
                cls
clus               0   1
  MRI1 MUTATED     4   2
  MRI1 WILD-TYPE 166 195
[1] "tbl2"
                cls
clus             [,1] [,2]
  MRI1 MUTATED      4    2
  MRI1 WILD-TYPE  166  195
        clus
vv       MRI1 MUTATED MRI1 WILD-TYPE
  FEMALE            4            166
  MALE              2            195
[1] 2 2
[1] FALSE
D731V8, binary
                cls
clus               0   1
  MRI1 MUTATED     3   3
  MRI1 WILD-TYPE 314  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  MRI1 MUTATED      3    3
  MRI1 WILD-TYPE  314   45
                               clus
vv                              MRI1 MUTATED MRI1 WILD-TYPE
  COLON ADENOCARCINOMA                     3            314
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MRI1 MUTATED     4   0   0   0
  MRI1 WILD-TYPE 253   2  22  21
D731V9, multiclass
    clus
vv   MRI1 MUTATED MRI1 WILD-TYPE
  R0            4            253
  R1            0              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"
D731V10, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MRI1 MUTATED                                  0     0
  MRI1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MRI1 MUTATED                           0     3
  MRI1 WILD-TYPE                        19   173
D731V11, multiclass
                                  clus
vv                                 MRI1 MUTATED MRI1 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(732) Variable = STK35 MUTATION ANALYSIS
D732V1, survival
                 sevent
clus2               0   1
  STK35 MUTATED     5   1
  STK35 WILD-TYPE 277  72
  STK35 MUTATED STK35 WILD-TYPE 
              6             349 
  STK35 MUTATED STK35 WILD-TYPE 
              1              72 
$`STK35 MUTATED`
TCGA-A6-6651 TCGA-AA-3977 TCGA-AU-6004 TCGA-AY-6386 TCGA-F4-6570 TCGA-G4-6588 
       21.76        25.02        27.09        17.82         6.18        26.17 

$`STK35 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        24.16        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       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        13.38        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 
       52.80 

  STK35 MUTATED STK35 WILD-TYPE 
           6.18            0.00 
  STK35 MUTATED STK35 WILD-TYPE 
          27.09          140.38 
  STK35 MUTATED STK35 WILD-TYPE 
          23.39           20.12 
[1] "6.2 - 27.1 (23.4)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1"  
D732V2, 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       25       107         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        19         10         39         31       35        13
                 vv
clus              STAGE IVB
  STK35 MUTATED           0
  STK35 WILD-TYPE         1
D732V3, multiclass
            clus
vv           STK35 MUTATED STK35 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              2             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  STK35 MUTATED     0   2   4   0
  STK35 WILD-TYPE   9  66 244  41
D732V4, multiclass
    clus
vv   STK35 MUTATED STK35 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             4             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
  STK35 MUTATED     4   2   0
  STK35 WILD-TYPE 216  78  66
D732V5, multiclass
    clus
vv   STK35 MUTATED STK35 WILD-TYPE
  N0             4             216
  N1             2              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"
D732V6, binary
                 cls
clus                0   1
  STK35 MUTATED     4   0
  STK35 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK35 MUTATED      4    0
  STK35 WILD-TYPE  279   48
   clus
vv  STK35 MUTATED STK35 WILD-TYPE
  0             4             279
  1             0              48
[1] 2 2
[1] FALSE
D732V7, 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
D732V8, binary
                 cls
clus                0   1
  STK35 MUTATED     6   0
  STK35 WILD-TYPE 311  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK35 MUTATED      6    0
  STK35 WILD-TYPE  311   48
                               clus
vv                              STK35 MUTATED STK35 WILD-TYPE
  COLON ADENOCARCINOMA                      6             311
  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 253   2  22  21
D732V9, multiclass
    clus
vv   STK35 MUTATED STK35 WILD-TYPE
  R0             4             253
  R1             0               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"
D732V10, 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
D732V11, 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(733) Variable = KDELR2 MUTATION ANALYSIS
D733V1, survival
                  sevent
clus2                0   1
  KDELR2 MUTATED     7   1
  KDELR2 WILD-TYPE 275  72
  KDELR2 MUTATED KDELR2 WILD-TYPE 
               8              347 
  KDELR2 MUTATED KDELR2 WILD-TYPE 
               1               72 
$`KDELR2 MUTATED`
TCGA-A6-5656 TCGA-AA-3950 TCGA-AZ-5407 TCGA-AZ-6608 TCGA-CM-4752 TCGA-CM-5868 
       32.91        24.00        61.41         1.94        13.02        17.03 
TCGA-D5-6532 TCGA-G4-6317 
       18.25        36.00 

$`KDELR2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13        83.80        22.36        62.79        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 
       19.59        13.51        11.51        20.19         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 
       55.04        51.75        45.11        36.72        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  KDELR2 MUTATED KDELR2 WILD-TYPE 
            1.94             0.00 
  KDELR2 MUTATED KDELR2 WILD-TYPE 
           61.41           140.38 
  KDELR2 MUTATED KDELR2 WILD-TYPE 
          21.125           20.190 
[1] "1.9 - 61.4 (21.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.6"
D733V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KDELR2 MUTATED         2        0        0         3         0         0
  KDELR2 WILD-TYPE      62        1       25       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KDELR2 MUTATED           0          1          0          1        0
  KDELR2 WILD-TYPE        19          9         41         30       35
                  vv
clus               STAGE IVA STAGE IVB
  KDELR2 MUTATED           1         0
  KDELR2 WILD-TYPE        12         1
D733V3, multiclass
            clus
vv           KDELR2 MUTATED KDELR2 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               3              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              1                9
  STAGE IIIB              0               41
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  KDELR2 MUTATED     1   2   4   1
  KDELR2 WILD-TYPE   8  66 244  40
D733V4, multiclass
    clus
vv   KDELR2 MUTATED KDELR2 WILD-TYPE
  T1              1                8
  T2              2               66
  T3              4              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
  KDELR2 MUTATED     5   2   1
  KDELR2 WILD-TYPE 215  78  65
D733V5, multiclass
    clus
vv   KDELR2 MUTATED KDELR2 WILD-TYPE
  N0              5              215
  N1              2               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"
D733V6, binary
                  cls
clus                 0   1
  KDELR2 MUTATED     6   1
  KDELR2 WILD-TYPE 277  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KDELR2 MUTATED      6    1
  KDELR2 WILD-TYPE  277   47
   clus
vv  KDELR2 MUTATED KDELR2 WILD-TYPE
  0              6              277
  1              1               47
[1] 2 2
[1] FALSE
D733V7, binary
                  cls
clus                 0   1
  KDELR2 MUTATED     5   3
  KDELR2 WILD-TYPE 165 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KDELR2 MUTATED      5    3
  KDELR2 WILD-TYPE  165  194
        clus
vv       KDELR2 MUTATED KDELR2 WILD-TYPE
  FEMALE              5              165
  MALE                3              194
[1] 2 2
[1] FALSE
D733V8, binary
                  cls
clus                 0   1
  KDELR2 MUTATED     7   1
  KDELR2 WILD-TYPE 310  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KDELR2 MUTATED      7    1
  KDELR2 WILD-TYPE  310   47
                               clus
vv                              KDELR2 MUTATED KDELR2 WILD-TYPE
  COLON ADENOCARCINOMA                       7              310
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  KDELR2 MUTATED     5   0   0   0
  KDELR2 WILD-TYPE 252   2  22  21
D733V9, multiclass
    clus
vv   KDELR2 MUTATED KDELR2 WILD-TYPE
  R0              5              252
  R1              0                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"
D733V10, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KDELR2 MUTATED                                  0     0
  KDELR2 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  KDELR2 MUTATED                           1     6
  KDELR2 WILD-TYPE                        18   170
D733V11, multiclass
                                  clus
vv                                 KDELR2 MUTATED KDELR2 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(734) Variable = HAUS6 MUTATION ANALYSIS
D734V1, survival
                 sevent
clus2               0   1
  HAUS6 MUTATED     6   3
  HAUS6 WILD-TYPE 276  70
  HAUS6 MUTATED HAUS6 WILD-TYPE 
              9             346 
  HAUS6 MUTATED HAUS6 WILD-TYPE 
              3              70 
$`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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
       40.34        15.62        49.08        51.32        21.99         2.93 
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-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       13.02        22.03        22.98        30.08        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 
       12.00        11.38        10.26       119.70        24.43       130.65 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  HAUS6 MUTATED HAUS6 WILD-TYPE 
          18.25            0.00 
  HAUS6 MUTATED HAUS6 WILD-TYPE 
         135.65          140.38 
  HAUS6 MUTATED HAUS6 WILD-TYPE 
          38.20           19.99 
[1] "18.2 - 135.7 (38.2)" "0.0 - 140.4 (20.0)" 
[1] "hr=" "1.2"
D734V2, 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       24       105         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        19          9         40         30       34        13
                 vv
clus              STAGE IVB
  HAUS6 MUTATED           0
  HAUS6 WILD-TYPE         1
D734V3, multiclass
            clus
vv           HAUS6 MUTATED HAUS6 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              4             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             1              40
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HAUS6 MUTATED     1   2   7   2
  HAUS6 WILD-TYPE   8  66 241  39
D734V4, multiclass
    clus
vv   HAUS6 MUTATED HAUS6 WILD-TYPE
  T1             1               8
  T2             2              66
  T3             7             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
  HAUS6 MUTATED     8   2   2
  HAUS6 WILD-TYPE 212  78  64
D734V5, multiclass
    clus
vv   HAUS6 MUTATED HAUS6 WILD-TYPE
  N0             8             212
  N1             2              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"
D734V6, binary
                 cls
clus                0   1
  HAUS6 MUTATED     9   1
  HAUS6 WILD-TYPE 274  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAUS6 MUTATED      9    1
  HAUS6 WILD-TYPE  274   47
   clus
vv  HAUS6 MUTATED HAUS6 WILD-TYPE
  0             9             274
  1             1              47
[1] 2 2
[1] FALSE
D734V7, 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
D734V8, binary
                 cls
clus                0   1
  HAUS6 MUTATED    10   2
  HAUS6 WILD-TYPE 307  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAUS6 MUTATED     10    2
  HAUS6 WILD-TYPE  307   46
                               clus
vv                              HAUS6 MUTATED HAUS6 WILD-TYPE
  COLON ADENOCARCINOMA                     10             307
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  HAUS6 MUTATED     5   0   1   2
  HAUS6 WILD-TYPE 252   2  21  19
D734V9, multiclass
    clus
vv   HAUS6 MUTATED HAUS6 WILD-TYPE
  R0             5             252
  R1             0               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"
D734V10, 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
D734V11, 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(735) Variable = HCRTR2 MUTATION ANALYSIS
D735V1, survival
                  sevent
clus2                0   1
  HCRTR2 MUTATED     6   1
  HCRTR2 WILD-TYPE 276  72
  HCRTR2 MUTATED HCRTR2 WILD-TYPE 
               7              348 
  HCRTR2 MUTATED HCRTR2 WILD-TYPE 
               1               72 
$`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        61.41        37.02        15.02 
TCGA-DM-A1DA 
        7.50 

$`HCRTR2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  HCRTR2 MUTATED HCRTR2 WILD-TYPE 
             7.5              0.0 
  HCRTR2 MUTATED HCRTR2 WILD-TYPE 
           61.41           140.38 
  HCRTR2 MUTATED HCRTR2 WILD-TYPE 
           30.05            20.07 
[1] "7.5 - 61.4 (30.1)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.6"
D735V2, 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       25       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HCRTR2 MUTATED           0          0          0          1        0
  HCRTR2 WILD-TYPE        19         10         41         30       35
                  vv
clus               STAGE IVA STAGE IVB
  HCRTR2 MUTATED           0         0
  HCRTR2 WILD-TYPE        13         1
D735V3, multiclass
            clus
vv           HCRTR2 MUTATED HCRTR2 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               3              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  HCRTR2 MUTATED     1   2   4   0
  HCRTR2 WILD-TYPE   8  66 244  41
D735V4, multiclass
    clus
vv   HCRTR2 MUTATED HCRTR2 WILD-TYPE
  T1              1                8
  T2              2               66
  T3              4              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
  HCRTR2 MUTATED     6   0   1
  HCRTR2 WILD-TYPE 214  80  65
D735V5, multiclass
    clus
vv   HCRTR2 MUTATED HCRTR2 WILD-TYPE
  N0              6              214
  N1              0               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"
D735V6, binary
                  cls
clus                 0   1
  HCRTR2 MUTATED     6   0
  HCRTR2 WILD-TYPE 277  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HCRTR2 MUTATED      6    0
  HCRTR2 WILD-TYPE  277   48
   clus
vv  HCRTR2 MUTATED HCRTR2 WILD-TYPE
  0              6              277
  1              0               48
[1] 2 2
[1] FALSE
D735V7, 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
D735V8, binary
                  cls
clus                 0   1
  HCRTR2 MUTATED     7   0
  HCRTR2 WILD-TYPE 310  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HCRTR2 MUTATED      7    0
  HCRTR2 WILD-TYPE  310   48
                               clus
vv                              HCRTR2 MUTATED HCRTR2 WILD-TYPE
  COLON ADENOCARCINOMA                       7              310
  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 253   2  22  21
D735V9, multiclass
    clus
vv   HCRTR2 MUTATED HCRTR2 WILD-TYPE
  R0              4              253
  R1              0                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"
D735V10, 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
D735V11, 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(736) Variable = CACNG3 MUTATION ANALYSIS
D736V1, survival
                  sevent
clus2                0   1
  CACNG3 MUTATED     6   2
  CACNG3 WILD-TYPE 276  71
  CACNG3 MUTATED CACNG3 WILD-TYPE 
               8              347 
  CACNG3 MUTATED CACNG3 WILD-TYPE 
               2               71 
$`CACNG3 MUTATED`
TCGA-A6-3808 TCGA-AA-3492 TCGA-AA-3672 TCGA-AA-3833 TCGA-AA-A010 TCGA-AA-A01D 
       33.34         3.02         0.92        15.95        34.98        10.98 
TCGA-CA-6717 TCGA-CM-4746 
        0.33        37.02 

$`CACNG3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 
       33.04         0.99        25.02         1.02        17.98        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  CACNG3 MUTATED CACNG3 WILD-TYPE 
            0.33             0.00 
  CACNG3 MUTATED CACNG3 WILD-TYPE 
           37.02           140.38 
  CACNG3 MUTATED CACNG3 WILD-TYPE 
          13.465           20.280 
[1] "0.3 - 37.0 (13.5)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "2.1"
D736V2, 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       24       106         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CACNG3 MUTATED           1          0          0          1        0
  CACNG3 WILD-TYPE        18         10         41         30       35
                  vv
clus               STAGE IVA STAGE IVB
  CACNG3 MUTATED           0         0
  CACNG3 WILD-TYPE        13         1
D736V3, multiclass
            clus
vv           CACNG3 MUTATED CACNG3 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               3              106
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CACNG3 MUTATED     0   1   6   1
  CACNG3 WILD-TYPE   9  67 242  40
D736V4, multiclass
    clus
vv   CACNG3 MUTATED CACNG3 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              6              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
  CACNG3 MUTATED     6   1   1
  CACNG3 WILD-TYPE 214  79  65
D736V5, multiclass
    clus
vv   CACNG3 MUTATED CACNG3 WILD-TYPE
  N0              6              214
  N1              1               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"
D736V6, binary
                  cls
clus                 0   1
  CACNG3 MUTATED     8   0
  CACNG3 WILD-TYPE 275  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CACNG3 MUTATED      8    0
  CACNG3 WILD-TYPE  275   48
   clus
vv  CACNG3 MUTATED CACNG3 WILD-TYPE
  0              8              275
  1              0               48
[1] 2 2
[1] FALSE
D736V7, 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
D736V8, binary
                  cls
clus                 0   1
  CACNG3 MUTATED     6   2
  CACNG3 WILD-TYPE 311  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CACNG3 MUTATED      6    2
  CACNG3 WILD-TYPE  311   46
                               clus
vv                              CACNG3 MUTATED CACNG3 WILD-TYPE
  COLON ADENOCARCINOMA                       6              311
  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 250   2  22  20
D736V9, multiclass
    clus
vv   CACNG3 MUTATED CACNG3 WILD-TYPE
  R0              7              250
  R1              0                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"
D736V10, 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
D736V11, 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(737) Variable = BST2 MUTATION ANALYSIS
D737V1, survival
                sevent
clus2              0   1
  BST2 MUTATED     5   1
  BST2 WILD-TYPE 277  72
  BST2 MUTATED BST2 WILD-TYPE 
             6            349 
  BST2 MUTATED BST2 WILD-TYPE 
             1             72 
$`BST2 MUTATED`
TCGA-AA-3833 TCGA-AY-6386 TCGA-AZ-6601 TCGA-CM-4743 TCGA-CM-5861 TCGA-D5-6541 
       15.95        17.82       100.01        23.05        15.02        15.58 

$`BST2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
        1.02        17.98        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93         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        16.01 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        16.14         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  BST2 MUTATED BST2 WILD-TYPE 
         15.02           0.00 
  BST2 MUTATED BST2 WILD-TYPE 
        100.01         140.38 
  BST2 MUTATED BST2 WILD-TYPE 
        16.885         20.280 
[1] "15.0 - 100.0 (16.9)" "0.0 - 140.4 (20.3)" 
[1] "hr=" "1.6"
D737V2, 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       24       105         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        19         10         40         31       35        13
                vv
clus             STAGE IVB
  BST2 MUTATED           0
  BST2 WILD-TYPE         1
D737V3, multiclass
            clus
vv           BST2 MUTATED BST2 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             4            105
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  BST2 MUTATED     0   0   6   0
  BST2 WILD-TYPE   9  68 242  41
D737V4, multiclass
    clus
vv   BST2 MUTATED BST2 WILD-TYPE
  T1            0              9
  T2            0             68
  T3            6            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
  BST2 MUTATED     5   1   0
  BST2 WILD-TYPE 215  79  66
D737V5, multiclass
    clus
vv   BST2 MUTATED BST2 WILD-TYPE
  N0            5            215
  N1            1             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"
D737V6, binary
                cls
clus               0   1
  BST2 MUTATED     6   0
  BST2 WILD-TYPE 277  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  BST2 MUTATED      6    0
  BST2 WILD-TYPE  277   48
   clus
vv  BST2 MUTATED BST2 WILD-TYPE
  0            6            277
  1            0             48
[1] 2 2
[1] FALSE
D737V7, 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
D737V8, binary
                cls
clus               0   1
  BST2 MUTATED     6   0
  BST2 WILD-TYPE 311  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  BST2 MUTATED      6    0
  BST2 WILD-TYPE  311   48
                               clus
vv                              BST2 MUTATED BST2 WILD-TYPE
  COLON ADENOCARCINOMA                     6            311
  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 252   2  22  21
D737V9, multiclass
    clus
vv   BST2 MUTATED BST2 WILD-TYPE
  R0            5            252
  R1            0              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"
D737V10, 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
D737V11, 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(738) Variable = OSTM1 MUTATION ANALYSIS
D738V1, survival
                 sevent
clus2               0   1
  OSTM1 MUTATED     4   1
  OSTM1 WILD-TYPE 278  72
  OSTM1 MUTATED OSTM1 WILD-TYPE 
              5             350 
  OSTM1 MUTATED OSTM1 WILD-TYPE 
              1              72 
$`OSTM1 MUTATED`
TCGA-AA-3496 TCGA-AA-3511 TCGA-AD-6889 TCGA-AZ-6598 TCGA-CM-6171 
        1.02         6.97        56.55        49.41        14.04 

$`OSTM1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  OSTM1 MUTATED OSTM1 WILD-TYPE 
           1.02            0.00 
  OSTM1 MUTATED OSTM1 WILD-TYPE 
          56.55          140.38 
  OSTM1 MUTATED OSTM1 WILD-TYPE 
         14.040          20.235 
[1] "1.0 - 56.5 (14.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D738V2, 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       22       108         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        19         10         41         31       35        13
                 vv
clus              STAGE IVB
  OSTM1 MUTATED           0
  OSTM1 WILD-TYPE         1
D738V3, multiclass
            clus
vv           OSTM1 MUTATED OSTM1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              1             108
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OSTM1 MUTATED     0   1   3   1
  OSTM1 WILD-TYPE   9  67 245  40
D738V4, multiclass
    clus
vv   OSTM1 MUTATED OSTM1 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             3             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
  OSTM1 MUTATED     5   0   0
  OSTM1 WILD-TYPE 215  80  66
D738V5, multiclass
    clus
vv   OSTM1 MUTATED OSTM1 WILD-TYPE
  N0             5             215
  N1             0              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"
D738V6, binary
                 cls
clus                0   1
  OSTM1 MUTATED     4   0
  OSTM1 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OSTM1 MUTATED      4    0
  OSTM1 WILD-TYPE  279   48
   clus
vv  OSTM1 MUTATED OSTM1 WILD-TYPE
  0             4             279
  1             0              48
[1] 2 2
[1] FALSE
D738V7, 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
D738V8, binary
                 cls
clus                0   1
  OSTM1 MUTATED     5   0
  OSTM1 WILD-TYPE 312  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OSTM1 MUTATED      5    0
  OSTM1 WILD-TYPE  312   48
                               clus
vv                              OSTM1 MUTATED OSTM1 WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  OSTM1 MUTATED     3   0   0   0
  OSTM1 WILD-TYPE 254   2  22  21
D738V9, multiclass
    clus
vv   OSTM1 MUTATED OSTM1 WILD-TYPE
  R0             3             254
  R1             0               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"
D738V10, 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
D738V11, 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(739) Variable = NGEF MUTATION ANALYSIS
D739V1, survival
                sevent
clus2              0   1
  NGEF MUTATED    12   3
  NGEF WILD-TYPE 270  70
  NGEF MUTATED NGEF WILD-TYPE 
            15            340 
  NGEF MUTATED NGEF WILD-TYPE 
             3             70 
$`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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.09        32.71        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       24.16        21.76        24.69        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 
       37.02        14.93         0.00        17.03        10.06        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 
       20.19        18.25         1.32        43.27        15.12         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 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-D5-6929 TCGA-D5-6930 
       12.43        14.30         9.44        11.64        13.41         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       19.43       107.67        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       51.75        45.11        36.72        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  NGEF MUTATED NGEF WILD-TYPE 
             0              0 
  NGEF MUTATED NGEF WILD-TYPE 
         78.08         140.38 
  NGEF MUTATED NGEF WILD-TYPE 
         22.06          20.07 
[1] "0.0 - 78.1 (22.1)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.2"
D739V2, 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       24       104         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NGEF MUTATED           1          1          2          3        0         0
  NGEF WILD-TYPE        18          9         39         28       35        13
                vv
clus             STAGE IVB
  NGEF MUTATED           0
  NGEF WILD-TYPE         1
D739V3, multiclass
            clus
vv           NGEF MUTATED NGEF WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             5            104
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            1              9
  STAGE IIIB            2             39
  STAGE IIIC            3             28
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NGEF MUTATED     0   3  11   2
  NGEF WILD-TYPE   9  65 237  39
D739V4, multiclass
    clus
vv   NGEF MUTATED NGEF WILD-TYPE
  T1            0              9
  T2            3             65
  T3           11            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
  NGEF MUTATED     9   3   4
  NGEF WILD-TYPE 211  77  62
D739V5, multiclass
    clus
vv   NGEF MUTATED NGEF WILD-TYPE
  N0            9            211
  N1            3             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"
D739V6, binary
                cls
clus               0   1
  NGEF MUTATED    14   0
  NGEF WILD-TYPE 269  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  NGEF MUTATED     14    0
  NGEF WILD-TYPE  269   48
   clus
vv  NGEF MUTATED NGEF WILD-TYPE
  0           14            269
  1            0             48
[1] 2 2
[1] FALSE
D739V7, 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
D739V8, binary
                cls
clus               0   1
  NGEF MUTATED    14   2
  NGEF WILD-TYPE 303  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  NGEF MUTATED     14    2
  NGEF WILD-TYPE  303   46
                               clus
vv                              NGEF MUTATED NGEF WILD-TYPE
  COLON ADENOCARCINOMA                    14            303
  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 245   2  22  21
D739V9, multiclass
    clus
vv   NGEF MUTATED NGEF WILD-TYPE
  R0           12            245
  R1            0              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"
D739V10, 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
D739V11, 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(740) Variable = ZHX1 MUTATION ANALYSIS
D740V1, survival
                sevent
clus2              0   1
  ZHX1 MUTATED     7   2
  ZHX1 WILD-TYPE 275  71
  ZHX1 MUTATED ZHX1 WILD-TYPE 
             9            346 
  ZHX1 MUTATED ZHX1 WILD-TYPE 
             2             71 
$`ZHX1 MUTATED`
TCGA-AA-3510 TCGA-AA-A010 TCGA-AD-5900 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CM-6678 
       63.98        34.98         0.07        49.41         0.33        11.01 
TCGA-D5-6929 TCGA-F4-6460 TCGA-G4-6626 
       13.41        13.38        46.75 

$`ZHX1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       35.80        26.17        91.79        52.80 

  ZHX1 MUTATED ZHX1 WILD-TYPE 
          0.07           0.00 
  ZHX1 MUTATED ZHX1 WILD-TYPE 
         63.98         140.38 
  ZHX1 MUTATED ZHX1 WILD-TYPE 
        13.410         20.235 
[1] "0.1 - 64.0 (13.4)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1"  
D740V2, 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       23       107         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        19         10         40         31       34        12
                vv
clus             STAGE IVB
  ZHX1 MUTATED           0
  ZHX1 WILD-TYPE         1
D740V3, multiclass
            clus
vv           ZHX1 MUTATED ZHX1 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             2            107
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 242  39
D740V4, multiclass
    clus
vv   ZHX1 MUTATED ZHX1 WILD-TYPE
  T1            0              9
  T2            1             67
  T3            6            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
  ZHX1 MUTATED     6   3   0
  ZHX1 WILD-TYPE 214  77  66
D740V5, multiclass
    clus
vv   ZHX1 MUTATED ZHX1 WILD-TYPE
  N0            6            214
  N1            3             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"
D740V6, binary
                cls
clus               0   1
  ZHX1 MUTATED     5   2
  ZHX1 WILD-TYPE 278  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZHX1 MUTATED      5    2
  ZHX1 WILD-TYPE  278   46
   clus
vv  ZHX1 MUTATED ZHX1 WILD-TYPE
  0            5            278
  1            2             46
[1] 2 2
[1] FALSE
D740V7, 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
D740V8, binary
                cls
clus               0   1
  ZHX1 MUTATED     7   2
  ZHX1 WILD-TYPE 310  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZHX1 MUTATED      7    2
  ZHX1 WILD-TYPE  310   46
                               clus
vv                              ZHX1 MUTATED ZHX1 WILD-TYPE
  COLON ADENOCARCINOMA                     7            310
  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 250   2  22  20
D740V9, multiclass
    clus
vv   ZHX1 MUTATED ZHX1 WILD-TYPE
  R0            7            250
  R1            0              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"
D740V10, 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
D740V11, 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(741) Variable = DUSP1 MUTATION ANALYSIS
D741V1, survival
                 sevent
clus2               0   1
  DUSP1 MUTATED     6   0
  DUSP1 WILD-TYPE 276  73
  DUSP1 MUTATED DUSP1 WILD-TYPE 
              6             349 
  DUSP1 MUTATED DUSP1 WILD-TYPE 
              0              73 
$`DUSP1 MUTATED`
TCGA-A6-5657 TCGA-AA-3514 TCGA-AA-3655 TCGA-AA-3660 TCGA-CA-5796 TCGA-G4-6628 
       31.63         1.02        61.02        78.08         3.25        52.80 

$`DUSP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         6.97        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        19.99         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        2.24         3.06         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 
       46.75 

  DUSP1 MUTATED DUSP1 WILD-TYPE 
           1.02            0.00 
  DUSP1 MUTATED DUSP1 WILD-TYPE 
          78.08          140.38 
  DUSP1 MUTATED DUSP1 WILD-TYPE 
         42.215          20.120 
[1] "1.0 - 78.1 (42.2)"  "0.0 - 140.4 (20.1)"
[1] "hr="     "9500000"
D741V2, 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       23       108         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        19         10         40         31       35        13
                 vv
clus              STAGE IVB
  DUSP1 MUTATED           0
  DUSP1 WILD-TYPE         1
D741V3, multiclass
            clus
vv           DUSP1 MUTATED DUSP1 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              1             108
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DUSP1 MUTATED     0   2   4   0
  DUSP1 WILD-TYPE   9  66 244  41
D741V4, multiclass
    clus
vv   DUSP1 MUTATED DUSP1 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             4             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
  DUSP1 MUTATED     5   1   0
  DUSP1 WILD-TYPE 215  79  66
D741V5, multiclass
    clus
vv   DUSP1 MUTATED DUSP1 WILD-TYPE
  N0             5             215
  N1             1              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"
D741V6, binary
                 cls
clus                0   1
  DUSP1 MUTATED     6   0
  DUSP1 WILD-TYPE 277  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DUSP1 MUTATED      6    0
  DUSP1 WILD-TYPE  277   48
   clus
vv  DUSP1 MUTATED DUSP1 WILD-TYPE
  0             6             277
  1             0              48
[1] 2 2
[1] FALSE
D741V7, 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
D741V8, binary
                 cls
clus                0   1
  DUSP1 MUTATED     5   1
  DUSP1 WILD-TYPE 312  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DUSP1 MUTATED      5    1
  DUSP1 WILD-TYPE  312   47
                               clus
vv                              DUSP1 MUTATED DUSP1 WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  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 251   2  22  21
D741V9, multiclass
    clus
vv   DUSP1 MUTATED DUSP1 WILD-TYPE
  R0             6             251
  R1             0               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"
D741V10, 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
D741V11, 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(742) Variable = TGFBR1 MUTATION ANALYSIS
D742V1, survival
                  sevent
clus2                0   1
  TGFBR1 MUTATED    12   2
  TGFBR1 WILD-TYPE 270  71
  TGFBR1 MUTATED TGFBR1 WILD-TYPE 
              14              341 
  TGFBR1 MUTATED TGFBR1 WILD-TYPE 
               2               71 
$`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         0.33       124.27        11.51 
TCGA-D5-6927 TCGA-F4-6806 
        9.44        29.59 

$`TGFBR1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        32.71        27.09         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U 
       34.03        18.05        38.04        27.02        42.02        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  TGFBR1 MUTATED TGFBR1 WILD-TYPE 
            0.33             0.00 
  TGFBR1 MUTATED TGFBR1 WILD-TYPE 
          124.27           140.38 
  TGFBR1 MUTATED TGFBR1 WILD-TYPE 
           14.78            20.28 
[1] "0.3 - 124.3 (14.8)" "0.0 - 140.4 (20.3)"
[1] "hr=" "1.3"
D742V2, 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       23       106         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TGFBR1 MUTATED           0          0          2          0        0
  TGFBR1 WILD-TYPE        19         10         39         31       35
                  vv
clus               STAGE IVA STAGE IVB
  TGFBR1 MUTATED           0         0
  TGFBR1 WILD-TYPE        13         1
D742V3, multiclass
            clus
vv           TGFBR1 MUTATED TGFBR1 WILD-TYPE
  STAGE I                 5               59
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               3              106
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TGFBR1 MUTATED     0   5   6   3
  TGFBR1 WILD-TYPE   9  63 242  38
D742V4, multiclass
    clus
vv   TGFBR1 MUTATED TGFBR1 WILD-TYPE
  T1              0                9
  T2              5               63
  T3              6              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
  TGFBR1 MUTATED    12   2   0
  TGFBR1 WILD-TYPE 208  78  66
D742V5, multiclass
    clus
vv   TGFBR1 MUTATED TGFBR1 WILD-TYPE
  N0             12              208
  N1              2               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"
D742V6, binary
                  cls
clus                 0   1
  TGFBR1 MUTATED    13   0
  TGFBR1 WILD-TYPE 270  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR1 MUTATED     13    0
  TGFBR1 WILD-TYPE  270   48
   clus
vv  TGFBR1 MUTATED TGFBR1 WILD-TYPE
  0             13              270
  1              0               48
[1] 2 2
[1] FALSE
D742V7, 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
D742V8, binary
                  cls
clus                 0   1
  TGFBR1 MUTATED    10   4
  TGFBR1 WILD-TYPE 307  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR1 MUTATED     10    4
  TGFBR1 WILD-TYPE  307   44
                               clus
vv                              TGFBR1 MUTATED TGFBR1 WILD-TYPE
  COLON ADENOCARCINOMA                      10              307
  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 247   2  22  19
D742V9, multiclass
    clus
vv   TGFBR1 MUTATED TGFBR1 WILD-TYPE
  R0             10              247
  R1              0                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"
D742V10, 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
D742V11, 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(743) Variable = C1QL3 MUTATION ANALYSIS
D743V1, survival
                 sevent
clus2               0   1
  C1QL3 MUTATED     4   0
  C1QL3 WILD-TYPE 278  73
  C1QL3 MUTATED C1QL3 WILD-TYPE 
              4             351 
  C1QL3 MUTATED C1QL3 WILD-TYPE 
              0              73 
$`C1QL3 MUTATED`
TCGA-A6-5665 TCGA-A6-6138 TCGA-CM-6166 TCGA-D5-6533 
       22.06        22.52        21.99         1.32 

$`C1QL3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.09        32.71        27.09         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        13.51        11.51 
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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  C1QL3 MUTATED C1QL3 WILD-TYPE 
           1.32            0.00 
  C1QL3 MUTATED C1QL3 WILD-TYPE 
          22.52          140.38 
  C1QL3 MUTATED C1QL3 WILD-TYPE 
         22.025          20.120 
[1] "1.3 - 22.5 (22.0)"  "0.0 - 140.4 (20.1)"
[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       25       108         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  C1QL3 MUTATED           0          0          1          0        0         0
  C1QL3 WILD-TYPE        19         10         40         31       35        13
                 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              25
  STAGE IIA              1             108
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  C1QL3 MUTATED     0   2   1   1
  C1QL3 WILD-TYPE   9  66 247  40
D743V4, multiclass
    clus
vv   C1QL3 MUTATED C1QL3 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             1             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
  C1QL3 MUTATED     4   0   0
  C1QL3 WILD-TYPE 216  80  66
D743V5, multiclass
    clus
vv   C1QL3 MUTATED C1QL3 WILD-TYPE
  N0             4             216
  N1             0              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"
D743V6, binary
                 cls
clus                0   1
  C1QL3 MUTATED     4   0
  C1QL3 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  C1QL3 MUTATED      4    0
  C1QL3 WILD-TYPE  279   48
   clus
vv  C1QL3 MUTATED C1QL3 WILD-TYPE
  0             4             279
  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 313  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  C1QL3 MUTATED      4    0
  C1QL3 WILD-TYPE  313   48
                               clus
vv                              C1QL3 MUTATED C1QL3 WILD-TYPE
  COLON ADENOCARCINOMA                      4             313
  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 254   2  22  21
D743V9, multiclass
    clus
vv   C1QL3 MUTATED C1QL3 WILD-TYPE
  R0             3             254
  R1             0               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"
D743V10, 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
D743V11, 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 = MTTP MUTATION ANALYSIS
D744V1, survival
                sevent
clus2              0   1
  MTTP MUTATED    14   8
  MTTP WILD-TYPE 268  65
  MTTP MUTATED MTTP WILD-TYPE 
            22            333 
  MTTP MUTATED MTTP WILD-TYPE 
             8             65 
$`MTTP MUTATED`
TCGA-A6-2676 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6653 TCGA-AA-3492 TCGA-AA-3811 
       42.90        33.53        22.06        24.39         3.02        10.06 
TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A02K TCGA-AD-6888 TCGA-AZ-6600 
        2.01        25.02         4.01        14.01         4.21        12.10 
TCGA-CA-6717 TCGA-CK-5916 TCGA-CM-4752 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6674 
        0.33        21.14        13.02        16.04        14.99        12.95 
TCGA-D5-6534 TCGA-F4-6459 TCGA-G4-6586 TCGA-G4-6588 
       43.27         8.61        35.80        26.17 

$`MTTP WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       31.63        30.44        29.19        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       21.76        24.69        23.87        20.12        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        7.04         1.02        35.01        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        19.04        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41        49.41         6.77       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99         2.93         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 
       16.01        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-6168 
       15.02        12.00        14.04        29.03        21.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        14.04        11.01        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 
      119.93        35.97        60.79       117.07        98.24        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  MTTP MUTATED MTTP WILD-TYPE 
          0.33           0.00 
  MTTP MUTATED MTTP WILD-TYPE 
         43.27         140.38 
  MTTP MUTATED MTTP WILD-TYPE 
         14.50          20.98 
[1] "0.3 - 43.3 (14.5)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "2.8"
D744V2, 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       24        98         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        18         10         39         30       33        13
                vv
clus             STAGE IVB
  MTTP MUTATED           0
  MTTP WILD-TYPE         1
D744V3, multiclass
            clus
vv           MTTP MUTATED MTTP WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA            11             98
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            2             39
  STAGE IIIC            1             30
  STAGE IV              2             33
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MTTP MUTATED     1   3  15   4
  MTTP WILD-TYPE   8  65 233  37
D744V4, multiclass
    clus
vv   MTTP MUTATED MTTP WILD-TYPE
  T1            1              8
  T2            3             65
  T3           15            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   1   4
  MTTP WILD-TYPE 203  79  62
D744V5, multiclass
    clus
vv   MTTP MUTATED MTTP WILD-TYPE
  N0           17            203
  N1            1             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"
D744V6, binary
                cls
clus               0   1
  MTTP MUTATED    20   2
  MTTP WILD-TYPE 263  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTTP MUTATED     20    2
  MTTP WILD-TYPE  263   46
   clus
vv  MTTP MUTATED MTTP WILD-TYPE
  0           20            263
  1            2             46
[1] 2 2
[1] FALSE
D744V7, 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
D744V8, binary
                cls
clus               0   1
  MTTP MUTATED    19   4
  MTTP WILD-TYPE 298  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTTP MUTATED     19    4
  MTTP WILD-TYPE  298   44
                               clus
vv                              MTTP MUTATED MTTP WILD-TYPE
  COLON ADENOCARCINOMA                    19            298
  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 241   2  21  19
D744V9, multiclass
    clus
vv   MTTP MUTATED MTTP WILD-TYPE
  R0           16            241
  R1            0              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"
D744V10, 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
D744V11, 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(745) Variable = PTTG1IP MUTATION ANALYSIS
D745V1, survival
                   sevent
clus2                 0   1
  PTTG1IP MUTATED     6   1
  PTTG1IP WILD-TYPE 276  72
  PTTG1IP MUTATED PTTG1IP WILD-TYPE 
                7               348 
  PTTG1IP MUTATED PTTG1IP WILD-TYPE 
                1                72 
$`PTTG1IP MUTATED`
TCGA-AA-3510 TCGA-CA-5255 TCGA-D5-6539 TCGA-DM-A1DB TCGA-G4-6304 TCGA-G4-6588 
       63.98         3.06        12.49        44.32        53.62        26.17 
TCGA-G4-6628 
       52.80 

$`PTTG1IP WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19         1.94         2.24         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32        12.59       140.38         7.50       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 

  PTTG1IP MUTATED PTTG1IP WILD-TYPE 
             3.06              0.00 
  PTTG1IP MUTATED PTTG1IP WILD-TYPE 
            63.98            140.38 
  PTTG1IP MUTATED PTTG1IP WILD-TYPE 
            44.32             20.07 
[1] "3.1 - 64.0 (44.3)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "2.2"
D745V2, 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       24       106         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PTTG1IP MUTATED           0          1          0          0        0
  PTTG1IP WILD-TYPE        19          9         41         31       35
                   vv
clus                STAGE IVA STAGE IVB
  PTTG1IP MUTATED           0         0
  PTTG1IP WILD-TYPE        13         1
D745V3, multiclass
            clus
vv           PTTG1IP MUTATED PTTG1IP WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                3               106
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               1                 9
  STAGE IIIB               0                41
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PTTG1IP MUTATED     0   1   5   1
  PTTG1IP WILD-TYPE   9  67 243  40
D745V4, multiclass
    clus
vv   PTTG1IP MUTATED PTTG1IP WILD-TYPE
  T1               0                 9
  T2               1                67
  T3               5               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
  PTTG1IP MUTATED     7   0   0
  PTTG1IP WILD-TYPE 213  80  66
D745V5, multiclass
    clus
vv   PTTG1IP MUTATED PTTG1IP WILD-TYPE
  N0               7               213
  N1               0                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"
D745V6, binary
                   cls
clus                  0   1
  PTTG1IP MUTATED     7   0
  PTTG1IP WILD-TYPE 276  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PTTG1IP MUTATED      7    0
  PTTG1IP WILD-TYPE  276   48
   clus
vv  PTTG1IP MUTATED PTTG1IP WILD-TYPE
  0               7               276
  1               0                48
[1] 2 2
[1] FALSE
D745V7, 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
D745V8, binary
                   cls
clus                  0   1
  PTTG1IP MUTATED     7   0
  PTTG1IP WILD-TYPE 310  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PTTG1IP MUTATED      7    0
  PTTG1IP WILD-TYPE  310   48
                               clus
vv                              PTTG1IP MUTATED PTTG1IP WILD-TYPE
  COLON ADENOCARCINOMA                        7               310
  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 252   2  22  20
D745V9, multiclass
    clus
vv   PTTG1IP MUTATED PTTG1IP WILD-TYPE
  R0               5               252
  R1               0                 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"
D745V10, 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
D745V11, 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(746) Variable = ADH1B MUTATION ANALYSIS
D746V1, survival
                 sevent
clus2               0   1
  ADH1B MUTATED     4   3
  ADH1B WILD-TYPE 278  70
  ADH1B MUTATED ADH1B WILD-TYPE 
              7             348 
  ADH1B MUTATED ADH1B WILD-TYPE 
              3              70 
$`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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        1.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       51.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 
      102.44        40.34        15.62        49.08        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 
        2.93         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        16.01 
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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-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        13.38        13.45        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  ADH1B MUTATED ADH1B WILD-TYPE 
           5.03            0.00 
  ADH1B MUTATED ADH1B WILD-TYPE 
          51.32          140.38 
  ADH1B MUTATED ADH1B WILD-TYPE 
         16.140          20.235 
[1] "5.0 - 51.3 (16.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2.2"
D746V2, 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       25       107         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        18         10         41         31       34        12
                 vv
clus              STAGE IVB
  ADH1B MUTATED           0
  ADH1B WILD-TYPE         1
D746V3, multiclass
            clus
vv           ADH1B MUTATED ADH1B WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              2             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 243  41
D746V4, multiclass
    clus
vv   ADH1B MUTATED ADH1B WILD-TYPE
  T1             0               9
  T2             2              66
  T3             5             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
  ADH1B MUTATED     4   2   1
  ADH1B WILD-TYPE 216  78  65
D746V5, multiclass
    clus
vv   ADH1B MUTATED ADH1B WILD-TYPE
  N0             4             216
  N1             2              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"
D746V6, binary
                 cls
clus                0   1
  ADH1B MUTATED     4   2
  ADH1B WILD-TYPE 279  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADH1B MUTATED      4    2
  ADH1B WILD-TYPE  279   46
   clus
vv  ADH1B MUTATED ADH1B WILD-TYPE
  0             4             279
  1             2              46
[1] 2 2
[1] FALSE
D746V7, 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
D746V8, binary
                 cls
clus                0   1
  ADH1B MUTATED     5   2
  ADH1B WILD-TYPE 312  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADH1B MUTATED      5    2
  ADH1B WILD-TYPE  312   46
                               clus
vv                              ADH1B MUTATED ADH1B WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  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 253   2  21  20
D746V9, multiclass
    clus
vv   ADH1B MUTATED ADH1B WILD-TYPE
  R0             4             253
  R1             0               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"
D746V10, 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
D746V11, 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(747) Variable = LAS1L MUTATION ANALYSIS
D747V1, survival
                 sevent
clus2               0   1
  LAS1L MUTATED     8   1
  LAS1L WILD-TYPE 274  72
  LAS1L MUTATED LAS1L WILD-TYPE 
              9             346 
  LAS1L MUTATED LAS1L WILD-TYPE 
              1              72 
$`LAS1L MUTATED`
TCGA-A6-2672 TCGA-A6-2676 TCGA-AU-3779 TCGA-AU-6004 TCGA-AZ-5407 TCGA-CM-6680 
       46.65        42.90        14.50        27.09        61.41        12.03 
TCGA-G4-6309 TCGA-G4-6321 TCGA-G4-6625 
       51.75        22.09        91.79 

$`LAS1L WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       43.76        43.76        24.33        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       33.34        32.75        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       10.88         0.20        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       44.68        55.04        45.11        36.72        36.00        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        46.75        52.80 

  LAS1L MUTATED LAS1L WILD-TYPE 
          12.03            0.00 
  LAS1L MUTATED LAS1L WILD-TYPE 
          91.79          140.38 
  LAS1L MUTATED LAS1L WILD-TYPE 
         42.900          20.005 
[1] "12.0 - 91.8 (42.9)" "0.0 - 140.4 (20.0)"
[1] "hr=" "3"  
D747V2, 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       25       107         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        18         10         38         31       35        13
                 vv
clus              STAGE IVB
  LAS1L MUTATED           0
  LAS1L WILD-TYPE         1
D747V3, multiclass
            clus
vv           LAS1L MUTATED LAS1L WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              2             107
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             3              38
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LAS1L MUTATED     1   2   5   1
  LAS1L WILD-TYPE   8  66 243  40
D747V4, multiclass
    clus
vv   LAS1L MUTATED LAS1L WILD-TYPE
  T1             1               8
  T2             2              66
  T3             5             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
  LAS1L MUTATED     5   3   1
  LAS1L WILD-TYPE 215  77  65
D747V5, multiclass
    clus
vv   LAS1L MUTATED LAS1L WILD-TYPE
  N0             5             215
  N1             3              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"
D747V6, binary
                 cls
clus                0   1
  LAS1L MUTATED     8   0
  LAS1L WILD-TYPE 275  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LAS1L MUTATED      8    0
  LAS1L WILD-TYPE  275   48
   clus
vv  LAS1L MUTATED LAS1L WILD-TYPE
  0             8             275
  1             0              48
[1] 2 2
[1] FALSE
D747V7, 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
D747V8, binary
                 cls
clus                0   1
  LAS1L MUTATED     9   0
  LAS1L WILD-TYPE 308  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LAS1L MUTATED      9    0
  LAS1L WILD-TYPE  308   48
                               clus
vv                              LAS1L MUTATED LAS1L WILD-TYPE
  COLON ADENOCARCINOMA                      9             308
  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 249   2  22  21
D747V9, multiclass
    clus
vv   LAS1L MUTATED LAS1L WILD-TYPE
  R0             8             249
  R1             0               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"
D747V10, 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
D747V11, 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(748) Variable = SNX2 MUTATION ANALYSIS
D748V1, survival
                sevent
clus2              0   1
  SNX2 MUTATED     8   2
  SNX2 WILD-TYPE 274  71
  SNX2 MUTATED SNX2 WILD-TYPE 
            10            345 
  SNX2 MUTATED SNX2 WILD-TYPE 
             2             71 
$`SNX2 MUTATED`
TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3811 TCGA-AA-3982 TCGA-AA-A010 TCGA-AA-A02H 
       19.66        63.98        10.06        27.02        34.98         2.01 
TCGA-CA-6717 TCGA-CM-6162 TCGA-D5-6540 TCGA-G4-6628 
        0.33        12.00        16.14        52.80 

$`SNX2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        19.04        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3986 
       34.06        26.01        25.02        24.00        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02K 
       37.02        39.06        51.98        39.98         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       26.17        91.79        46.75 

  SNX2 MUTATED SNX2 WILD-TYPE 
          0.33           0.00 
  SNX2 MUTATED SNX2 WILD-TYPE 
         63.98         140.38 
  SNX2 MUTATED SNX2 WILD-TYPE 
         17.90          20.28 
[1] "0.3 - 64.0 (17.9)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1"  
D748V2, 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       24       108         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        18         10         39         30       34        13
                vv
clus             STAGE IVB
  SNX2 MUTATED           0
  SNX2 WILD-TYPE         1
D748V3, multiclass
            clus
vv           SNX2 MUTATED SNX2 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             1            108
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            2             39
  STAGE IIIC            1             30
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SNX2 MUTATED     0   2   6   3
  SNX2 WILD-TYPE   9  66 242  38
D748V4, multiclass
    clus
vv   SNX2 MUTATED SNX2 WILD-TYPE
  T1            0              9
  T2            2             66
  T3            6            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
  SNX2 MUTATED     6   3   2
  SNX2 WILD-TYPE 214  77  64
D748V5, multiclass
    clus
vv   SNX2 MUTATED SNX2 WILD-TYPE
  N0            6            214
  N1            3             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"
D748V6, binary
                cls
clus               0   1
  SNX2 MUTATED     8   1
  SNX2 WILD-TYPE 275  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  SNX2 MUTATED      8    1
  SNX2 WILD-TYPE  275   47
   clus
vv  SNX2 MUTATED SNX2 WILD-TYPE
  0            8            275
  1            1             47
[1] 2 2
[1] FALSE
D748V7, 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
D748V8, binary
                cls
clus               0   1
  SNX2 MUTATED     7   4
  SNX2 WILD-TYPE 310  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  SNX2 MUTATED      7    4
  SNX2 WILD-TYPE  310   44
                               clus
vv                              SNX2 MUTATED SNX2 WILD-TYPE
  COLON ADENOCARCINOMA                     7            310
  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 250   2  21  19
D748V9, multiclass
    clus
vv   SNX2 MUTATED SNX2 WILD-TYPE
  R0            7            250
  R1            0              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"
D748V10, 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
D748V11, 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(749) Variable = SCN4A MUTATION ANALYSIS
D749V1, survival
                 sevent
clus2               0   1
  SCN4A MUTATED    17   4
  SCN4A WILD-TYPE 265  69
  SCN4A MUTATED SCN4A WILD-TYPE 
             21             334 
  SCN4A MUTATED SCN4A WILD-TYPE 
              4              69 
$`SCN4A MUTATED`
TCGA-A6-3809 TCGA-AA-3492 TCGA-AA-3715 TCGA-AA-3869 TCGA-AA-3947 TCGA-AA-3977 
       32.75         3.02        19.04        27.02        33.01        25.02 
TCGA-AA-3979 TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6895 TCGA-AU-6004 TCGA-AZ-4315 
       24.00         0.07        56.55         0.72        27.09        58.39 
TCGA-CA-5254 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4744 TCGA-CM-5344 TCGA-D5-6533 
        2.24         0.33         0.10        20.02        22.03         1.32 
TCGA-D5-6928 TCGA-DM-A1DB TCGA-F4-6856 
       11.64        44.32        19.43 

$`SCN4A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37         4.21 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19         1.94         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07         0.26         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 
        2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 
       16.24        33.67        13.25         0.53        35.41       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  SCN4A MUTATED SCN4A WILD-TYPE 
           0.07            0.00 
  SCN4A MUTATED SCN4A WILD-TYPE 
          58.39          140.38 
  SCN4A MUTATED SCN4A WILD-TYPE 
         20.020          20.235 
[1] "0.1 - 58.4 (20.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D749V2, 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       22       101         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        19         10         39         31       34        13
                 vv
clus              STAGE IVB
  SCN4A MUTATED           0
  SCN4A WILD-TYPE         1
D749V3, multiclass
            clus
vv           SCN4A MUTATED SCN4A WILD-TYPE
  STAGE I                5              59
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              8             101
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SCN4A MUTATED     0   6  12   5
  SCN4A WILD-TYPE   9  62 236  36
D749V4, multiclass
    clus
vv   SCN4A MUTATED SCN4A WILD-TYPE
  T1             0               9
  T2             6              62
  T3            12             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
  SCN4A MUTATED    20   2   1
  SCN4A WILD-TYPE 200  78  65
D749V5, multiclass
    clus
vv   SCN4A MUTATED SCN4A WILD-TYPE
  N0            20             200
  N1             2              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"
D749V6, binary
                 cls
clus                0   1
  SCN4A MUTATED    18   1
  SCN4A WILD-TYPE 265  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCN4A MUTATED     18    1
  SCN4A WILD-TYPE  265   47
   clus
vv  SCN4A MUTATED SCN4A WILD-TYPE
  0            18             265
  1             1              47
[1] 2 2
[1] FALSE
D749V7, 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
D749V8, binary
                 cls
clus                0   1
  SCN4A MUTATED    17   6
  SCN4A WILD-TYPE 300  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCN4A MUTATED     17    6
  SCN4A WILD-TYPE  300   42
                               clus
vv                              SCN4A MUTATED SCN4A WILD-TYPE
  COLON ADENOCARCINOMA                     17             300
  COLON MUCINOUS ADENOCARCINOMA             6              42
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SCN4A MUTATED    14   0   1   4
  SCN4A WILD-TYPE 243   2  21  17
D749V9, multiclass
    clus
vv   SCN4A MUTATED SCN4A WILD-TYPE
  R0            14             243
  R1             0               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"
D749V10, 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
D749V11, 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(750) Variable = B4GALT6 MUTATION ANALYSIS
D750V1, survival
                   sevent
clus2                 0   1
  B4GALT6 MUTATED     8   2
  B4GALT6 WILD-TYPE 274  71
  B4GALT6 MUTATED B4GALT6 WILD-TYPE 
               10               345 
  B4GALT6 MUTATED B4GALT6 WILD-TYPE 
                2                71 
$`B4GALT6 MUTATED`
TCGA-A6-2676 TCGA-A6-6649 TCGA-AA-3977 TCGA-AA-A00J TCGA-AA-A010 TCGA-AA-A01R 
       42.90        24.16        25.02        18.05        34.98        35.01 
TCGA-AD-6895 TCGA-AZ-4315 TCGA-AZ-6607 TCGA-CM-6162 
        0.72        58.39         3.19        12.00 

$`B4GALT6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.18        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21        56.55         0.79         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  B4GALT6 MUTATED B4GALT6 WILD-TYPE 
             0.72              0.00 
  B4GALT6 MUTATED B4GALT6 WILD-TYPE 
            58.39            140.38 
  B4GALT6 MUTATED B4GALT6 WILD-TYPE 
            24.59             20.12 
[1] "0.7 - 58.4 (24.6)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1"  
D750V2, 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       25       108         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  B4GALT6 MUTATED           1          0          3          0        1
  B4GALT6 WILD-TYPE        18         10         38         31       34
                   vv
clus                STAGE IVA STAGE IVB
  B4GALT6 MUTATED           0         0
  B4GALT6 WILD-TYPE        13         1
D750V3, multiclass
            clus
vv           B4GALT6 MUTATED B4GALT6 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                1               108
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               0                10
  STAGE IIIB               3                38
  STAGE IIIC               0                31
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  B4GALT6 MUTATED     0   1   5   4
  B4GALT6 WILD-TYPE   9  67 243  37
D750V4, multiclass
    clus
vv   B4GALT6 MUTATED B4GALT6 WILD-TYPE
  T1               0                 9
  T2               1                67
  T3               5               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
  B4GALT6 MUTATED     4   4   2
  B4GALT6 WILD-TYPE 216  76  64
D750V5, multiclass
    clus
vv   B4GALT6 MUTATED B4GALT6 WILD-TYPE
  N0               4               216
  N1               4                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"
D750V6, binary
                   cls
clus                  0   1
  B4GALT6 MUTATED     7   1
  B4GALT6 WILD-TYPE 276  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  B4GALT6 MUTATED      7    1
  B4GALT6 WILD-TYPE  276   47
   clus
vv  B4GALT6 MUTATED B4GALT6 WILD-TYPE
  0               7               276
  1               1                47
[1] 2 2
[1] FALSE
D750V7, 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
D750V8, binary
                   cls
clus                  0   1
  B4GALT6 MUTATED     7   3
  B4GALT6 WILD-TYPE 310  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  B4GALT6 MUTATED      7    3
  B4GALT6 WILD-TYPE  310   45
                               clus
vv                              B4GALT6 MUTATED B4GALT6 WILD-TYPE
  COLON ADENOCARCINOMA                        7               310
  COLON MUCINOUS ADENOCARCINOMA               3                45
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  B4GALT6 MUTATED     6   0   0   0
  B4GALT6 WILD-TYPE 251   2  22  21
D750V9, multiclass
    clus
vv   B4GALT6 MUTATED B4GALT6 WILD-TYPE
  R0               6               251
  R1               0                 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"
D750V10, 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
D750V11, 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(751) Variable = OR10J1 MUTATION ANALYSIS
D751V1, survival
                  sevent
clus2                0   1
  OR10J1 MUTATED     9   3
  OR10J1 WILD-TYPE 273  70
  OR10J1 MUTATED OR10J1 WILD-TYPE 
              12              343 
  OR10J1 MUTATED OR10J1 WILD-TYPE 
               3               70 
$`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         0.10        17.56 
TCGA-CM-5861 TCGA-CM-6172 TCGA-D5-6533 TCGA-F4-6569 TCGA-F4-6570 TCGA-G4-6306 
       15.02        11.01         1.32        13.45         6.18        44.68 

$`OR10J1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10       100.01        29.56         5.23         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        0.33         1.35       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       11.51        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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6703 
       60.79       117.07        98.24         8.61        13.38        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  OR10J1 MUTATED OR10J1 WILD-TYPE 
             0.1              0.0 
  OR10J1 MUTATED OR10J1 WILD-TYPE 
           44.68           140.38 
  OR10J1 MUTATED OR10J1 WILD-TYPE 
          12.595           20.980 
[1] "0.1 - 44.7 (12.6)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "2"  
D751V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR10J1 MUTATED         2        0        0         5         1         0
  OR10J1 WILD-TYPE      62        1       25       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        19         10         39         31       34
                  vv
clus               STAGE IVA STAGE IVB
  OR10J1 MUTATED           2         0
  OR10J1 WILD-TYPE        11         1
D751V3, multiclass
            clus
vv           OR10J1 MUTATED OR10J1 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               5              104
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               2               11
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 243  36
D751V4, multiclass
    clus
vv   OR10J1 MUTATED OR10J1 WILD-TYPE
  T1              1                8
  T2              2               66
  T3              5              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
  OR10J1 MUTATED     9   3   1
  OR10J1 WILD-TYPE 211  77  65
D751V5, multiclass
    clus
vv   OR10J1 MUTATED OR10J1 WILD-TYPE
  N0              9              211
  N1              3               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
  OR10J1 MUTATED    11   2
  OR10J1 WILD-TYPE 272  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR10J1 MUTATED     11    2
  OR10J1 WILD-TYPE  272   46
   clus
vv  OR10J1 MUTATED OR10J1 WILD-TYPE
  0             11              272
  1              2               46
[1] 2 2
[1] FALSE
D751V7, 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
D751V8, binary
                  cls
clus                 0   1
  OR10J1 MUTATED    11   2
  OR10J1 WILD-TYPE 306  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR10J1 MUTATED     11    2
  OR10J1 WILD-TYPE  306   46
                               clus
vv                              OR10J1 MUTATED OR10J1 WILD-TYPE
  COLON ADENOCARCINOMA                      11              306
  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 247   2  22  19
D751V9, multiclass
    clus
vv   OR10J1 MUTATED OR10J1 WILD-TYPE
  R0             10              247
  R1              0                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"
D751V10, 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
D751V11, 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(752) Variable = PDP2 MUTATION ANALYSIS
D752V1, survival
                sevent
clus2              0   1
  PDP2 MUTATED     5   0
  PDP2 WILD-TYPE 277  73
  PDP2 MUTATED PDP2 WILD-TYPE 
             5            350 
  PDP2 MUTATED PDP2 WILD-TYPE 
             0             73 
$`PDP2 MUTATED`
TCGA-AA-3713 TCGA-AD-6889 TCGA-AD-6895 TCGA-CA-6717 TCGA-CM-6165 
       19.04        56.55         0.72         0.33        16.04 

$`PDP2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        4.21         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  PDP2 MUTATED PDP2 WILD-TYPE 
          0.33           0.00 
  PDP2 MUTATED PDP2 WILD-TYPE 
         56.55         140.38 
  PDP2 MUTATED PDP2 WILD-TYPE 
         16.04          20.63 
[1] "0.3 - 56.5 (16.0)"  "0.0 - 140.4 (20.6)"
[1] "hr="     "9100000"
D752V2, 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       25       106         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PDP2 MUTATED           0          0          0          0        1         0
  PDP2 WILD-TYPE        19         10         41         31       34        13
                vv
clus             STAGE IVB
  PDP2 MUTATED           0
  PDP2 WILD-TYPE         1
D752V3, multiclass
            clus
vv           PDP2 MUTATED PDP2 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             3            106
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PDP2 MUTATED     0   0   5   0
  PDP2 WILD-TYPE   9  68 243  41
D752V4, multiclass
    clus
vv   PDP2 MUTATED PDP2 WILD-TYPE
  T1            0              9
  T2            0             68
  T3            5            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
  PDP2 MUTATED     4   1   0
  PDP2 WILD-TYPE 216  79  66
D752V5, multiclass
    clus
vv   PDP2 MUTATED PDP2 WILD-TYPE
  N0            4            216
  N1            1             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"
D752V6, binary
                cls
clus               0   1
  PDP2 MUTATED     3   1
  PDP2 WILD-TYPE 280  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  PDP2 MUTATED      3    1
  PDP2 WILD-TYPE  280   47
   clus
vv  PDP2 MUTATED PDP2 WILD-TYPE
  0            3            280
  1            1             47
[1] 2 2
[1] FALSE
D752V7, 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
D752V8, binary
                cls
clus               0   1
  PDP2 MUTATED     4   1
  PDP2 WILD-TYPE 313  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  PDP2 MUTATED      4    1
  PDP2 WILD-TYPE  313   47
                               clus
vv                              PDP2 MUTATED PDP2 WILD-TYPE
  COLON ADENOCARCINOMA                     4            313
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PDP2 MUTATED     1   0   1   1
  PDP2 WILD-TYPE 256   2  21  20
D752V9, multiclass
    clus
vv   PDP2 MUTATED PDP2 WILD-TYPE
  R0            1            256
  R1            0              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"
D752V10, 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
D752V11, 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(753) Variable = EXD2 MUTATION ANALYSIS
D753V1, survival
                sevent
clus2              0   1
  EXD2 MUTATED     8   3
  EXD2 WILD-TYPE 274  70
  EXD2 MUTATED EXD2 WILD-TYPE 
            11            344 
  EXD2 MUTATED EXD2 WILD-TYPE 
             3             70 
$`EXD2 MUTATED`
TCGA-AA-3713 TCGA-AA-3950 TCGA-AA-A00N TCGA-AD-6964 TCGA-CA-6717 TCGA-CM-5864 
       19.04        24.00         4.01        10.88         0.33        15.02 
TCGA-D5-6534 TCGA-D5-6539 TCGA-F4-6459 TCGA-F4-6856 TCGA-G4-6323 
       43.27        12.49         8.61        19.43        13.78 

$`EXD2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 
       35.97        60.79       117.07        98.24        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 
       33.67        13.25         0.53        35.41       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.72        36.00        22.09        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  EXD2 MUTATED EXD2 WILD-TYPE 
          0.33           0.00 
  EXD2 MUTATED EXD2 WILD-TYPE 
         43.27         140.38 
  EXD2 MUTATED EXD2 WILD-TYPE 
        13.780         20.995 
[1] "0.3 - 43.3 (13.8)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "2.1"
D753V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EXD2 MUTATED         2        1        0         3         1         0
  EXD2 WILD-TYPE      62        0       25       106         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EXD2 MUTATED           0          1          1          0        1         0
  EXD2 WILD-TYPE        19          9         40         31       34        13
                vv
clus             STAGE IVB
  EXD2 MUTATED           0
  EXD2 WILD-TYPE         1
D753V3, multiclass
            clus
vv           EXD2 MUTATED EXD2 WILD-TYPE
  STAGE I               2             62
  STAGE IA              1              0
  STAGE II              0             25
  STAGE IIA             3            106
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            1              9
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  EXD2 MUTATED     0   2   6   2
  EXD2 WILD-TYPE   9  66 242  39
D753V4, multiclass
    clus
vv   EXD2 MUTATED EXD2 WILD-TYPE
  T1            0              9
  T2            2             66
  T3            6            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
  EXD2 MUTATED     9   0   2
  EXD2 WILD-TYPE 211  80  64
D753V5, multiclass
    clus
vv   EXD2 MUTATED EXD2 WILD-TYPE
  N0            9            211
  N1            0             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"
D753V6, binary
                cls
clus               0   1
  EXD2 MUTATED     8   1
  EXD2 WILD-TYPE 275  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  EXD2 MUTATED      8    1
  EXD2 WILD-TYPE  275   47
   clus
vv  EXD2 MUTATED EXD2 WILD-TYPE
  0            8            275
  1            1             47
[1] 2 2
[1] FALSE
D753V7, binary
                cls
clus               0   1
  EXD2 MUTATED     4   7
  EXD2 WILD-TYPE 166 190
[1] "tbl2"
                cls
clus             [,1] [,2]
  EXD2 MUTATED      4    7
  EXD2 WILD-TYPE  166  190
        clus
vv       EXD2 MUTATED EXD2 WILD-TYPE
  FEMALE            4            166
  MALE              7            190
[1] 2 2
[1] FALSE
D753V8, binary
                cls
clus               0   1
  EXD2 MUTATED     6   5
  EXD2 WILD-TYPE 311  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  EXD2 MUTATED      6    5
  EXD2 WILD-TYPE  311   43
                               clus
vv                              EXD2 MUTATED EXD2 WILD-TYPE
  COLON ADENOCARCINOMA                     6            311
  COLON MUCINOUS ADENOCARCINOMA            5             43
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  EXD2 MUTATED     8   0   1   1
  EXD2 WILD-TYPE 249   2  21  20
D753V9, multiclass
    clus
vv   EXD2 MUTATED EXD2 WILD-TYPE
  R0            8            249
  R1            0              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"
D753V10, 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     6
  EXD2 WILD-TYPE                        18   170
D753V11, 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                                       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(754) Variable = SLC35A5 MUTATION ANALYSIS
D754V1, survival
                   sevent
clus2                 0   1
  SLC35A5 MUTATED     5   2
  SLC35A5 WILD-TYPE 277  71
  SLC35A5 MUTATED SLC35A5 WILD-TYPE 
                7               348 
  SLC35A5 MUTATED SLC35A5 WILD-TYPE 
                2                71 
$`SLC35A5 MUTATED`
TCGA-AA-3510 TCGA-AA-3663 TCGA-AZ-4682 TCGA-CM-6163 TCGA-CM-6164 TCGA-G4-6303 
       63.98         6.97        22.36        14.04        29.03        65.85 
TCGA-G4-6628 
       52.80 

$`SLC35A5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13        83.80        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 
        0.53        35.41        19.43       107.67        74.56        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 

  SLC35A5 MUTATED SLC35A5 WILD-TYPE 
             6.97              0.00 
  SLC35A5 MUTATED SLC35A5 WILD-TYPE 
            65.85            140.38 
  SLC35A5 MUTATED SLC35A5 WILD-TYPE 
            29.03             20.07 
[1] "7.0 - 65.8 (29.0)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.1"
D754V2, 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       23       108         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC35A5 MUTATED           0          0          0          0        1
  SLC35A5 WILD-TYPE        19         10         41         31       34
                   vv
clus                STAGE IVA STAGE IVB
  SLC35A5 MUTATED           1         0
  SLC35A5 WILD-TYPE        12         1
D754V3, multiclass
            clus
vv           SLC35A5 MUTATED SLC35A5 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 2                23
  STAGE IIA                1               108
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               0                31
  STAGE IV                 1                34
  STAGE IVA                1                12
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 243  41
D754V4, multiclass
    clus
vv   SLC35A5 MUTATED SLC35A5 WILD-TYPE
  T1               1                 8
  T2               1                67
  T3               5               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
  SLC35A5 MUTATED     6   1   0
  SLC35A5 WILD-TYPE 214  79  66
D754V5, multiclass
    clus
vv   SLC35A5 MUTATED SLC35A5 WILD-TYPE
  N0               6               214
  N1               1                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"
D754V6, binary
                   cls
clus                  0   1
  SLC35A5 MUTATED     5   2
  SLC35A5 WILD-TYPE 278  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC35A5 MUTATED      5    2
  SLC35A5 WILD-TYPE  278   46
   clus
vv  SLC35A5 MUTATED SLC35A5 WILD-TYPE
  0               5               278
  1               2                46
[1] 2 2
[1] FALSE
D754V7, 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
D754V8, binary
                   cls
clus                  0   1
  SLC35A5 MUTATED     7   0
  SLC35A5 WILD-TYPE 310  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC35A5 MUTATED      7    0
  SLC35A5 WILD-TYPE  310   48
                               clus
vv                              SLC35A5 MUTATED SLC35A5 WILD-TYPE
  COLON ADENOCARCINOMA                        7               310
  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 250   2  22  21
D754V9, multiclass
    clus
vv   SLC35A5 MUTATED SLC35A5 WILD-TYPE
  R0               7               250
  R1               0                 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"
D754V10, 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
D754V11, 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(755) Variable = CHEK2 MUTATION ANALYSIS
D755V1, survival
                 sevent
clus2               0   1
  CHEK2 MUTATED     9   1
  CHEK2 WILD-TYPE 273  72
  CHEK2 MUTATED CHEK2 WILD-TYPE 
             10             345 
  CHEK2 MUTATED CHEK2 WILD-TYPE 
              1              72 
$`CHEK2 MUTATED`
TCGA-A6-6653 TCGA-AA-3815 TCGA-AA-A01Q TCGA-AZ-6608 TCGA-CA-6717 TCGA-CA-6718 
       24.39        33.04         1.02         1.94         0.33         0.10 
TCGA-CM-4743 TCGA-D5-6529 TCGA-D5-6928 TCGA-G4-6317 
       23.05        20.19        11.64        36.00 

$`CHEK2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       13.51        11.51        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       45.11        36.72        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  CHEK2 MUTATED CHEK2 WILD-TYPE 
            0.1             0.0 
  CHEK2 MUTATED CHEK2 WILD-TYPE 
          36.00          140.38 
  CHEK2 MUTATED CHEK2 WILD-TYPE 
         15.915          20.280 
[1] "0.1 - 36.0 (15.9)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.2"
D755V2, 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       24       103         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        19          9         41         30       35        13
                 vv
clus              STAGE IVB
  CHEK2 MUTATED           0
  CHEK2 WILD-TYPE         1
D755V3, multiclass
            clus
vv           CHEK2 MUTATED CHEK2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              6             103
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CHEK2 MUTATED     0   2   8   0
  CHEK2 WILD-TYPE   9  66 240  41
D755V4, multiclass
    clus
vv   CHEK2 MUTATED CHEK2 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             8             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
  CHEK2 MUTATED     8   1   1
  CHEK2 WILD-TYPE 212  79  65
D755V5, multiclass
    clus
vv   CHEK2 MUTATED CHEK2 WILD-TYPE
  N0             8             212
  N1             1              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"
D755V6, binary
                 cls
clus                0   1
  CHEK2 MUTATED     9   0
  CHEK2 WILD-TYPE 274  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHEK2 MUTATED      9    0
  CHEK2 WILD-TYPE  274   48
   clus
vv  CHEK2 MUTATED CHEK2 WILD-TYPE
  0             9             274
  1             0              48
[1] 2 2
[1] FALSE
D755V7, 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
D755V8, binary
                 cls
clus                0   1
  CHEK2 MUTATED     8   2
  CHEK2 WILD-TYPE 309  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHEK2 MUTATED      8    2
  CHEK2 WILD-TYPE  309   46
                               clus
vv                              CHEK2 MUTATED CHEK2 WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  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 251   2  22  19
D755V9, multiclass
    clus
vv   CHEK2 MUTATED CHEK2 WILD-TYPE
  R0             6             251
  R1             0               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"
D755V10, 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
D755V11, 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(756) Variable = DCTN5 MUTATION ANALYSIS
D756V1, survival
                 sevent
clus2               0   1
  DCTN5 MUTATED     5   1
  DCTN5 WILD-TYPE 277  72
  DCTN5 MUTATED DCTN5 WILD-TYPE 
              6             349 
  DCTN5 MUTATED DCTN5 WILD-TYPE 
              1              72 
$`DCTN5 MUTATED`
TCGA-A6-3809 TCGA-AA-3713 TCGA-AZ-6598 TCGA-CK-5914 TCGA-CM-6164 TCGA-G4-6588 
       32.75        19.04        49.41        21.99        29.03        26.17 

$`DCTN5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13        83.80        22.36        62.79        61.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 
       40.34        15.62        49.08        51.32        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 
       52.80 

  DCTN5 MUTATED DCTN5 WILD-TYPE 
          19.04            0.00 
  DCTN5 MUTATED DCTN5 WILD-TYPE 
          49.41          140.38 
  DCTN5 MUTATED DCTN5 WILD-TYPE 
          27.60           20.02 
[1] "19.0 - 49.4 (27.6)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.4"
D756V2, 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       24       107         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        19         10         40         31       34        13
                 vv
clus              STAGE IVB
  DCTN5 MUTATED           0
  DCTN5 WILD-TYPE         1
D756V3, multiclass
            clus
vv           DCTN5 MUTATED DCTN5 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              2             107
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DCTN5 MUTATED     0   0   5   1
  DCTN5 WILD-TYPE   9  68 243  40
D756V4, multiclass
    clus
vv   DCTN5 MUTATED DCTN5 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             5             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
  DCTN5 MUTATED     5   1   0
  DCTN5 WILD-TYPE 215  79  66
D756V5, multiclass
    clus
vv   DCTN5 MUTATED DCTN5 WILD-TYPE
  N0             5             215
  N1             1              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
  DCTN5 MUTATED     3   1
  DCTN5 WILD-TYPE 280  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DCTN5 MUTATED      3    1
  DCTN5 WILD-TYPE  280   47
   clus
vv  DCTN5 MUTATED DCTN5 WILD-TYPE
  0             3             280
  1             1              47
[1] 2 2
[1] FALSE
D756V7, 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
D756V8, binary
                 cls
clus                0   1
  DCTN5 MUTATED     5   1
  DCTN5 WILD-TYPE 312  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DCTN5 MUTATED      5    1
  DCTN5 WILD-TYPE  312   47
                               clus
vv                              DCTN5 MUTATED DCTN5 WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  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 254   2  21  20
D756V9, multiclass
    clus
vv   DCTN5 MUTATED DCTN5 WILD-TYPE
  R0             3             254
  R1             0               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"
D756V10, 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
D756V11, 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(757) Variable = GABRA6 MUTATION ANALYSIS
D757V1, survival
                  sevent
clus2                0   1
  GABRA6 MUTATED    17   2
  GABRA6 WILD-TYPE 265  71
  GABRA6 MUTATED GABRA6 WILD-TYPE 
              19              336 
  GABRA6 MUTATED GABRA6 WILD-TYPE 
               2               71 
$`GABRA6 MUTATED`
TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3681 TCGA-AA-3715 TCGA-AA-3864 TCGA-AA-A010 
       63.98         6.97         5.98        19.04        53.00        34.98 
TCGA-AY-5543 TCGA-AZ-5407 TCGA-CK-6751 TCGA-CM-6164 TCGA-D5-6923 TCGA-D5-6928 
       15.75        61.41       124.27        29.03        12.43        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-DM-A285 TCGA-F4-6703 TCGA-G4-6304 TCGA-G4-6310 
        1.51        12.00         6.12        35.87        53.62        45.11 
TCGA-G4-6588 
       26.17 

$`GABRA6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       15.02        11.01        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 
        1.41         5.13        83.80        22.36        62.79        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14         2.93         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 
       16.01        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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-D5-6929 TCGA-D5-6932 
       10.13        14.30         9.04         9.44        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        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        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        51.75        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        52.80 

  GABRA6 MUTATED GABRA6 WILD-TYPE 
            1.51             0.00 
  GABRA6 MUTATED GABRA6 WILD-TYPE 
          124.27           140.38 
  GABRA6 MUTATED GABRA6 WILD-TYPE 
          26.170           20.155 
[1] "1.5 - 124.3 (26.2)" "0.0 - 140.4 (20.2)"
[1] "hr=" "2.6"
D757V2, 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       21       104         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GABRA6 MUTATED           1          0          1          1        1
  GABRA6 WILD-TYPE        18         10         40         30       34
                  vv
clus               STAGE IVA STAGE IVB
  GABRA6 MUTATED           1         0
  GABRA6 WILD-TYPE        12         1
D757V3, multiclass
            clus
vv           GABRA6 MUTATED GABRA6 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                4               21
  STAGE IIA               5              104
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              1               30
  STAGE IV                1               34
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 235  38
D757V4, multiclass
    clus
vv   GABRA6 MUTATED GABRA6 WILD-TYPE
  T1              1                8
  T2              2               66
  T3             13              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
  GABRA6 MUTATED    14   3   2
  GABRA6 WILD-TYPE 206  77  64
D757V5, multiclass
    clus
vv   GABRA6 MUTATED GABRA6 WILD-TYPE
  N0             14              206
  N1              3               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"
D757V6, binary
                  cls
clus                 0   1
  GABRA6 MUTATED    16   2
  GABRA6 WILD-TYPE 267  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GABRA6 MUTATED     16    2
  GABRA6 WILD-TYPE  267   46
   clus
vv  GABRA6 MUTATED GABRA6 WILD-TYPE
  0             16              267
  1              2               46
[1] 2 2
[1] FALSE
D757V7, 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
D757V8, binary
                  cls
clus                 0   1
  GABRA6 MUTATED    15   4
  GABRA6 WILD-TYPE 302  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GABRA6 MUTATED     15    4
  GABRA6 WILD-TYPE  302   44
                               clus
vv                              GABRA6 MUTATED GABRA6 WILD-TYPE
  COLON ADENOCARCINOMA                      15              302
  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 241   2  22  20
D757V9, multiclass
    clus
vv   GABRA6 MUTATED GABRA6 WILD-TYPE
  R0             16              241
  R1              0                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"
D757V10, 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
D757V11, 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(758) Variable = BAP1 MUTATION ANALYSIS
D758V1, survival
                sevent
clus2              0   1
  BAP1 MUTATED    13   3
  BAP1 WILD-TYPE 269  70
  BAP1 MUTATED BAP1 WILD-TYPE 
            16            339 
  BAP1 MUTATED BAP1 WILD-TYPE 
             3             70 
$`BAP1 MUTATED`
TCGA-A6-5662 TCGA-AA-3518 TCGA-AA-A010 TCGA-AU-6004 TCGA-AY-6196 TCGA-AZ-6599 
       23.61         1.02        34.98        27.09         0.20         6.77 
TCGA-AZ-6601 TCGA-CM-4743 TCGA-CM-5344 TCGA-CM-6161 TCGA-D5-5538 TCGA-D5-6928 
      100.01        23.05        22.03        15.02        12.26        11.64 
TCGA-DM-A282 TCGA-F4-6807 TCGA-G4-6588 TCGA-G4-6626 
      139.17        16.24        26.17        46.75 

$`BAP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        33.53        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        14.50        16.31         0.95        15.75        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       62.79        61.41        49.41        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
       21.99        21.14         2.93         2.01       124.27        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 
       16.01        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        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       135.65         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       29.59        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 
       35.80        91.79        52.80 

  BAP1 MUTATED BAP1 WILD-TYPE 
           0.2            0.0 
  BAP1 MUTATED BAP1 WILD-TYPE 
        139.17         140.38 
  BAP1 MUTATED BAP1 WILD-TYPE 
         22.54          20.12 
[1] "0.2 - 139.2 (22.5)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.3"
D758V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BAP1 MUTATED         4        0        1         6         1         0
  BAP1 WILD-TYPE      60        1       24       103         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BAP1 MUTATED           0          0          2          2        0         1
  BAP1 WILD-TYPE        19         10         39         29       35        12
                vv
clus             STAGE IVB
  BAP1 MUTATED           0
  BAP1 WILD-TYPE         1
D758V3, multiclass
            clus
vv           BAP1 MUTATED BAP1 WILD-TYPE
  STAGE I               4             60
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             6            103
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            2             39
  STAGE IIIC            2             29
  STAGE IV              0             35
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  BAP1 MUTATED     0   4  12   1
  BAP1 WILD-TYPE   9  64 236  40
D758V4, multiclass
    clus
vv   BAP1 MUTATED BAP1 WILD-TYPE
  T1            0              9
  T2            4             64
  T3           12            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
  BAP1 MUTATED    12   2   3
  BAP1 WILD-TYPE 208  78  63
D758V5, multiclass
    clus
vv   BAP1 MUTATED BAP1 WILD-TYPE
  N0           12            208
  N1            2             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"
D758V6, binary
                cls
clus               0   1
  BAP1 MUTATED    13   1
  BAP1 WILD-TYPE 270  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED     13    1
  BAP1 WILD-TYPE  270   47
   clus
vv  BAP1 MUTATED BAP1 WILD-TYPE
  0           13            270
  1            1             47
[1] 2 2
[1] FALSE
D758V7, binary
                cls
clus               0   1
  BAP1 MUTATED     9   8
  BAP1 WILD-TYPE 161 189
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED      9    8
  BAP1 WILD-TYPE  161  189
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  FEMALE            9            161
  MALE              8            189
[1] 2 2
[1] FALSE
D758V8, binary
                cls
clus               0   1
  BAP1 MUTATED    15   2
  BAP1 WILD-TYPE 302  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED     15    2
  BAP1 WILD-TYPE  302   46
                               clus
vv                              BAP1 MUTATED BAP1 WILD-TYPE
  COLON ADENOCARCINOMA                    15            302
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  BAP1 MUTATED    12   0   0   1
  BAP1 WILD-TYPE 245   2  22  20
D758V9, multiclass
    clus
vv   BAP1 MUTATED BAP1 WILD-TYPE
  R0           12            245
  R1            0              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"
D758V10, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BAP1 MUTATED                                  0     0
  BAP1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  BAP1 MUTATED                           0    15
  BAP1 WILD-TYPE                        19   161
D758V11, multiclass
                                  clus
vv                                 BAP1 MUTATED BAP1 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(759) Variable = ANKRD17 MUTATION ANALYSIS
D759V1, survival
                   sevent
clus2                 0   1
  ANKRD17 MUTATED    23   2
  ANKRD17 WILD-TYPE 259  71
  ANKRD17 MUTATED ANKRD17 WILD-TYPE 
               25               330 
  ANKRD17 MUTATED ANKRD17 WILD-TYPE 
                2                71 
$`ANKRD17 MUTATED`
TCGA-A6-5661 TCGA-A6-5666 TCGA-A6-6653 TCGA-AA-3510 TCGA-AA-3525 TCGA-AA-3715 
       33.53        32.71        24.39        63.98         8.05        19.04 
TCGA-AA-3833 TCGA-AA-3977 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A02W 
       15.95        25.02        18.05         4.01        34.98        41.00 
TCGA-AD-5900 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4952 TCGA-CK-6748 
        0.07        58.39         0.33         0.10        15.62         2.01 
TCGA-CM-4746 TCGA-CM-5860 TCGA-CM-5861 TCGA-D5-5539 TCGA-D5-6540 TCGA-F4-6856 
       37.02        16.01        15.02        19.59        16.14        19.43 
TCGA-G4-6309 
       51.75 

$`ANKRD17 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       24.16        21.76        24.69        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       37.05        36.03        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
        1.02        17.98        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       19.00        30.02        34.03        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
       14.01         0.92        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07         0.26         1.35        17.56       102.44        40.34 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 
       49.08        51.32        21.99        21.14         2.93       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-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-D5-5541 TCGA-D5-6529 
       12.03        45.40        12.26        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        35.41       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  ANKRD17 MUTATED ANKRD17 WILD-TYPE 
             0.07              0.00 
  ANKRD17 MUTATED ANKRD17 WILD-TYPE 
            63.98            140.38 
  ANKRD17 MUTATED ANKRD17 WILD-TYPE 
            19.04             20.98 
[1] "0.1 - 64.0 (19.0)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "2.4"
D759V2, 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       23       102         5         0
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANKRD17 MUTATED           1          1          3          0        1
  ANKRD17 WILD-TYPE        18          9         38         31       34
                   vv
clus                STAGE IVA STAGE IVB
  ANKRD17 MUTATED           0         0
  ANKRD17 WILD-TYPE        13         1
D759V3, multiclass
            clus
vv           ANKRD17 MUTATED ANKRD17 WILD-TYPE
  STAGE I                  6                58
  STAGE IA                 0                 1
  STAGE II                 2                23
  STAGE IIA                7               102
  STAGE IIB                3                 5
  STAGE IIC                1                 0
  STAGE III                1                18
  STAGE IIIA               1                 9
  STAGE IIIB               3                38
  STAGE IIIC               0                31
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ANKRD17 MUTATED     0   7  13   6
  ANKRD17 WILD-TYPE   9  61 235  35
D759V4, multiclass
    clus
vv   ANKRD17 MUTATED ANKRD17 WILD-TYPE
  T1               0                 9
  T2               7                61
  T3              13               235
  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  75  65
D759V5, multiclass
    clus
vv   ANKRD17 MUTATED ANKRD17 WILD-TYPE
  N0              20               200
  N1               5                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"
D759V6, binary
                   cls
clus                  0   1
  ANKRD17 MUTATED    22   1
  ANKRD17 WILD-TYPE 261  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD17 MUTATED     22    1
  ANKRD17 WILD-TYPE  261   47
   clus
vv  ANKRD17 MUTATED ANKRD17 WILD-TYPE
  0              22               261
  1               1                47
[1] 2 2
[1] FALSE
D759V7, 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
D759V8, binary
                   cls
clus                  0   1
  ANKRD17 MUTATED    17   9
  ANKRD17 WILD-TYPE 300  39
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD17 MUTATED     17    9
  ANKRD17 WILD-TYPE  300   39
                               clus
vv                              ANKRD17 MUTATED ANKRD17 WILD-TYPE
  COLON ADENOCARCINOMA                       17               300
  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 239   2  22  16
D759V9, multiclass
    clus
vv   ANKRD17 MUTATED ANKRD17 WILD-TYPE
  R0              18               239
  R1               0                 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"
D759V10, 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
D759V11, 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(760) Variable = STAU2 MUTATION ANALYSIS
D760V1, survival
                 sevent
clus2               0   1
  STAU2 MUTATED     8   1
  STAU2 WILD-TYPE 274  72
  STAU2 MUTATED STAU2 WILD-TYPE 
              9             346 
  STAU2 MUTATED STAU2 WILD-TYPE 
              1              72 
$`STAU2 MUTATED`
TCGA-AA-3821 TCGA-AA-A00A TCGA-AD-5900 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CK-5913 
        1.02        38.04         0.07        58.39         0.33        51.32 
TCGA-CK-5916 TCGA-F4-6460 TCGA-G4-6586 
       21.14        13.38        35.80 

$`STAU2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       49.08        21.99         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  STAU2 MUTATED STAU2 WILD-TYPE 
           0.07            0.00 
  STAU2 MUTATED STAU2 WILD-TYPE 
          58.39          140.38 
  STAU2 MUTATED STAU2 WILD-TYPE 
         21.140          20.155 
[1] "0.1 - 58.4 (21.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.8"
D760V2, 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       25       103         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        19         10         40         31       35        13
                 vv
clus              STAGE IVB
  STAU2 MUTATED           0
  STAU2 WILD-TYPE         1
D760V3, multiclass
            clus
vv           STAU2 MUTATED STAU2 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              6             103
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  STAU2 MUTATED     1   2   7   0
  STAU2 WILD-TYPE   8  66 241  41
D760V4, multiclass
    clus
vv   STAU2 MUTATED STAU2 WILD-TYPE
  T1             1               8
  T2             2              66
  T3             7             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
  STAU2 MUTATED     9   1   0
  STAU2 WILD-TYPE 211  79  66
D760V5, multiclass
    clus
vv   STAU2 MUTATED STAU2 WILD-TYPE
  N0             9             211
  N1             1              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"
D760V6, binary
                 cls
clus                0   1
  STAU2 MUTATED     8   0
  STAU2 WILD-TYPE 275  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAU2 MUTATED      8    0
  STAU2 WILD-TYPE  275   48
   clus
vv  STAU2 MUTATED STAU2 WILD-TYPE
  0             8             275
  1             0              48
[1] 2 2
[1] FALSE
D760V7, 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
D760V8, binary
                 cls
clus                0   1
  STAU2 MUTATED     7   3
  STAU2 WILD-TYPE 310  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAU2 MUTATED      7    3
  STAU2 WILD-TYPE  310   45
                               clus
vv                              STAU2 MUTATED STAU2 WILD-TYPE
  COLON ADENOCARCINOMA                      7             310
  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 250   2  22  18
D760V9, multiclass
    clus
vv   STAU2 MUTATED STAU2 WILD-TYPE
  R0             7             250
  R1             0               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"
D760V10, 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
D760V11, 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(761) Variable = ELFN2 MUTATION ANALYSIS
D761V1, survival
                 sevent
clus2               0   1
  ELFN2 MUTATED     8   1
  ELFN2 WILD-TYPE 274  72
  ELFN2 MUTATED ELFN2 WILD-TYPE 
              9             346 
  ELFN2 MUTATED ELFN2 WILD-TYPE 
              1              72 
$`ELFN2 MUTATED`
TCGA-AA-3979 TCGA-AD-6895 TCGA-CK-4947 TCGA-CM-5860 TCGA-D5-6533 TCGA-D5-6535 
       24.00         0.72        17.56        16.01         1.32        15.12 
TCGA-D5-6537 TCGA-D5-6927 TCGA-G4-6315 
        4.80         9.44        36.72 

$`ELFN2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        4.21        56.55         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 
        0.07         0.26         0.33         0.10         1.35       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       18.25        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-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04        11.64        13.41         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       51.75        45.11        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  ELFN2 MUTATED ELFN2 WILD-TYPE 
           0.72            0.00 
  ELFN2 MUTATED ELFN2 WILD-TYPE 
          36.72          140.38 
  ELFN2 MUTATED ELFN2 WILD-TYPE 
          15.12           20.98 
[1] "0.7 - 36.7 (15.1)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1"  
D761V2, 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       25       106         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ELFN2 MUTATED           0          0          3          0        1         1
  ELFN2 WILD-TYPE        19         10         38         31       34        12
                 vv
clus              STAGE IVB
  ELFN2 MUTATED           0
  ELFN2 WILD-TYPE         1
D761V3, multiclass
            clus
vv           ELFN2 MUTATED ELFN2 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              3             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             3              38
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  68 241  39
D761V4, multiclass
    clus
vv   ELFN2 MUTATED ELFN2 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             7             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
  ELFN2 MUTATED     4   5   0
  ELFN2 WILD-TYPE 216  75  66
D761V5, multiclass
    clus
vv   ELFN2 MUTATED ELFN2 WILD-TYPE
  N0             4             216
  N1             5              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"
D761V6, binary
                 cls
clus                0   1
  ELFN2 MUTATED     5   1
  ELFN2 WILD-TYPE 278  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ELFN2 MUTATED      5    1
  ELFN2 WILD-TYPE  278   47
   clus
vv  ELFN2 MUTATED ELFN2 WILD-TYPE
  0             5             278
  1             1              47
[1] 2 2
[1] FALSE
D761V7, 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
D761V8, binary
                 cls
clus                0   1
  ELFN2 MUTATED     9   0
  ELFN2 WILD-TYPE 308  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ELFN2 MUTATED      9    0
  ELFN2 WILD-TYPE  308   48
                               clus
vv                              ELFN2 MUTATED ELFN2 WILD-TYPE
  COLON ADENOCARCINOMA                      9             308
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ELFN2 MUTATED     6   0   0   2
  ELFN2 WILD-TYPE 251   2  22  19
D761V9, multiclass
    clus
vv   ELFN2 MUTATED ELFN2 WILD-TYPE
  R0             6             251
  R1             0               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"
D761V10, 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
D761V11, 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(762) Variable = TMEM45A MUTATION ANALYSIS
D762V1, survival
                   sevent
clus2                 0   1
  TMEM45A MUTATED     3   1
  TMEM45A WILD-TYPE 279  72
  TMEM45A MUTATED TMEM45A WILD-TYPE 
                4               351 
  TMEM45A MUTATED TMEM45A WILD-TYPE 
                1                72 
$`TMEM45A MUTATED`
TCGA-A6-6138 TCGA-AZ-6598 TCGA-G4-6323 TCGA-G4-6628 
       22.52        49.41        13.78        52.80 

$`TMEM45A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        32.71        27.09         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 
       51.75        45.11        36.72        36.00        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       26.17        91.79        46.75 

  TMEM45A MUTATED TMEM45A WILD-TYPE 
            13.78              0.00 
  TMEM45A MUTATED TMEM45A WILD-TYPE 
            52.80            140.38 
  TMEM45A MUTATED TMEM45A WILD-TYPE 
           35.965            20.120 
[1] "13.8 - 52.8 (36.0)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.2"
D762V2, 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       24       109         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM45A MUTATED           0          0          0          0        0
  TMEM45A WILD-TYPE        19         10         41         31       35
                   vv
clus                STAGE IVA STAGE IVB
  TMEM45A MUTATED           0         0
  TMEM45A WILD-TYPE        13         1
D762V3, multiclass
            clus
vv           TMEM45A MUTATED TMEM45A WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 1                 0
  STAGE II                 1                24
  STAGE IIA                0               109
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TMEM45A MUTATED     0   2   1   0
  TMEM45A WILD-TYPE   9  66 247  41
D762V4, multiclass
    clus
vv   TMEM45A MUTATED TMEM45A WILD-TYPE
  T1               0                 9
  T2               2                66
  T3               1               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
  TMEM45A MUTATED     4   0   0
  TMEM45A WILD-TYPE 216  80  66
D762V5, multiclass
    clus
vv   TMEM45A MUTATED TMEM45A WILD-TYPE
  N0               4               216
  N1               0                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"
D762V6, binary
                   cls
clus                  0   1
  TMEM45A MUTATED     2   0
  TMEM45A WILD-TYPE 281  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM45A MUTATED      2    0
  TMEM45A WILD-TYPE  281   48
   clus
vv  TMEM45A MUTATED TMEM45A WILD-TYPE
  0               2               281
  1               0                48
[1] 2 2
[1] FALSE
D762V7, 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
D762V8, binary
                   cls
clus                  0   1
  TMEM45A MUTATED     4   0
  TMEM45A WILD-TYPE 313  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM45A MUTATED      4    0
  TMEM45A WILD-TYPE  313   48
                               clus
vv                              TMEM45A MUTATED TMEM45A WILD-TYPE
  COLON ADENOCARCINOMA                        4               313
  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 255   2  22  21
D762V9, multiclass
[1] "Remove cluster labels:" "TMEM45A MUTATED"       
clus
  TMEM45A MUTATED TMEM45A WILD-TYPE 
                2               300 
       TCGA-A6-2671        TCGA-A6-2672        TCGA-A6-2674        TCGA-A6-2676 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-A6-2677        TCGA-A6-2678        TCGA-A6-2683        TCGA-A6-3807 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-A6-3808        TCGA-A6-3809        TCGA-A6-3810        TCGA-A6-5657 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-A6-5659        TCGA-A6-5661        TCGA-A6-5665        TCGA-A6-6781 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3489        TCGA-AA-3492        TCGA-AA-3496        TCGA-AA-3502 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3510        TCGA-AA-3511        TCGA-AA-3514        TCGA-AA-3517 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3518        TCGA-AA-3519        TCGA-AA-3520        TCGA-AA-3521 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3522        TCGA-AA-3524        TCGA-AA-3525        TCGA-AA-3526 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3527        TCGA-AA-3529        TCGA-AA-3530        TCGA-AA-3531 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3532        TCGA-AA-3534        TCGA-AA-3538        TCGA-AA-3542 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3543        TCGA-AA-3544        TCGA-AA-3548        TCGA-AA-3549 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3552        TCGA-AA-3553        TCGA-AA-3554        TCGA-AA-3555 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3556        TCGA-AA-3558        TCGA-AA-3560        TCGA-AA-3561 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3562        TCGA-AA-3655        TCGA-AA-3660        TCGA-AA-3662 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3663        TCGA-AA-3664        TCGA-AA-3666        TCGA-AA-3667 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3672        TCGA-AA-3673        TCGA-AA-3678        TCGA-AA-3679 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3680        TCGA-AA-3681        TCGA-AA-3684        TCGA-AA-3685 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3688        TCGA-AA-3692        TCGA-AA-3693        TCGA-AA-3695 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3696        TCGA-AA-3697        TCGA-AA-3710        TCGA-AA-3712 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3713        TCGA-AA-3715        TCGA-AA-3811        TCGA-AA-3812 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3814        TCGA-AA-3815        TCGA-AA-3818        TCGA-AA-3819 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3821        TCGA-AA-3831        TCGA-AA-3833        TCGA-AA-3837 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3842        TCGA-AA-3844        TCGA-AA-3845        TCGA-AA-3846 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3848        TCGA-AA-3850        TCGA-AA-3851        TCGA-AA-3852 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3854        TCGA-AA-3855        TCGA-AA-3856        TCGA-AA-3858 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3860        TCGA-AA-3861        TCGA-AA-3864        TCGA-AA-3866 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3867        TCGA-AA-3869        TCGA-AA-3870        TCGA-AA-3872 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3875        TCGA-AA-3877        TCGA-AA-3930        TCGA-AA-3939 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3941        TCGA-AA-3947        TCGA-AA-3949        TCGA-AA-3950 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3952        TCGA-AA-3955        TCGA-AA-3956        TCGA-AA-3968 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3971        TCGA-AA-3972        TCGA-AA-3973        TCGA-AA-3975 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3976        TCGA-AA-3979        TCGA-AA-3984        TCGA-AA-3986 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3989        TCGA-AA-3994        TCGA-AA-A004        TCGA-AA-A00A 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-A00D        TCGA-AA-A00E        TCGA-AA-A00F        TCGA-AA-A00J 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-A00K        TCGA-AA-A00L        TCGA-AA-A00N        TCGA-AA-A00O 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-A00Q        TCGA-AA-A00R        TCGA-AA-A00U        TCGA-AA-A00W 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-A00Z        TCGA-AA-A010        TCGA-AA-A017        TCGA-AA-A01D 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-A01F        TCGA-AA-A01G        TCGA-AA-A01I        TCGA-AA-A01K 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-A01P        TCGA-AA-A01Q        TCGA-AA-A01R        TCGA-AA-A01S 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-A01T        TCGA-AA-A01V        TCGA-AA-A01X        TCGA-AA-A01Z 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-A022        TCGA-AA-A024        TCGA-AA-A029        TCGA-AA-A02F 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-A02H        TCGA-AA-A02J        TCGA-AA-A02K        TCGA-AA-A02O 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-A02W        TCGA-AA-A02Y        TCGA-AA-A03F        TCGA-AA-A03J 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AD-5900        TCGA-AD-6548        TCGA-AD-6888        TCGA-AU-3779 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AU-6004        TCGA-AY-4070        TCGA-AY-4071        TCGA-AY-5543 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AY-6196        TCGA-AY-6197        TCGA-AY-6386        TCGA-AZ-4315 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AZ-4681        TCGA-AZ-4682        TCGA-CA-5254        TCGA-CA-5255 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-CA-5796        TCGA-CA-5797        TCGA-CA-6715        TCGA-CA-6716 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-CA-6717        TCGA-CA-6718        TCGA-CA-6719        TCGA-CK-4947 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-CK-4948        TCGA-CK-4950        TCGA-CK-4952        TCGA-CK-5912 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-CK-5913        TCGA-CK-5914        TCGA-CK-5915        TCGA-CK-5916 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-CK-6746        TCGA-CK-6747        TCGA-CK-6748        TCGA-CK-6751 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-CM-4743        TCGA-CM-4744        TCGA-CM-4746        TCGA-CM-4747 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-CM-4752        TCGA-CM-5341        TCGA-CM-5344        TCGA-CM-5348 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-CM-5349        TCGA-CM-5860        TCGA-CM-5861        TCGA-CM-5862 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-CM-5863        TCGA-CM-5864        TCGA-CM-5868        TCGA-CM-6161 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-CM-6162        TCGA-CM-6163        TCGA-CM-6164        TCGA-CM-6165 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-CM-6166        TCGA-CM-6167        TCGA-CM-6168        TCGA-CM-6169 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-CM-6170        TCGA-CM-6171        TCGA-CM-6172        TCGA-CM-6674 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-CM-6675        TCGA-CM-6676        TCGA-CM-6677        TCGA-CM-6678 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-CM-6679        TCGA-CM-6680        TCGA-D5-5537        TCGA-D5-5538 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-D5-5539        TCGA-D5-5540        TCGA-D5-5541        TCGA-D5-6529 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-D5-6532        TCGA-D5-6533        TCGA-D5-6534        TCGA-D5-6535 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-D5-6536        TCGA-D5-6537        TCGA-D5-6538        TCGA-D5-6539 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-D5-6540        TCGA-D5-6541        TCGA-D5-6898        TCGA-D5-6920 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-D5-6922        TCGA-D5-6923        TCGA-D5-6924        TCGA-D5-6926 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-D5-6927        TCGA-D5-6928        TCGA-D5-6929        TCGA-D5-6930 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-D5-6931        TCGA-D5-6932        TCGA-D5-7000        TCGA-F4-6459 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-F4-6460        TCGA-F4-6569        TCGA-F4-6570        TCGA-F4-6703 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-F4-6704        TCGA-F4-6805        TCGA-F4-6806        TCGA-F4-6807 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-F4-6808        TCGA-F4-6809        TCGA-F4-6854        TCGA-F4-6855 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-F4-6856        TCGA-G4-6293        TCGA-G4-6299        TCGA-G4-6303 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-G4-6304        TCGA-G4-6306        TCGA-G4-6307        TCGA-G4-6309 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-G4-6310        TCGA-G4-6315        TCGA-G4-6317        TCGA-G4-6321 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-G4-6586        TCGA-G4-6588        TCGA-G4-6625        TCGA-G4-6626 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
D762V10, 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
D762V11, 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(763) Variable = ASB11 MUTATION ANALYSIS
D763V1, survival
                 sevent
clus2               0   1
  ASB11 MUTATED     6   1
  ASB11 WILD-TYPE 276  72
  ASB11 MUTATED ASB11 WILD-TYPE 
              7             348 
  ASB11 MUTATED ASB11 WILD-TYPE 
              1              72 
$`ASB11 MUTATED`
TCGA-A6-5665 TCGA-AD-6901 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CK-5913 TCGA-F4-6856 
       22.06        22.42        58.39         0.33        51.32        19.43 
TCGA-G4-6628 
       52.80 

$`ASB11 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 
        4.21        56.55         0.79         0.72         5.79        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        35.41       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 

  ASB11 MUTATED ASB11 WILD-TYPE 
           0.33            0.00 
  ASB11 MUTATED ASB11 WILD-TYPE 
          58.39          140.38 
  ASB11 MUTATED ASB11 WILD-TYPE 
          22.42           20.07 
[1] "0.3 - 58.4 (22.4)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "2"  
D763V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ASB11 MUTATED         2        0        0         4         0         0
  ASB11 WILD-TYPE      62        1       25       105         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        19         10         41         31       35        13
                 vv
clus              STAGE IVB
  ASB11 MUTATED           0
  ASB11 WILD-TYPE         1
D763V3, multiclass
            clus
vv           ASB11 MUTATED ASB11 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              4             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ASB11 MUTATED     0   2   5   0
  ASB11 WILD-TYPE   9  66 243  41
D763V4, multiclass
    clus
vv   ASB11 MUTATED ASB11 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             5             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     7   0   0
  ASB11 WILD-TYPE 213  80  66
D763V5, multiclass
    clus
vv   ASB11 MUTATED ASB11 WILD-TYPE
  N0             7             213
  N1             0              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"
D763V6, binary
                 cls
clus                0   1
  ASB11 MUTATED     5   0
  ASB11 WILD-TYPE 278  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASB11 MUTATED      5    0
  ASB11 WILD-TYPE  278   48
   clus
vv  ASB11 MUTATED ASB11 WILD-TYPE
  0             5             278
  1             0              48
[1] 2 2
[1] FALSE
D763V7, binary
                 cls
clus                0   1
  ASB11 MUTATED     2   5
  ASB11 WILD-TYPE 168 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASB11 MUTATED      2    5
  ASB11 WILD-TYPE  168  192
        clus
vv       ASB11 MUTATED ASB11 WILD-TYPE
  FEMALE             2             168
  MALE               5             192
[1] 2 2
[1] FALSE
D763V8, binary
                 cls
clus                0   1
  ASB11 MUTATED     5   2
  ASB11 WILD-TYPE 312  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASB11 MUTATED      5    2
  ASB11 WILD-TYPE  312   46
                               clus
vv                              ASB11 MUTATED ASB11 WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ASB11 MUTATED     4   0   0   2
  ASB11 WILD-TYPE 253   2  22  19
D763V9, multiclass
    clus
vv   ASB11 MUTATED ASB11 WILD-TYPE
  R0             4             253
  R1             0               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"
D763V10, 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     6
  ASB11 WILD-TYPE                        19   170
D763V11, 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                                        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(764) Variable = NEB MUTATION ANALYSIS
D764V1, survival
               sevent
clus2             0   1
  NEB MUTATED    35  20
  NEB WILD-TYPE 247  53
  NEB MUTATED NEB WILD-TYPE 
           55           300 
  NEB MUTATED NEB WILD-TYPE 
           20            53 
$`NEB MUTATED`
TCGA-A6-3810 TCGA-A6-5661 TCGA-A6-6141 TCGA-A6-6653 TCGA-A6-6654 TCGA-AA-3496 
       36.53        33.53         8.38        24.39        23.87         1.02 
TCGA-AA-3510 TCGA-AA-3655 TCGA-AA-3672 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       63.98        61.02         0.92        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
       10.06         0.00        10.06        33.01        26.01         2.01 
TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-6964 
        2.01        25.02         4.01        34.98        35.01        10.88 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       21.44        58.39        62.79        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4948 
      100.01        11.74         3.19         0.33         0.10       102.44 
TCGA-CK-5912 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-6162 
       49.08         2.93       124.27        22.98        16.01        12.00 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6537 TCGA-D5-6538 TCGA-DM-A1D6 TCGA-DM-A1D7 
       20.19        18.25         4.80        17.13        49.91        13.32 
TCGA-DM-A1DA TCGA-DM-A28F TCGA-G4-6293 TCGA-G4-6309 TCGA-G4-6321 TCGA-G4-6588 
        7.50        35.97       107.67        51.75        22.09        26.17 
TCGA-G4-6628 
       52.80 

$`NEB WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       32.71        27.09        22.52        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 
       21.76        24.69        20.12        19.66        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        3.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       85.05        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
       17.98        15.95        38.99        37.02        14.93        17.03 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00        24.00        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       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        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        15.75         0.20        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6603 TCGA-AZ-6605 
        5.13        83.80        22.36        61.41        29.56         5.23 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 
        0.26         1.35        17.56        40.34        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.99        21.14         2.01        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-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       19.59        13.51        11.51         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.85        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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D8 TCGA-DM-A1D9 
       24.43        38.20       130.65        92.75        12.59       140.38 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
      119.93        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       74.56        65.85        53.62        44.68        55.04        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.72        36.00        13.78        35.80        91.79        46.75 

  NEB MUTATED NEB WILD-TYPE 
            0             0 
  NEB MUTATED NEB WILD-TYPE 
       124.27        140.38 
  NEB MUTATED NEB WILD-TYPE 
        21.44         20.07 
[1] "0.0 - 124.3 (21.4)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.8"
D764V2, 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       18        91         5         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NEB MUTATED           6          1          8          3        4         0
  NEB WILD-TYPE        13          9         33         28       31        13
               vv
clus            STAGE IVB
  NEB MUTATED           0
  NEB WILD-TYPE         1
D764V3, multiclass
            clus
vv           NEB MUTATED NEB WILD-TYPE
  STAGE I              5            59
  STAGE IA             0             1
  STAGE II             7            18
  STAGE IIA           18            91
  STAGE IIB            3             5
  STAGE IIC            0             1
  STAGE III            6            13
  STAGE IIIA           1             9
  STAGE IIIB           8            33
  STAGE IIIC           3            28
  STAGE IV             4            31
  STAGE IVA            0            13
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  NEB MUTATED     0   7  43   7
  NEB WILD-TYPE   9  61 205  34
D764V4, multiclass
    clus
vv   NEB MUTATED NEB WILD-TYPE
  T1           0             9
  T2           7            61
  T3          43           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
  NEB MUTATED    35  12  10
  NEB WILD-TYPE 185  68  56
D764V5, multiclass
    clus
vv   NEB MUTATED NEB WILD-TYPE
  N0          35           185
  N1          12            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"
D764V6, binary
               cls
clus              0   1
  NEB MUTATED    42   4
  NEB WILD-TYPE 241  44
[1] "tbl2"
               cls
clus            [,1] [,2]
  NEB MUTATED     42    4
  NEB WILD-TYPE  241   44
   clus
vv  NEB MUTATED NEB WILD-TYPE
  0          42           241
  1           4            44
[1] 2 2
[1] FALSE
D764V7, 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
D764V8, binary
               cls
clus              0   1
  NEB MUTATED    48   9
  NEB WILD-TYPE 269  39
[1] "tbl2"
               cls
clus            [,1] [,2]
  NEB MUTATED     48    9
  NEB WILD-TYPE  269   39
                               clus
vv                              NEB MUTATED NEB WILD-TYPE
  COLON ADENOCARCINOMA                   48           269
  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 223   2  21  16
D764V9, multiclass
    clus
vv   NEB MUTATED NEB WILD-TYPE
  R0          34           223
  R1           0             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"
D764V10, 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
D764V11, 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(765) Variable = ZNF691 MUTATION ANALYSIS
D765V1, survival
                  sevent
clus2                0   1
  ZNF691 MUTATED     5   2
  ZNF691 WILD-TYPE 277  71
  ZNF691 MUTATED ZNF691 WILD-TYPE 
               7              348 
  ZNF691 MUTATED ZNF691 WILD-TYPE 
               2               71 
$`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 
       36.72 

$`ZNF691 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        1.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      102.44        40.34        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        43.27        15.12         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A285 
      140.38         7.50        44.32       131.51       135.65         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        51.75        45.11        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  ZNF691 MUTATED ZNF691 WILD-TYPE 
           13.02             0.00 
  ZNF691 MUTATED ZNF691 WILD-TYPE 
          139.17           140.38 
  ZNF691 MUTATED ZNF691 WILD-TYPE 
          23.050           20.155 
[1] "13.0 - 139.2 (23.1)" "0.0 - 140.4 (20.2)" 
[1] "hr=" "1.1"
D765V2, 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       24       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF691 MUTATED           2          0          0          0        1
  ZNF691 WILD-TYPE        17         10         41         31       34
                  vv
clus               STAGE IVA STAGE IVB
  ZNF691 MUTATED           0         0
  ZNF691 WILD-TYPE        13         1
D765V3, multiclass
            clus
vv           ZNF691 MUTATED ZNF691 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               3              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               2               17
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF691 MUTATED     0   0   6   1
  ZNF691 WILD-TYPE   9  68 242  40
D765V4, multiclass
    clus
vv   ZNF691 MUTATED ZNF691 WILD-TYPE
  T1              0                9
  T2              0               68
  T3              6              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
  ZNF691 MUTATED     4   1   2
  ZNF691 WILD-TYPE 216  79  64
D765V5, multiclass
    clus
vv   ZNF691 MUTATED ZNF691 WILD-TYPE
  N0              4              216
  N1              1               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"
D765V6, binary
                  cls
clus                 0   1
  ZNF691 MUTATED     5   1
  ZNF691 WILD-TYPE 278  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF691 MUTATED      5    1
  ZNF691 WILD-TYPE  278   47
   clus
vv  ZNF691 MUTATED ZNF691 WILD-TYPE
  0              5              278
  1              1               47
[1] 2 2
[1] FALSE
D765V7, 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
D765V8, binary
                  cls
clus                 0   1
  ZNF691 MUTATED     5   2
  ZNF691 WILD-TYPE 312  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF691 MUTATED      5    2
  ZNF691 WILD-TYPE  312   46
                               clus
vv                              ZNF691 MUTATED ZNF691 WILD-TYPE
  COLON ADENOCARCINOMA                       5              312
  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 254   2  22  20
D765V9, multiclass
    clus
vv   ZNF691 MUTATED ZNF691 WILD-TYPE
  R0              3              254
  R1              0                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"
D765V10, 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
D765V11, 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(766) Variable = ODAM MUTATION ANALYSIS
D766V1, survival
                sevent
clus2              0   1
  ODAM MUTATED     4   1
  ODAM WILD-TYPE 278  72
  ODAM MUTATED ODAM WILD-TYPE 
             5            350 
  ODAM MUTATED ODAM WILD-TYPE 
             1             72 
$`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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 
       10.26       119.70        24.43        38.20       130.65        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  ODAM MUTATED ODAM WILD-TYPE 
         22.98           0.00 
  ODAM MUTATED ODAM WILD-TYPE 
        117.07         140.38 
  ODAM MUTATED ODAM WILD-TYPE 
        44.680         20.005 
[1] "23.0 - 117.1 (44.7)" "0.0 - 140.4 (20.0)" 
[1] "hr=" "2.3"
D766V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ODAM MUTATED         0        0        0         2         0         0
  ODAM WILD-TYPE      64        1       25       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        19         10         40         30       35        13
                vv
clus             STAGE IVB
  ODAM MUTATED           0
  ODAM WILD-TYPE         1
D766V3, multiclass
            clus
vv           ODAM MUTATED ODAM WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             2            107
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            1             30
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ODAM MUTATED     0   2   3   0
  ODAM WILD-TYPE   9  66 245  41
D766V4, multiclass
    clus
vv   ODAM MUTATED ODAM WILD-TYPE
  T1            0              9
  T2            2             66
  T3            3            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
  ODAM MUTATED     3   1   1
  ODAM WILD-TYPE 217  79  65
D766V5, multiclass
    clus
vv   ODAM MUTATED ODAM WILD-TYPE
  N0            3            217
  N1            1             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"
D766V6, binary
                cls
clus               0   1
  ODAM MUTATED     4   0
  ODAM WILD-TYPE 279  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  ODAM MUTATED      4    0
  ODAM WILD-TYPE  279   48
   clus
vv  ODAM MUTATED ODAM WILD-TYPE
  0            4            279
  1            0             48
[1] 2 2
[1] FALSE
D766V7, 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
D766V8, binary
                cls
clus               0   1
  ODAM MUTATED     5   0
  ODAM WILD-TYPE 312  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  ODAM MUTATED      5    0
  ODAM WILD-TYPE  312   48
                               clus
vv                              ODAM MUTATED ODAM WILD-TYPE
  COLON ADENOCARCINOMA                     5            312
  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 255   2  22  21
D766V9, multiclass
[1] "Remove cluster labels:" "ODAM MUTATED"          
clus
  ODAM MUTATED ODAM WILD-TYPE 
             2            300 
    TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810     TCGA-A6-5657 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-A6-5659     TCGA-A6-5661     TCGA-A6-5665     TCGA-A6-6781 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3489     TCGA-AA-3492     TCGA-AA-3496     TCGA-AA-3502 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3510     TCGA-AA-3511     TCGA-AA-3514     TCGA-AA-3517 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3518     TCGA-AA-3519     TCGA-AA-3520     TCGA-AA-3521 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3522     TCGA-AA-3524     TCGA-AA-3525     TCGA-AA-3526 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3527     TCGA-AA-3529     TCGA-AA-3530     TCGA-AA-3531 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3532     TCGA-AA-3534     TCGA-AA-3538     TCGA-AA-3542 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3543     TCGA-AA-3544     TCGA-AA-3548     TCGA-AA-3549 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3552     TCGA-AA-3553     TCGA-AA-3554     TCGA-AA-3555 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3556     TCGA-AA-3558     TCGA-AA-3560     TCGA-AA-3561 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3562     TCGA-AA-3655     TCGA-AA-3660     TCGA-AA-3662 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3663     TCGA-AA-3664     TCGA-AA-3666     TCGA-AA-3667 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3672     TCGA-AA-3673     TCGA-AA-3678     TCGA-AA-3679 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3680     TCGA-AA-3681     TCGA-AA-3684     TCGA-AA-3685 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3688     TCGA-AA-3692     TCGA-AA-3693     TCGA-AA-3695 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3696     TCGA-AA-3697     TCGA-AA-3710     TCGA-AA-3712 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3713     TCGA-AA-3715     TCGA-AA-3811     TCGA-AA-3812 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3814     TCGA-AA-3815     TCGA-AA-3818     TCGA-AA-3819 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3821     TCGA-AA-3831     TCGA-AA-3833     TCGA-AA-3837 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3842     TCGA-AA-3844     TCGA-AA-3845     TCGA-AA-3846 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3848     TCGA-AA-3850     TCGA-AA-3851     TCGA-AA-3852 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3854     TCGA-AA-3855     TCGA-AA-3856     TCGA-AA-3858 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3860     TCGA-AA-3861     TCGA-AA-3864     TCGA-AA-3866 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3867     TCGA-AA-3869     TCGA-AA-3870     TCGA-AA-3872 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3875     TCGA-AA-3877     TCGA-AA-3930     TCGA-AA-3939 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3941     TCGA-AA-3947     TCGA-AA-3949     TCGA-AA-3950 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3952     TCGA-AA-3955     TCGA-AA-3956     TCGA-AA-3968 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3971     TCGA-AA-3972     TCGA-AA-3973     TCGA-AA-3975 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3976     TCGA-AA-3979     TCGA-AA-3984     TCGA-AA-3986 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3989     TCGA-AA-3994     TCGA-AA-A004     TCGA-AA-A00A 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-A00D     TCGA-AA-A00E     TCGA-AA-A00F     TCGA-AA-A00J 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-A00K     TCGA-AA-A00L     TCGA-AA-A00N     TCGA-AA-A00O 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-A00Q     TCGA-AA-A00R     TCGA-AA-A00U     TCGA-AA-A00W 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-A00Z     TCGA-AA-A010     TCGA-AA-A017     TCGA-AA-A01D 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-A01F     TCGA-AA-A01G     TCGA-AA-A01I     TCGA-AA-A01K 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-A01P     TCGA-AA-A01Q     TCGA-AA-A01R     TCGA-AA-A01S 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-A01T     TCGA-AA-A01V     TCGA-AA-A01X     TCGA-AA-A01Z 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-A022     TCGA-AA-A024     TCGA-AA-A029     TCGA-AA-A02F 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-A02H     TCGA-AA-A02J     TCGA-AA-A02K     TCGA-AA-A02O 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-A02W     TCGA-AA-A02Y     TCGA-AA-A03F     TCGA-AA-A03J 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AD-5900     TCGA-AD-6548     TCGA-AD-6888     TCGA-AU-3779 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AU-6004     TCGA-AY-4070     TCGA-AY-4071     TCGA-AY-5543 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AY-6196     TCGA-AY-6197     TCGA-AY-6386     TCGA-AZ-4315 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AZ-4681     TCGA-AZ-4682     TCGA-CA-5254     TCGA-CA-5255 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-CA-5796     TCGA-CA-5797     TCGA-CA-6715     TCGA-CA-6716 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-CA-6717     TCGA-CA-6718     TCGA-CA-6719     TCGA-CK-4947 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-CK-4948     TCGA-CK-4950     TCGA-CK-4952     TCGA-CK-5912 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-CK-5913     TCGA-CK-5914     TCGA-CK-5915     TCGA-CK-5916 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-CK-6746     TCGA-CK-6747     TCGA-CK-6748     TCGA-CK-6751 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-CM-4743     TCGA-CM-4744     TCGA-CM-4746     TCGA-CM-4747 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-CM-4752     TCGA-CM-5341     TCGA-CM-5344     TCGA-CM-5349 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-CM-5860     TCGA-CM-5861     TCGA-CM-5862     TCGA-CM-5863 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-CM-5864     TCGA-CM-5868     TCGA-CM-6161     TCGA-CM-6162 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-CM-6163     TCGA-CM-6164     TCGA-CM-6165     TCGA-CM-6166 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-CM-6167     TCGA-CM-6168     TCGA-CM-6169     TCGA-CM-6170 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-CM-6171     TCGA-CM-6172     TCGA-CM-6674     TCGA-CM-6675 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-CM-6676     TCGA-CM-6677     TCGA-CM-6678     TCGA-CM-6679 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-CM-6680     TCGA-D5-5537     TCGA-D5-5538     TCGA-D5-5539 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-D5-5540     TCGA-D5-5541     TCGA-D5-6529     TCGA-D5-6532 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-D5-6533     TCGA-D5-6534     TCGA-D5-6535     TCGA-D5-6536 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-D5-6537     TCGA-D5-6538     TCGA-D5-6539     TCGA-D5-6540 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-D5-6541     TCGA-D5-6898     TCGA-D5-6920     TCGA-D5-6922 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-D5-6923     TCGA-D5-6924     TCGA-D5-6926     TCGA-D5-6927 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-D5-6928     TCGA-D5-6929     TCGA-D5-6930     TCGA-D5-6931 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-D5-6932     TCGA-D5-7000     TCGA-F4-6459     TCGA-F4-6460 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-F4-6569     TCGA-F4-6570     TCGA-F4-6703     TCGA-F4-6704 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-F4-6805     TCGA-F4-6806     TCGA-F4-6807     TCGA-F4-6808 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-F4-6809     TCGA-F4-6854     TCGA-F4-6855     TCGA-F4-6856 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-G4-6293     TCGA-G4-6299     TCGA-G4-6303     TCGA-G4-6304 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-G4-6307     TCGA-G4-6309     TCGA-G4-6310     TCGA-G4-6315 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-G4-6317     TCGA-G4-6321     TCGA-G4-6323     TCGA-G4-6586 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-G4-6588     TCGA-G4-6625     TCGA-G4-6626     TCGA-G4-6628 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
D766V10, 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
D766V11, 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(767) Variable = C12ORF49 MUTATION ANALYSIS
D767V1, survival
                    sevent
clus2                  0   1
  C12ORF49 MUTATED     1   3
  C12ORF49 WILD-TYPE 281  70
  C12ORF49 MUTATED C12ORF49 WILD-TYPE 
                 4                351 
  C12ORF49 MUTATED C12ORF49 WILD-TYPE 
                 3                 70 
$`C12ORF49 MUTATED`
TCGA-AA-3663 TCGA-AZ-6598 TCGA-DM-A1DA TCGA-G4-6626 
        6.97        49.41         7.50        46.75 

$`C12ORF49 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       26.17        91.79        52.80 

  C12ORF49 MUTATED C12ORF49 WILD-TYPE 
              6.97               0.00 
  C12ORF49 MUTATED C12ORF49 WILD-TYPE 
             49.41             140.38 
  C12ORF49 MUTATED C12ORF49 WILD-TYPE 
            27.125             20.190 
[1] "7.0 - 49.4 (27.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "3.1"
D767V2, 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       23       108         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C12ORF49 MUTATED           0          0          0          1        0
  C12ORF49 WILD-TYPE        19         10         41         30       35
                    vv
clus                 STAGE IVA STAGE IVB
  C12ORF49 MUTATED           0         0
  C12ORF49 WILD-TYPE        13         1
D767V3, multiclass
            clus
vv           C12ORF49 MUTATED C12ORF49 WILD-TYPE
  STAGE I                   0                 64
  STAGE IA                  0                  1
  STAGE II                  2                 23
  STAGE IIA                 1                108
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                0                 10
  STAGE IIIB                0                 41
  STAGE IIIC                1                 30
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C12ORF49 MUTATED     0   0   4   0
  C12ORF49 WILD-TYPE   9  68 244  41
D767V4, multiclass
    clus
vv   C12ORF49 MUTATED C12ORF49 WILD-TYPE
  T1                0                  9
  T2                0                 68
  T3                4                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
  C12ORF49 MUTATED     3   0   1
  C12ORF49 WILD-TYPE 217  80  65
D767V5, multiclass
    clus
vv   C12ORF49 MUTATED C12ORF49 WILD-TYPE
  N0                3                217
  N1                0                 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"
D767V6, binary
                    cls
clus                   0   1
  C12ORF49 MUTATED     3   0
  C12ORF49 WILD-TYPE 280  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF49 MUTATED      3    0
  C12ORF49 WILD-TYPE  280   48
   clus
vv  C12ORF49 MUTATED C12ORF49 WILD-TYPE
  0                3                280
  1                0                 48
[1] 2 2
[1] FALSE
D767V7, 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
D767V8, binary
                    cls
clus                   0   1
  C12ORF49 MUTATED     4   0
  C12ORF49 WILD-TYPE 313  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF49 MUTATED      4    0
  C12ORF49 WILD-TYPE  313   48
                               clus
vv                              C12ORF49 MUTATED C12ORF49 WILD-TYPE
  COLON ADENOCARCINOMA                         4                313
  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 255   2  22  21
D767V9, multiclass
[1] "Remove cluster labels:" "C12ORF49 MUTATED"      
clus
  C12ORF49 MUTATED C12ORF49 WILD-TYPE 
                 2                300 
        TCGA-A6-2671         TCGA-A6-2672         TCGA-A6-2674 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-A6-2676         TCGA-A6-2677         TCGA-A6-2678 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-A6-2683         TCGA-A6-3807         TCGA-A6-3808 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-A6-3809         TCGA-A6-3810         TCGA-A6-5657 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-A6-5659         TCGA-A6-5661         TCGA-A6-5665 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-A6-6781         TCGA-AA-3489         TCGA-AA-3492 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3496         TCGA-AA-3502         TCGA-AA-3510 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3511         TCGA-AA-3514         TCGA-AA-3517 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3518         TCGA-AA-3519         TCGA-AA-3520 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3521         TCGA-AA-3522         TCGA-AA-3524 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3525         TCGA-AA-3526         TCGA-AA-3527 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3529         TCGA-AA-3530         TCGA-AA-3531 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3532         TCGA-AA-3534         TCGA-AA-3538 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3542         TCGA-AA-3543         TCGA-AA-3544 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3548         TCGA-AA-3549         TCGA-AA-3552 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3553         TCGA-AA-3554         TCGA-AA-3555 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3556         TCGA-AA-3558         TCGA-AA-3560 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3561         TCGA-AA-3562         TCGA-AA-3655 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3660         TCGA-AA-3662         TCGA-AA-3664 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3666         TCGA-AA-3667         TCGA-AA-3672 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3673         TCGA-AA-3678         TCGA-AA-3679 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3680         TCGA-AA-3681         TCGA-AA-3684 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3685         TCGA-AA-3688         TCGA-AA-3692 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3693         TCGA-AA-3695         TCGA-AA-3696 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3697         TCGA-AA-3710         TCGA-AA-3712 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3713         TCGA-AA-3715         TCGA-AA-3811 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3812         TCGA-AA-3814         TCGA-AA-3815 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3818         TCGA-AA-3819         TCGA-AA-3821 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3831         TCGA-AA-3833         TCGA-AA-3837 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3842         TCGA-AA-3844         TCGA-AA-3845 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3846         TCGA-AA-3848         TCGA-AA-3850 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3851         TCGA-AA-3852         TCGA-AA-3854 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3855         TCGA-AA-3856         TCGA-AA-3858 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3860         TCGA-AA-3861         TCGA-AA-3864 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3866         TCGA-AA-3867         TCGA-AA-3869 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3870         TCGA-AA-3872         TCGA-AA-3875 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3877         TCGA-AA-3930         TCGA-AA-3939 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3941         TCGA-AA-3947         TCGA-AA-3949 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3950         TCGA-AA-3952         TCGA-AA-3955 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3956         TCGA-AA-3968         TCGA-AA-3971 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3972         TCGA-AA-3973         TCGA-AA-3975 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3976         TCGA-AA-3979         TCGA-AA-3984 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3986         TCGA-AA-3989         TCGA-AA-3994 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-A004         TCGA-AA-A00A         TCGA-AA-A00D 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-A00E         TCGA-AA-A00F         TCGA-AA-A00J 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-A00K         TCGA-AA-A00L         TCGA-AA-A00N 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-A00O         TCGA-AA-A00Q         TCGA-AA-A00R 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-A00U         TCGA-AA-A00W         TCGA-AA-A00Z 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-A010         TCGA-AA-A017         TCGA-AA-A01D 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-A01F         TCGA-AA-A01G         TCGA-AA-A01I 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-A01K         TCGA-AA-A01P         TCGA-AA-A01Q 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-A01R         TCGA-AA-A01S         TCGA-AA-A01T 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-A01V         TCGA-AA-A01X         TCGA-AA-A01Z 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-A022         TCGA-AA-A024         TCGA-AA-A029 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-A02F         TCGA-AA-A02H         TCGA-AA-A02J 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-A02K         TCGA-AA-A02O         TCGA-AA-A02W 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-A02Y         TCGA-AA-A03F         TCGA-AA-A03J 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AD-5900         TCGA-AD-6548         TCGA-AD-6888 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AU-3779         TCGA-AU-6004         TCGA-AY-4070 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AY-4071         TCGA-AY-5543         TCGA-AY-6196 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AY-6197         TCGA-AY-6386         TCGA-AZ-4315 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AZ-4681         TCGA-AZ-4682         TCGA-CA-5254 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-CA-5255         TCGA-CA-5796         TCGA-CA-5797 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-CA-6715         TCGA-CA-6716         TCGA-CA-6717 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-CA-6718         TCGA-CA-6719         TCGA-CK-4947 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-CK-4948         TCGA-CK-4950         TCGA-CK-4952 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-CK-5912         TCGA-CK-5913         TCGA-CK-5914 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-CK-5915         TCGA-CK-5916         TCGA-CK-6746 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-CK-6747         TCGA-CK-6748         TCGA-CK-6751 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-CM-4743         TCGA-CM-4744         TCGA-CM-4746 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-CM-4747         TCGA-CM-4752         TCGA-CM-5341 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-CM-5344         TCGA-CM-5348         TCGA-CM-5349 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-CM-5860         TCGA-CM-5861         TCGA-CM-5862 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-CM-5863         TCGA-CM-5864         TCGA-CM-5868 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-CM-6161         TCGA-CM-6162         TCGA-CM-6163 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-CM-6164         TCGA-CM-6165         TCGA-CM-6166 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-CM-6167         TCGA-CM-6168         TCGA-CM-6169 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-CM-6170         TCGA-CM-6171         TCGA-CM-6172 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-CM-6674         TCGA-CM-6675         TCGA-CM-6676 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-CM-6677         TCGA-CM-6678         TCGA-CM-6679 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-CM-6680         TCGA-D5-5537         TCGA-D5-5538 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-D5-5539         TCGA-D5-5540         TCGA-D5-5541 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-D5-6529         TCGA-D5-6532         TCGA-D5-6533 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-D5-6534         TCGA-D5-6535         TCGA-D5-6536 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-D5-6537         TCGA-D5-6538         TCGA-D5-6539 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-D5-6540         TCGA-D5-6541         TCGA-D5-6898 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-D5-6920         TCGA-D5-6922         TCGA-D5-6923 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-D5-6924         TCGA-D5-6926         TCGA-D5-6927 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-D5-6928         TCGA-D5-6929         TCGA-D5-6930 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-D5-6931         TCGA-D5-6932         TCGA-D5-7000 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-F4-6459         TCGA-F4-6460         TCGA-F4-6569 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-F4-6570         TCGA-F4-6703         TCGA-F4-6704 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-F4-6805         TCGA-F4-6806         TCGA-F4-6807 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-F4-6808         TCGA-F4-6809         TCGA-F4-6854 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-F4-6855         TCGA-F4-6856         TCGA-G4-6293 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-G4-6299         TCGA-G4-6303         TCGA-G4-6304 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-G4-6306         TCGA-G4-6307         TCGA-G4-6309 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-G4-6310         TCGA-G4-6315         TCGA-G4-6317 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-G4-6321         TCGA-G4-6323         TCGA-G4-6586 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-G4-6588         TCGA-G4-6625         TCGA-G4-6628 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
D767V10, 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
D767V11, 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(768) Variable = MAP3K4 MUTATION ANALYSIS
D768V1, survival
                  sevent
clus2                0   1
  MAP3K4 MUTATED    23  11
  MAP3K4 WILD-TYPE 259  62
  MAP3K4 MUTATED MAP3K4 WILD-TYPE 
              34              321 
  MAP3K4 MUTATED MAP3K4 WILD-TYPE 
              11               62 
$`MAP3K4 MUTATED`
TCGA-A6-2676 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3697 TCGA-AA-3715 
       42.90         3.02        63.98        13.02        85.05        19.04 
TCGA-AA-3821 TCGA-AA-3833 TCGA-AA-3947 TCGA-AA-3968 TCGA-AA-3977 TCGA-AA-A00J 
        1.02        15.95        33.01        21.99        25.02        18.05 
TCGA-AA-A00K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A02K TCGA-AD-6888 TCGA-AD-6889 
       18.05        38.07        35.01        14.01         4.21        56.55 
TCGA-AD-6964 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-5254 
       10.88        58.39         1.41        49.41       100.01         2.24 
TCGA-CA-6716 TCGA-CM-4746 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-6165 TCGA-D5-6534 
        0.26        37.02        30.08         5.03        16.04        43.27 
TCGA-D5-6927 TCGA-F4-6703 TCGA-F4-6806 TCGA-G4-6628 
        9.44        35.87        29.59        52.80 

$`MAP3K4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        6.97         1.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 
        5.98        37.05        19.00        36.00         5.03        26.99 
TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       17.98        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       40.96         0.07        21.37         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4616 
        0.95        15.75         0.20        21.44        17.82         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 
       29.56         5.23        11.74         3.19         1.94         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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 
       16.01        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 
       13.38        13.45         6.18         1.55        16.31        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       26.17        91.79        46.75 

  MAP3K4 MUTATED MAP3K4 WILD-TYPE 
            0.26             0.00 
  MAP3K4 MUTATED MAP3K4 WILD-TYPE 
          100.01           140.38 
  MAP3K4 MUTATED MAP3K4 WILD-TYPE 
          23.505           20.120 
[1] "0.3 - 100.0 (23.5)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.5"
D768V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MAP3K4 MUTATED         5        0        6        12         2         0
  MAP3K4 WILD-TYPE      59        1       19        97         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAP3K4 MUTATED           4          0          2          0        2
  MAP3K4 WILD-TYPE        15         10         39         31       33
                  vv
clus               STAGE IVA STAGE IVB
  MAP3K4 MUTATED           1         0
  MAP3K4 WILD-TYPE        12         1
D768V3, multiclass
            clus
vv           MAP3K4 MUTATED MAP3K4 WILD-TYPE
  STAGE I                 5               59
  STAGE IA                0                1
  STAGE II                6               19
  STAGE IIA              12               97
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               4               15
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              0               31
  STAGE IV                2               33
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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   7  22   7
  MAP3K4 WILD-TYPE   9  61 226  34
D768V4, multiclass
    clus
vv   MAP3K4 MUTATED MAP3K4 WILD-TYPE
  T1              0                9
  T2              7               61
  T3             22              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   3   5
  MAP3K4 WILD-TYPE 193  77  61
D768V5, multiclass
    clus
vv   MAP3K4 MUTATED MAP3K4 WILD-TYPE
  N0             27              193
  N1              3               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"
D768V6, binary
                  cls
clus                 0   1
  MAP3K4 MUTATED    30   3
  MAP3K4 WILD-TYPE 253  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP3K4 MUTATED     30    3
  MAP3K4 WILD-TYPE  253   45
   clus
vv  MAP3K4 MUTATED MAP3K4 WILD-TYPE
  0             30              253
  1              3               45
[1] 2 2
[1] FALSE
D768V7, 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
D768V8, binary
                  cls
clus                 0   1
  MAP3K4 MUTATED    30   6
  MAP3K4 WILD-TYPE 287  42
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP3K4 MUTATED     30    6
  MAP3K4 WILD-TYPE  287   42
                               clus
vv                              MAP3K4 MUTATED MAP3K4 WILD-TYPE
  COLON ADENOCARCINOMA                      30              287
  COLON MUCINOUS ADENOCARCINOMA              6               42
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  MAP3K4 MUTATED    26   0   1   2
  MAP3K4 WILD-TYPE 231   2  21  19
D768V9, multiclass
    clus
vv   MAP3K4 MUTATED MAP3K4 WILD-TYPE
  R0             26              231
  R1              0                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"
D768V10, 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
D768V11, 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(769) Variable = OSMR MUTATION ANALYSIS
D769V1, survival
                sevent
clus2              0   1
  OSMR MUTATED    14   6
  OSMR WILD-TYPE 268  67
  OSMR MUTATED OSMR WILD-TYPE 
            20            335 
  OSMR MUTATED OSMR WILD-TYPE 
             6             67 
$`OSMR MUTATED`
TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3818 TCGA-AA-3864 
       22.06        19.66         3.02        63.98         0.99        53.00 
TCGA-AA-3972 TCGA-AA-A00N TCGA-AY-6197 TCGA-AZ-6599 TCGA-AZ-6607 TCGA-CA-6717 
       50.99         4.01        21.44         6.77         3.19         0.33 
TCGA-CA-6718 TCGA-CM-4744 TCGA-CM-6171 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6540 
        0.10        20.02        14.04        17.85        17.13        16.14 
TCGA-DM-A28H TCGA-G4-6303 
      117.07        65.85 

$`OSMR WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.12        20.28         7.04         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       16.08        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41        49.41        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 
      100.01        29.56         5.23        11.74         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07         0.26         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 
       20.19        18.25         1.32        43.27        15.12         4.80 
TCGA-D5-6539 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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 
       81.37       119.93        35.97        60.79        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       19.43       107.67        74.56        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  OSMR MUTATED OSMR WILD-TYPE 
           0.1            0.0 
  OSMR MUTATED OSMR WILD-TYPE 
        117.07         140.38 
  OSMR MUTATED OSMR WILD-TYPE 
         17.49          20.98 
[1] "0.1 - 117.1 (17.5)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.4"
D769V2, 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       22       103         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        19         10         40         29       32        13
                vv
clus             STAGE IVB
  OSMR MUTATED           0
  OSMR WILD-TYPE         1
D769V3, multiclass
            clus
vv           OSMR MUTATED OSMR WILD-TYPE
  STAGE I               4             60
  STAGE IA              0              1
  STAGE II              3             22
  STAGE IIA             6            103
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            2             29
  STAGE IV              3             32
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  OSMR MUTATED     0   4  13   3
  OSMR WILD-TYPE   9  64 235  38
D769V4, multiclass
    clus
vv   OSMR MUTATED OSMR WILD-TYPE
  T1            0              9
  T2            4             64
  T3           13            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
  OSMR MUTATED    14   3   3
  OSMR WILD-TYPE 206  77  63
D769V5, multiclass
    clus
vv   OSMR MUTATED OSMR WILD-TYPE
  N0           14            206
  N1            3             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"
D769V6, binary
                cls
clus               0   1
  OSMR MUTATED    14   3
  OSMR WILD-TYPE 269  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  OSMR MUTATED     14    3
  OSMR WILD-TYPE  269   45
   clus
vv  OSMR MUTATED OSMR WILD-TYPE
  0           14            269
  1            3             45
[1] 2 2
[1] FALSE
D769V7, 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
D769V8, binary
                cls
clus               0   1
  OSMR MUTATED    16   4
  OSMR WILD-TYPE 301  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  OSMR MUTATED     16    4
  OSMR WILD-TYPE  301   44
                               clus
vv                              OSMR MUTATED OSMR WILD-TYPE
  COLON ADENOCARCINOMA                    16            301
  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 243   2  21  19
D769V9, multiclass
    clus
vv   OSMR MUTATED OSMR WILD-TYPE
  R0           14            243
  R1            0              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"
D769V10, 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
D769V11, 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(770) Variable = HIST1H1C MUTATION ANALYSIS
D770V1, survival
                    sevent
clus2                  0   1
  HIST1H1C MUTATED     7   0
  HIST1H1C WILD-TYPE 275  73
  HIST1H1C MUTATED HIST1H1C WILD-TYPE 
                 7                348 
  HIST1H1C MUTATED HIST1H1C WILD-TYPE 
                 0                 73 
$`HIST1H1C MUTATED`
TCGA-AA-3510 TCGA-AA-A01V TCGA-AD-6895 TCGA-CK-5913 TCGA-CK-5914 TCGA-DM-A0X9 
       63.98        35.01         0.72        51.32        21.99       119.70 
TCGA-DM-A1HA 
      131.51 

$`HIST1H1C WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 TCGA-AA-A029 
        1.02        33.04        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       40.34        15.62        49.08        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  HIST1H1C MUTATED HIST1H1C WILD-TYPE 
              0.72               0.00 
  HIST1H1C MUTATED HIST1H1C WILD-TYPE 
            131.51             140.38 
  HIST1H1C MUTATED HIST1H1C WILD-TYPE 
            51.320             20.005 
[1] "0.7 - 131.5 (51.3)" "0.0 - 140.4 (20.0)"
[1] "hr="     "2.7e+07"
D770V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HIST1H1C MUTATED         1        0        1         2         0         0
  HIST1H1C WILD-TYPE      63        1       24       107         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HIST1H1C MUTATED           0          0          1          1        0
  HIST1H1C WILD-TYPE        19         10         40         30       35
                    vv
clus                 STAGE IVA STAGE IVB
  HIST1H1C MUTATED           0         0
  HIST1H1C WILD-TYPE        13         1
D770V3, multiclass
            clus
vv           HIST1H1C MUTATED HIST1H1C WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  1                 24
  STAGE IIA                 2                107
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                0                 10
  STAGE IIIB                1                 40
  STAGE IIIC                1                 30
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  HIST1H1C MUTATED     0   1   6   0
  HIST1H1C WILD-TYPE   9  67 242  41
D770V4, multiclass
    clus
vv   HIST1H1C MUTATED HIST1H1C WILD-TYPE
  T1                0                  9
  T2                1                 67
  T3                6                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
  HIST1H1C MUTATED     4   2   1
  HIST1H1C WILD-TYPE 216  78  65
D770V5, multiclass
    clus
vv   HIST1H1C MUTATED HIST1H1C WILD-TYPE
  N0                4                216
  N1                2                 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"
D770V6, binary
                    cls
clus                   0   1
  HIST1H1C MUTATED     4   0
  HIST1H1C WILD-TYPE 279  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1C MUTATED      4    0
  HIST1H1C WILD-TYPE  279   48
   clus
vv  HIST1H1C MUTATED HIST1H1C WILD-TYPE
  0                4                279
  1                0                 48
[1] 2 2
[1] FALSE
D770V7, binary
                    cls
clus                   0   1
  HIST1H1C MUTATED     2   5
  HIST1H1C WILD-TYPE 168 192
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1C MUTATED      2    5
  HIST1H1C WILD-TYPE  168  192
        clus
vv       HIST1H1C MUTATED HIST1H1C WILD-TYPE
  FEMALE                2                168
  MALE                  5                192
[1] 2 2
[1] FALSE
D770V8, binary
                    cls
clus                   0   1
  HIST1H1C MUTATED     7   0
  HIST1H1C WILD-TYPE 310  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1C MUTATED      7    0
  HIST1H1C WILD-TYPE  310   48
                               clus
vv                              HIST1H1C MUTATED HIST1H1C WILD-TYPE
  COLON ADENOCARCINOMA                         7                310
  COLON MUCINOUS ADENOCARCINOMA                0                 48
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  HIST1H1C MUTATED     2   0   0   2
  HIST1H1C WILD-TYPE 255   2  22  19
D770V9, multiclass
    clus
vv   HIST1H1C MUTATED HIST1H1C WILD-TYPE
  R0                2                255
  R1                0                  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"
D770V10, 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     5
  HIST1H1C WILD-TYPE                        19   171
D770V11, multiclass
                                  clus
vv                                 HIST1H1C MUTATED HIST1H1C 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(771) Variable = KIAA1797 MUTATION ANALYSIS
D771V1, survival
                    sevent
clus2                  0   1
  KIAA1797 MUTATED    16   4
  KIAA1797 WILD-TYPE 266  69
  KIAA1797 MUTATED KIAA1797 WILD-TYPE 
                20                335 
  KIAA1797 MUTATED KIAA1797 WILD-TYPE 
                 4                 69 
$`KIAA1797 MUTATED`
TCGA-A6-5665 TCGA-A6-6141 TCGA-AA-3492 TCGA-AA-3864 TCGA-AA-A00N TCGA-AA-A00O 
       22.06         8.38         3.02        53.00         4.01        27.02 
TCGA-AA-A01Q TCGA-AD-5900 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 
        1.02         0.07        21.44        58.39        49.41         0.33 
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        35.87 
TCGA-G4-6293 TCGA-G4-6626 
      107.67        46.75 

$`KIAA1797 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.09        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        38.04        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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-4681 
       15.75         0.20        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       14.04        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 
       11.51        20.19         1.32        43.27        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        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        13.38        13.45         6.18         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.41        19.43        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        52.80 

  KIAA1797 MUTATED KIAA1797 WILD-TYPE 
              0.07               0.00 
  KIAA1797 MUTATED KIAA1797 WILD-TYPE 
            107.67             140.38 
  KIAA1797 MUTATED KIAA1797 WILD-TYPE 
            17.195             20.280 
[1] "0.1 - 107.7 (17.2)" "0.0 - 140.4 (20.3)"
[1] "hr=" "1.1"
D771V2, 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       21       100         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1797 MUTATED           1          0          2          1        0
  KIAA1797 WILD-TYPE        18         10         39         30       35
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA1797 MUTATED           0         0
  KIAA1797 WILD-TYPE        13         1
D771V3, multiclass
            clus
vv           KIAA1797 MUTATED KIAA1797 WILD-TYPE
  STAGE I                   2                 62
  STAGE IA                  0                  1
  STAGE II                  4                 21
  STAGE IIA                 9                100
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 1                 18
  STAGE IIIA                0                 10
  STAGE IIIB                2                 39
  STAGE IIIC                1                 30
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA1797 MUTATED     0   2  17   1
  KIAA1797 WILD-TYPE   9  66 231  40
D771V4, multiclass
    clus
vv   KIAA1797 MUTATED KIAA1797 WILD-TYPE
  T1                0                  9
  T2                2                 66
  T3               17                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
  KIAA1797 MUTATED    16   3   1
  KIAA1797 WILD-TYPE 204  77  65
D771V5, multiclass
    clus
vv   KIAA1797 MUTATED KIAA1797 WILD-TYPE
  N0               16                204
  N1                3                 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"
D771V6, binary
                    cls
clus                   0   1
  KIAA1797 MUTATED    16   0
  KIAA1797 WILD-TYPE 267  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1797 MUTATED     16    0
  KIAA1797 WILD-TYPE  267   48
   clus
vv  KIAA1797 MUTATED KIAA1797 WILD-TYPE
  0               16                267
  1                0                 48
[1] 2 2
[1] FALSE
D771V7, 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
D771V8, binary
                    cls
clus                   0   1
  KIAA1797 MUTATED    16   4
  KIAA1797 WILD-TYPE 301  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1797 MUTATED     16    4
  KIAA1797 WILD-TYPE  301   44
                               clus
vv                              KIAA1797 MUTATED KIAA1797 WILD-TYPE
  COLON ADENOCARCINOMA                        16                301
  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 241   2  22  19
D771V9, multiclass
    clus
vv   KIAA1797 MUTATED KIAA1797 WILD-TYPE
  R0               16                241
  R1                0                  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"
D771V10, 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
D771V11, 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(772) Variable = ZNF83 MUTATION ANALYSIS
D772V1, survival
                 sevent
clus2               0   1
  ZNF83 MUTATED    12   4
  ZNF83 WILD-TYPE 270  69
  ZNF83 MUTATED ZNF83 WILD-TYPE 
             16             339 
  ZNF83 MUTATED ZNF83 WILD-TYPE 
              4              69 
$`ZNF83 MUTATED`
TCGA-A6-3809 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3525 TCGA-AA-3864 
       32.75        19.66         3.02        63.98         8.05        53.00 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A02K TCGA-AZ-4315 TCGA-AZ-6601 TCGA-CM-4752 
        4.01        34.98        14.01        58.39       100.01        13.02 
TCGA-CM-6674 TCGA-D5-6923 TCGA-DM-A28K TCGA-G4-6586 
       12.95        12.43        98.24        35.80 

$`ZNF83 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.12        20.28         7.04         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       37.05        36.03        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
       39.98         2.01         5.03         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 
       15.58         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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       35.97        60.79       117.07         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 
       45.11        36.72        36.00        22.09        13.78        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  ZNF83 MUTATED ZNF83 WILD-TYPE 
           3.02            0.00 
  ZNF83 MUTATED ZNF83 WILD-TYPE 
         100.01          140.38 
  ZNF83 MUTATED ZNF83 WILD-TYPE 
         26.205          20.190 
[1] "3.0 - 100.0 (26.2)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D772V2, 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       21       103         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        19         10         40         30       34        13
                 vv
clus              STAGE IVB
  ZNF83 MUTATED           0
  ZNF83 WILD-TYPE         1
D772V3, multiclass
            clus
vv           ZNF83 MUTATED ZNF83 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               4              21
  STAGE IIA              6             103
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ZNF83 MUTATED     0   1  11   5
  ZNF83 WILD-TYPE   9  67 237  36
D772V4, multiclass
    clus
vv   ZNF83 MUTATED ZNF83 WILD-TYPE
  T1             0               9
  T2             1              67
  T3            11             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
  ZNF83 MUTATED    14   2   1
  ZNF83 WILD-TYPE 206  78  65
D772V5, multiclass
    clus
vv   ZNF83 MUTATED ZNF83 WILD-TYPE
  N0            14             206
  N1             2              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"
D772V6, binary
                 cls
clus                0   1
  ZNF83 MUTATED    15   1
  ZNF83 WILD-TYPE 268  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF83 MUTATED     15    1
  ZNF83 WILD-TYPE  268   47
   clus
vv  ZNF83 MUTATED ZNF83 WILD-TYPE
  0            15             268
  1             1              47
[1] 2 2
[1] FALSE
D772V7, 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
D772V8, binary
                 cls
clus                0   1
  ZNF83 MUTATED    13   4
  ZNF83 WILD-TYPE 304  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF83 MUTATED     13    4
  ZNF83 WILD-TYPE  304   44
                               clus
vv                              ZNF83 MUTATED ZNF83 WILD-TYPE
  COLON ADENOCARCINOMA                     13             304
  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 243   2  21  21
D772V9, multiclass
    clus
vv   ZNF83 MUTATED ZNF83 WILD-TYPE
  R0            14             243
  R1             0               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"
D772V10, 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
D772V11, 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(773) Variable = EIF4G2 MUTATION ANALYSIS
D773V1, survival
                  sevent
clus2                0   1
  EIF4G2 MUTATED     8   5
  EIF4G2 WILD-TYPE 274  68
  EIF4G2 MUTATED EIF4G2 WILD-TYPE 
              13              342 
  EIF4G2 MUTATED EIF4G2 WILD-TYPE 
               5               68 
$`EIF4G2 MUTATED`
TCGA-A6-5657 TCGA-AA-3811 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-A00N TCGA-AA-A010 
       31.63        10.06        33.01        26.01         4.01        34.98 
TCGA-AZ-4315 TCGA-CA-5797 TCGA-CK-5916 TCGA-CM-5862 TCGA-DM-A1D8 TCGA-DM-A28K 
       58.39         3.29        21.14         5.03        12.59        98.24 
TCGA-G4-6588 
       26.17 

$`EIF4G2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       12.99        24.00        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        52.80 

  EIF4G2 MUTATED EIF4G2 WILD-TYPE 
            3.29             0.00 
  EIF4G2 MUTATED EIF4G2 WILD-TYPE 
           98.24           140.38 
  EIF4G2 MUTATED EIF4G2 WILD-TYPE 
           26.01            20.07 
[1] "3.3 - 98.2 (26.0)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.9"
D773V2, 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       25       104         4         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EIF4G2 MUTATED           1          0          2          0        0
  EIF4G2 WILD-TYPE        18         10         39         31       35
                  vv
clus               STAGE IVA STAGE IVB
  EIF4G2 MUTATED           1         0
  EIF4G2 WILD-TYPE        12         1
D773V3, multiclass
            clus
vv           EIF4G2 MUTATED EIF4G2 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               5              104
  STAGE IIB               4                4
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  68 238  37
D773V4, multiclass
    clus
vv   EIF4G2 MUTATED EIF4G2 WILD-TYPE
  T1              1                8
  T2              0               68
  T3             10              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
  EIF4G2 MUTATED    10   4   1
  EIF4G2 WILD-TYPE 210  76  65
D773V5, multiclass
    clus
vv   EIF4G2 MUTATED EIF4G2 WILD-TYPE
  N0             10              210
  N1              4               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"
D773V6, binary
                  cls
clus                 0   1
  EIF4G2 MUTATED    12   1
  EIF4G2 WILD-TYPE 271  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF4G2 MUTATED     12    1
  EIF4G2 WILD-TYPE  271   47
   clus
vv  EIF4G2 MUTATED EIF4G2 WILD-TYPE
  0             12              271
  1              1               47
[1] 2 2
[1] FALSE
D773V7, 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
D773V8, binary
                  cls
clus                 0   1
  EIF4G2 MUTATED    11   4
  EIF4G2 WILD-TYPE 306  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF4G2 MUTATED     11    4
  EIF4G2 WILD-TYPE  306   44
                               clus
vv                              EIF4G2 MUTATED EIF4G2 WILD-TYPE
  COLON ADENOCARCINOMA                      11              306
  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 246   2  22  19
D773V9, multiclass
    clus
vv   EIF4G2 MUTATED EIF4G2 WILD-TYPE
  R0             11              246
  R1              0                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"
D773V10, 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
D773V11, 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(774) Variable = ALK MUTATION ANALYSIS
D774V1, survival
               sevent
clus2             0   1
  ALK MUTATED    23   9
  ALK WILD-TYPE 259  64
  ALK MUTATED ALK WILD-TYPE 
           32           323 
  ALK MUTATED ALK WILD-TYPE 
            9            64 
$`ALK MUTATED`
TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3518 TCGA-AA-3562 TCGA-AA-3663 
       14.53         1.02        63.98         1.02        19.99         6.97 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3818 TCGA-AA-3845 TCGA-AA-3950 
       26.99        19.04        19.04         0.99         0.00        24.00 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A01R TCGA-AZ-6601 TCGA-AZ-6608 
       26.01        25.02         4.01        35.01       100.01         1.94 
TCGA-CA-6717 TCGA-CM-4752 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6170 
        0.33        13.02        12.00        14.04        16.04        15.02 
TCGA-D5-6540 TCGA-D5-6930 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1HA TCGA-F4-6703 
       16.14         1.51        13.32        12.59       131.51        35.87 
TCGA-G4-6304 TCGA-G4-6307 
       53.62        55.04 

$`ALK WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 
        6.97         1.02        13.02        38.99         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 
       29.95        23.01        20.98        19.99        13.94        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       78.08         6.05        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3812 
       19.00        36.00         5.03        85.05        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       33.04        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02        14.93        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3979 TCGA-AA-3980 
       16.08        50.99        13.05        34.06        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
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        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        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         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       17.03        15.02        29.03        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 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-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 
       49.91       140.38         7.50        44.32       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 
       98.24         8.61        13.38        13.45         6.18         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 
       35.41        19.43       107.67        74.56        65.85        44.68 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  ALK MUTATED ALK WILD-TYPE 
            0             0 
  ALK MUTATED ALK WILD-TYPE 
       131.51        140.38 
  ALK MUTATED ALK WILD-TYPE 
        15.53         21.14 
[1] "0.0 - 131.5 (15.5)" "0.0 - 140.4 (21.1)"
[1] "hr=" "1.5"
D774V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ALK MUTATED         3        0        5        12         2         0
  ALK WILD-TYPE      61        1       20        97         6         1
               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        17          8         39         29       34        13
               vv
clus            STAGE IVB
  ALK MUTATED           0
  ALK WILD-TYPE         1
D774V3, multiclass
            clus
vv           ALK MUTATED ALK WILD-TYPE
  STAGE I              3            61
  STAGE IA             0             1
  STAGE II             5            20
  STAGE IIA           12            97
  STAGE IIB            2             6
  STAGE IIC            0             1
  STAGE III            2            17
  STAGE IIIA           2             8
  STAGE IIIB           2            39
  STAGE IIIC           2            29
  STAGE IV             1            34
  STAGE IVA            0            13
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  ALK MUTATED     1   5  25   2
  ALK WILD-TYPE   8  63 223  39
D774V4, multiclass
    clus
vv   ALK MUTATED ALK WILD-TYPE
  T1           1             8
  T2           5            63
  T3          25           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
  ALK MUTATED    24   5   4
  ALK WILD-TYPE 196  75  62
D774V5, multiclass
    clus
vv   ALK MUTATED ALK WILD-TYPE
  N0          24           196
  N1           5            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"
D774V6, binary
               cls
clus              0   1
  ALK MUTATED    30   1
  ALK WILD-TYPE 253  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  ALK MUTATED     30    1
  ALK WILD-TYPE  253   47
   clus
vv  ALK MUTATED ALK WILD-TYPE
  0          30           253
  1           1            47
[1] 2 2
[1] FALSE
D774V7, binary
               cls
clus              0   1
  ALK MUTATED    12  21
  ALK WILD-TYPE 158 176
[1] "tbl2"
               cls
clus            [,1] [,2]
  ALK MUTATED     12   21
  ALK WILD-TYPE  158  176
        clus
vv       ALK MUTATED ALK WILD-TYPE
  FEMALE          12           158
  MALE            21           176
[1] 2 2
[1] FALSE
D774V8, binary
               cls
clus              0   1
  ALK MUTATED    26   7
  ALK WILD-TYPE 291  41
[1] "tbl2"
               cls
clus            [,1] [,2]
  ALK MUTATED     26    7
  ALK WILD-TYPE  291   41
                               clus
vv                              ALK MUTATED ALK WILD-TYPE
  COLON ADENOCARCINOMA                   26           291
  COLON MUCINOUS ADENOCARCINOMA           7            41
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  ALK MUTATED    24   0   1   1
  ALK WILD-TYPE 233   2  21  20
D774V9, multiclass
    clus
vv   ALK MUTATED ALK WILD-TYPE
  R0          24           233
  R1           0             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"
D774V10, 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    15
  ALK WILD-TYPE                        18   161
D774V11, 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                                     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(775) Variable = FMO5 MUTATION ANALYSIS
D775V1, survival
                sevent
clus2              0   1
  FMO5 MUTATED     9   3
  FMO5 WILD-TYPE 273  70
  FMO5 MUTATED FMO5 WILD-TYPE 
            12            343 
  FMO5 MUTATED FMO5 WILD-TYPE 
             3             70 
$`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         0.10 
TCGA-CK-5916 TCGA-CM-5349 TCGA-CM-5861 TCGA-D5-6930 TCGA-G4-6303 TCGA-G4-6628 
       21.14        30.08        15.02         1.51        65.85        52.80 

$`FMO5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A02F 
       33.04        35.01        26.01        37.02        39.06        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.20        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
      100.01         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99         2.93         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        16.01         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 
       46.75 

  FMO5 MUTATED FMO5 WILD-TYPE 
           0.1            0.0 
  FMO5 MUTATED FMO5 WILD-TYPE 
         65.85         140.38 
  FMO5 MUTATED FMO5 WILD-TYPE 
         20.40          20.19 
[1] "0.1 - 65.8 (20.4)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D775V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FMO5 MUTATED         2        0        1         6         0         0
  FMO5 WILD-TYPE      62        1       24       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        19         10         41         30       34        13
                vv
clus             STAGE IVB
  FMO5 MUTATED           0
  FMO5 WILD-TYPE         1
D775V3, multiclass
            clus
vv           FMO5 MUTATED FMO5 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             6            103
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            1             30
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  FMO5 MUTATED     1   2   8   1
  FMO5 WILD-TYPE   8  66 240  40
D775V4, multiclass
    clus
vv   FMO5 MUTATED FMO5 WILD-TYPE
  T1            1              8
  T2            2             66
  T3            8            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
  FMO5 MUTATED     9   3   0
  FMO5 WILD-TYPE 211  77  66
D775V5, multiclass
    clus
vv   FMO5 MUTATED FMO5 WILD-TYPE
  N0            9            211
  N1            3             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"
D775V6, binary
                cls
clus               0   1
  FMO5 MUTATED     9   1
  FMO5 WILD-TYPE 274  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  FMO5 MUTATED      9    1
  FMO5 WILD-TYPE  274   47
   clus
vv  FMO5 MUTATED FMO5 WILD-TYPE
  0            9            274
  1            1             47
[1] 2 2
[1] FALSE
D775V7, binary
                cls
clus               0   1
  FMO5 MUTATED     6   6
  FMO5 WILD-TYPE 164 191
[1] "tbl2"
                cls
clus             [,1] [,2]
  FMO5 MUTATED      6    6
  FMO5 WILD-TYPE  164  191
        clus
vv       FMO5 MUTATED FMO5 WILD-TYPE
  FEMALE            6            164
  MALE              6            191
[1] 2 2
[1] FALSE
D775V8, binary
                cls
clus               0   1
  FMO5 MUTATED    10   2
  FMO5 WILD-TYPE 307  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  FMO5 MUTATED     10    2
  FMO5 WILD-TYPE  307   46
                               clus
vv                              FMO5 MUTATED FMO5 WILD-TYPE
  COLON ADENOCARCINOMA                    10            307
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  FMO5 MUTATED     8   0   0   2
  FMO5 WILD-TYPE 249   2  22  19
D775V9, multiclass
    clus
vv   FMO5 MUTATED FMO5 WILD-TYPE
  R0            8            249
  R1            0              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"
D775V10, 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     9
  FMO5 WILD-TYPE                        18   167
D775V11, 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                                       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(776) Variable = HGS MUTATION ANALYSIS
D776V1, survival
               sevent
clus2             0   1
  HGS MUTATED     7   3
  HGS WILD-TYPE 275  70
  HGS MUTATED HGS WILD-TYPE 
           10           345 
  HGS MUTATED HGS WILD-TYPE 
            3            70 
$`HGS MUTATED`
TCGA-AA-3496 TCGA-AY-6197 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CK-5913 TCGA-CK-6751 
        1.02        21.44        49.41       100.01        51.32       124.27 
TCGA-CM-5861 TCGA-D5-5540 TCGA-D5-6540 TCGA-F4-6570 
       15.02        13.51        16.14         6.18 

$`HGS WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        15.75         0.20        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13        83.80        22.36        62.79        61.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        21.99        21.14         2.93         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        16.01         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  HGS MUTATED HGS WILD-TYPE 
         1.02          0.00 
  HGS MUTATED HGS WILD-TYPE 
       124.27        140.38 
  HGS MUTATED HGS WILD-TYPE 
        18.79         20.19 
[1] "1.0 - 124.3 (18.8)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D776V2, 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       22       104         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        19         10         41         31       35        13
               vv
clus            STAGE IVB
  HGS MUTATED           0
  HGS WILD-TYPE         1
D776V3, multiclass
            clus
vv           HGS MUTATED HGS WILD-TYPE
  STAGE I              2            62
  STAGE IA             0             1
  STAGE II             3            22
  STAGE IIA            5           104
  STAGE IIB            0             8
  STAGE IIC            0             1
  STAGE III            0            19
  STAGE IIIA           0            10
  STAGE IIIB           0            41
  STAGE IIIC           0            31
  STAGE IV             0            35
  STAGE IVA            0            13
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  HGS MUTATED     0   2   8   0
  HGS WILD-TYPE   9  66 240  41
D776V4, multiclass
    clus
vv   HGS MUTATED HGS WILD-TYPE
  T1           0             9
  T2           2            66
  T3           8           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
  HGS MUTATED    10   0   0
  HGS WILD-TYPE 210  80  66
D776V5, multiclass
    clus
vv   HGS MUTATED HGS WILD-TYPE
  N0          10           210
  N1           0            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"
D776V6, binary
               cls
clus              0   1
  HGS MUTATED     6   0
  HGS WILD-TYPE 277  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  HGS MUTATED      6    0
  HGS WILD-TYPE  277   48
   clus
vv  HGS MUTATED HGS WILD-TYPE
  0           6           277
  1           0            48
[1] 2 2
[1] FALSE
D776V7, 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
D776V8, binary
               cls
clus              0   1
  HGS MUTATED     8   2
  HGS WILD-TYPE 309  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  HGS MUTATED      8    2
  HGS WILD-TYPE  309   46
                               clus
vv                              HGS MUTATED HGS WILD-TYPE
  COLON ADENOCARCINOMA                    8           309
  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 251   2  22  19
D776V9, multiclass
    clus
vv   HGS MUTATED HGS WILD-TYPE
  R0           6           251
  R1           0             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"
D776V10, 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
D776V11, 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(777) Variable = SLC41A2 MUTATION ANALYSIS
D777V1, survival
                   sevent
clus2                 0   1
  SLC41A2 MUTATED     7   0
  SLC41A2 WILD-TYPE 275  73
  SLC41A2 MUTATED SLC41A2 WILD-TYPE 
                7               348 
  SLC41A2 MUTATED SLC41A2 WILD-TYPE 
                0                73 
$`SLC41A2 MUTATED`
TCGA-CA-6717 TCGA-CM-6164 TCGA-CM-6168 TCGA-D5-5540 TCGA-D5-6928 TCGA-DM-A1HB 
        0.33        29.03        12.99        13.51        11.64       135.65 
TCGA-G4-6315 
       36.72 

$`SLC41A2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        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-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-D5-5541 TCGA-D5-6529 
       12.03        45.40        12.26        19.59        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        51.75        45.11        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  SLC41A2 MUTATED SLC41A2 WILD-TYPE 
             0.33              0.00 
  SLC41A2 MUTATED SLC41A2 WILD-TYPE 
           135.65            140.38 
  SLC41A2 MUTATED SLC41A2 WILD-TYPE 
           13.510            20.235 
[1] "0.3 - 135.7 (13.5)" "0.0 - 140.4 (20.2)"
[1] "hr="     "9300000"
D777V2, 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       25       103         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC41A2 MUTATED           0          0          1          0        1
  SLC41A2 WILD-TYPE        19         10         40         31       34
                   vv
clus                STAGE IVA STAGE IVB
  SLC41A2 MUTATED           0         0
  SLC41A2 WILD-TYPE        13         1
D777V3, multiclass
            clus
vv           SLC41A2 MUTATED SLC41A2 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                6               103
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               0                31
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC41A2 MUTATED     0   0   8   0
  SLC41A2 WILD-TYPE   9  68 240  41
D777V4, multiclass
    clus
vv   SLC41A2 MUTATED SLC41A2 WILD-TYPE
  T1               0                 9
  T2               0                68
  T3               8               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
  SLC41A2 MUTATED     6   2   0
  SLC41A2 WILD-TYPE 214  78  66
D777V5, multiclass
    clus
vv   SLC41A2 MUTATED SLC41A2 WILD-TYPE
  N0               6               214
  N1               2                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"
D777V6, binary
                   cls
clus                  0   1
  SLC41A2 MUTATED     7   1
  SLC41A2 WILD-TYPE 276  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC41A2 MUTATED      7    1
  SLC41A2 WILD-TYPE  276   47
   clus
vv  SLC41A2 MUTATED SLC41A2 WILD-TYPE
  0               7               276
  1               1                47
[1] 2 2
[1] FALSE
D777V7, 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
D777V8, binary
                   cls
clus                  0   1
  SLC41A2 MUTATED     6   2
  SLC41A2 WILD-TYPE 311  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC41A2 MUTATED      6    2
  SLC41A2 WILD-TYPE  311   46
                               clus
vv                              SLC41A2 MUTATED SLC41A2 WILD-TYPE
  COLON ADENOCARCINOMA                        6               311
  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 251   2  22  20
D777V9, multiclass
    clus
vv   SLC41A2 MUTATED SLC41A2 WILD-TYPE
  R0               6               251
  R1               0                 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"
D777V10, 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
D777V11, 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(778) Variable = UGT2A1 MUTATION ANALYSIS
D778V1, survival
                  sevent
clus2                0   1
  UGT2A1 MUTATED     7   2
  UGT2A1 WILD-TYPE 275  71
  UGT2A1 MUTATED UGT2A1 WILD-TYPE 
               9              346 
  UGT2A1 MUTATED UGT2A1 WILD-TYPE 
               2               71 
$`UGT2A1 MUTATED`
TCGA-AA-3821 TCGA-AA-3864 TCGA-AA-3952 TCGA-AA-3977 TCGA-AA-A010 TCGA-AA-A01R 
        1.02        53.00         2.01        25.02        34.98        35.01 
TCGA-CA-6717 TCGA-F4-6570 TCGA-G4-6293 
        0.33         6.18       107.67 

$`UGT2A1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 
       12.99        24.00        33.01        26.01        24.00        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.38        13.45        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  UGT2A1 MUTATED UGT2A1 WILD-TYPE 
            0.33             0.00 
  UGT2A1 MUTATED UGT2A1 WILD-TYPE 
          107.67           140.38 
  UGT2A1 MUTATED UGT2A1 WILD-TYPE 
          25.020           20.155 
[1] "0.3 - 107.7 (25.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1"  
D778V2, 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       23       107         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  UGT2A1 MUTATED           2          0          0          1        0
  UGT2A1 WILD-TYPE        17         10         41         30       35
                  vv
clus               STAGE IVA STAGE IVB
  UGT2A1 MUTATED           0         0
  UGT2A1 WILD-TYPE        13         1
D778V3, multiclass
            clus
vv           UGT2A1 MUTATED UGT2A1 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               2              107
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               2               17
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  UGT2A1 MUTATED     0   2   6   2
  UGT2A1 WILD-TYPE   9  66 242  39
D778V4, multiclass
    clus
vv   UGT2A1 MUTATED UGT2A1 WILD-TYPE
  T1              0                9
  T2              2               66
  T3              6              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
  UGT2A1 MUTATED     7   1   2
  UGT2A1 WILD-TYPE 213  79  64
D778V5, multiclass
    clus
vv   UGT2A1 MUTATED UGT2A1 WILD-TYPE
  N0              7              213
  N1              1               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"
D778V6, binary
                  cls
clus                 0   1
  UGT2A1 MUTATED     9   0
  UGT2A1 WILD-TYPE 274  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT2A1 MUTATED      9    0
  UGT2A1 WILD-TYPE  274   48
   clus
vv  UGT2A1 MUTATED UGT2A1 WILD-TYPE
  0              9              274
  1              0               48
[1] 2 2
[1] FALSE
D778V7, 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
D778V8, binary
                  cls
clus                 0   1
  UGT2A1 MUTATED     7   3
  UGT2A1 WILD-TYPE 310  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT2A1 MUTATED      7    3
  UGT2A1 WILD-TYPE  310   45
                               clus
vv                              UGT2A1 MUTATED UGT2A1 WILD-TYPE
  COLON ADENOCARCINOMA                       7              310
  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 249   2  22  20
D778V9, multiclass
    clus
vv   UGT2A1 MUTATED UGT2A1 WILD-TYPE
  R0              8              249
  R1              0                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"
D778V10, 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
D778V11, 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(779) Variable = STK36 MUTATION ANALYSIS
D779V1, survival
                 sevent
clus2               0   1
  STK36 MUTATED    14   1
  STK36 WILD-TYPE 268  72
  STK36 MUTATED STK36 WILD-TYPE 
             15             340 
  STK36 MUTATED STK36 WILD-TYPE 
              1              72 
$`STK36 MUTATED`
TCGA-A6-5657 TCGA-AA-3949 TCGA-AA-3966 TCGA-AA-A00E TCGA-AD-5900 TCGA-AY-6386 
       31.63        26.01         2.01        30.02         0.07        17.82 
TCGA-AZ-4315 TCGA-AZ-6600 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5913 TCGA-CM-5348 
       58.39        12.10         0.33         0.10        51.32        22.98 
TCGA-CM-5349 TCGA-DM-A1HB TCGA-G4-6323 
       30.08       135.65        13.78 

$`STK36 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07         0.26         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        21.99        21.14         2.93         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-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       29.06        22.03        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 
       51.75        45.11        36.72        36.00        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  STK36 MUTATED STK36 WILD-TYPE 
           0.07            0.00 
  STK36 MUTATED STK36 WILD-TYPE 
         135.65          140.38 
  STK36 MUTATED STK36 WILD-TYPE 
         22.980          20.155 
[1] "0.1 - 135.7 (23.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "3.4"
D779V2, 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       25       102         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  STK36 MUTATED           0          0          5          0        1         0
  STK36 WILD-TYPE        19         10         36         31       34        13
                 vv
clus              STAGE IVB
  STK36 MUTATED           0
  STK36 WILD-TYPE         1
D779V3, multiclass
            clus
vv           STK36 MUTATED STK36 WILD-TYPE
  STAGE I                1              63
  STAGE IA               1               0
  STAGE II               0              25
  STAGE IIA              7             102
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             5              36
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  STK36 MUTATED     0   1  12   1
  STK36 WILD-TYPE   9  67 236  40
D779V4, multiclass
    clus
vv   STK36 MUTATED STK36 WILD-TYPE
  T1             0               9
  T2             1              67
  T3            12             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
  STK36 MUTATED     9   6   0
  STK36 WILD-TYPE 211  74  66
D779V5, multiclass
    clus
vv   STK36 MUTATED STK36 WILD-TYPE
  N0             9             211
  N1             6              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"
D779V6, binary
                 cls
clus                0   1
  STK36 MUTATED    11   1
  STK36 WILD-TYPE 272  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK36 MUTATED     11    1
  STK36 WILD-TYPE  272   47
   clus
vv  STK36 MUTATED STK36 WILD-TYPE
  0            11             272
  1             1              47
[1] 2 2
[1] FALSE
D779V7, binary
                 cls
clus                0   1
  STK36 MUTATED     5  10
  STK36 WILD-TYPE 165 187
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK36 MUTATED      5   10
  STK36 WILD-TYPE  165  187
        clus
vv       STK36 MUTATED STK36 WILD-TYPE
  FEMALE             5             165
  MALE              10             187
[1] 2 2
[1] FALSE
D779V8, binary
                 cls
clus                0   1
  STK36 MUTATED    11   4
  STK36 WILD-TYPE 306  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK36 MUTATED     11    4
  STK36 WILD-TYPE  306   44
                               clus
vv                              STK36 MUTATED STK36 WILD-TYPE
  COLON ADENOCARCINOMA                     11             306
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  STK36 MUTATED     9   0   0   3
  STK36 WILD-TYPE 248   2  22  18
D779V9, multiclass
    clus
vv   STK36 MUTATED STK36 WILD-TYPE
  R0             9             248
  R1             0               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"
D779V10, 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
D779V11, 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(780) Variable = MACC1 MUTATION ANALYSIS
D780V1, survival
                 sevent
clus2               0   1
  MACC1 MUTATED    12   5
  MACC1 WILD-TYPE 270  68
  MACC1 MUTATED MACC1 WILD-TYPE 
             17             338 
  MACC1 MUTATED MACC1 WILD-TYPE 
              5              68 
$`MACC1 MUTATED`
TCGA-AA-3492 TCGA-AA-3516 TCGA-AA-3821 TCGA-AA-3837 TCGA-AA-3845 TCGA-AA-3977 
        3.02        13.02         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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 
       35.05        33.04         0.99        25.02        17.98        15.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02        14.93        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       15.75        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        49.08        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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-6676 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        12.95        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 
       11.51        20.19        18.25         1.32        43.27        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  MACC1 MUTATED MACC1 WILD-TYPE 
              0               0 
  MACC1 MUTATED MACC1 WILD-TYPE 
          51.32          140.38 
  MACC1 MUTATED MACC1 WILD-TYPE 
          14.99           20.63 
[1] "0.0 - 51.3 (15.0)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "1.9"
D780V2, 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       21       105         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        18         10         39         28       35        13
                 vv
clus              STAGE IVB
  MACC1 MUTATED           1
  MACC1 WILD-TYPE         0
D780V3, multiclass
            clus
vv           MACC1 MUTATED MACC1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               4              21
  STAGE IIA              4             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             3              28
  STAGE IV               0              35
  STAGE IVA              0              13
  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  66 234  39
D780V4, multiclass
    clus
vv   MACC1 MUTATED MACC1 WILD-TYPE
  T1             0               9
  T2             2              66
  T3            14             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
  MACC1 MUTATED    11   2   5
  MACC1 WILD-TYPE 209  78  61
D780V5, multiclass
    clus
vv   MACC1 MUTATED MACC1 WILD-TYPE
  N0            11             209
  N1             2              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"
D780V6, binary
                 cls
clus                0   1
  MACC1 MUTATED    11   1
  MACC1 WILD-TYPE 272  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MACC1 MUTATED     11    1
  MACC1 WILD-TYPE  272   47
   clus
vv  MACC1 MUTATED MACC1 WILD-TYPE
  0            11             272
  1             1              47
[1] 2 2
[1] FALSE
D780V7, 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
D780V8, binary
                 cls
clus                0   1
  MACC1 MUTATED    12   6
  MACC1 WILD-TYPE 305  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MACC1 MUTATED     12    6
  MACC1 WILD-TYPE  305   42
                               clus
vv                              MACC1 MUTATED MACC1 WILD-TYPE
  COLON ADENOCARCINOMA                     12             305
  COLON MUCINOUS ADENOCARCINOMA             6              42
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MACC1 MUTATED    11   0   0   3
  MACC1 WILD-TYPE 246   2  22  18
D780V9, multiclass
    clus
vv   MACC1 MUTATED MACC1 WILD-TYPE
  R0            11             246
  R1             0               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"
D780V10, 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
D780V11, 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(781) Variable = BAI3 MUTATION ANALYSIS
D781V1, survival
                sevent
clus2              0   1
  BAI3 MUTATED    31   7
  BAI3 WILD-TYPE 251  66
  BAI3 MUTATED BAI3 WILD-TYPE 
            38            317 
  BAI3 MUTATED BAI3 WILD-TYPE 
             7             66 
$`BAI3 MUTATED`
TCGA-A6-5656 TCGA-AA-3510 TCGA-AA-3526 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3663 
       32.91        63.98        19.07        17.95        29.95         6.97 
TCGA-AA-3679 TCGA-AA-3815 TCGA-AA-3821 TCGA-AA-3947 TCGA-AA-A00N TCGA-AA-A010 
       15.02        33.04         1.02        33.01         4.01        34.98 
TCGA-AA-A01G TCGA-AU-6004 TCGA-AY-6196 TCGA-AZ-6598 TCGA-AZ-6606 TCGA-CA-6717 
       12.00        27.09         0.20        49.41        11.74         0.33 
TCGA-CA-6718 TCGA-CK-4952 TCGA-CK-5913 TCGA-CM-5861 TCGA-CM-5868 TCGA-CM-6166 
        0.10        15.62        51.32        15.02        17.03        21.99 
TCGA-CM-6170 TCGA-D5-5537 TCGA-D5-6533 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6541 
       15.02        45.40         1.32        17.85        17.13        15.58 
TCGA-DM-A1D4 TCGA-DM-A1D8 TCGA-DM-A28G TCGA-G4-6306 TCGA-G4-6315 TCGA-G4-6321 
       92.75        12.59        60.79        44.68        36.72        22.09 
TCGA-G4-6625 TCGA-G4-6628 
       91.79        52.80 

$`BAI3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3529 
        9.07        24.03        37.05        36.03         8.05         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       78.08         6.05        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       50.04        47.01        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 
       10.06        35.05         0.99        25.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       15.75        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
      100.01        29.56         5.23         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07         0.26         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 
       17.56       102.44        40.34        49.08        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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-6161 TCGA-CM-6162 
       16.01         5.03        15.02        15.02        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-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       11.01        10.06        12.03        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 
       11.51        20.19        18.25        43.27        15.12         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-D5-6924 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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-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-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
      130.65        49.91        13.32       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       35.97       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        53.62        55.04        51.75        45.11 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 
       36.00        13.78        35.80        26.17        46.75 

  BAI3 MUTATED BAI3 WILD-TYPE 
           0.1            0.0 
  BAI3 MUTATED BAI3 WILD-TYPE 
         92.75         140.38 
  BAI3 MUTATED BAI3 WILD-TYPE 
         18.51          20.28 
[1] "0.1 - 92.8 (18.5)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.2"
D781V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BAI3 MUTATED         8        0        4        16         3         0
  BAI3 WILD-TYPE      56        1       21        93         5         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BAI3 MUTATED           2          0          2          1        4         1
  BAI3 WILD-TYPE        17         10         39         30       31        12
                vv
clus             STAGE IVB
  BAI3 MUTATED           0
  BAI3 WILD-TYPE         1
D781V3, multiclass
            clus
vv           BAI3 MUTATED BAI3 WILD-TYPE
  STAGE I               8             56
  STAGE IA              0              1
  STAGE II              4             21
  STAGE IIA            16             93
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             2             17
  STAGE IIIA            0             10
  STAGE IIIB            2             39
  STAGE IIIC            1             30
  STAGE IV              4             31
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  24   8
  BAI3 WILD-TYPE   9  58 224  33
D781V4, multiclass
    clus
vv   BAI3 MUTATED BAI3 WILD-TYPE
  T1            0              9
  T2           10             58
  T3           24            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   7
  BAI3 WILD-TYPE 189  76  59
D781V5, multiclass
    clus
vv   BAI3 MUTATED BAI3 WILD-TYPE
  N0           31            189
  N1            4             76
  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"
D781V6, binary
                cls
clus               0   1
  BAI3 MUTATED    30   5
  BAI3 WILD-TYPE 253  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAI3 MUTATED     30    5
  BAI3 WILD-TYPE  253   43
   clus
vv  BAI3 MUTATED BAI3 WILD-TYPE
  0           30            253
  1            5             43
[1] 2 2
[1] FALSE
D781V7, binary
                cls
clus               0   1
  BAI3 MUTATED    20  22
  BAI3 WILD-TYPE 150 175
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAI3 MUTATED     20   22
  BAI3 WILD-TYPE  150  175
        clus
vv       BAI3 MUTATED BAI3 WILD-TYPE
  FEMALE           20            150
  MALE             22            175
[1] 2 2
[1] FALSE
D781V8, binary
                cls
clus               0   1
  BAI3 MUTATED    34   8
  BAI3 WILD-TYPE 283  40
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAI3 MUTATED     34    8
  BAI3 WILD-TYPE  283   40
                               clus
vv                              BAI3 MUTATED BAI3 WILD-TYPE
  COLON ADENOCARCINOMA                    34            283
  COLON MUCINOUS ADENOCARCINOMA            8             40
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  BAI3 MUTATED    28   0   2   6
  BAI3 WILD-TYPE 229   2  20  15
D781V9, multiclass
    clus
vv   BAI3 MUTATED BAI3 WILD-TYPE
  R0           28            229
  R1            0              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"
D781V10, 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
D781V11, 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(782) Variable = POLE MUTATION ANALYSIS
D782V1, survival
                sevent
clus2              0   1
  POLE MUTATED    23   6
  POLE WILD-TYPE 259  67
  POLE MUTATED POLE WILD-TYPE 
            29            326 
  POLE MUTATED POLE WILD-TYPE 
             6             67 
$`POLE MUTATED`
TCGA-A6-4105 TCGA-A6-6141 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3518 TCGA-AA-3525 
       14.53         8.38        19.66        63.98         1.02         8.05 
TCGA-AA-3555 TCGA-AA-3660 TCGA-AA-3678 TCGA-AA-3710 TCGA-AA-3815 TCGA-AA-3833 
       29.95        78.08        47.01        26.99        33.04        15.95 
TCGA-AA-3864 TCGA-AA-3977 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6964 
       53.00        25.02        18.05         4.01        34.98        10.88 
TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-5861 
       58.39        49.41       100.01         0.33         0.10        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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
        1.02        13.02        38.99         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
       36.03        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        17.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        61.02         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3679 
       54.02         2.01        14.01         0.92        50.04        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       85.05        19.04        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
       25.02         1.02        17.98        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       19.00        30.02        34.03        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.26         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01         5.03 
TCGA-CM-5863 TCGA-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-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79       117.07         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  POLE MUTATED POLE WILD-TYPE 
           0.1            0.0 
  POLE MUTATED POLE WILD-TYPE 
        100.01         140.38 
  POLE MUTATED POLE WILD-TYPE 
        19.660         20.235 
[1] "0.1 - 100.0 (19.7)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.3"
D782V2, 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       20        96         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        18         10         39         30       34        12
                vv
clus             STAGE IVB
  POLE MUTATED           1
  POLE WILD-TYPE         0
D782V3, multiclass
            clus
vv           POLE MUTATED POLE WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              5             20
  STAGE IIA            13             96
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            2             39
  STAGE IIIC            1             30
  STAGE IV              1             34
  STAGE IVA             1             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
  POLE MUTATED     0   4  21   6
  POLE WILD-TYPE   9  64 227  35
D782V4, multiclass
    clus
vv   POLE MUTATED POLE WILD-TYPE
  T1            0              9
  T2            4             64
  T3           21            227
  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  74  64
D782V5, multiclass
    clus
vv   POLE MUTATED POLE WILD-TYPE
  N0           23            197
  N1            6             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"
D782V6, binary
                cls
clus               0   1
  POLE MUTATED    23   3
  POLE WILD-TYPE 260  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  POLE MUTATED     23    3
  POLE WILD-TYPE  260   45
   clus
vv  POLE MUTATED POLE WILD-TYPE
  0           23            260
  1            3             45
[1] 2 2
[1] FALSE
D782V7, 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
D782V8, binary
                cls
clus               0   1
  POLE MUTATED    24   7
  POLE WILD-TYPE 293  41
[1] "tbl2"
                cls
clus             [,1] [,2]
  POLE MUTATED     24    7
  POLE WILD-TYPE  293   41
                               clus
vv                              POLE MUTATED POLE WILD-TYPE
  COLON ADENOCARCINOMA                    24            293
  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 236   2  22  18
D782V9, multiclass
    clus
vv   POLE MUTATED POLE WILD-TYPE
  R0           21            236
  R1            0              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"
D782V10, 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
D782V11, 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(783) Variable = ABI3BP MUTATION ANALYSIS
D783V1, survival
                  sevent
clus2                0   1
  ABI3BP MUTATED    14   6
  ABI3BP WILD-TYPE 268  67
  ABI3BP MUTATED ABI3BP WILD-TYPE 
              20              335 
  ABI3BP MUTATED ABI3BP WILD-TYPE 
               6               67 
$`ABI3BP MUTATED`
TCGA-A6-6654 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R TCGA-AY-4071 
       23.87        25.02         4.01        34.98        35.01         0.95 
TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-6164 
       49.41       100.01         0.33        13.02        22.03        29.03 
TCGA-D5-6536 TCGA-D5-6926 TCGA-D5-6929 TCGA-DM-A0XF TCGA-F4-6570 TCGA-G4-6307 
       17.85         9.04        13.41        38.20         6.18        55.04 
TCGA-G4-6317 TCGA-G4-6586 
       36.00        35.80 

$`ABI3BP WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       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        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       61.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        24.43       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      117.07        98.24         8.61        13.38        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 
       53.62        44.68        51.75        45.11        36.72        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        26.17        91.79        46.75        52.80 

  ABI3BP MUTATED ABI3BP WILD-TYPE 
            0.33             0.00 
  ABI3BP MUTATED ABI3BP WILD-TYPE 
          100.01           140.38 
  ABI3BP MUTATED ABI3BP WILD-TYPE 
          24.445           20.020 
[1] "0.3 - 100.0 (24.4)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.4"
D783V2, 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       23       102         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ABI3BP MUTATED           1          1          3          2        1
  ABI3BP WILD-TYPE        18          9         38         29       34
                  vv
clus               STAGE IVA STAGE IVB
  ABI3BP MUTATED           0         0
  ABI3BP WILD-TYPE        13         1
D783V3, multiclass
            clus
vv           ABI3BP MUTATED ABI3BP WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               7              102
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              1                9
  STAGE IIIB              3               38
  STAGE IIIC              2               29
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ABI3BP MUTATED     1   1  16   3
  ABI3BP WILD-TYPE   8  67 232  38
D783V4, multiclass
    clus
vv   ABI3BP MUTATED ABI3BP WILD-TYPE
  T1              1                8
  T2              1               67
  T3             16              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
  ABI3BP MUTATED    13   5   3
  ABI3BP WILD-TYPE 207  75  63
D783V5, multiclass
    clus
vv   ABI3BP MUTATED ABI3BP WILD-TYPE
  N0             13              207
  N1              5               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"
D783V6, binary
                  cls
clus                 0   1
  ABI3BP MUTATED    16   1
  ABI3BP WILD-TYPE 267  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ABI3BP MUTATED     16    1
  ABI3BP WILD-TYPE  267   47
   clus
vv  ABI3BP MUTATED ABI3BP WILD-TYPE
  0             16              267
  1              1               47
[1] 2 2
[1] FALSE
D783V7, 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
D783V8, binary
                  cls
clus                 0   1
  ABI3BP MUTATED    16   4
  ABI3BP WILD-TYPE 301  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ABI3BP MUTATED     16    4
  ABI3BP WILD-TYPE  301   44
                               clus
vv                              ABI3BP MUTATED ABI3BP WILD-TYPE
  COLON ADENOCARCINOMA                      16              301
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ABI3BP MUTATED    15   0   0   1
  ABI3BP WILD-TYPE 242   2  22  20
D783V9, multiclass
    clus
vv   ABI3BP MUTATED ABI3BP WILD-TYPE
  R0             15              242
  R1              0                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"
D783V10, 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
D783V11, 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(784) Variable = INSRR MUTATION ANALYSIS
D784V1, survival
                 sevent
clus2               0   1
  INSRR MUTATED    20   5
  INSRR WILD-TYPE 262  68
  INSRR MUTATED INSRR WILD-TYPE 
             25             330 
  INSRR MUTATED INSRR WILD-TYPE 
              5              68 
$`INSRR MUTATED`
TCGA-A6-2676 TCGA-A6-6648 TCGA-AA-3518 TCGA-AA-3666 TCGA-AA-3941 TCGA-AA-3950 
       42.90        25.18         1.02         2.01        24.00        24.00 
TCGA-AA-3977 TCGA-AD-6895 TCGA-AU-3779 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CA-6718 
       25.02         0.72        14.50       100.01         0.33         0.10 
TCGA-CK-4948 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-5868 TCGA-CM-6162 TCGA-D5-6533 
      102.44        23.05        37.02        17.03        12.00         1.32 
TCGA-D5-6538 TCGA-D5-6929 TCGA-DM-A285 TCGA-F4-6570 TCGA-G4-6304 TCGA-G4-6588 
       17.13        13.41         6.12         6.18        53.62        26.17 
TCGA-G4-6628 
       52.80 

$`INSRR WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 
       63.98         6.97         1.02        13.02        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 
       29.98        18.05        31.00         2.01        12.99        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        4.21        56.55         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
        1.35        17.56        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
       21.99        21.14         2.93         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-6161 
       16.01        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
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-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44        11.64         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C TCGA-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        13.38        13.45 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 

  INSRR MUTATED INSRR WILD-TYPE 
            0.1             0.0 
  INSRR MUTATED INSRR WILD-TYPE 
         102.44          140.38 
  INSRR MUTATED INSRR WILD-TYPE 
         17.130          20.235 
[1] "0.1 - 102.4 (17.1)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1"  
D784V2, 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       23       101         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  INSRR MUTATED           1          1          3          0        2         3
  INSRR WILD-TYPE        18          9         38         31       33        10
                 vv
clus              STAGE IVB
  INSRR MUTATED           0
  INSRR WILD-TYPE         1
D784V3, multiclass
            clus
vv           INSRR MUTATED INSRR WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              8             101
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             1               9
  STAGE IIIB             3              38
  STAGE IIIC             0              31
  STAGE IV               2              33
  STAGE IVA              3              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
  INSRR MUTATED     0   3  17   6
  INSRR WILD-TYPE   9  65 231  35
D784V4, multiclass
    clus
vv   INSRR MUTATED INSRR WILD-TYPE
  T1             0               9
  T2             3              65
  T3            17             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
  INSRR MUTATED    17   7   2
  INSRR WILD-TYPE 203  73  64
D784V5, multiclass
    clus
vv   INSRR MUTATED INSRR WILD-TYPE
  N0            17             203
  N1             7              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"
D784V6, binary
                 cls
clus                0   1
  INSRR MUTATED    19   5
  INSRR WILD-TYPE 264  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INSRR MUTATED     19    5
  INSRR WILD-TYPE  264   43
   clus
vv  INSRR MUTATED INSRR WILD-TYPE
  0            19             264
  1             5              43
[1] 2 2
[1] FALSE
D784V7, 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
D784V8, binary
                 cls
clus                0   1
  INSRR MUTATED    22   4
  INSRR WILD-TYPE 295  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INSRR MUTATED     22    4
  INSRR WILD-TYPE  295   44
                               clus
vv                              INSRR MUTATED INSRR WILD-TYPE
  COLON ADENOCARCINOMA                     22             295
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  INSRR MUTATED    19   0   0   2
  INSRR WILD-TYPE 238   2  22  19
D784V9, multiclass
    clus
vv   INSRR MUTATED INSRR WILD-TYPE
  R0            19             238
  R1             0               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"
D784V10, 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
D784V11, 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(785) Variable = IQGAP2 MUTATION ANALYSIS
D785V1, survival
                  sevent
clus2                0   1
  IQGAP2 MUTATED    13   7
  IQGAP2 WILD-TYPE 269  66
  IQGAP2 MUTATED IQGAP2 WILD-TYPE 
              20              335 
  IQGAP2 MUTATED IQGAP2 WILD-TYPE 
               7               66 
$`IQGAP2 MUTATED`
TCGA-A6-2676 TCGA-AA-3543 TCGA-AA-3549 TCGA-AA-3950 TCGA-AA-3977 TCGA-AA-A00E 
       42.90         0.99        21.01        24.00        25.02        30.02 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AZ-4315 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6606 
       38.04         4.01        58.39        62.79        49.41        11.74 
TCGA-CA-6717 TCGA-CK-5913 TCGA-CM-6169 TCGA-CM-6674 TCGA-D5-6931 TCGA-DM-A1DB 
        0.33        51.32        13.02        12.95        12.00        44.32 
TCGA-F4-6570 TCGA-F4-6703 
        6.18        35.87 

$`IQGAP2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 
       26.01        12.99        14.01        33.99        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J 
       27.02        13.94        38.04        19.00        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       18.05        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       83.80        22.36        61.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
       17.56       102.44        40.34        15.62        49.08        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
        8.61        13.38        13.45         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  IQGAP2 MUTATED IQGAP2 WILD-TYPE 
            0.33             0.00 
  IQGAP2 MUTATED IQGAP2 WILD-TYPE 
           62.79           140.38 
  IQGAP2 MUTATED IQGAP2 WILD-TYPE 
           24.51            20.02 
[1] "0.3 - 62.8 (24.5)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1.6"
D785V2, 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       23        98         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IQGAP2 MUTATED           0          0          0          1        2
  IQGAP2 WILD-TYPE        19         10         41         30       33
                  vv
clus               STAGE IVA STAGE IVB
  IQGAP2 MUTATED           0         0
  IQGAP2 WILD-TYPE        13         1
D785V3, multiclass
            clus
vv           IQGAP2 MUTATED IQGAP2 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA              11               98
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              1               30
  STAGE IV                2               33
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  IQGAP2 MUTATED     0   3  14   4
  IQGAP2 WILD-TYPE   9  65 234  37
D785V4, multiclass
    clus
vv   IQGAP2 MUTATED IQGAP2 WILD-TYPE
  T1              0                9
  T2              3               65
  T3             14              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
  IQGAP2 MUTATED    18   0   3
  IQGAP2 WILD-TYPE 202  80  63
D785V5, multiclass
    clus
vv   IQGAP2 MUTATED IQGAP2 WILD-TYPE
  N0             18              202
  N1              0               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"
D785V6, binary
                  cls
clus                 0   1
  IQGAP2 MUTATED    15   2
  IQGAP2 WILD-TYPE 268  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IQGAP2 MUTATED     15    2
  IQGAP2 WILD-TYPE  268   46
   clus
vv  IQGAP2 MUTATED IQGAP2 WILD-TYPE
  0             15              268
  1              2               46
[1] 2 2
[1] FALSE
D785V7, 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
D785V8, binary
                  cls
clus                 0   1
  IQGAP2 MUTATED    17   4
  IQGAP2 WILD-TYPE 300  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IQGAP2 MUTATED     17    4
  IQGAP2 WILD-TYPE  300   44
                               clus
vv                              IQGAP2 MUTATED IQGAP2 WILD-TYPE
  COLON ADENOCARCINOMA                      17              300
  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 244   2  21  19
D785V9, multiclass
    clus
vv   IQGAP2 MUTATED IQGAP2 WILD-TYPE
  R0             13              244
  R1              0                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"
D785V10, 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
D785V11, 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(786) Variable = SCN2A MUTATION ANALYSIS
D786V1, survival
                 sevent
clus2               0   1
  SCN2A MUTATED    39   6
  SCN2A WILD-TYPE 243  67
  SCN2A MUTATED SCN2A WILD-TYPE 
             45             310 
  SCN2A MUTATED SCN2A WILD-TYPE 
              6              67 
$`SCN2A MUTATED`
TCGA-A6-2671 TCGA-A6-2676 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-6137 
       43.76        42.90        32.91        31.63        29.19        27.09 
TCGA-A6-6141 TCGA-A6-6651 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3663 TCGA-AA-3875 
        8.38        21.76         3.02         1.02         6.97        18.05 
TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3977 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00N 
       31.00        33.01        25.02        27.02        38.04         4.01 
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 
        0.07        14.50        58.39         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-5914 TCGA-CM-4743 TCGA-CM-5861 TCGA-CM-6163 
        1.35        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         1.51        60.79        98.24 
TCGA-G4-6306 TCGA-G4-6315 TCGA-G4-6628 
       44.68        36.72        52.80 

$`SCN2A WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        24.33        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5659 TCGA-A6-5661 
       33.34        32.75        36.53        14.53        30.44        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6142 
       23.61        22.09        22.06        32.71        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       19.66        20.28         7.04        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.05        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       19.07         7.96        13.94        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U 
       18.05        18.05        38.04        27.02        42.02        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        31.00        38.07         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       26.01        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 
      102.44        40.34        15.62        49.08        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93         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        16.01 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       29.03        16.04        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        12.95        13.05        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H 
      139.17         6.12        81.37       119.93        35.97       117.07 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        51.75        45.11        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       35.80        26.17        91.79        46.75 

  SCN2A MUTATED SCN2A WILD-TYPE 
           0.07            0.00 
  SCN2A MUTATED SCN2A WILD-TYPE 
          98.24          140.38 
  SCN2A MUTATED SCN2A WILD-TYPE 
          21.99           20.07 
[1] "0.1 - 98.2 (22.0)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.4"
D786V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SCN2A MUTATED        10        0        5        14         5         0
  SCN2A WILD-TYPE      54        1       20        95         3         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SCN2A MUTATED           1          0          5          1        3         1
  SCN2A WILD-TYPE        18         10         36         30       32        12
                 vv
clus              STAGE IVB
  SCN2A MUTATED           0
  SCN2A WILD-TYPE         1
D786V3, multiclass
            clus
vv           SCN2A MUTATED SCN2A WILD-TYPE
  STAGE I               10              54
  STAGE IA               0               1
  STAGE II               5              20
  STAGE IIA             14              95
  STAGE IIB              5               3
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             5              36
  STAGE IIIC             1              30
  STAGE IV               3              32
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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   7
  SCN2A WILD-TYPE   6  59 221  34
D786V4, multiclass
    clus
vv   SCN2A MUTATED SCN2A WILD-TYPE
  T1             3               6
  T2             9              59
  T3            27             221
  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
  SCN2A MUTATED    35   7   4
  SCN2A WILD-TYPE 185  73  62
D786V5, multiclass
    clus
vv   SCN2A MUTATED SCN2A WILD-TYPE
  N0            35             185
  N1             7              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"
D786V6, binary
                 cls
clus                0   1
  SCN2A MUTATED    38   3
  SCN2A WILD-TYPE 245  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCN2A MUTATED     38    3
  SCN2A WILD-TYPE  245   45
   clus
vv  SCN2A MUTATED SCN2A WILD-TYPE
  0            38             245
  1             3              45
[1] 2 2
[1] FALSE
D786V7, binary
                 cls
clus                0   1
  SCN2A MUTATED    15  31
  SCN2A WILD-TYPE 155 166
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCN2A MUTATED     15   31
  SCN2A WILD-TYPE  155  166
        clus
vv       SCN2A MUTATED SCN2A WILD-TYPE
  FEMALE            15             155
  MALE              31             166
[1] 2 2
[1] FALSE
D786V8, binary
                 cls
clus                0   1
  SCN2A MUTATED    36  10
  SCN2A WILD-TYPE 281  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCN2A MUTATED     36   10
  SCN2A WILD-TYPE  281   38
                               clus
vv                              SCN2A MUTATED SCN2A WILD-TYPE
  COLON ADENOCARCINOMA                     36             281
  COLON MUCINOUS ADENOCARCINOMA            10              38
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SCN2A MUTATED    30   0   1   7
  SCN2A WILD-TYPE 227   2  21  14
D786V9, multiclass
    clus
vv   SCN2A MUTATED SCN2A WILD-TYPE
  R0            30             227
  R1             0               2
  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"
D786V10, 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
D786V11, 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(787) Variable = KCNG4 MUTATION ANALYSIS
D787V1, survival
                 sevent
clus2               0   1
  KCNG4 MUTATED     7   3
  KCNG4 WILD-TYPE 275  70
  KCNG4 MUTATED KCNG4 WILD-TYPE 
             10             345 
  KCNG4 MUTATED KCNG4 WILD-TYPE 
              3              70 
$`KCNG4 MUTATED`
TCGA-A6-5665 TCGA-AA-3941 TCGA-AA-A010 TCGA-AD-6889 TCGA-AD-6965 TCGA-AY-6196 
       22.06        24.00        34.98        56.55         0.20         0.20 
TCGA-D5-6536 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A285 
       17.85        92.75        13.32         6.12 

$`KCNG4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37         4.21         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AU-3779 
        0.72         5.79        22.42        27.42        10.88        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        15.75        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-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        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  KCNG4 MUTATED KCNG4 WILD-TYPE 
            0.2             0.0 
  KCNG4 MUTATED KCNG4 WILD-TYPE 
          92.75          140.38 
  KCNG4 MUTATED KCNG4 WILD-TYPE 
         19.955          20.190 
[1] "0.2 - 92.8 (20.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.4"
D787V2, 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       25       104         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KCNG4 MUTATED           0          0          0          1        1         1
  KCNG4 WILD-TYPE        19         10         41         30       34        12
                 vv
clus              STAGE IVB
  KCNG4 MUTATED           0
  KCNG4 WILD-TYPE         1
D787V3, multiclass
            clus
vv           KCNG4 MUTATED KCNG4 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              5             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  68 241  38
D787V4, multiclass
    clus
vv   KCNG4 MUTATED KCNG4 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             7             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
  KCNG4 MUTATED     6   1   3
  KCNG4 WILD-TYPE 214  79  63
D787V5, multiclass
    clus
vv   KCNG4 MUTATED KCNG4 WILD-TYPE
  N0             6             214
  N1             1              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"
D787V6, binary
                 cls
clus                0   1
  KCNG4 MUTATED     6   2
  KCNG4 WILD-TYPE 277  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNG4 MUTATED      6    2
  KCNG4 WILD-TYPE  277   46
   clus
vv  KCNG4 MUTATED KCNG4 WILD-TYPE
  0             6             277
  1             2              46
[1] 2 2
[1] FALSE
D787V7, 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
D787V8, binary
                 cls
clus                0   1
  KCNG4 MUTATED     8   2
  KCNG4 WILD-TYPE 309  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNG4 MUTATED      8    2
  KCNG4 WILD-TYPE  309   46
                               clus
vv                              KCNG4 MUTATED KCNG4 WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  KCNG4 MUTATED     5   0   0   0
  KCNG4 WILD-TYPE 252   2  22  21
D787V9, multiclass
    clus
vv   KCNG4 MUTATED KCNG4 WILD-TYPE
  R0             5             252
  R1             0               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"
D787V10, 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
D787V11, 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(788) Variable = MANBA MUTATION ANALYSIS
D788V1, survival
                 sevent
clus2               0   1
  MANBA MUTATED    10   2
  MANBA WILD-TYPE 272  71
  MANBA MUTATED MANBA WILD-TYPE 
             12             343 
  MANBA MUTATED MANBA WILD-TYPE 
              2              71 
$`MANBA MUTATED`
TCGA-AA-3525 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3672 TCGA-AA-A00N TCGA-AA-A01Q 
        8.05        17.95        29.95         0.92         4.01         1.02 
TCGA-AD-6964 TCGA-AZ-4315 TCGA-CK-4947 TCGA-CK-5914 TCGA-CM-6168 TCGA-D5-6533 
       10.88        58.39        17.56        21.99        12.99         1.32 

$`MANBA WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       13.02        24.00        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 
        0.07         0.26         0.33         0.10         1.35       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 
       40.34        15.62        49.08        51.32        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-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 
       12.26        19.59        13.51        11.51        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  MANBA MUTATED MANBA WILD-TYPE 
           0.92            0.00 
  MANBA MUTATED MANBA WILD-TYPE 
          58.39          140.38 
  MANBA MUTATED MANBA WILD-TYPE 
         11.935          20.980 
[1] "0.9 - 58.4 (11.9)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.3"
D788V2, 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       24       105         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MANBA MUTATED           1          0          3          0        0         1
  MANBA WILD-TYPE        18         10         38         31       35        12
                 vv
clus              STAGE IVB
  MANBA MUTATED           0
  MANBA WILD-TYPE         1
D788V3, multiclass
            clus
vv           MANBA MUTATED MANBA WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              4             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             3              38
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  68 240  37
D788V4, multiclass
    clus
vv   MANBA MUTATED MANBA WILD-TYPE
  T1             0               9
  T2             0              68
  T3             8             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
  MANBA MUTATED     7   4   1
  MANBA WILD-TYPE 213  76  65
D788V5, multiclass
    clus
vv   MANBA MUTATED MANBA WILD-TYPE
  N0             7             213
  N1             4              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"
D788V6, binary
                 cls
clus                0   1
  MANBA MUTATED    10   0
  MANBA WILD-TYPE 273  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MANBA MUTATED     10    0
  MANBA WILD-TYPE  273   48
   clus
vv  MANBA MUTATED MANBA WILD-TYPE
  0            10             273
  1             0              48
[1] 2 2
[1] FALSE
D788V7, 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
D788V8, binary
                 cls
clus                0   1
  MANBA MUTATED    10   2
  MANBA WILD-TYPE 307  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MANBA MUTATED     10    2
  MANBA WILD-TYPE  307   46
                               clus
vv                              MANBA MUTATED MANBA WILD-TYPE
  COLON ADENOCARCINOMA                     10             307
  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 248   2  22  19
D788V9, multiclass
    clus
vv   MANBA MUTATED MANBA WILD-TYPE
  R0             9             248
  R1             0               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"
D788V10, 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
D788V11, 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(789) Variable = SLC22A16 MUTATION ANALYSIS
D789V1, survival
                    sevent
clus2                  0   1
  SLC22A16 MUTATED    10   2
  SLC22A16 WILD-TYPE 272  71
  SLC22A16 MUTATED SLC22A16 WILD-TYPE 
                12                343 
  SLC22A16 MUTATED SLC22A16 WILD-TYPE 
                 2                 71 
$`SLC22A16 MUTATED`
TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-A00R TCGA-AA-A01T TCGA-AD-6964 
       22.06        19.66         3.02         0.99        33.04        10.88 
TCGA-AU-6004 TCGA-CA-6718 TCGA-CK-5913 TCGA-CM-4746 TCGA-CM-6171 TCGA-G4-6588 
       27.09         0.10        51.32        37.02        14.04        26.17 

$`SLC22A16 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.12        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       27.02        42.02        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X 
       38.07         1.02        35.01         1.02        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
        5.79        22.42        27.42         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.33         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 
      102.44        40.34        15.62        49.08        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 
       52.80 

  SLC22A16 MUTATED SLC22A16 WILD-TYPE 
               0.1                0.0 
  SLC22A16 MUTATED SLC22A16 WILD-TYPE 
             51.32             140.38 
  SLC22A16 MUTATED SLC22A16 WILD-TYPE 
             20.86              20.19 
[1] "0.1 - 51.3 (20.9)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1"  
D789V2, 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       24       104         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC22A16 MUTATED           1          0          0          1        0
  SLC22A16 WILD-TYPE        18         10         41         30       35
                    vv
clus                 STAGE IVA STAGE IVB
  SLC22A16 MUTATED           0         0
  SLC22A16 WILD-TYPE        13         1
D789V3, multiclass
            clus
vv           SLC22A16 MUTATED SLC22A16 WILD-TYPE
  STAGE I                   4                 60
  STAGE IA                  0                  1
  STAGE II                  1                 24
  STAGE IIA                 5                104
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 1                 18
  STAGE IIIA                0                 10
  STAGE IIIB                0                 41
  STAGE IIIC                1                 30
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  SLC22A16 MUTATED     0   4   7   2
  SLC22A16 WILD-TYPE   9  64 241  39
D789V4, multiclass
    clus
vv   SLC22A16 MUTATED SLC22A16 WILD-TYPE
  T1                0                  9
  T2                4                 64
  T3                7                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
  SLC22A16 MUTATED    10   2   1
  SLC22A16 WILD-TYPE 210  78  65
D789V5, multiclass
    clus
vv   SLC22A16 MUTATED SLC22A16 WILD-TYPE
  N0               10                210
  N1                2                 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"
D789V6, binary
                    cls
clus                   0   1
  SLC22A16 MUTATED    10   0
  SLC22A16 WILD-TYPE 273  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC22A16 MUTATED     10    0
  SLC22A16 WILD-TYPE  273   48
   clus
vv  SLC22A16 MUTATED SLC22A16 WILD-TYPE
  0               10                273
  1                0                 48
[1] 2 2
[1] FALSE
D789V7, 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
D789V8, binary
                    cls
clus                   0   1
  SLC22A16 MUTATED    12   1
  SLC22A16 WILD-TYPE 305  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC22A16 MUTATED     12    1
  SLC22A16 WILD-TYPE  305   47
                               clus
vv                              SLC22A16 MUTATED SLC22A16 WILD-TYPE
  COLON ADENOCARCINOMA                        12                305
  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 247   2  22  19
D789V9, multiclass
    clus
vv   SLC22A16 MUTATED SLC22A16 WILD-TYPE
  R0               10                247
  R1                0                  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"
D789V10, 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
D789V11, 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(790) Variable = TAOK3 MUTATION ANALYSIS
D790V1, survival
                 sevent
clus2               0   1
  TAOK3 MUTATED    16   3
  TAOK3 WILD-TYPE 266  70
  TAOK3 MUTATED TAOK3 WILD-TYPE 
             19             336 
  TAOK3 MUTATED TAOK3 WILD-TYPE 
              3              70 
$`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         0.33        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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
       20.28         1.02        35.01        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       40.34        49.08        21.99        21.14         2.93         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        16.01         5.03 
TCGA-CM-5863 TCGA-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-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       11.51        20.19         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6930 
       10.13        12.43        14.30         9.04        11.64         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  TAOK3 MUTATED TAOK3 WILD-TYPE 
           0.33            0.00 
  TAOK3 MUTATED TAOK3 WILD-TYPE 
          55.04          140.38 
  TAOK3 MUTATED TAOK3 WILD-TYPE 
         15.620          20.995 
[1] "0.3 - 55.0 (15.6)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.1"
D790V2, 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       23       101         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TAOK3 MUTATED           1          0          1          1        1         0
  TAOK3 WILD-TYPE        18         10         40         30       34        13
                 vv
clus              STAGE IVB
  TAOK3 MUTATED           0
  TAOK3 WILD-TYPE         1
D790V3, multiclass
            clus
vv           TAOK3 MUTATED TAOK3 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              8             101
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TAOK3 MUTATED     0   3  12   5
  TAOK3 WILD-TYPE   9  65 236  36
D790V4, multiclass
    clus
vv   TAOK3 MUTATED TAOK3 WILD-TYPE
  T1             0               9
  T2             3              65
  T3            12             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
  TAOK3 MUTATED    16   3   1
  TAOK3 WILD-TYPE 204  77  65
D790V5, multiclass
    clus
vv   TAOK3 MUTATED TAOK3 WILD-TYPE
  N0            16             204
  N1             3              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"
D790V6, binary
                 cls
clus                0   1
  TAOK3 MUTATED    16   1
  TAOK3 WILD-TYPE 267  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAOK3 MUTATED     16    1
  TAOK3 WILD-TYPE  267   47
   clus
vv  TAOK3 MUTATED TAOK3 WILD-TYPE
  0            16             267
  1             1              47
[1] 2 2
[1] FALSE
D790V7, 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
D790V8, binary
                 cls
clus                0   1
  TAOK3 MUTATED    14   6
  TAOK3 WILD-TYPE 303  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAOK3 MUTATED     14    6
  TAOK3 WILD-TYPE  303   42
                               clus
vv                              TAOK3 MUTATED TAOK3 WILD-TYPE
  COLON ADENOCARCINOMA                     14             303
  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 241   2  22  18
D790V9, multiclass
    clus
vv   TAOK3 MUTATED TAOK3 WILD-TYPE
  R0            16             241
  R1             0               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"
D790V10, 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
D790V11, 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(791) Variable = RPGRIP1L MUTATION ANALYSIS
D791V1, survival
                    sevent
clus2                  0   1
  RPGRIP1L MUTATED    12   3
  RPGRIP1L WILD-TYPE 270  70
  RPGRIP1L MUTATED RPGRIP1L WILD-TYPE 
                15                340 
  RPGRIP1L MUTATED RPGRIP1L WILD-TYPE 
                 3                 70 
$`RPGRIP1L MUTATED`
TCGA-A6-5661 TCGA-A6-6141 TCGA-A6-6648 TCGA-AA-3511 TCGA-AA-3680 TCGA-AA-3949 
       33.53         8.38        25.18         6.97        11.01        26.01 
TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-6598 TCGA-CM-4752 
       24.00         2.01         4.01        34.98        49.41        13.02 
TCGA-D5-6536 TCGA-F4-6703 TCGA-F4-6808 
       17.85        35.87        33.67 

$`RPGRIP1L WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6649 
       22.06        32.71        27.09        22.52        25.08        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 
       14.01         0.92        50.04        47.01        15.02         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.38        13.45         6.18         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       16.24        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  RPGRIP1L MUTATED RPGRIP1L WILD-TYPE 
              2.01               0.00 
  RPGRIP1L MUTATED RPGRIP1L WILD-TYPE 
             49.41             140.38 
  RPGRIP1L MUTATED RPGRIP1L WILD-TYPE 
            24.000             20.155 
[1] "2.0 - 49.4 (24.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D791V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RPGRIP1L MUTATED         1        0        2         8         2         0
  RPGRIP1L WILD-TYPE      63        1       23       101         6         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RPGRIP1L MUTATED           0          0          1          0        1
  RPGRIP1L WILD-TYPE        19         10         40         31       34
                    vv
clus                 STAGE IVA STAGE IVB
  RPGRIP1L MUTATED           1         0
  RPGRIP1L WILD-TYPE        12         1
D791V3, multiclass
            clus
vv           RPGRIP1L MUTATED RPGRIP1L WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  2                 23
  STAGE IIA                 8                101
  STAGE IIB                 2                  6
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                0                 10
  STAGE IIIB                1                 40
  STAGE IIIC                0                 31
  STAGE IV                  1                 34
  STAGE IVA                 1                 12
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of 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  11   4
  RPGRIP1L WILD-TYPE   8  68 237  37
D791V4, multiclass
    clus
vv   RPGRIP1L MUTATED RPGRIP1L WILD-TYPE
  T1                1                  8
  T2                0                 68
  T3               11                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    14   1   1
  RPGRIP1L WILD-TYPE 206  79  65
D791V5, multiclass
    clus
vv   RPGRIP1L MUTATED RPGRIP1L WILD-TYPE
  N0               14                206
  N1                1                 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"
D791V6, binary
                    cls
clus                   0   1
  RPGRIP1L MUTATED    13   2
  RPGRIP1L WILD-TYPE 270  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  RPGRIP1L MUTATED     13    2
  RPGRIP1L WILD-TYPE  270   46
   clus
vv  RPGRIP1L MUTATED RPGRIP1L WILD-TYPE
  0               13                270
  1                2                 46
[1] 2 2
[1] FALSE
D791V7, binary
                    cls
clus                   0   1
  RPGRIP1L MUTATED     9   7
  RPGRIP1L WILD-TYPE 161 190
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  RPGRIP1L MUTATED      9    7
  RPGRIP1L WILD-TYPE  161  190
        clus
vv       RPGRIP1L MUTATED RPGRIP1L WILD-TYPE
  FEMALE                9                161
  MALE                  7                190
[1] 2 2
[1] FALSE
D791V8, binary
                    cls
clus                   0   1
  RPGRIP1L MUTATED    12   4
  RPGRIP1L WILD-TYPE 305  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  RPGRIP1L MUTATED     12    4
  RPGRIP1L WILD-TYPE  305   44
                               clus
vv                              RPGRIP1L MUTATED RPGRIP1L WILD-TYPE
  COLON ADENOCARCINOMA                        12                305
  COLON MUCINOUS ADENOCARCINOMA                4                 44
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  RPGRIP1L MUTATED    11   0   1   0
  RPGRIP1L WILD-TYPE 246   2  21  21
D791V9, multiclass
    clus
vv   RPGRIP1L MUTATED RPGRIP1L WILD-TYPE
  R0               11                246
  R1                0                  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"
D791V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RPGRIP1L MUTATED                                  0     0
  RPGRIP1L WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  RPGRIP1L MUTATED                           3     5
  RPGRIP1L WILD-TYPE                        16   171
D791V11, multiclass
                                  clus
vv                                 RPGRIP1L MUTATED RPGRIP1L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 10
  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(792) Variable = GRINA MUTATION ANALYSIS
D792V1, survival
                 sevent
clus2               0   1
  GRINA MUTATED     3   1
  GRINA WILD-TYPE 279  72
  GRINA MUTATED GRINA WILD-TYPE 
              4             351 
  GRINA MUTATED GRINA WILD-TYPE 
              1              72 
$`GRINA MUTATED`
TCGA-A6-5665 TCGA-CM-5341 TCGA-G4-6309 TCGA-G4-6626 
       22.06        29.06        51.75        46.75 

$`GRINA WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       26.17        91.79        52.80 

  GRINA MUTATED GRINA WILD-TYPE 
          22.06            0.00 
  GRINA MUTATED GRINA WILD-TYPE 
          51.75          140.38 
  GRINA MUTATED GRINA WILD-TYPE 
         37.905          20.020 
[1] "22.1 - 51.8 (37.9)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.2"
D792V2, 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       25       107         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        19          9         40         31       35        13
                 vv
clus              STAGE IVB
  GRINA MUTATED           0
  GRINA WILD-TYPE         1
D792V3, multiclass
            clus
vv           GRINA MUTATED GRINA WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              2             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GRINA MUTATED     0   1   3   0
  GRINA WILD-TYPE   9  67 245  41
D792V4, multiclass
    clus
vv   GRINA MUTATED GRINA WILD-TYPE
  T1             0               9
  T2             1              67
  T3             3             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
  GRINA MUTATED     2   2   0
  GRINA WILD-TYPE 218  78  66
D792V5, multiclass
    clus
vv   GRINA MUTATED GRINA WILD-TYPE
  N0             2             218
  N1             2              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"
D792V6, binary
                 cls
clus                0   1
  GRINA MUTATED     4   0
  GRINA WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GRINA MUTATED      4    0
  GRINA WILD-TYPE  279   48
   clus
vv  GRINA MUTATED GRINA WILD-TYPE
  0             4             279
  1             0              48
[1] 2 2
[1] FALSE
D792V7, 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
D792V8, binary
                 cls
clus                0   1
  GRINA MUTATED     4   0
  GRINA WILD-TYPE 313  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GRINA MUTATED      4    0
  GRINA WILD-TYPE  313   48
                               clus
vv                              GRINA MUTATED GRINA WILD-TYPE
  COLON ADENOCARCINOMA                      4             313
  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 253   2  22  21
D792V9, multiclass
    clus
vv   GRINA MUTATED GRINA WILD-TYPE
  R0             4             253
  R1             0               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"
D792V10, 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
D792V11, 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(793) Variable = SLC25A44 MUTATION ANALYSIS
D793V1, survival
                    sevent
clus2                  0   1
  SLC25A44 MUTATED     5   0
  SLC25A44 WILD-TYPE 277  73
  SLC25A44 MUTATED SLC25A44 WILD-TYPE 
                 5                350 
  SLC25A44 MUTATED SLC25A44 WILD-TYPE 
                 0                 73 
$`SLC25A44 MUTATED`
TCGA-AA-3966 TCGA-AA-A01Q TCGA-CA-6715 TCGA-CM-6162 TCGA-D5-5541 
        2.01         1.02         0.07        12.00        11.51 

$`SLC25A44 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        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-D5-6529 TCGA-D5-6532 
       45.40        12.26        19.59        13.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  SLC25A44 MUTATED SLC25A44 WILD-TYPE 
              0.07               0.00 
  SLC25A44 MUTATED SLC25A44 WILD-TYPE 
             12.00             140.38 
  SLC25A44 MUTATED SLC25A44 WILD-TYPE 
              2.01              20.98 
[1] "0.1 - 12.0 (2.0)"   "0.0 - 140.4 (21.0)"
[1] "hr="     "3300000"
D793V2, 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       24       108         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC25A44 MUTATED           0          0          3          0        0
  SLC25A44 WILD-TYPE        19         10         38         31       35
                    vv
clus                 STAGE IVA STAGE IVB
  SLC25A44 MUTATED           0         0
  SLC25A44 WILD-TYPE        13         1
D793V3, multiclass
            clus
vv           SLC25A44 MUTATED SLC25A44 WILD-TYPE
  STAGE I                   0                 64
  STAGE IA                  0                  1
  STAGE II                  1                 24
  STAGE IIA                 1                108
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                0                 10
  STAGE IIIB                3                 38
  STAGE IIIC                0                 31
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  SLC25A44 MUTATED     0   0   5   0
  SLC25A44 WILD-TYPE   9  68 243  41
D793V4, multiclass
    clus
vv   SLC25A44 MUTATED SLC25A44 WILD-TYPE
  T1                0                  9
  T2                0                 68
  T3                5                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
  SLC25A44 MUTATED     2   3   0
  SLC25A44 WILD-TYPE 218  77  66
D793V5, multiclass
    clus
vv   SLC25A44 MUTATED SLC25A44 WILD-TYPE
  N0                2                218
  N1                3                 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"
D793V6, binary
                    cls
clus                   0   1
  SLC25A44 MUTATED     5   0
  SLC25A44 WILD-TYPE 278  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC25A44 MUTATED      5    0
  SLC25A44 WILD-TYPE  278   48
   clus
vv  SLC25A44 MUTATED SLC25A44 WILD-TYPE
  0                5                278
  1                0                 48
[1] 2 2
[1] FALSE
D793V7, 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
D793V8, binary
                    cls
clus                   0   1
  SLC25A44 MUTATED     3   2
  SLC25A44 WILD-TYPE 314  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC25A44 MUTATED      3    2
  SLC25A44 WILD-TYPE  314   46
                               clus
vv                              SLC25A44 MUTATED SLC25A44 WILD-TYPE
  COLON ADENOCARCINOMA                         3                314
  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 254   2  22  20
D793V9, multiclass
    clus
vv   SLC25A44 MUTATED SLC25A44 WILD-TYPE
  R0                3                254
  R1                0                  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"
D793V10, 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
D793V11, 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(794) Variable = SGK3 MUTATION ANALYSIS
D794V1, survival
                sevent
clus2              0   1
  SGK3 MUTATED     4   4
  SGK3 WILD-TYPE 278  69
  SGK3 MUTATED SGK3 WILD-TYPE 
             8            347 
  SGK3 MUTATED SGK3 WILD-TYPE 
             4             69 
$`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 
        1.51        60.79 

$`SGK3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 
        4.21        56.55         0.79         0.72        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 
      100.01        29.56         5.23        11.74         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
      119.93        35.97       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  SGK3 MUTATED SGK3 WILD-TYPE 
          1.51           0.00 
  SGK3 MUTATED SGK3 WILD-TYPE 
         63.98         140.38 
  SGK3 MUTATED SGK3 WILD-TYPE 
        20.335         20.190 
[1] "1.5 - 64.0 (20.3)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2.1"
D794V2, 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       24       105         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        19         10         41         30       34        13
                vv
clus             STAGE IVB
  SGK3 MUTATED           0
  SGK3 WILD-TYPE         1
D794V3, multiclass
            clus
vv           SGK3 MUTATED SGK3 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             4            105
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            1             30
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SGK3 MUTATED     0   0   6   2
  SGK3 WILD-TYPE   9  68 242  39
D794V4, multiclass
    clus
vv   SGK3 MUTATED SGK3 WILD-TYPE
  T1            0              9
  T2            0             68
  T3            6            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
  SGK3 MUTATED     6   0   2
  SGK3 WILD-TYPE 214  80  64
D794V5, multiclass
    clus
vv   SGK3 MUTATED SGK3 WILD-TYPE
  N0            6            214
  N1            0             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"
D794V6, binary
                cls
clus               0   1
  SGK3 MUTATED     5   1
  SGK3 WILD-TYPE 278  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  SGK3 MUTATED      5    1
  SGK3 WILD-TYPE  278   47
   clus
vv  SGK3 MUTATED SGK3 WILD-TYPE
  0            5            278
  1            1             47
[1] 2 2
[1] FALSE
D794V7, 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
D794V8, binary
                cls
clus               0   1
  SGK3 MUTATED     6   2
  SGK3 WILD-TYPE 311  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  SGK3 MUTATED      6    2
  SGK3 WILD-TYPE  311   46
                               clus
vv                              SGK3 MUTATED SGK3 WILD-TYPE
  COLON ADENOCARCINOMA                     6            311
  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 253   2  22  21
D794V9, multiclass
    clus
vv   SGK3 MUTATED SGK3 WILD-TYPE
  R0            4            253
  R1            0              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"
D794V10, 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
D794V11, 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(795) Variable = TMEM48 MUTATION ANALYSIS
D795V1, survival
                  sevent
clus2                0   1
  TMEM48 MUTATED     7   2
  TMEM48 WILD-TYPE 275  71
  TMEM48 MUTATED TMEM48 WILD-TYPE 
               9              346 
  TMEM48 MUTATED TMEM48 WILD-TYPE 
               2               71 
$`TMEM48 MUTATED`
TCGA-A6-5661 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3525 TCGA-AZ-4315 TCGA-AZ-6598 
       33.53         3.02        63.98         8.05        58.39        49.41 
TCGA-CA-6717 TCGA-CA-6718 TCGA-G4-6317 
        0.33         0.10        36.00 

$`TMEM48 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       24.03        37.05        36.03        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07         0.26         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       51.75        45.11        36.72        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  TMEM48 MUTATED TMEM48 WILD-TYPE 
             0.1              0.0 
  TMEM48 MUTATED TMEM48 WILD-TYPE 
           63.98           140.38 
  TMEM48 MUTATED TMEM48 WILD-TYPE 
          33.530           20.155 
[1] "0.1 - 64.0 (33.5)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1"  
D795V2, 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       22       104         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM48 MUTATED           0          0          1          1        0
  TMEM48 WILD-TYPE        19         10         40         30       35
                  vv
clus               STAGE IVA STAGE IVB
  TMEM48 MUTATED           0         0
  TMEM48 WILD-TYPE        13         1
D795V3, multiclass
            clus
vv           TMEM48 MUTATED TMEM48 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                3               22
  STAGE IIA               5              104
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TMEM48 MUTATED     0   0  10   0
  TMEM48 WILD-TYPE   9  68 238  41
D795V4, multiclass
    clus
vv   TMEM48 MUTATED TMEM48 WILD-TYPE
  T1              0                9
  T2              0               68
  T3             10              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
  TMEM48 MUTATED     8   1   1
  TMEM48 WILD-TYPE 212  79  65
D795V5, multiclass
    clus
vv   TMEM48 MUTATED TMEM48 WILD-TYPE
  N0              8              212
  N1              1               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"
D795V6, binary
                  cls
clus                 0   1
  TMEM48 MUTATED     8   0
  TMEM48 WILD-TYPE 275  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM48 MUTATED      8    0
  TMEM48 WILD-TYPE  275   48
   clus
vv  TMEM48 MUTATED TMEM48 WILD-TYPE
  0              8              275
  1              0               48
[1] 2 2
[1] FALSE
D795V7, 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
D795V8, binary
                  cls
clus                 0   1
  TMEM48 MUTATED     9   1
  TMEM48 WILD-TYPE 308  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM48 MUTATED      9    1
  TMEM48 WILD-TYPE  308   47
                               clus
vv                              TMEM48 MUTATED TMEM48 WILD-TYPE
  COLON ADENOCARCINOMA                       9              308
  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 250   2  22  19
D795V9, multiclass
    clus
vv   TMEM48 MUTATED TMEM48 WILD-TYPE
  R0              7              250
  R1              0                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"
D795V10, 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
D795V11, 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(796) Variable = TXNDC6 MUTATION ANALYSIS
D796V1, survival
                  sevent
clus2                0   1
  TXNDC6 MUTATED     6   2
  TXNDC6 WILD-TYPE 276  71
  TXNDC6 MUTATED TXNDC6 WILD-TYPE 
               8              347 
  TXNDC6 MUTATED TXNDC6 WILD-TYPE 
               2               71 
$`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        61.41        13.02        17.85 
TCGA-DM-A1DA TCGA-DM-A1HB 
        7.50       135.65 

$`TXNDC6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        42.90        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 
       35.05        33.04         0.99        25.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        15.12         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  TXNDC6 MUTATED TXNDC6 WILD-TYPE 
            1.02             0.00 
  TXNDC6 MUTATED TXNDC6 WILD-TYPE 
          135.65           140.38 
  TXNDC6 MUTATED TXNDC6 WILD-TYPE 
           21.09            20.19 
[1] "1.0 - 135.7 (21.1)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D796V2, 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       24       107         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TXNDC6 MUTATED           0          0          1          2        0
  TXNDC6 WILD-TYPE        19         10         40         29       35
                  vv
clus               STAGE IVA STAGE IVB
  TXNDC6 MUTATED           0         0
  TXNDC6 WILD-TYPE        13         1
D796V3, multiclass
            clus
vv           TXNDC6 MUTATED TXNDC6 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               2              107
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              2               29
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TXNDC6 MUTATED     1   1   6   0
  TXNDC6 WILD-TYPE   8  67 242  41
D796V4, multiclass
    clus
vv   TXNDC6 MUTATED TXNDC6 WILD-TYPE
  T1              1                8
  T2              1               67
  T3              6              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
  TXNDC6 MUTATED     5   1   2
  TXNDC6 WILD-TYPE 215  79  64
D796V5, multiclass
    clus
vv   TXNDC6 MUTATED TXNDC6 WILD-TYPE
  N0              5              215
  N1              1               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"
D796V6, binary
                  cls
clus                 0   1
  TXNDC6 MUTATED     8   0
  TXNDC6 WILD-TYPE 275  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TXNDC6 MUTATED      8    0
  TXNDC6 WILD-TYPE  275   48
   clus
vv  TXNDC6 MUTATED TXNDC6 WILD-TYPE
  0              8              275
  1              0               48
[1] 2 2
[1] FALSE
D796V7, 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
D796V8, binary
                  cls
clus                 0   1
  TXNDC6 MUTATED     7   1
  TXNDC6 WILD-TYPE 310  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TXNDC6 MUTATED      7    1
  TXNDC6 WILD-TYPE  310   47
                               clus
vv                              TXNDC6 MUTATED TXNDC6 WILD-TYPE
  COLON ADENOCARCINOMA                       7              310
  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 252   2  22  21
D796V9, multiclass
    clus
vv   TXNDC6 MUTATED TXNDC6 WILD-TYPE
  R0              5              252
  R1              0                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"
D796V10, 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
D796V11, 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(797) Variable = UIMC1 MUTATION ANALYSIS
D797V1, survival
                 sevent
clus2               0   1
  UIMC1 MUTATED     4   2
  UIMC1 WILD-TYPE 278  71
  UIMC1 MUTATED UIMC1 WILD-TYPE 
              6             349 
  UIMC1 MUTATED UIMC1 WILD-TYPE 
              2              71 
$`UIMC1 MUTATED`
TCGA-AA-A01P TCGA-CA-6717 TCGA-CK-4948 TCGA-CM-5862 TCGA-D5-6927 TCGA-G4-6323 
       38.07         0.33       102.44         5.03         9.44        13.78 

$`UIMC1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  UIMC1 MUTATED UIMC1 WILD-TYPE 
           0.33            0.00 
  UIMC1 MUTATED UIMC1 WILD-TYPE 
         102.44          140.38 
  UIMC1 MUTATED UIMC1 WILD-TYPE 
          11.61           20.28 
[1] "0.3 - 102.4 (11.6)" "0.0 - 140.4 (20.3)"
[1] "hr=" "1.5"
D797V2, 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       25       107         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  UIMC1 MUTATED           1          1          0          0        0         1
  UIMC1 WILD-TYPE        18          9         41         31       35        12
                 vv
clus              STAGE IVB
  UIMC1 MUTATED           0
  UIMC1 WILD-TYPE         1
D797V3, multiclass
            clus
vv           UIMC1 MUTATED UIMC1 WILD-TYPE
  STAGE I                0              64
  STAGE IA               1               0
  STAGE II               0              25
  STAGE IIA              2             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             1               9
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  68 243  41
D797V4, multiclass
    clus
vv   UIMC1 MUTATED UIMC1 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             5             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
  UIMC1 MUTATED     3   3   0
  UIMC1 WILD-TYPE 217  77  66
D797V5, multiclass
    clus
vv   UIMC1 MUTATED UIMC1 WILD-TYPE
  N0             3             217
  N1             3              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"
D797V6, binary
                 cls
clus                0   1
  UIMC1 MUTATED     4   1
  UIMC1 WILD-TYPE 279  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UIMC1 MUTATED      4    1
  UIMC1 WILD-TYPE  279   47
   clus
vv  UIMC1 MUTATED UIMC1 WILD-TYPE
  0             4             279
  1             1              47
[1] 2 2
[1] FALSE
D797V7, 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
D797V8, binary
                 cls
clus                0   1
  UIMC1 MUTATED     5   1
  UIMC1 WILD-TYPE 312  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UIMC1 MUTATED      5    1
  UIMC1 WILD-TYPE  312   47
                               clus
vv                              UIMC1 MUTATED UIMC1 WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  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 252   2  22  20
D797V9, multiclass
    clus
vv   UIMC1 MUTATED UIMC1 WILD-TYPE
  R0             5             252
  R1             0               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"
D797V10, 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
D797V11, 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(798) Variable = TGFBR2 MUTATION ANALYSIS
D798V1, survival
                  sevent
clus2                0   1
  TGFBR2 MUTATED    18   4
  TGFBR2 WILD-TYPE 264  69
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
              22              333 
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
               4               69 
$`TGFBR2 MUTATED`
TCGA-A6-3808 TCGA-A6-5661 TCGA-A6-6141 TCGA-AA-3492 TCGA-AA-3514 TCGA-AA-3968 
       33.34        33.53         8.38         3.02         1.02        21.99 
TCGA-AA-A010 TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A029 TCGA-AA-A03F TCGA-AD-6964 
       34.98         1.02        35.01        51.98        18.05        10.88 
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        13.51        12.00 
TCGA-DM-A1HB TCGA-F4-6460 TCGA-G4-6303 TCGA-G4-6588 
      135.65        13.38        65.85        26.17 

$`TGFBR2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       32.71        27.09        22.52        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         1.02        35.01        63.98         6.97 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01S TCGA-AA-A01T 
       12.00        31.00        31.00        38.07         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02F TCGA-AA-A02H 
       35.01        26.01        37.02        39.06        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J 
        5.03        14.01         0.92        41.00        39.98        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 
        1.35        17.56       102.44        40.34        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
       21.99        21.14         2.93         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        16.01        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-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       45.40        12.26        19.59        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      107.67        74.56        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
            1.02             0.00 
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
          135.65           140.38 
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
          16.835           20.280 
[1] "1.0 - 135.7 (16.8)" "0.0 - 140.4 (20.3)"
[1] "hr=" "1.1"
D798V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TGFBR2 MUTATED         3        0        3         7         1         0
  TGFBR2 WILD-TYPE      61        1       22       102         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TGFBR2 MUTATED           3          0          2          1        1
  TGFBR2 WILD-TYPE        16         10         39         30       34
                  vv
clus               STAGE IVA STAGE IVB
  TGFBR2 MUTATED           0         0
  TGFBR2 WILD-TYPE        13         1
D798V3, multiclass
            clus
vv           TGFBR2 MUTATED TGFBR2 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                3               22
  STAGE IIA               7              102
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               3               16
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              1               30
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TGFBR2 MUTATED     0   3  15   4
  TGFBR2 WILD-TYPE   9  65 233  37
D798V4, multiclass
    clus
vv   TGFBR2 MUTATED TGFBR2 WILD-TYPE
  T1              0                9
  T2              3               65
  T3             15              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
  TGFBR2 MUTATED    14   3   5
  TGFBR2 WILD-TYPE 206  77  61
D798V5, multiclass
    clus
vv   TGFBR2 MUTATED TGFBR2 WILD-TYPE
  N0             14              206
  N1              3               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"
D798V6, binary
                  cls
clus                 0   1
  TGFBR2 MUTATED    20   1
  TGFBR2 WILD-TYPE 263  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR2 MUTATED     20    1
  TGFBR2 WILD-TYPE  263   47
   clus
vv  TGFBR2 MUTATED TGFBR2 WILD-TYPE
  0             20              263
  1              1               47
[1] 2 2
[1] FALSE
D798V7, binary
                  cls
clus                 0   1
  TGFBR2 MUTATED    12  10
  TGFBR2 WILD-TYPE 158 187
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR2 MUTATED     12   10
  TGFBR2 WILD-TYPE  158  187
        clus
vv       TGFBR2 MUTATED TGFBR2 WILD-TYPE
  FEMALE             12              158
  MALE               10              187
[1] 2 2
[1] FALSE
D798V8, binary
                  cls
clus                 0   1
  TGFBR2 MUTATED    19   3
  TGFBR2 WILD-TYPE 298  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR2 MUTATED     19    3
  TGFBR2 WILD-TYPE  298   45
                               clus
vv                              TGFBR2 MUTATED TGFBR2 WILD-TYPE
  COLON ADENOCARCINOMA                      19              298
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TGFBR2 MUTATED    18   0   0   1
  TGFBR2 WILD-TYPE 239   2  22  20
D798V9, multiclass
    clus
vv   TGFBR2 MUTATED TGFBR2 WILD-TYPE
  R0             18              239
  R1              0                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"
D798V10, 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                           2    12
  TGFBR2 WILD-TYPE                        17   164
D798V11, multiclass
                                  clus
vv                                 TGFBR2 MUTATED TGFBR2 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(799) Variable = DLL3 MUTATION ANALYSIS
D799V1, survival
                sevent
clus2              0   1
  DLL3 MUTATED     5   1
  DLL3 WILD-TYPE 277  72
  DLL3 MUTATED DLL3 WILD-TYPE 
             6            349 
  DLL3 MUTATED DLL3 WILD-TYPE 
             1             72 
$`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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  DLL3 MUTATED DLL3 WILD-TYPE 
          9.44           0.00 
  DLL3 MUTATED DLL3 WILD-TYPE 
         49.41         140.38 
  DLL3 MUTATED DLL3 WILD-TYPE 
         28.70          20.12 
[1] "9.4 - 49.4 (28.7)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.3"
D799V2, 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       24       108         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        19         10         40         31       35        13
                vv
clus             STAGE IVB
  DLL3 MUTATED           0
  DLL3 WILD-TYPE         1
D799V3, multiclass
            clus
vv           DLL3 MUTATED DLL3 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             1            108
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  DLL3 MUTATED     0   1   3   2
  DLL3 WILD-TYPE   9  67 245  39
D799V4, multiclass
    clus
vv   DLL3 MUTATED DLL3 WILD-TYPE
  T1            0              9
  T2            1             67
  T3            3            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
  DLL3 MUTATED     5   1   0
  DLL3 WILD-TYPE 215  79  66
D799V5, multiclass
    clus
vv   DLL3 MUTATED DLL3 WILD-TYPE
  N0            5            215
  N1            1             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"
D799V6, binary
                cls
clus               0   1
  DLL3 MUTATED     5   0
  DLL3 WILD-TYPE 278  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLL3 MUTATED      5    0
  DLL3 WILD-TYPE  278   48
   clus
vv  DLL3 MUTATED DLL3 WILD-TYPE
  0            5            278
  1            0             48
[1] 2 2
[1] FALSE
D799V7, 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
D799V8, binary
                cls
clus               0   1
  DLL3 MUTATED     4   2
  DLL3 WILD-TYPE 313  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLL3 MUTATED      4    2
  DLL3 WILD-TYPE  313   46
                               clus
vv                              DLL3 MUTATED DLL3 WILD-TYPE
  COLON ADENOCARCINOMA                     4            313
  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 253   2  22  21
D799V9, multiclass
    clus
vv   DLL3 MUTATED DLL3 WILD-TYPE
  R0            4            253
  R1            0              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"
D799V10, 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
D799V11, 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(800) Variable = ICOSLG MUTATION ANALYSIS
D800V1, survival
                  sevent
clus2                0   1
  ICOSLG MUTATED     3   1
  ICOSLG WILD-TYPE 279  72
  ICOSLG MUTATED ICOSLG WILD-TYPE 
               4              351 
  ICOSLG MUTATED ICOSLG WILD-TYPE 
               1               72 
$`ICOSLG MUTATED`
TCGA-AD-6889 TCGA-AZ-4315 TCGA-CK-5916 TCGA-CM-6674 
       56.55        58.39        21.14        12.95 

$`ICOSLG WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        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        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  ICOSLG MUTATED ICOSLG WILD-TYPE 
           12.95             0.00 
  ICOSLG MUTATED ICOSLG WILD-TYPE 
           58.39           140.38 
  ICOSLG MUTATED ICOSLG WILD-TYPE 
          38.845           20.120 
[1] "12.9 - 58.4 (38.8)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.2"
D800V2, 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       25       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ICOSLG MUTATED           0          0          0          0        0
  ICOSLG WILD-TYPE        19         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  ICOSLG MUTATED           0         0
  ICOSLG WILD-TYPE        13         1
D800V3, multiclass
            clus
vv           ICOSLG MUTATED ICOSLG WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               3              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ICOSLG MUTATED     1   0   3   0
  ICOSLG WILD-TYPE   8  68 245  41
D800V4, multiclass
    clus
vv   ICOSLG MUTATED ICOSLG WILD-TYPE
  T1              1                8
  T2              0               68
  T3              3              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
  ICOSLG MUTATED     4   0   0
  ICOSLG WILD-TYPE 216  80  66
D800V5, multiclass
    clus
vv   ICOSLG MUTATED ICOSLG WILD-TYPE
  N0              4              216
  N1              0               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"
D800V6, binary
                  cls
clus                 0   1
  ICOSLG MUTATED     4   0
  ICOSLG WILD-TYPE 279  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ICOSLG MUTATED      4    0
  ICOSLG WILD-TYPE  279   48
   clus
vv  ICOSLG MUTATED ICOSLG WILD-TYPE
  0              4              279
  1              0               48
[1] 2 2
[1] FALSE
D800V7, 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
D800V8, binary
                  cls
clus                 0   1
  ICOSLG MUTATED     4   0
  ICOSLG WILD-TYPE 313  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ICOSLG MUTATED      4    0
  ICOSLG WILD-TYPE  313   48
                               clus
vv                              ICOSLG MUTATED ICOSLG WILD-TYPE
  COLON ADENOCARCINOMA                       4              313
  COLON MUCINOUS ADENOCARCINOMA              0               48
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ICOSLG MUTATED     2   0   0   1
  ICOSLG WILD-TYPE 255   2  22  20
D800V9, multiclass
    clus
vv   ICOSLG MUTATED ICOSLG WILD-TYPE
  R0              2              255
  R1              0                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"
D800V10, continuous
[1] "Remove cluster labels:" "ICOSLG MUTATED"        
clus
  ICOSLG MUTATED ICOSLG WILD-TYPE 
               2              343 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-4105 
"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-A6-6649       TCGA-A6-6651 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-A6-6652       TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-A6-6781       TCGA-A6-6782       TCGA-AA-3489       TCGA-AA-3492 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3496       TCGA-AA-3502       TCGA-AA-3510       TCGA-AA-3511 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3514       TCGA-AA-3516       TCGA-AA-3517       TCGA-AA-3518 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3519       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-3526       TCGA-AA-3527 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3529       TCGA-AA-3530       TCGA-AA-3531       TCGA-AA-3532 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3534       TCGA-AA-3538       TCGA-AA-3542       TCGA-AA-3543 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3544       TCGA-AA-3548       TCGA-AA-3549       TCGA-AA-3552 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3553       TCGA-AA-3554       TCGA-AA-3555       TCGA-AA-3556 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3558       TCGA-AA-3560       TCGA-AA-3562       TCGA-AA-3655 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3660       TCGA-AA-3662       TCGA-AA-3663       TCGA-AA-3664 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3666       TCGA-AA-3667       TCGA-AA-3672       TCGA-AA-3673 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3678       TCGA-AA-3679       TCGA-AA-3680       TCGA-AA-3681 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3684       TCGA-AA-3685       TCGA-AA-3688       TCGA-AA-3692 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3693       TCGA-AA-3695       TCGA-AA-3696       TCGA-AA-3697 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3710       TCGA-AA-3712       TCGA-AA-3713       TCGA-AA-3715 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3811       TCGA-AA-3812       TCGA-AA-3814       TCGA-AA-3815 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3818       TCGA-AA-3819       TCGA-AA-3821       TCGA-AA-3831 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3833       TCGA-AA-3837       TCGA-AA-3842       TCGA-AA-3844 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3845       TCGA-AA-3846       TCGA-AA-3848       TCGA-AA-3850 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3851       TCGA-AA-3852       TCGA-AA-3854       TCGA-AA-3855 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3856       TCGA-AA-3858       TCGA-AA-3860       TCGA-AA-3861 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3864       TCGA-AA-3866       TCGA-AA-3867       TCGA-AA-3869 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3870       TCGA-AA-3872       TCGA-AA-3875       TCGA-AA-3877 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3930       TCGA-AA-3939       TCGA-AA-3941       TCGA-AA-3947 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3949       TCGA-AA-3950       TCGA-AA-3952       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-3972       TCGA-AA-3973       TCGA-AA-3975       TCGA-AA-3976 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3977       TCGA-AA-3979       TCGA-AA-3980       TCGA-AA-3982 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-3984       TCGA-AA-3986       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-A00L 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-A00N       TCGA-AA-A00O       TCGA-AA-A00Q       TCGA-AA-A00R 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-A00U       TCGA-AA-A00W       TCGA-AA-A00Z       TCGA-AA-A010 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-A017       TCGA-AA-A01D       TCGA-AA-A01F       TCGA-AA-A01G 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-A01I       TCGA-AA-A01K       TCGA-AA-A01P       TCGA-AA-A01Q 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-A01R       TCGA-AA-A01S       TCGA-AA-A01T       TCGA-AA-A01V 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-A01X       TCGA-AA-A01Z       TCGA-AA-A022       TCGA-AA-A024 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-A029       TCGA-AA-A02F       TCGA-AA-A02H       TCGA-AA-A02J 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-A02K       TCGA-AA-A02O       TCGA-AA-A02W       TCGA-AA-A02Y 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AA-A03F       TCGA-AA-A03J       TCGA-AD-5900       TCGA-AD-6548 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AD-6888       TCGA-AD-6890       TCGA-AD-6895       TCGA-AD-6899 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6964       TCGA-AD-6965 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070       TCGA-AY-4071 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4682       TCGA-AZ-5403 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AZ-5407       TCGA-AZ-6598       TCGA-AZ-6599       TCGA-AZ-6600 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-AZ-6601       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-AZ-6608       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-A285       TCGA-DM-A28C 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-DM-A28E       TCGA-DM-A28F       TCGA-DM-A28G       TCGA-DM-A28H 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-DM-A28K       TCGA-F4-6459       TCGA-F4-6460       TCGA-F4-6569 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704       TCGA-F4-6806 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-F4-6807       TCGA-F4-6808       TCGA-F4-6809       TCGA-F4-6854 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-F4-6855       TCGA-F4-6856       TCGA-G4-6293       TCGA-G4-6299 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-G4-6303       TCGA-G4-6304       TCGA-G4-6306       TCGA-G4-6307 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-G4-6309       TCGA-G4-6310       TCGA-G4-6315       TCGA-G4-6317 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-G4-6321       TCGA-G4-6323       TCGA-G4-6586       TCGA-G4-6588 
"ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" "ICOSLG WILD-TYPE" 
      TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628 
"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
D800V11, 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(801) Variable = GPR126 MUTATION ANALYSIS
D801V1, survival
                  sevent
clus2                0   1
  GPR126 MUTATED    12   2
  GPR126 WILD-TYPE 270  71
  GPR126 MUTATED GPR126 WILD-TYPE 
              14              341 
  GPR126 MUTATED GPR126 WILD-TYPE 
               2               71 
$`GPR126 MUTATED`
TCGA-A6-5665 TCGA-A6-6141 TCGA-AA-3492 TCGA-AA-3672 TCGA-AA-3715 TCGA-AA-3864 
       22.06         8.38         3.02         0.92        19.04        53.00 
TCGA-AA-3947 TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-CA-6717 TCGA-D5-6539 
       33.01        34.98        58.39        61.41         0.33        12.49 
TCGA-D5-6929 TCGA-F4-6856 
       13.41        19.43 

$`GPR126 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.09        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  GPR126 MUTATED GPR126 WILD-TYPE 
            0.33             0.00 
  GPR126 MUTATED GPR126 WILD-TYPE 
           61.41           140.38 
  GPR126 MUTATED GPR126 WILD-TYPE 
          19.235           20.280 
[1] "0.3 - 61.4 (19.2)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.4"
D801V2, 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       21       104         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPR126 MUTATED           1          1          0          0        1
  GPR126 WILD-TYPE        18          9         41         31       34
                  vv
clus               STAGE IVA STAGE IVB
  GPR126 MUTATED           0         0
  GPR126 WILD-TYPE        13         1
D801V3, multiclass
            clus
vv           GPR126 MUTATED GPR126 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                4               21
  STAGE IIA               5              104
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              1                9
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GPR126 MUTATED     1   1  11   3
  GPR126 WILD-TYPE   8  67 237  38
D801V4, multiclass
    clus
vv   GPR126 MUTATED GPR126 WILD-TYPE
  T1              1                8
  T2              1               67
  T3             11              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
  GPR126 MUTATED    14   2   0
  GPR126 WILD-TYPE 206  78  66
D801V5, multiclass
    clus
vv   GPR126 MUTATED GPR126 WILD-TYPE
  N0             14              206
  N1              2               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"
D801V6, binary
                  cls
clus                 0   1
  GPR126 MUTATED    15   1
  GPR126 WILD-TYPE 268  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR126 MUTATED     15    1
  GPR126 WILD-TYPE  268   47
   clus
vv  GPR126 MUTATED GPR126 WILD-TYPE
  0             15              268
  1              1               47
[1] 2 2
[1] FALSE
D801V7, 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
D801V8, binary
                  cls
clus                 0   1
  GPR126 MUTATED    13   3
  GPR126 WILD-TYPE 304  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR126 MUTATED     13    3
  GPR126 WILD-TYPE  304   45
                               clus
vv                              GPR126 MUTATED GPR126 WILD-TYPE
  COLON ADENOCARCINOMA                      13              304
  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 244   2  22  20
D801V9, multiclass
    clus
vv   GPR126 MUTATED GPR126 WILD-TYPE
  R0             13              244
  R1              0                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"
D801V10, 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
D801V11, 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(802) Variable = LYG1 MUTATION ANALYSIS
D802V1, survival
                sevent
clus2              0   1
  LYG1 MUTATED     6   0
  LYG1 WILD-TYPE 276  73
  LYG1 MUTATED LYG1 WILD-TYPE 
             6            349 
  LYG1 MUTATED LYG1 WILD-TYPE 
             0             73 
$`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         0.10 

$`LYG1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 
       10.06         0.00        33.07         0.00        36.03         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       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        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  LYG1 MUTATED LYG1 WILD-TYPE 
           0.1            0.0 
  LYG1 MUTATED LYG1 WILD-TYPE 
         63.98         140.38 
  LYG1 MUTATED LYG1 WILD-TYPE 
        28.535         20.120 
[1] "0.1 - 64.0 (28.5)"  "0.0 - 140.4 (20.1)"
[1] "hr="     "9200000"
D802V2, 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       23       108         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        18         10         41         31       35        13
                vv
clus             STAGE IVB
  LYG1 MUTATED           0
  LYG1 WILD-TYPE         1
D802V3, multiclass
            clus
vv           LYG1 MUTATED LYG1 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             1            108
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  LYG1 MUTATED     0   2   4   0
  LYG1 WILD-TYPE   9  66 244  41
D802V4, multiclass
    clus
vv   LYG1 MUTATED LYG1 WILD-TYPE
  T1            0              9
  T2            2             66
  T3            4            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
  LYG1 MUTATED     5   0   1
  LYG1 WILD-TYPE 215  80  65
D802V5, multiclass
    clus
vv   LYG1 MUTATED LYG1 WILD-TYPE
  N0            5            215
  N1            0             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"
D802V6, binary
                cls
clus               0   1
  LYG1 MUTATED     5   0
  LYG1 WILD-TYPE 278  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  LYG1 MUTATED      5    0
  LYG1 WILD-TYPE  278   48
   clus
vv  LYG1 MUTATED LYG1 WILD-TYPE
  0            5            278
  1            0             48
[1] 2 2
[1] FALSE
D802V7, 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
D802V8, binary
                cls
clus               0   1
  LYG1 MUTATED     5   1
  LYG1 WILD-TYPE 312  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  LYG1 MUTATED      5    1
  LYG1 WILD-TYPE  312   47
                               clus
vv                              LYG1 MUTATED LYG1 WILD-TYPE
  COLON ADENOCARCINOMA                     5            312
  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 253   2  22  20
D802V9, multiclass
    clus
vv   LYG1 MUTATED LYG1 WILD-TYPE
  R0            4            253
  R1            0              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"
D802V10, 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
D802V11, multiclass
[1] "Remove cluster labels:" "LYG1 MUTATED"          
clus
  LYG1 MUTATED LYG1 WILD-TYPE 
             1            205 
    TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810     TCGA-A6-4105 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-A6-5656     TCGA-A6-5657     TCGA-A6-5659     TCGA-A6-5660 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-A6-5661     TCGA-A6-5662     TCGA-A6-5664     TCGA-A6-5665 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-A6-5666     TCGA-A6-6137     TCGA-A6-6138     TCGA-A6-6141 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-A6-6142     TCGA-A6-6648     TCGA-A6-6649     TCGA-A6-6651 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-A6-6652     TCGA-A6-6653     TCGA-A6-6654     TCGA-A6-6780 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-A6-6781     TCGA-A6-6782     TCGA-AD-5900     TCGA-AD-6548 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-AD-6888     TCGA-AD-6889     TCGA-AD-6890     TCGA-AD-6895 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-AD-6899     TCGA-AD-6901     TCGA-AD-6963     TCGA-AD-6964 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-AD-6965     TCGA-AU-3779     TCGA-AU-6004     TCGA-AY-4070 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-AY-4071     TCGA-AY-5543     TCGA-AY-6196     TCGA-AY-6197 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-AY-6386     TCGA-AZ-4315     TCGA-AZ-4323     TCGA-AZ-4616 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-AZ-4681     TCGA-AZ-4682     TCGA-AZ-5403     TCGA-AZ-5407 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-AZ-6598     TCGA-AZ-6599     TCGA-AZ-6600     TCGA-AZ-6601 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-AZ-6603     TCGA-AZ-6605     TCGA-AZ-6606     TCGA-AZ-6607 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-AZ-6608     TCGA-CA-5254     TCGA-CA-5255     TCGA-CA-5796 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-CA-5797     TCGA-CA-6715     TCGA-CA-6716     TCGA-CA-6717 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-CA-6719     TCGA-CK-4947     TCGA-CK-4948     TCGA-CK-4950 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-CK-4952     TCGA-CK-5912     TCGA-CK-5913     TCGA-CK-5914 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-CK-5915     TCGA-CK-5916     TCGA-CK-6746     TCGA-CK-6747 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-CK-6748     TCGA-CK-6751     TCGA-CM-4743     TCGA-CM-4744 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-CM-4746     TCGA-CM-4747     TCGA-CM-4752     TCGA-CM-5341 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-CM-5344     TCGA-CM-5348     TCGA-CM-5349     TCGA-CM-5860 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-CM-5861     TCGA-CM-5862     TCGA-CM-5863     TCGA-CM-5864 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-CM-5868     TCGA-CM-6161     TCGA-CM-6162     TCGA-CM-6163 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-CM-6164     TCGA-CM-6165     TCGA-CM-6166     TCGA-CM-6167 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-CM-6168     TCGA-CM-6169     TCGA-CM-6170     TCGA-CM-6171 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-CM-6172     TCGA-CM-6674     TCGA-CM-6675     TCGA-CM-6676 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-CM-6677     TCGA-CM-6678     TCGA-CM-6679     TCGA-CM-6680 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-D5-5537     TCGA-D5-5538     TCGA-D5-5539     TCGA-D5-5540 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-D5-5541     TCGA-D5-6529     TCGA-D5-6532     TCGA-D5-6533 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-D5-6534     TCGA-D5-6535     TCGA-D5-6536     TCGA-D5-6537 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-D5-6538     TCGA-D5-6539     TCGA-D5-6540     TCGA-D5-6541 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-D5-6898     TCGA-D5-6920     TCGA-D5-6922     TCGA-D5-6923 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-D5-6924     TCGA-D5-6926     TCGA-D5-6927     TCGA-D5-6928 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-D5-6929     TCGA-D5-6930     TCGA-D5-6931     TCGA-D5-6932 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-D5-7000     TCGA-DM-A0X9     TCGA-DM-A0XD     TCGA-DM-A0XF 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-DM-A1D0     TCGA-DM-A1D4     TCGA-DM-A1D6     TCGA-DM-A1D7 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-DM-A1D8     TCGA-DM-A1D9     TCGA-DM-A1DA     TCGA-DM-A1DB 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-DM-A1HA     TCGA-DM-A1HB     TCGA-DM-A282     TCGA-DM-A285 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-DM-A28C     TCGA-DM-A28E     TCGA-DM-A28F     TCGA-DM-A28G 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-DM-A28H     TCGA-DM-A28K     TCGA-F4-6459     TCGA-F4-6460 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-F4-6569     TCGA-F4-6570     TCGA-F4-6703     TCGA-F4-6704 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-F4-6805     TCGA-F4-6806     TCGA-F4-6807     TCGA-F4-6808 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-F4-6809     TCGA-F4-6854     TCGA-F4-6855     TCGA-F4-6856 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-G4-6293     TCGA-G4-6299     TCGA-G4-6303     TCGA-G4-6304 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-G4-6306     TCGA-G4-6307     TCGA-G4-6309     TCGA-G4-6310 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-G4-6315     TCGA-G4-6317     TCGA-G4-6321     TCGA-G4-6323 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-G4-6586     TCGA-G4-6588     TCGA-G4-6625     TCGA-G4-6626 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-G4-6628 
"LYG1 WILD-TYPE" 

Clustering(803) Variable = REXO4 MUTATION ANALYSIS
D803V1, survival
                 sevent
clus2               0   1
  REXO4 MUTATED     3   2
  REXO4 WILD-TYPE 279  71
  REXO4 MUTATED REXO4 WILD-TYPE 
              5             350 
  REXO4 MUTATED REXO4 WILD-TYPE 
              2              71 
$`REXO4 MUTATED`
TCGA-AA-3715 TCGA-AA-A00J TCGA-CK-6747 TCGA-CM-5861 TCGA-F4-6570 
       19.04        18.05         2.93        15.02         6.18 

$`REXO4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        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-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       16.01         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       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        13.38        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  REXO4 MUTATED REXO4 WILD-TYPE 
           2.93            0.00 
  REXO4 MUTATED REXO4 WILD-TYPE 
          19.04          140.38 
  REXO4 MUTATED REXO4 WILD-TYPE 
          15.02           20.98 
[1] "2.9 - 19.0 (15.0)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "3.5"
D803V2, 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       24       106         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        19         10         40         31       35        13
                 vv
clus              STAGE IVB
  REXO4 MUTATED           0
  REXO4 WILD-TYPE         1
D803V3, multiclass
            clus
vv           REXO4 MUTATED REXO4 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              3             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  REXO4 MUTATED     0   0   4   1
  REXO4 WILD-TYPE   9  68 244  40
D803V4, multiclass
    clus
vv   REXO4 MUTATED REXO4 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             4             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
  REXO4 MUTATED     4   1   0
  REXO4 WILD-TYPE 216  79  66
D803V5, multiclass
    clus
vv   REXO4 MUTATED REXO4 WILD-TYPE
  N0             4             216
  N1             1              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"
D803V6, binary
                 cls
clus                0   1
  REXO4 MUTATED     4   0
  REXO4 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  REXO4 MUTATED      4    0
  REXO4 WILD-TYPE  279   48
   clus
vv  REXO4 MUTATED REXO4 WILD-TYPE
  0             4             279
  1             0              48
[1] 2 2
[1] FALSE
D803V7, 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
D803V8, binary
                 cls
clus                0   1
  REXO4 MUTATED     4   1
  REXO4 WILD-TYPE 313  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  REXO4 MUTATED      4    1
  REXO4 WILD-TYPE  313   47
                               clus
vv                              REXO4 MUTATED REXO4 WILD-TYPE
  COLON ADENOCARCINOMA                      4             313
  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 253   2  22  20
D803V9, multiclass
    clus
vv   REXO4 MUTATED REXO4 WILD-TYPE
  R0             4             253
  R1             0               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"
D803V10, 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
D803V11, 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(804) Variable = MSRB3 MUTATION ANALYSIS
D804V1, survival
                 sevent
clus2               0   1
  MSRB3 MUTATED     8   3
  MSRB3 WILD-TYPE 274  70
  MSRB3 MUTATED MSRB3 WILD-TYPE 
             11             344 
  MSRB3 MUTATED MSRB3 WILD-TYPE 
              3              70 
$`MSRB3 MUTATED`
TCGA-A6-2674 TCGA-AA-3664 TCGA-AA-A00N TCGA-AZ-6598 TCGA-AZ-6605 TCGA-CA-6717 
       43.76        54.02         4.01        49.41         5.23         0.33 
TCGA-CM-6168 TCGA-CM-6678 TCGA-D5-5538 TCGA-D5-6535 TCGA-D5-6536 
       12.99        11.01        12.26        15.12        17.85 

$`MSRB3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
        6.97         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
      100.01        29.56        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        45.40        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6537 TCGA-D5-6538 
       20.19        18.25         1.32        43.27         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  MSRB3 MUTATED MSRB3 WILD-TYPE 
           0.33            0.00 
  MSRB3 MUTATED MSRB3 WILD-TYPE 
          54.02          140.38 
  MSRB3 MUTATED MSRB3 WILD-TYPE 
          12.99           20.98 
[1] "0.3 - 54.0 (13.0)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.5"
D804V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MSRB3 MUTATED         0        0        2         3         1         0
  MSRB3 WILD-TYPE      64        1       23       106         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MSRB3 MUTATED           0          0          3          0        1         1
  MSRB3 WILD-TYPE        19         10         38         31       34        12
                 vv
clus              STAGE IVB
  MSRB3 MUTATED           0
  MSRB3 WILD-TYPE         1
D804V3, multiclass
            clus
vv           MSRB3 MUTATED MSRB3 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              3             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             3              38
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MSRB3 MUTATED     0   0   8   3
  MSRB3 WILD-TYPE   9  68 240  38
D804V4, multiclass
    clus
vv   MSRB3 MUTATED MSRB3 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             8             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
  MSRB3 MUTATED     6   4   1
  MSRB3 WILD-TYPE 214  76  65
D804V5, multiclass
    clus
vv   MSRB3 MUTATED MSRB3 WILD-TYPE
  N0             6             214
  N1             4              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"
D804V6, binary
                 cls
clus                0   1
  MSRB3 MUTATED     7   2
  MSRB3 WILD-TYPE 276  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MSRB3 MUTATED      7    2
  MSRB3 WILD-TYPE  276   46
   clus
vv  MSRB3 MUTATED MSRB3 WILD-TYPE
  0             7             276
  1             2              46
[1] 2 2
[1] FALSE
D804V7, binary
                 cls
clus                0   1
  MSRB3 MUTATED     6   5
  MSRB3 WILD-TYPE 164 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MSRB3 MUTATED      6    5
  MSRB3 WILD-TYPE  164  192
        clus
vv       MSRB3 MUTATED MSRB3 WILD-TYPE
  FEMALE             6             164
  MALE               5             192
[1] 2 2
[1] FALSE
D804V8, binary
                 cls
clus                0   1
  MSRB3 MUTATED     8   3
  MSRB3 WILD-TYPE 309  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MSRB3 MUTATED      8    3
  MSRB3 WILD-TYPE  309   45
                               clus
vv                              MSRB3 MUTATED MSRB3 WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MSRB3 MUTATED     7   0   0   2
  MSRB3 WILD-TYPE 250   2  22  19
D804V9, multiclass
    clus
vv   MSRB3 MUTATED MSRB3 WILD-TYPE
  R0             7             250
  R1             0               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"
D804V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MSRB3 MUTATED                                  0     1
  MSRB3 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MSRB3 MUTATED                           1     7
  MSRB3 WILD-TYPE                        18   169
D804V11, multiclass
                                  clus
vv                                 MSRB3 MUTATED MSRB3 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(805) Variable = GRIA4 MUTATION ANALYSIS
D805V1, survival
                 sevent
clus2               0   1
  GRIA4 MUTATED    28   2
  GRIA4 WILD-TYPE 254  71
  GRIA4 MUTATED GRIA4 WILD-TYPE 
             30             325 
  GRIA4 MUTATED GRIA4 WILD-TYPE 
              2              71 
$`GRIA4 MUTATED`
TCGA-A6-2676 TCGA-A6-5661 TCGA-A6-6782 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3554 
       42.90        33.53        20.28        63.98         6.97        17.95 
TCGA-AA-3678 TCGA-AA-3851 TCGA-AA-3867 TCGA-AA-3877 TCGA-AA-A010 TCGA-AA-A01Z 
       47.01        33.07        24.03        31.00        34.98        37.02 
TCGA-AZ-4315 TCGA-CA-6715 TCGA-CA-6717 TCGA-CM-4744 TCGA-CM-5348 TCGA-CM-5349 
       58.39         0.07         0.33        20.02        22.98        30.08 
TCGA-CM-5868 TCGA-CM-6675 TCGA-D5-6924 TCGA-DM-A1HB TCGA-DM-A28C TCGA-F4-6460 
       17.03        13.05        14.30       135.65        81.37        13.38 
TCGA-F4-6805 TCGA-F4-6808 TCGA-F4-6856 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6317 
       16.31        33.67        19.43        55.04        45.11        36.00 

$`GRIA4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3514 
       19.66         7.04         3.02         1.02        35.01         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3556 
       33.99        21.01        13.02        24.00        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       50.04        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       17.03        10.06         0.00         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       27.02        29.98        18.05         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 
        2.93         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        16.01        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
      139.17         6.12       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        13.45         6.18        35.87         1.55 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 
       29.59        16.24        13.25         0.53        35.41       107.67 
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        51.75        36.72 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  GRIA4 MUTATED GRIA4 WILD-TYPE 
           0.07            0.00 
  GRIA4 MUTATED GRIA4 WILD-TYPE 
         135.65          140.38 
  GRIA4 MUTATED GRIA4 WILD-TYPE 
          30.54           19.66 
[1] "0.1 - 135.7 (30.5)" "0.0 - 140.4 (19.7)"
[1] "hr=" "4.1"
D805V2, 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       22       100         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        18         10         35         30       34        12
                 vv
clus              STAGE IVB
  GRIA4 MUTATED           1
  GRIA4 WILD-TYPE         0
D805V3, multiclass
            clus
vv           GRIA4 MUTATED GRIA4 WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              9             100
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             6              35
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              1              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
  GRIA4 MUTATED     2   3  20   5
  GRIA4 WILD-TYPE   7  65 228  36
D805V4, multiclass
    clus
vv   GRIA4 MUTATED GRIA4 WILD-TYPE
  T1             2               7
  T2             3              65
  T3            20             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
  GRIA4 MUTATED    19   8   3
  GRIA4 WILD-TYPE 201  72  63
D805V5, multiclass
    clus
vv   GRIA4 MUTATED GRIA4 WILD-TYPE
  N0            19             201
  N1             8              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"
D805V6, binary
                 cls
clus                0   1
  GRIA4 MUTATED    25   3
  GRIA4 WILD-TYPE 258  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GRIA4 MUTATED     25    3
  GRIA4 WILD-TYPE  258   45
   clus
vv  GRIA4 MUTATED GRIA4 WILD-TYPE
  0            25             258
  1             3              45
[1] 2 2
[1] FALSE
D805V7, 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
D805V8, binary
                 cls
clus                0   1
  GRIA4 MUTATED    27   3
  GRIA4 WILD-TYPE 290  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GRIA4 MUTATED     27    3
  GRIA4 WILD-TYPE  290   45
                               clus
vv                              GRIA4 MUTATED GRIA4 WILD-TYPE
  COLON ADENOCARCINOMA                     27             290
  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 233   2  21  19
D805V9, multiclass
    clus
vv   GRIA4 MUTATED GRIA4 WILD-TYPE
  R0            24             233
  R1             0               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"
D805V10, 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
D805V11, 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(806) Variable = TP53RK MUTATION ANALYSIS
D806V1, survival
                  sevent
clus2                0   1
  TP53RK MUTATED     2   2
  TP53RK WILD-TYPE 280  71
  TP53RK MUTATED TP53RK WILD-TYPE 
               4              351 
  TP53RK MUTATED TP53RK WILD-TYPE 
               2               71 
$`TP53RK MUTATED`
TCGA-A6-6781 TCGA-AA-A00N TCGA-AZ-6598 TCGA-G4-6588 
       19.66         4.01        49.41        26.17 

$`TP53RK WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13        83.80        22.36        62.79        61.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  TP53RK MUTATED TP53RK WILD-TYPE 
            4.01             0.00 
  TP53RK MUTATED TP53RK WILD-TYPE 
           49.41           140.38 
  TP53RK MUTATED TP53RK WILD-TYPE 
          22.915           20.190 
[1] "4.0 - 49.4 (22.9)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2.4"
D806V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TP53RK MUTATED         0        0        1         1         1         0
  TP53RK WILD-TYPE      64        1       24       108         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TP53RK MUTATED           0          0          0          1        0
  TP53RK WILD-TYPE        19         10         41         30       35
                  vv
clus               STAGE IVA STAGE IVB
  TP53RK MUTATED           0         0
  TP53RK WILD-TYPE        13         1
D806V3, multiclass
            clus
vv           TP53RK MUTATED TP53RK WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               1              108
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TP53RK MUTATED     0   0   2   2
  TP53RK WILD-TYPE   9  68 246  39
D806V4, multiclass
    clus
vv   TP53RK MUTATED TP53RK WILD-TYPE
  T1              0                9
  T2              0               68
  T3              2              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
  TP53RK MUTATED     3   1   0
  TP53RK WILD-TYPE 217  79  66
D806V5, multiclass
    clus
vv   TP53RK MUTATED TP53RK WILD-TYPE
  N0              3              217
  N1              1               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"
D806V6, binary
                  cls
clus                 0   1
  TP53RK MUTATED     2   0
  TP53RK WILD-TYPE 281  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TP53RK MUTATED      2    0
  TP53RK WILD-TYPE  281   48
   clus
vv  TP53RK MUTATED TP53RK WILD-TYPE
  0              2              281
  1              0               48
[1] 2 2
[1] FALSE
D806V7, binary
                  cls
clus                 0   1
  TP53RK MUTATED     2   2
  TP53RK WILD-TYPE 168 195
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TP53RK MUTATED      2    2
  TP53RK WILD-TYPE  168  195
        clus
vv       TP53RK MUTATED TP53RK WILD-TYPE
  FEMALE              2              168
  MALE                2              195
[1] 2 2
[1] FALSE
D806V8, binary
                  cls
clus                 0   1
  TP53RK MUTATED     2   2
  TP53RK WILD-TYPE 315  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TP53RK MUTATED      2    2
  TP53RK WILD-TYPE  315   46
                               clus
vv                              TP53RK MUTATED TP53RK WILD-TYPE
  COLON ADENOCARCINOMA                       2              315
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TP53RK MUTATED     3   0   0   0
  TP53RK WILD-TYPE 254   2  22  21
D806V9, multiclass
    clus
vv   TP53RK MUTATED TP53RK WILD-TYPE
  R0              3              254
  R1              0                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"
D806V10, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TP53RK MUTATED                                  0     0
  TP53RK WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TP53RK MUTATED                           0     3
  TP53RK WILD-TYPE                        19   173
D806V11, multiclass
                                  clus
vv                                 TP53RK MUTATED TP53RK 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(807) Variable = TMEM50B MUTATION ANALYSIS
D807V1, survival
                   sevent
clus2                 0   1
  TMEM50B MUTATED     4   2
  TMEM50B WILD-TYPE 278  71
  TMEM50B MUTATED TMEM50B WILD-TYPE 
                6               349 
  TMEM50B MUTATED TMEM50B WILD-TYPE 
                2                71 
$`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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14         2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 
        1.55        16.31        29.59        16.24        33.67         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  TMEM50B MUTATED TMEM50B WILD-TYPE 
            10.13              0.00 
  TMEM50B MUTATED TMEM50B WILD-TYPE 
            58.39            140.38 
  TMEM50B MUTATED TMEM50B WILD-TYPE 
           18.115            20.190 
[1] "10.1 - 58.4 (18.1)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.7"
D807V2, 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       25       107         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM50B MUTATED           0          1          1          0        1
  TMEM50B WILD-TYPE        19          9         40         31       34
                   vv
clus                STAGE IVA STAGE IVB
  TMEM50B MUTATED           1         0
  TMEM50B WILD-TYPE        12         1
D807V3, multiclass
            clus
vv           TMEM50B MUTATED TMEM50B WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                2               107
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               1                 9
  STAGE IIIB               1                40
  STAGE IIIC               0                31
  STAGE IV                 1                34
  STAGE IVA                1                12
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of 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  68 243  40
D807V4, multiclass
    clus
vv   TMEM50B MUTATED TMEM50B WILD-TYPE
  T1               0                 9
  T2               0                68
  T3               5               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
  TMEM50B MUTATED     2   4   0
  TMEM50B WILD-TYPE 218  76  66
D807V5, multiclass
    clus
vv   TMEM50B MUTATED TMEM50B WILD-TYPE
  N0               2               218
  N1               4                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"
D807V6, binary
                   cls
clus                  0   1
  TMEM50B MUTATED     4   2
  TMEM50B WILD-TYPE 279  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM50B MUTATED      4    2
  TMEM50B WILD-TYPE  279   46
   clus
vv  TMEM50B MUTATED TMEM50B WILD-TYPE
  0               4               279
  1               2                46
[1] 2 2
[1] FALSE
D807V7, 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
D807V8, binary
                   cls
clus                  0   1
  TMEM50B MUTATED     6   0
  TMEM50B WILD-TYPE 311  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM50B MUTATED      6    0
  TMEM50B WILD-TYPE  311   48
                               clus
vv                              TMEM50B MUTATED TMEM50B WILD-TYPE
  COLON ADENOCARCINOMA                        6               311
  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 252   2  22  21
D807V9, multiclass
    clus
vv   TMEM50B MUTATED TMEM50B WILD-TYPE
  R0               5               252
  R1               0                 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"
D807V10, 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
D807V11, 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(808) Variable = CRYGA MUTATION ANALYSIS
D808V1, survival
                 sevent
clus2               0   1
  CRYGA MUTATED     4   1
  CRYGA WILD-TYPE 278  72
  CRYGA MUTATED CRYGA WILD-TYPE 
              5             350 
  CRYGA MUTATED CRYGA WILD-TYPE 
              1              72 
$`CRYGA MUTATED`
TCGA-A6-6653 TCGA-A6-6780 TCGA-AZ-6598 TCGA-G4-6586 TCGA-G4-6588 
       24.39        20.12        49.41        35.80        26.17 

$`CRYGA WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13        83.80        22.36        62.79        61.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 
       45.11        36.72        36.00        22.09        13.78        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  CRYGA MUTATED CRYGA WILD-TYPE 
          20.12            0.00 
  CRYGA MUTATED CRYGA WILD-TYPE 
          49.41          140.38 
  CRYGA MUTATED CRYGA WILD-TYPE 
         26.170          20.005 
[1] "20.1 - 49.4 (26.2)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.2"
D808V2, 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       24       106         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        19         10         41         31       35        13
                 vv
clus              STAGE IVB
  CRYGA MUTATED           0
  CRYGA WILD-TYPE         1
D808V3, multiclass
            clus
vv           CRYGA MUTATED CRYGA WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              3             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CRYGA MUTATED     0   1   4   0
  CRYGA WILD-TYPE   9  67 244  41
D808V4, multiclass
    clus
vv   CRYGA MUTATED CRYGA WILD-TYPE
  T1             0               9
  T2             1              67
  T3             4             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
  CRYGA MUTATED     5   0   0
  CRYGA WILD-TYPE 215  80  66
D808V5, multiclass
    clus
vv   CRYGA MUTATED CRYGA WILD-TYPE
  N0             5             215
  N1             0              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"
D808V6, binary
                 cls
clus                0   1
  CRYGA MUTATED     3   0
  CRYGA WILD-TYPE 280  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CRYGA MUTATED      3    0
  CRYGA WILD-TYPE  280   48
   clus
vv  CRYGA MUTATED CRYGA WILD-TYPE
  0             3             280
  1             0              48
[1] 2 2
[1] FALSE
D808V7, 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
D808V8, binary
                 cls
clus                0   1
  CRYGA MUTATED     4   1
  CRYGA WILD-TYPE 313  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CRYGA MUTATED      4    1
  CRYGA WILD-TYPE  313   47
                               clus
vv                              CRYGA MUTATED CRYGA WILD-TYPE
  COLON ADENOCARCINOMA                      4             313
  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 255   2  22  21
D808V9, multiclass
[1] "Remove cluster labels:" "CRYGA MUTATED"         
clus
  CRYGA MUTATED CRYGA WILD-TYPE 
              2             300 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-5657 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-A6-5659      TCGA-A6-5661      TCGA-A6-5665      TCGA-A6-6781 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3489      TCGA-AA-3492      TCGA-AA-3496      TCGA-AA-3502 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3510      TCGA-AA-3511      TCGA-AA-3514      TCGA-AA-3517 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3518      TCGA-AA-3519      TCGA-AA-3520      TCGA-AA-3521 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3522      TCGA-AA-3524      TCGA-AA-3525      TCGA-AA-3526 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3527      TCGA-AA-3529      TCGA-AA-3530      TCGA-AA-3531 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3532      TCGA-AA-3534      TCGA-AA-3538      TCGA-AA-3542 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3543      TCGA-AA-3544      TCGA-AA-3548      TCGA-AA-3549 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3552      TCGA-AA-3553      TCGA-AA-3554      TCGA-AA-3555 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3556      TCGA-AA-3558      TCGA-AA-3560      TCGA-AA-3561 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3562      TCGA-AA-3655      TCGA-AA-3660      TCGA-AA-3662 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3663      TCGA-AA-3664      TCGA-AA-3666      TCGA-AA-3667 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3672      TCGA-AA-3673      TCGA-AA-3678      TCGA-AA-3679 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3680      TCGA-AA-3681      TCGA-AA-3684      TCGA-AA-3685 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3688      TCGA-AA-3692      TCGA-AA-3693      TCGA-AA-3695 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3696      TCGA-AA-3697      TCGA-AA-3710      TCGA-AA-3712 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3713      TCGA-AA-3715      TCGA-AA-3811      TCGA-AA-3812 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3814      TCGA-AA-3815      TCGA-AA-3818      TCGA-AA-3819 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3821      TCGA-AA-3831      TCGA-AA-3833      TCGA-AA-3837 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3842      TCGA-AA-3844      TCGA-AA-3845      TCGA-AA-3846 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3848      TCGA-AA-3850      TCGA-AA-3851      TCGA-AA-3852 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3854      TCGA-AA-3855      TCGA-AA-3856      TCGA-AA-3858 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3860      TCGA-AA-3861      TCGA-AA-3864      TCGA-AA-3866 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3867      TCGA-AA-3869      TCGA-AA-3870      TCGA-AA-3872 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3875      TCGA-AA-3877      TCGA-AA-3930      TCGA-AA-3939 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3941      TCGA-AA-3947      TCGA-AA-3949      TCGA-AA-3950 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3952      TCGA-AA-3955      TCGA-AA-3956      TCGA-AA-3968 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3971      TCGA-AA-3972      TCGA-AA-3973      TCGA-AA-3975 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3976      TCGA-AA-3979      TCGA-AA-3984      TCGA-AA-3986 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3989      TCGA-AA-3994      TCGA-AA-A004      TCGA-AA-A00A 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-A00D      TCGA-AA-A00E      TCGA-AA-A00F      TCGA-AA-A00J 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-A00K      TCGA-AA-A00L      TCGA-AA-A00N      TCGA-AA-A00O 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-A00Q      TCGA-AA-A00R      TCGA-AA-A00U      TCGA-AA-A00W 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-A00Z      TCGA-AA-A010      TCGA-AA-A017      TCGA-AA-A01D 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-A01F      TCGA-AA-A01G      TCGA-AA-A01I      TCGA-AA-A01K 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-A01P      TCGA-AA-A01Q      TCGA-AA-A01R      TCGA-AA-A01S 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-A01T      TCGA-AA-A01V      TCGA-AA-A01X      TCGA-AA-A01Z 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-A022      TCGA-AA-A024      TCGA-AA-A029      TCGA-AA-A02F 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-A02H      TCGA-AA-A02J      TCGA-AA-A02K      TCGA-AA-A02O 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-A02W      TCGA-AA-A02Y      TCGA-AA-A03F      TCGA-AA-A03J 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AD-5900      TCGA-AD-6548      TCGA-AD-6888      TCGA-AU-3779 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AU-6004      TCGA-AY-4070      TCGA-AY-4071      TCGA-AY-5543 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AY-6196      TCGA-AY-6197      TCGA-AY-6386      TCGA-AZ-4315 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AZ-4681      TCGA-AZ-4682      TCGA-CA-5254      TCGA-CA-5255 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-CA-5796      TCGA-CA-5797      TCGA-CA-6715      TCGA-CA-6716 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-CA-6717      TCGA-CA-6718      TCGA-CA-6719      TCGA-CK-4947 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-CK-4948      TCGA-CK-4950      TCGA-CK-4952      TCGA-CK-5912 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-CK-5913      TCGA-CK-5914      TCGA-CK-5915      TCGA-CK-5916 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-CK-6746      TCGA-CK-6747      TCGA-CK-6748      TCGA-CK-6751 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-CM-4743      TCGA-CM-4744      TCGA-CM-4746      TCGA-CM-4747 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-CM-4752      TCGA-CM-5341      TCGA-CM-5344      TCGA-CM-5348 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-CM-5349      TCGA-CM-5860      TCGA-CM-5861      TCGA-CM-5862 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-CM-5863      TCGA-CM-5864      TCGA-CM-5868      TCGA-CM-6161 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-CM-6162      TCGA-CM-6163      TCGA-CM-6164      TCGA-CM-6165 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-CM-6166      TCGA-CM-6167      TCGA-CM-6168      TCGA-CM-6169 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-CM-6170      TCGA-CM-6171      TCGA-CM-6172      TCGA-CM-6674 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-CM-6675      TCGA-CM-6676      TCGA-CM-6677      TCGA-CM-6678 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-CM-6679      TCGA-CM-6680      TCGA-D5-5537      TCGA-D5-5538 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-D5-5539      TCGA-D5-5540      TCGA-D5-5541      TCGA-D5-6529 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-D5-6532      TCGA-D5-6533      TCGA-D5-6534      TCGA-D5-6535 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-D5-6536      TCGA-D5-6537      TCGA-D5-6538      TCGA-D5-6539 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-D5-6540      TCGA-D5-6541      TCGA-D5-6898      TCGA-D5-6920 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-D5-6922      TCGA-D5-6923      TCGA-D5-6924      TCGA-D5-6926 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-D5-6927      TCGA-D5-6928      TCGA-D5-6929      TCGA-D5-6930 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-D5-6931      TCGA-D5-6932      TCGA-D5-7000      TCGA-F4-6459 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-F4-6460      TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-F4-6704      TCGA-F4-6805      TCGA-F4-6806      TCGA-F4-6807 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-F4-6808      TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-F4-6856      TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-G4-6304      TCGA-G4-6306      TCGA-G4-6307      TCGA-G4-6309 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-G4-6310      TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6321 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-G4-6323      TCGA-G4-6625      TCGA-G4-6626      TCGA-G4-6628 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
D808V10, 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
D808V11, 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(809) Variable = IL2RG MUTATION ANALYSIS
D809V1, survival
                 sevent
clus2               0   1
  IL2RG MUTATED     5   2
  IL2RG WILD-TYPE 277  71
  IL2RG MUTATED IL2RG WILD-TYPE 
              7             348 
  IL2RG MUTATED IL2RG WILD-TYPE 
              2              71 
$`IL2RG MUTATED`
TCGA-A6-6781 TCGA-AA-3492 TCGA-AY-6386 TCGA-CA-6717 TCGA-F4-6570 TCGA-G4-6309 
       19.66         3.02        17.82         0.33         6.18        51.75 
TCGA-G4-6586 
       35.80 

$`IL2RG WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       23.87        20.12        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       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        13.38        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        26.17        91.79        46.75        52.80 

  IL2RG MUTATED IL2RG WILD-TYPE 
           0.33            0.00 
  IL2RG MUTATED IL2RG WILD-TYPE 
          51.75          140.38 
  IL2RG MUTATED IL2RG WILD-TYPE 
          17.82           20.63 
[1] "0.3 - 51.8 (17.8)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "1.8"
D809V2, 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       24       106         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        19         10         39         30       35        13
                 vv
clus              STAGE IVB
  IL2RG MUTATED           0
  IL2RG WILD-TYPE         1
D809V3, multiclass
            clus
vv           IL2RG MUTATED IL2RG WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              3             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  IL2RG MUTATED     0   0   6   1
  IL2RG WILD-TYPE   9  68 242  40
D809V4, multiclass
    clus
vv   IL2RG MUTATED IL2RG WILD-TYPE
  T1             0               9
  T2             0              68
  T3             6             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
  IL2RG MUTATED     4   3   0
  IL2RG WILD-TYPE 216  77  66
D809V5, multiclass
    clus
vv   IL2RG MUTATED IL2RG WILD-TYPE
  N0             4             216
  N1             3              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"
D809V6, binary
                 cls
clus                0   1
  IL2RG MUTATED     6   0
  IL2RG WILD-TYPE 277  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL2RG MUTATED      6    0
  IL2RG WILD-TYPE  277   48
   clus
vv  IL2RG MUTATED IL2RG WILD-TYPE
  0             6             277
  1             0              48
[1] 2 2
[1] FALSE
D809V7, 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
D809V8, binary
                 cls
clus                0   1
  IL2RG MUTATED     5   2
  IL2RG WILD-TYPE 312  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL2RG MUTATED      5    2
  IL2RG WILD-TYPE  312   46
                               clus
vv                              IL2RG MUTATED IL2RG WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  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 251   2  22  20
D809V9, multiclass
    clus
vv   IL2RG MUTATED IL2RG WILD-TYPE
  R0             6             251
  R1             0               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"
D809V10, 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
D809V11, 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(810) Variable = BAIAP2L1 MUTATION ANALYSIS
D810V1, survival
                    sevent
clus2                  0   1
  BAIAP2L1 MUTATED     9   3
  BAIAP2L1 WILD-TYPE 273  70
  BAIAP2L1 MUTATED BAIAP2L1 WILD-TYPE 
                12                343 
  BAIAP2L1 MUTATED BAIAP2L1 WILD-TYPE 
                 3                 70 
$`BAIAP2L1 MUTATED`
TCGA-AA-3663 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A01R TCGA-AD-5900 TCGA-AD-6964 
        6.97         2.01        25.02        35.01         0.07        10.88 
TCGA-AZ-4315 TCGA-D5-6927 TCGA-DM-A1DA TCGA-F4-6570 TCGA-G4-6586 TCGA-G4-6588 
       58.39         9.44         7.50         6.18        35.80        26.17 

$`BAIAP2L1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 
       36.72        36.00        22.09        13.78        91.79        46.75 
TCGA-G4-6628 
       52.80 

  BAIAP2L1 MUTATED BAIAP2L1 WILD-TYPE 
              0.07               0.00 
  BAIAP2L1 MUTATED BAIAP2L1 WILD-TYPE 
             58.39             140.38 
  BAIAP2L1 MUTATED BAIAP2L1 WILD-TYPE 
             10.16              20.28 
[1] "0.1 - 58.4 (10.2)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.7"
D810V2, 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       24       103         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BAIAP2L1 MUTATED           1          0          0          1        0
  BAIAP2L1 WILD-TYPE        18         10         41         30       35
                    vv
clus                 STAGE IVA STAGE IVB
  BAIAP2L1 MUTATED           0         0
  BAIAP2L1 WILD-TYPE        13         1
D810V3, multiclass
            clus
vv           BAIAP2L1 MUTATED BAIAP2L1 WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  1                 24
  STAGE IIA                 6                103
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 1                 18
  STAGE IIIA                0                 10
  STAGE IIIB                0                 41
  STAGE IIIC                1                 30
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  BAIAP2L1 MUTATED     0   2   9   1
  BAIAP2L1 WILD-TYPE   9  66 239  40
D810V4, multiclass
    clus
vv   BAIAP2L1 MUTATED BAIAP2L1 WILD-TYPE
  T1                0                  9
  T2                2                 66
  T3                9                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
  BAIAP2L1 MUTATED     9   0   3
  BAIAP2L1 WILD-TYPE 211  80  63
D810V5, multiclass
    clus
vv   BAIAP2L1 MUTATED BAIAP2L1 WILD-TYPE
  N0                9                211
  N1                0                 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"
D810V6, binary
                    cls
clus                   0   1
  BAIAP2L1 MUTATED     9   0
  BAIAP2L1 WILD-TYPE 274  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  BAIAP2L1 MUTATED      9    0
  BAIAP2L1 WILD-TYPE  274   48
   clus
vv  BAIAP2L1 MUTATED BAIAP2L1 WILD-TYPE
  0                9                274
  1                0                 48
[1] 2 2
[1] FALSE
D810V7, 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
D810V8, binary
                    cls
clus                   0   1
  BAIAP2L1 MUTATED     9   3
  BAIAP2L1 WILD-TYPE 308  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  BAIAP2L1 MUTATED      9    3
  BAIAP2L1 WILD-TYPE  308   45
                               clus
vv                              BAIAP2L1 MUTATED BAIAP2L1 WILD-TYPE
  COLON ADENOCARCINOMA                         9                308
  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 249   2  22  21
D810V9, multiclass
    clus
vv   BAIAP2L1 MUTATED BAIAP2L1 WILD-TYPE
  R0                8                249
  R1                0                  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"
D810V10, 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
D810V11, 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(811) Variable = C7ORF58 MUTATION ANALYSIS
D811V1, survival
                   sevent
clus2                 0   1
  C7ORF58 MUTATED    17   3
  C7ORF58 WILD-TYPE 265  70
  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
               20               335 
  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
                3                70 
$`C7ORF58 MUTATED`
TCGA-A6-2676 TCGA-A6-5662 TCGA-A6-6649 TCGA-A6-6780 TCGA-AA-3672 TCGA-AA-3697 
       42.90        23.61        24.16        20.12         0.92        85.05 
TCGA-AA-3949 TCGA-AA-A00N TCGA-AA-A010 TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-6601 
       26.01         4.01        34.98        27.09        58.39       100.01 
TCGA-CA-5254 TCGA-CA-6717 TCGA-CA-6718 TCGA-D5-6922 TCGA-D5-6930 TCGA-DM-A28H 
        2.24         0.33         0.10        10.13         1.51       117.07 
TCGA-F4-6856 TCGA-G4-6309 
       19.43        51.75 

$`C7ORF58 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        33.53        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 
       21.76        24.69        24.39        23.87        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        7.04         3.02         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 
       37.05        19.00        36.00         5.03        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        33.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.20        14.50        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        61.41        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19         1.94         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07         0.26         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         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-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K 
        6.12        81.37       119.93        35.97        60.79        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.41       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
              0.1               0.0 
  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
           117.07            140.38 
  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
           23.885            20.020 
[1] "0.1 - 117.1 (23.9)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.8"
D811V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C7ORF58 MUTATED         2        0        1         6         3         0
  C7ORF58 WILD-TYPE      62        1       24       103         5         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C7ORF58 MUTATED           3          1          3          1        0
  C7ORF58 WILD-TYPE        16          9         38         30       35
                   vv
clus                STAGE IVA STAGE IVB
  C7ORF58 MUTATED           1         0
  C7ORF58 WILD-TYPE        12         1
D811V3, multiclass
            clus
vv           C7ORF58 MUTATED C7ORF58 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                6               103
  STAGE IIB                3                 5
  STAGE IIC                0                 1
  STAGE III                3                16
  STAGE IIIA               1                 9
  STAGE IIIB               3                38
  STAGE IIIC               1                30
  STAGE IV                 0                35
  STAGE IVA                1                12
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 232  38
D811V4, multiclass
    clus
vv   C7ORF58 MUTATED C7ORF58 WILD-TYPE
  T1               0                 9
  T2               2                66
  T3              16               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
  C7ORF58 MUTATED    13   5   3
  C7ORF58 WILD-TYPE 207  75  63
D811V5, multiclass
    clus
vv   C7ORF58 MUTATED C7ORF58 WILD-TYPE
  N0              13               207
  N1               5                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"
D811V6, binary
                   cls
clus                  0   1
  C7ORF58 MUTATED    19   1
  C7ORF58 WILD-TYPE 264  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF58 MUTATED     19    1
  C7ORF58 WILD-TYPE  264   47
   clus
vv  C7ORF58 MUTATED C7ORF58 WILD-TYPE
  0              19               264
  1               1                47
[1] 2 2
[1] FALSE
D811V7, 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
D811V8, binary
                   cls
clus                  0   1
  C7ORF58 MUTATED    15   6
  C7ORF58 WILD-TYPE 302  42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF58 MUTATED     15    6
  C7ORF58 WILD-TYPE  302   42
                               clus
vv                              C7ORF58 MUTATED C7ORF58 WILD-TYPE
  COLON ADENOCARCINOMA                       15               302
  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 244   2  22  18
D811V9, multiclass
    clus
vv   C7ORF58 MUTATED C7ORF58 WILD-TYPE
  R0              13               244
  R1               0                 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"
D811V10, 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
D811V11, 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(812) Variable = ATP13A5 MUTATION ANALYSIS
D812V1, survival
                   sevent
clus2                 0   1
  ATP13A5 MUTATED    21   1
  ATP13A5 WILD-TYPE 261  72
  ATP13A5 MUTATED ATP13A5 WILD-TYPE 
               22               333 
  ATP13A5 MUTATED ATP13A5 WILD-TYPE 
                1                72 
$`ATP13A5 MUTATED`
TCGA-A6-5661 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-6780 TCGA-AA-3510 TCGA-AA-3713 
       33.53        25.08        21.76        20.12        63.98        19.04 
TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A010 TCGA-AD-5900 TCGA-AD-6963 TCGA-AZ-4315 
        2.01        25.02        34.98         0.07        27.42        58.39 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4952 TCGA-CK-6747 TCGA-CM-6167 TCGA-CM-6168 
        0.33         0.10        15.62         2.93        14.99        12.99 
TCGA-DM-A1HA TCGA-F4-6570 TCGA-G4-6293 TCGA-G4-6588 
      131.51         6.18       107.67        26.17 

$`ATP13A5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6648 
       22.06        32.71        27.09        22.52         8.38        25.18 
TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 
       24.16        24.69        24.39        23.87        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 
        7.04         3.02         1.02        35.01         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        0.72         5.79        22.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07         0.26         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      102.44        40.34        49.08        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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.38        13.45        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  ATP13A5 MUTATED ATP13A5 WILD-TYPE 
             0.07              0.00 
  ATP13A5 MUTATED ATP13A5 WILD-TYPE 
           131.51            140.38 
  ATP13A5 MUTATED ATP13A5 WILD-TYPE 
            20.94             20.19 
[1] "0.1 - 131.5 (20.9)" "0.0 - 140.4 (20.2)"
[1] "hr=" "5.3"
D812V2, 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       24        99         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP13A5 MUTATED           2          0          1          2        1
  ATP13A5 WILD-TYPE        17         10         40         29       34
                   vv
clus                STAGE IVA STAGE IVB
  ATP13A5 MUTATED           1         0
  ATP13A5 WILD-TYPE        12         1
D812V3, multiclass
            clus
vv           ATP13A5 MUTATED ATP13A5 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA               10                99
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                2                17
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               2                29
  STAGE IV                 1                34
  STAGE IVA                1                12
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 230  39
D812V4, multiclass
    clus
vv   ATP13A5 MUTATED ATP13A5 WILD-TYPE
  T1               0                 9
  T2               2                66
  T3              18               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
  ATP13A5 MUTATED    16   3   3
  ATP13A5 WILD-TYPE 204  77  63
D812V5, multiclass
    clus
vv   ATP13A5 MUTATED ATP13A5 WILD-TYPE
  N0              16               204
  N1               3                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"
D812V6, binary
                   cls
clus                  0   1
  ATP13A5 MUTATED    14   2
  ATP13A5 WILD-TYPE 269  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ATP13A5 MUTATED     14    2
  ATP13A5 WILD-TYPE  269   46
   clus
vv  ATP13A5 MUTATED ATP13A5 WILD-TYPE
  0              14               269
  1               2                46
[1] 2 2
[1] FALSE
D812V7, 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
D812V8, binary
                   cls
clus                  0   1
  ATP13A5 MUTATED    17   5
  ATP13A5 WILD-TYPE 300  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ATP13A5 MUTATED     17    5
  ATP13A5 WILD-TYPE  300   43
                               clus
vv                              ATP13A5 MUTATED ATP13A5 WILD-TYPE
  COLON ADENOCARCINOMA                       17               300
  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 247   2  21  17
D812V9, multiclass
    clus
vv   ATP13A5 MUTATED ATP13A5 WILD-TYPE
  R0              10               247
  R1               0                 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"
D812V10, 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
D812V11, 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(813) Variable = AMBRA1 MUTATION ANALYSIS
D813V1, survival
                  sevent
clus2                0   1
  AMBRA1 MUTATED    14   4
  AMBRA1 WILD-TYPE 268  69
  AMBRA1 MUTATED AMBRA1 WILD-TYPE 
              18              337 
  AMBRA1 MUTATED AMBRA1 WILD-TYPE 
               4               69 
$`AMBRA1 MUTATED`
TCGA-AA-3492 TCGA-AA-3518 TCGA-AA-3864 TCGA-AA-A01I TCGA-AA-A01Q TCGA-AU-6004 
        3.02         1.02        53.00        31.00         1.02        27.09 
TCGA-AZ-4315 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-CK-6748 TCGA-CM-5861 TCGA-CM-6171 
       58.39         6.77       100.01         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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       49.41        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        16.01 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
      139.17         6.12       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  AMBRA1 MUTATED AMBRA1 WILD-TYPE 
            1.02             0.00 
  AMBRA1 MUTATED AMBRA1 WILD-TYPE 
          135.65           140.38 
  AMBRA1 MUTATED AMBRA1 WILD-TYPE 
          16.435           20.280 
[1] "1.0 - 135.7 (16.4)" "0.0 - 140.4 (20.3)"
[1] "hr=" "1.3"
D813V2, 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       21       103         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AMBRA1 MUTATED           0          1          2          0        1
  AMBRA1 WILD-TYPE        19          9         39         31       34
                  vv
clus               STAGE IVA STAGE IVB
  AMBRA1 MUTATED           0         0
  AMBRA1 WILD-TYPE        13         1
D813V3, multiclass
            clus
vv           AMBRA1 MUTATED AMBRA1 WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                4               21
  STAGE IIA               6              103
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              1                9
  STAGE IIIB              2               39
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  AMBRA1 MUTATED     0   4  14   0
  AMBRA1 WILD-TYPE   9  64 234  41
D813V4, multiclass
    clus
vv   AMBRA1 MUTATED AMBRA1 WILD-TYPE
  T1              0                9
  T2              4               64
  T3             14              234
  T4              0               41
[1] 4 2
[1] TRUE
[1] "dimension 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  76  66
D813V5, multiclass
    clus
vv   AMBRA1 MUTATED AMBRA1 WILD-TYPE
  N0             14              206
  N1              4               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"
D813V6, binary
                  cls
clus                 0   1
  AMBRA1 MUTATED    16   1
  AMBRA1 WILD-TYPE 267  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AMBRA1 MUTATED     16    1
  AMBRA1 WILD-TYPE  267   47
   clus
vv  AMBRA1 MUTATED AMBRA1 WILD-TYPE
  0             16              267
  1              1               47
[1] 2 2
[1] FALSE
D813V7, 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
D813V8, binary
                  cls
clus                 0   1
  AMBRA1 MUTATED    17   1
  AMBRA1 WILD-TYPE 300  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AMBRA1 MUTATED     17    1
  AMBRA1 WILD-TYPE  300   47
                               clus
vv                              AMBRA1 MUTATED AMBRA1 WILD-TYPE
  COLON ADENOCARCINOMA                      17              300
  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 244   2  22  20
D813V9, multiclass
    clus
vv   AMBRA1 MUTATED AMBRA1 WILD-TYPE
  R0             13              244
  R1              0                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"
D813V10, 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
D813V11, 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(814) Variable = SKIL MUTATION ANALYSIS
D814V1, survival
                sevent
clus2              0   1
  SKIL MUTATED     4   3
  SKIL WILD-TYPE 278  70
  SKIL MUTATED SKIL WILD-TYPE 
             7            348 
  SKIL MUTATED SKIL WILD-TYPE 
             3             70 
$`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        19.43 
TCGA-G4-6303 
       65.85 

$`SKIL WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        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-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       11.01        12.95        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 
      119.70        24.43        38.20       130.65        92.75        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
      139.17         6.12        81.37       119.93        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 
        0.53        35.41       107.67        74.56        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  SKIL MUTATED SKIL WILD-TYPE 
          6.97           0.00 
  SKIL MUTATED SKIL WILD-TYPE 
         65.85         140.38 
  SKIL MUTATED SKIL WILD-TYPE 
        29.030         20.155 
[1] "7.0 - 65.8 (29.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.6"
D814V2, 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       24       107         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        19         10         40         31       34        13
                vv
clus             STAGE IVB
  SKIL MUTATED           1
  SKIL WILD-TYPE         0
D814V3, multiclass
            clus
vv           SKIL MUTATED SKIL WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             2            107
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             0             13
  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  67 242  41
D814V4, multiclass
    clus
vv   SKIL MUTATED SKIL WILD-TYPE
  T1            0              9
  T2            1             67
  T3            6            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
  SKIL MUTATED     4   2   1
  SKIL WILD-TYPE 216  78  65
D814V5, multiclass
    clus
vv   SKIL MUTATED SKIL WILD-TYPE
  N0            4            216
  N1            2             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"
D814V6, binary
                cls
clus               0   1
  SKIL MUTATED     5   2
  SKIL WILD-TYPE 278  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  SKIL MUTATED      5    2
  SKIL WILD-TYPE  278   46
   clus
vv  SKIL MUTATED SKIL WILD-TYPE
  0            5            278
  1            2             46
[1] 2 2
[1] FALSE
D814V7, 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
D814V8, binary
                cls
clus               0   1
  SKIL MUTATED     5   2
  SKIL WILD-TYPE 312  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  SKIL MUTATED      5    2
  SKIL WILD-TYPE  312   46
                               clus
vv                              SKIL MUTATED SKIL WILD-TYPE
  COLON ADENOCARCINOMA                     5            312
  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 252   2  22  21
D814V9, multiclass
    clus
vv   SKIL MUTATED SKIL WILD-TYPE
  R0            5            252
  R1            0              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"
D814V10, 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
D814V11, 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(815) Variable = ZNF570 MUTATION ANALYSIS
D815V1, survival
                  sevent
clus2                0   1
  ZNF570 MUTATED     7   1
  ZNF570 WILD-TYPE 275  72
  ZNF570 MUTATED ZNF570 WILD-TYPE 
               8              347 
  ZNF570 MUTATED ZNF570 WILD-TYPE 
               1               72 
$`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        51.75 

$`ZNF570 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
       40.34        15.62        49.08        51.32        21.99         2.93 
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        16.01        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  ZNF570 MUTATED ZNF570 WILD-TYPE 
           15.95             0.00 
  ZNF570 MUTATED ZNF570 WILD-TYPE 
          124.27           140.38 
  ZNF570 MUTATED ZNF570 WILD-TYPE 
           27.09            20.12 
[1] "15.9 - 124.3 (27.1)" "0.0 - 140.4 (20.1)" 
[1] "hr=" "2.4"
D815V2, 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       25       106         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF570 MUTATED           0          0          1          0        0
  ZNF570 WILD-TYPE        19         10         40         31       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF570 MUTATED           1         0
  ZNF570 WILD-TYPE        12         1
D815V3, multiclass
            clus
vv           ZNF570 MUTATED ZNF570 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               3              106
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 244  39
D815V4, multiclass
    clus
vv   ZNF570 MUTATED ZNF570 WILD-TYPE
  T1              1                8
  T2              2               66
  T3              4              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
  ZNF570 MUTATED     7   2   0
  ZNF570 WILD-TYPE 213  78  66
D815V5, multiclass
    clus
vv   ZNF570 MUTATED ZNF570 WILD-TYPE
  N0              7              213
  N1              2               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"
D815V6, binary
                  cls
clus                 0   1
  ZNF570 MUTATED     6   1
  ZNF570 WILD-TYPE 277  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF570 MUTATED      6    1
  ZNF570 WILD-TYPE  277   47
   clus
vv  ZNF570 MUTATED ZNF570 WILD-TYPE
  0              6              277
  1              1               47
[1] 2 2
[1] FALSE
D815V7, 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
D815V8, binary
                  cls
clus                 0   1
  ZNF570 MUTATED     7   2
  ZNF570 WILD-TYPE 310  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF570 MUTATED      7    2
  ZNF570 WILD-TYPE  310   46
                               clus
vv                              ZNF570 MUTATED ZNF570 WILD-TYPE
  COLON ADENOCARCINOMA                       7              310
  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 251   2  22  18
D815V9, multiclass
    clus
vv   ZNF570 MUTATED ZNF570 WILD-TYPE
  R0              6              251
  R1              0                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"
D815V10, 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
D815V11, 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(816) Variable = UCHL5 MUTATION ANALYSIS
D816V1, survival
                 sevent
clus2               0   1
  UCHL5 MUTATED     2   2
  UCHL5 WILD-TYPE 280  71
  UCHL5 MUTATED UCHL5 WILD-TYPE 
              4             351 
  UCHL5 MUTATED UCHL5 WILD-TYPE 
              2              71 
$`UCHL5 MUTATED`
TCGA-AA-3510 TCGA-AZ-6606 TCGA-CK-5912 TCGA-CM-4746 
       63.98        11.74        49.08        37.02 

$`UCHL5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      102.44        40.34        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 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  UCHL5 MUTATED UCHL5 WILD-TYPE 
          11.74            0.00 
  UCHL5 MUTATED UCHL5 WILD-TYPE 
          63.98          140.38 
  UCHL5 MUTATED UCHL5 WILD-TYPE 
          43.05           20.12 
[1] "11.7 - 64.0 (43.0)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.5"
D816V2, 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       24       109         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        19         10         41         31       34        13
                 vv
clus              STAGE IVB
  UCHL5 MUTATED           0
  UCHL5 WILD-TYPE         1
D816V3, multiclass
            clus
vv           UCHL5 MUTATED UCHL5 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              0             109
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  UCHL5 MUTATED     0   2   1   1
  UCHL5 WILD-TYPE   9  66 247  40
D816V4, multiclass
    clus
vv   UCHL5 MUTATED UCHL5 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             1             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
  UCHL5 MUTATED     3   0   1
  UCHL5 WILD-TYPE 217  80  65
D816V5, multiclass
    clus
vv   UCHL5 MUTATED UCHL5 WILD-TYPE
  N0             3             217
  N1             0              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"
D816V6, binary
                 cls
clus                0   1
  UCHL5 MUTATED     2   1
  UCHL5 WILD-TYPE 281  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UCHL5 MUTATED      2    1
  UCHL5 WILD-TYPE  281   47
   clus
vv  UCHL5 MUTATED UCHL5 WILD-TYPE
  0             2             281
  1             1              47
[1] 2 2
[1] FALSE
D816V7, 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
D816V8, binary
                 cls
clus                0   1
  UCHL5 MUTATED     4   0
  UCHL5 WILD-TYPE 313  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UCHL5 MUTATED      4    0
  UCHL5 WILD-TYPE  313   48
                               clus
vv                              UCHL5 MUTATED UCHL5 WILD-TYPE
  COLON ADENOCARCINOMA                      4             313
  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 255   2  22  20
D816V9, multiclass
    clus
vv   UCHL5 MUTATED UCHL5 WILD-TYPE
  R0             2             255
  R1             0               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"
D816V10, 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
D816V11, 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(817) Variable = CASC1 MUTATION ANALYSIS
D817V1, survival
                 sevent
clus2               0   1
  CASC1 MUTATED    10   2
  CASC1 WILD-TYPE 272  71
  CASC1 MUTATED CASC1 WILD-TYPE 
             12             343 
  CASC1 MUTATED CASC1 WILD-TYPE 
              2              71 
$`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 
        0.26         0.33        15.62        11.08        12.49        19.43 

$`CASC1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       38.99         1.02         9.07        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41        49.41        12.10       100.01 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      102.44        40.34        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        35.41       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  CASC1 MUTATED CASC1 WILD-TYPE 
           0.26            0.00 
  CASC1 MUTATED CASC1 WILD-TYPE 
          34.98          140.38 
  CASC1 MUTATED CASC1 WILD-TYPE 
         14.055          20.980 
[1] "0.3 - 35.0 (14.1)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.4"
D817V2, 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       24       106         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CASC1 MUTATED           1          1          0          0        0         0
  CASC1 WILD-TYPE        18          9         41         31       35        13
                 vv
clus              STAGE IVB
  CASC1 MUTATED           0
  CASC1 WILD-TYPE         1
D817V3, multiclass
            clus
vv           CASC1 MUTATED CASC1 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              3             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             1               9
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CASC1 MUTATED     0   5   5   2
  CASC1 WILD-TYPE   9  63 243  39
D817V4, multiclass
    clus
vv   CASC1 MUTATED CASC1 WILD-TYPE
  T1             0               9
  T2             5              63
  T3             5             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
  CASC1 MUTATED    10   1   1
  CASC1 WILD-TYPE 210  79  65
D817V5, multiclass
    clus
vv   CASC1 MUTATED CASC1 WILD-TYPE
  N0            10             210
  N1             1              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"
D817V6, binary
                 cls
clus                0   1
  CASC1 MUTATED     9   0
  CASC1 WILD-TYPE 274  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASC1 MUTATED      9    0
  CASC1 WILD-TYPE  274   48
   clus
vv  CASC1 MUTATED CASC1 WILD-TYPE
  0             9             274
  1             0              48
[1] 2 2
[1] FALSE
D817V7, 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
D817V8, binary
                 cls
clus                0   1
  CASC1 MUTATED     8   4
  CASC1 WILD-TYPE 309  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASC1 MUTATED      8    4
  CASC1 WILD-TYPE  309   44
                               clus
vv                              CASC1 MUTATED CASC1 WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  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 252   2  22  18
D817V9, multiclass
    clus
vv   CASC1 MUTATED CASC1 WILD-TYPE
  R0             5             252
  R1             0               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"
D817V10, 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
D817V11, 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(818) Variable = CBLL1 MUTATION ANALYSIS
D818V1, survival
                 sevent
clus2               0   1
  CBLL1 MUTATED     4   1
  CBLL1 WILD-TYPE 278  72
  CBLL1 MUTATED CBLL1 WILD-TYPE 
              5             350 
  CBLL1 MUTATED CBLL1 WILD-TYPE 
              1              72 
$`CBLL1 MUTATED`
TCGA-A6-5657 TCGA-AA-3663 TCGA-AY-6197 TCGA-AZ-5407 TCGA-F4-6570 
       31.63         6.97        21.44        61.41         6.18 

$`CBLL1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       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        13.38        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  CBLL1 MUTATED CBLL1 WILD-TYPE 
           6.18            0.00 
  CBLL1 MUTATED CBLL1 WILD-TYPE 
          61.41          140.38 
  CBLL1 MUTATED CBLL1 WILD-TYPE 
         21.440          20.155 
[1] "6.2 - 61.4 (21.4)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1"  
D818V2, 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       24       107         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        19         10         40         31       35        13
                 vv
clus              STAGE IVB
  CBLL1 MUTATED           0
  CBLL1 WILD-TYPE         1
D818V3, multiclass
            clus
vv           CBLL1 MUTATED CBLL1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              2             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CBLL1 MUTATED     1   0   4   0
  CBLL1 WILD-TYPE   8  68 244  41
D818V4, multiclass
    clus
vv   CBLL1 MUTATED CBLL1 WILD-TYPE
  T1             1               8
  T2             0              68
  T3             4             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
  CBLL1 MUTATED     4   1   0
  CBLL1 WILD-TYPE 216  79  66
D818V5, multiclass
    clus
vv   CBLL1 MUTATED CBLL1 WILD-TYPE
  N0             4             216
  N1             1              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"
D818V6, binary
                 cls
clus                0   1
  CBLL1 MUTATED     4   0
  CBLL1 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBLL1 MUTATED      4    0
  CBLL1 WILD-TYPE  279   48
   clus
vv  CBLL1 MUTATED CBLL1 WILD-TYPE
  0             4             279
  1             0              48
[1] 2 2
[1] FALSE
D818V7, 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
D818V8, binary
                 cls
clus                0   1
  CBLL1 MUTATED     5   0
  CBLL1 WILD-TYPE 312  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBLL1 MUTATED      5    0
  CBLL1 WILD-TYPE  312   48
                               clus
vv                              CBLL1 MUTATED CBLL1 WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  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 253   2  22  21
D818V9, multiclass
    clus
vv   CBLL1 MUTATED CBLL1 WILD-TYPE
  R0             4             253
  R1             0               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"
D818V10, 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
D818V11, 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(819) Variable = FOXN3 MUTATION ANALYSIS
D819V1, survival
                 sevent
clus2               0   1
  FOXN3 MUTATED    11   0
  FOXN3 WILD-TYPE 271  73
  FOXN3 MUTATED FOXN3 WILD-TYPE 
             11             344 
  FOXN3 MUTATED FOXN3 WILD-TYPE 
              0              73 
$`FOXN3 MUTATED`
TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3663 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3821 
       24.39        19.66         6.97        26.99        19.04         1.02 
TCGA-AA-3864 TCGA-CA-6717 TCGA-CM-4743 TCGA-CM-5864 TCGA-CM-6169 
       53.00         0.33        23.05        15.02        13.02 

$`FOXN3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       85.05        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
       25.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14         2.93         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-5868 TCGA-CM-6161 
       16.01        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-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       12.99        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  FOXN3 MUTATED FOXN3 WILD-TYPE 
           0.33            0.00 
  FOXN3 MUTATED FOXN3 WILD-TYPE 
          53.00          140.38 
  FOXN3 MUTATED FOXN3 WILD-TYPE 
          19.04           20.63 
[1] "0.3 - 53.0 (19.0)"  "0.0 - 140.4 (20.6)"
[1] "hr="     "9300000"
D819V2, 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       23       105         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        19         10         41         30       34        13
                 vv
clus              STAGE IVB
  FOXN3 MUTATED           0
  FOXN3 WILD-TYPE         1
D819V3, multiclass
            clus
vv           FOXN3 MUTATED FOXN3 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              4             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FOXN3 MUTATED     0   3   7   1
  FOXN3 WILD-TYPE   9  65 241  40
D819V4, multiclass
    clus
vv   FOXN3 MUTATED FOXN3 WILD-TYPE
  T1             0               9
  T2             3              65
  T3             7             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
  FOXN3 MUTATED    10   1   0
  FOXN3 WILD-TYPE 210  79  66
D819V5, multiclass
    clus
vv   FOXN3 MUTATED FOXN3 WILD-TYPE
  N0            10             210
  N1             1              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
  FOXN3 MUTATED     9   1
  FOXN3 WILD-TYPE 274  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXN3 MUTATED      9    1
  FOXN3 WILD-TYPE  274   47
   clus
vv  FOXN3 MUTATED FOXN3 WILD-TYPE
  0             9             274
  1             1              47
[1] 2 2
[1] FALSE
D819V7, 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
D819V8, binary
                 cls
clus                0   1
  FOXN3 MUTATED     8   3
  FOXN3 WILD-TYPE 309  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXN3 MUTATED      8    3
  FOXN3 WILD-TYPE  309   45
                               clus
vv                              FOXN3 MUTATED FOXN3 WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  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 249   2  21  20
D819V9, multiclass
    clus
vv   FOXN3 MUTATED FOXN3 WILD-TYPE
  R0             8             249
  R1             0               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"
D819V10, 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
D819V11, 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(820) Variable = AP1M1 MUTATION ANALYSIS
D820V1, survival
                 sevent
clus2               0   1
  AP1M1 MUTATED     8   1
  AP1M1 WILD-TYPE 274  72
  AP1M1 MUTATED AP1M1 WILD-TYPE 
              9             346 
  AP1M1 MUTATED AP1M1 WILD-TYPE 
              1              72 
$`AP1M1 MUTATED`
TCGA-A6-5665 TCGA-AA-3819 TCGA-AA-A01R TCGA-AY-6197 TCGA-AZ-5407 TCGA-AZ-6601 
       22.06        25.02        35.01        21.44        61.41       100.01 
TCGA-CK-5913 TCGA-D5-6533 TCGA-D5-6536 
       51.32         1.32        17.85 

$`AP1M1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05        33.04         0.99         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       22.36        62.79        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 
       13.51        11.51        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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  AP1M1 MUTATED AP1M1 WILD-TYPE 
           1.32            0.00 
  AP1M1 MUTATED AP1M1 WILD-TYPE 
         100.01          140.38 
  AP1M1 MUTATED AP1M1 WILD-TYPE 
         25.020          20.005 
[1] "1.3 - 100.0 (25.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "2.8"
D820V2, 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       24       104         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AP1M1 MUTATED           1          0          1          0        0         0
  AP1M1 WILD-TYPE        18         10         40         31       35        13
                 vv
clus              STAGE IVB
  AP1M1 MUTATED           0
  AP1M1 WILD-TYPE         1
D820V3, multiclass
            clus
vv           AP1M1 MUTATED AP1M1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              5             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  AP1M1 MUTATED     1   0   7   1
  AP1M1 WILD-TYPE   8  68 241  40
D820V4, multiclass
    clus
vv   AP1M1 MUTATED AP1M1 WILD-TYPE
  T1             1               8
  T2             0              68
  T3             7             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
  AP1M1 MUTATED     8   0   1
  AP1M1 WILD-TYPE 212  80  65
D820V5, multiclass
    clus
vv   AP1M1 MUTATED AP1M1 WILD-TYPE
  N0             8             212
  N1             0              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"
D820V6, binary
                 cls
clus                0   1
  AP1M1 MUTATED     7   0
  AP1M1 WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP1M1 MUTATED      7    0
  AP1M1 WILD-TYPE  276   48
   clus
vv  AP1M1 MUTATED AP1M1 WILD-TYPE
  0             7             276
  1             0              48
[1] 2 2
[1] FALSE
D820V7, 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
D820V8, binary
                 cls
clus                0   1
  AP1M1 MUTATED     8   1
  AP1M1 WILD-TYPE 309  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP1M1 MUTATED      8    1
  AP1M1 WILD-TYPE  309   47
                               clus
vv                              AP1M1 MUTATED AP1M1 WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  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 251   2  22  20
D820V9, multiclass
    clus
vv   AP1M1 MUTATED AP1M1 WILD-TYPE
  R0             6             251
  R1             0               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"
D820V10, 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
D820V11, 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(821) Variable = ARHGEF3 MUTATION ANALYSIS
D821V1, survival
                   sevent
clus2                 0   1
  ARHGEF3 MUTATED    11   1
  ARHGEF3 WILD-TYPE 271  72
  ARHGEF3 MUTATED ARHGEF3 WILD-TYPE 
               12               343 
  ARHGEF3 MUTATED ARHGEF3 WILD-TYPE 
                1                72 
$`ARHGEF3 MUTATED`
TCGA-A6-6653 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3977 TCGA-AA-A010 TCGA-AA-A01Q 
       24.39        63.98         6.97        25.02        34.98         1.02 
TCGA-AY-6196 TCGA-AZ-4315 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CM-5868 TCGA-D5-6540 
        0.20        58.39       100.01         0.33        17.03        16.14 

$`ARHGEF3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        15.75        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  ARHGEF3 MUTATED ARHGEF3 WILD-TYPE 
              0.2               0.0 
  ARHGEF3 MUTATED ARHGEF3 WILD-TYPE 
           100.01            140.38 
  ARHGEF3 MUTATED ARHGEF3 WILD-TYPE 
            20.71             20.19 
[1] "0.2 - 100.0 (20.7)" "0.0 - 140.4 (20.2)"
[1] "hr=" "2.9"
D821V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ARHGEF3 MUTATED         2        0        4         2         1         0
  ARHGEF3 WILD-TYPE      62        1       21       107         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARHGEF3 MUTATED           0          0          0          1        0
  ARHGEF3 WILD-TYPE        19         10         41         30       35
                   vv
clus                STAGE IVA STAGE IVB
  ARHGEF3 MUTATED           1         0
  ARHGEF3 WILD-TYPE        12         1
D821V3, multiclass
            clus
vv           ARHGEF3 MUTATED ARHGEF3 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 4                21
  STAGE IIA                2               107
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               1                30
  STAGE IV                 0                35
  STAGE IVA                1                12
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of 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   7   2
  ARHGEF3 WILD-TYPE   9  65 241  39
D821V4, multiclass
    clus
vv   ARHGEF3 MUTATED ARHGEF3 WILD-TYPE
  T1               0                 9
  T2               3                65
  T3               7               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
  ARHGEF3 MUTATED    10   1   1
  ARHGEF3 WILD-TYPE 210  79  65
D821V5, multiclass
    clus
vv   ARHGEF3 MUTATED ARHGEF3 WILD-TYPE
  N0              10               210
  N1               1                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"
D821V6, binary
                   cls
clus                  0   1
  ARHGEF3 MUTATED     9   1
  ARHGEF3 WILD-TYPE 274  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGEF3 MUTATED      9    1
  ARHGEF3 WILD-TYPE  274   47
   clus
vv  ARHGEF3 MUTATED ARHGEF3 WILD-TYPE
  0               9               274
  1               1                47
[1] 2 2
[1] FALSE
D821V7, binary
                   cls
clus                  0   1
  ARHGEF3 MUTATED     3   9
  ARHGEF3 WILD-TYPE 167 188
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGEF3 MUTATED      3    9
  ARHGEF3 WILD-TYPE  167  188
        clus
vv       ARHGEF3 MUTATED ARHGEF3 WILD-TYPE
  FEMALE               3               167
  MALE                 9               188
[1] 2 2
[1] FALSE
D821V8, binary
                   cls
clus                  0   1
  ARHGEF3 MUTATED     9   3
  ARHGEF3 WILD-TYPE 308  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGEF3 MUTATED      9    3
  ARHGEF3 WILD-TYPE  308   45
                               clus
vv                              ARHGEF3 MUTATED ARHGEF3 WILD-TYPE
  COLON ADENOCARCINOMA                        9               308
  COLON MUCINOUS ADENOCARCINOMA               3                45
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ARHGEF3 MUTATED     8   0   0   1
  ARHGEF3 WILD-TYPE 249   2  22  20
D821V9, multiclass
    clus
vv   ARHGEF3 MUTATED ARHGEF3 WILD-TYPE
  R0               8               249
  R1               0                 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"
D821V10, 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
D821V11, 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(822) Variable = KLKB1 MUTATION ANALYSIS
D822V1, survival
                 sevent
clus2               0   1
  KLKB1 MUTATED    11   2
  KLKB1 WILD-TYPE 271  71
  KLKB1 MUTATED KLKB1 WILD-TYPE 
             13             342 
  KLKB1 MUTATED KLKB1 WILD-TYPE 
              2              71 
$`KLKB1 MUTATED`
TCGA-A6-2676 TCGA-A6-5661 TCGA-A6-5665 TCGA-AA-3525 TCGA-AA-3950 TCGA-AA-A00J 
       42.90        33.53        22.06         8.05        24.00        18.05 
TCGA-AA-A00N TCGA-AD-5900 TCGA-CA-6715 TCGA-CM-4743 TCGA-CM-6171 TCGA-D5-6927 
        4.01         0.07         0.07        23.05        14.04         9.44 
TCGA-G4-6588 
       26.17 

$`KLKB1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       31.63        30.44        29.19        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       24.03        37.05        36.03        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        52.80 

  KLKB1 MUTATED KLKB1 WILD-TYPE 
           0.07            0.00 
  KLKB1 MUTATED KLKB1 WILD-TYPE 
          42.90          140.38 
  KLKB1 MUTATED KLKB1 WILD-TYPE 
         18.050          20.235 
[1] "0.1 - 42.9 (18.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D822V2, 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       25       103         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        19         10         38         31       35        13
                 vv
clus              STAGE IVB
  KLKB1 MUTATED           0
  KLKB1 WILD-TYPE         1
D822V3, multiclass
            clus
vv           KLKB1 MUTATED KLKB1 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              6             103
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             3              38
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KLKB1 MUTATED     0   2   8   3
  KLKB1 WILD-TYPE   9  66 240  38
D822V4, multiclass
    clus
vv   KLKB1 MUTATED KLKB1 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             8             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
  KLKB1 MUTATED    10   3   0
  KLKB1 WILD-TYPE 210  77  66
D822V5, multiclass
    clus
vv   KLKB1 MUTATED KLKB1 WILD-TYPE
  N0            10             210
  N1             3              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"
D822V6, binary
                 cls
clus                0   1
  KLKB1 MUTATED    12   0
  KLKB1 WILD-TYPE 271  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLKB1 MUTATED     12    0
  KLKB1 WILD-TYPE  271   48
   clus
vv  KLKB1 MUTATED KLKB1 WILD-TYPE
  0            12             271
  1             0              48
[1] 2 2
[1] FALSE
D822V7, 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
D822V8, binary
                 cls
clus                0   1
  KLKB1 MUTATED     9   4
  KLKB1 WILD-TYPE 308  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLKB1 MUTATED      9    4
  KLKB1 WILD-TYPE  308   44
                               clus
vv                              KLKB1 MUTATED KLKB1 WILD-TYPE
  COLON ADENOCARCINOMA                      9             308
  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 245   2  22  20
D822V9, multiclass
    clus
vv   KLKB1 MUTATED KLKB1 WILD-TYPE
  R0            12             245
  R1             0               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"
D822V10, 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
D822V11, 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(823) Variable = ZBTB33 MUTATION ANALYSIS
D823V1, survival
                  sevent
clus2                0   1
  ZBTB33 MUTATED    10   6
  ZBTB33 WILD-TYPE 272  67
  ZBTB33 MUTATED ZBTB33 WILD-TYPE 
              16              339 
  ZBTB33 MUTATED ZBTB33 WILD-TYPE 
               6               67 
$`ZBTB33 MUTATED`
TCGA-A6-6780 TCGA-AA-3510 TCGA-AA-3552 TCGA-AA-3660 TCGA-AA-3715 TCGA-AA-3947 
       20.12        63.98        13.02        78.08        19.04        33.01 
TCGA-AA-A01P TCGA-AA-A01R TCGA-AD-6889 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-CK-5916 
       38.07        35.01        56.55         6.77       100.01        21.14 
TCGA-CM-6170 TCGA-CM-6171 TCGA-D5-6541 TCGA-G4-6586 
       15.02        14.04        15.58        35.80 

$`ZBTB33 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 
       12.99         0.99        14.01        33.99        21.01        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 
       18.05        31.00         2.01        12.99        24.00        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41        49.41        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32        21.99         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        16.14         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 
       45.11        36.72        36.00        22.09        13.78        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  ZBTB33 MUTATED ZBTB33 WILD-TYPE 
            6.77             0.00 
  ZBTB33 MUTATED ZBTB33 WILD-TYPE 
          100.01           140.38 
  ZBTB33 MUTATED ZBTB33 WILD-TYPE 
          27.075           20.020 
[1] "6.8 - 100.0 (27.1)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.4"
D823V2, 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       21       105         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZBTB33 MUTATED           2          0          0          1        0
  ZBTB33 WILD-TYPE        17         10         41         30       35
                  vv
clus               STAGE IVA STAGE IVB
  ZBTB33 MUTATED           0         0
  ZBTB33 WILD-TYPE        13         1
D823V3, multiclass
            clus
vv           ZBTB33 MUTATED ZBTB33 WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                4               21
  STAGE IIA               4              105
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               2               17
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZBTB33 MUTATED     1   3  11   1
  ZBTB33 WILD-TYPE   8  65 237  40
D823V4, multiclass
    clus
vv   ZBTB33 MUTATED ZBTB33 WILD-TYPE
  T1              1                8
  T2              3               65
  T3             11              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
  ZBTB33 MUTATED    13   1   2
  ZBTB33 WILD-TYPE 207  79  64
D823V5, multiclass
    clus
vv   ZBTB33 MUTATED ZBTB33 WILD-TYPE
  N0             13              207
  N1              1               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"
D823V6, binary
                  cls
clus                 0   1
  ZBTB33 MUTATED    14   0
  ZBTB33 WILD-TYPE 269  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB33 MUTATED     14    0
  ZBTB33 WILD-TYPE  269   48
   clus
vv  ZBTB33 MUTATED ZBTB33 WILD-TYPE
  0             14              269
  1              0               48
[1] 2 2
[1] FALSE
D823V7, 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
D823V8, binary
                  cls
clus                 0   1
  ZBTB33 MUTATED    13   3
  ZBTB33 WILD-TYPE 304  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB33 MUTATED     13    3
  ZBTB33 WILD-TYPE  304   45
                               clus
vv                              ZBTB33 MUTATED ZBTB33 WILD-TYPE
  COLON ADENOCARCINOMA                      13              304
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZBTB33 MUTATED    11   0   0   1
  ZBTB33 WILD-TYPE 246   2  22  20
D823V9, multiclass
    clus
vv   ZBTB33 MUTATED ZBTB33 WILD-TYPE
  R0             11              246
  R1              0                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"
D823V10, 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
D823V11, 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(824) Variable = H2AFJ MUTATION ANALYSIS
D824V1, survival
                 sevent
clus2               0   1
  H2AFJ MUTATED     3   0
  H2AFJ WILD-TYPE 279  73
  H2AFJ MUTATED H2AFJ WILD-TYPE 
              3             352 
  H2AFJ MUTATED H2AFJ WILD-TYPE 
              0              73 
$`H2AFJ MUTATED`
TCGA-AA-3663 TCGA-AA-3713 TCGA-CM-5348 
        6.97        19.04        22.98 

$`H2AFJ WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  H2AFJ MUTATED H2AFJ WILD-TYPE 
           6.97            0.00 
  H2AFJ MUTATED H2AFJ WILD-TYPE 
          22.98          140.38 
  H2AFJ MUTATED H2AFJ WILD-TYPE 
         19.040          20.235 
[1] "7.0 - 23.0 (19.0)"  "0.0 - 140.4 (20.2)"
[1] "hr="     "3300000"
D824V2, 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       24       109         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        19         10         40         31       34        13
                 vv
clus              STAGE IVB
  H2AFJ MUTATED           0
  H2AFJ WILD-TYPE         1
D824V3, multiclass
            clus
vv           H2AFJ MUTATED H2AFJ WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              0             109
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  H2AFJ MUTATED     0   0   3   0
  H2AFJ WILD-TYPE   9  68 245  41
D824V4, multiclass
    clus
vv   H2AFJ MUTATED H2AFJ WILD-TYPE
  T1             0               9
  T2             0              68
  T3             3             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
  H2AFJ MUTATED     2   1   0
  H2AFJ WILD-TYPE 218  79  66
D824V5, multiclass
    clus
vv   H2AFJ MUTATED H2AFJ WILD-TYPE
  N0             2             218
  N1             1              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"
D824V6, binary
                 cls
clus                0   1
  H2AFJ MUTATED     2   1
  H2AFJ WILD-TYPE 281  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  H2AFJ MUTATED      2    1
  H2AFJ WILD-TYPE  281   47
   clus
vv  H2AFJ MUTATED H2AFJ WILD-TYPE
  0             2             281
  1             1              47
[1] 2 2
[1] FALSE
D824V7, 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
D824V8, binary
                 cls
clus                0   1
  H2AFJ MUTATED     3   0
  H2AFJ WILD-TYPE 314  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  H2AFJ MUTATED      3    0
  H2AFJ WILD-TYPE  314   48
                               clus
vv                              H2AFJ MUTATED H2AFJ WILD-TYPE
  COLON ADENOCARCINOMA                      3             314
  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 255   2  21  21
D824V9, multiclass
    clus
vv   H2AFJ MUTATED H2AFJ WILD-TYPE
  R0             2             255
  R1             0               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"
D824V10, 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
D824V11, multiclass
[1] "Remove cluster labels:" "H2AFJ MUTATED"         
clus
  H2AFJ MUTATED H2AFJ WILD-TYPE 
              1             205 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-4105 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-A6-5656      TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5660 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-A6-5661      TCGA-A6-5662      TCGA-A6-5664      TCGA-A6-5665 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-A6-5666      TCGA-A6-6137      TCGA-A6-6138      TCGA-A6-6141 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-A6-6142      TCGA-A6-6648      TCGA-A6-6649      TCGA-A6-6651 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-A6-6652      TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-A6-6781      TCGA-A6-6782      TCGA-AD-5900      TCGA-AD-6548 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-AD-6888      TCGA-AD-6889      TCGA-AD-6890      TCGA-AD-6895 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-AD-6899      TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6964 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-AD-6965      TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-AY-4071      TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-AY-6386      TCGA-AZ-4315      TCGA-AZ-4323      TCGA-AZ-4616 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-AZ-4681      TCGA-AZ-4682      TCGA-AZ-5403      TCGA-AZ-5407 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-AZ-6598      TCGA-AZ-6599      TCGA-AZ-6600      TCGA-AZ-6601 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-AZ-6603      TCGA-AZ-6605      TCGA-AZ-6606      TCGA-AZ-6607 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-AZ-6608      TCGA-CA-5254      TCGA-CA-5255      TCGA-CA-5796 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-CA-5797      TCGA-CA-6715      TCGA-CA-6716      TCGA-CA-6717 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-CA-6718      TCGA-CA-6719      TCGA-CK-4947      TCGA-CK-4948 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-CK-4950      TCGA-CK-4952      TCGA-CK-5912      TCGA-CK-5913 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-CK-5914      TCGA-CK-5915      TCGA-CK-5916      TCGA-CK-6746 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-CK-6747      TCGA-CK-6748      TCGA-CK-6751      TCGA-CM-4743 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-CM-4744      TCGA-CM-4746      TCGA-CM-4747      TCGA-CM-4752 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-CM-5341      TCGA-CM-5344      TCGA-CM-5349      TCGA-CM-5860 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-CM-5861      TCGA-CM-5862      TCGA-CM-5863      TCGA-CM-5864 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-CM-5868      TCGA-CM-6161      TCGA-CM-6162      TCGA-CM-6163 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-CM-6164      TCGA-CM-6165      TCGA-CM-6166      TCGA-CM-6167 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-CM-6168      TCGA-CM-6169      TCGA-CM-6170      TCGA-CM-6171 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-CM-6172      TCGA-CM-6674      TCGA-CM-6675      TCGA-CM-6676 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-CM-6677      TCGA-CM-6678      TCGA-CM-6679      TCGA-CM-6680 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-D5-5537      TCGA-D5-5538      TCGA-D5-5539      TCGA-D5-5540 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-D5-5541      TCGA-D5-6529      TCGA-D5-6532      TCGA-D5-6533 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-D5-6534      TCGA-D5-6535      TCGA-D5-6536      TCGA-D5-6537 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-D5-6538      TCGA-D5-6539      TCGA-D5-6540      TCGA-D5-6541 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-D5-6898      TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-D5-6924      TCGA-D5-6926      TCGA-D5-6927      TCGA-D5-6928 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-D5-6929      TCGA-D5-6930      TCGA-D5-6931      TCGA-D5-6932 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-D5-7000      TCGA-DM-A0X9      TCGA-DM-A0XD      TCGA-DM-A0XF 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-DM-A1D0      TCGA-DM-A1D4      TCGA-DM-A1D6      TCGA-DM-A1D7 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-DM-A1D8      TCGA-DM-A1D9      TCGA-DM-A1DA      TCGA-DM-A1DB 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-DM-A1HA      TCGA-DM-A1HB      TCGA-DM-A282      TCGA-DM-A285 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-DM-A28C      TCGA-DM-A28E      TCGA-DM-A28F      TCGA-DM-A28G 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-DM-A28H      TCGA-DM-A28K      TCGA-F4-6459      TCGA-F4-6460 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-F4-6805      TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-G4-6306      TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-G4-6586      TCGA-G4-6588      TCGA-G4-6625      TCGA-G4-6626 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-G4-6628 
"H2AFJ WILD-TYPE" 

Clustering(825) Variable = CBLN3 MUTATION ANALYSIS
D825V1, survival
                 sevent
clus2               0   1
  CBLN3 MUTATED     6   0
  CBLN3 WILD-TYPE 276  73
  CBLN3 MUTATED CBLN3 WILD-TYPE 
              6             349 
  CBLN3 MUTATED CBLN3 WILD-TYPE 
              0              73 
$`CBLN3 MUTATED`
TCGA-AA-3713 TCGA-CA-6717 TCGA-CM-6171 TCGA-D5-6536 TCGA-F4-6856 TCGA-G4-6321 
       19.04         0.33        14.04        17.85        19.43        22.09 

$`CBLN3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 
       20.19        18.25         1.32        43.27        15.12         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        35.41       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  CBLN3 MUTATED CBLN3 WILD-TYPE 
           0.33            0.00 
  CBLN3 MUTATED CBLN3 WILD-TYPE 
          22.09          140.38 
  CBLN3 MUTATED CBLN3 WILD-TYPE 
         18.445          20.980 
[1] "0.3 - 22.1 (18.4)"  "0.0 - 140.4 (21.0)"
[1] "hr="     "9100000"
D825V2, 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       25       107         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        18         10         41         31       34        13
                 vv
clus              STAGE IVB
  CBLN3 MUTATED           0
  CBLN3 WILD-TYPE         1
D825V3, multiclass
            clus
vv           CBLN3 MUTATED CBLN3 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              2             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CBLN3 MUTATED     0   3   3   0
  CBLN3 WILD-TYPE   9  65 245  41
D825V4, multiclass
    clus
vv   CBLN3 MUTATED CBLN3 WILD-TYPE
  T1             0               9
  T2             3              65
  T3             3             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
  CBLN3 MUTATED     5   1   0
  CBLN3 WILD-TYPE 215  79  66
D825V5, multiclass
    clus
vv   CBLN3 MUTATED CBLN3 WILD-TYPE
  N0             5             215
  N1             1              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"
D825V6, binary
                 cls
clus                0   1
  CBLN3 MUTATED     4   1
  CBLN3 WILD-TYPE 279  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBLN3 MUTATED      4    1
  CBLN3 WILD-TYPE  279   47
   clus
vv  CBLN3 MUTATED CBLN3 WILD-TYPE
  0             4             279
  1             1              47
[1] 2 2
[1] FALSE
D825V7, 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
D825V8, binary
                 cls
clus                0   1
  CBLN3 MUTATED     4   2
  CBLN3 WILD-TYPE 313  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBLN3 MUTATED      4    2
  CBLN3 WILD-TYPE  313   46
                               clus
vv                              CBLN3 MUTATED CBLN3 WILD-TYPE
  COLON ADENOCARCINOMA                      4             313
  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 253   2  21  20
D825V9, multiclass
    clus
vv   CBLN3 MUTATED CBLN3 WILD-TYPE
  R0             4             253
  R1             0               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"
D825V10, 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
D825V11, 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(826) Variable = TRIM46 MUTATION ANALYSIS
D826V1, survival
                  sevent
clus2                0   1
  TRIM46 MUTATED    10   4
  TRIM46 WILD-TYPE 272  69
  TRIM46 MUTATED TRIM46 WILD-TYPE 
              14              341 
  TRIM46 MUTATED TRIM46 WILD-TYPE 
               4               69 
$`TRIM46 MUTATED`
TCGA-AA-3715 TCGA-AA-3845 TCGA-AD-6889 TCGA-AD-6964 TCGA-AY-6197 TCGA-AZ-4315 
       19.04         0.00        56.55        10.88        21.44        58.39 
TCGA-AZ-6601 TCGA-CA-6718 TCGA-CM-4746 TCGA-CM-5344 TCGA-CM-5861 TCGA-D5-6539 
      100.01         0.10        37.02        22.03        15.02        12.49 
TCGA-DM-A0X9 TCGA-DM-A1HB 
      119.70       135.65 

$`TRIM46 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
       17.98        15.95        38.99        37.02        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.33         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         2.01       124.27        23.05        20.02 
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        16.01 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        11.38        10.26        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  TRIM46 MUTATED TRIM46 WILD-TYPE 
               0                0 
  TRIM46 MUTATED TRIM46 WILD-TYPE 
          135.65           140.38 
  TRIM46 MUTATED TRIM46 WILD-TYPE 
          21.735           20.120 
[1] "0.0 - 135.7 (21.7)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.1"
D826V2, 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       22       102         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRIM46 MUTATED           0          1          2          0        0
  TRIM46 WILD-TYPE        19          9         39         31       35
                  vv
clus               STAGE IVA STAGE IVB
  TRIM46 MUTATED           0         0
  TRIM46 WILD-TYPE        13         1
D826V3, multiclass
            clus
vv           TRIM46 MUTATED TRIM46 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                3               22
  STAGE IIA               7              102
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              1                9
  STAGE IIIB              2               39
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TRIM46 MUTATED     0   1  12   2
  TRIM46 WILD-TYPE   9  67 236  39
D826V4, multiclass
    clus
vv   TRIM46 MUTATED TRIM46 WILD-TYPE
  T1              0                9
  T2              1               67
  T3             12              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
  TRIM46 MUTATED    12   2   1
  TRIM46 WILD-TYPE 208  78  65
D826V5, multiclass
    clus
vv   TRIM46 MUTATED TRIM46 WILD-TYPE
  N0             12              208
  N1              2               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"
D826V6, binary
                  cls
clus                 0   1
  TRIM46 MUTATED    13   0
  TRIM46 WILD-TYPE 270  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM46 MUTATED     13    0
  TRIM46 WILD-TYPE  270   48
   clus
vv  TRIM46 MUTATED TRIM46 WILD-TYPE
  0             13              270
  1              0               48
[1] 2 2
[1] FALSE
D826V7, 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
D826V8, binary
                  cls
clus                 0   1
  TRIM46 MUTATED    15   0
  TRIM46 WILD-TYPE 302  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM46 MUTATED     15    0
  TRIM46 WILD-TYPE  302   48
                               clus
vv                              TRIM46 MUTATED TRIM46 WILD-TYPE
  COLON ADENOCARCINOMA                      15              302
  COLON MUCINOUS ADENOCARCINOMA              0               48
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TRIM46 MUTATED     9   0   0   1
  TRIM46 WILD-TYPE 248   2  22  20
D826V9, multiclass
    clus
vv   TRIM46 MUTATED TRIM46 WILD-TYPE
  R0              9              248
  R1              0                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"
D826V10, 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
D826V11, 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(827) Variable = CCDC88A MUTATION ANALYSIS
D827V1, survival
                   sevent
clus2                 0   1
  CCDC88A MUTATED    22   5
  CCDC88A WILD-TYPE 260  68
  CCDC88A MUTATED CCDC88A WILD-TYPE 
               27               328 
  CCDC88A MUTATED CCDC88A WILD-TYPE 
                5                68 
$`CCDC88A MUTATED`
TCGA-A6-2676 TCGA-A6-3809 TCGA-A6-5665 TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3510 
       42.90        32.75        22.06        24.39        19.66        63.98 
TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3524 TCGA-AA-3555 TCGA-AA-3663 TCGA-AA-3977 
       13.02         1.02        36.03        29.95         6.97        25.02 
TCGA-AA-A00U TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-6603 TCGA-CA-6717 
       17.03        34.98        58.39         1.41        29.56         0.33 
TCGA-CA-6718 TCGA-CM-4746 TCGA-CM-5348 TCGA-D5-5540 TCGA-DM-A0XD TCGA-DM-A1HA 
        0.10        37.02        22.98        13.51        24.43       131.51 
TCGA-DM-A28K TCGA-G4-6586 TCGA-G4-6628 
       98.24        35.80        52.80 

$`CCDC88A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       34.65        33.34        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       30.44        29.19        33.53        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 
       21.76        24.69        23.87        20.12        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02         1.02        35.01         6.97         1.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
        9.07        24.03        37.05         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.05        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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-4681 
       15.75         0.20        21.44        17.82         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
      100.01         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07         0.26         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 
       20.02        25.02        13.02        29.06        22.03        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-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 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       13.78        26.17        91.79        46.75 

  CCDC88A MUTATED CCDC88A WILD-TYPE 
              0.1               0.0 
  CCDC88A MUTATED CCDC88A WILD-TYPE 
           131.51            140.38 
  CCDC88A MUTATED CCDC88A WILD-TYPE 
            25.02             19.79 
[1] "0.1 - 131.5 (25.0)" "0.0 - 140.4 (19.8)"
[1] "hr=" "1.3"
D827V2, 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       22        98         4         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC88A MUTATED           1          0          2          2        2
  CCDC88A WILD-TYPE        18         10         39         29       33
                   vv
clus                STAGE IVA STAGE IVB
  CCDC88A MUTATED           0         0
  CCDC88A WILD-TYPE        13         1
D827V3, multiclass
            clus
vv           CCDC88A MUTATED CCDC88A WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 3                22
  STAGE IIA               11                98
  STAGE IIB                4                 4
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               0                10
  STAGE IIIB               2                39
  STAGE IIIC               2                29
  STAGE IV                 2                33
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CCDC88A MUTATED     0   5  19   6
  CCDC88A WILD-TYPE   9  63 229  35
D827V4, multiclass
    clus
vv   CCDC88A MUTATED CCDC88A WILD-TYPE
  T1               0                 9
  T2               5                63
  T3              19               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
  CCDC88A MUTATED    22   4   4
  CCDC88A WILD-TYPE 198  76  62
D827V5, multiclass
    clus
vv   CCDC88A MUTATED CCDC88A WILD-TYPE
  N0              22               198
  N1               4                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"
D827V6, binary
                   cls
clus                  0   1
  CCDC88A MUTATED    24   2
  CCDC88A WILD-TYPE 259  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC88A MUTATED     24    2
  CCDC88A WILD-TYPE  259   46
   clus
vv  CCDC88A MUTATED CCDC88A WILD-TYPE
  0              24               259
  1               2                46
[1] 2 2
[1] FALSE
D827V7, 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
D827V8, binary
                   cls
clus                  0   1
  CCDC88A MUTATED    24   6
  CCDC88A WILD-TYPE 293  42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC88A MUTATED     24    6
  CCDC88A WILD-TYPE  293   42
                               clus
vv                              CCDC88A MUTATED CCDC88A WILD-TYPE
  COLON ADENOCARCINOMA                       24               293
  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 239   2  21  18
D827V9, multiclass
    clus
vv   CCDC88A MUTATED CCDC88A WILD-TYPE
  R0              18               239
  R1               0                 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"
D827V10, 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
D827V11, 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(828) Variable = PRKCI MUTATION ANALYSIS
D828V1, survival
                 sevent
clus2               0   1
  PRKCI MUTATED    15   2
  PRKCI WILD-TYPE 267  71
  PRKCI MUTATED PRKCI WILD-TYPE 
             17             338 
  PRKCI MUTATED PRKCI WILD-TYPE 
              2              71 
$`PRKCI MUTATED`
TCGA-A6-6141 TCGA-A6-6780 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3663 TCGA-AA-3815 
        8.38        20.12        63.98        29.95         6.97        33.04 
TCGA-AA-3977 TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-6599 TCGA-CM-6169 TCGA-CM-6171 
       25.02        34.98        58.39         6.77        13.02        14.04 
TCGA-D5-5540 TCGA-D5-6535 TCGA-D5-6540 TCGA-DM-A1D4 TCGA-G4-6586 
       13.51        15.12        16.14        92.75        35.80 

$`PRKCI WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.05        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       19.04        19.04        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41        49.41        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-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        12.26 
TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       19.59        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        24.43        38.20       130.65        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  PRKCI MUTATED PRKCI WILD-TYPE 
           6.77            0.00 
  PRKCI MUTATED PRKCI WILD-TYPE 
          92.75          140.38 
  PRKCI MUTATED PRKCI WILD-TYPE 
         20.120          20.235 
[1] "6.8 - 92.8 (20.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2"  
D828V2, 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       23        99         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        19         10         40         31       35        13
                 vv
clus              STAGE IVB
  PRKCI MUTATED           0
  PRKCI WILD-TYPE         1
D828V3, multiclass
            clus
vv           PRKCI MUTATED PRKCI WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA             10              99
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PRKCI MUTATED     0   4  13   1
  PRKCI WILD-TYPE   9  64 235  40
D828V4, multiclass
    clus
vv   PRKCI MUTATED PRKCI WILD-TYPE
  T1             0               9
  T2             4              64
  T3            13             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
  PRKCI MUTATED    17   1   0
  PRKCI WILD-TYPE 203  79  66
D828V5, multiclass
    clus
vv   PRKCI MUTATED PRKCI WILD-TYPE
  N0            17             203
  N1             1              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"
D828V6, binary
                 cls
clus                0   1
  PRKCI MUTATED    14   0
  PRKCI WILD-TYPE 269  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCI MUTATED     14    0
  PRKCI WILD-TYPE  269   48
   clus
vv  PRKCI MUTATED PRKCI WILD-TYPE
  0            14             269
  1             0              48
[1] 2 2
[1] FALSE
D828V7, 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
D828V8, binary
                 cls
clus                0   1
  PRKCI MUTATED    15   3
  PRKCI WILD-TYPE 302  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCI MUTATED     15    3
  PRKCI WILD-TYPE  302   45
                               clus
vv                              PRKCI MUTATED PRKCI WILD-TYPE
  COLON ADENOCARCINOMA                     15             302
  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 245   2  22  20
D828V9, multiclass
    clus
vv   PRKCI MUTATED PRKCI WILD-TYPE
  R0            12             245
  R1             0               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"
D828V10, 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
D828V11, 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(829) Variable = C10ORF79 MUTATION ANALYSIS
D829V1, survival
                    sevent
clus2                  0   1
  C10ORF79 MUTATED    23   3
  C10ORF79 WILD-TYPE 259  70
  C10ORF79 MUTATED C10ORF79 WILD-TYPE 
                26                329 
  C10ORF79 MUTATED C10ORF79 WILD-TYPE 
                 3                 70 
$`C10ORF79 MUTATED`
TCGA-A6-5656 TCGA-A6-6141 TCGA-AA-3555 TCGA-AA-3660 TCGA-AA-3672 TCGA-AA-3864 
       32.91         8.38        29.95        78.08         0.92        53.00 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01K TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6964 
        4.01        34.98        31.00         0.07        56.55        10.88 
TCGA-AZ-4315 TCGA-AZ-4681 TCGA-AZ-6599 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4948 
       58.39        83.80         6.77         0.33         0.10       102.44 
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 
       16.31        44.68 

$`C10ORF79 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       18.05        40.96        21.37         4.21         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         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        61.41        49.41 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        0.26         1.35        17.56        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01         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-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       11.01        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
        6.12        81.37        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 
       19.43       107.67        74.56        65.85        53.62        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  C10ORF79 MUTATED C10ORF79 WILD-TYPE 
              0.07               0.00 
  C10ORF79 MUTATED C10ORF79 WILD-TYPE 
            119.93             140.38 
  C10ORF79 MUTATED C10ORF79 WILD-TYPE 
             17.28              20.28 
[1] "0.1 - 119.9 (17.3)" "0.0 - 140.4 (20.3)"
[1] "hr=" "2.4"
D829V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C10ORF79 MUTATED         5        0        3        13         2         0
  C10ORF79 WILD-TYPE      59        1       22        96         6         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C10ORF79 MUTATED           1          1          0          1        0
  C10ORF79 WILD-TYPE        18          9         41         30       35
                    vv
clus                 STAGE IVA STAGE IVB
  C10ORF79 MUTATED           0         0
  C10ORF79 WILD-TYPE        13         1
D829V3, multiclass
            clus
vv           C10ORF79 MUTATED C10ORF79 WILD-TYPE
  STAGE I                   5                 59
  STAGE IA                  0                  1
  STAGE II                  3                 22
  STAGE IIA                13                 96
  STAGE IIB                 2                  6
  STAGE IIC                 0                  1
  STAGE III                 1                 18
  STAGE IIIA                1                  9
  STAGE IIIB                0                 41
  STAGE IIIC                1                 30
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C10ORF79 MUTATED     1   5  17   4
  C10ORF79 WILD-TYPE   8  63 231  37
D829V4, multiclass
    clus
vv   C10ORF79 MUTATED C10ORF79 WILD-TYPE
  T1                1                  8
  T2                5                 63
  T3               17                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
  C10ORF79 MUTATED    23   2   2
  C10ORF79 WILD-TYPE 197  78  64
D829V5, multiclass
    clus
vv   C10ORF79 MUTATED C10ORF79 WILD-TYPE
  N0               23                197
  N1                2                 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"
D829V6, binary
                    cls
clus                   0   1
  C10ORF79 MUTATED    24   0
  C10ORF79 WILD-TYPE 259  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF79 MUTATED     24    0
  C10ORF79 WILD-TYPE  259   48
   clus
vv  C10ORF79 MUTATED C10ORF79 WILD-TYPE
  0               24                259
  1                0                 48
[1] 2 2
[1] FALSE
D829V7, 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
D829V8, binary
                    cls
clus                   0   1
  C10ORF79 MUTATED    23   4
  C10ORF79 WILD-TYPE 294  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF79 MUTATED     23    4
  C10ORF79 WILD-TYPE  294   44
                               clus
vv                              C10ORF79 MUTATED C10ORF79 WILD-TYPE
  COLON ADENOCARCINOMA                        23                294
  COLON MUCINOUS ADENOCARCINOMA                4                 44
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C10ORF79 MUTATED    19   0   0   2
  C10ORF79 WILD-TYPE 238   2  22  19
D829V9, multiclass
    clus
vv   C10ORF79 MUTATED C10ORF79 WILD-TYPE
  R0               19                238
  R1                0                  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"
D829V10, 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
D829V11, 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(830) Variable = WWTR1 MUTATION ANALYSIS
D830V1, survival
                 sevent
clus2               0   1
  WWTR1 MUTATED     5   1
  WWTR1 WILD-TYPE 277  72
  WWTR1 MUTATED WWTR1 WILD-TYPE 
              6             349 
  WWTR1 MUTATED WWTR1 WILD-TYPE 
              1              72 
$`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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        32.71        27.09         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 
        0.00        19.07        34.03        29.00        29.00        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32        21.99         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  WWTR1 MUTATED WWTR1 WILD-TYPE 
          20.12            0.00 
  WWTR1 MUTATED WWTR1 WILD-TYPE 
          29.95          140.38 
  WWTR1 MUTATED WWTR1 WILD-TYPE 
          21.98           19.99 
[1] "20.1 - 29.9 (22.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.1"
D830V2, 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       25       106         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        19         10         41         31       35        13
                 vv
clus              STAGE IVB
  WWTR1 MUTATED           0
  WWTR1 WILD-TYPE         1
D830V3, multiclass
            clus
vv           WWTR1 MUTATED WWTR1 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              3             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  WWTR1 MUTATED     1   2   3   0
  WWTR1 WILD-TYPE   8  66 245  41
D830V4, multiclass
    clus
vv   WWTR1 MUTATED WWTR1 WILD-TYPE
  T1             1               8
  T2             2              66
  T3             3             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
  WWTR1 MUTATED     6   0   0
  WWTR1 WILD-TYPE 214  80  66
D830V5, multiclass
    clus
vv   WWTR1 MUTATED WWTR1 WILD-TYPE
  N0             6             214
  N1             0              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"
D830V6, binary
                 cls
clus                0   1
  WWTR1 MUTATED     4   0
  WWTR1 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WWTR1 MUTATED      4    0
  WWTR1 WILD-TYPE  279   48
   clus
vv  WWTR1 MUTATED WWTR1 WILD-TYPE
  0             4             279
  1             0              48
[1] 2 2
[1] FALSE
D830V7, 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
D830V8, binary
                 cls
clus                0   1
  WWTR1 MUTATED     4   2
  WWTR1 WILD-TYPE 313  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WWTR1 MUTATED      4    2
  WWTR1 WILD-TYPE  313   46
                               clus
vv                              WWTR1 MUTATED WWTR1 WILD-TYPE
  COLON ADENOCARCINOMA                      4             313
  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 254   2  22  20
D830V9, multiclass
    clus
vv   WWTR1 MUTATED WWTR1 WILD-TYPE
  R0             3             254
  R1             0               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"
D830V10, 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
D830V11, 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(831) Variable = SLC25A17 MUTATION ANALYSIS
D831V1, survival
                    sevent
clus2                  0   1
  SLC25A17 MUTATED     4   3
  SLC25A17 WILD-TYPE 278  70
  SLC25A17 MUTATED SLC25A17 WILD-TYPE 
                 7                348 
  SLC25A17 MUTATED SLC25A17 WILD-TYPE 
                 3                 70 
$`SLC25A17 MUTATED`
TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3715 TCGA-AA-3950 TCGA-AA-A00N TCGA-AD-5900 
       22.06        63.98        19.04        24.00         4.01         0.07 
TCGA-AZ-6601 
      100.01 

$`SLC25A17 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  SLC25A17 MUTATED SLC25A17 WILD-TYPE 
              0.07               0.00 
  SLC25A17 MUTATED SLC25A17 WILD-TYPE 
            100.01             140.38 
  SLC25A17 MUTATED SLC25A17 WILD-TYPE 
            22.060             20.155 
[1] "0.1 - 100.0 (22.1)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.6"
D831V2, 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       22       107         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC25A17 MUTATED           0          0          0          0        0
  SLC25A17 WILD-TYPE        19         10         41         31       35
                    vv
clus                 STAGE IVA STAGE IVB
  SLC25A17 MUTATED           0         0
  SLC25A17 WILD-TYPE        13         1
D831V3, multiclass
            clus
vv           SLC25A17 MUTATED SLC25A17 WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  3                 22
  STAGE IIA                 2                107
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                0                 10
  STAGE IIIB                0                 41
  STAGE IIIC                0                 31
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  SLC25A17 MUTATED     0   1   5   1
  SLC25A17 WILD-TYPE   9  67 243  40
D831V4, multiclass
    clus
vv   SLC25A17 MUTATED SLC25A17 WILD-TYPE
  T1                0                  9
  T2                1                 67
  T3                5                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
  SLC25A17 MUTATED     7   0   0
  SLC25A17 WILD-TYPE 213  80  66
D831V5, multiclass
    clus
vv   SLC25A17 MUTATED SLC25A17 WILD-TYPE
  N0                7                213
  N1                0                 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"
D831V6, binary
                    cls
clus                   0   1
  SLC25A17 MUTATED     6   0
  SLC25A17 WILD-TYPE 277  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC25A17 MUTATED      6    0
  SLC25A17 WILD-TYPE  277   48
   clus
vv  SLC25A17 MUTATED SLC25A17 WILD-TYPE
  0                6                277
  1                0                 48
[1] 2 2
[1] FALSE
D831V7, 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
D831V8, binary
                    cls
clus                   0   1
  SLC25A17 MUTATED     4   3
  SLC25A17 WILD-TYPE 313  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC25A17 MUTATED      4    3
  SLC25A17 WILD-TYPE  313   45
                               clus
vv                              SLC25A17 MUTATED SLC25A17 WILD-TYPE
  COLON ADENOCARCINOMA                         4                313
  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 251   2  22  21
D831V9, multiclass
    clus
vv   SLC25A17 MUTATED SLC25A17 WILD-TYPE
  R0                6                251
  R1                0                  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"
D831V10, 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
D831V11, 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(832) Variable = ZNF334 MUTATION ANALYSIS
D832V1, survival
                  sevent
clus2                0   1
  ZNF334 MUTATED    17   2
  ZNF334 WILD-TYPE 265  71
  ZNF334 MUTATED ZNF334 WILD-TYPE 
              19              336 
  ZNF334 MUTATED ZNF334 WILD-TYPE 
               2               71 
$`ZNF334 MUTATED`
TCGA-AA-3510 TCGA-AA-3518 TCGA-AA-3544 TCGA-AA-3678 TCGA-AA-3821 TCGA-AA-3947 
       63.98         1.02        14.01        47.01         1.02        33.01 
TCGA-AA-3977 TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-6605 TCGA-CA-6717 TCGA-CM-4746 
       25.02        34.98        58.39         5.23         0.33        37.02 
TCGA-CM-5349 TCGA-CM-6166 TCGA-D5-6536 TCGA-D5-6931 TCGA-DM-A1D7 TCGA-F4-6569 
       30.08        21.99        17.85        12.00        13.32        13.45 
TCGA-G4-6628 
       52.80 

$`ZNF334 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
       12.99         0.99        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01         0.92        50.04        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
        0.99        25.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 
       18.05        31.00         2.01        12.99        24.00        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10       100.01        29.56        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 
       24.43        38.20       130.65        92.75        49.91        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        13.38         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 

  ZNF334 MUTATED ZNF334 WILD-TYPE 
            0.33             0.00 
  ZNF334 MUTATED ZNF334 WILD-TYPE 
           63.98           140.38 
  ZNF334 MUTATED ZNF334 WILD-TYPE 
          21.990           20.155 
[1] "0.3 - 64.0 (22.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2"  
D832V2, 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       24       103         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF334 MUTATED           1          0          1          1        0
  ZNF334 WILD-TYPE        18         10         40         30       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF334 MUTATED           0         0
  ZNF334 WILD-TYPE        13         1
D832V3, multiclass
            clus
vv           ZNF334 MUTATED ZNF334 WILD-TYPE
  STAGE I                 6               58
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               6              103
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF334 MUTATED     0   8   7   4
  ZNF334 WILD-TYPE   9  60 241  37
D832V4, multiclass
    clus
vv   ZNF334 MUTATED ZNF334 WILD-TYPE
  T1              0                9
  T2              8               60
  T3              7              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
  ZNF334 MUTATED    16   2   1
  ZNF334 WILD-TYPE 204  78  65
D832V5, multiclass
    clus
vv   ZNF334 MUTATED ZNF334 WILD-TYPE
  N0             16              204
  N1              2               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"
D832V6, binary
                  cls
clus                 0   1
  ZNF334 MUTATED    18   0
  ZNF334 WILD-TYPE 265  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF334 MUTATED     18    0
  ZNF334 WILD-TYPE  265   48
   clus
vv  ZNF334 MUTATED ZNF334 WILD-TYPE
  0             18              265
  1              0               48
[1] 2 2
[1] FALSE
D832V7, 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
D832V8, binary
                  cls
clus                 0   1
  ZNF334 MUTATED    16   3
  ZNF334 WILD-TYPE 301  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF334 MUTATED     16    3
  ZNF334 WILD-TYPE  301   45
                               clus
vv                              ZNF334 MUTATED ZNF334 WILD-TYPE
  COLON ADENOCARCINOMA                      16              301
  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 242   2  22  20
D832V9, multiclass
    clus
vv   ZNF334 MUTATED ZNF334 WILD-TYPE
  R0             15              242
  R1              0                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"
D832V10, 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
D832V11, 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(833) Variable = C9ORF71 MUTATION ANALYSIS
D833V1, survival
                   sevent
clus2                 0   1
  C9ORF71 MUTATED     4   0
  C9ORF71 WILD-TYPE 278  73
  C9ORF71 MUTATED C9ORF71 WILD-TYPE 
                4               351 
  C9ORF71 MUTATED C9ORF71 WILD-TYPE 
                0                73 
$`C9ORF71 MUTATED`
TCGA-CA-6717 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 
        0.33        35.80        26.17        52.80 

$`C9ORF71 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 
       13.78        91.79        46.75 

  C9ORF71 MUTATED C9ORF71 WILD-TYPE 
             0.33              0.00 
  C9ORF71 MUTATED C9ORF71 WILD-TYPE 
            52.80            140.38 
  C9ORF71 MUTATED C9ORF71 WILD-TYPE 
           30.985            20.120 
[1] "0.3 - 52.8 (31.0)"  "0.0 - 140.4 (20.1)"
[1] "hr="     "9100000"
D833V2, 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       25       106         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C9ORF71 MUTATED           0          0          0          0        0
  C9ORF71 WILD-TYPE        19         10         41         31       35
                   vv
clus                STAGE IVA STAGE IVB
  C9ORF71 MUTATED           0         0
  C9ORF71 WILD-TYPE        13         1
D833V3, multiclass
            clus
vv           C9ORF71 MUTATED C9ORF71 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                3               106
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C9ORF71 MUTATED     0   1   3   0
  C9ORF71 WILD-TYPE   9  67 245  41
D833V4, multiclass
    clus
vv   C9ORF71 MUTATED C9ORF71 WILD-TYPE
  T1               0                 9
  T2               1                67
  T3               3               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
  C9ORF71 MUTATED     4   0   0
  C9ORF71 WILD-TYPE 216  80  66
D833V5, multiclass
    clus
vv   C9ORF71 MUTATED C9ORF71 WILD-TYPE
  N0               4               216
  N1               0                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"
D833V6, binary
                   cls
clus                  0   1
  C9ORF71 MUTATED     4   0
  C9ORF71 WILD-TYPE 279  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF71 MUTATED      4    0
  C9ORF71 WILD-TYPE  279   48
   clus
vv  C9ORF71 MUTATED C9ORF71 WILD-TYPE
  0               4               279
  1               0                48
[1] 2 2
[1] FALSE
D833V7, 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
D833V8, binary
                   cls
clus                  0   1
  C9ORF71 MUTATED     3   1
  C9ORF71 WILD-TYPE 314  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF71 MUTATED      3    1
  C9ORF71 WILD-TYPE  314   47
                               clus
vv                              C9ORF71 MUTATED C9ORF71 WILD-TYPE
  COLON ADENOCARCINOMA                        3               314
  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 254   2  22  20
D833V9, multiclass
    clus
vv   C9ORF71 MUTATED C9ORF71 WILD-TYPE
  R0               3               254
  R1               0                 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"
D833V10, 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
D833V11, 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(834) Variable = CD55 MUTATION ANALYSIS
D834V1, survival
                sevent
clus2              0   1
  CD55 MUTATED     7   0
  CD55 WILD-TYPE 275  73
  CD55 MUTATED CD55 WILD-TYPE 
             7            348 
  CD55 MUTATED CD55 WILD-TYPE 
             0             73 
$`CD55 MUTATED`
TCGA-AA-3518 TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3877 TCGA-AZ-5407 TCGA-CA-5255 
        1.02         0.92        19.04        31.00        61.41         3.06 
TCGA-CM-6674 
       12.95 

$`CD55 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       38.99         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       27.02        29.98        18.05         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  CD55 MUTATED CD55 WILD-TYPE 
          0.92           0.00 
  CD55 MUTATED CD55 WILD-TYPE 
         61.41         140.38 
  CD55 MUTATED CD55 WILD-TYPE 
         12.95          20.63 
[1] "0.9 - 61.4 (12.9)"  "0.0 - 140.4 (20.6)"
[1] "hr="     "9100000"
D834V2, 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       25       106         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        18         10         41         31       34        13
                vv
clus             STAGE IVB
  CD55 MUTATED           0
  CD55 WILD-TYPE         1
D834V3, multiclass
            clus
vv           CD55 MUTATED CD55 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             3            106
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CD55 MUTATED     2   0   5   0
  CD55 WILD-TYPE   7  68 243  41
D834V4, multiclass
    clus
vv   CD55 MUTATED CD55 WILD-TYPE
  T1            2              7
  T2            0             68
  T3            5            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
  CD55 MUTATED     6   1   0
  CD55 WILD-TYPE 214  79  66
D834V5, multiclass
    clus
vv   CD55 MUTATED CD55 WILD-TYPE
  N0            6            214
  N1            1             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"
D834V6, binary
                cls
clus               0   1
  CD55 MUTATED     6   1
  CD55 WILD-TYPE 277  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD55 MUTATED      6    1
  CD55 WILD-TYPE  277   47
   clus
vv  CD55 MUTATED CD55 WILD-TYPE
  0            6            277
  1            1             47
[1] 2 2
[1] FALSE
D834V7, 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
D834V8, binary
                cls
clus               0   1
  CD55 MUTATED     6   1
  CD55 WILD-TYPE 311  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD55 MUTATED      6    1
  CD55 WILD-TYPE  311   47
                               clus
vv                              CD55 MUTATED CD55 WILD-TYPE
  COLON ADENOCARCINOMA                     6            311
  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 253   2  21  20
D834V9, multiclass
    clus
vv   CD55 MUTATED CD55 WILD-TYPE
  R0            4            253
  R1            0              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"
D834V10, 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
D834V11, 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(835) Variable = EXPH5 MUTATION ANALYSIS
D835V1, survival
                 sevent
clus2               0   1
  EXPH5 MUTATED    15   5
  EXPH5 WILD-TYPE 267  68
  EXPH5 MUTATED EXPH5 WILD-TYPE 
             20             335 
  EXPH5 MUTATED EXPH5 WILD-TYPE 
              5              68 
$`EXPH5 MUTATED`
TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6781 TCGA-AA-3555 TCGA-AA-3877 
       22.06         8.38        25.08        19.66        29.95        31.00 
TCGA-AA-3949 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A01R TCGA-AZ-5403 TCGA-AZ-6605 
       26.01        18.05         4.01        35.01        62.79         5.23 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4743 TCGA-CM-5862 TCGA-D5-5539 TCGA-DM-A28F 
        0.33         0.10        23.05         5.03        19.59        35.97 
TCGA-G4-6588 TCGA-G4-6628 
       26.17        52.80 

$`EXPH5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6648 TCGA-A6-6649 
       22.09        32.71        27.09        22.52        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 
       21.76        24.69        24.39        23.87        20.12        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        7.04         3.02         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 
       18.05         2.01        12.99        24.00        33.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
       29.56        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07         0.26         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14         2.93         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-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       16.01        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-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       45.40        12.26        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
        6.12        81.37       119.93        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        91.79        46.75 

  EXPH5 MUTATED EXPH5 WILD-TYPE 
            0.1             0.0 
  EXPH5 MUTATED EXPH5 WILD-TYPE 
          62.79          140.38 
  EXPH5 MUTATED EXPH5 WILD-TYPE 
         22.555          20.120 
[1] "0.1 - 62.8 (22.6)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.4"
D835V2, 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       24       101         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        18          9         37         30       35        11
                 vv
clus              STAGE IVB
  EXPH5 MUTATED           0
  EXPH5 WILD-TYPE         1
D835V3, multiclass
            clus
vv           EXPH5 MUTATED EXPH5 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              8             101
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             1               9
  STAGE IIIB             4              37
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              2              11
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 233  37
D835V4, multiclass
    clus
vv   EXPH5 MUTATED EXPH5 WILD-TYPE
  T1             1               8
  T2             1              67
  T3            15             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
  EXPH5 MUTATED    12   8   1
  EXPH5 WILD-TYPE 208  72  65
D835V5, multiclass
    clus
vv   EXPH5 MUTATED EXPH5 WILD-TYPE
  N0            12             208
  N1             8              72
  N2             1              65
[1] 3 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
  EXPH5 MUTATED    17   2
  EXPH5 WILD-TYPE 266  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EXPH5 MUTATED     17    2
  EXPH5 WILD-TYPE  266   46
   clus
vv  EXPH5 MUTATED EXPH5 WILD-TYPE
  0            17             266
  1             2              46
[1] 2 2
[1] FALSE
D835V7, 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
D835V8, binary
                 cls
clus                0   1
  EXPH5 MUTATED    12   9
  EXPH5 WILD-TYPE 305  39
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EXPH5 MUTATED     12    9
  EXPH5 WILD-TYPE  305   39
                               clus
vv                              EXPH5 MUTATED EXPH5 WILD-TYPE
  COLON ADENOCARCINOMA                     12             305
  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 243   2  22  19
D835V9, multiclass
    clus
vv   EXPH5 MUTATED EXPH5 WILD-TYPE
  R0            14             243
  R1             0               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"
D835V10, 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
D835V11, 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(836) Variable = TMEM41B MUTATION ANALYSIS
D836V1, survival
                   sevent
clus2                 0   1
  TMEM41B MUTATED     4   0
  TMEM41B WILD-TYPE 278  73
  TMEM41B MUTATED TMEM41B WILD-TYPE 
                4               351 
  TMEM41B MUTATED TMEM41B WILD-TYPE 
                0                73 
$`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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01        12.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        15.75         0.20        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        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-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  TMEM41B MUTATED TMEM41B WILD-TYPE 
             0.99              0.00 
  TMEM41B MUTATED TMEM41B WILD-TYPE 
            29.03            140.38 
  TMEM41B MUTATED TMEM41B WILD-TYPE 
            16.72             20.19 
[1] "1.0 - 29.0 (16.7)"  "0.0 - 140.4 (20.2)"
[1] "hr="     "3300000"
D836V2, 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       25       107         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM41B MUTATED           0          0          1          0        0
  TMEM41B WILD-TYPE        19         10         40         31       35
                   vv
clus                STAGE IVA STAGE IVB
  TMEM41B MUTATED           0         0
  TMEM41B WILD-TYPE        13         1
D836V3, multiclass
            clus
vv           TMEM41B MUTATED TMEM41B WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                2               107
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TMEM41B MUTATED     0   1   3   0
  TMEM41B WILD-TYPE   9  67 245  41
D836V4, multiclass
    clus
vv   TMEM41B MUTATED TMEM41B WILD-TYPE
  T1               0                 9
  T2               1                67
  T3               3               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
  TMEM41B MUTATED     3   1   0
  TMEM41B WILD-TYPE 217  79  66
D836V5, multiclass
    clus
vv   TMEM41B MUTATED TMEM41B WILD-TYPE
  N0               3               217
  N1               1                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"
D836V6, binary
                   cls
clus                  0   1
  TMEM41B MUTATED     3   0
  TMEM41B WILD-TYPE 280  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM41B MUTATED      3    0
  TMEM41B WILD-TYPE  280   48
   clus
vv  TMEM41B MUTATED TMEM41B WILD-TYPE
  0               3               280
  1               0                48
[1] 2 2
[1] FALSE
D836V7, 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
D836V8, binary
                   cls
clus                  0   1
  TMEM41B MUTATED     2   2
  TMEM41B WILD-TYPE 315  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM41B MUTATED      2    2
  TMEM41B WILD-TYPE  315   46
                               clus
vv                              TMEM41B MUTATED TMEM41B WILD-TYPE
  COLON ADENOCARCINOMA                        2               315
  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 253   2  22  21
D836V9, multiclass
    clus
vv   TMEM41B MUTATED TMEM41B WILD-TYPE
  R0               4               253
  R1               0                 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"
D836V10, 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
D836V11, 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(837) Variable = PLEKHB2 MUTATION ANALYSIS
D837V1, survival
                   sevent
clus2                 0   1
  PLEKHB2 MUTATED     3   2
  PLEKHB2 WILD-TYPE 279  71
  PLEKHB2 MUTATED PLEKHB2 WILD-TYPE 
                5               350 
  PLEKHB2 MUTATED PLEKHB2 WILD-TYPE 
                2                71 
$`PLEKHB2 MUTATED`
TCGA-A6-5666 TCGA-AA-3662 TCGA-AA-3977 TCGA-AD-6964 TCGA-AZ-6601 
       32.71         6.05        25.02        10.88       100.01 

$`PLEKHB2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       19.99        13.94        19.99        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  PLEKHB2 MUTATED PLEKHB2 WILD-TYPE 
             6.05              0.00 
  PLEKHB2 MUTATED PLEKHB2 WILD-TYPE 
           100.01            140.38 
  PLEKHB2 MUTATED PLEKHB2 WILD-TYPE 
           25.020            20.155 
[1] "6.0 - 100.0 (25.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.5"
D837V2, 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       24       109         8         0
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLEKHB2 MUTATED           1          0          0          0        1
  PLEKHB2 WILD-TYPE        18         10         41         31       34
                   vv
clus                STAGE IVA STAGE IVB
  PLEKHB2 MUTATED           0         0
  PLEKHB2 WILD-TYPE        13         1
D837V3, multiclass
            clus
vv           PLEKHB2 MUTATED PLEKHB2 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                0               109
  STAGE IIB                0                 8
  STAGE IIC                1                 0
  STAGE III                1                18
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               0                31
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PLEKHB2 MUTATED     0   1   2   3
  PLEKHB2 WILD-TYPE   9  67 246  38
D837V4, multiclass
    clus
vv   PLEKHB2 MUTATED PLEKHB2 WILD-TYPE
  T1               0                 9
  T2               1                67
  T3               2               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
  PLEKHB2 MUTATED     3   0   3
  PLEKHB2 WILD-TYPE 217  80  63
D837V5, multiclass
    clus
vv   PLEKHB2 MUTATED PLEKHB2 WILD-TYPE
  N0               3               217
  N1               0                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"
D837V6, binary
                   cls
clus                  0   1
  PLEKHB2 MUTATED     3   1
  PLEKHB2 WILD-TYPE 280  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHB2 MUTATED      3    1
  PLEKHB2 WILD-TYPE  280   47
   clus
vv  PLEKHB2 MUTATED PLEKHB2 WILD-TYPE
  0               3               280
  1               1                47
[1] 2 2
[1] FALSE
D837V7, 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
D837V8, binary
                   cls
clus                  0   1
  PLEKHB2 MUTATED     6   0
  PLEKHB2 WILD-TYPE 311  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHB2 MUTATED      6    0
  PLEKHB2 WILD-TYPE  311   48
                               clus
vv                              PLEKHB2 MUTATED PLEKHB2 WILD-TYPE
  COLON ADENOCARCINOMA                        6               311
  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 256   2  21  21
D837V9, multiclass
[1] "Remove cluster labels:" "PLEKHB2 MUTATED"       
clus
  PLEKHB2 MUTATED PLEKHB2 WILD-TYPE 
                2               300 
       TCGA-A6-2671        TCGA-A6-2672        TCGA-A6-2674        TCGA-A6-2676 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-A6-2677        TCGA-A6-2678        TCGA-A6-2683        TCGA-A6-3807 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-A6-3808        TCGA-A6-3809        TCGA-A6-3810        TCGA-A6-5657 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-A6-5659        TCGA-A6-5661        TCGA-A6-5665        TCGA-A6-6781 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3489        TCGA-AA-3492        TCGA-AA-3496        TCGA-AA-3502 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3510        TCGA-AA-3511        TCGA-AA-3514        TCGA-AA-3517 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3518        TCGA-AA-3519        TCGA-AA-3520        TCGA-AA-3521 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3522        TCGA-AA-3524        TCGA-AA-3525        TCGA-AA-3526 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3527        TCGA-AA-3529        TCGA-AA-3530        TCGA-AA-3531 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3532        TCGA-AA-3534        TCGA-AA-3538        TCGA-AA-3542 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3543        TCGA-AA-3544        TCGA-AA-3548        TCGA-AA-3549 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3552        TCGA-AA-3553        TCGA-AA-3554        TCGA-AA-3555 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3556        TCGA-AA-3558        TCGA-AA-3560        TCGA-AA-3561 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3562        TCGA-AA-3655        TCGA-AA-3660        TCGA-AA-3663 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3664        TCGA-AA-3666        TCGA-AA-3667        TCGA-AA-3672 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3673        TCGA-AA-3678        TCGA-AA-3679        TCGA-AA-3680 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3681        TCGA-AA-3684        TCGA-AA-3685        TCGA-AA-3688 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3692        TCGA-AA-3693        TCGA-AA-3695        TCGA-AA-3696 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3697        TCGA-AA-3710        TCGA-AA-3713        TCGA-AA-3715 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3811        TCGA-AA-3812        TCGA-AA-3814        TCGA-AA-3815 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3818        TCGA-AA-3819        TCGA-AA-3821        TCGA-AA-3831 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3833        TCGA-AA-3837        TCGA-AA-3842        TCGA-AA-3844 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3845        TCGA-AA-3846        TCGA-AA-3848        TCGA-AA-3850 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3851        TCGA-AA-3852        TCGA-AA-3854        TCGA-AA-3855 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3856        TCGA-AA-3858        TCGA-AA-3860        TCGA-AA-3861 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3864        TCGA-AA-3866        TCGA-AA-3867        TCGA-AA-3869 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3870        TCGA-AA-3872        TCGA-AA-3875        TCGA-AA-3877 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3930        TCGA-AA-3939        TCGA-AA-3941        TCGA-AA-3947 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3949        TCGA-AA-3950        TCGA-AA-3952        TCGA-AA-3955 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3956        TCGA-AA-3968        TCGA-AA-3971        TCGA-AA-3972 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3973        TCGA-AA-3975        TCGA-AA-3976        TCGA-AA-3979 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3984        TCGA-AA-3986        TCGA-AA-3989        TCGA-AA-3994 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-A004        TCGA-AA-A00A        TCGA-AA-A00D        TCGA-AA-A00E 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-A00F        TCGA-AA-A00J        TCGA-AA-A00K        TCGA-AA-A00L 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-A00N        TCGA-AA-A00O        TCGA-AA-A00Q        TCGA-AA-A00R 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-A00U        TCGA-AA-A00W        TCGA-AA-A00Z        TCGA-AA-A010 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-A017        TCGA-AA-A01D        TCGA-AA-A01F        TCGA-AA-A01G 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-A01I        TCGA-AA-A01K        TCGA-AA-A01P        TCGA-AA-A01Q 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-A01R        TCGA-AA-A01S        TCGA-AA-A01T        TCGA-AA-A01V 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-A01X        TCGA-AA-A01Z        TCGA-AA-A022        TCGA-AA-A024 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-A029        TCGA-AA-A02F        TCGA-AA-A02H        TCGA-AA-A02J 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-A02K        TCGA-AA-A02O        TCGA-AA-A02W        TCGA-AA-A02Y 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-A03F        TCGA-AA-A03J        TCGA-AD-5900        TCGA-AD-6548 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AD-6888        TCGA-AU-3779        TCGA-AU-6004        TCGA-AY-4070 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AY-4071        TCGA-AY-5543        TCGA-AY-6196        TCGA-AY-6197 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AY-6386        TCGA-AZ-4315        TCGA-AZ-4681        TCGA-AZ-4682 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-CA-5254        TCGA-CA-5255        TCGA-CA-5796        TCGA-CA-5797 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-CA-6715        TCGA-CA-6716        TCGA-CA-6717        TCGA-CA-6718 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-CA-6719        TCGA-CK-4947        TCGA-CK-4948        TCGA-CK-4950 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-CK-4952        TCGA-CK-5912        TCGA-CK-5913        TCGA-CK-5914 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-CK-5915        TCGA-CK-5916        TCGA-CK-6746        TCGA-CK-6747 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-CK-6748        TCGA-CK-6751        TCGA-CM-4743        TCGA-CM-4744 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-CM-4746        TCGA-CM-4747        TCGA-CM-4752        TCGA-CM-5341 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-CM-5344        TCGA-CM-5348        TCGA-CM-5349        TCGA-CM-5860 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-CM-5861        TCGA-CM-5862        TCGA-CM-5863        TCGA-CM-5864 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-CM-5868        TCGA-CM-6161        TCGA-CM-6162        TCGA-CM-6163 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-CM-6164        TCGA-CM-6165        TCGA-CM-6166        TCGA-CM-6167 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-CM-6168        TCGA-CM-6169        TCGA-CM-6170        TCGA-CM-6171 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-CM-6172        TCGA-CM-6674        TCGA-CM-6675        TCGA-CM-6676 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-CM-6677        TCGA-CM-6678        TCGA-CM-6679        TCGA-CM-6680 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-D5-5537        TCGA-D5-5538        TCGA-D5-5539        TCGA-D5-5540 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-D5-5541        TCGA-D5-6529        TCGA-D5-6532        TCGA-D5-6533 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-D5-6534        TCGA-D5-6535        TCGA-D5-6536        TCGA-D5-6537 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-D5-6538        TCGA-D5-6539        TCGA-D5-6540        TCGA-D5-6541 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-D5-6898        TCGA-D5-6920        TCGA-D5-6922        TCGA-D5-6923 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-D5-6924        TCGA-D5-6926        TCGA-D5-6927        TCGA-D5-6928 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-D5-6929        TCGA-D5-6930        TCGA-D5-6931        TCGA-D5-6932 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-D5-7000        TCGA-F4-6459        TCGA-F4-6460        TCGA-F4-6569 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-F4-6570        TCGA-F4-6703        TCGA-F4-6704        TCGA-F4-6805 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-F4-6806        TCGA-F4-6807        TCGA-F4-6808        TCGA-F4-6809 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-F4-6854        TCGA-F4-6855        TCGA-F4-6856        TCGA-G4-6293 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-G4-6299        TCGA-G4-6303        TCGA-G4-6304        TCGA-G4-6306 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-G4-6307        TCGA-G4-6309        TCGA-G4-6310        TCGA-G4-6315 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-G4-6317        TCGA-G4-6321        TCGA-G4-6323        TCGA-G4-6586 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-G4-6588        TCGA-G4-6625        TCGA-G4-6626        TCGA-G4-6628 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
D837V10, 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
D837V11, 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(838) Variable = SLC7A6 MUTATION ANALYSIS
D838V1, survival
                  sevent
clus2                0   1
  SLC7A6 MUTATED     6   0
  SLC7A6 WILD-TYPE 276  73
  SLC7A6 MUTATED SLC7A6 WILD-TYPE 
               6              349 
  SLC7A6 MUTATED SLC7A6 WILD-TYPE 
               0               73 
$`SLC7A6 MUTATED`
TCGA-AA-3660 TCGA-AZ-5407 TCGA-CA-5797 TCGA-CM-6680 TCGA-DM-A1HB TCGA-F4-6855 
       78.08        61.41         3.29        12.03       135.65        35.41 

$`SLC7A6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        61.02         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 
        1.41         5.13        83.80        22.36        62.79        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 
        3.19         1.94         2.24         3.06         3.25         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  SLC7A6 MUTATED SLC7A6 WILD-TYPE 
            3.29             0.00 
  SLC7A6 MUTATED SLC7A6 WILD-TYPE 
          135.65           140.38 
  SLC7A6 MUTATED SLC7A6 WILD-TYPE 
           48.41            20.12 
[1] "3.3 - 135.7 (48.4)" "0.0 - 140.4 (20.1)"
[1] "hr="     "2.6e+07"
D838V2, 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       24       107         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC7A6 MUTATED           0          0          2          0        0
  SLC7A6 WILD-TYPE        19         10         39         31       35
                  vv
clus               STAGE IVA STAGE IVB
  SLC7A6 MUTATED           0         0
  SLC7A6 WILD-TYPE        13         1
D838V3, multiclass
            clus
vv           SLC7A6 MUTATED SLC7A6 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               2              107
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SLC7A6 MUTATED     1   0   5   0
  SLC7A6 WILD-TYPE   8  68 243  41
D838V4, multiclass
    clus
vv   SLC7A6 MUTATED SLC7A6 WILD-TYPE
  T1              1                8
  T2              0               68
  T3              5              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
  SLC7A6 MUTATED     4   1   1
  SLC7A6 WILD-TYPE 216  79  65
D838V5, multiclass
    clus
vv   SLC7A6 MUTATED SLC7A6 WILD-TYPE
  N0              4              216
  N1              1               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"
D838V6, binary
                  cls
clus                 0   1
  SLC7A6 MUTATED     6   0
  SLC7A6 WILD-TYPE 277  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC7A6 MUTATED      6    0
  SLC7A6 WILD-TYPE  277   48
   clus
vv  SLC7A6 MUTATED SLC7A6 WILD-TYPE
  0              6              277
  1              0               48
[1] 2 2
[1] FALSE
D838V7, 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
D838V8, binary
                  cls
clus                 0   1
  SLC7A6 MUTATED     6   0
  SLC7A6 WILD-TYPE 311  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC7A6 MUTATED      6    0
  SLC7A6 WILD-TYPE  311   48
                               clus
vv                              SLC7A6 MUTATED SLC7A6 WILD-TYPE
  COLON ADENOCARCINOMA                       6              311
  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 253   2  22  21
D838V9, multiclass
    clus
vv   SLC7A6 MUTATED SLC7A6 WILD-TYPE
  R0              4              253
  R1              0                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"
D838V10, 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
D838V11, 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(839) Variable = TPK1 MUTATION ANALYSIS
D839V1, survival
                sevent
clus2              0   1
  TPK1 MUTATED     3   2
  TPK1 WILD-TYPE 279  71
  TPK1 MUTATED TPK1 WILD-TYPE 
             5            350 
  TPK1 MUTATED TPK1 WILD-TYPE 
             2             71 
$`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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        32.71        27.09         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         0.72         5.79        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79       117.07         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 
       91.79        52.80 

  TPK1 MUTATED TPK1 WILD-TYPE 
         20.12           0.00 
  TPK1 MUTATED TPK1 WILD-TYPE 
         98.24         140.38 
  TPK1 MUTATED TPK1 WILD-TYPE 
        22.520         20.005 
[1] "20.1 - 98.2 (22.5)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.2"
D839V2, 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       25       106         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        19         10         41         31       35        13
                vv
clus             STAGE IVB
  TPK1 MUTATED           0
  TPK1 WILD-TYPE         1
D839V3, multiclass
            clus
vv           TPK1 MUTATED TPK1 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             3            106
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TPK1 MUTATED     0   1   4   0
  TPK1 WILD-TYPE   9  67 244  41
D839V4, multiclass
    clus
vv   TPK1 MUTATED TPK1 WILD-TYPE
  T1            0              9
  T2            1             67
  T3            4            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
  TPK1 MUTATED     5   0   0
  TPK1 WILD-TYPE 215  80  66
D839V5, multiclass
    clus
vv   TPK1 MUTATED TPK1 WILD-TYPE
  N0            5            215
  N1            0             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"
D839V6, binary
                cls
clus               0   1
  TPK1 MUTATED     3   0
  TPK1 WILD-TYPE 280  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPK1 MUTATED      3    0
  TPK1 WILD-TYPE  280   48
   clus
vv  TPK1 MUTATED TPK1 WILD-TYPE
  0            3            280
  1            0             48
[1] 2 2
[1] FALSE
D839V7, 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
D839V8, binary
                cls
clus               0   1
  TPK1 MUTATED     3   2
  TPK1 WILD-TYPE 314  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPK1 MUTATED      3    2
  TPK1 WILD-TYPE  314   46
                               clus
vv                              TPK1 MUTATED TPK1 WILD-TYPE
  COLON ADENOCARCINOMA                     3            314
  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 256   2  22  21
D839V9, multiclass
[1] "Remove cluster labels:" "TPK1 MUTATED"          
clus
  TPK1 MUTATED TPK1 WILD-TYPE 
             1            301 
    TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-A6-2677     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-3496     TCGA-AA-3502 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-3510     TCGA-AA-3511     TCGA-AA-3514     TCGA-AA-3517 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-3518     TCGA-AA-3519     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-3526 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-3527     TCGA-AA-3529     TCGA-AA-3530     TCGA-AA-3531 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-3532     TCGA-AA-3534     TCGA-AA-3538     TCGA-AA-3542 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-3543     TCGA-AA-3544     TCGA-AA-3548     TCGA-AA-3549 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-3552     TCGA-AA-3553     TCGA-AA-3554     TCGA-AA-3555 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-3556     TCGA-AA-3558     TCGA-AA-3560     TCGA-AA-3561 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-3562     TCGA-AA-3655     TCGA-AA-3660     TCGA-AA-3662 
"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-3672     TCGA-AA-3673     TCGA-AA-3678     TCGA-AA-3679 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-3680     TCGA-AA-3681     TCGA-AA-3684     TCGA-AA-3685 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-3688     TCGA-AA-3692     TCGA-AA-3693     TCGA-AA-3695 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-3696     TCGA-AA-3697     TCGA-AA-3710     TCGA-AA-3712 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-3713     TCGA-AA-3715     TCGA-AA-3811     TCGA-AA-3812 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-3814     TCGA-AA-3815     TCGA-AA-3818     TCGA-AA-3819 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-3821     TCGA-AA-3831     TCGA-AA-3833     TCGA-AA-3837 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-3842     TCGA-AA-3844     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-3860     TCGA-AA-3861     TCGA-AA-3864     TCGA-AA-3866 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-3867     TCGA-AA-3869     TCGA-AA-3870     TCGA-AA-3872 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-3875     TCGA-AA-3877     TCGA-AA-3930     TCGA-AA-3939 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-3941     TCGA-AA-3947     TCGA-AA-3949     TCGA-AA-3950 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-3952     TCGA-AA-3955     TCGA-AA-3956     TCGA-AA-3968 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-3971     TCGA-AA-3972     TCGA-AA-3973     TCGA-AA-3975 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-3976     TCGA-AA-3979     TCGA-AA-3984     TCGA-AA-3986 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-3989     TCGA-AA-3994     TCGA-AA-A004     TCGA-AA-A00A 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-A00D     TCGA-AA-A00E     TCGA-AA-A00F     TCGA-AA-A00J 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-A00K     TCGA-AA-A00L     TCGA-AA-A00N     TCGA-AA-A00O 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-A00Q     TCGA-AA-A00R     TCGA-AA-A00U     TCGA-AA-A00W 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-A00Z     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-A024     TCGA-AA-A029     TCGA-AA-A02F 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-A02H     TCGA-AA-A02J     TCGA-AA-A02K     TCGA-AA-A02O 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AA-A02W     TCGA-AA-A02Y     TCGA-AA-A03F     TCGA-AA-A03J 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AD-5900     TCGA-AD-6548     TCGA-AD-6888     TCGA-AU-3779 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AU-6004     TCGA-AY-4070     TCGA-AY-4071     TCGA-AY-5543 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AY-6196     TCGA-AY-6197     TCGA-AY-6386     TCGA-AZ-4315 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-AZ-4681     TCGA-AZ-4682     TCGA-CA-5254     TCGA-CA-5255 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-CA-5796     TCGA-CA-5797     TCGA-CA-6715     TCGA-CA-6716 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-CA-6717     TCGA-CA-6718     TCGA-CA-6719     TCGA-CK-4947 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-CK-4948     TCGA-CK-4950     TCGA-CK-4952     TCGA-CK-5912 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-CK-5913     TCGA-CK-5914     TCGA-CK-5915     TCGA-CK-5916 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-CK-6746     TCGA-CK-6747     TCGA-CK-6748     TCGA-CK-6751 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-CM-4743     TCGA-CM-4744     TCGA-CM-4746     TCGA-CM-4747 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-CM-4752     TCGA-CM-5341     TCGA-CM-5344     TCGA-CM-5348 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-CM-5349     TCGA-CM-5860     TCGA-CM-5861     TCGA-CM-5862 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-CM-5863     TCGA-CM-5864     TCGA-CM-5868     TCGA-CM-6161 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-CM-6162     TCGA-CM-6163     TCGA-CM-6164     TCGA-CM-6165 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-CM-6166     TCGA-CM-6167     TCGA-CM-6168     TCGA-CM-6169 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-CM-6170     TCGA-CM-6171     TCGA-CM-6172     TCGA-CM-6674 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-CM-6675     TCGA-CM-6676     TCGA-CM-6677     TCGA-CM-6678 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-CM-6679     TCGA-CM-6680     TCGA-D5-5537     TCGA-D5-5538 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-D5-5539     TCGA-D5-5540     TCGA-D5-5541     TCGA-D5-6529 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-D5-6532     TCGA-D5-6533     TCGA-D5-6534     TCGA-D5-6535 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-D5-6536     TCGA-D5-6537     TCGA-D5-6538     TCGA-D5-6539 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-D5-6540     TCGA-D5-6541     TCGA-D5-6898     TCGA-D5-6920 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-D5-6922     TCGA-D5-6923     TCGA-D5-6924     TCGA-D5-6926 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-D5-6927     TCGA-D5-6928     TCGA-D5-6929     TCGA-D5-6930 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-D5-6931     TCGA-D5-6932     TCGA-D5-7000     TCGA-F4-6459 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-F4-6460     TCGA-F4-6569     TCGA-F4-6570     TCGA-F4-6703 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-F4-6704     TCGA-F4-6805     TCGA-F4-6806     TCGA-F4-6807 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-F4-6808     TCGA-F4-6809     TCGA-F4-6854     TCGA-F4-6855 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-F4-6856     TCGA-G4-6293     TCGA-G4-6299     TCGA-G4-6303 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-G4-6304     TCGA-G4-6306     TCGA-G4-6307     TCGA-G4-6309 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-G4-6310     TCGA-G4-6315     TCGA-G4-6317     TCGA-G4-6321 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-G4-6323     TCGA-G4-6586     TCGA-G4-6588     TCGA-G4-6625 
"TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" "TPK1 WILD-TYPE" 
    TCGA-G4-6628 
"TPK1 WILD-TYPE" 
D839V10, 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
D839V11, 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(840) Variable = CDH10 MUTATION ANALYSIS
D840V1, survival
                 sevent
clus2               0   1
  CDH10 MUTATED    33   5
  CDH10 WILD-TYPE 249  68
  CDH10 MUTATED CDH10 WILD-TYPE 
             38             317 
  CDH10 MUTATED CDH10 WILD-TYPE 
              5              68 
$`CDH10 MUTATED`
TCGA-A6-5662 TCGA-A6-5665 TCGA-AA-3525 TCGA-AA-3555 TCGA-AA-3660 TCGA-AA-3672 
       23.61        22.06         8.05        29.95        78.08         0.92 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3815 TCGA-AA-3821 TCGA-AA-3864 TCGA-AA-3977 
       26.99        19.04        33.04         1.02        53.00        25.02 
TCGA-AA-3989 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01I TCGA-AA-A01Z TCGA-AY-6196 
        7.96         4.01        34.98        31.00        37.02         0.20 
TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6603 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-6747 
       58.39        49.41        29.56         0.33         0.10         2.93 
TCGA-CM-4743 TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6171 TCGA-CM-6674 
       23.05        15.02        12.00        29.03        14.04        12.95 
TCGA-CM-6680 TCGA-D5-6536 TCGA-DM-A282 TCGA-F4-6570 TCGA-G4-6299 TCGA-G4-6317 
       12.03        17.85       139.17         6.18        74.56        36.00 
TCGA-G4-6323 TCGA-G4-6628 
       13.78        52.80 

$`CDH10 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        33.53        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 
        9.07        24.03        37.05        36.03        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3811 
       19.00        36.00         5.03        85.05        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       35.05         0.99        25.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 
       24.00        27.02        27.02        19.07        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K 
       21.99        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        35.01 
TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       26.01        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        15.75        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10       100.01         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.26         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 
       49.08        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        16.01         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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       135.65         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 
       13.25         0.53        35.41        19.43       107.67        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        35.80        26.17        91.79        46.75 

  CDH10 MUTATED CDH10 WILD-TYPE 
            0.1             0.0 
  CDH10 MUTATED CDH10 WILD-TYPE 
         139.17          140.38 
  CDH10 MUTATED CDH10 WILD-TYPE 
         22.555          20.120 
[1] "0.1 - 139.2 (22.6)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.7"
D840V2, 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       21        94         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        17         10         38         28       33        12
                 vv
clus              STAGE IVB
  CDH10 MUTATED           0
  CDH10 WILD-TYPE         1
D840V3, multiclass
            clus
vv           CDH10 MUTATED CDH10 WILD-TYPE
  STAGE I                4              60
  STAGE IA               1               0
  STAGE II               4              21
  STAGE IIA             15              94
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             0              10
  STAGE IIIB             3              38
  STAGE IIIC             3              28
  STAGE IV               2              33
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  62 218  39
D840V4, multiclass
    clus
vv   CDH10 MUTATED CDH10 WILD-TYPE
  T1             0               9
  T2             6              62
  T3            30             218
  T4             2              39
[1] 4 2
[1] TRUE
[1] "dimension 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  76  59
D840V5, multiclass
    clus
vv   CDH10 MUTATED CDH10 WILD-TYPE
  N0            28             192
  N1             4              76
  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"
D840V6, binary
                 cls
clus                0   1
  CDH10 MUTATED    29   3
  CDH10 WILD-TYPE 254  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH10 MUTATED     29    3
  CDH10 WILD-TYPE  254   45
   clus
vv  CDH10 MUTATED CDH10 WILD-TYPE
  0            29             254
  1             3              45
[1] 2 2
[1] FALSE
D840V7, 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
D840V8, binary
                 cls
clus                0   1
  CDH10 MUTATED    33   6
  CDH10 WILD-TYPE 284  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH10 MUTATED     33    6
  CDH10 WILD-TYPE  284   42
                               clus
vv                              CDH10 MUTATED CDH10 WILD-TYPE
  COLON ADENOCARCINOMA                     33             284
  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 228   2  20  18
D840V9, multiclass
    clus
vv   CDH10 MUTATED CDH10 WILD-TYPE
  R0            29             228
  R1             0               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"
D840V10, 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
D840V11, 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(841) Variable = PAX6 MUTATION ANALYSIS
D841V1, survival
                sevent
clus2              0   1
  PAX6 MUTATED    12   2
  PAX6 WILD-TYPE 270  71
  PAX6 MUTATED PAX6 WILD-TYPE 
            14            341 
  PAX6 MUTATED PAX6 WILD-TYPE 
             2             71 
$`PAX6 MUTATED`
TCGA-A6-6138 TCGA-A6-6781 TCGA-AA-3811 TCGA-AA-3950 TCGA-AA-A00J TCGA-AA-A00R 
       22.52        19.66        10.06        24.00        18.05         0.99 
TCGA-AZ-4315 TCGA-CA-6717 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-6171 TCGA-D5-6539 
       58.39         0.33        23.05        37.02        14.04        12.49 
TCGA-DM-A28F TCGA-DM-A28K 
       35.97        98.24 

$`PAX6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        32.71        27.09         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        19.04        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4747 
       21.14         2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 
       81.37       119.93        60.79       117.07         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  PAX6 MUTATED PAX6 WILD-TYPE 
          0.33           0.00 
  PAX6 MUTATED PAX6 WILD-TYPE 
         98.24         140.38 
  PAX6 MUTATED PAX6 WILD-TYPE 
         21.09          20.19 
[1] "0.3 - 98.2 (21.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.5"
D841V2, 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       25       104         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PAX6 MUTATED           1          1          2          1        0         0
  PAX6 WILD-TYPE        18          9         39         30       35        13
                vv
clus             STAGE IVB
  PAX6 MUTATED           0
  PAX6 WILD-TYPE         1
D841V3, multiclass
            clus
vv           PAX6 MUTATED PAX6 WILD-TYPE
  STAGE I               4             60
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             5            104
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            1              9
  STAGE IIIB            2             39
  STAGE IIIC            1             30
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PAX6 MUTATED     0   4   8   2
  PAX6 WILD-TYPE   9  64 240  39
D841V4, multiclass
    clus
vv   PAX6 MUTATED PAX6 WILD-TYPE
  T1            0              9
  T2            4             64
  T3            8            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
  PAX6 MUTATED    10   3   1
  PAX6 WILD-TYPE 210  77  65
D841V5, multiclass
    clus
vv   PAX6 MUTATED PAX6 WILD-TYPE
  N0           10            210
  N1            3             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"
D841V6, binary
                cls
clus               0   1
  PAX6 MUTATED    13   0
  PAX6 WILD-TYPE 270  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAX6 MUTATED     13    0
  PAX6 WILD-TYPE  270   48
   clus
vv  PAX6 MUTATED PAX6 WILD-TYPE
  0           13            270
  1            0             48
[1] 2 2
[1] FALSE
D841V7, 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
D841V8, binary
                cls
clus               0   1
  PAX6 MUTATED     9   5
  PAX6 WILD-TYPE 308  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAX6 MUTATED      9    5
  PAX6 WILD-TYPE  308   43
                               clus
vv                              PAX6 MUTATED PAX6 WILD-TYPE
  COLON ADENOCARCINOMA                     9            308
  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 247   2  22  20
D841V9, multiclass
    clus
vv   PAX6 MUTATED PAX6 WILD-TYPE
  R0           10            247
  R1            0              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"
D841V10, 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
D841V11, 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(842) Variable = SFRP2 MUTATION ANALYSIS
D842V1, survival
                 sevent
clus2               0   1
  SFRP2 MUTATED     7   1
  SFRP2 WILD-TYPE 275  72
  SFRP2 MUTATED SFRP2 WILD-TYPE 
              8             347 
  SFRP2 MUTATED SFRP2 WILD-TYPE 
              1              72 
$`SFRP2 MUTATED`
TCGA-A6-3810 TCGA-AA-3697 TCGA-AD-6963 TCGA-AZ-6601 TCGA-CK-4947 TCGA-CM-4743 
       36.53        85.05        27.42       100.01        17.56        23.05 
TCGA-D5-6930 TCGA-F4-6854 
        1.51         0.53 

$`SFRP2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 
       56.55         0.79         0.72         5.79        22.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.33         0.10         1.35       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6855 TCGA-F4-6856 
       29.59        16.24        33.67        13.25        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  SFRP2 MUTATED SFRP2 WILD-TYPE 
           0.53            0.00 
  SFRP2 MUTATED SFRP2 WILD-TYPE 
         100.01          140.38 
  SFRP2 MUTATED SFRP2 WILD-TYPE 
         25.235          20.120 
[1] "0.5 - 100.0 (25.2)" "0.0 - 140.4 (20.1)"
[1] "hr=" "2.3"
D842V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SFRP2 MUTATED         0        0        1         4         0         0
  SFRP2 WILD-TYPE      64        1       24       105         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SFRP2 MUTATED           1          0          0          0        0         1
  SFRP2 WILD-TYPE        18         10         41         31       35        12
                 vv
clus              STAGE IVB
  SFRP2 MUTATED           0
  SFRP2 WILD-TYPE         1
D842V3, multiclass
            clus
vv           SFRP2 MUTATED SFRP2 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              4             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  68 241  40
D842V4, multiclass
    clus
vv   SFRP2 MUTATED SFRP2 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             7             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
  SFRP2 MUTATED     7   1   0
  SFRP2 WILD-TYPE 213  79  66
D842V5, multiclass
    clus
vv   SFRP2 MUTATED SFRP2 WILD-TYPE
  N0             7             213
  N1             1              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"
D842V6, binary
                 cls
clus                0   1
  SFRP2 MUTATED     7   0
  SFRP2 WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SFRP2 MUTATED      7    0
  SFRP2 WILD-TYPE  276   48
   clus
vv  SFRP2 MUTATED SFRP2 WILD-TYPE
  0             7             276
  1             0              48
[1] 2 2
[1] FALSE
D842V7, 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
D842V8, binary
                 cls
clus                0   1
  SFRP2 MUTATED     7   1
  SFRP2 WILD-TYPE 310  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SFRP2 MUTATED      7    1
  SFRP2 WILD-TYPE  310   47
                               clus
vv                              SFRP2 MUTATED SFRP2 WILD-TYPE
  COLON ADENOCARCINOMA                      7             310
  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 252   2  22  20
D842V9, multiclass
    clus
vv   SFRP2 MUTATED SFRP2 WILD-TYPE
  R0             5             252
  R1             0               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"
D842V10, 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
D842V11, 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(843) Variable = THOC6 MUTATION ANALYSIS
D843V1, survival
                 sevent
clus2               0   1
  THOC6 MUTATED     5   2
  THOC6 WILD-TYPE 277  71
  THOC6 MUTATED THOC6 WILD-TYPE 
              7             348 
  THOC6 MUTATED THOC6 WILD-TYPE 
              2              71 
$`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       107.67 
TCGA-G4-6299 
       74.56 

$`THOC6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        1.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
        0.53        35.41        19.43        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  THOC6 MUTATED THOC6 WILD-TYPE 
           12.1             0.0 
  THOC6 MUTATED THOC6 WILD-TYPE 
         107.67          140.38 
  THOC6 MUTATED THOC6 WILD-TYPE 
         30.080          20.155 
[1] "12.1 - 107.7 (30.1)" "0.0 - 140.4 (20.2)" 
[1] "hr=" "1.1"
D843V2, 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       25       108         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        16         10         41         30       33        13
                 vv
clus              STAGE IVB
  THOC6 MUTATED           0
  THOC6 WILD-TYPE         1
D843V3, multiclass
            clus
vv           THOC6 MUTATED THOC6 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              1             108
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              3              16
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               2              33
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  THOC6 MUTATED     0   0   6   2
  THOC6 WILD-TYPE   9  68 242  39
D843V4, multiclass
    clus
vv   THOC6 MUTATED THOC6 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             6             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
  THOC6 MUTATED     3   2   3
  THOC6 WILD-TYPE 217  78  63
D843V5, multiclass
    clus
vv   THOC6 MUTATED THOC6 WILD-TYPE
  N0             3             217
  N1             2              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"
D843V6, binary
                 cls
clus                0   1
  THOC6 MUTATED     6   2
  THOC6 WILD-TYPE 277  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THOC6 MUTATED      6    2
  THOC6 WILD-TYPE  277   46
   clus
vv  THOC6 MUTATED THOC6 WILD-TYPE
  0             6             277
  1             2              46
[1] 2 2
[1] FALSE
D843V7, 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
D843V8, binary
                 cls
clus                0   1
  THOC6 MUTATED     7   1
  THOC6 WILD-TYPE 310  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THOC6 MUTATED      7    1
  THOC6 WILD-TYPE  310   47
                               clus
vv                              THOC6 MUTATED THOC6 WILD-TYPE
  COLON ADENOCARCINOMA                      7             310
  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 252   2  21  21
D843V9, multiclass
    clus
vv   THOC6 MUTATED THOC6 WILD-TYPE
  R0             5             252
  R1             0               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"
D843V10, 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
D843V11, 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(844) Variable = ZNF620 MUTATION ANALYSIS
D844V1, survival
                  sevent
clus2                0   1
  ZNF620 MUTATED     7   1
  ZNF620 WILD-TYPE 275  72
  ZNF620 MUTATED ZNF620 WILD-TYPE 
               8              347 
  ZNF620 MUTATED ZNF620 WILD-TYPE 
               1               72 
$`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 
        0.33       135.65 

$`ZNF620 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A03F 
        2.01         5.03        14.01         0.92        41.00        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41        49.41         6.77       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  ZNF620 MUTATED ZNF620 WILD-TYPE 
            0.33             0.00 
  ZNF620 MUTATED ZNF620 WILD-TYPE 
          135.65           140.38 
  ZNF620 MUTATED ZNF620 WILD-TYPE 
          19.745           20.190 
[1] "0.3 - 135.7 (19.7)" "0.0 - 140.4 (20.2)"
[1] "hr=" "2.3"
D844V2, 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       24       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF620 MUTATED           0          0          2          0        1
  ZNF620 WILD-TYPE        19         10         39         31       34
                  vv
clus               STAGE IVA STAGE IVB
  ZNF620 MUTATED           0         0
  ZNF620 WILD-TYPE        13         1
D844V3, multiclass
            clus
vv           ZNF620 MUTATED ZNF620 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               3              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF620 MUTATED     0   1   5   2
  ZNF620 WILD-TYPE   9  67 243  39
D844V4, multiclass
    clus
vv   ZNF620 MUTATED ZNF620 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              5              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
  ZNF620 MUTATED     5   3   0
  ZNF620 WILD-TYPE 215  77  66
D844V5, multiclass
    clus
vv   ZNF620 MUTATED ZNF620 WILD-TYPE
  N0              5              215
  N1              3               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"
D844V6, binary
                  cls
clus                 0   1
  ZNF620 MUTATED     6   1
  ZNF620 WILD-TYPE 277  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF620 MUTATED      6    1
  ZNF620 WILD-TYPE  277   47
   clus
vv  ZNF620 MUTATED ZNF620 WILD-TYPE
  0              6              277
  1              1               47
[1] 2 2
[1] FALSE
D844V7, 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
D844V8, binary
                  cls
clus                 0   1
  ZNF620 MUTATED     6   2
  ZNF620 WILD-TYPE 311  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF620 MUTATED      6    2
  ZNF620 WILD-TYPE  311   46
                               clus
vv                              ZNF620 MUTATED ZNF620 WILD-TYPE
  COLON ADENOCARCINOMA                       6              311
  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 252   2  22  20
D844V9, multiclass
    clus
vv   ZNF620 MUTATED ZNF620 WILD-TYPE
  R0              5              252
  R1              0                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"
D844V10, 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
D844V11, 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(845) Variable = NDUFAF1 MUTATION ANALYSIS
D845V1, survival
                   sevent
clus2                 0   1
  NDUFAF1 MUTATED     6   1
  NDUFAF1 WILD-TYPE 276  72
  NDUFAF1 MUTATED NDUFAF1 WILD-TYPE 
                7               348 
  NDUFAF1 MUTATED NDUFAF1 WILD-TYPE 
                1                72 
$`NDUFAF1 MUTATED`
TCGA-A6-6781 TCGA-AA-3713 TCGA-AY-6386 TCGA-D5-6537 TCGA-DM-A28H TCGA-G4-6310 
       19.66        19.04        17.82         4.80       117.07        45.11 
TCGA-G4-6588 
       26.17 

$`NDUFAF1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        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        51.75        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        52.80 

  NDUFAF1 MUTATED NDUFAF1 WILD-TYPE 
              4.8               0.0 
  NDUFAF1 MUTATED NDUFAF1 WILD-TYPE 
           117.07            140.38 
  NDUFAF1 MUTATED NDUFAF1 WILD-TYPE 
           19.660            20.235 
[1] "4.8 - 117.1 (19.7)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.9"
D845V2, 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       25       108         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NDUFAF1 MUTATED           0          0          3          2        1
  NDUFAF1 WILD-TYPE        19         10         38         29       34
                   vv
clus                STAGE IVA STAGE IVB
  NDUFAF1 MUTATED           0         0
  NDUFAF1 WILD-TYPE        13         1
D845V3, multiclass
            clus
vv           NDUFAF1 MUTATED NDUFAF1 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                1               108
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               3                38
  STAGE IIIC               2                29
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  NDUFAF1 MUTATED     0   0   6   1
  NDUFAF1 WILD-TYPE   9  68 242  40
D845V4, multiclass
    clus
vv   NDUFAF1 MUTATED NDUFAF1 WILD-TYPE
  T1               0                 9
  T2               0                68
  T3               6               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
  NDUFAF1 MUTATED     2   4   1
  NDUFAF1 WILD-TYPE 218  76  65
D845V5, multiclass
    clus
vv   NDUFAF1 MUTATED NDUFAF1 WILD-TYPE
  N0               2               218
  N1               4                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"
D845V6, binary
                   cls
clus                  0   1
  NDUFAF1 MUTATED     4   1
  NDUFAF1 WILD-TYPE 279  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NDUFAF1 MUTATED      4    1
  NDUFAF1 WILD-TYPE  279   47
   clus
vv  NDUFAF1 MUTATED NDUFAF1 WILD-TYPE
  0               4               279
  1               1                47
[1] 2 2
[1] FALSE
D845V7, 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
D845V8, binary
                   cls
clus                  0   1
  NDUFAF1 MUTATED     6   1
  NDUFAF1 WILD-TYPE 311  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NDUFAF1 MUTATED      6    1
  NDUFAF1 WILD-TYPE  311   47
                               clus
vv                              NDUFAF1 MUTATED NDUFAF1 WILD-TYPE
  COLON ADENOCARCINOMA                        6               311
  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 252   2  21  21
D845V9, multiclass
    clus
vv   NDUFAF1 MUTATED NDUFAF1 WILD-TYPE
  R0               5               252
  R1               0                 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"
D845V10, 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
D845V11, 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(846) Variable = CEL MUTATION ANALYSIS
D846V1, survival
               sevent
clus2             0   1
  CEL MUTATED     7   2
  CEL WILD-TYPE 275  71
  CEL MUTATED CEL WILD-TYPE 
            9           346 
  CEL MUTATED CEL WILD-TYPE 
            2            71 
$`CEL MUTATED`
TCGA-A6-6781 TCGA-AA-3713 TCGA-AA-3980 TCGA-AZ-6598 TCGA-CM-6171 TCGA-F4-6570 
       19.66        19.04        27.02        49.41        14.04         6.18 
TCGA-G4-6309 TCGA-G4-6588 TCGA-G4-6628 
       51.75        26.17        52.80 

$`CEL WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        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        13.38        13.45        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       13.78        35.80        91.79        46.75 

  CEL MUTATED CEL WILD-TYPE 
         6.18          0.00 
  CEL MUTATED CEL WILD-TYPE 
        52.80        140.38 
  CEL MUTATED CEL WILD-TYPE 
       26.170        20.155 
[1] "6.2 - 52.8 (26.2)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D846V2, 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       24       107         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        19         10         40         30       34        13
               vv
clus            STAGE IVB
  CEL MUTATED           0
  CEL WILD-TYPE         1
D846V3, multiclass
            clus
vv           CEL MUTATED CEL WILD-TYPE
  STAGE I              3            61
  STAGE IA             0             1
  STAGE II             1            24
  STAGE IIA            2           107
  STAGE IIB            0             8
  STAGE IIC            0             1
  STAGE III            0            19
  STAGE IIIA           0            10
  STAGE IIIB           1            40
  STAGE IIIC           1            30
  STAGE IV             1            34
  STAGE IVA            0            13
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  CEL MUTATED     0   3   5   1
  CEL WILD-TYPE   9  65 243  40
D846V4, multiclass
    clus
vv   CEL MUTATED CEL WILD-TYPE
  T1           0             9
  T2           3            65
  T3           5           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
  CEL MUTATED     7   2   0
  CEL WILD-TYPE 213  78  66
D846V5, multiclass
    clus
vv   CEL MUTATED CEL WILD-TYPE
  N0           7           213
  N1           2            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"
D846V6, binary
               cls
clus              0   1
  CEL MUTATED     6   1
  CEL WILD-TYPE 277  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  CEL MUTATED      6    1
  CEL WILD-TYPE  277   47
   clus
vv  CEL MUTATED CEL WILD-TYPE
  0           6           277
  1           1            47
[1] 2 2
[1] FALSE
D846V7, 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
D846V8, binary
               cls
clus              0   1
  CEL MUTATED     8   1
  CEL WILD-TYPE 309  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  CEL MUTATED      8    1
  CEL WILD-TYPE  309   47
                               clus
vv                              CEL MUTATED CEL WILD-TYPE
  COLON ADENOCARCINOMA                    8           309
  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 251   2  21  21
D846V9, multiclass
    clus
vv   CEL MUTATED CEL WILD-TYPE
  R0           6           251
  R1           0             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"
D846V10, 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
D846V11, 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(847) Variable = PTPN12 MUTATION ANALYSIS
D847V1, survival
                  sevent
clus2                0   1
  PTPN12 MUTATED    11   3
  PTPN12 WILD-TYPE 271  70
  PTPN12 MUTATED PTPN12 WILD-TYPE 
              14              341 
  PTPN12 MUTATED PTPN12 WILD-TYPE 
               3               70 
$`PTPN12 MUTATED`
TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3525 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3710 
       19.66        63.98         8.05         6.97         0.92        26.99 
TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6964 TCGA-AZ-6598 
       24.00        20.98         4.01        34.98        10.88        49.41 
TCGA-CA-6717 TCGA-G4-6586 
        0.33        35.80 

$`PTPN12 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 
        9.07        24.03        37.05        36.03        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 
       37.05        19.00        36.00         5.03        85.05        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
        0.72         5.79        22.42        27.42         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        26.17        91.79        46.75        52.80 

  PTPN12 MUTATED PTPN12 WILD-TYPE 
            0.33             0.00 
  PTPN12 MUTATED PTPN12 WILD-TYPE 
           63.98           140.38 
  PTPN12 MUTATED PTPN12 WILD-TYPE 
           20.32            20.19 
[1] "0.3 - 64.0 (20.3)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D847V2, 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       21       104         5         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PTPN12 MUTATED           1          0          2          1        0
  PTPN12 WILD-TYPE        18         10         39         30       35
                  vv
clus               STAGE IVA STAGE IVB
  PTPN12 MUTATED           0         0
  PTPN12 WILD-TYPE        13         1
D847V3, multiclass
            clus
vv           PTPN12 MUTATED PTPN12 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                4               21
  STAGE IIA               5              104
  STAGE IIB               3                5
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PTPN12 MUTATED     0   1  10   6
  PTPN12 WILD-TYPE   9  67 238  35
D847V4, multiclass
    clus
vv   PTPN12 MUTATED PTPN12 WILD-TYPE
  T1              0                9
  T2              1               67
  T3             10              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
  PTPN12 MUTATED    12   3   2
  PTPN12 WILD-TYPE 208  77  64
D847V5, multiclass
    clus
vv   PTPN12 MUTATED PTPN12 WILD-TYPE
  N0             12              208
  N1              3               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"
D847V6, binary
                  cls
clus                 0   1
  PTPN12 MUTATED    13   0
  PTPN12 WILD-TYPE 270  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN12 MUTATED     13    0
  PTPN12 WILD-TYPE  270   48
   clus
vv  PTPN12 MUTATED PTPN12 WILD-TYPE
  0             13              270
  1              0               48
[1] 2 2
[1] FALSE
D847V7, 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
D847V8, binary
                  cls
clus                 0   1
  PTPN12 MUTATED    13   4
  PTPN12 WILD-TYPE 304  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN12 MUTATED     13    4
  PTPN12 WILD-TYPE  304   44
                               clus
vv                              PTPN12 MUTATED PTPN12 WILD-TYPE
  COLON ADENOCARCINOMA                      13              304
  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 244   2  22  19
D847V9, multiclass
    clus
vv   PTPN12 MUTATED PTPN12 WILD-TYPE
  R0             13              244
  R1              0                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"
D847V10, 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
D847V11, 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(848) Variable = DHX32 MUTATION ANALYSIS
D848V1, survival
                 sevent
clus2               0   1
  DHX32 MUTATED     8   2
  DHX32 WILD-TYPE 274  71
  DHX32 MUTATED DHX32 WILD-TYPE 
             10             345 
  DHX32 MUTATED DHX32 WILD-TYPE 
              2              71 
$`DHX32 MUTATED`
TCGA-AA-3710 TCGA-AA-3977 TCGA-AD-5900 TCGA-AY-5543 TCGA-AZ-4315 TCGA-CM-6169 
       26.99        25.02         0.07        15.75        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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 
        0.20        14.50        27.09        16.31         0.95         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       33.67         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  DHX32 MUTATED DHX32 WILD-TYPE 
           0.07            0.00 
  DHX32 MUTATED DHX32 WILD-TYPE 
          58.39          140.38 
  DHX32 MUTATED DHX32 WILD-TYPE 
          14.50           20.28 
[1] "0.1 - 58.4 (14.5)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1"  
D848V2, 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       25       104         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        19         10         41         30       35        11
                 vv
clus              STAGE IVB
  DHX32 MUTATED           0
  DHX32 WILD-TYPE         1
D848V3, multiclass
            clus
vv           DHX32 MUTATED DHX32 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              5             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              2              11
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 241  40
D848V4, multiclass
    clus
vv   DHX32 MUTATED DHX32 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             7             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
  DHX32 MUTATED     7   2   1
  DHX32 WILD-TYPE 213  78  65
D848V5, multiclass
    clus
vv   DHX32 MUTATED DHX32 WILD-TYPE
  N0             7             213
  N1             2              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"
D848V6, binary
                 cls
clus                0   1
  DHX32 MUTATED     6   2
  DHX32 WILD-TYPE 277  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX32 MUTATED      6    2
  DHX32 WILD-TYPE  277   46
   clus
vv  DHX32 MUTATED DHX32 WILD-TYPE
  0             6             277
  1             2              46
[1] 2 2
[1] FALSE
D848V7, 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
D848V8, binary
                 cls
clus                0   1
  DHX32 MUTATED     8   2
  DHX32 WILD-TYPE 309  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX32 MUTATED      8    2
  DHX32 WILD-TYPE  309   46
                               clus
vv                              DHX32 MUTATED DHX32 WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  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 249   2  22  21
D848V9, multiclass
    clus
vv   DHX32 MUTATED DHX32 WILD-TYPE
  R0             8             249
  R1             0               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"
D848V10, 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
D848V11, 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(849) Variable = RIMBP3 MUTATION ANALYSIS
D849V1, survival
                  sevent
clus2                0   1
  RIMBP3 MUTATED     6   0
  RIMBP3 WILD-TYPE 276  73
  RIMBP3 MUTATED RIMBP3 WILD-TYPE 
               6              349 
  RIMBP3 MUTATED RIMBP3 WILD-TYPE 
               0               73 
$`RIMBP3 MUTATED`
TCGA-AA-A010 TCGA-AD-5900 TCGA-AU-3779 TCGA-D5-6928 TCGA-G4-6293 TCGA-G4-6310 
       34.98         0.07        14.50        11.64       107.67        45.11 

$`RIMBP3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        35.41        19.43        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        51.75        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  RIMBP3 MUTATED RIMBP3 WILD-TYPE 
            0.07             0.00 
  RIMBP3 MUTATED RIMBP3 WILD-TYPE 
          107.67           140.38 
  RIMBP3 MUTATED RIMBP3 WILD-TYPE 
           24.74            20.19 
[1] "0.1 - 107.7 (24.7)" "0.0 - 140.4 (20.2)"
[1] "hr="     "9300000"
D849V2, 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       25       107         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RIMBP3 MUTATED           1          0          1          0        0
  RIMBP3 WILD-TYPE        18         10         40         31       35
                  vv
clus               STAGE IVA STAGE IVB
  RIMBP3 MUTATED           0         0
  RIMBP3 WILD-TYPE        13         1
D849V3, multiclass
            clus
vv           RIMBP3 MUTATED RIMBP3 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               2              107
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  RIMBP3 MUTATED     0   1   4   1
  RIMBP3 WILD-TYPE   9  67 244  40
D849V4, multiclass
    clus
vv   RIMBP3 MUTATED RIMBP3 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              4              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
  RIMBP3 MUTATED     4   2   0
  RIMBP3 WILD-TYPE 216  78  66
D849V5, multiclass
    clus
vv   RIMBP3 MUTATED RIMBP3 WILD-TYPE
  N0              4              216
  N1              2               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"
D849V6, binary
                  cls
clus                 0   1
  RIMBP3 MUTATED     5   0
  RIMBP3 WILD-TYPE 278  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RIMBP3 MUTATED      5    0
  RIMBP3 WILD-TYPE  278   48
   clus
vv  RIMBP3 MUTATED RIMBP3 WILD-TYPE
  0              5              278
  1              0               48
[1] 2 2
[1] FALSE
D849V7, 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
D849V8, binary
                  cls
clus                 0   1
  RIMBP3 MUTATED     4   2
  RIMBP3 WILD-TYPE 313  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RIMBP3 MUTATED      4    2
  RIMBP3 WILD-TYPE  313   46
                               clus
vv                              RIMBP3 MUTATED RIMBP3 WILD-TYPE
  COLON ADENOCARCINOMA                       4              313
  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 251   2  22  21
D849V9, multiclass
    clus
vv   RIMBP3 MUTATED RIMBP3 WILD-TYPE
  R0              6              251
  R1              0                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"
D849V10, 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
D849V11, 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(850) Variable = CTTN MUTATION ANALYSIS
D850V1, survival
                sevent
clus2              0   1
  CTTN MUTATED     4   0
  CTTN WILD-TYPE 278  73
  CTTN MUTATED CTTN WILD-TYPE 
             4            351 
  CTTN MUTATED CTTN WILD-TYPE 
             0             73 
$`CTTN MUTATED`
TCGA-AU-6004 TCGA-AZ-4315 TCGA-CK-4950 TCGA-CK-4952 
       27.09        58.39        40.34        15.62 

$`CTTN WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
      102.44        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  CTTN MUTATED CTTN WILD-TYPE 
         15.62           0.00 
  CTTN MUTATED CTTN WILD-TYPE 
         58.39         140.38 
  CTTN MUTATED CTTN WILD-TYPE 
        33.715         20.120 
[1] "15.6 - 58.4 (33.7)" "0.0 - 140.4 (20.1)"
[1] "hr="     "9100000"
D850V2, 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       25       108         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CTTN MUTATED           1          1          0          0        0         0
  CTTN WILD-TYPE        18          9         41         31       35        13
                vv
clus             STAGE IVB
  CTTN MUTATED           0
  CTTN WILD-TYPE         1
D850V3, multiclass
            clus
vv           CTTN MUTATED CTTN WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             1            108
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            1              9
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CTTN MUTATED     0   1   2   1
  CTTN WILD-TYPE   9  67 246  40
D850V4, multiclass
    clus
vv   CTTN MUTATED CTTN WILD-TYPE
  T1            0              9
  T2            1             67
  T3            2            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
  CTTN MUTATED     2   1   1
  CTTN WILD-TYPE 218  79  65
D850V5, multiclass
    clus
vv   CTTN MUTATED CTTN WILD-TYPE
  N0            2            218
  N1            1             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"
D850V6, binary
                cls
clus               0   1
  CTTN MUTATED     4   0
  CTTN WILD-TYPE 279  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTTN MUTATED      4    0
  CTTN WILD-TYPE  279   48
   clus
vv  CTTN MUTATED CTTN WILD-TYPE
  0            4            279
  1            0             48
[1] 2 2
[1] FALSE
D850V7, 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
D850V8, binary
                cls
clus               0   1
  CTTN MUTATED     3   1
  CTTN WILD-TYPE 314  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTTN MUTATED      3    1
  CTTN WILD-TYPE  314   47
                               clus
vv                              CTTN MUTATED CTTN WILD-TYPE
  COLON ADENOCARCINOMA                     3            314
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CTTN MUTATED     2   1   0   1
  CTTN WILD-TYPE 255   1  22  20
D850V9, multiclass
    clus
vv   CTTN MUTATED CTTN WILD-TYPE
  R0            2            255
  R1            1              1
  R2            0             22
  RX            1             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D850V10, 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
D850V11, 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(851) Variable = SLC25A13 MUTATION ANALYSIS
D851V1, survival
                    sevent
clus2                  0   1
  SLC25A13 MUTATED    11   3
  SLC25A13 WILD-TYPE 271  70
  SLC25A13 MUTATED SLC25A13 WILD-TYPE 
                14                341 
  SLC25A13 MUTATED SLC25A13 WILD-TYPE 
                 3                 70 
$`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        61.41        49.41         1.35        51.32        13.02 
TCGA-D5-6923 TCGA-G4-6304 
       12.43        53.62 

$`SLC25A13 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       17.03        10.06        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       27.09        16.31         0.95        15.75         0.20        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6599 
        1.41         5.13        83.80        22.36        62.79         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.33         0.10        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 
       19.43       107.67        74.56        65.85        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  SLC25A13 MUTATED SLC25A13 WILD-TYPE 
                 0                  0 
  SLC25A13 MUTATED SLC25A13 WILD-TYPE 
             61.41             140.38 
  SLC25A13 MUTATED SLC25A13 WILD-TYPE 
             28.21              20.02 
[1] "0.0 - 61.4 (28.2)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1.2"
D851V2, 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       24       103         5         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC25A13 MUTATED           0          0          1          0        0
  SLC25A13 WILD-TYPE        19         10         40         31       35
                    vv
clus                 STAGE IVA STAGE IVB
  SLC25A13 MUTATED           0         0
  SLC25A13 WILD-TYPE        13         1
D851V3, multiclass
            clus
vv           SLC25A13 MUTATED SLC25A13 WILD-TYPE
  STAGE I                   3                 61
  STAGE IA                  0                  1
  STAGE II                  1                 24
  STAGE IIA                 6                103
  STAGE IIB                 3                  5
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                0                 10
  STAGE IIIB                1                 40
  STAGE IIIC                0                 31
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  SLC25A13 MUTATED     1   3   7   3
  SLC25A13 WILD-TYPE   8  65 241  38
D851V4, multiclass
    clus
vv   SLC25A13 MUTATED SLC25A13 WILD-TYPE
  T1                1                  8
  T2                3                 65
  T3                7                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
  SLC25A13 MUTATED    13   0   1
  SLC25A13 WILD-TYPE 207  80  65
D851V5, multiclass
    clus
vv   SLC25A13 MUTATED SLC25A13 WILD-TYPE
  N0               13                207
  N1                0                 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"
D851V6, binary
                    cls
clus                   0   1
  SLC25A13 MUTATED    11   0
  SLC25A13 WILD-TYPE 272  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC25A13 MUTATED     11    0
  SLC25A13 WILD-TYPE  272   48
   clus
vv  SLC25A13 MUTATED SLC25A13 WILD-TYPE
  0               11                272
  1                0                 48
[1] 2 2
[1] FALSE
D851V7, 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
D851V8, binary
                    cls
clus                   0   1
  SLC25A13 MUTATED    13   1
  SLC25A13 WILD-TYPE 304  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC25A13 MUTATED     13    1
  SLC25A13 WILD-TYPE  304   47
                               clus
vv                              SLC25A13 MUTATED SLC25A13 WILD-TYPE
  COLON ADENOCARCINOMA                        13                304
  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 247   2  22  19
D851V9, multiclass
    clus
vv   SLC25A13 MUTATED SLC25A13 WILD-TYPE
  R0               10                247
  R1                0                  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"
D851V10, 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
D851V11, 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(852) Variable = RBMX2 MUTATION ANALYSIS
D852V1, survival
                 sevent
clus2               0   1
  RBMX2 MUTATED    10   1
  RBMX2 WILD-TYPE 272  72
  RBMX2 MUTATED RBMX2 WILD-TYPE 
             11             344 
  RBMX2 MUTATED RBMX2 WILD-TYPE 
              1              72 
$`RBMX2 MUTATED`
TCGA-AA-3492 TCGA-AA-3710 TCGA-AY-6197 TCGA-AZ-4315 TCGA-CM-6171 TCGA-D5-6930 
        3.02        26.99        21.44        58.39        14.04         1.51 
TCGA-F4-6806 TCGA-G4-6299 TCGA-G4-6310 TCGA-G4-6588 TCGA-G4-6625 
       29.59        74.56        45.11        26.17        91.79 

$`RBMX2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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-4681 
       15.75         0.20        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       16.31        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       19.43       107.67        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       51.75        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  RBMX2 MUTATED RBMX2 WILD-TYPE 
           1.51            0.00 
  RBMX2 MUTATED RBMX2 WILD-TYPE 
          91.79          140.38 
  RBMX2 MUTATED RBMX2 WILD-TYPE 
         26.990          20.005 
[1] "1.5 - 91.8 (27.0)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "3.2"
D852V2, 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       24       103         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        19         10         40         30       35        13
                 vv
clus              STAGE IVB
  RBMX2 MUTATED           0
  RBMX2 WILD-TYPE         1
D852V3, multiclass
            clus
vv           RBMX2 MUTATED RBMX2 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              6             103
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RBMX2 MUTATED     0   2   9   0
  RBMX2 WILD-TYPE   9  66 239  41
D852V4, multiclass
    clus
vv   RBMX2 MUTATED RBMX2 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             9             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
  RBMX2 MUTATED     9   1   1
  RBMX2 WILD-TYPE 211  79  65
D852V5, multiclass
    clus
vv   RBMX2 MUTATED RBMX2 WILD-TYPE
  N0             9             211
  N1             1              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"
D852V6, binary
                 cls
clus                0   1
  RBMX2 MUTATED    10   0
  RBMX2 WILD-TYPE 273  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBMX2 MUTATED     10    0
  RBMX2 WILD-TYPE  273   48
   clus
vv  RBMX2 MUTATED RBMX2 WILD-TYPE
  0            10             273
  1             0              48
[1] 2 2
[1] FALSE
D852V7, 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
D852V8, binary
                 cls
clus                0   1
  RBMX2 MUTATED    10   1
  RBMX2 WILD-TYPE 307  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBMX2 MUTATED     10    1
  RBMX2 WILD-TYPE  307   47
                               clus
vv                              RBMX2 MUTATED RBMX2 WILD-TYPE
  COLON ADENOCARCINOMA                     10             307
  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 246   2  22  21
D852V9, multiclass
    clus
vv   RBMX2 MUTATED RBMX2 WILD-TYPE
  R0            11             246
  R1             0               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"
D852V10, 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
D852V11, 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(853) Variable = LEO1 MUTATION ANALYSIS
D853V1, survival
                sevent
clus2              0   1
  LEO1 MUTATED     8   2
  LEO1 WILD-TYPE 274  71
  LEO1 MUTATED LEO1 WILD-TYPE 
            10            345 
  LEO1 MUTATED LEO1 WILD-TYPE 
             2             71 
$`LEO1 MUTATED`
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3510 TCGA-AA-3864 TCGA-AA-A00N 
       23.87        20.12        20.28        63.98        53.00         4.01 
TCGA-AD-6895 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 
        0.72        58.39        49.41         0.33 

$`LEO1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       19.66         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21        56.55         0.79         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13        83.80        22.36        62.79        61.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  LEO1 MUTATED LEO1 WILD-TYPE 
          0.33           0.00 
  LEO1 MUTATED LEO1 WILD-TYPE 
         63.98         140.38 
  LEO1 MUTATED LEO1 WILD-TYPE 
        22.075         20.020 
[1] "0.3 - 64.0 (22.1)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1.3"
D853V2, 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       22       106         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LEO1 MUTATED           0          0          1          0        0         0
  LEO1 WILD-TYPE        19         10         40         31       35        13
                vv
clus             STAGE IVB
  LEO1 MUTATED           0
  LEO1 WILD-TYPE         1
D853V3, multiclass
            clus
vv           LEO1 MUTATED LEO1 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              3             22
  STAGE IIA             3            106
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  LEO1 MUTATED     0   0   8   2
  LEO1 WILD-TYPE   9  68 240  39
D853V4, multiclass
    clus
vv   LEO1 MUTATED LEO1 WILD-TYPE
  T1            0              9
  T2            0             68
  T3            8            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
  LEO1 MUTATED     8   2   0
  LEO1 WILD-TYPE 212  78  66
D853V5, multiclass
    clus
vv   LEO1 MUTATED LEO1 WILD-TYPE
  N0            8            212
  N1            2             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"
D853V6, binary
                cls
clus               0   1
  LEO1 MUTATED     6   0
  LEO1 WILD-TYPE 277  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  LEO1 MUTATED      6    0
  LEO1 WILD-TYPE  277   48
   clus
vv  LEO1 MUTATED LEO1 WILD-TYPE
  0            6            277
  1            0             48
[1] 2 2
[1] FALSE
D853V7, 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
D853V8, binary
                cls
clus               0   1
  LEO1 MUTATED     7   3
  LEO1 WILD-TYPE 310  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  LEO1 MUTATED      7    3
  LEO1 WILD-TYPE  310   45
                               clus
vv                              LEO1 MUTATED LEO1 WILD-TYPE
  COLON ADENOCARCINOMA                     7            310
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  LEO1 MUTATED     4   0   0   1
  LEO1 WILD-TYPE 253   2  22  20
D853V9, multiclass
    clus
vv   LEO1 MUTATED LEO1 WILD-TYPE
  R0            4            253
  R1            0              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"
D853V10, 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
D853V11, 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(854) Variable = SR140 MUTATION ANALYSIS
D854V1, survival
                 sevent
clus2               0   1
  SR140 MUTATED     7   3
  SR140 WILD-TYPE 275  70
  SR140 MUTATED SR140 WILD-TYPE 
             10             345 
  SR140 MUTATED SR140 WILD-TYPE 
              3              70 
$`SR140 MUTATED`
TCGA-A6-2671 TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-A00N TCGA-AD-6895 TCGA-AZ-4315 
       43.76        24.39        19.66         4.01         0.72        58.39 
TCGA-AZ-6601 TCGA-CK-6747 TCGA-CM-6674 TCGA-DM-A1HB 
      100.01         2.93        12.95       135.65 

$`SR140 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  SR140 MUTATED SR140 WILD-TYPE 
           0.72            0.00 
  SR140 MUTATED SR140 WILD-TYPE 
         135.65          140.38 
  SR140 MUTATED SR140 WILD-TYPE 
         22.025          20.190 
[1] "0.7 - 135.7 (22.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1"  
D854V2, 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       24       105         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SR140 MUTATED           0          0          1          1        1         0
  SR140 WILD-TYPE        19         10         40         30       34        13
                 vv
clus              STAGE IVB
  SR140 MUTATED           0
  SR140 WILD-TYPE         1
D854V3, multiclass
            clus
vv           SR140 MUTATED SR140 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              4             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SR140 MUTATED     0   1   8   2
  SR140 WILD-TYPE   9  67 240  39
D854V4, multiclass
    clus
vv   SR140 MUTATED SR140 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             8             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
  SR140 MUTATED     7   3   1
  SR140 WILD-TYPE 213  77  65
D854V5, multiclass
    clus
vv   SR140 MUTATED SR140 WILD-TYPE
  N0             7             213
  N1             3              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"
D854V6, binary
                 cls
clus                0   1
  SR140 MUTATED     7   1
  SR140 WILD-TYPE 276  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SR140 MUTATED      7    1
  SR140 WILD-TYPE  276   47
   clus
vv  SR140 MUTATED SR140 WILD-TYPE
  0             7             276
  1             1              47
[1] 2 2
[1] FALSE
D854V7, 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
D854V8, binary
                 cls
clus                0   1
  SR140 MUTATED     9   2
  SR140 WILD-TYPE 308  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SR140 MUTATED      9    2
  SR140 WILD-TYPE  308   46
                               clus
vv                              SR140 MUTATED SR140 WILD-TYPE
  COLON ADENOCARCINOMA                      9             308
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SR140 MUTATED     6   0   0   1
  SR140 WILD-TYPE 251   2  22  20
D854V9, multiclass
    clus
vv   SR140 MUTATED SR140 WILD-TYPE
  R0             6             251
  R1             0               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"
D854V10, 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
D854V11, 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(855) Variable = KBTBD4 MUTATION ANALYSIS
D855V1, survival
                  sevent
clus2                0   1
  KBTBD4 MUTATED     3   4
  KBTBD4 WILD-TYPE 279  69
  KBTBD4 MUTATED KBTBD4 WILD-TYPE 
               7              348 
  KBTBD4 MUTATED KBTBD4 WILD-TYPE 
               4               69 
$`KBTBD4 MUTATED`
TCGA-AA-3811 TCGA-AZ-6598 TCGA-CK-5913 TCGA-CK-5916 TCGA-F4-6570 TCGA-G4-6293 
       10.06        49.41        51.32        21.14         6.18       107.67 
TCGA-G4-6628 
       52.80 

$`KBTBD4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6747 
      102.44        40.34        15.62        49.08        21.99         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       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        13.38        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        35.41        19.43        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 

  KBTBD4 MUTATED KBTBD4 WILD-TYPE 
            6.18             0.00 
  KBTBD4 MUTATED KBTBD4 WILD-TYPE 
          107.67           140.38 
  KBTBD4 MUTATED KBTBD4 WILD-TYPE 
           49.41            20.07 
[1] "6.2 - 107.7 (49.4)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.6"
D855V2, 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       24       107         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KBTBD4 MUTATED           2          0          0          0        0
  KBTBD4 WILD-TYPE        17         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  KBTBD4 MUTATED           0         0
  KBTBD4 WILD-TYPE        13         1
D855V3, multiclass
            clus
vv           KBTBD4 MUTATED KBTBD4 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               2              107
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               2               17
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  KBTBD4 MUTATED     1   1   5   0
  KBTBD4 WILD-TYPE   8  67 243  41
D855V4, multiclass
    clus
vv   KBTBD4 MUTATED KBTBD4 WILD-TYPE
  T1              1                8
  T2              1               67
  T3              5              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
  KBTBD4 MUTATED     5   1   1
  KBTBD4 WILD-TYPE 215  79  65
D855V5, multiclass
    clus
vv   KBTBD4 MUTATED KBTBD4 WILD-TYPE
  N0              5              215
  N1              1               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"
D855V6, binary
                  cls
clus                 0   1
  KBTBD4 MUTATED     5   0
  KBTBD4 WILD-TYPE 278  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KBTBD4 MUTATED      5    0
  KBTBD4 WILD-TYPE  278   48
   clus
vv  KBTBD4 MUTATED KBTBD4 WILD-TYPE
  0              5              278
  1              0               48
[1] 2 2
[1] FALSE
D855V7, 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
D855V8, binary
                  cls
clus                 0   1
  KBTBD4 MUTATED     7   0
  KBTBD4 WILD-TYPE 310  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KBTBD4 MUTATED      7    0
  KBTBD4 WILD-TYPE  310   48
                               clus
vv                              KBTBD4 MUTATED KBTBD4 WILD-TYPE
  COLON ADENOCARCINOMA                       7              310
  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 253   2  22  19
D855V9, multiclass
    clus
vv   KBTBD4 MUTATED KBTBD4 WILD-TYPE
  R0              4              253
  R1              0                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"
D855V10, 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
D855V11, 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(856) Variable = HAUS1 MUTATION ANALYSIS
D856V1, survival
                 sevent
clus2               0   1
  HAUS1 MUTATED     4   2
  HAUS1 WILD-TYPE 278  71
  HAUS1 MUTATED HAUS1 WILD-TYPE 
              6             349 
  HAUS1 MUTATED HAUS1 WILD-TYPE 
              2              71 
$`HAUS1 MUTATED`
TCGA-A6-6141 TCGA-AA-3715 TCGA-AA-A01Q TCGA-AZ-4323 TCGA-CM-6161 TCGA-G4-6307 
        8.38        19.04         1.02         1.41        15.02        55.04 

$`HAUS1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82        58.39         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  HAUS1 MUTATED HAUS1 WILD-TYPE 
           1.02            0.00 
  HAUS1 MUTATED HAUS1 WILD-TYPE 
          55.04          140.38 
  HAUS1 MUTATED HAUS1 WILD-TYPE 
          11.70           20.98 
[1] "1.0 - 55.0 (11.7)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "2.2"
D856V2, 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       23       108         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        19         10         40         31       34        13
                 vv
clus              STAGE IVB
  HAUS1 MUTATED           0
  HAUS1 WILD-TYPE         1
D856V3, multiclass
            clus
vv           HAUS1 MUTATED HAUS1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              1             108
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HAUS1 MUTATED     0   1   4   1
  HAUS1 WILD-TYPE   9  67 244  40
D856V4, multiclass
    clus
vv   HAUS1 MUTATED HAUS1 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             4             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
  HAUS1 MUTATED     4   1   1
  HAUS1 WILD-TYPE 216  79  65
D856V5, multiclass
    clus
vv   HAUS1 MUTATED HAUS1 WILD-TYPE
  N0             4             216
  N1             1              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"
D856V6, binary
                 cls
clus                0   1
  HAUS1 MUTATED     5   1
  HAUS1 WILD-TYPE 278  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAUS1 MUTATED      5    1
  HAUS1 WILD-TYPE  278   47
   clus
vv  HAUS1 MUTATED HAUS1 WILD-TYPE
  0             5             278
  1             1              47
[1] 2 2
[1] FALSE
D856V7, 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
D856V8, binary
                 cls
clus                0   1
  HAUS1 MUTATED     6   0
  HAUS1 WILD-TYPE 311  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAUS1 MUTATED      6    0
  HAUS1 WILD-TYPE  311   48
                               clus
vv                              HAUS1 MUTATED HAUS1 WILD-TYPE
  COLON ADENOCARCINOMA                      6             311
  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 253   2  22  21
D856V9, multiclass
    clus
vv   HAUS1 MUTATED HAUS1 WILD-TYPE
  R0             4             253
  R1             0               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"
D856V10, 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
D856V11, 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(857) Variable = RNF145 MUTATION ANALYSIS
D857V1, survival
                  sevent
clus2                0   1
  RNF145 MUTATED    11   3
  RNF145 WILD-TYPE 271  70
  RNF145 MUTATED RNF145 WILD-TYPE 
              14              341 
  RNF145 MUTATED RNF145 WILD-TYPE 
               3               70 
$`RNF145 MUTATED`
TCGA-AA-3510 TCGA-AA-3950 TCGA-AD-6964 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-6598 
       63.98        24.00        10.88        17.82        58.39        49.41 
TCGA-AZ-6601 TCGA-CA-6718 TCGA-CM-5348 TCGA-CM-6162 TCGA-DM-A1D9 TCGA-F4-6569 
      100.01         0.10        22.98        12.00       140.38        13.45 
TCGA-F4-6856 TCGA-G4-6628 
       19.43        52.80 

$`RNF145 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
        0.20        21.44         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       62.79        61.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.33         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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 
       16.01        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       12.59         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        13.38         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.41       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       13.78        35.80        26.17        91.79        46.75 

  RNF145 MUTATED RNF145 WILD-TYPE 
             0.1              0.0 
  RNF145 MUTATED RNF145 WILD-TYPE 
          140.38           139.17 
  RNF145 MUTATED RNF145 WILD-TYPE 
           23.49            20.12 
[1] "0.1 - 140.4 (23.5)" "0.0 - 139.2 (20.1)"
[1] "hr=" "1.6"
D857V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RNF145 MUTATED         3        0        4         4         0         0
  RNF145 WILD-TYPE      61        1       21       105         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RNF145 MUTATED           0          0          3          0        0
  RNF145 WILD-TYPE        19         10         38         31       35
                  vv
clus               STAGE IVA STAGE IVB
  RNF145 MUTATED           0         0
  RNF145 WILD-TYPE        13         1
D857V3, multiclass
            clus
vv           RNF145 MUTATED RNF145 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                4               21
  STAGE IIA               4              105
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              3               38
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  RNF145 MUTATED     0   3  10   2
  RNF145 WILD-TYPE   9  65 238  39
D857V4, multiclass
    clus
vv   RNF145 MUTATED RNF145 WILD-TYPE
  T1              0                9
  T2              3               65
  T3             10              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
  RNF145 MUTATED    11   3   1
  RNF145 WILD-TYPE 209  77  65
D857V5, multiclass
    clus
vv   RNF145 MUTATED RNF145 WILD-TYPE
  N0             11              209
  N1              3               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"
D857V6, binary
                  cls
clus                 0   1
  RNF145 MUTATED    13   0
  RNF145 WILD-TYPE 270  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF145 MUTATED     13    0
  RNF145 WILD-TYPE  270   48
   clus
vv  RNF145 MUTATED RNF145 WILD-TYPE
  0             13              270
  1              0               48
[1] 2 2
[1] FALSE
D857V7, binary
                  cls
clus                 0   1
  RNF145 MUTATED     6   9
  RNF145 WILD-TYPE 164 188
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF145 MUTATED      6    9
  RNF145 WILD-TYPE  164  188
        clus
vv       RNF145 MUTATED RNF145 WILD-TYPE
  FEMALE              6              164
  MALE                9              188
[1] 2 2
[1] FALSE
D857V8, binary
                  cls
clus                 0   1
  RNF145 MUTATED    12   3
  RNF145 WILD-TYPE 305  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF145 MUTATED     12    3
  RNF145 WILD-TYPE  305   45
                               clus
vv                              RNF145 MUTATED RNF145 WILD-TYPE
  COLON ADENOCARCINOMA                      12              305
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  RNF145 MUTATED    10   0   0   1
  RNF145 WILD-TYPE 247   2  22  20
D857V9, multiclass
    clus
vv   RNF145 MUTATED RNF145 WILD-TYPE
  R0             10              247
  R1              0                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"
D857V10, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RNF145 MUTATED                                  0     1
  RNF145 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  RNF145 MUTATED                           1    10
  RNF145 WILD-TYPE                        18   166
D857V11, multiclass
                                  clus
vv                                 RNF145 MUTATED RNF145 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(858) Variable = WNK3 MUTATION ANALYSIS
D858V1, survival
                sevent
clus2              0   1
  WNK3 MUTATED    20   2
  WNK3 WILD-TYPE 262  71
  WNK3 MUTATED WNK3 WILD-TYPE 
            22            333 
  WNK3 MUTATED WNK3 WILD-TYPE 
             2             71 
$`WNK3 MUTATED`
TCGA-A6-5657 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6781 TCGA-AA-3555 TCGA-AA-3660 
       31.63        22.06        32.71        19.66        29.95        78.08 
TCGA-AA-3663 TCGA-AA-3667 TCGA-AA-3710 TCGA-AA-3875 TCGA-AA-A00J TCGA-AA-A00N 
        6.97        14.01        26.99        18.05        18.05         4.01 
TCGA-AD-6895 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CM-6168 TCGA-D5-6928 
        0.72        58.39        49.41         0.33        12.99        11.64 
TCGA-F4-6807 TCGA-F4-6856 TCGA-G4-6309 TCGA-G4-6310 
       16.24        19.43        51.75        45.11 

$`WNK3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 
       21.76        24.69        24.39        23.87        20.12        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        7.04         3.02         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
        6.05        54.02         2.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       27.02        29.98        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21        56.55         0.79         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13        83.80        22.36        62.79        61.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       16.31        29.59        33.67        13.25         0.53        35.41 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  WNK3 MUTATED WNK3 WILD-TYPE 
          0.33           0.00 
  WNK3 MUTATED WNK3 WILD-TYPE 
         78.08         140.38 
  WNK3 MUTATED WNK3 WILD-TYPE 
        19.545         20.280 
[1] "0.3 - 78.1 (19.5)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "2.4"
D858V2, 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       22       101         7         0
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  WNK3 MUTATED           0          0          4          2        1         0
  WNK3 WILD-TYPE        19         10         37         29       34        13
                vv
clus             STAGE IVB
  WNK3 MUTATED           0
  WNK3 WILD-TYPE         1
D858V3, multiclass
            clus
vv           WNK3 MUTATED WNK3 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              3             22
  STAGE IIA             8            101
  STAGE IIB             1              7
  STAGE IIC             1              0
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            4             37
  STAGE IIIC            2             29
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  WNK3 MUTATED     1   2  16   5
  WNK3 WILD-TYPE   8  66 232  36
D858V4, multiclass
    clus
vv   WNK3 MUTATED WNK3 WILD-TYPE
  T1            1              8
  T2            2             66
  T3           16            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
  WNK3 MUTATED    16   7   1
  WNK3 WILD-TYPE 204  73  65
D858V5, multiclass
    clus
vv   WNK3 MUTATED WNK3 WILD-TYPE
  N0           16            204
  N1            7             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"
D858V6, binary
                cls
clus               0   1
  WNK3 MUTATED    20   1
  WNK3 WILD-TYPE 263  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNK3 MUTATED     20    1
  WNK3 WILD-TYPE  263   47
   clus
vv  WNK3 MUTATED WNK3 WILD-TYPE
  0           20            263
  1            1             47
[1] 2 2
[1] FALSE
D858V7, 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
D858V8, binary
                cls
clus               0   1
  WNK3 MUTATED    17   7
  WNK3 WILD-TYPE 300  41
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNK3 MUTATED     17    7
  WNK3 WILD-TYPE  300   41
                               clus
vv                              WNK3 MUTATED WNK3 WILD-TYPE
  COLON ADENOCARCINOMA                    17            300
  COLON MUCINOUS ADENOCARCINOMA            7             41
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  WNK3 MUTATED    19   0   1   1
  WNK3 WILD-TYPE 238   2  21  20
D858V9, multiclass
    clus
vv   WNK3 MUTATED WNK3 WILD-TYPE
  R0           19            238
  R1            0              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"
D858V10, 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
D858V11, 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(859) Variable = TDRD7 MUTATION ANALYSIS
D859V1, survival
                 sevent
clus2               0   1
  TDRD7 MUTATED    12   3
  TDRD7 WILD-TYPE 270  70
  TDRD7 MUTATED TDRD7 WILD-TYPE 
             15             340 
  TDRD7 MUTATED TDRD7 WILD-TYPE 
              3              70 
$`TDRD7 MUTATED`
TCGA-A6-5659 TCGA-A6-5665 TCGA-A6-6141 TCGA-AA-3492 TCGA-AA-3681 TCGA-AA-3710 
       30.44        22.06         8.38         3.02         5.98        26.99 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CM-5864 
        4.01        34.98        58.39       100.01         0.33        15.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-D5-6532 
       15.02        14.04        18.25 

$`TDRD7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       32.71        27.09        22.52        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 
       37.05        19.00        36.00         5.03        85.05        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        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-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       11.51        20.19         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  TDRD7 MUTATED TDRD7 WILD-TYPE 
           0.33            0.00 
  TDRD7 MUTATED TDRD7 WILD-TYPE 
         100.01          140.38 
  TDRD7 MUTATED TDRD7 WILD-TYPE 
          15.02           20.63 
[1] "0.3 - 100.0 (15.0)" "0.0 - 140.4 (20.6)"
[1] "hr=" "1"  
D859V2, 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       23       103         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        18         10         41         31       35        13
                 vv
clus              STAGE IVB
  TDRD7 MUTATED           0
  TDRD7 WILD-TYPE         1
D859V3, multiclass
            clus
vv           TDRD7 MUTATED TDRD7 WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              6             103
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TDRD7 MUTATED     0   4   9   2
  TDRD7 WILD-TYPE   9  64 239  39
D859V4, multiclass
    clus
vv   TDRD7 MUTATED TDRD7 WILD-TYPE
  T1             0               9
  T2             4              64
  T3             9             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
  TDRD7 MUTATED    14   1   0
  TDRD7 WILD-TYPE 206  79  66
D859V5, multiclass
    clus
vv   TDRD7 MUTATED TDRD7 WILD-TYPE
  N0            14             206
  N1             1              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
  TDRD7 MUTATED    15   0
  TDRD7 WILD-TYPE 268  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TDRD7 MUTATED     15    0
  TDRD7 WILD-TYPE  268   48
   clus
vv  TDRD7 MUTATED TDRD7 WILD-TYPE
  0            15             268
  1             0              48
[1] 2 2
[1] FALSE
D859V7, 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
D859V8, binary
                 cls
clus                0   1
  TDRD7 MUTATED    13   2
  TDRD7 WILD-TYPE 304  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TDRD7 MUTATED     13    2
  TDRD7 WILD-TYPE  304   46
                               clus
vv                              TDRD7 MUTATED TDRD7 WILD-TYPE
  COLON ADENOCARCINOMA                     13             304
  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 245   2  22  20
D859V9, multiclass
    clus
vv   TDRD7 MUTATED TDRD7 WILD-TYPE
  R0            12             245
  R1             0               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"
D859V10, 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
D859V11, 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(860) Variable = BACE2 MUTATION ANALYSIS
D860V1, survival
                 sevent
clus2               0   1
  BACE2 MUTATED    10   0
  BACE2 WILD-TYPE 272  73
  BACE2 MUTATED BACE2 WILD-TYPE 
             10             345 
  BACE2 MUTATED BACE2 WILD-TYPE 
              0              73 
$`BACE2 MUTATED`
TCGA-A6-2672 TCGA-A6-6648 TCGA-A6-6651 TCGA-AA-3994 TCGA-AA-A010 TCGA-AD-6895 
       46.65        25.18        21.76        27.02        34.98         0.72 
TCGA-AY-6386 TCGA-CK-4952 TCGA-CM-6679 TCGA-G4-6309 
       17.82        15.62        10.06        51.75 

$`BACE2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       24.16        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       19.07         7.96        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
        0.07        21.37         4.21        56.55         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 
       16.31         0.95        15.75         0.20        21.44        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       102.44        40.34        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       74.56        65.85        53.62        44.68        55.04        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  BACE2 MUTATED BACE2 WILD-TYPE 
           0.72            0.00 
  BACE2 MUTATED BACE2 WILD-TYPE 
          51.75          140.38 
  BACE2 MUTATED BACE2 WILD-TYPE 
          23.47           20.12 
[1] "0.7 - 51.8 (23.5)"  "0.0 - 140.4 (20.1)"
[1] "hr="     "2.5e+07"
D860V2, 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       25       108         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BACE2 MUTATED           1          0          5          0        0         1
  BACE2 WILD-TYPE        18         10         36         31       35        12
                 vv
clus              STAGE IVB
  BACE2 MUTATED           0
  BACE2 WILD-TYPE         1
D860V3, multiclass
            clus
vv           BACE2 MUTATED BACE2 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              1             108
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             5              36
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  68 240  39
D860V4, multiclass
    clus
vv   BACE2 MUTATED BACE2 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             8             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
  BACE2 MUTATED     3   6   1
  BACE2 WILD-TYPE 217  74  65
D860V5, multiclass
    clus
vv   BACE2 MUTATED BACE2 WILD-TYPE
  N0             3             217
  N1             6              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"
D860V6, binary
                 cls
clus                0   1
  BACE2 MUTATED     7   1
  BACE2 WILD-TYPE 276  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BACE2 MUTATED      7    1
  BACE2 WILD-TYPE  276   47
   clus
vv  BACE2 MUTATED BACE2 WILD-TYPE
  0             7             276
  1             1              47
[1] 2 2
[1] FALSE
D860V7, 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
D860V8, binary
                 cls
clus                0   1
  BACE2 MUTATED     8   2
  BACE2 WILD-TYPE 309  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BACE2 MUTATED      8    2
  BACE2 WILD-TYPE  309   46
                               clus
vv                              BACE2 MUTATED BACE2 WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  BACE2 MUTATED     6   0   0   1
  BACE2 WILD-TYPE 251   2  22  20
D860V9, multiclass
    clus
vv   BACE2 MUTATED BACE2 WILD-TYPE
  R0             6             251
  R1             0               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"
D860V10, 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
D860V11, 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(861) Variable = DNMT1 MUTATION ANALYSIS
D861V1, survival
                 sevent
clus2               0   1
  DNMT1 MUTATED    14   4
  DNMT1 WILD-TYPE 268  69
  DNMT1 MUTATED DNMT1 WILD-TYPE 
             18             337 
  DNMT1 MUTATED DNMT1 WILD-TYPE 
              4              69 
$`DNMT1 MUTATED`
TCGA-A6-2683 TCGA-AA-3492 TCGA-AA-3555 TCGA-AA-3672 TCGA-AA-3845 TCGA-AA-3877 
       16.57         3.02        29.95         0.92         0.00        31.00 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q 
       34.03         2.01        18.05         4.01        34.98         1.02 
TCGA-AA-A01Z TCGA-AZ-4315 TCGA-CA-6718 TCGA-CK-5913 TCGA-CM-5861 TCGA-D5-6540 
       37.02        58.39         0.10        51.32        15.02        16.14 

$`DNMT1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02        14.93        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       24.00         2.01        20.98        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       19.00        30.02        34.03        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 
       35.01         1.02        33.04        35.01        26.01        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.33         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       40.34        15.62        49.08        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  DNMT1 MUTATED DNMT1 WILD-TYPE 
              0               0 
  DNMT1 MUTATED DNMT1 WILD-TYPE 
          58.39          140.38 
  DNMT1 MUTATED DNMT1 WILD-TYPE 
         16.355          20.980 
[1] "0.0 - 58.4 (16.4)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.4"
D861V2, 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       22       101         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        18         10         40         31       34        13
                 vv
clus              STAGE IVB
  DNMT1 MUTATED           0
  DNMT1 WILD-TYPE         1
D861V3, multiclass
            clus
vv           DNMT1 MUTATED DNMT1 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              8             101
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DNMT1 MUTATED     1   1  12   4
  DNMT1 WILD-TYPE   8  67 236  37
D861V4, multiclass
    clus
vv   DNMT1 MUTATED DNMT1 WILD-TYPE
  T1             1               8
  T2             1              67
  T3            12             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
  DNMT1 MUTATED    16   2   0
  DNMT1 WILD-TYPE 204  78  66
D861V5, multiclass
    clus
vv   DNMT1 MUTATED DNMT1 WILD-TYPE
  N0            16             204
  N1             2              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"
D861V6, binary
                 cls
clus                0   1
  DNMT1 MUTATED    16   1
  DNMT1 WILD-TYPE 267  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNMT1 MUTATED     16    1
  DNMT1 WILD-TYPE  267   47
   clus
vv  DNMT1 MUTATED DNMT1 WILD-TYPE
  0            16             267
  1             1              47
[1] 2 2
[1] FALSE
D861V7, 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
D861V8, binary
                 cls
clus                0   1
  DNMT1 MUTATED    12   6
  DNMT1 WILD-TYPE 305  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNMT1 MUTATED     12    6
  DNMT1 WILD-TYPE  305   42
                               clus
vv                              DNMT1 MUTATED DNMT1 WILD-TYPE
  COLON ADENOCARCINOMA                     12             305
  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 242   2  22  19
D861V9, multiclass
    clus
vv   DNMT1 MUTATED DNMT1 WILD-TYPE
  R0            15             242
  R1             0               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"
D861V10, 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
D861V11, 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(862) Variable = WDR65 MUTATION ANALYSIS
D862V1, survival
                 sevent
clus2               0   1
  WDR65 MUTATED     9   3
  WDR65 WILD-TYPE 273  70
  WDR65 MUTATED WDR65 WILD-TYPE 
             12             343 
  WDR65 MUTATED WDR65 WILD-TYPE 
              3              70 
$`WDR65 MUTATED`
TCGA-A6-5666 TCGA-A6-6780 TCGA-AA-3950 TCGA-AA-A00J TCGA-AA-A010 TCGA-AD-6889 
       32.71        20.12        24.00        18.05        34.98        56.55 
TCGA-CA-6718 TCGA-CK-5916 TCGA-DM-A0XD TCGA-DM-A1D9 TCGA-DM-A28G TCGA-G4-6628 
        0.10        21.14        24.43       140.38        60.79        52.80 

$`WDR65 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        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        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37         4.21         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.33         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       10.26       119.70        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32        12.59         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H 
      139.17         6.12        81.37       119.93        35.97       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 
       46.75 

  WDR65 MUTATED WDR65 WILD-TYPE 
            0.1             0.0 
  WDR65 MUTATED WDR65 WILD-TYPE 
         140.38          139.17 
  WDR65 MUTATED WDR65 WILD-TYPE 
          28.57           19.99 
[1] "0.1 - 140.4 (28.6)" "0.0 - 139.2 (20.0)"
[1] "hr=" "1.2"
D862V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  WDR65 MUTATED         2        0        0         8         1         1
  WDR65 WILD-TYPE      62        1       25       101         7         0
                 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        19         10         40         31       35        13
                 vv
clus              STAGE IVB
  WDR65 MUTATED           0
  WDR65 WILD-TYPE         1
D862V3, multiclass
            clus
vv           WDR65 MUTATED WDR65 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              8             101
  STAGE IIB              1               7
  STAGE IIC              1               0
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  WDR65 MUTATED     1   1   8   3
  WDR65 WILD-TYPE   8  67 240  38
D862V4, multiclass
    clus
vv   WDR65 MUTATED WDR65 WILD-TYPE
  T1             1               8
  T2             1              67
  T3             8             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
  WDR65 MUTATED    12   1   0
  WDR65 WILD-TYPE 208  79  66
D862V5, multiclass
    clus
vv   WDR65 MUTATED WDR65 WILD-TYPE
  N0            12             208
  N1             1              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"
D862V6, binary
                 cls
clus                0   1
  WDR65 MUTATED    12   0
  WDR65 WILD-TYPE 271  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR65 MUTATED     12    0
  WDR65 WILD-TYPE  271   48
   clus
vv  WDR65 MUTATED WDR65 WILD-TYPE
  0            12             271
  1             0              48
[1] 2 2
[1] FALSE
D862V7, binary
                 cls
clus                0   1
  WDR65 MUTATED     5   8
  WDR65 WILD-TYPE 165 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR65 MUTATED      5    8
  WDR65 WILD-TYPE  165  189
        clus
vv       WDR65 MUTATED WDR65 WILD-TYPE
  FEMALE             5             165
  MALE               8             189
[1] 2 2
[1] FALSE
D862V8, binary
                 cls
clus                0   1
  WDR65 MUTATED    10   3
  WDR65 WILD-TYPE 307  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR65 MUTATED     10    3
  WDR65 WILD-TYPE  307   45
                               clus
vv                              WDR65 MUTATED WDR65 WILD-TYPE
  COLON ADENOCARCINOMA                     10             307
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  WDR65 MUTATED     5   0   0   2
  WDR65 WILD-TYPE 252   2  22  19
D862V9, multiclass
    clus
vv   WDR65 MUTATED WDR65 WILD-TYPE
  R0             5             252
  R1             0               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"
D862V10, 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     7
  WDR65 WILD-TYPE                        19   169
D862V11, 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                                        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(863) Variable = ARAP3 MUTATION ANALYSIS
D863V1, survival
                 sevent
clus2               0   1
  ARAP3 MUTATED    14   5
  ARAP3 WILD-TYPE 268  68
  ARAP3 MUTATED ARAP3 WILD-TYPE 
             19             336 
  ARAP3 MUTATED ARAP3 WILD-TYPE 
              5              68 
$`ARAP3 MUTATED`
TCGA-AA-3518 TCGA-AA-3663 TCGA-AA-3715 TCGA-AA-3815 TCGA-AA-3833 TCGA-AA-A00N 
        1.02         6.97        19.04        33.04        15.95         4.01 
TCGA-AA-A01R TCGA-AU-3779 TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-5403 TCGA-AZ-6601 
       35.01        14.50        27.09        58.39        62.79       100.01 
TCGA-CK-5916 TCGA-CM-5860 TCGA-CM-6162 TCGA-F4-6460 TCGA-G4-6586 TCGA-G4-6588 
       21.14        16.01        12.00        13.38        35.80        26.17 
TCGA-G4-6628 
       52.80 

$`ARAP3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       38.99         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 
        0.99        25.02         1.02        17.98        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       27.42        10.88         0.20        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       22.36        61.41        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99         2.93         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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 
       60.79       117.07        98.24         8.61        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 
       36.72        36.00        22.09        13.78        91.79        46.75 

  ARAP3 MUTATED ARAP3 WILD-TYPE 
           1.02            0.00 
  ARAP3 MUTATED ARAP3 WILD-TYPE 
         100.01          140.38 
  ARAP3 MUTATED ARAP3 WILD-TYPE 
         21.140          20.155 
[1] "1.0 - 100.0 (21.1)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D863V2, 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       21       101         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        18         10         39         31       35        13
                 vv
clus              STAGE IVB
  ARAP3 MUTATED           0
  ARAP3 WILD-TYPE         1
D863V3, multiclass
            clus
vv           ARAP3 MUTATED ARAP3 WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               4              21
  STAGE IIA              8             101
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ARAP3 MUTATED     1   3  15   2
  ARAP3 WILD-TYPE   8  65 233  39
D863V4, multiclass
    clus
vv   ARAP3 MUTATED ARAP3 WILD-TYPE
  T1             1               8
  T2             3              65
  T3            15             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
  ARAP3 MUTATED    18   2   1
  ARAP3 WILD-TYPE 202  78  65
D863V5, multiclass
    clus
vv   ARAP3 MUTATED ARAP3 WILD-TYPE
  N0            18             202
  N1             2              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"
D863V6, binary
                 cls
clus                0   1
  ARAP3 MUTATED    18   0
  ARAP3 WILD-TYPE 265  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARAP3 MUTATED     18    0
  ARAP3 WILD-TYPE  265   48
   clus
vv  ARAP3 MUTATED ARAP3 WILD-TYPE
  0            18             265
  1             0              48
[1] 2 2
[1] FALSE
D863V7, 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
D863V8, binary
                 cls
clus                0   1
  ARAP3 MUTATED    18   3
  ARAP3 WILD-TYPE 299  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARAP3 MUTATED     18    3
  ARAP3 WILD-TYPE  299   45
                               clus
vv                              ARAP3 MUTATED ARAP3 WILD-TYPE
  COLON ADENOCARCINOMA                     18             299
  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 241   2  22  18
D863V9, multiclass
    clus
vv   ARAP3 MUTATED ARAP3 WILD-TYPE
  R0            16             241
  R1             0               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"
D863V10, 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
D863V11, 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(864) Variable = ZFYVE16 MUTATION ANALYSIS
D864V1, survival
                   sevent
clus2                 0   1
  ZFYVE16 MUTATED    14   1
  ZFYVE16 WILD-TYPE 268  72
  ZFYVE16 MUTATED ZFYVE16 WILD-TYPE 
               15               340 
  ZFYVE16 MUTATED ZFYVE16 WILD-TYPE 
                1                72 
$`ZFYVE16 MUTATED`
TCGA-A6-5661 TCGA-A6-5665 TCGA-AA-3667 TCGA-AA-3977 TCGA-AA-A00E TCGA-AA-A00N 
       33.53        22.06        14.01        25.02        30.02         4.01 
TCGA-AA-A010 TCGA-AD-5900 TCGA-AD-6895 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CM-5861 
       34.98         0.07         0.72        58.39         0.33        15.02 
TCGA-CM-6165 TCGA-D5-6540 TCGA-D5-6928 
       16.04        16.14        11.64 

$`ZFYVE16 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F 
        7.96        27.02        13.94        38.04        19.00        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  ZFYVE16 MUTATED ZFYVE16 WILD-TYPE 
             0.07              0.00 
  ZFYVE16 MUTATED ZFYVE16 WILD-TYPE 
            58.39            140.38 
  ZFYVE16 MUTATED ZFYVE16 WILD-TYPE 
            16.04             20.63 
[1] "0.1 - 58.4 (16.0)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "2.3"
D864V2, 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       25       100         5         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZFYVE16 MUTATED           0          0          0          0        0
  ZFYVE16 WILD-TYPE        19         10         41         31       35
                   vv
clus                STAGE IVA STAGE IVB
  ZFYVE16 MUTATED           0         0
  ZFYVE16 WILD-TYPE        13         1
D864V3, multiclass
            clus
vv           ZFYVE16 MUTATED ZFYVE16 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                9               100
  STAGE IIB                3                 5
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ZFYVE16 MUTATED     0   4  10   3
  ZFYVE16 WILD-TYPE   9  64 238  38
D864V4, multiclass
    clus
vv   ZFYVE16 MUTATED ZFYVE16 WILD-TYPE
  T1               0                 9
  T2               4                64
  T3              10               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
  ZFYVE16 MUTATED    16   1   0
  ZFYVE16 WILD-TYPE 204  79  66
D864V5, multiclass
    clus
vv   ZFYVE16 MUTATED ZFYVE16 WILD-TYPE
  N0              16               204
  N1               1                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"
D864V6, binary
                   cls
clus                  0   1
  ZFYVE16 MUTATED    13   0
  ZFYVE16 WILD-TYPE 270  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFYVE16 MUTATED     13    0
  ZFYVE16 WILD-TYPE  270   48
   clus
vv  ZFYVE16 MUTATED ZFYVE16 WILD-TYPE
  0              13               270
  1               0                48
[1] 2 2
[1] FALSE
D864V7, 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
D864V8, binary
                   cls
clus                  0   1
  ZFYVE16 MUTATED    12   5
  ZFYVE16 WILD-TYPE 305  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFYVE16 MUTATED     12    5
  ZFYVE16 WILD-TYPE  305   43
                               clus
vv                              ZFYVE16 MUTATED ZFYVE16 WILD-TYPE
  COLON ADENOCARCINOMA                       12               305
  COLON MUCINOUS ADENOCARCINOMA               5                43
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ZFYVE16 MUTATED    13   0   0   2
  ZFYVE16 WILD-TYPE 244   2  22  19
D864V9, multiclass
    clus
vv   ZFYVE16 MUTATED ZFYVE16 WILD-TYPE
  R0              13               244
  R1               0                 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"
D864V10, 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
D864V11, 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(865) Variable = LGALS9C MUTATION ANALYSIS
D865V1, survival
                   sevent
clus2                 0   1
  LGALS9C MUTATED     4   1
  LGALS9C WILD-TYPE 278  72
  LGALS9C MUTATED LGALS9C WILD-TYPE 
                5               350 
  LGALS9C MUTATED LGALS9C WILD-TYPE 
                1                72 
$`LGALS9C MUTATED`
TCGA-AA-3511 TCGA-AZ-6599 TCGA-CM-6164 TCGA-CM-6674 TCGA-G4-6586 
        6.97         6.77        29.03        12.95        35.80 

$`LGALS9C WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01        63.98         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  LGALS9C MUTATED LGALS9C WILD-TYPE 
             6.77              0.00 
  LGALS9C MUTATED LGALS9C WILD-TYPE 
            35.80            140.38 
  LGALS9C MUTATED LGALS9C WILD-TYPE 
           12.950            20.235 
[1] "6.8 - 35.8 (12.9)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.4"
D865V2, 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       24       106         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LGALS9C MUTATED           0          0          0          0        0
  LGALS9C WILD-TYPE        19         10         41         31       35
                   vv
clus                STAGE IVA STAGE IVB
  LGALS9C MUTATED           0         0
  LGALS9C WILD-TYPE        13         1
D865V3, multiclass
            clus
vv           LGALS9C MUTATED LGALS9C WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                3               106
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  LGALS9C MUTATED     0   1   3   1
  LGALS9C WILD-TYPE   9  67 245  40
D865V4, multiclass
    clus
vv   LGALS9C MUTATED LGALS9C WILD-TYPE
  T1               0                 9
  T2               1                67
  T3               3               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
  LGALS9C MUTATED     5   0   0
  LGALS9C WILD-TYPE 215  80  66
D865V5, multiclass
    clus
vv   LGALS9C MUTATED LGALS9C WILD-TYPE
  N0               5               215
  N1               0                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"
D865V6, binary
                   cls
clus                  0   1
  LGALS9C MUTATED     4   0
  LGALS9C WILD-TYPE 279  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  LGALS9C MUTATED      4    0
  LGALS9C WILD-TYPE  279   48
   clus
vv  LGALS9C MUTATED LGALS9C WILD-TYPE
  0               4               279
  1               0                48
[1] 2 2
[1] FALSE
D865V7, 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
D865V8, binary
                   cls
clus                  0   1
  LGALS9C MUTATED     5   0
  LGALS9C WILD-TYPE 312  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  LGALS9C MUTATED      5    0
  LGALS9C WILD-TYPE  312   48
                               clus
vv                              LGALS9C MUTATED LGALS9C WILD-TYPE
  COLON ADENOCARCINOMA                        5               312
  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 253   2  22  21
D865V9, multiclass
    clus
vv   LGALS9C MUTATED LGALS9C WILD-TYPE
  R0               4               253
  R1               0                 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"
D865V10, 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
D865V11, 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(866) Variable = DGKH MUTATION ANALYSIS
D866V1, survival
                sevent
clus2              0   1
  DGKH MUTATED    13   3
  DGKH WILD-TYPE 269  70
  DGKH MUTATED DGKH WILD-TYPE 
            16            339 
  DGKH MUTATED DGKH WILD-TYPE 
             3             70 
$`DGKH MUTATED`
TCGA-AA-3511 TCGA-AA-3544 TCGA-AA-3554 TCGA-AA-3815 TCGA-AA-3977 TCGA-AA-A01P 
        6.97        14.01        17.95        33.04        25.02        38.07 
TCGA-AD-6895 TCGA-AZ-6600 TCGA-AZ-6608 TCGA-CA-6717 TCGA-CK-6751 TCGA-CM-5864 
        0.72        12.10         1.94         0.33       124.27        15.02 
TCGA-D5-6536 TCGA-DM-A1D0 TCGA-F4-6807 TCGA-G4-6304 
       17.85       130.65        16.24        53.62 

$`DGKH WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01        63.98         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       26.01        12.99         0.99        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        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        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21        56.55         0.79         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 
       11.38        10.26       119.70        24.43        38.20        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  DGKH MUTATED DGKH WILD-TYPE 
          0.33           0.00 
  DGKH MUTATED DGKH WILD-TYPE 
        130.65         140.38 
  DGKH MUTATED DGKH WILD-TYPE 
        17.045         20.980 
[1] "0.3 - 130.7 (17.0)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.3"
D866V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DGKH MUTATED         3        0        1         5         1         0
  DGKH WILD-TYPE      61        1       24       104         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DGKH MUTATED           1          1          0          1        1         0
  DGKH WILD-TYPE        18          9         41         30       34        13
                vv
clus             STAGE IVB
  DGKH MUTATED           0
  DGKH WILD-TYPE         1
D866V3, multiclass
            clus
vv           DGKH MUTATED DGKH WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             5            104
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            1              9
  STAGE IIIB            0             41
  STAGE IIIC            1             30
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  DGKH MUTATED     0   5   8   3
  DGKH WILD-TYPE   9  63 240  38
D866V4, multiclass
    clus
vv   DGKH MUTATED DGKH WILD-TYPE
  T1            0              9
  T2            5             63
  T3            8            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
  DGKH MUTATED    11   4   1
  DGKH WILD-TYPE 209  76  65
D866V5, multiclass
    clus
vv   DGKH MUTATED DGKH WILD-TYPE
  N0           11            209
  N1            4             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"
D866V6, binary
                cls
clus               0   1
  DGKH MUTATED    12   1
  DGKH WILD-TYPE 271  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  DGKH MUTATED     12    1
  DGKH WILD-TYPE  271   47
   clus
vv  DGKH MUTATED DGKH WILD-TYPE
  0           12            271
  1            1             47
[1] 2 2
[1] FALSE
D866V7, binary
                cls
clus               0   1
  DGKH MUTATED     8   8
  DGKH WILD-TYPE 162 189
[1] "tbl2"
                cls
clus             [,1] [,2]
  DGKH MUTATED      8    8
  DGKH WILD-TYPE  162  189
        clus
vv       DGKH MUTATED DGKH WILD-TYPE
  FEMALE            8            162
  MALE              8            189
[1] 2 2
[1] FALSE
D866V8, binary
                cls
clus               0   1
  DGKH MUTATED    14   2
  DGKH WILD-TYPE 303  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  DGKH MUTATED     14    2
  DGKH WILD-TYPE  303   46
                               clus
vv                              DGKH MUTATED DGKH WILD-TYPE
  COLON ADENOCARCINOMA                    14            303
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  DGKH MUTATED     9   0   0   2
  DGKH WILD-TYPE 248   2  22  19
D866V9, multiclass
    clus
vv   DGKH MUTATED DGKH WILD-TYPE
  R0            9            248
  R1            0              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"
D866V10, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DGKH MUTATED                                  0     1
  DGKH WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  DGKH MUTATED                           1     8
  DGKH WILD-TYPE                        18   168
D866V11, multiclass
                                  clus
vv                                 DGKH MUTATED DGKH 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(867) Variable = RTN4 MUTATION ANALYSIS
D867V1, survival
                sevent
clus2              0   1
  RTN4 MUTATED    17   2
  RTN4 WILD-TYPE 265  71
  RTN4 MUTATED RTN4 WILD-TYPE 
            19            336 
  RTN4 MUTATED RTN4 WILD-TYPE 
             2             71 
$`RTN4 MUTATED`
TCGA-A6-3809 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3555 
       32.75         3.02        63.98         1.02         1.02        29.95 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-A00R TCGA-AA-A010 TCGA-AD-5900 TCGA-AZ-4315 
       19.04        19.04         0.99        34.98         0.07        58.39 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4950 TCGA-CM-6171 TCGA-D5-6540 
        0.26         0.33         0.10        40.34        14.04        16.14 
TCGA-G4-6628 
       52.80 

$`RTN4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
        6.97        13.02        38.99         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 
       33.99        21.01        13.02        24.00        17.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3811 
       19.00        36.00         5.03        85.05        26.99        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
        4.01        27.02        42.02        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.25         3.29         0.07         1.35        17.56       102.44 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 

  RTN4 MUTATED RTN4 WILD-TYPE 
          0.07           0.00 
  RTN4 MUTATED RTN4 WILD-TYPE 
         63.98         140.38 
  RTN4 MUTATED RTN4 WILD-TYPE 
         16.14          20.98 
[1] "0.1 - 64.0 (16.1)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.6"
D867V2, 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       22       103         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RTN4 MUTATED           0          1          0          0        1         0
  RTN4 WILD-TYPE        19          9         41         31       34        13
                vv
clus             STAGE IVB
  RTN4 MUTATED           0
  RTN4 WILD-TYPE         1
D867V3, multiclass
            clus
vv           RTN4 MUTATED RTN4 WILD-TYPE
  STAGE I               6             58
  STAGE IA              0              1
  STAGE II              3             22
  STAGE IIA             6            103
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            1              9
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RTN4 MUTATED     0   6  11   2
  RTN4 WILD-TYPE   9  62 237  39
D867V4, multiclass
    clus
vv   RTN4 MUTATED RTN4 WILD-TYPE
  T1            0              9
  T2            6             62
  T3           11            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
  RTN4 MUTATED    18   1   0
  RTN4 WILD-TYPE 202  79  66
D867V5, multiclass
    clus
vv   RTN4 MUTATED RTN4 WILD-TYPE
  N0           18            202
  N1            1             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"
D867V6, binary
                cls
clus               0   1
  RTN4 MUTATED    17   1
  RTN4 WILD-TYPE 266  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  RTN4 MUTATED     17    1
  RTN4 WILD-TYPE  266   47
   clus
vv  RTN4 MUTATED RTN4 WILD-TYPE
  0           17            266
  1            1             47
[1] 2 2
[1] FALSE
D867V7, 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
D867V8, binary
                cls
clus               0   1
  RTN4 MUTATED    14   5
  RTN4 WILD-TYPE 303  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  RTN4 MUTATED     14    5
  RTN4 WILD-TYPE  303   43
                               clus
vv                              RTN4 MUTATED RTN4 WILD-TYPE
  COLON ADENOCARCINOMA                    14            303
  COLON MUCINOUS ADENOCARCINOMA            5             43
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RTN4 MUTATED    14   1   1   3
  RTN4 WILD-TYPE 243   1  21  18
D867V9, multiclass
    clus
vv   RTN4 MUTATED RTN4 WILD-TYPE
  R0           14            243
  R1            1              1
  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"
D867V10, 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
D867V11, 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(868) Variable = TRMT5 MUTATION ANALYSIS
D868V1, survival
                 sevent
clus2               0   1
  TRMT5 MUTATED     6   2
  TRMT5 WILD-TYPE 276  71
  TRMT5 MUTATED TRMT5 WILD-TYPE 
              8             347 
  TRMT5 MUTATED TRMT5 WILD-TYPE 
              2              71 
$`TRMT5 MUTATED`
TCGA-AA-3663 TCGA-AA-3697 TCGA-AA-A00N TCGA-AZ-6600 TCGA-CM-5861 TCGA-CM-6161 
        6.97        85.05         4.01        12.10        15.02        15.02 
TCGA-D5-6536 TCGA-D5-6927 
       17.85         9.44 

$`TRMT5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  TRMT5 MUTATED TRMT5 WILD-TYPE 
           4.01            0.00 
  TRMT5 MUTATED TRMT5 WILD-TYPE 
          85.05          140.38 
  TRMT5 MUTATED TRMT5 WILD-TYPE 
          13.56           20.98 
[1] "4.0 - 85.0 (13.6)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.4"
D868V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TRMT5 MUTATED         1        0        1         3         1         0
  TRMT5 WILD-TYPE      63        1       24       106         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TRMT5 MUTATED           1          0          0          0        1         0
  TRMT5 WILD-TYPE        18         10         41         31       34        13
                 vv
clus              STAGE IVB
  TRMT5 MUTATED           0
  TRMT5 WILD-TYPE         1
D868V3, multiclass
            clus
vv           TRMT5 MUTATED TRMT5 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              3             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TRMT5 MUTATED     0   1   5   2
  TRMT5 WILD-TYPE   9  67 243  39
D868V4, multiclass
    clus
vv   TRMT5 MUTATED TRMT5 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             5             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
  TRMT5 MUTATED     7   1   0
  TRMT5 WILD-TYPE 213  79  66
D868V5, multiclass
    clus
vv   TRMT5 MUTATED TRMT5 WILD-TYPE
  N0             7             213
  N1             1              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"
D868V6, binary
                 cls
clus                0   1
  TRMT5 MUTATED     7   1
  TRMT5 WILD-TYPE 276  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRMT5 MUTATED      7    1
  TRMT5 WILD-TYPE  276   47
   clus
vv  TRMT5 MUTATED TRMT5 WILD-TYPE
  0             7             276
  1             1              47
[1] 2 2
[1] FALSE
D868V7, binary
                 cls
clus                0   1
  TRMT5 MUTATED     2   6
  TRMT5 WILD-TYPE 168 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRMT5 MUTATED      2    6
  TRMT5 WILD-TYPE  168  191
        clus
vv       TRMT5 MUTATED TRMT5 WILD-TYPE
  FEMALE             2             168
  MALE               6             191
[1] 2 2
[1] FALSE
D868V8, binary
                 cls
clus                0   1
  TRMT5 MUTATED     7   1
  TRMT5 WILD-TYPE 310  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRMT5 MUTATED      7    1
  TRMT5 WILD-TYPE  310   47
                               clus
vv                              TRMT5 MUTATED TRMT5 WILD-TYPE
  COLON ADENOCARCINOMA                      7             310
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TRMT5 MUTATED     7   0   0   0
  TRMT5 WILD-TYPE 250   2  22  21
D868V9, multiclass
    clus
vv   TRMT5 MUTATED TRMT5 WILD-TYPE
  R0             7             250
  R1             0               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"
D868V10, 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     4
  TRMT5 WILD-TYPE                        18   172
D868V11, 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                                        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(869) Variable = RYR2 MUTATION ANALYSIS
D869V1, survival
                sevent
clus2              0   1
  RYR2 MUTATED    60  21
  RYR2 WILD-TYPE 222  52
  RYR2 MUTATED RYR2 WILD-TYPE 
            81            274 
  RYR2 MUTATED RYR2 WILD-TYPE 
            21             52 
$`RYR2 MUTATED`
TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6653 TCGA-A6-6780 
       34.65        32.75        33.53        22.06        24.39        20.12 
TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3672 
        3.02        63.98         6.05         6.97         2.01         0.92 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3815 TCGA-AA-3864 
        5.03        26.99        19.04        19.04        33.04        53.00 
TCGA-AA-3870 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3977 
       29.98        26.01        24.00         2.01        21.99        25.02 
TCGA-AA-3982 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01K TCGA-AA-A01R TCGA-AA-A01Z 
       27.02         4.01        34.98        31.00        35.01        37.02 
TCGA-AA-A029 TCGA-AA-A02Y TCGA-AD-5900 TCGA-AD-6901 TCGA-AU-6004 TCGA-AY-4070 
       51.98        39.98         0.07        22.42        27.09        16.31 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 
       17.82        58.39        22.36        62.79        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6608 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4950 TCGA-CK-5916 
       12.10         1.94         0.33         0.10        40.34        21.14 
TCGA-CM-4746 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-6161 TCGA-CM-6171 TCGA-CM-6172 
       37.02        16.01        15.02        15.02        14.04        11.01 
TCGA-CM-6676 TCGA-D5-6534 TCGA-D5-6540 TCGA-D5-6924 TCGA-D5-6928 TCGA-D5-6930 
       11.08        43.27        16.14        14.30        11.64         1.51 
TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A282 TCGA-DM-A285 
       11.38        24.43        13.32        12.59       139.17         6.12 
TCGA-DM-A28F TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6805 TCGA-F4-6808 TCGA-G4-6293 
       35.97        13.38         6.18        16.31        33.67       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6317 
       74.56        65.85        53.62        44.68        55.04        36.00 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6628 
       22.09        26.17        52.80 

$`RYR2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       16.57        33.34        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 
       30.44        29.19        23.61        22.09        32.71        27.09 
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 
       22.52         8.38        25.08        25.18        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       24.69        23.87        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3667 
       13.94        19.99        61.02        78.08        54.02        14.01 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       19.00        36.00        85.05        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        17.03        24.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3952 TCGA-AA-3955 
        2.01        12.99        24.00        33.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       34.03        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       24.00        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07         1.02         1.02        33.04        35.01        26.01 
TCGA-AA-A024 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       39.06        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       41.00        18.05        40.96        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         0.72         5.79        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4323 
       14.50         0.95        15.75         0.20        21.44         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-5407 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
        5.13        83.80        61.41       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 
        0.07         0.26         1.35        17.56       102.44        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32        21.99         2.93         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-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       22.98        30.08         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-6674 TCGA-CM-6675 TCGA-CM-6677 
       12.99        13.02        15.02        12.95        13.05        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 
       13.51        11.51        20.19        18.25         1.32        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-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
       12.39        10.13        12.43         9.04         9.44        13.41 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       12.00        10.26       119.70        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       49.91       140.38         7.50        44.32       131.51       135.65 
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-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 
       13.45        35.87         1.55        29.59        16.24        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
        0.53        35.41        19.43        51.75        45.11        36.72 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       13.78        35.80        91.79        46.75 

  RYR2 MUTATED RYR2 WILD-TYPE 
          0.07           0.00 
  RYR2 MUTATED RYR2 WILD-TYPE 
        139.17         140.38 
  RYR2 MUTATED RYR2 WILD-TYPE 
        22.360         19.625 
[1] "0.1 - 139.2 (22.4)" "0.0 - 140.4 (19.6)"
[1] "hr=" "1.3"
D869V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RYR2 MUTATED        15        0       10        25         4         0
  RYR2 WILD-TYPE      49        1       15        84         4         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RYR2 MUTATED           5          2          7          5        7         1
  RYR2 WILD-TYPE        14          8         34         26       28        12
                vv
clus             STAGE IVB
  RYR2 MUTATED           0
  RYR2 WILD-TYPE         1
D869V3, multiclass
            clus
vv           RYR2 MUTATED RYR2 WILD-TYPE
  STAGE I              15             49
  STAGE IA              0              1
  STAGE II             10             15
  STAGE IIA            25             84
  STAGE IIB             4              4
  STAGE IIC             0              1
  STAGE III             5             14
  STAGE IIIA            2              8
  STAGE IIIB            7             34
  STAGE IIIC            5             26
  STAGE IV              7             28
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  51 190  34
D869V4, multiclass
    clus
vv   RYR2 MUTATED RYR2 WILD-TYPE
  T1            2              7
  T2           17             51
  T3           58            190
  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  63  57
D869V5, multiclass
    clus
vv   RYR2 MUTATED RYR2 WILD-TYPE
  N0           58            162
  N1           17             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"
D869V6, binary
                cls
clus               0   1
  RYR2 MUTATED    65   8
  RYR2 WILD-TYPE 218  40
[1] "tbl2"
                cls
clus             [,1] [,2]
  RYR2 MUTATED     65    8
  RYR2 WILD-TYPE  218   40
   clus
vv  RYR2 MUTATED RYR2 WILD-TYPE
  0           65            218
  1            8             40
[1] 2 2
[1] FALSE
D869V7, 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
D869V8, binary
                cls
clus               0   1
  RYR2 MUTATED    70  14
  RYR2 WILD-TYPE 247  34
[1] "tbl2"
                cls
clus             [,1] [,2]
  RYR2 MUTATED     70   14
  RYR2 WILD-TYPE  247   34
                               clus
vv                              RYR2 MUTATED RYR2 WILD-TYPE
  COLON ADENOCARCINOMA                    70            247
  COLON MUCINOUS ADENOCARCINOMA           14             34
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RYR2 MUTATED    58   2   3   4
  RYR2 WILD-TYPE 199   0  19  17
D869V9, multiclass
    clus
vv   RYR2 MUTATED RYR2 WILD-TYPE
  R0           58            199
  R1            2              0
  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"
D869V10, 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
D869V11, 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(870) Variable = INADL MUTATION ANALYSIS
D870V1, survival
                 sevent
clus2               0   1
  INADL MUTATED    10   3
  INADL WILD-TYPE 272  70
  INADL MUTATED INADL WILD-TYPE 
             13             342 
  INADL MUTATED INADL WILD-TYPE 
              3              70 
$`INADL MUTATED`
TCGA-AA-3663 TCGA-AA-3845 TCGA-AA-3977 TCGA-AA-A01R TCGA-AY-6196 TCGA-AZ-4315 
        6.97         0.00        25.02        35.01         0.20        58.39 
TCGA-AZ-6601 TCGA-CA-6717 TCGA-CM-5861 TCGA-DM-A1D8 TCGA-G4-6321 TCGA-G4-6323 
      100.01         0.33        15.02        12.59        22.09        13.78 
TCGA-G4-6586 
       35.80 

$`INADL WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
       17.98        15.95        38.99        37.02        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        15.75        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       36.72        36.00        26.17        91.79        46.75        52.80 

  INADL MUTATED INADL WILD-TYPE 
              0               0 
  INADL MUTATED INADL WILD-TYPE 
         100.01          140.38 
  INADL MUTATED INADL WILD-TYPE 
         15.020          20.235 
[1] "0.0 - 100.0 (15.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D870V2, 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       23       104         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        17         10         41         30       35        13
                 vv
clus              STAGE IVB
  INADL MUTATED           0
  INADL WILD-TYPE         1
D870V3, multiclass
            clus
vv           INADL MUTATED INADL WILD-TYPE
  STAGE I                0              64
  STAGE IA               1               0
  STAGE II               2              23
  STAGE IIA              5             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  INADL MUTATED     0   2  10   0
  INADL WILD-TYPE   9  66 238  41
D870V4, multiclass
    clus
vv   INADL MUTATED INADL WILD-TYPE
  T1             0               9
  T2             2              66
  T3            10             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
  INADL MUTATED     9   2   2
  INADL WILD-TYPE 211  78  64
D870V5, multiclass
    clus
vv   INADL MUTATED INADL WILD-TYPE
  N0             9             211
  N1             2              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"
D870V6, binary
                 cls
clus                0   1
  INADL MUTATED     8   0
  INADL WILD-TYPE 275  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INADL MUTATED      8    0
  INADL WILD-TYPE  275   48
   clus
vv  INADL MUTATED INADL WILD-TYPE
  0             8             275
  1             0              48
[1] 2 2
[1] FALSE
D870V7, 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
D870V8, binary
                 cls
clus                0   1
  INADL MUTATED    10   3
  INADL WILD-TYPE 307  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INADL MUTATED     10    3
  INADL WILD-TYPE  307   45
                               clus
vv                              INADL MUTATED INADL WILD-TYPE
  COLON ADENOCARCINOMA                     10             307
  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 248   2  22  20
D870V9, multiclass
    clus
vv   INADL MUTATED INADL WILD-TYPE
  R0             9             248
  R1             0               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"
D870V10, 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
D870V11, 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(871) Variable = JMJD6 MUTATION ANALYSIS
D871V1, survival
                 sevent
clus2               0   1
  JMJD6 MUTATED     8   0
  JMJD6 WILD-TYPE 274  73
  JMJD6 MUTATED JMJD6 WILD-TYPE 
              8             347 
  JMJD6 MUTATED JMJD6 WILD-TYPE 
              0              73 
$`JMJD6 MUTATED`
TCGA-A6-6142 TCGA-AA-3663 TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-5900 TCGA-CM-5348 
       25.08         6.97        34.98        35.01         0.07        22.98 
TCGA-D5-6540 TCGA-G4-6293 
       16.14       107.67 

$`JMJD6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       19.43        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  JMJD6 MUTATED JMJD6 WILD-TYPE 
           0.07            0.00 
  JMJD6 MUTATED JMJD6 WILD-TYPE 
         107.67          140.38 
  JMJD6 MUTATED JMJD6 WILD-TYPE 
          24.03           20.12 
[1] "0.1 - 107.7 (24.0)" "0.0 - 140.4 (20.1)"
[1] "hr="     "9300000"
D871V2, 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       24       109         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        17         10         40         31       35        12
                 vv
clus              STAGE IVB
  JMJD6 MUTATED           0
  JMJD6 WILD-TYPE         1
D871V3, multiclass
            clus
vv           JMJD6 MUTATED JMJD6 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              0             109
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 243  40
D871V4, multiclass
    clus
vv   JMJD6 MUTATED JMJD6 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             5             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
  JMJD6 MUTATED     4   3   1
  JMJD6 WILD-TYPE 216  77  65
D871V5, multiclass
    clus
vv   JMJD6 MUTATED JMJD6 WILD-TYPE
  N0             4             216
  N1             3              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"
D871V6, binary
                 cls
clus                0   1
  JMJD6 MUTATED     6   1
  JMJD6 WILD-TYPE 277  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  JMJD6 MUTATED      6    1
  JMJD6 WILD-TYPE  277   47
   clus
vv  JMJD6 MUTATED JMJD6 WILD-TYPE
  0             6             277
  1             1              47
[1] 2 2
[1] FALSE
D871V7, 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
D871V8, binary
                 cls
clus                0   1
  JMJD6 MUTATED     5   3
  JMJD6 WILD-TYPE 312  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  JMJD6 MUTATED      5    3
  JMJD6 WILD-TYPE  312   45
                               clus
vv                              JMJD6 MUTATED JMJD6 WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  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 250   2  22  21
D871V9, multiclass
    clus
vv   JMJD6 MUTATED JMJD6 WILD-TYPE
  R0             7             250
  R1             0               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"
D871V10, 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
D871V11, 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(872) Variable = MAOA MUTATION ANALYSIS
D872V1, survival
                sevent
clus2              0   1
  MAOA MUTATED     4   1
  MAOA WILD-TYPE 278  72
  MAOA MUTATED MAOA WILD-TYPE 
             5            350 
  MAOA MUTATED MAOA WILD-TYPE 
             1             72 
$`MAOA MUTATED`
TCGA-AA-3525 TCGA-AA-A00R TCGA-AZ-6601 TCGA-D5-6922 TCGA-G4-6317 
        8.05         0.99       100.01        10.13        36.00 

$`MAOA WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W 
       38.04         4.01        27.02        42.02        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.72        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  MAOA MUTATED MAOA WILD-TYPE 
          0.99           0.00 
  MAOA MUTATED MAOA WILD-TYPE 
        100.01         140.38 
  MAOA MUTATED MAOA WILD-TYPE 
        10.130         20.235 
[1] "1.0 - 100.0 (10.1)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.3"
D872V2, 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       24       109         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        19          9         40         30       35        13
                vv
clus             STAGE IVB
  MAOA MUTATED           0
  MAOA WILD-TYPE         1
D872V3, multiclass
            clus
vv           MAOA MUTATED MAOA WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             0            109
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            1              9
  STAGE IIIB            1             40
  STAGE IIIC            1             30
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MAOA MUTATED     0   1   4   0
  MAOA WILD-TYPE   9  67 244  41
D872V4, multiclass
    clus
vv   MAOA MUTATED MAOA WILD-TYPE
  T1            0              9
  T2            1             67
  T3            4            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
  MAOA MUTATED     2   2   1
  MAOA WILD-TYPE 218  78  65
D872V5, multiclass
    clus
vv   MAOA MUTATED MAOA WILD-TYPE
  N0            2            218
  N1            2             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"
D872V6, binary
                cls
clus               0   1
  MAOA MUTATED     4   0
  MAOA WILD-TYPE 279  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAOA MUTATED      4    0
  MAOA WILD-TYPE  279   48
   clus
vv  MAOA MUTATED MAOA WILD-TYPE
  0            4            279
  1            0             48
[1] 2 2
[1] FALSE
D872V7, 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
D872V8, binary
                cls
clus               0   1
  MAOA MUTATED     5   0
  MAOA WILD-TYPE 312  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAOA MUTATED      5    0
  MAOA WILD-TYPE  312   48
                               clus
vv                              MAOA MUTATED MAOA WILD-TYPE
  COLON ADENOCARCINOMA                     5            312
  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 253   2  22  21
D872V9, multiclass
    clus
vv   MAOA MUTATED MAOA WILD-TYPE
  R0            4            253
  R1            0              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"
D872V10, 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
D872V11, 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(873) Variable = ZNF555 MUTATION ANALYSIS
D873V1, survival
                  sevent
clus2                0   1
  ZNF555 MUTATED     7   1
  ZNF555 WILD-TYPE 275  72
  ZNF555 MUTATED ZNF555 WILD-TYPE 
               8              347 
  ZNF555 MUTATED ZNF555 WILD-TYPE 
               1               72 
$`ZNF555 MUTATED`
TCGA-AA-3510 TCGA-AA-3518 TCGA-AA-3555 TCGA-AA-3715 TCGA-AA-3833 TCGA-CK-6747 
       63.98         1.02        29.95        19.04        15.95         2.93 
TCGA-D5-5539 TCGA-G4-6293 
       19.59       107.67 

$`ZNF555 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 
        0.99        25.02         1.02        17.98        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 
       49.08        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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       19.43        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  ZNF555 MUTATED ZNF555 WILD-TYPE 
            1.02             0.00 
  ZNF555 MUTATED ZNF555 WILD-TYPE 
          107.67           140.38 
  ZNF555 MUTATED ZNF555 WILD-TYPE 
          19.315           20.280 
[1] "1.0 - 107.7 (19.3)" "0.0 - 140.4 (20.3)"
[1] "hr=" "2.1"
D873V2, 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       23       105         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF555 MUTATED           1          1          0          0        0
  ZNF555 WILD-TYPE        18          9         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF555 MUTATED           0         0
  ZNF555 WILD-TYPE        13         1
D873V3, multiclass
            clus
vv           ZNF555 MUTATED ZNF555 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               4              105
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              1                9
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF555 MUTATED     0   0   8   0
  ZNF555 WILD-TYPE   9  68 240  41
D873V4, multiclass
    clus
vv   ZNF555 MUTATED ZNF555 WILD-TYPE
  T1              0                9
  T2              0               68
  T3              8              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
  ZNF555 MUTATED     6   2   0
  ZNF555 WILD-TYPE 214  78  66
D873V5, multiclass
    clus
vv   ZNF555 MUTATED ZNF555 WILD-TYPE
  N0              6              214
  N1              2               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"
D873V6, binary
                  cls
clus                 0   1
  ZNF555 MUTATED     7   0
  ZNF555 WILD-TYPE 276  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF555 MUTATED      7    0
  ZNF555 WILD-TYPE  276   48
   clus
vv  ZNF555 MUTATED ZNF555 WILD-TYPE
  0              7              276
  1              0               48
[1] 2 2
[1] FALSE
D873V7, 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
D873V8, binary
                  cls
clus                 0   1
  ZNF555 MUTATED     6   2
  ZNF555 WILD-TYPE 311  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF555 MUTATED      6    2
  ZNF555 WILD-TYPE  311   46
                               clus
vv                              ZNF555 MUTATED ZNF555 WILD-TYPE
  COLON ADENOCARCINOMA                       6              311
  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 250   2  22  20
D873V9, multiclass
    clus
vv   ZNF555 MUTATED ZNF555 WILD-TYPE
  R0              7              250
  R1              0                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"
D873V10, 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
D873V11, 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(874) Variable = SAMD9L MUTATION ANALYSIS
D874V1, survival
                  sevent
clus2                0   1
  SAMD9L MUTATED    14   6
  SAMD9L WILD-TYPE 268  67
  SAMD9L MUTATED SAMD9L WILD-TYPE 
              20              335 
  SAMD9L MUTATED SAMD9L WILD-TYPE 
               6               67 
$`SAMD9L MUTATED`
TCGA-A6-3809 TCGA-AA-3496 TCGA-AA-3696 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3977 
       32.75         1.02         5.03        19.04        10.06        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6895 TCGA-AZ-4315 TCGA-AZ-4681 TCGA-AZ-6598 
        4.01        34.98         0.72        58.39        83.80        49.41 
TCGA-CA-6717 TCGA-CM-6170 TCGA-CM-6676 TCGA-DM-A0XD TCGA-DM-A282 TCGA-G4-6309 
        0.33        15.02        11.08        24.43       139.17        51.75 
TCGA-G4-6586 TCGA-G4-6588 
       35.80        26.17 

$`SAMD9L WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       85.05        26.99        19.04        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-6601 TCGA-AZ-6603 
       62.79        61.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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-6677 TCGA-CM-6678 TCGA-CM-6679 
       11.01        12.95        13.05        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        91.79        46.75        52.80 

  SAMD9L MUTATED SAMD9L WILD-TYPE 
            0.33             0.00 
  SAMD9L MUTATED SAMD9L WILD-TYPE 
          139.17           140.38 
  SAMD9L MUTATED SAMD9L WILD-TYPE 
          24.725           20.120 
[1] "0.3 - 139.2 (24.7)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.3"
D874V2, 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       22       101         5         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SAMD9L MUTATED           2          0          1          0        1
  SAMD9L WILD-TYPE        17         10         40         31       34
                  vv
clus               STAGE IVA STAGE IVB
  SAMD9L MUTATED           0         0
  SAMD9L WILD-TYPE        13         1
D874V3, multiclass
            clus
vv           SAMD9L MUTATED SAMD9L WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                3               22
  STAGE IIA               8              101
  STAGE IIB               3                5
  STAGE IIC               0                1
  STAGE III               2               17
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SAMD9L MUTATED     0   3  16   3
  SAMD9L WILD-TYPE   9  65 232  38
D874V4, multiclass
    clus
vv   SAMD9L MUTATED SAMD9L WILD-TYPE
  T1              0                9
  T2              3               65
  T3             16              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
  SAMD9L MUTATED    17   3   2
  SAMD9L WILD-TYPE 203  77  64
D874V5, multiclass
    clus
vv   SAMD9L MUTATED SAMD9L WILD-TYPE
  N0             17              203
  N1              3               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"
D874V6, binary
                  cls
clus                 0   1
  SAMD9L MUTATED    18   1
  SAMD9L WILD-TYPE 265  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SAMD9L MUTATED     18    1
  SAMD9L WILD-TYPE  265   47
   clus
vv  SAMD9L MUTATED SAMD9L WILD-TYPE
  0             18              265
  1              1               47
[1] 2 2
[1] FALSE
D874V7, 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
D874V8, binary
                  cls
clus                 0   1
  SAMD9L MUTATED    19   3
  SAMD9L WILD-TYPE 298  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SAMD9L MUTATED     19    3
  SAMD9L WILD-TYPE  298   45
                               clus
vv                              SAMD9L MUTATED SAMD9L WILD-TYPE
  COLON ADENOCARCINOMA                      19              298
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SAMD9L MUTATED    15   0   1   1
  SAMD9L WILD-TYPE 242   2  21  20
D874V9, multiclass
    clus
vv   SAMD9L MUTATED SAMD9L WILD-TYPE
  R0             15              242
  R1              0                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"
D874V10, 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
D874V11, 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(875) Variable = GDE1 MUTATION ANALYSIS
D875V1, survival
                sevent
clus2              0   1
  GDE1 MUTATED     5   0
  GDE1 WILD-TYPE 277  73
  GDE1 MUTATED GDE1 WILD-TYPE 
             5            350 
  GDE1 MUTATED GDE1 WILD-TYPE 
             0             73 
$`GDE1 MUTATED`
TCGA-A6-5656 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CK-4950 TCGA-D5-6898 
       32.91        58.39         0.33        40.34         7.53 

$`GDE1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        16.14        15.58        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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  GDE1 MUTATED GDE1 WILD-TYPE 
          0.33           0.00 
  GDE1 MUTATED GDE1 WILD-TYPE 
         58.39         140.38 
  GDE1 MUTATED GDE1 WILD-TYPE 
        32.910         20.155 
[1] "0.3 - 58.4 (32.9)"  "0.0 - 140.4 (20.2)"
[1] "hr="     "9100000"
D875V2, 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       25       107         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GDE1 MUTATED           0          1          0          0        0         0
  GDE1 WILD-TYPE        19          9         41         31       35        13
                vv
clus             STAGE IVB
  GDE1 MUTATED           0
  GDE1 WILD-TYPE         1
D875V3, multiclass
            clus
vv           GDE1 MUTATED GDE1 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             2            107
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            1              9
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GDE1 MUTATED     0   2   3   0
  GDE1 WILD-TYPE   9  66 245  41
D875V4, multiclass
    clus
vv   GDE1 MUTATED GDE1 WILD-TYPE
  T1            0              9
  T2            2             66
  T3            3            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
  GDE1 MUTATED     4   1   0
  GDE1 WILD-TYPE 216  79  66
D875V5, multiclass
    clus
vv   GDE1 MUTATED GDE1 WILD-TYPE
  N0            4            216
  N1            1             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"
D875V6, binary
                cls
clus               0   1
  GDE1 MUTATED     5   0
  GDE1 WILD-TYPE 278  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  GDE1 MUTATED      5    0
  GDE1 WILD-TYPE  278   48
   clus
vv  GDE1 MUTATED GDE1 WILD-TYPE
  0            5            278
  1            0             48
[1] 2 2
[1] FALSE
D875V7, 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
D875V8, binary
                cls
clus               0   1
  GDE1 MUTATED     4   1
  GDE1 WILD-TYPE 313  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  GDE1 MUTATED      4    1
  GDE1 WILD-TYPE  313   47
                               clus
vv                              GDE1 MUTATED GDE1 WILD-TYPE
  COLON ADENOCARCINOMA                     4            313
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  GDE1 MUTATED     2   1   0   1
  GDE1 WILD-TYPE 255   1  22  20
D875V9, multiclass
    clus
vv   GDE1 MUTATED GDE1 WILD-TYPE
  R0            2            255
  R1            1              1
  R2            0             22
  RX            1             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D875V10, 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
D875V11, 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(876) Variable = TCEAL5 MUTATION ANALYSIS
D876V1, survival
                  sevent
clus2                0   1
  TCEAL5 MUTATED     4   1
  TCEAL5 WILD-TYPE 278  72
  TCEAL5 MUTATED TCEAL5 WILD-TYPE 
               5              350 
  TCEAL5 MUTATED TCEAL5 WILD-TYPE 
               1               72 
$`TCEAL5 MUTATED`
TCGA-A6-6138 TCGA-AA-A01P TCGA-AD-6889 TCGA-CM-6162 TCGA-G4-6306 
       22.52        38.07        56.55        12.00        44.68 

$`TCEAL5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        32.71        27.09         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  TCEAL5 MUTATED TCEAL5 WILD-TYPE 
              12                0 
  TCEAL5 MUTATED TCEAL5 WILD-TYPE 
           56.55           140.38 
  TCEAL5 MUTATED TCEAL5 WILD-TYPE 
           38.07            20.07 
[1] "12.0 - 56.5 (38.1)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.4"
D876V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TCEAL5 MUTATED         1        0        0         2         0         0
  TCEAL5 WILD-TYPE      63        1       25       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        18         10         40         31       35
                  vv
clus               STAGE IVA STAGE IVB
  TCEAL5 MUTATED           0         0
  TCEAL5 WILD-TYPE        13         1
D876V3, multiclass
            clus
vv           TCEAL5 MUTATED TCEAL5 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               2              107
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TCEAL5 MUTATED     0   2   3   0
  TCEAL5 WILD-TYPE   9  66 245  41
D876V4, multiclass
    clus
vv   TCEAL5 MUTATED TCEAL5 WILD-TYPE
  T1              0                9
  T2              2               66
  T3              3              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
  TCEAL5 MUTATED     3   2   0
  TCEAL5 WILD-TYPE 217  78  66
D876V5, multiclass
    clus
vv   TCEAL5 MUTATED TCEAL5 WILD-TYPE
  N0              3              217
  N1              2               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
  TCEAL5 MUTATED     5   0
  TCEAL5 WILD-TYPE 278  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCEAL5 MUTATED      5    0
  TCEAL5 WILD-TYPE  278   48
   clus
vv  TCEAL5 MUTATED TCEAL5 WILD-TYPE
  0              5              278
  1              0               48
[1] 2 2
[1] FALSE
D876V7, 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
D876V8, binary
                  cls
clus                 0   1
  TCEAL5 MUTATED     4   1
  TCEAL5 WILD-TYPE 313  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCEAL5 MUTATED      4    1
  TCEAL5 WILD-TYPE  313   47
                               clus
vv                              TCEAL5 MUTATED TCEAL5 WILD-TYPE
  COLON ADENOCARCINOMA                       4              313
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TCEAL5 MUTATED     3   0   0   0
  TCEAL5 WILD-TYPE 254   2  22  21
D876V9, multiclass
    clus
vv   TCEAL5 MUTATED TCEAL5 WILD-TYPE
  R0              3              254
  R1              0                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"
D876V10, 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
D876V11, 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(877) Variable = MCF2 MUTATION ANALYSIS
D877V1, survival
                sevent
clus2              0   1
  MCF2 MUTATED    26   2
  MCF2 WILD-TYPE 256  71
  MCF2 MUTATED MCF2 WILD-TYPE 
            28            327 
  MCF2 MUTATED MCF2 WILD-TYPE 
             2             71 
$`MCF2 MUTATED`
TCGA-A6-5665 TCGA-A6-6653 TCGA-AA-3510 TCGA-AA-3538 TCGA-AA-3555 TCGA-AA-3662 
       22.06        24.39        63.98        26.01        29.95         6.05 
TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3930 TCGA-AA-3968 
        6.97         0.92        85.05        19.04         2.01        21.99 
TCGA-AA-3977 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-5407 
       25.02        18.05         4.01        34.98        58.39        61.41 
TCGA-CA-5254 TCGA-CA-6717 TCGA-CA-6718 TCGA-D5-6534 TCGA-D5-6541 TCGA-D5-7000 
        2.24         0.33         0.10        43.27        15.58        10.26 
TCGA-DM-A28E TCGA-G4-6304 TCGA-G4-6586 TCGA-G4-6588 
      119.93        53.62        35.80        26.17 

$`MCF2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3543 
       19.07        34.03        29.00        29.00        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
       78.08        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.03        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05        31.00        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19         1.94         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07         0.26         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19        18.25         1.32        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 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-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
        1.51        12.00        11.38       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-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 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 
       19.43       107.67        74.56        65.85        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  MCF2 MUTATED MCF2 WILD-TYPE 
           0.1            0.0 
  MCF2 MUTATED MCF2 WILD-TYPE 
        119.93         140.38 
  MCF2 MUTATED MCF2 WILD-TYPE 
        23.225         20.020 
[1] "0.1 - 119.9 (23.2)" "0.0 - 140.4 (20.0)"
[1] "hr=" "3.4"
D877V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MCF2 MUTATED         5        0        2        11         3         0
  MCF2 WILD-TYPE      59        1       23        98         5         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MCF2 MUTATED           2          0          1          0        3         0
  MCF2 WILD-TYPE        17         10         40         31       32        13
                vv
clus             STAGE IVB
  MCF2 MUTATED           0
  MCF2 WILD-TYPE         1
D877V3, multiclass
            clus
vv           MCF2 MUTATED MCF2 WILD-TYPE
  STAGE I               5             59
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA            11             98
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             2             17
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              3             32
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MCF2 MUTATED     1   5  17   5
  MCF2 WILD-TYPE   8  63 231  36
D877V4, multiclass
    clus
vv   MCF2 MUTATED MCF2 WILD-TYPE
  T1            1              8
  T2            5             63
  T3           17            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
  MCF2 MUTATED    24   2   2
  MCF2 WILD-TYPE 196  78  64
D877V5, multiclass
    clus
vv   MCF2 MUTATED MCF2 WILD-TYPE
  N0           24            196
  N1            2             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
  MCF2 MUTATED    24   3
  MCF2 WILD-TYPE 259  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCF2 MUTATED     24    3
  MCF2 WILD-TYPE  259   45
   clus
vv  MCF2 MUTATED MCF2 WILD-TYPE
  0           24            259
  1            3             45
[1] 2 2
[1] FALSE
D877V7, 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
D877V8, binary
                cls
clus               0   1
  MCF2 MUTATED    22   6
  MCF2 WILD-TYPE 295  42
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCF2 MUTATED     22    6
  MCF2 WILD-TYPE  295   42
                               clus
vv                              MCF2 MUTATED MCF2 WILD-TYPE
  COLON ADENOCARCINOMA                    22            295
  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 239   2  19  18
D877V9, multiclass
    clus
vv   MCF2 MUTATED MCF2 WILD-TYPE
  R0           18            239
  R1            0              2
  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"
D877V10, 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
D877V11, 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(878) Variable = DNASE1L3 MUTATION ANALYSIS
D878V1, survival
                    sevent
clus2                  0   1
  DNASE1L3 MUTATED     5   3
  DNASE1L3 WILD-TYPE 277  70
  DNASE1L3 MUTATED DNASE1L3 WILD-TYPE 
                 8                347 
  DNASE1L3 MUTATED DNASE1L3 WILD-TYPE 
                 3                 70 
$`DNASE1L3 MUTATED`
TCGA-A6-2671 TCGA-AA-3510 TCGA-AA-3877 TCGA-AA-A02W TCGA-AZ-5403 TCGA-AZ-6601 
       43.76        63.98        31.00        41.00        62.79       100.01 
TCGA-CA-6717 TCGA-CK-4952 
        0.33        15.62 

$`DNASE1L3 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        18.05         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03        14.01         0.92        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       22.36        61.41        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       102.44        40.34        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  DNASE1L3 MUTATED DNASE1L3 WILD-TYPE 
              0.33               0.00 
  DNASE1L3 MUTATED DNASE1L3 WILD-TYPE 
            100.01             140.38 
  DNASE1L3 MUTATED DNASE1L3 WILD-TYPE 
             42.38              20.02 
[1] "0.3 - 100.0 (42.4)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1"  
D878V2, 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       22       108         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DNASE1L3 MUTATED           1          0          0          0        1
  DNASE1L3 WILD-TYPE        18         10         41         31       34
                    vv
clus                 STAGE IVA STAGE IVB
  DNASE1L3 MUTATED           0         0
  DNASE1L3 WILD-TYPE        13         1
D878V3, multiclass
            clus
vv           DNASE1L3 MUTATED DNASE1L3 WILD-TYPE
  STAGE I                   2                 62
  STAGE IA                  0                  1
  STAGE II                  3                 22
  STAGE IIA                 1                108
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 1                 18
  STAGE IIIA                0                 10
  STAGE IIIB                0                 41
  STAGE IIIC                0                 31
  STAGE IV                  1                 34
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  DNASE1L3 MUTATED     1   1   5   1
  DNASE1L3 WILD-TYPE   8  67 243  40
D878V4, multiclass
    clus
vv   DNASE1L3 MUTATED DNASE1L3 WILD-TYPE
  T1                1                  8
  T2                1                 67
  T3                5                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
  DNASE1L3 MUTATED     6   0   2
  DNASE1L3 WILD-TYPE 214  80  64
D878V5, multiclass
    clus
vv   DNASE1L3 MUTATED DNASE1L3 WILD-TYPE
  N0                6                214
  N1                0                 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
  DNASE1L3 MUTATED     6   1
  DNASE1L3 WILD-TYPE 277  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  DNASE1L3 MUTATED      6    1
  DNASE1L3 WILD-TYPE  277   47
   clus
vv  DNASE1L3 MUTATED DNASE1L3 WILD-TYPE
  0                6                277
  1                1                 47
[1] 2 2
[1] FALSE
D878V7, 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
D878V8, binary
                    cls
clus                   0   1
  DNASE1L3 MUTATED     5   3
  DNASE1L3 WILD-TYPE 312  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  DNASE1L3 MUTATED      5    3
  DNASE1L3 WILD-TYPE  312   45
                               clus
vv                              DNASE1L3 MUTATED DNASE1L3 WILD-TYPE
  COLON ADENOCARCINOMA                         5                312
  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 253   2  22  19
D878V9, multiclass
    clus
vv   DNASE1L3 MUTATED DNASE1L3 WILD-TYPE
  R0                4                253
  R1                0                  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"
D878V10, 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
D878V11, 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(879) Variable = ZSWIM3 MUTATION ANALYSIS
D879V1, survival
                  sevent
clus2                0   1
  ZSWIM3 MUTATED    10   2
  ZSWIM3 WILD-TYPE 272  71
  ZSWIM3 MUTATED ZSWIM3 WILD-TYPE 
              12              343 
  ZSWIM3 MUTATED ZSWIM3 WILD-TYPE 
               2               71 
$`ZSWIM3 MUTATED`
TCGA-AA-3492 TCGA-AA-3518 TCGA-AA-3542 TCGA-AA-3554 TCGA-AA-A00A TCGA-AA-A010 
        3.02         1.02        12.99        17.95        38.04        34.98 
TCGA-CK-4950 TCGA-D5-6540 TCGA-D5-6541 TCGA-DM-A1D4 TCGA-DM-A1HB TCGA-G4-6310 
       40.34        16.14        15.58        92.75       135.65        45.11 

$`ZSWIM3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
        7.96        27.02        13.94        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
        1.35        17.56       102.44        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 
       15.12        17.85         4.80        17.13        12.49         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        24.43        38.20       130.65        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        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        51.75        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  ZSWIM3 MUTATED ZSWIM3 WILD-TYPE 
            1.02             0.00 
  ZSWIM3 MUTATED ZSWIM3 WILD-TYPE 
          135.65           140.38 
  ZSWIM3 MUTATED ZSWIM3 WILD-TYPE 
          26.465           20.190 
[1] "1.0 - 135.7 (26.5)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.7"
D879V2, 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       24       104         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZSWIM3 MUTATED           0          1          2          1        0
  ZSWIM3 WILD-TYPE        19          9         39         30       35
                  vv
clus               STAGE IVA STAGE IVB
  ZSWIM3 MUTATED           0         0
  ZSWIM3 WILD-TYPE        13         1
D879V3, multiclass
            clus
vv           ZSWIM3 MUTATED ZSWIM3 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               5              104
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              1                9
  STAGE IIIB              2               39
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZSWIM3 MUTATED     0   1  10   1
  ZSWIM3 WILD-TYPE   9  67 238  40
D879V4, multiclass
    clus
vv   ZSWIM3 MUTATED ZSWIM3 WILD-TYPE
  T1              0                9
  T2              1               67
  T3             10              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
  ZSWIM3 MUTATED     8   3   1
  ZSWIM3 WILD-TYPE 212  77  65
D879V5, multiclass
    clus
vv   ZSWIM3 MUTATED ZSWIM3 WILD-TYPE
  N0              8              212
  N1              3               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"
D879V6, binary
                  cls
clus                 0   1
  ZSWIM3 MUTATED    12   0
  ZSWIM3 WILD-TYPE 271  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZSWIM3 MUTATED     12    0
  ZSWIM3 WILD-TYPE  271   48
   clus
vv  ZSWIM3 MUTATED ZSWIM3 WILD-TYPE
  0             12              271
  1              0               48
[1] 2 2
[1] FALSE
D879V7, 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
D879V8, binary
                  cls
clus                 0   1
  ZSWIM3 MUTATED    11   1
  ZSWIM3 WILD-TYPE 306  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZSWIM3 MUTATED     11    1
  ZSWIM3 WILD-TYPE  306   47
                               clus
vv                              ZSWIM3 MUTATED ZSWIM3 WILD-TYPE
  COLON ADENOCARCINOMA                      11              306
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZSWIM3 MUTATED     9   1   0   0
  ZSWIM3 WILD-TYPE 248   1  22  21
D879V9, multiclass
    clus
vv   ZSWIM3 MUTATED ZSWIM3 WILD-TYPE
  R0              9              248
  R1              1                1
  R2              0               22
  RX              0               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D879V10, 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
D879V11, 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(880) Variable = CDH8 MUTATION ANALYSIS
D880V1, survival
                sevent
clus2              0   1
  CDH8 MUTATED    26   4
  CDH8 WILD-TYPE 256  69
  CDH8 MUTATED CDH8 WILD-TYPE 
            30            325 
  CDH8 MUTATED CDH8 WILD-TYPE 
             4             69 
$`CDH8 MUTATED`
TCGA-A6-6653 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3525 TCGA-AA-3662 TCGA-AA-3664 
       24.39         6.97         1.02         8.05         6.05        54.02 
TCGA-AA-3672 TCGA-AA-3697 TCGA-AA-3864 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A00R 
        0.92        85.05        53.00        25.02         4.01         0.99 
TCGA-AA-A01Q TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-4682 TCGA-AZ-6608 TCGA-CA-6717 
        1.02        27.09        58.39        22.36         1.94         0.33 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CM-4743 TCGA-CM-5861 TCGA-CM-6679 
       17.56       102.44        15.62        23.05        15.02        10.06 
TCGA-CM-6680 TCGA-DM-A28H TCGA-F4-6570 TCGA-F4-6703 TCGA-G4-6315 TCGA-G4-6628 
       12.03       117.07         6.18        35.87        36.72        52.80 

$`CDH8 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       35.01        63.98        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       24.03        37.05        36.03        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-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-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
      100.01        29.56         5.23        11.74         3.19         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
        1.35        40.34        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93         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        16.01 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.08        11.01        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
      119.93        35.97        60.79        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       13.45         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 
       46.75 

  CDH8 MUTATED CDH8 WILD-TYPE 
          0.33           0.00 
  CDH8 MUTATED CDH8 WILD-TYPE 
        117.07         140.38 
  CDH8 MUTATED CDH8 WILD-TYPE 
         16.59          20.28 
[1] "0.3 - 117.1 (16.6)" "0.0 - 140.4 (20.3)"
[1] "hr=" "1.7"
D880V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CDH8 MUTATED         5        0        4         7         2         0
  CDH8 WILD-TYPE      59        1       21       102         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CDH8 MUTATED           3          2          2          1        3         2
  CDH8 WILD-TYPE        16          8         39         30       32        11
                vv
clus             STAGE IVB
  CDH8 MUTATED           0
  CDH8 WILD-TYPE         1
D880V3, multiclass
            clus
vv           CDH8 MUTATED CDH8 WILD-TYPE
  STAGE I               5             59
  STAGE IA              0              1
  STAGE II              4             21
  STAGE IIA             7            102
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             3             16
  STAGE IIIA            2              8
  STAGE IIIB            2             39
  STAGE IIIC            1             30
  STAGE IV              3             32
  STAGE IVA             2             11
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  19   6
  CDH8 WILD-TYPE   9  61 229  35
D880V4, multiclass
    clus
vv   CDH8 MUTATED CDH8 WILD-TYPE
  T1            0              9
  T2            7             61
  T3           19            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    21   6   5
  CDH8 WILD-TYPE 199  74  61
D880V5, multiclass
    clus
vv   CDH8 MUTATED CDH8 WILD-TYPE
  N0           21            199
  N1            6             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"
D880V6, binary
                cls
clus               0   1
  CDH8 MUTATED    26   4
  CDH8 WILD-TYPE 257  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDH8 MUTATED     26    4
  CDH8 WILD-TYPE  257   44
   clus
vv  CDH8 MUTATED CDH8 WILD-TYPE
  0           26            257
  1            4             44
[1] 2 2
[1] FALSE
D880V7, binary
                cls
clus               0   1
  CDH8 MUTATED    16  16
  CDH8 WILD-TYPE 154 181
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDH8 MUTATED     16   16
  CDH8 WILD-TYPE  154  181
        clus
vv       CDH8 MUTATED CDH8 WILD-TYPE
  FEMALE           16            154
  MALE             16            181
[1] 2 2
[1] FALSE
D880V8, binary
                cls
clus               0   1
  CDH8 MUTATED    29   3
  CDH8 WILD-TYPE 288  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDH8 MUTATED     29    3
  CDH8 WILD-TYPE  288   45
                               clus
vv                              CDH8 MUTATED CDH8 WILD-TYPE
  COLON ADENOCARCINOMA                    29            288
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CDH8 MUTATED    22   0   2   4
  CDH8 WILD-TYPE 235   2  20  17
D880V9, multiclass
    clus
vv   CDH8 MUTATED CDH8 WILD-TYPE
  R0           22            235
  R1            0              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"
D880V10, 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
D880V11, 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(881) Variable = ADM MUTATION ANALYSIS
D881V1, survival
               sevent
clus2             0   1
  ADM MUTATED     5   1
  ADM WILD-TYPE 277  72
  ADM MUTATED ADM WILD-TYPE 
            6           349 
  ADM MUTATED ADM WILD-TYPE 
            1            72 
$`ADM MUTATED`
TCGA-A6-5661 TCGA-AA-3510 TCGA-AA-3977 TCGA-AA-A01D TCGA-CM-4743 TCGA-G4-6588 
       33.53        63.98        25.02        10.98        23.05        26.17 

$`ADM WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       34.98        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        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 
       52.80 

  ADM MUTATED ADM WILD-TYPE 
        10.98          0.00 
  ADM MUTATED ADM WILD-TYPE 
        63.98        140.38 
  ADM MUTATED ADM WILD-TYPE 
       25.595        20.020 
[1] "11.0 - 64.0 (25.6)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.5"
D881V2, 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       24       106         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        19         10         41         30       35        13
               vv
clus            STAGE IVB
  ADM MUTATED           0
  ADM WILD-TYPE         1
D881V3, multiclass
            clus
vv           ADM MUTATED ADM WILD-TYPE
  STAGE I              0            64
  STAGE IA             0             1
  STAGE II             1            24
  STAGE IIA            3           106
  STAGE IIB            0             8
  STAGE IIC            0             1
  STAGE III            0            19
  STAGE IIIA           0            10
  STAGE IIIB           0            41
  STAGE IIIC           1            30
  STAGE IV             0            35
  STAGE IVA            0            13
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  ADM MUTATED     0   1   5   0
  ADM WILD-TYPE   9  67 243  41
D881V4, multiclass
    clus
vv   ADM MUTATED ADM WILD-TYPE
  T1           0             9
  T2           1            67
  T3           5           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
  ADM MUTATED     5   0   1
  ADM WILD-TYPE 215  80  65
D881V5, multiclass
    clus
vv   ADM MUTATED ADM WILD-TYPE
  N0           5           215
  N1           0            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"
D881V6, binary
               cls
clus              0   1
  ADM MUTATED     5   0
  ADM WILD-TYPE 278  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  ADM MUTATED      5    0
  ADM WILD-TYPE  278   48
   clus
vv  ADM MUTATED ADM WILD-TYPE
  0           5           278
  1           0            48
[1] 2 2
[1] FALSE
D881V7, 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
D881V8, binary
               cls
clus              0   1
  ADM MUTATED     5   1
  ADM WILD-TYPE 312  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  ADM MUTATED      5    1
  ADM WILD-TYPE  312   47
                               clus
vv                              ADM MUTATED ADM WILD-TYPE
  COLON ADENOCARCINOMA                    5           312
  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 252   2  22  21
D881V9, multiclass
    clus
vv   ADM MUTATED ADM WILD-TYPE
  R0           5           252
  R1           0             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"
D881V10, 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
D881V11, 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(882) Variable = NIPBL MUTATION ANALYSIS
D882V1, survival
                 sevent
clus2               0   1
  NIPBL MUTATED    25   7
  NIPBL WILD-TYPE 257  66
  NIPBL MUTATED NIPBL WILD-TYPE 
             32             323 
  NIPBL MUTATED NIPBL WILD-TYPE 
              7              66 
$`NIPBL MUTATED`
TCGA-A6-2672 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5665 TCGA-A6-6780 TCGA-A6-6781 
       46.65        30.44        29.19        22.06        20.12        19.66 
TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       63.98         6.97         0.92        26.99        19.04        10.06 
TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-6895 
       31.00        33.01         4.01        34.98        35.01         0.72 
TCGA-AZ-4315 TCGA-AZ-4616 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CA-6718 
       58.39         5.13        12.10       100.01         0.33         0.10 
TCGA-CM-5868 TCGA-CM-6162 TCGA-D5-6539 TCGA-D5-6920 TCGA-DM-A28F TCGA-G4-6304 
       17.03        12.00        12.49        12.39        35.97        53.62 
TCGA-G4-6309 TCGA-G4-6315 
       51.75        36.72 

$`NIPBL WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 
       31.63        33.53        23.61        22.09        32.71        27.09 
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 
       22.52         8.38        25.08        25.18        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.69        24.39        23.87        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       85.05        19.04        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       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        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
        0.07        21.37         4.21        56.55         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        1.41        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
        6.77        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        15.02        15.02        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
      139.17         6.12        81.37       119.93        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       44.68        55.04        45.11        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  NIPBL MUTATED NIPBL WILD-TYPE 
            0.1             0.0 
  NIPBL MUTATED NIPBL WILD-TYPE 
         100.01          140.38 
  NIPBL MUTATED NIPBL WILD-TYPE 
          21.09           20.19 
[1] "0.1 - 100.0 (21.1)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1"  
D882V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NIPBL MUTATED         2        0        4         8         4         0
  NIPBL WILD-TYPE      62        1       21       101         4         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NIPBL MUTATED           3          1          4          2        3         1
  NIPBL WILD-TYPE        16          9         37         29       32        12
                 vv
clus              STAGE IVB
  NIPBL MUTATED           0
  NIPBL WILD-TYPE         1
D882V3, multiclass
            clus
vv           NIPBL MUTATED NIPBL WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               4              21
  STAGE IIA              8             101
  STAGE IIB              4               4
  STAGE IIC              0               1
  STAGE III              3              16
  STAGE IIIA             1               9
  STAGE IIIB             4              37
  STAGE IIIC             2              29
  STAGE IV               3              32
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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   7
  NIPBL WILD-TYPE   8  67 224  34
D882V4, multiclass
    clus
vv   NIPBL MUTATED NIPBL WILD-TYPE
  T1             1               8
  T2             1              67
  T3            24             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
  NIPBL MUTATED    19  10   4
  NIPBL WILD-TYPE 201  70  62
D882V5, multiclass
    clus
vv   NIPBL MUTATED NIPBL WILD-TYPE
  N0            19             201
  N1            10              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"
D882V6, binary
                 cls
clus                0   1
  NIPBL MUTATED    26   4
  NIPBL WILD-TYPE 257  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NIPBL MUTATED     26    4
  NIPBL WILD-TYPE  257   44
   clus
vv  NIPBL MUTATED NIPBL WILD-TYPE
  0            26             257
  1             4              44
[1] 2 2
[1] FALSE
D882V7, binary
                 cls
clus                0   1
  NIPBL MUTATED    16  17
  NIPBL WILD-TYPE 154 180
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NIPBL MUTATED     16   17
  NIPBL WILD-TYPE  154  180
        clus
vv       NIPBL MUTATED NIPBL WILD-TYPE
  FEMALE            16             154
  MALE              17             180
[1] 2 2
[1] FALSE
D882V8, binary
                 cls
clus                0   1
  NIPBL MUTATED    25   8
  NIPBL WILD-TYPE 292  40
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NIPBL MUTATED     25    8
  NIPBL WILD-TYPE  292   40
                               clus
vv                              NIPBL MUTATED NIPBL WILD-TYPE
  COLON ADENOCARCINOMA                     25             292
  COLON MUCINOUS ADENOCARCINOMA             8              40
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  NIPBL MUTATED    24   0   0   2
  NIPBL WILD-TYPE 233   2  22  19
D882V9, multiclass
    clus
vv   NIPBL MUTATED NIPBL WILD-TYPE
  R0            24             233
  R1             0               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"
D882V10, 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
D882V11, 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(883) Variable = FRMD6 MUTATION ANALYSIS
D883V1, survival
                 sevent
clus2               0   1
  FRMD6 MUTATED     8   1
  FRMD6 WILD-TYPE 274  72
  FRMD6 MUTATED FRMD6 WILD-TYPE 
              9             346 
  FRMD6 MUTATED FRMD6 WILD-TYPE 
              1              72 
$`FRMD6 MUTATED`
TCGA-A6-5662 TCGA-A6-5665 TCGA-AA-3663 TCGA-AA-A010 TCGA-AD-5900 TCGA-AY-6386 
       23.61        22.06         6.97        34.98         0.07        17.82 
TCGA-AZ-6598 TCGA-CM-5348 TCGA-G4-6321 
       49.41        22.98        22.09 

$`FRMD6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        33.53        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 
       51.75        45.11        36.72        36.00        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  FRMD6 MUTATED FRMD6 WILD-TYPE 
           0.07            0.00 
  FRMD6 MUTATED FRMD6 WILD-TYPE 
          49.41          140.38 
  FRMD6 MUTATED FRMD6 WILD-TYPE 
          22.09           20.07 
[1] "0.1 - 49.4 (22.1)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.6"
D883V2, 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       23       108         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        18         10         39         31       35        12
                 vv
clus              STAGE IVB
  FRMD6 MUTATED           0
  FRMD6 WILD-TYPE         1
D883V3, multiclass
            clus
vv           FRMD6 MUTATED FRMD6 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              1             108
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 242  39
D883V4, multiclass
    clus
vv   FRMD6 MUTATED FRMD6 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             6             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
  FRMD6 MUTATED     6   3   1
  FRMD6 WILD-TYPE 214  77  65
D883V5, multiclass
    clus
vv   FRMD6 MUTATED FRMD6 WILD-TYPE
  N0             6             214
  N1             3              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"
D883V6, binary
                 cls
clus                0   1
  FRMD6 MUTATED     5   1
  FRMD6 WILD-TYPE 278  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FRMD6 MUTATED      5    1
  FRMD6 WILD-TYPE  278   47
   clus
vv  FRMD6 MUTATED FRMD6 WILD-TYPE
  0             5             278
  1             1              47
[1] 2 2
[1] FALSE
D883V7, 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
D883V8, binary
                 cls
clus                0   1
  FRMD6 MUTATED     9   1
  FRMD6 WILD-TYPE 308  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FRMD6 MUTATED      9    1
  FRMD6 WILD-TYPE  308   47
                               clus
vv                              FRMD6 MUTATED FRMD6 WILD-TYPE
  COLON ADENOCARCINOMA                      9             308
  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 250   2  22  20
D883V9, multiclass
    clus
vv   FRMD6 MUTATED FRMD6 WILD-TYPE
  R0             7             250
  R1             0               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"
D883V10, 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
D883V11, 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(884) Variable = CYP4A22 MUTATION ANALYSIS
D884V1, survival
                   sevent
clus2                 0   1
  CYP4A22 MUTATED     8   4
  CYP4A22 WILD-TYPE 274  69
  CYP4A22 MUTATED CYP4A22 WILD-TYPE 
               12               343 
  CYP4A22 MUTATED CYP4A22 WILD-TYPE 
                4                69 
$`CYP4A22 MUTATED`
TCGA-AA-3821 TCGA-AD-6889 TCGA-AD-6895 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-6717 
        1.02        56.55         0.72        11.74         3.19         0.33 
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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        4.21         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-5254 
       12.10       100.01        29.56         5.23         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02        12.00        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85        17.13        12.49        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A285 
      140.38         7.50        44.32       131.51       135.65         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  CYP4A22 MUTATED CYP4A22 WILD-TYPE 
             0.33              0.00 
  CYP4A22 MUTATED CYP4A22 WILD-TYPE 
           139.17            140.38 
  CYP4A22 MUTATED CYP4A22 WILD-TYPE 
            12.89             20.98 
[1] "0.3 - 139.2 (12.9)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.9"
D884V2, 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       25       104         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CYP4A22 MUTATED           0          0          1          1        2
  CYP4A22 WILD-TYPE        19         10         40         30       33
                   vv
clus                STAGE IVA STAGE IVB
  CYP4A22 MUTATED           0         0
  CYP4A22 WILD-TYPE        13         1
D884V3, multiclass
            clus
vv           CYP4A22 MUTATED CYP4A22 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                5               104
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               1                30
  STAGE IV                 2                33
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CYP4A22 MUTATED     1   2   8   2
  CYP4A22 WILD-TYPE   8  66 240  39
D884V4, multiclass
    clus
vv   CYP4A22 MUTATED CYP4A22 WILD-TYPE
  T1               1                 8
  T2               2                66
  T3               8               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
  CYP4A22 MUTATED     8   2   3
  CYP4A22 WILD-TYPE 212  78  63
D884V5, multiclass
    clus
vv   CYP4A22 MUTATED CYP4A22 WILD-TYPE
  N0               8               212
  N1               2                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"
D884V6, binary
                   cls
clus                  0   1
  CYP4A22 MUTATED     9   2
  CYP4A22 WILD-TYPE 274  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP4A22 MUTATED      9    2
  CYP4A22 WILD-TYPE  274   46
   clus
vv  CYP4A22 MUTATED CYP4A22 WILD-TYPE
  0               9               274
  1               2                46
[1] 2 2
[1] FALSE
D884V7, 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
D884V8, binary
                   cls
clus                  0   1
  CYP4A22 MUTATED    10   3
  CYP4A22 WILD-TYPE 307  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP4A22 MUTATED     10    3
  CYP4A22 WILD-TYPE  307   45
                               clus
vv                              CYP4A22 MUTATED CYP4A22 WILD-TYPE
  COLON ADENOCARCINOMA                       10               307
  COLON MUCINOUS ADENOCARCINOMA               3                45
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  CYP4A22 MUTATED     6   0   0   1
  CYP4A22 WILD-TYPE 251   2  22  20
D884V9, multiclass
    clus
vv   CYP4A22 MUTATED CYP4A22 WILD-TYPE
  R0               6               251
  R1               0                 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"
D884V10, 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
D884V11, 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(885) Variable = KIF21A MUTATION ANALYSIS
D885V1, survival
                  sevent
clus2                0   1
  KIF21A MUTATED    18   5
  KIF21A WILD-TYPE 264  68
  KIF21A MUTATED KIF21A WILD-TYPE 
              23              332 
  KIF21A MUTATED KIF21A WILD-TYPE 
               5               68 
$`KIF21A MUTATED`
TCGA-A6-5665 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3663 TCGA-AA-3815 
       22.06        20.12        19.66         3.02         6.97        33.04 
TCGA-AA-3845 TCGA-AA-3867 TCGA-AA-3977 TCGA-AA-A00N TCGA-AD-6890 TCGA-AY-6197 
        0.00        24.03        25.02         4.01         0.79        21.44 
TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-4952 TCGA-CM-6162 TCGA-CM-6169 
       58.39        49.41         0.33        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        51.75 

$`KIF21A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.05        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       19.04        19.04        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       17.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 
       40.96         0.07        21.37         4.21        56.55         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       27.09        16.31         0.95        15.75         0.20        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       40.34        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-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-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
       14.30         9.44        13.41         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  KIF21A MUTATED KIF21A WILD-TYPE 
               0                0 
  KIF21A MUTATED KIF21A WILD-TYPE 
           74.56           140.38 
  KIF21A MUTATED KIF21A WILD-TYPE 
           15.62            20.98 
[1] "0.0 - 74.6 (15.6)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.2"
D885V2, 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       22        98         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIF21A MUTATED           1          1          2          2        1
  KIF21A WILD-TYPE        18          9         39         29       34
                  vv
clus               STAGE IVA STAGE IVB
  KIF21A MUTATED           0         0
  KIF21A WILD-TYPE        13         1
D885V3, multiclass
            clus
vv           KIF21A MUTATED KIF21A WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                3               22
  STAGE IIA              11               98
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              1                9
  STAGE IIIB              2               39
  STAGE IIIC              2               29
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  KIF21A MUTATED     1   1  18   4
  KIF21A WILD-TYPE   8  67 230  37
D885V4, multiclass
    clus
vv   KIF21A MUTATED KIF21A WILD-TYPE
  T1              1                8
  T2              1               67
  T3             18              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
  KIF21A MUTATED    17   4   3
  KIF21A WILD-TYPE 203  76  63
D885V5, multiclass
    clus
vv   KIF21A MUTATED KIF21A WILD-TYPE
  N0             17              203
  N1              4               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"
D885V6, binary
                  cls
clus                 0   1
  KIF21A MUTATED    17   1
  KIF21A WILD-TYPE 266  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF21A MUTATED     17    1
  KIF21A WILD-TYPE  266   47
   clus
vv  KIF21A MUTATED KIF21A WILD-TYPE
  0             17              266
  1              1               47
[1] 2 2
[1] FALSE
D885V7, 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
D885V8, binary
                  cls
clus                 0   1
  KIF21A MUTATED    17   7
  KIF21A WILD-TYPE 300  41
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF21A MUTATED     17    7
  KIF21A WILD-TYPE  300   41
                               clus
vv                              KIF21A MUTATED KIF21A WILD-TYPE
  COLON ADENOCARCINOMA                      17              300
  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 240   2  21  19
D885V9, multiclass
    clus
vv   KIF21A MUTATED KIF21A WILD-TYPE
  R0             17              240
  R1              0                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"
D885V10, 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
D885V11, 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(886) Variable = PSD3 MUTATION ANALYSIS
D886V1, survival
                sevent
clus2              0   1
  PSD3 MUTATED     8   2
  PSD3 WILD-TYPE 274  71
  PSD3 MUTATED PSD3 WILD-TYPE 
            10            345 
  PSD3 MUTATED PSD3 WILD-TYPE 
             2             71 
$`PSD3 MUTATED`
TCGA-A6-5661 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3815 TCGA-AD-6899 TCGA-AZ-6599 
       33.53        63.98         6.97        33.04         5.79         6.77 
TCGA-CM-4743 TCGA-CM-4747 TCGA-D5-6529 TCGA-G4-6588 
       23.05        25.02        20.19        26.17 

$`PSD3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        0.72        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41        49.41        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       11.51        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  PSD3 MUTATED PSD3 WILD-TYPE 
          5.79           0.00 
  PSD3 MUTATED PSD3 WILD-TYPE 
         63.98         140.38 
  PSD3 MUTATED PSD3 WILD-TYPE 
        24.035         20.020 
[1] "5.8 - 64.0 (24.0)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1"  
D886V2, 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       23       104         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        19         10         41         30       35        12
                vv
clus             STAGE IVB
  PSD3 MUTATED           0
  PSD3 WILD-TYPE         1
D886V3, multiclass
            clus
vv           PSD3 MUTATED PSD3 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             5            104
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            1             30
  STAGE IV              0             35
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 241  39
D886V4, multiclass
    clus
vv   PSD3 MUTATED PSD3 WILD-TYPE
  T1            0              9
  T2            1             67
  T3            7            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
  PSD3 MUTATED     8   1   1
  PSD3 WILD-TYPE 212  79  65
D886V5, multiclass
    clus
vv   PSD3 MUTATED PSD3 WILD-TYPE
  N0            8            212
  N1            1             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"
D886V6, binary
                cls
clus               0   1
  PSD3 MUTATED     7   1
  PSD3 WILD-TYPE 276  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  PSD3 MUTATED      7    1
  PSD3 WILD-TYPE  276   47
   clus
vv  PSD3 MUTATED PSD3 WILD-TYPE
  0            7            276
  1            1             47
[1] 2 2
[1] FALSE
D886V7, 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
D886V8, binary
                cls
clus               0   1
  PSD3 MUTATED     9   1
  PSD3 WILD-TYPE 308  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  PSD3 MUTATED      9    1
  PSD3 WILD-TYPE  308   47
                               clus
vv                              PSD3 MUTATED PSD3 WILD-TYPE
  COLON ADENOCARCINOMA                     9            308
  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 249   2  22  21
D886V9, multiclass
    clus
vv   PSD3 MUTATED PSD3 WILD-TYPE
  R0            8            249
  R1            0              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"
D886V10, 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
D886V11, 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(887) Variable = NCF2 MUTATION ANALYSIS
D887V1, survival
                sevent
clus2              0   1
  NCF2 MUTATED     8   0
  NCF2 WILD-TYPE 274  73
  NCF2 MUTATED NCF2 WILD-TYPE 
             8            347 
  NCF2 MUTATED NCF2 WILD-TYPE 
             0             73 
$`NCF2 MUTATED`
TCGA-AA-3660 TCGA-AA-3864 TCGA-AY-6197 TCGA-CA-6717 TCGA-CM-4743 TCGA-CM-5348 
       78.08        53.00        21.44         0.33        23.05        22.98 
TCGA-CM-6163 TCGA-G4-6588 
       14.04        26.17 

$`NCF2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        61.02         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 
       15.02        15.02        17.03        15.02        12.00        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        91.79        46.75        52.80 

  NCF2 MUTATED NCF2 WILD-TYPE 
          0.33           0.00 
  NCF2 MUTATED NCF2 WILD-TYPE 
         78.08         140.38 
  NCF2 MUTATED NCF2 WILD-TYPE 
        23.015         20.020 
[1] "0.3 - 78.1 (23.0)"  "0.0 - 140.4 (20.0)"
[1] "hr="     "2.5e+07"
D887V2, 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       23       105         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        19         10         40         31       35        13
                vv
clus             STAGE IVB
  NCF2 MUTATED           0
  NCF2 WILD-TYPE         1
D887V3, multiclass
            clus
vv           NCF2 MUTATED NCF2 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             4            105
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NCF2 MUTATED     1   0   7   0
  NCF2 WILD-TYPE   8  68 241  41
D887V4, multiclass
    clus
vv   NCF2 MUTATED NCF2 WILD-TYPE
  T1            1              8
  T2            0             68
  T3            7            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
  NCF2 MUTATED     7   1   0
  NCF2 WILD-TYPE 213  79  66
D887V5, multiclass
    clus
vv   NCF2 MUTATED NCF2 WILD-TYPE
  N0            7            213
  N1            1             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
  NCF2 MUTATED     7   0
  NCF2 WILD-TYPE 276  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  NCF2 MUTATED      7    0
  NCF2 WILD-TYPE  276   48
   clus
vv  NCF2 MUTATED NCF2 WILD-TYPE
  0            7            276
  1            0             48
[1] 2 2
[1] FALSE
D887V7, 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
D887V8, binary
                cls
clus               0   1
  NCF2 MUTATED     7   1
  NCF2 WILD-TYPE 310  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  NCF2 MUTATED      7    1
  NCF2 WILD-TYPE  310   47
                               clus
vv                              NCF2 MUTATED NCF2 WILD-TYPE
  COLON ADENOCARCINOMA                     7            310
  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 250   2  22  20
D887V9, multiclass
    clus
vv   NCF2 MUTATED NCF2 WILD-TYPE
  R0            7            250
  R1            0              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"
D887V10, 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
D887V11, 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(888) Variable = ZNF619 MUTATION ANALYSIS
D888V1, survival
                  sevent
clus2                0   1
  ZNF619 MUTATED     8   3
  ZNF619 WILD-TYPE 274  70
  ZNF619 MUTATED ZNF619 WILD-TYPE 
              11              344 
  ZNF619 MUTATED ZNF619 WILD-TYPE 
               3               70 
$`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 TCGA-DM-A1D8 
       34.98        35.01        58.39        11.64        12.59 

$`ZNF619 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       38.99        37.02        14.93        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  ZNF619 MUTATED ZNF619 WILD-TYPE 
               0                0 
  ZNF619 MUTATED ZNF619 WILD-TYPE 
           63.98           140.38 
  ZNF619 MUTATED ZNF619 WILD-TYPE 
          19.660           20.235 
[1] "0.0 - 64.0 (19.7)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.4"
D888V2, 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       23       106         5         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF619 MUTATED           1          0          0          1        0
  ZNF619 WILD-TYPE        18         10         41         30       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF619 MUTATED           0         0
  ZNF619 WILD-TYPE        13         1
D888V3, multiclass
            clus
vv           ZNF619 MUTATED ZNF619 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               3              106
  STAGE IIB               3                5
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF619 MUTATED     1   0   7   4
  ZNF619 WILD-TYPE   8  68 241  37
D888V4, multiclass
    clus
vv   ZNF619 MUTATED ZNF619 WILD-TYPE
  T1              1                8
  T2              0               68
  T3              7              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
  ZNF619 MUTATED     9   2   1
  ZNF619 WILD-TYPE 211  78  65
D888V5, multiclass
    clus
vv   ZNF619 MUTATED ZNF619 WILD-TYPE
  N0              9              211
  N1              2               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
  ZNF619 MUTATED     9   0
  ZNF619 WILD-TYPE 274  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF619 MUTATED      9    0
  ZNF619 WILD-TYPE  274   48
   clus
vv  ZNF619 MUTATED ZNF619 WILD-TYPE
  0              9              274
  1              0               48
[1] 2 2
[1] FALSE
D888V7, binary
                  cls
clus                 0   1
  ZNF619 MUTATED     5   7
  ZNF619 WILD-TYPE 165 190
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF619 MUTATED      5    7
  ZNF619 WILD-TYPE  165  190
        clus
vv       ZNF619 MUTATED ZNF619 WILD-TYPE
  FEMALE              5              165
  MALE                7              190
[1] 2 2
[1] FALSE
D888V8, binary
                  cls
clus                 0   1
  ZNF619 MUTATED     7   5
  ZNF619 WILD-TYPE 310  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF619 MUTATED      7    5
  ZNF619 WILD-TYPE  310   43
                               clus
vv                              ZNF619 MUTATED ZNF619 WILD-TYPE
  COLON ADENOCARCINOMA                       7              310
  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 247   2  22  20
D888V9, multiclass
    clus
vv   ZNF619 MUTATED ZNF619 WILD-TYPE
  R0             10              247
  R1              0                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"
D888V10, 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     5
  ZNF619 WILD-TYPE                        19   171
D888V11, 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                                         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(889) Variable = NOL9 MUTATION ANALYSIS
D889V1, survival
                sevent
clus2              0   1
  NOL9 MUTATED     7   0
  NOL9 WILD-TYPE 275  73
  NOL9 MUTATED NOL9 WILD-TYPE 
             7            348 
  NOL9 MUTATED NOL9 WILD-TYPE 
             0             73 
$`NOL9 MUTATED`
TCGA-AA-3982 TCGA-AA-A02F TCGA-CA-6719 TCGA-DM-A1HB TCGA-G4-6586 TCGA-G4-6588 
       27.02        39.98         1.35       135.65        35.80        26.17 
TCGA-G4-6628 
       52.80 

$`NOL9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       24.00        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       51.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.33         0.10        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 
       36.72        36.00        22.09        13.78        91.79        46.75 

  NOL9 MUTATED NOL9 WILD-TYPE 
          1.35           0.00 
  NOL9 MUTATED NOL9 WILD-TYPE 
        135.65         140.38 
  NOL9 MUTATED NOL9 WILD-TYPE 
        35.800         20.005 
[1] "1.4 - 135.7 (35.8)" "0.0 - 140.4 (20.0)"
[1] "hr="     "2.6e+07"
D889V2, 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       25       106         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        19         10         39         31       34        13
                vv
clus             STAGE IVB
  NOL9 MUTATED           0
  NOL9 WILD-TYPE         1
D889V3, multiclass
            clus
vv           NOL9 MUTATED NOL9 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             3            106
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            2             39
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NOL9 MUTATED     0   1   6   0
  NOL9 WILD-TYPE   9  67 242  41
D889V4, multiclass
    clus
vv   NOL9 MUTATED NOL9 WILD-TYPE
  T1            0              9
  T2            1             67
  T3            6            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
  NOL9 MUTATED     4   3   0
  NOL9 WILD-TYPE 216  77  66
D889V5, multiclass
    clus
vv   NOL9 MUTATED NOL9 WILD-TYPE
  N0            4            216
  N1            3             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"
D889V6, binary
                cls
clus               0   1
  NOL9 MUTATED     6   1
  NOL9 WILD-TYPE 277  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOL9 MUTATED      6    1
  NOL9 WILD-TYPE  277   47
   clus
vv  NOL9 MUTATED NOL9 WILD-TYPE
  0            6            277
  1            1             47
[1] 2 2
[1] FALSE
D889V7, 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
D889V8, binary
                cls
clus               0   1
  NOL9 MUTATED     7   0
  NOL9 WILD-TYPE 310  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOL9 MUTATED      7    0
  NOL9 WILD-TYPE  310   48
                               clus
vv                              NOL9 MUTATED NOL9 WILD-TYPE
  COLON ADENOCARCINOMA                     7            310
  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 254   2  21  20
D889V9, multiclass
    clus
vv   NOL9 MUTATED NOL9 WILD-TYPE
  R0            3            254
  R1            0              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"
D889V10, 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
D889V11, 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(890) Variable = PVRL4 MUTATION ANALYSIS
D890V1, survival
                 sevent
clus2               0   1
  PVRL4 MUTATED     8   1
  PVRL4 WILD-TYPE 274  72
  PVRL4 MUTATED PVRL4 WILD-TYPE 
              9             346 
  PVRL4 MUTATED PVRL4 WILD-TYPE 
              1              72 
$`PVRL4 MUTATED`
TCGA-A6-6141 TCGA-AA-3715 TCGA-AA-3877 TCGA-AA-3966 TCGA-AA-A00J TCGA-CM-5349 
        8.38        19.04        31.00         2.01        18.05        30.08 
TCGA-CM-5868 TCGA-DM-A1HB TCGA-G4-6293 
       17.03       135.65       107.67 

$`PVRL4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        18.05         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  PVRL4 MUTATED PVRL4 WILD-TYPE 
           2.01            0.00 
  PVRL4 MUTATED PVRL4 WILD-TYPE 
         135.65          140.38 
  PVRL4 MUTATED PVRL4 WILD-TYPE 
         19.040          20.235 
[1] "2.0 - 135.7 (19.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "2.8"
D890V2, 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       24       106         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        18         10         39         31       35        12
                 vv
clus              STAGE IVB
  PVRL4 MUTATED           0
  PVRL4 WILD-TYPE         1
D890V3, multiclass
            clus
vv           PVRL4 MUTATED PVRL4 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              3             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  68 242  39
D890V4, multiclass
    clus
vv   PVRL4 MUTATED PVRL4 WILD-TYPE
  T1             1               8
  T2             0              68
  T3             6             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
  PVRL4 MUTATED     5   4   0
  PVRL4 WILD-TYPE 215  76  66
D890V5, multiclass
    clus
vv   PVRL4 MUTATED PVRL4 WILD-TYPE
  N0             5             215
  N1             4              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"
D890V6, binary
                 cls
clus                0   1
  PVRL4 MUTATED     8   1
  PVRL4 WILD-TYPE 275  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PVRL4 MUTATED      8    1
  PVRL4 WILD-TYPE  275   47
   clus
vv  PVRL4 MUTATED PVRL4 WILD-TYPE
  0             8             275
  1             1              47
[1] 2 2
[1] FALSE
D890V7, 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
D890V8, binary
                 cls
clus                0   1
  PVRL4 MUTATED     6   3
  PVRL4 WILD-TYPE 311  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PVRL4 MUTATED      6    3
  PVRL4 WILD-TYPE  311   45
                               clus
vv                              PVRL4 MUTATED PVRL4 WILD-TYPE
  COLON ADENOCARCINOMA                      6             311
  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 251   2  22  21
D890V9, multiclass
    clus
vv   PVRL4 MUTATED PVRL4 WILD-TYPE
  R0             6             251
  R1             0               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"
D890V10, 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
D890V11, 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(891) Variable = FAM20B MUTATION ANALYSIS
D891V1, survival
                  sevent
clus2                0   1
  FAM20B MUTATED     9   1
  FAM20B WILD-TYPE 273  72
  FAM20B MUTATED FAM20B WILD-TYPE 
              10              345 
  FAM20B MUTATED FAM20B WILD-TYPE 
               1               72 
$`FAM20B MUTATED`
TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3966 TCGA-AA-A00N TCGA-AD-6889 
       22.06        19.66        63.98         2.01         4.01        56.55 
TCGA-CM-5344 TCGA-D5-6536 TCGA-D5-6929 TCGA-G4-6309 
       22.03        17.85        13.41        51.75 

$`FAM20B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37         4.21         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       74.56        65.85        53.62        44.68        55.04        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  FAM20B MUTATED FAM20B WILD-TYPE 
            2.01             0.00 
  FAM20B MUTATED FAM20B WILD-TYPE 
           63.98           140.38 
  FAM20B MUTATED FAM20B WILD-TYPE 
          20.845           20.190 
[1] "2.0 - 64.0 (20.8)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2.4"
D891V2, 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       24       105         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM20B MUTATED           0          0          2          1        1
  FAM20B WILD-TYPE        19         10         39         30       34
                  vv
clus               STAGE IVA STAGE IVB
  FAM20B MUTATED           0         0
  FAM20B WILD-TYPE        13         1
D891V3, multiclass
            clus
vv           FAM20B MUTATED FAM20B WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               4              105
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              1               30
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FAM20B MUTATED     0   0   8   2
  FAM20B WILD-TYPE   9  68 240  39
D891V4, multiclass
    clus
vv   FAM20B MUTATED FAM20B WILD-TYPE
  T1              0                9
  T2              0               68
  T3              8              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
  FAM20B MUTATED     6   4   0
  FAM20B WILD-TYPE 214  76  66
D891V5, multiclass
    clus
vv   FAM20B MUTATED FAM20B WILD-TYPE
  N0              6              214
  N1              4               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"
D891V6, binary
                  cls
clus                 0   1
  FAM20B MUTATED     8   1
  FAM20B WILD-TYPE 275  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM20B MUTATED      8    1
  FAM20B WILD-TYPE  275   47
   clus
vv  FAM20B MUTATED FAM20B WILD-TYPE
  0              8              275
  1              1               47
[1] 2 2
[1] FALSE
D891V7, 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
D891V8, binary
                  cls
clus                 0   1
  FAM20B MUTATED     7   3
  FAM20B WILD-TYPE 310  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM20B MUTATED      7    3
  FAM20B WILD-TYPE  310   45
                               clus
vv                              FAM20B MUTATED FAM20B WILD-TYPE
  COLON ADENOCARCINOMA                       7              310
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  FAM20B MUTATED     8   0   0   0
  FAM20B WILD-TYPE 249   2  22  21
D891V9, multiclass
    clus
vv   FAM20B MUTATED FAM20B WILD-TYPE
  R0              8              249
  R1              0                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"
D891V10, 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
D891V11, 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(892) Variable = TM9SF2 MUTATION ANALYSIS
D892V1, survival
                  sevent
clus2                0   1
  TM9SF2 MUTATED     8   2
  TM9SF2 WILD-TYPE 274  71
  TM9SF2 MUTATED TM9SF2 WILD-TYPE 
              10              345 
  TM9SF2 MUTATED TM9SF2 WILD-TYPE 
               2               71 
$`TM9SF2 MUTATED`
TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-A00R TCGA-AA-A01R TCGA-AD-6548 TCGA-AD-6964 
       22.06        63.98         0.99        35.01        21.37        10.88 
TCGA-AU-3779 TCGA-AY-6197 TCGA-AZ-6598 TCGA-CM-6680 
       14.50        21.44        49.41        12.03 

$`TM9SF2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
        4.01        27.02        42.02        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 
        5.79        22.42        27.42         0.20        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        15.75         0.20        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13        83.80        22.36        62.79        61.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  TM9SF2 MUTATED TM9SF2 WILD-TYPE 
            0.99             0.00 
  TM9SF2 MUTATED TM9SF2 WILD-TYPE 
           63.98           140.38 
  TM9SF2 MUTATED TM9SF2 WILD-TYPE 
          21.405           20.120 
[1] "1.0 - 64.0 (21.4)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.1"
D892V2, 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       23       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TM9SF2 MUTATED           1          0          1          0        0
  TM9SF2 WILD-TYPE        18         10         40         31       35
                  vv
clus               STAGE IVA STAGE IVB
  TM9SF2 MUTATED           0         0
  TM9SF2 WILD-TYPE        13         1
D892V3, multiclass
            clus
vv           TM9SF2 MUTATED TM9SF2 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               3              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TM9SF2 MUTATED     0   2   7   1
  TM9SF2 WILD-TYPE   9  66 241  40
D892V4, multiclass
    clus
vv   TM9SF2 MUTATED TM9SF2 WILD-TYPE
  T1              0                9
  T2              2               66
  T3              7              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
  TM9SF2 MUTATED     7   0   3
  TM9SF2 WILD-TYPE 213  80  63
D892V5, multiclass
    clus
vv   TM9SF2 MUTATED TM9SF2 WILD-TYPE
  N0              7              213
  N1              0               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"
D892V6, binary
                  cls
clus                 0   1
  TM9SF2 MUTATED     7   0
  TM9SF2 WILD-TYPE 276  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TM9SF2 MUTATED      7    0
  TM9SF2 WILD-TYPE  276   48
   clus
vv  TM9SF2 MUTATED TM9SF2 WILD-TYPE
  0              7              276
  1              0               48
[1] 2 2
[1] FALSE
D892V7, 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
D892V8, binary
                  cls
clus                 0   1
  TM9SF2 MUTATED     9   1
  TM9SF2 WILD-TYPE 308  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TM9SF2 MUTATED      9    1
  TM9SF2 WILD-TYPE  308   47
                               clus
vv                              TM9SF2 MUTATED TM9SF2 WILD-TYPE
  COLON ADENOCARCINOMA                       9              308
  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 249   2  22  21
D892V9, multiclass
    clus
vv   TM9SF2 MUTATED TM9SF2 WILD-TYPE
  R0              8              249
  R1              0                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"
D892V10, 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
D892V11, 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(893) Variable = PAGE2 MUTATION ANALYSIS
D893V1, survival
                 sevent
clus2               0   1
  PAGE2 MUTATED     6   0
  PAGE2 WILD-TYPE 276  73
  PAGE2 MUTATED PAGE2 WILD-TYPE 
              6             349 
  PAGE2 MUTATED PAGE2 WILD-TYPE 
              0              73 
$`PAGE2 MUTATED`
TCGA-AA-3861 TCGA-CM-6162 TCGA-D5-5539 TCGA-DM-A282 TCGA-G4-6299 TCGA-G4-6625 
       30.05        12.00        19.59       139.17        74.56        91.79 

$`PAGE2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        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        12.26        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      135.65         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 
       13.25         0.53        35.41        19.43       107.67        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        26.17        46.75 
TCGA-G4-6628 
       52.80 

  PAGE2 MUTATED PAGE2 WILD-TYPE 
             12               0 
  PAGE2 MUTATED PAGE2 WILD-TYPE 
         139.17          140.38 
  PAGE2 MUTATED PAGE2 WILD-TYPE 
         52.305          20.120 
[1] "12.0 - 139.2 (52.3)" "0.0 - 140.4 (20.1)" 
[1] "hr="     "2.7e+07"
D893V2, 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       25       105         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        19          9         40         30       34        13
                 vv
clus              STAGE IVB
  PAGE2 MUTATED           0
  PAGE2 WILD-TYPE         1
D893V3, multiclass
            clus
vv           PAGE2 MUTATED PAGE2 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              4             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             1              40
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PAGE2 MUTATED     0   0   7   1
  PAGE2 WILD-TYPE   9  68 241  40
D893V4, multiclass
    clus
vv   PAGE2 MUTATED PAGE2 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             7             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
  PAGE2 MUTATED     4   2   2
  PAGE2 WILD-TYPE 216  78  64
D893V5, multiclass
    clus
vv   PAGE2 MUTATED PAGE2 WILD-TYPE
  N0             4             216
  N1             2              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"
D893V6, binary
                 cls
clus                0   1
  PAGE2 MUTATED     7   1
  PAGE2 WILD-TYPE 276  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAGE2 MUTATED      7    1
  PAGE2 WILD-TYPE  276   47
   clus
vv  PAGE2 MUTATED PAGE2 WILD-TYPE
  0             7             276
  1             1              47
[1] 2 2
[1] FALSE
D893V7, 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
D893V8, binary
                 cls
clus                0   1
  PAGE2 MUTATED     5   3
  PAGE2 WILD-TYPE 312  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAGE2 MUTATED      5    3
  PAGE2 WILD-TYPE  312   45
                               clus
vv                              PAGE2 MUTATED PAGE2 WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  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 251   2  21  21
D893V9, multiclass
    clus
vv   PAGE2 MUTATED PAGE2 WILD-TYPE
  R0             6             251
  R1             0               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"
D893V10, 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
D893V11, 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(894) Variable = E2F5 MUTATION ANALYSIS
D894V1, survival
                sevent
clus2              0   1
  E2F5 MUTATED     6   0
  E2F5 WILD-TYPE 276  73
  E2F5 MUTATED E2F5 WILD-TYPE 
             6            349 
  E2F5 MUTATED E2F5 WILD-TYPE 
             0             73 
$`E2F5 MUTATED`
TCGA-AA-3947 TCGA-AZ-4315 TCGA-CA-6716 TCGA-CA-6717 TCGA-D5-6536 TCGA-F4-6856 
       33.01        58.39         0.26         0.33        17.85        19.43 

$`E2F5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        43.27        15.12         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        35.41       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  E2F5 MUTATED E2F5 WILD-TYPE 
          0.26           0.00 
  E2F5 MUTATED E2F5 WILD-TYPE 
         58.39         140.38 
  E2F5 MUTATED E2F5 WILD-TYPE 
         18.64          20.28 
[1] "0.3 - 58.4 (18.6)"  "0.0 - 140.4 (20.3)"
[1] "hr="     "9100000"
D894V2, 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       25       105         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        19         10         41         31       34        13
                vv
clus             STAGE IVB
  E2F5 MUTATED           0
  E2F5 WILD-TYPE         1
D894V3, multiclass
            clus
vv           E2F5 MUTATED E2F5 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             4            105
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  E2F5 MUTATED     0   1   4   2
  E2F5 WILD-TYPE   9  67 244  39
D894V4, multiclass
    clus
vv   E2F5 MUTATED E2F5 WILD-TYPE
  T1            0              9
  T2            1             67
  T3            4            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
  E2F5 MUTATED     6   1   0
  E2F5 WILD-TYPE 214  79  66
D894V5, multiclass
    clus
vv   E2F5 MUTATED E2F5 WILD-TYPE
  N0            6            214
  N1            1             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
  E2F5 MUTATED     6   1
  E2F5 WILD-TYPE 277  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  E2F5 MUTATED      6    1
  E2F5 WILD-TYPE  277   47
   clus
vv  E2F5 MUTATED E2F5 WILD-TYPE
  0            6            277
  1            1             47
[1] 2 2
[1] FALSE
D894V7, 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
D894V8, binary
                cls
clus               0   1
  E2F5 MUTATED     4   3
  E2F5 WILD-TYPE 313  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  E2F5 MUTATED      4    3
  E2F5 WILD-TYPE  313   45
                               clus
vv                              E2F5 MUTATED E2F5 WILD-TYPE
  COLON ADENOCARCINOMA                     4            313
  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 253   2  21  19
D894V9, multiclass
    clus
vv   E2F5 MUTATED E2F5 WILD-TYPE
  R0            4            253
  R1            0              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"
D894V10, 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
D894V11, 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(895) Variable = GNA14 MUTATION ANALYSIS
D895V1, survival
                 sevent
clus2               0   1
  GNA14 MUTATED     8   2
  GNA14 WILD-TYPE 274  71
  GNA14 MUTATED GNA14 WILD-TYPE 
             10             345 
  GNA14 MUTATED GNA14 WILD-TYPE 
              2              71 
$`GNA14 MUTATED`
TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3543 TCGA-AA-3821 TCGA-AA-3877 TCGA-AA-3966 
       63.98        13.02         0.99         1.02        31.00         2.01 
TCGA-AY-6197 TCGA-D5-5538 TCGA-DM-A1HB TCGA-DM-A28G 
       21.44        12.26       135.65        60.79 

$`GNA14 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        1.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
       12.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       33.04         0.99        25.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       26.01        24.00         2.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        15.75         0.20        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  GNA14 MUTATED GNA14 WILD-TYPE 
           0.99            0.00 
  GNA14 MUTATED GNA14 WILD-TYPE 
         135.65          140.38 
  GNA14 MUTATED GNA14 WILD-TYPE 
          17.23           20.19 
[1] "1.0 - 135.7 (17.2)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.3"
D895V2, 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       24       106         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        18         10         39         31       35        13
                 vv
clus              STAGE IVB
  GNA14 MUTATED           0
  GNA14 WILD-TYPE         1
D895V3, multiclass
            clus
vv           GNA14 MUTATED GNA14 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              3             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GNA14 MUTATED     1   2   7   0
  GNA14 WILD-TYPE   8  66 241  41
D895V4, multiclass
    clus
vv   GNA14 MUTATED GNA14 WILD-TYPE
  T1             1               8
  T2             2              66
  T3             7             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
  GNA14 MUTATED     7   2   1
  GNA14 WILD-TYPE 213  78  65
D895V5, multiclass
    clus
vv   GNA14 MUTATED GNA14 WILD-TYPE
  N0             7             213
  N1             2              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"
D895V6, binary
                 cls
clus                0   1
  GNA14 MUTATED     9   0
  GNA14 WILD-TYPE 274  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNA14 MUTATED      9    0
  GNA14 WILD-TYPE  274   48
   clus
vv  GNA14 MUTATED GNA14 WILD-TYPE
  0             9             274
  1             0              48
[1] 2 2
[1] FALSE
D895V7, 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
D895V8, binary
                 cls
clus                0   1
  GNA14 MUTATED     5   5
  GNA14 WILD-TYPE 312  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNA14 MUTATED      5    5
  GNA14 WILD-TYPE  312   43
                               clus
vv                              GNA14 MUTATED GNA14 WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  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 251   2  22  21
D895V9, multiclass
    clus
vv   GNA14 MUTATED GNA14 WILD-TYPE
  R0             6             251
  R1             0               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"
D895V10, 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
D895V11, 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(896) Variable = SLC2A3 MUTATION ANALYSIS
D896V1, survival
                  sevent
clus2                0   1
  SLC2A3 MUTATED    10   1
  SLC2A3 WILD-TYPE 272  72
  SLC2A3 MUTATED SLC2A3 WILD-TYPE 
              11              344 
  SLC2A3 MUTATED SLC2A3 WILD-TYPE 
               1               72 
$`SLC2A3 MUTATED`
TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6781 TCGA-AA-A01D TCGA-AY-5543 TCGA-AZ-4315 
       22.06         8.38        19.66        10.98        15.75        58.39 
TCGA-CK-4950 TCGA-CM-6676 TCGA-DM-A1HA TCGA-G4-6588 TCGA-G4-6628 
       40.34        11.08       131.51        26.17        52.80 

$`SLC2A3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.09        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       34.98        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        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-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-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
        1.35        17.56       102.44        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 
       91.79        46.75 

  SLC2A3 MUTATED SLC2A3 WILD-TYPE 
            8.38             0.00 
  SLC2A3 MUTATED SLC2A3 WILD-TYPE 
          131.51           140.38 
  SLC2A3 MUTATED SLC2A3 WILD-TYPE 
          22.060           20.155 
[1] "8.4 - 131.5 (22.1)" "0.0 - 140.4 (20.2)"
[1] "hr=" "3.1"
D896V2, 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       25       105         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC2A3 MUTATED           0          1          0          3        0
  SLC2A3 WILD-TYPE        19          9         41         28       35
                  vv
clus               STAGE IVA STAGE IVB
  SLC2A3 MUTATED           1         0
  SLC2A3 WILD-TYPE        12         1
D896V3, multiclass
            clus
vv           SLC2A3 MUTATED SLC2A3 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               4              105
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              1                9
  STAGE IIIB              0               41
  STAGE IIIC              3               28
  STAGE IV                0               35
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 240  40
D896V4, multiclass
    clus
vv   SLC2A3 MUTATED SLC2A3 WILD-TYPE
  T1              0                9
  T2              2               66
  T3              8              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
  SLC2A3 MUTATED     6   3   2
  SLC2A3 WILD-TYPE 214  77  64
D896V5, multiclass
    clus
vv   SLC2A3 MUTATED SLC2A3 WILD-TYPE
  N0              6              214
  N1              3               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"
D896V6, binary
                  cls
clus                 0   1
  SLC2A3 MUTATED     9   1
  SLC2A3 WILD-TYPE 274  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC2A3 MUTATED      9    1
  SLC2A3 WILD-TYPE  274   47
   clus
vv  SLC2A3 MUTATED SLC2A3 WILD-TYPE
  0              9              274
  1              1               47
[1] 2 2
[1] FALSE
D896V7, 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
D896V8, binary
                  cls
clus                 0   1
  SLC2A3 MUTATED     9   2
  SLC2A3 WILD-TYPE 308  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC2A3 MUTATED      9    2
  SLC2A3 WILD-TYPE  308   46
                               clus
vv                              SLC2A3 MUTATED SLC2A3 WILD-TYPE
  COLON ADENOCARCINOMA                       9              308
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SLC2A3 MUTATED     8   1   0   0
  SLC2A3 WILD-TYPE 249   1  22  21
D896V9, multiclass
    clus
vv   SLC2A3 MUTATED SLC2A3 WILD-TYPE
  R0              8              249
  R1              1                1
  R2              0               22
  RX              0               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D896V10, 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
D896V11, 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(897) Variable = UBA3 MUTATION ANALYSIS
D897V1, survival
                sevent
clus2              0   1
  UBA3 MUTATED     4   1
  UBA3 WILD-TYPE 278  72
  UBA3 MUTATED UBA3 WILD-TYPE 
             5            350 
  UBA3 MUTATED UBA3 WILD-TYPE 
             1             72 
$`UBA3 MUTATED`
TCGA-A6-3809 TCGA-AA-3489 TCGA-AA-3510 TCGA-AZ-5407 TCGA-CM-5349 
       32.75         7.04        63.98        61.41        30.08 

$`UBA3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  UBA3 MUTATED UBA3 WILD-TYPE 
          7.04           0.00 
  UBA3 MUTATED UBA3 WILD-TYPE 
         63.98         140.38 
  UBA3 MUTATED UBA3 WILD-TYPE 
         32.75          20.07 
[1] "7.0 - 64.0 (32.8)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.6"
D897V2, 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       23       107         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        19         10         41         31       35        13
                vv
clus             STAGE IVB
  UBA3 MUTATED           0
  UBA3 WILD-TYPE         1
D897V3, multiclass
            clus
vv           UBA3 MUTATED UBA3 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             2            107
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  UBA3 MUTATED     1   0   4   1
  UBA3 WILD-TYPE   8  68 244  40
D897V4, multiclass
    clus
vv   UBA3 MUTATED UBA3 WILD-TYPE
  T1            1              8
  T2            0             68
  T3            4            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
  UBA3 MUTATED     6   0   0
  UBA3 WILD-TYPE 214  80  66
D897V5, multiclass
    clus
vv   UBA3 MUTATED UBA3 WILD-TYPE
  N0            6            214
  N1            0             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
  UBA3 MUTATED     6   0
  UBA3 WILD-TYPE 277  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  UBA3 MUTATED      6    0
  UBA3 WILD-TYPE  277   48
   clus
vv  UBA3 MUTATED UBA3 WILD-TYPE
  0            6            277
  1            0             48
[1] 2 2
[1] FALSE
D897V7, 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
D897V8, binary
                cls
clus               0   1
  UBA3 MUTATED     5   1
  UBA3 WILD-TYPE 312  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  UBA3 MUTATED      5    1
  UBA3 WILD-TYPE  312   47
                               clus
vv                              UBA3 MUTATED UBA3 WILD-TYPE
  COLON ADENOCARCINOMA                     5            312
  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 252   2  22  21
D897V9, multiclass
    clus
vv   UBA3 MUTATED UBA3 WILD-TYPE
  R0            5            252
  R1            0              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"
D897V10, 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
D897V11, 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(898) Variable = KTN1 MUTATION ANALYSIS
D898V1, survival
                sevent
clus2              0   1
  KTN1 MUTATED    14   2
  KTN1 WILD-TYPE 268  71
  KTN1 MUTATED KTN1 WILD-TYPE 
            16            339 
  KTN1 MUTATED KTN1 WILD-TYPE 
             2             71 
$`KTN1 MUTATED`
TCGA-A6-2672 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5665 TCGA-AA-3518 TCGA-AA-A00E 
       46.65        33.53        23.61        22.06         1.02        30.02 
TCGA-AA-A00N TCGA-AA-A01R TCGA-AD-6889 TCGA-AD-6895 TCGA-AZ-4315 TCGA-CM-6162 
        4.01        35.01        56.55         0.72        58.39        12.00 
TCGA-CM-6171 TCGA-D5-6540 TCGA-F4-6703 TCGA-G4-6303 
       14.04        16.14        35.87        65.85 

$`KTN1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 
       31.63        30.44        29.19        22.09        32.71        27.09 
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 
       22.52         8.38        25.08        25.18        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        7.04         3.02         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
        1.02        13.02        38.99         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J 
       27.02        13.94        38.04        19.00        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45         6.18         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  KTN1 MUTATED KTN1 WILD-TYPE 
          0.72           0.00 
  KTN1 MUTATED KTN1 WILD-TYPE 
         65.85         140.38 
  KTN1 MUTATED KTN1 WILD-TYPE 
        26.815         20.020 
[1] "0.7 - 65.8 (26.8)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1.8"
D898V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KTN1 MUTATED         2        0        0         7         1         0
  KTN1 WILD-TYPE      62        1       25       102         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KTN1 MUTATED           2          0          2          0        1         1
  KTN1 WILD-TYPE        17         10         39         31       34        12
                vv
clus             STAGE IVB
  KTN1 MUTATED           0
  KTN1 WILD-TYPE         1
D898V3, multiclass
            clus
vv           KTN1 MUTATED KTN1 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             7            102
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             2             17
  STAGE IIIA            0             10
  STAGE IIIB            2             39
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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   1
  KTN1 WILD-TYPE   9  66 234  40
D898V4, multiclass
    clus
vv   KTN1 MUTATED KTN1 WILD-TYPE
  T1            0              9
  T2            2             66
  T3           14            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
  KTN1 MUTATED    10   4   3
  KTN1 WILD-TYPE 210  76  63
D898V5, multiclass
    clus
vv   KTN1 MUTATED KTN1 WILD-TYPE
  N0           10            210
  N1            4             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"
D898V6, binary
                cls
clus               0   1
  KTN1 MUTATED    14   2
  KTN1 WILD-TYPE 269  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  KTN1 MUTATED     14    2
  KTN1 WILD-TYPE  269   46
   clus
vv  KTN1 MUTATED KTN1 WILD-TYPE
  0           14            269
  1            2             46
[1] 2 2
[1] FALSE
D898V7, binary
                cls
clus               0   1
  KTN1 MUTATED     7  10
  KTN1 WILD-TYPE 163 187
[1] "tbl2"
                cls
clus             [,1] [,2]
  KTN1 MUTATED      7   10
  KTN1 WILD-TYPE  163  187
        clus
vv       KTN1 MUTATED KTN1 WILD-TYPE
  FEMALE            7            163
  MALE             10            187
[1] 2 2
[1] FALSE
D898V8, binary
                cls
clus               0   1
  KTN1 MUTATED    13   4
  KTN1 WILD-TYPE 304  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  KTN1 MUTATED     13    4
  KTN1 WILD-TYPE  304   44
                               clus
vv                              KTN1 MUTATED KTN1 WILD-TYPE
  COLON ADENOCARCINOMA                    13            304
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  KTN1 MUTATED    14   0   0   0
  KTN1 WILD-TYPE 243   2  22  21
D898V9, multiclass
    clus
vv   KTN1 MUTATED KTN1 WILD-TYPE
  R0           14            243
  R1            0              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"
D898V10, 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
D898V11, 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(899) Variable = MAGEB2 MUTATION ANALYSIS
D899V1, survival
                  sevent
clus2                0   1
  MAGEB2 MUTATED     6   4
  MAGEB2 WILD-TYPE 276  69
  MAGEB2 MUTATED MAGEB2 WILD-TYPE 
              10              345 
  MAGEB2 MUTATED MAGEB2 WILD-TYPE 
               4               69 
$`MAGEB2 MUTATED`
TCGA-AA-3950 TCGA-AA-A02H TCGA-AZ-4315 TCGA-AZ-6608 TCGA-CM-5349 TCGA-D5-6539 
       24.00         2.01        58.39         1.94        30.08        12.49 
TCGA-D5-6924 TCGA-DM-A0XF TCGA-F4-6809 TCGA-G4-6588 
       14.30        38.20        13.25        26.17 

$`MAGEB2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       51.98        39.98         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38        10.26       119.70        24.43       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       16.24        33.67         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  MAGEB2 MUTATED MAGEB2 WILD-TYPE 
            1.94             0.00 
  MAGEB2 MUTATED MAGEB2 WILD-TYPE 
           58.39           140.38 
  MAGEB2 MUTATED MAGEB2 WILD-TYPE 
           19.15            20.19 
[1] "1.9 - 58.4 (19.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2.3"
D899V2, 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       25       103         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAGEB2 MUTATED           0          2          0          1        1
  MAGEB2 WILD-TYPE        19          8         41         30       34
                  vv
clus               STAGE IVA STAGE IVB
  MAGEB2 MUTATED           1         0
  MAGEB2 WILD-TYPE        12         1
D899V3, multiclass
            clus
vv           MAGEB2 MUTATED MAGEB2 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               6              103
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              2                8
  STAGE IIIB              0               41
  STAGE IIIC              1               30
  STAGE IV                1               34
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 238  41
D899V4, multiclass
    clus
vv   MAGEB2 MUTATED MAGEB2 WILD-TYPE
  T1              0                9
  T2              1               67
  T3             10              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
  MAGEB2 MUTATED     7   2   2
  MAGEB2 WILD-TYPE 213  78  64
D899V5, multiclass
    clus
vv   MAGEB2 MUTATED MAGEB2 WILD-TYPE
  N0              7              213
  N1              2               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"
D899V6, binary
                  cls
clus                 0   1
  MAGEB2 MUTATED     9   2
  MAGEB2 WILD-TYPE 274  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGEB2 MUTATED      9    2
  MAGEB2 WILD-TYPE  274   46
   clus
vv  MAGEB2 MUTATED MAGEB2 WILD-TYPE
  0              9              274
  1              2               46
[1] 2 2
[1] FALSE
D899V7, 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
D899V8, binary
                  cls
clus                 0   1
  MAGEB2 MUTATED     9   2
  MAGEB2 WILD-TYPE 308  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGEB2 MUTATED      9    2
  MAGEB2 WILD-TYPE  308   46
                               clus
vv                              MAGEB2 MUTATED MAGEB2 WILD-TYPE
  COLON ADENOCARCINOMA                       9              308
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  MAGEB2 MUTATED     8   0   1   0
  MAGEB2 WILD-TYPE 249   2  21  21
D899V9, multiclass
    clus
vv   MAGEB2 MUTATED MAGEB2 WILD-TYPE
  R0              8              249
  R1              0                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"
D899V10, 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
D899V11, 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(900) Variable = AXIN2 MUTATION ANALYSIS
D900V1, survival
                 sevent
clus2               0   1
  AXIN2 MUTATED    13   7
  AXIN2 WILD-TYPE 269  66
  AXIN2 MUTATED AXIN2 WILD-TYPE 
             20             335 
  AXIN2 MUTATED AXIN2 WILD-TYPE 
              7              66 
$`AXIN2 MUTATED`
TCGA-A6-2676 TCGA-A6-5661 TCGA-AA-3492 TCGA-AA-3542 TCGA-AA-3672 TCGA-AA-3972 
       42.90        33.53         3.02        12.99         0.92        50.99 
TCGA-AA-A00E TCGA-AA-A010 TCGA-AD-5900 TCGA-AD-6964 TCGA-CA-5255 TCGA-CK-5916 
       30.02        34.98         0.07        10.88         3.06        21.14 
TCGA-CM-5349 TCGA-CM-6162 TCGA-D5-6537 TCGA-D5-6930 TCGA-DM-A1D6 TCGA-DM-A1DB 
       30.08        12.00         4.80         1.51        49.91        44.32 
TCGA-G4-6304 TCGA-G4-6628 
       53.62        52.80 

$`AXIN2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 
       19.07        34.03        29.00        29.00        26.01         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       21.99        16.08        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        19.00        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        2.24         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32        21.99         2.93         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        16.01        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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-A285 
      140.38         7.50       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 
       35.41        19.43       107.67        74.56        65.85        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       13.78        35.80        26.17        91.79        46.75 

  AXIN2 MUTATED AXIN2 WILD-TYPE 
           0.07            0.00 
  AXIN2 MUTATED AXIN2 WILD-TYPE 
          53.62          140.38 
  AXIN2 MUTATED AXIN2 WILD-TYPE 
          25.58           20.12 
[1] "0.1 - 53.6 (25.6)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.8"
D900V2, 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       23       102         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        18         10         39         30       34        13
                 vv
clus              STAGE IVB
  AXIN2 MUTATED           0
  AXIN2 WILD-TYPE         1
D900V3, multiclass
            clus
vv           AXIN2 MUTATED AXIN2 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              7             102
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  AXIN2 MUTATED     1   2  13   5
  AXIN2 WILD-TYPE   8  66 235  36
D900V4, multiclass
    clus
vv   AXIN2 MUTATED AXIN2 WILD-TYPE
  T1             1               8
  T2             2              66
  T3            13             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
  AXIN2 MUTATED    15   4   2
  AXIN2 WILD-TYPE 205  76  64
D900V5, multiclass
    clus
vv   AXIN2 MUTATED AXIN2 WILD-TYPE
  N0            15             205
  N1             4              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"
D900V6, binary
                 cls
clus                0   1
  AXIN2 MUTATED    17   1
  AXIN2 WILD-TYPE 266  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AXIN2 MUTATED     17    1
  AXIN2 WILD-TYPE  266   47
   clus
vv  AXIN2 MUTATED AXIN2 WILD-TYPE
  0            17             266
  1             1              47
[1] 2 2
[1] FALSE
D900V7, 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
D900V8, binary
                 cls
clus                0   1
  AXIN2 MUTATED    17   4
  AXIN2 WILD-TYPE 300  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AXIN2 MUTATED     17    4
  AXIN2 WILD-TYPE  300   44
                               clus
vv                              AXIN2 MUTATED AXIN2 WILD-TYPE
  COLON ADENOCARCINOMA                     17             300
  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 242   2  21  19
D900V9, multiclass
    clus
vv   AXIN2 MUTATED AXIN2 WILD-TYPE
  R0            15             242
  R1             0               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"
D900V10, 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
D900V11, 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(901) Variable = MTA2 MUTATION ANALYSIS
D901V1, survival
                sevent
clus2              0   1
  MTA2 MUTATED     7   5
  MTA2 WILD-TYPE 275  68
  MTA2 MUTATED MTA2 WILD-TYPE 
            12            343 
  MTA2 MUTATED MTA2 WILD-TYPE 
             5             68 
$`MTA2 MUTATED`
TCGA-A6-2672 TCGA-AA-3492 TCGA-AA-3713 TCGA-AA-3950 TCGA-AA-3977 TCGA-AA-A01D 
       46.65         3.02        19.04        24.00        25.02        10.98 
TCGA-AY-4071 TCGA-AZ-6601 TCGA-CM-5344 TCGA-F4-6809 TCGA-G4-6299 TCGA-G4-6588 
        0.95       100.01        22.03        13.25        74.56        26.17 

$`MTA2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 
       33.67         0.53        35.41        19.43       107.67        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 
       52.80 

  MTA2 MUTATED MTA2 WILD-TYPE 
          0.95           0.00 
  MTA2 MUTATED MTA2 WILD-TYPE 
        100.01         140.38 
  MTA2 MUTATED MTA2 WILD-TYPE 
        23.015         20.120 
[1] "0.9 - 100.0 (23.0)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.7"
D901V2, 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       23       107         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        19         10         39         29       34        12
                vv
clus             STAGE IVB
  MTA2 MUTATED           0
  MTA2 WILD-TYPE         1
D901V3, multiclass
            clus
vv           MTA2 MUTATED MTA2 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             2            107
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            2             39
  STAGE IIIC            2             29
  STAGE IV              1             34
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 238  41
D901V4, multiclass
    clus
vv   MTA2 MUTATED MTA2 WILD-TYPE
  T1            1              8
  T2            1             67
  T3           10            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
  MTA2 MUTATED     7   3   2
  MTA2 WILD-TYPE 213  77  64
D901V5, multiclass
    clus
vv   MTA2 MUTATED MTA2 WILD-TYPE
  N0            7            213
  N1            3             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"
D901V6, binary
                cls
clus               0   1
  MTA2 MUTATED     8   2
  MTA2 WILD-TYPE 275  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTA2 MUTATED      8    2
  MTA2 WILD-TYPE  275   46
   clus
vv  MTA2 MUTATED MTA2 WILD-TYPE
  0            8            275
  1            2             46
[1] 2 2
[1] FALSE
D901V7, 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
D901V8, binary
                cls
clus               0   1
  MTA2 MUTATED     9   2
  MTA2 WILD-TYPE 308  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTA2 MUTATED      9    2
  MTA2 WILD-TYPE  308   46
                               clus
vv                              MTA2 MUTATED MTA2 WILD-TYPE
  COLON ADENOCARCINOMA                     9            308
  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 248   2  21  21
D901V9, multiclass
    clus
vv   MTA2 MUTATED MTA2 WILD-TYPE
  R0            9            248
  R1            0              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"
D901V10, 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
D901V11, 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(902) Variable = CPS1 MUTATION ANALYSIS
D902V1, survival
                sevent
clus2              0   1
  CPS1 MUTATED    24   5
  CPS1 WILD-TYPE 258  68
  CPS1 MUTATED CPS1 WILD-TYPE 
            29            326 
  CPS1 MUTATED CPS1 WILD-TYPE 
             5             68 
$`CPS1 MUTATED`
TCGA-A6-5660 TCGA-A6-5665 TCGA-AA-3516 TCGA-AA-3672 TCGA-AA-3811 TCGA-AA-3861 
       29.19        22.06        13.02         0.92        10.06        30.05 
TCGA-AA-3947 TCGA-AA-3968 TCGA-AA-3977 TCGA-AA-A010 TCGA-AA-A01K TCGA-AD-6889 
       33.01        21.99        25.02        34.98        31.00        56.55 
TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-5861 
       58.39         0.33         0.10        23.05        37.02        15.02 
TCGA-CM-6169 TCGA-CM-6172 TCGA-D5-5541 TCGA-D5-6537 TCGA-D5-6930 TCGA-DM-A0XF 
       13.02        11.01        11.51         4.80         1.51        38.20 
TCGA-DM-A1D6 TCGA-G4-6299 TCGA-G4-6307 TCGA-G4-6321 TCGA-G4-6628 
       49.91        74.56        55.04        22.09        52.80 

$`CPS1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        19.04        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03         2.01        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P 
       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        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37         4.21         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07         0.26         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 
        2.93         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-5862 
       29.06        22.03        22.98        30.08        16.01         5.03 
TCGA-CM-5863 TCGA-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-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       14.04        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        13.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         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-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        92.75        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 
       19.43       107.67        65.85        53.62        44.68        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       45.11        36.72        36.00        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 
       91.79        46.75 

  CPS1 MUTATED CPS1 WILD-TYPE 
           0.1            0.0 
  CPS1 MUTATED CPS1 WILD-TYPE 
         74.56         140.38 
  CPS1 MUTATED CPS1 WILD-TYPE 
         23.05          19.99 
[1] "0.1 - 74.6 (23.1)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1.3"
D902V2, 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       25        97         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        15         10         37         27       35        13
                vv
clus             STAGE IVB
  CPS1 MUTATED           0
  CPS1 WILD-TYPE         1
D902V3, multiclass
            clus
vv           CPS1 MUTATED CPS1 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA            12             97
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             4             15
  STAGE IIIA            0             10
  STAGE IIIB            4             37
  STAGE IIIC            4             27
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CPS1 MUTATED     0   5  23   2
  CPS1 WILD-TYPE   9  63 225  39
D902V4, multiclass
    clus
vv   CPS1 MUTATED CPS1 WILD-TYPE
  T1            0              9
  T2            5             63
  T3           23            225
  T4            2             39
[1] 4 2
[1] TRUE
[1] "dimension 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  74  60
D902V5, multiclass
    clus
vv   CPS1 MUTATED CPS1 WILD-TYPE
  N0           18            202
  N1            6             74
  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"
D902V6, binary
                cls
clus               0   1
  CPS1 MUTATED    27   0
  CPS1 WILD-TYPE 256  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  CPS1 MUTATED     27    0
  CPS1 WILD-TYPE  256   48
   clus
vv  CPS1 MUTATED CPS1 WILD-TYPE
  0           27            256
  1            0             48
[1] 2 2
[1] FALSE
D902V7, 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
D902V8, binary
                cls
clus               0   1
  CPS1 MUTATED    24   6
  CPS1 WILD-TYPE 293  42
[1] "tbl2"
                cls
clus             [,1] [,2]
  CPS1 MUTATED     24    6
  CPS1 WILD-TYPE  293   42
                               clus
vv                              CPS1 MUTATED CPS1 WILD-TYPE
  COLON ADENOCARCINOMA                    24            293
  COLON MUCINOUS ADENOCARCINOMA            6             42
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CPS1 MUTATED    22   0   0   2
  CPS1 WILD-TYPE 235   2  22  19
D902V9, multiclass
    clus
vv   CPS1 MUTATED CPS1 WILD-TYPE
  R0           22            235
  R1            0              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"
D902V10, 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
D902V11, 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(903) Variable = SLC27A2 MUTATION ANALYSIS
D903V1, survival
                   sevent
clus2                 0   1
  SLC27A2 MUTATED     4   1
  SLC27A2 WILD-TYPE 278  72
  SLC27A2 MUTATED SLC27A2 WILD-TYPE 
                5               350 
  SLC27A2 MUTATED SLC27A2 WILD-TYPE 
                1                72 
$`SLC27A2 MUTATED`
TCGA-A6-5657 TCGA-AA-3510 TCGA-AA-A01D TCGA-D5-6533 TCGA-F4-6856 
       31.63        63.98        10.98         1.32        19.43 

$`SLC27A2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        35.41       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  SLC27A2 MUTATED SLC27A2 WILD-TYPE 
             1.32              0.00 
  SLC27A2 MUTATED SLC27A2 WILD-TYPE 
            63.98            140.38 
  SLC27A2 MUTATED SLC27A2 WILD-TYPE 
           19.430            20.235 
[1] "1.3 - 64.0 (19.4)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D903V2, 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       24       108         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC27A2 MUTATED           0          0          2          1        0
  SLC27A2 WILD-TYPE        19         10         39         30       35
                   vv
clus                STAGE IVA STAGE IVB
  SLC27A2 MUTATED           0         0
  SLC27A2 WILD-TYPE        13         1
D903V3, multiclass
            clus
vv           SLC27A2 MUTATED SLC27A2 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                1               108
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               2                39
  STAGE IIIC               1                30
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC27A2 MUTATED     0   1   4   1
  SLC27A2 WILD-TYPE   9  67 244  40
D903V4, multiclass
    clus
vv   SLC27A2 MUTATED SLC27A2 WILD-TYPE
  T1               0                 9
  T2               1                67
  T3               4               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
  SLC27A2 MUTATED     4   1   1
  SLC27A2 WILD-TYPE 216  79  65
D903V5, multiclass
    clus
vv   SLC27A2 MUTATED SLC27A2 WILD-TYPE
  N0               4               216
  N1               1                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"
D903V6, binary
                   cls
clus                  0   1
  SLC27A2 MUTATED     6   0
  SLC27A2 WILD-TYPE 277  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC27A2 MUTATED      6    0
  SLC27A2 WILD-TYPE  277   48
   clus
vv  SLC27A2 MUTATED SLC27A2 WILD-TYPE
  0               6               277
  1               0                48
[1] 2 2
[1] FALSE
D903V7, 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
D903V8, binary
                   cls
clus                  0   1
  SLC27A2 MUTATED     4   2
  SLC27A2 WILD-TYPE 313  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC27A2 MUTATED      4    2
  SLC27A2 WILD-TYPE  313   46
                               clus
vv                              SLC27A2 MUTATED SLC27A2 WILD-TYPE
  COLON ADENOCARCINOMA                        4               313
  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 251   2  22  21
D903V9, multiclass
    clus
vv   SLC27A2 MUTATED SLC27A2 WILD-TYPE
  R0               6               251
  R1               0                 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"
D903V10, 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
D903V11, 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(904) Variable = MOV10 MUTATION ANALYSIS
D904V1, survival
                 sevent
clus2               0   1
  MOV10 MUTATED    13   0
  MOV10 WILD-TYPE 269  73
  MOV10 MUTATED MOV10 WILD-TYPE 
             13             342 
  MOV10 MUTATED MOV10 WILD-TYPE 
              0              73 
$`MOV10 MUTATED`
TCGA-A6-6781 TCGA-AA-3655 TCGA-AA-3812 TCGA-AA-3966 TCGA-AA-A00E TCGA-AU-3779 
       19.66        61.02        35.05         2.01        30.02        14.50 
TCGA-CK-4947 TCGA-CK-5914 TCGA-CM-5344 TCGA-CM-5349 TCGA-DM-A1HA TCGA-G4-6293 
       17.56        21.99        22.03        30.08       131.51       107.67 
TCGA-G4-6586 
       35.80 

$`MOV10 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F 
        7.96        27.02        13.94        38.04        19.00        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 
        5.79        22.42        27.42        10.88         0.20        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
        1.35       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 
       12.59       140.38         7.50        44.32       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        35.41        19.43        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        26.17        91.79        46.75        52.80 

  MOV10 MUTATED MOV10 WILD-TYPE 
           2.01            0.00 
  MOV10 MUTATED MOV10 WILD-TYPE 
         131.51          140.38 
  MOV10 MUTATED MOV10 WILD-TYPE 
         30.020          20.005 
[1] "2.0 - 131.5 (30.0)" "0.0 - 140.4 (20.0)"
[1] "hr="     "2.7e+07"
D904V2, 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       24       103         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MOV10 MUTATED           1          0          2          2        0         1
  MOV10 WILD-TYPE        18         10         39         29       35        12
                 vv
clus              STAGE IVB
  MOV10 MUTATED           0
  MOV10 WILD-TYPE         1
D904V3, multiclass
            clus
vv           MOV10 MUTATED MOV10 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              6             103
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             2              29
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  68 237  39
D904V4, multiclass
    clus
vv   MOV10 MUTATED MOV10 WILD-TYPE
  T1             0               9
  T2             0              68
  T3            11             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
  MOV10 MUTATED     7   5   1
  MOV10 WILD-TYPE 213  75  65
D904V5, multiclass
    clus
vv   MOV10 MUTATED MOV10 WILD-TYPE
  N0             7             213
  N1             5              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"
D904V6, binary
                 cls
clus                0   1
  MOV10 MUTATED    11   0
  MOV10 WILD-TYPE 272  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MOV10 MUTATED     11    0
  MOV10 WILD-TYPE  272   48
   clus
vv  MOV10 MUTATED MOV10 WILD-TYPE
  0            11             272
  1             0              48
[1] 2 2
[1] FALSE
D904V7, 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
D904V8, binary
                 cls
clus                0   1
  MOV10 MUTATED    11   2
  MOV10 WILD-TYPE 306  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MOV10 MUTATED     11    2
  MOV10 WILD-TYPE  306   46
                               clus
vv                              MOV10 MUTATED MOV10 WILD-TYPE
  COLON ADENOCARCINOMA                     11             306
  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 248   2  22  19
D904V9, multiclass
    clus
vv   MOV10 MUTATED MOV10 WILD-TYPE
  R0             9             248
  R1             0               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"
D904V10, 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
D904V11, 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(905) Variable = IFNAR1 MUTATION ANALYSIS
D905V1, survival
                  sevent
clus2                0   1
  IFNAR1 MUTATED     6   1
  IFNAR1 WILD-TYPE 276  72
  IFNAR1 MUTATED IFNAR1 WILD-TYPE 
               7              348 
  IFNAR1 MUTATED IFNAR1 WILD-TYPE 
               1               72 
$`IFNAR1 MUTATED`
TCGA-AA-3672 TCGA-AA-3815 TCGA-AA-3855 TCGA-AA-A010 TCGA-CK-5912 TCGA-CM-5860 
        0.92        33.04        32.05        34.98        49.08        16.01 
TCGA-CM-6678 
       11.01 

$`IFNAR1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
        6.05         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 
       10.06         0.00        33.07         0.00        36.03         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
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         2.93         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-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  IFNAR1 MUTATED IFNAR1 WILD-TYPE 
            0.92             0.00 
  IFNAR1 MUTATED IFNAR1 WILD-TYPE 
           49.08           140.38 
  IFNAR1 MUTATED IFNAR1 WILD-TYPE 
          32.050           20.155 
[1] "0.9 - 49.1 (32.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.3"
D905V2, 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       25       107         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IFNAR1 MUTATED           1          0          0          0        0
  IFNAR1 WILD-TYPE        18         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  IFNAR1 MUTATED           1         0
  IFNAR1 WILD-TYPE        12         1
D905V3, multiclass
            clus
vv           IFNAR1 MUTATED IFNAR1 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               2              107
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 245  39
D905V4, multiclass
    clus
vv   IFNAR1 MUTATED IFNAR1 WILD-TYPE
  T1              0                9
  T2              2               66
  T3              3              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
  IFNAR1 MUTATED     5   2   0
  IFNAR1 WILD-TYPE 215  78  66
D905V5, multiclass
    clus
vv   IFNAR1 MUTATED IFNAR1 WILD-TYPE
  N0              5              215
  N1              2               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"
D905V6, binary
                  cls
clus                 0   1
  IFNAR1 MUTATED     5   1
  IFNAR1 WILD-TYPE 278  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFNAR1 MUTATED      5    1
  IFNAR1 WILD-TYPE  278   47
   clus
vv  IFNAR1 MUTATED IFNAR1 WILD-TYPE
  0              5              278
  1              1               47
[1] 2 2
[1] FALSE
D905V7, 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
D905V8, binary
                  cls
clus                 0   1
  IFNAR1 MUTATED     7   0
  IFNAR1 WILD-TYPE 310  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFNAR1 MUTATED      7    0
  IFNAR1 WILD-TYPE  310   48
                               clus
vv                              IFNAR1 MUTATED IFNAR1 WILD-TYPE
  COLON ADENOCARCINOMA                       7              310
  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 251   2  22  20
D905V9, multiclass
    clus
vv   IFNAR1 MUTATED IFNAR1 WILD-TYPE
  R0              6              251
  R1              0                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"
D905V10, 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
D905V11, 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(906) Variable = DCBLD1 MUTATION ANALYSIS
D906V1, survival
                  sevent
clus2                0   1
  DCBLD1 MUTATED     4   1
  DCBLD1 WILD-TYPE 278  72
  DCBLD1 MUTATED DCBLD1 WILD-TYPE 
               5              350 
  DCBLD1 MUTATED DCBLD1 WILD-TYPE 
               1               72 
$`DCBLD1 MUTATED`
TCGA-A6-6781 TCGA-AA-3697 TCGA-AA-3977 TCGA-D5-6922 TCGA-DM-A28G 
       19.66        85.05        25.02        10.13        60.79 

$`DCBLD1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H 
      139.17         6.12        81.37       119.93        35.97       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  DCBLD1 MUTATED DCBLD1 WILD-TYPE 
           10.13             0.00 
  DCBLD1 MUTATED DCBLD1 WILD-TYPE 
           85.05           140.38 
  DCBLD1 MUTATED DCBLD1 WILD-TYPE 
          25.020           20.155 
[1] "10.1 - 85.0 (25.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.6"
D906V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DCBLD1 MUTATED         0        0        0         1         0         0
  DCBLD1 WILD-TYPE      64        1       25       108         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DCBLD1 MUTATED           1          1          0          1        0
  DCBLD1 WILD-TYPE        18          9         41         30       35
                  vv
clus               STAGE IVA STAGE IVB
  DCBLD1 MUTATED           0         0
  DCBLD1 WILD-TYPE        13         1
D906V3, multiclass
            clus
vv           DCBLD1 MUTATED DCBLD1 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               1              108
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              1                9
  STAGE IIIB              0               41
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  DCBLD1 MUTATED     0   1   3   1
  DCBLD1 WILD-TYPE   9  67 245  40
D906V4, multiclass
    clus
vv   DCBLD1 MUTATED DCBLD1 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              3              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
  DCBLD1 MUTATED     3   2   0
  DCBLD1 WILD-TYPE 217  78  66
D906V5, multiclass
    clus
vv   DCBLD1 MUTATED DCBLD1 WILD-TYPE
  N0              3              217
  N1              2               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"
D906V6, binary
                  cls
clus                 0   1
  DCBLD1 MUTATED     3   0
  DCBLD1 WILD-TYPE 280  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DCBLD1 MUTATED      3    0
  DCBLD1 WILD-TYPE  280   48
   clus
vv  DCBLD1 MUTATED DCBLD1 WILD-TYPE
  0              3              280
  1              0               48
[1] 2 2
[1] FALSE
D906V7, 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
D906V8, binary
                  cls
clus                 0   1
  DCBLD1 MUTATED     4   1
  DCBLD1 WILD-TYPE 313  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DCBLD1 MUTATED      4    1
  DCBLD1 WILD-TYPE  313   47
                               clus
vv                              DCBLD1 MUTATED DCBLD1 WILD-TYPE
  COLON ADENOCARCINOMA                       4              313
  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 254   2  22  21
D906V9, multiclass
    clus
vv   DCBLD1 MUTATED DCBLD1 WILD-TYPE
  R0              3              254
  R1              0                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"
D906V10, 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
D906V11, 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(907) Variable = SYNE1 MUTATION ANALYSIS
D907V1, survival
                 sevent
clus2               0   1
  SYNE1 MUTATED    91  24
  SYNE1 WILD-TYPE 191  49
  SYNE1 MUTATED SYNE1 WILD-TYPE 
            115             240 
  SYNE1 MUTATED SYNE1 WILD-TYPE 
             24              49 
$`SYNE1 MUTATED`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2683 TCGA-A6-3808 
       43.76        46.65        42.90        24.33        16.57        33.34 
TCGA-A6-4105 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6141 
       14.53        29.19        33.53        22.06        32.71         8.38 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3492 
       25.18        24.16        21.76        19.66        20.28         3.02 
TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3543 
       63.98        13.02         1.02        37.05         8.05         0.99 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3562 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       29.95        20.98        19.99         6.97        54.02         2.01 
TCGA-AA-3672 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3833 TCGA-AA-3845 
        0.92        85.05        26.99        19.04        15.95         0.00 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3875 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3977 
        0.00        36.03        18.05        26.01        24.00        25.02 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A00E TCGA-AA-A00N TCGA-AA-A00U 
       27.02         7.96        27.02        30.02         4.01        17.03 
TCGA-AA-A010 TCGA-AA-A01Q TCGA-AA-A02K TCGA-AA-A02W TCGA-AD-5900 TCGA-AD-6888 
       34.98         1.02        14.01        41.00         0.07         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6197 
       56.55         0.79         0.72        27.09        15.75        21.44 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-CA-5797 
       58.39         1.41        61.41        49.41         6.77         3.29 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4952 TCGA-CK-6751 
        0.26         0.33         0.10         1.35        15.62       124.27 
TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       23.05        37.02        13.02        29.06        22.03        22.98 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6171 
       15.02        15.02        15.02        15.02        12.00        14.04 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 
       11.01        10.06        12.03        12.26        13.51        11.51 
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 
        1.51        12.00        38.20       140.38        44.32       135.65 
TCGA-DM-A285 TCGA-DM-A28F TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6809 
        6.12        35.97        13.38         6.18        35.87        13.25 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 
       51.75        45.11        22.09        35.80        26.17        46.75 
TCGA-G4-6628 
       52.80 

$`SYNE1 WILD-TYPE`
TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       43.76        42.28        34.65        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-6137 TCGA-A6-6138 
       31.63        30.44        23.61        22.09        27.09        22.52 
TCGA-A6-6142 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-AA-3489 
       25.08        24.69        24.39        23.87        20.12         7.04 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 
        1.02        35.01         6.97         1.02        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       24.03        36.03        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
       29.00        29.00        26.01        12.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       21.01        13.02        24.00        17.95        23.01        19.99 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3667 TCGA-AA-3673 
       13.94        61.02        78.08         6.05        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       36.00         5.03        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 
        0.99        25.02         1.02        17.98        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3855 
       14.93        17.03        10.06         0.00        33.07        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3986 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       24.00        27.02        19.07        13.94        38.04        19.00 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03F 
       39.98         2.01         5.03         0.92        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       40.96        21.37         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6386 
        0.20        14.50        16.31         0.95         0.20        17.82 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6600 TCGA-AZ-6601 
        5.13        83.80        22.36        62.79        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        3.06         3.25         0.07        17.56       102.44        40.34 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         2.01 
TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5868 
       20.02        25.02        30.08        16.01         5.03        17.03 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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-D5-5537 TCGA-D5-5539 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       11.08        45.40        19.59        20.19        18.25         1.32 
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-D5-6926 TCGA-D5-6932 
        7.53        12.39        10.13        12.43         9.04        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-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-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 
      119.93        60.79       117.07        98.24         8.61        13.45 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 
        1.55        16.31        29.59        16.24        33.67         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6625 
       44.68        55.04        36.72        36.00        13.78        91.79 

  SYNE1 MUTATED SYNE1 WILD-TYPE 
              0               0 
  SYNE1 MUTATED SYNE1 WILD-TYPE 
         140.38          139.17 
  SYNE1 MUTATED SYNE1 WILD-TYPE 
         19.040          21.075 
[1] "0.0 - 140.4 (19.0)" "0.0 - 139.2 (21.1)"
[1] "hr=" "1.1"
D907V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SYNE1 MUTATED        15        0        7        40         5         1
  SYNE1 WILD-TYPE      49        1       18        69         3         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SYNE1 MUTATED           6          2         21          6        8         4
  SYNE1 WILD-TYPE        13          8         20         25       27         9
                 vv
clus              STAGE IVB
  SYNE1 MUTATED           0
  SYNE1 WILD-TYPE         1
D907V3, multiclass
            clus
vv           SYNE1 MUTATED SYNE1 WILD-TYPE
  STAGE I               15              49
  STAGE IA               0               1
  STAGE II               7              18
  STAGE IIA             40              69
  STAGE IIB              5               3
  STAGE IIC              1               0
  STAGE III              6              13
  STAGE IIIA             2               8
  STAGE IIIB            21              20
  STAGE IIIC             6              25
  STAGE IV               8              27
  STAGE IVA              4               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
  SYNE1 MUTATED     3  17  84  14
  SYNE1 WILD-TYPE   6  51 164  27
D907V4, multiclass
    clus
vv   SYNE1 MUTATED SYNE1 WILD-TYPE
  T1             3               6
  T2            17              51
  T3            84             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  30  13
  SYNE1 WILD-TYPE 146  50  53
D907V5, multiclass
    clus
vv   SYNE1 MUTATED SYNE1 WILD-TYPE
  N0            74             146
  N1            30              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"
D907V6, binary
                 cls
clus                0   1
  SYNE1 MUTATED    93  12
  SYNE1 WILD-TYPE 190  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYNE1 MUTATED     93   12
  SYNE1 WILD-TYPE  190   36
   clus
vv  SYNE1 MUTATED SYNE1 WILD-TYPE
  0            93             190
  1            12              36
[1] 2 2
[1] FALSE
D907V7, 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
D907V8, binary
                 cls
clus                0   1
  SYNE1 MUTATED    97  21
  SYNE1 WILD-TYPE 220  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYNE1 MUTATED     97   21
  SYNE1 WILD-TYPE  220   27
                               clus
vv                              SYNE1 MUTATED SYNE1 WILD-TYPE
  COLON ADENOCARCINOMA                     97             220
  COLON MUCINOUS ADENOCARCINOMA            21              27
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SYNE1 MUTATED    83   0   4   7
  SYNE1 WILD-TYPE 174   2  18  14
D907V9, multiclass
    clus
vv   SYNE1 MUTATED SYNE1 WILD-TYPE
  R0            83             174
  R1             0               2
  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"
D907V10, 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
D907V11, 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(908) Variable = PTPDC1 MUTATION ANALYSIS
D908V1, survival
                  sevent
clus2                0   1
  PTPDC1 MUTATED     8   1
  PTPDC1 WILD-TYPE 274  72
  PTPDC1 MUTATED PTPDC1 WILD-TYPE 
               9              346 
  PTPDC1 MUTATED PTPDC1 WILD-TYPE 
               1               72 
$`PTPDC1 MUTATED`
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3672 TCGA-AD-6895 TCGA-AU-6004 TCGA-CM-4743 
       24.00        17.95         0.92         0.72        27.09        23.05 
TCGA-CM-6675 TCGA-DM-A1DA TCGA-G4-6588 
       13.05         7.50        26.17 

$`PTPDC1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       21.01        13.02        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB 
       92.75        49.91        13.32        12.59       140.38        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        91.79        46.75        52.80 

  PTPDC1 MUTATED PTPDC1 WILD-TYPE 
            0.72             0.00 
  PTPDC1 MUTATED PTPDC1 WILD-TYPE 
           27.09           140.38 
  PTPDC1 MUTATED PTPDC1 WILD-TYPE 
          17.950           20.235 
[1] "0.7 - 27.1 (17.9)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D908V2, 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       25       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PTPDC1 MUTATED           1          0          0          1        0
  PTPDC1 WILD-TYPE        18         10         41         30       35
                  vv
clus               STAGE IVA STAGE IVB
  PTPDC1 MUTATED           0         1
  PTPDC1 WILD-TYPE        13         0
D908V3, multiclass
            clus
vv           PTPDC1 MUTATED PTPDC1 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               3              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  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   7   0
  PTPDC1 WILD-TYPE   9  66 241  41
D908V4, multiclass
    clus
vv   PTPDC1 MUTATED PTPDC1 WILD-TYPE
  T1              0                9
  T2              2               66
  T3              7              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
  PTPDC1 MUTATED     5   2   2
  PTPDC1 WILD-TYPE 215  78  64
D908V5, multiclass
    clus
vv   PTPDC1 MUTATED PTPDC1 WILD-TYPE
  N0              5              215
  N1              2               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"
D908V6, binary
                  cls
clus                 0   1
  PTPDC1 MUTATED     7   1
  PTPDC1 WILD-TYPE 276  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPDC1 MUTATED      7    1
  PTPDC1 WILD-TYPE  276   47
   clus
vv  PTPDC1 MUTATED PTPDC1 WILD-TYPE
  0              7              276
  1              1               47
[1] 2 2
[1] FALSE
D908V7, binary
                  cls
clus                 0   1
  PTPDC1 MUTATED     6   3
  PTPDC1 WILD-TYPE 164 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPDC1 MUTATED      6    3
  PTPDC1 WILD-TYPE  164  194
        clus
vv       PTPDC1 MUTATED PTPDC1 WILD-TYPE
  FEMALE              6              164
  MALE                3              194
[1] 2 2
[1] FALSE
D908V8, binary
                  cls
clus                 0   1
  PTPDC1 MUTATED     9   0
  PTPDC1 WILD-TYPE 308  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPDC1 MUTATED      9    0
  PTPDC1 WILD-TYPE  308   48
                               clus
vv                              PTPDC1 MUTATED PTPDC1 WILD-TYPE
  COLON ADENOCARCINOMA                       9              308
  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 250   2  22  21
D908V9, multiclass
    clus
vv   PTPDC1 MUTATED PTPDC1 WILD-TYPE
  R0              7              250
  R1              0                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"
D908V10, 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
D908V11, 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(909) Variable = RSPO2 MUTATION ANALYSIS
D909V1, survival
                 sevent
clus2               0   1
  RSPO2 MUTATED    13   3
  RSPO2 WILD-TYPE 269  70
  RSPO2 MUTATED RSPO2 WILD-TYPE 
             16             339 
  RSPO2 MUTATED RSPO2 WILD-TYPE 
              3              70 
$`RSPO2 MUTATED`
TCGA-A6-5659 TCGA-A6-6651 TCGA-A6-6654 TCGA-AA-3855 TCGA-AA-3947 TCGA-AA-A010 
       30.44        21.76        23.87        32.05        33.01        34.98 
TCGA-AZ-6605 TCGA-CA-5796 TCGA-CA-6718 TCGA-CM-5349 TCGA-CM-6680 TCGA-D5-6929 
        5.23         3.25         0.10        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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       25.18        24.16        24.69        24.39        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 
        0.00        33.07         0.00        36.03         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5797 
       11.74         3.19         1.94         2.24         3.06         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.33         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
      119.93        35.97        60.79         8.61        13.38        13.45 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  RSPO2 MUTATED RSPO2 WILD-TYPE 
            0.1             0.0 
  RSPO2 MUTATED RSPO2 WILD-TYPE 
         117.07          140.38 
  RSPO2 MUTATED RSPO2 WILD-TYPE 
         26.975          20.020 
[1] "0.1 - 117.1 (27.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.4"
D909V2, 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       25       102         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        19         10         37         30       34        13
                 vv
clus              STAGE IVB
  RSPO2 MUTATED           0
  RSPO2 WILD-TYPE         1
D909V3, multiclass
            clus
vv           RSPO2 MUTATED RSPO2 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              7             102
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             4              37
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RSPO2 MUTATED     0   2  12   3
  RSPO2 WILD-TYPE   9  66 236  38
D909V4, multiclass
    clus
vv   RSPO2 MUTATED RSPO2 WILD-TYPE
  T1             0               9
  T2             2              66
  T3            12             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
  RSPO2 MUTATED    11   4   2
  RSPO2 WILD-TYPE 209  76  64
D909V5, multiclass
    clus
vv   RSPO2 MUTATED RSPO2 WILD-TYPE
  N0            11             209
  N1             4              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"
D909V6, binary
                 cls
clus                0   1
  RSPO2 MUTATED    15   1
  RSPO2 WILD-TYPE 268  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RSPO2 MUTATED     15    1
  RSPO2 WILD-TYPE  268   47
   clus
vv  RSPO2 MUTATED RSPO2 WILD-TYPE
  0            15             268
  1             1              47
[1] 2 2
[1] FALSE
D909V7, 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
D909V8, binary
                 cls
clus                0   1
  RSPO2 MUTATED    14   3
  RSPO2 WILD-TYPE 303  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RSPO2 MUTATED     14    3
  RSPO2 WILD-TYPE  303   45
                               clus
vv                              RSPO2 MUTATED RSPO2 WILD-TYPE
  COLON ADENOCARCINOMA                     14             303
  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 247   2  22  20
D909V9, multiclass
    clus
vv   RSPO2 MUTATED RSPO2 WILD-TYPE
  R0            10             247
  R1             0               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"
D909V10, 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
D909V11, 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(910) Variable = ZNF605 MUTATION ANALYSIS
D910V1, survival
                  sevent
clus2                0   1
  ZNF605 MUTATED     6   2
  ZNF605 WILD-TYPE 276  71
  ZNF605 MUTATED ZNF605 WILD-TYPE 
               8              347 
  ZNF605 MUTATED ZNF605 WILD-TYPE 
               2               71 
$`ZNF605 MUTATED`
TCGA-A6-2672 TCGA-A6-6141 TCGA-AZ-4315 TCGA-AZ-6608 TCGA-CA-6718 TCGA-D5-6539 
       46.65         8.38        58.39         1.94         0.10        12.49 
TCGA-DM-A0XD TCGA-G4-6588 
       24.43        26.17 

$`ZNF605 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.33         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        11.38        10.26       119.70        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        91.79        46.75        52.80 

  ZNF605 MUTATED ZNF605 WILD-TYPE 
             0.1              0.0 
  ZNF605 MUTATED ZNF605 WILD-TYPE 
           58.39           140.38 
  ZNF605 MUTATED ZNF605 WILD-TYPE 
           18.46            20.19 
[1] "0.1 - 58.4 (18.5)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.4"
D910V2, 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       25       104         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF605 MUTATED           0          2          1          0        0
  ZNF605 WILD-TYPE        19          8         40         31       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF605 MUTATED           0         0
  ZNF605 WILD-TYPE        13         1
D910V3, multiclass
            clus
vv           ZNF605 MUTATED ZNF605 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               5              104
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              2                8
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF605 MUTATED     0   1   7   0
  ZNF605 WILD-TYPE   9  67 241  41
D910V4, multiclass
    clus
vv   ZNF605 MUTATED ZNF605 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              7              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
  ZNF605 MUTATED     6   2   0
  ZNF605 WILD-TYPE 214  78  66
D910V5, multiclass
    clus
vv   ZNF605 MUTATED ZNF605 WILD-TYPE
  N0              6              214
  N1              2               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"
D910V6, binary
                  cls
clus                 0   1
  ZNF605 MUTATED     8   0
  ZNF605 WILD-TYPE 275  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF605 MUTATED      8    0
  ZNF605 WILD-TYPE  275   48
   clus
vv  ZNF605 MUTATED ZNF605 WILD-TYPE
  0              8              275
  1              0               48
[1] 2 2
[1] FALSE
D910V7, 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
D910V8, binary
                  cls
clus                 0   1
  ZNF605 MUTATED     8   0
  ZNF605 WILD-TYPE 309  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF605 MUTATED      8    0
  ZNF605 WILD-TYPE  309   48
                               clus
vv                              ZNF605 MUTATED ZNF605 WILD-TYPE
  COLON ADENOCARCINOMA                       8              309
  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 253   2  22  20
D910V9, multiclass
    clus
vv   ZNF605 MUTATED ZNF605 WILD-TYPE
  R0              4              253
  R1              0                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"
D910V10, 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
D910V11, 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(911) Variable = WDR75 MUTATION ANALYSIS
D911V1, survival
                 sevent
clus2               0   1
  WDR75 MUTATED     4   3
  WDR75 WILD-TYPE 278  70
  WDR75 MUTATED WDR75 WILD-TYPE 
              7             348 
  WDR75 MUTATED WDR75 WILD-TYPE 
              3              70 
$`WDR75 MUTATED`
TCGA-AA-3856 TCGA-AA-3977 TCGA-AA-A00E TCGA-AA-A00N TCGA-AD-6899 TCGA-CM-4747 
        0.99        25.02        30.02         4.01         5.79        25.02 
TCGA-F4-6570 
        6.18 

$`WDR75 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       19.00        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        0.72        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-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        13.38        13.45        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  WDR75 MUTATED WDR75 WILD-TYPE 
           0.99            0.00 
  WDR75 MUTATED WDR75 WILD-TYPE 
          30.02          140.38 
  WDR75 MUTATED WDR75 WILD-TYPE 
          6.180          20.235 
[1] "1.0 - 30.0 (6.2)"   "0.0 - 140.4 (20.2)"
[1] "hr=" "3.8"
D911V2, 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       25       105         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        19         10         41         30       35        12
                 vv
clus              STAGE IVB
  WDR75 MUTATED           0
  WDR75 WILD-TYPE         1
D911V3, multiclass
            clus
vv           WDR75 MUTATED WDR75 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              4             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 244  38
D911V4, multiclass
    clus
vv   WDR75 MUTATED WDR75 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             4             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
  WDR75 MUTATED     6   1   1
  WDR75 WILD-TYPE 214  79  65
D911V5, multiclass
    clus
vv   WDR75 MUTATED WDR75 WILD-TYPE
  N0             6             214
  N1             1              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"
D911V6, binary
                 cls
clus                0   1
  WDR75 MUTATED     5   1
  WDR75 WILD-TYPE 278  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR75 MUTATED      5    1
  WDR75 WILD-TYPE  278   47
   clus
vv  WDR75 MUTATED WDR75 WILD-TYPE
  0             5             278
  1             1              47
[1] 2 2
[1] FALSE
D911V7, 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
D911V8, binary
                 cls
clus                0   1
  WDR75 MUTATED     6   2
  WDR75 WILD-TYPE 311  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR75 MUTATED      6    2
  WDR75 WILD-TYPE  311   46
                               clus
vv                              WDR75 MUTATED WDR75 WILD-TYPE
  COLON ADENOCARCINOMA                      6             311
  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 251   2  22  21
D911V9, multiclass
    clus
vv   WDR75 MUTATED WDR75 WILD-TYPE
  R0             6             251
  R1             0               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"
D911V10, 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
D911V11, 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(912) Variable = SLITRK2 MUTATION ANALYSIS
D912V1, survival
                   sevent
clus2                 0   1
  SLITRK2 MUTATED    17   3
  SLITRK2 WILD-TYPE 265  70
  SLITRK2 MUTATED SLITRK2 WILD-TYPE 
               20               335 
  SLITRK2 MUTATED SLITRK2 WILD-TYPE 
                3                70 
$`SLITRK2 MUTATED`
TCGA-A6-2678 TCGA-A6-5666 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3672 
       42.28        32.71         3.02        63.98        29.95         0.92 
TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-3977 TCGA-AA-A010 TCGA-AU-6004 TCGA-AZ-6601 
       53.00        33.01        25.02        34.98        27.09       100.01 
TCGA-AZ-6608 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5913 TCGA-CM-5348 TCGA-D5-6532 
        1.94         0.33         0.10        51.32        22.98        18.25 
TCGA-D5-6930 TCGA-F4-6808 
        1.51        33.67 

$`SLITRK2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2683 
       43.76        46.65        43.76        42.90        24.33        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       19.66        20.28         7.04         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        61.41        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         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07         0.26         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       40.34        15.62        49.08        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       29.59        16.24        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  SLITRK2 MUTATED SLITRK2 WILD-TYPE 
              0.1               0.0 
  SLITRK2 MUTATED SLITRK2 WILD-TYPE 
           100.01            140.38 
  SLITRK2 MUTATED SLITRK2 WILD-TYPE 
            28.52             19.99 
[1] "0.1 - 100.0 (28.5)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.5"
D912V2, 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       21       103         6         0
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLITRK2 MUTATED           1          1          2          0        0
  SLITRK2 WILD-TYPE        18          9         39         31       35
                   vv
clus                STAGE IVA STAGE IVB
  SLITRK2 MUTATED           0         0
  SLITRK2 WILD-TYPE        13         1
D912V3, multiclass
            clus
vv           SLITRK2 MUTATED SLITRK2 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 4                21
  STAGE IIA                6               103
  STAGE IIB                2                 6
  STAGE IIC                1                 0
  STAGE III                1                18
  STAGE IIIA               1                 9
  STAGE IIIB               2                39
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLITRK2 MUTATED     1   4  13   3
  SLITRK2 WILD-TYPE   8  64 235  38
D912V4, multiclass
    clus
vv   SLITRK2 MUTATED SLITRK2 WILD-TYPE
  T1               1                 8
  T2               4                64
  T3              13               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
  SLITRK2 MUTATED    17   4   0
  SLITRK2 WILD-TYPE 203  76  66
D912V5, multiclass
    clus
vv   SLITRK2 MUTATED SLITRK2 WILD-TYPE
  N0              17               203
  N1               4                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"
D912V6, binary
                   cls
clus                  0   1
  SLITRK2 MUTATED    18   0
  SLITRK2 WILD-TYPE 265  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLITRK2 MUTATED     18    0
  SLITRK2 WILD-TYPE  265   48
   clus
vv  SLITRK2 MUTATED SLITRK2 WILD-TYPE
  0              18               265
  1               0                48
[1] 2 2
[1] FALSE
D912V7, 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
D912V8, binary
                   cls
clus                  0   1
  SLITRK2 MUTATED    17   4
  SLITRK2 WILD-TYPE 300  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLITRK2 MUTATED     17    4
  SLITRK2 WILD-TYPE  300   44
                               clus
vv                              SLITRK2 MUTATED SLITRK2 WILD-TYPE
  COLON ADENOCARCINOMA                       17               300
  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 244   2  22  17
D912V9, multiclass
    clus
vv   SLITRK2 MUTATED SLITRK2 WILD-TYPE
  R0              13               244
  R1               0                 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"
D912V10, 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
D912V11, 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(913) Variable = OR51A4 MUTATION ANALYSIS
D913V1, survival
                  sevent
clus2                0   1
  OR51A4 MUTATED     5   1
  OR51A4 WILD-TYPE 277  72
  OR51A4 MUTATED OR51A4 WILD-TYPE 
               6              349 
  OR51A4 MUTATED OR51A4 WILD-TYPE 
               1               72 
$`OR51A4 MUTATED`
TCGA-A6-6781 TCGA-AA-3821 TCGA-AA-3864 TCGA-AD-6899 TCGA-D5-6535 TCGA-D5-6540 
       19.66         1.02        53.00         5.79        15.12        16.14 

$`OR51A4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 
       10.06        35.05        33.04         0.99        25.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         0.72        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        43.27        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  OR51A4 MUTATED OR51A4 WILD-TYPE 
            1.02             0.00 
  OR51A4 MUTATED OR51A4 WILD-TYPE 
           53.00           140.38 
  OR51A4 MUTATED OR51A4 WILD-TYPE 
           15.63            20.98 
[1] "1.0 - 53.0 (15.6)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1"  
D913V2, 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       24       108         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR51A4 MUTATED           0          0          1          2        0
  OR51A4 WILD-TYPE        19         10         40         29       35
                  vv
clus               STAGE IVA STAGE IVB
  OR51A4 MUTATED           0         0
  OR51A4 WILD-TYPE        13         1
D913V3, multiclass
            clus
vv           OR51A4 MUTATED OR51A4 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               1              108
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              2               29
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  OR51A4 MUTATED     0   2   3   3
  OR51A4 WILD-TYPE   9  66 245  38
D913V4, multiclass
    clus
vv   OR51A4 MUTATED OR51A4 WILD-TYPE
  T1              0                9
  T2              2               66
  T3              3              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
  OR51A4 MUTATED     5   2   1
  OR51A4 WILD-TYPE 215  78  65
D913V5, multiclass
    clus
vv   OR51A4 MUTATED OR51A4 WILD-TYPE
  N0              5              215
  N1              2               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"
D913V6, binary
                  cls
clus                 0   1
  OR51A4 MUTATED     4   0
  OR51A4 WILD-TYPE 279  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51A4 MUTATED      4    0
  OR51A4 WILD-TYPE  279   48
   clus
vv  OR51A4 MUTATED OR51A4 WILD-TYPE
  0              4              279
  1              0               48
[1] 2 2
[1] FALSE
D913V7, 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
D913V8, binary
                  cls
clus                 0   1
  OR51A4 MUTATED     4   4
  OR51A4 WILD-TYPE 313  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51A4 MUTATED      4    4
  OR51A4 WILD-TYPE  313   44
                               clus
vv                              OR51A4 MUTATED OR51A4 WILD-TYPE
  COLON ADENOCARCINOMA                       4              313
  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 252   2  22  19
D913V9, multiclass
    clus
vv   OR51A4 MUTATED OR51A4 WILD-TYPE
  R0              5              252
  R1              0                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"
D913V10, 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
D913V11, 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(914) Variable = UBR2 MUTATION ANALYSIS
D914V1, survival
                sevent
clus2              0   1
  UBR2 MUTATED    11   3
  UBR2 WILD-TYPE 271  70
  UBR2 MUTATED UBR2 WILD-TYPE 
            14            341 
  UBR2 MUTATED UBR2 WILD-TYPE 
             3             70 
$`UBR2 MUTATED`
TCGA-A6-5666 TCGA-AA-3558 TCGA-AA-3864 TCGA-AA-3966 TCGA-AA-A010 TCGA-AA-A01Q 
       32.71        20.98        53.00         2.01        34.98         1.02 
TCGA-AZ-4315 TCGA-CA-6715 TCGA-CA-6717 TCGA-D5-6922 TCGA-D5-6930 TCGA-DM-A1DA 
       58.39         0.07         0.33        10.13         1.51         7.50 
TCGA-DM-A285 TCGA-DM-A28F 
        6.12        35.97 

$`UBR2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3560 
       13.02        24.00        17.95        29.95        23.01        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         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        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  UBR2 MUTATED UBR2 WILD-TYPE 
          0.07           0.00 
  UBR2 MUTATED UBR2 WILD-TYPE 
         58.39         140.38 
  UBR2 MUTATED UBR2 WILD-TYPE 
         8.815         20.280 
[1] "0.1 - 58.4 (8.8)"   "0.0 - 140.4 (20.3)"
[1] "hr=" "1.4"
D914V2, 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       23       104         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        19          9         39         30       34        13
                vv
clus             STAGE IVB
  UBR2 MUTATED           0
  UBR2 WILD-TYPE         1
D914V3, multiclass
            clus
vv           UBR2 MUTATED UBR2 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             5            104
  STAGE IIB             1              7
  STAGE IIC             1              0
  STAGE III             0             19
  STAGE IIIA            1              9
  STAGE IIIB            2             39
  STAGE IIIC            1             30
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  UBR2 MUTATED     0   1  12   2
  UBR2 WILD-TYPE   9  67 236  39
D914V4, multiclass
    clus
vv   UBR2 MUTATED UBR2 WILD-TYPE
  T1            0              9
  T2            1             67
  T3           12            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
  UBR2 MUTATED    10   3   2
  UBR2 WILD-TYPE 210  77  64
D914V5, multiclass
    clus
vv   UBR2 MUTATED UBR2 WILD-TYPE
  N0           10            210
  N1            3             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"
D914V6, binary
                cls
clus               0   1
  UBR2 MUTATED    14   1
  UBR2 WILD-TYPE 269  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  UBR2 MUTATED     14    1
  UBR2 WILD-TYPE  269   47
   clus
vv  UBR2 MUTATED UBR2 WILD-TYPE
  0           14            269
  1            1             47
[1] 2 2
[1] FALSE
D914V7, 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
D914V8, binary
                cls
clus               0   1
  UBR2 MUTATED    11   4
  UBR2 WILD-TYPE 306  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  UBR2 MUTATED     11    4
  UBR2 WILD-TYPE  306   44
                               clus
vv                              UBR2 MUTATED UBR2 WILD-TYPE
  COLON ADENOCARCINOMA                    11            306
  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 250   2  21  19
D914V9, multiclass
    clus
vv   UBR2 MUTATED UBR2 WILD-TYPE
  R0            7            250
  R1            0              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"
D914V10, 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
D914V11, 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(915) Variable = ZKSCAN1 MUTATION ANALYSIS
D915V1, survival
                   sevent
clus2                 0   1
  ZKSCAN1 MUTATED     5   2
  ZKSCAN1 WILD-TYPE 277  71
  ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE 
                7               348 
  ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE 
                2                71 
$`ZKSCAN1 MUTATED`
TCGA-AA-3492 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3864 TCGA-AA-A00J TCGA-AD-5900 
        3.02        13.02         1.02        53.00        18.05         0.07 
TCGA-G4-6293 
      107.67 

$`ZKSCAN1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 
       35.01        63.98         6.97         1.02        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.41        19.43        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE 
             0.07              0.00 
  ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE 
           107.67            140.38 
  ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE 
            13.02             20.63 
[1] "0.1 - 107.7 (13.0)" "0.0 - 140.4 (20.6)"
[1] "hr=" "1.2"
D915V2, 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       23       108         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZKSCAN1 MUTATED           2          0          1          0        0
  ZKSCAN1 WILD-TYPE        17         10         40         31       35
                   vv
clus                STAGE IVA STAGE IVB
  ZKSCAN1 MUTATED           0         0
  ZKSCAN1 WILD-TYPE        13         1
D915V3, multiclass
            clus
vv           ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 2                23
  STAGE IIA                1               108
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                2                17
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ZKSCAN1 MUTATED     0   1   5   1
  ZKSCAN1 WILD-TYPE   9  67 243  40
D915V4, multiclass
    clus
vv   ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE
  T1               0                 9
  T2               1                67
  T3               5               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
  ZKSCAN1 MUTATED     4   2   1
  ZKSCAN1 WILD-TYPE 216  78  65
D915V5, multiclass
    clus
vv   ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE
  N0               4               216
  N1               2                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"
D915V6, binary
                   cls
clus                  0   1
  ZKSCAN1 MUTATED     6   0
  ZKSCAN1 WILD-TYPE 277  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZKSCAN1 MUTATED      6    0
  ZKSCAN1 WILD-TYPE  277   48
   clus
vv  ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE
  0               6               277
  1               0                48
[1] 2 2
[1] FALSE
D915V7, 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
D915V8, binary
                   cls
clus                  0   1
  ZKSCAN1 MUTATED     4   3
  ZKSCAN1 WILD-TYPE 313  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZKSCAN1 MUTATED      4    3
  ZKSCAN1 WILD-TYPE  313   45
                               clus
vv                              ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE
  COLON ADENOCARCINOMA                        4               313
  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 251   2  22  21
D915V9, multiclass
    clus
vv   ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE
  R0               6               251
  R1               0                 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"
D915V10, 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
D915V11, multiclass
[1] "Remove cluster labels:" "ZKSCAN1 MUTATED"       
clus
  ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE 
                2               204 
       TCGA-A6-2671        TCGA-A6-2672        TCGA-A6-2674        TCGA-A6-2676 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-A6-2677        TCGA-A6-2678        TCGA-A6-2683        TCGA-A6-3807 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-A6-3808        TCGA-A6-3809        TCGA-A6-3810        TCGA-A6-4105 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-A6-5656        TCGA-A6-5657        TCGA-A6-5659        TCGA-A6-5660 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-A6-5661        TCGA-A6-5662        TCGA-A6-5664        TCGA-A6-5665 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-A6-5666        TCGA-A6-6137        TCGA-A6-6138        TCGA-A6-6141 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-A6-6142        TCGA-A6-6648        TCGA-A6-6649        TCGA-A6-6651 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-A6-6652        TCGA-A6-6653        TCGA-A6-6654        TCGA-A6-6780 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-A6-6781        TCGA-A6-6782        TCGA-AD-6548        TCGA-AD-6888 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-AD-6889        TCGA-AD-6890        TCGA-AD-6895        TCGA-AD-6899 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-AD-6901        TCGA-AD-6963        TCGA-AD-6964        TCGA-AD-6965 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-AU-3779        TCGA-AU-6004        TCGA-AY-4070        TCGA-AY-4071 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-AY-5543        TCGA-AY-6196        TCGA-AY-6197        TCGA-AY-6386 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-AZ-4315        TCGA-AZ-4323        TCGA-AZ-4616        TCGA-AZ-4681 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-AZ-4682        TCGA-AZ-5403        TCGA-AZ-5407        TCGA-AZ-6598 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-AZ-6599        TCGA-AZ-6600        TCGA-AZ-6601        TCGA-AZ-6603 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-AZ-6605        TCGA-AZ-6606        TCGA-AZ-6607        TCGA-AZ-6608 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-CA-5254        TCGA-CA-5255        TCGA-CA-5796        TCGA-CA-5797 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-CA-6715        TCGA-CA-6716        TCGA-CA-6717        TCGA-CA-6718 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-CA-6719        TCGA-CK-4947        TCGA-CK-4948        TCGA-CK-4950 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-CK-4952        TCGA-CK-5912        TCGA-CK-5913        TCGA-CK-5914 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-CK-5915        TCGA-CK-5916        TCGA-CK-6746        TCGA-CK-6747 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-CK-6748        TCGA-CK-6751        TCGA-CM-4743        TCGA-CM-4744 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-CM-4746        TCGA-CM-4747        TCGA-CM-4752        TCGA-CM-5341 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-CM-5344        TCGA-CM-5348        TCGA-CM-5349        TCGA-CM-5860 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-CM-5861        TCGA-CM-5862        TCGA-CM-5863        TCGA-CM-5864 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-CM-5868        TCGA-CM-6161        TCGA-CM-6162        TCGA-CM-6163 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-CM-6164        TCGA-CM-6165        TCGA-CM-6166        TCGA-CM-6167 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-CM-6168        TCGA-CM-6169        TCGA-CM-6170        TCGA-CM-6171 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-CM-6172        TCGA-CM-6674        TCGA-CM-6675        TCGA-CM-6676 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-CM-6677        TCGA-CM-6678        TCGA-CM-6679        TCGA-CM-6680 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-D5-5537        TCGA-D5-5538        TCGA-D5-5539        TCGA-D5-5540 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-D5-5541        TCGA-D5-6529        TCGA-D5-6532        TCGA-D5-6533 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-D5-6534        TCGA-D5-6535        TCGA-D5-6536        TCGA-D5-6537 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-D5-6538        TCGA-D5-6539        TCGA-D5-6540        TCGA-D5-6541 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-D5-6898        TCGA-D5-6920        TCGA-D5-6922        TCGA-D5-6923 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-D5-6924        TCGA-D5-6926        TCGA-D5-6927        TCGA-D5-6928 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-D5-6929        TCGA-D5-6930        TCGA-D5-6931        TCGA-D5-6932 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-D5-7000        TCGA-DM-A0X9        TCGA-DM-A0XD        TCGA-DM-A0XF 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-DM-A1D0        TCGA-DM-A1D4        TCGA-DM-A1D6        TCGA-DM-A1D7 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-DM-A1D8        TCGA-DM-A1D9        TCGA-DM-A1DA        TCGA-DM-A1DB 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-DM-A1HA        TCGA-DM-A1HB        TCGA-DM-A282        TCGA-DM-A285 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-DM-A28C        TCGA-DM-A28E        TCGA-DM-A28F        TCGA-DM-A28G 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-DM-A28H        TCGA-DM-A28K        TCGA-F4-6459        TCGA-F4-6460 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-F4-6569        TCGA-F4-6570        TCGA-F4-6703        TCGA-F4-6704 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-F4-6805        TCGA-F4-6806        TCGA-F4-6807        TCGA-F4-6808 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-F4-6809        TCGA-F4-6854        TCGA-F4-6855        TCGA-F4-6856 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-G4-6299        TCGA-G4-6303        TCGA-G4-6304        TCGA-G4-6306 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-G4-6307        TCGA-G4-6309        TCGA-G4-6310        TCGA-G4-6315 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-G4-6317        TCGA-G4-6321        TCGA-G4-6323        TCGA-G4-6586 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-G4-6588        TCGA-G4-6625        TCGA-G4-6626        TCGA-G4-6628 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 

Clustering(916) Variable = HCLS1 MUTATION ANALYSIS
D916V1, survival
                 sevent
clus2               0   1
  HCLS1 MUTATED    13   2
  HCLS1 WILD-TYPE 269  71
  HCLS1 MUTATED HCLS1 WILD-TYPE 
             15             340 
  HCLS1 MUTATED HCLS1 WILD-TYPE 
              2              71 
$`HCLS1 MUTATED`
TCGA-AA-3511 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3548 TCGA-AA-3663 TCGA-AA-3977 
        6.97        13.02         1.02        33.99         6.97        25.02 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-6601 TCGA-CA-6717 
       18.05        18.05        34.98        58.39       100.01         0.33 
TCGA-CM-5861 TCGA-D5-6930 TCGA-G4-6588 
       15.02         1.51        26.17 

$`HCLS1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 
        1.02        35.01        63.98         1.02        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
        0.99        14.01        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.05        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00L 
       13.94        38.04        19.00        30.02        34.03        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        91.79        46.75        52.80 

  HCLS1 MUTATED HCLS1 WILD-TYPE 
           0.33            0.00 
  HCLS1 MUTATED HCLS1 WILD-TYPE 
         100.01          140.38 
  HCLS1 MUTATED HCLS1 WILD-TYPE 
          18.05           20.63 
[1] "0.3 - 100.0 (18.1)" "0.0 - 140.4 (20.6)"
[1] "hr=" "1.5"
D916V2, 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       22       102         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        18         10         40         30       35        13
                 vv
clus              STAGE IVB
  HCLS1 MUTATED           0
  HCLS1 WILD-TYPE         1
D916V3, multiclass
            clus
vv           HCLS1 MUTATED HCLS1 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              7             102
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HCLS1 MUTATED     0   1  11   3
  HCLS1 WILD-TYPE   9  67 237  38
D916V4, multiclass
    clus
vv   HCLS1 MUTATED HCLS1 WILD-TYPE
  T1             0               9
  T2             1              67
  T3            11             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
  HCLS1 MUTATED    12   1   2
  HCLS1 WILD-TYPE 208  79  64
D916V5, multiclass
    clus
vv   HCLS1 MUTATED HCLS1 WILD-TYPE
  N0            12             208
  N1             1              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"
D916V6, binary
                 cls
clus                0   1
  HCLS1 MUTATED    14   0
  HCLS1 WILD-TYPE 269  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HCLS1 MUTATED     14    0
  HCLS1 WILD-TYPE  269   48
   clus
vv  HCLS1 MUTATED HCLS1 WILD-TYPE
  0            14             269
  1             0              48
[1] 2 2
[1] FALSE
D916V7, 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
D916V8, binary
                 cls
clus                0   1
  HCLS1 MUTATED    11   4
  HCLS1 WILD-TYPE 306  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HCLS1 MUTATED     11    4
  HCLS1 WILD-TYPE  306   44
                               clus
vv                              HCLS1 MUTATED HCLS1 WILD-TYPE
  COLON ADENOCARCINOMA                     11             306
  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 246   2  22  20
D916V9, multiclass
    clus
vv   HCLS1 MUTATED HCLS1 WILD-TYPE
  R0            11             246
  R1             0               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"
D916V10, 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
D916V11, 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(917) Variable = PLA2G15 MUTATION ANALYSIS
D917V1, survival
                   sevent
clus2                 0   1
  PLA2G15 MUTATED     2   3
  PLA2G15 WILD-TYPE 280  70
  PLA2G15 MUTATED PLA2G15 WILD-TYPE 
                5               350 
  PLA2G15 MUTATED PLA2G15 WILD-TYPE 
                3                70 
$`PLA2G15 MUTATED`
TCGA-AA-3811 TCGA-AZ-6601 TCGA-CM-4743 TCGA-D5-6534 TCGA-DM-A1D7 
       10.06       100.01        23.05        43.27        13.32 

$`PLA2G15 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14         2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19        18.25         1.32        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 
       24.43        38.20       130.65        92.75        49.91        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  PLA2G15 MUTATED PLA2G15 WILD-TYPE 
            10.06              0.00 
  PLA2G15 MUTATED PLA2G15 WILD-TYPE 
           100.01            140.38 
  PLA2G15 MUTATED PLA2G15 WILD-TYPE 
           23.050            20.155 
[1] "10.1 - 100.0 (23.1)" "0.0 - 140.4 (20.2)" 
[1] "hr=" "2"  
D917V2, 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       24       106         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLA2G15 MUTATED           1          0          0          0        0
  PLA2G15 WILD-TYPE        18         10         41         31       35
                   vv
clus                STAGE IVA STAGE IVB
  PLA2G15 MUTATED           0         0
  PLA2G15 WILD-TYPE        13         1
D917V3, multiclass
            clus
vv           PLA2G15 MUTATED PLA2G15 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                3               106
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PLA2G15 MUTATED     0   0   5   0
  PLA2G15 WILD-TYPE   9  68 243  41
D917V4, multiclass
    clus
vv   PLA2G15 MUTATED PLA2G15 WILD-TYPE
  T1               0                 9
  T2               0                68
  T3               5               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
  PLA2G15 MUTATED     4   0   1
  PLA2G15 WILD-TYPE 216  80  65
D917V5, multiclass
    clus
vv   PLA2G15 MUTATED PLA2G15 WILD-TYPE
  N0               4               216
  N1               0                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"
D917V6, binary
                   cls
clus                  0   1
  PLA2G15 MUTATED     5   0
  PLA2G15 WILD-TYPE 278  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLA2G15 MUTATED      5    0
  PLA2G15 WILD-TYPE  278   48
   clus
vv  PLA2G15 MUTATED PLA2G15 WILD-TYPE
  0               5               278
  1               0                48
[1] 2 2
[1] FALSE
D917V7, 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
D917V8, binary
                   cls
clus                  0   1
  PLA2G15 MUTATED     4   1
  PLA2G15 WILD-TYPE 313  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLA2G15 MUTATED      4    1
  PLA2G15 WILD-TYPE  313   47
                               clus
vv                              PLA2G15 MUTATED PLA2G15 WILD-TYPE
  COLON ADENOCARCINOMA                        4               313
  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 254   2  22  21
D917V9, multiclass
    clus
vv   PLA2G15 MUTATED PLA2G15 WILD-TYPE
  R0               3               254
  R1               0                 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"
D917V10, 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
D917V11, 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(918) Variable = LRRC23 MUTATION ANALYSIS
D918V1, survival
                  sevent
clus2                0   1
  LRRC23 MUTATED     8   2
  LRRC23 WILD-TYPE 274  71
  LRRC23 MUTATED LRRC23 WILD-TYPE 
              10              345 
  LRRC23 MUTATED LRRC23 WILD-TYPE 
               2               71 
$`LRRC23 MUTATED`
TCGA-AA-A00N TCGA-AD-6889 TCGA-AZ-5403 TCGA-CA-6717 TCGA-CM-5864 TCGA-CM-6163 
        4.01        56.55        62.79         0.33        15.02        14.04 
TCGA-CM-6677 TCGA-CM-6680 TCGA-D5-6923 TCGA-D5-6927 
       11.08        12.03        12.43         9.44 

$`LRRC23 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        4.21         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13        83.80        22.36        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       15.02         5.03        15.02        17.03        15.02        12.00 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       11.01        10.06        45.40        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 
        7.53        12.39        10.13        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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  LRRC23 MUTATED LRRC23 WILD-TYPE 
            0.33             0.00 
  LRRC23 MUTATED LRRC23 WILD-TYPE 
           62.79           140.38 
  LRRC23 MUTATED LRRC23 WILD-TYPE 
           12.23            20.98 
[1] "0.3 - 62.8 (12.2)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.1"
D918V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LRRC23 MUTATED         3        0        1         4         1         0
  LRRC23 WILD-TYPE      61        1       24       105         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LRRC23 MUTATED           0          0          1          0        0
  LRRC23 WILD-TYPE        19         10         40         31       35
                  vv
clus               STAGE IVA STAGE IVB
  LRRC23 MUTATED           0         0
  LRRC23 WILD-TYPE        13         1
D918V3, multiclass
            clus
vv           LRRC23 MUTATED LRRC23 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               4              105
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  LRRC23 MUTATED     1   2   6   1
  LRRC23 WILD-TYPE   8  66 242  40
D918V4, multiclass
    clus
vv   LRRC23 MUTATED LRRC23 WILD-TYPE
  T1              1                8
  T2              2               66
  T3              6              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
  LRRC23 MUTATED     9   0   1
  LRRC23 WILD-TYPE 211  80  65
D918V5, multiclass
    clus
vv   LRRC23 MUTATED LRRC23 WILD-TYPE
  N0              9              211
  N1              0               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"
D918V6, binary
                  cls
clus                 0   1
  LRRC23 MUTATED     9   0
  LRRC23 WILD-TYPE 274  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRC23 MUTATED      9    0
  LRRC23 WILD-TYPE  274   48
   clus
vv  LRRC23 MUTATED LRRC23 WILD-TYPE
  0              9              274
  1              0               48
[1] 2 2
[1] FALSE
D918V7, binary
                  cls
clus                 0   1
  LRRC23 MUTATED     2   8
  LRRC23 WILD-TYPE 168 189
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRC23 MUTATED      2    8
  LRRC23 WILD-TYPE  168  189
        clus
vv       LRRC23 MUTATED LRRC23 WILD-TYPE
  FEMALE              2              168
  MALE                8              189
[1] 2 2
[1] FALSE
D918V8, binary
                  cls
clus                 0   1
  LRRC23 MUTATED     8   2
  LRRC23 WILD-TYPE 309  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRC23 MUTATED      8    2
  LRRC23 WILD-TYPE  309   46
                               clus
vv                              LRRC23 MUTATED LRRC23 WILD-TYPE
  COLON ADENOCARCINOMA                       8              309
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  LRRC23 MUTATED     7   0   0   1
  LRRC23 WILD-TYPE 250   2  22  20
D918V9, multiclass
    clus
vv   LRRC23 MUTATED LRRC23 WILD-TYPE
  R0              7              250
  R1              0                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"
D918V10, 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
D918V11, 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(919) Variable = CLDN10 MUTATION ANALYSIS
D919V1, survival
                  sevent
clus2                0   1
  CLDN10 MUTATED     8   3
  CLDN10 WILD-TYPE 274  70
  CLDN10 MUTATED CLDN10 WILD-TYPE 
              11              344 
  CLDN10 MUTATED CLDN10 WILD-TYPE 
               3               70 
$`CLDN10 MUTATED`
TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3715 TCGA-AU-6004 TCGA-AZ-6598 TCGA-CM-4746 
       19.66        63.98        19.04        27.09        49.41        37.02 
TCGA-D5-6929 TCGA-DM-A0X9 TCGA-DM-A28E TCGA-F4-6570 TCGA-F4-6856 
       13.41       119.70       119.93         6.18        19.43 

$`CLDN10 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.20        14.50        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38        10.26        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28F 
      131.51       135.65       139.17         6.12        81.37        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        35.41       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  CLDN10 MUTATED CLDN10 WILD-TYPE 
            6.18             0.00 
  CLDN10 MUTATED CLDN10 WILD-TYPE 
          119.93           140.38 
  CLDN10 MUTATED CLDN10 WILD-TYPE 
          27.090           20.155 
[1] "6.2 - 119.9 (27.1)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.3"
D919V2, 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       22       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CLDN10 MUTATED           0          0          0          1        1
  CLDN10 WILD-TYPE        19         10         41         30       34
                  vv
clus               STAGE IVA STAGE IVB
  CLDN10 MUTATED           0         0
  CLDN10 WILD-TYPE        13         1
D919V3, multiclass
            clus
vv           CLDN10 MUTATED CLDN10 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                3               22
  STAGE IIA               3              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              1               30
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CLDN10 MUTATED     0   3   7   1
  CLDN10 WILD-TYPE   9  65 241  40
D919V4, multiclass
    clus
vv   CLDN10 MUTATED CLDN10 WILD-TYPE
  T1              0                9
  T2              3               65
  T3              7              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
  CLDN10 MUTATED     9   2   0
  CLDN10 WILD-TYPE 211  78  66
D919V5, multiclass
    clus
vv   CLDN10 MUTATED CLDN10 WILD-TYPE
  N0              9              211
  N1              2               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"
D919V6, binary
                  cls
clus                 0   1
  CLDN10 MUTATED     8   1
  CLDN10 WILD-TYPE 275  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLDN10 MUTATED      8    1
  CLDN10 WILD-TYPE  275   47
   clus
vv  CLDN10 MUTATED CLDN10 WILD-TYPE
  0              8              275
  1              1               47
[1] 2 2
[1] FALSE
D919V7, 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
D919V8, binary
                  cls
clus                 0   1
  CLDN10 MUTATED     9   2
  CLDN10 WILD-TYPE 308  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLDN10 MUTATED      9    2
  CLDN10 WILD-TYPE  308   46
                               clus
vv                              CLDN10 MUTATED CLDN10 WILD-TYPE
  COLON ADENOCARCINOMA                       9              308
  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 249   2  22  21
D919V9, multiclass
    clus
vv   CLDN10 MUTATED CLDN10 WILD-TYPE
  R0              8              249
  R1              0                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"
D919V10, 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
D919V11, 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(920) Variable = DUSP19 MUTATION ANALYSIS
D920V1, survival
                  sevent
clus2                0   1
  DUSP19 MUTATED     7   2
  DUSP19 WILD-TYPE 275  71
  DUSP19 MUTATED DUSP19 WILD-TYPE 
               9              346 
  DUSP19 MUTATED DUSP19 WILD-TYPE 
               2               71 
$`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         1.35        13.02        12.26 
TCGA-D5-6537 TCGA-D5-6923 TCGA-D5-6930 
        4.80        12.43         1.51 

$`DUSP19 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.33         0.10        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12        17.85        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 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-D5-6931 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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  DUSP19 MUTATED DUSP19 WILD-TYPE 
            1.35             0.00 
  DUSP19 MUTATED DUSP19 WILD-TYPE 
           58.39           140.38 
  DUSP19 MUTATED DUSP19 WILD-TYPE 
           12.26            20.98 
[1] "1.4 - 58.4 (12.3)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.8"
D920V2, 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       25       104         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DUSP19 MUTATED           0          0          2          0        0
  DUSP19 WILD-TYPE        19         10         39         31       35
                  vv
clus               STAGE IVA STAGE IVB
  DUSP19 MUTATED           0         0
  DUSP19 WILD-TYPE        13         1
D920V3, multiclass
            clus
vv           DUSP19 MUTATED DUSP19 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               5              104
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  DUSP19 MUTATED     0   1   7   1
  DUSP19 WILD-TYPE   9  67 241  40
D920V4, multiclass
    clus
vv   DUSP19 MUTATED DUSP19 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              7              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
  DUSP19 MUTATED     7   2   0
  DUSP19 WILD-TYPE 213  78  66
D920V5, multiclass
    clus
vv   DUSP19 MUTATED DUSP19 WILD-TYPE
  N0              7              213
  N1              2               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"
D920V6, binary
                  cls
clus                 0   1
  DUSP19 MUTATED     8   0
  DUSP19 WILD-TYPE 275  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DUSP19 MUTATED      8    0
  DUSP19 WILD-TYPE  275   48
   clus
vv  DUSP19 MUTATED DUSP19 WILD-TYPE
  0              8              275
  1              0               48
[1] 2 2
[1] FALSE
D920V7, 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
D920V8, binary
                  cls
clus                 0   1
  DUSP19 MUTATED     7   2
  DUSP19 WILD-TYPE 310  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DUSP19 MUTATED      7    2
  DUSP19 WILD-TYPE  310   46
                               clus
vv                              DUSP19 MUTATED DUSP19 WILD-TYPE
  COLON ADENOCARCINOMA                       7              310
  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 249   2  22  20
D920V9, multiclass
    clus
vv   DUSP19 MUTATED DUSP19 WILD-TYPE
  R0              8              249
  R1              0                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"
D920V10, 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
D920V11, 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(921) Variable = CBX3 MUTATION ANALYSIS
D921V1, survival
                sevent
clus2              0   1
  CBX3 MUTATED     6   0
  CBX3 WILD-TYPE 276  73
  CBX3 MUTATED CBX3 WILD-TYPE 
             6            349 
  CBX3 MUTATED CBX3 WILD-TYPE 
             0             73 
$`CBX3 MUTATED`
TCGA-A6-5661 TCGA-A6-6780 TCGA-AA-3950 TCGA-AA-3977 TCGA-AD-6889 TCGA-G4-6586 
       33.53        20.12        24.00        25.02        56.55        35.80 

$`CBX3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37         4.21         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  CBX3 MUTATED CBX3 WILD-TYPE 
         20.12           0.00 
  CBX3 MUTATED CBX3 WILD-TYPE 
         56.55         140.38 
  CBX3 MUTATED CBX3 WILD-TYPE 
        29.275         19.990 
[1] "20.1 - 56.5 (29.3)" "0.0 - 140.4 (20.0)"
[1] "hr="     "9200000"
D921V2, 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       25       104         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        19         10         41         31       35        13
                vv
clus             STAGE IVB
  CBX3 MUTATED           0
  CBX3 WILD-TYPE         1
D921V3, multiclass
            clus
vv           CBX3 MUTATED CBX3 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             5            104
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CBX3 MUTATED     0   1   5   0
  CBX3 WILD-TYPE   9  67 243  41
D921V4, multiclass
    clus
vv   CBX3 MUTATED CBX3 WILD-TYPE
  T1            0              9
  T2            1             67
  T3            5            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
  CBX3 MUTATED     6   0   0
  CBX3 WILD-TYPE 214  80  66
D921V5, multiclass
    clus
vv   CBX3 MUTATED CBX3 WILD-TYPE
  N0            6            214
  N1            0             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"
D921V6, binary
                cls
clus               0   1
  CBX3 MUTATED     4   0
  CBX3 WILD-TYPE 279  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  CBX3 MUTATED      4    0
  CBX3 WILD-TYPE  279   48
   clus
vv  CBX3 MUTATED CBX3 WILD-TYPE
  0            4            279
  1            0             48
[1] 2 2
[1] FALSE
D921V7, 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
D921V8, binary
                cls
clus               0   1
  CBX3 MUTATED     4   2
  CBX3 WILD-TYPE 313  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  CBX3 MUTATED      4    2
  CBX3 WILD-TYPE  313   46
                               clus
vv                              CBX3 MUTATED CBX3 WILD-TYPE
  COLON ADENOCARCINOMA                     4            313
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CBX3 MUTATED     3   0   0   0
  CBX3 WILD-TYPE 254   2  22  21
D921V9, multiclass
    clus
vv   CBX3 MUTATED CBX3 WILD-TYPE
  R0            3            254
  R1            0              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"
D921V10, 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
D921V11, 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(922) Variable = TBC1D10C MUTATION ANALYSIS
D922V1, survival
                    sevent
clus2                  0   1
  TBC1D10C MUTATED     6   2
  TBC1D10C WILD-TYPE 276  71
  TBC1D10C MUTATED TBC1D10C WILD-TYPE 
                 8                347 
  TBC1D10C MUTATED TBC1D10C WILD-TYPE 
                 2                 71 
$`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         2.24        45.40        12.49 
TCGA-F4-6570 TCGA-G4-6299 
        6.18        74.56 

$`TBC1D10C WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 
       10.06        35.05        33.04         0.99        25.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        1.94         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-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        13.38        13.45        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       19.43       107.67        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  TBC1D10C MUTATED TBC1D10C WILD-TYPE 
              1.02               0.00 
  TBC1D10C MUTATED TBC1D10C WILD-TYPE 
             74.56             140.38 
  TBC1D10C MUTATED TBC1D10C WILD-TYPE 
             19.25              20.19 
[1] "1.0 - 74.6 (19.2)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D922V2, 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       25       105         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TBC1D10C MUTATED           0          1          1          1        0
  TBC1D10C WILD-TYPE        19          9         40         30       35
                    vv
clus                 STAGE IVA STAGE IVB
  TBC1D10C MUTATED           0         0
  TBC1D10C WILD-TYPE        13         1
D922V3, multiclass
            clus
vv           TBC1D10C MUTATED TBC1D10C WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  0                 25
  STAGE IIA                 4                105
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                1                  9
  STAGE IIIB                1                 40
  STAGE IIIC                1                 30
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  TBC1D10C MUTATED     0   1   7   0
  TBC1D10C WILD-TYPE   9  67 241  41
D922V4, multiclass
    clus
vv   TBC1D10C MUTATED TBC1D10C WILD-TYPE
  T1                0                  9
  T2                1                 67
  T3                7                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
  TBC1D10C MUTATED     5   1   2
  TBC1D10C WILD-TYPE 215  79  64
D922V5, multiclass
    clus
vv   TBC1D10C MUTATED TBC1D10C WILD-TYPE
  N0                5                215
  N1                1                 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"
D922V6, binary
                    cls
clus                   0   1
  TBC1D10C MUTATED     7   0
  TBC1D10C WILD-TYPE 276  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TBC1D10C MUTATED      7    0
  TBC1D10C WILD-TYPE  276   48
   clus
vv  TBC1D10C MUTATED TBC1D10C WILD-TYPE
  0                7                276
  1                0                 48
[1] 2 2
[1] FALSE
D922V7, 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
D922V8, binary
                    cls
clus                   0   1
  TBC1D10C MUTATED     6   2
  TBC1D10C WILD-TYPE 311  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TBC1D10C MUTATED      6    2
  TBC1D10C WILD-TYPE  311   46
                               clus
vv                              TBC1D10C MUTATED TBC1D10C WILD-TYPE
  COLON ADENOCARCINOMA                         6                311
  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 251   2  22  19
D922V9, multiclass
    clus
vv   TBC1D10C MUTATED TBC1D10C WILD-TYPE
  R0                6                251
  R1                0                  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"
D922V10, 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
D922V11, 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(923) Variable = BRD8 MUTATION ANALYSIS
D923V1, survival
                sevent
clus2              0   1
  BRD8 MUTATED    12   3
  BRD8 WILD-TYPE 270  70
  BRD8 MUTATED BRD8 WILD-TYPE 
            15            340 
  BRD8 MUTATED BRD8 WILD-TYPE 
             3             70 
$`BRD8 MUTATED`
TCGA-A6-5665 TCGA-A6-6653 TCGA-AA-3555 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3994 
       22.06        24.39        29.95        19.04        19.04        27.02 
TCGA-AA-A00N TCGA-AD-5900 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CK-5913 TCGA-CM-5860 
        4.01         0.07        58.39        49.41        51.32        16.01 
TCGA-CM-6171 TCGA-CM-6674 TCGA-DM-A28K 
       14.04        12.95        98.24 

$`BRD8 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       85.05        26.99        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        21.99        21.14         2.93         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-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       15.02        11.01        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       35.97        60.79       117.07         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  BRD8 MUTATED BRD8 WILD-TYPE 
          0.07           0.00 
  BRD8 MUTATED BRD8 WILD-TYPE 
         98.24         140.38 
  BRD8 MUTATED BRD8 WILD-TYPE 
        22.060         20.155 
[1] "0.1 - 98.2 (22.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D923V2, 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       23       102         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        19         10         40         31       34        13
                vv
clus             STAGE IVB
  BRD8 MUTATED           0
  BRD8 WILD-TYPE         1
D923V3, multiclass
            clus
vv           BRD8 MUTATED BRD8 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             7            102
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  BRD8 MUTATED     0   3  11   1
  BRD8 WILD-TYPE   9  65 237  40
D923V4, multiclass
    clus
vv   BRD8 MUTATED BRD8 WILD-TYPE
  T1            0              9
  T2            3             65
  T3           11            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
  BRD8 MUTATED    14   1   0
  BRD8 WILD-TYPE 206  79  66
D923V5, multiclass
    clus
vv   BRD8 MUTATED BRD8 WILD-TYPE
  N0           14            206
  N1            1             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"
D923V6, binary
                cls
clus               0   1
  BRD8 MUTATED    11   1
  BRD8 WILD-TYPE 272  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD8 MUTATED     11    1
  BRD8 WILD-TYPE  272   47
   clus
vv  BRD8 MUTATED BRD8 WILD-TYPE
  0           11            272
  1            1             47
[1] 2 2
[1] FALSE
D923V7, 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
D923V8, binary
                cls
clus               0   1
  BRD8 MUTATED    10   5
  BRD8 WILD-TYPE 307  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD8 MUTATED     10    5
  BRD8 WILD-TYPE  307   43
                               clus
vv                              BRD8 MUTATED BRD8 WILD-TYPE
  COLON ADENOCARCINOMA                    10            307
  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 247   2  21  20
D923V9, multiclass
    clus
vv   BRD8 MUTATED BRD8 WILD-TYPE
  R0           10            247
  R1            0              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"
D923V10, 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
D923V11, 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(924) Variable = MYH15 MUTATION ANALYSIS
D924V1, survival
                 sevent
clus2               0   1
  MYH15 MUTATED    18   4
  MYH15 WILD-TYPE 264  69
  MYH15 MUTATED MYH15 WILD-TYPE 
             22             333 
  MYH15 MUTATED MYH15 WILD-TYPE 
              4              69 
$`MYH15 MUTATED`
TCGA-A6-6138 TCGA-A6-6653 TCGA-A6-6654 TCGA-AA-3510 TCGA-AA-3662 TCGA-AA-3663 
       22.52        24.39        23.87        63.98         6.05         6.97 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3864 TCGA-AD-6890 TCGA-AD-6964 TCGA-AZ-4315 
       26.99        19.04        53.00         0.79        10.88        58.39 
TCGA-CA-6717 TCGA-CM-5861 TCGA-CM-6674 TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6534 
        0.33        15.02        12.95        11.51        18.25        43.27 
TCGA-D5-6930 TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-G4-6628 
        1.51        38.20        92.75        52.80 

$`MYH15 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        32.71        27.09         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6780 TCGA-A6-6781 
       25.18        24.16        21.76        24.69        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       61.02        78.08        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3811 
       19.00        36.00         5.03        85.05        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
        0.72         5.79        22.42        27.42         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01         5.03        15.02        15.02 
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-D5-6529 
       12.03        45.40        12.26        19.59        13.51        20.19 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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-A1D0 TCGA-DM-A1D6 
       11.38        10.26       119.70        24.43       130.65        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       26.17        91.79        46.75 

  MYH15 MUTATED MYH15 WILD-TYPE 
           0.33            0.00 
  MYH15 MUTATED MYH15 WILD-TYPE 
          92.75          140.38 
  MYH15 MUTATED MYH15 WILD-TYPE 
          20.78           20.19 
[1] "0.3 - 92.8 (20.8)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.3"
D924V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MYH15 MUTATED         3        0        4        10         0         0
  MYH15 WILD-TYPE      61        1       21        99         8         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        19         10         39         30       34        13
                 vv
clus              STAGE IVB
  MYH15 MUTATED           0
  MYH15 WILD-TYPE         1
D924V3, multiclass
            clus
vv           MYH15 MUTATED MYH15 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               4              21
  STAGE IIA             10              99
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MYH15 MUTATED     1   3  17   2
  MYH15 WILD-TYPE   8  65 231  39
D924V4, multiclass
    clus
vv   MYH15 MUTATED MYH15 WILD-TYPE
  T1             1               8
  T2             3              65
  T3            17             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
  MYH15 MUTATED    18   2   3
  MYH15 WILD-TYPE 202  78  63
D924V5, multiclass
    clus
vv   MYH15 MUTATED MYH15 WILD-TYPE
  N0            18             202
  N1             2              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"
D924V6, binary
                 cls
clus                0   1
  MYH15 MUTATED    20   1
  MYH15 WILD-TYPE 263  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYH15 MUTATED     20    1
  MYH15 WILD-TYPE  263   47
   clus
vv  MYH15 MUTATED MYH15 WILD-TYPE
  0            20             263
  1             1              47
[1] 2 2
[1] FALSE
D924V7, binary
                 cls
clus                0   1
  MYH15 MUTATED     7  16
  MYH15 WILD-TYPE 163 181
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYH15 MUTATED      7   16
  MYH15 WILD-TYPE  163  181
        clus
vv       MYH15 MUTATED MYH15 WILD-TYPE
  FEMALE             7             163
  MALE              16             181
[1] 2 2
[1] FALSE
D924V8, binary
                 cls
clus                0   1
  MYH15 MUTATED    19   4
  MYH15 WILD-TYPE 298  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYH15 MUTATED     19    4
  MYH15 WILD-TYPE  298   44
                               clus
vv                              MYH15 MUTATED MYH15 WILD-TYPE
  COLON ADENOCARCINOMA                     19             298
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MYH15 MUTATED    14   0   1   1
  MYH15 WILD-TYPE 243   2  21  20
D924V9, multiclass
    clus
vv   MYH15 MUTATED MYH15 WILD-TYPE
  R0            14             243
  R1             0               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"
D924V10, 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
D924V11, 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(925) Variable = PFN4 MUTATION ANALYSIS
D925V1, survival
                sevent
clus2              0   1
  PFN4 MUTATED     5   1
  PFN4 WILD-TYPE 277  72
  PFN4 MUTATED PFN4 WILD-TYPE 
             6            349 
  PFN4 MUTATED PFN4 WILD-TYPE 
             1             72 
$`PFN4 MUTATED`
TCGA-AA-3492 TCGA-AA-3663 TCGA-AA-3977 TCGA-AY-6197 TCGA-CM-5349 TCGA-CM-5861 
        3.02         6.97        25.02        21.44        30.08        15.02 

$`PFN4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  PFN4 MUTATED PFN4 WILD-TYPE 
          3.02           0.00 
  PFN4 MUTATED PFN4 WILD-TYPE 
         30.08         140.38 
  PFN4 MUTATED PFN4 WILD-TYPE 
         18.23          20.19 
[1] "3.0 - 30.1 (18.2)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D925V2, 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       23       106         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        19         10         41         31       35        13
                vv
clus             STAGE IVB
  PFN4 MUTATED           0
  PFN4 WILD-TYPE         1
D925V3, multiclass
            clus
vv           PFN4 MUTATED PFN4 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             3            106
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PFN4 MUTATED     0   1   5   0
  PFN4 WILD-TYPE   9  67 243  41
D925V4, multiclass
    clus
vv   PFN4 MUTATED PFN4 WILD-TYPE
  T1            0              9
  T2            1             67
  T3            5            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
  PFN4 MUTATED     6   0   0
  PFN4 WILD-TYPE 214  80  66
D925V5, multiclass
    clus
vv   PFN4 MUTATED PFN4 WILD-TYPE
  N0            6            214
  N1            0             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"
D925V6, binary
                cls
clus               0   1
  PFN4 MUTATED     4   0
  PFN4 WILD-TYPE 279  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  PFN4 MUTATED      4    0
  PFN4 WILD-TYPE  279   48
   clus
vv  PFN4 MUTATED PFN4 WILD-TYPE
  0            4            279
  1            0             48
[1] 2 2
[1] FALSE
D925V7, 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
D925V8, binary
                cls
clus               0   1
  PFN4 MUTATED     6   0
  PFN4 WILD-TYPE 311  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  PFN4 MUTATED      6    0
  PFN4 WILD-TYPE  311   48
                               clus
vv                              PFN4 MUTATED PFN4 WILD-TYPE
  COLON ADENOCARCINOMA                     6            311
  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 252   2  22  21
D925V9, multiclass
    clus
vv   PFN4 MUTATED PFN4 WILD-TYPE
  R0            5            252
  R1            0              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"
D925V10, 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
D925V11, 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(926) Variable = MRPS5 MUTATION ANALYSIS
D926V1, survival
                 sevent
clus2               0   1
  MRPS5 MUTATED     7   4
  MRPS5 WILD-TYPE 275  69
  MRPS5 MUTATED MRPS5 WILD-TYPE 
             11             344 
  MRPS5 MUTATED MRPS5 WILD-TYPE 
              4              69 
$`MRPS5 MUTATED`
TCGA-AA-3672 TCGA-AA-A00N TCGA-AD-6890 TCGA-AY-6197 TCGA-AZ-6599 TCGA-AZ-6600 
        0.92         4.01         0.79        21.44         6.77        12.10 
TCGA-CA-5796 TCGA-CM-6165 TCGA-D5-6532 TCGA-D5-6537 TCGA-G4-6304 
        3.25        16.04        18.25         4.80        53.62 

$`MRPS5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
        6.05         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-AZ-6603 
       22.36        62.79        61.41        49.41       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       11.51        20.19         1.32        43.27        15.12        17.85 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  MRPS5 MUTATED MRPS5 WILD-TYPE 
           0.79            0.00 
  MRPS5 MUTATED MRPS5 WILD-TYPE 
          53.62          140.38 
  MRPS5 MUTATED MRPS5 WILD-TYPE 
          6.770          20.995 
[1] "0.8 - 53.6 (6.8)"   "0.0 - 140.4 (21.0)"
[1] "hr=" "3.2"
D926V2, 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       25       105         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        18         10         40         31       34        13
                 vv
clus              STAGE IVB
  MRPS5 MUTATED           0
  MRPS5 WILD-TYPE         1
D926V3, multiclass
            clus
vv           MRPS5 MUTATED MRPS5 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              4             105
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MRPS5 MUTATED     1   1   6   3
  MRPS5 WILD-TYPE   8  67 242  38
D926V4, multiclass
    clus
vv   MRPS5 MUTATED MRPS5 WILD-TYPE
  T1             1               8
  T2             1              67
  T3             6             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
  MRPS5 MUTATED     8   3   0
  MRPS5 WILD-TYPE 212  77  66
D926V5, multiclass
    clus
vv   MRPS5 MUTATED MRPS5 WILD-TYPE
  N0             8             212
  N1             3              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"
D926V6, binary
                 cls
clus                0   1
  MRPS5 MUTATED     6   1
  MRPS5 WILD-TYPE 277  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MRPS5 MUTATED      6    1
  MRPS5 WILD-TYPE  277   47
   clus
vv  MRPS5 MUTATED MRPS5 WILD-TYPE
  0             6             277
  1             1              47
[1] 2 2
[1] FALSE
D926V7, 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
D926V8, binary
                 cls
clus                0   1
  MRPS5 MUTATED     9   2
  MRPS5 WILD-TYPE 308  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MRPS5 MUTATED      9    2
  MRPS5 WILD-TYPE  308   46
                               clus
vv                              MRPS5 MUTATED MRPS5 WILD-TYPE
  COLON ADENOCARCINOMA                      9             308
  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 249   2  22  21
D926V9, multiclass
    clus
vv   MRPS5 MUTATED MRPS5 WILD-TYPE
  R0             8             249
  R1             0               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"
D926V10, 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
D926V11, 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(927) Variable = ATP10B MUTATION ANALYSIS
D927V1, survival
                  sevent
clus2                0   1
  ATP10B MUTATED    11   4
  ATP10B WILD-TYPE 271  69
  ATP10B MUTATED ATP10B WILD-TYPE 
              15              340 
  ATP10B MUTATED ATP10B WILD-TYPE 
               4               69 
$`ATP10B MUTATED`
TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3655 TCGA-AA-3715 TCGA-AA-3845 TCGA-AD-6889 
       22.06        19.66        61.02        19.04         0.00        56.55 
TCGA-AY-5543 TCGA-AZ-6599 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4743 TCGA-CM-4747 
       15.75         6.77         0.33         0.10        23.05        25.02 
TCGA-D5-6926 TCGA-DM-A285 TCGA-F4-6854 
        9.04         6.12         0.53 

$`ATP10B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02        14.93        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37         4.21         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07         0.26         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        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        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       16.24        33.67        13.25        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  ATP10B MUTATED ATP10B WILD-TYPE 
               0                0 
  ATP10B MUTATED ATP10B WILD-TYPE 
           61.02           140.38 
  ATP10B MUTATED ATP10B WILD-TYPE 
           15.75            20.98 
[1] "0.0 - 61.0 (15.8)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.8"
D927V2, 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       23       102         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP10B MUTATED           0          1          0          1        1
  ATP10B WILD-TYPE        19          9         41         30       34
                  vv
clus               STAGE IVA STAGE IVB
  ATP10B MUTATED           2         0
  ATP10B WILD-TYPE        11         1
D927V3, multiclass
            clus
vv           ATP10B MUTATED ATP10B WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               7              102
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              1                9
  STAGE IIIB              0               41
  STAGE IIIC              1               30
  STAGE IV                1               34
  STAGE IVA               2               11
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 237  38
D927V4, multiclass
    clus
vv   ATP10B MUTATED ATP10B WILD-TYPE
  T1              0                9
  T2              1               67
  T3             11              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
  ATP10B MUTATED    10   4   1
  ATP10B WILD-TYPE 210  76  65
D927V5, multiclass
    clus
vv   ATP10B MUTATED ATP10B WILD-TYPE
  N0             10              210
  N1              4               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"
D927V6, binary
                  cls
clus                 0   1
  ATP10B MUTATED    10   3
  ATP10B WILD-TYPE 273  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP10B MUTATED     10    3
  ATP10B WILD-TYPE  273   45
   clus
vv  ATP10B MUTATED ATP10B WILD-TYPE
  0             10              273
  1              3               45
[1] 2 2
[1] FALSE
D927V7, 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
D927V8, binary
                  cls
clus                 0   1
  ATP10B MUTATED    12   3
  ATP10B WILD-TYPE 305  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP10B MUTATED     12    3
  ATP10B WILD-TYPE  305   45
                               clus
vv                              ATP10B MUTATED ATP10B WILD-TYPE
  COLON ADENOCARCINOMA                      12              305
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ATP10B MUTATED    10   0   0   2
  ATP10B WILD-TYPE 247   2  22  19
D927V9, multiclass
    clus
vv   ATP10B MUTATED ATP10B WILD-TYPE
  R0             10              247
  R1              0                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"
D927V10, 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
D927V11, 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(928) Variable = EPC1 MUTATION ANALYSIS
D928V1, survival
                sevent
clus2              0   1
  EPC1 MUTATED     8   5
  EPC1 WILD-TYPE 274  68
  EPC1 MUTATED EPC1 WILD-TYPE 
            13            342 
  EPC1 MUTATED EPC1 WILD-TYPE 
             5             68 
$`EPC1 MUTATED`
TCGA-A6-2676 TCGA-A6-5659 TCGA-A6-6781 TCGA-AA-A010 TCGA-AZ-6598 TCGA-AZ-6599 
       42.90        30.44        19.66        34.98        49.41         6.77 
TCGA-AZ-6608 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CM-5349 TCGA-CM-5860 
        1.94         0.33         0.10        17.56        30.08        16.01 
TCGA-G4-6303 
       65.85 

$`EPC1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       22.36        62.79        61.41        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 
        3.29         0.07         0.26         1.35       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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-5861 TCGA-CM-5862 
       13.02        29.06        22.03        22.98        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 
       35.41        19.43       107.67        74.56        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  EPC1 MUTATED EPC1 WILD-TYPE 
           0.1            0.0 
  EPC1 MUTATED EPC1 WILD-TYPE 
         65.85         140.38 
  EPC1 MUTATED EPC1 WILD-TYPE 
        19.660         20.235 
[1] "0.1 - 65.8 (19.7)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2"  
D928V2, 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       24       105         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EPC1 MUTATED           0          1          0          1        1         1
  EPC1 WILD-TYPE        19          9         41         30       34        12
                vv
clus             STAGE IVB
  EPC1 MUTATED           0
  EPC1 WILD-TYPE         1
D928V3, multiclass
            clus
vv           EPC1 MUTATED EPC1 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             4            105
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            1              9
  STAGE IIIB            0             41
  STAGE IIIC            1             30
  STAGE IV              1             34
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  65 242  37
D928V4, multiclass
    clus
vv   EPC1 MUTATED EPC1 WILD-TYPE
  T1            0              9
  T2            3             65
  T3            6            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
  EPC1 MUTATED     9   4   0
  EPC1 WILD-TYPE 211  76  66
D928V5, multiclass
    clus
vv   EPC1 MUTATED EPC1 WILD-TYPE
  N0            9            211
  N1            4             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"
D928V6, binary
                cls
clus               0   1
  EPC1 MUTATED     9   1
  EPC1 WILD-TYPE 274  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  EPC1 MUTATED      9    1
  EPC1 WILD-TYPE  274   47
   clus
vv  EPC1 MUTATED EPC1 WILD-TYPE
  0            9            274
  1            1             47
[1] 2 2
[1] FALSE
D928V7, 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
D928V8, binary
                cls
clus               0   1
  EPC1 MUTATED    11   2
  EPC1 WILD-TYPE 306  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  EPC1 MUTATED     11    2
  EPC1 WILD-TYPE  306   46
                               clus
vv                              EPC1 MUTATED EPC1 WILD-TYPE
  COLON ADENOCARCINOMA                    11            306
  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 250   2  22  18
D928V9, multiclass
    clus
vv   EPC1 MUTATED EPC1 WILD-TYPE
  R0            7            250
  R1            0              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"
D928V10, 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
D928V11, 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(929) Variable = TBL1XR1 MUTATION ANALYSIS
D929V1, survival
                   sevent
clus2                 0   1
  TBL1XR1 MUTATED    10   1
  TBL1XR1 WILD-TYPE 272  72
  TBL1XR1 MUTATED TBL1XR1 WILD-TYPE 
               11               344 
  TBL1XR1 MUTATED TBL1XR1 WILD-TYPE 
                1                72 
$`TBL1XR1 MUTATED`
TCGA-A6-6654 TCGA-AA-3510 TCGA-AA-3713 TCGA-AA-3877 TCGA-AA-3977 TCGA-AA-A00N 
       23.87        63.98        19.04        31.00        25.02         4.01 
TCGA-AA-A010 TCGA-CK-6748 TCGA-D5-6927 TCGA-D5-6928 TCGA-F4-6856 
       34.98         2.01         9.44        11.64        19.43 

$`TBL1XR1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       27.02        29.98        18.05         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99        21.14         2.93       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        35.41       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  TBL1XR1 MUTATED TBL1XR1 WILD-TYPE 
             2.01              0.00 
  TBL1XR1 MUTATED TBL1XR1 WILD-TYPE 
            63.98            140.38 
  TBL1XR1 MUTATED TBL1XR1 WILD-TYPE 
           19.430            20.235 
[1] "2.0 - 64.0 (19.4)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2"  
D929V2, 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       23       106         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TBL1XR1 MUTATED           0          0          1          0        2
  TBL1XR1 WILD-TYPE        19         10         40         31       33
                   vv
clus                STAGE IVA STAGE IVB
  TBL1XR1 MUTATED           0         0
  TBL1XR1 WILD-TYPE        13         1
D929V3, multiclass
            clus
vv           TBL1XR1 MUTATED TBL1XR1 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 2                23
  STAGE IIA                3               106
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               0                31
  STAGE IV                 2                33
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TBL1XR1 MUTATED     1   2   7   3
  TBL1XR1 WILD-TYPE   8  66 241  38
D929V4, multiclass
    clus
vv   TBL1XR1 MUTATED TBL1XR1 WILD-TYPE
  T1               1                 8
  T2               2                66
  T3               7               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
  TBL1XR1 MUTATED    11   2   0
  TBL1XR1 WILD-TYPE 209  78  66
D929V5, multiclass
    clus
vv   TBL1XR1 MUTATED TBL1XR1 WILD-TYPE
  N0              11               209
  N1               2                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"
D929V6, binary
                   cls
clus                  0   1
  TBL1XR1 MUTATED    10   2
  TBL1XR1 WILD-TYPE 273  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TBL1XR1 MUTATED     10    2
  TBL1XR1 WILD-TYPE  273   46
   clus
vv  TBL1XR1 MUTATED TBL1XR1 WILD-TYPE
  0              10               273
  1               2                46
[1] 2 2
[1] FALSE
D929V7, 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
D929V8, binary
                   cls
clus                  0   1
  TBL1XR1 MUTATED     8   5
  TBL1XR1 WILD-TYPE 309  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TBL1XR1 MUTATED      8    5
  TBL1XR1 WILD-TYPE  309   43
                               clus
vv                              TBL1XR1 MUTATED TBL1XR1 WILD-TYPE
  COLON ADENOCARCINOMA                        8               309
  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 248   2  21  20
D929V9, multiclass
    clus
vv   TBL1XR1 MUTATED TBL1XR1 WILD-TYPE
  R0               9               248
  R1               0                 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"
D929V10, 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
D929V11, 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(930) Variable = DNAJC7 MUTATION ANALYSIS
D930V1, survival
                  sevent
clus2                0   1
  DNAJC7 MUTATED     6   0
  DNAJC7 WILD-TYPE 276  73
  DNAJC7 MUTATED DNAJC7 WILD-TYPE 
               6              349 
  DNAJC7 MUTATED DNAJC7 WILD-TYPE 
               0               73 
$`DNAJC7 MUTATED`
TCGA-AA-3950 TCGA-AA-A010 TCGA-AY-6197 TCGA-CA-6717 TCGA-CK-5913 TCGA-G4-6628 
       24.00        34.98        21.44         0.33        51.32        52.80 

$`DNAJC7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 
       46.75 

  DNAJC7 MUTATED DNAJC7 WILD-TYPE 
            0.33             0.00 
  DNAJC7 MUTATED DNAJC7 WILD-TYPE 
           52.80           140.38 
  DNAJC7 MUTATED DNAJC7 WILD-TYPE 
           29.49            20.02 
[1] "0.3 - 52.8 (29.5)"  "0.0 - 140.4 (20.0)"
[1] "hr="     "9300000"
D930V2, 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       25       105         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DNAJC7 MUTATED           0          0          0          0        0
  DNAJC7 WILD-TYPE        19         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  DNAJC7 MUTATED           0         0
  DNAJC7 WILD-TYPE        13         1
D930V3, multiclass
            clus
vv           DNAJC7 MUTATED DNAJC7 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               4              105
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  DNAJC7 MUTATED     0   1   4   2
  DNAJC7 WILD-TYPE   9  67 244  39
D930V4, multiclass
    clus
vv   DNAJC7 MUTATED DNAJC7 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              4              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
  DNAJC7 MUTATED     7   0   0
  DNAJC7 WILD-TYPE 213  80  66
D930V5, multiclass
    clus
vv   DNAJC7 MUTATED DNAJC7 WILD-TYPE
  N0              7              213
  N1              0               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"
D930V6, binary
                  cls
clus                 0   1
  DNAJC7 MUTATED     4   0
  DNAJC7 WILD-TYPE 279  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAJC7 MUTATED      4    0
  DNAJC7 WILD-TYPE  279   48
   clus
vv  DNAJC7 MUTATED DNAJC7 WILD-TYPE
  0              4              279
  1              0               48
[1] 2 2
[1] FALSE
D930V7, 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
D930V8, binary
                  cls
clus                 0   1
  DNAJC7 MUTATED     5   2
  DNAJC7 WILD-TYPE 312  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAJC7 MUTATED      5    2
  DNAJC7 WILD-TYPE  312   46
                               clus
vv                              DNAJC7 MUTATED DNAJC7 WILD-TYPE
  COLON ADENOCARCINOMA                       5              312
  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 253   2  22  18
D930V9, multiclass
    clus
vv   DNAJC7 MUTATED DNAJC7 WILD-TYPE
  R0              4              253
  R1              0                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"
D930V10, 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
D930V11, 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(931) Variable = AWAT1 MUTATION ANALYSIS
D931V1, survival
                 sevent
clus2               0   1
  AWAT1 MUTATED     7   1
  AWAT1 WILD-TYPE 275  72
  AWAT1 MUTATED AWAT1 WILD-TYPE 
              8             347 
  AWAT1 MUTATED AWAT1 WILD-TYPE 
              1              72 
$`AWAT1 MUTATED`
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-A024 TCGA-CA-6717 TCGA-D5-5540 TCGA-D5-6536 
       33.01        26.01        39.06         0.33        13.51        17.85 
TCGA-D5-6538 TCGA-G4-6588 
       17.13        26.17 

$`AWAT1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3950 TCGA-AA-3952 
       31.00         2.01        12.99        24.00        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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        35.01        26.01        37.02        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 
        1.32        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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        91.79        46.75        52.80 

  AWAT1 MUTATED AWAT1 WILD-TYPE 
           0.33            0.00 
  AWAT1 MUTATED AWAT1 WILD-TYPE 
          39.06          140.38 
  AWAT1 MUTATED AWAT1 WILD-TYPE 
          21.93           20.19 
[1] "0.3 - 39.1 (21.9)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.4"
D931V2, 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       24       105         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        19         10         39         31       35        13
                 vv
clus              STAGE IVB
  AWAT1 MUTATED           0
  AWAT1 WILD-TYPE         1
D931V3, multiclass
            clus
vv           AWAT1 MUTATED AWAT1 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              4             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  AWAT1 MUTATED     0   0   7   1
  AWAT1 WILD-TYPE   9  68 241  40
D931V4, multiclass
    clus
vv   AWAT1 MUTATED AWAT1 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             7             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
  AWAT1 MUTATED     6   1   1
  AWAT1 WILD-TYPE 214  79  65
D931V5, multiclass
    clus
vv   AWAT1 MUTATED AWAT1 WILD-TYPE
  N0             6             214
  N1             1              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"
D931V6, binary
                 cls
clus                0   1
  AWAT1 MUTATED     8   0
  AWAT1 WILD-TYPE 275  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AWAT1 MUTATED      8    0
  AWAT1 WILD-TYPE  275   48
   clus
vv  AWAT1 MUTATED AWAT1 WILD-TYPE
  0             8             275
  1             0              48
[1] 2 2
[1] FALSE
D931V7, 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
D931V8, binary
                 cls
clus                0   1
  AWAT1 MUTATED     4   4
  AWAT1 WILD-TYPE 313  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AWAT1 MUTATED      4    4
  AWAT1 WILD-TYPE  313   44
                               clus
vv                              AWAT1 MUTATED AWAT1 WILD-TYPE
  COLON ADENOCARCINOMA                      4             313
  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 250   2  22  20
D931V9, multiclass
    clus
vv   AWAT1 MUTATED AWAT1 WILD-TYPE
  R0             7             250
  R1             0               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"
D931V10, 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
D931V11, 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(932) Variable = NEK1 MUTATION ANALYSIS
D932V1, survival
                sevent
clus2              0   1
  NEK1 MUTATED    10   1
  NEK1 WILD-TYPE 272  72
  NEK1 MUTATED NEK1 WILD-TYPE 
            11            344 
  NEK1 MUTATED NEK1 WILD-TYPE 
             1             72 
$`NEK1 MUTATED`
TCGA-A6-5665 TCGA-A6-6653 TCGA-AA-3950 TCGA-AA-3977 TCGA-AA-A010 TCGA-AD-5900 
       22.06        24.39        24.00        25.02        34.98         0.07 
TCGA-AU-6004 TCGA-CA-6717 TCGA-D5-6539 TCGA-D5-6931 TCGA-DM-A28F 
       27.09         0.33        12.49        12.00        35.97 

$`NEK1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
      139.17         6.12        81.37       119.93        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  NEK1 MUTATED NEK1 WILD-TYPE 
          0.07           0.00 
  NEK1 MUTATED NEK1 WILD-TYPE 
         35.97         140.38 
  NEK1 MUTATED NEK1 WILD-TYPE 
         24.00          20.07 
[1] "0.1 - 36.0 (24.0)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.7"
D932V2, 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       25       105         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NEK1 MUTATED           0          1          1          1        0         0
  NEK1 WILD-TYPE        19          9         40         30       35        13
                vv
clus             STAGE IVB
  NEK1 MUTATED           0
  NEK1 WILD-TYPE         1
D932V3, multiclass
            clus
vv           NEK1 MUTATED NEK1 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             4            105
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            1              9
  STAGE IIIB            1             40
  STAGE IIIC            1             30
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NEK1 MUTATED     0   4   6   2
  NEK1 WILD-TYPE   9  64 242  39
D932V4, multiclass
    clus
vv   NEK1 MUTATED NEK1 WILD-TYPE
  T1            0              9
  T2            4             64
  T3            6            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
  NEK1 MUTATED    10   1   1
  NEK1 WILD-TYPE 210  79  65
D932V5, multiclass
    clus
vv   NEK1 MUTATED NEK1 WILD-TYPE
  N0           10            210
  N1            1             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"
D932V6, binary
                cls
clus               0   1
  NEK1 MUTATED    10   0
  NEK1 WILD-TYPE 273  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEK1 MUTATED     10    0
  NEK1 WILD-TYPE  273   48
   clus
vv  NEK1 MUTATED NEK1 WILD-TYPE
  0           10            273
  1            0             48
[1] 2 2
[1] FALSE
D932V7, 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
D932V8, binary
                cls
clus               0   1
  NEK1 MUTATED     9   3
  NEK1 WILD-TYPE 308  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEK1 MUTATED      9    3
  NEK1 WILD-TYPE  308   45
                               clus
vv                              NEK1 MUTATED NEK1 WILD-TYPE
  COLON ADENOCARCINOMA                     9            308
  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 249   2  22  20
D932V9, multiclass
    clus
vv   NEK1 MUTATED NEK1 WILD-TYPE
  R0            8            249
  R1            0              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"
D932V10, 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
D932V11, 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(933) Variable = SLC24A2 MUTATION ANALYSIS
D933V1, survival
                   sevent
clus2                 0   1
  SLC24A2 MUTATED    12   5
  SLC24A2 WILD-TYPE 270  68
  SLC24A2 MUTATED SLC24A2 WILD-TYPE 
               17               338 
  SLC24A2 MUTATED SLC24A2 WILD-TYPE 
                5                68 
$`SLC24A2 MUTATED`
TCGA-A6-6780 TCGA-AA-3492 TCGA-AA-3713 TCGA-AA-3947 TCGA-AA-3977 TCGA-AA-A00A 
       20.12         3.02        19.04        33.01        25.02        38.04 
TCGA-AA-A010 TCGA-AY-4070 TCGA-AZ-4315 TCGA-AZ-6603 TCGA-CA-6717 TCGA-CA-6718 
       34.98        16.31        58.39        29.56         0.33         0.10 
TCGA-D5-6540 TCGA-D5-6930 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DB 
       16.14         1.51        13.32       140.38        44.32 

$`SLC24A2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       23.87        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       27.02        13.94        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 
       27.42        10.88         0.20        14.50        27.09         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10       100.01         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 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-A1D8 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       49.91        12.59         7.50       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  SLC24A2 MUTATED SLC24A2 WILD-TYPE 
              0.1               0.0 
  SLC24A2 MUTATED SLC24A2 WILD-TYPE 
           140.38            139.17 
  SLC24A2 MUTATED SLC24A2 WILD-TYPE 
           20.120            20.235 
[1] "0.1 - 140.4 (20.1)" "0.0 - 139.2 (20.2)"
[1] "hr=" "1.4"
D933V2, 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       24       100         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC24A2 MUTATED           0          0          0          1        1
  SLC24A2 WILD-TYPE        19         10         41         30       34
                   vv
clus                STAGE IVA STAGE IVB
  SLC24A2 MUTATED           0         0
  SLC24A2 WILD-TYPE        13         1
D933V3, multiclass
            clus
vv           SLC24A2 MUTATED SLC24A2 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                9               100
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               1                30
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC24A2 MUTATED     0   3  12   2
  SLC24A2 WILD-TYPE   9  65 236  39
D933V4, multiclass
    clus
vv   SLC24A2 MUTATED SLC24A2 WILD-TYPE
  T1               0                 9
  T2               3                65
  T3              12               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
  SLC24A2 MUTATED    15   1   1
  SLC24A2 WILD-TYPE 205  79  65
D933V5, multiclass
    clus
vv   SLC24A2 MUTATED SLC24A2 WILD-TYPE
  N0              15               205
  N1               1                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"
D933V6, binary
                   cls
clus                  0   1
  SLC24A2 MUTATED    13   1
  SLC24A2 WILD-TYPE 270  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC24A2 MUTATED     13    1
  SLC24A2 WILD-TYPE  270   47
   clus
vv  SLC24A2 MUTATED SLC24A2 WILD-TYPE
  0              13               270
  1               1                47
[1] 2 2
[1] FALSE
D933V7, 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
D933V8, binary
                   cls
clus                  0   1
  SLC24A2 MUTATED    12   5
  SLC24A2 WILD-TYPE 305  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC24A2 MUTATED     12    5
  SLC24A2 WILD-TYPE  305   43
                               clus
vv                              SLC24A2 MUTATED SLC24A2 WILD-TYPE
  COLON ADENOCARCINOMA                       12               305
  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 250   1  21  19
D933V9, multiclass
    clus
vv   SLC24A2 MUTATED SLC24A2 WILD-TYPE
  R0               7               250
  R1               1                 1
  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"
D933V10, 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
D933V11, 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(934) Variable = RRM2B MUTATION ANALYSIS
D934V1, survival
                 sevent
clus2               0   1
  RRM2B MUTATED     3   2
  RRM2B WILD-TYPE 279  71
  RRM2B MUTATED RRM2B WILD-TYPE 
              5             350 
  RRM2B MUTATED RRM2B WILD-TYPE 
              2              71 
$`RRM2B MUTATED`
TCGA-AA-3510 TCGA-AY-6197 TCGA-CA-6718 TCGA-D5-6537 TCGA-DM-A1DB 
       63.98        21.44         0.10         4.80        44.32 

$`RRM2B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        15.75         0.20        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.33         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       12.59       140.38         7.50       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  RRM2B MUTATED RRM2B WILD-TYPE 
            0.1             0.0 
  RRM2B MUTATED RRM2B WILD-TYPE 
          63.98          140.38 
  RRM2B MUTATED RRM2B WILD-TYPE 
         21.440          20.155 
[1] "0.1 - 64.0 (21.4)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.8"
D934V2, 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       24       106         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        19         10         40         31       35        13
                 vv
clus              STAGE IVB
  RRM2B MUTATED           0
  RRM2B WILD-TYPE         1
D934V3, multiclass
            clus
vv           RRM2B MUTATED RRM2B WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              3             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RRM2B MUTATED     0   0   5   0
  RRM2B WILD-TYPE   9  68 243  41
D934V4, multiclass
    clus
vv   RRM2B MUTATED RRM2B WILD-TYPE
  T1             0               9
  T2             0              68
  T3             5             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
  RRM2B MUTATED     4   1   0
  RRM2B WILD-TYPE 216  79  66
D934V5, multiclass
    clus
vv   RRM2B MUTATED RRM2B WILD-TYPE
  N0             4             216
  N1             1              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"
D934V6, binary
                 cls
clus                0   1
  RRM2B MUTATED     3   0
  RRM2B WILD-TYPE 280  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RRM2B MUTATED      3    0
  RRM2B WILD-TYPE  280   48
   clus
vv  RRM2B MUTATED RRM2B WILD-TYPE
  0             3             280
  1             0              48
[1] 2 2
[1] FALSE
D934V7, 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
D934V8, binary
                 cls
clus                0   1
  RRM2B MUTATED     5   0
  RRM2B WILD-TYPE 312  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RRM2B MUTATED      5    0
  RRM2B WILD-TYPE  312   48
                               clus
vv                              RRM2B MUTATED RRM2B WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  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 254   2  22  20
D934V9, multiclass
    clus
vv   RRM2B MUTATED RRM2B WILD-TYPE
  R0             3             254
  R1             0               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"
D934V10, 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
D934V11, 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(935) Variable = SCN3A MUTATION ANALYSIS
D935V1, survival
                 sevent
clus2               0   1
  SCN3A MUTATED    32   8
  SCN3A WILD-TYPE 250  65
  SCN3A MUTATED SCN3A WILD-TYPE 
             40             315 
  SCN3A MUTATED SCN3A WILD-TYPE 
              8              65 
$`SCN3A MUTATED`
TCGA-A6-2671 TCGA-A6-3809 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6652 
       43.76        32.75        33.53        22.06        32.71        24.69 
TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3556 TCGA-AA-3713 TCGA-AA-3715 
       24.39        19.66        63.98        23.01        19.04        19.04 
TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 
       31.00        33.01        24.00        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 
        0.33        22.03        12.95        11.01        10.06        11.51 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6930 TCGA-D5-6931 TCGA-DM-A1D9 
        1.32        15.12         4.80         1.51        12.00       140.38 
TCGA-DM-A1HB TCGA-F4-6459 TCGA-G4-6321 TCGA-G4-6323 
      135.65         8.61        22.09        13.78 

$`SCN3A WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       34.65        33.34        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-6137 TCGA-A6-6138 
       30.44        29.19        23.61        22.09        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6654 
        8.38        25.08        25.18        24.16        21.76        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        29.95        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       26.99        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
        2.01        12.99        24.00        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        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        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       39.06        51.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        15.75         0.20        21.44         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       83.80        22.36        61.41        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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-6680 TCGA-D5-5537 
       11.01        13.05        11.08        11.08        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 
       12.26        19.59        13.51        20.19        18.25        43.27 
TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 
      119.93        35.97        60.79       117.07        98.24        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6586 TCGA-G4-6588 
       51.75        45.11        36.72        36.00        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  SCN3A MUTATED SCN3A WILD-TYPE 
           0.33            0.00 
  SCN3A MUTATED SCN3A WILD-TYPE 
         140.38          139.17 
  SCN3A MUTATED SCN3A WILD-TYPE 
         22.075          20.020 
[1] "0.3 - 140.4 (22.1)" "0.0 - 139.2 (20.0)"
[1] "hr=" "1.1"
D935V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SCN3A MUTATED         4        1        5        10         4         1
  SCN3A WILD-TYPE      60        0       20        99         4         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SCN3A MUTATED           2          0          8          2        3         2
  SCN3A WILD-TYPE        17         10         33         29       32        11
                 vv
clus              STAGE IVB
  SCN3A MUTATED           0
  SCN3A WILD-TYPE         1
D935V3, multiclass
            clus
vv           SCN3A MUTATED SCN3A WILD-TYPE
  STAGE I                4              60
  STAGE IA               1               0
  STAGE II               5              20
  STAGE IIA             10              99
  STAGE IIB              4               4
  STAGE IIC              1               0
  STAGE III              2              17
  STAGE IIIA             0              10
  STAGE IIIB             8              33
  STAGE IIIC             2              29
  STAGE IV               3              32
  STAGE IVA              2              11
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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   5  26  10
  SCN3A WILD-TYPE   8  63 222  31
D935V4, multiclass
    clus
vv   SCN3A MUTATED SCN3A WILD-TYPE
  T1             1               8
  T2             5              63
  T3            26             222
  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    29  10   4
  SCN3A WILD-TYPE 191  70  62
D935V5, multiclass
    clus
vv   SCN3A MUTATED SCN3A WILD-TYPE
  N0            29             191
  N1            10              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"
D935V6, binary
                 cls
clus                0   1
  SCN3A MUTATED    29   5
  SCN3A WILD-TYPE 254  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCN3A MUTATED     29    5
  SCN3A WILD-TYPE  254   43
   clus
vv  SCN3A MUTATED SCN3A WILD-TYPE
  0            29             254
  1             5              43
[1] 2 2
[1] FALSE
D935V7, binary
                 cls
clus                0   1
  SCN3A MUTATED    19  24
  SCN3A WILD-TYPE 151 173
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCN3A MUTATED     19   24
  SCN3A WILD-TYPE  151  173
        clus
vv       SCN3A MUTATED SCN3A WILD-TYPE
  FEMALE            19             151
  MALE              24             173
[1] 2 2
[1] FALSE
D935V8, binary
                 cls
clus                0   1
  SCN3A MUTATED    34   8
  SCN3A WILD-TYPE 283  40
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCN3A MUTATED     34    8
  SCN3A WILD-TYPE  283   40
                               clus
vv                              SCN3A MUTATED SCN3A WILD-TYPE
  COLON ADENOCARCINOMA                     34             283
  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 227   2  20  19
D935V9, multiclass
    clus
vv   SCN3A MUTATED SCN3A WILD-TYPE
  R0            30             227
  R1             0               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"
D935V10, 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    24
  SCN3A WILD-TYPE                        15   152
D935V11, 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                                       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(936) Variable = KIAA0240 MUTATION ANALYSIS
D936V1, survival
                    sevent
clus2                  0   1
  KIAA0240 MUTATED     7   2
  KIAA0240 WILD-TYPE 275  71
  KIAA0240 MUTATED KIAA0240 WILD-TYPE 
                 9                346 
  KIAA0240 MUTATED KIAA0240 WILD-TYPE 
                 2                 71 
$`KIAA0240 MUTATED`
TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3713 TCGA-AA-3949 TCGA-AA-A00N 
       63.98        13.02         1.02        19.04        26.01         4.01 
TCGA-CM-6171 TCGA-D5-6928 TCGA-G4-6628 
       14.04        11.64        52.80 

$`KIAA0240 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 
        1.02        35.01         6.97         1.02        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       35.80        26.17        91.79        46.75 

  KIAA0240 MUTATED KIAA0240 WILD-TYPE 
              1.02               0.00 
  KIAA0240 MUTATED KIAA0240 WILD-TYPE 
             63.98             140.38 
  KIAA0240 MUTATED KIAA0240 WILD-TYPE 
             14.04              20.63 
[1] "1.0 - 64.0 (14.0)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "1.1"
D936V2, 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       24       107         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0240 MUTATED           1          0          1          0        1
  KIAA0240 WILD-TYPE        18         10         40         31       34
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA0240 MUTATED           0         0
  KIAA0240 WILD-TYPE        13         1
D936V3, multiclass
            clus
vv           KIAA0240 MUTATED KIAA0240 WILD-TYPE
  STAGE I                   2                 62
  STAGE IA                  0                  1
  STAGE II                  1                 24
  STAGE IIA                 2                107
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 1                 18
  STAGE IIIA                0                 10
  STAGE IIIB                1                 40
  STAGE IIIC                0                 31
  STAGE IV                  1                 34
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA0240 MUTATED     0   2   6   1
  KIAA0240 WILD-TYPE   9  66 242  40
D936V4, multiclass
    clus
vv   KIAA0240 MUTATED KIAA0240 WILD-TYPE
  T1                0                  9
  T2                2                 66
  T3                6                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
  KIAA0240 MUTATED     7   1   1
  KIAA0240 WILD-TYPE 213  79  65
D936V5, multiclass
    clus
vv   KIAA0240 MUTATED KIAA0240 WILD-TYPE
  N0                7                213
  N1                1                 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"
D936V6, binary
                    cls
clus                   0   1
  KIAA0240 MUTATED     8   1
  KIAA0240 WILD-TYPE 275  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0240 MUTATED      8    1
  KIAA0240 WILD-TYPE  275   47
   clus
vv  KIAA0240 MUTATED KIAA0240 WILD-TYPE
  0                8                275
  1                1                 47
[1] 2 2
[1] FALSE
D936V7, 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
D936V8, binary
                    cls
clus                   0   1
  KIAA0240 MUTATED     5   4
  KIAA0240 WILD-TYPE 312  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0240 MUTATED      5    4
  KIAA0240 WILD-TYPE  312   44
                               clus
vv                              KIAA0240 MUTATED KIAA0240 WILD-TYPE
  COLON ADENOCARCINOMA                         5                312
  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 250   2  21  21
D936V9, multiclass
    clus
vv   KIAA0240 MUTATED KIAA0240 WILD-TYPE
  R0                7                250
  R1                0                  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"
D936V10, 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
D936V11, 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(937) Variable = IVD MUTATION ANALYSIS
D937V1, survival
               sevent
clus2             0   1
  IVD MUTATED     5   0
  IVD WILD-TYPE 277  73
  IVD MUTATED IVD WILD-TYPE 
            5           350 
  IVD MUTATED IVD WILD-TYPE 
            0            73 
$`IVD MUTATED`
TCGA-A6-6781 TCGA-AU-6004 TCGA-CA-6716 TCGA-D5-6539 TCGA-F4-6703 
       19.66        27.09         0.26        12.49        35.87 

$`IVD WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  IVD MUTATED IVD WILD-TYPE 
         0.26          0.00 
  IVD MUTATED IVD WILD-TYPE 
        35.87        140.38 
  IVD MUTATED IVD WILD-TYPE 
       19.660        20.235 
[1] "0.3 - 35.9 (19.7)"  "0.0 - 140.4 (20.2)"
[1] "hr="     "9100000"
D937V2, 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       25       107         8         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IVD MUTATED           0          1          0          1        0         0
  IVD WILD-TYPE        19          9         41         30       35        13
               vv
clus            STAGE IVB
  IVD MUTATED           0
  IVD WILD-TYPE         1
D937V3, multiclass
            clus
vv           IVD MUTATED IVD WILD-TYPE
  STAGE I              1            63
  STAGE IA             0             1
  STAGE II             0            25
  STAGE IIA            2           107
  STAGE IIB            0             8
  STAGE IIC            0             1
  STAGE III            0            19
  STAGE IIIA           1             9
  STAGE IIIB           0            41
  STAGE IIIC           1            30
  STAGE IV             0            35
  STAGE IVA            0            13
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  IVD MUTATED     0   1   3   1
  IVD WILD-TYPE   9  67 245  40
D937V4, multiclass
    clus
vv   IVD MUTATED IVD WILD-TYPE
  T1           0             9
  T2           1            67
  T3           3           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
  IVD MUTATED     4   1   0
  IVD WILD-TYPE 216  79  66
D937V5, multiclass
    clus
vv   IVD MUTATED IVD WILD-TYPE
  N0           4           216
  N1           1            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"
D937V6, binary
               cls
clus              0   1
  IVD MUTATED     4   0
  IVD WILD-TYPE 279  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  IVD MUTATED      4    0
  IVD WILD-TYPE  279   48
   clus
vv  IVD MUTATED IVD WILD-TYPE
  0           4           279
  1           0            48
[1] 2 2
[1] FALSE
D937V7, 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
D937V8, binary
               cls
clus              0   1
  IVD MUTATED     4   1
  IVD WILD-TYPE 313  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  IVD MUTATED      4    1
  IVD WILD-TYPE  313   47
                               clus
vv                              IVD MUTATED IVD WILD-TYPE
  COLON ADENOCARCINOMA                    4           313
  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 253   2  22  20
D937V9, multiclass
    clus
vv   IVD MUTATED IVD WILD-TYPE
  R0           4           253
  R1           0             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"
D937V10, 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
D937V11, 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(938) Variable = ZFP57 MUTATION ANALYSIS
D938V1, survival
                 sevent
clus2               0   1
  ZFP57 MUTATED    10   2
  ZFP57 WILD-TYPE 272  71
  ZFP57 MUTATED ZFP57 WILD-TYPE 
             12             343 
  ZFP57 MUTATED ZFP57 WILD-TYPE 
              2              71 
$`ZFP57 MUTATED`
TCGA-A6-5665 TCGA-A6-6138 TCGA-AA-3672 TCGA-AA-3815 TCGA-AA-3966 TCGA-AA-A010 
       22.06        22.52         0.92        33.04         2.01        34.98 
TCGA-AZ-4315 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CA-6717 TCGA-G4-6304 TCGA-G4-6588 
       58.39       100.01         1.94         0.33        53.62        26.17 

$`ZFP57 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.09        32.71        27.09         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
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         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 
       52.80 

  ZFP57 MUTATED ZFP57 WILD-TYPE 
           0.33            0.00 
  ZFP57 MUTATED ZFP57 WILD-TYPE 
         100.01          140.38 
  ZFP57 MUTATED ZFP57 WILD-TYPE 
         24.345          20.020 
[1] "0.3 - 100.0 (24.3)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.4"
D938V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZFP57 MUTATED         1        0        1         6         2         0
  ZFP57 WILD-TYPE      63        1       24       103         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ZFP57 MUTATED           1          1          0          0        0         0
  ZFP57 WILD-TYPE        18          9         41         31       35        13
                 vv
clus              STAGE IVB
  ZFP57 MUTATED           0
  ZFP57 WILD-TYPE         1
D938V3, multiclass
            clus
vv           ZFP57 MUTATED ZFP57 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              6             103
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             1               9
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ZFP57 MUTATED     0   2   8   2
  ZFP57 WILD-TYPE   9  66 240  39
D938V4, multiclass
    clus
vv   ZFP57 MUTATED ZFP57 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             8             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
  ZFP57 MUTATED    10   2   0
  ZFP57 WILD-TYPE 210  78  66
D938V5, multiclass
    clus
vv   ZFP57 MUTATED ZFP57 WILD-TYPE
  N0            10             210
  N1             2              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"
D938V6, binary
                 cls
clus                0   1
  ZFP57 MUTATED    12   0
  ZFP57 WILD-TYPE 271  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFP57 MUTATED     12    0
  ZFP57 WILD-TYPE  271   48
   clus
vv  ZFP57 MUTATED ZFP57 WILD-TYPE
  0            12             271
  1             0              48
[1] 2 2
[1] FALSE
D938V7, binary
                 cls
clus                0   1
  ZFP57 MUTATED     8   4
  ZFP57 WILD-TYPE 162 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFP57 MUTATED      8    4
  ZFP57 WILD-TYPE  162  193
        clus
vv       ZFP57 MUTATED ZFP57 WILD-TYPE
  FEMALE             8             162
  MALE               4             193
[1] 2 2
[1] FALSE
D938V8, binary
                 cls
clus                0   1
  ZFP57 MUTATED    10   2
  ZFP57 WILD-TYPE 307  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFP57 MUTATED     10    2
  ZFP57 WILD-TYPE  307   46
                               clus
vv                              ZFP57 MUTATED ZFP57 WILD-TYPE
  COLON ADENOCARCINOMA                     10             307
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ZFP57 MUTATED     7   0   0   1
  ZFP57 WILD-TYPE 250   2  22  20
D938V9, multiclass
    clus
vv   ZFP57 MUTATED ZFP57 WILD-TYPE
  R0             7             250
  R1             0               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"
D938V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZFP57 MUTATED                                  0     1
  ZFP57 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ZFP57 MUTATED                           0     7
  ZFP57 WILD-TYPE                        19   169
D938V11, multiclass
                                  clus
vv                                 ZFP57 MUTATED ZFP57 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(939) Variable = RC3H2 MUTATION ANALYSIS
D939V1, survival
                 sevent
clus2               0   1
  RC3H2 MUTATED    10   0
  RC3H2 WILD-TYPE 272  73
  RC3H2 MUTATED RC3H2 WILD-TYPE 
             10             345 
  RC3H2 MUTATED RC3H2 WILD-TYPE 
              0              73 
$`RC3H2 MUTATED`
TCGA-A6-6780 TCGA-AA-3864 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-6169 TCGA-CM-6674 
       20.12        53.00         2.01        23.05        13.02        12.95 
TCGA-D5-6541 TCGA-F4-6460 TCGA-F4-6806 TCGA-G4-6586 
       15.58        13.38        29.59        35.80 

$`RC3H2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       21.14         2.93       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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-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-6675 TCGA-CM-6676 
       12.99        15.02        14.04        11.01        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 
       13.45         6.18        35.87         1.55        16.31        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 
       45.11        36.72        36.00        22.09        13.78        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  RC3H2 MUTATED RC3H2 WILD-TYPE 
           2.01            0.00 
  RC3H2 MUTATED RC3H2 WILD-TYPE 
          53.00          140.38 
  RC3H2 MUTATED RC3H2 WILD-TYPE 
          17.85           20.28 
[1] "2.0 - 53.0 (17.9)"  "0.0 - 140.4 (20.3)"
[1] "hr="     "9300000"
D939V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RC3H2 MUTATED         1        0        1         6         0         0
  RC3H2 WILD-TYPE      63        1       24       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        19         10         40         31       34        13
                 vv
clus              STAGE IVB
  RC3H2 MUTATED           0
  RC3H2 WILD-TYPE         1
D939V3, multiclass
            clus
vv           RC3H2 MUTATED RC3H2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              6             103
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RC3H2 MUTATED     0   1   9   0
  RC3H2 WILD-TYPE   9  67 239  41
D939V4, multiclass
    clus
vv   RC3H2 MUTATED RC3H2 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             9             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
  RC3H2 MUTATED     8   2   0
  RC3H2 WILD-TYPE 212  78  66
D939V5, multiclass
    clus
vv   RC3H2 MUTATED RC3H2 WILD-TYPE
  N0             8             212
  N1             2              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"
D939V6, binary
                 cls
clus                0   1
  RC3H2 MUTATED     8   1
  RC3H2 WILD-TYPE 275  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RC3H2 MUTATED      8    1
  RC3H2 WILD-TYPE  275   47
   clus
vv  RC3H2 MUTATED RC3H2 WILD-TYPE
  0             8             275
  1             1              47
[1] 2 2
[1] FALSE
D939V7, binary
                 cls
clus                0   1
  RC3H2 MUTATED     4   6
  RC3H2 WILD-TYPE 166 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RC3H2 MUTATED      4    6
  RC3H2 WILD-TYPE  166  191
        clus
vv       RC3H2 MUTATED RC3H2 WILD-TYPE
  FEMALE             4             166
  MALE               6             191
[1] 2 2
[1] FALSE
D939V8, binary
                 cls
clus                0   1
  RC3H2 MUTATED     8   2
  RC3H2 WILD-TYPE 309  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RC3H2 MUTATED      8    2
  RC3H2 WILD-TYPE  309   46
                               clus
vv                              RC3H2 MUTATED RC3H2 WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RC3H2 MUTATED     8   0   0   1
  RC3H2 WILD-TYPE 249   2  22  20
D939V9, multiclass
    clus
vv   RC3H2 MUTATED RC3H2 WILD-TYPE
  R0             8             249
  R1             0               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"
D939V10, 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     8
  RC3H2 WILD-TYPE                        18   168
D939V11, 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                                        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(940) Variable = CCDC141 MUTATION ANALYSIS
D940V1, survival
                   sevent
clus2                 0   1
  CCDC141 MUTATED    20   4
  CCDC141 WILD-TYPE 262  69
  CCDC141 MUTATED CCDC141 WILD-TYPE 
               24               331 
  CCDC141 MUTATED CCDC141 WILD-TYPE 
                4                69 
$`CCDC141 MUTATED`
TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3864 TCGA-AA-3941 TCGA-AA-3977 TCGA-AA-A00N 
        1.02        63.98        53.00        24.00        25.02         4.01 
TCGA-AA-A010 TCGA-AA-A01R TCGA-AZ-4315 TCGA-CA-5797 TCGA-CA-6717 TCGA-CK-5912 
       34.98        35.01        58.39         3.29         0.33        49.08 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-6161 TCGA-CM-6166 TCGA-CM-6171 TCGA-D5-6541 
       22.03        22.98        15.02        21.99        14.04        15.58 
TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D8 TCGA-F4-6459 TCGA-G4-6304 TCGA-G4-6628 
       13.41        11.38        12.59         8.61        53.62        52.80 

$`CCDC141 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 
        1.94         2.24         3.06         3.25         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        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         2.93         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-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        16.01        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-6167 
       17.03        12.00        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        16.14         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         1.51        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79       117.07        98.24        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 
       46.75 

  CCDC141 MUTATED CCDC141 WILD-TYPE 
             0.33              0.00 
  CCDC141 MUTATED CCDC141 WILD-TYPE 
            63.98            140.38 
  CCDC141 MUTATED CCDC141 WILD-TYPE 
            22.01             20.12 
[1] "0.3 - 64.0 (22.0)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.3"
D940V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CCDC141 MUTATED         5        0        3         5         3         0
  CCDC141 WILD-TYPE      59        1       22       104         5         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC141 MUTATED           1          0          3          0        1
  CCDC141 WILD-TYPE        18         10         38         31       34
                   vv
clus                STAGE IVA STAGE IVB
  CCDC141 MUTATED           1         0
  CCDC141 WILD-TYPE        12         1
D940V3, multiclass
            clus
vv           CCDC141 MUTATED CCDC141 WILD-TYPE
  STAGE I                  5                59
  STAGE IA                 0                 1
  STAGE II                 3                22
  STAGE IIA                5               104
  STAGE IIB                3                 5
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               0                10
  STAGE IIIB               3                38
  STAGE IIIC               0                31
  STAGE IV                 1                34
  STAGE IVA                1                12
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of 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  14   4
  CCDC141 WILD-TYPE   9  62 234  37
D940V4, multiclass
    clus
vv   CCDC141 MUTATED CCDC141 WILD-TYPE
  T1               0                 9
  T2               6                62
  T3              14               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
  CCDC141 MUTATED    17   5   2
  CCDC141 WILD-TYPE 203  75  64
D940V5, multiclass
    clus
vv   CCDC141 MUTATED CCDC141 WILD-TYPE
  N0              17               203
  N1               5                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"
D940V6, binary
                   cls
clus                  0   1
  CCDC141 MUTATED    19   2
  CCDC141 WILD-TYPE 264  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC141 MUTATED     19    2
  CCDC141 WILD-TYPE  264   46
   clus
vv  CCDC141 MUTATED CCDC141 WILD-TYPE
  0              19               264
  1               2                46
[1] 2 2
[1] FALSE
D940V7, binary
                   cls
clus                  0   1
  CCDC141 MUTATED    11  13
  CCDC141 WILD-TYPE 159 184
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC141 MUTATED     11   13
  CCDC141 WILD-TYPE  159  184
        clus
vv       CCDC141 MUTATED CCDC141 WILD-TYPE
  FEMALE              11               159
  MALE                13               184
[1] 2 2
[1] FALSE
D940V8, binary
                   cls
clus                  0   1
  CCDC141 MUTATED    21   3
  CCDC141 WILD-TYPE 296  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC141 MUTATED     21    3
  CCDC141 WILD-TYPE  296   45
                               clus
vv                              CCDC141 MUTATED CCDC141 WILD-TYPE
  COLON ADENOCARCINOMA                       21               296
  COLON MUCINOUS ADENOCARCINOMA               3                45
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  CCDC141 MUTATED    20   0   0   2
  CCDC141 WILD-TYPE 237   2  22  19
D940V9, multiclass
    clus
vv   CCDC141 MUTATED CCDC141 WILD-TYPE
  R0              20               237
  R1               0                 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"
D940V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCDC141 MUTATED                                  0     2
  CCDC141 WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CCDC141 MUTATED                           0    14
  CCDC141 WILD-TYPE                        19   162
D940V11, multiclass
                                  clus
vv                                 CCDC141 MUTATED CCDC141 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(941) Variable = HEATR4 MUTATION ANALYSIS
D941V1, survival
                  sevent
clus2                0   1
  HEATR4 MUTATED    11   3
  HEATR4 WILD-TYPE 271  70
  HEATR4 MUTATED HEATR4 WILD-TYPE 
              14              341 
  HEATR4 MUTATED HEATR4 WILD-TYPE 
               3               70 
$`HEATR4 MUTATED`
TCGA-A6-5661 TCGA-AA-3492 TCGA-AA-3672 TCGA-AA-3819 TCGA-AA-A00A TCGA-AA-A01R 
       33.53         3.02         0.92        25.02        38.04        35.01 
TCGA-AD-6964 TCGA-CA-6717 TCGA-CA-6718 TCGA-D5-6920 TCGA-DM-A0XF TCGA-G4-6299 
       10.88         0.33         0.10        12.39        38.20        74.56 
TCGA-G4-6304 TCGA-G4-6588 
       53.62        26.17 

$`HEATR4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       33.04         0.99         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
        7.96        27.02        13.94        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07         0.26         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6306 
        0.53        35.41        19.43       107.67        65.85        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        91.79        46.75        52.80 

  HEATR4 MUTATED HEATR4 WILD-TYPE 
             0.1              0.0 
  HEATR4 MUTATED HEATR4 WILD-TYPE 
           74.56           140.38 
  HEATR4 MUTATED HEATR4 WILD-TYPE 
          25.595           20.120 
[1] "0.1 - 74.6 (25.6)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.1"
D941V2, 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       24       102         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HEATR4 MUTATED           2          0          0          2        0
  HEATR4 WILD-TYPE        17         10         41         29       35
                  vv
clus               STAGE IVA STAGE IVB
  HEATR4 MUTATED           0         0
  HEATR4 WILD-TYPE        13         1
D941V3, multiclass
            clus
vv           HEATR4 MUTATED HEATR4 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               7              102
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               2               17
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              2               29
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  HEATR4 MUTATED     0   0  12   2
  HEATR4 WILD-TYPE   9  68 236  39
D941V4, multiclass
    clus
vv   HEATR4 MUTATED HEATR4 WILD-TYPE
  T1              0                9
  T2              0               68
  T3             12              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
  HEATR4 MUTATED     9   1   4
  HEATR4 WILD-TYPE 211  79  62
D941V5, multiclass
    clus
vv   HEATR4 MUTATED HEATR4 WILD-TYPE
  N0              9              211
  N1              1               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"
D941V6, binary
                  cls
clus                 0   1
  HEATR4 MUTATED    13   0
  HEATR4 WILD-TYPE 270  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HEATR4 MUTATED     13    0
  HEATR4 WILD-TYPE  270   48
   clus
vv  HEATR4 MUTATED HEATR4 WILD-TYPE
  0             13              270
  1              0               48
[1] 2 2
[1] FALSE
D941V7, 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
D941V8, binary
                  cls
clus                 0   1
  HEATR4 MUTATED    11   3
  HEATR4 WILD-TYPE 306  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HEATR4 MUTATED     11    3
  HEATR4 WILD-TYPE  306   45
                               clus
vv                              HEATR4 MUTATED HEATR4 WILD-TYPE
  COLON ADENOCARCINOMA                      11              306
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  HEATR4 MUTATED    10   0   0   2
  HEATR4 WILD-TYPE 247   2  22  19
D941V9, multiclass
    clus
vv   HEATR4 MUTATED HEATR4 WILD-TYPE
  R0             10              247
  R1              0                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"
D941V10, 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
D941V11, 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(942) Variable = ASPM MUTATION ANALYSIS
D942V1, survival
                sevent
clus2              0   1
  ASPM MUTATED    33   7
  ASPM WILD-TYPE 249  66
  ASPM MUTATED ASPM WILD-TYPE 
            40            315 
  ASPM MUTATED ASPM WILD-TYPE 
             7             66 
$`ASPM MUTATED`
TCGA-A6-5665 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3543 
       22.06        24.39        20.12        19.66        63.98         0.99 
TCGA-AA-3555 TCGA-AA-3811 TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-3977 TCGA-AA-A00E 
       29.95        10.06        53.00        33.01        25.02        30.02 
TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A00Z TCGA-AA-A010 TCGA-AD-6889 TCGA-AD-6895 
       18.05         4.01        21.99        34.98        56.55         0.72 
TCGA-AD-6901 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
       22.42        58.39         1.41         0.07         0.26         0.33 
TCGA-CK-5916 TCGA-CK-6748 TCGA-CM-6161 TCGA-CM-6171 TCGA-CM-6678 TCGA-D5-6540 
       21.14         2.01        15.02        14.04        11.01        16.14 
TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-DM-A1HB TCGA-DM-A285 TCGA-DM-A28C 
        9.04        11.64        13.41       135.65         6.12        81.37 
TCGA-F4-6703 TCGA-F4-6856 TCGA-G4-6588 TCGA-G4-6628 
       35.87        19.43        26.17        52.80 

$`ASPM WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 
       25.18        24.16        21.76        24.69        23.87        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 
        7.04         3.02         1.02        35.01         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
       29.00        29.00        26.01        12.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        17.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00K 
       27.02        13.94        38.04        19.00        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        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        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 
       40.96         0.07        21.37         4.21         0.79         5.79 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4616 
        0.95        15.75         0.20        21.44        17.82         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6718 
        1.94         2.24         3.06         3.25         3.29         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       51.32        21.99         2.93       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        16.01        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-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-6679 TCGA-CM-6680 TCGA-D5-5537 
       13.05        11.08        11.08        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       14.30         9.44         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-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-F4-6704 TCGA-F4-6805 
        8.61        13.38        13.45         6.18         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       35.80        91.79        46.75 

  ASPM MUTATED ASPM WILD-TYPE 
          0.07           0.00 
  ASPM MUTATED ASPM WILD-TYPE 
        135.65         140.38 
  ASPM MUTATED ASPM WILD-TYPE 
         19.89          20.28 
[1] "0.1 - 135.7 (19.9)" "0.0 - 140.4 (20.3)"
[1] "hr=" "1.2"
D942V2, 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       23        95         5         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ASPM MUTATED           1          1          3          1        4         1
  ASPM WILD-TYPE        18          9         38         30       31        12
                vv
clus             STAGE IVB
  ASPM MUTATED           0
  ASPM WILD-TYPE         1
D942V3, multiclass
            clus
vv           ASPM MUTATED ASPM WILD-TYPE
  STAGE I               8             56
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA            14             95
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            1              9
  STAGE IIIB            3             38
  STAGE IIIC            1             30
  STAGE IV              4             31
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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   8
  ASPM WILD-TYPE   8  60 224  33
D942V4, multiclass
    clus
vv   ASPM MUTATED ASPM WILD-TYPE
  T1            1              8
  T2            8             60
  T3           24            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
  ASPM MUTATED    29   9   3
  ASPM WILD-TYPE 191  71  63
D942V5, multiclass
    clus
vv   ASPM MUTATED ASPM WILD-TYPE
  N0           29            191
  N1            9             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"
D942V6, binary
                cls
clus               0   1
  ASPM MUTATED    31   5
  ASPM WILD-TYPE 252  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASPM MUTATED     31    5
  ASPM WILD-TYPE  252   43
   clus
vv  ASPM MUTATED ASPM WILD-TYPE
  0           31            252
  1            5             43
[1] 2 2
[1] FALSE
D942V7, binary
                cls
clus               0   1
  ASPM MUTATED    14  27
  ASPM WILD-TYPE 156 170
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASPM MUTATED     14   27
  ASPM WILD-TYPE  156  170
        clus
vv       ASPM MUTATED ASPM WILD-TYPE
  FEMALE           14            156
  MALE             27            170
[1] 2 2
[1] FALSE
D942V8, binary
                cls
clus               0   1
  ASPM MUTATED    28  13
  ASPM WILD-TYPE 289  35
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASPM MUTATED     28   13
  ASPM WILD-TYPE  289   35
                               clus
vv                              ASPM MUTATED ASPM WILD-TYPE
  COLON ADENOCARCINOMA                    28            289
  COLON MUCINOUS ADENOCARCINOMA           13             35
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ASPM MUTATED    26   0   0   5
  ASPM WILD-TYPE 231   2  22  16
D942V9, multiclass
    clus
vv   ASPM MUTATED ASPM WILD-TYPE
  R0           26            231
  R1            0              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"
D942V10, 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
D942V11, 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(943) Variable = COL6A5 MUTATION ANALYSIS
D943V1, survival
                  sevent
clus2                0   1
  COL6A5 MUTATED    27   4
  COL6A5 WILD-TYPE 255  69
  COL6A5 MUTATED COL6A5 WILD-TYPE 
              31              324 
  COL6A5 MUTATED COL6A5 WILD-TYPE 
               4               69 
$`COL6A5 MUTATED`
TCGA-A6-5661 TCGA-A6-6141 TCGA-A6-6653 TCGA-AA-3510 TCGA-AA-3815 TCGA-AA-3955 
       33.53         8.38        24.39        63.98        33.04        20.98 
TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A01R TCGA-AU-3779 TCGA-AZ-4315 TCGA-AZ-6598 
       25.02         4.01        35.01        14.50        58.39        49.41 
TCGA-AZ-6608 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4743 TCGA-CM-5864 TCGA-CM-6164 
        1.94         0.33         0.10        23.05        15.02        29.03 
TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6675 TCGA-CM-6676 TCGA-D5-6923 TCGA-D5-6924 
       12.99        14.04        13.05        11.08        12.43        14.30 
TCGA-D5-6930 TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-F4-6460 TCGA-F4-6805 TCGA-G4-6588 
        1.51       130.65        92.75        13.38        16.31        26.17 
TCGA-G4-6628 
       52.80 

$`COL6A5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       24.16        21.76        24.69        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01        24.00         2.01        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.20        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07         0.26         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93         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        16.01 
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-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-6172 TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       11.01        12.95        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 
       10.13         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-A1D6 
       11.38        10.26       119.70        24.43        38.20        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 
       60.79       117.07        98.24         8.61        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       35.87         1.55        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 

  COL6A5 MUTATED COL6A5 WILD-TYPE 
             0.1              0.0 
  COL6A5 MUTATED COL6A5 WILD-TYPE 
          130.65           140.38 
  COL6A5 MUTATED COL6A5 WILD-TYPE 
          16.310           20.235 
[1] "0.1 - 130.7 (16.3)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.8"
D943V2, 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       23        92         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  COL6A5 MUTATED           1          1          2          0        0
  COL6A5 WILD-TYPE        18          9         39         31       35
                  vv
clus               STAGE IVA STAGE IVB
  COL6A5 MUTATED           0         1
  COL6A5 WILD-TYPE        13         0
D943V3, multiclass
            clus
vv           COL6A5 MUTATED COL6A5 WILD-TYPE
  STAGE I                 6               58
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA              17               92
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              1                9
  STAGE IIIB              2               39
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  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  59 226  39
D943V4, multiclass
    clus
vv   COL6A5 MUTATED COL6A5 WILD-TYPE
  T1              0                9
  T2              9               59
  T3             22              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
  COL6A5 MUTATED    28   2   3
  COL6A5 WILD-TYPE 192  78  63
D943V5, multiclass
    clus
vv   COL6A5 MUTATED COL6A5 WILD-TYPE
  N0             28              192
  N1              2               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"
D943V6, binary
                  cls
clus                 0   1
  COL6A5 MUTATED    29   1
  COL6A5 WILD-TYPE 254  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL6A5 MUTATED     29    1
  COL6A5 WILD-TYPE  254   47
   clus
vv  COL6A5 MUTATED COL6A5 WILD-TYPE
  0             29              254
  1              1               47
[1] 2 2
[1] FALSE
D943V7, 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
D943V8, binary
                  cls
clus                 0   1
  COL6A5 MUTATED    29   4
  COL6A5 WILD-TYPE 288  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL6A5 MUTATED     29    4
  COL6A5 WILD-TYPE  288   44
                               clus
vv                              COL6A5 MUTATED COL6A5 WILD-TYPE
  COLON ADENOCARCINOMA                      29              288
  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 234   2  22  18
D943V9, multiclass
    clus
vv   COL6A5 MUTATED COL6A5 WILD-TYPE
  R0             23              234
  R1              0                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"
D943V10, 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
D943V11, 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(944) Variable = PREX2 MUTATION ANALYSIS
D944V1, survival
                 sevent
clus2               0   1
  PREX2 MUTATED    24   5
  PREX2 WILD-TYPE 258  68
  PREX2 MUTATED PREX2 WILD-TYPE 
             29             326 
  PREX2 MUTATED PREX2 WILD-TYPE 
              5              68 
$`PREX2 MUTATED`
TCGA-A6-2676 TCGA-A6-5659 TCGA-A6-6142 TCGA-A6-6653 TCGA-AA-3510 TCGA-AA-3544 
       42.90        30.44        25.08        24.39        63.98        14.01 
TCGA-AA-3660 TCGA-AA-3672 TCGA-AA-3815 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-A00N 
       78.08         0.92        33.04        24.00        33.01         4.01 
TCGA-AA-A01R TCGA-AD-6548 TCGA-AZ-4315 TCGA-CA-6716 TCGA-CA-6717 TCGA-CK-4950 
       35.01        21.37        58.39         0.26         0.33        40.34 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6676 TCGA-D5-6537 
       51.32        21.99        12.99        15.02        11.08         4.80 
TCGA-D5-6538 TCGA-D5-6540 TCGA-DM-A285 TCGA-F4-6570 TCGA-G4-6323 
       17.13        16.14         6.12         6.18        13.78 

$`PREX2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 
       32.71        27.09        22.52         8.38        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       21.76        24.69        23.87        20.12        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 
        7.04         3.02         1.02        35.01         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3548 
       29.00        29.00        26.01        12.99         0.99        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        61.02         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6888 
       41.00        39.98        18.05        40.96         0.07         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 
        0.10         1.35        17.56       102.44        15.62        49.08 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6541 
        1.32        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        13.38        13.45 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.72        36.00        22.09        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  PREX2 MUTATED PREX2 WILD-TYPE 
           0.26            0.00 
  PREX2 MUTATED PREX2 WILD-TYPE 
          78.08          140.38 
  PREX2 MUTATED PREX2 WILD-TYPE 
         21.370          20.155 
[1] "0.3 - 78.1 (21.4)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D944V2, 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       23       102         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PREX2 MUTATED           2          1          3          0        3         2
  PREX2 WILD-TYPE        17          9         38         31       32        11
                 vv
clus              STAGE IVB
  PREX2 MUTATED           0
  PREX2 WILD-TYPE         1
D944V3, multiclass
            clus
vv           PREX2 MUTATED PREX2 WILD-TYPE
  STAGE I                7              57
  STAGE IA               1               0
  STAGE II               2              23
  STAGE IIA              7             102
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             1               9
  STAGE IIIB             3              38
  STAGE IIIC             0              31
  STAGE IV               3              32
  STAGE IVA              2              11
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  61 230  36
D944V4, multiclass
    clus
vv   PREX2 MUTATED PREX2 WILD-TYPE
  T1             0               9
  T2             7              61
  T3            18             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
  PREX2 MUTATED    20   7   4
  PREX2 WILD-TYPE 200  73  62
D944V5, multiclass
    clus
vv   PREX2 MUTATED PREX2 WILD-TYPE
  N0            20             200
  N1             7              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"
D944V6, binary
                 cls
clus                0   1
  PREX2 MUTATED    22   5
  PREX2 WILD-TYPE 261  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PREX2 MUTATED     22    5
  PREX2 WILD-TYPE  261   43
   clus
vv  PREX2 MUTATED PREX2 WILD-TYPE
  0            22             261
  1             5              43
[1] 2 2
[1] FALSE
D944V7, 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
D944V8, binary
                 cls
clus                0   1
  PREX2 MUTATED    25   6
  PREX2 WILD-TYPE 292  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PREX2 MUTATED     25    6
  PREX2 WILD-TYPE  292   42
                               clus
vv                              PREX2 MUTATED PREX2 WILD-TYPE
  COLON ADENOCARCINOMA                     25             292
  COLON MUCINOUS ADENOCARCINOMA             6              42
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PREX2 MUTATED    21   1   2   4
  PREX2 WILD-TYPE 236   1  20  17
D944V9, multiclass
    clus
vv   PREX2 MUTATED PREX2 WILD-TYPE
  R0            21             236
  R1             1               1
  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"
D944V10, 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
D944V11, 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(945) Variable = ZNF280C MUTATION ANALYSIS
D945V1, survival
                   sevent
clus2                 0   1
  ZNF280C MUTATED     9   0
  ZNF280C WILD-TYPE 273  73
  ZNF280C MUTATED ZNF280C WILD-TYPE 
                9               346 
  ZNF280C MUTATED ZNF280C WILD-TYPE 
                0                73 
$`ZNF280C MUTATED`
TCGA-A6-5665 TCGA-A6-5666 TCGA-AA-3518 TCGA-AA-3866 TCGA-AZ-4315 TCGA-CM-6168 
       22.06        32.71         1.02        17.03        58.39        12.99 
TCGA-CM-6678 TCGA-F4-6460 TCGA-G4-6628 
       11.01        13.38        52.80 

$`ZNF280C WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.09        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 
       63.98         6.97         1.02        13.02        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        53.00        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       35.80        26.17        91.79        46.75 

  ZNF280C MUTATED ZNF280C WILD-TYPE 
             1.02              0.00 
  ZNF280C MUTATED ZNF280C WILD-TYPE 
            58.39            140.38 
  ZNF280C MUTATED ZNF280C WILD-TYPE 
           17.030            20.235 
[1] "1.0 - 58.4 (17.0)"  "0.0 - 140.4 (20.2)"
[1] "hr="     "9300000"
D945V2, 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       25       105         8         0
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF280C MUTATED           0          0          1          0        0
  ZNF280C WILD-TYPE        19         10         40         31       35
                   vv
clus                STAGE IVA STAGE IVB
  ZNF280C MUTATED           1         0
  ZNF280C WILD-TYPE        12         1
D945V3, multiclass
            clus
vv           ZNF280C MUTATED ZNF280C WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                4               105
  STAGE IIB                0                 8
  STAGE IIC                1                 0
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                1                12
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 243  39
D945V4, multiclass
    clus
vv   ZNF280C MUTATED ZNF280C WILD-TYPE
  T1               0                 9
  T2               2                66
  T3               5               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
  ZNF280C MUTATED     7   2   0
  ZNF280C WILD-TYPE 213  78  66
D945V5, multiclass
    clus
vv   ZNF280C MUTATED ZNF280C WILD-TYPE
  N0               7               213
  N1               2                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"
D945V6, binary
                   cls
clus                  0   1
  ZNF280C MUTATED     8   1
  ZNF280C WILD-TYPE 275  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF280C MUTATED      8    1
  ZNF280C WILD-TYPE  275   47
   clus
vv  ZNF280C MUTATED ZNF280C WILD-TYPE
  0               8               275
  1               1                47
[1] 2 2
[1] FALSE
D945V7, 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
D945V8, binary
                   cls
clus                  0   1
  ZNF280C MUTATED     9   0
  ZNF280C WILD-TYPE 308  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF280C MUTATED      9    0
  ZNF280C WILD-TYPE  308   48
                               clus
vv                              ZNF280C MUTATED ZNF280C WILD-TYPE
  COLON ADENOCARCINOMA                        9               308
  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 249   2  22  21
D945V9, multiclass
    clus
vv   ZNF280C MUTATED ZNF280C WILD-TYPE
  R0               8               249
  R1               0                 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"
D945V10, 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
D945V11, 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(946) Variable = TSHZ1 MUTATION ANALYSIS
D946V1, survival
                 sevent
clus2               0   1
  TSHZ1 MUTATED    10   2
  TSHZ1 WILD-TYPE 272  71
  TSHZ1 MUTATED TSHZ1 WILD-TYPE 
             12             343 
  TSHZ1 MUTATED TSHZ1 WILD-TYPE 
              2              71 
$`TSHZ1 MUTATED`
TCGA-A6-5661 TCGA-A6-6780 TCGA-AA-3697 TCGA-AA-3821 TCGA-AA-3877 TCGA-AA-A00N 
       33.53        20.12        85.05         1.02        31.00         4.01 
TCGA-AA-A010 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-D5-6928 TCGA-G4-6628 
       34.98        21.44        58.39        49.41        11.64        52.80 

$`TSHZ1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       33.04         0.99        25.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        15.75         0.20        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 
       46.75 

  TSHZ1 MUTATED TSHZ1 WILD-TYPE 
           1.02            0.00 
  TSHZ1 MUTATED TSHZ1 WILD-TYPE 
          85.05          140.38 
  TSHZ1 MUTATED TSHZ1 WILD-TYPE 
         32.265          19.990 
[1] "1.0 - 85.0 (32.3)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1.6"
D946V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TSHZ1 MUTATED         3        0        1         5         2         0
  TSHZ1 WILD-TYPE      61        1       24       104         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TSHZ1 MUTATED           1          0          0          0        0         0
  TSHZ1 WILD-TYPE        18         10         41         31       35        13
                 vv
clus              STAGE IVB
  TSHZ1 MUTATED           0
  TSHZ1 WILD-TYPE         1
D946V3, multiclass
            clus
vv           TSHZ1 MUTATED TSHZ1 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              5             104
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TSHZ1 MUTATED     1   2   7   2
  TSHZ1 WILD-TYPE   8  66 241  39
D946V4, multiclass
    clus
vv   TSHZ1 MUTATED TSHZ1 WILD-TYPE
  T1             1               8
  T2             2              66
  T3             7             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
  TSHZ1 MUTATED    12   0   0
  TSHZ1 WILD-TYPE 208  80  66
D946V5, multiclass
    clus
vv   TSHZ1 MUTATED TSHZ1 WILD-TYPE
  N0            12             208
  N1             0              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"
D946V6, binary
                 cls
clus                0   1
  TSHZ1 MUTATED     9   0
  TSHZ1 WILD-TYPE 274  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TSHZ1 MUTATED      9    0
  TSHZ1 WILD-TYPE  274   48
   clus
vv  TSHZ1 MUTATED TSHZ1 WILD-TYPE
  0             9             274
  1             0              48
[1] 2 2
[1] FALSE
D946V7, 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
D946V8, binary
                 cls
clus                0   1
  TSHZ1 MUTATED     7   5
  TSHZ1 WILD-TYPE 310  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TSHZ1 MUTATED      7    5
  TSHZ1 WILD-TYPE  310   43
                               clus
vv                              TSHZ1 MUTATED TSHZ1 WILD-TYPE
  COLON ADENOCARCINOMA                      7             310
  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 247   2  22  21
D946V9, multiclass
    clus
vv   TSHZ1 MUTATED TSHZ1 WILD-TYPE
  R0            10             247
  R1             0               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"
D946V10, 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
D946V11, 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(947) Variable = IKBKB MUTATION ANALYSIS
D947V1, survival
                 sevent
clus2               0   1
  IKBKB MUTATED     6   1
  IKBKB WILD-TYPE 276  72
  IKBKB MUTATED IKBKB WILD-TYPE 
              7             348 
  IKBKB MUTATED IKBKB WILD-TYPE 
              1              72 
$`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         0.26         0.33 
TCGA-D5-6532 
       18.25 

$`IKBKB WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41        49.41        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6718 
        2.24         3.06         3.25         3.29         0.07         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 
       19.59        13.51        11.51        20.19         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  IKBKB MUTATED IKBKB WILD-TYPE 
           0.26            0.00 
  IKBKB MUTATED IKBKB WILD-TYPE 
          34.98          140.38 
  IKBKB MUTATED IKBKB WILD-TYPE 
         18.250          20.235 
[1] "0.3 - 35.0 (18.2)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D947V2, 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       25       106         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        18         10         41         31       35        13
                 vv
clus              STAGE IVB
  IKBKB MUTATED           0
  IKBKB WILD-TYPE         1
D947V3, multiclass
            clus
vv           IKBKB MUTATED IKBKB WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              3             106
  STAGE IIB              1               7
  STAGE IIC              1               0
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  IKBKB MUTATED     0   1   4   2
  IKBKB WILD-TYPE   9  67 244  39
D947V4, multiclass
    clus
vv   IKBKB MUTATED IKBKB WILD-TYPE
  T1             0               9
  T2             1              67
  T3             4             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
  IKBKB MUTATED     6   1   0
  IKBKB WILD-TYPE 214  79  66
D947V5, multiclass
    clus
vv   IKBKB MUTATED IKBKB WILD-TYPE
  N0             6             214
  N1             1              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"
D947V6, binary
                 cls
clus                0   1
  IKBKB MUTATED     6   0
  IKBKB WILD-TYPE 277  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IKBKB MUTATED      6    0
  IKBKB WILD-TYPE  277   48
   clus
vv  IKBKB MUTATED IKBKB WILD-TYPE
  0             6             277
  1             0              48
[1] 2 2
[1] FALSE
D947V7, 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
D947V8, binary
                 cls
clus                0   1
  IKBKB MUTATED     6   1
  IKBKB WILD-TYPE 311  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IKBKB MUTATED      6    1
  IKBKB WILD-TYPE  311   47
                               clus
vv                              IKBKB MUTATED IKBKB WILD-TYPE
  COLON ADENOCARCINOMA                      6             311
  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 254   2  22  19
D947V9, multiclass
    clus
vv   IKBKB MUTATED IKBKB WILD-TYPE
  R0             3             254
  R1             0               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"
D947V10, 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
D947V11, 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(948) Variable = DNAH17 MUTATION ANALYSIS
D948V1, survival
                  sevent
clus2                0   1
  DNAH17 MUTATED    28   6
  DNAH17 WILD-TYPE 254  67
  DNAH17 MUTATED DNAH17 WILD-TYPE 
              34              321 
  DNAH17 MUTATED DNAH17 WILD-TYPE 
               6               67 
$`DNAH17 MUTATED`
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-6141 TCGA-A6-6780 TCGA-A6-6781 
       29.19        33.53        23.61         8.38        20.12        19.66 
TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3713 TCGA-AA-3968 
        3.02        63.98        78.08         6.97        19.04        21.99 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6964 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.07        56.55        10.88        17.82        58.39         1.41 
TCGA-AZ-6601 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5912 TCGA-CM-4752 
      100.01         0.26         0.33         0.10        49.08        13.02 
TCGA-CM-5344 TCGA-CM-5861 TCGA-CM-5868 TCGA-CM-6168 TCGA-D5-5537 TCGA-D5-6540 
       22.03        15.02        17.03        12.99        45.40        16.14 
TCGA-D5-6541 TCGA-DM-A1HB TCGA-G4-6293 TCGA-G4-6628 
       15.58       135.65       107.67        52.80 

$`DNAH17 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       32.91        31.63        30.44        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 
       27.09        22.52        25.08        25.18        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       24.69        24.39        23.87        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       13.94        19.99        61.02         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        4.21         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
        0.20        21.44         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        3.29         0.07         1.35        17.56       102.44        40.34 
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         2.93         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-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        16.01         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-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-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       12.49         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       26.17        91.79        46.75 

  DNAH17 MUTATED DNAH17 WILD-TYPE 
            0.07             0.00 
  DNAH17 MUTATED DNAH17 WILD-TYPE 
          135.65           140.38 
  DNAH17 MUTATED DNAH17 WILD-TYPE 
           19.35            20.98 
[1] "0.1 - 135.7 (19.4)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.5"
D948V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DNAH17 MUTATED         5        0        5        13         0         0
  DNAH17 WILD-TYPE      59        1       20        96         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DNAH17 MUTATED           1          0          3          2        2
  DNAH17 WILD-TYPE        18         10         38         29       33
                  vv
clus               STAGE IVA STAGE IVB
  DNAH17 MUTATED           2         0
  DNAH17 WILD-TYPE        11         1
D948V3, multiclass
            clus
vv           DNAH17 MUTATED DNAH17 WILD-TYPE
  STAGE I                 5               59
  STAGE IA                0                1
  STAGE II                5               20
  STAGE IIA              13               96
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              3               38
  STAGE IIIC              2               29
  STAGE IV                2               33
  STAGE IVA               2               11
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  DNAH17 MUTATED     0   5  25   4
  DNAH17 WILD-TYPE   9  63 223  37
D948V4, multiclass
    clus
vv   DNAH17 MUTATED DNAH17 WILD-TYPE
  T1              0                9
  T2              5               63
  T3             25              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
  DNAH17 MUTATED    23   6   5
  DNAH17 WILD-TYPE 197  74  61
D948V5, multiclass
    clus
vv   DNAH17 MUTATED DNAH17 WILD-TYPE
  N0             23              197
  N1              6               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"
D948V6, binary
                  cls
clus                 0   1
  DNAH17 MUTATED    24   4
  DNAH17 WILD-TYPE 259  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAH17 MUTATED     24    4
  DNAH17 WILD-TYPE  259   44
   clus
vv  DNAH17 MUTATED DNAH17 WILD-TYPE
  0             24              259
  1              4               44
[1] 2 2
[1] FALSE
D948V7, binary
                  cls
clus                 0   1
  DNAH17 MUTATED    10  24
  DNAH17 WILD-TYPE 160 173
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAH17 MUTATED     10   24
  DNAH17 WILD-TYPE  160  173
        clus
vv       DNAH17 MUTATED DNAH17 WILD-TYPE
  FEMALE             10              160
  MALE               24              173
[1] 2 2
[1] FALSE
D948V8, binary
                  cls
clus                 0   1
  DNAH17 MUTATED    29   5
  DNAH17 WILD-TYPE 288  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAH17 MUTATED     29    5
  DNAH17 WILD-TYPE  288   43
                               clus
vv                              DNAH17 MUTATED DNAH17 WILD-TYPE
  COLON ADENOCARCINOMA                      29              288
  COLON MUCINOUS ADENOCARCINOMA              5               43
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  DNAH17 MUTATED    19   0   1   5
  DNAH17 WILD-TYPE 238   2  21  16
D948V9, multiclass
    clus
vv   DNAH17 MUTATED DNAH17 WILD-TYPE
  R0             19              238
  R1              0                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"
D948V10, 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                           6    18
  DNAH17 WILD-TYPE                        13   158
D948V11, multiclass
                                  clus
vv                                 DNAH17 MUTATED DNAH17 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         4                6
  BLACK OR AFRICAN AMERICAN                     6               13
  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(949) Variable = SLC9A9 MUTATION ANALYSIS
D949V1, survival
                  sevent
clus2                0   1
  SLC9A9 MUTATED    16   2
  SLC9A9 WILD-TYPE 266  71
  SLC9A9 MUTATED SLC9A9 WILD-TYPE 
              18              337 
  SLC9A9 MUTATED SLC9A9 WILD-TYPE 
               2               71 
$`SLC9A9 MUTATED`
TCGA-A6-2676 TCGA-A6-6654 TCGA-AA-3543 TCGA-AA-3555 TCGA-AA-3949 TCGA-AA-3977 
       42.90        23.87         0.99        29.95        26.01        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q TCGA-AA-A01R TCGA-CA-5796 TCGA-CA-6717 
        4.01        34.98         1.02        35.01         3.25         0.33 
TCGA-CA-6718 TCGA-CM-6164 TCGA-CM-6171 TCGA-D5-5538 TCGA-D5-6535 TCGA-G4-6310 
        0.10        29.03        14.04        12.26        15.12        45.11 

$`SLC9A9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
       12.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        31.00        38.07         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        2.24         3.06         3.29         0.07         0.26         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        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        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        43.27        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        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        51.75        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  SLC9A9 MUTATED SLC9A9 WILD-TYPE 
             0.1              0.0 
  SLC9A9 MUTATED SLC9A9 WILD-TYPE 
           45.11           140.38 
  SLC9A9 MUTATED SLC9A9 WILD-TYPE 
          19.495           20.190 
[1] "0.1 - 45.1 (19.5)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.3"
D949V2, 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       24       103         5         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC9A9 MUTATED           2          0          5          0        0
  SLC9A9 WILD-TYPE        17         10         36         31       35
                  vv
clus               STAGE IVA STAGE IVB
  SLC9A9 MUTATED           0         0
  SLC9A9 WILD-TYPE        13         1
D949V3, multiclass
            clus
vv           SLC9A9 MUTATED SLC9A9 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               6              103
  STAGE IIB               3                5
  STAGE IIC               0                1
  STAGE III               2               17
  STAGE IIIA              0               10
  STAGE IIIB              5               36
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SLC9A9 MUTATED     0   4  14   3
  SLC9A9 WILD-TYPE   9  64 234  38
D949V4, multiclass
    clus
vv   SLC9A9 MUTATED SLC9A9 WILD-TYPE
  T1              0                9
  T2              4               64
  T3             14              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
  SLC9A9 MUTATED    14   5   2
  SLC9A9 WILD-TYPE 206  75  64
D949V5, multiclass
    clus
vv   SLC9A9 MUTATED SLC9A9 WILD-TYPE
  N0             14              206
  N1              5               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"
D949V6, binary
                  cls
clus                 0   1
  SLC9A9 MUTATED    18   0
  SLC9A9 WILD-TYPE 265  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC9A9 MUTATED     18    0
  SLC9A9 WILD-TYPE  265   48
   clus
vv  SLC9A9 MUTATED SLC9A9 WILD-TYPE
  0             18              265
  1              0               48
[1] 2 2
[1] FALSE
D949V7, 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
D949V8, binary
                  cls
clus                 0   1
  SLC9A9 MUTATED    14   7
  SLC9A9 WILD-TYPE 303  41
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC9A9 MUTATED     14    7
  SLC9A9 WILD-TYPE  303   41
                               clus
vv                              SLC9A9 MUTATED SLC9A9 WILD-TYPE
  COLON ADENOCARCINOMA                      14              303
  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 242   2  22  17
D949V9, multiclass
    clus
vv   SLC9A9 MUTATED SLC9A9 WILD-TYPE
  R0             15              242
  R1              0                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"
D949V10, 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
D949V11, 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(950) Variable = PCDH19 MUTATION ANALYSIS
D950V1, survival
                  sevent
clus2                0   1
  PCDH19 MUTATED     9   4
  PCDH19 WILD-TYPE 273  69
  PCDH19 MUTATED PCDH19 WILD-TYPE 
              13              342 
  PCDH19 MUTATED PCDH19 WILD-TYPE 
               4               69 
$`PCDH19 MUTATED`
TCGA-AA-3492 TCGA-AA-3672 TCGA-AA-3845 TCGA-AA-3854 TCGA-AA-3947 TCGA-AA-A004 
        3.02         0.92         0.00        36.03        33.01        13.94 
TCGA-AZ-4315 TCGA-AZ-5403 TCGA-DM-A1HB TCGA-F4-6570 TCGA-G4-6586 TCGA-G4-6588 
       58.39        62.79       135.65         6.18        35.80        26.17 
TCGA-G4-6625 
       91.79 

$`PCDH19 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02        14.93        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
        0.00        33.07         0.00        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       27.02        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 
        1.41         5.13        83.80        22.36        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6628 
       36.72        36.00        22.09        13.78        46.75        52.80 

  PCDH19 MUTATED PCDH19 WILD-TYPE 
               0                0 
  PCDH19 MUTATED PCDH19 WILD-TYPE 
          135.65           140.38 
  PCDH19 MUTATED PCDH19 WILD-TYPE 
           33.01            20.07 
[1] "0.0 - 135.7 (33.0)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.1"
D950V2, 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       23       101         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PCDH19 MUTATED           1          0          1          0        0
  PCDH19 WILD-TYPE        18         10         40         31       35
                  vv
clus               STAGE IVA STAGE IVB
  PCDH19 MUTATED           0         0
  PCDH19 WILD-TYPE        13         1
D950V3, multiclass
            clus
vv           PCDH19 MUTATED PCDH19 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               8              101
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PCDH19 MUTATED     0   1  12   1
  PCDH19 WILD-TYPE   9  67 236  40
D950V4, multiclass
    clus
vv   PCDH19 MUTATED PCDH19 WILD-TYPE
  T1              0                9
  T2              1               67
  T3             12              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
  PCDH19 MUTATED    12   2   0
  PCDH19 WILD-TYPE 208  78  66
D950V5, multiclass
    clus
vv   PCDH19 MUTATED PCDH19 WILD-TYPE
  N0             12              208
  N1              2               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"
D950V6, binary
                  cls
clus                 0   1
  PCDH19 MUTATED    13   0
  PCDH19 WILD-TYPE 270  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH19 MUTATED     13    0
  PCDH19 WILD-TYPE  270   48
   clus
vv  PCDH19 MUTATED PCDH19 WILD-TYPE
  0             13              270
  1              0               48
[1] 2 2
[1] FALSE
D950V7, 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
D950V8, binary
                  cls
clus                 0   1
  PCDH19 MUTATED    12   2
  PCDH19 WILD-TYPE 305  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH19 MUTATED     12    2
  PCDH19 WILD-TYPE  305   46
                               clus
vv                              PCDH19 MUTATED PCDH19 WILD-TYPE
  COLON ADENOCARCINOMA                      12              305
  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 245   2  22  21
D950V9, multiclass
    clus
vv   PCDH19 MUTATED PCDH19 WILD-TYPE
  R0             12              245
  R1              0                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"
D950V10, 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
D950V11, 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(951) Variable = TMCO6 MUTATION ANALYSIS
D951V1, survival
                 sevent
clus2               0   1
  TMCO6 MUTATED     6   1
  TMCO6 WILD-TYPE 276  72
  TMCO6 MUTATED TMCO6 WILD-TYPE 
              7             348 
  TMCO6 MUTATED TMCO6 WILD-TYPE 
              1              72 
$`TMCO6 MUTATED`
TCGA-AA-3821 TCGA-AA-3947 TCGA-AA-A010 TCGA-AD-6895 TCGA-AZ-6598 TCGA-CM-4746 
        1.02        33.01        34.98         0.72        49.41        37.02 
TCGA-G4-6307 
       55.04 

$`TMCO6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  TMCO6 MUTATED TMCO6 WILD-TYPE 
           0.72            0.00 
  TMCO6 MUTATED TMCO6 WILD-TYPE 
          55.04          140.38 
  TMCO6 MUTATED TMCO6 WILD-TYPE 
          34.98           20.07 
[1] "0.7 - 55.0 (35.0)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.6"
D951V2, 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       24       109         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TMCO6 MUTATED           0          0          1          0        0         0
  TMCO6 WILD-TYPE        19         10         40         31       35        13
                 vv
clus              STAGE IVB
  TMCO6 MUTATED           0
  TMCO6 WILD-TYPE         1
D951V3, multiclass
            clus
vv           TMCO6 MUTATED TMCO6 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              0             109
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TMCO6 MUTATED     0   2   3   2
  TMCO6 WILD-TYPE   9  66 245  39
D951V4, multiclass
    clus
vv   TMCO6 MUTATED TMCO6 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             3             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
  TMCO6 MUTATED     5   2   0
  TMCO6 WILD-TYPE 215  78  66
D951V5, multiclass
    clus
vv   TMCO6 MUTATED TMCO6 WILD-TYPE
  N0             5             215
  N1             2              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"
D951V6, binary
                 cls
clus                0   1
  TMCO6 MUTATED     5   0
  TMCO6 WILD-TYPE 278  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMCO6 MUTATED      5    0
  TMCO6 WILD-TYPE  278   48
   clus
vv  TMCO6 MUTATED TMCO6 WILD-TYPE
  0             5             278
  1             0              48
[1] 2 2
[1] FALSE
D951V7, 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
D951V8, binary
                 cls
clus                0   1
  TMCO6 MUTATED     5   2
  TMCO6 WILD-TYPE 312  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMCO6 MUTATED      5    2
  TMCO6 WILD-TYPE  312   46
                               clus
vv                              TMCO6 MUTATED TMCO6 WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TMCO6 MUTATED     5   0   0   0
  TMCO6 WILD-TYPE 252   2  22  21
D951V9, multiclass
    clus
vv   TMCO6 MUTATED TMCO6 WILD-TYPE
  R0             5             252
  R1             0               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"
D951V10, 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
D951V11, 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(952) Variable = FBXL21 MUTATION ANALYSIS
D952V1, survival
                  sevent
clus2                0   1
  FBXL21 MUTATED     5   1
  FBXL21 WILD-TYPE 277  72
  FBXL21 MUTATED FBXL21 WILD-TYPE 
               6              349 
  FBXL21 MUTATED FBXL21 WILD-TYPE 
               1               72 
$`FBXL21 MUTATED`
TCGA-AA-3947 TCGA-AA-3977 TCGA-AY-6386 TCGA-AZ-6605 TCGA-CK-4950 TCGA-F4-6855 
       33.01        25.02        17.82         5.23        40.34        35.41 

$`FBXL21 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10       100.01        29.56        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 
        0.33         0.10         1.35        17.56       102.44        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  FBXL21 MUTATED FBXL21 WILD-TYPE 
            5.23             0.00 
  FBXL21 MUTATED FBXL21 WILD-TYPE 
           40.34           140.38 
  FBXL21 MUTATED FBXL21 WILD-TYPE 
          29.015           20.120 
[1] "5.2 - 40.3 (29.0)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.1"
D952V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FBXL21 MUTATED         0        0        0         2         2         0
  FBXL21 WILD-TYPE      64        1       25       107         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FBXL21 MUTATED           0          1          2          0        0
  FBXL21 WILD-TYPE        19          9         39         31       35
                  vv
clus               STAGE IVA STAGE IVB
  FBXL21 MUTATED           0         0
  FBXL21 WILD-TYPE        13         1
D952V3, multiclass
            clus
vv           FBXL21 MUTATED FBXL21 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               2              107
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              1                9
  STAGE IIIB              2               39
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FBXL21 MUTATED     0   1   4   3
  FBXL21 WILD-TYPE   9  67 244  38
D952V4, multiclass
    clus
vv   FBXL21 MUTATED FBXL21 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              4              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
  FBXL21 MUTATED     5   3   0
  FBXL21 WILD-TYPE 215  77  66
D952V5, multiclass
    clus
vv   FBXL21 MUTATED FBXL21 WILD-TYPE
  N0              5              215
  N1              3               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"
D952V6, binary
                  cls
clus                 0   1
  FBXL21 MUTATED     6   0
  FBXL21 WILD-TYPE 277  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXL21 MUTATED      6    0
  FBXL21 WILD-TYPE  277   48
   clus
vv  FBXL21 MUTATED FBXL21 WILD-TYPE
  0              6              277
  1              0               48
[1] 2 2
[1] FALSE
D952V7, binary
                  cls
clus                 0   1
  FBXL21 MUTATED     6   2
  FBXL21 WILD-TYPE 164 195
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXL21 MUTATED      6    2
  FBXL21 WILD-TYPE  164  195
        clus
vv       FBXL21 MUTATED FBXL21 WILD-TYPE
  FEMALE              6              164
  MALE                2              195
[1] 2 2
[1] FALSE
D952V8, binary
                  cls
clus                 0   1
  FBXL21 MUTATED     7   1
  FBXL21 WILD-TYPE 310  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXL21 MUTATED      7    1
  FBXL21 WILD-TYPE  310   47
                               clus
vv                              FBXL21 MUTATED FBXL21 WILD-TYPE
  COLON ADENOCARCINOMA                       7              310
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  FBXL21 MUTATED     4   1   0   1
  FBXL21 WILD-TYPE 253   1  22  20
D952V9, multiclass
    clus
vv   FBXL21 MUTATED FBXL21 WILD-TYPE
  R0              4              253
  R1              1                1
  R2              0               22
  RX              1               20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D952V10, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FBXL21 MUTATED                                  0     0
  FBXL21 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  FBXL21 MUTATED                           2     3
  FBXL21 WILD-TYPE                        17   173
D952V11, multiclass
                                  clus
vv                                 FBXL21 MUTATED FBXL21 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(953) Variable = CCDC55 MUTATION ANALYSIS
D953V1, survival
                  sevent
clus2                0   1
  CCDC55 MUTATED    10   1
  CCDC55 WILD-TYPE 272  72
  CCDC55 MUTATED CCDC55 WILD-TYPE 
              11              344 
  CCDC55 MUTATED CCDC55 WILD-TYPE 
               1               72 
$`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         0.33        23.05        98.24        51.75 

$`CCDC55 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       30.44        29.19        33.53        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
        7.96        27.02        13.94        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14         2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79       117.07         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  CCDC55 MUTATED CCDC55 WILD-TYPE 
            0.33             0.00 
  CCDC55 MUTATED CCDC55 WILD-TYPE 
           98.24           140.38 
  CCDC55 MUTATED CCDC55 WILD-TYPE 
          27.420           20.005 
[1] "0.3 - 98.2 (27.4)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "3"  
D953V2, 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       25       101         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC55 MUTATED           0          0          2          0        0
  CCDC55 WILD-TYPE        19         10         39         31       35
                  vv
clus               STAGE IVA STAGE IVB
  CCDC55 MUTATED           0         0
  CCDC55 WILD-TYPE        13         1
D953V3, multiclass
            clus
vv           CCDC55 MUTATED CCDC55 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               8              101
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CCDC55 MUTATED     0   1  11   1
  CCDC55 WILD-TYPE   9  67 237  40
D953V4, multiclass
    clus
vv   CCDC55 MUTATED CCDC55 WILD-TYPE
  T1              0                9
  T2              1               67
  T3             11              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
  CCDC55 MUTATED    11   2   0
  CCDC55 WILD-TYPE 209  78  66
D953V5, multiclass
    clus
vv   CCDC55 MUTATED CCDC55 WILD-TYPE
  N0             11              209
  N1              2               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"
D953V6, binary
                  cls
clus                 0   1
  CCDC55 MUTATED    10   0
  CCDC55 WILD-TYPE 273  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC55 MUTATED     10    0
  CCDC55 WILD-TYPE  273   48
   clus
vv  CCDC55 MUTATED CCDC55 WILD-TYPE
  0             10              273
  1              0               48
[1] 2 2
[1] FALSE
D953V7, 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
D953V8, binary
                  cls
clus                 0   1
  CCDC55 MUTATED    10   3
  CCDC55 WILD-TYPE 307  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC55 MUTATED     10    3
  CCDC55 WILD-TYPE  307   45
                               clus
vv                              CCDC55 MUTATED CCDC55 WILD-TYPE
  COLON ADENOCARCINOMA                      10              307
  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 251   2  22  18
D953V9, multiclass
    clus
vv   CCDC55 MUTATED CCDC55 WILD-TYPE
  R0              6              251
  R1              0                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"
D953V10, 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
D953V11, 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(954) Variable = ZNF462 MUTATION ANALYSIS
D954V1, survival
                  sevent
clus2                0   1
  ZNF462 MUTATED    16   7
  ZNF462 WILD-TYPE 266  66
  ZNF462 MUTATED ZNF462 WILD-TYPE 
              23              332 
  ZNF462 MUTATED ZNF462 WILD-TYPE 
               7               66 
$`ZNF462 MUTATED`
TCGA-A6-5665 TCGA-A6-6653 TCGA-A6-6780 TCGA-AA-3516 TCGA-AA-3811 TCGA-AA-3877 
       22.06        24.39        20.12        13.02        10.06        31.00 
TCGA-AA-A00A TCGA-AA-A010 TCGA-AA-A01P TCGA-AD-5900 TCGA-AD-6890 TCGA-AD-6901 
       38.04        34.98        38.07         0.07         0.79        22.42 
TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6607 TCGA-CM-4743 TCGA-CM-5868 
       27.09        58.39        49.41         3.19        23.05        17.03 
TCGA-CM-6162 TCGA-CM-6171 TCGA-D5-6930 TCGA-DM-A28F TCGA-G4-6588 
       12.00        14.04         1.51        35.97        26.17 

$`ZNF462 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6781 
       25.18        24.16        21.76        24.69        23.87        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        6.97         1.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        19.04        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       13.94        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 
       18.05        40.96        21.37         4.21        56.55         0.72 
TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
        5.79        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13        83.80        22.36        62.79        61.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 
       12.10       100.01        29.56         5.23        11.74         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G 
      135.65       139.17         6.12        81.37       119.93        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  ZNF462 MUTATED ZNF462 WILD-TYPE 
            0.07             0.00 
  ZNF462 MUTATED ZNF462 WILD-TYPE 
           58.39           140.38 
  ZNF462 MUTATED ZNF462 WILD-TYPE 
          22.420           20.005 
[1] "0.1 - 58.4 (22.4)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1.8"
D954V2, 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       23       101         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF462 MUTATED           3          0          2          0        2
  ZNF462 WILD-TYPE        16         10         39         31       33
                  vv
clus               STAGE IVA STAGE IVB
  ZNF462 MUTATED           1         0
  ZNF462 WILD-TYPE        12         1
D954V3, multiclass
            clus
vv           ZNF462 MUTATED ZNF462 WILD-TYPE
  STAGE I                 5               59
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               8              101
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               3               16
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              0               31
  STAGE IV                2               33
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  64 233  36
D954V4, multiclass
    clus
vv   ZNF462 MUTATED ZNF462 WILD-TYPE
  T1              2                7
  T2              4               64
  T3             15              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
  ZNF462 MUTATED    18   5   3
  ZNF462 WILD-TYPE 202  75  63
D954V5, multiclass
    clus
vv   ZNF462 MUTATED ZNF462 WILD-TYPE
  N0             18              202
  N1              5               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"
D954V6, binary
                  cls
clus                 0   1
  ZNF462 MUTATED    18   3
  ZNF462 WILD-TYPE 265  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF462 MUTATED     18    3
  ZNF462 WILD-TYPE  265   45
   clus
vv  ZNF462 MUTATED ZNF462 WILD-TYPE
  0             18              265
  1              3               45
[1] 2 2
[1] FALSE
D954V7, 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
D954V8, binary
                  cls
clus                 0   1
  ZNF462 MUTATED    20   6
  ZNF462 WILD-TYPE 297  42
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF462 MUTATED     20    6
  ZNF462 WILD-TYPE  297   42
                               clus
vv                              ZNF462 MUTATED ZNF462 WILD-TYPE
  COLON ADENOCARCINOMA                      20              297
  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 240   2  21  21
D954V9, multiclass
    clus
vv   ZNF462 MUTATED ZNF462 WILD-TYPE
  R0             17              240
  R1              0                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"
D954V10, 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
D954V11, 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(955) Variable = SMC2 MUTATION ANALYSIS
D955V1, survival
                sevent
clus2              0   1
  SMC2 MUTATED    15   9
  SMC2 WILD-TYPE 267  64
  SMC2 MUTATED SMC2 WILD-TYPE 
            24            331 
  SMC2 MUTATED SMC2 WILD-TYPE 
             9             64 
$`SMC2 MUTATED`
TCGA-AA-3492 TCGA-AA-3819 TCGA-AA-3979 TCGA-AA-A01Z TCGA-AD-6889 TCGA-AD-6890 
        3.02        25.02        24.00        37.02        56.55         0.79 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-6598 TCGA-CA-6716 TCGA-CA-6717 
       15.75        17.82         1.41        49.41         0.26         0.33 
TCGA-CM-4743 TCGA-CM-5862 TCGA-CM-6168 TCGA-D5-6533 TCGA-D5-6537 TCGA-D5-6540 
       23.05         5.03        12.99         1.32         4.80        16.14 
TCGA-D5-6920 TCGA-DM-A1D6 TCGA-DM-A28F TCGA-F4-6570 TCGA-G4-6293 TCGA-G4-6626 
       12.39        49.91        35.97         6.18       107.67        46.75 

$`SMC2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05        33.04         0.99         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        25.02        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       35.01        26.01        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6899 
       40.96         0.07        21.37         4.21         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4616 
       16.31         0.95         0.20        21.44        58.39         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6718 
        2.24         3.06         3.25         3.29         0.07         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        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-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       21.99        14.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 
       20.19        18.25        43.27        15.12        17.85        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       12.49        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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        35.41        19.43        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6628 
       52.80 

  SMC2 MUTATED SMC2 WILD-TYPE 
          0.26           0.00 
  SMC2 MUTATED SMC2 WILD-TYPE 
        107.67         140.38 
  SMC2 MUTATED SMC2 WILD-TYPE 
        15.945         20.980 
[1] "0.3 - 107.7 (15.9)" "0.0 - 140.4 (21.0)"
[1] "hr=" "2.1"
D955V2, 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       22        98         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SMC2 MUTATED           1          0          4          0        1         2
  SMC2 WILD-TYPE        18         10         37         31       34        11
                vv
clus             STAGE IVB
  SMC2 MUTATED           0
  SMC2 WILD-TYPE         1
D955V3, multiclass
            clus
vv           SMC2 MUTATED SMC2 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              3             22
  STAGE IIA            11             98
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            4             37
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             2             11
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 228  38
D955V4, multiclass
    clus
vv   SMC2 MUTATED SMC2 WILD-TYPE
  T1            1              8
  T2            1             67
  T3           20            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
  SMC2 MUTATED    18   6   1
  SMC2 WILD-TYPE 202  74  65
D955V5, multiclass
    clus
vv   SMC2 MUTATED SMC2 WILD-TYPE
  N0           18            202
  N1            6             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"
D955V6, binary
                cls
clus               0   1
  SMC2 MUTATED    18   3
  SMC2 WILD-TYPE 265  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMC2 MUTATED     18    3
  SMC2 WILD-TYPE  265   45
   clus
vv  SMC2 MUTATED SMC2 WILD-TYPE
  0           18            265
  1            3             45
[1] 2 2
[1] FALSE
D955V7, 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
D955V8, binary
                cls
clus               0   1
  SMC2 MUTATED    22   3
  SMC2 WILD-TYPE 295  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMC2 MUTATED     22    3
  SMC2 WILD-TYPE  295   45
                               clus
vv                              SMC2 MUTATED SMC2 WILD-TYPE
  COLON ADENOCARCINOMA                    22            295
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SMC2 MUTATED    16   0   0   3
  SMC2 WILD-TYPE 241   2  22  18
D955V9, multiclass
    clus
vv   SMC2 MUTATED SMC2 WILD-TYPE
  R0           16            241
  R1            0              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"
D955V10, 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
D955V11, 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(956) Variable = SBNO1 MUTATION ANALYSIS
D956V1, survival
                 sevent
clus2               0   1
  SBNO1 MUTATED    14   1
  SBNO1 WILD-TYPE 268  72
  SBNO1 MUTATED SBNO1 WILD-TYPE 
             15             340 
  SBNO1 MUTATED SBNO1 WILD-TYPE 
              1              72 
$`SBNO1 MUTATED`
TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3864 TCGA-AA-A010 
       24.39        19.66         0.92        19.00        53.00        34.98 
TCGA-AZ-5407 TCGA-AZ-6601 TCGA-CA-6718 TCGA-CK-4952 TCGA-CM-4743 TCGA-CM-5344 
       61.41       100.01         0.10        15.62        23.05        22.03 
TCGA-CM-5349 TCGA-CM-5868 TCGA-G4-6588 
       30.08        17.03        26.17 

$`SBNO1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
       11.01         5.98        37.05        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.33         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       40.34        49.08        51.32        21.99        21.14         2.93 
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        16.01        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        91.79        46.75        52.80 

  SBNO1 MUTATED SBNO1 WILD-TYPE 
            0.1             0.0 
  SBNO1 MUTATED SBNO1 WILD-TYPE 
         100.01          140.38 
  SBNO1 MUTATED SBNO1 WILD-TYPE 
          23.05           20.07 
[1] "0.1 - 100.0 (23.1)" "0.0 - 140.4 (20.1)"
[1] "hr=" "3.8"
D956V2, 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       23       105         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SBNO1 MUTATED           2          0          1          1        1         1
  SBNO1 WILD-TYPE        17         10         40         30       34        12
                 vv
clus              STAGE IVB
  SBNO1 MUTATED           0
  SBNO1 WILD-TYPE         1
D956V3, multiclass
            clus
vv           SBNO1 MUTATED SBNO1 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              4             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 239  37
D956V4, multiclass
    clus
vv   SBNO1 MUTATED SBNO1 WILD-TYPE
  T1             1               8
  T2             1              67
  T3             9             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
  SBNO1 MUTATED     9   5   1
  SBNO1 WILD-TYPE 211  75  65
D956V5, multiclass
    clus
vv   SBNO1 MUTATED SBNO1 WILD-TYPE
  N0             9             211
  N1             5              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"
D956V6, binary
                 cls
clus                0   1
  SBNO1 MUTATED    12   2
  SBNO1 WILD-TYPE 271  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SBNO1 MUTATED     12    2
  SBNO1 WILD-TYPE  271   46
   clus
vv  SBNO1 MUTATED SBNO1 WILD-TYPE
  0            12             271
  1             2              46
[1] 2 2
[1] FALSE
D956V7, 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
D956V8, binary
                 cls
clus                0   1
  SBNO1 MUTATED    13   2
  SBNO1 WILD-TYPE 304  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SBNO1 MUTATED     13    2
  SBNO1 WILD-TYPE  304   46
                               clus
vv                              SBNO1 MUTATED SBNO1 WILD-TYPE
  COLON ADENOCARCINOMA                     13             304
  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 248   2  21  19
D956V9, multiclass
    clus
vv   SBNO1 MUTATED SBNO1 WILD-TYPE
  R0             9             248
  R1             0               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"
D956V10, 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
D956V11, 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(957) Variable = ALDOB MUTATION ANALYSIS
D957V1, survival
                 sevent
clus2               0   1
  ALDOB MUTATED    12   3
  ALDOB WILD-TYPE 270  70
  ALDOB MUTATED ALDOB WILD-TYPE 
             15             340 
  ALDOB MUTATED ALDOB WILD-TYPE 
              3              70 
$`ALDOB MUTATED`
TCGA-A6-2676 TCGA-A6-6141 TCGA-AA-3821 TCGA-AA-3845 TCGA-AA-3949 TCGA-AA-A01Q 
       42.90         8.38         1.02         0.00        26.01         1.02 
TCGA-AD-6895 TCGA-AZ-6599 TCGA-CK-4948 TCGA-CK-6747 TCGA-D5-6534 TCGA-D5-6540 
        0.72         6.77       102.44         2.93        43.27        16.14 
TCGA-D5-6928 TCGA-G4-6586 TCGA-G4-6628 
       11.64        35.80        52.80 

$`ALDOB WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 
       35.05        33.04         0.99        25.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       38.99        37.02        14.93        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21        56.55         0.79         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       13.78        26.17        91.79        46.75 

  ALDOB MUTATED ALDOB WILD-TYPE 
              0               0 
  ALDOB MUTATED ALDOB WILD-TYPE 
         102.44          140.38 
  ALDOB MUTATED ALDOB WILD-TYPE 
          11.64           20.63 
[1] "0.0 - 102.4 (11.6)" "0.0 - 140.4 (20.6)"
[1] "hr=" "1.1"
D957V2, 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       24       103         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ALDOB MUTATED           0          1          1          0        0         0
  ALDOB WILD-TYPE        19          9         40         31       35        13
                 vv
clus              STAGE IVB
  ALDOB MUTATED           0
  ALDOB WILD-TYPE         1
D957V3, multiclass
            clus
vv           ALDOB MUTATED ALDOB WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              6             103
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ALDOB MUTATED     0   4  10   1
  ALDOB WILD-TYPE   9  64 238  40
D957V4, multiclass
    clus
vv   ALDOB MUTATED ALDOB WILD-TYPE
  T1             0               9
  T2             4              64
  T3            10             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
  ALDOB MUTATED    12   3   0
  ALDOB WILD-TYPE 208  77  66
D957V5, multiclass
    clus
vv   ALDOB MUTATED ALDOB WILD-TYPE
  N0            12             208
  N1             3              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"
D957V6, binary
                 cls
clus                0   1
  ALDOB MUTATED    12   0
  ALDOB WILD-TYPE 271  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALDOB MUTATED     12    0
  ALDOB WILD-TYPE  271   48
   clus
vv  ALDOB MUTATED ALDOB WILD-TYPE
  0            12             271
  1             0              48
[1] 2 2
[1] FALSE
D957V7, 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
D957V8, binary
                 cls
clus                0   1
  ALDOB MUTATED    10   5
  ALDOB WILD-TYPE 307  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALDOB MUTATED     10    5
  ALDOB WILD-TYPE  307   43
                               clus
vv                              ALDOB MUTATED ALDOB WILD-TYPE
  COLON ADENOCARCINOMA                     10             307
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ALDOB MUTATED    11   0   0   1
  ALDOB WILD-TYPE 246   2  22  20
D957V9, multiclass
    clus
vv   ALDOB MUTATED ALDOB WILD-TYPE
  R0            11             246
  R1             0               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"
D957V10, 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
D957V11, 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(958) Variable = TAF6 MUTATION ANALYSIS
D958V1, survival
                sevent
clus2              0   1
  TAF6 MUTATED     6   2
  TAF6 WILD-TYPE 276  71
  TAF6 MUTATED TAF6 WILD-TYPE 
             8            347 
  TAF6 MUTATED TAF6 WILD-TYPE 
             2             71 
$`TAF6 MUTATED`
TCGA-AA-3516 TCGA-AA-A00N TCGA-AD-5900 TCGA-CM-6161 TCGA-D5-6540 TCGA-F4-6460 
       13.02         4.01         0.07        15.02        16.14        13.38 
TCGA-G4-6307 TCGA-G4-6317 
       55.04        36.00 

$`TAF6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        1.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 
       44.68        51.75        45.11        36.72        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  TAF6 MUTATED TAF6 WILD-TYPE 
          0.07           0.00 
  TAF6 MUTATED TAF6 WILD-TYPE 
         55.04         140.38 
  TAF6 MUTATED TAF6 WILD-TYPE 
         14.20          20.98 
[1] "0.1 - 55.0 (14.2)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.5"
D958V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TAF6 MUTATED         3        0        0         0         1         0
  TAF6 WILD-TYPE      61        1       25       109         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        18         10         39         30       35        13
                vv
clus             STAGE IVB
  TAF6 MUTATED           0
  TAF6 WILD-TYPE         1
D958V3, multiclass
            clus
vv           TAF6 MUTATED TAF6 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             0            109
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            2             39
  STAGE IIIC            1             30
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TAF6 MUTATED     0   3   4   1
  TAF6 WILD-TYPE   9  65 244  40
D958V4, multiclass
    clus
vv   TAF6 MUTATED TAF6 WILD-TYPE
  T1            0              9
  T2            3             65
  T3            4            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     4   2   2
  TAF6 WILD-TYPE 216  78  64
D958V5, multiclass
    clus
vv   TAF6 MUTATED TAF6 WILD-TYPE
  N0            4            216
  N1            2             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"
D958V6, binary
                cls
clus               0   1
  TAF6 MUTATED     6   0
  TAF6 WILD-TYPE 277  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF6 MUTATED      6    0
  TAF6 WILD-TYPE  277   48
   clus
vv  TAF6 MUTATED TAF6 WILD-TYPE
  0            6            277
  1            0             48
[1] 2 2
[1] FALSE
D958V7, binary
                cls
clus               0   1
  TAF6 MUTATED     5   3
  TAF6 WILD-TYPE 165 194
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF6 MUTATED      5    3
  TAF6 WILD-TYPE  165  194
        clus
vv       TAF6 MUTATED TAF6 WILD-TYPE
  FEMALE            5            165
  MALE              3            194
[1] 2 2
[1] FALSE
D958V8, binary
                cls
clus               0   1
  TAF6 MUTATED     4   4
  TAF6 WILD-TYPE 313  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF6 MUTATED      4    4
  TAF6 WILD-TYPE  313   44
                               clus
vv                              TAF6 MUTATED TAF6 WILD-TYPE
  COLON ADENOCARCINOMA                     4            313
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TAF6 MUTATED     7   0   0   0
  TAF6 WILD-TYPE 250   2  22  21
D958V9, multiclass
    clus
vv   TAF6 MUTATED TAF6 WILD-TYPE
  R0            7            250
  R1            0              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"
D958V10, 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
D958V11, 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(959) Variable = MKI67 MUTATION ANALYSIS
D959V1, survival
                 sevent
clus2               0   1
  MKI67 MUTATED    28   7
  MKI67 WILD-TYPE 254  66
  MKI67 MUTATED MKI67 WILD-TYPE 
             35             320 
  MKI67 MUTATED MKI67 WILD-TYPE 
              7              66 
$`MKI67 MUTATED`
TCGA-A6-2676 TCGA-A6-3809 TCGA-A6-5660 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       42.90        32.75        29.19        24.39        23.87        20.12 
TCGA-AA-3510 TCGA-AA-3525 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3815 TCGA-AA-3845 
       63.98         8.05        85.05        19.04        33.04         0.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00A TCGA-AA-A00E 
       33.01        26.01         2.01        25.02        38.04        30.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q TCGA-AU-3779 TCGA-AU-6004 TCGA-AZ-6598 
        4.01        34.98         1.02        14.50        27.09        49.41 
TCGA-CA-6718 TCGA-CK-4952 TCGA-CM-5349 TCGA-CM-6162 TCGA-D5-6924 TCGA-DM-A1DB 
        0.10        15.62        30.08        12.00        14.30        44.32 
TCGA-DM-A28K TCGA-F4-6570 TCGA-F4-6703 TCGA-G4-6315 TCGA-G4-6628 
       98.24         6.18        35.87        36.72        52.80 

$`MKI67 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       34.65        33.34        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       30.44        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       21.76        24.69        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 
        1.02         9.07        24.03        37.05        36.03        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
        5.03        26.99        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       14.93        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3950 TCGA-AA-3952 
       31.00         2.01        12.99        24.00        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J 
        7.96        27.02        13.94        19.00        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
        0.20        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.33         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       102.44        40.34        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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 
       16.01        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 
       81.37       119.93        35.97        60.79       117.07         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.38        13.45         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       45.11        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 
       91.79        46.75 

  MKI67 MUTATED MKI67 WILD-TYPE 
              0               0 
  MKI67 MUTATED MKI67 WILD-TYPE 
          98.24          140.38 
  MKI67 MUTATED MKI67 WILD-TYPE 
         27.090          19.625 
[1] "0.0 - 98.2 (27.1)"  "0.0 - 140.4 (19.6)"
[1] "hr=" "1.1"
D959V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MKI67 MUTATED         3        0        4        15         5         0
  MKI67 WILD-TYPE      61        1       21        94         3         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MKI67 MUTATED           2          0          4          1        1         0
  MKI67 WILD-TYPE        17         10         37         30       34        13
                 vv
clus              STAGE IVB
  MKI67 MUTATED           0
  MKI67 WILD-TYPE         1
D959V3, multiclass
            clus
vv           MKI67 MUTATED MKI67 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               4              21
  STAGE IIA             15              94
  STAGE IIB              5               3
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             0              10
  STAGE IIIB             4              37
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MKI67 MUTATED     0   4  26   6
  MKI67 WILD-TYPE   9  64 222  35
D959V4, multiclass
    clus
vv   MKI67 MUTATED MKI67 WILD-TYPE
  T1             0               9
  T2             4              64
  T3            26             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
  MKI67 MUTATED    29   5   2
  MKI67 WILD-TYPE 191  75  64
D959V5, multiclass
    clus
vv   MKI67 MUTATED MKI67 WILD-TYPE
  N0            29             191
  N1             5              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"
D959V6, binary
                 cls
clus                0   1
  MKI67 MUTATED    32   1
  MKI67 WILD-TYPE 251  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MKI67 MUTATED     32    1
  MKI67 WILD-TYPE  251   47
   clus
vv  MKI67 MUTATED MKI67 WILD-TYPE
  0            32             251
  1             1              47
[1] 2 2
[1] FALSE
D959V7, 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
D959V8, binary
                 cls
clus                0   1
  MKI67 MUTATED    27   9
  MKI67 WILD-TYPE 290  39
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MKI67 MUTATED     27    9
  MKI67 WILD-TYPE  290   39
                               clus
vv                              MKI67 MUTATED MKI67 WILD-TYPE
  COLON ADENOCARCINOMA                     27             290
  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 232   2  22  19
D959V9, multiclass
    clus
vv   MKI67 MUTATED MKI67 WILD-TYPE
  R0            25             232
  R1             0               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"
D959V10, 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
D959V11, 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(960) Variable = KCNN4 MUTATION ANALYSIS
D960V1, survival
                 sevent
clus2               0   1
  KCNN4 MUTATED     5   1
  KCNN4 WILD-TYPE 277  72
  KCNN4 MUTATED KCNN4 WILD-TYPE 
              6             349 
  KCNN4 MUTATED KCNN4 WILD-TYPE 
              1              72 
$`KCNN4 MUTATED`
TCGA-AD-6901 TCGA-CK-4950 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5860 TCGA-G4-6304 
       22.42        40.34        13.02        22.03        16.01        53.62 

$`KCNN4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       102.44        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  KCNN4 MUTATED KCNN4 WILD-TYPE 
          13.02            0.00 
  KCNN4 MUTATED KCNN4 WILD-TYPE 
          53.62          140.38 
  KCNN4 MUTATED KCNN4 WILD-TYPE 
         22.225          20.120 
[1] "13.0 - 53.6 (22.2)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.4"
D960V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KCNN4 MUTATED         0        0        0         2         1         0
  KCNN4 WILD-TYPE      64        1       25       107         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KCNN4 MUTATED           0          1          1          0        0         0
  KCNN4 WILD-TYPE        19          9         40         31       35        13
                 vv
clus              STAGE IVB
  KCNN4 MUTATED           0
  KCNN4 WILD-TYPE         1
D960V3, multiclass
            clus
vv           KCNN4 MUTATED KCNN4 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              2             107
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KCNN4 MUTATED     0   0   5   1
  KCNN4 WILD-TYPE   9  68 243  40
D960V4, multiclass
    clus
vv   KCNN4 MUTATED KCNN4 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             5             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
  KCNN4 MUTATED     4   2   0
  KCNN4 WILD-TYPE 216  78  66
D960V5, multiclass
    clus
vv   KCNN4 MUTATED KCNN4 WILD-TYPE
  N0             4             216
  N1             2              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"
D960V6, binary
                 cls
clus                0   1
  KCNN4 MUTATED     5   0
  KCNN4 WILD-TYPE 278  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNN4 MUTATED      5    0
  KCNN4 WILD-TYPE  278   48
   clus
vv  KCNN4 MUTATED KCNN4 WILD-TYPE
  0             5             278
  1             0              48
[1] 2 2
[1] FALSE
D960V7, binary
                 cls
clus                0   1
  KCNN4 MUTATED     3   3
  KCNN4 WILD-TYPE 167 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNN4 MUTATED      3    3
  KCNN4 WILD-TYPE  167  194
        clus
vv       KCNN4 MUTATED KCNN4 WILD-TYPE
  FEMALE             3             167
  MALE               3             194
[1] 2 2
[1] FALSE
D960V8, binary
                 cls
clus                0   1
  KCNN4 MUTATED     6   0
  KCNN4 WILD-TYPE 311  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNN4 MUTATED      6    0
  KCNN4 WILD-TYPE  311   48
                               clus
vv                              KCNN4 MUTATED KCNN4 WILD-TYPE
  COLON ADENOCARCINOMA                      6             311
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  KCNN4 MUTATED     4   1   0   0
  KCNN4 WILD-TYPE 253   1  22  21
D960V9, multiclass
    clus
vv   KCNN4 MUTATED KCNN4 WILD-TYPE
  R0             4             253
  R1             1               1
  R2             0              22
  RX             0              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D960V10, 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     4
  KCNN4 WILD-TYPE                        17   172
D960V11, 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                                        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(961) Variable = STX16 MUTATION ANALYSIS
D961V1, survival
                 sevent
clus2               0   1
  STX16 MUTATED     5   2
  STX16 WILD-TYPE 277  71
  STX16 MUTATED STX16 WILD-TYPE 
              7             348 
  STX16 MUTATED STX16 WILD-TYPE 
              2              71 
$`STX16 MUTATED`
TCGA-A6-2676 TCGA-A6-5657 TCGA-AA-3679 TCGA-AA-3947 TCGA-CM-6162 TCGA-F4-6809 
       42.90        31.63        15.02        33.01        12.00        13.25 
TCGA-G4-6317 
       36.00 

$`STX16 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 
        1.55        16.31        29.59        16.24        33.67         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 
       44.68        55.04        51.75        45.11        36.72        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  STX16 MUTATED STX16 WILD-TYPE 
             12               0 
  STX16 MUTATED STX16 WILD-TYPE 
          42.90          140.38 
  STX16 MUTATED STX16 WILD-TYPE 
         31.630          20.155 
[1] "12.0 - 42.9 (31.6)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.5"
D961V2, 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       25       109         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        19         10         39         30       34        12
                 vv
clus              STAGE IVB
  STX16 MUTATED           0
  STX16 WILD-TYPE         1
D961V3, multiclass
            clus
vv           STX16 MUTATED STX16 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              0             109
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  68 243  39
D961V4, multiclass
    clus
vv   STX16 MUTATED STX16 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             5             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
  STX16 MUTATED     2   3   2
  STX16 WILD-TYPE 218  77  64
D961V5, multiclass
    clus
vv   STX16 MUTATED STX16 WILD-TYPE
  N0             2             218
  N1             3              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"
D961V6, binary
                 cls
clus                0   1
  STX16 MUTATED     4   2
  STX16 WILD-TYPE 279  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STX16 MUTATED      4    2
  STX16 WILD-TYPE  279   46
   clus
vv  STX16 MUTATED STX16 WILD-TYPE
  0             4             279
  1             2              46
[1] 2 2
[1] FALSE
D961V7, 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
D961V8, binary
                 cls
clus                0   1
  STX16 MUTATED     5   2
  STX16 WILD-TYPE 312  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STX16 MUTATED      5    2
  STX16 WILD-TYPE  312   46
                               clus
vv                              STX16 MUTATED STX16 WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  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 251   2  21  21
D961V9, multiclass
    clus
vv   STX16 MUTATED STX16 WILD-TYPE
  R0             6             251
  R1             0               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"
D961V10, 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
D961V11, 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(962) Variable = OR2A5 MUTATION ANALYSIS
D962V1, survival
                 sevent
clus2               0   1
  OR2A5 MUTATED     7   1
  OR2A5 WILD-TYPE 275  72
  OR2A5 MUTATED OR2A5 WILD-TYPE 
              8             347 
  OR2A5 MUTATED OR2A5 WILD-TYPE 
              1              72 
$`OR2A5 MUTATED`
TCGA-AA-3713 TCGA-AA-3947 TCGA-AA-3977 TCGA-CA-6717 TCGA-CM-5349 TCGA-CM-6676 
       19.04        33.01        25.02         0.33        30.08        11.08 
TCGA-DM-A0XF TCGA-G4-6628 
       38.20        52.80 

$`OR2A5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 
       12.00        11.38        10.26       119.70        24.43       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       13.78        35.80        26.17        91.79        46.75 

  OR2A5 MUTATED OR2A5 WILD-TYPE 
           0.33            0.00 
  OR2A5 MUTATED OR2A5 WILD-TYPE 
          52.80          140.38 
  OR2A5 MUTATED OR2A5 WILD-TYPE 
          27.55           20.12 
[1] "0.3 - 52.8 (27.5)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.7"
D962V2, 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       25       106         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        19         10         41         30       33        13
                 vv
clus              STAGE IVB
  OR2A5 MUTATED           0
  OR2A5 WILD-TYPE         1
D962V3, multiclass
            clus
vv           OR2A5 MUTATED OR2A5 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              3             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               2              33
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR2A5 MUTATED     0   3   6   1
  OR2A5 WILD-TYPE   9  65 242  40
D962V4, multiclass
    clus
vv   OR2A5 MUTATED OR2A5 WILD-TYPE
  T1             0               9
  T2             3              65
  T3             6             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
  OR2A5 MUTATED     8   0   2
  OR2A5 WILD-TYPE 212  80  64
D962V5, multiclass
    clus
vv   OR2A5 MUTATED OR2A5 WILD-TYPE
  N0             8             212
  N1             0              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"
D962V6, binary
                 cls
clus                0   1
  OR2A5 MUTATED     7   2
  OR2A5 WILD-TYPE 276  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2A5 MUTATED      7    2
  OR2A5 WILD-TYPE  276   46
   clus
vv  OR2A5 MUTATED OR2A5 WILD-TYPE
  0             7             276
  1             2              46
[1] 2 2
[1] FALSE
D962V7, 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
D962V8, binary
                 cls
clus                0   1
  OR2A5 MUTATED     7   3
  OR2A5 WILD-TYPE 310  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2A5 MUTATED      7    3
  OR2A5 WILD-TYPE  310   45
                               clus
vv                              OR2A5 MUTATED OR2A5 WILD-TYPE
  COLON ADENOCARCINOMA                      7             310
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  OR2A5 MUTATED     5   0   2   1
  OR2A5 WILD-TYPE 252   2  20  20
D962V9, multiclass
    clus
vv   OR2A5 MUTATED OR2A5 WILD-TYPE
  R0             5             252
  R1             0               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"
D962V10, 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
D962V11, 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(963) Variable = CSNK2A2 MUTATION ANALYSIS
D963V1, survival
                   sevent
clus2                 0   1
  CSNK2A2 MUTATED     4   2
  CSNK2A2 WILD-TYPE 278  71
  CSNK2A2 MUTATED CSNK2A2 WILD-TYPE 
                6               349 
  CSNK2A2 MUTATED CSNK2A2 WILD-TYPE 
                2                71 
$`CSNK2A2 MUTATED`
TCGA-AZ-6599 TCGA-CM-5868 TCGA-D5-6535 TCGA-D5-6927 TCGA-F4-6570 TCGA-G4-6588 
        6.77        17.03        15.12         9.44         6.18        26.17 

$`CSNK2A2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41        49.41        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 
       11.51        20.19        18.25         1.32        43.27        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       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        13.38        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 
       52.80 

  CSNK2A2 MUTATED CSNK2A2 WILD-TYPE 
             6.18              0.00 
  CSNK2A2 MUTATED CSNK2A2 WILD-TYPE 
            26.17            140.38 
  CSNK2A2 MUTATED CSNK2A2 WILD-TYPE 
            12.28             20.98 
[1] "6.2 - 26.2 (12.3)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "2.8"
D963V2, 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       25       106         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CSNK2A2 MUTATED           0          0          1          0        1
  CSNK2A2 WILD-TYPE        19         10         40         31       34
                   vv
clus                STAGE IVA STAGE IVB
  CSNK2A2 MUTATED           1         0
  CSNK2A2 WILD-TYPE        12         1
D963V3, multiclass
            clus
vv           CSNK2A2 MUTATED CSNK2A2 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                3               106
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               0                31
  STAGE IV                 1                34
  STAGE IVA                1                12
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 244  39
D963V4, multiclass
    clus
vv   CSNK2A2 MUTATED CSNK2A2 WILD-TYPE
  T1               0                 9
  T2               1                67
  T3               4               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
  CSNK2A2 MUTATED     4   3   0
  CSNK2A2 WILD-TYPE 216  77  66
D963V5, multiclass
    clus
vv   CSNK2A2 MUTATED CSNK2A2 WILD-TYPE
  N0               4               216
  N1               3                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"
D963V6, binary
                   cls
clus                  0   1
  CSNK2A2 MUTATED     3   2
  CSNK2A2 WILD-TYPE 280  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CSNK2A2 MUTATED      3    2
  CSNK2A2 WILD-TYPE  280   46
   clus
vv  CSNK2A2 MUTATED CSNK2A2 WILD-TYPE
  0               3               280
  1               2                46
[1] 2 2
[1] FALSE
D963V7, 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
D963V8, binary
                   cls
clus                  0   1
  CSNK2A2 MUTATED     7   0
  CSNK2A2 WILD-TYPE 310  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CSNK2A2 MUTATED      7    0
  CSNK2A2 WILD-TYPE  310   48
                               clus
vv                              CSNK2A2 MUTATED CSNK2A2 WILD-TYPE
  COLON ADENOCARCINOMA                        7               310
  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 253   2  21  20
D963V9, multiclass
    clus
vv   CSNK2A2 MUTATED CSNK2A2 WILD-TYPE
  R0               4               253
  R1               0                 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"
D963V10, 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
D963V11, 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(964) Variable = CASP4 MUTATION ANALYSIS
D964V1, survival
                 sevent
clus2               0   1
  CASP4 MUTATED     7   1
  CASP4 WILD-TYPE 275  72
  CASP4 MUTATED CASP4 WILD-TYPE 
              8             347 
  CASP4 MUTATED CASP4 WILD-TYPE 
              1              72 
$`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         0.33        15.62        13.05 
TCGA-D5-5538 TCGA-D5-6529 
       12.26        20.19 

$`CASP4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       16.08        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        15.75         0.20        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10       100.01         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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-D5-5539 
       11.08        11.01        10.06        12.03        45.40        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       13.51        11.51        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  CASP4 MUTATED CASP4 WILD-TYPE 
           0.33            0.00 
  CASP4 MUTATED CASP4 WILD-TYPE 
          50.99          140.38 
  CASP4 MUTATED CASP4 WILD-TYPE 
         17.905          20.280 
[1] "0.3 - 51.0 (17.9)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.4"
D964V2, 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       25       106         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CASP4 MUTATED           1          0          1          0        1         0
  CASP4 WILD-TYPE        18         10         40         31       34        13
                 vv
clus              STAGE IVB
  CASP4 MUTATED           1
  CASP4 WILD-TYPE         0
D964V3, multiclass
            clus
vv           CASP4 MUTATED CASP4 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              3             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  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  67 242  40
D964V4, multiclass
    clus
vv   CASP4 MUTATED CASP4 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             6             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
  CASP4 MUTATED     3   3   2
  CASP4 WILD-TYPE 217  77  64
D964V5, multiclass
    clus
vv   CASP4 MUTATED CASP4 WILD-TYPE
  N0             3             217
  N1             3              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"
D964V6, binary
                 cls
clus                0   1
  CASP4 MUTATED     4   2
  CASP4 WILD-TYPE 279  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP4 MUTATED      4    2
  CASP4 WILD-TYPE  279   46
   clus
vv  CASP4 MUTATED CASP4 WILD-TYPE
  0             4             279
  1             2              46
[1] 2 2
[1] FALSE
D964V7, 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
D964V8, binary
                 cls
clus                0   1
  CASP4 MUTATED     6   2
  CASP4 WILD-TYPE 311  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP4 MUTATED      6    2
  CASP4 WILD-TYPE  311   46
                               clus
vv                              CASP4 MUTATED CASP4 WILD-TYPE
  COLON ADENOCARCINOMA                      6             311
  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 253   2  21  19
D964V9, multiclass
    clus
vv   CASP4 MUTATED CASP4 WILD-TYPE
  R0             4             253
  R1             0               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"
D964V10, 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
D964V11, 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(965) Variable = WDR5 MUTATION ANALYSIS
D965V1, survival
                sevent
clus2              0   1
  WDR5 MUTATED     5   1
  WDR5 WILD-TYPE 277  72
  WDR5 MUTATED WDR5 WILD-TYPE 
             6            349 
  WDR5 MUTATED WDR5 WILD-TYPE 
             1             72 
$`WDR5 MUTATED`
TCGA-AA-3864 TCGA-AU-6004 TCGA-D5-6538 TCGA-F4-6809 TCGA-G4-6309 TCGA-G4-6586 
       53.00        27.09        17.13        13.25        51.75        35.80 

$`WDR5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       33.67         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  WDR5 MUTATED WDR5 WILD-TYPE 
         13.25           0.00 
  WDR5 MUTATED WDR5 WILD-TYPE 
         53.00         140.38 
  WDR5 MUTATED WDR5 WILD-TYPE 
        31.445         20.120 
[1] "13.2 - 53.0 (31.4)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.7"
D965V2, 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       24       108         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        19         10         39         31       35        12
                vv
clus             STAGE IVB
  WDR5 MUTATED           0
  WDR5 WILD-TYPE         1
D965V3, multiclass
            clus
vv           WDR5 MUTATED WDR5 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             1            108
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            2             39
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 243  41
D965V4, multiclass
    clus
vv   WDR5 MUTATED WDR5 WILD-TYPE
  T1            0              9
  T2            1             67
  T3            5            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
  WDR5 MUTATED     3   2   1
  WDR5 WILD-TYPE 217  78  65
D965V5, multiclass
    clus
vv   WDR5 MUTATED WDR5 WILD-TYPE
  N0            3            217
  N1            2             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"
D965V6, binary
                cls
clus               0   1
  WDR5 MUTATED     5   1
  WDR5 WILD-TYPE 278  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  WDR5 MUTATED      5    1
  WDR5 WILD-TYPE  278   47
   clus
vv  WDR5 MUTATED WDR5 WILD-TYPE
  0            5            278
  1            1             47
[1] 2 2
[1] FALSE
D965V7, 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
D965V8, binary
                cls
clus               0   1
  WDR5 MUTATED     6   0
  WDR5 WILD-TYPE 311  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  WDR5 MUTATED      6    0
  WDR5 WILD-TYPE  311   48
                               clus
vv                              WDR5 MUTATED WDR5 WILD-TYPE
  COLON ADENOCARCINOMA                     6            311
  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 251   2  22  21
D965V9, multiclass
    clus
vv   WDR5 MUTATED WDR5 WILD-TYPE
  R0            6            251
  R1            0              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"
D965V10, 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
D965V11, 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(966) Variable = ADORA3 MUTATION ANALYSIS
D966V1, survival
                  sevent
clus2                0   1
  ADORA3 MUTATED    10   4
  ADORA3 WILD-TYPE 272  69
  ADORA3 MUTATED ADORA3 WILD-TYPE 
              14              341 
  ADORA3 MUTATED ADORA3 WILD-TYPE 
               4               69 
$`ADORA3 MUTATED`
TCGA-A6-3807 TCGA-AA-3864 TCGA-AA-3955 TCGA-AU-3779 TCGA-CA-6718 TCGA-CK-5916 
       34.65        53.00        20.98        14.50         0.10        21.14 
TCGA-CK-6751 TCGA-CM-5348 TCGA-CM-6676 TCGA-DM-A1D8 TCGA-F4-6570 TCGA-F4-6809 
      124.27        22.98        11.08        12.59         6.18        13.25 
TCGA-F4-6855 TCGA-G4-6588 
       35.41        26.17 

$`ADORA3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.20        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.33         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 
       49.08        51.32        21.99         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      117.07        98.24         8.61        13.38        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 
        1.55        16.31        29.59        16.24        33.67         0.53 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        91.79        46.75        52.80 

  ADORA3 MUTATED ADORA3 WILD-TYPE 
             0.1              0.0 
  ADORA3 MUTATED ADORA3 WILD-TYPE 
          124.27           140.38 
  ADORA3 MUTATED ADORA3 WILD-TYPE 
           21.06            20.12 
[1] "0.1 - 124.3 (21.1)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.3"
D966V2, 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       24       104         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ADORA3 MUTATED           0          0          2          1        0
  ADORA3 WILD-TYPE        19         10         39         30       35
                  vv
clus               STAGE IVA STAGE IVB
  ADORA3 MUTATED           1         0
  ADORA3 WILD-TYPE        12         1
D966V3, multiclass
            clus
vv           ADORA3 MUTATED ADORA3 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               5              104
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  65 238  41
D966V4, multiclass
    clus
vv   ADORA3 MUTATED ADORA3 WILD-TYPE
  T1              1                8
  T2              3               65
  T3             10              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
  ADORA3 MUTATED     9   3   2
  ADORA3 WILD-TYPE 211  77  64
D966V5, multiclass
    clus
vv   ADORA3 MUTATED ADORA3 WILD-TYPE
  N0              9              211
  N1              3               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"
D966V6, binary
                  cls
clus                 0   1
  ADORA3 MUTATED    11   1
  ADORA3 WILD-TYPE 272  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADORA3 MUTATED     11    1
  ADORA3 WILD-TYPE  272   47
   clus
vv  ADORA3 MUTATED ADORA3 WILD-TYPE
  0             11              272
  1              1               47
[1] 2 2
[1] FALSE
D966V7, 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
D966V8, binary
                  cls
clus                 0   1
  ADORA3 MUTATED    13   1
  ADORA3 WILD-TYPE 304  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADORA3 MUTATED     13    1
  ADORA3 WILD-TYPE  304   47
                               clus
vv                              ADORA3 MUTATED ADORA3 WILD-TYPE
  COLON ADENOCARCINOMA                      13              304
  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 247   2  22  18
D966V9, multiclass
    clus
vv   ADORA3 MUTATED ADORA3 WILD-TYPE
  R0             10              247
  R1              0                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"
D966V10, 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
D966V11, 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(967) Variable = USP29 MUTATION ANALYSIS
D967V1, survival
                 sevent
clus2               0   1
  USP29 MUTATED    13   3
  USP29 WILD-TYPE 269  70
  USP29 MUTATED USP29 WILD-TYPE 
             16             339 
  USP29 MUTATED USP29 WILD-TYPE 
              3              70 
$`USP29 MUTATED`
TCGA-AA-3492 TCGA-AA-3543 TCGA-AA-3672 TCGA-AA-3710 TCGA-AA-3950 TCGA-AA-A00N 
        3.02         0.99         0.92        26.99        24.00         4.01 
TCGA-AA-A010 TCGA-AD-5900 TCGA-AZ-4315 TCGA-CA-6718 TCGA-CK-4950 TCGA-D5-6535 
       34.98         0.07        58.39         0.10        40.34        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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       26.01        12.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 
        0.26         0.33         1.35        17.56       102.44        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 
       14.30         9.04         9.44        13.41         1.51        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       35.97        60.79        98.24         8.61        13.38        13.45 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  USP29 MUTATED USP29 WILD-TYPE 
           0.07            0.00 
  USP29 MUTATED USP29 WILD-TYPE 
         117.07          140.38 
  USP29 MUTATED USP29 WILD-TYPE 
          11.82           20.98 
[1] "0.1 - 117.1 (11.8)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.1"
D967V2, 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       24       102         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  USP29 MUTATED           1          1          1          2        0         0
  USP29 WILD-TYPE        18          9         40         29       35        13
                 vv
clus              STAGE IVB
  USP29 MUTATED           0
  USP29 WILD-TYPE         1
D967V3, multiclass
            clus
vv           USP29 MUTATED USP29 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              7             102
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             1               9
  STAGE IIIB             1              40
  STAGE IIIC             2              29
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  USP29 MUTATED     0   3  12   3
  USP29 WILD-TYPE   9  65 236  38
D967V4, multiclass
    clus
vv   USP29 MUTATED USP29 WILD-TYPE
  T1             0               9
  T2             3              65
  T3            12             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
  USP29 MUTATED    13   3   2
  USP29 WILD-TYPE 207  77  64
D967V5, multiclass
    clus
vv   USP29 MUTATED USP29 WILD-TYPE
  N0            13             207
  N1             3              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"
D967V6, binary
                 cls
clus                0   1
  USP29 MUTATED    15   0
  USP29 WILD-TYPE 268  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP29 MUTATED     15    0
  USP29 WILD-TYPE  268   48
   clus
vv  USP29 MUTATED USP29 WILD-TYPE
  0            15             268
  1             0              48
[1] 2 2
[1] FALSE
D967V7, 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
D967V8, binary
                 cls
clus                0   1
  USP29 MUTATED    13   5
  USP29 WILD-TYPE 304  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP29 MUTATED     13    5
  USP29 WILD-TYPE  304   43
                               clus
vv                              USP29 MUTATED USP29 WILD-TYPE
  COLON ADENOCARCINOMA                     13             304
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  USP29 MUTATED    13   1   0   3
  USP29 WILD-TYPE 244   1  22  18
D967V9, multiclass
    clus
vv   USP29 MUTATED USP29 WILD-TYPE
  R0            13             244
  R1             1               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"
D967V10, 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
D967V11, 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(968) Variable = IL13RA2 MUTATION ANALYSIS
D968V1, survival
                   sevent
clus2                 0   1
  IL13RA2 MUTATED    13   2
  IL13RA2 WILD-TYPE 269  71
  IL13RA2 MUTATED IL13RA2 WILD-TYPE 
               15               340 
  IL13RA2 MUTATED IL13RA2 WILD-TYPE 
                2                71 
$`IL13RA2 MUTATED`
TCGA-A6-5660 TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3662 TCGA-AA-3697 TCGA-AA-A00E 
       29.19        22.06        63.98         6.05        85.05        30.02 
TCGA-AA-A010 TCGA-CM-6165 TCGA-D5-6536 TCGA-D5-6920 TCGA-DM-A1DB TCGA-DM-A285 
       34.98        16.04        17.85        12.39        44.32         6.12 
TCGA-DM-A28H TCGA-G4-6315 TCGA-G4-6588 
      117.07        36.72        26.17 

$`IL13RA2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 
        5.98        37.05        19.00        36.00         5.03        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J 
       27.02        13.94        38.04        19.00        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-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 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        51.75        45.11        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        91.79        46.75        52.80 

  IL13RA2 MUTATED IL13RA2 WILD-TYPE 
             6.05              0.00 
  IL13RA2 MUTATED IL13RA2 WILD-TYPE 
           117.07            140.38 
  IL13RA2 MUTATED IL13RA2 WILD-TYPE 
           29.190            20.005 
[1] "6.0 - 117.1 (29.2)" "0.0 - 140.4 (20.0)"
[1] "hr=" "2.2"
D968V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IL13RA2 MUTATED         0        0        1         7         1         0
  IL13RA2 WILD-TYPE      64        1       24       102         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IL13RA2 MUTATED           1          0          0          2        3
  IL13RA2 WILD-TYPE        18         10         41         29       32
                   vv
clus                STAGE IVA STAGE IVB
  IL13RA2 MUTATED           0         0
  IL13RA2 WILD-TYPE        13         1
D968V3, multiclass
            clus
vv           IL13RA2 MUTATED IL13RA2 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                7               102
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               2                29
  STAGE IV                 3                32
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  IL13RA2 MUTATED     0   0  13   2
  IL13RA2 WILD-TYPE   9  68 235  39
D968V4, multiclass
    clus
vv   IL13RA2 MUTATED IL13RA2 WILD-TYPE
  T1               0                 9
  T2               0                68
  T3              13               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
  IL13RA2 MUTATED    10   1   4
  IL13RA2 WILD-TYPE 210  79  62
D968V5, multiclass
    clus
vv   IL13RA2 MUTATED IL13RA2 WILD-TYPE
  N0              10               210
  N1               1                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"
D968V6, binary
                   cls
clus                  0   1
  IL13RA2 MUTATED    12   3
  IL13RA2 WILD-TYPE 271  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  IL13RA2 MUTATED     12    3
  IL13RA2 WILD-TYPE  271   45
   clus
vv  IL13RA2 MUTATED IL13RA2 WILD-TYPE
  0              12               271
  1               3                45
[1] 2 2
[1] FALSE
D968V7, binary
                   cls
clus                  0   1
  IL13RA2 MUTATED     6   9
  IL13RA2 WILD-TYPE 164 188
[1] "tbl2"
                   cls
clus                [,1] [,2]
  IL13RA2 MUTATED      6    9
  IL13RA2 WILD-TYPE  164  188
        clus
vv       IL13RA2 MUTATED IL13RA2 WILD-TYPE
  FEMALE               6               164
  MALE                 9               188
[1] 2 2
[1] FALSE
D968V8, binary
                   cls
clus                  0   1
  IL13RA2 MUTATED    14   1
  IL13RA2 WILD-TYPE 303  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  IL13RA2 MUTATED     14    1
  IL13RA2 WILD-TYPE  303   47
                               clus
vv                              IL13RA2 MUTATED IL13RA2 WILD-TYPE
  COLON ADENOCARCINOMA                       14               303
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  IL13RA2 MUTATED    10   0   1   0
  IL13RA2 WILD-TYPE 247   2  21  21
D968V9, multiclass
    clus
vv   IL13RA2 MUTATED IL13RA2 WILD-TYPE
  R0              10               247
  R1               0                 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"
D968V10, 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     9
  IL13RA2 WILD-TYPE                        18   167
D968V11, 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                                          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(969) Variable = RARRES3 MUTATION ANALYSIS
D969V1, survival
                   sevent
clus2                 0   1
  RARRES3 MUTATED     4   1
  RARRES3 WILD-TYPE 278  72
  RARRES3 MUTATED RARRES3 WILD-TYPE 
                5               350 
  RARRES3 MUTATED RARRES3 WILD-TYPE 
                1                72 
$`RARRES3 MUTATED`
TCGA-AA-3710 TCGA-AY-6196 TCGA-CA-5797 TCGA-CM-6168 TCGA-DM-A1DA 
       26.99         0.20         3.29        12.99         7.50 

$`RARRES3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        15.75        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 
        3.19         1.94         2.24         3.06         3.25         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       12.59       140.38        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  RARRES3 MUTATED RARRES3 WILD-TYPE 
              0.2               0.0 
  RARRES3 MUTATED RARRES3 WILD-TYPE 
            26.99            140.38 
  RARRES3 MUTATED RARRES3 WILD-TYPE 
             7.50             20.63 
[1] "0.2 - 27.0 (7.5)"   "0.0 - 140.4 (20.6)"
[1] "hr=" "2.2"
D969V2, 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       25       106         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RARRES3 MUTATED           0          0          0          2        0
  RARRES3 WILD-TYPE        19         10         41         29       35
                   vv
clus                STAGE IVA STAGE IVB
  RARRES3 MUTATED           0         0
  RARRES3 WILD-TYPE        13         1
D969V3, multiclass
            clus
vv           RARRES3 MUTATED RARRES3 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                3               106
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               2                29
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  RARRES3 MUTATED     0   0   5   0
  RARRES3 WILD-TYPE   9  68 243  41
D969V4, multiclass
    clus
vv   RARRES3 MUTATED RARRES3 WILD-TYPE
  T1               0                 9
  T2               0                68
  T3               5               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
  RARRES3 MUTATED     3   0   2
  RARRES3 WILD-TYPE 217  80  64
D969V5, multiclass
    clus
vv   RARRES3 MUTATED RARRES3 WILD-TYPE
  N0               3               217
  N1               0                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"
D969V6, binary
                   cls
clus                  0   1
  RARRES3 MUTATED     4   0
  RARRES3 WILD-TYPE 279  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RARRES3 MUTATED      4    0
  RARRES3 WILD-TYPE  279   48
   clus
vv  RARRES3 MUTATED RARRES3 WILD-TYPE
  0               4               279
  1               0                48
[1] 2 2
[1] FALSE
D969V7, 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
D969V8, binary
                   cls
clus                  0   1
  RARRES3 MUTATED     4   1
  RARRES3 WILD-TYPE 313  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RARRES3 MUTATED      4    1
  RARRES3 WILD-TYPE  313   47
                               clus
vv                              RARRES3 MUTATED RARRES3 WILD-TYPE
  COLON ADENOCARCINOMA                        4               313
  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 253   2  22  21
D969V9, multiclass
    clus
vv   RARRES3 MUTATED RARRES3 WILD-TYPE
  R0               4               253
  R1               0                 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"
D969V10, 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
D969V11, 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(970) Variable = EFTUD2 MUTATION ANALYSIS
D970V1, survival
                  sevent
clus2                0   1
  EFTUD2 MUTATED     9   5
  EFTUD2 WILD-TYPE 273  68
  EFTUD2 MUTATED EFTUD2 WILD-TYPE 
              14              341 
  EFTUD2 MUTATED EFTUD2 WILD-TYPE 
               5               68 
$`EFTUD2 MUTATED`
TCGA-A6-3809 TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3543 TCGA-AA-3662 
       32.75        63.98        13.02        38.99         0.99         6.05 
TCGA-AA-A01R TCGA-AD-6964 TCGA-AZ-6601 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6676 
       35.01        10.88       100.01        14.04        12.95        11.08 
TCGA-DM-A0XD TCGA-DM-A0XF 
       24.43        38.20 

$`EFTUD2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
       35.01         6.97         1.02         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
       34.03        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       78.08         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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-6675 
       14.99        12.99        13.02        15.02        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D0 TCGA-DM-A1D4 
       12.00        11.38        10.26       119.70       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  EFTUD2 MUTATED EFTUD2 WILD-TYPE 
            0.99             0.00 
  EFTUD2 MUTATED EFTUD2 WILD-TYPE 
          100.01           140.38 
  EFTUD2 MUTATED EFTUD2 WILD-TYPE 
          19.235           20.190 
[1] "1.0 - 100.0 (19.2)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.6"
D970V2, 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       23       106         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EFTUD2 MUTATED           2          0          0          1        1
  EFTUD2 WILD-TYPE        17         10         41         30       34
                  vv
clus               STAGE IVA STAGE IVB
  EFTUD2 MUTATED           0         0
  EFTUD2 WILD-TYPE        13         1
D970V3, multiclass
            clus
vv           EFTUD2 MUTATED EFTUD2 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               3              106
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               2               17
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              1               30
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  EFTUD2 MUTATED     0   3   8   3
  EFTUD2 WILD-TYPE   9  65 240  38
D970V4, multiclass
    clus
vv   EFTUD2 MUTATED EFTUD2 WILD-TYPE
  T1              0                9
  T2              3               65
  T3              8              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
  EFTUD2 MUTATED     9   0   5
  EFTUD2 WILD-TYPE 211  80  61
D970V5, multiclass
    clus
vv   EFTUD2 MUTATED EFTUD2 WILD-TYPE
  N0              9              211
  N1              0               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"
D970V6, binary
                  cls
clus                 0   1
  EFTUD2 MUTATED    12   1
  EFTUD2 WILD-TYPE 271  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EFTUD2 MUTATED     12    1
  EFTUD2 WILD-TYPE  271   47
   clus
vv  EFTUD2 MUTATED EFTUD2 WILD-TYPE
  0             12              271
  1              1               47
[1] 2 2
[1] FALSE
D970V7, 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
D970V8, binary
                  cls
clus                 0   1
  EFTUD2 MUTATED     9   5
  EFTUD2 WILD-TYPE 308  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EFTUD2 MUTATED      9    5
  EFTUD2 WILD-TYPE  308   43
                               clus
vv                              EFTUD2 MUTATED EFTUD2 WILD-TYPE
  COLON ADENOCARCINOMA                       9              308
  COLON MUCINOUS ADENOCARCINOMA              5               43
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  EFTUD2 MUTATED     8   0   1   0
  EFTUD2 WILD-TYPE 249   2  21  21
D970V9, multiclass
    clus
vv   EFTUD2 MUTATED EFTUD2 WILD-TYPE
  R0              8              249
  R1              0                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"
D970V10, 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
D970V11, 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(971) Variable = GGNBP2 MUTATION ANALYSIS
D971V1, survival
                  sevent
clus2                0   1
  GGNBP2 MUTATED     8   2
  GGNBP2 WILD-TYPE 274  71
  GGNBP2 MUTATED GGNBP2 WILD-TYPE 
              10              345 
  GGNBP2 MUTATED GGNBP2 WILD-TYPE 
               2               71 
$`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       102.44 
TCGA-CM-6169 TCGA-CM-6677 TCGA-DM-A28E TCGA-F4-6570 
       13.02        11.08       119.93         6.18 

$`GGNBP2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
        0.20        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        0.10         1.35        17.56        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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-6678 
       14.04        11.01        12.95        13.05        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28F 
      131.51       135.65       139.17         6.12        81.37        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  GGNBP2 MUTATED GGNBP2 WILD-TYPE 
            4.01             0.00 
  GGNBP2 MUTATED GGNBP2 WILD-TYPE 
          119.93           140.38 
  GGNBP2 MUTATED GGNBP2 WILD-TYPE 
          24.265           20.120 
[1] "4.0 - 119.9 (24.3)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.6"
D971V2, 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       25       103         5         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GGNBP2 MUTATED           0          1          0          0        0
  GGNBP2 WILD-TYPE        19          9         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  GGNBP2 MUTATED           0         0
  GGNBP2 WILD-TYPE        13         1
D971V3, multiclass
            clus
vv           GGNBP2 MUTATED GGNBP2 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               6              103
  STAGE IIB               3                5
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              1                9
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GGNBP2 MUTATED     0   1   7   3
  GGNBP2 WILD-TYPE   9  67 241  38
D971V4, multiclass
    clus
vv   GGNBP2 MUTATED GGNBP2 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              7              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
  GGNBP2 MUTATED    10   1   0
  GGNBP2 WILD-TYPE 210  79  66
D971V5, multiclass
    clus
vv   GGNBP2 MUTATED GGNBP2 WILD-TYPE
  N0             10              210
  N1              1               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
  GGNBP2 MUTATED     9   0
  GGNBP2 WILD-TYPE 274  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GGNBP2 MUTATED      9    0
  GGNBP2 WILD-TYPE  274   48
   clus
vv  GGNBP2 MUTATED GGNBP2 WILD-TYPE
  0              9              274
  1              0               48
[1] 2 2
[1] FALSE
D971V7, 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
D971V8, binary
                  cls
clus                 0   1
  GGNBP2 MUTATED    10   1
  GGNBP2 WILD-TYPE 307  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GGNBP2 MUTATED     10    1
  GGNBP2 WILD-TYPE  307   47
                               clus
vv                              GGNBP2 MUTATED GGNBP2 WILD-TYPE
  COLON ADENOCARCINOMA                      10              307
  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 248   2  22  20
D971V9, multiclass
    clus
vv   GGNBP2 MUTATED GGNBP2 WILD-TYPE
  R0              9              248
  R1              0                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"
D971V10, 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
D971V11, 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(972) Variable = RAB42 MUTATION ANALYSIS
D972V1, survival
                 sevent
clus2               0   1
  RAB42 MUTATED     3   0
  RAB42 WILD-TYPE 279  73
  RAB42 MUTATED RAB42 WILD-TYPE 
              3             352 
  RAB42 MUTATED RAB42 WILD-TYPE 
              0              73 
$`RAB42 MUTATED`
TCGA-A6-6781 TCGA-AA-3663 TCGA-G4-6304 
       19.66         6.97        53.62 

$`RAB42 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      107.67        74.56        65.85        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  RAB42 MUTATED RAB42 WILD-TYPE 
           6.97            0.00 
  RAB42 MUTATED RAB42 WILD-TYPE 
          53.62          140.38 
  RAB42 MUTATED RAB42 WILD-TYPE 
         19.660          20.235 
[1] "7.0 - 53.6 (19.7)"  "0.0 - 140.4 (20.2)"
[1] "hr="     "9100000"
D972V2, 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       23       109         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        19         10         41         30       35        13
                 vv
clus              STAGE IVB
  RAB42 MUTATED           0
  RAB42 WILD-TYPE         1
D972V3, multiclass
            clus
vv           RAB42 MUTATED RAB42 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              0             109
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RAB42 MUTATED     0   0   1   3
  RAB42 WILD-TYPE   9  68 247  38
D972V4, multiclass
    clus
vv   RAB42 MUTATED RAB42 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             1             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
  RAB42 MUTATED     3   1   0
  RAB42 WILD-TYPE 217  79  66
D972V5, multiclass
    clus
vv   RAB42 MUTATED RAB42 WILD-TYPE
  N0             3             217
  N1             1              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"
D972V6, binary
                 cls
clus                0   1
  RAB42 MUTATED     3   0
  RAB42 WILD-TYPE 280  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB42 MUTATED      3    0
  RAB42 WILD-TYPE  280   48
   clus
vv  RAB42 MUTATED RAB42 WILD-TYPE
  0             3             280
  1             0              48
[1] 2 2
[1] FALSE
D972V7, 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
D972V8, binary
                 cls
clus                0   1
  RAB42 MUTATED     3   1
  RAB42 WILD-TYPE 314  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB42 MUTATED      3    1
  RAB42 WILD-TYPE  314   47
                               clus
vv                              RAB42 MUTATED RAB42 WILD-TYPE
  COLON ADENOCARCINOMA                      3             314
  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 253   2  22  21
D972V9, multiclass
    clus
vv   RAB42 MUTATED RAB42 WILD-TYPE
  R0             4             253
  R1             0               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"
D972V10, 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
D972V11, multiclass
[1] "Remove cluster labels:" "RAB42 MUTATED"         
clus
  RAB42 MUTATED RAB42 WILD-TYPE 
              2             204 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-4105 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-A6-5656      TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5660 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-A6-5661      TCGA-A6-5662      TCGA-A6-5664      TCGA-A6-5665 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-A6-5666      TCGA-A6-6137      TCGA-A6-6138      TCGA-A6-6141 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-A6-6142      TCGA-A6-6648      TCGA-A6-6649      TCGA-A6-6651 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-A6-6652      TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-A6-6782      TCGA-AD-5900      TCGA-AD-6548      TCGA-AD-6888 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-AD-6889      TCGA-AD-6890      TCGA-AD-6895      TCGA-AD-6899 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6964      TCGA-AD-6965 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070      TCGA-AY-4071 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197      TCGA-AY-6386 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-AZ-4315      TCGA-AZ-4323      TCGA-AZ-4616      TCGA-AZ-4681 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-AZ-4682      TCGA-AZ-5403      TCGA-AZ-5407      TCGA-AZ-6598 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-AZ-6599      TCGA-AZ-6600      TCGA-AZ-6601      TCGA-AZ-6603 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-AZ-6605      TCGA-AZ-6606      TCGA-AZ-6607      TCGA-AZ-6608 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-CA-5254      TCGA-CA-5255      TCGA-CA-5796      TCGA-CA-5797 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-CA-6715      TCGA-CA-6716      TCGA-CA-6717      TCGA-CA-6718 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-CA-6719      TCGA-CK-4947      TCGA-CK-4948      TCGA-CK-4950 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-CK-4952      TCGA-CK-5912      TCGA-CK-5913      TCGA-CK-5914 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-CK-5915      TCGA-CK-5916      TCGA-CK-6746      TCGA-CK-6747 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-CK-6748      TCGA-CK-6751      TCGA-CM-4743      TCGA-CM-4744 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-CM-4746      TCGA-CM-4747      TCGA-CM-4752      TCGA-CM-5341 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-CM-5344      TCGA-CM-5348      TCGA-CM-5349      TCGA-CM-5860 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-CM-5861      TCGA-CM-5862      TCGA-CM-5863      TCGA-CM-5864 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-CM-5868      TCGA-CM-6161      TCGA-CM-6162      TCGA-CM-6163 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-CM-6164      TCGA-CM-6165      TCGA-CM-6166      TCGA-CM-6167 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-CM-6168      TCGA-CM-6169      TCGA-CM-6170      TCGA-CM-6171 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-CM-6172      TCGA-CM-6674      TCGA-CM-6675      TCGA-CM-6676 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-CM-6677      TCGA-CM-6678      TCGA-CM-6679      TCGA-CM-6680 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-D5-5537      TCGA-D5-5538      TCGA-D5-5539      TCGA-D5-5540 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-D5-5541      TCGA-D5-6529      TCGA-D5-6532      TCGA-D5-6533 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-D5-6534      TCGA-D5-6535      TCGA-D5-6536      TCGA-D5-6537 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-D5-6538      TCGA-D5-6539      TCGA-D5-6540      TCGA-D5-6541 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-D5-6898      TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-D5-6924      TCGA-D5-6926      TCGA-D5-6927      TCGA-D5-6928 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-D5-6929      TCGA-D5-6930      TCGA-D5-6931      TCGA-D5-6932 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-D5-7000      TCGA-DM-A0X9      TCGA-DM-A0XD      TCGA-DM-A0XF 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-DM-A1D0      TCGA-DM-A1D4      TCGA-DM-A1D6      TCGA-DM-A1D7 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-DM-A1D8      TCGA-DM-A1D9      TCGA-DM-A1DA      TCGA-DM-A1DB 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-DM-A1HA      TCGA-DM-A1HB      TCGA-DM-A282      TCGA-DM-A285 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-DM-A28C      TCGA-DM-A28E      TCGA-DM-A28F      TCGA-DM-A28G 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-DM-A28H      TCGA-DM-A28K      TCGA-F4-6459      TCGA-F4-6460 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-F4-6805      TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6306 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310      TCGA-G4-6315 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323      TCGA-G4-6586 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-G4-6588      TCGA-G4-6625      TCGA-G4-6626      TCGA-G4-6628 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 

Clustering(973) Variable = PER3 MUTATION ANALYSIS
D973V1, survival
                sevent
clus2              0   1
  PER3 MUTATED    12   4
  PER3 WILD-TYPE 270  69
  PER3 MUTATED PER3 WILD-TYPE 
            16            339 
  PER3 MUTATED PER3 WILD-TYPE 
             4             69 
$`PER3 MUTATED`
TCGA-A6-5665 TCGA-A6-5666 TCGA-AA-3663 TCGA-AA-3673 TCGA-AA-3680 TCGA-AA-3818 
       22.06        32.71         6.97        50.04        11.01         0.99 
TCGA-AA-3949 TCGA-AA-A00E TCGA-AA-A00N TCGA-AD-6889 TCGA-AZ-4315 TCGA-AZ-6601 
       26.01        30.02         4.01        56.55        58.39       100.01 
TCGA-CK-4947 TCGA-CM-4746 TCGA-CM-5860 TCGA-CM-6162 
       17.56        37.02        16.01        12.00 

$`PER3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.09        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 
        2.01        14.01         0.92        47.01        15.02         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3819 
       19.04        19.04        10.06        35.05        33.04        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        33.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37         4.21         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        61.41        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
        1.35       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  PER3 MUTATED PER3 WILD-TYPE 
          0.99           0.00 
  PER3 MUTATED PER3 WILD-TYPE 
        100.01         140.38 
  PER3 MUTATED PER3 WILD-TYPE 
        24.035         20.120 
[1] "1.0 - 100.0 (24.0)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1"  
D973V2, 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       22       102         7         0
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PER3 MUTATED           0          0          2          0        1         1
  PER3 WILD-TYPE        19         10         39         31       34        12
                vv
clus             STAGE IVB
  PER3 MUTATED           0
  PER3 WILD-TYPE         1
D973V3, multiclass
            clus
vv           PER3 MUTATED PER3 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              3             22
  STAGE IIA             7            102
  STAGE IIB             1              7
  STAGE IIC             1              0
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            2             39
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 236  37
D973V4, multiclass
    clus
vv   PER3 MUTATED PER3 WILD-TYPE
  T1            0              9
  T2            1             67
  T3           12            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
  PER3 MUTATED    13   3   1
  PER3 WILD-TYPE 207  77  65
D973V5, multiclass
    clus
vv   PER3 MUTATED PER3 WILD-TYPE
  N0           13            207
  N1            3             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"
D973V6, binary
                cls
clus               0   1
  PER3 MUTATED    16   1
  PER3 WILD-TYPE 267  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  PER3 MUTATED     16    1
  PER3 WILD-TYPE  267   47
   clus
vv  PER3 MUTATED PER3 WILD-TYPE
  0           16            267
  1            1             47
[1] 2 2
[1] FALSE
D973V7, 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
D973V8, binary
                cls
clus               0   1
  PER3 MUTATED    14   3
  PER3 WILD-TYPE 303  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  PER3 MUTATED     14    3
  PER3 WILD-TYPE  303   45
                               clus
vv                              PER3 MUTATED PER3 WILD-TYPE
  COLON ADENOCARCINOMA                    14            303
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PER3 MUTATED    12   0   1   1
  PER3 WILD-TYPE 245   2  21  20
D973V9, multiclass
    clus
vv   PER3 MUTATED PER3 WILD-TYPE
  R0           12            245
  R1            0              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"
D973V10, 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
D973V11, 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(974) Variable = KCTD9 MUTATION ANALYSIS
D974V1, survival
                 sevent
clus2               0   1
  KCTD9 MUTATED     5   0
  KCTD9 WILD-TYPE 277  73
  KCTD9 MUTATED KCTD9 WILD-TYPE 
              5             350 
  KCTD9 MUTATED KCTD9 WILD-TYPE 
              0              73 
$`KCTD9 MUTATED`
TCGA-A6-6781 TCGA-AD-5900 TCGA-CM-6162 TCGA-CM-6674 TCGA-G4-6628 
       19.66         0.07        12.00        12.95        52.80 

$`KCTD9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 
       91.79        46.75 

  KCTD9 MUTATED KCTD9 WILD-TYPE 
           0.07            0.00 
  KCTD9 MUTATED KCTD9 WILD-TYPE 
          52.80          140.38 
  KCTD9 MUTATED KCTD9 WILD-TYPE 
          12.95           20.63 
[1] "0.1 - 52.8 (12.9)"  "0.0 - 140.4 (20.6)"
[1] "hr="     "9100000"
D974V2, 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       25       108         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        19         10         40         30       35        13
                 vv
clus              STAGE IVB
  KCTD9 MUTATED           0
  KCTD9 WILD-TYPE         1
D974V3, multiclass
            clus
vv           KCTD9 MUTATED KCTD9 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              1             108
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KCTD9 MUTATED     0   2   2   1
  KCTD9 WILD-TYPE   9  66 246  40
D974V4, multiclass
    clus
vv   KCTD9 MUTATED KCTD9 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             2             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
  KCTD9 MUTATED     3   2   0
  KCTD9 WILD-TYPE 217  78  66
D974V5, multiclass
    clus
vv   KCTD9 MUTATED KCTD9 WILD-TYPE
  N0             3             217
  N1             2              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
  KCTD9 MUTATED     3   0
  KCTD9 WILD-TYPE 280  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCTD9 MUTATED      3    0
  KCTD9 WILD-TYPE  280   48
   clus
vv  KCTD9 MUTATED KCTD9 WILD-TYPE
  0             3             280
  1             0              48
[1] 2 2
[1] FALSE
D974V7, 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
D974V8, binary
                 cls
clus                0   1
  KCTD9 MUTATED     2   3
  KCTD9 WILD-TYPE 315  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCTD9 MUTATED      2    3
  KCTD9 WILD-TYPE  315   45
                               clus
vv                              KCTD9 MUTATED KCTD9 WILD-TYPE
  COLON ADENOCARCINOMA                      2             315
  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 252   2  22  21
D974V9, multiclass
    clus
vv   KCTD9 MUTATED KCTD9 WILD-TYPE
  R0             5             252
  R1             0               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"
D974V10, 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
D974V11, 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(975) Variable = CCT5 MUTATION ANALYSIS
D975V1, survival
                sevent
clus2              0   1
  CCT5 MUTATED     7   0
  CCT5 WILD-TYPE 275  73
  CCT5 MUTATED CCT5 WILD-TYPE 
             7            348 
  CCT5 MUTATED CCT5 WILD-TYPE 
             0             73 
$`CCT5 MUTATED`
TCGA-A6-5661 TCGA-AA-3544 TCGA-AA-3949 TCGA-AA-A010 TCGA-CM-5861 TCGA-D5-6928 
       33.53        14.01        26.01        34.98        15.02        11.64 
TCGA-G4-6321 
       22.09 

$`CCT5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       26.01        12.99         0.99        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  CCT5 MUTATED CCT5 WILD-TYPE 
         11.64           0.00 
  CCT5 MUTATED CCT5 WILD-TYPE 
         34.98         140.38 
  CCT5 MUTATED CCT5 WILD-TYPE 
        22.090         20.155 
[1] "11.6 - 35.0 (22.1)" "0.0 - 140.4 (20.2)"
[1] "hr="     "9200000"
D975V2, 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       25       106         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        17         10         40         31       35        13
                vv
clus             STAGE IVB
  CCT5 MUTATED           0
  CCT5 WILD-TYPE         1
D975V3, multiclass
            clus
vv           CCT5 MUTATED CCT5 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             3            106
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             2             17
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CCT5 MUTATED     0   2   5   1
  CCT5 WILD-TYPE   9  66 243  40
D975V4, multiclass
    clus
vv   CCT5 MUTATED CCT5 WILD-TYPE
  T1            0              9
  T2            2             66
  T3            5            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
  CCT5 MUTATED     5   2   1
  CCT5 WILD-TYPE 215  78  65
D975V5, multiclass
    clus
vv   CCT5 MUTATED CCT5 WILD-TYPE
  N0            5            215
  N1            2             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"
D975V6, binary
                cls
clus               0   1
  CCT5 MUTATED     7   0
  CCT5 WILD-TYPE 276  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCT5 MUTATED      7    0
  CCT5 WILD-TYPE  276   48
   clus
vv  CCT5 MUTATED CCT5 WILD-TYPE
  0            7            276
  1            0             48
[1] 2 2
[1] FALSE
D975V7, 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
D975V8, binary
                cls
clus               0   1
  CCT5 MUTATED     6   2
  CCT5 WILD-TYPE 311  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCT5 MUTATED      6    2
  CCT5 WILD-TYPE  311   46
                               clus
vv                              CCT5 MUTATED CCT5 WILD-TYPE
  COLON ADENOCARCINOMA                     6            311
  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 249   2  22  21
D975V9, multiclass
    clus
vv   CCT5 MUTATED CCT5 WILD-TYPE
  R0            8            249
  R1            0              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"
D975V10, 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
D975V11, 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(976) Variable = C18ORF19 MUTATION ANALYSIS
D976V1, survival
                    sevent
clus2                  0   1
  C18ORF19 MUTATED     8   0
  C18ORF19 WILD-TYPE 274  73
  C18ORF19 MUTATED C18ORF19 WILD-TYPE 
                 8                347 
  C18ORF19 MUTATED C18ORF19 WILD-TYPE 
                 0                 73 
$`C18ORF19 MUTATED`
TCGA-A6-6654 TCGA-AA-3710 TCGA-AA-3821 TCGA-AA-A00J TCGA-AD-6889 TCGA-AY-5543 
       23.87        26.99         1.02        18.05        56.55        15.75 
TCGA-CM-5349 TCGA-D5-6930 
       30.08         1.51 

$`C18ORF19 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 
       35.05        33.04         0.99        25.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37         4.21         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-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-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  C18ORF19 MUTATED C18ORF19 WILD-TYPE 
              1.02               0.00 
  C18ORF19 MUTATED C18ORF19 WILD-TYPE 
             56.55             140.38 
  C18ORF19 MUTATED C18ORF19 WILD-TYPE 
             20.96              20.19 
[1] "1.0 - 56.5 (21.0)"  "0.0 - 140.4 (20.2)"
[1] "hr="     "9200000"
D976V2, 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       25       105         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C18ORF19 MUTATED           0          0          2          0        0
  C18ORF19 WILD-TYPE        19         10         39         31       35
                    vv
clus                 STAGE IVA STAGE IVB
  C18ORF19 MUTATED           1         0
  C18ORF19 WILD-TYPE        12         1
D976V3, multiclass
            clus
vv           C18ORF19 MUTATED C18ORF19 WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  0                 25
  STAGE IIA                 4                105
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                0                 10
  STAGE IIIB                2                 39
  STAGE IIIC                0                 31
  STAGE IV                  0                 35
  STAGE IVA                 1                 12
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 242  40
D976V4, multiclass
    clus
vv   C18ORF19 MUTATED C18ORF19 WILD-TYPE
  T1                0                  9
  T2                1                 67
  T3                6                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
  C18ORF19 MUTATED     5   3   0
  C18ORF19 WILD-TYPE 215  77  66
D976V5, multiclass
    clus
vv   C18ORF19 MUTATED C18ORF19 WILD-TYPE
  N0                5                215
  N1                3                 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"
D976V6, binary
                    cls
clus                   0   1
  C18ORF19 MUTATED     7   1
  C18ORF19 WILD-TYPE 276  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C18ORF19 MUTATED      7    1
  C18ORF19 WILD-TYPE  276   47
   clus
vv  C18ORF19 MUTATED C18ORF19 WILD-TYPE
  0                7                276
  1                1                 47
[1] 2 2
[1] FALSE
D976V7, 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
D976V8, binary
                    cls
clus                   0   1
  C18ORF19 MUTATED     5   3
  C18ORF19 WILD-TYPE 312  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C18ORF19 MUTATED      5    3
  C18ORF19 WILD-TYPE  312   45
                               clus
vv                              C18ORF19 MUTATED C18ORF19 WILD-TYPE
  COLON ADENOCARCINOMA                         5                312
  COLON MUCINOUS ADENOCARCINOMA                3                 45
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C18ORF19 MUTATED     6   0   0   0
  C18ORF19 WILD-TYPE 251   2  22  21
D976V9, multiclass
    clus
vv   C18ORF19 MUTATED C18ORF19 WILD-TYPE
  R0                6                251
  R1                0                  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"
D976V10, 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
D976V11, 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(977) Variable = NONO MUTATION ANALYSIS
D977V1, survival
                sevent
clus2              0   1
  NONO MUTATED    10   1
  NONO WILD-TYPE 272  72
  NONO MUTATED NONO WILD-TYPE 
            11            344 
  NONO MUTATED NONO WILD-TYPE 
             1             72 
$`NONO MUTATED`
TCGA-A6-6141 TCGA-AA-A010 TCGA-AD-6889 TCGA-AZ-4315 TCGA-CK-4948 TCGA-CK-5912 
        8.38        34.98        56.55        58.39       102.44        49.08 
TCGA-CK-6751 TCGA-CM-6677 TCGA-D5-6539 TCGA-D5-6930 TCGA-G4-6306 
      124.27        11.08        12.49         1.51        44.68 

$`NONO WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 
        0.33         0.10         1.35        17.56        40.34        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         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  NONO MUTATED NONO WILD-TYPE 
          1.51           0.00 
  NONO MUTATED NONO WILD-TYPE 
        124.27         140.38 
  NONO MUTATED NONO WILD-TYPE 
         44.68          20.07 
[1] "1.5 - 124.3 (44.7)" "0.0 - 140.4 (20.1)"
[1] "hr=" "4.1"
D977V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NONO MUTATED         2        0        0         6         1         0
  NONO WILD-TYPE      62        1       25       103         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NONO MUTATED           0          2          0          0        0         0
  NONO WILD-TYPE        19          8         41         31       35        13
                vv
clus             STAGE IVB
  NONO MUTATED           0
  NONO WILD-TYPE         1
D977V3, multiclass
            clus
vv           NONO MUTATED NONO WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             6            103
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            2              8
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NONO MUTATED     0   3   7   1
  NONO WILD-TYPE   9  65 241  40
D977V4, multiclass
    clus
vv   NONO MUTATED NONO WILD-TYPE
  T1            0              9
  T2            3             65
  T3            7            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
  NONO MUTATED    10   1   0
  NONO WILD-TYPE 210  79  66
D977V5, multiclass
    clus
vv   NONO MUTATED NONO WILD-TYPE
  N0           10            210
  N1            1             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"
D977V6, binary
                cls
clus               0   1
  NONO MUTATED     9   0
  NONO WILD-TYPE 274  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  NONO MUTATED      9    0
  NONO WILD-TYPE  274   48
   clus
vv  NONO MUTATED NONO WILD-TYPE
  0            9            274
  1            0             48
[1] 2 2
[1] FALSE
D977V7, 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
D977V8, binary
                cls
clus               0   1
  NONO MUTATED     9   2
  NONO WILD-TYPE 308  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  NONO MUTATED      9    2
  NONO WILD-TYPE  308   46
                               clus
vv                              NONO MUTATED NONO WILD-TYPE
  COLON ADENOCARCINOMA                     9            308
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  NONO MUTATED     7   0   0   2
  NONO WILD-TYPE 250   2  22  19
D977V9, multiclass
    clus
vv   NONO MUTATED NONO WILD-TYPE
  R0            7            250
  R1            0              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"
D977V10, 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
D977V11, 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(978) Variable = ZC3H12C MUTATION ANALYSIS
D978V1, survival
                   sevent
clus2                 0   1
  ZC3H12C MUTATED     9   2
  ZC3H12C WILD-TYPE 273  71
  ZC3H12C MUTATED ZC3H12C WILD-TYPE 
               11               344 
  ZC3H12C MUTATED ZC3H12C WILD-TYPE 
                2                71 
$`ZC3H12C MUTATED`
TCGA-AA-3672 TCGA-AA-3679 TCGA-AA-3811 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00N 
        0.92        15.02        10.06         2.01        25.02         4.01 
TCGA-AA-A010 TCGA-AZ-4315 TCGA-CA-6717 TCGA-F4-6856 TCGA-G4-6586 
       34.98        58.39         0.33        19.43        35.80 

$`ZC3H12C WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
        6.05         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       47.01        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        19.04        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 
       33.67        13.25         0.53        35.41       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  ZC3H12C MUTATED ZC3H12C WILD-TYPE 
             0.33              0.00 
  ZC3H12C MUTATED ZC3H12C WILD-TYPE 
            58.39            140.38 
  ZC3H12C MUTATED ZC3H12C WILD-TYPE 
            15.02             20.63 
[1] "0.3 - 58.4 (15.0)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "1.2"
D978V2, 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       25       104         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZC3H12C MUTATED           2          0          0          0        1
  ZC3H12C WILD-TYPE        17         10         41         31       34
                   vv
clus                STAGE IVA STAGE IVB
  ZC3H12C MUTATED           0         0
  ZC3H12C WILD-TYPE        13         1
D978V3, multiclass
            clus
vv           ZC3H12C MUTATED ZC3H12C WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                5               104
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                2                17
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               0                31
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ZC3H12C MUTATED     0   2   8   2
  ZC3H12C WILD-TYPE   9  66 240  39
D978V4, multiclass
    clus
vv   ZC3H12C MUTATED ZC3H12C WILD-TYPE
  T1               0                 9
  T2               2                66
  T3               8               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
  ZC3H12C MUTATED     9   1   2
  ZC3H12C WILD-TYPE 211  79  64
D978V5, multiclass
    clus
vv   ZC3H12C MUTATED ZC3H12C WILD-TYPE
  N0               9               211
  N1               1                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"
D978V6, binary
                   cls
clus                  0   1
  ZC3H12C MUTATED    10   1
  ZC3H12C WILD-TYPE 273  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZC3H12C MUTATED     10    1
  ZC3H12C WILD-TYPE  273   47
   clus
vv  ZC3H12C MUTATED ZC3H12C WILD-TYPE
  0              10               273
  1               1                47
[1] 2 2
[1] FALSE
D978V7, 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
D978V8, binary
                   cls
clus                  0   1
  ZC3H12C MUTATED     8   4
  ZC3H12C WILD-TYPE 309  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZC3H12C MUTATED      8    4
  ZC3H12C WILD-TYPE  309   44
                               clus
vv                              ZC3H12C MUTATED ZC3H12C WILD-TYPE
  COLON ADENOCARCINOMA                        8               309
  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 249   2  21  20
D978V9, multiclass
    clus
vv   ZC3H12C MUTATED ZC3H12C WILD-TYPE
  R0               8               249
  R1               0                 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"
D978V10, 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
D978V11, 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(979) Variable = PIK3R4 MUTATION ANALYSIS
D979V1, survival
                  sevent
clus2                0   1
  PIK3R4 MUTATED    11   4
  PIK3R4 WILD-TYPE 271  69
  PIK3R4 MUTATED PIK3R4 WILD-TYPE 
              15              340 
  PIK3R4 MUTATED PIK3R4 WILD-TYPE 
               4               69 
$`PIK3R4 MUTATED`
TCGA-A6-2676 TCGA-A6-5660 TCGA-AA-3555 TCGA-AA-3713 TCGA-AA-3851 TCGA-AA-A00A 
       42.90        29.19        29.95        19.04        33.07        38.04 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q TCGA-AD-6965 TCGA-AZ-6598 TCGA-CA-5255 
        4.01        34.98         1.02         0.20        49.41         3.06 
TCGA-CM-5861 TCGA-F4-6459 TCGA-G4-6588 
       15.02         8.61        26.17 

$`PIK3R4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       27.02        13.94        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 
      119.93        35.97        60.79       117.07        98.24        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        91.79        46.75        52.80 

  PIK3R4 MUTATED PIK3R4 WILD-TYPE 
             0.2              0.0 
  PIK3R4 MUTATED PIK3R4 WILD-TYPE 
           49.41           140.38 
  PIK3R4 MUTATED PIK3R4 WILD-TYPE 
          26.170           20.155 
[1] "0.2 - 49.4 (26.2)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.6"
D979V2, 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       23       102         5         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PIK3R4 MUTATED           0          0          1          1        1
  PIK3R4 WILD-TYPE        19         10         40         30       34
                  vv
clus               STAGE IVA STAGE IVB
  PIK3R4 MUTATED           0         0
  PIK3R4 WILD-TYPE        13         1
D979V3, multiclass
            clus
vv           PIK3R4 MUTATED PIK3R4 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               7              102
  STAGE IIB               3                5
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              1               30
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PIK3R4 MUTATED     0   0  12   4
  PIK3R4 WILD-TYPE   9  68 236  37
D979V4, multiclass
    clus
vv   PIK3R4 MUTATED PIK3R4 WILD-TYPE
  T1              0                9
  T2              0               68
  T3             12              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
  PIK3R4 MUTATED    13   0   3
  PIK3R4 WILD-TYPE 207  80  63
D979V5, multiclass
    clus
vv   PIK3R4 MUTATED PIK3R4 WILD-TYPE
  N0             13              207
  N1              0               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"
D979V6, binary
                  cls
clus                 0   1
  PIK3R4 MUTATED    13   1
  PIK3R4 WILD-TYPE 270  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R4 MUTATED     13    1
  PIK3R4 WILD-TYPE  270   47
   clus
vv  PIK3R4 MUTATED PIK3R4 WILD-TYPE
  0             13              270
  1              1               47
[1] 2 2
[1] FALSE
D979V7, 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
D979V8, binary
                  cls
clus                 0   1
  PIK3R4 MUTATED    14   2
  PIK3R4 WILD-TYPE 303  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R4 MUTATED     14    2
  PIK3R4 WILD-TYPE  303   46
                               clus
vv                              PIK3R4 MUTATED PIK3R4 WILD-TYPE
  COLON ADENOCARCINOMA                      14              303
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PIK3R4 MUTATED    11   0   1   1
  PIK3R4 WILD-TYPE 246   2  21  20
D979V9, multiclass
    clus
vv   PIK3R4 MUTATED PIK3R4 WILD-TYPE
  R0             11              246
  R1              0                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"
D979V10, 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
D979V11, 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(980) Variable = CHRNA3 MUTATION ANALYSIS
D980V1, survival
                  sevent
clus2                0   1
  CHRNA3 MUTATED     6   4
  CHRNA3 WILD-TYPE 276  69
  CHRNA3 MUTATED CHRNA3 WILD-TYPE 
              10              345 
  CHRNA3 MUTATED CHRNA3 WILD-TYPE 
               4               69 
$`CHRNA3 MUTATED`
TCGA-A6-5659 TCGA-AA-3655 TCGA-AA-3811 TCGA-AD-6964 TCGA-AZ-6598 TCGA-AZ-6601 
       30.44        61.02        10.06        10.88        49.41       100.01 
TCGA-CK-4952 TCGA-CM-5348 TCGA-F4-6808 TCGA-F4-6856 
       15.62        22.98        33.67        19.43 

$`CHRNA3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        19.04        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       22.36        62.79        61.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 
        1.35        17.56       102.44        40.34        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 
       16.24        13.25         0.53        35.41       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  CHRNA3 MUTATED CHRNA3 WILD-TYPE 
           10.06             0.00 
  CHRNA3 MUTATED CHRNA3 WILD-TYPE 
          100.01           140.38 
  CHRNA3 MUTATED CHRNA3 WILD-TYPE 
           26.71            20.12 
[1] "10.1 - 100.0 (26.7)" "0.0 - 140.4 (20.1)" 
[1] "hr=" "1.4"
D980V2, 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       22       109         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CHRNA3 MUTATED           2          0          1          0        0
  CHRNA3 WILD-TYPE        17         10         40         31       35
                  vv
clus               STAGE IVA STAGE IVB
  CHRNA3 MUTATED           0         0
  CHRNA3 WILD-TYPE        13         1
D980V3, multiclass
            clus
vv           CHRNA3 MUTATED CHRNA3 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                3               22
  STAGE IIA               0              109
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               2               17
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CHRNA3 MUTATED     1   2   5   2
  CHRNA3 WILD-TYPE   8  66 243  39
D980V4, multiclass
    clus
vv   CHRNA3 MUTATED CHRNA3 WILD-TYPE
  T1              1                8
  T2              2               66
  T3              5              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
  CHRNA3 MUTATED     6   1   3
  CHRNA3 WILD-TYPE 214  79  63
D980V5, multiclass
    clus
vv   CHRNA3 MUTATED CHRNA3 WILD-TYPE
  N0              6              214
  N1              1               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"
D980V6, binary
                  cls
clus                 0   1
  CHRNA3 MUTATED     8   0
  CHRNA3 WILD-TYPE 275  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHRNA3 MUTATED      8    0
  CHRNA3 WILD-TYPE  275   48
   clus
vv  CHRNA3 MUTATED CHRNA3 WILD-TYPE
  0              8              275
  1              0               48
[1] 2 2
[1] FALSE
D980V7, 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
D980V8, binary
                  cls
clus                 0   1
  CHRNA3 MUTATED     8   2
  CHRNA3 WILD-TYPE 309  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHRNA3 MUTATED      8    2
  CHRNA3 WILD-TYPE  309   46
                               clus
vv                              CHRNA3 MUTATED CHRNA3 WILD-TYPE
  COLON ADENOCARCINOMA                       8              309
  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 251   2  22  20
D980V9, multiclass
    clus
vv   CHRNA3 MUTATED CHRNA3 WILD-TYPE
  R0              6              251
  R1              0                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"
D980V10, 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
D980V11, 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(981) Variable = PRRT2 MUTATION ANALYSIS
D981V1, survival
                 sevent
clus2               0   1
  PRRT2 MUTATED     6   0
  PRRT2 WILD-TYPE 276  73
  PRRT2 MUTATED PRRT2 WILD-TYPE 
              6             349 
  PRRT2 MUTATED PRRT2 WILD-TYPE 
              0              73 
$`PRRT2 MUTATED`
TCGA-AA-3663 TCGA-AD-5900 TCGA-AY-6197 TCGA-CK-4948 TCGA-G4-6306 TCGA-G4-6588 
        6.97         0.07        21.44       102.44        44.68        26.17 

$`PRRT2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 
        0.26         0.33         0.10         1.35        17.56        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 
       52.80 

  PRRT2 MUTATED PRRT2 WILD-TYPE 
           0.07            0.00 
  PRRT2 MUTATED PRRT2 WILD-TYPE 
         102.44          140.38 
  PRRT2 MUTATED PRRT2 WILD-TYPE 
         23.805          20.120 
[1] "0.1 - 102.4 (23.8)" "0.0 - 140.4 (20.1)"
[1] "hr="     "9300000"
D981V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PRRT2 MUTATED         1        0        1         3         0         0
  PRRT2 WILD-TYPE      63        1       24       106         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PRRT2 MUTATED           0          1          0          0        0         0
  PRRT2 WILD-TYPE        19          9         41         31       35        13
                 vv
clus              STAGE IVB
  PRRT2 MUTATED           0
  PRRT2 WILD-TYPE         1
D981V3, multiclass
            clus
vv           PRRT2 MUTATED PRRT2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              3             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PRRT2 MUTATED     0   2   4   0
  PRRT2 WILD-TYPE   9  66 244  41
D981V4, multiclass
    clus
vv   PRRT2 MUTATED PRRT2 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             4             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
  PRRT2 MUTATED     5   1   0
  PRRT2 WILD-TYPE 215  79  66
D981V5, multiclass
    clus
vv   PRRT2 MUTATED PRRT2 WILD-TYPE
  N0             5             215
  N1             1              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"
D981V6, binary
                 cls
clus                0   1
  PRRT2 MUTATED     4   0
  PRRT2 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRRT2 MUTATED      4    0
  PRRT2 WILD-TYPE  279   48
   clus
vv  PRRT2 MUTATED PRRT2 WILD-TYPE
  0             4             279
  1             0              48
[1] 2 2
[1] FALSE
D981V7, 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
D981V8, binary
                 cls
clus                0   1
  PRRT2 MUTATED     5   1
  PRRT2 WILD-TYPE 312  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRRT2 MUTATED      5    1
  PRRT2 WILD-TYPE  312   47
                               clus
vv                              PRRT2 MUTATED PRRT2 WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  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 251   2  22  21
D981V9, multiclass
    clus
vv   PRRT2 MUTATED PRRT2 WILD-TYPE
  R0             6             251
  R1             0               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"
D981V10, 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
D981V11, 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(982) Variable = C4ORF49 MUTATION ANALYSIS
D982V1, survival
                   sevent
clus2                 0   1
  C4ORF49 MUTATED     5   0
  C4ORF49 WILD-TYPE 277  73
  C4ORF49 MUTATED C4ORF49 WILD-TYPE 
                5               350 
  C4ORF49 MUTATED C4ORF49 WILD-TYPE 
                0                73 
$`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       107.67 

$`C4ORF49 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        35.41        19.43        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  C4ORF49 MUTATED C4ORF49 WILD-TYPE 
            19.59              0.00 
  C4ORF49 MUTATED C4ORF49 WILD-TYPE 
           135.65            140.38 
  C4ORF49 MUTATED C4ORF49 WILD-TYPE 
            63.98             20.07 
[1] "19.6 - 135.7 (64.0)" "0.0 - 140.4 (20.1)" 
[1] "hr="     "2.7e+07"
D982V2, 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       24       109         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C4ORF49 MUTATED           1          1          2          0        0
  C4ORF49 WILD-TYPE        18          9         39         31       35
                   vv
clus                STAGE IVA STAGE IVB
  C4ORF49 MUTATED           0         0
  C4ORF49 WILD-TYPE        13         1
D982V3, multiclass
            clus
vv           C4ORF49 MUTATED C4ORF49 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                0               109
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               1                 9
  STAGE IIIB               2                39
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C4ORF49 MUTATED     0   0   5   0
  C4ORF49 WILD-TYPE   9  68 243  41
D982V4, multiclass
    clus
vv   C4ORF49 MUTATED C4ORF49 WILD-TYPE
  T1               0                 9
  T2               0                68
  T3               5               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
  C4ORF49 MUTATED     1   4   0
  C4ORF49 WILD-TYPE 219  76  66
D982V5, multiclass
    clus
vv   C4ORF49 MUTATED C4ORF49 WILD-TYPE
  N0               1               219
  N1               4                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"
D982V6, binary
                   cls
clus                  0   1
  C4ORF49 MUTATED     4   0
  C4ORF49 WILD-TYPE 279  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C4ORF49 MUTATED      4    0
  C4ORF49 WILD-TYPE  279   48
   clus
vv  C4ORF49 MUTATED C4ORF49 WILD-TYPE
  0               4               279
  1               0                48
[1] 2 2
[1] FALSE
D982V7, 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
D982V8, binary
                   cls
clus                  0   1
  C4ORF49 MUTATED     4   1
  C4ORF49 WILD-TYPE 313  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C4ORF49 MUTATED      4    1
  C4ORF49 WILD-TYPE  313   47
                               clus
vv                              C4ORF49 MUTATED C4ORF49 WILD-TYPE
  COLON ADENOCARCINOMA                        4               313
  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 254   2  22  20
D982V9, multiclass
    clus
vv   C4ORF49 MUTATED C4ORF49 WILD-TYPE
  R0               3               254
  R1               0                 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"
D982V10, 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
D982V11, 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(983) Variable = ANKRD23 MUTATION ANALYSIS
D983V1, survival
                   sevent
clus2                 0   1
  ANKRD23 MUTATED     3   1
  ANKRD23 WILD-TYPE 279  72
  ANKRD23 MUTATED ANKRD23 WILD-TYPE 
                4               351 
  ANKRD23 MUTATED ANKRD23 WILD-TYPE 
                1                72 
$`ANKRD23 MUTATED`
TCGA-AA-3492 TCGA-CM-4743 TCGA-CM-6171 TCGA-G4-6628 
        3.02        23.05        14.04        52.80 

$`ANKRD23 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       26.17        91.79        46.75 

  ANKRD23 MUTATED ANKRD23 WILD-TYPE 
             3.02              0.00 
  ANKRD23 MUTATED ANKRD23 WILD-TYPE 
            52.80            140.38 
  ANKRD23 MUTATED ANKRD23 WILD-TYPE 
           18.545            20.190 
[1] "3.0 - 52.8 (18.5)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D983V2, 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       24       108         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANKRD23 MUTATED           0          0          0          0        0
  ANKRD23 WILD-TYPE        19         10         41         31       35
                   vv
clus                STAGE IVA STAGE IVB
  ANKRD23 MUTATED           0         0
  ANKRD23 WILD-TYPE        13         1
D983V3, multiclass
            clus
vv           ANKRD23 MUTATED ANKRD23 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                1               108
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ANKRD23 MUTATED     0   2   2   0
  ANKRD23 WILD-TYPE   9  66 246  41
D983V4, multiclass
    clus
vv   ANKRD23 MUTATED ANKRD23 WILD-TYPE
  T1               0                 9
  T2               2                66
  T3               2               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
  ANKRD23 MUTATED     4   0   0
  ANKRD23 WILD-TYPE 216  80  66
D983V5, multiclass
    clus
vv   ANKRD23 MUTATED ANKRD23 WILD-TYPE
  N0               4               216
  N1               0                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"
D983V6, binary
                   cls
clus                  0   1
  ANKRD23 MUTATED     4   0
  ANKRD23 WILD-TYPE 279  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD23 MUTATED      4    0
  ANKRD23 WILD-TYPE  279   48
   clus
vv  ANKRD23 MUTATED ANKRD23 WILD-TYPE
  0               4               279
  1               0                48
[1] 2 2
[1] FALSE
D983V7, 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
D983V8, binary
                   cls
clus                  0   1
  ANKRD23 MUTATED     4   0
  ANKRD23 WILD-TYPE 313  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD23 MUTATED      4    0
  ANKRD23 WILD-TYPE  313   48
                               clus
vv                              ANKRD23 MUTATED ANKRD23 WILD-TYPE
  COLON ADENOCARCINOMA                        4               313
  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 253   2  22  21
D983V9, multiclass
    clus
vv   ANKRD23 MUTATED ANKRD23 WILD-TYPE
  R0               4               253
  R1               0                 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"
D983V10, 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
D983V11, 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(984) Variable = AP1G2 MUTATION ANALYSIS
D984V1, survival
                 sevent
clus2               0   1
  AP1G2 MUTATED    12   1
  AP1G2 WILD-TYPE 270  72
  AP1G2 MUTATED AP1G2 WILD-TYPE 
             13             342 
  AP1G2 MUTATED AP1G2 WILD-TYPE 
              1              72 
$`AP1G2 MUTATED`
TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3518 TCGA-AA-3554 TCGA-AA-3672 TCGA-AA-3966 
       20.12        19.66         1.02        17.95         0.92         2.01 
TCGA-AA-3977 TCGA-AA-A00A TCGA-AA-A01P TCGA-CM-5348 TCGA-CM-5861 TCGA-D5-6536 
       25.02        38.04        38.07        22.98        15.02        17.85 
TCGA-G4-6299 
       74.56 

$`AP1G2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       23.87        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 
       63.98         6.97         1.02        13.02        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       26.01        24.00         2.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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        16.01 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        15.12         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.41        19.43       107.67        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  AP1G2 MUTATED AP1G2 WILD-TYPE 
           0.92            0.00 
  AP1G2 MUTATED AP1G2 WILD-TYPE 
          74.56          140.38 
  AP1G2 MUTATED AP1G2 WILD-TYPE 
          19.66           20.63 
[1] "0.9 - 74.6 (19.7)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "2.4"
D984V2, 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       25       102         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        17         10         40         29       35        13
                 vv
clus              STAGE IVB
  AP1G2 MUTATED           0
  AP1G2 WILD-TYPE         1
D984V3, multiclass
            clus
vv           AP1G2 MUTATED AP1G2 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              7             102
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             2              29
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  AP1G2 MUTATED     0   1  11   1
  AP1G2 WILD-TYPE   9  67 237  40
D984V4, multiclass
    clus
vv   AP1G2 MUTATED AP1G2 WILD-TYPE
  T1             0               9
  T2             1              67
  T3            11             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
  AP1G2 MUTATED     8   4   1
  AP1G2 WILD-TYPE 212  76  65
D984V5, multiclass
    clus
vv   AP1G2 MUTATED AP1G2 WILD-TYPE
  N0             8             212
  N1             4              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"
D984V6, binary
                 cls
clus                0   1
  AP1G2 MUTATED    10   0
  AP1G2 WILD-TYPE 273  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP1G2 MUTATED     10    0
  AP1G2 WILD-TYPE  273   48
   clus
vv  AP1G2 MUTATED AP1G2 WILD-TYPE
  0            10             273
  1             0              48
[1] 2 2
[1] FALSE
D984V7, 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
D984V8, binary
                 cls
clus                0   1
  AP1G2 MUTATED    10   3
  AP1G2 WILD-TYPE 307  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP1G2 MUTATED     10    3
  AP1G2 WILD-TYPE  307   45
                               clus
vv                              AP1G2 MUTATED AP1G2 WILD-TYPE
  COLON ADENOCARCINOMA                     10             307
  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 247   2  22  21
D984V9, multiclass
    clus
vv   AP1G2 MUTATED AP1G2 WILD-TYPE
  R0            10             247
  R1             0               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"
D984V10, 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
D984V11, 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(985) Variable = SATB1 MUTATION ANALYSIS
D985V1, survival
                 sevent
clus2               0   1
  SATB1 MUTATED    12   2
  SATB1 WILD-TYPE 270  71
  SATB1 MUTATED SATB1 WILD-TYPE 
             14             341 
  SATB1 MUTATED SATB1 WILD-TYPE 
              2              71 
$`SATB1 MUTATED`
TCGA-A6-6648 TCGA-A6-6780 TCGA-AA-3815 TCGA-AD-6889 TCGA-AZ-6598 TCGA-CA-6718 
       25.18        20.12        33.04        56.55        49.41         0.10 
TCGA-D5-6532 TCGA-D5-6540 TCGA-D5-6928 TCGA-DM-A1HB TCGA-F4-6856 TCGA-G4-6315 
       18.25        16.14        11.64       135.65        19.43        36.72 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

$`SATB1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37         4.21         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 
       19.59        13.51        11.51        20.19         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        35.41       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 
       53.62        44.68        55.04        51.75        45.11        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       22.09        13.78        35.80        26.17        91.79 

  SATB1 MUTATED SATB1 WILD-TYPE 
            0.1             0.0 
  SATB1 MUTATED SATB1 WILD-TYPE 
         135.65          140.38 
  SATB1 MUTATED SATB1 WILD-TYPE 
          29.11           20.02 
[1] "0.1 - 135.7 (29.1)" "0.0 - 140.4 (20.0)"
[1] "hr=" "2.1"
D985V2, 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       24       102         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        18         10         40         31       33        12
                 vv
clus              STAGE IVB
  SATB1 MUTATED           0
  SATB1 WILD-TYPE         1
D985V3, multiclass
            clus
vv           SATB1 MUTATED SATB1 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              7             102
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               2              33
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  65 236  40
D985V4, multiclass
    clus
vv   SATB1 MUTATED SATB1 WILD-TYPE
  T1             0               9
  T2             3              65
  T3            12             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
  SATB1 MUTATED    12   3   1
  SATB1 WILD-TYPE 208  77  65
D985V5, multiclass
    clus
vv   SATB1 MUTATED SATB1 WILD-TYPE
  N0            12             208
  N1             3              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"
D985V6, binary
                 cls
clus                0   1
  SATB1 MUTATED    11   3
  SATB1 WILD-TYPE 272  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SATB1 MUTATED     11    3
  SATB1 WILD-TYPE  272   45
   clus
vv  SATB1 MUTATED SATB1 WILD-TYPE
  0            11             272
  1             3              45
[1] 2 2
[1] FALSE
D985V7, 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
D985V8, binary
                 cls
clus                0   1
  SATB1 MUTATED    12   4
  SATB1 WILD-TYPE 305  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SATB1 MUTATED     12    4
  SATB1 WILD-TYPE  305   44
                               clus
vv                              SATB1 MUTATED SATB1 WILD-TYPE
  COLON ADENOCARCINOMA                     12             305
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SATB1 MUTATED     9   0   1   1
  SATB1 WILD-TYPE 248   2  21  20
D985V9, multiclass
    clus
vv   SATB1 MUTATED SATB1 WILD-TYPE
  R0             9             248
  R1             0               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"
D985V10, 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
D985V11, 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(986) Variable = PPP1R12A MUTATION ANALYSIS
D986V1, survival
                    sevent
clus2                  0   1
  PPP1R12A MUTATED    10   3
  PPP1R12A WILD-TYPE 272  70
  PPP1R12A MUTATED PPP1R12A WILD-TYPE 
                13                342 
  PPP1R12A MUTATED PPP1R12A WILD-TYPE 
                 3                 70 
$`PPP1R12A MUTATED`
TCGA-A6-2671 TCGA-A6-6781 TCGA-AA-3502 TCGA-AA-3845 TCGA-AA-3864 TCGA-AZ-6608 
       43.76        19.66        35.01         0.00        53.00         1.94 
TCGA-CA-6718 TCGA-CK-5913 TCGA-CK-6751 TCGA-D5-5540 TCGA-D5-6539 TCGA-DM-A1HA 
        0.10        51.32       124.27        13.51        12.49       131.51 
TCGA-F4-6808 
       33.67 

$`PPP1R12A WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3510 
       20.12        20.28         7.04         3.02         1.02        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       38.99        37.02        14.93        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.33         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
       17.56       102.44        40.34        15.62        49.08        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14         2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       16.31        29.59        16.24        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  PPP1R12A MUTATED PPP1R12A WILD-TYPE 
                 0                  0 
  PPP1R12A MUTATED PPP1R12A WILD-TYPE 
            131.51             140.38 
  PPP1R12A MUTATED PPP1R12A WILD-TYPE 
            33.670             20.155 
[1] "0.0 - 131.5 (33.7)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.3"
D986V2, 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       24       105         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PPP1R12A MUTATED           0          2          0          2        1
  PPP1R12A WILD-TYPE        19          8         41         29       34
                    vv
clus                 STAGE IVA STAGE IVB
  PPP1R12A MUTATED           0         0
  PPP1R12A WILD-TYPE        13         1
D986V3, multiclass
            clus
vv           PPP1R12A MUTATED PPP1R12A WILD-TYPE
  STAGE I                   3                 61
  STAGE IA                  0                  1
  STAGE II                  1                 24
  STAGE IIA                 4                105
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                2                  8
  STAGE IIIB                0                 41
  STAGE IIIC                2                 29
  STAGE IV                  1                 34
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  PPP1R12A MUTATED     1   3   8   1
  PPP1R12A WILD-TYPE   8  65 240  40
D986V4, multiclass
    clus
vv   PPP1R12A MUTATED PPP1R12A WILD-TYPE
  T1                1                  8
  T2                3                 65
  T3                8                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
  PPP1R12A MUTATED     9   2   2
  PPP1R12A WILD-TYPE 211  78  64
D986V5, multiclass
    clus
vv   PPP1R12A MUTATED PPP1R12A WILD-TYPE
  N0                9                211
  N1                2                 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"
D986V6, binary
                    cls
clus                   0   1
  PPP1R12A MUTATED     9   1
  PPP1R12A WILD-TYPE 274  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R12A MUTATED      9    1
  PPP1R12A WILD-TYPE  274   47
   clus
vv  PPP1R12A MUTATED PPP1R12A WILD-TYPE
  0                9                274
  1                1                 47
[1] 2 2
[1] FALSE
D986V7, 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
D986V8, binary
                    cls
clus                   0   1
  PPP1R12A MUTATED    11   2
  PPP1R12A WILD-TYPE 306  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R12A MUTATED     11    2
  PPP1R12A WILD-TYPE  306   46
                               clus
vv                              PPP1R12A MUTATED PPP1R12A WILD-TYPE
  COLON ADENOCARCINOMA                        11                306
  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 249   2  22  18
D986V9, multiclass
    clus
vv   PPP1R12A MUTATED PPP1R12A WILD-TYPE
  R0                8                249
  R1                0                  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"
D986V10, 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
D986V11, 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(987) Variable = GIMAP5 MUTATION ANALYSIS
D987V1, survival
                  sevent
clus2                0   1
  GIMAP5 MUTATED     2   2
  GIMAP5 WILD-TYPE 280  71
  GIMAP5 MUTATED GIMAP5 WILD-TYPE 
               4              351 
  GIMAP5 MUTATED GIMAP5 WILD-TYPE 
               2               71 
$`GIMAP5 MUTATED`
TCGA-AA-3555 TCGA-AA-3811 TCGA-AA-A00N TCGA-AA-A01F 
       29.95        10.06         4.01        32.02 

$`GIMAP5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        17.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       34.98        15.02        10.98        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  GIMAP5 MUTATED GIMAP5 WILD-TYPE 
            4.01             0.00 
  GIMAP5 MUTATED GIMAP5 WILD-TYPE 
           32.02           140.38 
  GIMAP5 MUTATED GIMAP5 WILD-TYPE 
          20.005           20.190 
[1] "4.0 - 32.0 (20.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "3.6"
D987V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GIMAP5 MUTATED         0        0        0         1         1         0
  GIMAP5 WILD-TYPE      64        1       25       108         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GIMAP5 MUTATED           1          0          1          0        0
  GIMAP5 WILD-TYPE        18         10         40         31       35
                  vv
clus               STAGE IVA STAGE IVB
  GIMAP5 MUTATED           0         0
  GIMAP5 WILD-TYPE        13         1
D987V3, multiclass
            clus
vv           GIMAP5 MUTATED GIMAP5 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               1              108
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GIMAP5 MUTATED     0   0   3   1
  GIMAP5 WILD-TYPE   9  68 245  40
D987V4, multiclass
    clus
vv   GIMAP5 MUTATED GIMAP5 WILD-TYPE
  T1              0                9
  T2              0               68
  T3              3              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
  GIMAP5 MUTATED     2   1   1
  GIMAP5 WILD-TYPE 218  79  65
D987V5, multiclass
    clus
vv   GIMAP5 MUTATED GIMAP5 WILD-TYPE
  N0              2              218
  N1              1               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"
D987V6, binary
                  cls
clus                 0   1
  GIMAP5 MUTATED     4   0
  GIMAP5 WILD-TYPE 279  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GIMAP5 MUTATED      4    0
  GIMAP5 WILD-TYPE  279   48
   clus
vv  GIMAP5 MUTATED GIMAP5 WILD-TYPE
  0              4              279
  1              0               48
[1] 2 2
[1] FALSE
D987V7, binary
                  cls
clus                 0   1
  GIMAP5 MUTATED     2   2
  GIMAP5 WILD-TYPE 168 195
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GIMAP5 MUTATED      2    2
  GIMAP5 WILD-TYPE  168  195
        clus
vv       GIMAP5 MUTATED GIMAP5 WILD-TYPE
  FEMALE              2              168
  MALE                2              195
[1] 2 2
[1] FALSE
D987V8, binary
                  cls
clus                 0   1
  GIMAP5 MUTATED     2   2
  GIMAP5 WILD-TYPE 315  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GIMAP5 MUTATED      2    2
  GIMAP5 WILD-TYPE  315   46
                               clus
vv                              GIMAP5 MUTATED GIMAP5 WILD-TYPE
  COLON ADENOCARCINOMA                       2              315
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  GIMAP5 MUTATED     4   0   0   0
  GIMAP5 WILD-TYPE 253   2  22  21
D987V9, multiclass
    clus
vv   GIMAP5 MUTATED GIMAP5 WILD-TYPE
  R0              4              253
  R1              0                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"
D987V10, 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     0
  GIMAP5 WILD-TYPE                        19   176
D987V11, multiclass

Clustering(988) Variable = ALCAM MUTATION ANALYSIS
D988V1, survival
                 sevent
clus2               0   1
  ALCAM MUTATED     8   3
  ALCAM WILD-TYPE 274  70
  ALCAM MUTATED ALCAM WILD-TYPE 
             11             344 
  ALCAM MUTATED ALCAM WILD-TYPE 
              3              70 
$`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         0.33 
TCGA-CA-6718 TCGA-D5-6923 TCGA-DM-A1HA TCGA-G4-6303 TCGA-G4-6315 
        0.10        12.43       131.51        65.85        36.72 

$`ALCAM WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
        6.05         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         0.72        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07         0.26         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 
       15.58         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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  ALCAM MUTATED ALCAM WILD-TYPE 
            0.1             0.0 
  ALCAM MUTATED ALCAM WILD-TYPE 
         131.51          140.38 
  ALCAM MUTATED ALCAM WILD-TYPE 
         21.440          20.155 
[1] "0.1 - 131.5 (21.4)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1"  
D988V2, 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       23       106         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        18         10         41         29       33        13
                 vv
clus              STAGE IVB
  ALCAM MUTATED           0
  ALCAM WILD-TYPE         1
D988V3, multiclass
            clus
vv           ALCAM MUTATED ALCAM WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              3             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             2              29
  STAGE IV               2              33
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ALCAM MUTATED     0   1   9   1
  ALCAM WILD-TYPE   9  67 239  40
D988V4, multiclass
    clus
vv   ALCAM MUTATED ALCAM WILD-TYPE
  T1             0               9
  T2             1              67
  T3             9             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
  ALCAM MUTATED     6   3   2
  ALCAM WILD-TYPE 214  77  64
D988V5, multiclass
    clus
vv   ALCAM MUTATED ALCAM WILD-TYPE
  N0             6             214
  N1             3              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"
D988V6, binary
                 cls
clus                0   1
  ALCAM MUTATED     6   2
  ALCAM WILD-TYPE 277  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALCAM MUTATED      6    2
  ALCAM WILD-TYPE  277   46
   clus
vv  ALCAM MUTATED ALCAM WILD-TYPE
  0             6             277
  1             2              46
[1] 2 2
[1] FALSE
D988V7, 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
D988V8, binary
                 cls
clus                0   1
  ALCAM MUTATED     9   2
  ALCAM WILD-TYPE 308  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALCAM MUTATED      9    2
  ALCAM WILD-TYPE  308   46
                               clus
vv                              ALCAM MUTATED ALCAM WILD-TYPE
  COLON ADENOCARCINOMA                      9             308
  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 251   2  22  19
D988V9, multiclass
    clus
vv   ALCAM MUTATED ALCAM WILD-TYPE
  R0             6             251
  R1             0               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"
D988V10, 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
D988V11, 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(989) Variable = THUMPD3 MUTATION ANALYSIS
D989V1, survival
                   sevent
clus2                 0   1
  THUMPD3 MUTATED     8   2
  THUMPD3 WILD-TYPE 274  71
  THUMPD3 MUTATED THUMPD3 WILD-TYPE 
               10               345 
  THUMPD3 MUTATED THUMPD3 WILD-TYPE 
                2                71 
$`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         0.33        13.02 
TCGA-D5-6539 TCGA-F4-6569 TCGA-G4-6303 TCGA-G4-6304 
       12.49        13.45        65.85        53.62 

$`THUMPD3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        19.00        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 
       43.27        15.12        17.85         4.80        17.13        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.38         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
      107.67        74.56        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  THUMPD3 MUTATED THUMPD3 WILD-TYPE 
             0.33              0.00 
  THUMPD3 MUTATED THUMPD3 WILD-TYPE 
            65.85            140.38 
  THUMPD3 MUTATED THUMPD3 WILD-TYPE 
           21.735            20.190 
[1] "0.3 - 65.8 (21.7)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D989V2, 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       25       105         5         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  THUMPD3 MUTATED           0          1          0          0        2
  THUMPD3 WILD-TYPE        19          9         41         31       33
                   vv
clus                STAGE IVA STAGE IVB
  THUMPD3 MUTATED           0         0
  THUMPD3 WILD-TYPE        13         1
D989V3, multiclass
            clus
vv           THUMPD3 MUTATED THUMPD3 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                4               105
  STAGE IIB                3                 5
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               1                 9
  STAGE IIIB               0                41
  STAGE IIIC               0                31
  STAGE IV                 2                33
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  THUMPD3 MUTATED     0   1   6   4
  THUMPD3 WILD-TYPE   9  67 242  37
D989V4, multiclass
    clus
vv   THUMPD3 MUTATED THUMPD3 WILD-TYPE
  T1               0                 9
  T2               1                67
  T3               6               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
  THUMPD3 MUTATED     9   2   0
  THUMPD3 WILD-TYPE 211  78  66
D989V5, multiclass
    clus
vv   THUMPD3 MUTATED THUMPD3 WILD-TYPE
  N0               9               211
  N1               2                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"
D989V6, binary
                   cls
clus                  0   1
  THUMPD3 MUTATED     8   2
  THUMPD3 WILD-TYPE 275  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  THUMPD3 MUTATED      8    2
  THUMPD3 WILD-TYPE  275   46
   clus
vv  THUMPD3 MUTATED THUMPD3 WILD-TYPE
  0               8               275
  1               2                46
[1] 2 2
[1] FALSE
D989V7, 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
D989V8, binary
                   cls
clus                  0   1
  THUMPD3 MUTATED    10   1
  THUMPD3 WILD-TYPE 307  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  THUMPD3 MUTATED     10    1
  THUMPD3 WILD-TYPE  307   47
                               clus
vv                              THUMPD3 MUTATED THUMPD3 WILD-TYPE
  COLON ADENOCARCINOMA                       10               307
  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 249   2  22  19
D989V9, multiclass
    clus
vv   THUMPD3 MUTATED THUMPD3 WILD-TYPE
  R0               8               249
  R1               0                 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"
D989V10, 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
D989V11, 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(990) Variable = SMARCA1 MUTATION ANALYSIS
D990V1, survival
                   sevent
clus2                 0   1
  SMARCA1 MUTATED    13   5
  SMARCA1 WILD-TYPE 269  68
  SMARCA1 MUTATED SMARCA1 WILD-TYPE 
               18               337 
  SMARCA1 MUTATED SMARCA1 WILD-TYPE 
                5                68 
$`SMARCA1 MUTATED`
TCGA-A6-3809 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3529 TCGA-AA-3555 TCGA-AA-3977 
       32.75        22.06        19.66         0.00        29.95        25.02 
TCGA-AA-A00K TCGA-AA-A01P TCGA-AD-6964 TCGA-AU-3779 TCGA-AY-6197 TCGA-AZ-6599 
       18.05        38.07        10.88        14.50        21.44         6.77 
TCGA-CA-6717 TCGA-CK-6747 TCGA-CM-5861 TCGA-D5-6536 TCGA-DM-A28G TCGA-G4-6586 
        0.33         2.93        15.02        17.85        60.79        35.80 

$`SMARCA1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 
       24.03        37.05        36.03         8.05        19.07        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.20        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41        49.41        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        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        16.01         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 
       20.19        18.25         1.32        43.27        15.12         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H 
      139.17         6.12        81.37       119.93        35.97       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  SMARCA1 MUTATED SMARCA1 WILD-TYPE 
                0                 0 
  SMARCA1 MUTATED SMARCA1 WILD-TYPE 
            60.79            140.38 
  SMARCA1 MUTATED SMARCA1 WILD-TYPE 
           18.855            20.280 
[1] "0.0 - 60.8 (18.9)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.8"
D990V2, 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       24        98         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SMARCA1 MUTATED           1          0          0          2        0
  SMARCA1 WILD-TYPE        18         10         41         29       35
                   vv
clus                STAGE IVA STAGE IVB
  SMARCA1 MUTATED           0         0
  SMARCA1 WILD-TYPE        13         1
D990V3, multiclass
            clus
vv           SMARCA1 MUTATED SMARCA1 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA               11                98
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               2                29
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SMARCA1 MUTATED     0   2  13   4
  SMARCA1 WILD-TYPE   9  66 235  37
D990V4, multiclass
    clus
vv   SMARCA1 MUTATED SMARCA1 WILD-TYPE
  T1               0                 9
  T2               2                66
  T3              13               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
  SMARCA1 MUTATED    15   2   2
  SMARCA1 WILD-TYPE 205  78  64
D990V5, multiclass
    clus
vv   SMARCA1 MUTATED SMARCA1 WILD-TYPE
  N0              15               205
  N1               2                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"
D990V6, binary
                   cls
clus                  0   1
  SMARCA1 MUTATED    13   0
  SMARCA1 WILD-TYPE 270  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA1 MUTATED     13    0
  SMARCA1 WILD-TYPE  270   48
   clus
vv  SMARCA1 MUTATED SMARCA1 WILD-TYPE
  0              13               270
  1               0                48
[1] 2 2
[1] FALSE
D990V7, 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
D990V8, binary
                   cls
clus                  0   1
  SMARCA1 MUTATED    15   4
  SMARCA1 WILD-TYPE 302  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA1 MUTATED     15    4
  SMARCA1 WILD-TYPE  302   44
                               clus
vv                              SMARCA1 MUTATED SMARCA1 WILD-TYPE
  COLON ADENOCARCINOMA                       15               302
  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 244   2  22  19
D990V9, multiclass
    clus
vv   SMARCA1 MUTATED SMARCA1 WILD-TYPE
  R0              13               244
  R1               0                 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"
D990V10, 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
D990V11, 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(991) Variable = SPANXC MUTATION ANALYSIS
D991V1, survival
                  sevent
clus2                0   1
  SPANXC MUTATED     3   0
  SPANXC WILD-TYPE 279  73
  SPANXC MUTATED SPANXC WILD-TYPE 
               3              352 
  SPANXC MUTATED SPANXC WILD-TYPE 
               0               73 
$`SPANXC MUTATED`
TCGA-A6-5661 TCGA-A6-6653 TCGA-CK-5913 
       33.53        24.39        51.32 

$`SPANXC WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 
      102.44        40.34        15.62        49.08        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  SPANXC MUTATED SPANXC WILD-TYPE 
           24.39             0.00 
  SPANXC MUTATED SPANXC WILD-TYPE 
           51.32           140.38 
  SPANXC MUTATED SPANXC WILD-TYPE 
           33.53            20.07 
[1] "24.4 - 51.3 (33.5)" "0.0 - 140.4 (20.1)"
[1] "hr="     "9100000"
D991V2, 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       25       107         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SPANXC MUTATED           0          0          0          0        1
  SPANXC WILD-TYPE        19         10         41         31       34
                  vv
clus               STAGE IVA STAGE IVB
  SPANXC MUTATED           0         0
  SPANXC WILD-TYPE        13         1
D991V3, multiclass
            clus
vv           SPANXC MUTATED SPANXC WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               2              107
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SPANXC MUTATED     0   1   2   1
  SPANXC WILD-TYPE   9  67 246  40
D991V4, multiclass
    clus
vv   SPANXC MUTATED SPANXC WILD-TYPE
  T1              0                9
  T2              1               67
  T3              2              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
  SPANXC MUTATED     3   0   1
  SPANXC WILD-TYPE 217  80  65
D991V5, multiclass
    clus
vv   SPANXC MUTATED SPANXC WILD-TYPE
  N0              3              217
  N1              0               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"
D991V6, binary
                  cls
clus                 0   1
  SPANXC MUTATED     2   1
  SPANXC WILD-TYPE 281  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPANXC MUTATED      2    1
  SPANXC WILD-TYPE  281   47
   clus
vv  SPANXC MUTATED SPANXC WILD-TYPE
  0              2              281
  1              1               47
[1] 2 2
[1] FALSE
D991V7, 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
D991V8, binary
                  cls
clus                 0   1
  SPANXC MUTATED     4   0
  SPANXC WILD-TYPE 313  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPANXC MUTATED      4    0
  SPANXC WILD-TYPE  313   48
                               clus
vv                              SPANXC MUTATED SPANXC WILD-TYPE
  COLON ADENOCARCINOMA                       4              313
  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 256   2  21  20
D991V9, multiclass
    clus
vv   SPANXC MUTATED SPANXC WILD-TYPE
  R0              1              256
  R1              0                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"
D991V10, 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
D991V11, 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(992) Variable = RRAGD MUTATION ANALYSIS
D992V1, survival
                 sevent
clus2               0   1
  RRAGD MUTATED     7   0
  RRAGD WILD-TYPE 275  73
  RRAGD MUTATED RRAGD WILD-TYPE 
              7             348 
  RRAGD MUTATED RRAGD WILD-TYPE 
              0              73 
$`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        61.41        15.12 
TCGA-D5-6538 
       17.13 

$`RRAGD WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        33.53        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3560 
       13.02        24.00        17.95        29.95        23.01        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 
        1.32        43.27        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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  RRAGD MUTATED RRAGD WILD-TYPE 
           14.5             0.0 
  RRAGD MUTATED RRAGD WILD-TYPE 
          61.41          140.38 
  RRAGD MUTATED RRAGD WILD-TYPE 
         20.980          20.155 
[1] "14.5 - 61.4 (21.0)" "0.0 - 140.4 (20.2)"
[1] "hr="     "9300000"
D992V2, 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       25       107         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        19         10         39         31       35        12
                 vv
clus              STAGE IVB
  RRAGD MUTATED           0
  RRAGD WILD-TYPE         1
D992V3, multiclass
            clus
vv           RRAGD MUTATED RRAGD WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              2             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 243  41
D992V4, multiclass
    clus
vv   RRAGD MUTATED RRAGD WILD-TYPE
  T1             1               8
  T2             1              67
  T3             5             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
  RRAGD MUTATED     4   1   2
  RRAGD WILD-TYPE 216  79  64
D992V5, multiclass
    clus
vv   RRAGD MUTATED RRAGD WILD-TYPE
  N0             4             216
  N1             1              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"
D992V6, binary
                 cls
clus                0   1
  RRAGD MUTATED     5   1
  RRAGD WILD-TYPE 278  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RRAGD MUTATED      5    1
  RRAGD WILD-TYPE  278   47
   clus
vv  RRAGD MUTATED RRAGD WILD-TYPE
  0             5             278
  1             1              47
[1] 2 2
[1] FALSE
D992V7, 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
D992V8, binary
                 cls
clus                0   1
  RRAGD MUTATED     7   0
  RRAGD WILD-TYPE 310  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RRAGD MUTATED      7    0
  RRAGD WILD-TYPE  310   48
                               clus
vv                              RRAGD MUTATED RRAGD WILD-TYPE
  COLON ADENOCARCINOMA                      7             310
  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 254   2  21  20
D992V9, multiclass
    clus
vv   RRAGD MUTATED RRAGD WILD-TYPE
  R0             3             254
  R1             0               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"
D992V10, 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
D992V11, 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(993) Variable = MYB MUTATION ANALYSIS
D993V1, survival
               sevent
clus2             0   1
  MYB MUTATED     7   1
  MYB WILD-TYPE 275  72
  MYB MUTATED MYB WILD-TYPE 
            8           347 
  MYB MUTATED MYB WILD-TYPE 
            1            72 
$`MYB MUTATED`
TCGA-A6-3809 TCGA-AA-3864 TCGA-AA-A01R TCGA-CA-6718 TCGA-CM-6171 TCGA-D5-6540 
       32.75        53.00        35.01         0.10        14.04        16.14 
TCGA-F4-6570 TCGA-G4-6586 
        6.18        35.80 

$`MYB WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.33         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-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        13.38        13.45        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        26.17        91.79        46.75        52.80 

  MYB MUTATED MYB WILD-TYPE 
          0.1           0.0 
  MYB MUTATED MYB WILD-TYPE 
        53.00        140.38 
  MYB MUTATED MYB WILD-TYPE 
       24.445        20.190 
[1] "0.1 - 53.0 (24.4)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.5"
D993V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MYB MUTATED         2        0        1         3         1         0
  MYB WILD-TYPE      62        1       24       106         7         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MYB MUTATED           1          0          0          0        0         0
  MYB WILD-TYPE        18         10         41         31       35        13
               vv
clus            STAGE IVB
  MYB MUTATED           0
  MYB WILD-TYPE         1
D993V3, multiclass
            clus
vv           MYB MUTATED MYB WILD-TYPE
  STAGE I              2            62
  STAGE IA             0             1
  STAGE II             1            24
  STAGE IIA            3           106
  STAGE IIB            1             7
  STAGE IIC            0             1
  STAGE III            1            18
  STAGE IIIA           0            10
  STAGE IIIB           0            41
  STAGE IIIC           0            31
  STAGE IV             0            35
  STAGE IVA            0            13
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  MYB MUTATED     0   2   5   1
  MYB WILD-TYPE   9  66 243  40
D993V4, multiclass
    clus
vv   MYB MUTATED MYB WILD-TYPE
  T1           0             9
  T2           2            66
  T3           5           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
  MYB MUTATED     7   0   1
  MYB WILD-TYPE 213  80  65
D993V5, multiclass
    clus
vv   MYB MUTATED MYB WILD-TYPE
  N0           7           213
  N1           0            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"
D993V6, binary
               cls
clus              0   1
  MYB MUTATED     8   0
  MYB WILD-TYPE 275  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  MYB MUTATED      8    0
  MYB WILD-TYPE  275   48
   clus
vv  MYB MUTATED MYB WILD-TYPE
  0           8           275
  1           0            48
[1] 2 2
[1] FALSE
D993V7, binary
               cls
clus              0   1
  MYB MUTATED     4   4
  MYB WILD-TYPE 166 193
[1] "tbl2"
               cls
clus            [,1] [,2]
  MYB MUTATED      4    4
  MYB WILD-TYPE  166  193
        clus
vv       MYB MUTATED MYB WILD-TYPE
  FEMALE           4           166
  MALE             4           193
[1] 2 2
[1] FALSE
D993V8, binary
               cls
clus              0   1
  MYB MUTATED     5   3
  MYB WILD-TYPE 312  45
[1] "tbl2"
               cls
clus            [,1] [,2]
  MYB MUTATED      5    3
  MYB WILD-TYPE  312   45
                               clus
vv                              MYB MUTATED MYB WILD-TYPE
  COLON ADENOCARCINOMA                    5           312
  COLON MUCINOUS ADENOCARCINOMA           3            45
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  MYB MUTATED     7   0   0   1
  MYB WILD-TYPE 250   2  22  20
D993V9, multiclass
    clus
vv   MYB MUTATED MYB WILD-TYPE
  R0           7           250
  R1           0             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"
D993V10, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MYB MUTATED                                  0     1
  MYB WILD-TYPE                                1     9
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  MYB MUTATED                           0     5
  MYB WILD-TYPE                        19   171
D993V11, multiclass
                                  clus
vv                                 MYB MUTATED MYB 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(994) Variable = CHD1 MUTATION ANALYSIS
D994V1, survival
                sevent
clus2              0   1
  CHD1 MUTATED    20   3
  CHD1 WILD-TYPE 262  70
  CHD1 MUTATED CHD1 WILD-TYPE 
            23            332 
  CHD1 MUTATED CHD1 WILD-TYPE 
             3             70 
$`CHD1 MUTATED`
TCGA-A6-5659 TCGA-A6-6138 TCGA-A6-6649 TCGA-AA-3526 TCGA-AA-3672 TCGA-AA-3713 
       30.44        22.52        24.16        19.07         0.92        19.04 
TCGA-AA-3815 TCGA-AA-3821 TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-3977 TCGA-AA-3982 
       33.04         1.02        53.00        33.01        25.02        27.02 
TCGA-AA-A00A TCGA-AD-5900 TCGA-AZ-4315 TCGA-AZ-6606 TCGA-CA-6717 TCGA-CA-6718 
       38.04         0.07        58.39        11.74         0.33         0.10 
TCGA-CK-5916 TCGA-CM-6162 TCGA-D5-6930 TCGA-DM-A0XF TCGA-F4-6856 
       21.14        12.00         1.51        38.20        19.43 

$`CHD1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09         8.38        25.08        25.18 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3529 TCGA-AA-3530 
       24.03        37.05        36.03         8.05         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 
       19.04        10.06        35.05         0.99        25.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       26.01        24.00        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       13.94        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10       100.01        29.56         5.23         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99         2.93         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        16.01        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        24.43       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        35.41       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  CHD1 MUTATED CHD1 WILD-TYPE 
          0.07           0.00 
  CHD1 MUTATED CHD1 WILD-TYPE 
         58.39         140.38 
  CHD1 MUTATED CHD1 WILD-TYPE 
        21.140         20.155 
[1] "0.1 - 58.4 (21.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.3"
D994V2, 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       24       103         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        18         10         38         30       33        13
                vv
clus             STAGE IVB
  CHD1 MUTATED           0
  CHD1 WILD-TYPE         1
D994V3, multiclass
            clus
vv           CHD1 MUTATED CHD1 WILD-TYPE
  STAGE I               7             57
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             6            103
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            3             38
  STAGE IIIC            1             30
  STAGE IV              2             33
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CHD1 MUTATED     1   7  13   2
  CHD1 WILD-TYPE   8  61 235  39
D994V4, multiclass
    clus
vv   CHD1 MUTATED CHD1 WILD-TYPE
  T1            1              8
  T2            7             61
  T3           13            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
  CHD1 MUTATED    17   4   2
  CHD1 WILD-TYPE 203  76  64
D994V5, multiclass
    clus
vv   CHD1 MUTATED CHD1 WILD-TYPE
  N0           17            203
  N1            4             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"
D994V6, binary
                cls
clus               0   1
  CHD1 MUTATED    19   2
  CHD1 WILD-TYPE 264  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD1 MUTATED     19    2
  CHD1 WILD-TYPE  264   46
   clus
vv  CHD1 MUTATED CHD1 WILD-TYPE
  0           19            264
  1            2             46
[1] 2 2
[1] FALSE
D994V7, 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
D994V8, binary
                cls
clus               0   1
  CHD1 MUTATED    15   8
  CHD1 WILD-TYPE 302  40
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD1 MUTATED     15    8
  CHD1 WILD-TYPE  302   40
                               clus
vv                              CHD1 MUTATED CHD1 WILD-TYPE
  COLON ADENOCARCINOMA                    15            302
  COLON MUCINOUS ADENOCARCINOMA            8             40
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CHD1 MUTATED    13   0   1   3
  CHD1 WILD-TYPE 244   2  21  18
D994V9, multiclass
    clus
vv   CHD1 MUTATED CHD1 WILD-TYPE
  R0           13            244
  R1            0              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"
D994V10, 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
D994V11, 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(995) Variable = OR10G4 MUTATION ANALYSIS
D995V1, survival
                  sevent
clus2                0   1
  OR10G4 MUTATED     2   3
  OR10G4 WILD-TYPE 280  70
  OR10G4 MUTATED OR10G4 WILD-TYPE 
               5              350 
  OR10G4 MUTATED OR10G4 WILD-TYPE 
               3               70 
$`OR10G4 MUTATED`
TCGA-A6-6653 TCGA-AA-3715 TCGA-AA-A00N TCGA-AZ-6599 TCGA-CM-5348 
       24.39        19.04         4.01         6.77        22.98 

$`OR10G4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41        49.41        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  OR10G4 MUTATED OR10G4 WILD-TYPE 
            4.01             0.00 
  OR10G4 MUTATED OR10G4 WILD-TYPE 
           24.39           140.38 
  OR10G4 MUTATED OR10G4 WILD-TYPE 
          19.040           20.235 
[1] "4.0 - 24.4 (19.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "4.7"
D995V2, 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       24       109         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR10G4 MUTATED           0          0          1          0        0
  OR10G4 WILD-TYPE        19         10         40         31       35
                  vv
clus               STAGE IVA STAGE IVB
  OR10G4 MUTATED           0         0
  OR10G4 WILD-TYPE        13         1
D995V3, multiclass
            clus
vv           OR10G4 MUTATED OR10G4 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               0              109
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  OR10G4 MUTATED     0   2   2   1
  OR10G4 WILD-TYPE   9  66 246  40
D995V4, multiclass
    clus
vv   OR10G4 MUTATED OR10G4 WILD-TYPE
  T1              0                9
  T2              2               66
  T3              2              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
  OR10G4 MUTATED     4   1   0
  OR10G4 WILD-TYPE 216  79  66
D995V5, multiclass
    clus
vv   OR10G4 MUTATED OR10G4 WILD-TYPE
  N0              4              216
  N1              1               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"
D995V6, binary
                  cls
clus                 0   1
  OR10G4 MUTATED     4   0
  OR10G4 WILD-TYPE 279  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR10G4 MUTATED      4    0
  OR10G4 WILD-TYPE  279   48
   clus
vv  OR10G4 MUTATED OR10G4 WILD-TYPE
  0              4              279
  1              0               48
[1] 2 2
[1] FALSE
D995V7, 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
D995V8, binary
                  cls
clus                 0   1
  OR10G4 MUTATED     4   1
  OR10G4 WILD-TYPE 313  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR10G4 MUTATED      4    1
  OR10G4 WILD-TYPE  313   47
                               clus
vv                              OR10G4 MUTATED OR10G4 WILD-TYPE
  COLON ADENOCARCINOMA                       4              313
  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 254   2  22  21
D995V9, multiclass
    clus
vv   OR10G4 MUTATED OR10G4 WILD-TYPE
  R0              3              254
  R1              0                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"
D995V10, 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
D995V11, 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(996) Variable = ACAT2 MUTATION ANALYSIS
D996V1, survival
                 sevent
clus2               0   1
  ACAT2 MUTATED     5   3
  ACAT2 WILD-TYPE 277  70
  ACAT2 MUTATED ACAT2 WILD-TYPE 
              8             347 
  ACAT2 MUTATED ACAT2 WILD-TYPE 
              3              70 
$`ACAT2 MUTATED`
TCGA-AA-3715 TCGA-AA-A010 TCGA-AD-6889 TCGA-CA-6718 TCGA-CK-4948 TCGA-CK-6747 
       19.04        34.98        56.55         0.10       102.44         2.93 
TCGA-CM-5862 TCGA-D5-6537 
        5.03         4.80 

$`ACAT2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 
        0.26         0.33         1.35        17.56        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 
       49.08        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-5863 
       22.03        22.98        30.08        16.01        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  ACAT2 MUTATED ACAT2 WILD-TYPE 
            0.1             0.0 
  ACAT2 MUTATED ACAT2 WILD-TYPE 
         102.44          140.38 
  ACAT2 MUTATED ACAT2 WILD-TYPE 
         12.035          20.280 
[1] "0.1 - 102.4 (12.0)" "0.0 - 140.4 (20.3)"
[1] "hr=" "1.7"
D996V2, 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       24       106         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ACAT2 MUTATED           0          1          1          0        0         1
  ACAT2 WILD-TYPE        19          9         40         31       35        12
                 vv
clus              STAGE IVB
  ACAT2 MUTATED           0
  ACAT2 WILD-TYPE         1
D996V3, multiclass
            clus
vv           ACAT2 MUTATED ACAT2 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              3             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  68 241  40
D996V4, multiclass
    clus
vv   ACAT2 MUTATED ACAT2 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             7             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
  ACAT2 MUTATED     5   3   0
  ACAT2 WILD-TYPE 215  77  66
D996V5, multiclass
    clus
vv   ACAT2 MUTATED ACAT2 WILD-TYPE
  N0             5             215
  N1             3              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"
D996V6, binary
                 cls
clus                0   1
  ACAT2 MUTATED     5   1
  ACAT2 WILD-TYPE 278  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACAT2 MUTATED      5    1
  ACAT2 WILD-TYPE  278   47
   clus
vv  ACAT2 MUTATED ACAT2 WILD-TYPE
  0             5             278
  1             1              47
[1] 2 2
[1] FALSE
D996V7, 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
D996V8, binary
                 cls
clus                0   1
  ACAT2 MUTATED     8   0
  ACAT2 WILD-TYPE 309  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACAT2 MUTATED      8    0
  ACAT2 WILD-TYPE  309   48
                               clus
vv                              ACAT2 MUTATED ACAT2 WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ACAT2 MUTATED     5   0   0   2
  ACAT2 WILD-TYPE 252   2  22  19
D996V9, multiclass
    clus
vv   ACAT2 MUTATED ACAT2 WILD-TYPE
  R0             5             252
  R1             0               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"
D996V10, 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
D996V11, 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(997) Variable = MTF1 MUTATION ANALYSIS
D997V1, survival
                sevent
clus2              0   1
  MTF1 MUTATED     8   0
  MTF1 WILD-TYPE 274  73
  MTF1 MUTATED MTF1 WILD-TYPE 
             8            347 
  MTF1 MUTATED MTF1 WILD-TYPE 
             0             73 
$`MTF1 MUTATED`
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-A00J TCGA-AD-6895 TCGA-CA-6717 TCGA-CM-5861 
       24.00        33.01        18.05         0.72         0.33        15.02 
TCGA-D5-6536 TCGA-D5-6541 
       17.85        15.58 

$`MTF1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       31.00         2.01        12.99        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12         4.80        17.13        12.49        16.14 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  MTF1 MUTATED MTF1 WILD-TYPE 
          0.33           0.00 
  MTF1 MUTATED MTF1 WILD-TYPE 
         33.01         140.38 
  MTF1 MUTATED MTF1 WILD-TYPE 
        16.715         20.980 
[1] "0.3 - 33.0 (16.7)"  "0.0 - 140.4 (21.0)"
[1] "hr="     "9200000"
D997V2, 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       25       104         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MTF1 MUTATED           0          0          1          0        0         1
  MTF1 WILD-TYPE        19         10         40         31       35        12
                vv
clus             STAGE IVB
  MTF1 MUTATED           0
  MTF1 WILD-TYPE         1
D997V3, multiclass
            clus
vv           MTF1 MUTATED MTF1 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             5            104
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  68 242  38
D997V4, multiclass
    clus
vv   MTF1 MUTATED MTF1 WILD-TYPE
  T1            0              9
  T2            0             68
  T3            6            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
  MTF1 MUTATED     6   3   0
  MTF1 WILD-TYPE 214  77  66
D997V5, multiclass
    clus
vv   MTF1 MUTATED MTF1 WILD-TYPE
  N0            6            214
  N1            3             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"
D997V6, binary
                cls
clus               0   1
  MTF1 MUTATED     7   1
  MTF1 WILD-TYPE 276  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTF1 MUTATED      7    1
  MTF1 WILD-TYPE  276   47
   clus
vv  MTF1 MUTATED MTF1 WILD-TYPE
  0            7            276
  1            1             47
[1] 2 2
[1] FALSE
D997V7, 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
D997V8, binary
                cls
clus               0   1
  MTF1 MUTATED     6   3
  MTF1 WILD-TYPE 311  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTF1 MUTATED      6    3
  MTF1 WILD-TYPE  311   45
                               clus
vv                              MTF1 MUTATED MTF1 WILD-TYPE
  COLON ADENOCARCINOMA                     6            311
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MTF1 MUTATED     7   0   0   1
  MTF1 WILD-TYPE 250   2  22  20
D997V9, multiclass
    clus
vv   MTF1 MUTATED MTF1 WILD-TYPE
  R0            7            250
  R1            0              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"
D997V10, 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
D997V11, 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(998) Variable = HDAC5 MUTATION ANALYSIS
D998V1, survival
                 sevent
clus2               0   1
  HDAC5 MUTATED     6   5
  HDAC5 WILD-TYPE 276  68
  HDAC5 MUTATED HDAC5 WILD-TYPE 
             11             344 
  HDAC5 MUTATED HDAC5 WILD-TYPE 
              5              68 
$`HDAC5 MUTATED`
TCGA-AA-3492 TCGA-AA-A01R TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CK-5916 
        3.02        35.01        62.79        49.41       100.01        21.14 
TCGA-CM-5860 TCGA-D5-6930 TCGA-F4-6703 TCGA-F4-6856 TCGA-G4-6315 
       16.01         1.51        35.87        19.43        36.72 

$`HDAC5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
        5.13        83.80        22.36        61.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32        21.99         2.93         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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45         6.18         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 
       33.67        13.25         0.53        35.41       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  HDAC5 MUTATED HDAC5 WILD-TYPE 
           1.51            0.00 
  HDAC5 MUTATED HDAC5 WILD-TYPE 
         100.01          140.38 
  HDAC5 MUTATED HDAC5 WILD-TYPE 
          35.01           20.07 
[1] "1.5 - 100.0 (35.0)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.7"
D998V2, 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       21       106         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        18         10         41         31       34        13
                 vv
clus              STAGE IVB
  HDAC5 MUTATED           0
  HDAC5 WILD-TYPE         1
D998V3, multiclass
            clus
vv           HDAC5 MUTATED HDAC5 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               4              21
  STAGE IIA              3             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HDAC5 MUTATED     1   1   9   0
  HDAC5 WILD-TYPE   8  67 239  41
D998V4, multiclass
    clus
vv   HDAC5 MUTATED HDAC5 WILD-TYPE
  T1             1               8
  T2             1              67
  T3             9             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
  HDAC5 MUTATED     9   1   1
  HDAC5 WILD-TYPE 211  79  65
D998V5, multiclass
    clus
vv   HDAC5 MUTATED HDAC5 WILD-TYPE
  N0             9             211
  N1             1              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"
D998V6, binary
                 cls
clus                0   1
  HDAC5 MUTATED     8   1
  HDAC5 WILD-TYPE 275  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HDAC5 MUTATED      8    1
  HDAC5 WILD-TYPE  275   47
   clus
vv  HDAC5 MUTATED HDAC5 WILD-TYPE
  0             8             275
  1             1              47
[1] 2 2
[1] FALSE
D998V7, 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
D998V8, binary
                 cls
clus                0   1
  HDAC5 MUTATED     8   3
  HDAC5 WILD-TYPE 309  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HDAC5 MUTATED      8    3
  HDAC5 WILD-TYPE  309   45
                               clus
vv                              HDAC5 MUTATED HDAC5 WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  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 250   2  22  20
D998V9, multiclass
    clus
vv   HDAC5 MUTATED HDAC5 WILD-TYPE
  R0             7             250
  R1             0               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"
D998V10, 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
D998V11, 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(999) Variable = ZNF443 MUTATION ANALYSIS
D999V1, survival
                  sevent
clus2                0   1
  ZNF443 MUTATED     6   2
  ZNF443 WILD-TYPE 276  71
  ZNF443 MUTATED ZNF443 WILD-TYPE 
               8              347 
  ZNF443 MUTATED ZNF443 WILD-TYPE 
               2               71 
$`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         0.33 
TCGA-CM-6674 TCGA-CM-6675 
       12.95        13.05 

$`ZNF443 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
        1.02        17.98        15.95        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       27.02        19.07        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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-6676 TCGA-CM-6677 TCGA-CM-6678 
       15.02        14.04        11.01        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  ZNF443 MUTATED ZNF443 WILD-TYPE 
            0.33             0.00 
  ZNF443 MUTATED ZNF443 WILD-TYPE 
           38.99           140.38 
  ZNF443 MUTATED ZNF443 WILD-TYPE 
           13.00            20.28 
[1] "0.3 - 39.0 (13.0)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.9"
D999V2, 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       25       106         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF443 MUTATED           0          0          0          0        1
  ZNF443 WILD-TYPE        19         10         41         31       34
                  vv
clus               STAGE IVA STAGE IVB
  ZNF443 MUTATED           0         1
  ZNF443 WILD-TYPE        13         0
D999V3, multiclass
            clus
vv           ZNF443 MUTATED ZNF443 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               3              106
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  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  68 243  39
D999V4, multiclass
    clus
vv   ZNF443 MUTATED ZNF443 WILD-TYPE
  T1              1                8
  T2              0               68
  T3              5              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
  ZNF443 MUTATED     6   0   2
  ZNF443 WILD-TYPE 214  80  64
D999V5, multiclass
    clus
vv   ZNF443 MUTATED ZNF443 WILD-TYPE
  N0              6              214
  N1              0               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"
D999V6, binary
                  cls
clus                 0   1
  ZNF443 MUTATED     6   2
  ZNF443 WILD-TYPE 277  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF443 MUTATED      6    2
  ZNF443 WILD-TYPE  277   46
   clus
vv  ZNF443 MUTATED ZNF443 WILD-TYPE
  0              6              277
  1              2               46
[1] 2 2
[1] FALSE
D999V7, 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
D999V8, binary
                  cls
clus                 0   1
  ZNF443 MUTATED     4   4
  ZNF443 WILD-TYPE 313  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF443 MUTATED      4    4
  ZNF443 WILD-TYPE  313   44
                               clus
vv                              ZNF443 MUTATED ZNF443 WILD-TYPE
  COLON ADENOCARCINOMA                       4              313
  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 251   2  21  20
D999V9, multiclass
    clus
vv   ZNF443 MUTATED ZNF443 WILD-TYPE
  R0              6              251
  R1              0                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"
D999V10, 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
D999V11, 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(1000) Variable = DCAF12L2 MUTATION ANALYSIS
D1000V1, survival
                    sevent
clus2                  0   1
  DCAF12L2 MUTATED    13   3
  DCAF12L2 WILD-TYPE 269  70
  DCAF12L2 MUTATED DCAF12L2 WILD-TYPE 
                16                339 
  DCAF12L2 MUTATED DCAF12L2 WILD-TYPE 
                 3                 70 
$`DCAF12L2 MUTATED`
TCGA-A6-5665 TCGA-A6-6654 TCGA-AA-3660 TCGA-AA-3713 TCGA-AA-3821 TCGA-AA-3977 
       22.06        23.87        78.08        19.04         1.02        25.02 
TCGA-AA-A010 TCGA-AD-6901 TCGA-AU-6004 TCGA-CK-5916 TCGA-CM-5860 TCGA-CM-5868 
       34.98        22.42        27.09        21.14        16.01        17.03 
TCGA-CM-6171 TCGA-F4-6460 TCGA-F4-6570 TCGA-G4-6307 
       14.04        13.38         6.18        55.04 

$`DCAF12L2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
        0.99        25.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 
        4.21        56.55         0.79         0.72         5.79        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
       40.34        15.62        49.08        51.32        21.99         2.93 
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-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-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        53.62        44.68        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  DCAF12L2 MUTATED DCAF12L2 WILD-TYPE 
              1.02               0.00 
  DCAF12L2 MUTATED DCAF12L2 WILD-TYPE 
             78.08             140.38 
  DCAF12L2 MUTATED DCAF12L2 WILD-TYPE 
             21.60              20.12 
[1] "1.0 - 78.1 (21.6)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.1"
D1000V2, 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       24       106         6         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DCAF12L2 MUTATED           0          0          3          0        1
  DCAF12L2 WILD-TYPE        19         10         38         31       34
                    vv
clus                 STAGE IVA STAGE IVB
  DCAF12L2 MUTATED           1         0
  DCAF12L2 WILD-TYPE        12         1
D1000V3, multiclass
            clus
vv           DCAF12L2 MUTATED DCAF12L2 WILD-TYPE
  STAGE I                   4                 60
  STAGE IA                  0                  1
  STAGE II                  1                 24
  STAGE IIA                 3                106
  STAGE IIB                 2                  6
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                0                 10
  STAGE IIIB                3                 38
  STAGE IIIC                0                 31
  STAGE IV                  1                 34
  STAGE IVA                 1                 12
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of 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  64 239  38
D1000V4, multiclass
    clus
vv   DCAF12L2 MUTATED DCAF12L2 WILD-TYPE
  T1                1                  8
  T2                4                 64
  T3                9                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
  DCAF12L2 MUTATED    13   4   0
  DCAF12L2 WILD-TYPE 207  76  66
D1000V5, multiclass
    clus
vv   DCAF12L2 MUTATED DCAF12L2 WILD-TYPE
  N0               13                207
  N1                4                 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"
D1000V6, binary
                    cls
clus                   0   1
  DCAF12L2 MUTATED    12   2
  DCAF12L2 WILD-TYPE 271  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  DCAF12L2 MUTATED     12    2
  DCAF12L2 WILD-TYPE  271   46
   clus
vv  DCAF12L2 MUTATED DCAF12L2 WILD-TYPE
  0               12                271
  1                2                 46
[1] 2 2
[1] FALSE
D1000V7, 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
D1000V8, binary
                    cls
clus                   0   1
  DCAF12L2 MUTATED    16   1
  DCAF12L2 WILD-TYPE 301  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  DCAF12L2 MUTATED     16    1
  DCAF12L2 WILD-TYPE  301   47
                               clus
vv                              DCAF12L2 MUTATED DCAF12L2 WILD-TYPE
  COLON ADENOCARCINOMA                        16                301
  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 246   2  21  19
D1000V9, multiclass
    clus
vv   DCAF12L2 MUTATED DCAF12L2 WILD-TYPE
  R0               11                246
  R1                0                  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"
D1000V10, 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
D1000V11, 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(1001) Variable = CD244 MUTATION ANALYSIS
D1001V1, survival
                 sevent
clus2               0   1
  CD244 MUTATED     6   1
  CD244 WILD-TYPE 276  72
  CD244 MUTATED CD244 WILD-TYPE 
              7             348 
  CD244 MUTATED CD244 WILD-TYPE 
              1              72 
$`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        13.38 
TCGA-G4-6306 
       44.68 

$`CD244 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  CD244 MUTATED CD244 WILD-TYPE 
           4.01            0.00 
  CD244 MUTATED CD244 WILD-TYPE 
          63.98          140.38 
  CD244 MUTATED CD244 WILD-TYPE 
          34.98           20.07 
[1] "4.0 - 64.0 (35.0)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "2"  
D1001V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CD244 MUTATED         0        0        2         1         2         0
  CD244 WILD-TYPE      64        1       23       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        19         10         39         31       35        13
                 vv
clus              STAGE IVB
  CD244 MUTATED           0
  CD244 WILD-TYPE         1
D1001V3, multiclass
            clus
vv           CD244 MUTATED CD244 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              1             108
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CD244 MUTATED     0   1   4   2
  CD244 WILD-TYPE   9  67 244  39
D1001V4, multiclass
    clus
vv   CD244 MUTATED CD244 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             4             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
  CD244 MUTATED     5   2   0
  CD244 WILD-TYPE 215  78  66
D1001V5, multiclass
    clus
vv   CD244 MUTATED CD244 WILD-TYPE
  N0             5             215
  N1             2              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"
D1001V6, binary
                 cls
clus                0   1
  CD244 MUTATED     7   0
  CD244 WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD244 MUTATED      7    0
  CD244 WILD-TYPE  276   48
   clus
vv  CD244 MUTATED CD244 WILD-TYPE
  0             7             276
  1             0              48
[1] 2 2
[1] FALSE
D1001V7, 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
D1001V8, binary
                 cls
clus                0   1
  CD244 MUTATED     6   1
  CD244 WILD-TYPE 311  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD244 MUTATED      6    1
  CD244 WILD-TYPE  311   47
                               clus
vv                              CD244 MUTATED CD244 WILD-TYPE
  COLON ADENOCARCINOMA                      6             311
  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 250   2  22  21
D1001V9, multiclass
    clus
vv   CD244 MUTATED CD244 WILD-TYPE
  R0             7             250
  R1             0               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"
D1001V10, 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
D1001V11, 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(1002) Variable = LIMCH1 MUTATION ANALYSIS
D1002V1, survival
                  sevent
clus2                0   1
  LIMCH1 MUTATED    13   0
  LIMCH1 WILD-TYPE 269  73
  LIMCH1 MUTATED LIMCH1 WILD-TYPE 
              13              342 
  LIMCH1 MUTATED LIMCH1 WILD-TYPE 
               0               73 
$`LIMCH1 MUTATED`
TCGA-A6-3808 TCGA-A6-5661 TCGA-A6-6780 TCGA-AA-3510 TCGA-AA-3534 TCGA-AA-3672 
       33.34        33.53        20.12        63.98        29.00         0.92 
TCGA-AA-3815 TCGA-AA-A00A TCGA-AA-A01Q TCGA-AZ-4315 TCGA-CA-6717 TCGA-CM-4743 
       33.04        38.04         1.02        58.39         0.33        23.05 
TCGA-D5-5539 
       19.59 

$`LIMCH1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 
       24.16        21.76        24.69        24.39        23.87        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       34.03        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  LIMCH1 MUTATED LIMCH1 WILD-TYPE 
            0.33             0.00 
  LIMCH1 MUTATED LIMCH1 WILD-TYPE 
           63.98           140.38 
  LIMCH1 MUTATED LIMCH1 WILD-TYPE 
          29.000           20.005 
[1] "0.3 - 64.0 (29.0)"  "0.0 - 140.4 (20.0)"
[1] "hr="     "2.6e+07"
D1002V2, 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       23       100         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LIMCH1 MUTATED           1          1          0          0        0
  LIMCH1 WILD-TYPE        18          9         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  LIMCH1 MUTATED           0         0
  LIMCH1 WILD-TYPE        13         1
D1002V3, multiclass
            clus
vv           LIMCH1 MUTATED LIMCH1 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               9              100
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              1                9
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  LIMCH1 MUTATED     0   0  13   0
  LIMCH1 WILD-TYPE   9  68 235  41
D1002V4, multiclass
    clus
vv   LIMCH1 MUTATED LIMCH1 WILD-TYPE
  T1              0                9
  T2              0               68
  T3             13              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
  LIMCH1 MUTATED    11   2   0
  LIMCH1 WILD-TYPE 209  78  66
D1002V5, multiclass
    clus
vv   LIMCH1 MUTATED LIMCH1 WILD-TYPE
  N0             11              209
  N1              2               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"
D1002V6, binary
                  cls
clus                 0   1
  LIMCH1 MUTATED    12   0
  LIMCH1 WILD-TYPE 271  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LIMCH1 MUTATED     12    0
  LIMCH1 WILD-TYPE  271   48
   clus
vv  LIMCH1 MUTATED LIMCH1 WILD-TYPE
  0             12              271
  1              0               48
[1] 2 2
[1] FALSE
D1002V7, 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
D1002V8, binary
                  cls
clus                 0   1
  LIMCH1 MUTATED    10   3
  LIMCH1 WILD-TYPE 307  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LIMCH1 MUTATED     10    3
  LIMCH1 WILD-TYPE  307   45
                               clus
vv                              LIMCH1 MUTATED LIMCH1 WILD-TYPE
  COLON ADENOCARCINOMA                      10              307
  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 246   2  22  20
D1002V9, multiclass
    clus
vv   LIMCH1 MUTATED LIMCH1 WILD-TYPE
  R0             11              246
  R1              0                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"
D1002V10, 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
D1002V11, 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(1003) Variable = ESCO2 MUTATION ANALYSIS
D1003V1, survival
                 sevent
clus2               0   1
  ESCO2 MUTATED     8   2
  ESCO2 WILD-TYPE 274  71
  ESCO2 MUTATED ESCO2 WILD-TYPE 
             10             345 
  ESCO2 MUTATED ESCO2 WILD-TYPE 
              2              71 
$`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 
        0.33         0.10        23.05        30.08 

$`ESCO2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07         0.26         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14         2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  ESCO2 MUTATED ESCO2 WILD-TYPE 
            0.1             0.0 
  ESCO2 MUTATED ESCO2 WILD-TYPE 
          58.39          140.38 
  ESCO2 MUTATED ESCO2 WILD-TYPE 
          15.75           20.19 
[1] "0.1 - 58.4 (15.8)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.3"
D1003V2, 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       24       103         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        18         10         41         31       35        13
                 vv
clus              STAGE IVB
  ESCO2 MUTATED           0
  ESCO2 WILD-TYPE         1
D1003V3, multiclass
            clus
vv           ESCO2 MUTATED ESCO2 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              6             103
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ESCO2 MUTATED     0   0   8   2
  ESCO2 WILD-TYPE   9  68 240  39
D1003V4, multiclass
    clus
vv   ESCO2 MUTATED ESCO2 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             8             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
  ESCO2 MUTATED     9   0   1
  ESCO2 WILD-TYPE 211  80  65
D1003V5, multiclass
    clus
vv   ESCO2 MUTATED ESCO2 WILD-TYPE
  N0             9             211
  N1             0              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"
D1003V6, binary
                 cls
clus                0   1
  ESCO2 MUTATED     9   0
  ESCO2 WILD-TYPE 274  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESCO2 MUTATED      9    0
  ESCO2 WILD-TYPE  274   48
   clus
vv  ESCO2 MUTATED ESCO2 WILD-TYPE
  0             9             274
  1             0              48
[1] 2 2
[1] FALSE
D1003V7, 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
D1003V8, binary
                 cls
clus                0   1
  ESCO2 MUTATED     8   2
  ESCO2 WILD-TYPE 309  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESCO2 MUTATED      8    2
  ESCO2 WILD-TYPE  309   46
                               clus
vv                              ESCO2 MUTATED ESCO2 WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  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 249   2  22  19
D1003V9, multiclass
    clus
vv   ESCO2 MUTATED ESCO2 WILD-TYPE
  R0             8             249
  R1             0               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"
D1003V10, 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
D1003V11, 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(1004) Variable = ABCD4 MUTATION ANALYSIS
D1004V1, survival
                 sevent
clus2               0   1
  ABCD4 MUTATED     8   1
  ABCD4 WILD-TYPE 274  72
  ABCD4 MUTATED ABCD4 WILD-TYPE 
              9             346 
  ABCD4 MUTATED ABCD4 WILD-TYPE 
              1              72 
$`ABCD4 MUTATED`
TCGA-AA-3672 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-A00E TCGA-CK-4950 TCGA-D5-6930 
        0.92        53.00        31.00        30.02        40.34         1.51 
TCGA-F4-6570 TCGA-G4-6588 TCGA-G4-6628 
        6.18        26.17        52.80 

$`ABCD4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
        6.05         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        18.05         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 
        0.33         0.10         1.35        17.56       102.44        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-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        13.38        13.45        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       13.78        35.80        91.79        46.75 

  ABCD4 MUTATED ABCD4 WILD-TYPE 
           0.92            0.00 
  ABCD4 MUTATED ABCD4 WILD-TYPE 
          53.00          140.38 
  ABCD4 MUTATED ABCD4 WILD-TYPE 
          30.02           20.07 
[1] "0.9 - 53.0 (30.0)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "2"  
D1004V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ABCD4 MUTATED         2        0        1         4         0         0
  ABCD4 WILD-TYPE      62        1       24       105         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ABCD4 MUTATED           1          1          0          0        0         0
  ABCD4 WILD-TYPE        18          9         41         31       35        13
                 vv
clus              STAGE IVB
  ABCD4 MUTATED           0
  ABCD4 WILD-TYPE         1
D1004V3, multiclass
            clus
vv           ABCD4 MUTATED ABCD4 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              4             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             1               9
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ABCD4 MUTATED     1   1   7   0
  ABCD4 WILD-TYPE   8  67 241  41
D1004V4, multiclass
    clus
vv   ABCD4 MUTATED ABCD4 WILD-TYPE
  T1             1               8
  T2             1              67
  T3             7             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     7   2   0
  ABCD4 WILD-TYPE 213  78  66
D1004V5, multiclass
    clus
vv   ABCD4 MUTATED ABCD4 WILD-TYPE
  N0             7             213
  N1             2              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"
D1004V6, binary
                 cls
clus                0   1
  ABCD4 MUTATED     9   0
  ABCD4 WILD-TYPE 274  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCD4 MUTATED      9    0
  ABCD4 WILD-TYPE  274   48
   clus
vv  ABCD4 MUTATED ABCD4 WILD-TYPE
  0             9             274
  1             0              48
[1] 2 2
[1] FALSE
D1004V7, binary
                 cls
clus                0   1
  ABCD4 MUTATED     5   4
  ABCD4 WILD-TYPE 165 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCD4 MUTATED      5    4
  ABCD4 WILD-TYPE  165  193
        clus
vv       ABCD4 MUTATED ABCD4 WILD-TYPE
  FEMALE             5             165
  MALE               4             193
[1] 2 2
[1] FALSE
D1004V8, binary
                 cls
clus                0   1
  ABCD4 MUTATED     7   2
  ABCD4 WILD-TYPE 310  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCD4 MUTATED      7    2
  ABCD4 WILD-TYPE  310   46
                               clus
vv                              ABCD4 MUTATED ABCD4 WILD-TYPE
  COLON ADENOCARCINOMA                      7             310
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ABCD4 MUTATED     8   1   0   0
  ABCD4 WILD-TYPE 249   1  22  21
D1004V9, multiclass
    clus
vv   ABCD4 MUTATED ABCD4 WILD-TYPE
  R0             8             249
  R1             1               1
  R2             0              22
  RX             0              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1004V10, 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
D1004V11, 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(1005) Variable = EPHA7 MUTATION ANALYSIS
D1005V1, survival
                 sevent
clus2               0   1
  EPHA7 MUTATED    25   9
  EPHA7 WILD-TYPE 257  64
  EPHA7 MUTATED EPHA7 WILD-TYPE 
             34             321 
  EPHA7 MUTATED EPHA7 WILD-TYPE 
              9              64 
$`EPHA7 MUTATED`
TCGA-A6-3809 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3555 TCGA-AA-3663 TCGA-AA-3710 
       32.75         3.02         1.02        29.95         6.97        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3815 TCGA-AA-3858 TCGA-AA-3966 TCGA-AA-A00N 
       19.04        19.04        33.04        31.07         2.01         4.01 
TCGA-AA-A010 TCGA-AD-5900 TCGA-AD-6901 TCGA-AD-6964 TCGA-AY-6196 TCGA-AZ-4315 
       34.98         0.07        22.42        10.88         0.20        58.39 
TCGA-AZ-6605 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-6751 TCGA-CM-5349 
        5.23         0.33         0.10        17.56       124.27        30.08 
TCGA-CM-6162 TCGA-CM-6171 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6930 
       12.00        14.04        17.85        12.49        15.58         1.51 
TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-DM-A28G TCGA-G4-6321 
       49.91         7.50        60.79        22.09 

$`EPHA7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3510 
       20.12        19.66        20.28         7.04        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.05        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3811 
       37.05        19.00        36.00         5.03        85.05        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 
       56.55         0.79         0.72         5.79        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        15.75        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 
        3.29         0.07         0.26         1.35       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
        4.80        17.13        16.14         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-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       35.97       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       45.11        36.72        36.00        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  EPHA7 MUTATED EPHA7 WILD-TYPE 
           0.07            0.00 
  EPHA7 MUTATED EPHA7 WILD-TYPE 
         124.27          140.38 
  EPHA7 MUTATED EPHA7 WILD-TYPE 
          16.57           21.01 
[1] "0.1 - 124.3 (16.6)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.6"
D1005V2, 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       21        96         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EPHA7 MUTATED           2          1          2          2        1         1
  EPHA7 WILD-TYPE        17          9         39         29       34        12
                 vv
clus              STAGE IVB
  EPHA7 MUTATED           0
  EPHA7 WILD-TYPE         1
D1005V3, multiclass
            clus
vv           EPHA7 MUTATED EPHA7 WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               4              21
  STAGE IIA             13              96
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             1               9
  STAGE IIIB             2              39
  STAGE IIIC             2              29
  STAGE IV               1              34
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  63 224  35
D1005V4, multiclass
    clus
vv   EPHA7 MUTATED EPHA7 WILD-TYPE
  T1             0               9
  T2             5              63
  T3            24             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
  EPHA7 MUTATED    27   4   4
  EPHA7 WILD-TYPE 193  76  62
D1005V5, multiclass
    clus
vv   EPHA7 MUTATED EPHA7 WILD-TYPE
  N0            27             193
  N1             4              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"
D1005V6, binary
                 cls
clus                0   1
  EPHA7 MUTATED    28   1
  EPHA7 WILD-TYPE 255  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA7 MUTATED     28    1
  EPHA7 WILD-TYPE  255   47
   clus
vv  EPHA7 MUTATED EPHA7 WILD-TYPE
  0            28             255
  1             1              47
[1] 2 2
[1] FALSE
D1005V7, 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
D1005V8, binary
                 cls
clus                0   1
  EPHA7 MUTATED    24  11
  EPHA7 WILD-TYPE 293  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA7 MUTATED     24   11
  EPHA7 WILD-TYPE  293   37
                               clus
vv                              EPHA7 MUTATED EPHA7 WILD-TYPE
  COLON ADENOCARCINOMA                     24             293
  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 234   2  21  17
D1005V9, multiclass
    clus
vv   EPHA7 MUTATED EPHA7 WILD-TYPE
  R0            23             234
  R1             0               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"
D1005V10, 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
D1005V11, 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(1006) Variable = CCDC3 MUTATION ANALYSIS
D1006V1, survival
                 sevent
clus2               0   1
  CCDC3 MUTATED     2   2
  CCDC3 WILD-TYPE 280  71
  CCDC3 MUTATED CCDC3 WILD-TYPE 
              4             351 
  CCDC3 MUTATED CCDC3 WILD-TYPE 
              2              71 
$`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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        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-6679 
       11.01        12.95        13.05        11.08        11.08        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  CCDC3 MUTATED CCDC3 WILD-TYPE 
            4.8             0.0 
  CCDC3 MUTATED CCDC3 WILD-TYPE 
          19.04          140.38 
  CCDC3 MUTATED CCDC3 WILD-TYPE 
           8.02           20.98 
[1] "4.8 - 19.0 (8.0)"   "0.0 - 140.4 (21.0)"
[1] "hr=" "5.5"
D1006V2, 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       25       109         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        19         10         40         31       34        11
                 vv
clus              STAGE IVB
  CCDC3 MUTATED           0
  CCDC3 WILD-TYPE         1
D1006V3, multiclass
            clus
vv           CCDC3 MUTATED CCDC3 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              0             109
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              2              11
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  68 245  40
D1006V4, multiclass
    clus
vv   CCDC3 MUTATED CCDC3 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             3             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
  CCDC3 MUTATED     1   3   0
  CCDC3 WILD-TYPE 219  77  66
D1006V5, multiclass
    clus
vv   CCDC3 MUTATED CCDC3 WILD-TYPE
  N0             1             219
  N1             3              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"
D1006V6, binary
                 cls
clus                0   1
  CCDC3 MUTATED     0   3
  CCDC3 WILD-TYPE 283  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCDC3 MUTATED      0    3
  CCDC3 WILD-TYPE  283   45
   clus
vv  CCDC3 MUTATED CCDC3 WILD-TYPE
  0             0             283
  1             3              45
[1] 2 2
[1] FALSE
D1006V7, 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
D1006V8, binary
                 cls
clus                0   1
  CCDC3 MUTATED     4   0
  CCDC3 WILD-TYPE 313  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCDC3 MUTATED      4    0
  CCDC3 WILD-TYPE  313   48
                               clus
vv                              CCDC3 MUTATED CCDC3 WILD-TYPE
  COLON ADENOCARCINOMA                      4             313
  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 254   2  21  21
D1006V9, multiclass
    clus
vv   CCDC3 MUTATED CCDC3 WILD-TYPE
  R0             3             254
  R1             0               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"
D1006V10, 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
D1006V11, 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(1007) Variable = TMEM131 MUTATION ANALYSIS
D1007V1, survival
                   sevent
clus2                 0   1
  TMEM131 MUTATED    16   4
  TMEM131 WILD-TYPE 266  69
  TMEM131 MUTATED TMEM131 WILD-TYPE 
               20               335 
  TMEM131 MUTATED TMEM131 WILD-TYPE 
                4                69 
$`TMEM131 MUTATED`
TCGA-A6-5666 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3672 TCGA-AA-3845 
       32.71         1.02        35.01        63.98         0.92         0.00 
TCGA-AA-3861 TCGA-AY-6197 TCGA-AZ-4682 TCGA-CA-6717 TCGA-CK-4952 TCGA-CM-4743 
       30.05        21.44        22.36         0.33        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        35.41 
TCGA-F4-6856 TCGA-G4-6309 
       19.43        51.75 

$`TMEM131 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3511 
       20.12        19.66        20.28         7.04         3.02         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       14.93        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        15.75         0.20        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13        83.80        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       43.27        17.85         4.80        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       10.26       119.70        24.43       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G 
      135.65       139.17         6.12        81.37        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      117.07        98.24         8.61        13.38        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
        0.53       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  TMEM131 MUTATED TMEM131 WILD-TYPE 
                0                 0 
  TMEM131 MUTATED TMEM131 WILD-TYPE 
           119.93            140.38 
  TMEM131 MUTATED TMEM131 WILD-TYPE 
            21.90             20.12 
[1] "0.0 - 119.9 (21.9)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.1"
D1007V2, 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       23       100         8         0
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM131 MUTATED           2          0          2          1        0
  TMEM131 WILD-TYPE        17         10         39         30       35
                   vv
clus                STAGE IVA STAGE IVB
  TMEM131 MUTATED           1         0
  TMEM131 WILD-TYPE        12         1
D1007V3, multiclass
            clus
vv           TMEM131 MUTATED TMEM131 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 2                23
  STAGE IIA                9               100
  STAGE IIB                0                 8
  STAGE IIC                1                 0
  STAGE III                2                17
  STAGE IIIA               0                10
  STAGE IIIB               2                39
  STAGE IIIC               1                30
  STAGE IV                 0                35
  STAGE IVA                1                12
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of 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  65 232  39
D1007V4, multiclass
    clus
vv   TMEM131 MUTATED TMEM131 WILD-TYPE
  T1               0                 9
  T2               3                65
  T3              16               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
  TMEM131 MUTATED    16   3   2
  TMEM131 WILD-TYPE 204  77  64
D1007V5, multiclass
    clus
vv   TMEM131 MUTATED TMEM131 WILD-TYPE
  N0              16               204
  N1               3                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"
D1007V6, binary
                   cls
clus                  0   1
  TMEM131 MUTATED    18   1
  TMEM131 WILD-TYPE 265  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM131 MUTATED     18    1
  TMEM131 WILD-TYPE  265   47
   clus
vv  TMEM131 MUTATED TMEM131 WILD-TYPE
  0              18               265
  1               1                47
[1] 2 2
[1] FALSE
D1007V7, 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
D1007V8, binary
                   cls
clus                  0   1
  TMEM131 MUTATED    16   5
  TMEM131 WILD-TYPE 301  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM131 MUTATED     16    5
  TMEM131 WILD-TYPE  301   43
                               clus
vv                              TMEM131 MUTATED TMEM131 WILD-TYPE
  COLON ADENOCARCINOMA                       16               301
  COLON MUCINOUS ADENOCARCINOMA               5                43
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  TMEM131 MUTATED    15   0   0   3
  TMEM131 WILD-TYPE 242   2  22  18
D1007V9, multiclass
    clus
vv   TMEM131 MUTATED TMEM131 WILD-TYPE
  R0              15               242
  R1               0                 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"
D1007V10, 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
D1007V11, 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(1008) Variable = TRIM54 MUTATION ANALYSIS
D1008V1, survival
                  sevent
clus2                0   1
  TRIM54 MUTATED     6   2
  TRIM54 WILD-TYPE 276  71
  TRIM54 MUTATED TRIM54 WILD-TYPE 
               8              347 
  TRIM54 MUTATED TRIM54 WILD-TYPE 
               2               71 
$`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         0.26        14.04         1.32 
TCGA-DM-A1D4 TCGA-F4-6460 
       92.75        13.38 

$`TRIM54 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13        83.80        22.36        62.79        61.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       12.00        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        13.51        11.51        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  TRIM54 MUTATED TRIM54 WILD-TYPE 
            0.26             0.00 
  TRIM54 MUTATED TRIM54 WILD-TYPE 
           92.75           140.38 
  TRIM54 MUTATED TRIM54 WILD-TYPE 
           22.03            20.19 
[1] "0.3 - 92.8 (22.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D1008V2, 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       24       105         8         0
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRIM54 MUTATED           0          0          2          0        0
  TRIM54 WILD-TYPE        19         10         39         31       35
                  vv
clus               STAGE IVA STAGE IVB
  TRIM54 MUTATED           0         0
  TRIM54 WILD-TYPE        13         1
D1008V3, multiclass
            clus
vv           TRIM54 MUTATED TRIM54 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               4              105
  STAGE IIB               0                8
  STAGE IIC               1                0
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TRIM54 MUTATED     1   0   6   2
  TRIM54 WILD-TYPE   8  68 242  39
D1008V4, multiclass
    clus
vv   TRIM54 MUTATED TRIM54 WILD-TYPE
  T1              1                8
  T2              0               68
  T3              6              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
  TRIM54 MUTATED     8   1   0
  TRIM54 WILD-TYPE 212  79  66
D1008V5, multiclass
    clus
vv   TRIM54 MUTATED TRIM54 WILD-TYPE
  N0              8              212
  N1              1               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"
D1008V6, binary
                  cls
clus                 0   1
  TRIM54 MUTATED     8   0
  TRIM54 WILD-TYPE 275  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM54 MUTATED      8    0
  TRIM54 WILD-TYPE  275   48
   clus
vv  TRIM54 MUTATED TRIM54 WILD-TYPE
  0              8              275
  1              0               48
[1] 2 2
[1] FALSE
D1008V7, 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
D1008V8, binary
                  cls
clus                 0   1
  TRIM54 MUTATED     9   0
  TRIM54 WILD-TYPE 308  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM54 MUTATED      9    0
  TRIM54 WILD-TYPE  308   48
                               clus
vv                              TRIM54 MUTATED TRIM54 WILD-TYPE
  COLON ADENOCARCINOMA                       9              308
  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 252   2  22  20
D1008V9, multiclass
    clus
vv   TRIM54 MUTATED TRIM54 WILD-TYPE
  R0              5              252
  R1              0                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"
D1008V10, 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
D1008V11, 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(1009) Variable = NAP1L1 MUTATION ANALYSIS
D1009V1, survival
                  sevent
clus2                0   1
  NAP1L1 MUTATED     6   1
  NAP1L1 WILD-TYPE 276  72
  NAP1L1 MUTATED NAP1L1 WILD-TYPE 
               7              348 
  NAP1L1 MUTATED NAP1L1 WILD-TYPE 
               1               72 
$`NAP1L1 MUTATED`
TCGA-A6-4105 TCGA-A6-5666 TCGA-AA-3977 TCGA-AD-6890 TCGA-AZ-4315 TCGA-CA-6717 
       14.53        32.71        25.02         0.79        58.39         0.33 
TCGA-DM-A1HB 
      135.65 

$`NAP1L1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  NAP1L1 MUTATED NAP1L1 WILD-TYPE 
            0.33             0.00 
  NAP1L1 MUTATED NAP1L1 WILD-TYPE 
          135.65           140.38 
  NAP1L1 MUTATED NAP1L1 WILD-TYPE 
          25.020           20.155 
[1] "0.3 - 135.7 (25.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.9"
D1009V2, 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       25       106         8         0
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NAP1L1 MUTATED           0          0          1          0        0
  NAP1L1 WILD-TYPE        19         10         40         31       35
                  vv
clus               STAGE IVA STAGE IVB
  NAP1L1 MUTATED           0         0
  NAP1L1 WILD-TYPE        13         1
D1009V3, multiclass
            clus
vv           NAP1L1 MUTATED NAP1L1 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               3              106
  STAGE IIB               0                8
  STAGE IIC               1                0
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  NAP1L1 MUTATED     1   1   4   1
  NAP1L1 WILD-TYPE   8  67 244  40
D1009V4, multiclass
    clus
vv   NAP1L1 MUTATED NAP1L1 WILD-TYPE
  T1              1                8
  T2              1               67
  T3              4              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
  NAP1L1 MUTATED     6   1   0
  NAP1L1 WILD-TYPE 214  79  66
D1009V5, multiclass
    clus
vv   NAP1L1 MUTATED NAP1L1 WILD-TYPE
  N0              6              214
  N1              1               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"
D1009V6, binary
                  cls
clus                 0   1
  NAP1L1 MUTATED     5   0
  NAP1L1 WILD-TYPE 278  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NAP1L1 MUTATED      5    0
  NAP1L1 WILD-TYPE  278   48
   clus
vv  NAP1L1 MUTATED NAP1L1 WILD-TYPE
  0              5              278
  1              0               48
[1] 2 2
[1] FALSE
D1009V7, 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
D1009V8, binary
                  cls
clus                 0   1
  NAP1L1 MUTATED     6   1
  NAP1L1 WILD-TYPE 311  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NAP1L1 MUTATED      6    1
  NAP1L1 WILD-TYPE  311   47
                               clus
vv                              NAP1L1 MUTATED NAP1L1 WILD-TYPE
  COLON ADENOCARCINOMA                       6              311
  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 256   2  22  20
D1009V9, multiclass
[1] "Remove cluster labels:" "NAP1L1 MUTATED"        
clus
  NAP1L1 MUTATED NAP1L1 WILD-TYPE 
               2              300 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-A6-2677       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-3496       TCGA-AA-3502 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-3510       TCGA-AA-3511       TCGA-AA-3514       TCGA-AA-3517 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-3518       TCGA-AA-3519       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-3526 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-3527       TCGA-AA-3529       TCGA-AA-3530       TCGA-AA-3531 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-3532       TCGA-AA-3534       TCGA-AA-3538       TCGA-AA-3542 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-3543       TCGA-AA-3544       TCGA-AA-3548       TCGA-AA-3549 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-3552       TCGA-AA-3553       TCGA-AA-3554       TCGA-AA-3555 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-3556       TCGA-AA-3558       TCGA-AA-3560       TCGA-AA-3561 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-3562       TCGA-AA-3655       TCGA-AA-3660       TCGA-AA-3662 
"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-3672       TCGA-AA-3673       TCGA-AA-3678       TCGA-AA-3679 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-3680       TCGA-AA-3681       TCGA-AA-3684       TCGA-AA-3685 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-3688       TCGA-AA-3692       TCGA-AA-3693       TCGA-AA-3695 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-3696       TCGA-AA-3697       TCGA-AA-3710       TCGA-AA-3712 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-3713       TCGA-AA-3715       TCGA-AA-3811       TCGA-AA-3812 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-3814       TCGA-AA-3815       TCGA-AA-3818       TCGA-AA-3819 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-3821       TCGA-AA-3831       TCGA-AA-3833       TCGA-AA-3837 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-3842       TCGA-AA-3844       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-3860       TCGA-AA-3861       TCGA-AA-3864       TCGA-AA-3866 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-3867       TCGA-AA-3869       TCGA-AA-3870       TCGA-AA-3872 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-3875       TCGA-AA-3877       TCGA-AA-3930       TCGA-AA-3939 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-3941       TCGA-AA-3947       TCGA-AA-3949       TCGA-AA-3950 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-3952       TCGA-AA-3955       TCGA-AA-3956       TCGA-AA-3968 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-3971       TCGA-AA-3972       TCGA-AA-3973       TCGA-AA-3975 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-3976       TCGA-AA-3979       TCGA-AA-3984       TCGA-AA-3986 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-3989       TCGA-AA-3994       TCGA-AA-A004       TCGA-AA-A00A 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-A00D       TCGA-AA-A00E       TCGA-AA-A00F       TCGA-AA-A00J 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-A00K       TCGA-AA-A00L       TCGA-AA-A00N       TCGA-AA-A00O 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-A00Q       TCGA-AA-A00R       TCGA-AA-A00U       TCGA-AA-A00W 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-A00Z       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-A024       TCGA-AA-A029       TCGA-AA-A02F 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-A02H       TCGA-AA-A02J       TCGA-AA-A02K       TCGA-AA-A02O 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AA-A02W       TCGA-AA-A02Y       TCGA-AA-A03F       TCGA-AA-A03J 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AD-5900       TCGA-AD-6548       TCGA-AD-6888       TCGA-AU-3779 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AU-6004       TCGA-AY-4070       TCGA-AY-4071       TCGA-AY-5543 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386       TCGA-AZ-4681 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-AZ-4682       TCGA-CA-5254       TCGA-CA-5255       TCGA-CA-5796 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-CA-5797       TCGA-CA-6715       TCGA-CA-6716       TCGA-CA-6718 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-CA-6719       TCGA-CK-4947       TCGA-CK-4948       TCGA-CK-4950 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-CK-4952       TCGA-CK-5912       TCGA-CK-5913       TCGA-CK-5914 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-CK-5915       TCGA-CK-5916       TCGA-CK-6746       TCGA-CK-6747 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-CK-6748       TCGA-CK-6751       TCGA-CM-4743       TCGA-CM-4744 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-CM-4746       TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-CM-5344       TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-CM-5861       TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-CM-5868       TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-CM-6164       TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-CM-6168       TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-CM-6172       TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-CM-6677       TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-D5-5537       TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-D5-5541       TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-D5-6534       TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-D5-6538       TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-D5-6898       TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-D5-6924       TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-D5-6929       TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-D5-7000       TCGA-F4-6459       TCGA-F4-6460       TCGA-F4-6569 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704       TCGA-F4-6805 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808       TCGA-F4-6809 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856       TCGA-G4-6293 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304       TCGA-G4-6306 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310       TCGA-G4-6315 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323       TCGA-G4-6586 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
      TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628 
"NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" "NAP1L1 WILD-TYPE" 
D1009V10, 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
D1009V11, 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(1010) Variable = PARP1 MUTATION ANALYSIS
D1010V1, survival
                 sevent
clus2               0   1
  PARP1 MUTATED    13   1
  PARP1 WILD-TYPE 269  72
  PARP1 MUTATED PARP1 WILD-TYPE 
             14             341 
  PARP1 MUTATED PARP1 WILD-TYPE 
              1              72 
$`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         0.33        17.56        15.02        11.08 
TCGA-DM-A1HB TCGA-F4-6704 
      135.65         1.55 

$`PARP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        33.53        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       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        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 
       14.01         0.92        41.00        39.98        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        15.75        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 
        0.07         0.26         0.10         1.35       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 
       13.38        13.45         6.18        35.87        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  PARP1 MUTATED PARP1 WILD-TYPE 
            0.2             0.0 
  PARP1 MUTATED PARP1 WILD-TYPE 
         135.65          140.38 
  PARP1 MUTATED PARP1 WILD-TYPE 
         20.055          20.190 
[1] "0.2 - 135.7 (20.1)" "0.0 - 140.4 (20.2)"
[1] "hr=" "3"  
D1010V2, 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       25       105         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PARP1 MUTATED           2          0          2          2        0         2
  PARP1 WILD-TYPE        17         10         39         29       35        11
                 vv
clus              STAGE IVB
  PARP1 MUTATED           0
  PARP1 WILD-TYPE         1
D1010V3, multiclass
            clus
vv           PARP1 MUTATED PARP1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              4             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             2              29
  STAGE IV               0              35
  STAGE IVA              2              11
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 237  39
D1010V4, multiclass
    clus
vv   PARP1 MUTATED PARP1 WILD-TYPE
  T1             0               9
  T2             1              67
  T3            11             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
  PARP1 MUTATED     6   3   5
  PARP1 WILD-TYPE 214  77  61
D1010V5, multiclass
    clus
vv   PARP1 MUTATED PARP1 WILD-TYPE
  N0             6             214
  N1             3              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"
D1010V6, binary
                 cls
clus                0   1
  PARP1 MUTATED    11   1
  PARP1 WILD-TYPE 272  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PARP1 MUTATED     11    1
  PARP1 WILD-TYPE  272   47
   clus
vv  PARP1 MUTATED PARP1 WILD-TYPE
  0            11             272
  1             1              47
[1] 2 2
[1] FALSE
D1010V7, 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
D1010V8, binary
                 cls
clus                0   1
  PARP1 MUTATED     8   6
  PARP1 WILD-TYPE 309  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PARP1 MUTATED      8    6
  PARP1 WILD-TYPE  309   42
                               clus
vv                              PARP1 MUTATED PARP1 WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  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 247   2  22  19
D1010V9, multiclass
    clus
vv   PARP1 MUTATED PARP1 WILD-TYPE
  R0            10             247
  R1             0               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"
D1010V10, 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
D1010V11, 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(1011) Variable = TUT1 MUTATION ANALYSIS
D1011V1, survival
                sevent
clus2              0   1
  TUT1 MUTATED     9   0
  TUT1 WILD-TYPE 273  73
  TUT1 MUTATED TUT1 WILD-TYPE 
             9            346 
  TUT1 MUTATED TUT1 WILD-TYPE 
             0             73 
$`TUT1 MUTATED`
TCGA-A6-5661 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3518 TCGA-AA-3837 TCGA-AA-3950 
       33.53        20.12        19.66         1.02        38.99        24.00 
TCGA-AU-6004 TCGA-CM-5860 TCGA-D5-6529 
       27.09        16.01        20.19 

$`TUT1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 
        6.97         1.02        13.02        38.99         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3842 
        0.99        25.02         1.02        17.98        15.95        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       11.51        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  TUT1 MUTATED TUT1 WILD-TYPE 
          1.02           0.00 
  TUT1 MUTATED TUT1 WILD-TYPE 
         38.99         140.38 
  TUT1 MUTATED TUT1 WILD-TYPE 
         20.19          20.15 
[1] "1.0 - 39.0 (20.2)"  "0.0 - 140.4 (20.1)"
[1] "hr="     "9300000"
D1011V2, 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       25       102         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        19         10         41         30       35        13
                vv
clus             STAGE IVB
  TUT1 MUTATED           0
  TUT1 WILD-TYPE         1
D1011V3, multiclass
            clus
vv           TUT1 MUTATED TUT1 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             7            102
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            1             30
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TUT1 MUTATED     0   1   7   1
  TUT1 WILD-TYPE   9  67 241  40
D1011V4, multiclass
    clus
vv   TUT1 MUTATED TUT1 WILD-TYPE
  T1            0              9
  T2            1             67
  T3            7            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
  TUT1 MUTATED     8   1   0
  TUT1 WILD-TYPE 212  79  66
D1011V5, multiclass
    clus
vv   TUT1 MUTATED TUT1 WILD-TYPE
  N0            8            212
  N1            1             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"
D1011V6, binary
                cls
clus               0   1
  TUT1 MUTATED     7   0
  TUT1 WILD-TYPE 276  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  TUT1 MUTATED      7    0
  TUT1 WILD-TYPE  276   48
   clus
vv  TUT1 MUTATED TUT1 WILD-TYPE
  0            7            276
  1            0             48
[1] 2 2
[1] FALSE
D1011V7, 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
D1011V8, binary
                cls
clus               0   1
  TUT1 MUTATED     5   4
  TUT1 WILD-TYPE 312  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  TUT1 MUTATED      5    4
  TUT1 WILD-TYPE  312   44
                               clus
vv                              TUT1 MUTATED TUT1 WILD-TYPE
  COLON ADENOCARCINOMA                     5            312
  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 249   2  22  21
D1011V9, multiclass
    clus
vv   TUT1 MUTATED TUT1 WILD-TYPE
  R0            8            249
  R1            0              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"
D1011V10, 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
D1011V11, 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(1012) Variable = OR4C15 MUTATION ANALYSIS
D1012V1, survival
                  sevent
clus2                0   1
  OR4C15 MUTATED     8   4
  OR4C15 WILD-TYPE 274  69
  OR4C15 MUTATED OR4C15 WILD-TYPE 
              12              343 
  OR4C15 MUTATED OR4C15 WILD-TYPE 
               4               69 
$`OR4C15 MUTATED`
TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3713 TCGA-AA-A00N TCGA-AZ-4315 TCGA-AZ-6605 
       22.06        63.98        19.04         4.01        58.39         5.23 
TCGA-AZ-6608 TCGA-CA-6718 TCGA-CM-6162 TCGA-D5-6920 TCGA-DM-A1D9 TCGA-DM-A28G 
        1.94         0.10        12.00        12.39       140.38        60.79 

$`OR4C15 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       29.56        11.74         3.19         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.33         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       12.59         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K 
        6.12        81.37       119.93        35.97       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  OR4C15 MUTATED OR4C15 WILD-TYPE 
             0.1              0.0 
  OR4C15 MUTATED OR4C15 WILD-TYPE 
          140.38           139.17 
  OR4C15 MUTATED OR4C15 WILD-TYPE 
          15.715           20.280 
[1] "0.1 - 140.4 (15.7)" "0.0 - 139.2 (20.3)"
[1] "hr=" "1.3"
D1012V2, 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       23       103         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR4C15 MUTATED           0          1          2          0        1
  OR4C15 WILD-TYPE        19          9         39         31       34
                  vv
clus               STAGE IVA STAGE IVB
  OR4C15 MUTATED           0         0
  OR4C15 WILD-TYPE        13         1
D1012V3, multiclass
            clus
vv           OR4C15 MUTATED OR4C15 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               6              103
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              1                9
  STAGE IIIB              2               39
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  OR4C15 MUTATED     0   1   9   3
  OR4C15 WILD-TYPE   9  67 239  38
D1012V4, multiclass
    clus
vv   OR4C15 MUTATED OR4C15 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              9              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
  OR4C15 MUTATED    10   3   0
  OR4C15 WILD-TYPE 210  77  66
D1012V5, multiclass
    clus
vv   OR4C15 MUTATED OR4C15 WILD-TYPE
  N0             10              210
  N1              3               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"
D1012V6, binary
                  cls
clus                 0   1
  OR4C15 MUTATED    12   1
  OR4C15 WILD-TYPE 271  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR4C15 MUTATED     12    1
  OR4C15 WILD-TYPE  271   47
   clus
vv  OR4C15 MUTATED OR4C15 WILD-TYPE
  0             12              271
  1              1               47
[1] 2 2
[1] FALSE
D1012V7, 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
D1012V8, binary
                  cls
clus                 0   1
  OR4C15 MUTATED    11   2
  OR4C15 WILD-TYPE 306  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR4C15 MUTATED     11    2
  OR4C15 WILD-TYPE  306   46
                               clus
vv                              OR4C15 MUTATED OR4C15 WILD-TYPE
  COLON ADENOCARCINOMA                      11              306
  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 250   2  21  20
D1012V9, multiclass
    clus
vv   OR4C15 MUTATED OR4C15 WILD-TYPE
  R0              7              250
  R1              0                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"
D1012V10, 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
D1012V11, 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(1013) Variable = ATIC MUTATION ANALYSIS
D1013V1, survival
                sevent
clus2              0   1
  ATIC MUTATED     8   5
  ATIC WILD-TYPE 274  68
  ATIC MUTATED ATIC WILD-TYPE 
            13            342 
  ATIC MUTATED ATIC WILD-TYPE 
             5             68 
$`ATIC MUTATED`
TCGA-A6-5666 TCGA-A6-6781 TCGA-AA-3516 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-A00N 
       32.71        19.66        13.02         6.97         0.92         4.01 
TCGA-AA-A01R TCGA-AZ-6599 TCGA-CA-5796 TCGA-CK-4950 TCGA-CK-5916 TCGA-DM-A1D4 
       35.01         6.77         3.25        40.34        21.14        92.75 
TCGA-G4-6310 
       45.11 

$`ATIC WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5797 TCGA-CA-6715 
        3.19         1.94         2.24         3.06         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        51.32        21.99         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20       130.65        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        51.75        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  ATIC MUTATED ATIC WILD-TYPE 
          0.92           0.00 
  ATIC MUTATED ATIC WILD-TYPE 
         92.75         140.38 
  ATIC MUTATED ATIC WILD-TYPE 
        19.660         20.235 
[1] "0.9 - 92.8 (19.7)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2.1"
D1013V2, 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       24       107         7         0
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ATIC MUTATED           3          1          1          1        0         0
  ATIC WILD-TYPE        16          9         40         30       35        13
                vv
clus             STAGE IVB
  ATIC MUTATED           0
  ATIC WILD-TYPE         1
D1013V3, multiclass
            clus
vv           ATIC MUTATED ATIC WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             2            107
  STAGE IIB             1              7
  STAGE IIC             1              0
  STAGE III             3             16
  STAGE IIIA            1              9
  STAGE IIIB            1             40
  STAGE IIIC            1             30
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ATIC MUTATED     1   1   8   3
  ATIC WILD-TYPE   8  67 240  38
D1013V4, multiclass
    clus
vv   ATIC MUTATED ATIC WILD-TYPE
  T1            1              8
  T2            1             67
  T3            8            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
  ATIC MUTATED     7   4   2
  ATIC WILD-TYPE 213  76  64
D1013V5, multiclass
    clus
vv   ATIC MUTATED ATIC WILD-TYPE
  N0            7            213
  N1            4             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"
D1013V6, binary
                cls
clus               0   1
  ATIC MUTATED    11   0
  ATIC WILD-TYPE 272  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATIC MUTATED     11    0
  ATIC WILD-TYPE  272   48
   clus
vv  ATIC MUTATED ATIC WILD-TYPE
  0           11            272
  1            0             48
[1] 2 2
[1] FALSE
D1013V7, 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
D1013V8, binary
                cls
clus               0   1
  ATIC MUTATED     8   5
  ATIC WILD-TYPE 309  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATIC MUTATED      8    5
  ATIC WILD-TYPE  309   43
                               clus
vv                              ATIC MUTATED ATIC WILD-TYPE
  COLON ADENOCARCINOMA                     8            309
  COLON MUCINOUS ADENOCARCINOMA            5             43
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ATIC MUTATED     7   1   0   1
  ATIC WILD-TYPE 250   1  22  20
D1013V9, multiclass
    clus
vv   ATIC MUTATED ATIC WILD-TYPE
  R0            7            250
  R1            1              1
  R2            0             22
  RX            1             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1013V10, 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
D1013V11, 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(1014) Variable = LMOD1 MUTATION ANALYSIS
D1014V1, survival
                 sevent
clus2               0   1
  LMOD1 MUTATED    11   1
  LMOD1 WILD-TYPE 271  72
  LMOD1 MUTATED LMOD1 WILD-TYPE 
             12             343 
  LMOD1 MUTATED LMOD1 WILD-TYPE 
              1              72 
$`LMOD1 MUTATED`
TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3672 TCGA-AA-3947 TCGA-AZ-4315 TCGA-CA-6717 
        3.02        63.98         0.92        33.01        58.39         0.33 
TCGA-CM-5861 TCGA-CM-6166 TCGA-CM-6170 TCGA-D5-5538 TCGA-D5-6540 TCGA-D5-6926 
       15.02        21.99        15.02        12.26        16.14         9.04 

$`LMOD1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-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-6171 TCGA-CM-6172 
       16.04        14.99        12.99        13.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       12.03        45.40        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  LMOD1 MUTATED LMOD1 WILD-TYPE 
           0.33            0.00 
  LMOD1 MUTATED LMOD1 WILD-TYPE 
          63.98          140.38 
  LMOD1 MUTATED LMOD1 WILD-TYPE 
          15.02           20.98 
[1] "0.3 - 64.0 (15.0)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "2.2"
D1014V2, 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       23       106         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LMOD1 MUTATED           1          1          1          0        0         0
  LMOD1 WILD-TYPE        18          9         40         31       35        13
                 vv
clus              STAGE IVB
  LMOD1 MUTATED           0
  LMOD1 WILD-TYPE         1
D1014V3, multiclass
            clus
vv           LMOD1 MUTATED LMOD1 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              3             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             1               9
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LMOD1 MUTATED     0   3   7   2
  LMOD1 WILD-TYPE   9  65 241  39
D1014V4, multiclass
    clus
vv   LMOD1 MUTATED LMOD1 WILD-TYPE
  T1             0               9
  T2             3              65
  T3             7             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
  LMOD1 MUTATED     9   3   0
  LMOD1 WILD-TYPE 211  77  66
D1014V5, multiclass
    clus
vv   LMOD1 MUTATED LMOD1 WILD-TYPE
  N0             9             211
  N1             3              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"
D1014V6, binary
                 cls
clus                0   1
  LMOD1 MUTATED    12   0
  LMOD1 WILD-TYPE 271  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LMOD1 MUTATED     12    0
  LMOD1 WILD-TYPE  271   48
   clus
vv  LMOD1 MUTATED LMOD1 WILD-TYPE
  0            12             271
  1             0              48
[1] 2 2
[1] FALSE
D1014V7, 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
D1014V8, binary
                 cls
clus                0   1
  LMOD1 MUTATED     9   3
  LMOD1 WILD-TYPE 308  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LMOD1 MUTATED      9    3
  LMOD1 WILD-TYPE  308   45
                               clus
vv                              LMOD1 MUTATED LMOD1 WILD-TYPE
  COLON ADENOCARCINOMA                      9             308
  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 246   2  22  20
D1014V9, multiclass
    clus
vv   LMOD1 MUTATED LMOD1 WILD-TYPE
  R0            11             246
  R1             0               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"
D1014V10, 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
D1014V11, 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(1015) Variable = GAD2 MUTATION ANALYSIS
D1015V1, survival
                sevent
clus2              0   1
  GAD2 MUTATED    11   4
  GAD2 WILD-TYPE 271  69
  GAD2 MUTATED GAD2 WILD-TYPE 
            15            340 
  GAD2 MUTATED GAD2 WILD-TYPE 
             4             69 
$`GAD2 MUTATED`
TCGA-A6-2676 TCGA-A6-6141 TCGA-A6-6654 TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-3989 
       42.90         8.38        23.87        24.00         2.01         7.96 
TCGA-AA-A00A TCGA-CM-4743 TCGA-CM-5862 TCGA-CM-6165 TCGA-D5-6537 TCGA-D5-6931 
       38.04        23.05         5.03        16.04         4.80        12.00 
TCGA-D5-7000 TCGA-DM-A1HB TCGA-F4-6460 
       10.26       135.65        13.38 

$`GAD2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       24.16        21.76        24.69        24.39        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01         2.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 
       25.02        24.00        27.02        27.02        19.07        27.02 
TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       13.94        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
       21.99        21.14         2.93         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-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        16.01        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 
       18.25         1.32        43.27        15.12        17.85        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        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-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 
       35.97        60.79       117.07        98.24         8.61        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  GAD2 MUTATED GAD2 WILD-TYPE 
          2.01           0.00 
  GAD2 MUTATED GAD2 WILD-TYPE 
        135.65         140.38 
  GAD2 MUTATED GAD2 WILD-TYPE 
         13.38          20.63 
[1] "2.0 - 135.7 (13.4)" "0.0 - 140.4 (20.6)"
[1] "hr=" "1.5"
D1015V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GAD2 MUTATED         1        0        0         6         1         0
  GAD2 WILD-TYPE      63        1       25       103         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        19         10         37         30       34        12
                vv
clus             STAGE IVB
  GAD2 MUTATED           0
  GAD2 WILD-TYPE         1
D1015V3, multiclass
            clus
vv           GAD2 MUTATED GAD2 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             6            103
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            4             37
  STAGE IIIC            1             30
  STAGE IV              1             34
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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   1  12   2
  GAD2 WILD-TYPE   9  67 236  39
D1015V4, multiclass
    clus
vv   GAD2 MUTATED GAD2 WILD-TYPE
  T1            0              9
  T2            1             67
  T3           12            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
  GAD2 MUTATED     8   5   2
  GAD2 WILD-TYPE 212  75  64
D1015V5, multiclass
    clus
vv   GAD2 MUTATED GAD2 WILD-TYPE
  N0            8            212
  N1            5             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"
D1015V6, binary
                cls
clus               0   1
  GAD2 MUTATED    12   2
  GAD2 WILD-TYPE 271  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAD2 MUTATED     12    2
  GAD2 WILD-TYPE  271   46
   clus
vv  GAD2 MUTATED GAD2 WILD-TYPE
  0           12            271
  1            2             46
[1] 2 2
[1] FALSE
D1015V7, binary
                cls
clus               0   1
  GAD2 MUTATED     6   9
  GAD2 WILD-TYPE 164 188
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAD2 MUTATED      6    9
  GAD2 WILD-TYPE  164  188
        clus
vv       GAD2 MUTATED GAD2 WILD-TYPE
  FEMALE            6            164
  MALE              9            188
[1] 2 2
[1] FALSE
D1015V8, binary
                cls
clus               0   1
  GAD2 MUTATED    12   3
  GAD2 WILD-TYPE 305  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAD2 MUTATED     12    3
  GAD2 WILD-TYPE  305   45
                               clus
vv                              GAD2 MUTATED GAD2 WILD-TYPE
  COLON ADENOCARCINOMA                    12            305
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  GAD2 MUTATED    10   0   1   0
  GAD2 WILD-TYPE 247   2  21  21
D1015V9, multiclass
    clus
vv   GAD2 MUTATED GAD2 WILD-TYPE
  R0           10            247
  R1            0              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"
D1015V10, 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    10
  GAD2 WILD-TYPE                        18   166
D1015V11, 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                                      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(1016) Variable = SF3B2 MUTATION ANALYSIS
D1016V1, survival
                 sevent
clus2               0   1
  SF3B2 MUTATED     6   4
  SF3B2 WILD-TYPE 276  69
  SF3B2 MUTATED SF3B2 WILD-TYPE 
             10             345 
  SF3B2 MUTATED SF3B2 WILD-TYPE 
              4              69 
$`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        61.41        49.41 
TCGA-AZ-6599 TCGA-CM-6166 TCGA-D5-6539 TCGA-F4-6570 
        6.77        21.99        12.49         6.18 

$`SF3B2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        19.04        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       22.36        62.79        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  SF3B2 MUTATED SF3B2 WILD-TYPE 
           6.18            0.00 
  SF3B2 MUTATED SF3B2 WILD-TYPE 
          61.41          140.38 
  SF3B2 MUTATED SF3B2 WILD-TYPE 
         20.825          20.190 
[1] "6.2 - 61.4 (20.8)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2"  
D1016V2, 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       24       107         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SF3B2 MUTATED           1          1          0          1        0         0
  SF3B2 WILD-TYPE        18          9         41         30       35        13
                 vv
clus              STAGE IVB
  SF3B2 MUTATED           0
  SF3B2 WILD-TYPE         1
D1016V3, multiclass
            clus
vv           SF3B2 MUTATED SF3B2 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              2             107
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             1               9
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SF3B2 MUTATED     1   2   5   2
  SF3B2 WILD-TYPE   8  66 243  39
D1016V4, multiclass
    clus
vv   SF3B2 MUTATED SF3B2 WILD-TYPE
  T1             1               8
  T2             2              66
  T3             5             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
  SF3B2 MUTATED     8   1   1
  SF3B2 WILD-TYPE 212  79  65
D1016V5, multiclass
    clus
vv   SF3B2 MUTATED SF3B2 WILD-TYPE
  N0             8             212
  N1             1              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"
D1016V6, binary
                 cls
clus                0   1
  SF3B2 MUTATED     7   0
  SF3B2 WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SF3B2 MUTATED      7    0
  SF3B2 WILD-TYPE  276   48
   clus
vv  SF3B2 MUTATED SF3B2 WILD-TYPE
  0             7             276
  1             0              48
[1] 2 2
[1] FALSE
D1016V7, 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
D1016V8, binary
                 cls
clus                0   1
  SF3B2 MUTATED     9   1
  SF3B2 WILD-TYPE 308  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SF3B2 MUTATED      9    1
  SF3B2 WILD-TYPE  308   47
                               clus
vv                              SF3B2 MUTATED SF3B2 WILD-TYPE
  COLON ADENOCARCINOMA                      9             308
  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 250   2  22  21
D1016V9, multiclass
    clus
vv   SF3B2 MUTATED SF3B2 WILD-TYPE
  R0             7             250
  R1             0               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"
D1016V10, 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
D1016V11, 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(1017) Variable = EMR3 MUTATION ANALYSIS
D1017V1, survival
                sevent
clus2              0   1
  EMR3 MUTATED    12   4
  EMR3 WILD-TYPE 270  69
  EMR3 MUTATED EMR3 WILD-TYPE 
            16            339 
  EMR3 MUTATED EMR3 WILD-TYPE 
             4             69 
$`EMR3 MUTATED`
TCGA-A6-2671 TCGA-A6-4105 TCGA-A6-5665 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3525 
       43.76        14.53        22.06        35.01        63.98         8.05 
TCGA-AA-3710 TCGA-AA-3870 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6895 TCGA-AY-6196 
       26.99        29.98         4.01        34.98         0.72         0.20 
TCGA-CM-4743 TCGA-CM-6172 TCGA-D5-6537 TCGA-G4-6588 
       23.05        11.01         4.80        26.17 

$`EMR3 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 
       34.65        33.34        32.75        36.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       30.44        29.19        33.53        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3511 TCGA-AA-3514 
       20.28         7.04         3.02         1.02         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
       36.03        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       17.03        24.03        27.02        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        15.75        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  EMR3 MUTATED EMR3 WILD-TYPE 
           0.2            0.0 
  EMR3 MUTATED EMR3 WILD-TYPE 
         63.98         140.38 
  EMR3 MUTATED EMR3 WILD-TYPE 
        22.555         20.120 
[1] "0.2 - 64.0 (22.6)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.5"
D1017V2, 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       24       104         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EMR3 MUTATED           0          0          3          1        2         0
  EMR3 WILD-TYPE        19         10         38         30       33        13
                vv
clus             STAGE IVB
  EMR3 MUTATED           0
  EMR3 WILD-TYPE         1
D1017V3, multiclass
            clus
vv           EMR3 MUTATED EMR3 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             5            104
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            3             38
  STAGE IIIC            1             30
  STAGE IV              2             33
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  EMR3 MUTATED     0   1  13   2
  EMR3 WILD-TYPE   9  67 235  39
D1017V4, multiclass
    clus
vv   EMR3 MUTATED EMR3 WILD-TYPE
  T1            0              9
  T2            1             67
  T3           13            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
  EMR3 MUTATED     9   4   3
  EMR3 WILD-TYPE 211  76  63
D1017V5, multiclass
    clus
vv   EMR3 MUTATED EMR3 WILD-TYPE
  N0            9            211
  N1            4             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"
D1017V6, binary
                cls
clus               0   1
  EMR3 MUTATED    11   2
  EMR3 WILD-TYPE 272  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMR3 MUTATED     11    2
  EMR3 WILD-TYPE  272   46
   clus
vv  EMR3 MUTATED EMR3 WILD-TYPE
  0           11            272
  1            2             46
[1] 2 2
[1] FALSE
D1017V7, 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
D1017V8, binary
                cls
clus               0   1
  EMR3 MUTATED    14   2
  EMR3 WILD-TYPE 303  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMR3 MUTATED     14    2
  EMR3 WILD-TYPE  303   46
                               clus
vv                              EMR3 MUTATED EMR3 WILD-TYPE
  COLON ADENOCARCINOMA                    14            303
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  EMR3 MUTATED    14   0   0   0
  EMR3 WILD-TYPE 243   2  22  21
D1017V9, multiclass
    clus
vv   EMR3 MUTATED EMR3 WILD-TYPE
  R0           14            243
  R1            0              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"
D1017V10, 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
D1017V11, 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(1018) Variable = CYP4F11 MUTATION ANALYSIS
D1018V1, survival
                   sevent
clus2                 0   1
  CYP4F11 MUTATED     4   2
  CYP4F11 WILD-TYPE 278  71
  CYP4F11 MUTATED CYP4F11 WILD-TYPE 
                6               349 
  CYP4F11 MUTATED CYP4F11 WILD-TYPE 
                2                71 
$`CYP4F11 MUTATED`
TCGA-AA-3713 TCGA-AA-A00N TCGA-AD-5900 TCGA-AY-6196 TCGA-AZ-6601 TCGA-CM-6171 
       19.04         4.01         0.07         0.20       100.01        14.04 

$`CYP4F11 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  CYP4F11 MUTATED CYP4F11 WILD-TYPE 
             0.07              0.00 
  CYP4F11 MUTATED CYP4F11 WILD-TYPE 
           100.01            140.38 
  CYP4F11 MUTATED CYP4F11 WILD-TYPE 
            9.025            20.980 
[1] "0.1 - 100.0 (9.0)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.7"
D1018V2, 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       24       109         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CYP4F11 MUTATED           0          0          0          1        1
  CYP4F11 WILD-TYPE        19         10         41         30       34
                   vv
clus                STAGE IVA STAGE IVB
  CYP4F11 MUTATED           0         0
  CYP4F11 WILD-TYPE        13         1
D1018V3, multiclass
            clus
vv           CYP4F11 MUTATED CYP4F11 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                0               109
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               1                30
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CYP4F11 MUTATED     0   2   3   1
  CYP4F11 WILD-TYPE   9  66 245  40
D1018V4, multiclass
    clus
vv   CYP4F11 MUTATED CYP4F11 WILD-TYPE
  T1               0                 9
  T2               2                66
  T3               3               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
  CYP4F11 MUTATED     5   0   1
  CYP4F11 WILD-TYPE 215  80  65
D1018V5, multiclass
    clus
vv   CYP4F11 MUTATED CYP4F11 WILD-TYPE
  N0               5               215
  N1               0                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"
D1018V6, binary
                   cls
clus                  0   1
  CYP4F11 MUTATED     3   1
  CYP4F11 WILD-TYPE 280  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP4F11 MUTATED      3    1
  CYP4F11 WILD-TYPE  280   47
   clus
vv  CYP4F11 MUTATED CYP4F11 WILD-TYPE
  0               3               280
  1               1                47
[1] 2 2
[1] FALSE
D1018V7, 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
D1018V8, binary
                   cls
clus                  0   1
  CYP4F11 MUTATED     3   3
  CYP4F11 WILD-TYPE 314  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP4F11 MUTATED      3    3
  CYP4F11 WILD-TYPE  314   45
                               clus
vv                              CYP4F11 MUTATED CYP4F11 WILD-TYPE
  COLON ADENOCARCINOMA                        3               314
  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 253   2  21  21
D1018V9, multiclass
    clus
vv   CYP4F11 MUTATED CYP4F11 WILD-TYPE
  R0               4               253
  R1               0                 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"
D1018V10, 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
D1018V11, 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(1019) Variable = USP9X MUTATION ANALYSIS
D1019V1, survival
                 sevent
clus2               0   1
  USP9X MUTATED    20  10
  USP9X WILD-TYPE 262  63
  USP9X MUTATED USP9X WILD-TYPE 
             30             325 
  USP9X MUTATED USP9X WILD-TYPE 
             10              63 
$`USP9X MUTATED`
TCGA-A6-5660 TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3713 
       29.19        22.06         3.02        63.98         6.97        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3815 TCGA-AA-3864 TCGA-AA-A00N TCGA-AZ-4315 
       19.04        10.06        33.04        53.00         4.01        58.39 
TCGA-AZ-4682 TCGA-AZ-6598 TCGA-CA-6718 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 
       22.36        49.41         0.10        40.34        49.08        51.32 
TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6680 TCGA-D5-6537 
        5.03        15.02        12.00        16.04        12.03         4.80 
TCGA-D5-6538 TCGA-D5-6898 TCGA-F4-6570 TCGA-F4-6856 TCGA-G4-6588 TCGA-G4-6628 
       17.13         7.53         6.18        19.43        26.17        52.80 

$`USP9X WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       19.66        20.28         7.04         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.05        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-5407 
       17.82         1.41         5.13        83.80        62.79        61.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.33         1.35        17.56       102.44 
TCGA-CK-4952 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        21.99        21.14         2.93         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        16.01        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 
       17.03        15.02        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-D5-5537 
       13.05        11.08        11.08        11.01        10.06        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6540 
        1.32        43.27        15.12        17.85        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6920 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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 
       33.67        13.25         0.53        35.41       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 
       46.75 

  USP9X MUTATED USP9X WILD-TYPE 
            0.1             0.0 
  USP9X MUTATED USP9X WILD-TYPE 
          63.98          140.38 
  USP9X MUTATED USP9X WILD-TYPE 
          19.04           20.98 
[1] "0.1 - 64.0 (19.0)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.7"
D1019V2, 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       19       100         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  USP9X MUTATED           1          1          4          1        1         2
  USP9X WILD-TYPE        18          9         37         30       34        11
                 vv
clus              STAGE IVB
  USP9X MUTATED           0
  USP9X WILD-TYPE         1
D1019V3, multiclass
            clus
vv           USP9X MUTATED USP9X WILD-TYPE
  STAGE I                5              59
  STAGE IA               0               1
  STAGE II               6              19
  STAGE IIA              9             100
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             1               9
  STAGE IIIB             4              37
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              2              11
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  63 223  40
D1019V4, multiclass
    clus
vv   USP9X MUTATED USP9X WILD-TYPE
  T1             0               9
  T2             5              63
  T3            25             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
  USP9X MUTATED    23   4   4
  USP9X WILD-TYPE 197  76  62
D1019V5, multiclass
    clus
vv   USP9X MUTATED USP9X WILD-TYPE
  N0            23             197
  N1             4              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"
D1019V6, binary
                 cls
clus                0   1
  USP9X MUTATED    24   3
  USP9X WILD-TYPE 259  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP9X MUTATED     24    3
  USP9X WILD-TYPE  259   45
   clus
vv  USP9X MUTATED USP9X WILD-TYPE
  0            24             259
  1             3              45
[1] 2 2
[1] FALSE
D1019V7, 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
D1019V8, binary
                 cls
clus                0   1
  USP9X MUTATED    28   3
  USP9X WILD-TYPE 289  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP9X MUTATED     28    3
  USP9X WILD-TYPE  289   45
                               clus
vv                              USP9X MUTATED USP9X WILD-TYPE
  COLON ADENOCARCINOMA                     28             289
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  USP9X MUTATED    24   1   1   3
  USP9X WILD-TYPE 233   1  21  18
D1019V9, multiclass
    clus
vv   USP9X MUTATED USP9X WILD-TYPE
  R0            24             233
  R1             1               1
  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"
D1019V10, 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
D1019V11, 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(1020) Variable = ADH7 MUTATION ANALYSIS
D1020V1, survival
                sevent
clus2              0   1
  ADH7 MUTATED     7   0
  ADH7 WILD-TYPE 275  73
  ADH7 MUTATED ADH7 WILD-TYPE 
             7            348 
  ADH7 MUTATED ADH7 WILD-TYPE 
             0             73 
$`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         0.26        15.02 
TCGA-CM-6161 
       15.02 

$`ADH7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        17.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 
        2.24         3.06         3.25         3.29         0.07         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01         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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  ADH7 MUTATED ADH7 WILD-TYPE 
          0.26           0.00 
  ADH7 MUTATED ADH7 WILD-TYPE 
         58.39         140.38 
  ADH7 MUTATED ADH7 WILD-TYPE 
        29.950         20.155 
[1] "0.3 - 58.4 (29.9)"  "0.0 - 140.4 (20.2)"
[1] "hr="     "9200000"
D1020V2, 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       25       104         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        19         10         41         31       35        13
                vv
clus             STAGE IVB
  ADH7 MUTATED           0
  ADH7 WILD-TYPE         1
D1020V3, multiclass
            clus
vv           ADH7 MUTATED ADH7 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             5            104
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ADH7 MUTATED     0   1   5   1
  ADH7 WILD-TYPE   9  67 243  40
D1020V4, multiclass
    clus
vv   ADH7 MUTATED ADH7 WILD-TYPE
  T1            0              9
  T2            1             67
  T3            5            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
  ADH7 MUTATED     7   0   0
  ADH7 WILD-TYPE 213  80  66
D1020V5, multiclass
    clus
vv   ADH7 MUTATED ADH7 WILD-TYPE
  N0            7            213
  N1            0             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"
D1020V6, binary
                cls
clus               0   1
  ADH7 MUTATED     7   0
  ADH7 WILD-TYPE 276  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  ADH7 MUTATED      7    0
  ADH7 WILD-TYPE  276   48
   clus
vv  ADH7 MUTATED ADH7 WILD-TYPE
  0            7            276
  1            0             48
[1] 2 2
[1] FALSE
D1020V7, 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
D1020V8, binary
                cls
clus               0   1
  ADH7 MUTATED     6   1
  ADH7 WILD-TYPE 311  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  ADH7 MUTATED      6    1
  ADH7 WILD-TYPE  311   47
                               clus
vv                              ADH7 MUTATED ADH7 WILD-TYPE
  COLON ADENOCARCINOMA                     6            311
  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 251   2  22  20
D1020V9, multiclass
    clus
vv   ADH7 MUTATED ADH7 WILD-TYPE
  R0            6            251
  R1            0              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"
D1020V10, 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
D1020V11, 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(1021) Variable = RUSC2 MUTATION ANALYSIS
D1021V1, survival
                 sevent
clus2               0   1
  RUSC2 MUTATED    10   1
  RUSC2 WILD-TYPE 272  72
  RUSC2 MUTATED RUSC2 WILD-TYPE 
             11             344 
  RUSC2 MUTATED RUSC2 WILD-TYPE 
              1              72 
$`RUSC2 MUTATED`
TCGA-A6-6648 TCGA-AA-3715 TCGA-AA-3819 TCGA-AA-3864 TCGA-AA-A00J TCGA-AA-A010 
       25.18        19.04        25.02        53.00        18.05        34.98 
TCGA-AD-5900 TCGA-CK-4950 TCGA-CM-4746 TCGA-CM-6674 TCGA-DM-A1HB 
        0.07        40.34        37.02        12.95       135.65 

$`RUSC2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05        33.04         0.99         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       102.44        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  RUSC2 MUTATED RUSC2 WILD-TYPE 
           0.07            0.00 
  RUSC2 MUTATED RUSC2 WILD-TYPE 
         135.65          140.38 
  RUSC2 MUTATED RUSC2 WILD-TYPE 
          25.18           20.07 
[1] "0.1 - 135.7 (25.2)" "0.0 - 140.4 (20.1)"
[1] "hr=" "3"  
D1021V2, 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       23       107         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RUSC2 MUTATED           0          1          2          0        0         1
  RUSC2 WILD-TYPE        19          9         39         31       35        12
                 vv
clus              STAGE IVB
  RUSC2 MUTATED           0
  RUSC2 WILD-TYPE         1
D1021V3, multiclass
            clus
vv           RUSC2 MUTATED RUSC2 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              2             107
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 241  38
D1021V4, multiclass
    clus
vv   RUSC2 MUTATED RUSC2 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             7             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
  RUSC2 MUTATED     9   3   0
  RUSC2 WILD-TYPE 211  77  66
D1021V5, multiclass
    clus
vv   RUSC2 MUTATED RUSC2 WILD-TYPE
  N0             9             211
  N1             3              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"
D1021V6, binary
                 cls
clus                0   1
  RUSC2 MUTATED     9   1
  RUSC2 WILD-TYPE 274  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUSC2 MUTATED      9    1
  RUSC2 WILD-TYPE  274   47
   clus
vv  RUSC2 MUTATED RUSC2 WILD-TYPE
  0             9             274
  1             1              47
[1] 2 2
[1] FALSE
D1021V7, 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
D1021V8, binary
                 cls
clus                0   1
  RUSC2 MUTATED    10   2
  RUSC2 WILD-TYPE 307  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUSC2 MUTATED     10    2
  RUSC2 WILD-TYPE  307   46
                               clus
vv                              RUSC2 MUTATED RUSC2 WILD-TYPE
  COLON ADENOCARCINOMA                     10             307
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RUSC2 MUTATED     8   1   0   1
  RUSC2 WILD-TYPE 249   1  22  20
D1021V9, multiclass
    clus
vv   RUSC2 MUTATED RUSC2 WILD-TYPE
  R0             8             249
  R1             1               1
  R2             0              22
  RX             1              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1021V10, 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
D1021V11, 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(1022) Variable = URGCP MUTATION ANALYSIS
D1022V1, survival
                 sevent
clus2               0   1
  URGCP MUTATED    12   3
  URGCP WILD-TYPE 270  70
  URGCP MUTATED URGCP WILD-TYPE 
             15             340 
  URGCP MUTATED URGCP WILD-TYPE 
              3              70 
$`URGCP MUTATED`
TCGA-A6-5665 TCGA-A6-6138 TCGA-AA-3655 TCGA-AA-3977 TCGA-AA-A01D TCGA-AD-6964 
       22.06        22.52        61.02        25.02        10.98        10.88 
TCGA-AZ-4315 TCGA-AZ-6601 TCGA-CA-6716 TCGA-CA-6717 TCGA-CM-5344 TCGA-CM-6167 
       58.39       100.01         0.26         0.33        22.03        14.99 
TCGA-CM-6172 TCGA-D5-6927 TCGA-G4-6309 
       11.01         9.44        51.75 

$`URGCP WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.09        32.71        27.09         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       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        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        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-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        14.04        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  URGCP MUTATED URGCP WILD-TYPE 
           0.26            0.00 
  URGCP MUTATED URGCP WILD-TYPE 
         100.01          140.38 
  URGCP MUTATED URGCP WILD-TYPE 
         22.030          20.155 
[1] "0.3 - 100.0 (22.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D1022V2, 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       23       104         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        19         10         38         29       35        13
                 vv
clus              STAGE IVB
  URGCP MUTATED           0
  URGCP WILD-TYPE         1
D1022V3, multiclass
            clus
vv           URGCP MUTATED URGCP WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              5             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             3              38
  STAGE IIIC             2              29
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  URGCP MUTATED     0   2  12   1
  URGCP WILD-TYPE   9  66 236  40
D1022V4, multiclass
    clus
vv   URGCP MUTATED URGCP WILD-TYPE
  T1             0               9
  T2             2              66
  T3            12             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
  URGCP MUTATED     9   3   3
  URGCP WILD-TYPE 211  77  63
D1022V5, multiclass
    clus
vv   URGCP MUTATED URGCP WILD-TYPE
  N0             9             211
  N1             3              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"
D1022V6, binary
                 cls
clus                0   1
  URGCP MUTATED    13   0
  URGCP WILD-TYPE 270  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  URGCP MUTATED     13    0
  URGCP WILD-TYPE  270   48
   clus
vv  URGCP MUTATED URGCP WILD-TYPE
  0            13             270
  1             0              48
[1] 2 2
[1] FALSE
D1022V7, 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
D1022V8, binary
                 cls
clus                0   1
  URGCP MUTATED    13   2
  URGCP WILD-TYPE 304  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  URGCP MUTATED     13    2
  URGCP WILD-TYPE  304   46
                               clus
vv                              URGCP MUTATED URGCP WILD-TYPE
  COLON ADENOCARCINOMA                     13             304
  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 248   2  22  19
D1022V9, multiclass
    clus
vv   URGCP MUTATED URGCP WILD-TYPE
  R0             9             248
  R1             0               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"
D1022V10, 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
D1022V11, 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(1023) Variable = C1ORF35 MUTATION ANALYSIS
D1023V1, survival
                   sevent
clus2                 0   1
  C1ORF35 MUTATED     3   1
  C1ORF35 WILD-TYPE 279  72
  C1ORF35 MUTATED C1ORF35 WILD-TYPE 
                4               351 
  C1ORF35 MUTATED C1ORF35 WILD-TYPE 
                1                72 
$`C1ORF35 MUTATED`
TCGA-AA-3713 TCGA-CA-6717 TCGA-CK-5913 TCGA-CK-5916 
       19.04         0.33        51.32        21.14 

$`C1ORF35 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6747 
      102.44        40.34        15.62        49.08        21.99         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  C1ORF35 MUTATED C1ORF35 WILD-TYPE 
             0.33              0.00 
  C1ORF35 MUTATED C1ORF35 WILD-TYPE 
            51.32            140.38 
  C1ORF35 MUTATED C1ORF35 WILD-TYPE 
            20.09             20.19 
[1] "0.3 - 51.3 (20.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D1023V2, 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       25       107         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C1ORF35 MUTATED           0          0          0          0        1
  C1ORF35 WILD-TYPE        19         10         41         31       34
                   vv
clus                STAGE IVA STAGE IVB
  C1ORF35 MUTATED           0         0
  C1ORF35 WILD-TYPE        13         1
D1023V3, multiclass
            clus
vv           C1ORF35 MUTATED C1ORF35 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                2               107
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               0                31
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C1ORF35 MUTATED     1   0   3   0
  C1ORF35 WILD-TYPE   8  68 245  41
D1023V4, multiclass
    clus
vv   C1ORF35 MUTATED C1ORF35 WILD-TYPE
  T1               1                 8
  T2               0                68
  T3               3               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
  C1ORF35 MUTATED     4   0   0
  C1ORF35 WILD-TYPE 216  80  66
D1023V5, multiclass
    clus
vv   C1ORF35 MUTATED C1ORF35 WILD-TYPE
  N0               4               216
  N1               0                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"
D1023V6, binary
                   cls
clus                  0   1
  C1ORF35 MUTATED     2   1
  C1ORF35 WILD-TYPE 281  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1ORF35 MUTATED      2    1
  C1ORF35 WILD-TYPE  281   47
   clus
vv  C1ORF35 MUTATED C1ORF35 WILD-TYPE
  0               2               281
  1               1                47
[1] 2 2
[1] FALSE
D1023V7, 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
D1023V8, binary
                   cls
clus                  0   1
  C1ORF35 MUTATED     3   1
  C1ORF35 WILD-TYPE 314  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1ORF35 MUTATED      3    1
  C1ORF35 WILD-TYPE  314   47
                               clus
vv                              C1ORF35 MUTATED C1ORF35 WILD-TYPE
  COLON ADENOCARCINOMA                        3               314
  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 257   2  21  18
D1023V9, multiclass
    clus
vv   C1ORF35 MUTATED C1ORF35 WILD-TYPE
  R0               0               257
  R1               0                 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"
D1023V10, continuous
[1] "Remove cluster labels:" "C1ORF35 MUTATED"       
clus
  C1ORF35 MUTATED C1ORF35 WILD-TYPE 
                1               344 
       TCGA-A6-2671        TCGA-A6-2672        TCGA-A6-2674        TCGA-A6-2676 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-A6-2677        TCGA-A6-2678        TCGA-A6-2683        TCGA-A6-3807 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-A6-3808        TCGA-A6-3809        TCGA-A6-3810        TCGA-A6-4105 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-A6-5656        TCGA-A6-5657        TCGA-A6-5659        TCGA-A6-5660 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-A6-5661        TCGA-A6-5662        TCGA-A6-5664        TCGA-A6-5665 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-A6-5666        TCGA-A6-6137        TCGA-A6-6138        TCGA-A6-6141 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-A6-6142        TCGA-A6-6648        TCGA-A6-6649        TCGA-A6-6651 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-A6-6652        TCGA-A6-6653        TCGA-A6-6654        TCGA-A6-6780 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-A6-6781        TCGA-A6-6782        TCGA-AA-3489        TCGA-AA-3492 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3496        TCGA-AA-3502        TCGA-AA-3510        TCGA-AA-3511 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3514        TCGA-AA-3516        TCGA-AA-3517        TCGA-AA-3518 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3519        TCGA-AA-3520        TCGA-AA-3521        TCGA-AA-3522 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3524        TCGA-AA-3525        TCGA-AA-3526        TCGA-AA-3527 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3529        TCGA-AA-3530        TCGA-AA-3531        TCGA-AA-3532 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3534        TCGA-AA-3538        TCGA-AA-3542        TCGA-AA-3543 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3544        TCGA-AA-3548        TCGA-AA-3549        TCGA-AA-3552 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3553        TCGA-AA-3554        TCGA-AA-3555        TCGA-AA-3556 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3558        TCGA-AA-3560        TCGA-AA-3562        TCGA-AA-3655 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3660        TCGA-AA-3662        TCGA-AA-3663        TCGA-AA-3664 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3666        TCGA-AA-3667        TCGA-AA-3672        TCGA-AA-3673 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3678        TCGA-AA-3679        TCGA-AA-3680        TCGA-AA-3681 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3684        TCGA-AA-3685        TCGA-AA-3688        TCGA-AA-3692 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3693        TCGA-AA-3695        TCGA-AA-3696        TCGA-AA-3697 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3710        TCGA-AA-3712        TCGA-AA-3715        TCGA-AA-3811 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3812        TCGA-AA-3814        TCGA-AA-3815        TCGA-AA-3818 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3819        TCGA-AA-3821        TCGA-AA-3831        TCGA-AA-3833 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3837        TCGA-AA-3842        TCGA-AA-3844        TCGA-AA-3845 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3846        TCGA-AA-3848        TCGA-AA-3850        TCGA-AA-3851 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3852        TCGA-AA-3854        TCGA-AA-3855        TCGA-AA-3856 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3858        TCGA-AA-3860        TCGA-AA-3861        TCGA-AA-3864 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3866        TCGA-AA-3867        TCGA-AA-3869        TCGA-AA-3870 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3872        TCGA-AA-3875        TCGA-AA-3877        TCGA-AA-3930 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3939        TCGA-AA-3941        TCGA-AA-3947        TCGA-AA-3949 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3950        TCGA-AA-3952        TCGA-AA-3955        TCGA-AA-3956 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3966        TCGA-AA-3968        TCGA-AA-3971        TCGA-AA-3972 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3973        TCGA-AA-3975        TCGA-AA-3976        TCGA-AA-3977 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3979        TCGA-AA-3980        TCGA-AA-3982        TCGA-AA-3984 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3986        TCGA-AA-3989        TCGA-AA-3994        TCGA-AA-A004 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-A00A        TCGA-AA-A00D        TCGA-AA-A00E        TCGA-AA-A00F 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-A00J        TCGA-AA-A00K        TCGA-AA-A00L        TCGA-AA-A00N 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-A00O        TCGA-AA-A00Q        TCGA-AA-A00R        TCGA-AA-A00U 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-A00W        TCGA-AA-A00Z        TCGA-AA-A010        TCGA-AA-A017 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-A01D        TCGA-AA-A01F        TCGA-AA-A01G        TCGA-AA-A01I 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-A01K        TCGA-AA-A01P        TCGA-AA-A01Q        TCGA-AA-A01R 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-A01S        TCGA-AA-A01T        TCGA-AA-A01V        TCGA-AA-A01X 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-A01Z        TCGA-AA-A022        TCGA-AA-A024        TCGA-AA-A029 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-A02F        TCGA-AA-A02H        TCGA-AA-A02J        TCGA-AA-A02K 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-A02O        TCGA-AA-A02W        TCGA-AA-A02Y        TCGA-AA-A03F 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-A03J        TCGA-AD-5900        TCGA-AD-6548        TCGA-AD-6888 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AD-6889        TCGA-AD-6890        TCGA-AD-6895        TCGA-AD-6899 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AD-6901        TCGA-AD-6963        TCGA-AD-6964        TCGA-AD-6965 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AU-3779        TCGA-AU-6004        TCGA-AY-4070        TCGA-AY-4071 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AY-5543        TCGA-AY-6196        TCGA-AY-6197        TCGA-AY-6386 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AZ-4323        TCGA-AZ-4616        TCGA-AZ-4682        TCGA-AZ-5403 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AZ-5407        TCGA-AZ-6598        TCGA-AZ-6599        TCGA-AZ-6600 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AZ-6601        TCGA-AZ-6603        TCGA-AZ-6605        TCGA-AZ-6606 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AZ-6607        TCGA-AZ-6608        TCGA-CK-4947        TCGA-CK-4948 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-CK-4950        TCGA-CK-4952        TCGA-CM-4743        TCGA-CM-4744 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-CM-4746        TCGA-CM-4747        TCGA-CM-4752        TCGA-CM-5341 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-CM-5344        TCGA-CM-5348        TCGA-CM-5349        TCGA-CM-5860 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-CM-5861        TCGA-CM-5862        TCGA-CM-5863        TCGA-CM-5864 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-CM-5868        TCGA-CM-6161        TCGA-CM-6162        TCGA-CM-6163 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-CM-6164        TCGA-CM-6165        TCGA-CM-6166        TCGA-CM-6167 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-CM-6168        TCGA-CM-6169        TCGA-CM-6170        TCGA-CM-6171 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-CM-6172        TCGA-CM-6674        TCGA-CM-6675        TCGA-CM-6676 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-CM-6677        TCGA-CM-6678        TCGA-CM-6679        TCGA-CM-6680 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-D5-5537        TCGA-D5-5538        TCGA-D5-5539        TCGA-D5-5540 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-D5-5541        TCGA-D5-6529        TCGA-D5-6532        TCGA-D5-6533 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-D5-6534        TCGA-D5-6535        TCGA-D5-6536        TCGA-D5-6537 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-D5-6538        TCGA-D5-6539        TCGA-D5-6540        TCGA-D5-6541 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-D5-6898        TCGA-D5-6920        TCGA-D5-6922        TCGA-D5-6923 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-D5-6924        TCGA-D5-6926        TCGA-D5-6927        TCGA-D5-6928 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-D5-6929        TCGA-D5-6930        TCGA-D5-6931        TCGA-D5-6932 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-D5-7000        TCGA-DM-A0X9        TCGA-DM-A0XD        TCGA-DM-A0XF 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-DM-A1D0        TCGA-DM-A1D4        TCGA-DM-A1D6        TCGA-DM-A1D7 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-DM-A1D8        TCGA-DM-A1D9        TCGA-DM-A1DA        TCGA-DM-A1DB 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-DM-A1HA        TCGA-DM-A1HB        TCGA-DM-A282        TCGA-DM-A285 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-DM-A28C        TCGA-DM-A28E        TCGA-DM-A28F        TCGA-DM-A28G 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-DM-A28H        TCGA-DM-A28K        TCGA-F4-6459        TCGA-F4-6460 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-F4-6569        TCGA-F4-6570        TCGA-F4-6703        TCGA-F4-6704 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-F4-6806        TCGA-F4-6807        TCGA-F4-6808        TCGA-F4-6809 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-F4-6854        TCGA-F4-6855        TCGA-F4-6856        TCGA-G4-6293 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-G4-6299        TCGA-G4-6303        TCGA-G4-6304        TCGA-G4-6306 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-G4-6307        TCGA-G4-6309        TCGA-G4-6310        TCGA-G4-6315 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-G4-6317        TCGA-G4-6321        TCGA-G4-6323        TCGA-G4-6586 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-G4-6588        TCGA-G4-6625        TCGA-G4-6626        TCGA-G4-6628 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
                   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
D1023V11, 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(1024) Variable = SLC30A8 MUTATION ANALYSIS
D1024V1, survival
                   sevent
clus2                 0   1
  SLC30A8 MUTATED    11   2
  SLC30A8 WILD-TYPE 271  71
  SLC30A8 MUTATED SLC30A8 WILD-TYPE 
               13               342 
  SLC30A8 MUTATED SLC30A8 WILD-TYPE 
                2                71 
$`SLC30A8 MUTATED`
TCGA-A6-6648 TCGA-A6-6649 TCGA-AA-3713 TCGA-AA-3815 TCGA-AA-3845 TCGA-AA-3869 
       25.18        24.16        19.04        33.04         0.00        27.02 
TCGA-AA-3949 TCGA-AA-3966 TCGA-CA-6717 TCGA-CK-5913 TCGA-CK-6751 TCGA-F4-6460 
       26.01         2.01         0.33        51.32       124.27        13.38 
TCGA-G4-6315 
       36.72 

$`SLC30A8 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.08        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02        14.93        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3875 
       30.05        53.00        17.03        24.03        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        33.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       40.34        15.62        49.08        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        51.75        45.11        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  SLC30A8 MUTATED SLC30A8 WILD-TYPE 
                0                 0 
  SLC30A8 MUTATED SLC30A8 WILD-TYPE 
           124.27            140.38 
  SLC30A8 MUTATED SLC30A8 WILD-TYPE 
            25.18             20.07 
[1] "0.0 - 124.3 (25.2)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.5"
D1024V2, 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       24       104         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC30A8 MUTATED           0          0          3          0        3
  SLC30A8 WILD-TYPE        19         10         38         31       32
                   vv
clus                STAGE IVA STAGE IVB
  SLC30A8 MUTATED           1         0
  SLC30A8 WILD-TYPE        12         1
D1024V3, multiclass
            clus
vv           SLC30A8 MUTATED SLC30A8 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                5               104
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               3                38
  STAGE IIIC               0                31
  STAGE IV                 3                32
  STAGE IVA                1                12
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 237  39
D1024V4, multiclass
    clus
vv   SLC30A8 MUTATED SLC30A8 WILD-TYPE
  T1               0                 9
  T2               1                67
  T3              11               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
  SLC30A8 MUTATED     9   4   1
  SLC30A8 WILD-TYPE 211  76  65
D1024V5, multiclass
    clus
vv   SLC30A8 MUTATED SLC30A8 WILD-TYPE
  N0               9               211
  N1               4                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"
D1024V6, binary
                   cls
clus                  0   1
  SLC30A8 MUTATED     8   4
  SLC30A8 WILD-TYPE 275  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC30A8 MUTATED      8    4
  SLC30A8 WILD-TYPE  275   44
   clus
vv  SLC30A8 MUTATED SLC30A8 WILD-TYPE
  0               8               275
  1               4                44
[1] 2 2
[1] FALSE
D1024V7, 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
D1024V8, binary
                   cls
clus                  0   1
  SLC30A8 MUTATED    10   4
  SLC30A8 WILD-TYPE 307  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC30A8 MUTATED     10    4
  SLC30A8 WILD-TYPE  307   44
                               clus
vv                              SLC30A8 MUTATED SLC30A8 WILD-TYPE
  COLON ADENOCARCINOMA                       10               307
  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 251   2  20  18
D1024V9, multiclass
    clus
vv   SLC30A8 MUTATED SLC30A8 WILD-TYPE
  R0               6               251
  R1               0                 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"
D1024V10, 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
D1024V11, 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(1025) Variable = NSUN6 MUTATION ANALYSIS
D1025V1, survival
                 sevent
clus2               0   1
  NSUN6 MUTATED     6   2
  NSUN6 WILD-TYPE 276  71
  NSUN6 MUTATED NSUN6 WILD-TYPE 
              8             347 
  NSUN6 MUTATED NSUN6 WILD-TYPE 
              2              71 
$`NSUN6 MUTATED`
TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-A010 TCGA-AD-5900 TCGA-AZ-6607 
       19.66         3.02        63.98        34.98         0.07         3.19 
TCGA-CM-5861 TCGA-D5-6540 
       15.02        16.14 

$`NSUN6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       23.87        20.12        20.28         7.04         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  NSUN6 MUTATED NSUN6 WILD-TYPE 
           0.07            0.00 
  NSUN6 MUTATED NSUN6 WILD-TYPE 
          63.98          140.38 
  NSUN6 MUTATED NSUN6 WILD-TYPE 
          15.58           20.98 
[1] "0.1 - 64.0 (15.6)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.5"
D1025V2, 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       23       108         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        19         10         41         30       34        13
                 vv
clus              STAGE IVB
  NSUN6 MUTATED           0
  NSUN6 WILD-TYPE         1
D1025V3, multiclass
            clus
vv           NSUN6 MUTATED NSUN6 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              1             108
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NSUN6 MUTATED     0   2   3   3
  NSUN6 WILD-TYPE   9  66 245  38
D1025V4, multiclass
    clus
vv   NSUN6 MUTATED NSUN6 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             3             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
  NSUN6 MUTATED     6   1   1
  NSUN6 WILD-TYPE 214  79  65
D1025V5, multiclass
    clus
vv   NSUN6 MUTATED NSUN6 WILD-TYPE
  N0             6             214
  N1             1              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"
D1025V6, binary
                 cls
clus                0   1
  NSUN6 MUTATED     5   1
  NSUN6 WILD-TYPE 278  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NSUN6 MUTATED      5    1
  NSUN6 WILD-TYPE  278   47
   clus
vv  NSUN6 MUTATED NSUN6 WILD-TYPE
  0             5             278
  1             1              47
[1] 2 2
[1] FALSE
D1025V7, 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
D1025V8, binary
                 cls
clus                0   1
  NSUN6 MUTATED     5   3
  NSUN6 WILD-TYPE 312  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NSUN6 MUTATED      5    3
  NSUN6 WILD-TYPE  312   45
                               clus
vv                              NSUN6 MUTATED NSUN6 WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  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 250   2  22  21
D1025V9, multiclass
    clus
vv   NSUN6 MUTATED NSUN6 WILD-TYPE
  R0             7             250
  R1             0               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"
D1025V10, 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
D1025V11, 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(1026) Variable = SMARCB1 MUTATION ANALYSIS
D1026V1, survival
                   sevent
clus2                 0   1
  SMARCB1 MUTATED    17   5
  SMARCB1 WILD-TYPE 265  68
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
               22               333 
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
                5                68 
$`SMARCB1 MUTATED`
TCGA-AA-3542 TCGA-AA-3663 TCGA-AA-3713 TCGA-AA-A010 TCGA-AA-A02W TCGA-AU-3779 
       12.99         6.97        19.04        34.98        41.00        14.50 
TCGA-AZ-4315 TCGA-AZ-6599 TCGA-CM-4746 TCGA-CM-5344 TCGA-CM-6172 TCGA-CM-6674 
       58.39         6.77        37.02        22.03        11.01        12.95 
TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6928 TCGA-DM-A1D7 TCGA-G4-6293 TCGA-G4-6303 
        4.80        16.14        11.64        13.32       107.67        65.85 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6626 
       36.00        22.09        26.17        46.75 

$`SMARCB1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03        14.01         0.92        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 
        5.79        22.42        27.42        10.88         0.20        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         2.01       124.27        23.05        20.02 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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-6675 TCGA-CM-6676 
       12.99        13.02        15.02        14.04        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       43.27        15.12        17.85        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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6304 
       13.25         0.53        35.41        19.43        74.56        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6323 
       44.68        55.04        51.75        45.11        36.72        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 
       35.80        91.79        52.80 

  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
              4.8               0.0 
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
           107.67            140.38 
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
           20.535            20.190 
[1] "4.8 - 107.7 (20.5)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1"  
D1026V2, 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       24       102         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SMARCB1 MUTATED           2          0          3          2        2
  SMARCB1 WILD-TYPE        17         10         38         29       33
                   vv
clus                STAGE IVA STAGE IVB
  SMARCB1 MUTATED           0         0
  SMARCB1 WILD-TYPE        13         1
D1026V3, multiclass
            clus
vv           SMARCB1 MUTATED SMARCB1 WILD-TYPE
  STAGE I                  5                59
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                7               102
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                2                17
  STAGE IIIA               0                10
  STAGE IIIB               3                38
  STAGE IIIC               2                29
  STAGE IV                 2                33
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SMARCB1 MUTATED     0   6  16   1
  SMARCB1 WILD-TYPE   9  62 232  40
D1026V4, multiclass
    clus
vv   SMARCB1 MUTATED SMARCB1 WILD-TYPE
  T1               0                 9
  T2               6                62
  T3              16               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
  SMARCB1 MUTATED    15   6   2
  SMARCB1 WILD-TYPE 205  74  64
D1026V5, multiclass
    clus
vv   SMARCB1 MUTATED SMARCB1 WILD-TYPE
  N0              15               205
  N1               6                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"
D1026V6, binary
                   cls
clus                  0   1
  SMARCB1 MUTATED    16   2
  SMARCB1 WILD-TYPE 267  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCB1 MUTATED     16    2
  SMARCB1 WILD-TYPE  267   46
   clus
vv  SMARCB1 MUTATED SMARCB1 WILD-TYPE
  0              16               267
  1               2                46
[1] 2 2
[1] FALSE
D1026V7, 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
D1026V8, binary
                   cls
clus                  0   1
  SMARCB1 MUTATED    21   2
  SMARCB1 WILD-TYPE 296  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCB1 MUTATED     21    2
  SMARCB1 WILD-TYPE  296   46
                               clus
vv                              SMARCB1 MUTATED SMARCB1 WILD-TYPE
  COLON ADENOCARCINOMA                       21               296
  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 238   2  21  20
D1026V9, multiclass
    clus
vv   SMARCB1 MUTATED SMARCB1 WILD-TYPE
  R0              19               238
  R1               0                 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"
D1026V10, 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
D1026V11, 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(1027) Variable = FAM155B MUTATION ANALYSIS
D1027V1, survival
                   sevent
clus2                 0   1
  FAM155B MUTATED     7   1
  FAM155B WILD-TYPE 275  72
  FAM155B MUTATED FAM155B WILD-TYPE 
                8               347 
  FAM155B MUTATED FAM155B WILD-TYPE 
                1                72 
$`FAM155B MUTATED`
TCGA-AA-3815 TCGA-AA-3819 TCGA-AD-6889 TCGA-AY-5543 TCGA-AZ-4315 TCGA-AZ-5403 
       33.04        25.02        56.55        15.75        58.39        62.79 
TCGA-CK-5913 TCGA-CM-5348 
       51.32        22.98 

$`FAM155B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 
       19.04        10.06        35.05         0.99         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 
        0.20        14.50        27.09        16.31         0.95         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  FAM155B MUTATED FAM155B WILD-TYPE 
            15.75              0.00 
  FAM155B MUTATED FAM155B WILD-TYPE 
            62.79            140.38 
  FAM155B MUTATED FAM155B WILD-TYPE 
            42.18             19.99 
[1] "15.8 - 62.8 (42.2)" "0.0 - 140.4 (20.0)"
[1] "hr=" "2.8"
D1027V2, 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       24       104         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM155B MUTATED           0          0          1          0        0
  FAM155B WILD-TYPE        19         10         40         31       35
                   vv
clus                STAGE IVA STAGE IVB
  FAM155B MUTATED           1         0
  FAM155B WILD-TYPE        12         1
D1027V3, multiclass
            clus
vv           FAM155B MUTATED FAM155B WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                5               104
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                1                12
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of 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  68 240  41
D1027V4, multiclass
    clus
vv   FAM155B MUTATED FAM155B WILD-TYPE
  T1               0                 9
  T2               0                68
  T3               8               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
  FAM155B MUTATED     6   2   0
  FAM155B WILD-TYPE 214  78  66
D1027V5, multiclass
    clus
vv   FAM155B MUTATED FAM155B WILD-TYPE
  N0               6               214
  N1               2                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
  FAM155B MUTATED     5   1
  FAM155B WILD-TYPE 278  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM155B MUTATED      5    1
  FAM155B WILD-TYPE  278   47
   clus
vv  FAM155B MUTATED FAM155B WILD-TYPE
  0               5               278
  1               1                47
[1] 2 2
[1] FALSE
D1027V7, 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
D1027V8, binary
                   cls
clus                  0   1
  FAM155B MUTATED     8   0
  FAM155B WILD-TYPE 309  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM155B MUTATED      8    0
  FAM155B WILD-TYPE  309   48
                               clus
vv                              FAM155B MUTATED FAM155B WILD-TYPE
  COLON ADENOCARCINOMA                        8               309
  COLON MUCINOUS ADENOCARCINOMA               0                48
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  FAM155B MUTATED     5   0   0   1
  FAM155B WILD-TYPE 252   2  22  20
D1027V9, multiclass
    clus
vv   FAM155B MUTATED FAM155B WILD-TYPE
  R0               5               252
  R1               0                 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"
D1027V10, 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
D1027V11, 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(1028) Variable = EXT1 MUTATION ANALYSIS
D1028V1, survival
                sevent
clus2              0   1
  EXT1 MUTATED    14   4
  EXT1 WILD-TYPE 268  69
  EXT1 MUTATED EXT1 WILD-TYPE 
            18            337 
  EXT1 MUTATED EXT1 WILD-TYPE 
             4             69 
$`EXT1 MUTATED`
TCGA-A6-5656 TCGA-AA-3517 TCGA-AA-3555 TCGA-AA-3666 TCGA-AA-3715 TCGA-AA-3977 
       32.91        38.99        29.95         2.01        19.04        25.02 
TCGA-AA-A00A TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-5900 TCGA-AD-6963 
       38.04         4.01        34.98        35.01         0.07        27.42 
TCGA-AY-6197 TCGA-AY-6386 TCGA-CK-5912 TCGA-CK-6751 TCGA-CM-6676 TCGA-D5-6536 
       21.44        17.82        49.08       124.27        11.08        17.85 

$`EXT1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        13.02         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       13.94        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AZ-4315 TCGA-AZ-4323 
       16.31         0.95        15.75         0.20        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      102.44        40.34        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 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        15.12         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  EXT1 MUTATED EXT1 WILD-TYPE 
          0.07           0.00 
  EXT1 MUTATED EXT1 WILD-TYPE 
        124.27         140.38 
  EXT1 MUTATED EXT1 WILD-TYPE 
         26.22          20.02 
[1] "0.1 - 124.3 (26.2)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1"  
D1028V2, 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       24       104         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        17         10         40         31       35        13
                vv
clus             STAGE IVB
  EXT1 MUTATED           0
  EXT1 WILD-TYPE         1
D1028V3, multiclass
            clus
vv           EXT1 MUTATED EXT1 WILD-TYPE
  STAGE I               5             59
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             5            104
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             2             17
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  EXT1 MUTATED     0   6  10   2
  EXT1 WILD-TYPE   9  62 238  39
D1028V4, multiclass
    clus
vv   EXT1 MUTATED EXT1 WILD-TYPE
  T1            0              9
  T2            6             62
  T3           10            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
  EXT1 MUTATED    15   2   1
  EXT1 WILD-TYPE 205  78  65
D1028V5, multiclass
    clus
vv   EXT1 MUTATED EXT1 WILD-TYPE
  N0           15            205
  N1            2             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"
D1028V6, binary
                cls
clus               0   1
  EXT1 MUTATED    12   0
  EXT1 WILD-TYPE 271  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  EXT1 MUTATED     12    0
  EXT1 WILD-TYPE  271   48
   clus
vv  EXT1 MUTATED EXT1 WILD-TYPE
  0           12            271
  1            0             48
[1] 2 2
[1] FALSE
D1028V7, 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
D1028V8, binary
                cls
clus               0   1
  EXT1 MUTATED    13   5
  EXT1 WILD-TYPE 304  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  EXT1 MUTATED     13    5
  EXT1 WILD-TYPE  304   43
                               clus
vv                              EXT1 MUTATED EXT1 WILD-TYPE
  COLON ADENOCARCINOMA                    13            304
  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 244   2  22  19
D1028V9, multiclass
    clus
vv   EXT1 MUTATED EXT1 WILD-TYPE
  R0           13            244
  R1            0              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"
D1028V10, 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
D1028V11, 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(1029) Variable = TCF7 MUTATION ANALYSIS
D1029V1, survival
                sevent
clus2              0   1
  TCF7 MUTATED     9   2
  TCF7 WILD-TYPE 273  71
  TCF7 MUTATED TCF7 WILD-TYPE 
            11            344 
  TCF7 MUTATED TCF7 WILD-TYPE 
             2             71 
$`TCF7 MUTATED`
TCGA-A6-5661 TCGA-A6-6780 TCGA-AA-3554 TCGA-AA-3558 TCGA-AA-3713 TCGA-AA-A00N 
       33.53        20.12        17.95        20.98        19.04         4.01 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CM-4746 
        0.07        21.37        49.41         0.33        37.02 

$`TCF7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       24.00        29.95        23.01        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6888 
        0.92        41.00        39.98        18.05        40.96         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13        83.80        22.36        62.79        61.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  TCF7 MUTATED TCF7 WILD-TYPE 
          0.07           0.00 
  TCF7 MUTATED TCF7 WILD-TYPE 
         49.41         140.38 
  TCF7 MUTATED TCF7 WILD-TYPE 
        20.120         20.235 
[1] "0.1 - 49.4 (20.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D1029V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TCF7 MUTATED         4        0        1         4         1         0
  TCF7 WILD-TYPE      60        1       24       105         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TCF7 MUTATED           0          0          0          0        1         0
  TCF7 WILD-TYPE        19         10         41         31       34        13
                vv
clus             STAGE IVB
  TCF7 MUTATED           0
  TCF7 WILD-TYPE         1
D1029V3, multiclass
            clus
vv           TCF7 MUTATED TCF7 WILD-TYPE
  STAGE I               4             60
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             4            105
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TCF7 MUTATED     0   4   6   1
  TCF7 WILD-TYPE   9  64 242  40
D1029V4, multiclass
    clus
vv   TCF7 MUTATED TCF7 WILD-TYPE
  T1            0              9
  T2            4             64
  T3            6            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
  TCF7 MUTATED    11   0   0
  TCF7 WILD-TYPE 209  80  66
D1029V5, multiclass
    clus
vv   TCF7 MUTATED TCF7 WILD-TYPE
  N0           11            209
  N1            0             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"
D1029V6, binary
                cls
clus               0   1
  TCF7 MUTATED     7   1
  TCF7 WILD-TYPE 276  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  TCF7 MUTATED      7    1
  TCF7 WILD-TYPE  276   47
   clus
vv  TCF7 MUTATED TCF7 WILD-TYPE
  0            7            276
  1            1             47
[1] 2 2
[1] FALSE
D1029V7, binary
                cls
clus               0   1
  TCF7 MUTATED     4   7
  TCF7 WILD-TYPE 166 190
[1] "tbl2"
                cls
clus             [,1] [,2]
  TCF7 MUTATED      4    7
  TCF7 WILD-TYPE  166  190
        clus
vv       TCF7 MUTATED TCF7 WILD-TYPE
  FEMALE            4            166
  MALE              7            190
[1] 2 2
[1] FALSE
D1029V8, binary
                cls
clus               0   1
  TCF7 MUTATED     7   4
  TCF7 WILD-TYPE 310  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  TCF7 MUTATED      7    4
  TCF7 WILD-TYPE  310   44
                               clus
vv                              TCF7 MUTATED TCF7 WILD-TYPE
  COLON ADENOCARCINOMA                     7            310
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TCF7 MUTATED     6   0   2   1
  TCF7 WILD-TYPE 251   2  20  20
D1029V9, multiclass
    clus
vv   TCF7 MUTATED TCF7 WILD-TYPE
  R0            6            251
  R1            0              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"
D1029V10, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TCF7 MUTATED                                  0     1
  TCF7 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TCF7 MUTATED                           2     4
  TCF7 WILD-TYPE                        17   172
D1029V11, multiclass
                                  clus
vv                                 TCF7 MUTATED TCF7 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(1030) Variable = HEPACAM2 MUTATION ANALYSIS
D1030V1, survival
                    sevent
clus2                  0   1
  HEPACAM2 MUTATED    11   2
  HEPACAM2 WILD-TYPE 271  71
  HEPACAM2 MUTATED HEPACAM2 WILD-TYPE 
                13                342 
  HEPACAM2 MUTATED HEPACAM2 WILD-TYPE 
                 2                 71 
$`HEPACAM2 MUTATED`
TCGA-A6-3809 TCGA-A6-6781 TCGA-AA-3845 TCGA-AA-3977 TCGA-AU-6004 TCGA-AZ-6600 
       32.75        19.66         0.00        25.02        27.09        12.10 
TCGA-CA-6718 TCGA-CK-4952 TCGA-CM-4743 TCGA-CM-5348 TCGA-D5-6930 TCGA-G4-6315 
        0.10        15.62        23.05        22.98         1.51        36.72 
TCGA-G4-6628 
       52.80 

$`HEPACAM2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02        14.93        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41        49.41         6.77       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.33         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       102.44        40.34        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14         2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 
       53.62        44.68        55.04        51.75        45.11        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 

  HEPACAM2 MUTATED HEPACAM2 WILD-TYPE 
                 0                  0 
  HEPACAM2 MUTATED HEPACAM2 WILD-TYPE 
             52.80             140.38 
  HEPACAM2 MUTATED HEPACAM2 WILD-TYPE 
            22.980             20.155 
[1] "0.0 - 52.8 (23.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D1030V2, 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       25       105         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HEPACAM2 MUTATED           1          0          1          1        2
  HEPACAM2 WILD-TYPE        18         10         40         30       33
                    vv
clus                 STAGE IVA STAGE IVB
  HEPACAM2 MUTATED           0         0
  HEPACAM2 WILD-TYPE        13         1
D1030V3, multiclass
            clus
vv           HEPACAM2 MUTATED HEPACAM2 WILD-TYPE
  STAGE I                   2                 62
  STAGE IA                  0                  1
  STAGE II                  0                 25
  STAGE IIA                 4                105
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 1                 18
  STAGE IIIA                0                 10
  STAGE IIIB                1                 40
  STAGE IIIC                1                 30
  STAGE IV                  2                 33
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  HEPACAM2 MUTATED     0   3   6   4
  HEPACAM2 WILD-TYPE   9  65 242  37
D1030V4, multiclass
    clus
vv   HEPACAM2 MUTATED HEPACAM2 WILD-TYPE
  T1                0                  9
  T2                3                 65
  T3                6                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
  HEPACAM2 MUTATED     8   4   1
  HEPACAM2 WILD-TYPE 212  76  65
D1030V5, multiclass
    clus
vv   HEPACAM2 MUTATED HEPACAM2 WILD-TYPE
  N0                8                212
  N1                4                 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"
D1030V6, binary
                    cls
clus                   0   1
  HEPACAM2 MUTATED     9   2
  HEPACAM2 WILD-TYPE 274  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HEPACAM2 MUTATED      9    2
  HEPACAM2 WILD-TYPE  274   46
   clus
vv  HEPACAM2 MUTATED HEPACAM2 WILD-TYPE
  0                9                274
  1                2                 46
[1] 2 2
[1] FALSE
D1030V7, 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
D1030V8, binary
                    cls
clus                   0   1
  HEPACAM2 MUTATED     9   4
  HEPACAM2 WILD-TYPE 308  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HEPACAM2 MUTATED      9    4
  HEPACAM2 WILD-TYPE  308   44
                               clus
vv                              HEPACAM2 MUTATED HEPACAM2 WILD-TYPE
  COLON ADENOCARCINOMA                         9                308
  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 248   2  22  19
D1030V9, multiclass
    clus
vv   HEPACAM2 MUTATED HEPACAM2 WILD-TYPE
  R0                9                248
  R1                0                  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"
D1030V10, 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
D1030V11, 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(1031) Variable = PSMB8 MUTATION ANALYSIS
D1031V1, survival
                 sevent
clus2               0   1
  PSMB8 MUTATED     4   2
  PSMB8 WILD-TYPE 278  71
  PSMB8 MUTATED PSMB8 WILD-TYPE 
              6             349 
  PSMB8 MUTATED PSMB8 WILD-TYPE 
              2              71 
$`PSMB8 MUTATED`
TCGA-A6-5661 TCGA-AA-3489 TCGA-AD-6895 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CM-5861 
       33.53         7.04         0.72        58.39        49.41        15.02 

$`PSMB8 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  PSMB8 MUTATED PSMB8 WILD-TYPE 
           0.72            0.00 
  PSMB8 MUTATED PSMB8 WILD-TYPE 
          58.39          140.38 
  PSMB8 MUTATED PSMB8 WILD-TYPE 
         24.275          20.190 
[1] "0.7 - 58.4 (24.3)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.5"
D1031V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PSMB8 MUTATED         0        0        2         3         0         0
  PSMB8 WILD-TYPE      64        1       23       106         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        19         10         41         31       35        13
                 vv
clus              STAGE IVB
  PSMB8 MUTATED           0
  PSMB8 WILD-TYPE         1
D1031V3, multiclass
            clus
vv           PSMB8 MUTATED PSMB8 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              3             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PSMB8 MUTATED     0   0   6   0
  PSMB8 WILD-TYPE   9  68 242  41
D1031V4, multiclass
    clus
vv   PSMB8 MUTATED PSMB8 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             6             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
  PSMB8 MUTATED     5   1   0
  PSMB8 WILD-TYPE 215  79  66
D1031V5, multiclass
    clus
vv   PSMB8 MUTATED PSMB8 WILD-TYPE
  N0             5             215
  N1             1              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
  PSMB8 MUTATED     4   0
  PSMB8 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSMB8 MUTATED      4    0
  PSMB8 WILD-TYPE  279   48
   clus
vv  PSMB8 MUTATED PSMB8 WILD-TYPE
  0             4             279
  1             0              48
[1] 2 2
[1] FALSE
D1031V7, binary
                 cls
clus                0   1
  PSMB8 MUTATED     3   3
  PSMB8 WILD-TYPE 167 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSMB8 MUTATED      3    3
  PSMB8 WILD-TYPE  167  194
        clus
vv       PSMB8 MUTATED PSMB8 WILD-TYPE
  FEMALE             3             167
  MALE               3             194
[1] 2 2
[1] FALSE
D1031V8, binary
                 cls
clus                0   1
  PSMB8 MUTATED     6   0
  PSMB8 WILD-TYPE 311  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSMB8 MUTATED      6    0
  PSMB8 WILD-TYPE  311   48
                               clus
vv                              PSMB8 MUTATED PSMB8 WILD-TYPE
  COLON ADENOCARCINOMA                      6             311
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PSMB8 MUTATED     4   0   0   0
  PSMB8 WILD-TYPE 253   2  22  21
D1031V9, multiclass
    clus
vv   PSMB8 MUTATED PSMB8 WILD-TYPE
  R0             4             253
  R1             0               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"
D1031V10, 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     4
  PSMB8 WILD-TYPE                        18   172
D1031V11, 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                                        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(1032) Variable = RDBP MUTATION ANALYSIS
D1032V1, survival
                sevent
clus2              0   1
  RDBP MUTATED     6   0
  RDBP WILD-TYPE 276  73
  RDBP MUTATED RDBP WILD-TYPE 
             6            349 
  RDBP MUTATED RDBP WILD-TYPE 
             0             73 
$`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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        21.99        21.14         2.93         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        16.01        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  RDBP MUTATED RDBP WILD-TYPE 
          6.97           0.00 
  RDBP MUTATED RDBP WILD-TYPE 
         51.32         140.38 
  RDBP MUTATED RDBP WILD-TYPE 
        22.915         20.120 
[1] "7.0 - 51.3 (22.9)"  "0.0 - 140.4 (20.1)"
[1] "hr="     "9200000"
D1032V2, 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       24       107         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        19         10         40         31       35        13
                vv
clus             STAGE IVB
  RDBP MUTATED           0
  RDBP WILD-TYPE         1
D1032V3, multiclass
            clus
vv           RDBP MUTATED RDBP WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             2            107
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RDBP MUTATED     0   1   4   1
  RDBP WILD-TYPE   9  67 244  40
D1032V4, multiclass
    clus
vv   RDBP MUTATED RDBP WILD-TYPE
  T1            0              9
  T2            1             67
  T3            4            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
  RDBP MUTATED     5   1   0
  RDBP WILD-TYPE 215  79  66
D1032V5, multiclass
    clus
vv   RDBP MUTATED RDBP WILD-TYPE
  N0            5            215
  N1            1             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
  RDBP MUTATED     4   0
  RDBP WILD-TYPE 279  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  RDBP MUTATED      4    0
  RDBP WILD-TYPE  279   48
   clus
vv  RDBP MUTATED RDBP WILD-TYPE
  0            4            279
  1            0             48
[1] 2 2
[1] FALSE
D1032V7, 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
D1032V8, binary
                cls
clus               0   1
  RDBP MUTATED     4   2
  RDBP WILD-TYPE 313  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  RDBP MUTATED      4    2
  RDBP WILD-TYPE  313   46
                               clus
vv                              RDBP MUTATED RDBP WILD-TYPE
  COLON ADENOCARCINOMA                     4            313
  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 253   2  22  20
D1032V9, multiclass
    clus
vv   RDBP MUTATED RDBP WILD-TYPE
  R0            4            253
  R1            0              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"
D1032V10, 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
D1032V11, 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(1033) Variable = F2R MUTATION ANALYSIS
D1033V1, survival
               sevent
clus2             0   1
  F2R MUTATED    10   1
  F2R WILD-TYPE 272  72
  F2R MUTATED F2R WILD-TYPE 
           11           344 
  F2R MUTATED F2R WILD-TYPE 
            1            72 
$`F2R MUTATED`
TCGA-A6-6780 TCGA-AA-3511 TCGA-AA-3663 TCGA-AA-3950 TCGA-AZ-6599 TCGA-CA-6717 
       20.12         6.97         6.97        24.00         6.77         0.33 
TCGA-CK-4950 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-6161 TCGA-D5-6540 
       40.34        30.08        15.02        15.02        16.14 

$`F2R WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41        49.41        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
        1.35        17.56       102.44        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01         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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  F2R MUTATED F2R WILD-TYPE 
         0.33          0.00 
  F2R MUTATED F2R WILD-TYPE 
        40.34        140.38 
  F2R MUTATED F2R WILD-TYPE 
        15.02         20.98 
[1] "0.3 - 40.3 (15.0)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.6"
D1033V2, 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       23       104         8         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  F2R MUTATED           0          1          0          0        0         0
  F2R WILD-TYPE        19          9         41         31       35        13
               vv
clus            STAGE IVB
  F2R MUTATED           0
  F2R WILD-TYPE         1
D1033V3, multiclass
            clus
vv           F2R MUTATED F2R WILD-TYPE
  STAGE I              3            61
  STAGE IA             0             1
  STAGE II             2            23
  STAGE IIA            5           104
  STAGE IIB            0             8
  STAGE IIC            0             1
  STAGE III            0            19
  STAGE IIIA           1             9
  STAGE IIIB           0            41
  STAGE IIIC           0            31
  STAGE IV             0            35
  STAGE IVA            0            13
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  F2R MUTATED     0   3   7   1
  F2R WILD-TYPE   9  65 241  40
D1033V4, multiclass
    clus
vv   F2R MUTATED F2R WILD-TYPE
  T1           0             9
  T2           3            65
  T3           7           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
  F2R MUTATED    10   1   0
  F2R WILD-TYPE 210  79  66
D1033V5, multiclass
    clus
vv   F2R MUTATED F2R WILD-TYPE
  N0          10           210
  N1           1            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"
D1033V6, binary
               cls
clus              0   1
  F2R MUTATED     9   0
  F2R WILD-TYPE 274  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  F2R MUTATED      9    0
  F2R WILD-TYPE  274   48
   clus
vv  F2R MUTATED F2R WILD-TYPE
  0           9           274
  1           0            48
[1] 2 2
[1] FALSE
D1033V7, 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
D1033V8, binary
               cls
clus              0   1
  F2R MUTATED     7   4
  F2R WILD-TYPE 310  44
[1] "tbl2"
               cls
clus            [,1] [,2]
  F2R MUTATED      7    4
  F2R WILD-TYPE  310   44
                               clus
vv                              F2R MUTATED F2R WILD-TYPE
  COLON ADENOCARCINOMA                    7           310
  COLON MUCINOUS ADENOCARCINOMA           4            44
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  F2R MUTATED     7   1   0   1
  F2R WILD-TYPE 250   1  22  20
D1033V9, multiclass
    clus
vv   F2R MUTATED F2R WILD-TYPE
  R0           7           250
  R1           1             1
  R2           0            22
  RX           1            20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1033V10, 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
D1033V11, 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(1034) Variable = TRYX3 MUTATION ANALYSIS
D1034V1, survival
                 sevent
clus2               0   1
  TRYX3 MUTATED     4   2
  TRYX3 WILD-TYPE 278  71
  TRYX3 MUTATED TRYX3 WILD-TYPE 
              6             349 
  TRYX3 MUTATED TRYX3 WILD-TYPE 
              2              71 
$`TRYX3 MUTATED`
TCGA-A6-5665 TCGA-AA-3660 TCGA-AA-3852 TCGA-AD-6964 TCGA-CA-6718 TCGA-D5-6926 
       22.06        78.08         0.00        10.88         0.10         9.04 

$`TRYX3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        61.02         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       10.06         0.00        33.07        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.33         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  TRYX3 MUTATED TRYX3 WILD-TYPE 
              0               0 
  TRYX3 MUTATED TRYX3 WILD-TYPE 
          78.08          140.38 
  TRYX3 MUTATED TRYX3 WILD-TYPE 
           9.96           20.28 
[1] "0.0 - 78.1 (10.0)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "2.1"
D1034V2, 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       24       106         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TRYX3 MUTATED           0          1          0          0        0         0
  TRYX3 WILD-TYPE        19          9         41         31       35        13
                 vv
clus              STAGE IVB
  TRYX3 MUTATED           0
  TRYX3 WILD-TYPE         1
D1034V3, multiclass
            clus
vv           TRYX3 MUTATED TRYX3 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              3             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TRYX3 MUTATED     0   0   4   2
  TRYX3 WILD-TYPE   9  68 244  39
D1034V4, multiclass
    clus
vv   TRYX3 MUTATED TRYX3 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             4             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
  TRYX3 MUTATED     4   1   1
  TRYX3 WILD-TYPE 216  79  65
D1034V5, multiclass
    clus
vv   TRYX3 MUTATED TRYX3 WILD-TYPE
  N0             4             216
  N1             1              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"
D1034V6, binary
                 cls
clus                0   1
  TRYX3 MUTATED     5   0
  TRYX3 WILD-TYPE 278  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRYX3 MUTATED      5    0
  TRYX3 WILD-TYPE  278   48
   clus
vv  TRYX3 MUTATED TRYX3 WILD-TYPE
  0             5             278
  1             0              48
[1] 2 2
[1] FALSE
D1034V7, 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
D1034V8, binary
                 cls
clus                0   1
  TRYX3 MUTATED     5   1
  TRYX3 WILD-TYPE 312  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRYX3 MUTATED      5    1
  TRYX3 WILD-TYPE  312   47
                               clus
vv                              TRYX3 MUTATED TRYX3 WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  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 253   2  22  20
D1034V9, multiclass
    clus
vv   TRYX3 MUTATED TRYX3 WILD-TYPE
  R0             4             253
  R1             0               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"
D1034V10, 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
D1034V11, 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(1035) Variable = SLC27A3 MUTATION ANALYSIS
D1035V1, survival
                   sevent
clus2                 0   1
  SLC27A3 MUTATED     5   1
  SLC27A3 WILD-TYPE 277  72
  SLC27A3 MUTATED SLC27A3 WILD-TYPE 
                6               349 
  SLC27A3 MUTATED SLC27A3 WILD-TYPE 
                1                72 
$`SLC27A3 MUTATED`
TCGA-A6-6780 TCGA-AA-3815 TCGA-AD-6889 TCGA-F4-6570 TCGA-G4-6588 TCGA-G4-6628 
       20.12        33.04        56.55         6.18        26.17        52.80 

$`SLC27A3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 
       46.75 

  SLC27A3 MUTATED SLC27A3 WILD-TYPE 
             6.18              0.00 
  SLC27A3 MUTATED SLC27A3 WILD-TYPE 
            56.55            140.38 
  SLC27A3 MUTATED SLC27A3 WILD-TYPE 
           29.605            20.020 
[1] "6.2 - 56.5 (29.6)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1.6"
D1035V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC27A3 MUTATED         1        0        0         5         0         0
  SLC27A3 WILD-TYPE      63        1       25       104         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC27A3 MUTATED           0          0          0          0        0
  SLC27A3 WILD-TYPE        19         10         41         31       35
                   vv
clus                STAGE IVA STAGE IVB
  SLC27A3 MUTATED           0         0
  SLC27A3 WILD-TYPE        13         1
D1035V3, multiclass
            clus
vv           SLC27A3 MUTATED SLC27A3 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                5               104
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC27A3 MUTATED     0   1   5   0
  SLC27A3 WILD-TYPE   9  67 243  41
D1035V4, multiclass
    clus
vv   SLC27A3 MUTATED SLC27A3 WILD-TYPE
  T1               0                 9
  T2               1                67
  T3               5               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
  SLC27A3 MUTATED     6   0   0
  SLC27A3 WILD-TYPE 214  80  66
D1035V5, multiclass
    clus
vv   SLC27A3 MUTATED SLC27A3 WILD-TYPE
  N0               6               214
  N1               0                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"
D1035V6, binary
                   cls
clus                  0   1
  SLC27A3 MUTATED     5   0
  SLC27A3 WILD-TYPE 278  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC27A3 MUTATED      5    0
  SLC27A3 WILD-TYPE  278   48
   clus
vv  SLC27A3 MUTATED SLC27A3 WILD-TYPE
  0               5               278
  1               0                48
[1] 2 2
[1] FALSE
D1035V7, binary
                   cls
clus                  0   1
  SLC27A3 MUTATED     3   3
  SLC27A3 WILD-TYPE 167 194
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC27A3 MUTATED      3    3
  SLC27A3 WILD-TYPE  167  194
        clus
vv       SLC27A3 MUTATED SLC27A3 WILD-TYPE
  FEMALE               3               167
  MALE                 3               194
[1] 2 2
[1] FALSE
D1035V8, binary
                   cls
clus                  0   1
  SLC27A3 MUTATED     5   1
  SLC27A3 WILD-TYPE 312  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC27A3 MUTATED      5    1
  SLC27A3 WILD-TYPE  312   47
                               clus
vv                              SLC27A3 MUTATED SLC27A3 WILD-TYPE
  COLON ADENOCARCINOMA                        5               312
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SLC27A3 MUTATED     4   0   0   0
  SLC27A3 WILD-TYPE 253   2  22  21
D1035V9, multiclass
    clus
vv   SLC27A3 MUTATED SLC27A3 WILD-TYPE
  R0               4               253
  R1               0                 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"
D1035V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC27A3 MUTATED                                  0     1
  SLC27A3 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC27A3 MUTATED                           0     4
  SLC27A3 WILD-TYPE                        19   172
D1035V11, multiclass
                                  clus
vv                                 SLC27A3 MUTATED SLC27A3 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(1036) Variable = AKAP11 MUTATION ANALYSIS
D1036V1, survival
                  sevent
clus2                0   1
  AKAP11 MUTATED    18   3
  AKAP11 WILD-TYPE 264  70
  AKAP11 MUTATED AKAP11 WILD-TYPE 
              21              334 
  AKAP11 MUTATED AKAP11 WILD-TYPE 
               3               70 
$`AKAP11 MUTATED`
TCGA-A6-3809 TCGA-AA-3663 TCGA-AA-3861 TCGA-AA-3950 TCGA-AA-A00E TCGA-AA-A00R 
       32.75         6.97        30.05        24.00        30.02         0.99 
TCGA-AA-A010 TCGA-AD-6895 TCGA-AD-6901 TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6718 
       34.98         0.72        22.42         3.29         0.33         0.10 
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        12.26        13.41 
TCGA-DM-A1DA TCGA-F4-6856 TCGA-G4-6307 
        7.50        19.43        55.04 

$`AKAP11 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F 
        7.96        27.02        13.94        38.04        19.00        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 
        4.21        56.55         0.79         5.79        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 
        1.94         2.24         3.06         3.25         0.07         0.26 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 
        1.35        17.56       102.44        40.34        49.08        51.32 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99         2.93         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 
       16.01        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-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       45.40        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 
      107.67        74.56        65.85        53.62        44.68        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  AKAP11 MUTATED AKAP11 WILD-TYPE 
             0.1              0.0 
  AKAP11 MUTATED AKAP11 WILD-TYPE 
           55.04           140.38 
  AKAP11 MUTATED AKAP11 WILD-TYPE 
           15.62            20.63 
[1] "0.1 - 55.0 (15.6)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "1"  
D1036V2, 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       24       102         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AKAP11 MUTATED           1          0          3          1        1
  AKAP11 WILD-TYPE        18         10         38         30       34
                  vv
clus               STAGE IVA STAGE IVB
  AKAP11 MUTATED           0         0
  AKAP11 WILD-TYPE        13         1
D1036V3, multiclass
            clus
vv           AKAP11 MUTATED AKAP11 WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               7              102
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              3               38
  STAGE IIIC              1               30
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  AKAP11 MUTATED     2   2  15   3
  AKAP11 WILD-TYPE   7  66 233  38
D1036V4, multiclass
    clus
vv   AKAP11 MUTATED AKAP11 WILD-TYPE
  T1              2                7
  T2              2               66
  T3             15              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
  AKAP11 MUTATED    15   5   2
  AKAP11 WILD-TYPE 205  75  64
D1036V5, multiclass
    clus
vv   AKAP11 MUTATED AKAP11 WILD-TYPE
  N0             15              205
  N1              5               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"
D1036V6, binary
                  cls
clus                 0   1
  AKAP11 MUTATED    19   1
  AKAP11 WILD-TYPE 264  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKAP11 MUTATED     19    1
  AKAP11 WILD-TYPE  264   47
   clus
vv  AKAP11 MUTATED AKAP11 WILD-TYPE
  0             19              264
  1              1               47
[1] 2 2
[1] FALSE
D1036V7, 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
D1036V8, binary
                  cls
clus                 0   1
  AKAP11 MUTATED    17   5
  AKAP11 WILD-TYPE 300  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKAP11 MUTATED     17    5
  AKAP11 WILD-TYPE  300   43
                               clus
vv                              AKAP11 MUTATED AKAP11 WILD-TYPE
  COLON ADENOCARCINOMA                      17              300
  COLON MUCINOUS ADENOCARCINOMA              5               43
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  AKAP11 MUTATED    15   0   0   4
  AKAP11 WILD-TYPE 242   2  22  17
D1036V9, multiclass
    clus
vv   AKAP11 MUTATED AKAP11 WILD-TYPE
  R0             15              242
  R1              0                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"
D1036V10, 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
D1036V11, 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(1037) Variable = TRIM24 MUTATION ANALYSIS
D1037V1, survival
                  sevent
clus2                0   1
  TRIM24 MUTATED     8   8
  TRIM24 WILD-TYPE 274  65
  TRIM24 MUTATED TRIM24 WILD-TYPE 
              16              339 
  TRIM24 MUTATED TRIM24 WILD-TYPE 
               8               65 
$`TRIM24 MUTATED`
TCGA-A6-6782 TCGA-AA-3811 TCGA-AA-3833 TCGA-AA-A00N TCGA-AA-A02W TCGA-AD-5900 
       20.28        10.06        15.95         4.01        41.00         0.07 
TCGA-AZ-5403 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-CA-6718 TCGA-D5-6535 
       62.79         6.77        12.10        29.56         0.10        15.12 
TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-G4-6293 TCGA-G4-6628 
       12.59         7.50       107.67        52.80 

$`TRIM24 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        19.66         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03        14.01         0.92        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 
       58.39         1.41         5.13        83.80        22.36        61.41 
TCGA-AZ-6598 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       49.41       100.01         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.33         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        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-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       26.17        91.79        46.75 

  TRIM24 MUTATED TRIM24 WILD-TYPE 
            0.07             0.00 
  TRIM24 MUTATED TRIM24 WILD-TYPE 
          107.67           140.38 
  TRIM24 MUTATED TRIM24 WILD-TYPE 
          13.855           20.980 
[1] "0.1 - 107.7 (13.9)" "0.0 - 140.4 (21.0)"
[1] "hr=" "2.6"
D1037V2, 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       24       106         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRIM24 MUTATED           2          0          1          1        1
  TRIM24 WILD-TYPE        17         10         40         30       34
                  vv
clus               STAGE IVA STAGE IVB
  TRIM24 MUTATED           0         0
  TRIM24 WILD-TYPE        13         1
D1037V3, multiclass
            clus
vv           TRIM24 MUTATED TRIM24 WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               3              106
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               2               17
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              1               30
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TRIM24 MUTATED     0   5   9   3
  TRIM24 WILD-TYPE   9  63 239  38
D1037V4, multiclass
    clus
vv   TRIM24 MUTATED TRIM24 WILD-TYPE
  T1              0                9
  T2              5               63
  T3              9              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
  TRIM24 MUTATED    10   5   2
  TRIM24 WILD-TYPE 210  75  64
D1037V5, multiclass
    clus
vv   TRIM24 MUTATED TRIM24 WILD-TYPE
  N0             10              210
  N1              5               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"
D1037V6, binary
                  cls
clus                 0   1
  TRIM24 MUTATED     9   1
  TRIM24 WILD-TYPE 274  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM24 MUTATED      9    1
  TRIM24 WILD-TYPE  274   47
   clus
vv  TRIM24 MUTATED TRIM24 WILD-TYPE
  0              9              274
  1              1               47
[1] 2 2
[1] FALSE
D1037V7, 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
D1037V8, binary
                  cls
clus                 0   1
  TRIM24 MUTATED    15   2
  TRIM24 WILD-TYPE 302  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM24 MUTATED     15    2
  TRIM24 WILD-TYPE  302   46
                               clus
vv                              TRIM24 MUTATED TRIM24 WILD-TYPE
  COLON ADENOCARCINOMA                      15              302
  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 249   2  22  19
D1037V9, multiclass
    clus
vv   TRIM24 MUTATED TRIM24 WILD-TYPE
  R0              8              249
  R1              0                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"
D1037V10, 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
D1037V11, 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(1038) Variable = ASB18 MUTATION ANALYSIS
D1038V1, survival
                 sevent
clus2               0   1
  ASB18 MUTATED     6   0
  ASB18 WILD-TYPE 276  73
  ASB18 MUTATED ASB18 WILD-TYPE 
              6             349 
  ASB18 MUTATED ASB18 WILD-TYPE 
              0              73 
$`ASB18 MUTATED`
TCGA-AD-6895 TCGA-AZ-4315 TCGA-CA-6715 TCGA-DM-A1HB TCGA-G4-6309 TCGA-G4-6588 
        0.72        58.39         0.07       135.65        51.75        26.17 

$`ASB18 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21        56.55         0.79         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 
       52.80 

  ASB18 MUTATED ASB18 WILD-TYPE 
           0.07            0.00 
  ASB18 MUTATED ASB18 WILD-TYPE 
         135.65          140.38 
  ASB18 MUTATED ASB18 WILD-TYPE 
          38.96           20.12 
[1] "0.1 - 135.7 (39.0)" "0.0 - 140.4 (20.1)"
[1] "hr="     "2.6e+07"
D1038V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ASB18 MUTATED         0        0        0         2         0         0
  ASB18 WILD-TYPE      64        1       25       107         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ASB18 MUTATED           0          0          3          0        1         0
  ASB18 WILD-TYPE        19         10         38         31       34        13
                 vv
clus              STAGE IVB
  ASB18 MUTATED           0
  ASB18 WILD-TYPE         1
D1038V3, multiclass
            clus
vv           ASB18 MUTATED ASB18 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              2             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             3              38
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ASB18 MUTATED     0   0   6   1
  ASB18 WILD-TYPE   9  68 242  40
D1038V4, multiclass
    clus
vv   ASB18 MUTATED ASB18 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             6             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
  ASB18 MUTATED     2   5   0
  ASB18 WILD-TYPE 218  75  66
D1038V5, multiclass
    clus
vv   ASB18 MUTATED ASB18 WILD-TYPE
  N0             2             218
  N1             5              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"
D1038V6, binary
                 cls
clus                0   1
  ASB18 MUTATED     5   1
  ASB18 WILD-TYPE 278  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASB18 MUTATED      5    1
  ASB18 WILD-TYPE  278   47
   clus
vv  ASB18 MUTATED ASB18 WILD-TYPE
  0             5             278
  1             1              47
[1] 2 2
[1] FALSE
D1038V7, binary
                 cls
clus                0   1
  ASB18 MUTATED     3   4
  ASB18 WILD-TYPE 167 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASB18 MUTATED      3    4
  ASB18 WILD-TYPE  167  193
        clus
vv       ASB18 MUTATED ASB18 WILD-TYPE
  FEMALE             3             167
  MALE               4             193
[1] 2 2
[1] FALSE
D1038V8, binary
                 cls
clus                0   1
  ASB18 MUTATED     7   0
  ASB18 WILD-TYPE 310  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASB18 MUTATED      7    0
  ASB18 WILD-TYPE  310   48
                               clus
vv                              ASB18 MUTATED ASB18 WILD-TYPE
  COLON ADENOCARCINOMA                      7             310
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ASB18 MUTATED     3   0   1   1
  ASB18 WILD-TYPE 254   2  21  20
D1038V9, multiclass
    clus
vv   ASB18 MUTATED ASB18 WILD-TYPE
  R0             3             254
  R1             0               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"
D1038V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ASB18 MUTATED                                  0     1
  ASB18 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ASB18 MUTATED                           1     4
  ASB18 WILD-TYPE                        18   172
D1038V11, multiclass
                                  clus
vv                                 ASB18 MUTATED ASB18 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(1039) Variable = RNASEL MUTATION ANALYSIS
D1039V1, survival
                  sevent
clus2                0   1
  RNASEL MUTATED     9   3
  RNASEL WILD-TYPE 273  70
  RNASEL MUTATED RNASEL WILD-TYPE 
              12              343 
  RNASEL MUTATED RNASEL WILD-TYPE 
               3               70 
$`RNASEL MUTATED`
TCGA-A6-3809 TCGA-AA-3517 TCGA-AA-A00N TCGA-AD-5900 TCGA-AD-6895 TCGA-AZ-4315 
       32.75        38.99         4.01         0.07         0.72        58.39 
TCGA-AZ-6600 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5916 TCGA-D5-6922 TCGA-F4-6808 
       12.10         0.33         0.10        21.14        10.13        33.67 

$`RNASEL WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        13.02         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37         4.21        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41        49.41         6.77       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07         0.26         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
       40.34        15.62        49.08        51.32        21.99         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 
        1.55        16.31        29.59        16.24        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  RNASEL MUTATED RNASEL WILD-TYPE 
            0.07             0.00 
  RNASEL MUTATED RNASEL WILD-TYPE 
           58.39           140.38 
  RNASEL MUTATED RNASEL WILD-TYPE 
          11.115           20.280 
[1] "0.1 - 58.4 (11.1)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.9"
D1039V2, 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       25       105         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RNASEL MUTATED           0          1          0          0        1
  RNASEL WILD-TYPE        19          9         41         31       34
                  vv
clus               STAGE IVA STAGE IVB
  RNASEL MUTATED           0         0
  RNASEL WILD-TYPE        13         1
D1039V3, multiclass
            clus
vv           RNASEL MUTATED RNASEL WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               4              105
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              1                9
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  RNASEL MUTATED     2   1   6   3
  RNASEL WILD-TYPE   7  67 242  38
D1039V4, multiclass
    clus
vv   RNASEL MUTATED RNASEL WILD-TYPE
  T1              2                7
  T2              1               67
  T3              6              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
  RNASEL MUTATED     9   3   0
  RNASEL WILD-TYPE 211  77  66
D1039V5, multiclass
    clus
vv   RNASEL MUTATED RNASEL WILD-TYPE
  N0              9              211
  N1              3               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"
D1039V6, binary
                  cls
clus                 0   1
  RNASEL MUTATED     9   1
  RNASEL WILD-TYPE 274  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNASEL MUTATED      9    1
  RNASEL WILD-TYPE  274   47
   clus
vv  RNASEL MUTATED RNASEL WILD-TYPE
  0              9              274
  1              1               47
[1] 2 2
[1] FALSE
D1039V7, 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
D1039V8, binary
                  cls
clus                 0   1
  RNASEL MUTATED     8   4
  RNASEL WILD-TYPE 309  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNASEL MUTATED      8    4
  RNASEL WILD-TYPE  309   44
                               clus
vv                              RNASEL MUTATED RNASEL WILD-TYPE
  COLON ADENOCARCINOMA                       8              309
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  RNASEL MUTATED     7   0   0   3
  RNASEL WILD-TYPE 250   2  22  18
D1039V9, multiclass
    clus
vv   RNASEL MUTATED RNASEL WILD-TYPE
  R0              7              250
  R1              0                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"
D1039V10, 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
D1039V11, 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(1040) Variable = YES1 MUTATION ANALYSIS
D1040V1, survival
                sevent
clus2              0   1
  YES1 MUTATED     6   3
  YES1 WILD-TYPE 276  70
  YES1 MUTATED YES1 WILD-TYPE 
             9            346 
  YES1 MUTATED YES1 WILD-TYPE 
             3             70 
$`YES1 MUTATED`
TCGA-AA-3663 TCGA-AA-3819 TCGA-AU-3779 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-CA-6718 
        6.97        25.02        14.50         6.77       100.01         0.10 
TCGA-D5-6928 TCGA-DM-A1HB TCGA-F4-6809 
       11.64       135.65        13.25 

$`YES1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05        33.04         0.99         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41        49.41        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       16.24        33.67         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  YES1 MUTATED YES1 WILD-TYPE 
           0.1            0.0 
  YES1 MUTATED YES1 WILD-TYPE 
        135.65         140.38 
  YES1 MUTATED YES1 WILD-TYPE 
         13.25          20.63 
[1] "0.1 - 135.7 (13.2)" "0.0 - 140.4 (20.6)"
[1] "hr=" "1.3"
D1040V2, 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       23       105         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        19         10         40         31       35        12
                vv
clus             STAGE IVB
  YES1 MUTATED           0
  YES1 WILD-TYPE         1
D1040V3, multiclass
            clus
vv           YES1 MUTATED YES1 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             4            105
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 240  41
D1040V4, multiclass
    clus
vv   YES1 MUTATED YES1 WILD-TYPE
  T1            0              9
  T2            1             67
  T3            8            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
  YES1 MUTATED     7   2   0
  YES1 WILD-TYPE 213  78  66
D1040V5, multiclass
    clus
vv   YES1 MUTATED YES1 WILD-TYPE
  N0            7            213
  N1            2             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"
D1040V6, binary
                cls
clus               0   1
  YES1 MUTATED     7   1
  YES1 WILD-TYPE 276  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  YES1 MUTATED      7    1
  YES1 WILD-TYPE  276   47
   clus
vv  YES1 MUTATED YES1 WILD-TYPE
  0            7            276
  1            1             47
[1] 2 2
[1] FALSE
D1040V7, 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
D1040V8, binary
                cls
clus               0   1
  YES1 MUTATED     8   1
  YES1 WILD-TYPE 309  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  YES1 MUTATED      8    1
  YES1 WILD-TYPE  309   47
                               clus
vv                              YES1 MUTATED YES1 WILD-TYPE
  COLON ADENOCARCINOMA                     8            309
  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 252   2  22  20
D1040V9, multiclass
    clus
vv   YES1 MUTATED YES1 WILD-TYPE
  R0            5            252
  R1            0              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"
D1040V10, 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
D1040V11, 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(1041) Variable = MAP3K10 MUTATION ANALYSIS
D1041V1, survival
                   sevent
clus2                 0   1
  MAP3K10 MUTATED     8   2
  MAP3K10 WILD-TYPE 274  71
  MAP3K10 MUTATED MAP3K10 WILD-TYPE 
               10               345 
  MAP3K10 MUTATED MAP3K10 WILD-TYPE 
                2                71 
$`MAP3K10 MUTATED`
TCGA-AA-3663 TCGA-AA-3821 TCGA-AA-3947 TCGA-AD-6964 TCGA-D5-6535 TCGA-D5-6540 
        6.97         1.02        33.01        10.88        15.12        16.14 
TCGA-D5-6928 TCGA-DM-A1D6 TCGA-DM-A1HB TCGA-G4-6628 
       11.64        49.91       135.65        52.80 

$`MAP3K10 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 
       10.06        35.05        33.04         0.99        25.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        43.27        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       26.17        91.79        46.75 

  MAP3K10 MUTATED MAP3K10 WILD-TYPE 
             1.02              0.00 
  MAP3K10 MUTATED MAP3K10 WILD-TYPE 
           135.65            140.38 
  MAP3K10 MUTATED MAP3K10 WILD-TYPE 
            15.63             20.28 
[1] "1.0 - 135.7 (15.6)" "0.0 - 140.4 (20.3)"
[1] "hr=" "1.3"
D1041V2, 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       24       107         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAP3K10 MUTATED           0          0          2          0        0
  MAP3K10 WILD-TYPE        19         10         39         31       35
                   vv
clus                STAGE IVA STAGE IVB
  MAP3K10 MUTATED           0         0
  MAP3K10 WILD-TYPE        13         1
D1041V3, multiclass
            clus
vv           MAP3K10 MUTATED MAP3K10 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                2               107
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               2                39
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  MAP3K10 MUTATED     0   3   5   2
  MAP3K10 WILD-TYPE   9  65 243  39
D1041V4, multiclass
    clus
vv   MAP3K10 MUTATED MAP3K10 WILD-TYPE
  T1               0                 9
  T2               3                65
  T3               5               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
  MAP3K10 MUTATED     7   2   1
  MAP3K10 WILD-TYPE 213  78  65
D1041V5, multiclass
    clus
vv   MAP3K10 MUTATED MAP3K10 WILD-TYPE
  N0               7               213
  N1               2                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"
D1041V6, binary
                   cls
clus                  0   1
  MAP3K10 MUTATED     8   0
  MAP3K10 WILD-TYPE 275  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MAP3K10 MUTATED      8    0
  MAP3K10 WILD-TYPE  275   48
   clus
vv  MAP3K10 MUTATED MAP3K10 WILD-TYPE
  0               8               275
  1               0                48
[1] 2 2
[1] FALSE
D1041V7, 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
D1041V8, binary
                   cls
clus                  0   1
  MAP3K10 MUTATED     5   5
  MAP3K10 WILD-TYPE 312  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MAP3K10 MUTATED      5    5
  MAP3K10 WILD-TYPE  312   43
                               clus
vv                              MAP3K10 MUTATED MAP3K10 WILD-TYPE
  COLON ADENOCARCINOMA                        5               312
  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 251   2  22  20
D1041V9, multiclass
    clus
vv   MAP3K10 MUTATED MAP3K10 WILD-TYPE
  R0               6               251
  R1               0                 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"
D1041V10, 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
D1041V11, 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(1042) Variable = SV2A MUTATION ANALYSIS
D1042V1, survival
                sevent
clus2              0   1
  SV2A MUTATED    17   3
  SV2A WILD-TYPE 265  70
  SV2A MUTATED SV2A WILD-TYPE 
            20            335 
  SV2A MUTATED SV2A WILD-TYPE 
             3             70 
$`SV2A MUTATED`
TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3672 TCGA-AA-3864 TCGA-AA-3950 
       19.66         3.02        63.98         0.92        53.00        24.00 
TCGA-AA-3956 TCGA-AA-A010 TCGA-AU-6004 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-CA-6717 
       34.03        34.98        27.09        49.41        12.10         0.33 
TCGA-CK-4952 TCGA-CM-5349 TCGA-CM-6161 TCGA-CM-6163 TCGA-D5-6928 TCGA-D5-6930 
       15.62        30.08        15.02        14.04        11.64         1.51 
TCGA-DM-A28E TCGA-G4-6321 
      119.93        22.09 

$`SV2A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       23.87        20.12        20.28         7.04         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01         2.01        20.98         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 
       83.80        22.36        62.79        61.41         6.77       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 
        1.35        17.56       102.44        40.34        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
       81.37        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       55.04        51.75        45.11        36.72        36.00        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  SV2A MUTATED SV2A WILD-TYPE 
          0.33           0.00 
  SV2A MUTATED SV2A WILD-TYPE 
        119.93         140.38 
  SV2A MUTATED SV2A WILD-TYPE 
        20.875         20.190 
[1] "0.3 - 119.9 (20.9)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.5"
D1042V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SV2A MUTATED         3        0        4         7         1         0
  SV2A WILD-TYPE      61        1       21       102         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SV2A MUTATED           3          0          0          1        1         0
  SV2A WILD-TYPE        16         10         41         30       34        13
                vv
clus             STAGE IVB
  SV2A MUTATED           0
  SV2A WILD-TYPE         1
D1042V3, multiclass
            clus
vv           SV2A MUTATED SV2A WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              4             21
  STAGE IIA             7            102
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             3             16
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            1             30
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SV2A MUTATED     1   3  12   4
  SV2A WILD-TYPE   8  65 236  37
D1042V4, multiclass
    clus
vv   SV2A MUTATED SV2A WILD-TYPE
  T1            1              8
  T2            3             65
  T3           12            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
  SV2A MUTATED    15   4   1
  SV2A WILD-TYPE 205  76  65
D1042V5, multiclass
    clus
vv   SV2A MUTATED SV2A WILD-TYPE
  N0           15            205
  N1            4             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"
D1042V6, binary
                cls
clus               0   1
  SV2A MUTATED    16   1
  SV2A WILD-TYPE 267  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  SV2A MUTATED     16    1
  SV2A WILD-TYPE  267   47
   clus
vv  SV2A MUTATED SV2A WILD-TYPE
  0           16            267
  1            1             47
[1] 2 2
[1] FALSE
D1042V7, binary
                cls
clus               0   1
  SV2A MUTATED    11   9
  SV2A WILD-TYPE 159 188
[1] "tbl2"
                cls
clus             [,1] [,2]
  SV2A MUTATED     11    9
  SV2A WILD-TYPE  159  188
        clus
vv       SV2A MUTATED SV2A WILD-TYPE
  FEMALE           11            159
  MALE              9            188
[1] 2 2
[1] FALSE
D1042V8, binary
                cls
clus               0   1
  SV2A MUTATED    14   6
  SV2A WILD-TYPE 303  42
[1] "tbl2"
                cls
clus             [,1] [,2]
  SV2A MUTATED     14    6
  SV2A WILD-TYPE  303   42
                               clus
vv                              SV2A MUTATED SV2A WILD-TYPE
  COLON ADENOCARCINOMA                    14            303
  COLON MUCINOUS ADENOCARCINOMA            6             42
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SV2A MUTATED    15   0   0   2
  SV2A WILD-TYPE 242   2  22  19
D1042V9, multiclass
    clus
vv   SV2A MUTATED SV2A WILD-TYPE
  R0           15            242
  R1            0              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"
D1042V10, 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    11
  SV2A WILD-TYPE                        18   165
D1042V11, 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                                      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(1043) Variable = RPN2 MUTATION ANALYSIS
D1043V1, survival
                sevent
clus2              0   1
  RPN2 MUTATED     5   0
  RPN2 WILD-TYPE 277  73
  RPN2 MUTATED RPN2 WILD-TYPE 
             5            350 
  RPN2 MUTATED RPN2 WILD-TYPE 
             0             73 
$`RPN2 MUTATED`
TCGA-A6-5666 TCGA-AA-3697 TCGA-CM-5861 TCGA-CM-5868 TCGA-G4-6293 
       32.71        85.05        15.02        17.03       107.67 

$`RPN2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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-6161 
       30.08        16.01         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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        35.41        19.43        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  RPN2 MUTATED RPN2 WILD-TYPE 
         15.02           0.00 
  RPN2 MUTATED RPN2 WILD-TYPE 
        107.67         140.38 
  RPN2 MUTATED RPN2 WILD-TYPE 
        32.710         20.155 
[1] "15.0 - 107.7 (32.7)" "0.0 - 140.4 (20.2)" 
[1] "hr="     "2.6e+07"
D1043V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RPN2 MUTATED         0        0        0         1         0         1
  RPN2 WILD-TYPE      64        1       25       108         8         0
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RPN2 MUTATED           2          0          0          0        0         1
  RPN2 WILD-TYPE        17         10         41         31       35        12
                vv
clus             STAGE IVB
  RPN2 MUTATED           0
  RPN2 WILD-TYPE         1
D1043V3, multiclass
            clus
vv           RPN2 MUTATED RPN2 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             1            108
  STAGE IIB             0              8
  STAGE IIC             1              0
  STAGE III             2             17
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RPN2 MUTATED     0   0   3   2
  RPN2 WILD-TYPE   9  68 245  39
D1043V4, multiclass
    clus
vv   RPN2 MUTATED RPN2 WILD-TYPE
  T1            0              9
  T2            0             68
  T3            3            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
  RPN2 MUTATED     3   2   0
  RPN2 WILD-TYPE 217  78  66
D1043V5, multiclass
    clus
vv   RPN2 MUTATED RPN2 WILD-TYPE
  N0            3            217
  N1            2             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"
D1043V6, binary
                cls
clus               0   1
  RPN2 MUTATED     4   1
  RPN2 WILD-TYPE 279  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPN2 MUTATED      4    1
  RPN2 WILD-TYPE  279   47
   clus
vv  RPN2 MUTATED RPN2 WILD-TYPE
  0            4            279
  1            1             47
[1] 2 2
[1] FALSE
D1043V7, binary
                cls
clus               0   1
  RPN2 MUTATED     3   2
  RPN2 WILD-TYPE 167 195
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPN2 MUTATED      3    2
  RPN2 WILD-TYPE  167  195
        clus
vv       RPN2 MUTATED RPN2 WILD-TYPE
  FEMALE            3            167
  MALE              2            195
[1] 2 2
[1] FALSE
D1043V8, binary
                cls
clus               0   1
  RPN2 MUTATED     5   0
  RPN2 WILD-TYPE 312  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPN2 MUTATED      5    0
  RPN2 WILD-TYPE  312   48
                               clus
vv                              RPN2 MUTATED RPN2 WILD-TYPE
  COLON ADENOCARCINOMA                     5            312
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RPN2 MUTATED     4   0   0   0
  RPN2 WILD-TYPE 253   2  22  21
D1043V9, multiclass
    clus
vv   RPN2 MUTATED RPN2 WILD-TYPE
  R0            4            253
  R1            0              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"
D1043V10, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RPN2 MUTATED                                  0     0
  RPN2 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RPN2 MUTATED                           0     4
  RPN2 WILD-TYPE                        19   172
D1043V11, multiclass
                                  clus
vv                                 RPN2 MUTATED RPN2 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(1044) Variable = LRIG2 MUTATION ANALYSIS
D1044V1, survival
                 sevent
clus2               0   1
  LRIG2 MUTATED     6   3
  LRIG2 WILD-TYPE 276  70
  LRIG2 MUTATED LRIG2 WILD-TYPE 
              9             346 
  LRIG2 MUTATED LRIG2 WILD-TYPE 
              3              70 
$`LRIG2 MUTATED`
TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3845 TCGA-AA-3947 TCGA-AY-6197 TCGA-AZ-6599 
       22.06        63.98         0.00        33.01        21.44         6.77 
TCGA-CK-4947 TCGA-D5-6541 TCGA-F4-6570 
       17.56        15.58         6.18 

$`LRIG2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02        14.93        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41        49.41        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
        1.35       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  LRIG2 MUTATED LRIG2 WILD-TYPE 
              0               0 
  LRIG2 MUTATED LRIG2 WILD-TYPE 
          63.98          140.38 
  LRIG2 MUTATED LRIG2 WILD-TYPE 
         17.560          20.235 
[1] "0.0 - 64.0 (17.6)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2"  
D1044V2, 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       24       104         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LRIG2 MUTATED           0          0          0          0        0         1
  LRIG2 WILD-TYPE        19         10         41         31       35        12
                 vv
clus              STAGE IVB
  LRIG2 MUTATED           0
  LRIG2 WILD-TYPE         1
D1044V3, multiclass
            clus
vv           LRIG2 MUTATED LRIG2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              5             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 242  39
D1044V4, multiclass
    clus
vv   LRIG2 MUTATED LRIG2 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             6             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
  LRIG2 MUTATED     8   1   0
  LRIG2 WILD-TYPE 212  79  66
D1044V5, multiclass
    clus
vv   LRIG2 MUTATED LRIG2 WILD-TYPE
  N0             8             212
  N1             1              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"
D1044V6, binary
                 cls
clus                0   1
  LRIG2 MUTATED     7   0
  LRIG2 WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRIG2 MUTATED      7    0
  LRIG2 WILD-TYPE  276   48
   clus
vv  LRIG2 MUTATED LRIG2 WILD-TYPE
  0             7             276
  1             0              48
[1] 2 2
[1] FALSE
D1044V7, 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
D1044V8, binary
                 cls
clus                0   1
  LRIG2 MUTATED     8   1
  LRIG2 WILD-TYPE 309  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRIG2 MUTATED      8    1
  LRIG2 WILD-TYPE  309   47
                               clus
vv                              LRIG2 MUTATED LRIG2 WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  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 250   2  22  20
D1044V9, multiclass
    clus
vv   LRIG2 MUTATED LRIG2 WILD-TYPE
  R0             7             250
  R1             0               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"
D1044V10, 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
D1044V11, 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(1045) Variable = OR4A16 MUTATION ANALYSIS
D1045V1, survival
                  sevent
clus2                0   1
  OR4A16 MUTATED    10   3
  OR4A16 WILD-TYPE 272  70
  OR4A16 MUTATED OR4A16 WILD-TYPE 
              13              342 
  OR4A16 MUTATED OR4A16 WILD-TYPE 
               3               70 
$`OR4A16 MUTATED`
TCGA-AA-3510 TCGA-AA-3950 TCGA-AA-A02J TCGA-AZ-6608 TCGA-CA-6717 TCGA-CM-4743 
       63.98        24.00         5.03         1.94         0.33        23.05 
TCGA-CM-5344 TCGA-CM-5860 TCGA-CM-6161 TCGA-CM-6677 TCGA-D5-6928 TCGA-DM-A0X9 
       22.03        16.01        15.02        11.08        11.64       119.70 
TCGA-F4-6809 
       13.25 

$`OR4A16 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
       39.98         2.01        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        12.00        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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 
        1.51        12.00        11.38        10.26        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 
       16.31        29.59        16.24        33.67         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  OR4A16 MUTATED OR4A16 WILD-TYPE 
            0.33             0.00 
  OR4A16 MUTATED OR4A16 WILD-TYPE 
          119.70           140.38 
  OR4A16 MUTATED OR4A16 WILD-TYPE 
           15.02            20.63 
[1] "0.3 - 119.7 (15.0)" "0.0 - 140.4 (20.6)"
[1] "hr=" "1.1"
D1045V2, 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       24       101         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR4A16 MUTATED           0          1          1          0        1
  OR4A16 WILD-TYPE        19          9         40         31       34
                  vv
clus               STAGE IVA STAGE IVB
  OR4A16 MUTATED           1         0
  OR4A16 WILD-TYPE        12         1
D1045V3, multiclass
            clus
vv           OR4A16 MUTATED OR4A16 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               8              101
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              1                9
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 236  41
D1045V4, multiclass
    clus
vv   OR4A16 MUTATED OR4A16 WILD-TYPE
  T1              0                9
  T2              2               66
  T3             12              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
  OR4A16 MUTATED    11   3   0
  OR4A16 WILD-TYPE 209  77  66
D1045V5, multiclass
    clus
vv   OR4A16 MUTATED OR4A16 WILD-TYPE
  N0             11              209
  N1              3               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"
D1045V6, binary
                  cls
clus                 0   1
  OR4A16 MUTATED    12   2
  OR4A16 WILD-TYPE 271  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR4A16 MUTATED     12    2
  OR4A16 WILD-TYPE  271   46
   clus
vv  OR4A16 MUTATED OR4A16 WILD-TYPE
  0             12              271
  1              2               46
[1] 2 2
[1] FALSE
D1045V7, 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
D1045V8, binary
                  cls
clus                 0   1
  OR4A16 MUTATED    11   3
  OR4A16 WILD-TYPE 306  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR4A16 MUTATED     11    3
  OR4A16 WILD-TYPE  306   45
                               clus
vv                              OR4A16 MUTATED OR4A16 WILD-TYPE
  COLON ADENOCARCINOMA                      11              306
  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 247   2  21  20
D1045V9, multiclass
    clus
vv   OR4A16 MUTATED OR4A16 WILD-TYPE
  R0             10              247
  R1              0                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"
D1045V10, 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
D1045V11, 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(1046) Variable = GAS6 MUTATION ANALYSIS
D1046V1, survival
                sevent
clus2              0   1
  GAS6 MUTATED     8   0
  GAS6 WILD-TYPE 274  73
  GAS6 MUTATED GAS6 WILD-TYPE 
             8            347 
  GAS6 MUTATED GAS6 WILD-TYPE 
             0             73 
$`GAS6 MUTATED`
TCGA-A6-6782 TCGA-AA-3662 TCGA-AA-A010 TCGA-AD-6889 TCGA-F4-6460 TCGA-G4-6321 
       20.28         6.05        34.98        56.55        13.38        22.09 
TCGA-G4-6586 TCGA-G4-6588 
       35.80        26.17 

$`GAS6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        19.66         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       19.99        13.94        19.99        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37         4.21         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
      117.07        98.24         8.61        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       36.00        13.78        91.79        46.75        52.80 

  GAS6 MUTATED GAS6 WILD-TYPE 
          6.05           0.00 
  GAS6 MUTATED GAS6 WILD-TYPE 
         56.55         140.38 
  GAS6 MUTATED GAS6 WILD-TYPE 
         24.13          20.02 
[1] "6.0 - 56.5 (24.1)"  "0.0 - 140.4 (20.0)"
[1] "hr="     "9200000"
D1046V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GAS6 MUTATED         0        0        0         3         2         0
  GAS6 WILD-TYPE      64        1       25       106         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GAS6 MUTATED           1          0          1          0        1         0
  GAS6 WILD-TYPE        18         10         40         31       34        13
                vv
clus             STAGE IVB
  GAS6 MUTATED           0
  GAS6 WILD-TYPE         1
D1046V3, multiclass
            clus
vv           GAS6 MUTATED GAS6 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             3            106
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GAS6 MUTATED     0   1   4   3
  GAS6 WILD-TYPE   9  67 244  38
D1046V4, multiclass
    clus
vv   GAS6 MUTATED GAS6 WILD-TYPE
  T1            0              9
  T2            1             67
  T3            4            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
  GAS6 MUTATED     5   2   1
  GAS6 WILD-TYPE 215  78  65
D1046V5, multiclass
    clus
vv   GAS6 MUTATED GAS6 WILD-TYPE
  N0            5            215
  N1            2             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"
D1046V6, binary
                cls
clus               0   1
  GAS6 MUTATED     5   1
  GAS6 WILD-TYPE 278  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAS6 MUTATED      5    1
  GAS6 WILD-TYPE  278   47
   clus
vv  GAS6 MUTATED GAS6 WILD-TYPE
  0            5            278
  1            1             47
[1] 2 2
[1] FALSE
D1046V7, binary
                cls
clus               0   1
  GAS6 MUTATED     6   2
  GAS6 WILD-TYPE 164 195
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAS6 MUTATED      6    2
  GAS6 WILD-TYPE  164  195
        clus
vv       GAS6 MUTATED GAS6 WILD-TYPE
  FEMALE            6            164
  MALE              2            195
[1] 2 2
[1] FALSE
D1046V8, binary
                cls
clus               0   1
  GAS6 MUTATED     8   0
  GAS6 WILD-TYPE 309  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAS6 MUTATED      8    0
  GAS6 WILD-TYPE  309   48
                               clus
vv                              GAS6 MUTATED GAS6 WILD-TYPE
  COLON ADENOCARCINOMA                     8            309
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  GAS6 MUTATED     5   0   1   0
  GAS6 WILD-TYPE 252   2  21  21
D1046V9, multiclass
    clus
vv   GAS6 MUTATED GAS6 WILD-TYPE
  R0            5            252
  R1            0              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"
D1046V10, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GAS6 MUTATED                                  0     1
  GAS6 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GAS6 MUTATED                           0     5
  GAS6 WILD-TYPE                        19   171
D1046V11, multiclass
                                  clus
vv                                 GAS6 MUTATED GAS6 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(1047) Variable = MLL4 MUTATION ANALYSIS
D1047V1, survival
                sevent
clus2              0   1
  MLL4 MUTATED    26   6
  MLL4 WILD-TYPE 256  67
  MLL4 MUTATED MLL4 WILD-TYPE 
            32            323 
  MLL4 MUTATED MLL4 WILD-TYPE 
             6             67 
$`MLL4 MUTATED`
TCGA-A6-5661 TCGA-A6-6653 TCGA-AA-3492 TCGA-AA-3663 TCGA-AA-3685 TCGA-AA-3713 
       33.53        24.39         3.02         6.97        37.05        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3864 TCGA-AA-3950 
       19.04        10.06        17.98        15.95        53.00        24.00 
TCGA-AA-A010 TCGA-AY-6386 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-CA-5255 TCGA-CA-6718 
       34.98        17.82        61.41        49.41         3.06         0.10 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CM-4743 TCGA-CM-5861 TCGA-CM-5862 
       15.62        51.32        21.14        23.05        15.02         5.03 
TCGA-CM-6171 TCGA-CM-6674 TCGA-D5-6540 TCGA-DM-A1D9 TCGA-G4-6299 TCGA-G4-6304 
       14.04        12.95        16.14       140.38        74.56        53.62 
TCGA-G4-6588 TCGA-G4-6628 
       26.17        52.80 

$`MLL4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
        5.98        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3837 
       35.05        33.04         0.99        25.02         1.02        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6599 TCGA-AZ-6600 
        5.13        83.80        22.36        62.79         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        2.24         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5914 
        1.35        17.56       102.44        40.34        49.08        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93         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        16.01 
TCGA-CM-5863 TCGA-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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32        12.59         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 
       13.25         0.53        35.41        19.43       107.67        65.85 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        91.79        46.75 

  MLL4 MUTATED MLL4 WILD-TYPE 
           0.1            0.0 
  MLL4 MUTATED MLL4 WILD-TYPE 
        140.38         139.17 
  MLL4 MUTATED MLL4 WILD-TYPE 
         20.09          20.19 
[1] "0.1 - 140.4 (20.1)" "0.0 - 139.2 (20.2)"
[1] "hr=" "1.3"
D1047V2, 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       19        96         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MLL4 MUTATED           2          0          1          1        1         1
  MLL4 WILD-TYPE        17         10         40         30       34        12
                vv
clus             STAGE IVB
  MLL4 MUTATED           0
  MLL4 WILD-TYPE         1
D1047V3, multiclass
            clus
vv           MLL4 MUTATED MLL4 WILD-TYPE
  STAGE I               6             58
  STAGE IA              0              1
  STAGE II              6             19
  STAGE IIA            13             96
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             2             17
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            1             30
  STAGE IV              1             34
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  64 224  38
D1047V4, multiclass
    clus
vv   MLL4 MUTATED MLL4 WILD-TYPE
  T1            2              7
  T2            4             64
  T3           24            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
  MLL4 MUTATED    28   2   3
  MLL4 WILD-TYPE 192  78  63
D1047V5, multiclass
    clus
vv   MLL4 MUTATED MLL4 WILD-TYPE
  N0           28            192
  N1            2             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"
D1047V6, binary
                cls
clus               0   1
  MLL4 MUTATED    29   2
  MLL4 WILD-TYPE 254  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL4 MUTATED     29    2
  MLL4 WILD-TYPE  254   46
   clus
vv  MLL4 MUTATED MLL4 WILD-TYPE
  0           29            254
  1            2             46
[1] 2 2
[1] FALSE
D1047V7, 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
D1047V8, binary
                cls
clus               0   1
  MLL4 MUTATED    30   3
  MLL4 WILD-TYPE 287  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL4 MUTATED     30    3
  MLL4 WILD-TYPE  287   45
                               clus
vv                              MLL4 MUTATED MLL4 WILD-TYPE
  COLON ADENOCARCINOMA                    30            287
  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 234   2  21  16
D1047V9, multiclass
    clus
vv   MLL4 MUTATED MLL4 WILD-TYPE
  R0           23            234
  R1            0              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"
D1047V10, 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
D1047V11, 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(1048) Variable = TAX1BP1 MUTATION ANALYSIS
D1048V1, survival
                   sevent
clus2                 0   1
  TAX1BP1 MUTATED     8   4
  TAX1BP1 WILD-TYPE 274  69
  TAX1BP1 MUTATED TAX1BP1 WILD-TYPE 
               12               343 
  TAX1BP1 MUTATED TAX1BP1 WILD-TYPE 
                4                69 
$`TAX1BP1 MUTATED`
TCGA-A6-5665 TCGA-AA-3864 TCGA-AA-A010 TCGA-AY-4071 TCGA-AZ-6598 TCGA-AZ-6601 
       22.06        53.00        34.98         0.95        49.41       100.01 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CM-4743 TCGA-D5-6540 TCGA-D5-6927 TCGA-DM-A1HB 
       51.32        21.14        23.05        16.14         9.44       135.65 

$`TAX1BP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6196 
        0.20        14.50        27.09        16.31        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       22.36        62.79        61.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.99         2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  TAX1BP1 MUTATED TAX1BP1 WILD-TYPE 
             0.95              0.00 
  TAX1BP1 MUTATED TAX1BP1 WILD-TYPE 
           135.65            140.38 
  TAX1BP1 MUTATED TAX1BP1 WILD-TYPE 
           29.015            19.990 
[1] "0.9 - 135.7 (29.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1"  
D1048V2, 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       22       105         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TAX1BP1 MUTATED           0          0          1          0        0
  TAX1BP1 WILD-TYPE        19         10         40         31       35
                   vv
clus                STAGE IVA STAGE IVB
  TAX1BP1 MUTATED           0         0
  TAX1BP1 WILD-TYPE        13         1
D1048V3, multiclass
            clus
vv           TAX1BP1 MUTATED TAX1BP1 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 3                22
  STAGE IIA                4               105
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TAX1BP1 MUTATED     2   1   8   1
  TAX1BP1 WILD-TYPE   7  67 240  40
D1048V4, multiclass
    clus
vv   TAX1BP1 MUTATED TAX1BP1 WILD-TYPE
  T1               2                 7
  T2               1                67
  T3               8               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
  TAX1BP1 MUTATED    11   1   0
  TAX1BP1 WILD-TYPE 209  79  66
D1048V5, multiclass
    clus
vv   TAX1BP1 MUTATED TAX1BP1 WILD-TYPE
  N0              11               209
  N1               1                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
  TAX1BP1 MUTATED     9   0
  TAX1BP1 WILD-TYPE 274  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TAX1BP1 MUTATED      9    0
  TAX1BP1 WILD-TYPE  274   48
   clus
vv  TAX1BP1 MUTATED TAX1BP1 WILD-TYPE
  0               9               274
  1               0                48
[1] 2 2
[1] FALSE
D1048V7, 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
D1048V8, binary
                   cls
clus                  0   1
  TAX1BP1 MUTATED    10   1
  TAX1BP1 WILD-TYPE 307  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TAX1BP1 MUTATED     10    1
  TAX1BP1 WILD-TYPE  307   47
                               clus
vv                              TAX1BP1 MUTATED TAX1BP1 WILD-TYPE
  COLON ADENOCARCINOMA                       10               307
  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 250   2  22  19
D1048V9, multiclass
    clus
vv   TAX1BP1 MUTATED TAX1BP1 WILD-TYPE
  R0               7               250
  R1               0                 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"
D1048V10, 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
D1048V11, 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(1049) Variable = ASPG MUTATION ANALYSIS
D1049V1, survival
                sevent
clus2              0   1
  ASPG MUTATED     6   1
  ASPG WILD-TYPE 276  72
  ASPG MUTATED ASPG WILD-TYPE 
             7            348 
  ASPG MUTATED ASPG WILD-TYPE 
             1             72 
$`ASPG MUTATED`
TCGA-A6-5661 TCGA-AA-3877 TCGA-AU-3779 TCGA-AZ-4315 TCGA-AZ-6601 TCGA-CM-5861 
       33.53        31.00        14.50        58.39       100.01        15.02 
TCGA-CM-6674 
       12.95 

$`ASPG WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  ASPG MUTATED ASPG WILD-TYPE 
         12.95           0.00 
  ASPG MUTATED ASPG WILD-TYPE 
        100.01         140.38 
  ASPG MUTATED ASPG WILD-TYPE 
        31.000         20.155 
[1] "12.9 - 100.0 (31.0)" "0.0 - 140.4 (20.2)" 
[1] "hr=" "2.2"
D1049V2, 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       24       104         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        19         10         41         31       35        13
                vv
clus             STAGE IVB
  ASPG MUTATED           0
  ASPG WILD-TYPE         1
D1049V3, multiclass
            clus
vv           ASPG MUTATED ASPG WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             5            104
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ASPG MUTATED     1   0   6   0
  ASPG WILD-TYPE   8  68 242  41
D1049V4, multiclass
    clus
vv   ASPG MUTATED ASPG WILD-TYPE
  T1            1              8
  T2            0             68
  T3            6            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
  ASPG MUTATED     7   0   0
  ASPG WILD-TYPE 213  80  66
D1049V5, multiclass
    clus
vv   ASPG MUTATED ASPG WILD-TYPE
  N0            7            213
  N1            0             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"
D1049V6, binary
                cls
clus               0   1
  ASPG MUTATED     7   0
  ASPG WILD-TYPE 276  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASPG MUTATED      7    0
  ASPG WILD-TYPE  276   48
   clus
vv  ASPG MUTATED ASPG WILD-TYPE
  0            7            276
  1            0             48
[1] 2 2
[1] FALSE
D1049V7, 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
D1049V8, binary
                cls
clus               0   1
  ASPG MUTATED     6   1
  ASPG WILD-TYPE 311  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASPG MUTATED      6    1
  ASPG WILD-TYPE  311   47
                               clus
vv                              ASPG MUTATED ASPG WILD-TYPE
  COLON ADENOCARCINOMA                     6            311
  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 251   2  22  21
D1049V9, multiclass
    clus
vv   ASPG MUTATED ASPG WILD-TYPE
  R0            6            251
  R1            0              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"
D1049V10, 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
D1049V11, 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(1050) Variable = KLF3 MUTATION ANALYSIS
D1050V1, survival
                sevent
clus2              0   1
  KLF3 MUTATED     4   1
  KLF3 WILD-TYPE 278  72
  KLF3 MUTATED KLF3 WILD-TYPE 
             5            350 
  KLF3 MUTATED KLF3 WILD-TYPE 
             1             72 
$`KLF3 MUTATED`
TCGA-A6-5665 TCGA-AA-3663 TCGA-AA-3930 TCGA-AD-6895 TCGA-AZ-4315 
       22.06         6.97         2.01         0.72        58.39 

$`KLF3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3939 
       24.03        27.02        29.98        18.05        31.00        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  KLF3 MUTATED KLF3 WILD-TYPE 
          0.72           0.00 
  KLF3 MUTATED KLF3 WILD-TYPE 
         58.39         140.38 
  KLF3 MUTATED KLF3 WILD-TYPE 
         6.970         20.235 
[1] "0.7 - 58.4 (7.0)"   "0.0 - 140.4 (20.2)"
[1] "hr=" "1.3"
D1050V2, 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       24       106         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KLF3 MUTATED           0          0          0          0        1         0
  KLF3 WILD-TYPE        19         10         41         31       34        13
                vv
clus             STAGE IVB
  KLF3 MUTATED           0
  KLF3 WILD-TYPE         1
D1050V3, multiclass
            clus
vv           KLF3 MUTATED KLF3 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             3            106
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  KLF3 MUTATED     0   0   6   1
  KLF3 WILD-TYPE   9  68 242  40
D1050V4, multiclass
    clus
vv   KLF3 MUTATED KLF3 WILD-TYPE
  T1            0              9
  T2            0             68
  T3            6            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
  KLF3 MUTATED     5   1   1
  KLF3 WILD-TYPE 215  79  65
D1050V5, multiclass
    clus
vv   KLF3 MUTATED KLF3 WILD-TYPE
  N0            5            215
  N1            1             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"
D1050V6, binary
                cls
clus               0   1
  KLF3 MUTATED     4   1
  KLF3 WILD-TYPE 279  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLF3 MUTATED      4    1
  KLF3 WILD-TYPE  279   47
   clus
vv  KLF3 MUTATED KLF3 WILD-TYPE
  0            4            279
  1            1             47
[1] 2 2
[1] FALSE
D1050V7, 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
D1050V8, binary
                cls
clus               0   1
  KLF3 MUTATED     7   0
  KLF3 WILD-TYPE 310  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLF3 MUTATED      7    0
  KLF3 WILD-TYPE  310   48
                               clus
vv                              KLF3 MUTATED KLF3 WILD-TYPE
  COLON ADENOCARCINOMA                     7            310
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  KLF3 MUTATED     4   0   1   1
  KLF3 WILD-TYPE 253   2  21  20
D1050V9, multiclass
    clus
vv   KLF3 MUTATED KLF3 WILD-TYPE
  R0            4            253
  R1            0              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"
D1050V10, 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
D1050V11, 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(1051) Variable = TUBB4 MUTATION ANALYSIS
D1051V1, survival
                 sevent
clus2               0   1
  TUBB4 MUTATED     3   0
  TUBB4 WILD-TYPE 279  73
  TUBB4 MUTATED TUBB4 WILD-TYPE 
              3             352 
  TUBB4 MUTATED TUBB4 WILD-TYPE 
              0              73 
$`TUBB4 MUTATED`
TCGA-A6-5665 TCGA-AA-3864 TCGA-D5-6930 
       22.06        53.00         1.51 

$`TUBB4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  TUBB4 MUTATED TUBB4 WILD-TYPE 
           1.51            0.00 
  TUBB4 MUTATED TUBB4 WILD-TYPE 
          53.00          140.38 
  TUBB4 MUTATED TUBB4 WILD-TYPE 
         22.060          20.155 
[1] "1.5 - 53.0 (22.1)"  "0.0 - 140.4 (20.2)"
[1] "hr="     "3300000"
D1051V2, 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       24       107         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        19         10         41         31       34        13
                 vv
clus              STAGE IVB
  TUBB4 MUTATED           0
  TUBB4 WILD-TYPE         1
D1051V3, multiclass
            clus
vv           TUBB4 MUTATED TUBB4 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              2             107
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TUBB4 MUTATED     0   0   3   2
  TUBB4 WILD-TYPE   9  68 245  39
D1051V4, multiclass
    clus
vv   TUBB4 MUTATED TUBB4 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             3             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
  TUBB4 MUTATED     4   0   1
  TUBB4 WILD-TYPE 216  80  65
D1051V5, multiclass
    clus
vv   TUBB4 MUTATED TUBB4 WILD-TYPE
  N0             4             216
  N1             0              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"
D1051V6, binary
                 cls
clus                0   1
  TUBB4 MUTATED     3   1
  TUBB4 WILD-TYPE 280  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TUBB4 MUTATED      3    1
  TUBB4 WILD-TYPE  280   47
   clus
vv  TUBB4 MUTATED TUBB4 WILD-TYPE
  0             3             280
  1             1              47
[1] 2 2
[1] FALSE
D1051V7, 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
D1051V8, binary
                 cls
clus                0   1
  TUBB4 MUTATED     3   2
  TUBB4 WILD-TYPE 314  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TUBB4 MUTATED      3    2
  TUBB4 WILD-TYPE  314   46
                               clus
vv                              TUBB4 MUTATED TUBB4 WILD-TYPE
  COLON ADENOCARCINOMA                      3             314
  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 254   2  21  20
D1051V9, multiclass
    clus
vv   TUBB4 MUTATED TUBB4 WILD-TYPE
  R0             3             254
  R1             0               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"
D1051V10, 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
D1051V11, 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(1052) Variable = P2RX7 MUTATION ANALYSIS
D1052V1, survival
                 sevent
clus2               0   1
  P2RX7 MUTATED    10   2
  P2RX7 WILD-TYPE 272  71
  P2RX7 MUTATED P2RX7 WILD-TYPE 
             12             343 
  P2RX7 MUTATED P2RX7 WILD-TYPE 
              2              71 
$`P2RX7 MUTATED`
TCGA-A6-4105 TCGA-AA-3966 TCGA-AA-A02J TCGA-AD-6895 TCGA-CK-6747 TCGA-CM-5863 
       14.53         2.01         5.03         0.72         2.93        15.02 
TCGA-CM-6165 TCGA-D5-5538 TCGA-D5-6927 TCGA-DM-A1HA TCGA-DM-A28H TCGA-G4-6588 
       16.04        12.26         9.44       131.51       117.07        26.17 

$`P2RX7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
       39.98         2.01        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 
       15.62        49.08        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        16.01        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        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB 
       13.32        12.59       140.38         7.50        44.32       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 
       52.80 

  P2RX7 MUTATED P2RX7 WILD-TYPE 
           0.72            0.00 
  P2RX7 MUTATED P2RX7 WILD-TYPE 
         131.51          140.38 
  P2RX7 MUTATED P2RX7 WILD-TYPE 
         13.395          20.980 
[1] "0.7 - 131.5 (13.4)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.3"
D1052V2, 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       25       103         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  P2RX7 MUTATED           0          0          2          2        1         0
  P2RX7 WILD-TYPE        19         10         39         29       34        13
                 vv
clus              STAGE IVB
  P2RX7 MUTATED           0
  P2RX7 WILD-TYPE         1
D1052V3, multiclass
            clus
vv           P2RX7 MUTATED P2RX7 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              6             103
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             2              29
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  P2RX7 MUTATED     0   0  12   0
  P2RX7 WILD-TYPE   9  68 236  41
D1052V4, multiclass
    clus
vv   P2RX7 MUTATED P2RX7 WILD-TYPE
  T1             0               9
  T2             0              68
  T3            12             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
  P2RX7 MUTATED     7   3   2
  P2RX7 WILD-TYPE 213  77  64
D1052V5, multiclass
    clus
vv   P2RX7 MUTATED P2RX7 WILD-TYPE
  N0             7             213
  N1             3              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"
D1052V6, binary
                 cls
clus                0   1
  P2RX7 MUTATED     9   1
  P2RX7 WILD-TYPE 274  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  P2RX7 MUTATED      9    1
  P2RX7 WILD-TYPE  274   47
   clus
vv  P2RX7 MUTATED P2RX7 WILD-TYPE
  0             9             274
  1             1              47
[1] 2 2
[1] FALSE
D1052V7, 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
D1052V8, binary
                 cls
clus                0   1
  P2RX7 MUTATED    10   2
  P2RX7 WILD-TYPE 307  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  P2RX7 MUTATED     10    2
  P2RX7 WILD-TYPE  307   46
                               clus
vv                              P2RX7 MUTATED P2RX7 WILD-TYPE
  COLON ADENOCARCINOMA                     10             307
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  P2RX7 MUTATED     5   0   1   1
  P2RX7 WILD-TYPE 252   2  21  20
D1052V9, multiclass
    clus
vv   P2RX7 MUTATED P2RX7 WILD-TYPE
  R0             5             252
  R1             0               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"
D1052V10, 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
D1052V11, 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(1053) Variable = SNAPC2 MUTATION ANALYSIS
D1053V1, survival
                  sevent
clus2                0   1
  SNAPC2 MUTATED     5   1
  SNAPC2 WILD-TYPE 277  72
  SNAPC2 MUTATED SNAPC2 WILD-TYPE 
               6              349 
  SNAPC2 MUTATED SNAPC2 WILD-TYPE 
               1               72 
$`SNAPC2 MUTATED`
TCGA-AA-3516 TCGA-AA-3663 TCGA-AA-3713 TCGA-AA-3977 TCGA-AD-6889 TCGA-DM-A1HB 
       13.02         6.97        19.04        25.02        56.55       135.65 

$`SNAPC2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        1.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37         4.21         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  SNAPC2 MUTATED SNAPC2 WILD-TYPE 
            6.97             0.00 
  SNAPC2 MUTATED SNAPC2 WILD-TYPE 
          135.65           140.38 
  SNAPC2 MUTATED SNAPC2 WILD-TYPE 
           22.03            20.19 
[1] "7.0 - 135.7 (22.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.9"
D1053V2, 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       24       108         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SNAPC2 MUTATED           1          0          1          0        1
  SNAPC2 WILD-TYPE        18         10         40         31       34
                  vv
clus               STAGE IVA STAGE IVB
  SNAPC2 MUTATED           0         0
  SNAPC2 WILD-TYPE        13         1
D1053V3, multiclass
            clus
vv           SNAPC2 MUTATED SNAPC2 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               1              108
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SNAPC2 MUTATED     0   1   5   0
  SNAPC2 WILD-TYPE   9  67 243  41
D1053V4, multiclass
    clus
vv   SNAPC2 MUTATED SNAPC2 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              5              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
  SNAPC2 MUTATED     4   1   1
  SNAPC2 WILD-TYPE 216  79  65
D1053V5, multiclass
    clus
vv   SNAPC2 MUTATED SNAPC2 WILD-TYPE
  N0              4              216
  N1              1               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"
D1053V6, binary
                  cls
clus                 0   1
  SNAPC2 MUTATED     4   1
  SNAPC2 WILD-TYPE 279  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SNAPC2 MUTATED      4    1
  SNAPC2 WILD-TYPE  279   47
   clus
vv  SNAPC2 MUTATED SNAPC2 WILD-TYPE
  0              4              279
  1              1               47
[1] 2 2
[1] FALSE
D1053V7, 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
D1053V8, binary
                  cls
clus                 0   1
  SNAPC2 MUTATED     5   1
  SNAPC2 WILD-TYPE 312  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SNAPC2 MUTATED      5    1
  SNAPC2 WILD-TYPE  312   47
                               clus
vv                              SNAPC2 MUTATED SNAPC2 WILD-TYPE
  COLON ADENOCARCINOMA                       5              312
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SNAPC2 MUTATED     1   0   1   0
  SNAPC2 WILD-TYPE 256   2  21  21
D1053V9, multiclass
[1] "Remove cluster labels:" "SNAPC2 MUTATED"        
clus
  SNAPC2 MUTATED SNAPC2 WILD-TYPE 
               2              300 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-5657 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-A6-5659       TCGA-A6-5661       TCGA-A6-5665       TCGA-A6-6781 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3489       TCGA-AA-3492       TCGA-AA-3496       TCGA-AA-3502 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3510       TCGA-AA-3511       TCGA-AA-3514       TCGA-AA-3517 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3518       TCGA-AA-3519       TCGA-AA-3520       TCGA-AA-3521 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3522       TCGA-AA-3524       TCGA-AA-3525       TCGA-AA-3526 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3527       TCGA-AA-3529       TCGA-AA-3530       TCGA-AA-3531 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3532       TCGA-AA-3534       TCGA-AA-3538       TCGA-AA-3542 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3543       TCGA-AA-3544       TCGA-AA-3548       TCGA-AA-3549 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3552       TCGA-AA-3553       TCGA-AA-3554       TCGA-AA-3555 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3556       TCGA-AA-3558       TCGA-AA-3560       TCGA-AA-3561 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3562       TCGA-AA-3655       TCGA-AA-3660       TCGA-AA-3662 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3664       TCGA-AA-3666       TCGA-AA-3667       TCGA-AA-3672 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3673       TCGA-AA-3678       TCGA-AA-3679       TCGA-AA-3680 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3681       TCGA-AA-3684       TCGA-AA-3685       TCGA-AA-3688 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3692       TCGA-AA-3693       TCGA-AA-3695       TCGA-AA-3696 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3697       TCGA-AA-3710       TCGA-AA-3712       TCGA-AA-3715 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3811       TCGA-AA-3812       TCGA-AA-3814       TCGA-AA-3815 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3818       TCGA-AA-3819       TCGA-AA-3821       TCGA-AA-3831 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3833       TCGA-AA-3837       TCGA-AA-3842       TCGA-AA-3844 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3845       TCGA-AA-3846       TCGA-AA-3848       TCGA-AA-3850 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3851       TCGA-AA-3852       TCGA-AA-3854       TCGA-AA-3855 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3856       TCGA-AA-3858       TCGA-AA-3860       TCGA-AA-3861 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3864       TCGA-AA-3866       TCGA-AA-3867       TCGA-AA-3869 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3870       TCGA-AA-3872       TCGA-AA-3875       TCGA-AA-3877 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3930       TCGA-AA-3939       TCGA-AA-3941       TCGA-AA-3947 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3949       TCGA-AA-3950       TCGA-AA-3952       TCGA-AA-3955 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3956       TCGA-AA-3968       TCGA-AA-3971       TCGA-AA-3972 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3973       TCGA-AA-3975       TCGA-AA-3976       TCGA-AA-3979 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3984       TCGA-AA-3986       TCGA-AA-3989       TCGA-AA-3994 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-A004       TCGA-AA-A00A       TCGA-AA-A00D       TCGA-AA-A00E 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-A00F       TCGA-AA-A00J       TCGA-AA-A00K       TCGA-AA-A00L 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-A00N       TCGA-AA-A00O       TCGA-AA-A00Q       TCGA-AA-A00R 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-A00U       TCGA-AA-A00W       TCGA-AA-A00Z       TCGA-AA-A010 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-A017       TCGA-AA-A01D       TCGA-AA-A01F       TCGA-AA-A01G 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-A01I       TCGA-AA-A01K       TCGA-AA-A01P       TCGA-AA-A01Q 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-A01R       TCGA-AA-A01S       TCGA-AA-A01T       TCGA-AA-A01V 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-A01X       TCGA-AA-A01Z       TCGA-AA-A022       TCGA-AA-A024 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-A029       TCGA-AA-A02F       TCGA-AA-A02H       TCGA-AA-A02J 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-A02K       TCGA-AA-A02O       TCGA-AA-A02W       TCGA-AA-A02Y 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-A03F       TCGA-AA-A03J       TCGA-AD-5900       TCGA-AD-6548 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AD-6888       TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AY-4071       TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AY-6386       TCGA-AZ-4315       TCGA-AZ-4681       TCGA-AZ-4682 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CA-5254       TCGA-CA-5255       TCGA-CA-5796       TCGA-CA-5797 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CA-6715       TCGA-CA-6716       TCGA-CA-6717       TCGA-CA-6718 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CA-6719       TCGA-CK-4947       TCGA-CK-4948       TCGA-CK-4950 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CK-4952       TCGA-CK-5912       TCGA-CK-5913       TCGA-CK-5914 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CK-5915       TCGA-CK-5916       TCGA-CK-6746       TCGA-CK-6747 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CK-6748       TCGA-CK-6751       TCGA-CM-4743       TCGA-CM-4744 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CM-4746       TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CM-5344       TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CM-5861       TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CM-5868       TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CM-6164       TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CM-6168       TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CM-6172       TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CM-6677       TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-D5-5537       TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-D5-5541       TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-D5-6534       TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-D5-6538       TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-D5-6898       TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-D5-6924       TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-D5-6929       TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-D5-7000       TCGA-F4-6459       TCGA-F4-6460       TCGA-F4-6569 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704       TCGA-F4-6805 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808       TCGA-F4-6809 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856       TCGA-G4-6293 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304       TCGA-G4-6306 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310       TCGA-G4-6315 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323       TCGA-G4-6586 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
D1053V10, 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
D1053V11, multiclass
[1] "Remove cluster labels:" "SNAPC2 MUTATED"        
clus
  SNAPC2 MUTATED SNAPC2 WILD-TYPE 
               2              204 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-4105 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-A6-5661       TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5665 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-A6-5666       TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-A6-6142       TCGA-A6-6648       TCGA-A6-6649       TCGA-A6-6651 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-A6-6652       TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-A6-6781       TCGA-A6-6782       TCGA-AD-5900       TCGA-AD-6548 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AD-6888       TCGA-AD-6890       TCGA-AD-6895       TCGA-AD-6899 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6964       TCGA-AD-6965 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070       TCGA-AY-4071 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AZ-4315       TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4681 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AZ-4682       TCGA-AZ-5403       TCGA-AZ-5407       TCGA-AZ-6598 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AZ-6599       TCGA-AZ-6600       TCGA-AZ-6601       TCGA-AZ-6603 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AZ-6605       TCGA-AZ-6606       TCGA-AZ-6607       TCGA-AZ-6608 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CA-5254       TCGA-CA-5255       TCGA-CA-5796       TCGA-CA-5797 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CA-6715       TCGA-CA-6716       TCGA-CA-6717       TCGA-CA-6718 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CA-6719       TCGA-CK-4947       TCGA-CK-4948       TCGA-CK-4950 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CK-4952       TCGA-CK-5912       TCGA-CK-5913       TCGA-CK-5914 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CK-5915       TCGA-CK-5916       TCGA-CK-6746       TCGA-CK-6747 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CK-6748       TCGA-CK-6751       TCGA-CM-4743       TCGA-CM-4744 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CM-4746       TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CM-5344       TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CM-5861       TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CM-5868       TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CM-6164       TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CM-6168       TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CM-6172       TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CM-6677       TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-D5-5537       TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-D5-5541       TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-D5-6534       TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-D5-6538       TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-D5-6898       TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-D5-6924       TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-D5-6929       TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-D5-7000       TCGA-DM-A0X9       TCGA-DM-A0XD       TCGA-DM-A0XF 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-DM-A1D0       TCGA-DM-A1D4       TCGA-DM-A1D6       TCGA-DM-A1D7 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-DM-A1D8       TCGA-DM-A1D9       TCGA-DM-A1DA       TCGA-DM-A1DB 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-DM-A1HA       TCGA-DM-A282       TCGA-DM-A285       TCGA-DM-A28C 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-DM-A28E       TCGA-DM-A28F       TCGA-DM-A28G       TCGA-DM-A28H 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-DM-A28K       TCGA-F4-6459       TCGA-F4-6460       TCGA-F4-6569 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704       TCGA-F4-6805 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808       TCGA-F4-6809 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856       TCGA-G4-6293 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304       TCGA-G4-6306 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310       TCGA-G4-6315 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323       TCGA-G4-6586 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 

Clustering(1054) Variable = USF1 MUTATION ANALYSIS
D1054V1, survival
                sevent
clus2              0   1
  USF1 MUTATED     4   1
  USF1 WILD-TYPE 278  72
  USF1 MUTATED USF1 WILD-TYPE 
             5            350 
  USF1 MUTATED USF1 WILD-TYPE 
             1             72 
$`USF1 MUTATED`
TCGA-AA-3947 TCGA-AA-A010 TCGA-AD-5900 TCGA-AZ-5407 TCGA-AZ-6598 
       33.01        34.98         0.07        61.41        49.41 

$`USF1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       83.80        22.36        62.79         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  USF1 MUTATED USF1 WILD-TYPE 
          0.07           0.00 
  USF1 MUTATED USF1 WILD-TYPE 
         61.41         140.38 
  USF1 MUTATED USF1 WILD-TYPE 
         34.98          20.07 
[1] "0.1 - 61.4 (35.0)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.4"
D1054V2, 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       24       109         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        19         10         41         31       35        13
                vv
clus             STAGE IVB
  USF1 MUTATED           0
  USF1 WILD-TYPE         1
D1054V3, multiclass
            clus
vv           USF1 MUTATED USF1 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             0            109
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  USF1 MUTATED     1   1   1   2
  USF1 WILD-TYPE   8  67 247  39
D1054V4, multiclass
    clus
vv   USF1 MUTATED USF1 WILD-TYPE
  T1            1              8
  T2            1             67
  T3            1            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
  USF1 MUTATED     5   0   0
  USF1 WILD-TYPE 215  80  66
D1054V5, multiclass
    clus
vv   USF1 MUTATED USF1 WILD-TYPE
  N0            5            215
  N1            0             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"
D1054V6, binary
                cls
clus               0   1
  USF1 MUTATED     3   0
  USF1 WILD-TYPE 280  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  USF1 MUTATED      3    0
  USF1 WILD-TYPE  280   48
   clus
vv  USF1 MUTATED USF1 WILD-TYPE
  0            3            280
  1            0             48
[1] 2 2
[1] FALSE
D1054V7, 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
D1054V8, binary
                cls
clus               0   1
  USF1 MUTATED     3   2
  USF1 WILD-TYPE 314  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  USF1 MUTATED      3    2
  USF1 WILD-TYPE  314   46
                               clus
vv                              USF1 MUTATED USF1 WILD-TYPE
  COLON ADENOCARCINOMA                     3            314
  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 254   2  22  21
D1054V9, multiclass
    clus
vv   USF1 MUTATED USF1 WILD-TYPE
  R0            3            254
  R1            0              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"
D1054V10, 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
D1054V11, 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(1055) Variable = CATSPER4 MUTATION ANALYSIS
D1055V1, survival
                    sevent
clus2                  0   1
  CATSPER4 MUTATED     7   2
  CATSPER4 WILD-TYPE 275  71
  CATSPER4 MUTATED CATSPER4 WILD-TYPE 
                 9                346 
  CATSPER4 MUTATED CATSPER4 WILD-TYPE 
                 2                 71 
$`CATSPER4 MUTATED`
TCGA-A6-6654 TCGA-A6-6780 TCGA-AA-3525 TCGA-AA-3947 TCGA-AD-6895 TCGA-AD-6901 
       23.87        20.12         8.05        33.01         0.72        22.42 
TCGA-AU-6004 TCGA-AZ-6606 TCGA-CA-6718 
       27.09        11.74         0.10 

$`CATSPER4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 
        9.07        24.03        37.05        36.03        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
        5.79        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.33         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  CATSPER4 MUTATED CATSPER4 WILD-TYPE 
               0.1                0.0 
  CATSPER4 MUTATED CATSPER4 WILD-TYPE 
             33.01             140.38 
  CATSPER4 MUTATED CATSPER4 WILD-TYPE 
            20.120             20.235 
[1] "0.1 - 33.0 (20.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.7"
D1055V2, 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       25       106         6         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CATSPER4 MUTATED           0          0          2          0        1
  CATSPER4 WILD-TYPE        19         10         39         31       34
                    vv
clus                 STAGE IVA STAGE IVB
  CATSPER4 MUTATED           0         0
  CATSPER4 WILD-TYPE        13         1
D1055V3, multiclass
            clus
vv           CATSPER4 MUTATED CATSPER4 WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  0                 25
  STAGE IIA                 3                106
  STAGE IIB                 2                  6
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                0                 10
  STAGE IIIB                2                 39
  STAGE IIIC                0                 31
  STAGE IV                  1                 34
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  CATSPER4 MUTATED     0   1   7   3
  CATSPER4 WILD-TYPE   9  67 241  38
D1055V4, multiclass
    clus
vv   CATSPER4 MUTATED CATSPER4 WILD-TYPE
  T1                0                  9
  T2                1                 67
  T3                7                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
  CATSPER4 MUTATED     7   3   1
  CATSPER4 WILD-TYPE 213  77  65
D1055V5, multiclass
    clus
vv   CATSPER4 MUTATED CATSPER4 WILD-TYPE
  N0                7                213
  N1                3                 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"
D1055V6, binary
                    cls
clus                   0   1
  CATSPER4 MUTATED     6   1
  CATSPER4 WILD-TYPE 277  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CATSPER4 MUTATED      6    1
  CATSPER4 WILD-TYPE  277   47
   clus
vv  CATSPER4 MUTATED CATSPER4 WILD-TYPE
  0                6                277
  1                1                 47
[1] 2 2
[1] FALSE
D1055V7, 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
D1055V8, binary
                    cls
clus                   0   1
  CATSPER4 MUTATED     9   2
  CATSPER4 WILD-TYPE 308  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CATSPER4 MUTATED      9    2
  CATSPER4 WILD-TYPE  308   46
                               clus
vv                              CATSPER4 MUTATED CATSPER4 WILD-TYPE
  COLON ADENOCARCINOMA                         9                308
  COLON MUCINOUS ADENOCARCINOMA                2                 46
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  CATSPER4 MUTATED     4   0   0   2
  CATSPER4 WILD-TYPE 253   2  22  19
D1055V9, multiclass
    clus
vv   CATSPER4 MUTATED CATSPER4 WILD-TYPE
  R0                4                253
  R1                0                  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"
D1055V10, 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
D1055V11, 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(1056) Variable = PIK3C3 MUTATION ANALYSIS
D1056V1, survival
                  sevent
clus2                0   1
  PIK3C3 MUTATED    19   3
  PIK3C3 WILD-TYPE 263  70
  PIK3C3 MUTATED PIK3C3 WILD-TYPE 
              22              333 
  PIK3C3 MUTATED PIK3C3 WILD-TYPE 
               3               70 
$`PIK3C3 MUTATED`
TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3660 TCGA-AA-3864 
       22.06         3.02        17.95        29.95        78.08        53.00 
TCGA-AA-A00J TCGA-AD-6888 TCGA-AD-6889 TCGA-AU-6004 TCGA-AY-6197 TCGA-AZ-6601 
       18.05         4.21        56.55        27.09        21.44       100.01 
TCGA-CA-6717 TCGA-CK-6748 TCGA-CM-4752 TCGA-CM-6168 TCGA-D5-6533 TCGA-D5-6536 
        0.33         2.01        13.02        12.99         1.32        17.85 
TCGA-D5-6540 TCGA-F4-6703 TCGA-G4-6586 TCGA-G4-6626 
       16.14        35.87        35.80        46.75 

$`PIK3C3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       24.00        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.20        14.50        16.31         0.95        15.75         0.20 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        61.41        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99        21.14         2.93       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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51        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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.38        13.45         6.18         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       26.17        91.79        52.80 

  PIK3C3 MUTATED PIK3C3 WILD-TYPE 
            0.33             0.00 
  PIK3C3 MUTATED PIK3C3 WILD-TYPE 
          100.01           140.38 
  PIK3C3 MUTATED PIK3C3 WILD-TYPE 
          19.745           20.190 
[1] "0.3 - 100.0 (19.7)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.7"
D1056V2, 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       20        97         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PIK3C3 MUTATED           0          0          3          0        1
  PIK3C3 WILD-TYPE        19         10         38         31       34
                  vv
clus               STAGE IVA STAGE IVB
  PIK3C3 MUTATED           0         0
  PIK3C3 WILD-TYPE        13         1
D1056V3, multiclass
            clus
vv           PIK3C3 MUTATED PIK3C3 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                5               20
  STAGE IIA              12               97
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              3               38
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PIK3C3 MUTATED     0   3  17   3
  PIK3C3 WILD-TYPE   9  65 231  38
D1056V4, multiclass
    clus
vv   PIK3C3 MUTATED PIK3C3 WILD-TYPE
  T1              0                9
  T2              3               65
  T3             17              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   2   0
  PIK3C3 WILD-TYPE 200  78  66
D1056V5, multiclass
    clus
vv   PIK3C3 MUTATED PIK3C3 WILD-TYPE
  N0             20              200
  N1              2               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"
D1056V6, binary
                  cls
clus                 0   1
  PIK3C3 MUTATED    21   1
  PIK3C3 WILD-TYPE 262  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3C3 MUTATED     21    1
  PIK3C3 WILD-TYPE  262   47
   clus
vv  PIK3C3 MUTATED PIK3C3 WILD-TYPE
  0             21              262
  1              1               47
[1] 2 2
[1] FALSE
D1056V7, 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
D1056V8, binary
                  cls
clus                 0   1
  PIK3C3 MUTATED    18   5
  PIK3C3 WILD-TYPE 299  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3C3 MUTATED     18    5
  PIK3C3 WILD-TYPE  299   43
                               clus
vv                              PIK3C3 MUTATED PIK3C3 WILD-TYPE
  COLON ADENOCARCINOMA                      18              299
  COLON MUCINOUS ADENOCARCINOMA              5               43
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PIK3C3 MUTATED    19   0   0   2
  PIK3C3 WILD-TYPE 238   2  22  19
D1056V9, multiclass
    clus
vv   PIK3C3 MUTATED PIK3C3 WILD-TYPE
  R0             19              238
  R1              0                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"
D1056V10, 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
D1056V11, 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(1057) Variable = IBTK MUTATION ANALYSIS
D1057V1, survival
                sevent
clus2              0   1
  IBTK MUTATED    13   6
  IBTK WILD-TYPE 269  67
  IBTK MUTATED IBTK WILD-TYPE 
            19            336 
  IBTK MUTATED IBTK WILD-TYPE 
             6             67 
$`IBTK MUTATED`
TCGA-A6-5661 TCGA-AA-3516 TCGA-AA-3543 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3715 
       33.53        13.02         0.99         6.97         0.92        19.04 
TCGA-AA-3815 TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6603 TCGA-AZ-6607 
       33.04        34.98        58.39        49.41        29.56         3.19 
TCGA-CK-5913 TCGA-CK-6748 TCGA-DM-A1D0 TCGA-F4-6459 TCGA-F4-6806 TCGA-G4-6321 
       51.32         2.01       130.65         8.61        29.59        22.09 
TCGA-G4-6628 
       52.80 

$`IBTK WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
       12.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
      100.01         5.23        11.74         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99        21.14         2.93       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79       117.07        98.24        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       35.87         1.55        16.31        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        13.78        35.80        26.17        91.79        46.75 

  IBTK MUTATED IBTK WILD-TYPE 
          0.92           0.00 
  IBTK MUTATED IBTK WILD-TYPE 
        130.65         140.38 
  IBTK MUTATED IBTK WILD-TYPE 
         29.56          20.07 
[1] "0.9 - 130.7 (29.6)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.4"
D1057V2, 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       22       104         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        16         10         40         31       33        13
                vv
clus             STAGE IVB
  IBTK MUTATED           0
  IBTK WILD-TYPE         1
D1057V3, multiclass
            clus
vv           IBTK MUTATED IBTK WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              3             22
  STAGE IIA             5            104
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             3             16
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              2             33
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  IBTK MUTATED     0   5  12   2
  IBTK WILD-TYPE   9  63 236  39
D1057V4, multiclass
    clus
vv   IBTK MUTATED IBTK WILD-TYPE
  T1            0              9
  T2            5             63
  T3           12            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
  IBTK MUTATED    12   4   3
  IBTK WILD-TYPE 208  76  63
D1057V5, multiclass
    clus
vv   IBTK MUTATED IBTK WILD-TYPE
  N0           12            208
  N1            4             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"
D1057V6, binary
                cls
clus               0   1
  IBTK MUTATED    13   2
  IBTK WILD-TYPE 270  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  IBTK MUTATED     13    2
  IBTK WILD-TYPE  270   46
   clus
vv  IBTK MUTATED IBTK WILD-TYPE
  0           13            270
  1            2             46
[1] 2 2
[1] FALSE
D1057V7, 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
D1057V8, binary
                cls
clus               0   1
  IBTK MUTATED    16   3
  IBTK WILD-TYPE 301  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  IBTK MUTATED     16    3
  IBTK WILD-TYPE  301   45
                               clus
vv                              IBTK MUTATED IBTK WILD-TYPE
  COLON ADENOCARCINOMA                    16            301
  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 245   2  22  19
D1057V9, multiclass
    clus
vv   IBTK MUTATED IBTK WILD-TYPE
  R0           12            245
  R1            0              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"
D1057V10, 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
D1057V11, 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(1058) Variable = C5ORF34 MUTATION ANALYSIS
D1058V1, survival
                   sevent
clus2                 0   1
  C5ORF34 MUTATED     8   2
  C5ORF34 WILD-TYPE 274  71
  C5ORF34 MUTATED C5ORF34 WILD-TYPE 
               10               345 
  C5ORF34 MUTATED C5ORF34 WILD-TYPE 
                2                71 
$`C5ORF34 MUTATED`
TCGA-A6-6137 TCGA-AA-3815 TCGA-AA-A00N TCGA-AU-6004 TCGA-CA-6717 TCGA-D5-5539 
       27.09        33.04         4.01        27.09         0.33        19.59 
TCGA-D5-6540 TCGA-D5-6930 TCGA-DM-A1DA TCGA-G4-6588 
       16.14         1.51         7.50        26.17 

$`C5ORF34 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        32.71        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.20        14.50        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  C5ORF34 MUTATED C5ORF34 WILD-TYPE 
             0.33              0.00 
  C5ORF34 MUTATED C5ORF34 WILD-TYPE 
            33.04            140.38 
  C5ORF34 MUTATED C5ORF34 WILD-TYPE 
           17.865            20.280 
[1] "0.3 - 33.0 (17.9)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.6"
D1058V2, 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       25       105         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C5ORF34 MUTATED           0          1          1          1        0
  C5ORF34 WILD-TYPE        19          9         40         30       35
                   vv
clus                STAGE IVA STAGE IVB
  C5ORF34 MUTATED           0         0
  C5ORF34 WILD-TYPE        13         1
D1058V3, multiclass
            clus
vv           C5ORF34 MUTATED C5ORF34 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                4               105
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               1                 9
  STAGE IIIB               1                40
  STAGE IIIC               1                30
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C5ORF34 MUTATED     0   2   7   1
  C5ORF34 WILD-TYPE   9  66 241  40
D1058V4, multiclass
    clus
vv   C5ORF34 MUTATED C5ORF34 WILD-TYPE
  T1               0                 9
  T2               2                66
  T3               7               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
  C5ORF34 MUTATED     7   2   1
  C5ORF34 WILD-TYPE 213  78  65
D1058V5, multiclass
    clus
vv   C5ORF34 MUTATED C5ORF34 WILD-TYPE
  N0               7               213
  N1               2                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"
D1058V6, binary
                   cls
clus                  0   1
  C5ORF34 MUTATED    10   0
  C5ORF34 WILD-TYPE 273  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF34 MUTATED     10    0
  C5ORF34 WILD-TYPE  273   48
   clus
vv  C5ORF34 MUTATED C5ORF34 WILD-TYPE
  0              10               273
  1               0                48
[1] 2 2
[1] FALSE
D1058V7, 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
D1058V8, binary
                   cls
clus                  0   1
  C5ORF34 MUTATED     5   5
  C5ORF34 WILD-TYPE 312  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF34 MUTATED      5    5
  C5ORF34 WILD-TYPE  312   43
                               clus
vv                              C5ORF34 MUTATED C5ORF34 WILD-TYPE
  COLON ADENOCARCINOMA                        5               312
  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 250   2  22  20
D1058V9, multiclass
    clus
vv   C5ORF34 MUTATED C5ORF34 WILD-TYPE
  R0               7               250
  R1               0                 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"
D1058V10, 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
D1058V11, 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(1059) Variable = GPR98 MUTATION ANALYSIS
D1059V1, survival
                 sevent
clus2               0   1
  GPR98 MUTATED    50  10
  GPR98 WILD-TYPE 232  63
  GPR98 MUTATED GPR98 WILD-TYPE 
             60             295 
  GPR98 MUTATED GPR98 WILD-TYPE 
             10              63 
$`GPR98 MUTATED`
TCGA-A6-3809 TCGA-A6-5660 TCGA-A6-5665 TCGA-A6-6651 TCGA-A6-6654 TCGA-AA-3489 
       32.75        29.19        22.06        21.76        23.87         7.04 
TCGA-AA-3492 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3819 
        3.02         6.97         0.92        85.05        19.04        25.02 
TCGA-AA-3833 TCGA-AA-3852 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3950 
       15.95         0.00        53.00        31.00        24.00        24.00 
TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R 
       20.98         2.01        25.02         4.01        34.98        35.01 
TCGA-AD-6889 TCGA-AD-6895 TCGA-AU-3779 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4616 
       56.55         0.72        14.50        21.44        58.39         5.13 
TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5912 
       62.79        49.41         6.77         0.33         0.10        49.08 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-6171 
      124.27        23.05        37.02        30.08        15.02        14.04 
TCGA-CM-6674 TCGA-CM-6678 TCGA-D5-5541 TCGA-D5-6535 TCGA-D5-6927 TCGA-D5-6928 
       12.95        11.01        11.51        15.12         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6932 TCGA-DM-A1HB TCGA-DM-A28H TCGA-F4-6570 TCGA-F4-6856 
        1.51        11.38       135.65       117.07         6.18        19.43 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6586 TCGA-G4-6588 
       44.68        55.04        51.75        36.72        35.80        26.17 

$`GPR98 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       31.63        30.44        33.53        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3496 
       24.69        24.39        20.12        19.66        20.28         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
        1.02        17.98        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 
       17.03        10.06         0.00        33.07        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 
       27.02        29.98        18.05         2.01        12.99        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       26.01         2.01        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       21.37         4.21         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 
        0.20        17.82         1.41        83.80        22.36        61.41 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.26         1.35        17.56       102.44        40.34        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         2.93         2.01        20.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 
       25.02        13.02        29.06        22.03        22.98        16.01 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        13.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 
       20.19        18.25         1.32        43.27        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         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-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
       60.79        98.24         8.61        13.38        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        35.41       107.67        74.56        65.85        53.62 
TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 
       45.11        36.00        22.09        13.78        91.79        46.75 
TCGA-G4-6628 
       52.80 

  GPR98 MUTATED GPR98 WILD-TYPE 
              0               0 
  GPR98 MUTATED GPR98 WILD-TYPE 
         135.65          140.38 
  GPR98 MUTATED GPR98 WILD-TYPE 
          21.91           19.99 
[1] "0.0 - 135.7 (21.9)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.4"
D1059V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GPR98 MUTATED         7        0        6        25         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           3          0          8          2        3         2
  GPR98 WILD-TYPE        16         10         33         29       32        11
                 vv
clus              STAGE IVB
  GPR98 MUTATED           0
  GPR98 WILD-TYPE         1
D1059V3, multiclass
            clus
vv           GPR98 MUTATED GPR98 WILD-TYPE
  STAGE I                7              57
  STAGE IA               0               1
  STAGE II               6              19
  STAGE IIA             25              84
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              3              16
  STAGE IIIA             0              10
  STAGE IIIB             8              33
  STAGE IIIC             2              29
  STAGE IV               3              32
  STAGE IVA              2              11
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  59 202  36
D1059V4, multiclass
    clus
vv   GPR98 MUTATED GPR98 WILD-TYPE
  T1             1               8
  T2             9              59
  T3            46             202
  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  68  61
D1059V5, multiclass
    clus
vv   GPR98 MUTATED GPR98 WILD-TYPE
  N0            44             176
  N1            12              68
  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"
D1059V6, binary
                 cls
clus                0   1
  GPR98 MUTATED    46   5
  GPR98 WILD-TYPE 237  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR98 MUTATED     46    5
  GPR98 WILD-TYPE  237   43
   clus
vv  GPR98 MUTATED GPR98 WILD-TYPE
  0            46             237
  1             5              43
[1] 2 2
[1] FALSE
D1059V7, 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
D1059V8, binary
                 cls
clus                0   1
  GPR98 MUTATED    49  12
  GPR98 WILD-TYPE 268  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR98 MUTATED     49   12
  GPR98 WILD-TYPE  268   36
                               clus
vv                              GPR98 MUTATED GPR98 WILD-TYPE
  COLON ADENOCARCINOMA                     49             268
  COLON MUCINOUS ADENOCARCINOMA            12              36
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  GPR98 MUTATED    42   0   1   5
  GPR98 WILD-TYPE 215   2  21  16
D1059V9, multiclass
    clus
vv   GPR98 MUTATED GPR98 WILD-TYPE
  R0            42             215
  R1             0               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"
D1059V10, 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
D1059V11, 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(1060) Variable = UAP1L1 MUTATION ANALYSIS
D1060V1, survival
                  sevent
clus2                0   1
  UAP1L1 MUTATED     4   2
  UAP1L1 WILD-TYPE 278  71
  UAP1L1 MUTATED UAP1L1 WILD-TYPE 
               6              349 
  UAP1L1 MUTATED UAP1L1 WILD-TYPE 
               2               71 
$`UAP1L1 MUTATED`
TCGA-AA-3662 TCGA-AA-3930 TCGA-AA-3977 TCGA-AD-5900 TCGA-DM-A28F TCGA-G4-6299 
        6.05         2.01        25.02         0.07        35.97        74.56 

$`UAP1L1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
      139.17         6.12        81.37       119.93        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 
        0.53        35.41        19.43       107.67        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  UAP1L1 MUTATED UAP1L1 WILD-TYPE 
            0.07             0.00 
  UAP1L1 MUTATED UAP1L1 WILD-TYPE 
           74.56           140.38 
  UAP1L1 MUTATED UAP1L1 WILD-TYPE 
          15.535           20.190 
[1] "0.1 - 74.6 (15.5)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.8"
D1060V2, 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       25       109         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  UAP1L1 MUTATED           0          0          1          1        2
  UAP1L1 WILD-TYPE        19         10         40         30       33
                  vv
clus               STAGE IVA STAGE IVB
  UAP1L1 MUTATED           0         0
  UAP1L1 WILD-TYPE        13         1
D1060V3, multiclass
            clus
vv           UAP1L1 MUTATED UAP1L1 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               0              109
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              1               30
  STAGE IV                2               33
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  UAP1L1 MUTATED     0   2   3   1
  UAP1L1 WILD-TYPE   9  66 245  40
D1060V4, multiclass
    clus
vv   UAP1L1 MUTATED UAP1L1 WILD-TYPE
  T1              0                9
  T2              2               66
  T3              3              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   1   3
  UAP1L1 WILD-TYPE 218  79  63
D1060V5, multiclass
    clus
vv   UAP1L1 MUTATED UAP1L1 WILD-TYPE
  N0              2              218
  N1              1               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"
D1060V6, binary
                  cls
clus                 0   1
  UAP1L1 MUTATED     2   2
  UAP1L1 WILD-TYPE 281  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UAP1L1 MUTATED      2    2
  UAP1L1 WILD-TYPE  281   46
   clus
vv  UAP1L1 MUTATED UAP1L1 WILD-TYPE
  0              2              281
  1              2               46
[1] 2 2
[1] FALSE
D1060V7, binary
                  cls
clus                 0   1
  UAP1L1 MUTATED     1   5
  UAP1L1 WILD-TYPE 169 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UAP1L1 MUTATED      1    5
  UAP1L1 WILD-TYPE  169  192
        clus
vv       UAP1L1 MUTATED UAP1L1 WILD-TYPE
  FEMALE              1              169
  MALE                5              192
[1] 2 2
[1] FALSE
D1060V8, binary
                  cls
clus                 0   1
  UAP1L1 MUTATED     5   1
  UAP1L1 WILD-TYPE 312  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UAP1L1 MUTATED      5    1
  UAP1L1 WILD-TYPE  312   47
                               clus
vv                              UAP1L1 MUTATED UAP1L1 WILD-TYPE
  COLON ADENOCARCINOMA                       5              312
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  UAP1L1 MUTATED     2   0   2   0
  UAP1L1 WILD-TYPE 255   2  20  21
D1060V9, multiclass
    clus
vv   UAP1L1 MUTATED UAP1L1 WILD-TYPE
  R0              2              255
  R1              0                2
  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"
D1060V10, 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     3
  UAP1L1 WILD-TYPE                        19   173
D1060V11, 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                                         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 = CDC7 MUTATION ANALYSIS
D1061V1, survival
                sevent
clus2              0   1
  CDC7 MUTATED     8   1
  CDC7 WILD-TYPE 274  72
  CDC7 MUTATED CDC7 WILD-TYPE 
             9            346 
  CDC7 MUTATED CDC7 WILD-TYPE 
             1             72 
$`CDC7 MUTATED`
TCGA-A6-2672 TCGA-AA-3496 TCGA-AA-3977 TCGA-AU-6004 TCGA-AZ-6599 TCGA-CA-5255 
       46.65         1.02        25.02        27.09         6.77         3.06 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-6676 
        0.33         0.10        11.08 

$`CDC7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.20        14.50        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41        49.41        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07         0.26         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  CDC7 MUTATED CDC7 WILD-TYPE 
           0.1            0.0 
  CDC7 MUTATED CDC7 WILD-TYPE 
         46.65         140.38 
  CDC7 MUTATED CDC7 WILD-TYPE 
          6.77          20.63 
[1] "0.1 - 46.6 (6.8)"   "0.0 - 140.4 (20.6)"
[1] "hr=" "1"  
D1061V2, 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       24       106         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        19         10         40         31       35        13
                vv
clus             STAGE IVB
  CDC7 MUTATED           0
  CDC7 WILD-TYPE         1
D1061V3, multiclass
            clus
vv           CDC7 MUTATED CDC7 WILD-TYPE
  STAGE I               4             60
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             3            106
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CDC7 MUTATED     0   5   5   0
  CDC7 WILD-TYPE   9  63 243  41
D1061V4, multiclass
    clus
vv   CDC7 MUTATED CDC7 WILD-TYPE
  T1            0              9
  T2            5             63
  T3            5            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
  CDC7 MUTATED     9   1   0
  CDC7 WILD-TYPE 211  79  66
D1061V5, multiclass
    clus
vv   CDC7 MUTATED CDC7 WILD-TYPE
  N0            9            211
  N1            1             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
  CDC7 MUTATED     7   0
  CDC7 WILD-TYPE 276  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDC7 MUTATED      7    0
  CDC7 WILD-TYPE  276   48
   clus
vv  CDC7 MUTATED CDC7 WILD-TYPE
  0            7            276
  1            0             48
[1] 2 2
[1] FALSE
D1061V7, 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
D1061V8, binary
                cls
clus               0   1
  CDC7 MUTATED     9   1
  CDC7 WILD-TYPE 308  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDC7 MUTATED      9    1
  CDC7 WILD-TYPE  308   47
                               clus
vv                              CDC7 MUTATED CDC7 WILD-TYPE
  COLON ADENOCARCINOMA                     9            308
  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 253   2  22  17
D1061V9, multiclass
    clus
vv   CDC7 MUTATED CDC7 WILD-TYPE
  R0            4            253
  R1            0              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"
D1061V10, 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
D1061V11, 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(1062) Variable = ST8SIA6 MUTATION ANALYSIS
D1062V1, survival
                   sevent
clus2                 0   1
  ST8SIA6 MUTATED     7   2
  ST8SIA6 WILD-TYPE 275  71
  ST8SIA6 MUTATED ST8SIA6 WILD-TYPE 
                9               346 
  ST8SIA6 MUTATED ST8SIA6 WILD-TYPE 
                2                71 
$`ST8SIA6 MUTATED`
TCGA-AA-3492 TCGA-AA-A00E TCGA-AA-A010 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4315 
        3.02        30.02        34.98         0.72        10.88        58.39 
TCGA-CA-6717 TCGA-CK-5913 TCGA-CK-6751 
        0.33        51.32       124.27 

$`ST8SIA6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
        0.79         5.79        22.42        27.42         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
       17.56       102.44        40.34        15.62        49.08        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14         2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  ST8SIA6 MUTATED ST8SIA6 WILD-TYPE 
             0.33              0.00 
  ST8SIA6 MUTATED ST8SIA6 WILD-TYPE 
           124.27            140.38 
  ST8SIA6 MUTATED ST8SIA6 WILD-TYPE 
           30.020            20.155 
[1] "0.3 - 124.3 (30.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D1062V2, 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       24       105         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ST8SIA6 MUTATED           0          0          0          0        0
  ST8SIA6 WILD-TYPE        19         10         41         31       35
                   vv
clus                STAGE IVA STAGE IVB
  ST8SIA6 MUTATED           0         0
  ST8SIA6 WILD-TYPE        13         1
D1062V3, multiclass
            clus
vv           ST8SIA6 MUTATED ST8SIA6 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                4               105
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ST8SIA6 MUTATED     0   1   6   3
  ST8SIA6 WILD-TYPE   9  67 242  38
D1062V4, multiclass
    clus
vv   ST8SIA6 MUTATED ST8SIA6 WILD-TYPE
  T1               0                 9
  T2               1                67
  T3               6               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
  ST8SIA6 MUTATED     8   1   1
  ST8SIA6 WILD-TYPE 212  79  65
D1062V5, multiclass
    clus
vv   ST8SIA6 MUTATED ST8SIA6 WILD-TYPE
  N0               8               212
  N1               1                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"
D1062V6, binary
                   cls
clus                  0   1
  ST8SIA6 MUTATED     5   0
  ST8SIA6 WILD-TYPE 278  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ST8SIA6 MUTATED      5    0
  ST8SIA6 WILD-TYPE  278   48
   clus
vv  ST8SIA6 MUTATED ST8SIA6 WILD-TYPE
  0               5               278
  1               0                48
[1] 2 2
[1] FALSE
D1062V7, 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
D1062V8, binary
                   cls
clus                  0   1
  ST8SIA6 MUTATED     8   2
  ST8SIA6 WILD-TYPE 309  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ST8SIA6 MUTATED      8    2
  ST8SIA6 WILD-TYPE  309   46
                               clus
vv                              ST8SIA6 MUTATED ST8SIA6 WILD-TYPE
  COLON ADENOCARCINOMA                        8               309
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ST8SIA6 MUTATED     4   0   0   4
  ST8SIA6 WILD-TYPE 253   2  22  17
D1062V9, multiclass
    clus
vv   ST8SIA6 MUTATED ST8SIA6 WILD-TYPE
  R0               4               253
  R1               0                 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"
D1062V10, 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
D1062V11, 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(1063) Variable = MRPS18B MUTATION ANALYSIS
D1063V1, survival
                   sevent
clus2                 0   1
  MRPS18B MUTATED     4   0
  MRPS18B WILD-TYPE 278  73
  MRPS18B MUTATED MRPS18B WILD-TYPE 
                4               351 
  MRPS18B MUTATED MRPS18B WILD-TYPE 
                0                73 
$`MRPS18B MUTATED`
TCGA-A6-2672 TCGA-AA-3662 TCGA-DM-A28K TCGA-G4-6315 
       46.65         6.05        98.24        36.72 

$`MRPS18B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       19.99        13.94        19.99        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       35.97        60.79       117.07         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       45.11        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  MRPS18B MUTATED MRPS18B WILD-TYPE 
             6.05              0.00 
  MRPS18B MUTATED MRPS18B WILD-TYPE 
            98.24            140.38 
  MRPS18B MUTATED MRPS18B WILD-TYPE 
           41.685            20.120 
[1] "6.0 - 98.2 (41.7)"  "0.0 - 140.4 (20.1)"
[1] "hr="     "9300000"
D1063V2, 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       25       108         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MRPS18B MUTATED           0          0          1          0        2
  MRPS18B WILD-TYPE        19         10         40         31       33
                   vv
clus                STAGE IVA STAGE IVB
  MRPS18B MUTATED           0         0
  MRPS18B WILD-TYPE        13         1
D1063V3, multiclass
            clus
vv           MRPS18B MUTATED MRPS18B WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                1               108
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               0                31
  STAGE IV                 2                33
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  MRPS18B MUTATED     0   0   3   1
  MRPS18B WILD-TYPE   9  68 245  40
D1063V4, multiclass
    clus
vv   MRPS18B MUTATED MRPS18B WILD-TYPE
  T1               0                 9
  T2               0                68
  T3               3               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
  MRPS18B MUTATED     1   2   1
  MRPS18B WILD-TYPE 219  78  65
D1063V5, multiclass
    clus
vv   MRPS18B MUTATED MRPS18B WILD-TYPE
  N0               1               219
  N1               2                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"
D1063V6, binary
                   cls
clus                  0   1
  MRPS18B MUTATED     2   2
  MRPS18B WILD-TYPE 281  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MRPS18B MUTATED      2    2
  MRPS18B WILD-TYPE  281   46
   clus
vv  MRPS18B MUTATED MRPS18B WILD-TYPE
  0               2               281
  1               2                46
[1] 2 2
[1] FALSE
D1063V7, 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
D1063V8, binary
                   cls
clus                  0   1
  MRPS18B MUTATED     3   1
  MRPS18B WILD-TYPE 314  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MRPS18B MUTATED      3    1
  MRPS18B WILD-TYPE  314   47
                               clus
vv                              MRPS18B MUTATED MRPS18B WILD-TYPE
  COLON ADENOCARCINOMA                        3               314
  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 255   2  21  21
D1063V9, multiclass
    clus
vv   MRPS18B MUTATED MRPS18B WILD-TYPE
  R0               2               255
  R1               0                 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"
D1063V10, 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
D1063V11, 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(1064) Variable = ARHGAP28 MUTATION ANALYSIS
D1064V1, survival
                    sevent
clus2                  0   1
  ARHGAP28 MUTATED    12   1
  ARHGAP28 WILD-TYPE 270  72
  ARHGAP28 MUTATED ARHGAP28 WILD-TYPE 
                13                342 
  ARHGAP28 MUTATED ARHGAP28 WILD-TYPE 
                 1                 72 
$`ARHGAP28 MUTATED`
TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3554 TCGA-AA-3715 TCGA-AA-3947 TCGA-AA-3949 
       24.39        19.66        17.95        19.04        33.01        26.01 
TCGA-AA-A00J TCGA-AA-A010 TCGA-AD-6889 TCGA-CM-4743 TCGA-CM-5861 TCGA-CM-6674 
       18.05        34.98        56.55        23.05        15.02        12.95 
TCGA-G4-6628 
       52.80 

$`ARHGAP28 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93         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        16.01 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 

  ARHGAP28 MUTATED ARHGAP28 WILD-TYPE 
             12.95               0.00 
  ARHGAP28 MUTATED ARHGAP28 WILD-TYPE 
             56.55             140.38 
  ARHGAP28 MUTATED ARHGAP28 WILD-TYPE 
            23.050             20.155 
[1] "12.9 - 56.5 (23.1)" "0.0 - 140.4 (20.2)"
[1] "hr=" "2.9"
D1064V2, 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       24       104         6         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARHGAP28 MUTATED           0          0          2          1        0
  ARHGAP28 WILD-TYPE        19         10         39         30       35
                    vv
clus                 STAGE IVA STAGE IVB
  ARHGAP28 MUTATED           0         0
  ARHGAP28 WILD-TYPE        13         1
D1064V3, multiclass
            clus
vv           ARHGAP28 MUTATED ARHGAP28 WILD-TYPE
  STAGE I                   2                 62
  STAGE IA                  0                  1
  STAGE II                  1                 24
  STAGE IIA                 5                104
  STAGE IIB                 2                  6
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                0                 10
  STAGE IIIB                2                 39
  STAGE IIIC                1                 30
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  ARHGAP28 MUTATED     0   2   7   4
  ARHGAP28 WILD-TYPE   9  66 241  37
D1064V4, multiclass
    clus
vv   ARHGAP28 MUTATED ARHGAP28 WILD-TYPE
  T1                0                  9
  T2                2                 66
  T3                7                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
  ARHGAP28 MUTATED    10   3   0
  ARHGAP28 WILD-TYPE 210  77  66
D1064V5, multiclass
    clus
vv   ARHGAP28 MUTATED ARHGAP28 WILD-TYPE
  N0               10                210
  N1                3                 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"
D1064V6, binary
                    cls
clus                   0   1
  ARHGAP28 MUTATED    12   0
  ARHGAP28 WILD-TYPE 271  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP28 MUTATED     12    0
  ARHGAP28 WILD-TYPE  271   48
   clus
vv  ARHGAP28 MUTATED ARHGAP28 WILD-TYPE
  0               12                271
  1                0                 48
[1] 2 2
[1] FALSE
D1064V7, 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
D1064V8, binary
                    cls
clus                   0   1
  ARHGAP28 MUTATED     9   4
  ARHGAP28 WILD-TYPE 308  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP28 MUTATED      9    4
  ARHGAP28 WILD-TYPE  308   44
                               clus
vv                              ARHGAP28 MUTATED ARHGAP28 WILD-TYPE
  COLON ADENOCARCINOMA                         9                308
  COLON MUCINOUS ADENOCARCINOMA                4                 44
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  ARHGAP28 MUTATED    11   0   0   0
  ARHGAP28 WILD-TYPE 246   2  22  21
D1064V9, multiclass
    clus
vv   ARHGAP28 MUTATED ARHGAP28 WILD-TYPE
  R0               11                246
  R1                0                  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"
D1064V10, 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
D1064V11, 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(1065) Variable = SSX2IP MUTATION ANALYSIS
D1065V1, survival
                  sevent
clus2                0   1
  SSX2IP MUTATED     5   2
  SSX2IP WILD-TYPE 277  71
  SSX2IP MUTATED SSX2IP WILD-TYPE 
               7              348 
  SSX2IP MUTATED SSX2IP WILD-TYPE 
               2               71 
$`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        16.01        12.00 
TCGA-D5-5539 
       19.59 

$`SSX2IP WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3560 
       13.02        24.00        17.95        29.95        23.01        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        12.26 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  SSX2IP MUTATED SSX2IP WILD-TYPE 
            3.02             0.00 
  SSX2IP MUTATED SSX2IP WILD-TYPE 
           62.79           140.38 
  SSX2IP MUTATED SSX2IP WILD-TYPE 
          19.590           20.235 
[1] "3.0 - 62.8 (19.6)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.4"
D1065V2, 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       22       108         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SSX2IP MUTATED           0          1          1          0        0
  SSX2IP WILD-TYPE        19          9         40         31       35
                  vv
clus               STAGE IVA STAGE IVB
  SSX2IP MUTATED           0         0
  SSX2IP WILD-TYPE        13         1
D1065V3, multiclass
            clus
vv           SSX2IP MUTATED SSX2IP WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                3               22
  STAGE IIA               1              108
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              1                9
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SSX2IP MUTATED     0   1   5   2
  SSX2IP WILD-TYPE   9  67 243  39
D1065V4, multiclass
    clus
vv   SSX2IP MUTATED SSX2IP WILD-TYPE
  T1              0                9
  T2              1               67
  T3              5              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
  SSX2IP MUTATED     6   2   0
  SSX2IP WILD-TYPE 214  78  66
D1065V5, multiclass
    clus
vv   SSX2IP MUTATED SSX2IP WILD-TYPE
  N0              6              214
  N1              2               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"
D1065V6, binary
                  cls
clus                 0   1
  SSX2IP MUTATED     7   0
  SSX2IP WILD-TYPE 276  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SSX2IP MUTATED      7    0
  SSX2IP WILD-TYPE  276   48
   clus
vv  SSX2IP MUTATED SSX2IP WILD-TYPE
  0              7              276
  1              0               48
[1] 2 2
[1] FALSE
D1065V7, 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
D1065V8, binary
                  cls
clus                 0   1
  SSX2IP MUTATED     6   2
  SSX2IP WILD-TYPE 311  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SSX2IP MUTATED      6    2
  SSX2IP WILD-TYPE  311   46
                               clus
vv                              SSX2IP MUTATED SSX2IP WILD-TYPE
  COLON ADENOCARCINOMA                       6              311
  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 251   2  21  21
D1065V9, multiclass
    clus
vv   SSX2IP MUTATED SSX2IP WILD-TYPE
  R0              6              251
  R1              0                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"
D1065V10, 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
D1065V11, 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(1066) Variable = SPOPL MUTATION ANALYSIS
D1066V1, survival
                 sevent
clus2               0   1
  SPOPL MUTATED     8   2
  SPOPL WILD-TYPE 274  71
  SPOPL MUTATED SPOPL WILD-TYPE 
             10             345 
  SPOPL MUTATED SPOPL WILD-TYPE 
              2              71 
$`SPOPL MUTATED`
TCGA-AA-3666 TCGA-AA-3672 TCGA-AZ-4315 TCGA-AZ-6603 TCGA-CA-6716 TCGA-D5-6532 
        2.01         0.92        58.39        29.56         0.26        18.25 
TCGA-D5-6541 TCGA-DM-A28E TCGA-F4-6704 TCGA-G4-6586 
       15.58       119.93         1.55        35.80 

$`SPOPL WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.05         6.97        54.02        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10       100.01         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 
        2.24         3.06         3.25         3.29         0.07         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45         6.18        35.87        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 
       45.11        36.72        36.00        22.09        13.78        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  SPOPL MUTATED SPOPL WILD-TYPE 
           0.26            0.00 
  SPOPL MUTATED SPOPL WILD-TYPE 
         119.93          140.38 
  SPOPL MUTATED SPOPL WILD-TYPE 
         16.915          20.280 
[1] "0.3 - 119.9 (16.9)" "0.0 - 140.4 (20.3)"
[1] "hr=" "1"  
D1066V2, 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       25       103         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        17         10         41         30       35        13
                 vv
clus              STAGE IVB
  SPOPL MUTATED           0
  SPOPL WILD-TYPE         1
D1066V3, multiclass
            clus
vv           SPOPL MUTATED SPOPL WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              6             103
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SPOPL MUTATED     0   1   9   0
  SPOPL WILD-TYPE   9  67 239  41
D1066V4, multiclass
    clus
vv   SPOPL MUTATED SPOPL WILD-TYPE
  T1             0               9
  T2             1              67
  T3             9             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
  SPOPL MUTATED     6   3   1
  SPOPL WILD-TYPE 214  77  65
D1066V5, multiclass
    clus
vv   SPOPL MUTATED SPOPL WILD-TYPE
  N0             6             214
  N1             3              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"
D1066V6, binary
                 cls
clus                0   1
  SPOPL MUTATED     8   0
  SPOPL WILD-TYPE 275  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPOPL MUTATED      8    0
  SPOPL WILD-TYPE  275   48
   clus
vv  SPOPL MUTATED SPOPL WILD-TYPE
  0             8             275
  1             0              48
[1] 2 2
[1] FALSE
D1066V7, 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
D1066V8, binary
                 cls
clus                0   1
  SPOPL MUTATED     9   1
  SPOPL WILD-TYPE 308  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPOPL MUTATED      9    1
  SPOPL WILD-TYPE  308   47
                               clus
vv                              SPOPL MUTATED SPOPL WILD-TYPE
  COLON ADENOCARCINOMA                      9             308
  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 250   2  22  20
D1066V9, multiclass
    clus
vv   SPOPL MUTATED SPOPL WILD-TYPE
  R0             7             250
  R1             0               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"
D1066V10, 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
D1066V11, 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(1067) Variable = DACT1 MUTATION ANALYSIS
D1067V1, survival
                 sevent
clus2               0   1
  DACT1 MUTATED     9   3
  DACT1 WILD-TYPE 273  70
  DACT1 MUTATED DACT1 WILD-TYPE 
             12             343 
  DACT1 MUTATED DACT1 WILD-TYPE 
              3              70 
$`DACT1 MUTATED`
TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3713 TCGA-AA-3815 TCGA-AA-A00N TCGA-AA-A01P 
       20.12        19.66        19.04        33.04         4.01        38.07 
TCGA-AZ-6598 TCGA-CA-6717 TCGA-CM-5348 TCGA-D5-6927 TCGA-DM-A28K TCGA-G4-6588 
       49.41         0.33        22.98         9.44        98.24        26.17 

$`DACT1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       23.87        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        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        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
      117.07         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 
       52.80 

  DACT1 MUTATED DACT1 WILD-TYPE 
           0.33            0.00 
  DACT1 MUTATED DACT1 WILD-TYPE 
          98.24          140.38 
  DACT1 MUTATED DACT1 WILD-TYPE 
          21.55           20.19 
[1] "0.3 - 98.2 (21.6)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D1067V2, 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       23       102         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        18         10         40         30       34        13
                 vv
clus              STAGE IVB
  DACT1 MUTATED           0
  DACT1 WILD-TYPE         1
D1067V3, multiclass
            clus
vv           DACT1 MUTATED DACT1 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              7             102
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DACT1 MUTATED     0   0  11   4
  DACT1 WILD-TYPE   9  68 237  37
D1067V4, multiclass
    clus
vv   DACT1 MUTATED DACT1 WILD-TYPE
  T1             0               9
  T2             0              68
  T3            11             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
  DACT1 MUTATED    12   3   0
  DACT1 WILD-TYPE 208  77  66
D1067V5, multiclass
    clus
vv   DACT1 MUTATED DACT1 WILD-TYPE
  N0            12             208
  N1             3              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"
D1067V6, binary
                 cls
clus                0   1
  DACT1 MUTATED    10   1
  DACT1 WILD-TYPE 273  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DACT1 MUTATED     10    1
  DACT1 WILD-TYPE  273   47
   clus
vv  DACT1 MUTATED DACT1 WILD-TYPE
  0            10             273
  1             1              47
[1] 2 2
[1] FALSE
D1067V7, 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
D1067V8, binary
                 cls
clus                0   1
  DACT1 MUTATED    10   5
  DACT1 WILD-TYPE 307  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DACT1 MUTATED     10    5
  DACT1 WILD-TYPE  307   43
                               clus
vv                              DACT1 MUTATED DACT1 WILD-TYPE
  COLON ADENOCARCINOMA                     10             307
  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 248   2  21  19
D1067V9, multiclass
    clus
vv   DACT1 MUTATED DACT1 WILD-TYPE
  R0             9             248
  R1             0               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"
D1067V10, 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
D1067V11, 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(1068) Variable = FAM193A MUTATION ANALYSIS
D1068V1, survival
                   sevent
clus2                 0   1
  FAM193A MUTATED    15   2
  FAM193A WILD-TYPE 267  71
  FAM193A MUTATED FAM193A WILD-TYPE 
               17               338 
  FAM193A MUTATED FAM193A WILD-TYPE 
                2                71 
$`FAM193A MUTATED`
TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-3660 TCGA-AA-3947 TCGA-AD-5900 TCGA-AD-6895 
       22.06        20.12        78.08        33.01         0.07         0.72 
TCGA-AD-6964 TCGA-AZ-6598 TCGA-CA-6718 TCGA-CK-4952 TCGA-CK-5913 TCGA-CM-5861 
       10.88        49.41         0.10        15.62        51.32        15.02 
TCGA-CM-6169 TCGA-D5-6927 TCGA-D5-7000 TCGA-G4-6304 TCGA-G4-6588 
       13.02         9.44        10.26        53.62        26.17 

$`FAM193A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
       40.96        21.37         4.21        56.55         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.33         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       40.34        49.08        21.99        21.14         2.93         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        16.01         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00        11.38 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  FAM193A MUTATED FAM193A WILD-TYPE 
             0.07              0.00 
  FAM193A MUTATED FAM193A WILD-TYPE 
            78.08            140.38 
  FAM193A MUTATED FAM193A WILD-TYPE 
            15.62             20.63 
[1] "0.1 - 78.1 (15.6)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "1.8"
D1068V2, 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       23       101         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM193A MUTATED           1          0          0          0        0
  FAM193A WILD-TYPE        18         10         41         31       35
                   vv
clus                STAGE IVA STAGE IVB
  FAM193A MUTATED           0         0
  FAM193A WILD-TYPE        13         1
D1068V3, multiclass
            clus
vv           FAM193A MUTATED FAM193A WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 2                23
  STAGE IIA                8               101
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  FAM193A MUTATED     0   2  11   4
  FAM193A WILD-TYPE   9  66 237  37
D1068V4, multiclass
    clus
vv   FAM193A MUTATED FAM193A WILD-TYPE
  T1               0                 9
  T2               2                66
  T3              11               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
  FAM193A MUTATED    14   1   2
  FAM193A WILD-TYPE 206  79  64
D1068V5, multiclass
    clus
vv   FAM193A MUTATED FAM193A WILD-TYPE
  N0              14               206
  N1               1                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
  FAM193A MUTATED    11   0
  FAM193A WILD-TYPE 272  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM193A MUTATED     11    0
  FAM193A WILD-TYPE  272   48
   clus
vv  FAM193A MUTATED FAM193A WILD-TYPE
  0              11               272
  1               0                48
[1] 2 2
[1] FALSE
D1068V7, 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
D1068V8, binary
                   cls
clus                  0   1
  FAM193A MUTATED    12   5
  FAM193A WILD-TYPE 305  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM193A MUTATED     12    5
  FAM193A WILD-TYPE  305   43
                               clus
vv                              FAM193A MUTATED FAM193A WILD-TYPE
  COLON ADENOCARCINOMA                       12               305
  COLON MUCINOUS ADENOCARCINOMA               5                43
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  FAM193A MUTATED    10   0   0   3
  FAM193A WILD-TYPE 247   2  22  18
D1068V9, multiclass
    clus
vv   FAM193A MUTATED FAM193A WILD-TYPE
  R0              10               247
  R1               0                 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"
D1068V10, 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
D1068V11, 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(1069) Variable = ZFP91 MUTATION ANALYSIS
D1069V1, survival
                 sevent
clus2               0   1
  ZFP91 MUTATED     5   2
  ZFP91 WILD-TYPE 277  71
  ZFP91 MUTATED ZFP91 WILD-TYPE 
              7             348 
  ZFP91 MUTATED ZFP91 WILD-TYPE 
              2              71 
$`ZFP91 MUTATED`
TCGA-A6-5661 TCGA-AA-3860 TCGA-AA-A00L TCGA-AA-A01R TCGA-CM-6162 TCGA-DM-A28G 
       33.53        31.07        38.04        35.01        12.00        60.79 
TCGA-G4-6303 
       65.85 

$`ZFP91 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
       32.05         0.99        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K 
        6.12        81.37       119.93        35.97       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 
       35.41        19.43       107.67        74.56        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  ZFP91 MUTATED ZFP91 WILD-TYPE 
             12               0 
  ZFP91 MUTATED ZFP91 WILD-TYPE 
          65.85          140.38 
  ZFP91 MUTATED ZFP91 WILD-TYPE 
         35.010          20.005 
[1] "12.0 - 65.8 (35.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.1"
D1069V2, 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       25       106         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        18         10         39         31       34        13
                 vv
clus              STAGE IVB
  ZFP91 MUTATED           0
  ZFP91 WILD-TYPE         1
D1069V3, multiclass
            clus
vv           ZFP91 MUTATED ZFP91 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              3             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ZFP91 MUTATED     0   0   7   0
  ZFP91 WILD-TYPE   9  68 241  41
D1069V4, multiclass
    clus
vv   ZFP91 MUTATED ZFP91 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             7             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
  ZFP91 MUTATED     3   3   1
  ZFP91 WILD-TYPE 217  77  65
D1069V5, multiclass
    clus
vv   ZFP91 MUTATED ZFP91 WILD-TYPE
  N0             3             217
  N1             3              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"
D1069V6, binary
                 cls
clus                0   1
  ZFP91 MUTATED     6   1
  ZFP91 WILD-TYPE 277  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFP91 MUTATED      6    1
  ZFP91 WILD-TYPE  277   47
   clus
vv  ZFP91 MUTATED ZFP91 WILD-TYPE
  0             6             277
  1             1              47
[1] 2 2
[1] FALSE
D1069V7, 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
D1069V8, binary
                 cls
clus                0   1
  ZFP91 MUTATED     5   2
  ZFP91 WILD-TYPE 312  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFP91 MUTATED      5    2
  ZFP91 WILD-TYPE  312   46
                               clus
vv                              ZFP91 MUTATED ZFP91 WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  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 251   2  22  21
D1069V9, multiclass
    clus
vv   ZFP91 MUTATED ZFP91 WILD-TYPE
  R0             6             251
  R1             0               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"
D1069V10, 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
D1069V11, 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(1070) Variable = USP44 MUTATION ANALYSIS
D1070V1, survival
                 sevent
clus2               0   1
  USP44 MUTATED    12   2
  USP44 WILD-TYPE 270  71
  USP44 MUTATED USP44 WILD-TYPE 
             14             341 
  USP44 MUTATED USP44 WILD-TYPE 
              2              71 
$`USP44 MUTATED`
TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3864 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00A 
        0.92        19.04        53.00         2.01        25.02        38.04 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6889 TCGA-CM-5344 TCGA-DM-A1D0 TCGA-DM-A1DA 
        4.01        34.98        56.55        22.03       130.65         7.50 
TCGA-F4-6807 TCGA-G4-6588 
       16.24        26.17 

$`USP44 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
        6.05         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       27.02        13.94        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43        38.20        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
      140.38        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       16.31        29.59        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        91.79        46.75        52.80 

  USP44 MUTATED USP44 WILD-TYPE 
           0.92            0.00 
  USP44 MUTATED USP44 WILD-TYPE 
         130.65          140.38 
  USP44 MUTATED USP44 WILD-TYPE 
         23.525          20.120 
[1] "0.9 - 130.7 (23.5)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.7"
D1070V2, 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       23       103         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        18         10         40         29       34        13
                 vv
clus              STAGE IVB
  USP44 MUTATED           0
  USP44 WILD-TYPE         1
D1070V3, multiclass
            clus
vv           USP44 MUTATED USP44 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              6             103
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             2              29
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  USP44 MUTATED     0   1  12   3
  USP44 WILD-TYPE   9  67 236  38
D1070V4, multiclass
    clus
vv   USP44 MUTATED USP44 WILD-TYPE
  T1             0               9
  T2             1              67
  T3            12             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
  USP44 MUTATED    12   2   2
  USP44 WILD-TYPE 208  78  64
D1070V5, multiclass
    clus
vv   USP44 MUTATED USP44 WILD-TYPE
  N0            12             208
  N1             2              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"
D1070V6, binary
                 cls
clus                0   1
  USP44 MUTATED    14   1
  USP44 WILD-TYPE 269  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP44 MUTATED     14    1
  USP44 WILD-TYPE  269   47
   clus
vv  USP44 MUTATED USP44 WILD-TYPE
  0            14             269
  1             1              47
[1] 2 2
[1] FALSE
D1070V7, 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
D1070V8, binary
                 cls
clus                0   1
  USP44 MUTATED    14   2
  USP44 WILD-TYPE 303  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP44 MUTATED     14    2
  USP44 WILD-TYPE  303   46
                               clus
vv                              USP44 MUTATED USP44 WILD-TYPE
  COLON ADENOCARCINOMA                     14             303
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  USP44 MUTATED    10   0   1   0
  USP44 WILD-TYPE 247   2  21  21
D1070V9, multiclass
    clus
vv   USP44 MUTATED USP44 WILD-TYPE
  R0            10             247
  R1             0               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"
D1070V10, 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
D1070V11, 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(1071) Variable = ZNF559 MUTATION ANALYSIS
D1071V1, survival
                  sevent
clus2                0   1
  ZNF559 MUTATED    13   2
  ZNF559 WILD-TYPE 269  71
  ZNF559 MUTATED ZNF559 WILD-TYPE 
              15              340 
  ZNF559 MUTATED ZNF559 WILD-TYPE 
               2               71 
$`ZNF559 MUTATED`
TCGA-A6-3810 TCGA-A6-6141 TCGA-AA-3672 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-A00A 
       36.53         8.38         0.92        26.99        19.04        38.04 
TCGA-AA-A00J TCGA-AA-A010 TCGA-AY-6197 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 
       18.05        34.98        21.44        58.39         0.33         0.10 
TCGA-CM-6166 TCGA-DM-A28F TCGA-F4-6856 
       21.99        35.97        19.43 

$`ZNF559 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       85.05        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K 
       27.02        13.94        19.00        30.02        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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-4681 
       15.75         0.20        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
      119.93        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 
       16.24        33.67        13.25         0.53        35.41       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  ZNF559 MUTATED ZNF559 WILD-TYPE 
             0.1              0.0 
  ZNF559 MUTATED ZNF559 WILD-TYPE 
           58.39           140.38 
  ZNF559 MUTATED ZNF559 WILD-TYPE 
          21.440           20.155 
[1] "0.1 - 58.4 (21.4)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.3"
D1071V2, 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       24       101         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF559 MUTATED           1          0          2          0        0
  ZNF559 WILD-TYPE        18         10         39         31       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF559 MUTATED           0         0
  ZNF559 WILD-TYPE        13         1
D1071V3, multiclass
            clus
vv           ZNF559 MUTATED ZNF559 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               8              101
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF559 MUTATED     0   2  11   2
  ZNF559 WILD-TYPE   9  66 237  39
D1071V4, multiclass
    clus
vv   ZNF559 MUTATED ZNF559 WILD-TYPE
  T1              0                9
  T2              2               66
  T3             11              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
  ZNF559 MUTATED    12   3   0
  ZNF559 WILD-TYPE 208  77  66
D1071V5, multiclass
    clus
vv   ZNF559 MUTATED ZNF559 WILD-TYPE
  N0             12              208
  N1              3               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"
D1071V6, binary
                  cls
clus                 0   1
  ZNF559 MUTATED    14   0
  ZNF559 WILD-TYPE 269  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF559 MUTATED     14    0
  ZNF559 WILD-TYPE  269   48
   clus
vv  ZNF559 MUTATED ZNF559 WILD-TYPE
  0             14              269
  1              0               48
[1] 2 2
[1] FALSE
D1071V7, 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
D1071V8, binary
                  cls
clus                 0   1
  ZNF559 MUTATED    12   3
  ZNF559 WILD-TYPE 305  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF559 MUTATED     12    3
  ZNF559 WILD-TYPE  305   45
                               clus
vv                              ZNF559 MUTATED ZNF559 WILD-TYPE
  COLON ADENOCARCINOMA                      12              305
  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 246   2  22  19
D1071V9, multiclass
    clus
vv   ZNF559 MUTATED ZNF559 WILD-TYPE
  R0             11              246
  R1              0                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"
D1071V10, 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
D1071V11, 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(1072) Variable = ATR MUTATION ANALYSIS
D1072V1, survival
               sevent
clus2             0   1
  ATR MUTATED    22   5
  ATR WILD-TYPE 260  68
  ATR MUTATED ATR WILD-TYPE 
           27           328 
  ATR MUTATED ATR WILD-TYPE 
            5            68 
$`ATR MUTATED`
TCGA-A6-2676 TCGA-A6-6648 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3543 TCGA-AA-3664 
       42.90        25.18         1.02        35.01         0.99        54.02 
TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3864 TCGA-AA-3977 TCGA-AA-A010 TCGA-AY-4070 
       19.04        10.06        53.00        25.02        34.98        16.31 
TCGA-AY-6197 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5912 
       21.44         1.94         3.06         0.33         0.10        49.08 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-6165 TCGA-CM-6675 TCGA-D5-5538 TCGA-D5-6536 
      124.27        23.05        16.04        13.05        12.26        17.85 
TCGA-F4-6806 TCGA-F4-6808 TCGA-G4-6315 
       29.59        33.67        36.72 

$`ATR WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3511 
       19.66        20.28         7.04         3.02        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
       34.03        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       78.08         6.05         6.97         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 
       27.09         0.95        15.75         0.20        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
       11.74         3.19         2.24         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.26         1.35        17.56       102.44        40.34        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         2.93         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        16.01        15.02         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-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        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        15.12         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.31        16.24        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       51.75        45.11        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  ATR MUTATED ATR WILD-TYPE 
          0.1           0.0 
  ATR MUTATED ATR WILD-TYPE 
       124.27        140.38 
  ATR MUTATED ATR WILD-TYPE 
       21.440        20.155 
[1] "0.1 - 124.3 (21.4)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D1072V2, 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       22       101         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        18          9         40         30       33        12
               vv
clus            STAGE IVB
  ATR MUTATED           1
  ATR WILD-TYPE         0
D1072V3, multiclass
            clus
vv           ATR MUTATED ATR WILD-TYPE
  STAGE I              6            58
  STAGE IA             0             1
  STAGE II             3            22
  STAGE IIA            8           101
  STAGE IIB            2             6
  STAGE IIC            0             1
  STAGE III            1            18
  STAGE IIIA           1             9
  STAGE IIIB           1            40
  STAGE IIIC           1            30
  STAGE IV             2            33
  STAGE IVA            1            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
  ATR MUTATED     1   7  18   2
  ATR WILD-TYPE   8  61 230  39
D1072V4, multiclass
    clus
vv   ATR MUTATED ATR WILD-TYPE
  T1           1             8
  T2           7            61
  T3          18           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
  ATR MUTATED    22   3   3
  ATR WILD-TYPE 198  77  63
D1072V5, multiclass
    clus
vv   ATR MUTATED ATR WILD-TYPE
  N0          22           198
  N1           3            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"
D1072V6, binary
               cls
clus              0   1
  ATR MUTATED    20   4
  ATR WILD-TYPE 263  44
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATR MUTATED     20    4
  ATR WILD-TYPE  263   44
   clus
vv  ATR MUTATED ATR WILD-TYPE
  0          20           263
  1           4            44
[1] 2 2
[1] FALSE
D1072V7, 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
D1072V8, binary
               cls
clus              0   1
  ATR MUTATED    25   3
  ATR WILD-TYPE 292  45
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATR MUTATED     25    3
  ATR WILD-TYPE  292   45
                               clus
vv                              ATR MUTATED ATR WILD-TYPE
  COLON ADENOCARCINOMA                   25           292
  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 239   1  21  16
D1072V9, multiclass
    clus
vv   ATR MUTATED ATR WILD-TYPE
  R0          18           239
  R1           1             1
  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"
D1072V10, 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
D1072V11, 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(1073) Variable = FSHR MUTATION ANALYSIS
D1073V1, survival
                sevent
clus2              0   1
  FSHR MUTATED    11   3
  FSHR WILD-TYPE 271  70
  FSHR MUTATED FSHR WILD-TYPE 
            14            341 
  FSHR MUTATED FSHR WILD-TYPE 
             3             70 
$`FSHR MUTATED`
TCGA-A6-5657 TCGA-A6-5666 TCGA-A6-6649 TCGA-AA-3662 TCGA-AA-3710 TCGA-AA-A00J 
       31.63        32.71        24.16         6.05        26.99        18.05 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AY-4071 TCGA-AZ-4323 TCGA-CA-6717 TCGA-CM-6164 
        4.01        34.98         0.95         1.41         0.33        29.03 
TCGA-CM-6171 TCGA-CM-6172 
       14.04        11.01 

$`FSHR WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 
       10.88         0.20        14.50        27.09        16.31        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82        58.39         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-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-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       15.02        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  FSHR MUTATED FSHR WILD-TYPE 
          0.33           0.00 
  FSHR MUTATED FSHR WILD-TYPE 
         34.98         140.38 
  FSHR MUTATED FSHR WILD-TYPE 
        16.045         20.280 
[1] "0.3 - 35.0 (16.0)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.7"
D1073V2, 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       25       105         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        19         10         37         31       33        13
                vv
clus             STAGE IVB
  FSHR MUTATED           0
  FSHR WILD-TYPE         1
D1073V3, multiclass
            clus
vv           FSHR MUTATED FSHR WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             4            105
  STAGE IIB             2              6
  STAGE IIC             1              0
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            4             37
  STAGE IIIC            0             31
  STAGE IV              2             33
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  FSHR MUTATED     1   1   7   6
  FSHR WILD-TYPE   8  67 241  35
D1073V4, multiclass
    clus
vv   FSHR MUTATED FSHR WILD-TYPE
  T1            1              8
  T2            1             67
  T3            7            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
  FSHR MUTATED     9   4   2
  FSHR WILD-TYPE 211  76  64
D1073V5, multiclass
    clus
vv   FSHR MUTATED FSHR WILD-TYPE
  N0            9            211
  N1            4             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"
D1073V6, binary
                cls
clus               0   1
  FSHR MUTATED    12   2
  FSHR WILD-TYPE 271  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  FSHR MUTATED     12    2
  FSHR WILD-TYPE  271   46
   clus
vv  FSHR MUTATED FSHR WILD-TYPE
  0           12            271
  1            2             46
[1] 2 2
[1] FALSE
D1073V7, 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
D1073V8, binary
                cls
clus               0   1
  FSHR MUTATED    11   3
  FSHR WILD-TYPE 306  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  FSHR MUTATED     11    3
  FSHR WILD-TYPE  306   45
                               clus
vv                              FSHR MUTATED FSHR WILD-TYPE
  COLON ADENOCARCINOMA                    11            306
  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 247   2  21  20
D1073V9, multiclass
    clus
vv   FSHR MUTATED FSHR WILD-TYPE
  R0           10            247
  R1            0              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"
D1073V10, 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
D1073V11, 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(1074) Variable = HIF3A MUTATION ANALYSIS
D1074V1, survival
                 sevent
clus2               0   1
  HIF3A MUTATED     9   5
  HIF3A WILD-TYPE 273  68
  HIF3A MUTATED HIF3A WILD-TYPE 
             14             341 
  HIF3A MUTATED HIF3A WILD-TYPE 
              5              68 
$`HIF3A MUTATED`
TCGA-A6-2676 TCGA-A6-6653 TCGA-AA-3877 TCGA-AA-3949 TCGA-AA-A00N TCGA-AA-A010 
       42.90        24.39        31.00        26.01         4.01        34.98 
TCGA-AD-6889 TCGA-AD-6964 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-CM-5349 TCGA-CM-5861 
       56.55        10.88       100.01        11.74        30.08        15.02 
TCGA-G4-6588 TCGA-G4-6628 
       26.17        52.80 

$`HIF3A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        18.05         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 
        6.77        12.10        29.56         5.23         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        91.79        46.75 

  HIF3A MUTATED HIF3A WILD-TYPE 
           4.01            0.00 
  HIF3A MUTATED HIF3A WILD-TYPE 
         100.01          140.38 
  HIF3A MUTATED HIF3A WILD-TYPE 
         28.125          19.990 
[1] "4.0 - 100.0 (28.1)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.4"
D1074V2, 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       23       105         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        19         10         40         31       34        13
                 vv
clus              STAGE IVB
  HIF3A MUTATED           0
  HIF3A WILD-TYPE         1
D1074V3, multiclass
            clus
vv           HIF3A MUTATED HIF3A WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              4             105
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HIF3A MUTATED     1   2   6   6
  HIF3A WILD-TYPE   8  66 242  35
D1074V4, multiclass
    clus
vv   HIF3A MUTATED HIF3A WILD-TYPE
  T1             1               8
  T2             2              66
  T3             6             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
  HIF3A MUTATED    12   1   2
  HIF3A WILD-TYPE 208  79  64
D1074V5, multiclass
    clus
vv   HIF3A MUTATED HIF3A WILD-TYPE
  N0            12             208
  N1             1              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"
D1074V6, binary
                 cls
clus                0   1
  HIF3A MUTATED    13   1
  HIF3A WILD-TYPE 270  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HIF3A MUTATED     13    1
  HIF3A WILD-TYPE  270   47
   clus
vv  HIF3A MUTATED HIF3A WILD-TYPE
  0            13             270
  1             1              47
[1] 2 2
[1] FALSE
D1074V7, 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
D1074V8, binary
                 cls
clus                0   1
  HIF3A MUTATED    12   3
  HIF3A WILD-TYPE 305  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HIF3A MUTATED     12    3
  HIF3A WILD-TYPE  305   45
                               clus
vv                              HIF3A MUTATED HIF3A WILD-TYPE
  COLON ADENOCARCINOMA                     12             305
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  HIF3A MUTATED    10   0   0   0
  HIF3A WILD-TYPE 247   2  22  21
D1074V9, multiclass
    clus
vv   HIF3A MUTATED HIF3A WILD-TYPE
  R0            10             247
  R1             0               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"
D1074V10, 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
D1074V11, 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(1075) Variable = RUNX2 MUTATION ANALYSIS
D1075V1, survival
                 sevent
clus2               0   1
  RUNX2 MUTATED     5   2
  RUNX2 WILD-TYPE 277  71
  RUNX2 MUTATED RUNX2 WILD-TYPE 
              7             348 
  RUNX2 MUTATED RUNX2 WILD-TYPE 
              2              71 
$`RUNX2 MUTATED`
TCGA-A6-3809 TCGA-AA-3710 TCGA-AA-3864 TCGA-AD-5900 TCGA-AU-6004 TCGA-CK-5916 
       32.75        26.99        53.00         0.07        27.09        21.14 
TCGA-F4-6570 
        6.18 

$`RUNX2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32        21.99         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-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        13.38        13.45        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  RUNX2 MUTATED RUNX2 WILD-TYPE 
           0.07            0.00 
  RUNX2 MUTATED RUNX2 WILD-TYPE 
          53.00          140.38 
  RUNX2 MUTATED RUNX2 WILD-TYPE 
          26.99           20.07 
[1] "0.1 - 53.0 (27.0)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.5"
D1075V2, 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       24       106         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        19         10         41         31       35        13
                 vv
clus              STAGE IVB
  RUNX2 MUTATED           0
  RUNX2 WILD-TYPE         1
D1075V3, multiclass
            clus
vv           RUNX2 MUTATED RUNX2 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              3             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RUNX2 MUTATED     1   2   4   1
  RUNX2 WILD-TYPE   8  66 244  40
D1075V4, multiclass
    clus
vv   RUNX2 MUTATED RUNX2 WILD-TYPE
  T1             1               8
  T2             2              66
  T3             4             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
  RUNX2 MUTATED     8   0   0
  RUNX2 WILD-TYPE 212  80  66
D1075V5, multiclass
    clus
vv   RUNX2 MUTATED RUNX2 WILD-TYPE
  N0             8             212
  N1             0              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"
D1075V6, binary
                 cls
clus                0   1
  RUNX2 MUTATED     7   0
  RUNX2 WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUNX2 MUTATED      7    0
  RUNX2 WILD-TYPE  276   48
   clus
vv  RUNX2 MUTATED RUNX2 WILD-TYPE
  0             7             276
  1             0              48
[1] 2 2
[1] FALSE
D1075V7, 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
D1075V8, binary
                 cls
clus                0   1
  RUNX2 MUTATED     6   2
  RUNX2 WILD-TYPE 311  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUNX2 MUTATED      6    2
  RUNX2 WILD-TYPE  311   46
                               clus
vv                              RUNX2 MUTATED RUNX2 WILD-TYPE
  COLON ADENOCARCINOMA                      6             311
  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 250   2  22  20
D1075V9, multiclass
    clus
vv   RUNX2 MUTATED RUNX2 WILD-TYPE
  R0             7             250
  R1             0               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"
D1075V10, 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
D1075V11, 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(1076) Variable = SNAPC1 MUTATION ANALYSIS
D1076V1, survival
                  sevent
clus2                0   1
  SNAPC1 MUTATED     3   4
  SNAPC1 WILD-TYPE 279  69
  SNAPC1 MUTATED SNAPC1 WILD-TYPE 
               7              348 
  SNAPC1 MUTATED SNAPC1 WILD-TYPE 
               4               69 
$`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         0.33 
TCGA-F4-6570 
        6.18 

$`SNAPC1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3855 
       17.03        10.06         0.00        33.07         0.00        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-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        13.38        13.45        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  SNAPC1 MUTATED SNAPC1 WILD-TYPE 
            0.33             0.00 
  SNAPC1 MUTATED SNAPC1 WILD-TYPE 
           53.00           140.38 
  SNAPC1 MUTATED SNAPC1 WILD-TYPE 
          36.030           20.155 
[1] "0.3 - 53.0 (36.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2.6"
D1076V2, 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       23       107         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SNAPC1 MUTATED           0          0          0          0        0
  SNAPC1 WILD-TYPE        19         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  SNAPC1 MUTATED           0         0
  SNAPC1 WILD-TYPE        13         1
D1076V3, multiclass
            clus
vv           SNAPC1 MUTATED SNAPC1 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               2              107
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SNAPC1 MUTATED     0   1   4   2
  SNAPC1 WILD-TYPE   9  67 244  39
D1076V4, multiclass
    clus
vv   SNAPC1 MUTATED SNAPC1 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              4              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
  SNAPC1 MUTATED     7   0   0
  SNAPC1 WILD-TYPE 213  80  66
D1076V5, multiclass
    clus
vv   SNAPC1 MUTATED SNAPC1 WILD-TYPE
  N0              7              213
  N1              0               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
  SNAPC1 MUTATED     6   0
  SNAPC1 WILD-TYPE 277  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SNAPC1 MUTATED      6    0
  SNAPC1 WILD-TYPE  277   48
   clus
vv  SNAPC1 MUTATED SNAPC1 WILD-TYPE
  0              6              277
  1              0               48
[1] 2 2
[1] FALSE
D1076V7, 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
D1076V8, binary
                  cls
clus                 0   1
  SNAPC1 MUTATED     4   3
  SNAPC1 WILD-TYPE 313  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SNAPC1 MUTATED      4    3
  SNAPC1 WILD-TYPE  313   45
                               clus
vv                              SNAPC1 MUTATED SNAPC1 WILD-TYPE
  COLON ADENOCARCINOMA                       4              313
  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 252   2  22  20
D1076V9, multiclass
    clus
vv   SNAPC1 MUTATED SNAPC1 WILD-TYPE
  R0              5              252
  R1              0                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"
D1076V10, 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
D1076V11, 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(1077) Variable = MATN3 MUTATION ANALYSIS
D1077V1, survival
                 sevent
clus2               0   1
  MATN3 MUTATED     4   2
  MATN3 WILD-TYPE 278  71
  MATN3 MUTATED MATN3 WILD-TYPE 
              6             349 
  MATN3 MUTATED MATN3 WILD-TYPE 
              2              71 
$`MATN3 MUTATED`
TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3672 TCGA-AA-3715 TCGA-AA-3950 TCGA-AA-A00N 
       22.06        19.66         0.92        19.04        24.00         4.01 

$`MATN3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  MATN3 MUTATED MATN3 WILD-TYPE 
           0.92            0.00 
  MATN3 MUTATED MATN3 WILD-TYPE 
          24.00          140.38 
  MATN3 MUTATED MATN3 WILD-TYPE 
          19.35           20.28 
[1] "0.9 - 24.0 (19.4)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "2.8"
D1077V2, 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       24       107         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        18         10         41         30       35        13
                 vv
clus              STAGE IVB
  MATN3 MUTATED           0
  MATN3 WILD-TYPE         1
D1077V3, multiclass
            clus
vv           MATN3 MUTATED MATN3 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              2             107
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MATN3 MUTATED     0   0   4   2
  MATN3 WILD-TYPE   9  68 244  39
D1077V4, multiclass
    clus
vv   MATN3 MUTATED MATN3 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             4             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
  MATN3 MUTATED     4   2   0
  MATN3 WILD-TYPE 216  78  66
D1077V5, multiclass
    clus
vv   MATN3 MUTATED MATN3 WILD-TYPE
  N0             4             216
  N1             2              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"
D1077V6, binary
                 cls
clus                0   1
  MATN3 MUTATED     5   0
  MATN3 WILD-TYPE 278  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MATN3 MUTATED      5    0
  MATN3 WILD-TYPE  278   48
   clus
vv  MATN3 MUTATED MATN3 WILD-TYPE
  0             5             278
  1             0              48
[1] 2 2
[1] FALSE
D1077V7, 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
D1077V8, binary
                 cls
clus                0   1
  MATN3 MUTATED     3   3
  MATN3 WILD-TYPE 314  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MATN3 MUTATED      3    3
  MATN3 WILD-TYPE  314   45
                               clus
vv                              MATN3 MUTATED MATN3 WILD-TYPE
  COLON ADENOCARCINOMA                      3             314
  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 251   2  22  21
D1077V9, multiclass
    clus
vv   MATN3 MUTATED MATN3 WILD-TYPE
  R0             6             251
  R1             0               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"
D1077V10, 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
D1077V11, multiclass
[1] "Remove cluster labels:" "MATN3 MUTATED"         
clus
  MATN3 MUTATED MATN3 WILD-TYPE 
              2             204 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-4105 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-A6-5656      TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5660 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-A6-5661      TCGA-A6-5662      TCGA-A6-5664      TCGA-A6-5666 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-A6-6137      TCGA-A6-6138      TCGA-A6-6141      TCGA-A6-6142 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-A6-6648      TCGA-A6-6649      TCGA-A6-6651      TCGA-A6-6652 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780      TCGA-A6-6782 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-AD-5900      TCGA-AD-6548      TCGA-AD-6888      TCGA-AD-6889 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-AD-6890      TCGA-AD-6895      TCGA-AD-6899      TCGA-AD-6901 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-AD-6963      TCGA-AD-6964      TCGA-AD-6965      TCGA-AU-3779 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-AU-6004      TCGA-AY-4070      TCGA-AY-4071      TCGA-AY-5543 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-AY-6196      TCGA-AY-6197      TCGA-AY-6386      TCGA-AZ-4315 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-AZ-4323      TCGA-AZ-4616      TCGA-AZ-4681      TCGA-AZ-4682 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-AZ-5403      TCGA-AZ-5407      TCGA-AZ-6598      TCGA-AZ-6599 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-AZ-6600      TCGA-AZ-6601      TCGA-AZ-6603      TCGA-AZ-6605 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-AZ-6606      TCGA-AZ-6607      TCGA-AZ-6608      TCGA-CA-5254 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-CA-5255      TCGA-CA-5796      TCGA-CA-5797      TCGA-CA-6715 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-CA-6716      TCGA-CA-6717      TCGA-CA-6718      TCGA-CA-6719 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-CK-4947      TCGA-CK-4948      TCGA-CK-4950      TCGA-CK-4952 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-CK-5912      TCGA-CK-5913      TCGA-CK-5914      TCGA-CK-5915 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-CK-5916      TCGA-CK-6746      TCGA-CK-6747      TCGA-CK-6748 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-CK-6751      TCGA-CM-4743      TCGA-CM-4744      TCGA-CM-4746 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-CM-4747      TCGA-CM-4752      TCGA-CM-5341      TCGA-CM-5344 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-CM-5348      TCGA-CM-5349      TCGA-CM-5860      TCGA-CM-5861 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-CM-5862      TCGA-CM-5863      TCGA-CM-5864      TCGA-CM-5868 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-CM-6161      TCGA-CM-6162      TCGA-CM-6163      TCGA-CM-6164 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-CM-6165      TCGA-CM-6166      TCGA-CM-6167      TCGA-CM-6168 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-CM-6169      TCGA-CM-6170      TCGA-CM-6171      TCGA-CM-6172 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-CM-6674      TCGA-CM-6675      TCGA-CM-6676      TCGA-CM-6677 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-CM-6678      TCGA-CM-6679      TCGA-CM-6680      TCGA-D5-5537 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-D5-5538      TCGA-D5-5539      TCGA-D5-5540      TCGA-D5-5541 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-D5-6529      TCGA-D5-6532      TCGA-D5-6533      TCGA-D5-6534 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-D5-6535      TCGA-D5-6536      TCGA-D5-6537      TCGA-D5-6538 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-D5-6539      TCGA-D5-6540      TCGA-D5-6541      TCGA-D5-6898 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923      TCGA-D5-6924 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-D5-6926      TCGA-D5-6927      TCGA-D5-6928      TCGA-D5-6929 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-D5-6930      TCGA-D5-6931      TCGA-D5-6932      TCGA-D5-7000 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-DM-A0X9      TCGA-DM-A0XD      TCGA-DM-A0XF      TCGA-DM-A1D0 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-DM-A1D4      TCGA-DM-A1D6      TCGA-DM-A1D7      TCGA-DM-A1D8 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-DM-A1D9      TCGA-DM-A1DA      TCGA-DM-A1DB      TCGA-DM-A1HA 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-DM-A1HB      TCGA-DM-A282      TCGA-DM-A285      TCGA-DM-A28C 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-DM-A28E      TCGA-DM-A28F      TCGA-DM-A28G      TCGA-DM-A28H 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-DM-A28K      TCGA-F4-6459      TCGA-F4-6460      TCGA-F4-6569 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704      TCGA-F4-6805 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808      TCGA-F4-6809 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856      TCGA-G4-6293 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304      TCGA-G4-6306 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310      TCGA-G4-6315 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323      TCGA-G4-6586 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-G4-6588      TCGA-G4-6625      TCGA-G4-6626      TCGA-G4-6628 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 

Clustering(1078) Variable = CD34 MUTATION ANALYSIS
D1078V1, survival
                sevent
clus2              0   1
  CD34 MUTATED     4   2
  CD34 WILD-TYPE 278  71
  CD34 MUTATED CD34 WILD-TYPE 
             6            349 
  CD34 MUTATED CD34 WILD-TYPE 
             2             71 
$`CD34 MUTATED`
TCGA-AA-3489 TCGA-AA-3662 TCGA-AA-3966 TCGA-AZ-4315 TCGA-AZ-6606 TCGA-CA-6717 
        7.04         6.05         2.01        58.39        11.74         0.33 

$`CD34 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       19.99        13.94        19.99        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
      100.01        29.56         5.23         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  CD34 MUTATED CD34 WILD-TYPE 
          0.33           0.00 
  CD34 MUTATED CD34 WILD-TYPE 
         58.39         140.38 
  CD34 MUTATED CD34 WILD-TYPE 
         6.545         20.980 
[1] "0.3 - 58.4 (6.5)"   "0.0 - 140.4 (21.0)"
[1] "hr=" "2.6"
D1078V2, 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       24       106         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        19         10         41         31       33        13
                vv
clus             STAGE IVB
  CD34 MUTATED           0
  CD34 WILD-TYPE         1
D1078V3, multiclass
            clus
vv           CD34 MUTATED CD34 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             3            106
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              2             33
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CD34 MUTATED     0   0   4   2
  CD34 WILD-TYPE   9  68 244  39
D1078V4, multiclass
    clus
vv   CD34 MUTATED CD34 WILD-TYPE
  T1            0              9
  T2            0             68
  T3            4            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
  CD34 MUTATED     4   0   2
  CD34 WILD-TYPE 216  80  64
D1078V5, multiclass
    clus
vv   CD34 MUTATED CD34 WILD-TYPE
  N0            4            216
  N1            0             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"
D1078V6, binary
                cls
clus               0   1
  CD34 MUTATED     4   2
  CD34 WILD-TYPE 279  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD34 MUTATED      4    2
  CD34 WILD-TYPE  279   46
   clus
vv  CD34 MUTATED CD34 WILD-TYPE
  0            4            279
  1            2             46
[1] 2 2
[1] FALSE
D1078V7, 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
D1078V8, binary
                cls
clus               0   1
  CD34 MUTATED     4   2
  CD34 WILD-TYPE 313  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD34 MUTATED      4    2
  CD34 WILD-TYPE  313   46
                               clus
vv                              CD34 MUTATED CD34 WILD-TYPE
  COLON ADENOCARCINOMA                     4            313
  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 255   2  21  20
D1078V9, multiclass
    clus
vv   CD34 MUTATED CD34 WILD-TYPE
  R0            2            255
  R1            0              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"
D1078V10, 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
D1078V11, 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(1079) Variable = TPR MUTATION ANALYSIS
D1079V1, survival
               sevent
clus2             0   1
  TPR MUTATED    18   3
  TPR WILD-TYPE 264  70
  TPR MUTATED TPR WILD-TYPE 
           21           334 
  TPR MUTATED TPR WILD-TYPE 
            3            70 
$`TPR MUTATED`
TCGA-A6-5666 TCGA-A6-6141 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3679 
       32.71         8.38        19.66         3.02         1.02        15.02 
TCGA-AA-3811 TCGA-AA-3864 TCGA-AA-3941 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00N 
       10.06        53.00        24.00         2.01        25.02         4.01 
TCGA-AA-A010 TCGA-AA-A01R TCGA-AZ-4681 TCGA-CA-5254 TCGA-CA-6717 TCGA-CM-4746 
       34.98        35.01        83.80         2.24         0.33        37.02 
TCGA-CM-5861 TCGA-DM-A28H TCGA-G4-6299 
       15.02       117.07        74.56 

$`TPR WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.09        22.06        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
       20.28         7.04        35.01        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
        0.92        50.04        47.01        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         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        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        1.94         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
      119.93        35.97        60.79        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      107.67        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  TPR MUTATED TPR WILD-TYPE 
         0.33          0.00 
  TPR MUTATED TPR WILD-TYPE 
       117.07        140.38 
  TPR MUTATED TPR WILD-TYPE 
       19.660        20.235 
[1] "0.3 - 117.1 (19.7)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.6"
D1079V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TPR MUTATED         1        0        3         7         2         1
  TPR WILD-TYPE      63        1       22       102         6         0
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TPR MUTATED           2          0          0          3        1         1
  TPR WILD-TYPE        17         10         41         28       34        12
               vv
clus            STAGE IVB
  TPR MUTATED           0
  TPR WILD-TYPE         1
D1079V3, multiclass
            clus
vv           TPR MUTATED TPR WILD-TYPE
  STAGE I              1            63
  STAGE IA             0             1
  STAGE II             3            22
  STAGE IIA            7           102
  STAGE IIB            2             6
  STAGE IIC            1             0
  STAGE III            2            17
  STAGE IIIA           0            10
  STAGE IIIB           0            41
  STAGE IIIC           3            28
  STAGE IV             1            34
  STAGE IVA            1            12
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of 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  15   5
  TPR WILD-TYPE   9  66 233  36
D1079V4, multiclass
    clus
vv   TPR MUTATED TPR WILD-TYPE
  T1           0             9
  T2           2            66
  T3          15           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
  TPR MUTATED    15   2   5
  TPR WILD-TYPE 205  78  61
D1079V5, multiclass
    clus
vv   TPR MUTATED TPR WILD-TYPE
  N0          15           205
  N1           2            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"
D1079V6, binary
               cls
clus              0   1
  TPR MUTATED    18   2
  TPR WILD-TYPE 265  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  TPR MUTATED     18    2
  TPR WILD-TYPE  265   46
   clus
vv  TPR MUTATED TPR WILD-TYPE
  0          18           265
  1           2            46
[1] 2 2
[1] FALSE
D1079V7, binary
               cls
clus              0   1
  TPR MUTATED    10  12
  TPR WILD-TYPE 160 185
[1] "tbl2"
               cls
clus            [,1] [,2]
  TPR MUTATED     10   12
  TPR WILD-TYPE  160  185
        clus
vv       TPR MUTATED TPR WILD-TYPE
  FEMALE          10           160
  MALE            12           185
[1] 2 2
[1] FALSE
D1079V8, binary
               cls
clus              0   1
  TPR MUTATED    17   5
  TPR WILD-TYPE 300  43
[1] "tbl2"
               cls
clus            [,1] [,2]
  TPR MUTATED     17    5
  TPR WILD-TYPE  300   43
                               clus
vv                              TPR MUTATED TPR WILD-TYPE
  COLON ADENOCARCINOMA                   17           300
  COLON MUCINOUS ADENOCARCINOMA           5            43
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  TPR MUTATED    14   0   1   2
  TPR WILD-TYPE 243   2  21  19
D1079V9, multiclass
    clus
vv   TPR MUTATED TPR WILD-TYPE
  R0          14           243
  R1           0             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"
D1079V10, 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                           2     6
  TPR WILD-TYPE                        17   170
D1079V11, multiclass
                                  clus
vv                                 TPR MUTATED TPR 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(1080) Variable = OR9Q2 MUTATION ANALYSIS
D1080V1, survival
                 sevent
clus2               0   1
  OR9Q2 MUTATED     8   5
  OR9Q2 WILD-TYPE 274  68
  OR9Q2 MUTATED OR9Q2 WILD-TYPE 
             13             342 
  OR9Q2 MUTATED OR9Q2 WILD-TYPE 
              5              68 
$`OR9Q2 MUTATED`
TCGA-AA-3510 TCGA-AA-3715 TCGA-AA-A010 TCGA-AY-6197 TCGA-AZ-6606 TCGA-CM-5862 
       63.98        19.04        34.98        21.44        11.74         5.03 
TCGA-CM-6680 TCGA-D5-6540 TCGA-DM-A1DB TCGA-DM-A28H TCGA-G4-6303 TCGA-G4-6310 
       12.03        16.14        44.32       117.07        65.85        45.11 
TCGA-G4-6586 
       35.80 

$`OR9Q2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
      100.01        29.56         5.23         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        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-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.01        10.06        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38         7.50       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        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        51.75        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        26.17        91.79        46.75        52.80 

  OR9Q2 MUTATED OR9Q2 WILD-TYPE 
           5.03            0.00 
  OR9Q2 MUTATED OR9Q2 WILD-TYPE 
         117.07          140.38 
  OR9Q2 MUTATED OR9Q2 WILD-TYPE 
          34.98           20.07 
[1] "5.0 - 117.1 (35.0)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.3"
D1080V2, 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       23       105         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        19         10         39         30       33        12
                 vv
clus              STAGE IVB
  OR9Q2 MUTATED           0
  OR9Q2 WILD-TYPE         1
D1080V3, multiclass
            clus
vv           OR9Q2 MUTATED OR9Q2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              4             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             1              30
  STAGE IV               2              33
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 237  39
D1080V4, multiclass
    clus
vv   OR9Q2 MUTATED OR9Q2 WILD-TYPE
  T1             0               9
  T2             1              67
  T3            11             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
  OR9Q2 MUTATED     8   3   3
  OR9Q2 WILD-TYPE 212  77  63
D1080V5, multiclass
    clus
vv   OR9Q2 MUTATED OR9Q2 WILD-TYPE
  N0             8             212
  N1             3              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"
D1080V6, binary
                 cls
clus                0   1
  OR9Q2 MUTATED    10   3
  OR9Q2 WILD-TYPE 273  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR9Q2 MUTATED     10    3
  OR9Q2 WILD-TYPE  273   45
   clus
vv  OR9Q2 MUTATED OR9Q2 WILD-TYPE
  0            10             273
  1             3              45
[1] 2 2
[1] FALSE
D1080V7, 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
D1080V8, binary
                 cls
clus                0   1
  OR9Q2 MUTATED    13   1
  OR9Q2 WILD-TYPE 304  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR9Q2 MUTATED     13    1
  OR9Q2 WILD-TYPE  304   47
                               clus
vv                              OR9Q2 MUTATED OR9Q2 WILD-TYPE
  COLON ADENOCARCINOMA                     13             304
  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 246   2  22  21
D1080V9, multiclass
    clus
vv   OR9Q2 MUTATED OR9Q2 WILD-TYPE
  R0            11             246
  R1             0               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"
D1080V10, 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
D1080V11, 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(1081) Variable = KRTAP10-11 MUTATION ANALYSIS
D1081V1, survival
                      sevent
clus2                    0   1
  KRTAP10-11 MUTATED     4   1
  KRTAP10-11 WILD-TYPE 278  72
  KRTAP10-11 MUTATED KRTAP10-11 WILD-TYPE 
                   5                  350 
  KRTAP10-11 MUTATED KRTAP10-11 WILD-TYPE 
                   1                   72 
$`KRTAP10-11 MUTATED`
TCGA-A6-5660 TCGA-A6-6781 TCGA-AA-A010 TCGA-DM-A0XF TCGA-G4-6588 
       29.19        19.66        34.98        38.20        26.17 

$`KRTAP10-11 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        24.43       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  KRTAP10-11 MUTATED KRTAP10-11 WILD-TYPE 
               19.66                 0.00 
  KRTAP10-11 MUTATED KRTAP10-11 WILD-TYPE 
               38.20               140.38 
  KRTAP10-11 MUTATED KRTAP10-11 WILD-TYPE 
               29.19                20.07 
[1] "19.7 - 38.2 (29.2)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.1"
D1081V2, 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       25       108         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        19         10         41         28       35
                      vv
clus                   STAGE IVA STAGE IVB
  KRTAP10-11 MUTATED           0         0
  KRTAP10-11 WILD-TYPE        13         1
D1081V3, multiclass
            clus
vv           KRTAP10-11 MUTATED KRTAP10-11 WILD-TYPE
  STAGE I                     0                   64
  STAGE IA                    0                    1
  STAGE II                    0                   25
  STAGE IIA                   1                  108
  STAGE IIB                   1                    7
  STAGE IIC                   0                    1
  STAGE III                   0                   19
  STAGE IIIA                  0                   10
  STAGE IIIB                  0                   41
  STAGE IIIC                  3                   28
  STAGE IV                    0                   35
  STAGE IVA                   0                   13
  STAGE IVB                   0                    1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                      vv
clus                    T1  T2  T3  T4
  KRTAP10-11 MUTATED     0   0   3   2
  KRTAP10-11 WILD-TYPE   9  68 245  39
D1081V4, multiclass
    clus
vv   KRTAP10-11 MUTATED KRTAP10-11 WILD-TYPE
  T1                  0                    9
  T2                  0                   68
  T3                  3                  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
  KRTAP10-11 MUTATED     2   1   2
  KRTAP10-11 WILD-TYPE 218  79  64
D1081V5, multiclass
    clus
vv   KRTAP10-11 MUTATED KRTAP10-11 WILD-TYPE
  N0                  2                  218
  N1                  1                   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"
D1081V6, binary
                      cls
clus                     0   1
  KRTAP10-11 MUTATED     4   0
  KRTAP10-11 WILD-TYPE 279  48
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  KRTAP10-11 MUTATED      4    0
  KRTAP10-11 WILD-TYPE  279   48
   clus
vv  KRTAP10-11 MUTATED KRTAP10-11 WILD-TYPE
  0                  4                  279
  1                  0                   48
[1] 2 2
[1] FALSE
D1081V7, 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
D1081V8, binary
                      cls
clus                     0   1
  KRTAP10-11 MUTATED     3   2
  KRTAP10-11 WILD-TYPE 314  46
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  KRTAP10-11 MUTATED      3    2
  KRTAP10-11 WILD-TYPE  314   46
                               clus
vv                              KRTAP10-11 MUTATED KRTAP10-11 WILD-TYPE
  COLON ADENOCARCINOMA                           3                  314
  COLON MUCINOUS ADENOCARCINOMA                  2                   46
[1] 2 2
[1] FALSE
                      vv
clus                    R0  R1  R2  RX
  KRTAP10-11 MUTATED     3   0   0   0
  KRTAP10-11 WILD-TYPE 254   2  22  21
D1081V9, multiclass
    clus
vv   KRTAP10-11 MUTATED KRTAP10-11 WILD-TYPE
  R0                  3                  254
  R1                  0                    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"
D1081V10, 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
D1081V11, 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(1082) Variable = SERPINB7 MUTATION ANALYSIS
D1082V1, survival
                    sevent
clus2                  0   1
  SERPINB7 MUTATED     7   1
  SERPINB7 WILD-TYPE 275  72
  SERPINB7 MUTATED SERPINB7 WILD-TYPE 
                 8                347 
  SERPINB7 MUTATED SERPINB7 WILD-TYPE 
                 1                 72 
$`SERPINB7 MUTATED`
TCGA-A6-5665 TCGA-A6-6654 TCGA-AA-3555 TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-6598 
       22.06        23.87        29.95        34.98        58.39        49.41 
TCGA-F4-6460 TCGA-G4-6628 
       13.38        52.80 

$`SERPINB7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-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        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       13.78        35.80        26.17        91.79        46.75 

  SERPINB7 MUTATED SERPINB7 WILD-TYPE 
             13.38               0.00 
  SERPINB7 MUTATED SERPINB7 WILD-TYPE 
             58.39             140.38 
  SERPINB7 MUTATED SERPINB7 WILD-TYPE 
            32.465             19.990 
[1] "13.4 - 58.4 (32.5)" "0.0 - 140.4 (20.0)"
[1] "hr=" "2.4"
D1082V2, 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       24       106         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SERPINB7 MUTATED           0          0          2          0        0
  SERPINB7 WILD-TYPE        19         10         39         31       35
                    vv
clus                 STAGE IVA STAGE IVB
  SERPINB7 MUTATED           0         0
  SERPINB7 WILD-TYPE        13         1
D1082V3, multiclass
            clus
vv           SERPINB7 MUTATED SERPINB7 WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  1                 24
  STAGE IIA                 3                106
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                0                 10
  STAGE IIIB                2                 39
  STAGE IIIC                0                 31
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  SERPINB7 MUTATED     0   1   6   1
  SERPINB7 WILD-TYPE   9  67 242  40
D1082V4, multiclass
    clus
vv   SERPINB7 MUTATED SERPINB7 WILD-TYPE
  T1                0                  9
  T2                1                 67
  T3                6                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
  SERPINB7 MUTATED     6   2   0
  SERPINB7 WILD-TYPE 214  78  66
D1082V5, multiclass
    clus
vv   SERPINB7 MUTATED SERPINB7 WILD-TYPE
  N0                6                214
  N1                2                 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"
D1082V6, binary
                    cls
clus                   0   1
  SERPINB7 MUTATED     7   0
  SERPINB7 WILD-TYPE 276  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINB7 MUTATED      7    0
  SERPINB7 WILD-TYPE  276   48
   clus
vv  SERPINB7 MUTATED SERPINB7 WILD-TYPE
  0                7                276
  1                0                 48
[1] 2 2
[1] FALSE
D1082V7, 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
D1082V8, binary
                    cls
clus                   0   1
  SERPINB7 MUTATED     7   1
  SERPINB7 WILD-TYPE 310  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINB7 MUTATED      7    1
  SERPINB7 WILD-TYPE  310   47
                               clus
vv                              SERPINB7 MUTATED SERPINB7 WILD-TYPE
  COLON ADENOCARCINOMA                         7                310
  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 251   2  22  21
D1082V9, multiclass
    clus
vv   SERPINB7 MUTATED SERPINB7 WILD-TYPE
  R0                6                251
  R1                0                  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"
D1082V10, 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
D1082V11, 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(1083) Variable = IFNA2 MUTATION ANALYSIS
D1083V1, survival
                 sevent
clus2               0   1
  IFNA2 MUTATED     7   2
  IFNA2 WILD-TYPE 275  71
  IFNA2 MUTATED IFNA2 WILD-TYPE 
              9             346 
  IFNA2 MUTATED IFNA2 WILD-TYPE 
              2              71 
$`IFNA2 MUTATED`
TCGA-A6-2676 TCGA-AA-3672 TCGA-AA-A00N TCGA-AU-3779 TCGA-CM-6161 TCGA-CM-6171 
       42.90         0.92         4.01        14.50        15.02        14.04 
TCGA-D5-6930 TCGA-F4-6806 TCGA-F4-6856 
        1.51        29.59        19.43 

$`IFNA2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.20        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
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-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 
       16.24        33.67        13.25         0.53        35.41       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  IFNA2 MUTATED IFNA2 WILD-TYPE 
           0.92            0.00 
  IFNA2 MUTATED IFNA2 WILD-TYPE 
          42.90          140.38 
  IFNA2 MUTATED IFNA2 WILD-TYPE 
          14.50           20.98 
[1] "0.9 - 42.9 (14.5)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.7"
D1083V2, 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       25       107         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        18         10         41         31       35        13
                 vv
clus              STAGE IVB
  IFNA2 MUTATED           0
  IFNA2 WILD-TYPE         1
D1083V3, multiclass
            clus
vv           IFNA2 MUTATED IFNA2 WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              2             107
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  IFNA2 MUTATED     0   4   3   2
  IFNA2 WILD-TYPE   9  64 245  39
D1083V4, multiclass
    clus
vv   IFNA2 MUTATED IFNA2 WILD-TYPE
  T1             0               9
  T2             4              64
  T3             3             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
  IFNA2 MUTATED     8   1   0
  IFNA2 WILD-TYPE 212  79  66
D1083V5, multiclass
    clus
vv   IFNA2 MUTATED IFNA2 WILD-TYPE
  N0             8             212
  N1             1              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"
D1083V6, binary
                 cls
clus                0   1
  IFNA2 MUTATED     9   0
  IFNA2 WILD-TYPE 274  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFNA2 MUTATED      9    0
  IFNA2 WILD-TYPE  274   48
   clus
vv  IFNA2 MUTATED IFNA2 WILD-TYPE
  0             9             274
  1             0              48
[1] 2 2
[1] FALSE
D1083V7, 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
D1083V8, binary
                 cls
clus                0   1
  IFNA2 MUTATED     6   3
  IFNA2 WILD-TYPE 311  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFNA2 MUTATED      6    3
  IFNA2 WILD-TYPE  311   45
                               clus
vv                              IFNA2 MUTATED IFNA2 WILD-TYPE
  COLON ADENOCARCINOMA                      6             311
  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 248   2  22  21
D1083V9, multiclass
    clus
vv   IFNA2 MUTATED IFNA2 WILD-TYPE
  R0             9             248
  R1             0               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"
D1083V10, 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
D1083V11, 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(1084) Variable = SPARCL1 MUTATION ANALYSIS
D1084V1, survival
                   sevent
clus2                 0   1
  SPARCL1 MUTATED    13   1
  SPARCL1 WILD-TYPE 269  72
  SPARCL1 MUTATED SPARCL1 WILD-TYPE 
               14               341 
  SPARCL1 MUTATED SPARCL1 WILD-TYPE 
                1                72 
$`SPARCL1 MUTATED`
TCGA-A6-6653 TCGA-AA-3510 TCGA-AA-3543 TCGA-AA-3663 TCGA-AA-3713 TCGA-AA-3950 
       24.39        63.98         0.99         6.97        19.04        24.00 
TCGA-AA-A00J TCGA-AD-6889 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4746 
       18.05        56.55        58.39         0.33         0.10        37.02 
TCGA-DM-A0XD TCGA-G4-6628 
       24.43        52.80 

$`SPARCL1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
       12.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        4.21         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.26         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        11.38        10.26       119.70        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       13.78        35.80        26.17        91.79        46.75 

  SPARCL1 MUTATED SPARCL1 WILD-TYPE 
              0.1               0.0 
  SPARCL1 MUTATED SPARCL1 WILD-TYPE 
            63.98            140.38 
  SPARCL1 MUTATED SPARCL1 WILD-TYPE 
           24.195            20.120 
[1] "0.1 - 64.0 (24.2)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "3.3"
D1084V2, 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       23       103         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SPARCL1 MUTATED           0          0          1          0        1
  SPARCL1 WILD-TYPE        19         10         40         31       34
                   vv
clus                STAGE IVA STAGE IVB
  SPARCL1 MUTATED           0         0
  SPARCL1 WILD-TYPE        13         1
D1084V3, multiclass
            clus
vv           SPARCL1 MUTATED SPARCL1 WILD-TYPE
  STAGE I                  4                60
  STAGE IA                 0                 1
  STAGE II                 2                23
  STAGE IIA                6               103
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               0                31
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SPARCL1 MUTATED     0   4   9   1
  SPARCL1 WILD-TYPE   9  64 239  40
D1084V4, multiclass
    clus
vv   SPARCL1 MUTATED SPARCL1 WILD-TYPE
  T1               0                 9
  T2               4                64
  T3               9               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
  SPARCL1 MUTATED    13   1   0
  SPARCL1 WILD-TYPE 207  79  66
D1084V5, multiclass
    clus
vv   SPARCL1 MUTATED SPARCL1 WILD-TYPE
  N0              13               207
  N1               1                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"
D1084V6, binary
                   cls
clus                  0   1
  SPARCL1 MUTATED    13   1
  SPARCL1 WILD-TYPE 270  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPARCL1 MUTATED     13    1
  SPARCL1 WILD-TYPE  270   47
   clus
vv  SPARCL1 MUTATED SPARCL1 WILD-TYPE
  0              13               270
  1               1                47
[1] 2 2
[1] FALSE
D1084V7, 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
D1084V8, binary
                   cls
clus                  0   1
  SPARCL1 MUTATED    10   4
  SPARCL1 WILD-TYPE 307  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPARCL1 MUTATED     10    4
  SPARCL1 WILD-TYPE  307   44
                               clus
vv                              SPARCL1 MUTATED SPARCL1 WILD-TYPE
  COLON ADENOCARCINOMA                       10               307
  COLON MUCINOUS ADENOCARCINOMA               4                44
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SPARCL1 MUTATED     8   0   1   2
  SPARCL1 WILD-TYPE 249   2  21  19
D1084V9, multiclass
    clus
vv   SPARCL1 MUTATED SPARCL1 WILD-TYPE
  R0               8               249
  R1               0                 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"
D1084V10, 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
D1084V11, 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(1085) Variable = MRPL13 MUTATION ANALYSIS
D1085V1, survival
                  sevent
clus2                0   1
  MRPL13 MUTATED     5   1
  MRPL13 WILD-TYPE 277  72
  MRPL13 MUTATED MRPL13 WILD-TYPE 
               6              349 
  MRPL13 MUTATED MRPL13 WILD-TYPE 
               1               72 
$`MRPL13 MUTATED`
TCGA-AA-3950 TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-5403 TCGA-CM-6161 TCGA-D5-5538 
       24.00        27.09        58.39        62.79        15.02        12.26 

$`MRPL13 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
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-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  MRPL13 MUTATED MRPL13 WILD-TYPE 
           12.26             0.00 
  MRPL13 MUTATED MRPL13 WILD-TYPE 
           62.79           140.38 
  MRPL13 MUTATED MRPL13 WILD-TYPE 
          25.545           20.120 
[1] "12.3 - 62.8 (25.5)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.7"
D1085V2, 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       24       107         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MRPL13 MUTATED           0          0          1          0        0
  MRPL13 WILD-TYPE        19         10         40         31       35
                  vv
clus               STAGE IVA STAGE IVB
  MRPL13 MUTATED           0         0
  MRPL13 WILD-TYPE        13         1
D1085V3, multiclass
            clus
vv           MRPL13 MUTATED MRPL13 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               2              107
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MRPL13 MUTATED     0   2   4   0
  MRPL13 WILD-TYPE   9  66 244  41
D1085V4, multiclass
    clus
vv   MRPL13 MUTATED MRPL13 WILD-TYPE
  T1              0                9
  T2              2               66
  T3              4              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
  MRPL13 MUTATED     5   1   0
  MRPL13 WILD-TYPE 215  79  66
D1085V5, multiclass
    clus
vv   MRPL13 MUTATED MRPL13 WILD-TYPE
  N0              5              215
  N1              1               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"
D1085V6, binary
                  cls
clus                 0   1
  MRPL13 MUTATED     5   0
  MRPL13 WILD-TYPE 278  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPL13 MUTATED      5    0
  MRPL13 WILD-TYPE  278   48
   clus
vv  MRPL13 MUTATED MRPL13 WILD-TYPE
  0              5              278
  1              0               48
[1] 2 2
[1] FALSE
D1085V7, 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
D1085V8, binary
                  cls
clus                 0   1
  MRPL13 MUTATED     5   1
  MRPL13 WILD-TYPE 312  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPL13 MUTATED      5    1
  MRPL13 WILD-TYPE  312   47
                               clus
vv                              MRPL13 MUTATED MRPL13 WILD-TYPE
  COLON ADENOCARCINOMA                       5              312
  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 252   2  22  21
D1085V9, multiclass
    clus
vv   MRPL13 MUTATED MRPL13 WILD-TYPE
  R0              5              252
  R1              0                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"
D1085V10, 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
D1085V11, 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(1086) Variable = IL1RL1 MUTATION ANALYSIS
D1086V1, survival
                  sevent
clus2                0   1
  IL1RL1 MUTATED    11   2
  IL1RL1 WILD-TYPE 271  71
  IL1RL1 MUTATED IL1RL1 WILD-TYPE 
              13              342 
  IL1RL1 MUTATED IL1RL1 WILD-TYPE 
               2               71 
$`IL1RL1 MUTATED`
TCGA-A6-5666 TCGA-A6-6782 TCGA-AA-3811 TCGA-AY-6197 TCGA-CA-6717 TCGA-CA-6718 
       32.71        20.28        10.06        21.44         0.33         0.10 
TCGA-CM-6674 TCGA-CM-6677 TCGA-D5-6930 TCGA-DM-A285 TCGA-F4-6569 TCGA-F4-6856 
       12.95        11.08         1.51         6.12        13.45        19.43 
TCGA-G4-6309 
       51.75 

$`IL1RL1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        19.04        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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        13.38         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        35.41       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  IL1RL1 MUTATED IL1RL1 WILD-TYPE 
             0.1              0.0 
  IL1RL1 MUTATED IL1RL1 WILD-TYPE 
           51.75           140.38 
  IL1RL1 MUTATED IL1RL1 WILD-TYPE 
          12.950           20.995 
[1] "0.1 - 51.8 (12.9)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.1"
D1086V2, 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       24       103         7         0
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IL1RL1 MUTATED           1          0          1          0        1
  IL1RL1 WILD-TYPE        18         10         40         31       34
                  vv
clus               STAGE IVA STAGE IVB
  IL1RL1 MUTATED           0         0
  IL1RL1 WILD-TYPE        13         1
D1086V3, multiclass
            clus
vv           IL1RL1 MUTATED IL1RL1 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               6              103
  STAGE IIB               1                7
  STAGE IIC               1                0
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  IL1RL1 MUTATED     0   2   9   3
  IL1RL1 WILD-TYPE   9  66 239  38
D1086V4, multiclass
    clus
vv   IL1RL1 MUTATED IL1RL1 WILD-TYPE
  T1              0                9
  T2              2               66
  T3              9              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
  IL1RL1 MUTATED    11   1   2
  IL1RL1 WILD-TYPE 209  79  64
D1086V5, multiclass
    clus
vv   IL1RL1 MUTATED IL1RL1 WILD-TYPE
  N0             11              209
  N1              1               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"
D1086V6, binary
                  cls
clus                 0   1
  IL1RL1 MUTATED    11   1
  IL1RL1 WILD-TYPE 272  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IL1RL1 MUTATED     11    1
  IL1RL1 WILD-TYPE  272   47
   clus
vv  IL1RL1 MUTATED IL1RL1 WILD-TYPE
  0             11              272
  1              1               47
[1] 2 2
[1] FALSE
D1086V7, 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
D1086V8, binary
                  cls
clus                 0   1
  IL1RL1 MUTATED    10   4
  IL1RL1 WILD-TYPE 307  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IL1RL1 MUTATED     10    4
  IL1RL1 WILD-TYPE  307   44
                               clus
vv                              IL1RL1 MUTATED IL1RL1 WILD-TYPE
  COLON ADENOCARCINOMA                      10              307
  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 248   2  22  19
D1086V9, multiclass
    clus
vv   IL1RL1 MUTATED IL1RL1 WILD-TYPE
  R0              9              248
  R1              0                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"
D1086V10, 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
D1086V11, 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(1087) Variable = C7ORF50 MUTATION ANALYSIS
D1087V1, survival
                   sevent
clus2                 0   1
  C7ORF50 MUTATED     4   1
  C7ORF50 WILD-TYPE 278  72
  C7ORF50 MUTATED C7ORF50 WILD-TYPE 
                5               350 
  C7ORF50 MUTATED C7ORF50 WILD-TYPE 
                1                72 
$`C7ORF50 MUTATED`
TCGA-A6-5665 TCGA-AA-3667 TCGA-AZ-6598 TCGA-CM-6171 TCGA-DM-A1HB 
       22.06        14.01        49.41        14.04       135.65 

$`C7ORF50 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13        83.80        22.36        62.79        61.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  C7ORF50 MUTATED C7ORF50 WILD-TYPE 
            14.01              0.00 
  C7ORF50 MUTATED C7ORF50 WILD-TYPE 
           135.65            140.38 
  C7ORF50 MUTATED C7ORF50 WILD-TYPE 
           22.060            20.155 
[1] "14.0 - 135.7 (22.1)" "0.0 - 140.4 (20.2)" 
[1] "hr=" "1.7"
D1087V2, 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       24       108         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C7ORF50 MUTATED           0          0          1          0        0
  C7ORF50 WILD-TYPE        19         10         40         31       35
                   vv
clus                STAGE IVA STAGE IVB
  C7ORF50 MUTATED           0         0
  C7ORF50 WILD-TYPE        13         1
D1087V3, multiclass
            clus
vv           C7ORF50 MUTATED C7ORF50 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                1               108
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C7ORF50 MUTATED     0   2   3   0
  C7ORF50 WILD-TYPE   9  66 245  41
D1087V4, multiclass
    clus
vv   C7ORF50 MUTATED C7ORF50 WILD-TYPE
  T1               0                 9
  T2               2                66
  T3               3               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
  C7ORF50 MUTATED     4   1   0
  C7ORF50 WILD-TYPE 216  79  66
D1087V5, multiclass
    clus
vv   C7ORF50 MUTATED C7ORF50 WILD-TYPE
  N0               4               216
  N1               1                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"
D1087V6, binary
                   cls
clus                  0   1
  C7ORF50 MUTATED     4   0
  C7ORF50 WILD-TYPE 279  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF50 MUTATED      4    0
  C7ORF50 WILD-TYPE  279   48
   clus
vv  C7ORF50 MUTATED C7ORF50 WILD-TYPE
  0               4               279
  1               0                48
[1] 2 2
[1] FALSE
D1087V7, 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
D1087V8, binary
                   cls
clus                  0   1
  C7ORF50 MUTATED     5   0
  C7ORF50 WILD-TYPE 312  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF50 MUTATED      5    0
  C7ORF50 WILD-TYPE  312   48
                               clus
vv                              C7ORF50 MUTATED C7ORF50 WILD-TYPE
  COLON ADENOCARCINOMA                        5               312
  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 254   2  22  21
D1087V9, multiclass
    clus
vv   C7ORF50 MUTATED C7ORF50 WILD-TYPE
  R0               3               254
  R1               0                 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"
D1087V10, 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
D1087V11, 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(1088) Variable = CEACAM6 MUTATION ANALYSIS
D1088V1, survival
                   sevent
clus2                 0   1
  CEACAM6 MUTATED     2   2
  CEACAM6 WILD-TYPE 280  71
  CEACAM6 MUTATED CEACAM6 WILD-TYPE 
                4               351 
  CEACAM6 MUTATED CEACAM6 WILD-TYPE 
                2                71 
$`CEACAM6 MUTATED`
TCGA-AZ-6600 TCGA-DM-A28H TCGA-F4-6570 TCGA-G4-6293 
       12.10       117.07         6.18       107.67 

$`CEACAM6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41        49.41         6.77       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
      119.93        35.97        60.79        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 
       33.67        13.25         0.53        35.41        19.43        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  CEACAM6 MUTATED CEACAM6 WILD-TYPE 
             6.18              0.00 
  CEACAM6 MUTATED CEACAM6 WILD-TYPE 
           117.07            140.38 
  CEACAM6 MUTATED CEACAM6 WILD-TYPE 
           59.885            20.190 
[1] "6.2 - 117.1 (59.9)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D1088V2, 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       25       108         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CEACAM6 MUTATED           1          0          0          1        1
  CEACAM6 WILD-TYPE        18         10         41         30       34
                   vv
clus                STAGE IVA STAGE IVB
  CEACAM6 MUTATED           0         0
  CEACAM6 WILD-TYPE        13         1
D1088V3, multiclass
            clus
vv           CEACAM6 MUTATED CEACAM6 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                1               108
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               1                30
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CEACAM6 MUTATED     0   0   3   1
  CEACAM6 WILD-TYPE   9  68 245  40
D1088V4, multiclass
    clus
vv   CEACAM6 MUTATED CEACAM6 WILD-TYPE
  T1               0                 9
  T2               0                68
  T3               3               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
  CEACAM6 MUTATED     1   2   1
  CEACAM6 WILD-TYPE 219  78  65
D1088V5, multiclass
    clus
vv   CEACAM6 MUTATED CEACAM6 WILD-TYPE
  N0               1               219
  N1               2                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"
D1088V6, binary
                   cls
clus                  0   1
  CEACAM6 MUTATED     3   1
  CEACAM6 WILD-TYPE 280  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CEACAM6 MUTATED      3    1
  CEACAM6 WILD-TYPE  280   47
   clus
vv  CEACAM6 MUTATED CEACAM6 WILD-TYPE
  0               3               280
  1               1                47
[1] 2 2
[1] FALSE
D1088V7, 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
D1088V8, binary
                   cls
clus                  0   1
  CEACAM6 MUTATED     4   0
  CEACAM6 WILD-TYPE 313  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CEACAM6 MUTATED      4    0
  CEACAM6 WILD-TYPE  313   48
                               clus
vv                              CEACAM6 MUTATED CEACAM6 WILD-TYPE
  COLON ADENOCARCINOMA                        4               313
  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 255   2  22  21
D1088V9, multiclass
[1] "Remove cluster labels:" "CEACAM6 MUTATED"       
clus
  CEACAM6 MUTATED CEACAM6 WILD-TYPE 
                2               300 
       TCGA-A6-2671        TCGA-A6-2672        TCGA-A6-2674        TCGA-A6-2676 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-A6-2677        TCGA-A6-2678        TCGA-A6-2683        TCGA-A6-3807 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-A6-3808        TCGA-A6-3809        TCGA-A6-3810        TCGA-A6-5657 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-A6-5659        TCGA-A6-5661        TCGA-A6-5665        TCGA-A6-6781 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3489        TCGA-AA-3492        TCGA-AA-3496        TCGA-AA-3502 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3510        TCGA-AA-3511        TCGA-AA-3514        TCGA-AA-3517 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3518        TCGA-AA-3519        TCGA-AA-3520        TCGA-AA-3521 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3522        TCGA-AA-3524        TCGA-AA-3525        TCGA-AA-3526 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3527        TCGA-AA-3529        TCGA-AA-3530        TCGA-AA-3531 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3532        TCGA-AA-3534        TCGA-AA-3538        TCGA-AA-3542 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3543        TCGA-AA-3544        TCGA-AA-3548        TCGA-AA-3549 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3552        TCGA-AA-3553        TCGA-AA-3554        TCGA-AA-3555 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3556        TCGA-AA-3558        TCGA-AA-3560        TCGA-AA-3561 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3562        TCGA-AA-3655        TCGA-AA-3660        TCGA-AA-3662 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3663        TCGA-AA-3664        TCGA-AA-3666        TCGA-AA-3667 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3672        TCGA-AA-3673        TCGA-AA-3678        TCGA-AA-3679 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3680        TCGA-AA-3681        TCGA-AA-3684        TCGA-AA-3685 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3688        TCGA-AA-3692        TCGA-AA-3693        TCGA-AA-3695 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3696        TCGA-AA-3697        TCGA-AA-3710        TCGA-AA-3712 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3713        TCGA-AA-3715        TCGA-AA-3811        TCGA-AA-3812 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3814        TCGA-AA-3815        TCGA-AA-3818        TCGA-AA-3819 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3821        TCGA-AA-3831        TCGA-AA-3833        TCGA-AA-3837 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3842        TCGA-AA-3844        TCGA-AA-3845        TCGA-AA-3846 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3848        TCGA-AA-3850        TCGA-AA-3851        TCGA-AA-3852 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3854        TCGA-AA-3855        TCGA-AA-3856        TCGA-AA-3858 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3860        TCGA-AA-3861        TCGA-AA-3864        TCGA-AA-3866 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3867        TCGA-AA-3869        TCGA-AA-3870        TCGA-AA-3872 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3875        TCGA-AA-3877        TCGA-AA-3930        TCGA-AA-3939 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3941        TCGA-AA-3947        TCGA-AA-3949        TCGA-AA-3950 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3952        TCGA-AA-3955        TCGA-AA-3956        TCGA-AA-3968 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3971        TCGA-AA-3972        TCGA-AA-3973        TCGA-AA-3975 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3976        TCGA-AA-3979        TCGA-AA-3984        TCGA-AA-3986 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3989        TCGA-AA-3994        TCGA-AA-A004        TCGA-AA-A00A 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-A00D        TCGA-AA-A00E        TCGA-AA-A00F        TCGA-AA-A00J 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-A00K        TCGA-AA-A00L        TCGA-AA-A00N        TCGA-AA-A00O 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-A00Q        TCGA-AA-A00R        TCGA-AA-A00U        TCGA-AA-A00W 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-A00Z        TCGA-AA-A010        TCGA-AA-A017        TCGA-AA-A01D 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-A01F        TCGA-AA-A01G        TCGA-AA-A01I        TCGA-AA-A01K 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-A01P        TCGA-AA-A01Q        TCGA-AA-A01R        TCGA-AA-A01S 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-A01T        TCGA-AA-A01V        TCGA-AA-A01X        TCGA-AA-A01Z 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-A022        TCGA-AA-A024        TCGA-AA-A029        TCGA-AA-A02F 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-A02H        TCGA-AA-A02J        TCGA-AA-A02K        TCGA-AA-A02O 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-A02W        TCGA-AA-A02Y        TCGA-AA-A03F        TCGA-AA-A03J 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AD-5900        TCGA-AD-6548        TCGA-AD-6888        TCGA-AU-3779 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AU-6004        TCGA-AY-4070        TCGA-AY-4071        TCGA-AY-5543 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AY-6196        TCGA-AY-6197        TCGA-AY-6386        TCGA-AZ-4315 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AZ-4681        TCGA-AZ-4682        TCGA-CA-5254        TCGA-CA-5255 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-CA-5796        TCGA-CA-5797        TCGA-CA-6715        TCGA-CA-6716 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-CA-6717        TCGA-CA-6718        TCGA-CA-6719        TCGA-CK-4947 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-CK-4948        TCGA-CK-4950        TCGA-CK-4952        TCGA-CK-5912 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-CK-5913        TCGA-CK-5914        TCGA-CK-5915        TCGA-CK-5916 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-CK-6746        TCGA-CK-6747        TCGA-CK-6748        TCGA-CK-6751 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-CM-4743        TCGA-CM-4744        TCGA-CM-4746        TCGA-CM-4747 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-CM-4752        TCGA-CM-5341        TCGA-CM-5344        TCGA-CM-5348 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-CM-5349        TCGA-CM-5860        TCGA-CM-5861        TCGA-CM-5862 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-CM-5863        TCGA-CM-5864        TCGA-CM-5868        TCGA-CM-6161 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-CM-6162        TCGA-CM-6163        TCGA-CM-6164        TCGA-CM-6165 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-CM-6166        TCGA-CM-6167        TCGA-CM-6168        TCGA-CM-6169 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-CM-6170        TCGA-CM-6171        TCGA-CM-6172        TCGA-CM-6674 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-CM-6675        TCGA-CM-6676        TCGA-CM-6677        TCGA-CM-6678 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-CM-6679        TCGA-CM-6680        TCGA-D5-5537        TCGA-D5-5538 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-D5-5539        TCGA-D5-5540        TCGA-D5-5541        TCGA-D5-6529 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-D5-6532        TCGA-D5-6533        TCGA-D5-6534        TCGA-D5-6535 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-D5-6536        TCGA-D5-6537        TCGA-D5-6538        TCGA-D5-6539 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-D5-6540        TCGA-D5-6541        TCGA-D5-6898        TCGA-D5-6920 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-D5-6922        TCGA-D5-6923        TCGA-D5-6924        TCGA-D5-6926 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-D5-6927        TCGA-D5-6928        TCGA-D5-6929        TCGA-D5-6930 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-D5-6931        TCGA-D5-6932        TCGA-D5-7000        TCGA-F4-6459 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-F4-6460        TCGA-F4-6569        TCGA-F4-6703        TCGA-F4-6704 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-F4-6805        TCGA-F4-6806        TCGA-F4-6807        TCGA-F4-6808 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-F4-6809        TCGA-F4-6854        TCGA-F4-6855        TCGA-F4-6856 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-G4-6299        TCGA-G4-6303        TCGA-G4-6304        TCGA-G4-6306 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-G4-6307        TCGA-G4-6309        TCGA-G4-6310        TCGA-G4-6315 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-G4-6317        TCGA-G4-6321        TCGA-G4-6323        TCGA-G4-6586 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-G4-6588        TCGA-G4-6625        TCGA-G4-6626        TCGA-G4-6628 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
D1088V10, 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
D1088V11, 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(1089) Variable = CASP1 MUTATION ANALYSIS
D1089V1, survival
                 sevent
clus2               0   1
  CASP1 MUTATED     4   1
  CASP1 WILD-TYPE 278  72
  CASP1 MUTATED CASP1 WILD-TYPE 
              5             350 
  CASP1 MUTATED CASP1 WILD-TYPE 
              1              72 
$`CASP1 MUTATED`
TCGA-AA-3663 TCGA-AA-3811 TCGA-AA-3977 TCGA-CK-4952 TCGA-G4-6628 
        6.97        10.06        25.02        15.62        52.80 

$`CASP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       40.34        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 
       91.79        46.75 

  CASP1 MUTATED CASP1 WILD-TYPE 
           6.97            0.00 
  CASP1 MUTATED CASP1 WILD-TYPE 
          52.80          140.38 
  CASP1 MUTATED CASP1 WILD-TYPE 
         15.620          20.235 
[1] "7.0 - 52.8 (15.6)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1"  
D1089V2, 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       24       109         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CASP1 MUTATED           2          0          0          0        0         0
  CASP1 WILD-TYPE        17         10         41         31       35        13
                 vv
clus              STAGE IVB
  CASP1 MUTATED           0
  CASP1 WILD-TYPE         1
D1089V3, multiclass
            clus
vv           CASP1 MUTATED CASP1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              0             109
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CASP1 MUTATED     0   2   2   2
  CASP1 WILD-TYPE   9  66 246  39
D1089V4, multiclass
    clus
vv   CASP1 MUTATED CASP1 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             2             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
  CASP1 MUTATED     4   0   2
  CASP1 WILD-TYPE 216  80  64
D1089V5, multiclass
    clus
vv   CASP1 MUTATED CASP1 WILD-TYPE
  N0             4             216
  N1             0              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"
D1089V6, binary
                 cls
clus                0   1
  CASP1 MUTATED     4   0
  CASP1 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP1 MUTATED      4    0
  CASP1 WILD-TYPE  279   48
   clus
vv  CASP1 MUTATED CASP1 WILD-TYPE
  0             4             279
  1             0              48
[1] 2 2
[1] FALSE
D1089V7, 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
D1089V8, binary
                 cls
clus                0   1
  CASP1 MUTATED     5   1
  CASP1 WILD-TYPE 312  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP1 MUTATED      5    1
  CASP1 WILD-TYPE  312   47
                               clus
vv                              CASP1 MUTATED CASP1 WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  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 254   2  22  19
D1089V9, multiclass
    clus
vv   CASP1 MUTATED CASP1 WILD-TYPE
  R0             3             254
  R1             0               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"
D1089V10, 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
D1089V11, 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(1090) Variable = RANBP17 MUTATION ANALYSIS
D1090V1, survival
                   sevent
clus2                 0   1
  RANBP17 MUTATED     8   2
  RANBP17 WILD-TYPE 274  71
  RANBP17 MUTATED RANBP17 WILD-TYPE 
               10               345 
  RANBP17 MUTATED RANBP17 WILD-TYPE 
                2                71 
$`RANBP17 MUTATED`
TCGA-AA-3696 TCGA-AA-3713 TCGA-AA-A01Q TCGA-AD-6889 TCGA-CA-6717 TCGA-CA-6718 
        5.03        19.04         1.02        56.55         0.33         0.10 
TCGA-CK-5916 TCGA-CM-6163 TCGA-D5-6924 TCGA-G4-6588 
       21.14        14.04        14.30        26.17 

$`RANBP17 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       19.00        36.00        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37         4.21         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02        12.00        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  RANBP17 MUTATED RANBP17 WILD-TYPE 
              0.1               0.0 
  RANBP17 MUTATED RANBP17 WILD-TYPE 
            56.55            140.38 
  RANBP17 MUTATED RANBP17 WILD-TYPE 
            14.17             20.98 
[1] "0.1 - 56.5 (14.2)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.5"
D1090V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RANBP17 MUTATED         2        0        1         5         1         0
  RANBP17 WILD-TYPE      62        1       24       104         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RANBP17 MUTATED           0          0          0          0        2
  RANBP17 WILD-TYPE        19         10         41         31       33
                   vv
clus                STAGE IVA STAGE IVB
  RANBP17 MUTATED           0         0
  RANBP17 WILD-TYPE        13         1
D1090V3, multiclass
            clus
vv           RANBP17 MUTATED RANBP17 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                5               104
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               0                31
  STAGE IV                 2                33
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  RANBP17 MUTATED     2   0   8   1
  RANBP17 WILD-TYPE   7  68 240  40
D1090V4, multiclass
    clus
vv   RANBP17 MUTATED RANBP17 WILD-TYPE
  T1               2                 7
  T2               0                68
  T3               8               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
  RANBP17 MUTATED    10   1   0
  RANBP17 WILD-TYPE 210  79  66
D1090V5, multiclass
    clus
vv   RANBP17 MUTATED RANBP17 WILD-TYPE
  N0              10               210
  N1               1                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"
D1090V6, binary
                   cls
clus                  0   1
  RANBP17 MUTATED     8   2
  RANBP17 WILD-TYPE 275  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RANBP17 MUTATED      8    2
  RANBP17 WILD-TYPE  275   46
   clus
vv  RANBP17 MUTATED RANBP17 WILD-TYPE
  0               8               275
  1               2                46
[1] 2 2
[1] FALSE
D1090V7, binary
                   cls
clus                  0   1
  RANBP17 MUTATED     5   6
  RANBP17 WILD-TYPE 165 191
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RANBP17 MUTATED      5    6
  RANBP17 WILD-TYPE  165  191
        clus
vv       RANBP17 MUTATED RANBP17 WILD-TYPE
  FEMALE               5               165
  MALE                 6               191
[1] 2 2
[1] FALSE
D1090V8, binary
                   cls
clus                  0   1
  RANBP17 MUTATED    10   1
  RANBP17 WILD-TYPE 307  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RANBP17 MUTATED     10    1
  RANBP17 WILD-TYPE  307   47
                               clus
vv                              RANBP17 MUTATED RANBP17 WILD-TYPE
  COLON ADENOCARCINOMA                       10               307
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  RANBP17 MUTATED     4   0   2   4
  RANBP17 WILD-TYPE 253   2  20  17
D1090V9, multiclass
    clus
vv   RANBP17 MUTATED RANBP17 WILD-TYPE
  R0               4               253
  R1               0                 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"
D1090V10, 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     5
  RANBP17 WILD-TYPE                        19   171
D1090V11, 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                                          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(1091) Variable = JAK3 MUTATION ANALYSIS
D1091V1, survival
                sevent
clus2              0   1
  JAK3 MUTATED    19   3
  JAK3 WILD-TYPE 263  70
  JAK3 MUTATED JAK3 WILD-TYPE 
            22            333 
  JAK3 MUTATED JAK3 WILD-TYPE 
             3             70 
$`JAK3 MUTATED`
TCGA-A6-5662 TCGA-A6-6648 TCGA-A6-6651 TCGA-AA-3555 TCGA-AA-3662 TCGA-AA-3877 
       23.61        25.18        21.76        29.95         6.05        31.00 
TCGA-AA-3977 TCGA-AA-A00E TCGA-AU-6004 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
       25.02        30.02        27.09        62.79        61.41        49.41 
TCGA-CA-6717 TCGA-CK-4952 TCGA-CK-5913 TCGA-CM-4752 TCGA-D5-6537 TCGA-DM-A28H 
        0.33        15.62        51.32        13.02         4.80       117.07 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6586 TCGA-G4-6588 
       55.04        45.11        35.80        26.17 

$`JAK3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        33.53        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       24.16        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       83.80        22.36         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 
       17.56       102.44        40.34        49.08        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 
       18.25         1.32        43.27        15.12        17.85        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K 
        6.12        81.37       119.93        35.97        60.79        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       44.68        51.75        36.72        36.00        22.09        13.78 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  JAK3 MUTATED JAK3 WILD-TYPE 
          0.33           0.00 
  JAK3 MUTATED JAK3 WILD-TYPE 
        117.07         140.38 
  JAK3 MUTATED JAK3 WILD-TYPE 
         28.52          19.59 
[1] "0.3 - 117.1 (28.5)" "0.0 - 140.4 (19.6)"
[1] "hr=" "2.1"
D1091V2, 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       22       102         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  JAK3 MUTATED           1          0          4          1        1         2
  JAK3 WILD-TYPE        18         10         37         30       34        11
                vv
clus             STAGE IVB
  JAK3 MUTATED           0
  JAK3 WILD-TYPE         1
D1091V3, multiclass
            clus
vv           JAK3 MUTATED JAK3 WILD-TYPE
  STAGE I               4             60
  STAGE IA              0              1
  STAGE II              3             22
  STAGE IIA             7            102
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            4             37
  STAGE IIIC            1             30
  STAGE IV              1             34
  STAGE IVA             2             11
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  65 232  38
D1091V4, multiclass
    clus
vv   JAK3 MUTATED JAK3 WILD-TYPE
  T1            2              7
  T2            3             65
  T3           16            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
  JAK3 MUTATED    16   4   4
  JAK3 WILD-TYPE 204  76  62
D1091V5, multiclass
    clus
vv   JAK3 MUTATED JAK3 WILD-TYPE
  N0           16            204
  N1            4             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"
D1091V6, binary
                cls
clus               0   1
  JAK3 MUTATED    14   3
  JAK3 WILD-TYPE 269  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  JAK3 MUTATED     14    3
  JAK3 WILD-TYPE  269   45
   clus
vv  JAK3 MUTATED JAK3 WILD-TYPE
  0           14            269
  1            3             45
[1] 2 2
[1] FALSE
D1091V7, 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
D1091V8, binary
                cls
clus               0   1
  JAK3 MUTATED    20   4
  JAK3 WILD-TYPE 297  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  JAK3 MUTATED     20    4
  JAK3 WILD-TYPE  297   44
                               clus
vv                              JAK3 MUTATED JAK3 WILD-TYPE
  COLON ADENOCARCINOMA                    20            297
  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 246   2  21  17
D1091V9, multiclass
    clus
vv   JAK3 MUTATED JAK3 WILD-TYPE
  R0           11            246
  R1            0              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"
D1091V10, 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
D1091V11, 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(1092) Variable = NFKBIB MUTATION ANALYSIS
D1092V1, survival
                  sevent
clus2                0   1
  NFKBIB MUTATED     2   3
  NFKBIB WILD-TYPE 280  70
  NFKBIB MUTATED NFKBIB WILD-TYPE 
               5              350 
  NFKBIB MUTATED NFKBIB WILD-TYPE 
               3               70 
$`NFKBIB MUTATED`
TCGA-AA-3875 TCGA-AZ-6605 TCGA-DM-A1D7 TCGA-G4-6303 TCGA-G4-6588 
       18.05         5.23        13.32        65.85        26.17 

$`NFKBIB WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3877 
       53.00        17.03        24.03        27.02        29.98        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 
       49.41         6.77        12.10       100.01        29.56        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  NFKBIB MUTATED NFKBIB WILD-TYPE 
            5.23             0.00 
  NFKBIB MUTATED NFKBIB WILD-TYPE 
           65.85           140.38 
  NFKBIB MUTATED NFKBIB WILD-TYPE 
          18.050           20.235 
[1] "5.2 - 65.8 (18.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2.7"
D1092V2, 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       25       107         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NFKBIB MUTATED           0          0          1          0        1
  NFKBIB WILD-TYPE        19         10         40         31       34
                  vv
clus               STAGE IVA STAGE IVB
  NFKBIB MUTATED           0         0
  NFKBIB WILD-TYPE        13         1
D1092V3, multiclass
            clus
vv           NFKBIB MUTATED NFKBIB WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               2              107
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  NFKBIB MUTATED     1   0   3   1
  NFKBIB WILD-TYPE   8  68 245  40
D1092V4, multiclass
    clus
vv   NFKBIB MUTATED NFKBIB WILD-TYPE
  T1              1                8
  T2              0               68
  T3              3              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
  NFKBIB MUTATED     3   2   0
  NFKBIB WILD-TYPE 217  78  66
D1092V5, multiclass
    clus
vv   NFKBIB MUTATED NFKBIB WILD-TYPE
  N0              3              217
  N1              2               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"
D1092V6, binary
                  cls
clus                 0   1
  NFKBIB MUTATED     4   1
  NFKBIB WILD-TYPE 279  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFKBIB MUTATED      4    1
  NFKBIB WILD-TYPE  279   47
   clus
vv  NFKBIB MUTATED NFKBIB WILD-TYPE
  0              4              279
  1              1               47
[1] 2 2
[1] FALSE
D1092V7, 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
D1092V8, binary
                  cls
clus                 0   1
  NFKBIB MUTATED     5   0
  NFKBIB WILD-TYPE 312  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFKBIB MUTATED      5    0
  NFKBIB WILD-TYPE  312   48
                               clus
vv                              NFKBIB MUTATED NFKBIB WILD-TYPE
  COLON ADENOCARCINOMA                       5              312
  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 254   2  22  21
D1092V9, multiclass
    clus
vv   NFKBIB MUTATED NFKBIB WILD-TYPE
  R0              3              254
  R1              0                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"
D1092V10, 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
D1092V11, 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(1093) Variable = CHD7 MUTATION ANALYSIS
D1093V1, survival
                sevent
clus2              0   1
  CHD7 MUTATED    31   4
  CHD7 WILD-TYPE 251  69
  CHD7 MUTATED CHD7 WILD-TYPE 
            35            320 
  CHD7 MUTATED CHD7 WILD-TYPE 
             4             69 
$`CHD7 MUTATED`
TCGA-A6-3809 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3672 TCGA-AA-3681 TCGA-AA-3697 
       32.75         3.02        63.98         0.92         5.98        85.05 
TCGA-AA-3713 TCGA-AA-3815 TCGA-AA-3861 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3977 
       19.04        33.04        30.05        26.01        24.00        25.02 
TCGA-AA-A004 TCGA-AA-A010 TCGA-AA-A01K TCGA-AD-6889 TCGA-AD-6895 TCGA-AU-6004 
       13.94        34.98        31.00        56.55         0.72        27.09 
TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-4952 TCGA-CM-4743 TCGA-CM-5348 
       58.39        49.41         0.33        15.62        23.05        22.98 
TCGA-CM-6161 TCGA-CM-6674 TCGA-CM-6679 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6928 
       15.02        12.95        10.06        17.13        16.14        11.64 
TCGA-DM-A0XF TCGA-DM-A1DB TCGA-G4-6309 TCGA-G4-6588 TCGA-G4-6628 
       38.20        44.32        51.75        26.17        52.80 

$`CHD7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 
       37.05        19.00        36.00         5.03        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37         4.21         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       40.34        49.08        51.32        21.99        21.14         2.93 
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        16.01        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-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        13.05        11.08        11.08        11.01 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 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-D5-6929 TCGA-D5-6930 
       12.43        14.30         9.04         9.44        13.41         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 
       12.00        11.38        10.26       119.70        24.43       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 
       91.79        46.75 

  CHD7 MUTATED CHD7 WILD-TYPE 
          0.33           0.00 
  CHD7 MUTATED CHD7 WILD-TYPE 
         85.05         140.38 
  CHD7 MUTATED CHD7 WILD-TYPE 
         25.02          19.99 
[1] "0.3 - 85.0 (25.0)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "2.1"
D1093V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CHD7 MUTATED         4        0        3        14         3         0
  CHD7 WILD-TYPE      60        1       22        95         5         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CHD7 MUTATED           4          0          4          2        1         0
  CHD7 WILD-TYPE        15         10         37         29       34        13
                vv
clus             STAGE IVB
  CHD7 MUTATED           0
  CHD7 WILD-TYPE         1
D1093V3, multiclass
            clus
vv           CHD7 MUTATED CHD7 WILD-TYPE
  STAGE I               4             60
  STAGE IA              0              1
  STAGE II              3             22
  STAGE IIA            14             95
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             4             15
  STAGE IIIA            0             10
  STAGE IIIB            4             37
  STAGE IIIC            2             29
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CHD7 MUTATED     0   5  28   4
  CHD7 WILD-TYPE   9  63 220  37
D1093V4, multiclass
    clus
vv   CHD7 MUTATED CHD7 WILD-TYPE
  T1            0              9
  T2            5             63
  T3           28            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
  CHD7 MUTATED    27   6   4
  CHD7 WILD-TYPE 193  74  62
D1093V5, multiclass
    clus
vv   CHD7 MUTATED CHD7 WILD-TYPE
  N0           27            193
  N1            6             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"
D1093V6, binary
                cls
clus               0   1
  CHD7 MUTATED    32   1
  CHD7 WILD-TYPE 251  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD7 MUTATED     32    1
  CHD7 WILD-TYPE  251   47
   clus
vv  CHD7 MUTATED CHD7 WILD-TYPE
  0           32            251
  1            1             47
[1] 2 2
[1] FALSE
D1093V7, 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
D1093V8, binary
                cls
clus               0   1
  CHD7 MUTATED    29   8
  CHD7 WILD-TYPE 288  40
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD7 MUTATED     29    8
  CHD7 WILD-TYPE  288   40
                               clus
vv                              CHD7 MUTATED CHD7 WILD-TYPE
  COLON ADENOCARCINOMA                    29            288
  COLON MUCINOUS ADENOCARCINOMA            8             40
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CHD7 MUTATED    27   0   1   3
  CHD7 WILD-TYPE 230   2  21  18
D1093V9, multiclass
    clus
vv   CHD7 MUTATED CHD7 WILD-TYPE
  R0           27            230
  R1            0              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"
D1093V10, 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
D1093V11, 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(1094) Variable = FBXO34 MUTATION ANALYSIS
D1094V1, survival
                  sevent
clus2                0   1
  FBXO34 MUTATED     6   3
  FBXO34 WILD-TYPE 276  70
  FBXO34 MUTATED FBXO34 WILD-TYPE 
               9              346 
  FBXO34 MUTATED FBXO34 WILD-TYPE 
               3               70 
$`FBXO34 MUTATED`
TCGA-AA-3663 TCGA-AA-3672 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6718 TCGA-CK-6747 
        6.97         0.92        58.39        49.41         0.10         2.93 
TCGA-CM-6171 TCGA-D5-6537 TCGA-DM-A1D4 
       14.04         4.80        92.75 

$`FBXO34 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.05        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.33         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 
       49.08        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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 
       10.26       119.70        24.43        38.20       130.65        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  FBXO34 MUTATED FBXO34 WILD-TYPE 
             0.1              0.0 
  FBXO34 MUTATED FBXO34 WILD-TYPE 
           92.75           140.38 
  FBXO34 MUTATED FBXO34 WILD-TYPE 
            6.97            20.63 
[1] "0.1 - 92.8 (7.0)"   "0.0 - 140.4 (20.6)"
[1] "hr=" "1.6"
D1094V2, 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       23       105         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FBXO34 MUTATED           1          0          1          0        0
  FBXO34 WILD-TYPE        18         10         40         31       35
                  vv
clus               STAGE IVA STAGE IVB
  FBXO34 MUTATED           0         0
  FBXO34 WILD-TYPE        13         1
D1094V3, multiclass
            clus
vv           FBXO34 MUTATED FBXO34 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               4              105
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FBXO34 MUTATED     0   1   8   0
  FBXO34 WILD-TYPE   9  67 240  41
D1094V4, multiclass
    clus
vv   FBXO34 MUTATED FBXO34 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              8              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
  FBXO34 MUTATED     7   2   0
  FBXO34 WILD-TYPE 213  78  66
D1094V5, multiclass
    clus
vv   FBXO34 MUTATED FBXO34 WILD-TYPE
  N0              7              213
  N1              2               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"
D1094V6, binary
                  cls
clus                 0   1
  FBXO34 MUTATED     6   0
  FBXO34 WILD-TYPE 277  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO34 MUTATED      6    0
  FBXO34 WILD-TYPE  277   48
   clus
vv  FBXO34 MUTATED FBXO34 WILD-TYPE
  0              6              277
  1              0               48
[1] 2 2
[1] FALSE
D1094V7, 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
D1094V8, binary
                  cls
clus                 0   1
  FBXO34 MUTATED     9   0
  FBXO34 WILD-TYPE 308  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO34 MUTATED      9    0
  FBXO34 WILD-TYPE  308   48
                               clus
vv                              FBXO34 MUTATED FBXO34 WILD-TYPE
  COLON ADENOCARCINOMA                       9              308
  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 252   2  22  19
D1094V9, multiclass
    clus
vv   FBXO34 MUTATED FBXO34 WILD-TYPE
  R0              5              252
  R1              0                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"
D1094V10, 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
D1094V11, 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(1095) Variable = AP1G1 MUTATION ANALYSIS
D1095V1, survival
                 sevent
clus2               0   1
  AP1G1 MUTATED     8   2
  AP1G1 WILD-TYPE 274  71
  AP1G1 MUTATED AP1G1 WILD-TYPE 
             10             345 
  AP1G1 MUTATED AP1G1 WILD-TYPE 
              2              71 
$`AP1G1 MUTATED`
TCGA-A6-4105 TCGA-AA-3710 TCGA-AA-A00N TCGA-AZ-4315 TCGA-CA-6715 TCGA-CA-6717 
       14.53        26.99         4.01        58.39         0.07         0.33 
TCGA-CM-6171 TCGA-CM-6675 TCGA-D5-6929 TCGA-F4-6460 
       14.04        13.05        13.41        13.38 

$`AP1G1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6718 
        2.24         3.06         3.25         3.29         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 
       60.79       117.07        98.24         8.61        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  AP1G1 MUTATED AP1G1 WILD-TYPE 
           0.07            0.00 
  AP1G1 MUTATED AP1G1 WILD-TYPE 
          58.39          140.38 
  AP1G1 MUTATED AP1G1 WILD-TYPE 
         13.395          20.980 
[1] "0.1 - 58.4 (13.4)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.4"
D1095V2, 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       25       104         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        19         10         39         31       34        13
                 vv
clus              STAGE IVB
  AP1G1 MUTATED           1
  AP1G1 WILD-TYPE         0
D1095V3, multiclass
            clus
vv           AP1G1 MUTATED AP1G1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              5             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  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  67 239  40
D1095V4, multiclass
    clus
vv   AP1G1 MUTATED AP1G1 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             9             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
  AP1G1 MUTATED     7   3   1
  AP1G1 WILD-TYPE 213  77  65
D1095V5, multiclass
    clus
vv   AP1G1 MUTATED AP1G1 WILD-TYPE
  N0             7             213
  N1             3              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
  AP1G1 MUTATED     9   2
  AP1G1 WILD-TYPE 274  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP1G1 MUTATED      9    2
  AP1G1 WILD-TYPE  274   46
   clus
vv  AP1G1 MUTATED AP1G1 WILD-TYPE
  0             9             274
  1             2              46
[1] 2 2
[1] FALSE
D1095V7, 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
D1095V8, binary
                 cls
clus                0   1
  AP1G1 MUTATED     9   2
  AP1G1 WILD-TYPE 308  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP1G1 MUTATED      9    2
  AP1G1 WILD-TYPE  308   46
                               clus
vv                              AP1G1 MUTATED AP1G1 WILD-TYPE
  COLON ADENOCARCINOMA                      9             308
  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 249   2  22  19
D1095V9, multiclass
    clus
vv   AP1G1 MUTATED AP1G1 WILD-TYPE
  R0             8             249
  R1             0               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"
D1095V10, 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
D1095V11, 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(1096) Variable = PLEKHH2 MUTATION ANALYSIS
D1096V1, survival
                   sevent
clus2                 0   1
  PLEKHH2 MUTATED    15   3
  PLEKHH2 WILD-TYPE 267  70
  PLEKHH2 MUTATED PLEKHH2 WILD-TYPE 
               18               337 
  PLEKHH2 MUTATED PLEKHH2 WILD-TYPE 
                3                70 
$`PLEKHH2 MUTATED`
TCGA-A6-2676 TCGA-A6-6141 TCGA-AA-3525 TCGA-AA-3663 TCGA-AA-3950 TCGA-AA-3977 
       42.90         8.38         8.05         6.97        24.00        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R TCGA-AA-A02K TCGA-AD-6889 TCGA-AY-6197 
        4.01        34.98        35.01        14.01        56.55        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4743 TCGA-D5-6930 
       17.82        58.39         0.33         0.10        23.05         1.51 

$`PLEKHH2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 
        9.07        24.03        37.05        36.03        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37         4.21         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AZ-4323 
       27.09        16.31         0.95        15.75         0.20         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07         0.26         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  PLEKHH2 MUTATED PLEKHH2 WILD-TYPE 
              0.1               0.0 
  PLEKHH2 MUTATED PLEKHH2 WILD-TYPE 
            58.39            140.38 
  PLEKHH2 MUTATED PLEKHH2 WILD-TYPE 
            19.63             20.19 
[1] "0.1 - 58.4 (19.6)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1"  
D1096V2, 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       24        99         5         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLEKHH2 MUTATED           1          0          2          0        1
  PLEKHH2 WILD-TYPE        18         10         39         31       34
                   vv
clus                STAGE IVA STAGE IVB
  PLEKHH2 MUTATED           0         0
  PLEKHH2 WILD-TYPE        13         1
D1096V3, multiclass
            clus
vv           PLEKHH2 MUTATED PLEKHH2 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA               10                99
  STAGE IIB                3                 5
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               0                10
  STAGE IIIB               2                39
  STAGE IIIC               0                31
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PLEKHH2 MUTATED     0   1  14   4
  PLEKHH2 WILD-TYPE   9  67 234  37
D1096V4, multiclass
    clus
vv   PLEKHH2 MUTATED PLEKHH2 WILD-TYPE
  T1               0                 9
  T2               1                67
  T3              14               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
  PLEKHH2 MUTATED    15   2   2
  PLEKHH2 WILD-TYPE 205  78  64
D1096V5, multiclass
    clus
vv   PLEKHH2 MUTATED PLEKHH2 WILD-TYPE
  N0              15               205
  N1               2                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"
D1096V6, binary
                   cls
clus                  0   1
  PLEKHH2 MUTATED    16   1
  PLEKHH2 WILD-TYPE 267  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHH2 MUTATED     16    1
  PLEKHH2 WILD-TYPE  267   47
   clus
vv  PLEKHH2 MUTATED PLEKHH2 WILD-TYPE
  0              16               267
  1               1                47
[1] 2 2
[1] FALSE
D1096V7, 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
D1096V8, binary
                   cls
clus                  0   1
  PLEKHH2 MUTATED    14   5
  PLEKHH2 WILD-TYPE 303  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHH2 MUTATED     14    5
  PLEKHH2 WILD-TYPE  303   43
                               clus
vv                              PLEKHH2 MUTATED PLEKHH2 WILD-TYPE
  COLON ADENOCARCINOMA                       14               303
  COLON MUCINOUS ADENOCARCINOMA               5                43
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  PLEKHH2 MUTATED    13   0   1   2
  PLEKHH2 WILD-TYPE 244   2  21  19
D1096V9, multiclass
    clus
vv   PLEKHH2 MUTATED PLEKHH2 WILD-TYPE
  R0              13               244
  R1               0                 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"
D1096V10, 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
D1096V11, 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(1097) Variable = FBXL19 MUTATION ANALYSIS
D1097V1, survival
                  sevent
clus2                0   1
  FBXL19 MUTATED     6   1
  FBXL19 WILD-TYPE 276  72
  FBXL19 MUTATED FBXL19 WILD-TYPE 
               7              348 
  FBXL19 MUTATED FBXL19 WILD-TYPE 
               1               72 
$`FBXL19 MUTATED`
TCGA-AA-3877 TCGA-AA-3980 TCGA-CM-4746 TCGA-D5-6532 TCGA-F4-6809 TCGA-G4-6293 
       31.00        27.02        37.02        18.25        13.25       107.67 
TCGA-G4-6309 
       51.75 

$`FBXL19 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        35.41        19.43        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  FBXL19 MUTATED FBXL19 WILD-TYPE 
           13.25             0.00 
  FBXL19 MUTATED FBXL19 WILD-TYPE 
          107.67           140.38 
  FBXL19 MUTATED FBXL19 WILD-TYPE 
           31.00            20.07 
[1] "13.2 - 107.7 (31.0)" "0.0 - 140.4 (20.1)" 
[1] "hr=" "2.3"
D1097V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FBXL19 MUTATED         3        0        0         1         0         0
  FBXL19 WILD-TYPE      61        1       25       108         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FBXL19 MUTATED           2          0          1          0        0
  FBXL19 WILD-TYPE        17         10         40         31       35
                  vv
clus               STAGE IVA STAGE IVB
  FBXL19 MUTATED           1         0
  FBXL19 WILD-TYPE        12         1
D1097V3, multiclass
            clus
vv           FBXL19 MUTATED FBXL19 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               1              108
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               2               17
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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   2   5   0
  FBXL19 WILD-TYPE   8  66 243  41
D1097V4, multiclass
    clus
vv   FBXL19 MUTATED FBXL19 WILD-TYPE
  T1              1                8
  T2              2               66
  T3              5              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
  FBXL19 MUTATED     4   3   1
  FBXL19 WILD-TYPE 216  77  65
D1097V5, multiclass
    clus
vv   FBXL19 MUTATED FBXL19 WILD-TYPE
  N0              4              216
  N1              3               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"
D1097V6, binary
                  cls
clus                 0   1
  FBXL19 MUTATED     7   1
  FBXL19 WILD-TYPE 276  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXL19 MUTATED      7    1
  FBXL19 WILD-TYPE  276   47
   clus
vv  FBXL19 MUTATED FBXL19 WILD-TYPE
  0              7              276
  1              1               47
[1] 2 2
[1] FALSE
D1097V7, binary
                  cls
clus                 0   1
  FBXL19 MUTATED     5   3
  FBXL19 WILD-TYPE 165 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXL19 MUTATED      5    3
  FBXL19 WILD-TYPE  165  194
        clus
vv       FBXL19 MUTATED FBXL19 WILD-TYPE
  FEMALE              5              165
  MALE                3              194
[1] 2 2
[1] FALSE
D1097V8, binary
                  cls
clus                 0   1
  FBXL19 MUTATED     7   1
  FBXL19 WILD-TYPE 310  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXL19 MUTATED      7    1
  FBXL19 WILD-TYPE  310   47
                               clus
vv                              FBXL19 MUTATED FBXL19 WILD-TYPE
  COLON ADENOCARCINOMA                       7              310
  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 250   2  22  21
D1097V9, multiclass
    clus
vv   FBXL19 MUTATED FBXL19 WILD-TYPE
  R0              7              250
  R1              0                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"
D1097V10, 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
D1097V11, 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(1098) Variable = MFSD6 MUTATION ANALYSIS
D1098V1, survival
                 sevent
clus2               0   1
  MFSD6 MUTATED     6   1
  MFSD6 WILD-TYPE 276  72
  MFSD6 MUTATED MFSD6 WILD-TYPE 
              7             348 
  MFSD6 MUTATED MFSD6 WILD-TYPE 
              1              72 
$`MFSD6 MUTATED`
TCGA-A6-5662 TCGA-AA-3949 TCGA-AD-5900 TCGA-AZ-4616 TCGA-D5-6533 TCGA-D5-6539 
       23.61        26.01         0.07         5.13         1.32        12.49 
TCGA-F4-6808 
       33.67 

$`MFSD6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        33.53        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4681 
        0.20        21.44        17.82        58.39         1.41        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        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-D5-6540 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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       16.31        29.59        16.24        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  MFSD6 MUTATED MFSD6 WILD-TYPE 
           0.07            0.00 
  MFSD6 MUTATED MFSD6 WILD-TYPE 
          33.67          140.38 
  MFSD6 MUTATED MFSD6 WILD-TYPE 
         12.490          20.235 
[1] "0.1 - 33.7 (12.5)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D1098V2, 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       25       109         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MFSD6 MUTATED           0          1          2          0        1         1
  MFSD6 WILD-TYPE        19          9         39         31       34        12
                 vv
clus              STAGE IVB
  MFSD6 MUTATED           0
  MFSD6 WILD-TYPE         1
D1098V3, multiclass
            clus
vv           MFSD6 MUTATED MFSD6 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              0             109
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 244  40
D1098V4, multiclass
    clus
vv   MFSD6 MUTATED MFSD6 WILD-TYPE
  T1             1               8
  T2             1              67
  T3             4             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
  MFSD6 MUTATED     4   1   2
  MFSD6 WILD-TYPE 216  79  64
D1098V5, multiclass
    clus
vv   MFSD6 MUTATED MFSD6 WILD-TYPE
  N0             4             216
  N1             1              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"
D1098V6, binary
                 cls
clus                0   1
  MFSD6 MUTATED     4   2
  MFSD6 WILD-TYPE 279  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MFSD6 MUTATED      4    2
  MFSD6 WILD-TYPE  279   46
   clus
vv  MFSD6 MUTATED MFSD6 WILD-TYPE
  0             4             279
  1             2              46
[1] 2 2
[1] FALSE
D1098V7, 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
D1098V8, binary
                 cls
clus                0   1
  MFSD6 MUTATED     5   2
  MFSD6 WILD-TYPE 312  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MFSD6 MUTATED      5    2
  MFSD6 WILD-TYPE  312   46
                               clus
vv                              MFSD6 MUTATED MFSD6 WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  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 252   2  22  21
D1098V9, multiclass
    clus
vv   MFSD6 MUTATED MFSD6 WILD-TYPE
  R0             5             252
  R1             0               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"
D1098V10, 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
D1098V11, 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(1099) Variable = SBSN MUTATION ANALYSIS
D1099V1, survival
                sevent
clus2              0   1
  SBSN MUTATED     8   2
  SBSN WILD-TYPE 274  71
  SBSN MUTATED SBSN WILD-TYPE 
            10            345 
  SBSN MUTATED SBSN WILD-TYPE 
             2             71 
$`SBSN MUTATED`
TCGA-AA-3554 TCGA-AA-3655 TCGA-AA-3977 TCGA-AA-A00A TCGA-AA-A00E TCGA-AD-5900 
       17.95        61.02        25.02        38.04        30.02         0.07 
TCGA-AD-6895 TCGA-AZ-6600 TCGA-CM-6171 TCGA-DM-A28F 
        0.72        12.10        14.04        35.97 

$`SBSN WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F 
       19.07         7.96        27.02        13.94        19.00        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21        56.55         0.79         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G 
      135.65       139.17         6.12        81.37       119.93        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  SBSN MUTATED SBSN WILD-TYPE 
          0.07           0.00 
  SBSN MUTATED SBSN WILD-TYPE 
         61.02         140.38 
  SBSN MUTATED SBSN WILD-TYPE 
        21.485         20.190 
[1] "0.1 - 61.0 (21.5)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D1099V2, 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       24       106         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SBSN MUTATED           0          0          1          0        1         0
  SBSN WILD-TYPE        19         10         40         31       34        13
                vv
clus             STAGE IVB
  SBSN MUTATED           0
  SBSN WILD-TYPE         1
D1099V3, multiclass
            clus
vv           SBSN MUTATED SBSN WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             3            106
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SBSN MUTATED     0   3   6   1
  SBSN WILD-TYPE   9  65 242  40
D1099V4, multiclass
    clus
vv   SBSN MUTATED SBSN WILD-TYPE
  T1            0              9
  T2            3             65
  T3            6            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
  SBSN MUTATED     7   3   0
  SBSN WILD-TYPE 213  77  66
D1099V5, multiclass
    clus
vv   SBSN MUTATED SBSN WILD-TYPE
  N0            7            213
  N1            3             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"
D1099V6, binary
                cls
clus               0   1
  SBSN MUTATED     6   1
  SBSN WILD-TYPE 277  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  SBSN MUTATED      6    1
  SBSN WILD-TYPE  277   47
   clus
vv  SBSN MUTATED SBSN WILD-TYPE
  0            6            277
  1            1             47
[1] 2 2
[1] FALSE
D1099V7, 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
D1099V8, binary
                cls
clus               0   1
  SBSN MUTATED     9   1
  SBSN WILD-TYPE 308  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  SBSN MUTATED      9    1
  SBSN WILD-TYPE  308   47
                               clus
vv                              SBSN MUTATED SBSN WILD-TYPE
  COLON ADENOCARCINOMA                     9            308
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SBSN MUTATED     6   0   0   0
  SBSN WILD-TYPE 251   2  22  21
D1099V9, multiclass
    clus
vv   SBSN MUTATED SBSN WILD-TYPE
  R0            6            251
  R1            0              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"
D1099V10, 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
D1099V11, 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(1100) Variable = ZCWPW2 MUTATION ANALYSIS
D1100V1, survival
                  sevent
clus2                0   1
  ZCWPW2 MUTATED    10   1
  ZCWPW2 WILD-TYPE 272  72
  ZCWPW2 MUTATED ZCWPW2 WILD-TYPE 
              11              344 
  ZCWPW2 MUTATED ZCWPW2 WILD-TYPE 
               1               72 
$`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 
       56.55        58.39        11.01        11.01        13.78 

$`ZCWPW2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        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        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.08        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.72        36.00        22.09        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  ZCWPW2 MUTATED ZCWPW2 WILD-TYPE 
            2.01             0.00 
  ZCWPW2 MUTATED ZCWPW2 WILD-TYPE 
           61.02           140.38 
  ZCWPW2 MUTATED ZCWPW2 WILD-TYPE 
          19.660           20.235 
[1] "2.0 - 61.0 (19.7)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2.6"
D1100V2, 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       24       105         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZCWPW2 MUTATED           0          0          1          1        1
  ZCWPW2 WILD-TYPE        19         10         40         30       34
                  vv
clus               STAGE IVA STAGE IVB
  ZCWPW2 MUTATED           1         0
  ZCWPW2 WILD-TYPE        12         1
D1100V3, multiclass
            clus
vv           ZCWPW2 MUTATED ZCWPW2 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                1                0
  STAGE II                1               24
  STAGE IIA               4              105
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              1               30
  STAGE IV                1               34
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  68 242  37
D1100V4, multiclass
    clus
vv   ZCWPW2 MUTATED ZCWPW2 WILD-TYPE
  T1              0                9
  T2              0               68
  T3              6              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
  ZCWPW2 MUTATED     8   3   0
  ZCWPW2 WILD-TYPE 212  77  66
D1100V5, multiclass
    clus
vv   ZCWPW2 MUTATED ZCWPW2 WILD-TYPE
  N0              8              212
  N1              3               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"
D1100V6, binary
                  cls
clus                 0   1
  ZCWPW2 MUTATED     7   2
  ZCWPW2 WILD-TYPE 276  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZCWPW2 MUTATED      7    2
  ZCWPW2 WILD-TYPE  276   46
   clus
vv  ZCWPW2 MUTATED ZCWPW2 WILD-TYPE
  0              7              276
  1              2               46
[1] 2 2
[1] FALSE
D1100V7, 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
D1100V8, binary
                  cls
clus                 0   1
  ZCWPW2 MUTATED     9   2
  ZCWPW2 WILD-TYPE 308  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZCWPW2 MUTATED      9    2
  ZCWPW2 WILD-TYPE  308   46
                               clus
vv                              ZCWPW2 MUTATED ZCWPW2 WILD-TYPE
  COLON ADENOCARCINOMA                       9              308
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZCWPW2 MUTATED     9   0   0   0
  ZCWPW2 WILD-TYPE 248   2  22  21
D1100V9, multiclass
    clus
vv   ZCWPW2 MUTATED ZCWPW2 WILD-TYPE
  R0              9              248
  R1              0                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"
D1100V10, 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
D1100V11, 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(1101) Variable = PAK4 MUTATION ANALYSIS
D1101V1, survival
                sevent
clus2              0   1
  PAK4 MUTATED     6   0
  PAK4 WILD-TYPE 276  73
  PAK4 MUTATED PAK4 WILD-TYPE 
             6            349 
  PAK4 MUTATED PAK4 WILD-TYPE 
             0             73 
$`PAK4 MUTATED`
TCGA-AY-5543 TCGA-AY-6196 TCGA-CM-4743 TCGA-CM-6171 TCGA-DM-A1HB TCGA-G4-6628 
       15.75         0.20        23.05        14.04       135.65        52.80 

$`PAK4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       16.31         0.95        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14         2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 
       46.75 

  PAK4 MUTATED PAK4 WILD-TYPE 
           0.2            0.0 
  PAK4 MUTATED PAK4 WILD-TYPE 
        135.65         140.38 
  PAK4 MUTATED PAK4 WILD-TYPE 
         19.40          20.19 
[1] "0.2 - 135.7 (19.4)" "0.0 - 140.4 (20.2)"
[1] "hr="     "9400000"
D1101V2, 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       25       108         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        19         10         40         30       35        12
                vv
clus             STAGE IVB
  PAK4 MUTATED           0
  PAK4 WILD-TYPE         1
D1101V3, multiclass
            clus
vv           PAK4 MUTATED PAK4 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             1            108
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            1             30
  STAGE IV              0             35
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 244  41
D1101V4, multiclass
    clus
vv   PAK4 MUTATED PAK4 WILD-TYPE
  T1            0              9
  T2            2             66
  T3            4            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
  PAK4 MUTATED     3   2   1
  PAK4 WILD-TYPE 217  78  65
D1101V5, multiclass
    clus
vv   PAK4 MUTATED PAK4 WILD-TYPE
  N0            3            217
  N1            2             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"
D1101V6, binary
                cls
clus               0   1
  PAK4 MUTATED     4   1
  PAK4 WILD-TYPE 279  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK4 MUTATED      4    1
  PAK4 WILD-TYPE  279   47
   clus
vv  PAK4 MUTATED PAK4 WILD-TYPE
  0            4            279
  1            1             47
[1] 2 2
[1] FALSE
D1101V7, 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
D1101V8, binary
                cls
clus               0   1
  PAK4 MUTATED     5   1
  PAK4 WILD-TYPE 312  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK4 MUTATED      5    1
  PAK4 WILD-TYPE  312   47
                               clus
vv                              PAK4 MUTATED PAK4 WILD-TYPE
  COLON ADENOCARCINOMA                     5            312
  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 252   2  22  21
D1101V9, multiclass
    clus
vv   PAK4 MUTATED PAK4 WILD-TYPE
  R0            5            252
  R1            0              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"
D1101V10, 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
D1101V11, 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(1102) Variable = NTRK2 MUTATION ANALYSIS
D1102V1, survival
                 sevent
clus2               0   1
  NTRK2 MUTATED    17   5
  NTRK2 WILD-TYPE 265  68
  NTRK2 MUTATED NTRK2 WILD-TYPE 
             22             333 
  NTRK2 MUTATED NTRK2 WILD-TYPE 
              5              68 
$`NTRK2 MUTATED`
TCGA-A6-3810 TCGA-A6-5662 TCGA-A6-5665 TCGA-A6-5666 TCGA-AA-3492 TCGA-AA-3510 
       36.53        23.61        22.06        32.71         3.02        63.98 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A02K TCGA-AD-6895 TCGA-AU-6004 TCGA-AZ-6598 
        4.01        34.98        14.01         0.72        27.09        49.41 
TCGA-CA-6717 TCGA-CM-5348 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-D5-6541 
        0.33        22.98        14.04        29.03        16.04        15.58 
TCGA-D5-6922 TCGA-D5-6930 TCGA-DM-A1DB TCGA-G4-6315 
       10.13         1.51        44.32        36.72 

$`NTRK2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-6137 
       31.63        30.44        29.19        33.53        22.09        27.09 
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 
       22.52         8.38        25.08        25.18        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        7.04         1.02        35.01         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
       39.98         2.01         5.03         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       17.03        15.02        12.00        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 
       12.49        16.14         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-A1HA 
       49.91        13.32        12.59       140.38         7.50       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       45.11        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  NTRK2 MUTATED NTRK2 WILD-TYPE 
           0.33            0.00 
  NTRK2 MUTATED NTRK2 WILD-TYPE 
          63.98          140.38 
  NTRK2 MUTATED NTRK2 WILD-TYPE 
          22.52           20.12 
[1] "0.3 - 64.0 (22.5)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.3"
D1102V2, 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       22       101         5         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NTRK2 MUTATED           0          1          1          0        2         1
  NTRK2 WILD-TYPE        19          9         40         31       33        12
                 vv
clus              STAGE IVB
  NTRK2 MUTATED           0
  NTRK2 WILD-TYPE         1
D1102V3, multiclass
            clus
vv           NTRK2 MUTATED NTRK2 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              8             101
  STAGE IIB              3               5
  STAGE IIC              1               0
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               2              33
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 232  36
D1102V4, multiclass
    clus
vv   NTRK2 MUTATED NTRK2 WILD-TYPE
  T1             1               8
  T2             1              67
  T3            16             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
  NTRK2 MUTATED    17   4   2
  NTRK2 WILD-TYPE 203  76  64
D1102V5, multiclass
    clus
vv   NTRK2 MUTATED NTRK2 WILD-TYPE
  N0            17             203
  N1             4              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"
D1102V6, binary
                 cls
clus                0   1
  NTRK2 MUTATED    17   3
  NTRK2 WILD-TYPE 266  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTRK2 MUTATED     17    3
  NTRK2 WILD-TYPE  266   45
   clus
vv  NTRK2 MUTATED NTRK2 WILD-TYPE
  0            17             266
  1             3              45
[1] 2 2
[1] FALSE
D1102V7, 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
D1102V8, binary
                 cls
clus                0   1
  NTRK2 MUTATED    20   3
  NTRK2 WILD-TYPE 297  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTRK2 MUTATED     20    3
  NTRK2 WILD-TYPE  297   45
                               clus
vv                              NTRK2 MUTATED NTRK2 WILD-TYPE
  COLON ADENOCARCINOMA                     20             297
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  NTRK2 MUTATED    15   0   1   2
  NTRK2 WILD-TYPE 242   2  21  19
D1102V9, multiclass
    clus
vv   NTRK2 MUTATED NTRK2 WILD-TYPE
  R0            15             242
  R1             0               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"
D1102V10, 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
D1102V11, 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(1103) Variable = FRMPD4 MUTATION ANALYSIS
D1103V1, survival
                  sevent
clus2                0   1
  FRMPD4 MUTATED    18   5
  FRMPD4 WILD-TYPE 264  68
  FRMPD4 MUTATED FRMPD4 WILD-TYPE 
              23              332 
  FRMPD4 MUTATED FRMPD4 WILD-TYPE 
               5               68 
$`FRMPD4 MUTATED`
TCGA-A6-2672 TCGA-A6-5662 TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-A00N TCGA-AA-A01P 
       46.65        23.61        22.06        20.12         4.01        38.07 
TCGA-AD-6899 TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-5403 TCGA-CA-6717 TCGA-CM-5861 
        5.79        27.09        58.39        62.79         0.33        15.02 
TCGA-CM-5868 TCGA-CM-6163 TCGA-D5-5540 TCGA-D5-6532 TCGA-DM-A0X9 TCGA-DM-A1DA 
       17.03        14.04        13.51        18.25       119.70         7.50 
TCGA-DM-A282 TCGA-DM-A28H TCGA-F4-6856 TCGA-G4-6310 TCGA-G4-6586 
      139.17       117.07        19.43        45.11        35.80 

$`FRMPD4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5666 
       31.63        30.44        29.19        33.53        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 
       21.76        24.69        24.39        23.87        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        7.04         3.02         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        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        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 
       21.37         4.21        56.55         0.79         0.72        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 
       15.02        15.02        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-D5-5541 
       10.06        12.03        45.40        12.26        19.59        11.51 
TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         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         1.51        12.00        11.38        10.26        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A285 TCGA-DM-A28C 
      140.38        44.32       131.51       135.65         6.12        81.37 
TCGA-DM-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        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 
       16.24        33.67        13.25         0.53        35.41       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  FRMPD4 MUTATED FRMPD4 WILD-TYPE 
            0.33             0.00 
  FRMPD4 MUTATED FRMPD4 WILD-TYPE 
          139.17           140.38 
  FRMPD4 MUTATED FRMPD4 WILD-TYPE 
          22.060           20.105 
[1] "0.3 - 139.2 (22.1)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.3"
D1103V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FRMPD4 MUTATED         3        0        1        10         1         0
  FRMPD4 WILD-TYPE      61        1       24        99         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FRMPD4 MUTATED           1          0          2          3        1
  FRMPD4 WILD-TYPE        18         10         39         28       34
                  vv
clus               STAGE IVA STAGE IVB
  FRMPD4 MUTATED           2         0
  FRMPD4 WILD-TYPE        11         1
D1103V3, multiclass
            clus
vv           FRMPD4 MUTATED FRMPD4 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA              10               99
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              3               28
  STAGE IV                1               34
  STAGE IVA               2               11
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  18   3
  FRMPD4 WILD-TYPE   8  66 230  38
D1103V4, multiclass
    clus
vv   FRMPD4 MUTATED FRMPD4 WILD-TYPE
  T1              1                8
  T2              2               66
  T3             18              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
  FRMPD4 MUTATED    15   4   5
  FRMPD4 WILD-TYPE 205  76  61
D1103V5, multiclass
    clus
vv   FRMPD4 MUTATED FRMPD4 WILD-TYPE
  N0             15              205
  N1              4               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"
D1103V6, binary
                  cls
clus                 0   1
  FRMPD4 MUTATED    18   3
  FRMPD4 WILD-TYPE 265  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FRMPD4 MUTATED     18    3
  FRMPD4 WILD-TYPE  265   45
   clus
vv  FRMPD4 MUTATED FRMPD4 WILD-TYPE
  0             18              265
  1              3               45
[1] 2 2
[1] FALSE
D1103V7, binary
                  cls
clus                 0   1
  FRMPD4 MUTATED    11  13
  FRMPD4 WILD-TYPE 159 184
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FRMPD4 MUTATED     11   13
  FRMPD4 WILD-TYPE  159  184
        clus
vv       FRMPD4 MUTATED FRMPD4 WILD-TYPE
  FEMALE             11              159
  MALE               13              184
[1] 2 2
[1] FALSE
D1103V8, binary
                  cls
clus                 0   1
  FRMPD4 MUTATED    19   5
  FRMPD4 WILD-TYPE 298  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FRMPD4 MUTATED     19    5
  FRMPD4 WILD-TYPE  298   43
                               clus
vv                              FRMPD4 MUTATED FRMPD4 WILD-TYPE
  COLON ADENOCARCINOMA                      19              298
  COLON MUCINOUS ADENOCARCINOMA              5               43
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  FRMPD4 MUTATED    14   0   1   1
  FRMPD4 WILD-TYPE 243   2  21  20
D1103V9, multiclass
    clus
vv   FRMPD4 MUTATED FRMPD4 WILD-TYPE
  R0             14              243
  R1              0                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"
D1103V10, 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                           0    20
  FRMPD4 WILD-TYPE                        19   156
D1103V11, multiclass
                                  clus
vv                                 FRMPD4 MUTATED FRMPD4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                9
  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(1104) Variable = CCDC11 MUTATION ANALYSIS
D1104V1, survival
                  sevent
clus2                0   1
  CCDC11 MUTATED     7   3
  CCDC11 WILD-TYPE 275  70
  CCDC11 MUTATED CCDC11 WILD-TYPE 
              10              345 
  CCDC11 MUTATED CCDC11 WILD-TYPE 
               3               70 
$`CCDC11 MUTATED`
TCGA-AA-3510 TCGA-AA-3697 TCGA-AA-3966 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A03F 
       63.98        85.05         2.01         4.01        34.98        18.05 
TCGA-AD-5900 TCGA-CK-4950 TCGA-DM-A28F TCGA-G4-6315 
        0.07        40.34        35.97        36.72 

$`CCDC11 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-6548 
       14.01         0.92        41.00        39.98        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       102.44        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       45.11        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  CCDC11 MUTATED CCDC11 WILD-TYPE 
            0.07             0.00 
  CCDC11 MUTATED CCDC11 WILD-TYPE 
           85.05           140.38 
  CCDC11 MUTATED CCDC11 WILD-TYPE 
          35.475           20.120 
[1] "0.1 - 85.0 (35.5)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.2"
D1104V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CCDC11 MUTATED         1        0        1         1         2         0
  CCDC11 WILD-TYPE      63        1       24       108         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC11 MUTATED           2          1          1          0        1
  CCDC11 WILD-TYPE        17          9         40         31       34
                  vv
clus               STAGE IVA STAGE IVB
  CCDC11 MUTATED           0         0
  CCDC11 WILD-TYPE        13         1
D1104V3, multiclass
            clus
vv           CCDC11 MUTATED CCDC11 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               1              108
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               2               17
  STAGE IIIA              1                9
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CCDC11 MUTATED     0   1   7   2
  CCDC11 WILD-TYPE   9  67 241  39
D1104V4, multiclass
    clus
vv   CCDC11 MUTATED CCDC11 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              7              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
  CCDC11 MUTATED     6   3   1
  CCDC11 WILD-TYPE 214  77  65
D1104V5, multiclass
    clus
vv   CCDC11 MUTATED CCDC11 WILD-TYPE
  N0              6              214
  N1              3               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"
D1104V6, binary
                  cls
clus                 0   1
  CCDC11 MUTATED     8   1
  CCDC11 WILD-TYPE 275  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC11 MUTATED      8    1
  CCDC11 WILD-TYPE  275   47
   clus
vv  CCDC11 MUTATED CCDC11 WILD-TYPE
  0              8              275
  1              1               47
[1] 2 2
[1] FALSE
D1104V7, binary
                  cls
clus                 0   1
  CCDC11 MUTATED     4   6
  CCDC11 WILD-TYPE 166 191
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC11 MUTATED      4    6
  CCDC11 WILD-TYPE  166  191
        clus
vv       CCDC11 MUTATED CCDC11 WILD-TYPE
  FEMALE              4              166
  MALE                6              191
[1] 2 2
[1] FALSE
D1104V8, binary
                  cls
clus                 0   1
  CCDC11 MUTATED     6   4
  CCDC11 WILD-TYPE 311  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC11 MUTATED      6    4
  CCDC11 WILD-TYPE  311   44
                               clus
vv                              CCDC11 MUTATED CCDC11 WILD-TYPE
  COLON ADENOCARCINOMA                       6              311
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CCDC11 MUTATED     7   1   0   0
  CCDC11 WILD-TYPE 250   1  22  21
D1104V9, multiclass
    clus
vv   CCDC11 MUTATED CCDC11 WILD-TYPE
  R0              7              250
  R1              1                1
  R2              0               22
  RX              0               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1104V10, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCDC11 MUTATED                                  0     0
  CCDC11 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CCDC11 MUTATED                           1     3
  CCDC11 WILD-TYPE                        18   173
D1104V11, multiclass
                                  clus
vv                                 CCDC11 MUTATED CCDC11 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(1105) Variable = OSR1 MUTATION ANALYSIS
D1105V1, survival
                sevent
clus2              0   1
  OSR1 MUTATED     3   1
  OSR1 WILD-TYPE 279  72
  OSR1 MUTATED OSR1 WILD-TYPE 
             4            351 
  OSR1 MUTATED OSR1 WILD-TYPE 
             1             72 
$`OSR1 MUTATED`
TCGA-CK-4950 TCGA-CM-5863 TCGA-G4-6293 TCGA-G4-6626 
       40.34        15.02       107.67        46.75 

$`OSR1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
        1.35        17.56       102.44        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        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-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       26.17        91.79        52.80 

  OSR1 MUTATED OSR1 WILD-TYPE 
         15.02           0.00 
  OSR1 MUTATED OSR1 WILD-TYPE 
        107.67         140.38 
  OSR1 MUTATED OSR1 WILD-TYPE 
        43.545         20.120 
[1] "15.0 - 107.7 (43.5)" "0.0 - 140.4 (20.1)" 
[1] "hr=" "1.7"
D1105V2, 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       25       108         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OSR1 MUTATED           1          1          1          0        0         0
  OSR1 WILD-TYPE        18          9         40         31       35        13
                vv
clus             STAGE IVB
  OSR1 MUTATED           0
  OSR1 WILD-TYPE         1
D1105V3, multiclass
            clus
vv           OSR1 MUTATED OSR1 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             1            108
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            1              9
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  OSR1 MUTATED     0   0   4   0
  OSR1 WILD-TYPE   9  68 244  41
D1105V4, multiclass
    clus
vv   OSR1 MUTATED OSR1 WILD-TYPE
  T1            0              9
  T2            0             68
  T3            4            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
  OSR1 MUTATED     1   3   0
  OSR1 WILD-TYPE 219  77  66
D1105V5, multiclass
    clus
vv   OSR1 MUTATED OSR1 WILD-TYPE
  N0            1            219
  N1            3             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"
D1105V6, binary
                cls
clus               0   1
  OSR1 MUTATED     4   0
  OSR1 WILD-TYPE 279  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  OSR1 MUTATED      4    0
  OSR1 WILD-TYPE  279   48
   clus
vv  OSR1 MUTATED OSR1 WILD-TYPE
  0            4            279
  1            0             48
[1] 2 2
[1] FALSE
D1105V7, 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
D1105V8, binary
                cls
clus               0   1
  OSR1 MUTATED     3   1
  OSR1 WILD-TYPE 314  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  OSR1 MUTATED      3    1
  OSR1 WILD-TYPE  314   47
                               clus
vv                              OSR1 MUTATED OSR1 WILD-TYPE
  COLON ADENOCARCINOMA                     3            314
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  OSR1 MUTATED     3   1   0   0
  OSR1 WILD-TYPE 254   1  22  21
D1105V9, multiclass
    clus
vv   OSR1 MUTATED OSR1 WILD-TYPE
  R0            3            254
  R1            1              1
  R2            0             22
  RX            0             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1105V10, 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
D1105V11, 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(1106) Variable = CREG2 MUTATION ANALYSIS
D1106V1, survival
                 sevent
clus2               0   1
  CREG2 MUTATED     3   2
  CREG2 WILD-TYPE 279  71
  CREG2 MUTATED CREG2 WILD-TYPE 
              5             350 
  CREG2 MUTATED CREG2 WILD-TYPE 
              2              71 
$`CREG2 MUTATED`
TCGA-AA-3516 TCGA-AA-3552 TCGA-AU-3779 TCGA-CM-6170 TCGA-G4-6306 
       13.02        13.02        14.50        15.02        44.68 

$`CREG2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        1.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  CREG2 MUTATED CREG2 WILD-TYPE 
          13.02            0.00 
  CREG2 MUTATED CREG2 WILD-TYPE 
          44.68          140.38 
  CREG2 MUTATED CREG2 WILD-TYPE 
          14.50           20.63 
[1] "13.0 - 44.7 (14.5)" "0.0 - 140.4 (20.6)"
[1] "hr=" "2.3"
D1106V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CREG2 MUTATED         1        0        0         2         0         0
  CREG2 WILD-TYPE      63        1       25       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        18         10         41         30       35        13
                 vv
clus              STAGE IVB
  CREG2 MUTATED           0
  CREG2 WILD-TYPE         1
D1106V3, multiclass
            clus
vv           CREG2 MUTATED CREG2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              2             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CREG2 MUTATED     0   2   3   0
  CREG2 WILD-TYPE   9  66 245  41
D1106V4, multiclass
    clus
vv   CREG2 MUTATED CREG2 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             3             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
  CREG2 MUTATED     3   0   2
  CREG2 WILD-TYPE 217  80  64
D1106V5, multiclass
    clus
vv   CREG2 MUTATED CREG2 WILD-TYPE
  N0             3             217
  N1             0              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"
D1106V6, binary
                 cls
clus                0   1
  CREG2 MUTATED     5   0
  CREG2 WILD-TYPE 278  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CREG2 MUTATED      5    0
  CREG2 WILD-TYPE  278   48
   clus
vv  CREG2 MUTATED CREG2 WILD-TYPE
  0             5             278
  1             0              48
[1] 2 2
[1] FALSE
D1106V7, 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
D1106V8, binary
                 cls
clus                0   1
  CREG2 MUTATED     4   1
  CREG2 WILD-TYPE 313  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CREG2 MUTATED      4    1
  CREG2 WILD-TYPE  313   47
                               clus
vv                              CREG2 MUTATED CREG2 WILD-TYPE
  COLON ADENOCARCINOMA                      4             313
  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 253   2  22  21
D1106V9, multiclass
    clus
vv   CREG2 MUTATED CREG2 WILD-TYPE
  R0             4             253
  R1             0               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"
D1106V10, 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
D1106V11, 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(1107) Variable = CDH22 MUTATION ANALYSIS
D1107V1, survival
                 sevent
clus2               0   1
  CDH22 MUTATED    10   4
  CDH22 WILD-TYPE 272  69
  CDH22 MUTATED CDH22 WILD-TYPE 
             14             341 
  CDH22 MUTATED CDH22 WILD-TYPE 
              4              69 
$`CDH22 MUTATED`
TCGA-A6-5665 TCGA-AA-3516 TCGA-AA-3681 TCGA-AA-3837 TCGA-AA-3950 TCGA-AY-6196 
       22.06        13.02         5.98        38.99        24.00         0.20 
TCGA-AZ-6599 TCGA-AZ-6606 TCGA-D5-6540 TCGA-DM-A1HA TCGA-G4-6303 TCGA-G4-6306 
        6.77        11.74        16.14       131.51        65.85        44.68 
TCGA-G4-6315 TCGA-G4-6586 
       36.72        35.80 

$`CDH22 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       15.02        11.01        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        15.75        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41        49.41        12.10       100.01        29.56         5.23 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB 
       13.32        12.59       140.38         7.50        44.32       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 
       53.62        55.04        51.75        45.11        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        26.17        91.79        46.75        52.80 

  CDH22 MUTATED CDH22 WILD-TYPE 
            0.2             0.0 
  CDH22 MUTATED CDH22 WILD-TYPE 
         131.51          140.38 
  CDH22 MUTATED CDH22 WILD-TYPE 
          23.03           20.12 
[1] "0.2 - 131.5 (23.0)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.2"
D1107V2, 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       25       103         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        17         10         41         29       32        13
                 vv
clus              STAGE IVB
  CDH22 MUTATED           0
  CDH22 WILD-TYPE         1
D1107V3, multiclass
            clus
vv           CDH22 MUTATED CDH22 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              6             103
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             2              29
  STAGE IV               3              32
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CDH22 MUTATED     0   3  11   1
  CDH22 WILD-TYPE   9  65 237  40
D1107V4, multiclass
    clus
vv   CDH22 MUTATED CDH22 WILD-TYPE
  T1             0               9
  T2             3              65
  T3            11             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     8   3   4
  CDH22 WILD-TYPE 212  77  62
D1107V5, multiclass
    clus
vv   CDH22 MUTATED CDH22 WILD-TYPE
  N0             8             212
  N1             3              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"
D1107V6, binary
                 cls
clus                0   1
  CDH22 MUTATED    10   3
  CDH22 WILD-TYPE 273  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH22 MUTATED     10    3
  CDH22 WILD-TYPE  273   45
   clus
vv  CDH22 MUTATED CDH22 WILD-TYPE
  0            10             273
  1             3              45
[1] 2 2
[1] FALSE
D1107V7, binary
                 cls
clus                0   1
  CDH22 MUTATED     7   8
  CDH22 WILD-TYPE 163 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH22 MUTATED      7    8
  CDH22 WILD-TYPE  163  189
        clus
vv       CDH22 MUTATED CDH22 WILD-TYPE
  FEMALE             7             163
  MALE               8             189
[1] 2 2
[1] FALSE
D1107V8, binary
                 cls
clus                0   1
  CDH22 MUTATED    10   5
  CDH22 WILD-TYPE 307  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH22 MUTATED     10    5
  CDH22 WILD-TYPE  307   43
                               clus
vv                              CDH22 MUTATED CDH22 WILD-TYPE
  COLON ADENOCARCINOMA                     10             307
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CDH22 MUTATED    11   0   0   0
  CDH22 WILD-TYPE 246   2  22  21
D1107V9, multiclass
    clus
vv   CDH22 MUTATED CDH22 WILD-TYPE
  R0            11             246
  R1             0               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"
D1107V10, 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    10
  CDH22 WILD-TYPE                        19   166
D1107V11, 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                                       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(1108) Variable = GUCY2F MUTATION ANALYSIS
D1108V1, survival
                  sevent
clus2                0   1
  GUCY2F MUTATED    15   3
  GUCY2F WILD-TYPE 267  70
  GUCY2F MUTATED GUCY2F WILD-TYPE 
              18              337 
  GUCY2F MUTATED GUCY2F WILD-TYPE 
               3               70 
$`GUCY2F MUTATED`
TCGA-A6-6141 TCGA-AA-3511 TCGA-AA-3555 TCGA-AA-3660 TCGA-AA-3864 TCGA-AA-3877 
        8.38         6.97        29.95        78.08        53.00        31.00 
TCGA-AA-3977 TCGA-AA-A01P TCGA-AD-6965 TCGA-AZ-6608 TCGA-CM-5860 TCGA-D5-5537 
       25.02        38.07         0.20         1.94        16.01        45.40 
TCGA-D5-6533 TCGA-D5-6927 TCGA-D5-6931 TCGA-DM-A1HB TCGA-DM-A28K TCGA-G4-6588 
        1.32         9.44        12.00       135.65        98.24        26.17 

$`GUCY2F WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 
       19.59        13.51        11.51        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         1.51        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
      117.07         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 
       52.80 

  GUCY2F MUTATED GUCY2F WILD-TYPE 
             0.2              0.0 
  GUCY2F MUTATED GUCY2F WILD-TYPE 
          135.65           140.38 
  GUCY2F MUTATED GUCY2F WILD-TYPE 
          25.595           20.120 
[1] "0.2 - 135.7 (25.6)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.6"
D1108V2, 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       22       101         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GUCY2F MUTATED           1          1          2          1        0
  GUCY2F WILD-TYPE        18          9         39         30       35
                  vv
clus               STAGE IVA STAGE IVB
  GUCY2F MUTATED           0         0
  GUCY2F WILD-TYPE        13         1
D1108V3, multiclass
            clus
vv           GUCY2F MUTATED GUCY2F WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                3               22
  STAGE IIA               8              101
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              1                9
  STAGE IIIB              2               39
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GUCY2F MUTATED     1   2  12   4
  GUCY2F WILD-TYPE   8  66 236  37
D1108V4, multiclass
    clus
vv   GUCY2F MUTATED GUCY2F WILD-TYPE
  T1              1                8
  T2              2               66
  T3             12              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
  GUCY2F MUTATED    13   3   3
  GUCY2F WILD-TYPE 207  77  63
D1108V5, multiclass
    clus
vv   GUCY2F MUTATED GUCY2F WILD-TYPE
  N0             13              207
  N1              3               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"
D1108V6, binary
                  cls
clus                 0   1
  GUCY2F MUTATED    16   0
  GUCY2F WILD-TYPE 267  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GUCY2F MUTATED     16    0
  GUCY2F WILD-TYPE  267   48
   clus
vv  GUCY2F MUTATED GUCY2F WILD-TYPE
  0             16              267
  1              0               48
[1] 2 2
[1] FALSE
D1108V7, 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
D1108V8, binary
                  cls
clus                 0   1
  GUCY2F MUTATED    16   3
  GUCY2F WILD-TYPE 301  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GUCY2F MUTATED     16    3
  GUCY2F WILD-TYPE  301   45
                               clus
vv                              GUCY2F MUTATED GUCY2F WILD-TYPE
  COLON ADENOCARCINOMA                      16              301
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  GUCY2F MUTATED    12   0   0   1
  GUCY2F WILD-TYPE 245   2  22  20
D1108V9, multiclass
    clus
vv   GUCY2F MUTATED GUCY2F WILD-TYPE
  R0             12              245
  R1              0                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"
D1108V10, 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
D1108V11, 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(1109) Variable = CHMP4C MUTATION ANALYSIS
D1109V1, survival
                  sevent
clus2                0   1
  CHMP4C MUTATED     2   1
  CHMP4C WILD-TYPE 280  72
  CHMP4C MUTATED CHMP4C WILD-TYPE 
               3              352 
  CHMP4C MUTATED CHMP4C WILD-TYPE 
               1               72 
$`CHMP4C MUTATED`
TCGA-AU-6004 TCGA-AZ-6606 TCGA-CK-4952 
       27.09        11.74        15.62 

$`CHMP4C WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      102.44        40.34        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  CHMP4C MUTATED CHMP4C WILD-TYPE 
           11.74             0.00 
  CHMP4C MUTATED CHMP4C WILD-TYPE 
           27.09           140.38 
  CHMP4C MUTATED CHMP4C WILD-TYPE 
          15.620           20.235 
[1] "11.7 - 27.1 (15.6)" "0.0 - 140.4 (20.2)"
[1] "hr=" "2.2"
D1109V2, 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       25       109         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CHMP4C MUTATED           1          0          0          0        1
  CHMP4C WILD-TYPE        18         10         41         31       34
                  vv
clus               STAGE IVA STAGE IVB
  CHMP4C MUTATED           0         0
  CHMP4C WILD-TYPE        13         1
D1109V3, multiclass
            clus
vv           CHMP4C MUTATED CHMP4C WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               0              109
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CHMP4C MUTATED     0   1   0   2
  CHMP4C WILD-TYPE   9  67 248  39
D1109V4, multiclass
    clus
vv   CHMP4C MUTATED CHMP4C WILD-TYPE
  T1              0                9
  T2              1               67
  T3              0              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
  CHMP4C MUTATED     1   0   2
  CHMP4C WILD-TYPE 219  80  64
D1109V5, multiclass
    clus
vv   CHMP4C MUTATED CHMP4C WILD-TYPE
  N0              1              219
  N1              0               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"
D1109V6, binary
                  cls
clus                 0   1
  CHMP4C MUTATED     2   1
  CHMP4C WILD-TYPE 281  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHMP4C MUTATED      2    1
  CHMP4C WILD-TYPE  281   47
   clus
vv  CHMP4C MUTATED CHMP4C WILD-TYPE
  0              2              281
  1              1               47
[1] 2 2
[1] FALSE
D1109V7, 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
D1109V8, binary
                  cls
clus                 0   1
  CHMP4C MUTATED     2   1
  CHMP4C WILD-TYPE 315  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHMP4C MUTATED      2    1
  CHMP4C WILD-TYPE  315   47
                               clus
vv                              CHMP4C MUTATED CHMP4C WILD-TYPE
  COLON ADENOCARCINOMA                       2              315
  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 256   2  22  20
D1109V9, multiclass
[1] "Remove cluster labels:" "CHMP4C MUTATED"        
clus
  CHMP4C MUTATED CHMP4C WILD-TYPE 
               2              300 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-A6-2677       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-3496       TCGA-AA-3502 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-3510       TCGA-AA-3511       TCGA-AA-3514       TCGA-AA-3517 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-3518       TCGA-AA-3519       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-3526 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-3527       TCGA-AA-3529       TCGA-AA-3530       TCGA-AA-3531 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-3532       TCGA-AA-3534       TCGA-AA-3538       TCGA-AA-3542 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-3543       TCGA-AA-3544       TCGA-AA-3548       TCGA-AA-3549 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-3552       TCGA-AA-3553       TCGA-AA-3554       TCGA-AA-3555 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-3556       TCGA-AA-3558       TCGA-AA-3560       TCGA-AA-3561 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-3562       TCGA-AA-3655       TCGA-AA-3660       TCGA-AA-3662 
"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-3672       TCGA-AA-3673       TCGA-AA-3678       TCGA-AA-3679 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-3680       TCGA-AA-3681       TCGA-AA-3684       TCGA-AA-3685 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-3688       TCGA-AA-3692       TCGA-AA-3693       TCGA-AA-3695 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-3696       TCGA-AA-3697       TCGA-AA-3710       TCGA-AA-3712 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-3713       TCGA-AA-3715       TCGA-AA-3811       TCGA-AA-3812 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-3814       TCGA-AA-3815       TCGA-AA-3818       TCGA-AA-3819 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-3821       TCGA-AA-3831       TCGA-AA-3833       TCGA-AA-3837 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-3842       TCGA-AA-3844       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-3860       TCGA-AA-3861       TCGA-AA-3864       TCGA-AA-3866 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-3867       TCGA-AA-3869       TCGA-AA-3870       TCGA-AA-3872 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-3875       TCGA-AA-3877       TCGA-AA-3930       TCGA-AA-3939 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-3941       TCGA-AA-3947       TCGA-AA-3949       TCGA-AA-3950 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-3952       TCGA-AA-3955       TCGA-AA-3956       TCGA-AA-3968 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-3971       TCGA-AA-3972       TCGA-AA-3973       TCGA-AA-3975 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-3976       TCGA-AA-3979       TCGA-AA-3984       TCGA-AA-3986 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-3989       TCGA-AA-3994       TCGA-AA-A004       TCGA-AA-A00A 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-A00D       TCGA-AA-A00E       TCGA-AA-A00F       TCGA-AA-A00J 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-A00K       TCGA-AA-A00L       TCGA-AA-A00N       TCGA-AA-A00O 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-A00Q       TCGA-AA-A00R       TCGA-AA-A00U       TCGA-AA-A00W 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-A00Z       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-A024       TCGA-AA-A029       TCGA-AA-A02F 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-A02H       TCGA-AA-A02J       TCGA-AA-A02K       TCGA-AA-A02O 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AA-A02W       TCGA-AA-A02Y       TCGA-AA-A03F       TCGA-AA-A03J 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AD-5900       TCGA-AD-6548       TCGA-AD-6888       TCGA-AU-3779 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AY-4070       TCGA-AY-4071       TCGA-AY-5543       TCGA-AY-6196 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AY-6197       TCGA-AY-6386       TCGA-AZ-4315       TCGA-AZ-4681 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-AZ-4682       TCGA-CA-5254       TCGA-CA-5255       TCGA-CA-5796 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-CA-5797       TCGA-CA-6715       TCGA-CA-6716       TCGA-CA-6717 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-CA-6718       TCGA-CA-6719       TCGA-CK-4947       TCGA-CK-4948 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-CK-4950       TCGA-CK-5912       TCGA-CK-5913       TCGA-CK-5914 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-CK-5915       TCGA-CK-5916       TCGA-CK-6746       TCGA-CK-6747 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-CK-6748       TCGA-CK-6751       TCGA-CM-4743       TCGA-CM-4744 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-CM-4746       TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-CM-5344       TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-CM-5861       TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-CM-5868       TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-CM-6164       TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-CM-6168       TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-CM-6172       TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-CM-6677       TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-D5-5537       TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-D5-5541       TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-D5-6534       TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-D5-6538       TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-D5-6898       TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-D5-6924       TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-D5-6929       TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-D5-7000       TCGA-F4-6459       TCGA-F4-6460       TCGA-F4-6569 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704       TCGA-F4-6805 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808       TCGA-F4-6809 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856       TCGA-G4-6293 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304       TCGA-G4-6306 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310       TCGA-G4-6315 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323       TCGA-G4-6586 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
      TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628 
"CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" "CHMP4C WILD-TYPE" 
D1109V10, 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
D1109V11, 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(1110) Variable = CTSZ MUTATION ANALYSIS
D1110V1, survival
                sevent
clus2              0   1
  CTSZ MUTATED     4   2
  CTSZ WILD-TYPE 278  71
  CTSZ MUTATED CTSZ WILD-TYPE 
             6            349 
  CTSZ MUTATED CTSZ WILD-TYPE 
             2             71 
$`CTSZ MUTATED`
TCGA-A6-6652 TCGA-AA-3715 TCGA-AA-3968 TCGA-D5-6932 TCGA-F4-6856 TCGA-G4-6303 
       24.69        19.04        21.99        11.38        19.43        65.85 

$`CTSZ WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03         2.01        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 
       13.25         0.53        35.41       107.67        74.56        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  CTSZ MUTATED CTSZ WILD-TYPE 
         11.38           0.00 
  CTSZ MUTATED CTSZ WILD-TYPE 
         65.85         140.38 
  CTSZ MUTATED CTSZ WILD-TYPE 
         20.71          20.19 
[1] "11.4 - 65.8 (20.7)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.4"
D1110V2, 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       24       108         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        19         10         41         31       34        12
                vv
clus             STAGE IVB
  CTSZ MUTATED           0
  CTSZ WILD-TYPE         1
D1110V3, multiclass
            clus
vv           CTSZ MUTATED CTSZ WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             1            108
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 244  41
D1110V4, multiclass
    clus
vv   CTSZ MUTATED CTSZ WILD-TYPE
  T1            0              9
  T2            2             66
  T3            4            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
  CTSZ MUTATED     5   1   0
  CTSZ WILD-TYPE 215  79  66
D1110V5, multiclass
    clus
vv   CTSZ MUTATED CTSZ WILD-TYPE
  N0            5            215
  N1            1             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"
D1110V6, binary
                cls
clus               0   1
  CTSZ MUTATED     4   2
  CTSZ WILD-TYPE 279  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSZ MUTATED      4    2
  CTSZ WILD-TYPE  279   46
   clus
vv  CTSZ MUTATED CTSZ WILD-TYPE
  0            4            279
  1            2             46
[1] 2 2
[1] FALSE
D1110V7, 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
D1110V8, binary
                cls
clus               0   1
  CTSZ MUTATED     5   1
  CTSZ WILD-TYPE 312  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSZ MUTATED      5    1
  CTSZ WILD-TYPE  312   47
                               clus
vv                              CTSZ MUTATED CTSZ WILD-TYPE
  COLON ADENOCARCINOMA                     5            312
  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 252   2  22  21
D1110V9, multiclass
    clus
vv   CTSZ MUTATED CTSZ WILD-TYPE
  R0            5            252
  R1            0              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"
D1110V10, 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
D1110V11, 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(1111) Variable = LRP2 MUTATION ANALYSIS
D1111V1, survival
                sevent
clus2              0   1
  LRP2 MUTATED    64  12
  LRP2 WILD-TYPE 218  61
  LRP2 MUTATED LRP2 WILD-TYPE 
            76            279 
  LRP2 MUTATED LRP2 WILD-TYPE 
            12             61 
$`LRP2 MUTATED`
TCGA-A6-5657 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6654 
       31.63        22.06        32.71         8.38        25.08        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3555 TCGA-AA-3662 
       20.12        19.66        13.02         1.02        29.95         6.05 
TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3833 TCGA-AA-3845 
        6.97         0.92        85.05        19.04        15.95         0.00 
TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3949 
       32.05        53.00        17.03        31.00        33.01        26.01 
TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N 
       13.05        25.02        34.03        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A010 TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01T 
       27.02        34.98        38.07         1.02        35.01        33.04 
TCGA-AA-A02O TCGA-AD-5900 TCGA-AD-6895 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6598 
        0.92         0.07         0.72        21.44        58.39        49.41 
TCGA-AZ-6601 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4952 TCGA-CK-5912 
      100.01         0.33         0.10         1.35        15.62        49.08 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5864 
       29.06        22.03        22.98        16.01        15.02        15.02 
TCGA-CM-6163 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6677 TCGA-D5-5540 
       14.04        14.04        11.01        13.05        11.08        13.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6540 TCGA-DM-A0XD TCGA-DM-A0XF 
       20.19        18.25         1.32        16.14        24.43        38.20 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6703 TCGA-F4-6854 
      131.51       135.65        60.79       117.07        35.87         0.53 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6588 TCGA-G4-6628 
       65.85        53.62        26.17        52.80 

$`LRP2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 
       27.09        22.52        25.18        24.16        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       24.39        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 
       63.98         6.97         1.02        38.99         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
       78.08        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.03        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 
        0.99        25.02         1.02        17.98        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       14.93        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3867 
       36.03         0.99        31.07        31.07        30.05        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       27.02        29.98        18.05         2.01        12.99        24.00 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       16.08        50.99        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00K TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       19.00        30.02        18.05        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       31.00        31.00         1.02        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
        0.20        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       62.79        61.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        3.29         0.07         0.26        17.56       102.44        40.34 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5349 
       23.05        20.02        37.02        25.02        13.02        30.08 
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-6674 TCGA-CM-6676 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-D5-5541 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       12.26        19.59        11.51        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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
        7.50        44.32       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       35.97        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6306 TCGA-G4-6307 
       35.41        19.43       107.67        74.56        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       35.80        91.79        46.75 

  LRP2 MUTATED LRP2 WILD-TYPE 
             0              0 
  LRP2 MUTATED LRP2 WILD-TYPE 
        135.65         140.38 
  LRP2 MUTATED LRP2 WILD-TYPE 
        21.735         19.990 
[1] "0.0 - 135.7 (21.7)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.5"
D1111V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LRP2 MUTATED        10        0        7        25         4         1
  LRP2 WILD-TYPE      54        1       18        84         4         0
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LRP2 MUTATED           7          1          9          6        3         1
  LRP2 WILD-TYPE        12          9         32         25       32        12
                vv
clus             STAGE IVB
  LRP2 MUTATED           1
  LRP2 WILD-TYPE         0
D1111V3, multiclass
            clus
vv           LRP2 MUTATED LRP2 WILD-TYPE
  STAGE I              10             54
  STAGE IA              0              1
  STAGE II              7             18
  STAGE IIA            25             84
  STAGE IIB             4              4
  STAGE IIC             1              0
  STAGE III             7             12
  STAGE IIIA            1              9
  STAGE IIIB            9             32
  STAGE IIIC            6             25
  STAGE IV              3             32
  STAGE IVA             1             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
  LRP2 MUTATED     2  10  54  11
  LRP2 WILD-TYPE   7  58 194  30
D1111V4, multiclass
    clus
vv   LRP2 MUTATED LRP2 WILD-TYPE
  T1            2              7
  T2           10             58
  T3           54            194
  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  63  56
D1111V5, multiclass
    clus
vv   LRP2 MUTATED LRP2 WILD-TYPE
  N0           50            170
  N1           17             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"
D1111V6, binary
                cls
clus               0   1
  LRP2 MUTATED    64   5
  LRP2 WILD-TYPE 219  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  LRP2 MUTATED     64    5
  LRP2 WILD-TYPE  219   43
   clus
vv  LRP2 MUTATED LRP2 WILD-TYPE
  0           64            219
  1            5             43
[1] 2 2
[1] FALSE
D1111V7, 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
D1111V8, binary
                cls
clus               0   1
  LRP2 MUTATED    62  15
  LRP2 WILD-TYPE 255  33
[1] "tbl2"
                cls
clus             [,1] [,2]
  LRP2 MUTATED     62   15
  LRP2 WILD-TYPE  255   33
                               clus
vv                              LRP2 MUTATED LRP2 WILD-TYPE
  COLON ADENOCARCINOMA                    62            255
  COLON MUCINOUS ADENOCARCINOMA           15             33
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  LRP2 MUTATED    54   0   2   5
  LRP2 WILD-TYPE 203   2  20  16
D1111V9, multiclass
    clus
vv   LRP2 MUTATED LRP2 WILD-TYPE
  R0           54            203
  R1            0              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"
D1111V10, 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
D1111V11, 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(1112) Variable = DOCK7 MUTATION ANALYSIS
D1112V1, survival
                 sevent
clus2               0   1
  DOCK7 MUTATED    15   2
  DOCK7 WILD-TYPE 267  71
  DOCK7 MUTATED DOCK7 WILD-TYPE 
             17             338 
  DOCK7 MUTATED DOCK7 WILD-TYPE 
              2              71 
$`DOCK7 MUTATED`
TCGA-A6-5665 TCGA-AA-3518 TCGA-AA-3710 TCGA-AA-3956 TCGA-AA-A00J TCGA-AA-A00N 
       22.06         1.02        26.99        34.03        18.05         4.01 
TCGA-AA-A010 TCGA-AD-6895 TCGA-AZ-4315 TCGA-CK-4950 TCGA-CK-5916 TCGA-CM-4746 
       34.98         0.72        58.39        40.34        21.14        37.02 
TCGA-D5-6927 TCGA-D5-6929 TCGA-DM-A1HB TCGA-G4-6310 TCGA-G4-6628 
        9.44        13.41       135.65        45.11        52.80 

$`DOCK7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        4.21        56.55         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        51.32        21.99         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
       14.30         9.04        11.64         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 
       91.79        46.75 

  DOCK7 MUTATED DOCK7 WILD-TYPE 
           0.72            0.00 
  DOCK7 MUTATED DOCK7 WILD-TYPE 
         135.65          140.38 
  DOCK7 MUTATED DOCK7 WILD-TYPE 
         26.990          20.005 
[1] "0.7 - 135.7 (27.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "2.1"
D1112V2, 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       25       103         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DOCK7 MUTATED           0          1          3          0        1         0
  DOCK7 WILD-TYPE        19          9         38         31       34        13
                 vv
clus              STAGE IVB
  DOCK7 MUTATED           0
  DOCK7 WILD-TYPE         1
D1112V3, multiclass
            clus
vv           DOCK7 MUTATED DOCK7 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              6             103
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             3              38
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DOCK7 MUTATED     1   2  11   3
  DOCK7 WILD-TYPE   8  66 237  38
D1112V4, multiclass
    clus
vv   DOCK7 MUTATED DOCK7 WILD-TYPE
  T1             1               8
  T2             2              66
  T3            11             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
  DOCK7 MUTATED    11   6   0
  DOCK7 WILD-TYPE 209  74  66
D1112V5, multiclass
    clus
vv   DOCK7 MUTATED DOCK7 WILD-TYPE
  N0            11             209
  N1             6              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"
D1112V6, binary
                 cls
clus                0   1
  DOCK7 MUTATED    15   1
  DOCK7 WILD-TYPE 268  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK7 MUTATED     15    1
  DOCK7 WILD-TYPE  268   47
   clus
vv  DOCK7 MUTATED DOCK7 WILD-TYPE
  0            15             268
  1             1              47
[1] 2 2
[1] FALSE
D1112V7, 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
D1112V8, binary
                 cls
clus                0   1
  DOCK7 MUTATED    15   2
  DOCK7 WILD-TYPE 302  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK7 MUTATED     15    2
  DOCK7 WILD-TYPE  302   46
                               clus
vv                              DOCK7 MUTATED DOCK7 WILD-TYPE
  COLON ADENOCARCINOMA                     15             302
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DOCK7 MUTATED    13   1   0   1
  DOCK7 WILD-TYPE 244   1  22  20
D1112V9, multiclass
    clus
vv   DOCK7 MUTATED DOCK7 WILD-TYPE
  R0            13             244
  R1             1               1
  R2             0              22
  RX             1              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1112V10, 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
D1112V11, 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(1113) Variable = DCLRE1A MUTATION ANALYSIS
D1113V1, survival
                   sevent
clus2                 0   1
  DCLRE1A MUTATED     6   3
  DCLRE1A WILD-TYPE 276  70
  DCLRE1A MUTATED DCLRE1A WILD-TYPE 
                9               346 
  DCLRE1A MUTATED DCLRE1A WILD-TYPE 
                3                70 
$`DCLRE1A MUTATED`
TCGA-AA-3710 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A01P TCGA-AD-6889 TCGA-AU-6004 
       26.99        25.02         4.01        38.07        56.55        27.09 
TCGA-AZ-6608 TCGA-CM-6676 TCGA-CM-6680 
        1.94        11.08        12.03 

$`DCLRE1A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37         4.21         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       10.06        45.40        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  DCLRE1A MUTATED DCLRE1A WILD-TYPE 
             1.94              0.00 
  DCLRE1A MUTATED DCLRE1A WILD-TYPE 
            56.55            140.38 
  DCLRE1A MUTATED DCLRE1A WILD-TYPE 
           25.020            20.155 
[1] "1.9 - 56.5 (25.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.9"
D1113V2, 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       24       107         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DCLRE1A MUTATED           1          1          1          0        0
  DCLRE1A WILD-TYPE        18          9         40         31       35
                   vv
clus                STAGE IVA STAGE IVB
  DCLRE1A MUTATED           0         0
  DCLRE1A WILD-TYPE        13         1
D1113V3, multiclass
            clus
vv           DCLRE1A MUTATED DCLRE1A WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                2               107
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               1                 9
  STAGE IIIB               1                40
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  DCLRE1A MUTATED     0   4   4   2
  DCLRE1A WILD-TYPE   9  64 244  39
D1113V4, multiclass
    clus
vv   DCLRE1A MUTATED DCLRE1A WILD-TYPE
  T1               0                 9
  T2               4                64
  T3               4               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
  DCLRE1A MUTATED     7   2   1
  DCLRE1A WILD-TYPE 213  78  65
D1113V5, multiclass
    clus
vv   DCLRE1A MUTATED DCLRE1A WILD-TYPE
  N0               7               213
  N1               2                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"
D1113V6, binary
                   cls
clus                  0   1
  DCLRE1A MUTATED     9   0
  DCLRE1A WILD-TYPE 274  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DCLRE1A MUTATED      9    0
  DCLRE1A WILD-TYPE  274   48
   clus
vv  DCLRE1A MUTATED DCLRE1A WILD-TYPE
  0               9               274
  1               0                48
[1] 2 2
[1] FALSE
D1113V7, 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
D1113V8, binary
                   cls
clus                  0   1
  DCLRE1A MUTATED     9   1
  DCLRE1A WILD-TYPE 308  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DCLRE1A MUTATED      9    1
  DCLRE1A WILD-TYPE  308   47
                               clus
vv                              DCLRE1A MUTATED DCLRE1A WILD-TYPE
  COLON ADENOCARCINOMA                        9               308
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  DCLRE1A MUTATED     7   0   0   0
  DCLRE1A WILD-TYPE 250   2  22  21
D1113V9, multiclass
    clus
vv   DCLRE1A MUTATED DCLRE1A WILD-TYPE
  R0               7               250
  R1               0                 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"
D1113V10, 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
D1113V11, 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(1114) Variable = SLC44A4 MUTATION ANALYSIS
D1114V1, survival
                   sevent
clus2                 0   1
  SLC44A4 MUTATED     7   3
  SLC44A4 WILD-TYPE 275  70
  SLC44A4 MUTATED SLC44A4 WILD-TYPE 
               10               345 
  SLC44A4 MUTATED SLC44A4 WILD-TYPE 
                3                70 
$`SLC44A4 MUTATED`
TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3811 TCGA-AA-A010 TCGA-AD-6889 TCGA-AZ-6598 
       22.06        19.66        10.06        34.98        56.55        49.41 
TCGA-CK-5916 TCGA-CM-4743 TCGA-CM-5861 TCGA-D5-6540 
       21.14        23.05        15.02        16.14 

$`SLC44A4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        19.04        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37         4.21         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
       51.32        21.99         2.93         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        16.01         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  SLC44A4 MUTATED SLC44A4 WILD-TYPE 
            10.06              0.00 
  SLC44A4 MUTATED SLC44A4 WILD-TYPE 
            56.55            140.38 
  SLC44A4 MUTATED SLC44A4 WILD-TYPE 
            21.60             20.12 
[1] "10.1 - 56.5 (21.6)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.4"
D1114V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC44A4 MUTATED         2        0        1         5         1         0
  SLC44A4 WILD-TYPE      62        1       24       104         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC44A4 MUTATED           1          0          0          1        0
  SLC44A4 WILD-TYPE        18         10         41         30       35
                   vv
clus                STAGE IVA STAGE IVB
  SLC44A4 MUTATED           0         0
  SLC44A4 WILD-TYPE        13         1
D1114V3, multiclass
            clus
vv           SLC44A4 MUTATED SLC44A4 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                5               104
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               1                30
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC44A4 MUTATED     1   1   7   2
  SLC44A4 WILD-TYPE   8  67 241  39
D1114V4, multiclass
    clus
vv   SLC44A4 MUTATED SLC44A4 WILD-TYPE
  T1               1                 8
  T2               1                67
  T3               7               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     9   1   1
  SLC44A4 WILD-TYPE 211  79  65
D1114V5, multiclass
    clus
vv   SLC44A4 MUTATED SLC44A4 WILD-TYPE
  N0               9               211
  N1               1                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
  SLC44A4 MUTATED     9   0
  SLC44A4 WILD-TYPE 274  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC44A4 MUTATED      9    0
  SLC44A4 WILD-TYPE  274   48
   clus
vv  SLC44A4 MUTATED SLC44A4 WILD-TYPE
  0               9               274
  1               0                48
[1] 2 2
[1] FALSE
D1114V7, binary
                   cls
clus                  0   1
  SLC44A4 MUTATED     7   4
  SLC44A4 WILD-TYPE 163 193
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC44A4 MUTATED      7    4
  SLC44A4 WILD-TYPE  163  193
        clus
vv       SLC44A4 MUTATED SLC44A4 WILD-TYPE
  FEMALE               7               163
  MALE                 4               193
[1] 2 2
[1] FALSE
D1114V8, binary
                   cls
clus                  0   1
  SLC44A4 MUTATED     9   2
  SLC44A4 WILD-TYPE 308  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC44A4 MUTATED      9    2
  SLC44A4 WILD-TYPE  308   46
                               clus
vv                              SLC44A4 MUTATED SLC44A4 WILD-TYPE
  COLON ADENOCARCINOMA                        9               308
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SLC44A4 MUTATED     8   0   0   1
  SLC44A4 WILD-TYPE 249   2  22  20
D1114V9, multiclass
    clus
vv   SLC44A4 MUTATED SLC44A4 WILD-TYPE
  R0               8               249
  R1               0                 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"
D1114V10, 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                           0     7
  SLC44A4 WILD-TYPE                        19   169
D1114V11, multiclass
                                  clus
vv                                 SLC44A4 MUTATED SLC44A4 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(1115) Variable = SGOL2 MUTATION ANALYSIS
D1115V1, survival
                 sevent
clus2               0   1
  SGOL2 MUTATED    11   1
  SGOL2 WILD-TYPE 271  72
  SGOL2 MUTATED SGOL2 WILD-TYPE 
             12             343 
  SGOL2 MUTATED SGOL2 WILD-TYPE 
              1              72 
$`SGOL2 MUTATED`
TCGA-AA-3710 TCGA-AA-A010 TCGA-AD-6895 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CK-5916 
       26.99        34.98         0.72        58.39         0.33        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        11.51        53.62        55.04 

$`SGOL2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4744 
       49.08        51.32        21.99         2.93       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        16.01        15.02         5.03        15.02        15.02 
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-D5-6529 
       12.03        45.40        12.26        19.59        13.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       65.85        44.68        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  SGOL2 MUTATED SGOL2 WILD-TYPE 
           0.33            0.00 
  SGOL2 MUTATED SGOL2 WILD-TYPE 
          58.39          140.38 
  SGOL2 MUTATED SGOL2 WILD-TYPE 
         22.095          20.120 
[1] "0.3 - 58.4 (22.1)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "2.5"
D1115V2, 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       25       105         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SGOL2 MUTATED           0          0          2          0        1         0
  SGOL2 WILD-TYPE        19         10         39         31       34        13
                 vv
clus              STAGE IVB
  SGOL2 MUTATED           1
  SGOL2 WILD-TYPE         0
D1115V3, multiclass
            clus
vv           SGOL2 MUTATED SGOL2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              4             105
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  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  68 239  39
D1115V4, multiclass
    clus
vv   SGOL2 MUTATED SGOL2 WILD-TYPE
  T1             1               8
  T2             0              68
  T3             9             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
  SGOL2 MUTATED     7   4   1
  SGOL2 WILD-TYPE 213  76  65
D1115V5, multiclass
    clus
vv   SGOL2 MUTATED SGOL2 WILD-TYPE
  N0             7             213
  N1             4              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"
D1115V6, binary
                 cls
clus                0   1
  SGOL2 MUTATED     9   2
  SGOL2 WILD-TYPE 274  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SGOL2 MUTATED      9    2
  SGOL2 WILD-TYPE  274   46
   clus
vv  SGOL2 MUTATED SGOL2 WILD-TYPE
  0             9             274
  1             2              46
[1] 2 2
[1] FALSE
D1115V7, 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
D1115V8, binary
                 cls
clus                0   1
  SGOL2 MUTATED    10   2
  SGOL2 WILD-TYPE 307  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SGOL2 MUTATED     10    2
  SGOL2 WILD-TYPE  307   46
                               clus
vv                              SGOL2 MUTATED SGOL2 WILD-TYPE
  COLON ADENOCARCINOMA                     10             307
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SGOL2 MUTATED     8   0   0   3
  SGOL2 WILD-TYPE 249   2  22  18
D1115V9, multiclass
    clus
vv   SGOL2 MUTATED SGOL2 WILD-TYPE
  R0             8             249
  R1             0               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"
D1115V10, 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
D1115V11, 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(1116) Variable = MAGI1 MUTATION ANALYSIS
D1116V1, survival
                 sevent
clus2               0   1
  MAGI1 MUTATED    19   3
  MAGI1 WILD-TYPE 263  70
  MAGI1 MUTATED MAGI1 WILD-TYPE 
             22             333 
  MAGI1 MUTATED MAGI1 WILD-TYPE 
              3              70 
$`MAGI1 MUTATED`
TCGA-A6-6652 TCGA-A6-6653 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3518 
       24.69        24.39         3.02        35.01        63.98         1.02 
TCGA-AA-3543 TCGA-AA-3560 TCGA-AA-3672 TCGA-AA-3831 TCGA-AA-3864 TCGA-AA-A01I 
        0.99        19.99         0.92        17.98        53.00        31.00 
TCGA-AA-A01R TCGA-AY-6197 TCGA-AZ-4323 TCGA-CA-6717 TCGA-CM-5861 TCGA-CM-6171 
       35.01        21.44         1.41         0.33        15.02        14.04 
TCGA-CM-6172 TCGA-F4-6570 TCGA-G4-6309 TCGA-G4-6315 
       11.01         6.18        51.75        36.72 

$`MAGI1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-6780 
       25.08        25.18        24.16        21.76        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3511 TCGA-AA-3514 
       19.66        20.28         7.04         1.02         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       13.02        38.99         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01        12.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3833 TCGA-AA-3837 
       33.04         0.99        25.02         1.02        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        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-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4616 
        0.95        15.75         0.20        17.82        58.39         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.38        13.45        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       45.11        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  MAGI1 MUTATED MAGI1 WILD-TYPE 
           0.33            0.00 
  MAGI1 MUTATED MAGI1 WILD-TYPE 
          63.98          140.38 
  MAGI1 MUTATED MAGI1 WILD-TYPE 
         18.985          20.280 
[1] "0.3 - 64.0 (19.0)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.3"
D1116V2, 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       22       102         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        17         10         39         30       33        12
                 vv
clus              STAGE IVB
  MAGI1 MUTATED           0
  MAGI1 WILD-TYPE         1
D1116V3, multiclass
            clus
vv           MAGI1 MUTATED MAGI1 WILD-TYPE
  STAGE I                5              59
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              7             102
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             1              30
  STAGE IV               2              33
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  63 231  40
D1116V4, multiclass
    clus
vv   MAGI1 MUTATED MAGI1 WILD-TYPE
  T1             0               9
  T2             5              63
  T3            17             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
  MAGI1 MUTATED    16   4   3
  MAGI1 WILD-TYPE 204  76  63
D1116V5, multiclass
    clus
vv   MAGI1 MUTATED MAGI1 WILD-TYPE
  N0            16             204
  N1             4              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"
D1116V6, binary
                 cls
clus                0   1
  MAGI1 MUTATED    19   3
  MAGI1 WILD-TYPE 264  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAGI1 MUTATED     19    3
  MAGI1 WILD-TYPE  264   45
   clus
vv  MAGI1 MUTATED MAGI1 WILD-TYPE
  0            19             264
  1             3              45
[1] 2 2
[1] FALSE
D1116V7, 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
D1116V8, binary
                 cls
clus                0   1
  MAGI1 MUTATED    20   3
  MAGI1 WILD-TYPE 297  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAGI1 MUTATED     20    3
  MAGI1 WILD-TYPE  297   45
                               clus
vv                              MAGI1 MUTATED MAGI1 WILD-TYPE
  COLON ADENOCARCINOMA                     20             297
  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 238   2  22  20
D1116V9, multiclass
    clus
vv   MAGI1 MUTATED MAGI1 WILD-TYPE
  R0            19             238
  R1             0               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"
D1116V10, 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
D1116V11, 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(1117) Variable = EPHA2 MUTATION ANALYSIS
D1117V1, survival
                 sevent
clus2               0   1
  EPHA2 MUTATED     8   3
  EPHA2 WILD-TYPE 274  70
  EPHA2 MUTATED EPHA2 WILD-TYPE 
             11             344 
  EPHA2 MUTATED EPHA2 WILD-TYPE 
              3              70 
$`EPHA2 MUTATED`
TCGA-A6-5661 TCGA-A6-6781 TCGA-AA-3715 TCGA-AA-3821 TCGA-AA-3966 TCGA-AA-A00A 
       33.53        19.66        19.04         1.02         2.01        38.04 
TCGA-AZ-6598 TCGA-CM-4743 TCGA-CM-4746 TCGA-D5-6927 TCGA-DM-A1DA 
       49.41        23.05        37.02         9.44         7.50 

$`EPHA2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       33.04         0.99        25.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       27.02        13.94        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
       21.99        21.14         2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       12.59       140.38        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  EPHA2 MUTATED EPHA2 WILD-TYPE 
           1.02            0.00 
  EPHA2 MUTATED EPHA2 WILD-TYPE 
          49.41          140.38 
  EPHA2 MUTATED EPHA2 WILD-TYPE 
         19.660          20.235 
[1] "1.0 - 49.4 (19.7)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.6"
D1117V2, 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       23       104         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        19         10         41         29       35        13
                 vv
clus              STAGE IVB
  EPHA2 MUTATED           0
  EPHA2 WILD-TYPE         1
D1117V3, multiclass
            clus
vv           EPHA2 MUTATED EPHA2 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              5             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             2              29
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EPHA2 MUTATED     0   2   8   1
  EPHA2 WILD-TYPE   9  66 240  40
D1117V4, multiclass
    clus
vv   EPHA2 MUTATED EPHA2 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             8             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
  EPHA2 MUTATED     9   1   1
  EPHA2 WILD-TYPE 211  79  65
D1117V5, multiclass
    clus
vv   EPHA2 MUTATED EPHA2 WILD-TYPE
  N0             9             211
  N1             1              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"
D1117V6, binary
                 cls
clus                0   1
  EPHA2 MUTATED     9   0
  EPHA2 WILD-TYPE 274  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA2 MUTATED      9    0
  EPHA2 WILD-TYPE  274   48
   clus
vv  EPHA2 MUTATED EPHA2 WILD-TYPE
  0             9             274
  1             0              48
[1] 2 2
[1] FALSE
D1117V7, 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
D1117V8, binary
                 cls
clus                0   1
  EPHA2 MUTATED     8   3
  EPHA2 WILD-TYPE 309  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA2 MUTATED      8    3
  EPHA2 WILD-TYPE  309   45
                               clus
vv                              EPHA2 MUTATED EPHA2 WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  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 249   2  22  21
D1117V9, multiclass
    clus
vv   EPHA2 MUTATED EPHA2 WILD-TYPE
  R0             8             249
  R1             0               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"
D1117V10, 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
D1117V11, 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(1118) Variable = STK38L MUTATION ANALYSIS
D1118V1, survival
                  sevent
clus2                0   1
  STK38L MUTATED     6   1
  STK38L WILD-TYPE 276  72
  STK38L MUTATED STK38L WILD-TYPE 
               7              348 
  STK38L MUTATED STK38L WILD-TYPE 
               1               72 
$`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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 
       56.55         0.79         0.72         5.79        22.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        35.80        26.17        91.79        46.75        52.80 

  STK38L MUTATED STK38L WILD-TYPE 
            4.01             0.00 
  STK38L MUTATED STK38L WILD-TYPE 
           34.98           140.38 
  STK38L MUTATED STK38L WILD-TYPE 
          17.820           20.235 
[1] "4.0 - 35.0 (17.8)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D1118V2, 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       25       109         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  STK38L MUTATED           0          1          2          0        0
  STK38L WILD-TYPE        19          9         39         31       35
                  vv
clus               STAGE IVA STAGE IVB
  STK38L MUTATED           0         0
  STK38L WILD-TYPE        13         1
D1118V3, multiclass
            clus
vv           STK38L MUTATED STK38L WILD-TYPE
  STAGE I                 0               64
  STAGE IA                1                0
  STAGE II                0               25
  STAGE IIA               0              109
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              1                9
  STAGE IIIB              2               39
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  STK38L MUTATED     0   0   4   2
  STK38L WILD-TYPE   9  68 244  39
D1118V4, multiclass
    clus
vv   STK38L MUTATED STK38L WILD-TYPE
  T1              0                9
  T2              0               68
  T3              4              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
  STK38L MUTATED     5   2   0
  STK38L WILD-TYPE 215  78  66
D1118V5, multiclass
    clus
vv   STK38L MUTATED STK38L WILD-TYPE
  N0              5              215
  N1              2               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"
D1118V6, binary
                  cls
clus                 0   1
  STK38L MUTATED     5   0
  STK38L WILD-TYPE 278  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STK38L MUTATED      5    0
  STK38L WILD-TYPE  278   48
   clus
vv  STK38L MUTATED STK38L WILD-TYPE
  0              5              278
  1              0               48
[1] 2 2
[1] FALSE
D1118V7, 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
D1118V8, binary
                  cls
clus                 0   1
  STK38L MUTATED     6   1
  STK38L WILD-TYPE 311  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STK38L MUTATED      6    1
  STK38L WILD-TYPE  311   47
                               clus
vv                              STK38L MUTATED STK38L WILD-TYPE
  COLON ADENOCARCINOMA                       6              311
  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 251   2  22  21
D1118V9, multiclass
    clus
vv   STK38L MUTATED STK38L WILD-TYPE
  R0              6              251
  R1              0                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"
D1118V10, 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
D1118V11, 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(1119) Variable = YLPM1 MUTATION ANALYSIS
D1119V1, survival
                 sevent
clus2               0   1
  YLPM1 MUTATED    17   4
  YLPM1 WILD-TYPE 265  69
  YLPM1 MUTATED YLPM1 WILD-TYPE 
             21             334 
  YLPM1 MUTATED YLPM1 WILD-TYPE 
              4              69 
$`YLPM1 MUTATED`
TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3815 
       19.66        63.98         6.97        36.00        19.04        33.04 
TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3972 TCGA-AA-A010 TCGA-AA-A01P TCGA-AY-6386 
        0.99         1.02        50.99        34.98        38.07        17.82 
TCGA-CA-6717 TCGA-CK-5913 TCGA-CK-5916 TCGA-CM-4743 TCGA-CM-5861 TCGA-CM-6171 
        0.33        51.32        21.14        23.05        15.02        14.04 
TCGA-D5-6540 TCGA-G4-6309 TCGA-G4-6586 
       16.14        51.75        35.80 

$`YLPM1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3697 
       11.01         5.98        37.05        19.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3819 TCGA-AA-3831 
       26.99        19.04        10.06        35.05        25.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       20.98        34.03         2.01        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       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        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
       17.56       102.44        40.34        15.62        49.08        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93         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        16.01 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  YLPM1 MUTATED YLPM1 WILD-TYPE 
           0.33            0.00 
  YLPM1 MUTATED YLPM1 WILD-TYPE 
          63.98          140.38 
  YLPM1 MUTATED YLPM1 WILD-TYPE 
         21.140          20.155 
[1] "0.3 - 64.0 (21.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D1119V2, 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       23       101         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        18         10         39         30       32        13
                 vv
clus              STAGE IVB
  YLPM1 MUTATED           0
  YLPM1 WILD-TYPE         1
D1119V3, multiclass
            clus
vv           YLPM1 MUTATED YLPM1 WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              8             101
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             1              30
  STAGE IV               3              32
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  YLPM1 MUTATED     1   3  16   2
  YLPM1 WILD-TYPE   8  65 232  39
D1119V4, multiclass
    clus
vv   YLPM1 MUTATED YLPM1 WILD-TYPE
  T1             1               8
  T2             3              65
  T3            16             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
  YLPM1 MUTATED    16   5   1
  YLPM1 WILD-TYPE 204  75  65
D1119V5, multiclass
    clus
vv   YLPM1 MUTATED YLPM1 WILD-TYPE
  N0            16             204
  N1             5              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"
D1119V6, binary
                 cls
clus                0   1
  YLPM1 MUTATED    17   3
  YLPM1 WILD-TYPE 266  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YLPM1 MUTATED     17    3
  YLPM1 WILD-TYPE  266   45
   clus
vv  YLPM1 MUTATED YLPM1 WILD-TYPE
  0            17             266
  1             3              45
[1] 2 2
[1] FALSE
D1119V7, 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
D1119V8, binary
                 cls
clus                0   1
  YLPM1 MUTATED    17   5
  YLPM1 WILD-TYPE 300  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YLPM1 MUTATED     17    5
  YLPM1 WILD-TYPE  300   43
                               clus
vv                              YLPM1 MUTATED YLPM1 WILD-TYPE
  COLON ADENOCARCINOMA                     17             300
  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 241   2  19  18
D1119V9, multiclass
    clus
vv   YLPM1 MUTATED YLPM1 WILD-TYPE
  R0            16             241
  R1             0               2
  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"
D1119V10, 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
D1119V11, 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(1120) Variable = FAM189B MUTATION ANALYSIS
D1120V1, survival
                   sevent
clus2                 0   1
  FAM189B MUTATED     8   1
  FAM189B WILD-TYPE 274  72
  FAM189B MUTATED FAM189B WILD-TYPE 
                9               346 
  FAM189B MUTATED FAM189B WILD-TYPE 
                1                72 
$`FAM189B MUTATED`
TCGA-A6-5657 TCGA-AA-3663 TCGA-AA-3672 TCGA-AD-6895 TCGA-AY-6196 TCGA-AZ-6598 
       31.63         6.97         0.92         0.72         0.20        49.41 
TCGA-D5-6540 TCGA-D5-6930 TCGA-DM-A1HB 
       16.14         1.51       135.65 

$`FAM189B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        15.75        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 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-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  FAM189B MUTATED FAM189B WILD-TYPE 
              0.2               0.0 
  FAM189B MUTATED FAM189B WILD-TYPE 
           135.65            140.38 
  FAM189B MUTATED FAM189B WILD-TYPE 
             6.97             20.63 
[1] "0.2 - 135.7 (7.0)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "1.8"
D1120V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FAM189B MUTATED         1        0        2         1         0         0
  FAM189B WILD-TYPE      63        1       23       108         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM189B MUTATED           1          0          2          1        0
  FAM189B WILD-TYPE        18         10         39         30       35
                   vv
clus                STAGE IVA STAGE IVB
  FAM189B MUTATED           0         0
  FAM189B WILD-TYPE        13         1
D1120V3, multiclass
            clus
vv           FAM189B MUTATED FAM189B WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 2                23
  STAGE IIA                1               108
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               0                10
  STAGE IIIB               2                39
  STAGE IIIC               1                30
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  FAM189B MUTATED     0   1   8   0
  FAM189B WILD-TYPE   9  67 240  41
D1120V4, multiclass
    clus
vv   FAM189B MUTATED FAM189B WILD-TYPE
  T1               0                 9
  T2               1                67
  T3               8               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
  FAM189B MUTATED     4   4   1
  FAM189B WILD-TYPE 216  76  65
D1120V5, multiclass
    clus
vv   FAM189B MUTATED FAM189B WILD-TYPE
  N0               4               216
  N1               4                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"
D1120V6, binary
                   cls
clus                  0   1
  FAM189B MUTATED     6   0
  FAM189B WILD-TYPE 277  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM189B MUTATED      6    0
  FAM189B WILD-TYPE  277   48
   clus
vv  FAM189B MUTATED FAM189B WILD-TYPE
  0               6               277
  1               0                48
[1] 2 2
[1] FALSE
D1120V7, binary
                   cls
clus                  0   1
  FAM189B MUTATED     2   7
  FAM189B WILD-TYPE 168 190
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM189B MUTATED      2    7
  FAM189B WILD-TYPE  168  190
        clus
vv       FAM189B MUTATED FAM189B WILD-TYPE
  FEMALE               2               168
  MALE                 7               190
[1] 2 2
[1] FALSE
D1120V8, binary
                   cls
clus                  0   1
  FAM189B MUTATED     6   3
  FAM189B WILD-TYPE 311  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM189B MUTATED      6    3
  FAM189B WILD-TYPE  311   45
                               clus
vv                              FAM189B MUTATED FAM189B WILD-TYPE
  COLON ADENOCARCINOMA                        6               311
  COLON MUCINOUS ADENOCARCINOMA               3                45
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  FAM189B MUTATED     6   0   0   0
  FAM189B WILD-TYPE 251   2  22  21
D1120V9, multiclass
    clus
vv   FAM189B MUTATED FAM189B WILD-TYPE
  R0               6               251
  R1               0                 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"
D1120V10, 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
D1120V11, 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(1121) Variable = ATG10 MUTATION ANALYSIS
D1121V1, survival
                 sevent
clus2               0   1
  ATG10 MUTATED     4   0
  ATG10 WILD-TYPE 278  73
  ATG10 MUTATED ATG10 WILD-TYPE 
              4             351 
  ATG10 MUTATED ATG10 WILD-TYPE 
              0              73 
$`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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  ATG10 MUTATED ATG10 WILD-TYPE 
           9.44            0.00 
  ATG10 MUTATED ATG10 WILD-TYPE 
          34.98          140.38 
  ATG10 MUTATED ATG10 WILD-TYPE 
          19.51           20.19 
[1] "9.4 - 35.0 (19.5)"  "0.0 - 140.4 (20.2)"
[1] "hr="     "3300000"
D1121V2, 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       25       106         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        19         10         41         31       35        13
                 vv
clus              STAGE IVB
  ATG10 MUTATED           0
  ATG10 WILD-TYPE         1
D1121V3, multiclass
            clus
vv           ATG10 MUTATED ATG10 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              3             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ATG10 MUTATED     0   0   3   1
  ATG10 WILD-TYPE   9  68 245  40
D1121V4, multiclass
    clus
vv   ATG10 MUTATED ATG10 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             3             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
  ATG10 MUTATED     4   0   0
  ATG10 WILD-TYPE 216  80  66
D1121V5, multiclass
    clus
vv   ATG10 MUTATED ATG10 WILD-TYPE
  N0             4             216
  N1             0              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"
D1121V6, binary
                 cls
clus                0   1
  ATG10 MUTATED     4   0
  ATG10 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATG10 MUTATED      4    0
  ATG10 WILD-TYPE  279   48
   clus
vv  ATG10 MUTATED ATG10 WILD-TYPE
  0             4             279
  1             0              48
[1] 2 2
[1] FALSE
D1121V7, 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
D1121V8, binary
                 cls
clus                0   1
  ATG10 MUTATED     3   1
  ATG10 WILD-TYPE 314  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATG10 MUTATED      3    1
  ATG10 WILD-TYPE  314   47
                               clus
vv                              ATG10 MUTATED ATG10 WILD-TYPE
  COLON ADENOCARCINOMA                      3             314
  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 253   2  22  21
D1121V9, multiclass
    clus
vv   ATG10 MUTATED ATG10 WILD-TYPE
  R0             4             253
  R1             0               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"
D1121V10, 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
D1121V11, multiclass
[1] "Remove cluster labels:" "ATG10 MUTATED"         
clus
  ATG10 MUTATED ATG10 WILD-TYPE 
              2             204 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-4105 
"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-A6-6649      TCGA-A6-6651 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-A6-6652      TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-A6-6781      TCGA-A6-6782      TCGA-AD-5900      TCGA-AD-6548 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-AD-6888      TCGA-AD-6889      TCGA-AD-6890      TCGA-AD-6895 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-AD-6899      TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6964 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-AD-6965      TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-AY-4071      TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-AY-6386      TCGA-AZ-4315      TCGA-AZ-4323      TCGA-AZ-4616 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-AZ-4681      TCGA-AZ-4682      TCGA-AZ-5403      TCGA-AZ-5407 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-AZ-6598      TCGA-AZ-6599      TCGA-AZ-6600      TCGA-AZ-6601 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-AZ-6603      TCGA-AZ-6605      TCGA-AZ-6606      TCGA-AZ-6607 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-AZ-6608      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-5912      TCGA-CK-5913 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-CK-5914      TCGA-CK-5915      TCGA-CK-5916      TCGA-CK-6746 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-CK-6747      TCGA-CK-6748      TCGA-CK-6751      TCGA-CM-4743 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-CM-4744      TCGA-CM-4746      TCGA-CM-4747      TCGA-CM-4752 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-CM-5341      TCGA-CM-5344      TCGA-CM-5348      TCGA-CM-5349 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-CM-5860      TCGA-CM-5862      TCGA-CM-5863      TCGA-CM-5864 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-CM-5868      TCGA-CM-6161      TCGA-CM-6162      TCGA-CM-6163 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-CM-6164      TCGA-CM-6165      TCGA-CM-6166      TCGA-CM-6167 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-CM-6168      TCGA-CM-6169      TCGA-CM-6170      TCGA-CM-6171 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-CM-6172      TCGA-CM-6674      TCGA-CM-6675      TCGA-CM-6676 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-CM-6677      TCGA-CM-6678      TCGA-CM-6679      TCGA-CM-6680 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-D5-5537      TCGA-D5-5538      TCGA-D5-5539      TCGA-D5-5540 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-D5-5541      TCGA-D5-6529      TCGA-D5-6532      TCGA-D5-6533 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-D5-6534      TCGA-D5-6535      TCGA-D5-6536      TCGA-D5-6537 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-D5-6538      TCGA-D5-6539      TCGA-D5-6540      TCGA-D5-6541 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-D5-6898      TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-D5-6924      TCGA-D5-6926      TCGA-D5-6928      TCGA-D5-6929 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-D5-6930      TCGA-D5-6931      TCGA-D5-6932      TCGA-D5-7000 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-DM-A0X9      TCGA-DM-A0XD      TCGA-DM-A0XF      TCGA-DM-A1D0 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-DM-A1D4      TCGA-DM-A1D6      TCGA-DM-A1D7      TCGA-DM-A1D8 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-DM-A1D9      TCGA-DM-A1DA      TCGA-DM-A1DB      TCGA-DM-A1HA 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-DM-A1HB      TCGA-DM-A282      TCGA-DM-A285      TCGA-DM-A28C 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-DM-A28E      TCGA-DM-A28F      TCGA-DM-A28G      TCGA-DM-A28H 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-DM-A28K      TCGA-F4-6459      TCGA-F4-6460      TCGA-F4-6569 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704      TCGA-F4-6805 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808      TCGA-F4-6809 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856      TCGA-G4-6293 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304      TCGA-G4-6306 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310      TCGA-G4-6315 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323      TCGA-G4-6586 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 
     TCGA-G4-6588      TCGA-G4-6625      TCGA-G4-6626      TCGA-G4-6628 
"ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" "ATG10 WILD-TYPE" 

Clustering(1122) Variable = OR5H15 MUTATION ANALYSIS
D1122V1, survival
                  sevent
clus2                0   1
  OR5H15 MUTATED     5   0
  OR5H15 WILD-TYPE 277  73
  OR5H15 MUTATED OR5H15 WILD-TYPE 
               5              350 
  OR5H15 MUTATED OR5H15 WILD-TYPE 
               0               73 
$`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        13.45 

$`OR5H15 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       16.01         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6703 
      117.07        98.24         8.61        13.38         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  OR5H15 MUTATED OR5H15 WILD-TYPE 
           13.45             0.00 
  OR5H15 MUTATED OR5H15 WILD-TYPE 
           30.44           140.38 
  OR5H15 MUTATED OR5H15 WILD-TYPE 
          20.020           20.235 
[1] "13.4 - 30.4 (20.0)" "0.0 - 140.4 (20.2)"
[1] "hr="     "9100000"
D1122V2, 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       25       107         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR5H15 MUTATED           0          0          0          0        0
  OR5H15 WILD-TYPE        19         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  OR5H15 MUTATED           0         0
  OR5H15 WILD-TYPE        13         1
D1122V3, multiclass
            clus
vv           OR5H15 MUTATED OR5H15 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               2              107
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  OR5H15 MUTATED     0   3   2   0
  OR5H15 WILD-TYPE   9  65 246  41
D1122V4, multiclass
    clus
vv   OR5H15 MUTATED OR5H15 WILD-TYPE
  T1              0                9
  T2              3               65
  T3              2              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
  OR5H15 MUTATED     5   0   0
  OR5H15 WILD-TYPE 215  80  66
D1122V5, multiclass
    clus
vv   OR5H15 MUTATED OR5H15 WILD-TYPE
  N0              5              215
  N1              0               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
  OR5H15 MUTATED     5   0
  OR5H15 WILD-TYPE 278  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR5H15 MUTATED      5    0
  OR5H15 WILD-TYPE  278   48
   clus
vv  OR5H15 MUTATED OR5H15 WILD-TYPE
  0              5              278
  1              0               48
[1] 2 2
[1] FALSE
D1122V7, 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
D1122V8, binary
                  cls
clus                 0   1
  OR5H15 MUTATED     5   0
  OR5H15 WILD-TYPE 312  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR5H15 MUTATED      5    0
  OR5H15 WILD-TYPE  312   48
                               clus
vv                              OR5H15 MUTATED OR5H15 WILD-TYPE
  COLON ADENOCARCINOMA                       5              312
  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 252   2  22  21
D1122V9, multiclass
    clus
vv   OR5H15 MUTATED OR5H15 WILD-TYPE
  R0              5              252
  R1              0                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"
D1122V10, 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
D1122V11, 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(1123) Variable = CSGALNACT1 MUTATION ANALYSIS
D1123V1, survival
                      sevent
clus2                    0   1
  CSGALNACT1 MUTATED     6   2
  CSGALNACT1 WILD-TYPE 276  71
  CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE 
                   8                  347 
  CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE 
                   2                   71 
$`CSGALNACT1 MUTATED`
TCGA-A6-6781 TCGA-AA-3489 TCGA-AD-6899 TCGA-AU-3779 TCGA-CA-6716 TCGA-CA-6717 
       19.66         7.04         5.79        14.50         0.26         0.33 
TCGA-G4-6586 TCGA-G4-6588 
       35.80        26.17 

$`CSGALNACT1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       23.87        20.12        20.28         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         0.72        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.20        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6718 
        2.24         3.06         3.25         3.29         0.07         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        91.79        46.75        52.80 

  CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE 
                0.26                 0.00 
  CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE 
               35.80               140.38 
  CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE 
               10.77                20.98 
[1] "0.3 - 35.8 (10.8)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "2.3"
D1123V2, 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       24       104         8         1
                      vv
clus                   STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CSGALNACT1 MUTATED           0          0          0          2        0
  CSGALNACT1 WILD-TYPE        19         10         41         29       35
                      vv
clus                   STAGE IVA STAGE IVB
  CSGALNACT1 MUTATED           0         0
  CSGALNACT1 WILD-TYPE        13         1
D1123V3, multiclass
            clus
vv           CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE
  STAGE I                     0                   64
  STAGE IA                    0                    1
  STAGE II                    1                   24
  STAGE IIA                   5                  104
  STAGE IIB                   0                    8
  STAGE IIC                   0                    1
  STAGE III                   0                   19
  STAGE IIIA                  0                   10
  STAGE IIIB                  0                   41
  STAGE IIIC                  2                   29
  STAGE IV                    0                   35
  STAGE IVA                   0                   13
  STAGE IVB                   0                    1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                      vv
clus                    T1  T2  T3  T4
  CSGALNACT1 MUTATED     0   0   6   2
  CSGALNACT1 WILD-TYPE   9  68 242  39
D1123V4, multiclass
    clus
vv   CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE
  T1                  0                    9
  T2                  0                   68
  T3                  6                  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
  CSGALNACT1 MUTATED     6   1   1
  CSGALNACT1 WILD-TYPE 214  79  65
D1123V5, multiclass
    clus
vv   CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE
  N0                  6                  214
  N1                  1                   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"
D1123V6, binary
                      cls
clus                     0   1
  CSGALNACT1 MUTATED     6   0
  CSGALNACT1 WILD-TYPE 277  48
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  CSGALNACT1 MUTATED      6    0
  CSGALNACT1 WILD-TYPE  277   48
   clus
vv  CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE
  0                  6                  277
  1                  0                   48
[1] 2 2
[1] FALSE
D1123V7, 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
D1123V8, binary
                      cls
clus                     0   1
  CSGALNACT1 MUTATED     5   3
  CSGALNACT1 WILD-TYPE 312  45
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  CSGALNACT1 MUTATED      5    3
  CSGALNACT1 WILD-TYPE  312   45
                               clus
vv                              CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE
  COLON ADENOCARCINOMA                           5                  312
  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 252   2  22  19
D1123V9, multiclass
    clus
vv   CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE
  R0                  5                  252
  R1                  0                    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"
D1123V10, 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
D1123V11, 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(1124) Variable = KRTAP5-3 MUTATION ANALYSIS
D1124V1, survival
                    sevent
clus2                  0   1
  KRTAP5-3 MUTATED     4   0
  KRTAP5-3 WILD-TYPE 278  73
  KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE 
                 4                351 
  KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE 
                 0                 73 
$`KRTAP5-3 MUTATED`
TCGA-AA-3966 TCGA-CA-6717 TCGA-CM-6169 TCGA-G4-6310 
        2.01         0.33        13.02        45.11 

$`KRTAP5-3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE 
              0.33               0.00 
  KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE 
             45.11             140.38 
  KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE 
             7.515             20.280 
[1] "0.3 - 45.1 (7.5)"   "0.0 - 140.4 (20.3)"
[1] "hr="     "3300000"
D1124V2, 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       25       106         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        19         10         40         31       35
                    vv
clus                 STAGE IVA STAGE IVB
  KRTAP5-3 MUTATED           0         0
  KRTAP5-3 WILD-TYPE        13         1
D1124V3, multiclass
            clus
vv           KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE
  STAGE I                   0                 64
  STAGE IA                  0                  1
  STAGE II                  0                 25
  STAGE IIA                 3                106
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                0                 10
  STAGE IIIB                1                 40
  STAGE IIIC                0                 31
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KRTAP5-3 MUTATED     0   0   4   0
  KRTAP5-3 WILD-TYPE   9  68 244  41
D1124V4, multiclass
    clus
vv   KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE
  T1                0                  9
  T2                0                 68
  T3                4                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
  KRTAP5-3 MUTATED     3   1   0
  KRTAP5-3 WILD-TYPE 217  79  66
D1124V5, multiclass
    clus
vv   KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE
  N0                3                217
  N1                1                 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"
D1124V6, binary
                    cls
clus                   0   1
  KRTAP5-3 MUTATED     4   0
  KRTAP5-3 WILD-TYPE 279  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP5-3 MUTATED      4    0
  KRTAP5-3 WILD-TYPE  279   48
   clus
vv  KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE
  0                4                279
  1                0                 48
[1] 2 2
[1] FALSE
D1124V7, 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
D1124V8, binary
                    cls
clus                   0   1
  KRTAP5-3 MUTATED     2   2
  KRTAP5-3 WILD-TYPE 315  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP5-3 MUTATED      2    2
  KRTAP5-3 WILD-TYPE  315   46
                               clus
vv                              KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE
  COLON ADENOCARCINOMA                         2                315
  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 255   2  22  20
D1124V9, multiclass
    clus
vv   KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE
  R0                2                255
  R1                0                  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"
D1124V10, 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
D1124V11, 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(1125) Variable = ATP11C MUTATION ANALYSIS
D1125V1, survival
                  sevent
clus2                0   1
  ATP11C MUTATED    19   5
  ATP11C WILD-TYPE 263  68
  ATP11C MUTATED ATP11C WILD-TYPE 
              24              331 
  ATP11C MUTATED ATP11C WILD-TYPE 
               5               68 
$`ATP11C MUTATED`
TCGA-A6-4105 TCGA-A6-5661 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3660 
       14.53        33.53        23.87        19.66        20.28        78.08 
TCGA-AA-3947 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A010 
       33.01        25.02        27.02         4.01         0.99        34.98 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CA-6718 
       21.44        58.39        12.10       100.01         0.33         0.10 
TCGA-CK-4947 TCGA-D5-6535 TCGA-DM-A1HA TCGA-DM-A28F TCGA-G4-6586 TCGA-G4-6588 
       17.56        15.12       131.51        35.97        35.80        26.17 

$`ATP11C WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-AA-3489 
       24.16        21.76        24.69        24.39        20.12         7.04 
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        3.02         1.02        35.01        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
       42.02        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        15.75         0.20        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
        6.77        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
        1.35       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G 
      135.65       139.17         6.12        81.37       119.93        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 
       36.72        36.00        22.09        13.78        91.79        46.75 
TCGA-G4-6628 
       52.80 

  ATP11C MUTATED ATP11C WILD-TYPE 
             0.1              0.0 
  ATP11C MUTATED ATP11C WILD-TYPE 
          131.51           140.38 
  ATP11C MUTATED ATP11C WILD-TYPE 
          24.445           19.990 
[1] "0.1 - 131.5 (24.4)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.2"
D1125V2, 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       23       100         4         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP11C MUTATED           0          0          3          2        1
  ATP11C WILD-TYPE        19         10         38         29       34
                  vv
clus               STAGE IVA STAGE IVB
  ATP11C MUTATED           1         0
  ATP11C WILD-TYPE        12         1
D1125V3, multiclass
            clus
vv           ATP11C MUTATED ATP11C WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               9              100
  STAGE IIB               4                4
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              3               38
  STAGE IIIC              2               29
  STAGE IV                1               34
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  65 233  34
D1125V4, multiclass
    clus
vv   ATP11C MUTATED ATP11C WILD-TYPE
  T1              0                9
  T2              3               65
  T3             15              233
  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  74  65
D1125V5, multiclass
    clus
vv   ATP11C MUTATED ATP11C WILD-TYPE
  N0             18              202
  N1              6               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"
D1125V6, binary
                  cls
clus                 0   1
  ATP11C MUTATED    19   1
  ATP11C WILD-TYPE 264  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP11C MUTATED     19    1
  ATP11C WILD-TYPE  264   47
   clus
vv  ATP11C MUTATED ATP11C WILD-TYPE
  0             19              264
  1              1               47
[1] 2 2
[1] FALSE
D1125V7, 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
D1125V8, binary
                  cls
clus                 0   1
  ATP11C MUTATED    21   4
  ATP11C WILD-TYPE 296  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP11C MUTATED     21    4
  ATP11C WILD-TYPE  296   44
                               clus
vv                              ATP11C MUTATED ATP11C WILD-TYPE
  COLON ADENOCARCINOMA                      21              296
  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 245   2  22  17
D1125V9, multiclass
    clus
vv   ATP11C MUTATED ATP11C WILD-TYPE
  R0             12              245
  R1              0                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"
D1125V10, 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
D1125V11, 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(1126) Variable = MAGEA4 MUTATION ANALYSIS
D1126V1, survival
                  sevent
clus2                0   1
  MAGEA4 MUTATED     3   2
  MAGEA4 WILD-TYPE 279  71
  MAGEA4 MUTATED MAGEA4 WILD-TYPE 
               5              350 
  MAGEA4 MUTATED MAGEA4 WILD-TYPE 
               2               71 
$`MAGEA4 MUTATED`
TCGA-AA-3496 TCGA-AZ-6598 TCGA-CA-6718 TCGA-F4-6459 TCGA-G4-6588 
        1.02        49.41         0.10         8.61        26.17 

$`MAGEA4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.33         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79       117.07        98.24        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  MAGEA4 MUTATED MAGEA4 WILD-TYPE 
             0.1              0.0 
  MAGEA4 MUTATED MAGEA4 WILD-TYPE 
           49.41           140.38 
  MAGEA4 MUTATED MAGEA4 WILD-TYPE 
           8.610           20.235 
[1] "0.1 - 49.4 (8.6)"   "0.0 - 140.4 (20.2)"
[1] "hr=" "2.7"
D1126V2, 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       23       107         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAGEA4 MUTATED           0          0          1          0        1
  MAGEA4 WILD-TYPE        19         10         40         31       34
                  vv
clus               STAGE IVA STAGE IVB
  MAGEA4 MUTATED           0         0
  MAGEA4 WILD-TYPE        13         1
D1126V3, multiclass
            clus
vv           MAGEA4 MUTATED MAGEA4 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               2              107
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MAGEA4 MUTATED     0   0   6   0
  MAGEA4 WILD-TYPE   9  68 242  41
D1126V4, multiclass
    clus
vv   MAGEA4 MUTATED MAGEA4 WILD-TYPE
  T1              0                9
  T2              0               68
  T3              6              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
  MAGEA4 MUTATED     4   0   2
  MAGEA4 WILD-TYPE 216  80  64
D1126V5, multiclass
    clus
vv   MAGEA4 MUTATED MAGEA4 WILD-TYPE
  N0              4              216
  N1              0               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"
D1126V6, binary
                  cls
clus                 0   1
  MAGEA4 MUTATED     4   1
  MAGEA4 WILD-TYPE 279  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGEA4 MUTATED      4    1
  MAGEA4 WILD-TYPE  279   47
   clus
vv  MAGEA4 MUTATED MAGEA4 WILD-TYPE
  0              4              279
  1              1               47
[1] 2 2
[1] FALSE
D1126V7, 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
D1126V8, binary
                  cls
clus                 0   1
  MAGEA4 MUTATED     6   0
  MAGEA4 WILD-TYPE 311  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGEA4 MUTATED      6    0
  MAGEA4 WILD-TYPE  311   48
                               clus
vv                              MAGEA4 MUTATED MAGEA4 WILD-TYPE
  COLON ADENOCARCINOMA                       6              311
  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 254   2  21  20
D1126V9, multiclass
    clus
vv   MAGEA4 MUTATED MAGEA4 WILD-TYPE
  R0              3              254
  R1              0                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"
D1126V10, 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
D1126V11, 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(1127) Variable = SMC1B MUTATION ANALYSIS
D1127V1, survival
                 sevent
clus2               0   1
  SMC1B MUTATED    14   4
  SMC1B WILD-TYPE 268  69
  SMC1B MUTATED SMC1B WILD-TYPE 
             18             337 
  SMC1B MUTATED SMC1B WILD-TYPE 
              4              69 
$`SMC1B MUTATED`
TCGA-A6-3809 TCGA-A6-6653 TCGA-A6-6654 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3511 
       32.75        24.39        23.87         3.02        63.98         6.97 
TCGA-AA-3715 TCGA-AA-3950 TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-6601 TCGA-CA-6717 
       19.04        24.00        34.98        58.39       100.01         0.33 
TCGA-CA-6718 TCGA-CM-6680 TCGA-D5-6931 TCGA-F4-6809 TCGA-G4-6309 TCGA-G4-6586 
        0.10        12.03        12.00        13.25        51.75        35.80 

$`SMC1B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6780 TCGA-A6-6781 
       25.18        24.16        21.76        24.69        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3514 TCGA-AA-3516 
       20.28         7.04         1.02        35.01         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07         0.26         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       33.67         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  SMC1B MUTATED SMC1B WILD-TYPE 
            0.1             0.0 
  SMC1B MUTATED SMC1B WILD-TYPE 
         100.01          140.38 
  SMC1B MUTATED SMC1B WILD-TYPE 
         23.935          20.120 
[1] "0.1 - 100.0 (23.9)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1"  
D1127V2, 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       20       103         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        19         10         38         30       35        12
                 vv
clus              STAGE IVB
  SMC1B MUTATED           0
  SMC1B WILD-TYPE         1
D1127V3, multiclass
            clus
vv           SMC1B MUTATED SMC1B WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               5              20
  STAGE IIA              6             103
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             3              38
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 234  37
D1127V4, multiclass
    clus
vv   SMC1B MUTATED SMC1B WILD-TYPE
  T1             0               9
  T2             1              67
  T3            14             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
  SMC1B MUTATED    14   3   2
  SMC1B WILD-TYPE 206  77  64
D1127V5, multiclass
    clus
vv   SMC1B MUTATED SMC1B WILD-TYPE
  N0            14             206
  N1             3              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"
D1127V6, binary
                 cls
clus                0   1
  SMC1B MUTATED    18   1
  SMC1B WILD-TYPE 265  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMC1B MUTATED     18    1
  SMC1B WILD-TYPE  265   47
   clus
vv  SMC1B MUTATED SMC1B WILD-TYPE
  0            18             265
  1             1              47
[1] 2 2
[1] FALSE
D1127V7, 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
D1127V8, binary
                 cls
clus                0   1
  SMC1B MUTATED    16   3
  SMC1B WILD-TYPE 301  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMC1B MUTATED     16    3
  SMC1B WILD-TYPE  301   45
                               clus
vv                              SMC1B MUTATED SMC1B WILD-TYPE
  COLON ADENOCARCINOMA                     16             301
  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 243   2  22  19
D1127V9, multiclass
    clus
vv   SMC1B MUTATED SMC1B WILD-TYPE
  R0            14             243
  R1             0               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"
D1127V10, 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
D1127V11, 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(1128) Variable = BCAP29 MUTATION ANALYSIS
D1128V1, survival
                  sevent
clus2                0   1
  BCAP29 MUTATED     9   0
  BCAP29 WILD-TYPE 273  73
  BCAP29 MUTATED BCAP29 WILD-TYPE 
               9              346 
  BCAP29 MUTATED BCAP29 WILD-TYPE 
               0               73 
$`BCAP29 MUTATED`
TCGA-AA-3713 TCGA-AA-3977 TCGA-AA-A010 TCGA-AD-5900 TCGA-CA-6717 TCGA-CK-4948 
       19.04        25.02        34.98         0.07         0.33       102.44 
TCGA-CM-6169 TCGA-CM-6675 TCGA-DM-A28K 
       13.02        13.05        98.24 

$`BCAP29 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        0.10         1.35        17.56        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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-6676 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        12.95        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       35.97        60.79       117.07         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  BCAP29 MUTATED BCAP29 WILD-TYPE 
            0.07             0.00 
  BCAP29 MUTATED BCAP29 WILD-TYPE 
          102.44           140.38 
  BCAP29 MUTATED BCAP29 WILD-TYPE 
          19.040           20.235 
[1] "0.1 - 102.4 (19.0)" "0.0 - 140.4 (20.2)"
[1] "hr="     "2.6e+07"
D1128V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BCAP29 MUTATED         1        0        0         3         1         0
  BCAP29 WILD-TYPE      63        1       25       106         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BCAP29 MUTATED           0          1          0          0        1
  BCAP29 WILD-TYPE        19          9         41         31       34
                  vv
clus               STAGE IVA STAGE IVB
  BCAP29 MUTATED           0         1
  BCAP29 WILD-TYPE        13         0
D1128V3, multiclass
            clus
vv           BCAP29 MUTATED BCAP29 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               3              106
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              1                9
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               1                0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  BCAP29 MUTATED     0   2   6   1
  BCAP29 WILD-TYPE   9  66 242  40
D1128V4, multiclass
    clus
vv   BCAP29 MUTATED BCAP29 WILD-TYPE
  T1              0                9
  T2              2               66
  T3              6              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
  BCAP29 MUTATED     7   1   1
  BCAP29 WILD-TYPE 213  79  65
D1128V5, multiclass
    clus
vv   BCAP29 MUTATED BCAP29 WILD-TYPE
  N0              7              213
  N1              1               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"
D1128V6, binary
                  cls
clus                 0   1
  BCAP29 MUTATED     5   2
  BCAP29 WILD-TYPE 278  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCAP29 MUTATED      5    2
  BCAP29 WILD-TYPE  278   46
   clus
vv  BCAP29 MUTATED BCAP29 WILD-TYPE
  0              5              278
  1              2               46
[1] 2 2
[1] FALSE
D1128V7, binary
                  cls
clus                 0   1
  BCAP29 MUTATED     2   7
  BCAP29 WILD-TYPE 168 190
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCAP29 MUTATED      2    7
  BCAP29 WILD-TYPE  168  190
        clus
vv       BCAP29 MUTATED BCAP29 WILD-TYPE
  FEMALE              2              168
  MALE                7              190
[1] 2 2
[1] FALSE
D1128V8, binary
                  cls
clus                 0   1
  BCAP29 MUTATED     6   3
  BCAP29 WILD-TYPE 311  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCAP29 MUTATED      6    3
  BCAP29 WILD-TYPE  311   45
                               clus
vv                              BCAP29 MUTATED BCAP29 WILD-TYPE
  COLON ADENOCARCINOMA                       6              311
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  BCAP29 MUTATED     5   0   1   1
  BCAP29 WILD-TYPE 252   2  21  20
D1128V9, multiclass
    clus
vv   BCAP29 MUTATED BCAP29 WILD-TYPE
  R0              5              252
  R1              0                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"
D1128V10, 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                           2     3
  BCAP29 WILD-TYPE                        17   173
D1128V11, multiclass
                                  clus
vv                                 BCAP29 MUTATED BCAP29 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(1129) Variable = MIPEP MUTATION ANALYSIS
D1129V1, survival
                 sevent
clus2               0   1
  MIPEP MUTATED     7   0
  MIPEP WILD-TYPE 275  73
  MIPEP MUTATED MIPEP WILD-TYPE 
              7             348 
  MIPEP MUTATED MIPEP WILD-TYPE 
              0              73 
$`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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        17.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-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-D5-5537 TCGA-D5-5538 
       11.08        11.08        11.01        10.06        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  MIPEP MUTATED MIPEP WILD-TYPE 
          12.03            0.00 
  MIPEP MUTATED MIPEP WILD-TYPE 
         124.27          140.38 
  MIPEP MUTATED MIPEP WILD-TYPE 
         29.950          20.155 
[1] "12.0 - 124.3 (29.9)" "0.0 - 140.4 (20.2)" 
[1] "hr="     "2.6e+07"
D1129V2, 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       22       106         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        19         10         40         31       35        13
                 vv
clus              STAGE IVB
  MIPEP MUTATED           0
  MIPEP WILD-TYPE         1
D1129V3, multiclass
            clus
vv           MIPEP MUTATED MIPEP WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              3             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MIPEP MUTATED     0   1   6   1
  MIPEP WILD-TYPE   9  67 242  40
D1129V4, multiclass
    clus
vv   MIPEP MUTATED MIPEP WILD-TYPE
  T1             0               9
  T2             1              67
  T3             6             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
  MIPEP MUTATED     7   0   1
  MIPEP WILD-TYPE 213  80  65
D1129V5, multiclass
    clus
vv   MIPEP MUTATED MIPEP WILD-TYPE
  N0             7             213
  N1             0              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"
D1129V6, binary
                 cls
clus                0   1
  MIPEP MUTATED     7   0
  MIPEP WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MIPEP MUTATED      7    0
  MIPEP WILD-TYPE  276   48
   clus
vv  MIPEP MUTATED MIPEP WILD-TYPE
  0             7             276
  1             0              48
[1] 2 2
[1] FALSE
D1129V7, 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
D1129V8, binary
                 cls
clus                0   1
  MIPEP MUTATED     6   2
  MIPEP WILD-TYPE 311  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MIPEP MUTATED      6    2
  MIPEP WILD-TYPE  311   46
                               clus
vv                              MIPEP MUTATED MIPEP WILD-TYPE
  COLON ADENOCARCINOMA                      6             311
  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 250   2  22  20
D1129V9, multiclass
    clus
vv   MIPEP MUTATED MIPEP WILD-TYPE
  R0             7             250
  R1             0               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"
D1129V10, 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
D1129V11, 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(1130) Variable = HMCN1 MUTATION ANALYSIS
D1130V1, survival
                 sevent
clus2               0   1
  HMCN1 MUTATED    57  10
  HMCN1 WILD-TYPE 225  63
  HMCN1 MUTATED HMCN1 WILD-TYPE 
             67             288 
  HMCN1 MUTATED HMCN1 WILD-TYPE 
             10              63 
$`HMCN1 MUTATED`
TCGA-A6-2674 TCGA-A6-3809 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6651 TCGA-A6-6781 
       43.76        32.75        33.53        22.06        21.76        19.66 
TCGA-AA-3510 TCGA-AA-3525 TCGA-AA-3554 TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3815 
       63.98         8.05        17.95         0.92        19.04        33.04 
TCGA-AA-3845 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3956 
        0.00        31.07        53.00        33.01        26.01        34.03 
TCGA-AA-3977 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J 
       25.02         7.96        13.94        38.04        30.02        18.05 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A024 TCGA-AA-A03J TCGA-AD-6895 TCGA-AY-6197 
        4.01        34.98        39.06        40.96         0.72        21.44 
TCGA-AZ-4315 TCGA-AZ-5407 TCGA-AZ-6601 TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6718 
       58.39        61.41       100.01         3.29         0.33         0.10 
TCGA-CK-4952 TCGA-CK-5914 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-5348 TCGA-CM-5349 
       15.62        21.99       124.27        23.05        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-6674 TCGA-CM-6679 TCGA-CM-6680 
       16.01        15.02         5.03        12.95        10.06        12.03 
TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6536 TCGA-D5-6541 TCGA-D5-6922 TCGA-D5-6923 
       45.40        20.19        17.85        15.58        10.13        12.43 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A1DB TCGA-DM-A1HB TCGA-F4-6459 
        1.51        12.00        11.38        44.32       135.65         8.61 
TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6703 TCGA-G4-6307 TCGA-G4-6321 TCGA-G4-6586 
       13.38         6.18        35.87        55.04        22.09        35.80 
TCGA-G4-6588 
       26.17 

$`HMCN1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       34.65        33.34        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 
       30.44        29.19        23.61        22.09        32.71        27.09 
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 
       22.52         8.38        25.08        25.18        24.16        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        20.12        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 
        1.02         9.07        24.03        37.05        36.03        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       26.99        19.04        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
       32.05         0.99        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 
       24.00        24.00         2.01        20.98         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A00D TCGA-AA-A00F 
       27.02        27.02        19.07        27.02        19.00        34.03 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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        35.01        26.01        37.02        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       27.09        16.31         0.95        15.75         0.20        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 
        1.41         5.13        83.80        22.36        62.79        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 
        1.94         2.24         3.06         3.25         0.07         0.26 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 
        1.35        17.56       102.44        40.34        49.08        51.32 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       21.14         2.93         2.01        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       13.02        29.06        22.03        15.02        15.02        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-D5-5538 TCGA-D5-5539 
       13.05        11.08        11.08        11.01        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       13.51        11.51        18.25         1.32        43.27        15.12 
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-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-7000 
       14.30         9.04         9.44        11.64        13.41        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        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-A282 
       13.32        12.59       140.38         7.50       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       98.24        13.45         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        53.62        44.68        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       36.72        36.00        13.78        91.79        46.75        52.80 

  HMCN1 MUTATED HMCN1 WILD-TYPE 
              0               0 
  HMCN1 MUTATED HMCN1 WILD-TYPE 
         135.65          140.38 
  HMCN1 MUTATED HMCN1 WILD-TYPE 
         21.760          20.005 
[1] "0.0 - 135.7 (21.8)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.5"
D1130V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HMCN1 MUTATED         5        0        4        32         5         0
  HMCN1 WILD-TYPE      59        1       21        77         3         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HMCN1 MUTATED           4          1         11          2        3         1
  HMCN1 WILD-TYPE        15          9         30         29       32        12
                 vv
clus              STAGE IVB
  HMCN1 MUTATED           0
  HMCN1 WILD-TYPE         1
D1130V3, multiclass
            clus
vv           HMCN1 MUTATED HMCN1 WILD-TYPE
  STAGE I                5              59
  STAGE IA               0               1
  STAGE II               4              21
  STAGE IIA             32              77
  STAGE IIB              5               3
  STAGE IIC              0               1
  STAGE III              4              15
  STAGE IIIA             1               9
  STAGE IIIB            11              30
  STAGE IIIC             2              29
  STAGE IV               3              32
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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   6  54   9
  HMCN1 WILD-TYPE   8  62 194  32
D1130V4, multiclass
    clus
vv   HMCN1 MUTATED HMCN1 WILD-TYPE
  T1             1               8
  T2             6              62
  T3            54             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    47  15   8
  HMCN1 WILD-TYPE 173  65  58
D1130V5, multiclass
    clus
vv   HMCN1 MUTATED HMCN1 WILD-TYPE
  N0            47             173
  N1            15              65
  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"
D1130V6, binary
                 cls
clus                0   1
  HMCN1 MUTATED    56   4
  HMCN1 WILD-TYPE 227  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HMCN1 MUTATED     56    4
  HMCN1 WILD-TYPE  227   44
   clus
vv  HMCN1 MUTATED HMCN1 WILD-TYPE
  0            56             227
  1             4              44
[1] 2 2
[1] FALSE
D1130V7, binary
                 cls
clus                0   1
  HMCN1 MUTATED    27  43
  HMCN1 WILD-TYPE 143 154
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HMCN1 MUTATED     27   43
  HMCN1 WILD-TYPE  143  154
        clus
vv       HMCN1 MUTATED HMCN1 WILD-TYPE
  FEMALE            27             143
  MALE              43             154
[1] 2 2
[1] FALSE
D1130V8, binary
                 cls
clus                0   1
  HMCN1 MUTATED    58  12
  HMCN1 WILD-TYPE 259  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HMCN1 MUTATED     58   12
  HMCN1 WILD-TYPE  259   36
                               clus
vv                              HMCN1 MUTATED HMCN1 WILD-TYPE
  COLON ADENOCARCINOMA                     58             259
  COLON MUCINOUS ADENOCARCINOMA            12              36
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  HMCN1 MUTATED    54   0   2   7
  HMCN1 WILD-TYPE 203   2  20  14
D1130V9, multiclass
    clus
vv   HMCN1 MUTATED HMCN1 WILD-TYPE
  R0            54             203
  R1             0               2
  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"
D1130V10, 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                           1    42
  HMCN1 WILD-TYPE                        18   134
D1130V11, multiclass
                                  clus
vv                                 HMCN1 MUTATED HMCN1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               7
  BLACK OR AFRICAN AMERICAN                    1              18
  WHITE                                       42             134
[1] 4 2
[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 = RAPGEF6 MUTATION ANALYSIS
D1131V1, survival
                   sevent
clus2                 0   1
  RAPGEF6 MUTATED    13   4
  RAPGEF6 WILD-TYPE 269  69
  RAPGEF6 MUTATED RAPGEF6 WILD-TYPE 
               17               338 
  RAPGEF6 MUTATED RAPGEF6 WILD-TYPE 
                4                69 
$`RAPGEF6 MUTATED`
TCGA-A6-5664 TCGA-A6-6781 TCGA-AA-3516 TCGA-AA-3554 TCGA-AA-3660 TCGA-AA-3848 
       22.09        19.66        13.02        17.95        78.08        10.06 
TCGA-AA-A010 TCGA-AA-A01F TCGA-AD-6895 TCGA-AU-6004 TCGA-CA-6717 TCGA-CK-5913 
       34.98        32.02         0.72        27.09         0.33        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        51.75 

$`RAPGEF6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       14.93         0.00        17.03         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01G 
       17.03        14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.20        14.50        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 
       35.97        60.79       117.07        98.24        13.38        13.45 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  RAPGEF6 MUTATED RAPGEF6 WILD-TYPE 
             0.33              0.00 
  RAPGEF6 MUTATED RAPGEF6 WILD-TYPE 
            78.08            140.38 
  RAPGEF6 MUTATED RAPGEF6 WILD-TYPE 
           19.660            20.235 
[1] "0.3 - 78.1 (19.7)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D1131V2, 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       24       104         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RAPGEF6 MUTATED           1          0          4          3        0
  RAPGEF6 WILD-TYPE        18         10         37         28       35
                   vv
clus                STAGE IVA STAGE IVB
  RAPGEF6 MUTATED           0         0
  RAPGEF6 WILD-TYPE        13         1
D1131V3, multiclass
            clus
vv           RAPGEF6 MUTATED RAPGEF6 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                5               104
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               0                10
  STAGE IIIB               4                37
  STAGE IIIC               3                28
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  RAPGEF6 MUTATED     0   1  13   3
  RAPGEF6 WILD-TYPE   9  67 235  38
D1131V4, multiclass
    clus
vv   RAPGEF6 MUTATED RAPGEF6 WILD-TYPE
  T1               0                 9
  T2               1                67
  T3              13               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
  RAPGEF6 MUTATED     8   5   4
  RAPGEF6 WILD-TYPE 212  75  62
D1131V5, multiclass
    clus
vv   RAPGEF6 MUTATED RAPGEF6 WILD-TYPE
  N0               8               212
  N1               5                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"
D1131V6, binary
                   cls
clus                  0   1
  RAPGEF6 MUTATED    13   0
  RAPGEF6 WILD-TYPE 270  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RAPGEF6 MUTATED     13    0
  RAPGEF6 WILD-TYPE  270   48
   clus
vv  RAPGEF6 MUTATED RAPGEF6 WILD-TYPE
  0              13               270
  1               0                48
[1] 2 2
[1] FALSE
D1131V7, 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
D1131V8, binary
                   cls
clus                  0   1
  RAPGEF6 MUTATED    13   4
  RAPGEF6 WILD-TYPE 304  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RAPGEF6 MUTATED     13    4
  RAPGEF6 WILD-TYPE  304   44
                               clus
vv                              RAPGEF6 MUTATED RAPGEF6 WILD-TYPE
  COLON ADENOCARCINOMA                       13               304
  COLON MUCINOUS ADENOCARCINOMA               4                44
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  RAPGEF6 MUTATED    12   0   0   2
  RAPGEF6 WILD-TYPE 245   2  22  19
D1131V9, multiclass
    clus
vv   RAPGEF6 MUTATED RAPGEF6 WILD-TYPE
  R0              12               245
  R1               0                 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"
D1131V10, 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
D1131V11, 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(1132) Variable = BAZ2B MUTATION ANALYSIS
D1132V1, survival
                 sevent
clus2               0   1
  BAZ2B MUTATED    12   2
  BAZ2B WILD-TYPE 270  71
  BAZ2B MUTATED BAZ2B WILD-TYPE 
             14             341 
  BAZ2B MUTATED BAZ2B WILD-TYPE 
              2              71 
$`BAZ2B MUTATED`
TCGA-A6-5660 TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3715 TCGA-AA-3950 TCGA-AA-3966 
       29.19         1.02        63.98        19.04        24.00         2.01 
TCGA-AA-A010 TCGA-CA-5255 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5912 TCGA-D5-6922 
       34.98         3.06         0.33         0.10        49.08        10.13 
TCGA-DM-A1HB TCGA-G4-6588 
      135.65        26.17 

$`BAZ2B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       33.01        26.01         2.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19         1.94         2.24         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07         0.26         1.35        17.56       102.44        40.34 
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         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 
       12.49        16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        91.79        46.75        52.80 

  BAZ2B MUTATED BAZ2B WILD-TYPE 
            0.1             0.0 
  BAZ2B MUTATED BAZ2B WILD-TYPE 
         135.65          140.38 
  BAZ2B MUTATED BAZ2B WILD-TYPE 
          21.52           20.19 
[1] "0.1 - 135.7 (21.5)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.5"
D1132V2, 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       22       103         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        19          9         40         30       35        13
                 vv
clus              STAGE IVB
  BAZ2B MUTATED           0
  BAZ2B WILD-TYPE         1
D1132V3, multiclass
            clus
vv           BAZ2B MUTATED BAZ2B WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              6             103
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             1              40
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  BAZ2B MUTATED     0   1  12   2
  BAZ2B WILD-TYPE   9  67 236  39
D1132V4, multiclass
    clus
vv   BAZ2B MUTATED BAZ2B WILD-TYPE
  T1             0               9
  T2             1              67
  T3            12             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
  BAZ2B MUTATED    12   2   1
  BAZ2B WILD-TYPE 208  78  65
D1132V5, multiclass
    clus
vv   BAZ2B MUTATED BAZ2B WILD-TYPE
  N0            12             208
  N1             2              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"
D1132V6, binary
                 cls
clus                0   1
  BAZ2B MUTATED    13   0
  BAZ2B WILD-TYPE 270  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BAZ2B MUTATED     13    0
  BAZ2B WILD-TYPE  270   48
   clus
vv  BAZ2B MUTATED BAZ2B WILD-TYPE
  0            13             270
  1             0              48
[1] 2 2
[1] FALSE
D1132V7, 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
D1132V8, binary
                 cls
clus                0   1
  BAZ2B MUTATED    12   3
  BAZ2B WILD-TYPE 305  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BAZ2B MUTATED     12    3
  BAZ2B WILD-TYPE  305   45
                               clus
vv                              BAZ2B MUTATED BAZ2B WILD-TYPE
  COLON ADENOCARCINOMA                     12             305
  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 250   2  22  16
D1132V9, multiclass
    clus
vv   BAZ2B MUTATED BAZ2B WILD-TYPE
  R0             7             250
  R1             0               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"
D1132V10, 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
D1132V11, 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(1133) Variable = GLDN MUTATION ANALYSIS
D1133V1, survival
                sevent
clus2              0   1
  GLDN MUTATED     5   1
  GLDN WILD-TYPE 277  72
  GLDN MUTATED GLDN WILD-TYPE 
             6            349 
  GLDN MUTATED GLDN WILD-TYPE 
             1             72 
$`GLDN MUTATED`
TCGA-AA-3977 TCGA-CA-6718 TCGA-D5-6537 TCGA-D5-6927 TCGA-F4-6856 TCGA-G4-6306 
       25.02         0.10         4.80         9.44        19.43        44.68 

$`GLDN WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.33         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85        17.13        12.49        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        35.41       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  GLDN MUTATED GLDN WILD-TYPE 
           0.1            0.0 
  GLDN MUTATED GLDN WILD-TYPE 
         44.68         140.38 
  GLDN MUTATED GLDN WILD-TYPE 
        14.435         20.280 
[1] "0.1 - 44.7 (14.4)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.2"
D1133V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GLDN MUTATED         1        0        0         4         0         0
  GLDN WILD-TYPE      63        1       25       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        19         10         40         31       35        13
                vv
clus             STAGE IVB
  GLDN MUTATED           0
  GLDN WILD-TYPE         1
D1133V3, multiclass
            clus
vv           GLDN MUTATED GLDN WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             4            105
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GLDN MUTATED     0   3   4   0
  GLDN WILD-TYPE   9  65 244  41
D1133V4, multiclass
    clus
vv   GLDN MUTATED GLDN WILD-TYPE
  T1            0              9
  T2            3             65
  T3            4            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
  GLDN MUTATED     6   1   0
  GLDN WILD-TYPE 214  79  66
D1133V5, multiclass
    clus
vv   GLDN MUTATED GLDN WILD-TYPE
  N0            6            214
  N1            1             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"
D1133V6, binary
                cls
clus               0   1
  GLDN MUTATED     5   0
  GLDN WILD-TYPE 278  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLDN MUTATED      5    0
  GLDN WILD-TYPE  278   48
   clus
vv  GLDN MUTATED GLDN WILD-TYPE
  0            5            278
  1            0             48
[1] 2 2
[1] FALSE
D1133V7, 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
D1133V8, binary
                cls
clus               0   1
  GLDN MUTATED     6   1
  GLDN WILD-TYPE 311  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLDN MUTATED      6    1
  GLDN WILD-TYPE  311   47
                               clus
vv                              GLDN MUTATED GLDN WILD-TYPE
  COLON ADENOCARCINOMA                     6            311
  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 252   2  22  20
D1133V9, multiclass
    clus
vv   GLDN MUTATED GLDN WILD-TYPE
  R0            5            252
  R1            0              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"
D1133V10, 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
D1133V11, 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(1134) Variable = RNF215 MUTATION ANALYSIS
D1134V1, survival
                  sevent
clus2                0   1
  RNF215 MUTATED     3   0
  RNF215 WILD-TYPE 279  73
  RNF215 MUTATED RNF215 WILD-TYPE 
               3              352 
  RNF215 MUTATED RNF215 WILD-TYPE 
               0               73 
$`RNF215 MUTATED`
TCGA-CA-5796 TCGA-CM-6163 TCGA-G4-6586 
        3.25        14.04        35.80 

$`RNF215 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02        12.00        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  RNF215 MUTATED RNF215 WILD-TYPE 
            3.25             0.00 
  RNF215 MUTATED RNF215 WILD-TYPE 
           35.80           140.38 
  RNF215 MUTATED RNF215 WILD-TYPE 
          14.040           20.235 
[1] "3.2 - 35.8 (14.0)"  "0.0 - 140.4 (20.2)"
[1] "hr="     "3300000"
D1134V2, 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       25       107         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RNF215 MUTATED           0          0          0          0        0
  RNF215 WILD-TYPE        19         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  RNF215 MUTATED           0         0
  RNF215 WILD-TYPE        13         1
D1134V3, multiclass
            clus
vv           RNF215 MUTATED RNF215 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               2              107
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  RNF215 MUTATED     1   0   2   0
  RNF215 WILD-TYPE   8  68 246  41
D1134V4, multiclass
    clus
vv   RNF215 MUTATED RNF215 WILD-TYPE
  T1              1                8
  T2              0               68
  T3              2              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
  RNF215 MUTATED     3   0   0
  RNF215 WILD-TYPE 217  80  66
D1134V5, multiclass
    clus
vv   RNF215 MUTATED RNF215 WILD-TYPE
  N0              3              217
  N1              0               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"
D1134V6, binary
                  cls
clus                 0   1
  RNF215 MUTATED     3   0
  RNF215 WILD-TYPE 280  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF215 MUTATED      3    0
  RNF215 WILD-TYPE  280   48
   clus
vv  RNF215 MUTATED RNF215 WILD-TYPE
  0              3              280
  1              0               48
[1] 2 2
[1] FALSE
D1134V7, 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
D1134V8, binary
                  cls
clus                 0   1
  RNF215 MUTATED     2   1
  RNF215 WILD-TYPE 315  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF215 MUTATED      2    1
  RNF215 WILD-TYPE  315   47
                               clus
vv                              RNF215 MUTATED RNF215 WILD-TYPE
  COLON ADENOCARCINOMA                       2              315
  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 254   2  22  21
D1134V9, multiclass
    clus
vv   RNF215 MUTATED RNF215 WILD-TYPE
  R0              3              254
  R1              0                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"
D1134V10, continuous
[1] "Remove cluster labels:" "RNF215 MUTATED"        
clus
  RNF215 MUTATED RNF215 WILD-TYPE 
               2              343 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-4105 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-A6-5661       TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5665 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-A6-5666       TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-A6-6142       TCGA-A6-6648       TCGA-A6-6649       TCGA-A6-6651 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-A6-6652       TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-A6-6781       TCGA-A6-6782       TCGA-AA-3489       TCGA-AA-3492 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3496       TCGA-AA-3502       TCGA-AA-3510       TCGA-AA-3511 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3514       TCGA-AA-3516       TCGA-AA-3517       TCGA-AA-3518 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3519       TCGA-AA-3520       TCGA-AA-3521       TCGA-AA-3522 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3524       TCGA-AA-3525       TCGA-AA-3526       TCGA-AA-3527 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3529       TCGA-AA-3530       TCGA-AA-3531       TCGA-AA-3532 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3534       TCGA-AA-3538       TCGA-AA-3542       TCGA-AA-3543 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3544       TCGA-AA-3548       TCGA-AA-3549       TCGA-AA-3552 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3553       TCGA-AA-3554       TCGA-AA-3555       TCGA-AA-3556 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3558       TCGA-AA-3560       TCGA-AA-3562       TCGA-AA-3655 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3660       TCGA-AA-3662       TCGA-AA-3663       TCGA-AA-3664 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3666       TCGA-AA-3667       TCGA-AA-3672       TCGA-AA-3673 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3678       TCGA-AA-3679       TCGA-AA-3680       TCGA-AA-3681 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3684       TCGA-AA-3685       TCGA-AA-3688       TCGA-AA-3692 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3693       TCGA-AA-3695       TCGA-AA-3696       TCGA-AA-3697 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3710       TCGA-AA-3712       TCGA-AA-3713       TCGA-AA-3715 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3811       TCGA-AA-3812       TCGA-AA-3814       TCGA-AA-3815 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3818       TCGA-AA-3819       TCGA-AA-3821       TCGA-AA-3831 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3833       TCGA-AA-3837       TCGA-AA-3842       TCGA-AA-3844 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3845       TCGA-AA-3846       TCGA-AA-3848       TCGA-AA-3850 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3851       TCGA-AA-3852       TCGA-AA-3854       TCGA-AA-3855 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3856       TCGA-AA-3858       TCGA-AA-3860       TCGA-AA-3861 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3864       TCGA-AA-3866       TCGA-AA-3867       TCGA-AA-3869 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3870       TCGA-AA-3872       TCGA-AA-3875       TCGA-AA-3877 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3930       TCGA-AA-3939       TCGA-AA-3941       TCGA-AA-3947 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3949       TCGA-AA-3950       TCGA-AA-3952       TCGA-AA-3955 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3956       TCGA-AA-3966       TCGA-AA-3968       TCGA-AA-3971 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3972       TCGA-AA-3973       TCGA-AA-3975       TCGA-AA-3976 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3977       TCGA-AA-3979       TCGA-AA-3980       TCGA-AA-3982 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3984       TCGA-AA-3986       TCGA-AA-3989       TCGA-AA-3994 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-A004       TCGA-AA-A00A       TCGA-AA-A00D       TCGA-AA-A00E 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-A00F       TCGA-AA-A00J       TCGA-AA-A00K       TCGA-AA-A00L 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-A00N       TCGA-AA-A00O       TCGA-AA-A00Q       TCGA-AA-A00R 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-A00U       TCGA-AA-A00W       TCGA-AA-A00Z       TCGA-AA-A010 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-A017       TCGA-AA-A01D       TCGA-AA-A01F       TCGA-AA-A01G 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-A01I       TCGA-AA-A01K       TCGA-AA-A01P       TCGA-AA-A01Q 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-A01R       TCGA-AA-A01S       TCGA-AA-A01T       TCGA-AA-A01V 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-A01X       TCGA-AA-A01Z       TCGA-AA-A022       TCGA-AA-A024 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-A029       TCGA-AA-A02F       TCGA-AA-A02H       TCGA-AA-A02J 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-A02K       TCGA-AA-A02O       TCGA-AA-A02W       TCGA-AA-A02Y 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-A03F       TCGA-AA-A03J       TCGA-AD-5900       TCGA-AD-6548 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AD-6888       TCGA-AD-6889       TCGA-AD-6890       TCGA-AD-6895 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AD-6899       TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6964 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AD-6965       TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AY-4071       TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AY-6386       TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4682 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AZ-5403       TCGA-AZ-5407       TCGA-AZ-6598       TCGA-AZ-6599 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AZ-6600       TCGA-AZ-6601       TCGA-AZ-6603       TCGA-AZ-6605 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AZ-6606       TCGA-AZ-6607       TCGA-AZ-6608       TCGA-CK-4947 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-CK-4948       TCGA-CK-4950       TCGA-CK-4952       TCGA-CM-4743 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-CM-4744       TCGA-CM-4746       TCGA-CM-4747       TCGA-CM-4752 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-CM-5341       TCGA-CM-5344       TCGA-CM-5348       TCGA-CM-5349 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-CM-5860       TCGA-CM-5861       TCGA-CM-5862       TCGA-CM-5863 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-CM-5864       TCGA-CM-5868       TCGA-CM-6161       TCGA-CM-6162 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-CM-6164       TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-CM-6168       TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-CM-6172       TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-CM-6677       TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-D5-5537       TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-D5-5541       TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-D5-6534       TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-D5-6538       TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-D5-6898       TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-D5-6924       TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-D5-6929       TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-D5-7000       TCGA-DM-A0X9       TCGA-DM-A0XD       TCGA-DM-A0XF 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-DM-A1D0       TCGA-DM-A1D4       TCGA-DM-A1D6       TCGA-DM-A1D7 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-DM-A1D8       TCGA-DM-A1D9       TCGA-DM-A1DA       TCGA-DM-A1DB 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-DM-A1HA       TCGA-DM-A1HB       TCGA-DM-A282       TCGA-DM-A285 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-DM-A28C       TCGA-DM-A28E       TCGA-DM-A28F       TCGA-DM-A28G 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-DM-A28H       TCGA-DM-A28K       TCGA-F4-6459       TCGA-F4-6460 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-F4-6569       TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808       TCGA-F4-6809 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856       TCGA-G4-6293 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304       TCGA-G4-6306 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310       TCGA-G4-6315 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323       TCGA-G4-6588 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628 
"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
D1134V11, 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(1135) Variable = TYW3 MUTATION ANALYSIS
D1135V1, survival
                sevent
clus2              0   1
  TYW3 MUTATED     3   2
  TYW3 WILD-TYPE 279  71
  TYW3 MUTATED TYW3 WILD-TYPE 
             5            350 
  TYW3 MUTATED TYW3 WILD-TYPE 
             2             71 
$`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        16.31 

$`TYW3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 
       20.19        18.25         1.32        43.27        15.12         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       35.87         1.55        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  TYW3 MUTATED TYW3 WILD-TYPE 
         10.88           0.00 
  TYW3 MUTATED TYW3 WILD-TYPE 
         17.85         140.38 
  TYW3 MUTATED TYW3 WILD-TYPE 
         15.02          20.98 
[1] "10.9 - 17.9 (15.0)" "0.0 - 140.4 (21.0)"
[1] "hr=" "3.1"
D1135V2, 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       25       107         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        18         10         41         31       34        13
                vv
clus             STAGE IVB
  TYW3 MUTATED           0
  TYW3 WILD-TYPE         1
D1135V3, multiclass
            clus
vv           TYW3 MUTATED TYW3 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             2            107
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TYW3 MUTATED     0   1   3   2
  TYW3 WILD-TYPE   9  67 245  39
D1135V4, multiclass
    clus
vv   TYW3 MUTATED TYW3 WILD-TYPE
  T1            0              9
  T2            1             67
  T3            3            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
  TYW3 MUTATED     3   1   2
  TYW3 WILD-TYPE 217  79  64
D1135V5, multiclass
    clus
vv   TYW3 MUTATED TYW3 WILD-TYPE
  N0            3            217
  N1            1             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"
D1135V6, binary
                cls
clus               0   1
  TYW3 MUTATED     4   1
  TYW3 WILD-TYPE 279  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  TYW3 MUTATED      4    1
  TYW3 WILD-TYPE  279   47
   clus
vv  TYW3 MUTATED TYW3 WILD-TYPE
  0            4            279
  1            1             47
[1] 2 2
[1] FALSE
D1135V7, 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
D1135V8, binary
                cls
clus               0   1
  TYW3 MUTATED     6   0
  TYW3 WILD-TYPE 311  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  TYW3 MUTATED      6    0
  TYW3 WILD-TYPE  311   48
                               clus
vv                              TYW3 MUTATED TYW3 WILD-TYPE
  COLON ADENOCARCINOMA                     6            311
  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 253   2  22  21
D1135V9, multiclass
    clus
vv   TYW3 MUTATED TYW3 WILD-TYPE
  R0            4            253
  R1            0              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"
D1135V10, 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
D1135V11, 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(1136) Variable = HLA-B MUTATION ANALYSIS
D1136V1, survival
                 sevent
clus2               0   1
  HLA-B MUTATED    10   0
  HLA-B WILD-TYPE 272  73
  HLA-B MUTATED HLA-B WILD-TYPE 
             10             345 
  HLA-B MUTATED HLA-B WILD-TYPE 
              0              73 
$`HLA-B MUTATED`
TCGA-A6-5665 TCGA-AA-3555 TCGA-AD-5900 TCGA-CK-4950 TCGA-CK-6751 TCGA-D5-6920 
       22.06        29.95         0.07        40.34       124.27        12.39 
TCGA-D5-6930 TCGA-D5-6931 TCGA-G4-6304 TCGA-G4-6588 
        1.51        12.00        53.62        26.17 

$`HLA-B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        17.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 
       12.49        16.14        15.58         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-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      107.67        74.56        65.85        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  HLA-B MUTATED HLA-B WILD-TYPE 
           0.07            0.00 
  HLA-B MUTATED HLA-B WILD-TYPE 
         124.27          140.38 
  HLA-B MUTATED HLA-B WILD-TYPE 
         24.115          20.120 
[1] "0.1 - 124.3 (24.1)" "0.0 - 140.4 (20.1)"
[1] "hr="     "2.6e+07"
D1136V2, 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       25       104         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HLA-B MUTATED           0          1          0          1        0         0
  HLA-B WILD-TYPE        19          9         41         30       35        13
                 vv
clus              STAGE IVB
  HLA-B MUTATED           0
  HLA-B WILD-TYPE         1
D1136V3, multiclass
            clus
vv           HLA-B MUTATED HLA-B WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              5             104
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HLA-B MUTATED     0   2   6   3
  HLA-B WILD-TYPE   9  66 242  38
D1136V4, multiclass
    clus
vv   HLA-B MUTATED HLA-B WILD-TYPE
  T1             0               9
  T2             2              66
  T3             6             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
  HLA-B MUTATED     9   1   1
  HLA-B WILD-TYPE 211  79  65
D1136V5, multiclass
    clus
vv   HLA-B MUTATED HLA-B WILD-TYPE
  N0             9             211
  N1             1              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"
D1136V6, binary
                 cls
clus                0   1
  HLA-B MUTATED     8   0
  HLA-B WILD-TYPE 275  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      8    0
  HLA-B WILD-TYPE  275   48
   clus
vv  HLA-B MUTATED HLA-B WILD-TYPE
  0             8             275
  1             0              48
[1] 2 2
[1] FALSE
D1136V7, 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
D1136V8, binary
                 cls
clus                0   1
  HLA-B MUTATED     7   4
  HLA-B WILD-TYPE 310  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      7    4
  HLA-B WILD-TYPE  310   44
                               clus
vv                              HLA-B MUTATED HLA-B WILD-TYPE
  COLON ADENOCARCINOMA                      7             310
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  HLA-B MUTATED     8   1   0   2
  HLA-B WILD-TYPE 249   1  22  19
D1136V9, multiclass
    clus
vv   HLA-B MUTATED HLA-B WILD-TYPE
  R0             8             249
  R1             1               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"
D1136V10, 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
D1136V11, 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(1137) Variable = LRRN1 MUTATION ANALYSIS
D1137V1, survival
                 sevent
clus2               0   1
  LRRN1 MUTATED    11   5
  LRRN1 WILD-TYPE 271  68
  LRRN1 MUTATED LRRN1 WILD-TYPE 
             16             339 
  LRRN1 MUTATED LRRN1 WILD-TYPE 
              5              68 
$`LRRN1 MUTATED`
TCGA-A6-6141 TCGA-A6-6653 TCGA-AA-3516 TCGA-AA-3526 TCGA-AA-3713 TCGA-AA-3715 
        8.38        24.39        13.02        19.07        19.04        19.04 
TCGA-AA-A01Q TCGA-AD-5900 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4952 
        1.02         0.07       100.01         0.33         0.10        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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3529 TCGA-AA-3530 
       24.03        37.05        36.03         8.05         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       26.99        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 
        0.26         1.35        17.56       102.44        40.34        49.08 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99         2.93         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        16.01         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  LRRN1 MUTATED LRRN1 WILD-TYPE 
           0.07            0.00 
  LRRN1 MUTATED LRRN1 WILD-TYPE 
         100.01          140.38 
  LRRN1 MUTATED LRRN1 WILD-TYPE 
          15.32           21.01 
[1] "0.1 - 100.0 (15.3)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.9"
D1137V2, 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       22       103         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LRRN1 MUTATED           2          0          0          0        1         0
  LRRN1 WILD-TYPE        17         10         41         31       34        13
                 vv
clus              STAGE IVB
  LRRN1 MUTATED           0
  LRRN1 WILD-TYPE         1
D1137V3, multiclass
            clus
vv           LRRN1 MUTATED LRRN1 WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              6             103
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LRRN1 MUTATED     1   3  11   2
  LRRN1 WILD-TYPE   8  65 237  39
D1137V4, multiclass
    clus
vv   LRRN1 MUTATED LRRN1 WILD-TYPE
  T1             1               8
  T2             3              65
  T3            11             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
  LRRN1 MUTATED    15   0   2
  LRRN1 WILD-TYPE 205  80  64
D1137V5, multiclass
    clus
vv   LRRN1 MUTATED LRRN1 WILD-TYPE
  N0            15             205
  N1             0              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"
D1137V6, binary
                 cls
clus                0   1
  LRRN1 MUTATED    13   1
  LRRN1 WILD-TYPE 270  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRRN1 MUTATED     13    1
  LRRN1 WILD-TYPE  270   47
   clus
vv  LRRN1 MUTATED LRRN1 WILD-TYPE
  0            13             270
  1             1              47
[1] 2 2
[1] FALSE
D1137V7, 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
D1137V8, binary
                 cls
clus                0   1
  LRRN1 MUTATED    13   4
  LRRN1 WILD-TYPE 304  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRRN1 MUTATED     13    4
  LRRN1 WILD-TYPE  304   44
                               clus
vv                              LRRN1 MUTATED LRRN1 WILD-TYPE
  COLON ADENOCARCINOMA                     13             304
  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 251   2  21  15
D1137V9, multiclass
    clus
vv   LRRN1 MUTATED LRRN1 WILD-TYPE
  R0             6             251
  R1             0               2
  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"
D1137V10, 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
D1137V11, 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(1138) Variable = VASH1 MUTATION ANALYSIS
D1138V1, survival
                 sevent
clus2               0   1
  VASH1 MUTATED     4   0
  VASH1 WILD-TYPE 278  73
  VASH1 MUTATED VASH1 WILD-TYPE 
              4             351 
  VASH1 MUTATED VASH1 WILD-TYPE 
              0              73 
$`VASH1 MUTATED`
TCGA-A6-5665 TCGA-CM-5861 TCGA-D5-6540 TCGA-DM-A1HB 
       22.06        15.02        16.14       135.65 

$`VASH1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  VASH1 MUTATED VASH1 WILD-TYPE 
          15.02            0.00 
  VASH1 MUTATED VASH1 WILD-TYPE 
         135.65          140.38 
  VASH1 MUTATED VASH1 WILD-TYPE 
          19.10           20.19 
[1] "15.0 - 135.7 (19.1)" "0.0 - 140.4 (20.2)" 
[1] "hr="     "9300000"
D1138V2, 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       25       107         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        19         10         40         31       35        13
                 vv
clus              STAGE IVB
  VASH1 MUTATED           0
  VASH1 WILD-TYPE         1
D1138V3, multiclass
            clus
vv           VASH1 MUTATED VASH1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              2             107
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  VASH1 MUTATED     0   1   3   1
  VASH1 WILD-TYPE   9  67 245  40
D1138V4, multiclass
    clus
vv   VASH1 MUTATED VASH1 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             3             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
  VASH1 MUTATED     4   1   0
  VASH1 WILD-TYPE 216  79  66
D1138V5, multiclass
    clus
vv   VASH1 MUTATED VASH1 WILD-TYPE
  N0             4             216
  N1             1              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"
D1138V6, binary
                 cls
clus                0   1
  VASH1 MUTATED     4   0
  VASH1 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VASH1 MUTATED      4    0
  VASH1 WILD-TYPE  279   48
   clus
vv  VASH1 MUTATED VASH1 WILD-TYPE
  0             4             279
  1             0              48
[1] 2 2
[1] FALSE
D1138V7, 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
D1138V8, binary
                 cls
clus                0   1
  VASH1 MUTATED     4   1
  VASH1 WILD-TYPE 313  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VASH1 MUTATED      4    1
  VASH1 WILD-TYPE  313   47
                               clus
vv                              VASH1 MUTATED VASH1 WILD-TYPE
  COLON ADENOCARCINOMA                      4             313
  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 254   2  22  20
D1138V9, multiclass
    clus
vv   VASH1 MUTATED VASH1 WILD-TYPE
  R0             3             254
  R1             0               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"
D1138V10, 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
D1138V11, 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(1139) Variable = PIGC MUTATION ANALYSIS
D1139V1, survival
                sevent
clus2              0   1
  PIGC MUTATED     2   1
  PIGC WILD-TYPE 280  72
  PIGC MUTATED PIGC WILD-TYPE 
             3            352 
  PIGC MUTATED PIGC WILD-TYPE 
             1             72 
$`PIGC MUTATED`
TCGA-AZ-6599 TCGA-CM-5349 TCGA-CM-6161 
        6.77        30.08        15.02 

$`PIGC WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41        49.41        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  PIGC MUTATED PIGC WILD-TYPE 
          6.77           0.00 
  PIGC MUTATED PIGC WILD-TYPE 
         30.08         140.38 
  PIGC MUTATED PIGC WILD-TYPE 
        15.020         20.235 
[1] "6.8 - 30.1 (15.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2.3"
D1139V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PIGC MUTATED         2        0        0         1         0         0
  PIGC WILD-TYPE      62        1       25       108         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        19         10         41         31       35        13
                vv
clus             STAGE IVB
  PIGC MUTATED           0
  PIGC WILD-TYPE         1
D1139V3, multiclass
            clus
vv           PIGC MUTATED PIGC WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             1            108
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PIGC MUTATED     0   2   1   0
  PIGC WILD-TYPE   9  66 247  41
D1139V4, multiclass
    clus
vv   PIGC MUTATED PIGC WILD-TYPE
  T1            0              9
  T2            2             66
  T3            1            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     3   0   0
  PIGC WILD-TYPE 217  80  66
D1139V5, multiclass
    clus
vv   PIGC MUTATED PIGC WILD-TYPE
  N0            3            217
  N1            0             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"
D1139V6, binary
                cls
clus               0   1
  PIGC MUTATED     2   0
  PIGC WILD-TYPE 281  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGC MUTATED      2    0
  PIGC WILD-TYPE  281   48
   clus
vv  PIGC MUTATED PIGC WILD-TYPE
  0            2            281
  1            0             48
[1] 2 2
[1] FALSE
D1139V7, binary
                cls
clus               0   1
  PIGC MUTATED     2   1
  PIGC WILD-TYPE 168 196
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGC MUTATED      2    1
  PIGC WILD-TYPE  168  196
        clus
vv       PIGC MUTATED PIGC WILD-TYPE
  FEMALE            2            168
  MALE              1            196
[1] 2 2
[1] FALSE
D1139V8, binary
                cls
clus               0   1
  PIGC MUTATED     3   0
  PIGC WILD-TYPE 314  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGC MUTATED      3    0
  PIGC WILD-TYPE  314   48
                               clus
vv                              PIGC MUTATED PIGC WILD-TYPE
  COLON ADENOCARCINOMA                     3            314
  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 255   2  22  21
D1139V9, multiclass
[1] "Remove cluster labels:" "PIGC MUTATED"          
clus
  PIGC MUTATED PIGC WILD-TYPE 
             2            300 
    TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810     TCGA-A6-5657 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-A6-5659     TCGA-A6-5661     TCGA-A6-5665     TCGA-A6-6781 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3489     TCGA-AA-3492     TCGA-AA-3496     TCGA-AA-3502 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3510     TCGA-AA-3511     TCGA-AA-3514     TCGA-AA-3517 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3518     TCGA-AA-3519     TCGA-AA-3520     TCGA-AA-3521 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3522     TCGA-AA-3524     TCGA-AA-3525     TCGA-AA-3526 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3527     TCGA-AA-3529     TCGA-AA-3530     TCGA-AA-3531 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3532     TCGA-AA-3534     TCGA-AA-3538     TCGA-AA-3542 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3543     TCGA-AA-3544     TCGA-AA-3548     TCGA-AA-3549 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3552     TCGA-AA-3553     TCGA-AA-3554     TCGA-AA-3555 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3556     TCGA-AA-3558     TCGA-AA-3560     TCGA-AA-3561 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3562     TCGA-AA-3655     TCGA-AA-3660     TCGA-AA-3662 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3663     TCGA-AA-3664     TCGA-AA-3666     TCGA-AA-3667 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3672     TCGA-AA-3673     TCGA-AA-3678     TCGA-AA-3679 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3680     TCGA-AA-3681     TCGA-AA-3684     TCGA-AA-3685 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3688     TCGA-AA-3692     TCGA-AA-3693     TCGA-AA-3695 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3696     TCGA-AA-3697     TCGA-AA-3710     TCGA-AA-3712 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3713     TCGA-AA-3715     TCGA-AA-3811     TCGA-AA-3812 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3814     TCGA-AA-3815     TCGA-AA-3818     TCGA-AA-3819 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3821     TCGA-AA-3831     TCGA-AA-3833     TCGA-AA-3837 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3842     TCGA-AA-3844     TCGA-AA-3845     TCGA-AA-3846 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3848     TCGA-AA-3850     TCGA-AA-3851     TCGA-AA-3852 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3854     TCGA-AA-3855     TCGA-AA-3856     TCGA-AA-3858 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3860     TCGA-AA-3861     TCGA-AA-3864     TCGA-AA-3866 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3867     TCGA-AA-3869     TCGA-AA-3870     TCGA-AA-3872 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3875     TCGA-AA-3877     TCGA-AA-3930     TCGA-AA-3939 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3941     TCGA-AA-3947     TCGA-AA-3949     TCGA-AA-3950 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3952     TCGA-AA-3955     TCGA-AA-3956     TCGA-AA-3968 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3971     TCGA-AA-3972     TCGA-AA-3973     TCGA-AA-3975 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3976     TCGA-AA-3979     TCGA-AA-3984     TCGA-AA-3986 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3989     TCGA-AA-3994     TCGA-AA-A004     TCGA-AA-A00A 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-A00D     TCGA-AA-A00E     TCGA-AA-A00F     TCGA-AA-A00J 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-A00K     TCGA-AA-A00L     TCGA-AA-A00N     TCGA-AA-A00O 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-A00Q     TCGA-AA-A00R     TCGA-AA-A00U     TCGA-AA-A00W 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-A00Z     TCGA-AA-A010     TCGA-AA-A017     TCGA-AA-A01D 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-A01F     TCGA-AA-A01G     TCGA-AA-A01I     TCGA-AA-A01K 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-A01P     TCGA-AA-A01Q     TCGA-AA-A01R     TCGA-AA-A01S 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-A01T     TCGA-AA-A01V     TCGA-AA-A01X     TCGA-AA-A01Z 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-A022     TCGA-AA-A024     TCGA-AA-A029     TCGA-AA-A02F 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-A02H     TCGA-AA-A02J     TCGA-AA-A02K     TCGA-AA-A02O 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-A02W     TCGA-AA-A02Y     TCGA-AA-A03F     TCGA-AA-A03J 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AD-5900     TCGA-AD-6548     TCGA-AD-6888     TCGA-AU-3779 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AU-6004     TCGA-AY-4070     TCGA-AY-4071     TCGA-AY-5543 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AY-6196     TCGA-AY-6197     TCGA-AY-6386     TCGA-AZ-4315 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AZ-4681     TCGA-AZ-4682     TCGA-CA-5254     TCGA-CA-5255 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-CA-5796     TCGA-CA-5797     TCGA-CA-6715     TCGA-CA-6716 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-CA-6717     TCGA-CA-6718     TCGA-CA-6719     TCGA-CK-4947 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-CK-4948     TCGA-CK-4950     TCGA-CK-4952     TCGA-CK-5912 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-CK-5913     TCGA-CK-5914     TCGA-CK-5915     TCGA-CK-5916 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-CK-6746     TCGA-CK-6747     TCGA-CK-6748     TCGA-CK-6751 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-CM-4743     TCGA-CM-4744     TCGA-CM-4746     TCGA-CM-4747 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-CM-4752     TCGA-CM-5341     TCGA-CM-5344     TCGA-CM-5348 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-CM-5860     TCGA-CM-5861     TCGA-CM-5862     TCGA-CM-5863 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-CM-5864     TCGA-CM-5868     TCGA-CM-6162     TCGA-CM-6163 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-CM-6164     TCGA-CM-6165     TCGA-CM-6166     TCGA-CM-6167 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-CM-6168     TCGA-CM-6169     TCGA-CM-6170     TCGA-CM-6171 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-CM-6172     TCGA-CM-6674     TCGA-CM-6675     TCGA-CM-6676 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-CM-6677     TCGA-CM-6678     TCGA-CM-6679     TCGA-CM-6680 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-D5-5537     TCGA-D5-5538     TCGA-D5-5539     TCGA-D5-5540 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-D5-5541     TCGA-D5-6529     TCGA-D5-6532     TCGA-D5-6533 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-D5-6534     TCGA-D5-6535     TCGA-D5-6536     TCGA-D5-6537 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-D5-6538     TCGA-D5-6539     TCGA-D5-6540     TCGA-D5-6541 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-D5-6898     TCGA-D5-6920     TCGA-D5-6922     TCGA-D5-6923 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-D5-6924     TCGA-D5-6926     TCGA-D5-6927     TCGA-D5-6928 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-D5-6929     TCGA-D5-6930     TCGA-D5-6931     TCGA-D5-6932 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-D5-7000     TCGA-F4-6459     TCGA-F4-6460     TCGA-F4-6569 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-F4-6570     TCGA-F4-6703     TCGA-F4-6704     TCGA-F4-6805 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-F4-6806     TCGA-F4-6807     TCGA-F4-6808     TCGA-F4-6809 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-F4-6854     TCGA-F4-6855     TCGA-F4-6856     TCGA-G4-6293 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-G4-6299     TCGA-G4-6303     TCGA-G4-6304     TCGA-G4-6306 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-G4-6307     TCGA-G4-6309     TCGA-G4-6310     TCGA-G4-6315 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-G4-6317     TCGA-G4-6321     TCGA-G4-6323     TCGA-G4-6586 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-G4-6588     TCGA-G4-6625     TCGA-G4-6626     TCGA-G4-6628 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
D1139V10, 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     3
  PIGC WILD-TYPE                        19   173
D1139V11, 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                                       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(1140) Variable = VPS33A MUTATION ANALYSIS
D1140V1, survival
                  sevent
clus2                0   1
  VPS33A MUTATED     6   1
  VPS33A WILD-TYPE 276  72
  VPS33A MUTATED VPS33A WILD-TYPE 
               7              348 
  VPS33A MUTATED VPS33A WILD-TYPE 
               1               72 
$`VPS33A MUTATED`
TCGA-AA-3525 TCGA-AA-3833 TCGA-AA-3845 TCGA-AA-3950 TCGA-AD-5900 TCGA-AD-6895 
        8.05        15.95         0.00        24.00         0.07         0.72 
TCGA-G4-6588 
       26.17 

$`VPS33A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       17.98        38.99        37.02        14.93        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
       40.96        21.37         4.21        56.55         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        52.80 

  VPS33A MUTATED VPS33A WILD-TYPE 
               0                0 
  VPS33A MUTATED VPS33A WILD-TYPE 
           26.17           140.38 
  VPS33A MUTATED VPS33A WILD-TYPE 
            8.05            20.63 
[1] "0.0 - 26.2 (8.1)"   "0.0 - 140.4 (20.6)"
[1] "hr=" "1.6"
D1140V2, 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       25       105         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  VPS33A MUTATED           0          0          1          0        0
  VPS33A WILD-TYPE        19         10         40         31       35
                  vv
clus               STAGE IVA STAGE IVB
  VPS33A MUTATED           0         0
  VPS33A WILD-TYPE        13         1
D1140V3, multiclass
            clus
vv           VPS33A MUTATED VPS33A WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               4              105
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  VPS33A MUTATED     0   1   6   1
  VPS33A WILD-TYPE   9  67 242  40
D1140V4, multiclass
    clus
vv   VPS33A MUTATED VPS33A WILD-TYPE
  T1              0                9
  T2              1               67
  T3              6              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
  VPS33A MUTATED     6   2   0
  VPS33A WILD-TYPE 214  78  66
D1140V5, multiclass
    clus
vv   VPS33A MUTATED VPS33A WILD-TYPE
  N0              6              214
  N1              2               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"
D1140V6, binary
                  cls
clus                 0   1
  VPS33A MUTATED     5   0
  VPS33A WILD-TYPE 278  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VPS33A MUTATED      5    0
  VPS33A WILD-TYPE  278   48
   clus
vv  VPS33A MUTATED VPS33A WILD-TYPE
  0              5              278
  1              0               48
[1] 2 2
[1] FALSE
D1140V7, 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
D1140V8, binary
                  cls
clus                 0   1
  VPS33A MUTATED     6   2
  VPS33A WILD-TYPE 311  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VPS33A MUTATED      6    2
  VPS33A WILD-TYPE  311   46
                               clus
vv                              VPS33A MUTATED VPS33A WILD-TYPE
  COLON ADENOCARCINOMA                       6              311
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  VPS33A MUTATED     6   0   0   1
  VPS33A WILD-TYPE 251   2  22  20
D1140V9, multiclass
    clus
vv   VPS33A MUTATED VPS33A WILD-TYPE
  R0              6              251
  R1              0                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"
D1140V10, 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
D1140V11, 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(1141) Variable = UPF2 MUTATION ANALYSIS
D1141V1, survival
                sevent
clus2              0   1
  UPF2 MUTATED    10   5
  UPF2 WILD-TYPE 272  68
  UPF2 MUTATED UPF2 WILD-TYPE 
            15            340 
  UPF2 MUTATED UPF2 WILD-TYPE 
             5             68 
$`UPF2 MUTATED`
TCGA-A6-2676 TCGA-A6-5661 TCGA-A6-5665 TCGA-AA-3525 TCGA-AA-3662 TCGA-AA-3713 
       42.90        33.53        22.06         8.05         6.05        19.04 
TCGA-AA-3818 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A02Y TCGA-AZ-4315 TCGA-AZ-6601 
        0.99        25.02         4.01        39.98        58.39       100.01 
TCGA-CA-6717 TCGA-CK-5916 TCGA-CM-6162 
        0.33        21.14        12.00 

$`UPF2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       31.63        30.44        29.19        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       24.03        37.05        36.03        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3819 TCGA-AA-3821 
       19.04        10.06        35.05        33.04        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A03F 
        2.01         5.03        14.01         0.92        41.00        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        61.41        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99         2.93         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        16.01        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  UPF2 MUTATED UPF2 WILD-TYPE 
          0.33           0.00 
  UPF2 MUTATED UPF2 WILD-TYPE 
        100.01         140.38 
  UPF2 MUTATED UPF2 WILD-TYPE 
        21.140         20.155 
[1] "0.3 - 100.0 (21.1)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.6"
D1141V2, 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       24       104         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        19         10         39         31       33        13
                vv
clus             STAGE IVB
  UPF2 MUTATED           0
  UPF2 WILD-TYPE         1
D1141V3, multiclass
            clus
vv           UPF2 MUTATED UPF2 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             5            104
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            2             39
  STAGE IIIC            0             31
  STAGE IV              2             33
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  UPF2 MUTATED     1   2   9   4
  UPF2 WILD-TYPE   8  66 239  37
D1141V4, multiclass
    clus
vv   UPF2 MUTATED UPF2 WILD-TYPE
  T1            1              8
  T2            2             66
  T3            9            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
  UPF2 MUTATED    13   2   1
  UPF2 WILD-TYPE 207  78  65
D1141V5, multiclass
    clus
vv   UPF2 MUTATED UPF2 WILD-TYPE
  N0           13            207
  N1            2             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
  UPF2 MUTATED    12   2
  UPF2 WILD-TYPE 271  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  UPF2 MUTATED     12    2
  UPF2 WILD-TYPE  271   46
   clus
vv  UPF2 MUTATED UPF2 WILD-TYPE
  0           12            271
  1            2             46
[1] 2 2
[1] FALSE
D1141V7, 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
D1141V8, binary
                cls
clus               0   1
  UPF2 MUTATED    13   3
  UPF2 WILD-TYPE 304  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  UPF2 MUTATED     13    3
  UPF2 WILD-TYPE  304   45
                               clus
vv                              UPF2 MUTATED UPF2 WILD-TYPE
  COLON ADENOCARCINOMA                    13            304
  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 248   2  20  18
D1141V9, multiclass
    clus
vv   UPF2 MUTATED UPF2 WILD-TYPE
  R0            9            248
  R1            0              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"
D1141V10, 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
D1141V11, 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(1142) Variable = TMEM92 MUTATION ANALYSIS
D1142V1, survival
                  sevent
clus2                0   1
  TMEM92 MUTATED     3   0
  TMEM92 WILD-TYPE 279  73
  TMEM92 MUTATED TMEM92 WILD-TYPE 
               3              352 
  TMEM92 MUTATED TMEM92 WILD-TYPE 
               0               73 
$`TMEM92 MUTATED`
TCGA-AA-3947 TCGA-AD-6889 TCGA-CK-5913 
       33.01        56.55        51.32 

$`TMEM92 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        4.21         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 
      102.44        40.34        15.62        49.08        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  TMEM92 MUTATED TMEM92 WILD-TYPE 
           33.01             0.00 
  TMEM92 MUTATED TMEM92 WILD-TYPE 
           56.55           140.38 
  TMEM92 MUTATED TMEM92 WILD-TYPE 
           51.32            20.07 
[1] "33.0 - 56.5 (51.3)" "0.0 - 140.4 (20.1)"
[1] "hr="     "9300000"
D1142V2, continuous
[1] "Remove cluster labels:" "TMEM92 MUTATED"        
clus
  TMEM92 MUTATED TMEM92 WILD-TYPE 
               2              364 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-4105 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-5661       TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5665 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-5666       TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-6142       TCGA-A6-6648       TCGA-A6-6649       TCGA-A6-6651 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-6652       TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-6781       TCGA-A6-6782       TCGA-AA-3489       TCGA-AA-3492 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3496       TCGA-AA-3502       TCGA-AA-3510       TCGA-AA-3511 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3514       TCGA-AA-3516       TCGA-AA-3517       TCGA-AA-3518 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3519       TCGA-AA-3520       TCGA-AA-3521       TCGA-AA-3522 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3524       TCGA-AA-3525       TCGA-AA-3526       TCGA-AA-3527 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3529       TCGA-AA-3530       TCGA-AA-3531       TCGA-AA-3532 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3534       TCGA-AA-3538       TCGA-AA-3542       TCGA-AA-3543 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3544       TCGA-AA-3548       TCGA-AA-3549       TCGA-AA-3552 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3553       TCGA-AA-3554       TCGA-AA-3555       TCGA-AA-3556 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3558       TCGA-AA-3560       TCGA-AA-3561       TCGA-AA-3562 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3655       TCGA-AA-3660       TCGA-AA-3662       TCGA-AA-3663 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3664       TCGA-AA-3666       TCGA-AA-3667       TCGA-AA-3672 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3673       TCGA-AA-3678       TCGA-AA-3679       TCGA-AA-3680 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3681       TCGA-AA-3684       TCGA-AA-3685       TCGA-AA-3688 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3692       TCGA-AA-3693       TCGA-AA-3695       TCGA-AA-3696 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3697       TCGA-AA-3710       TCGA-AA-3712       TCGA-AA-3713 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3715       TCGA-AA-3811       TCGA-AA-3812       TCGA-AA-3814 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3815       TCGA-AA-3818       TCGA-AA-3819       TCGA-AA-3821 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3831       TCGA-AA-3833       TCGA-AA-3837       TCGA-AA-3842 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3844       TCGA-AA-3845       TCGA-AA-3846       TCGA-AA-3848 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3850       TCGA-AA-3851       TCGA-AA-3852       TCGA-AA-3854 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3855       TCGA-AA-3856       TCGA-AA-3858       TCGA-AA-3860 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3861       TCGA-AA-3864       TCGA-AA-3866       TCGA-AA-3867 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3869       TCGA-AA-3870       TCGA-AA-3872       TCGA-AA-3875 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3877       TCGA-AA-3930       TCGA-AA-3939       TCGA-AA-3941 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3949       TCGA-AA-3950       TCGA-AA-3952       TCGA-AA-3955 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3956       TCGA-AA-3966       TCGA-AA-3968       TCGA-AA-3971 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3972       TCGA-AA-3973       TCGA-AA-3975       TCGA-AA-3976 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3977       TCGA-AA-3979       TCGA-AA-3980       TCGA-AA-3982 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3984       TCGA-AA-3986       TCGA-AA-3989       TCGA-AA-3994 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A004       TCGA-AA-A00A       TCGA-AA-A00D       TCGA-AA-A00E 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A00F       TCGA-AA-A00J       TCGA-AA-A00K       TCGA-AA-A00L 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A00N       TCGA-AA-A00O       TCGA-AA-A00Q       TCGA-AA-A00R 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A00U       TCGA-AA-A00W       TCGA-AA-A00Z       TCGA-AA-A010 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A017       TCGA-AA-A01D       TCGA-AA-A01F       TCGA-AA-A01G 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A01I       TCGA-AA-A01K       TCGA-AA-A01P       TCGA-AA-A01Q 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A01R       TCGA-AA-A01S       TCGA-AA-A01T       TCGA-AA-A01V 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A01X       TCGA-AA-A01Z       TCGA-AA-A022       TCGA-AA-A024 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A029       TCGA-AA-A02F       TCGA-AA-A02H       TCGA-AA-A02J 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A02K       TCGA-AA-A02O       TCGA-AA-A02W       TCGA-AA-A02Y 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A03F       TCGA-AA-A03J       TCGA-AD-5900       TCGA-AD-6548 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AD-6888       TCGA-AD-6890       TCGA-AD-6895       TCGA-AD-6899 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6964       TCGA-AD-6965 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070       TCGA-AY-4071 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AZ-4315       TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4681 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AZ-4682       TCGA-AZ-5403       TCGA-AZ-5407       TCGA-AZ-6598 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AZ-6599       TCGA-AZ-6600       TCGA-AZ-6601       TCGA-AZ-6603 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AZ-6605       TCGA-AZ-6606       TCGA-AZ-6607       TCGA-AZ-6608 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CA-5254       TCGA-CA-5255       TCGA-CA-5796       TCGA-CA-5797 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CA-6715       TCGA-CA-6716       TCGA-CA-6717       TCGA-CA-6718 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CA-6719       TCGA-CK-4947       TCGA-CK-4948       TCGA-CK-4950 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CK-4952       TCGA-CK-5912       TCGA-CK-5914       TCGA-CK-5915 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CK-5916       TCGA-CK-6746       TCGA-CK-6747       TCGA-CK-6748 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CK-6751       TCGA-CM-4743       TCGA-CM-4744       TCGA-CM-4746 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341       TCGA-CM-5344 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860       TCGA-CM-5861 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864       TCGA-CM-5868 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163       TCGA-CM-6164 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167       TCGA-CM-6168 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171       TCGA-CM-6172 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676       TCGA-CM-6677 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680       TCGA-D5-5537 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540       TCGA-D5-5541 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533       TCGA-D5-6534 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537       TCGA-D5-6538 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541       TCGA-D5-6898 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923       TCGA-D5-6924 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928       TCGA-D5-6929 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932       TCGA-D5-7000 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DM-A0X9       TCGA-DM-A0XD       TCGA-DM-A0XF       TCGA-DM-A1D0 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DM-A1D4       TCGA-DM-A1D6       TCGA-DM-A1D7       TCGA-DM-A1D8 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DM-A1D9       TCGA-DM-A1DA       TCGA-DM-A1DB       TCGA-DM-A1HA 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DM-A1HB       TCGA-DM-A282       TCGA-DM-A285       TCGA-DM-A28C 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DM-A28E       TCGA-DM-A28F       TCGA-DM-A28G       TCGA-DM-A28H 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DM-A28K       TCGA-F4-6459       TCGA-F4-6460       TCGA-F4-6569 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704       TCGA-F4-6805 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808       TCGA-F4-6809 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856       TCGA-G4-6293 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304       TCGA-G4-6306 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310       TCGA-G4-6315 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323       TCGA-G4-6586 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
                  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       25       107         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM92 MUTATED           0          0          0          0        0
  TMEM92 WILD-TYPE        19         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  TMEM92 MUTATED           0         0
  TMEM92 WILD-TYPE        13         1
D1142V3, multiclass
            clus
vv           TMEM92 MUTATED TMEM92 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               2              107
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TMEM92 MUTATED     0   0   2   1
  TMEM92 WILD-TYPE   9  68 246  40
D1142V4, multiclass
    clus
vv   TMEM92 MUTATED TMEM92 WILD-TYPE
  T1              0                9
  T2              0               68
  T3              2              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
  TMEM92 MUTATED     3   0   0
  TMEM92 WILD-TYPE 217  80  66
D1142V5, multiclass
    clus
vv   TMEM92 MUTATED TMEM92 WILD-TYPE
  N0              3              217
  N1              0               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"
D1142V6, binary
                  cls
clus                 0   1
  TMEM92 MUTATED     2   0
  TMEM92 WILD-TYPE 281  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM92 MUTATED      2    0
  TMEM92 WILD-TYPE  281   48
   clus
vv  TMEM92 MUTATED TMEM92 WILD-TYPE
  0              2              281
  1              0               48
[1] 2 2
[1] FALSE
D1142V7, 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
D1142V8, binary
                  cls
clus                 0   1
  TMEM92 MUTATED     2   1
  TMEM92 WILD-TYPE 315  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM92 MUTATED      2    1
  TMEM92 WILD-TYPE  315   47
                               clus
vv                              TMEM92 MUTATED TMEM92 WILD-TYPE
  COLON ADENOCARCINOMA                       2              315
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TMEM92 MUTATED     1   0   0   1
  TMEM92 WILD-TYPE 256   2  22  20
D1142V9, multiclass
[1] "Remove cluster labels:" "TMEM92 MUTATED"        
clus
  TMEM92 MUTATED TMEM92 WILD-TYPE 
               2              300 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-5657 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-5659       TCGA-A6-5661       TCGA-A6-5665       TCGA-A6-6781 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3489       TCGA-AA-3492       TCGA-AA-3496       TCGA-AA-3502 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3510       TCGA-AA-3511       TCGA-AA-3514       TCGA-AA-3517 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3518       TCGA-AA-3519       TCGA-AA-3520       TCGA-AA-3521 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3522       TCGA-AA-3524       TCGA-AA-3525       TCGA-AA-3526 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3527       TCGA-AA-3529       TCGA-AA-3530       TCGA-AA-3531 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3532       TCGA-AA-3534       TCGA-AA-3538       TCGA-AA-3542 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3543       TCGA-AA-3544       TCGA-AA-3548       TCGA-AA-3549 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3552       TCGA-AA-3553       TCGA-AA-3554       TCGA-AA-3555 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3556       TCGA-AA-3558       TCGA-AA-3560       TCGA-AA-3561 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3562       TCGA-AA-3655       TCGA-AA-3660       TCGA-AA-3662 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3663       TCGA-AA-3664       TCGA-AA-3666       TCGA-AA-3667 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3672       TCGA-AA-3673       TCGA-AA-3678       TCGA-AA-3679 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3680       TCGA-AA-3681       TCGA-AA-3684       TCGA-AA-3685 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3688       TCGA-AA-3692       TCGA-AA-3693       TCGA-AA-3695 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3696       TCGA-AA-3697       TCGA-AA-3710       TCGA-AA-3712 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3713       TCGA-AA-3715       TCGA-AA-3811       TCGA-AA-3812 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3814       TCGA-AA-3815       TCGA-AA-3818       TCGA-AA-3819 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3821       TCGA-AA-3831       TCGA-AA-3833       TCGA-AA-3837 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3842       TCGA-AA-3844       TCGA-AA-3845       TCGA-AA-3846 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3848       TCGA-AA-3850       TCGA-AA-3851       TCGA-AA-3852 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3854       TCGA-AA-3855       TCGA-AA-3856       TCGA-AA-3858 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3860       TCGA-AA-3861       TCGA-AA-3864       TCGA-AA-3866 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3867       TCGA-AA-3869       TCGA-AA-3870       TCGA-AA-3872 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3875       TCGA-AA-3877       TCGA-AA-3930       TCGA-AA-3939 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3941       TCGA-AA-3949       TCGA-AA-3950       TCGA-AA-3952 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3955       TCGA-AA-3956       TCGA-AA-3968       TCGA-AA-3971 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3972       TCGA-AA-3973       TCGA-AA-3975       TCGA-AA-3976 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3979       TCGA-AA-3984       TCGA-AA-3986       TCGA-AA-3989 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3994       TCGA-AA-A004       TCGA-AA-A00A       TCGA-AA-A00D 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A00E       TCGA-AA-A00F       TCGA-AA-A00J       TCGA-AA-A00K 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A00L       TCGA-AA-A00N       TCGA-AA-A00O       TCGA-AA-A00Q 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A00R       TCGA-AA-A00U       TCGA-AA-A00W       TCGA-AA-A00Z 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A010       TCGA-AA-A017       TCGA-AA-A01D       TCGA-AA-A01F 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A01G       TCGA-AA-A01I       TCGA-AA-A01K       TCGA-AA-A01P 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A01Q       TCGA-AA-A01R       TCGA-AA-A01S       TCGA-AA-A01T 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A01V       TCGA-AA-A01X       TCGA-AA-A01Z       TCGA-AA-A022 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A024       TCGA-AA-A029       TCGA-AA-A02F       TCGA-AA-A02H 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A02J       TCGA-AA-A02K       TCGA-AA-A02O       TCGA-AA-A02W 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A02Y       TCGA-AA-A03F       TCGA-AA-A03J       TCGA-AD-5900 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AD-6548       TCGA-AD-6888       TCGA-AU-3779       TCGA-AU-6004 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AY-4070       TCGA-AY-4071       TCGA-AY-5543       TCGA-AY-6196 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AY-6197       TCGA-AY-6386       TCGA-AZ-4315       TCGA-AZ-4681 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AZ-4682       TCGA-CA-5254       TCGA-CA-5255       TCGA-CA-5796 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CA-5797       TCGA-CA-6715       TCGA-CA-6716       TCGA-CA-6717 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CA-6718       TCGA-CA-6719       TCGA-CK-4947       TCGA-CK-4948 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CK-4950       TCGA-CK-4952       TCGA-CK-5912       TCGA-CK-5914 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CK-5915       TCGA-CK-5916       TCGA-CK-6746       TCGA-CK-6747 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CK-6748       TCGA-CK-6751       TCGA-CM-4743       TCGA-CM-4744 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-4746       TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-5344       TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-5861       TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-5868       TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-6164       TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-6168       TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-6172       TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-6677       TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-5537       TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-5541       TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6534       TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6538       TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6898       TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6924       TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6929       TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-7000       TCGA-F4-6459       TCGA-F4-6460       TCGA-F4-6569 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704       TCGA-F4-6805 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808       TCGA-F4-6809 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856       TCGA-G4-6293 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304       TCGA-G4-6306 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310       TCGA-G4-6315 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323       TCGA-G4-6586 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
D1142V10, continuous
[1] "Remove cluster labels:" "TMEM92 MUTATED"        
clus
  TMEM92 MUTATED TMEM92 WILD-TYPE 
               2              343 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-4105 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-5661       TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5665 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-5666       TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-6142       TCGA-A6-6648       TCGA-A6-6649       TCGA-A6-6651 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-6652       TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-6781       TCGA-A6-6782       TCGA-AA-3489       TCGA-AA-3492 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3496       TCGA-AA-3502       TCGA-AA-3510       TCGA-AA-3511 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3514       TCGA-AA-3516       TCGA-AA-3517       TCGA-AA-3518 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3519       TCGA-AA-3520       TCGA-AA-3521       TCGA-AA-3522 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3524       TCGA-AA-3525       TCGA-AA-3526       TCGA-AA-3527 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3529       TCGA-AA-3530       TCGA-AA-3531       TCGA-AA-3532 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3534       TCGA-AA-3538       TCGA-AA-3542       TCGA-AA-3543 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3544       TCGA-AA-3548       TCGA-AA-3549       TCGA-AA-3552 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3553       TCGA-AA-3554       TCGA-AA-3555       TCGA-AA-3556 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3558       TCGA-AA-3560       TCGA-AA-3562       TCGA-AA-3655 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3660       TCGA-AA-3662       TCGA-AA-3663       TCGA-AA-3664 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3666       TCGA-AA-3667       TCGA-AA-3672       TCGA-AA-3673 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3678       TCGA-AA-3679       TCGA-AA-3680       TCGA-AA-3681 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3684       TCGA-AA-3685       TCGA-AA-3688       TCGA-AA-3692 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3693       TCGA-AA-3695       TCGA-AA-3696       TCGA-AA-3697 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3710       TCGA-AA-3712       TCGA-AA-3713       TCGA-AA-3715 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3811       TCGA-AA-3812       TCGA-AA-3814       TCGA-AA-3815 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3818       TCGA-AA-3819       TCGA-AA-3821       TCGA-AA-3831 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3833       TCGA-AA-3837       TCGA-AA-3842       TCGA-AA-3844 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3845       TCGA-AA-3846       TCGA-AA-3848       TCGA-AA-3850 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3851       TCGA-AA-3852       TCGA-AA-3854       TCGA-AA-3855 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3856       TCGA-AA-3858       TCGA-AA-3860       TCGA-AA-3861 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3864       TCGA-AA-3866       TCGA-AA-3867       TCGA-AA-3869 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3870       TCGA-AA-3872       TCGA-AA-3875       TCGA-AA-3877 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3930       TCGA-AA-3939       TCGA-AA-3941       TCGA-AA-3949 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3950       TCGA-AA-3952       TCGA-AA-3955       TCGA-AA-3956 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3966       TCGA-AA-3968       TCGA-AA-3971       TCGA-AA-3972 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3973       TCGA-AA-3975       TCGA-AA-3976       TCGA-AA-3977 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3979       TCGA-AA-3980       TCGA-AA-3982       TCGA-AA-3984 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3986       TCGA-AA-3989       TCGA-AA-3994       TCGA-AA-A004 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A00A       TCGA-AA-A00D       TCGA-AA-A00E       TCGA-AA-A00F 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A00J       TCGA-AA-A00K       TCGA-AA-A00L       TCGA-AA-A00N 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A00O       TCGA-AA-A00Q       TCGA-AA-A00R       TCGA-AA-A00U 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A00W       TCGA-AA-A00Z       TCGA-AA-A010       TCGA-AA-A017 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A01D       TCGA-AA-A01F       TCGA-AA-A01G       TCGA-AA-A01I 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A01K       TCGA-AA-A01P       TCGA-AA-A01Q       TCGA-AA-A01R 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A01S       TCGA-AA-A01T       TCGA-AA-A01V       TCGA-AA-A01X 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A01Z       TCGA-AA-A022       TCGA-AA-A024       TCGA-AA-A029 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A02F       TCGA-AA-A02H       TCGA-AA-A02J       TCGA-AA-A02K 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A02O       TCGA-AA-A02W       TCGA-AA-A02Y       TCGA-AA-A03F 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A03J       TCGA-AD-5900       TCGA-AD-6548       TCGA-AD-6888 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AD-6890       TCGA-AD-6895       TCGA-AD-6899       TCGA-AD-6901 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AD-6963       TCGA-AD-6964       TCGA-AD-6965       TCGA-AU-3779 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AU-6004       TCGA-AY-4070       TCGA-AY-4071       TCGA-AY-5543 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386       TCGA-AZ-4323 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AZ-4616       TCGA-AZ-4682       TCGA-AZ-5403       TCGA-AZ-5407 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AZ-6598       TCGA-AZ-6599       TCGA-AZ-6600       TCGA-AZ-6601 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AZ-6603       TCGA-AZ-6605       TCGA-AZ-6606       TCGA-AZ-6607 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AZ-6608       TCGA-CK-4947       TCGA-CK-4948       TCGA-CK-4950 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CK-4952       TCGA-CM-4743       TCGA-CM-4744       TCGA-CM-4746 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341       TCGA-CM-5344 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860       TCGA-CM-5861 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864       TCGA-CM-5868 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163       TCGA-CM-6164 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167       TCGA-CM-6168 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171       TCGA-CM-6172 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676       TCGA-CM-6677 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680       TCGA-D5-5537 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540       TCGA-D5-5541 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533       TCGA-D5-6534 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537       TCGA-D5-6538 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541       TCGA-D5-6898 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923       TCGA-D5-6924 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928       TCGA-D5-6929 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932       TCGA-D5-7000 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DM-A0X9       TCGA-DM-A0XD       TCGA-DM-A0XF       TCGA-DM-A1D0 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DM-A1D4       TCGA-DM-A1D6       TCGA-DM-A1D7       TCGA-DM-A1D8 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DM-A1D9       TCGA-DM-A1DA       TCGA-DM-A1DB       TCGA-DM-A1HA 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DM-A1HB       TCGA-DM-A282       TCGA-DM-A285       TCGA-DM-A28C 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DM-A28E       TCGA-DM-A28F       TCGA-DM-A28G       TCGA-DM-A28H 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DM-A28K       TCGA-F4-6459       TCGA-F4-6460       TCGA-F4-6569 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704       TCGA-F4-6806 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-F4-6807       TCGA-F4-6808       TCGA-F4-6809       TCGA-F4-6854 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-F4-6855       TCGA-F4-6856       TCGA-G4-6293       TCGA-G4-6299 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-G4-6303       TCGA-G4-6304       TCGA-G4-6306       TCGA-G4-6307 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-G4-6309       TCGA-G4-6310       TCGA-G4-6315       TCGA-G4-6317 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-G4-6321       TCGA-G4-6323       TCGA-G4-6586       TCGA-G4-6588 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628 
"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
D1142V11, multiclass
[1] "Remove cluster labels:" "TMEM92 MUTATED"        
clus
  TMEM92 MUTATED TMEM92 WILD-TYPE 
               2              204 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-4105 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-5661       TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5665 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-5666       TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-6142       TCGA-A6-6648       TCGA-A6-6649       TCGA-A6-6651 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-6652       TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-6781       TCGA-A6-6782       TCGA-AD-5900       TCGA-AD-6548 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AD-6888       TCGA-AD-6890       TCGA-AD-6895       TCGA-AD-6899 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6964       TCGA-AD-6965 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070       TCGA-AY-4071 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AZ-4315       TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4681 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AZ-4682       TCGA-AZ-5403       TCGA-AZ-5407       TCGA-AZ-6598 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AZ-6599       TCGA-AZ-6600       TCGA-AZ-6601       TCGA-AZ-6603 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AZ-6605       TCGA-AZ-6606       TCGA-AZ-6607       TCGA-AZ-6608 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CA-5254       TCGA-CA-5255       TCGA-CA-5796       TCGA-CA-5797 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CA-6715       TCGA-CA-6716       TCGA-CA-6717       TCGA-CA-6718 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CA-6719       TCGA-CK-4947       TCGA-CK-4948       TCGA-CK-4950 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CK-4952       TCGA-CK-5912       TCGA-CK-5914       TCGA-CK-5915 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CK-5916       TCGA-CK-6746       TCGA-CK-6747       TCGA-CK-6748 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CK-6751       TCGA-CM-4743       TCGA-CM-4744       TCGA-CM-4746 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341       TCGA-CM-5344 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860       TCGA-CM-5861 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864       TCGA-CM-5868 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163       TCGA-CM-6164 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167       TCGA-CM-6168 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171       TCGA-CM-6172 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676       TCGA-CM-6677 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680       TCGA-D5-5537 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540       TCGA-D5-5541 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533       TCGA-D5-6534 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537       TCGA-D5-6538 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541       TCGA-D5-6898 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923       TCGA-D5-6924 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928       TCGA-D5-6929 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932       TCGA-D5-7000 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DM-A0X9       TCGA-DM-A0XD       TCGA-DM-A0XF       TCGA-DM-A1D0 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DM-A1D4       TCGA-DM-A1D6       TCGA-DM-A1D7       TCGA-DM-A1D8 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DM-A1D9       TCGA-DM-A1DA       TCGA-DM-A1DB       TCGA-DM-A1HA 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DM-A1HB       TCGA-DM-A282       TCGA-DM-A285       TCGA-DM-A28C 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DM-A28E       TCGA-DM-A28F       TCGA-DM-A28G       TCGA-DM-A28H 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DM-A28K       TCGA-F4-6459       TCGA-F4-6460       TCGA-F4-6569 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704       TCGA-F4-6805 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808       TCGA-F4-6809 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856       TCGA-G4-6293 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304       TCGA-G4-6306 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310       TCGA-G4-6315 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323       TCGA-G4-6586 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 

Clustering(1143) Variable = MALT1 MUTATION ANALYSIS
D1143V1, survival
                 sevent
clus2               0   1
  MALT1 MUTATED     8   3
  MALT1 WILD-TYPE 274  70
  MALT1 MUTATED MALT1 WILD-TYPE 
             11             344 
  MALT1 MUTATED MALT1 WILD-TYPE 
              3              70 
$`MALT1 MUTATED`
TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3516 TCGA-AA-3662 TCGA-AA-3815 TCGA-AA-3864 
       22.06         3.02        13.02         6.05        33.04        53.00 
TCGA-AA-3877 TCGA-AA-3977 TCGA-AA-A010 TCGA-AD-6901 TCGA-G4-6625 
       31.00        25.02        34.98        22.42        91.79 

$`MALT1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         0.72         5.79        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  MALT1 MUTATED MALT1 WILD-TYPE 
           3.02            0.00 
  MALT1 MUTATED MALT1 WILD-TYPE 
          91.79          140.38 
  MALT1 MUTATED MALT1 WILD-TYPE 
         25.020          20.005 
[1] "3.0 - 91.8 (25.0)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1.2"
D1143V2, 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       23       106         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        18         10         41         31       34        13
                 vv
clus              STAGE IVB
  MALT1 MUTATED           0
  MALT1 WILD-TYPE         1
D1143V3, multiclass
            clus
vv           MALT1 MUTATED MALT1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              3             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MALT1 MUTATED     1   1   7   2
  MALT1 WILD-TYPE   8  67 241  39
D1143V4, multiclass
    clus
vv   MALT1 MUTATED MALT1 WILD-TYPE
  T1             1               8
  T2             1              67
  T3             7             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
  MALT1 MUTATED     9   0   2
  MALT1 WILD-TYPE 211  80  64
D1143V5, multiclass
    clus
vv   MALT1 MUTATED MALT1 WILD-TYPE
  N0             9             211
  N1             0              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"
D1143V6, binary
                 cls
clus                0   1
  MALT1 MUTATED     8   1
  MALT1 WILD-TYPE 275  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MALT1 MUTATED      8    1
  MALT1 WILD-TYPE  275   47
   clus
vv  MALT1 MUTATED MALT1 WILD-TYPE
  0             8             275
  1             1              47
[1] 2 2
[1] FALSE
D1143V7, 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
D1143V8, binary
                 cls
clus                0   1
  MALT1 MUTATED     9   2
  MALT1 WILD-TYPE 308  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MALT1 MUTATED      9    2
  MALT1 WILD-TYPE  308   46
                               clus
vv                              MALT1 MUTATED MALT1 WILD-TYPE
  COLON ADENOCARCINOMA                      9             308
  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 250   2  21  21
D1143V9, multiclass
    clus
vv   MALT1 MUTATED MALT1 WILD-TYPE
  R0             7             250
  R1             0               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"
D1143V10, 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
D1143V11, 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(1144) Variable = OR13C5 MUTATION ANALYSIS
D1144V1, survival
                  sevent
clus2                0   1
  OR13C5 MUTATED     9   2
  OR13C5 WILD-TYPE 273  71
  OR13C5 MUTATED OR13C5 WILD-TYPE 
              11              344 
  OR13C5 MUTATED OR13C5 WILD-TYPE 
               2               71 
$`OR13C5 MUTATED`
TCGA-A6-5657 TCGA-AA-3815 TCGA-AA-3982 TCGA-AZ-6607 TCGA-CA-5797 TCGA-CA-6715 
       31.63        33.04        27.02         3.19         3.29         0.07 
TCGA-CM-4752 TCGA-CM-6171 TCGA-D5-6540 TCGA-D5-6930 TCGA-DM-A1D8 
       13.02        14.04        16.14         1.51        12.59 

$`OR13C5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 
       12.10       100.01        29.56         5.23        11.74         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        2.24         3.06         3.25         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  OR13C5 MUTATED OR13C5 WILD-TYPE 
            0.07             0.00 
  OR13C5 MUTATED OR13C5 WILD-TYPE 
           33.04           140.38 
  OR13C5 MUTATED OR13C5 WILD-TYPE 
           13.02            20.98 
[1] "0.1 - 33.0 (13.0)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.6"
D1144V2, 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       25       105         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR13C5 MUTATED           0          0          3          0        1
  OR13C5 WILD-TYPE        19         10         38         31       34
                  vv
clus               STAGE IVA STAGE IVB
  OR13C5 MUTATED           0         0
  OR13C5 WILD-TYPE        13         1
D1144V3, multiclass
            clus
vv           OR13C5 MUTATED OR13C5 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               4              105
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              3               38
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  OR13C5 MUTATED     0   2   8   1
  OR13C5 WILD-TYPE   9  66 240  40
D1144V4, multiclass
    clus
vv   OR13C5 MUTATED OR13C5 WILD-TYPE
  T1              0                9
  T2              2               66
  T3              8              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
  OR13C5 MUTATED     6   4   1
  OR13C5 WILD-TYPE 214  76  65
D1144V5, multiclass
    clus
vv   OR13C5 MUTATED OR13C5 WILD-TYPE
  N0              6              214
  N1              4               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"
D1144V6, binary
                  cls
clus                 0   1
  OR13C5 MUTATED     9   1
  OR13C5 WILD-TYPE 274  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR13C5 MUTATED      9    1
  OR13C5 WILD-TYPE  274   47
   clus
vv  OR13C5 MUTATED OR13C5 WILD-TYPE
  0              9              274
  1              1               47
[1] 2 2
[1] FALSE
D1144V7, 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
D1144V8, binary
                  cls
clus                 0   1
  OR13C5 MUTATED     9   2
  OR13C5 WILD-TYPE 308  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR13C5 MUTATED      9    2
  OR13C5 WILD-TYPE  308   46
                               clus
vv                              OR13C5 MUTATED OR13C5 WILD-TYPE
  COLON ADENOCARCINOMA                       9              308
  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 250   2  22  20
D1144V9, multiclass
    clus
vv   OR13C5 MUTATED OR13C5 WILD-TYPE
  R0              7              250
  R1              0                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"
D1144V10, 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
D1144V11, 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(1145) Variable = SPAG7 MUTATION ANALYSIS
D1145V1, survival
                 sevent
clus2               0   1
  SPAG7 MUTATED     2   1
  SPAG7 WILD-TYPE 280  72
  SPAG7 MUTATED SPAG7 WILD-TYPE 
              3             352 
  SPAG7 MUTATED SPAG7 WILD-TYPE 
              1              72 
$`SPAG7 MUTATED`
TCGA-AY-6386 TCGA-AZ-6598 TCGA-D5-5540 
       17.82        49.41        13.51 

$`SPAG7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 
       16.31         0.95        15.75         0.20        21.44        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  SPAG7 MUTATED SPAG7 WILD-TYPE 
          13.51            0.00 
  SPAG7 MUTATED SPAG7 WILD-TYPE 
          49.41          140.38 
  SPAG7 MUTATED SPAG7 WILD-TYPE 
         17.820          20.235 
[1] "13.5 - 49.4 (17.8)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.4"
D1145V2, 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       24       108         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        19         10         40         31       35        13
                 vv
clus              STAGE IVB
  SPAG7 MUTATED           0
  SPAG7 WILD-TYPE         1
D1145V3, multiclass
            clus
vv           SPAG7 MUTATED SPAG7 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              1             108
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SPAG7 MUTATED     0   0   3   0
  SPAG7 WILD-TYPE   9  68 245  41
D1145V4, multiclass
    clus
vv   SPAG7 MUTATED SPAG7 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             3             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
  SPAG7 MUTATED     2   1   0
  SPAG7 WILD-TYPE 218  79  66
D1145V5, multiclass
    clus
vv   SPAG7 MUTATED SPAG7 WILD-TYPE
  N0             2             218
  N1             1              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"
D1145V6, binary
                 cls
clus                0   1
  SPAG7 MUTATED     2   0
  SPAG7 WILD-TYPE 281  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPAG7 MUTATED      2    0
  SPAG7 WILD-TYPE  281   48
   clus
vv  SPAG7 MUTATED SPAG7 WILD-TYPE
  0             2             281
  1             0              48
[1] 2 2
[1] FALSE
D1145V7, 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
D1145V8, binary
                 cls
clus                0   1
  SPAG7 MUTATED     3   0
  SPAG7 WILD-TYPE 314  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPAG7 MUTATED      3    0
  SPAG7 WILD-TYPE  314   48
                               clus
vv                              SPAG7 MUTATED SPAG7 WILD-TYPE
  COLON ADENOCARCINOMA                      3             314
  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 255   2  22  21
D1145V9, multiclass
[1] "Remove cluster labels:" "SPAG7 MUTATED"         
clus
  SPAG7 MUTATED SPAG7 WILD-TYPE 
              2             300 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-5657 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-A6-5659      TCGA-A6-5661      TCGA-A6-5665      TCGA-A6-6781 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3489      TCGA-AA-3492      TCGA-AA-3496      TCGA-AA-3502 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3510      TCGA-AA-3511      TCGA-AA-3514      TCGA-AA-3517 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3518      TCGA-AA-3519      TCGA-AA-3520      TCGA-AA-3521 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3522      TCGA-AA-3524      TCGA-AA-3525      TCGA-AA-3526 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3527      TCGA-AA-3529      TCGA-AA-3530      TCGA-AA-3531 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3532      TCGA-AA-3534      TCGA-AA-3538      TCGA-AA-3542 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3543      TCGA-AA-3544      TCGA-AA-3548      TCGA-AA-3549 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3552      TCGA-AA-3553      TCGA-AA-3554      TCGA-AA-3555 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3556      TCGA-AA-3558      TCGA-AA-3560      TCGA-AA-3561 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3562      TCGA-AA-3655      TCGA-AA-3660      TCGA-AA-3662 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3663      TCGA-AA-3664      TCGA-AA-3666      TCGA-AA-3667 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3672      TCGA-AA-3673      TCGA-AA-3678      TCGA-AA-3679 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3680      TCGA-AA-3681      TCGA-AA-3684      TCGA-AA-3685 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3688      TCGA-AA-3692      TCGA-AA-3693      TCGA-AA-3695 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3696      TCGA-AA-3697      TCGA-AA-3710      TCGA-AA-3712 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3713      TCGA-AA-3715      TCGA-AA-3811      TCGA-AA-3812 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3814      TCGA-AA-3815      TCGA-AA-3818      TCGA-AA-3819 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3821      TCGA-AA-3831      TCGA-AA-3833      TCGA-AA-3837 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3842      TCGA-AA-3844      TCGA-AA-3845      TCGA-AA-3846 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3848      TCGA-AA-3850      TCGA-AA-3851      TCGA-AA-3852 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3854      TCGA-AA-3855      TCGA-AA-3856      TCGA-AA-3858 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3860      TCGA-AA-3861      TCGA-AA-3864      TCGA-AA-3866 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3867      TCGA-AA-3869      TCGA-AA-3870      TCGA-AA-3872 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3875      TCGA-AA-3877      TCGA-AA-3930      TCGA-AA-3939 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3941      TCGA-AA-3947      TCGA-AA-3949      TCGA-AA-3950 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3952      TCGA-AA-3955      TCGA-AA-3956      TCGA-AA-3968 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3971      TCGA-AA-3972      TCGA-AA-3973      TCGA-AA-3975 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3976      TCGA-AA-3979      TCGA-AA-3984      TCGA-AA-3986 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3989      TCGA-AA-3994      TCGA-AA-A004      TCGA-AA-A00A 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-A00D      TCGA-AA-A00E      TCGA-AA-A00F      TCGA-AA-A00J 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-A00K      TCGA-AA-A00L      TCGA-AA-A00N      TCGA-AA-A00O 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-A00Q      TCGA-AA-A00R      TCGA-AA-A00U      TCGA-AA-A00W 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-A00Z      TCGA-AA-A010      TCGA-AA-A017      TCGA-AA-A01D 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-A01F      TCGA-AA-A01G      TCGA-AA-A01I      TCGA-AA-A01K 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-A01P      TCGA-AA-A01Q      TCGA-AA-A01R      TCGA-AA-A01S 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-A01T      TCGA-AA-A01V      TCGA-AA-A01X      TCGA-AA-A01Z 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-A022      TCGA-AA-A024      TCGA-AA-A029      TCGA-AA-A02F 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-A02H      TCGA-AA-A02J      TCGA-AA-A02K      TCGA-AA-A02O 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-A02W      TCGA-AA-A02Y      TCGA-AA-A03F      TCGA-AA-A03J 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AD-5900      TCGA-AD-6548      TCGA-AD-6888      TCGA-AU-3779 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AU-6004      TCGA-AY-4070      TCGA-AY-4071      TCGA-AY-5543 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AY-6196      TCGA-AY-6197      TCGA-AZ-4315      TCGA-AZ-4681 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AZ-4682      TCGA-CA-5254      TCGA-CA-5255      TCGA-CA-5796 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-CA-5797      TCGA-CA-6715      TCGA-CA-6716      TCGA-CA-6717 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-CA-6718      TCGA-CA-6719      TCGA-CK-4947      TCGA-CK-4948 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-CK-4950      TCGA-CK-4952      TCGA-CK-5912      TCGA-CK-5913 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-CK-5914      TCGA-CK-5915      TCGA-CK-5916      TCGA-CK-6746 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-CK-6747      TCGA-CK-6748      TCGA-CK-6751      TCGA-CM-4743 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-CM-4744      TCGA-CM-4746      TCGA-CM-4747      TCGA-CM-4752 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-CM-5341      TCGA-CM-5344      TCGA-CM-5348      TCGA-CM-5349 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-CM-5860      TCGA-CM-5861      TCGA-CM-5862      TCGA-CM-5863 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-CM-5864      TCGA-CM-5868      TCGA-CM-6161      TCGA-CM-6162 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-CM-6163      TCGA-CM-6164      TCGA-CM-6165      TCGA-CM-6166 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-CM-6167      TCGA-CM-6168      TCGA-CM-6169      TCGA-CM-6170 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-CM-6171      TCGA-CM-6172      TCGA-CM-6674      TCGA-CM-6675 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-CM-6676      TCGA-CM-6677      TCGA-CM-6678      TCGA-CM-6679 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-CM-6680      TCGA-D5-5537      TCGA-D5-5538      TCGA-D5-5539 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-D5-5541      TCGA-D5-6529      TCGA-D5-6532      TCGA-D5-6533 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-D5-6534      TCGA-D5-6535      TCGA-D5-6536      TCGA-D5-6537 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-D5-6538      TCGA-D5-6539      TCGA-D5-6540      TCGA-D5-6541 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-D5-6898      TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-D5-6924      TCGA-D5-6926      TCGA-D5-6927      TCGA-D5-6928 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-D5-6929      TCGA-D5-6930      TCGA-D5-6931      TCGA-D5-6932 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-D5-7000      TCGA-F4-6459      TCGA-F4-6460      TCGA-F4-6569 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704      TCGA-F4-6805 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808      TCGA-F4-6809 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856      TCGA-G4-6293 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304      TCGA-G4-6306 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310      TCGA-G4-6315 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323      TCGA-G4-6586 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-G4-6588      TCGA-G4-6625      TCGA-G4-6626      TCGA-G4-6628 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
D1145V10, 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
D1145V11, 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(1146) Variable = DEK MUTATION ANALYSIS
D1146V1, survival
               sevent
clus2             0   1
  DEK MUTATED     4   2
  DEK WILD-TYPE 278  71
  DEK MUTATED DEK WILD-TYPE 
            6           349 
  DEK MUTATED DEK WILD-TYPE 
            2            71 
$`DEK MUTATED`
TCGA-A6-5660 TCGA-AA-A00N TCGA-AY-6197 TCGA-CA-6717 TCGA-G4-6586 TCGA-G4-6626 
       29.19         4.01        21.44         0.33        35.80        46.75 

$`DEK WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        26.17        91.79 
TCGA-G4-6628 
       52.80 

  DEK MUTATED DEK WILD-TYPE 
         0.33          0.00 
  DEK MUTATED DEK WILD-TYPE 
        46.75        140.38 
  DEK MUTATED DEK WILD-TYPE 
       25.315        20.120 
[1] "0.3 - 46.8 (25.3)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.9"
D1146V2, 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       25       105         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        19         10         41         30       35        13
               vv
clus            STAGE IVB
  DEK MUTATED           0
  DEK WILD-TYPE         1
D1146V3, multiclass
            clus
vv           DEK MUTATED DEK WILD-TYPE
  STAGE I              0            64
  STAGE IA             0             1
  STAGE II             0            25
  STAGE IIA            4           105
  STAGE IIB            1             7
  STAGE IIC            0             1
  STAGE III            0            19
  STAGE IIIA           0            10
  STAGE IIIB           0            41
  STAGE IIIC           1            30
  STAGE IV             0            35
  STAGE IVA            0            13
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  DEK MUTATED     0   0   5   1
  DEK WILD-TYPE   9  68 243  40
D1146V4, multiclass
    clus
vv   DEK MUTATED DEK WILD-TYPE
  T1           0             9
  T2           0            68
  T3           5           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
  DEK MUTATED     5   0   1
  DEK WILD-TYPE 215  80  65
D1146V5, multiclass
    clus
vv   DEK MUTATED DEK WILD-TYPE
  N0           5           215
  N1           0            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"
D1146V6, binary
               cls
clus              0   1
  DEK MUTATED     5   0
  DEK WILD-TYPE 278  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  DEK MUTATED      5    0
  DEK WILD-TYPE  278   48
   clus
vv  DEK MUTATED DEK WILD-TYPE
  0           5           278
  1           0            48
[1] 2 2
[1] FALSE
D1146V7, 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
D1146V8, binary
               cls
clus              0   1
  DEK MUTATED     4   2
  DEK WILD-TYPE 313  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  DEK MUTATED      4    2
  DEK WILD-TYPE  313   46
                               clus
vv                              DEK MUTATED DEK WILD-TYPE
  COLON ADENOCARCINOMA                    4           313
  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 253   2  22  20
D1146V9, multiclass
    clus
vv   DEK MUTATED DEK WILD-TYPE
  R0           4           253
  R1           0             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"
D1146V10, 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
D1146V11, 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(1147) Variable = DIAPH2 MUTATION ANALYSIS
D1147V1, survival
                  sevent
clus2                0   1
  DIAPH2 MUTATED    15   4
  DIAPH2 WILD-TYPE 267  69
  DIAPH2 MUTATED DIAPH2 WILD-TYPE 
              19              336 
  DIAPH2 MUTATED DIAPH2 WILD-TYPE 
               4               69 
$`DIAPH2 MUTATED`
TCGA-A6-6782 TCGA-AA-3552 TCGA-AA-3555 TCGA-AA-3692 TCGA-AA-3815 TCGA-AA-3977 
       20.28        13.02        29.95        36.00        33.04        25.02 
TCGA-AA-A00N TCGA-AD-6548 TCGA-AD-6899 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        4.01        21.37         5.79         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CM-5860 TCGA-CM-6675 TCGA-DM-A28H TCGA-F4-6460 TCGA-G4-6306 
        1.35        16.01        13.05       117.07        13.38        44.68 
TCGA-G4-6323 
       13.78 

$`DIAPH2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        19.66         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3697 
       11.01         5.98        37.05        19.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6888 
       41.00        39.98        18.05        40.96         0.07         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         0.72        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       11.01        12.95        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       60.79        98.24         8.61        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        35.80        26.17        91.79        46.75        52.80 

  DIAPH2 MUTATED DIAPH2 WILD-TYPE 
             0.1              0.0 
  DIAPH2 MUTATED DIAPH2 WILD-TYPE 
          117.07           140.38 
  DIAPH2 MUTATED DIAPH2 WILD-TYPE 
           13.78            20.98 
[1] "0.1 - 117.1 (13.8)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.3"
D1147V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DIAPH2 MUTATED         1        1        1         9         2         0
  DIAPH2 WILD-TYPE      63        0       24       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        19         10         40         28       34
                  vv
clus               STAGE IVA STAGE IVB
  DIAPH2 MUTATED           0         1
  DIAPH2 WILD-TYPE        13         0
D1147V3, multiclass
            clus
vv           DIAPH2 MUTATED DIAPH2 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                1                0
  STAGE II                1               24
  STAGE IIA               9              100
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              3               28
  STAGE IV                1               34
  STAGE IVA               0               13
  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  65 235  37
D1147V4, multiclass
    clus
vv   DIAPH2 MUTATED DIAPH2 WILD-TYPE
  T1              0                9
  T2              3               65
  T3             13              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
  DIAPH2 MUTATED    15   1   5
  DIAPH2 WILD-TYPE 205  79  61
D1147V5, multiclass
    clus
vv   DIAPH2 MUTATED DIAPH2 WILD-TYPE
  N0             15              205
  N1              1               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"
D1147V6, binary
                  cls
clus                 0   1
  DIAPH2 MUTATED    15   2
  DIAPH2 WILD-TYPE 268  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DIAPH2 MUTATED     15    2
  DIAPH2 WILD-TYPE  268   46
   clus
vv  DIAPH2 MUTATED DIAPH2 WILD-TYPE
  0             15              268
  1              2               46
[1] 2 2
[1] FALSE
D1147V7, 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
D1147V8, binary
                  cls
clus                 0   1
  DIAPH2 MUTATED    16   5
  DIAPH2 WILD-TYPE 301  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DIAPH2 MUTATED     16    5
  DIAPH2 WILD-TYPE  301   43
                               clus
vv                              DIAPH2 MUTATED DIAPH2 WILD-TYPE
  COLON ADENOCARCINOMA                      16              301
  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 245   2  21  17
D1147V9, multiclass
    clus
vv   DIAPH2 MUTATED DIAPH2 WILD-TYPE
  R0             12              245
  R1              0                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"
D1147V10, 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
D1147V11, 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(1148) Variable = C10ORF81 MUTATION ANALYSIS
D1148V1, survival
                    sevent
clus2                  0   1
  C10ORF81 MUTATED     5   0
  C10ORF81 WILD-TYPE 277  73
  C10ORF81 MUTATED C10ORF81 WILD-TYPE 
                 5                350 
  C10ORF81 MUTATED C10ORF81 WILD-TYPE 
                 0                 73 
$`C10ORF81 MUTATED`
TCGA-AA-3560 TCGA-CA-5797 TCGA-CA-6717 TCGA-D5-5539 TCGA-F4-6808 
       19.99         3.29         0.33        19.59        33.67 

$`C10ORF81 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       20.98        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 
       35.87         1.55        16.31        29.59        16.24        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  C10ORF81 MUTATED C10ORF81 WILD-TYPE 
              0.33               0.00 
  C10ORF81 MUTATED C10ORF81 WILD-TYPE 
             33.67             140.38 
  C10ORF81 MUTATED C10ORF81 WILD-TYPE 
             19.59              20.63 
[1] "0.3 - 33.7 (19.6)"  "0.0 - 140.4 (20.6)"
[1] "hr="     "3300000"
D1148V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C10ORF81 MUTATED         1        0        0         3         0         0
  C10ORF81 WILD-TYPE      63        1       25       106         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C10ORF81 MUTATED           0          1          0          1        0
  C10ORF81 WILD-TYPE        19          9         41         30       35
                    vv
clus                 STAGE IVA STAGE IVB
  C10ORF81 MUTATED           0         0
  C10ORF81 WILD-TYPE        13         1
D1148V3, multiclass
            clus
vv           C10ORF81 MUTATED C10ORF81 WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  0                 25
  STAGE IIA                 3                106
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                1                  9
  STAGE IIIB                0                 41
  STAGE IIIC                1                 30
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C10ORF81 MUTATED     1   0   5   0
  C10ORF81 WILD-TYPE   8  68 243  41
D1148V4, multiclass
    clus
vv   C10ORF81 MUTATED C10ORF81 WILD-TYPE
  T1                1                  8
  T2                0                 68
  T3                5                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
  C10ORF81 MUTATED     4   1   1
  C10ORF81 WILD-TYPE 216  79  65
D1148V5, multiclass
    clus
vv   C10ORF81 MUTATED C10ORF81 WILD-TYPE
  N0                4                216
  N1                1                 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"
D1148V6, binary
                    cls
clus                   0   1
  C10ORF81 MUTATED     6   0
  C10ORF81 WILD-TYPE 277  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF81 MUTATED      6    0
  C10ORF81 WILD-TYPE  277   48
   clus
vv  C10ORF81 MUTATED C10ORF81 WILD-TYPE
  0                6                277
  1                0                 48
[1] 2 2
[1] FALSE
D1148V7, binary
                    cls
clus                   0   1
  C10ORF81 MUTATED     3   3
  C10ORF81 WILD-TYPE 167 194
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF81 MUTATED      3    3
  C10ORF81 WILD-TYPE  167  194
        clus
vv       C10ORF81 MUTATED C10ORF81 WILD-TYPE
  FEMALE                3                167
  MALE                  3                194
[1] 2 2
[1] FALSE
D1148V8, binary
                    cls
clus                   0   1
  C10ORF81 MUTATED     4   2
  C10ORF81 WILD-TYPE 313  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF81 MUTATED      4    2
  C10ORF81 WILD-TYPE  313   46
                               clus
vv                              C10ORF81 MUTATED C10ORF81 WILD-TYPE
  COLON ADENOCARCINOMA                         4                313
  COLON MUCINOUS ADENOCARCINOMA                2                 46
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C10ORF81 MUTATED     5   0   0   1
  C10ORF81 WILD-TYPE 252   2  22  20
D1148V9, multiclass
    clus
vv   C10ORF81 MUTATED C10ORF81 WILD-TYPE
  R0                5                252
  R1                0                  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"
D1148V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C10ORF81 MUTATED                                  0     2
  C10ORF81 WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C10ORF81 MUTATED                           0     2
  C10ORF81 WILD-TYPE                        19   174
D1148V11, multiclass
                                  clus
vv                                 C10ORF81 MUTATED C10ORF81 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(1149) Variable = DPCR1 MUTATION ANALYSIS
D1149V1, survival
                 sevent
clus2               0   1
  DPCR1 MUTATED    11   1
  DPCR1 WILD-TYPE 271  72
  DPCR1 MUTATED DPCR1 WILD-TYPE 
             12             343 
  DPCR1 MUTATED DPCR1 WILD-TYPE 
              1              72 
$`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        11.51        43.27         6.18        19.43 

$`DPCR1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01         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        12.26        19.59        13.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19        18.25         1.32        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       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        13.38        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        35.41       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  DPCR1 MUTATED DPCR1 WILD-TYPE 
           6.18            0.00 
  DPCR1 MUTATED DPCR1 WILD-TYPE 
          63.98          140.38 
  DPCR1 MUTATED DPCR1 WILD-TYPE 
         19.545          20.980 
[1] "6.2 - 64.0 (19.5)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "2.4"
D1149V2, 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       24       104         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        19         10         40         30       35        12
                 vv
clus              STAGE IVB
  DPCR1 MUTATED           0
  DPCR1 WILD-TYPE         1
D1149V3, multiclass
            clus
vv           DPCR1 MUTATED DPCR1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              5             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 240  38
D1149V4, multiclass
    clus
vv   DPCR1 MUTATED DPCR1 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             8             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
  DPCR1 MUTATED     9   3   0
  DPCR1 WILD-TYPE 211  77  66
D1149V5, multiclass
    clus
vv   DPCR1 MUTATED DPCR1 WILD-TYPE
  N0             9             211
  N1             3              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"
D1149V6, binary
                 cls
clus                0   1
  DPCR1 MUTATED     8   1
  DPCR1 WILD-TYPE 275  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DPCR1 MUTATED      8    1
  DPCR1 WILD-TYPE  275   47
   clus
vv  DPCR1 MUTATED DPCR1 WILD-TYPE
  0             8             275
  1             1              47
[1] 2 2
[1] FALSE
D1149V7, 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
D1149V8, binary
                 cls
clus                0   1
  DPCR1 MUTATED     8   4
  DPCR1 WILD-TYPE 309  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DPCR1 MUTATED      8    4
  DPCR1 WILD-TYPE  309   44
                               clus
vv                              DPCR1 MUTATED DPCR1 WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  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 248   2  22  21
D1149V9, multiclass
    clus
vv   DPCR1 MUTATED DPCR1 WILD-TYPE
  R0             9             248
  R1             0               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"
D1149V10, 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
D1149V11, 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(1150) Variable = ICA1 MUTATION ANALYSIS
D1150V1, survival
                sevent
clus2              0   1
  ICA1 MUTATED     6   0
  ICA1 WILD-TYPE 276  73
  ICA1 MUTATED ICA1 WILD-TYPE 
             6            349 
  ICA1 MUTATED ICA1 WILD-TYPE 
             0             73 
$`ICA1 MUTATED`
TCGA-AA-3949 TCGA-AA-3950 TCGA-AD-6895 TCGA-CA-6717 TCGA-CM-5860 TCGA-D5-5540 
       26.01        24.00         0.72         0.33        16.01        13.51 

$`ICA1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3952 
       31.00         2.01        12.99        24.00        33.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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 
       12.26        19.59        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  ICA1 MUTATED ICA1 WILD-TYPE 
          0.33           0.00 
  ICA1 MUTATED ICA1 WILD-TYPE 
         26.01         140.38 
  ICA1 MUTATED ICA1 WILD-TYPE 
         14.76          20.28 
[1] "0.3 - 26.0 (14.8)"  "0.0 - 140.4 (20.3)"
[1] "hr="     "3300000"
D1150V2, 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       25       105         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ICA1 MUTATED           0          0          1          0        0         0
  ICA1 WILD-TYPE        19         10         40         31       35        13
                vv
clus             STAGE IVB
  ICA1 MUTATED           0
  ICA1 WILD-TYPE         1
D1150V3, multiclass
            clus
vv           ICA1 MUTATED ICA1 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             4            105
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ICA1 MUTATED     0   0   6   0
  ICA1 WILD-TYPE   9  68 242  41
D1150V4, multiclass
    clus
vv   ICA1 MUTATED ICA1 WILD-TYPE
  T1            0              9
  T2            0             68
  T3            6            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
  ICA1 MUTATED     4   2   0
  ICA1 WILD-TYPE 216  78  66
D1150V5, multiclass
    clus
vv   ICA1 MUTATED ICA1 WILD-TYPE
  N0            4            216
  N1            2             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"
D1150V6, binary
                cls
clus               0   1
  ICA1 MUTATED     5   0
  ICA1 WILD-TYPE 278  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  ICA1 MUTATED      5    0
  ICA1 WILD-TYPE  278   48
   clus
vv  ICA1 MUTATED ICA1 WILD-TYPE
  0            5            278
  1            0             48
[1] 2 2
[1] FALSE
D1150V7, 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
D1150V8, binary
                cls
clus               0   1
  ICA1 MUTATED     3   3
  ICA1 WILD-TYPE 314  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  ICA1 MUTATED      3    3
  ICA1 WILD-TYPE  314   45
                               clus
vv                              ICA1 MUTATED ICA1 WILD-TYPE
  COLON ADENOCARCINOMA                     3            314
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ICA1 MUTATED     4   0   0   1
  ICA1 WILD-TYPE 253   2  22  20
D1150V9, multiclass
    clus
vv   ICA1 MUTATED ICA1 WILD-TYPE
  R0            4            253
  R1            0              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"
D1150V10, 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
D1150V11, 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(1151) Variable = PRPF4B MUTATION ANALYSIS
D1151V1, survival
                  sevent
clus2                0   1
  PRPF4B MUTATED    14   1
  PRPF4B WILD-TYPE 268  72
  PRPF4B MUTATED PRPF4B WILD-TYPE 
              15              340 
  PRPF4B MUTATED PRPF4B WILD-TYPE 
               1               72 
$`PRPF4B MUTATED`
TCGA-A6-6781 TCGA-AA-3663 TCGA-AA-3697 TCGA-AA-3955 TCGA-AA-A00A TCGA-AA-A010 
       19.66         6.97        85.05        20.98        38.04        34.98 
TCGA-AD-6895 TCGA-CA-6717 TCGA-CK-4948 TCGA-CK-5913 TCGA-CK-5916 TCGA-CM-4746 
        0.72         0.33       102.44        51.32        21.14        37.02 
TCGA-CM-6166 TCGA-CM-6674 TCGA-D5-6533 
       21.99        12.95         1.32 

$`PRPF4B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3956 
       24.00        33.01        26.01        24.00         2.01        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
        7.96        27.02        13.94        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21        56.55         0.79         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       40.34        15.62        49.08        21.99         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       11.51        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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  PRPF4B MUTATED PRPF4B WILD-TYPE 
            0.33             0.00 
  PRPF4B MUTATED PRPF4B WILD-TYPE 
          102.44           140.38 
  PRPF4B MUTATED PRPF4B WILD-TYPE 
           21.14            20.07 
[1] "0.3 - 102.4 (21.1)" "0.0 - 140.4 (20.1)"
[1] "hr=" "3.7"
D1151V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PRPF4B MUTATED         3        0        1         4         1         0
  PRPF4B WILD-TYPE      61        1       24       105         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PRPF4B MUTATED           1          1          2          1        0
  PRPF4B WILD-TYPE        18          9         39         30       35
                  vv
clus               STAGE IVA STAGE IVB
  PRPF4B MUTATED           0         0
  PRPF4B WILD-TYPE        13         1
D1151V3, multiclass
            clus
vv           PRPF4B MUTATED PRPF4B WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               4              105
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              1                9
  STAGE IIIB              2               39
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PRPF4B MUTATED     1   3   8   3
  PRPF4B WILD-TYPE   8  65 240  38
D1151V4, multiclass
    clus
vv   PRPF4B MUTATED PRPF4B WILD-TYPE
  T1              1                8
  T2              3               65
  T3              8              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
  PRPF4B MUTATED    11   3   1
  PRPF4B WILD-TYPE 209  77  65
D1151V5, multiclass
    clus
vv   PRPF4B MUTATED PRPF4B WILD-TYPE
  N0             11              209
  N1              3               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"
D1151V6, binary
                  cls
clus                 0   1
  PRPF4B MUTATED    12   0
  PRPF4B WILD-TYPE 271  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRPF4B MUTATED     12    0
  PRPF4B WILD-TYPE  271   48
   clus
vv  PRPF4B MUTATED PRPF4B WILD-TYPE
  0             12              271
  1              0               48
[1] 2 2
[1] FALSE
D1151V7, 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
D1151V8, binary
                  cls
clus                 0   1
  PRPF4B MUTATED    13   2
  PRPF4B WILD-TYPE 304  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRPF4B MUTATED     13    2
  PRPF4B WILD-TYPE  304   46
                               clus
vv                              PRPF4B MUTATED PRPF4B WILD-TYPE
  COLON ADENOCARCINOMA                      13              304
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PRPF4B MUTATED    11   0   0   3
  PRPF4B WILD-TYPE 246   2  22  18
D1151V9, multiclass
    clus
vv   PRPF4B MUTATED PRPF4B WILD-TYPE
  R0             11              246
  R1              0                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"
D1151V10, 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
D1151V11, 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(1152) Variable = TRAPPC10 MUTATION ANALYSIS
D1152V1, survival
                    sevent
clus2                  0   1
  TRAPPC10 MUTATED    16   1
  TRAPPC10 WILD-TYPE 266  72
  TRAPPC10 MUTATED TRAPPC10 WILD-TYPE 
                17                338 
  TRAPPC10 MUTATED TRAPPC10 WILD-TYPE 
                 1                 72 
$`TRAPPC10 MUTATED`
TCGA-AA-3492 TCGA-AA-3662 TCGA-AA-3679 TCGA-AA-3812 TCGA-AA-3864 TCGA-AA-A01Q 
        3.02         6.05        15.02        35.05        53.00         1.02 
TCGA-AA-A01X TCGA-AD-5900 TCGA-AD-6889 TCGA-CA-6718 TCGA-CK-5914 TCGA-CM-5349 
       26.01         0.07        56.55         0.10        21.99        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-D5-6930 TCGA-G4-6586 TCGA-G4-6628 
       16.01        15.02         1.51        35.80        52.80 

$`TRAPPC10 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       19.99        13.94        19.99        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3815 
       85.05        26.99        19.04        19.04        10.06        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-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-A01Z TCGA-AA-A024 
       35.01         1.02        33.04        35.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37         4.21 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.33         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        51.32        21.14         2.93         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-5862 TCGA-CM-5863 TCGA-CM-5864 
       29.06        22.03        22.98         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 
       45.11        36.72        36.00        22.09        13.78        26.17 
TCGA-G4-6625 TCGA-G4-6626 
       91.79        46.75 

  TRAPPC10 MUTATED TRAPPC10 WILD-TYPE 
              0.07               0.00 
  TRAPPC10 MUTATED TRAPPC10 WILD-TYPE 
             56.55             140.38 
  TRAPPC10 MUTATED TRAPPC10 WILD-TYPE 
            16.010             20.235 
[1] "0.1 - 56.5 (16.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "3.1"
D1152V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TRAPPC10 MUTATED         2        0        3         9         1         0
  TRAPPC10 WILD-TYPE      62        1       22       100         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRAPPC10 MUTATED           1          0          1          0        2
  TRAPPC10 WILD-TYPE        18         10         40         31       33
                    vv
clus                 STAGE IVA STAGE IVB
  TRAPPC10 MUTATED           0         0
  TRAPPC10 WILD-TYPE        13         1
D1152V3, multiclass
            clus
vv           TRAPPC10 MUTATED TRAPPC10 WILD-TYPE
  STAGE I                   2                 62
  STAGE IA                  0                  1
  STAGE II                  3                 22
  STAGE IIA                 9                100
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 1                 18
  STAGE IIIA                0                 10
  STAGE IIIB                1                 40
  STAGE IIIC                0                 31
  STAGE IV                  2                 33
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  TRAPPC10 MUTATED     0   3  14   2
  TRAPPC10 WILD-TYPE   9  65 234  39
D1152V4, multiclass
    clus
vv   TRAPPC10 MUTATED TRAPPC10 WILD-TYPE
  T1                0                  9
  T2                3                 65
  T3               14                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
  TRAPPC10 MUTATED    15   2   2
  TRAPPC10 WILD-TYPE 205  78  64
D1152V5, multiclass
    clus
vv   TRAPPC10 MUTATED TRAPPC10 WILD-TYPE
  N0               15                205
  N1                2                 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"
D1152V6, binary
                    cls
clus                   0   1
  TRAPPC10 MUTATED    14   2
  TRAPPC10 WILD-TYPE 269  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TRAPPC10 MUTATED     14    2
  TRAPPC10 WILD-TYPE  269   46
   clus
vv  TRAPPC10 MUTATED TRAPPC10 WILD-TYPE
  0               14                269
  1                2                 46
[1] 2 2
[1] FALSE
D1152V7, binary
                    cls
clus                   0   1
  TRAPPC10 MUTATED    10   9
  TRAPPC10 WILD-TYPE 160 188
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TRAPPC10 MUTATED     10    9
  TRAPPC10 WILD-TYPE  160  188
        clus
vv       TRAPPC10 MUTATED TRAPPC10 WILD-TYPE
  FEMALE               10                160
  MALE                  9                188
[1] 2 2
[1] FALSE
D1152V8, binary
                    cls
clus                   0   1
  TRAPPC10 MUTATED    17   2
  TRAPPC10 WILD-TYPE 300  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TRAPPC10 MUTATED     17    2
  TRAPPC10 WILD-TYPE  300   46
                               clus
vv                              TRAPPC10 MUTATED TRAPPC10 WILD-TYPE
  COLON ADENOCARCINOMA                        17                300
  COLON MUCINOUS ADENOCARCINOMA                2                 46
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  TRAPPC10 MUTATED    12   0   2   4
  TRAPPC10 WILD-TYPE 245   2  20  17
D1152V9, multiclass
    clus
vv   TRAPPC10 MUTATED TRAPPC10 WILD-TYPE
  R0               12                245
  R1                0                  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"
D1152V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRAPPC10 MUTATED                                  0     2
  TRAPPC10 WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  TRAPPC10 MUTATED                           0     9
  TRAPPC10 WILD-TYPE                        19   167
D1152V11, multiclass
                                  clus
vv                                 TRAPPC10 MUTATED TRAPPC10 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(1153) Variable = STAG2 MUTATION ANALYSIS
D1153V1, survival
                 sevent
clus2               0   1
  STAG2 MUTATED    11   1
  STAG2 WILD-TYPE 271  72
  STAG2 MUTATED STAG2 WILD-TYPE 
             12             343 
  STAG2 MUTATED STAG2 WILD-TYPE 
              1              72 
$`STAG2 MUTATED`
TCGA-A6-2678 TCGA-A6-5662 TCGA-A6-5666 TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3555 
       42.28        23.61        32.71         1.02        63.98        29.95 
TCGA-AA-3821 TCGA-AA-A010 TCGA-AZ-6601 TCGA-CK-4948 TCGA-CM-6678 TCGA-G4-6317 
        1.02        34.98       100.01       102.44        11.01        36.00 

$`STAG2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2683 
       43.76        46.65        43.76        42.90        24.33        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 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-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 
       20.28         7.04         3.02        35.01         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 
       33.99        21.01        13.02        24.00        17.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 
        0.26         0.33         0.10         1.35        17.56        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  STAG2 MUTATED STAG2 WILD-TYPE 
           1.02            0.00 
  STAG2 MUTATED STAG2 WILD-TYPE 
         102.44          140.38 
  STAG2 MUTATED STAG2 WILD-TYPE 
         33.845          19.990 
[1] "1.0 - 102.4 (33.8)" "0.0 - 140.4 (20.0)"
[1] "hr=" "3.9"
D1153V2, 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       22       107         7         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  STAG2 MUTATED           0          1          1          1        0         2
  STAG2 WILD-TYPE        19          9         40         30       35        11
                 vv
clus              STAGE IVB
  STAG2 MUTATED           0
  STAG2 WILD-TYPE         1
D1153V3, multiclass
            clus
vv           STAG2 MUTATED STAG2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              2             107
  STAGE IIB              1               7
  STAGE IIC              1               0
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             1              40
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              2              11
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 239  38
D1153V4, multiclass
    clus
vv   STAG2 MUTATED STAG2 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             9             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
  STAG2 MUTATED     8   3   2
  STAG2 WILD-TYPE 212  77  64
D1153V5, multiclass
    clus
vv   STAG2 MUTATED STAG2 WILD-TYPE
  N0             8             212
  N1             3              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"
D1153V6, binary
                 cls
clus                0   1
  STAG2 MUTATED    10   2
  STAG2 WILD-TYPE 273  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAG2 MUTATED     10    2
  STAG2 WILD-TYPE  273   46
   clus
vv  STAG2 MUTATED STAG2 WILD-TYPE
  0            10             273
  1             2              46
[1] 2 2
[1] FALSE
D1153V7, 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
D1153V8, binary
                 cls
clus                0   1
  STAG2 MUTATED    11   2
  STAG2 WILD-TYPE 306  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAG2 MUTATED     11    2
  STAG2 WILD-TYPE  306   46
                               clus
vv                              STAG2 MUTATED STAG2 WILD-TYPE
  COLON ADENOCARCINOMA                     11             306
  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 247   2  22  21
D1153V9, multiclass
    clus
vv   STAG2 MUTATED STAG2 WILD-TYPE
  R0            10             247
  R1             0               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"
D1153V10, 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
D1153V11, 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(1154) Variable = SFRS15 MUTATION ANALYSIS
D1154V1, survival
                  sevent
clus2                0   1
  SFRS15 MUTATED    15   2
  SFRS15 WILD-TYPE 267  71
  SFRS15 MUTATED SFRS15 WILD-TYPE 
              17              338 
  SFRS15 MUTATED SFRS15 WILD-TYPE 
               2               71 
$`SFRS15 MUTATED`
TCGA-A6-3809 TCGA-AA-3510 TCGA-AA-3524 TCGA-AA-3555 TCGA-AA-3710 TCGA-AA-3877 
       32.75        63.98        36.03        29.95        26.99        31.00 
TCGA-AA-3977 TCGA-AA-A010 TCGA-AD-6889 TCGA-AD-6964 TCGA-AZ-4315 TCGA-AZ-6598 
       25.02        34.98        56.55        10.88        58.39        49.41 
TCGA-CA-6717 TCGA-D5-6538 TCGA-D5-6927 TCGA-D5-6928 TCGA-G4-6309 
        0.33        17.13         9.44        11.64        51.75 

$`SFRS15 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
        9.07        24.03        37.05         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85         4.80        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  SFRS15 MUTATED SFRS15 WILD-TYPE 
            0.33             0.00 
  SFRS15 MUTATED SFRS15 WILD-TYPE 
           63.98           140.38 
  SFRS15 MUTATED SFRS15 WILD-TYPE 
           31.00            19.99 
[1] "0.3 - 64.0 (31.0)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "2.3"
D1154V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SFRS15 MUTATED         1        0        3         8         2         0
  SFRS15 WILD-TYPE      63        1       22       101         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SFRS15 MUTATED           0          0          2          0        0
  SFRS15 WILD-TYPE        19         10         39         31       35
                  vv
clus               STAGE IVA STAGE IVB
  SFRS15 MUTATED           0         0
  SFRS15 WILD-TYPE        13         1
D1154V3, multiclass
            clus
vv           SFRS15 MUTATED SFRS15 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                3               22
  STAGE IIA               8              101
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SFRS15 MUTATED     1   1  13   3
  SFRS15 WILD-TYPE   8  67 235  38
D1154V4, multiclass
    clus
vv   SFRS15 MUTATED SFRS15 WILD-TYPE
  T1              1                8
  T2              1               67
  T3             13              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    15   1   2
  SFRS15 WILD-TYPE 205  79  64
D1154V5, multiclass
    clus
vv   SFRS15 MUTATED SFRS15 WILD-TYPE
  N0             15              205
  N1              1               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"
D1154V6, binary
                  cls
clus                 0   1
  SFRS15 MUTATED    15   0
  SFRS15 WILD-TYPE 268  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SFRS15 MUTATED     15    0
  SFRS15 WILD-TYPE  268   48
   clus
vv  SFRS15 MUTATED SFRS15 WILD-TYPE
  0             15              268
  1              0               48
[1] 2 2
[1] FALSE
D1154V7, binary
                  cls
clus                 0   1
  SFRS15 MUTATED     9   9
  SFRS15 WILD-TYPE 161 188
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SFRS15 MUTATED      9    9
  SFRS15 WILD-TYPE  161  188
        clus
vv       SFRS15 MUTATED SFRS15 WILD-TYPE
  FEMALE              9              161
  MALE                9              188
[1] 2 2
[1] FALSE
D1154V8, binary
                  cls
clus                 0   1
  SFRS15 MUTATED    13   5
  SFRS15 WILD-TYPE 304  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SFRS15 MUTATED     13    5
  SFRS15 WILD-TYPE  304   43
                               clus
vv                              SFRS15 MUTATED SFRS15 WILD-TYPE
  COLON ADENOCARCINOMA                      13              304
  COLON MUCINOUS ADENOCARCINOMA              5               43
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SFRS15 MUTATED    13   0   0   1
  SFRS15 WILD-TYPE 244   2  22  20
D1154V9, multiclass
    clus
vv   SFRS15 MUTATED SFRS15 WILD-TYPE
  R0             13              244
  R1              0                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"
D1154V10, 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     7
  SFRS15 WILD-TYPE                        18   169
D1154V11, 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                                         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(1155) Variable = ABHD2 MUTATION ANALYSIS
D1155V1, survival
                 sevent
clus2               0   1
  ABHD2 MUTATED     6   4
  ABHD2 WILD-TYPE 276  69
  ABHD2 MUTATED ABHD2 WILD-TYPE 
             10             345 
  ABHD2 MUTATED ABHD2 WILD-TYPE 
              4              69 
$`ABHD2 MUTATED`
TCGA-AA-3516 TCGA-AA-A00J TCGA-AA-A00N TCGA-AD-6889 TCGA-AD-6964 TCGA-CK-5912 
       13.02        18.05         4.01        56.55        10.88        49.08 
TCGA-CM-4746 TCGA-CM-5344 TCGA-CM-5864 TCGA-G4-6628 
       37.02        22.03        15.02        52.80 

$`ABHD2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        1.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37         4.21         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
        0.72         5.79        22.42        27.42         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        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         2.93         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        16.01        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       26.17        91.79        46.75 

  ABHD2 MUTATED ABHD2 WILD-TYPE 
           4.01            0.00 
  ABHD2 MUTATED ABHD2 WILD-TYPE 
          56.55          140.38 
  ABHD2 MUTATED ABHD2 WILD-TYPE 
          20.04           20.19 
[1] "4.0 - 56.5 (20.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.8"
D1155V2, 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       25       108         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        18         10         39         31       35        13
                 vv
clus              STAGE IVB
  ABHD2 MUTATED           0
  ABHD2 WILD-TYPE         1
D1155V3, multiclass
            clus
vv           ABHD2 MUTATED ABHD2 WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              1             108
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ABHD2 MUTATED     0   4   3   3
  ABHD2 WILD-TYPE   9  64 245  38
D1155V4, multiclass
    clus
vv   ABHD2 MUTATED ABHD2 WILD-TYPE
  T1             0               9
  T2             4              64
  T3             3             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
  ABHD2 MUTATED     6   2   2
  ABHD2 WILD-TYPE 214  78  64
D1155V5, multiclass
    clus
vv   ABHD2 MUTATED ABHD2 WILD-TYPE
  N0             6             214
  N1             2              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"
D1155V6, binary
                 cls
clus                0   1
  ABHD2 MUTATED     8   0
  ABHD2 WILD-TYPE 275  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABHD2 MUTATED      8    0
  ABHD2 WILD-TYPE  275   48
   clus
vv  ABHD2 MUTATED ABHD2 WILD-TYPE
  0             8             275
  1             0              48
[1] 2 2
[1] FALSE
D1155V7, 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
D1155V8, binary
                 cls
clus                0   1
  ABHD2 MUTATED     7   3
  ABHD2 WILD-TYPE 310  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABHD2 MUTATED      7    3
  ABHD2 WILD-TYPE  310   45
                               clus
vv                              ABHD2 MUTATED ABHD2 WILD-TYPE
  COLON ADENOCARCINOMA                      7             310
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ABHD2 MUTATED     6   0   0   1
  ABHD2 WILD-TYPE 251   2  22  20
D1155V9, multiclass
    clus
vv   ABHD2 MUTATED ABHD2 WILD-TYPE
  R0             6             251
  R1             0               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"
D1155V10, 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
D1155V11, 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(1156) Variable = CRTC1 MUTATION ANALYSIS
D1156V1, survival
                 sevent
clus2               0   1
  CRTC1 MUTATED    11   2
  CRTC1 WILD-TYPE 271  71
  CRTC1 MUTATED CRTC1 WILD-TYPE 
             13             342 
  CRTC1 MUTATED CRTC1 WILD-TYPE 
              2              71 
$`CRTC1 MUTATED`
TCGA-A6-5665 TCGA-A6-6653 TCGA-A6-6780 TCGA-AA-3492 TCGA-AA-3667 TCGA-AD-6964 
       22.06        24.39        20.12         3.02        14.01        10.88 
TCGA-AY-6197 TCGA-CM-6162 TCGA-D5-6930 TCGA-G4-6315 TCGA-G4-6586 TCGA-G4-6588 
       21.44        12.00         1.51        36.72        35.80        26.17 
TCGA-G4-6628 
       52.80 

$`CRTC1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6781 
       25.18        24.16        21.76        24.69        23.87        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        15.75         0.20        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 
       45.11        36.00        22.09        13.78        91.79        46.75 

  CRTC1 MUTATED CRTC1 WILD-TYPE 
           1.51            0.00 
  CRTC1 MUTATED CRTC1 WILD-TYPE 
          52.80          140.38 
  CRTC1 MUTATED CRTC1 WILD-TYPE 
         21.440          20.105 
[1] "1.5 - 52.8 (21.4)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.1"
D1156V2, 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       24       103         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        19         10         40         31       34        13
                 vv
clus              STAGE IVB
  CRTC1 MUTATED           0
  CRTC1 WILD-TYPE         1
D1156V3, multiclass
            clus
vv           CRTC1 MUTATED CRTC1 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              6             103
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CRTC1 MUTATED     0   3   9   1
  CRTC1 WILD-TYPE   9  65 239  40
D1156V4, multiclass
    clus
vv   CRTC1 MUTATED CRTC1 WILD-TYPE
  T1             0               9
  T2             3              65
  T3             9             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
  CRTC1 MUTATED    10   2   1
  CRTC1 WILD-TYPE 210  78  65
D1156V5, multiclass
    clus
vv   CRTC1 MUTATED CRTC1 WILD-TYPE
  N0            10             210
  N1             2              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"
D1156V6, binary
                 cls
clus                0   1
  CRTC1 MUTATED     9   1
  CRTC1 WILD-TYPE 274  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CRTC1 MUTATED      9    1
  CRTC1 WILD-TYPE  274   47
   clus
vv  CRTC1 MUTATED CRTC1 WILD-TYPE
  0             9             274
  1             1              47
[1] 2 2
[1] FALSE
D1156V7, 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
D1156V8, binary
                 cls
clus                0   1
  CRTC1 MUTATED    10   3
  CRTC1 WILD-TYPE 307  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CRTC1 MUTATED     10    3
  CRTC1 WILD-TYPE  307   45
                               clus
vv                              CRTC1 MUTATED CRTC1 WILD-TYPE
  COLON ADENOCARCINOMA                     10             307
  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 247   2  22  21
D1156V9, multiclass
    clus
vv   CRTC1 MUTATED CRTC1 WILD-TYPE
  R0            10             247
  R1             0               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"
D1156V10, 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
D1156V11, 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(1157) Variable = TMC8 MUTATION ANALYSIS
D1157V1, survival
                sevent
clus2              0   1
  TMC8 MUTATED     6   1
  TMC8 WILD-TYPE 276  72
  TMC8 MUTATED TMC8 WILD-TYPE 
             7            348 
  TMC8 MUTATED TMC8 WILD-TYPE 
             1             72 
$`TMC8 MUTATED`
TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3966 TCGA-AD-5900 TCGA-AU-6004 TCGA-CK-5913 
        3.02        63.98         2.01         0.07        27.09        51.32 
TCGA-CM-6162 
       12.00 

$`TMC8 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        21.99        21.14         2.93         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        16.01        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  TMC8 MUTATED TMC8 WILD-TYPE 
          0.07           0.00 
  TMC8 MUTATED TMC8 WILD-TYPE 
         63.98         140.38 
  TMC8 MUTATED TMC8 WILD-TYPE 
        12.000         20.235 
[1] "0.1 - 64.0 (12.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.4"
D1157V2, 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       23       107         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        19         10         40         31       35        13
                vv
clus             STAGE IVB
  TMC8 MUTATED           0
  TMC8 WILD-TYPE         1
D1157V3, multiclass
            clus
vv           TMC8 MUTATED TMC8 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             2            107
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TMC8 MUTATED     0   2   5   0
  TMC8 WILD-TYPE   9  66 243  41
D1157V4, multiclass
    clus
vv   TMC8 MUTATED TMC8 WILD-TYPE
  T1            0              9
  T2            2             66
  T3            5            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
  TMC8 MUTATED     6   1   0
  TMC8 WILD-TYPE 214  79  66
D1157V5, multiclass
    clus
vv   TMC8 MUTATED TMC8 WILD-TYPE
  N0            6            214
  N1            1             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"
D1157V6, binary
                cls
clus               0   1
  TMC8 MUTATED     5   0
  TMC8 WILD-TYPE 278  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  TMC8 MUTATED      5    0
  TMC8 WILD-TYPE  278   48
   clus
vv  TMC8 MUTATED TMC8 WILD-TYPE
  0            5            278
  1            0             48
[1] 2 2
[1] FALSE
D1157V7, 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
D1157V8, binary
                cls
clus               0   1
  TMC8 MUTATED     4   3
  TMC8 WILD-TYPE 313  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  TMC8 MUTATED      4    3
  TMC8 WILD-TYPE  313   45
                               clus
vv                              TMC8 MUTATED TMC8 WILD-TYPE
  COLON ADENOCARCINOMA                     4            313
  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 252   2  22  20
D1157V9, multiclass
    clus
vv   TMC8 MUTATED TMC8 WILD-TYPE
  R0            5            252
  R1            0              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"
D1157V10, 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
D1157V11, 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(1158) Variable = LIX1 MUTATION ANALYSIS
D1158V1, survival
                sevent
clus2              0   1
  LIX1 MUTATED     6   2
  LIX1 WILD-TYPE 276  71
  LIX1 MUTATED LIX1 WILD-TYPE 
             8            347 
  LIX1 MUTATED LIX1 WILD-TYPE 
             2             71 
$`LIX1 MUTATED`
TCGA-AA-3555 TCGA-AA-3713 TCGA-AA-3977 TCGA-AA-A010 TCGA-AZ-6600 TCGA-AZ-6601 
       29.95        19.04        25.02        34.98        12.10       100.01 
TCGA-CM-4744 TCGA-D5-6928 
       20.02        11.64 

$`LIX1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        17.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6603 
       22.36        62.79        61.41        49.41         6.77        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  LIX1 MUTATED LIX1 WILD-TYPE 
         11.64           0.00 
  LIX1 MUTATED LIX1 WILD-TYPE 
        100.01         140.38 
  LIX1 MUTATED LIX1 WILD-TYPE 
         22.52          20.19 
[1] "11.6 - 100.0 (22.5)" "0.0 - 140.4 (20.2)" 
[1] "hr=" "1"  
D1158V2, 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       24       107         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        18         10         41         31       33        13
                vv
clus             STAGE IVB
  LIX1 MUTATED           0
  LIX1 WILD-TYPE         1
D1158V3, multiclass
            clus
vv           LIX1 MUTATED LIX1 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             2            107
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              2             33
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  LIX1 MUTATED     0   2   5   2
  LIX1 WILD-TYPE   9  66 243  39
D1158V4, multiclass
    clus
vv   LIX1 MUTATED LIX1 WILD-TYPE
  T1            0              9
  T2            2             66
  T3            5            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
  LIX1 MUTATED     7   1   1
  LIX1 WILD-TYPE 213  79  65
D1158V5, multiclass
    clus
vv   LIX1 MUTATED LIX1 WILD-TYPE
  N0            7            213
  N1            1             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"
D1158V6, binary
                cls
clus               0   1
  LIX1 MUTATED     6   2
  LIX1 WILD-TYPE 277  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIX1 MUTATED      6    2
  LIX1 WILD-TYPE  277   46
   clus
vv  LIX1 MUTATED LIX1 WILD-TYPE
  0            6            277
  1            2             46
[1] 2 2
[1] FALSE
D1158V7, 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
D1158V8, binary
                cls
clus               0   1
  LIX1 MUTATED     7   2
  LIX1 WILD-TYPE 310  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIX1 MUTATED      7    2
  LIX1 WILD-TYPE  310   46
                               clus
vv                              LIX1 MUTATED LIX1 WILD-TYPE
  COLON ADENOCARCINOMA                     7            310
  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 252   2  21  21
D1158V9, multiclass
    clus
vv   LIX1 MUTATED LIX1 WILD-TYPE
  R0            5            252
  R1            0              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"
D1158V10, 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
D1158V11, 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(1159) Variable = DBF4B MUTATION ANALYSIS
D1159V1, survival
                 sevent
clus2               0   1
  DBF4B MUTATED     5   1
  DBF4B WILD-TYPE 277  72
  DBF4B MUTATED DBF4B WILD-TYPE 
              6             349 
  DBF4B MUTATED DBF4B WILD-TYPE 
              1              72 
$`DBF4B MUTATED`
TCGA-A6-5656 TCGA-AA-3715 TCGA-AA-A010 TCGA-CA-6717 TCGA-CM-6171 TCGA-D5-6930 
       32.91        19.04        34.98         0.33        14.04         1.51 

$`DBF4B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  DBF4B MUTATED DBF4B WILD-TYPE 
           0.33            0.00 
  DBF4B MUTATED DBF4B WILD-TYPE 
          34.98          140.38 
  DBF4B MUTATED DBF4B WILD-TYPE 
          16.54           20.28 
[1] "0.3 - 35.0 (16.5)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.3"
D1159V2, 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       24       106         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        19         10         41         31       35        13
                 vv
clus              STAGE IVB
  DBF4B MUTATED           0
  DBF4B WILD-TYPE         1
D1159V3, multiclass
            clus
vv           DBF4B MUTATED DBF4B WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              3             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DBF4B MUTATED     0   2   4   1
  DBF4B WILD-TYPE   9  66 244  40
D1159V4, multiclass
    clus
vv   DBF4B MUTATED DBF4B WILD-TYPE
  T1             0               9
  T2             2              66
  T3             4             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
  DBF4B MUTATED     7   0   0
  DBF4B WILD-TYPE 213  80  66
D1159V5, multiclass
    clus
vv   DBF4B MUTATED DBF4B WILD-TYPE
  N0             7             213
  N1             0              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"
D1159V6, binary
                 cls
clus                0   1
  DBF4B MUTATED     7   0
  DBF4B WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DBF4B MUTATED      7    0
  DBF4B WILD-TYPE  276   48
   clus
vv  DBF4B MUTATED DBF4B WILD-TYPE
  0             7             276
  1             0              48
[1] 2 2
[1] FALSE
D1159V7, 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
D1159V8, binary
                 cls
clus                0   1
  DBF4B MUTATED     5   2
  DBF4B WILD-TYPE 312  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DBF4B MUTATED      5    2
  DBF4B WILD-TYPE  312   46
                               clus
vv                              DBF4B MUTATED DBF4B WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  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 252   2  22  20
D1159V9, multiclass
    clus
vv   DBF4B MUTATED DBF4B WILD-TYPE
  R0             5             252
  R1             0               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"
D1159V10, 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
D1159V11, 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(1160) Variable = C7ORF66 MUTATION ANALYSIS
D1160V1, survival
                   sevent
clus2                 0   1
  C7ORF66 MUTATED     6   0
  C7ORF66 WILD-TYPE 276  73
  C7ORF66 MUTATED C7ORF66 WILD-TYPE 
                6               349 
  C7ORF66 MUTATED C7ORF66 WILD-TYPE 
                0                73 
$`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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       16.04        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  C7ORF66 MUTATED C7ORF66 WILD-TYPE 
            10.26              0.00 
  C7ORF66 MUTATED C7ORF66 WILD-TYPE 
           135.65            140.38 
  C7ORF66 MUTATED C7ORF66 WILD-TYPE 
           17.325            20.280 
[1] "10.3 - 135.7 (17.3)" "0.0 - 140.4 (20.3)" 
[1] "hr="     "9300000"
D1160V2, 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       25       107         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C7ORF66 MUTATED           0          0          1          2        0
  C7ORF66 WILD-TYPE        19         10         40         29       35
                   vv
clus                STAGE IVA STAGE IVB
  C7ORF66 MUTATED           0         0
  C7ORF66 WILD-TYPE        13         1
D1160V3, multiclass
            clus
vv           C7ORF66 MUTATED C7ORF66 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                2               107
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               2                29
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C7ORF66 MUTATED     0   2   4   1
  C7ORF66 WILD-TYPE   9  66 244  40
D1160V4, multiclass
    clus
vv   C7ORF66 MUTATED C7ORF66 WILD-TYPE
  T1               0                 9
  T2               2                66
  T3               4               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
  C7ORF66 MUTATED     4   2   1
  C7ORF66 WILD-TYPE 216  78  65
D1160V5, multiclass
    clus
vv   C7ORF66 MUTATED C7ORF66 WILD-TYPE
  N0               4               216
  N1               2                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"
D1160V6, binary
                   cls
clus                  0   1
  C7ORF66 MUTATED     6   0
  C7ORF66 WILD-TYPE 277  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF66 MUTATED      6    0
  C7ORF66 WILD-TYPE  277   48
   clus
vv  C7ORF66 MUTATED C7ORF66 WILD-TYPE
  0               6               277
  1               0                48
[1] 2 2
[1] FALSE
D1160V7, 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
D1160V8, binary
                   cls
clus                  0   1
  C7ORF66 MUTATED     5   2
  C7ORF66 WILD-TYPE 312  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF66 MUTATED      5    2
  C7ORF66 WILD-TYPE  312   46
                               clus
vv                              C7ORF66 MUTATED C7ORF66 WILD-TYPE
  COLON ADENOCARCINOMA                        5               312
  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 251   2  22  21
D1160V9, multiclass
    clus
vv   C7ORF66 MUTATED C7ORF66 WILD-TYPE
  R0               6               251
  R1               0                 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"
D1160V10, 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
D1160V11, 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(1161) Variable = HIST1H1A MUTATION ANALYSIS
D1161V1, survival
                    sevent
clus2                  0   1
  HIST1H1A MUTATED     6   3
  HIST1H1A WILD-TYPE 276  70
  HIST1H1A MUTATED HIST1H1A WILD-TYPE 
                 9                346 
  HIST1H1A MUTATED HIST1H1A WILD-TYPE 
                 3                 70 
$`HIST1H1A MUTATED`
TCGA-A6-6141 TCGA-AA-3492 TCGA-AA-3710 TCGA-AA-A01R TCGA-AA-A024 TCGA-AZ-4315 
        8.38         3.02        26.99        35.01        39.06        58.39 
TCGA-AZ-6608 TCGA-F4-6855 TCGA-G4-6588 
        1.94        35.41        26.17 

$`HIST1H1A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       26.01        37.02        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 
       29.59        16.24        33.67        13.25         0.53        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        91.79        46.75        52.80 

  HIST1H1A MUTATED HIST1H1A WILD-TYPE 
              1.94               0.00 
  HIST1H1A MUTATED HIST1H1A WILD-TYPE 
             58.39             140.38 
  HIST1H1A MUTATED HIST1H1A WILD-TYPE 
             26.99              20.07 
[1] "1.9 - 58.4 (27.0)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.8"
D1161V2, 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       23       104         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HIST1H1A MUTATED           1          1          0          0        0
  HIST1H1A WILD-TYPE        18          9         41         31       35
                    vv
clus                 STAGE IVA STAGE IVB
  HIST1H1A MUTATED           0         0
  HIST1H1A WILD-TYPE        13         1
D1161V3, multiclass
            clus
vv           HIST1H1A MUTATED HIST1H1A WILD-TYPE
  STAGE I                   0                 64
  STAGE IA                  0                  1
  STAGE II                  2                 23
  STAGE IIA                 5                104
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 1                 18
  STAGE IIIA                1                  9
  STAGE IIIB                0                 41
  STAGE IIIC                0                 31
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  HIST1H1A MUTATED     0   1   8   0
  HIST1H1A WILD-TYPE   9  67 240  41
D1161V4, multiclass
    clus
vv   HIST1H1A MUTATED HIST1H1A WILD-TYPE
  T1                0                  9
  T2                1                 67
  T3                8                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
  HIST1H1A MUTATED     7   1   1
  HIST1H1A WILD-TYPE 213  79  65
D1161V5, multiclass
    clus
vv   HIST1H1A MUTATED HIST1H1A WILD-TYPE
  N0                7                213
  N1                1                 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"
D1161V6, binary
                    cls
clus                   0   1
  HIST1H1A MUTATED     9   0
  HIST1H1A WILD-TYPE 274  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1A MUTATED      9    0
  HIST1H1A WILD-TYPE  274   48
   clus
vv  HIST1H1A MUTATED HIST1H1A WILD-TYPE
  0                9                274
  1                0                 48
[1] 2 2
[1] FALSE
D1161V7, 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
D1161V8, binary
                    cls
clus                   0   1
  HIST1H1A MUTATED     7   2
  HIST1H1A WILD-TYPE 310  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1A MUTATED      7    2
  HIST1H1A WILD-TYPE  310   46
                               clus
vv                              HIST1H1A MUTATED HIST1H1A WILD-TYPE
  COLON ADENOCARCINOMA                         7                310
  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 250   2  22  21
D1161V9, multiclass
    clus
vv   HIST1H1A MUTATED HIST1H1A WILD-TYPE
  R0                7                250
  R1                0                  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"
D1161V10, 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
D1161V11, 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(1162) Variable = OR51T1 MUTATION ANALYSIS
D1162V1, survival
                  sevent
clus2                0   1
  OR51T1 MUTATED     9   1
  OR51T1 WILD-TYPE 273  72
  OR51T1 MUTATED OR51T1 WILD-TYPE 
              10              345 
  OR51T1 MUTATED OR51T1 WILD-TYPE 
               1               72 
$`OR51T1 MUTATED`
TCGA-AA-3697 TCGA-AA-3815 TCGA-AD-6889 TCGA-AZ-4315 TCGA-CM-5864 TCGA-CM-6171 
       85.05        33.04        56.55        58.39        15.02        14.04 
TCGA-CM-6674 TCGA-D5-5538 TCGA-F4-6569 TCGA-G4-6626 
       12.95        12.26        13.45        46.75 

$`OR51T1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
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-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-D5-5539 TCGA-D5-5540 
       11.01        10.06        12.03        45.40        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       26.17        91.79        52.80 

  OR51T1 MUTATED OR51T1 WILD-TYPE 
           12.26             0.00 
  OR51T1 MUTATED OR51T1 WILD-TYPE 
           85.05           140.38 
  OR51T1 MUTATED OR51T1 WILD-TYPE 
           24.03            20.19 
[1] "12.3 - 85.0 (24.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "3"  
D1162V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR51T1 MUTATED         3        0        0         6         0         0
  OR51T1 WILD-TYPE      61        1       25       103         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR51T1 MUTATED           1          0          1          0        0
  OR51T1 WILD-TYPE        18         10         40         31       35
                  vv
clus               STAGE IVA STAGE IVB
  OR51T1 MUTATED           0         0
  OR51T1 WILD-TYPE        13         1
D1162V3, multiclass
            clus
vv           OR51T1 MUTATED OR51T1 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               6              103
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  OR51T1 MUTATED     0   3   8   0
  OR51T1 WILD-TYPE   9  65 240  41
D1162V4, multiclass
    clus
vv   OR51T1 MUTATED OR51T1 WILD-TYPE
  T1              0                9
  T2              3               65
  T3              8              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
  OR51T1 MUTATED    10   1   0
  OR51T1 WILD-TYPE 210  79  66
D1162V5, multiclass
    clus
vv   OR51T1 MUTATED OR51T1 WILD-TYPE
  N0             10              210
  N1              1               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"
D1162V6, binary
                  cls
clus                 0   1
  OR51T1 MUTATED    11   0
  OR51T1 WILD-TYPE 272  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51T1 MUTATED     11    0
  OR51T1 WILD-TYPE  272   48
   clus
vv  OR51T1 MUTATED OR51T1 WILD-TYPE
  0             11              272
  1              0               48
[1] 2 2
[1] FALSE
D1162V7, 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
D1162V8, binary
                  cls
clus                 0   1
  OR51T1 MUTATED    11   0
  OR51T1 WILD-TYPE 306  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51T1 MUTATED     11    0
  OR51T1 WILD-TYPE  306   48
                               clus
vv                              OR51T1 MUTATED OR51T1 WILD-TYPE
  COLON ADENOCARCINOMA                      11              306
  COLON MUCINOUS ADENOCARCINOMA              0               48
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  OR51T1 MUTATED    10   0   0   0
  OR51T1 WILD-TYPE 247   2  22  21
D1162V9, multiclass
    clus
vv   OR51T1 MUTATED OR51T1 WILD-TYPE
  R0             10              247
  R1              0                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"
D1162V10, 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
D1162V11, 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(1163) Variable = KIAA0649 MUTATION ANALYSIS
D1163V1, survival
                    sevent
clus2                  0   1
  KIAA0649 MUTATED     7   3
  KIAA0649 WILD-TYPE 275  70
  KIAA0649 MUTATED KIAA0649 WILD-TYPE 
                10                345 
  KIAA0649 MUTATED KIAA0649 WILD-TYPE 
                 3                 70 
$`KIAA0649 MUTATED`
TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3818 TCGA-AD-5900 
       22.06         3.02         6.97         0.92         0.99         0.07 
TCGA-CK-5913 TCGA-CM-5348 TCGA-F4-6570 TCGA-G4-6588 
       51.32        22.98         6.18        26.17 

$`KIAA0649 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  KIAA0649 MUTATED KIAA0649 WILD-TYPE 
              0.07               0.00 
  KIAA0649 MUTATED KIAA0649 WILD-TYPE 
             51.32             140.38 
  KIAA0649 MUTATED KIAA0649 WILD-TYPE 
             6.575             20.280 
[1] "0.1 - 51.3 (6.6)"   "0.0 - 140.4 (20.3)"
[1] "hr=" "2.5"
D1163V2, 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       23       104         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0649 MUTATED           1          0          1          0        0
  KIAA0649 WILD-TYPE        18         10         40         31       35
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA0649 MUTATED           0         0
  KIAA0649 WILD-TYPE        13         1
D1163V3, multiclass
            clus
vv           KIAA0649 MUTATED KIAA0649 WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  2                 23
  STAGE IIA                 5                104
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 1                 18
  STAGE IIIA                0                 10
  STAGE IIIB                1                 40
  STAGE IIIC                0                 31
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA0649 MUTATED     0   1   9   0
  KIAA0649 WILD-TYPE   9  67 239  41
D1163V4, multiclass
    clus
vv   KIAA0649 MUTATED KIAA0649 WILD-TYPE
  T1                0                  9
  T2                1                 67
  T3                9                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
  KIAA0649 MUTATED     8   2   0
  KIAA0649 WILD-TYPE 212  78  66
D1163V5, multiclass
    clus
vv   KIAA0649 MUTATED KIAA0649 WILD-TYPE
  N0                8                212
  N1                2                 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"
D1163V6, binary
                    cls
clus                   0   1
  KIAA0649 MUTATED     8   0
  KIAA0649 WILD-TYPE 275  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0649 MUTATED      8    0
  KIAA0649 WILD-TYPE  275   48
   clus
vv  KIAA0649 MUTATED KIAA0649 WILD-TYPE
  0                8                275
  1                0                 48
[1] 2 2
[1] FALSE
D1163V7, 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
D1163V8, binary
                    cls
clus                   0   1
  KIAA0649 MUTATED     9   1
  KIAA0649 WILD-TYPE 308  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0649 MUTATED      9    1
  KIAA0649 WILD-TYPE  308   47
                               clus
vv                              KIAA0649 MUTATED KIAA0649 WILD-TYPE
  COLON ADENOCARCINOMA                         9                308
  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 248   2  22  20
D1163V9, multiclass
    clus
vv   KIAA0649 MUTATED KIAA0649 WILD-TYPE
  R0                9                248
  R1                0                  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"
D1163V10, 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
D1163V11, 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(1164) Variable = MSH4 MUTATION ANALYSIS
D1164V1, survival
                sevent
clus2              0   1
  MSH4 MUTATED    10   2
  MSH4 WILD-TYPE 272  71
  MSH4 MUTATED MSH4 WILD-TYPE 
            12            343 
  MSH4 MUTATED MSH4 WILD-TYPE 
             2             71 
$`MSH4 MUTATED`
TCGA-A6-2678 TCGA-AA-3510 TCGA-AA-3543 TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-4681 
       42.28        63.98         0.99        34.98        58.39        83.80 
TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-4948 TCGA-CM-5348 TCGA-G4-6303 TCGA-G4-6586 
       49.41         0.33       102.44        22.98        65.85        35.80 

$`MSH4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2683 
       43.76        46.65        43.76        42.90        24.33        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
       12.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         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-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  MSH4 MUTATED MSH4 WILD-TYPE 
          0.33           0.00 
  MSH4 MUTATED MSH4 WILD-TYPE 
        102.44         140.38 
  MSH4 MUTATED MSH4 WILD-TYPE 
        45.845         19.990 
[1] "0.3 - 102.4 (45.8)" "0.0 - 140.4 (20.0)"
[1] "hr=" "2.3"
D1164V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MSH4 MUTATED         1        0        2         5         1         0
  MSH4 WILD-TYPE      63        1       23       104         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MSH4 MUTATED           0          1          2          0        1         0
  MSH4 WILD-TYPE        19          9         39         31       34        13
                vv
clus             STAGE IVB
  MSH4 MUTATED           0
  MSH4 WILD-TYPE         1
D1164V3, multiclass
            clus
vv           MSH4 MUTATED MSH4 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             5            104
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            1              9
  STAGE IIIB            2             39
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MSH4 MUTATED     0   1  11   1
  MSH4 WILD-TYPE   9  67 237  40
D1164V4, multiclass
    clus
vv   MSH4 MUTATED MSH4 WILD-TYPE
  T1            0              9
  T2            1             67
  T3           11            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
  MSH4 MUTATED     9   4   0
  MSH4 WILD-TYPE 211  76  66
D1164V5, multiclass
    clus
vv   MSH4 MUTATED MSH4 WILD-TYPE
  N0            9            211
  N1            4             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"
D1164V6, binary
                cls
clus               0   1
  MSH4 MUTATED    11   1
  MSH4 WILD-TYPE 272  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH4 MUTATED     11    1
  MSH4 WILD-TYPE  272   47
   clus
vv  MSH4 MUTATED MSH4 WILD-TYPE
  0           11            272
  1            1             47
[1] 2 2
[1] FALSE
D1164V7, binary
                cls
clus               0   1
  MSH4 MUTATED     8   5
  MSH4 WILD-TYPE 162 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH4 MUTATED      8    5
  MSH4 WILD-TYPE  162  192
        clus
vv       MSH4 MUTATED MSH4 WILD-TYPE
  FEMALE            8            162
  MALE              5            192
[1] 2 2
[1] FALSE
D1164V8, binary
                cls
clus               0   1
  MSH4 MUTATED    11   2
  MSH4 WILD-TYPE 306  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH4 MUTATED     11    2
  MSH4 WILD-TYPE  306   46
                               clus
vv                              MSH4 MUTATED MSH4 WILD-TYPE
  COLON ADENOCARCINOMA                    11            306
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MSH4 MUTATED    11   0   0   1
  MSH4 WILD-TYPE 246   2  22  20
D1164V9, multiclass
    clus
vv   MSH4 MUTATED MSH4 WILD-TYPE
  R0           11            246
  R1            0              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"
D1164V10, 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
D1164V11, 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(1165) Variable = TRAF3IP1 MUTATION ANALYSIS
D1165V1, survival
                    sevent
clus2                  0   1
  TRAF3IP1 MUTATED     5   1
  TRAF3IP1 WILD-TYPE 277  72
  TRAF3IP1 MUTATED TRAF3IP1 WILD-TYPE 
                 6                349 
  TRAF3IP1 MUTATED TRAF3IP1 WILD-TYPE 
                 1                 72 
$`TRAF3IP1 MUTATED`
TCGA-A6-6781 TCGA-AA-A010 TCGA-AD-6964 TCGA-CA-6717 TCGA-D5-5539 TCGA-F4-6856 
       19.66        34.98        10.88         0.33        19.59        19.43 

$`TRAF3IP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        35.41       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  TRAF3IP1 MUTATED TRAF3IP1 WILD-TYPE 
              0.33               0.00 
  TRAF3IP1 MUTATED TRAF3IP1 WILD-TYPE 
             34.98             140.38 
  TRAF3IP1 MUTATED TRAF3IP1 WILD-TYPE 
             19.51              20.98 
[1] "0.3 - 35.0 (19.5)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.2"
D1165V2, 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       25       108         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRAF3IP1 MUTATED           0          1          0          1        0
  TRAF3IP1 WILD-TYPE        19          9         41         30       35
                    vv
clus                 STAGE IVA STAGE IVB
  TRAF3IP1 MUTATED           0         0
  TRAF3IP1 WILD-TYPE        13         1
D1165V3, multiclass
            clus
vv           TRAF3IP1 MUTATED TRAF3IP1 WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  0                 25
  STAGE IIA                 1                108
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                1                  9
  STAGE IIIB                0                 41
  STAGE IIIC                1                 30
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  TRAF3IP1 MUTATED     0   1   2   3
  TRAF3IP1 WILD-TYPE   9  67 246  38
D1165V4, multiclass
    clus
vv   TRAF3IP1 MUTATED TRAF3IP1 WILD-TYPE
  T1                0                  9
  T2                1                 67
  T3                2                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
  TRAF3IP1 MUTATED     3   2   1
  TRAF3IP1 WILD-TYPE 217  78  65
D1165V5, multiclass
    clus
vv   TRAF3IP1 MUTATED TRAF3IP1 WILD-TYPE
  N0                3                217
  N1                2                 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"
D1165V6, binary
                    cls
clus                   0   1
  TRAF3IP1 MUTATED     4   0
  TRAF3IP1 WILD-TYPE 279  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TRAF3IP1 MUTATED      4    0
  TRAF3IP1 WILD-TYPE  279   48
   clus
vv  TRAF3IP1 MUTATED TRAF3IP1 WILD-TYPE
  0                4                279
  1                0                 48
[1] 2 2
[1] FALSE
D1165V7, 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
D1165V8, binary
                    cls
clus                   0   1
  TRAF3IP1 MUTATED     2   4
  TRAF3IP1 WILD-TYPE 315  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TRAF3IP1 MUTATED      2    4
  TRAF3IP1 WILD-TYPE  315   44
                               clus
vv                              TRAF3IP1 MUTATED TRAF3IP1 WILD-TYPE
  COLON ADENOCARCINOMA                         2                315
  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 253   2  22  20
D1165V9, multiclass
    clus
vv   TRAF3IP1 MUTATED TRAF3IP1 WILD-TYPE
  R0                4                253
  R1                0                  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"
D1165V10, 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
D1165V11, 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(1166) Variable = GPR160 MUTATION ANALYSIS
D1166V1, survival
                  sevent
clus2                0   1
  GPR160 MUTATED     2   2
  GPR160 WILD-TYPE 280  71
  GPR160 MUTATED GPR160 WILD-TYPE 
               4              351 
  GPR160 MUTATED GPR160 WILD-TYPE 
               2               71 
$`GPR160 MUTATED`
TCGA-AA-3950 TCGA-AA-A00N TCGA-F4-6570 TCGA-G4-6588 
       24.00         4.01         6.18        26.17 

$`GPR160 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  GPR160 MUTATED GPR160 WILD-TYPE 
            4.01             0.00 
  GPR160 MUTATED GPR160 WILD-TYPE 
           26.17           140.38 
  GPR160 MUTATED GPR160 WILD-TYPE 
           15.09            20.19 
[1] "4.0 - 26.2 (15.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "4.1"
D1166V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GPR160 MUTATED         0        0        0         3         1         0
  GPR160 WILD-TYPE      64        1       25       106         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPR160 MUTATED           0          0          0          0        0
  GPR160 WILD-TYPE        19         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  GPR160 MUTATED           0         0
  GPR160 WILD-TYPE        13         1
D1166V3, multiclass
            clus
vv           GPR160 MUTATED GPR160 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               3              106
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GPR160 MUTATED     0   0   3   1
  GPR160 WILD-TYPE   9  68 245  40
D1166V4, multiclass
    clus
vv   GPR160 MUTATED GPR160 WILD-TYPE
  T1              0                9
  T2              0               68
  T3              3              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
  GPR160 MUTATED     4   0   0
  GPR160 WILD-TYPE 216  80  66
D1166V5, multiclass
    clus
vv   GPR160 MUTATED GPR160 WILD-TYPE
  N0              4              216
  N1              0               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"
D1166V6, binary
                  cls
clus                 0   1
  GPR160 MUTATED     4   0
  GPR160 WILD-TYPE 279  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR160 MUTATED      4    0
  GPR160 WILD-TYPE  279   48
   clus
vv  GPR160 MUTATED GPR160 WILD-TYPE
  0              4              279
  1              0               48
[1] 2 2
[1] FALSE
D1166V7, binary
                  cls
clus                 0   1
  GPR160 MUTATED     3   1
  GPR160 WILD-TYPE 167 196
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR160 MUTATED      3    1
  GPR160 WILD-TYPE  167  196
        clus
vv       GPR160 MUTATED GPR160 WILD-TYPE
  FEMALE              3              167
  MALE                1              196
[1] 2 2
[1] FALSE
D1166V8, binary
                  cls
clus                 0   1
  GPR160 MUTATED     2   2
  GPR160 WILD-TYPE 315  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR160 MUTATED      2    2
  GPR160 WILD-TYPE  315   46
                               clus
vv                              GPR160 MUTATED GPR160 WILD-TYPE
  COLON ADENOCARCINOMA                       2              315
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  GPR160 MUTATED     4   0   0   0
  GPR160 WILD-TYPE 253   2  22  21
D1166V9, multiclass
    clus
vv   GPR160 MUTATED GPR160 WILD-TYPE
  R0              4              253
  R1              0                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"
D1166V10, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GPR160 MUTATED                                  0     0
  GPR160 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GPR160 MUTATED                           0     2
  GPR160 WILD-TYPE                        19   174
D1166V11, multiclass
[1] "Remove cluster labels:" "GPR160 MUTATED"        
clus
  GPR160 MUTATED GPR160 WILD-TYPE 
               2              204 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-4105 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-A6-5661       TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5665 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-A6-5666       TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-A6-6142       TCGA-A6-6648       TCGA-A6-6649       TCGA-A6-6651 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-A6-6652       TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-A6-6781       TCGA-A6-6782       TCGA-AD-5900       TCGA-AD-6548 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-AD-6888       TCGA-AD-6889       TCGA-AD-6890       TCGA-AD-6895 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-AD-6899       TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6964 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-AD-6965       TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-AY-4071       TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-AY-6386       TCGA-AZ-4315       TCGA-AZ-4323       TCGA-AZ-4616 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-AZ-4681       TCGA-AZ-4682       TCGA-AZ-5403       TCGA-AZ-5407 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-AZ-6598       TCGA-AZ-6599       TCGA-AZ-6600       TCGA-AZ-6601 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-AZ-6603       TCGA-AZ-6605       TCGA-AZ-6606       TCGA-AZ-6607 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-AZ-6608       TCGA-CA-5254       TCGA-CA-5255       TCGA-CA-5796 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-CA-5797       TCGA-CA-6715       TCGA-CA-6716       TCGA-CA-6717 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-CA-6718       TCGA-CA-6719       TCGA-CK-4947       TCGA-CK-4948 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-CK-4950       TCGA-CK-4952       TCGA-CK-5912       TCGA-CK-5913 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-CK-5914       TCGA-CK-5915       TCGA-CK-5916       TCGA-CK-6746 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-CK-6747       TCGA-CK-6748       TCGA-CK-6751       TCGA-CM-4743 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-CM-4744       TCGA-CM-4746       TCGA-CM-4747       TCGA-CM-4752 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-CM-5341       TCGA-CM-5344       TCGA-CM-5348       TCGA-CM-5349 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-CM-5860       TCGA-CM-5861       TCGA-CM-5862       TCGA-CM-5863 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-CM-5864       TCGA-CM-5868       TCGA-CM-6161       TCGA-CM-6162 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-CM-6163       TCGA-CM-6164       TCGA-CM-6165       TCGA-CM-6166 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-CM-6167       TCGA-CM-6168       TCGA-CM-6169       TCGA-CM-6170 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-CM-6171       TCGA-CM-6172       TCGA-CM-6674       TCGA-CM-6675 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-CM-6676       TCGA-CM-6677       TCGA-CM-6678       TCGA-CM-6679 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-CM-6680       TCGA-D5-5537       TCGA-D5-5538       TCGA-D5-5539 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-D5-5540       TCGA-D5-5541       TCGA-D5-6529       TCGA-D5-6532 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-D5-6533       TCGA-D5-6534       TCGA-D5-6535       TCGA-D5-6536 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-D5-6537       TCGA-D5-6538       TCGA-D5-6539       TCGA-D5-6540 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-D5-6541       TCGA-D5-6898       TCGA-D5-6920       TCGA-D5-6922 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-D5-6923       TCGA-D5-6924       TCGA-D5-6926       TCGA-D5-6927 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-D5-6928       TCGA-D5-6929       TCGA-D5-6930       TCGA-D5-6931 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-D5-6932       TCGA-D5-7000       TCGA-DM-A0X9       TCGA-DM-A0XD 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-DM-A0XF       TCGA-DM-A1D0       TCGA-DM-A1D4       TCGA-DM-A1D6 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-DM-A1D7       TCGA-DM-A1D8       TCGA-DM-A1D9       TCGA-DM-A1DA 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-DM-A1DB       TCGA-DM-A1HA       TCGA-DM-A1HB       TCGA-DM-A282 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-DM-A285       TCGA-DM-A28C       TCGA-DM-A28E       TCGA-DM-A28F 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-DM-A28G       TCGA-DM-A28H       TCGA-DM-A28K       TCGA-F4-6459 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-F4-6460       TCGA-F4-6569       TCGA-F4-6703       TCGA-F4-6704 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-F4-6805       TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-F4-6809       TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-G4-6293       TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-G4-6306       TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-G4-6315       TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-G4-6586       TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 

Clustering(1167) Variable = KIAA1407 MUTATION ANALYSIS
D1167V1, survival
                    sevent
clus2                  0   1
  KIAA1407 MUTATED     9   2
  KIAA1407 WILD-TYPE 273  71
  KIAA1407 MUTATED KIAA1407 WILD-TYPE 
                11                344 
  KIAA1407 MUTATED KIAA1407 WILD-TYPE 
                 2                 71 
$`KIAA1407 MUTATED`
TCGA-A6-6654 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3815 TCGA-AA-3977 TCGA-AA-A010 
       23.87        85.05        26.99        33.04        25.02        34.98 
TCGA-AZ-6598 TCGA-AZ-6605 TCGA-CA-6718 TCGA-CM-6171 TCGA-CM-6676 
       49.41         5.23         0.10        14.04        11.08 

$`KIAA1407 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       36.00         5.03        19.04        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 
       61.41         6.77        12.10       100.01        29.56        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.33         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       13.05        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  KIAA1407 MUTATED KIAA1407 WILD-TYPE 
               0.1                0.0 
  KIAA1407 MUTATED KIAA1407 WILD-TYPE 
             85.05             140.38 
  KIAA1407 MUTATED KIAA1407 WILD-TYPE 
             25.02              20.07 
[1] "0.1 - 85.0 (25.0)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.2"
D1167V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIAA1407 MUTATED         2        0        1         3         1         0
  KIAA1407 WILD-TYPE      62        1       24       106         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1407 MUTATED           1          0          2          0        0
  KIAA1407 WILD-TYPE        18         10         39         31       35
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA1407 MUTATED           0         0
  KIAA1407 WILD-TYPE        13         1
D1167V3, multiclass
            clus
vv           KIAA1407 MUTATED KIAA1407 WILD-TYPE
  STAGE I                   2                 62
  STAGE IA                  0                  1
  STAGE II                  1                 24
  STAGE IIA                 3                106
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 1                 18
  STAGE IIIA                0                 10
  STAGE IIIB                2                 39
  STAGE IIIC                0                 31
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA1407 MUTATED     0   3   6   2
  KIAA1407 WILD-TYPE   9  65 242  39
D1167V4, multiclass
    clus
vv   KIAA1407 MUTATED KIAA1407 WILD-TYPE
  T1                0                  9
  T2                3                 65
  T3                6                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
  KIAA1407 MUTATED     9   2   0
  KIAA1407 WILD-TYPE 211  78  66
D1167V5, multiclass
    clus
vv   KIAA1407 MUTATED KIAA1407 WILD-TYPE
  N0                9                211
  N1                2                 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"
D1167V6, binary
                    cls
clus                   0   1
  KIAA1407 MUTATED     9   0
  KIAA1407 WILD-TYPE 274  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1407 MUTATED      9    0
  KIAA1407 WILD-TYPE  274   48
   clus
vv  KIAA1407 MUTATED KIAA1407 WILD-TYPE
  0                9                274
  1                0                 48
[1] 2 2
[1] FALSE
D1167V7, 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
D1167V8, binary
                    cls
clus                   0   1
  KIAA1407 MUTATED    11   0
  KIAA1407 WILD-TYPE 306  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1407 MUTATED     11    0
  KIAA1407 WILD-TYPE  306   48
                               clus
vv                              KIAA1407 MUTATED KIAA1407 WILD-TYPE
  COLON ADENOCARCINOMA                        11                306
  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 251   2  22  20
D1167V9, multiclass
    clus
vv   KIAA1407 MUTATED KIAA1407 WILD-TYPE
  R0                6                251
  R1                0                  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"
D1167V10, 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
D1167V11, 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(1168) Variable = DTX3L MUTATION ANALYSIS
D1168V1, survival
                 sevent
clus2               0   1
  DTX3L MUTATED     5   4
  DTX3L WILD-TYPE 277  69
  DTX3L MUTATED DTX3L WILD-TYPE 
              9             346 
  DTX3L MUTATED DTX3L WILD-TYPE 
              4              69 
$`DTX3L MUTATED`
TCGA-AA-3977 TCGA-AA-A010 TCGA-AD-6964 TCGA-AZ-6599 TCGA-CK-5912 TCGA-CM-4743 
       25.02        34.98        10.88         6.77        49.08        23.05 
TCGA-D5-6533 TCGA-DM-A1D4 TCGA-G4-6586 
        1.32        92.75        35.80 

$`DTX3L WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41        49.41        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
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         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 
       19.59        13.51        11.51        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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  DTX3L MUTATED DTX3L WILD-TYPE 
           1.32            0.00 
  DTX3L MUTATED DTX3L WILD-TYPE 
          92.75          140.38 
  DTX3L MUTATED DTX3L WILD-TYPE 
          25.02           20.07 
[1] "1.3 - 92.8 (25.0)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.9"
D1168V2, 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       25       105         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DTX3L MUTATED           0          0          1          0        0         0
  DTX3L WILD-TYPE        19         10         40         31       35        13
                 vv
clus              STAGE IVB
  DTX3L MUTATED           0
  DTX3L WILD-TYPE         1
D1168V3, multiclass
            clus
vv           DTX3L MUTATED DTX3L WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              4             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DTX3L MUTATED     0   3   4   3
  DTX3L WILD-TYPE   9  65 244  38
D1168V4, multiclass
    clus
vv   DTX3L MUTATED DTX3L WILD-TYPE
  T1             0               9
  T2             3              65
  T3             4             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
  DTX3L MUTATED     9   0   1
  DTX3L WILD-TYPE 211  80  65
D1168V5, multiclass
    clus
vv   DTX3L MUTATED DTX3L WILD-TYPE
  N0             9             211
  N1             0              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"
D1168V6, binary
                 cls
clus                0   1
  DTX3L MUTATED     6   0
  DTX3L WILD-TYPE 277  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DTX3L MUTATED      6    0
  DTX3L WILD-TYPE  277   48
   clus
vv  DTX3L MUTATED DTX3L WILD-TYPE
  0             6             277
  1             0              48
[1] 2 2
[1] FALSE
D1168V7, 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
D1168V8, binary
                 cls
clus                0   1
  DTX3L MUTATED    10   0
  DTX3L WILD-TYPE 307  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DTX3L MUTATED     10    0
  DTX3L WILD-TYPE  307   48
                               clus
vv                              DTX3L MUTATED DTX3L WILD-TYPE
  COLON ADENOCARCINOMA                     10             307
  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 252   2  22  20
D1168V9, multiclass
    clus
vv   DTX3L MUTATED DTX3L WILD-TYPE
  R0             5             252
  R1             0               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"
D1168V10, 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
D1168V11, 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(1169) Variable = DST MUTATION ANALYSIS
D1169V1, survival
               sevent
clus2             0   1
  DST MUTATED    53  11
  DST WILD-TYPE 229  62
  DST MUTATED DST WILD-TYPE 
           64           291 
  DST MUTATED DST WILD-TYPE 
           11            62 
$`DST MUTATED`
TCGA-A6-2676 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5661 TCGA-A6-6649 
       42.90        33.34        36.53        32.91        33.53        24.16 
TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3496 
       21.76        24.39        20.12        19.66         3.02         1.02 
TCGA-AA-3510 TCGA-AA-3660 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3821 TCGA-AA-3845 
       63.98        78.08        14.01         0.92         1.02         0.00 
TCGA-AA-3941 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R 
       24.00         2.01        25.02         4.01        34.98        35.01 
TCGA-AD-5900 TCGA-AD-6964 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-6196 TCGA-AY-6197 
        0.07        10.88        14.50        27.09         0.20        21.44 
TCGA-AZ-4315 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-CA-5254 TCGA-CA-6717 TCGA-CA-6718 
       58.39        61.41         6.77         2.24         0.33         0.10 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CM-4746 TCGA-CM-5341 TCGA-CM-5860 
       21.99        21.14         2.93        37.02        29.06        16.01 
TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6166 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-6540 
       15.02        12.00        21.99        45.40        12.26        16.14 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 TCGA-DM-A1D6 TCGA-DM-A1HA 
       11.64        13.41         1.51        11.38        49.91       131.51 
TCGA-DM-A1HB TCGA-DM-A28F TCGA-F4-6460 TCGA-F4-6703 TCGA-G4-6303 TCGA-G4-6304 
      135.65        35.97        13.38        35.87        65.85        53.62 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6588 TCGA-G4-6628 
       51.75        45.11        26.17        52.80 

$`DST WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-4105 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       34.65        32.75        14.53        31.63        30.44        29.19 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       23.61        22.09        22.06        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 
        8.38        25.08        25.18        24.69        23.87        20.28 
TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        7.04        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        61.02         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       54.02         2.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
        0.99        25.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       14.93        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 
       27.42         0.20        16.31         0.95        15.75        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 
        1.41         5.13        83.80        22.36        62.79        49.41 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        1.94         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 
       51.32         2.01       124.27        23.05        20.02        25.02 
TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5863 
       13.02        22.03        22.98        30.08         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02        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-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.03        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
       14.30         9.04         9.44        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43        38.20       130.65        92.75        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
      140.38         7.50        44.32       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 
      119.93        60.79       117.07        98.24         8.61        13.45 
TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       44.68        55.04        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       35.80        91.79        46.75 

  DST MUTATED DST WILD-TYPE 
            0             0 
  DST MUTATED DST WILD-TYPE 
       135.65        140.38 
  DST MUTATED DST WILD-TYPE 
       21.875        19.990 
[1] "0.0 - 135.7 (21.9)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.3"
D1169V2, 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       20        86         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        17          9         31         28       33        12
               vv
clus            STAGE IVB
  DST MUTATED           0
  DST WILD-TYPE         1
D1169V3, multiclass
            clus
vv           DST MUTATED DST WILD-TYPE
  STAGE I             13            51
  STAGE IA             0             1
  STAGE II             5            20
  STAGE IIA           23            86
  STAGE IIB            4             4
  STAGE IIC            0             1
  STAGE III            2            17
  STAGE IIIA           1             9
  STAGE IIIB          10            31
  STAGE IIIC           3            28
  STAGE IV             2            33
  STAGE IVA            1            12
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of 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  55 205  33
D1169V4, multiclass
    clus
vv   DST MUTATED DST WILD-TYPE
  T1           2             7
  T2          13            55
  T3          43           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
  DST MUTATED    45  16   5
  DST WILD-TYPE 175  64  61
D1169V5, multiclass
    clus
vv   DST MUTATED DST WILD-TYPE
  N0          45           175
  N1          16            64
  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"
D1169V6, binary
               cls
clus              0   1
  DST MUTATED    51   3
  DST WILD-TYPE 232  45
[1] "tbl2"
               cls
clus            [,1] [,2]
  DST MUTATED     51    3
  DST WILD-TYPE  232   45
   clus
vv  DST MUTATED DST WILD-TYPE
  0          51           232
  1           3            45
[1] 2 2
[1] FALSE
D1169V7, 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
D1169V8, binary
               cls
clus              0   1
  DST MUTATED    52  14
  DST WILD-TYPE 265  34
[1] "tbl2"
               cls
clus            [,1] [,2]
  DST MUTATED     52   14
  DST WILD-TYPE  265   34
                               clus
vv                              DST MUTATED DST WILD-TYPE
  COLON ADENOCARCINOMA                   52           265
  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 212   2  22  14
D1169V9, multiclass
    clus
vv   DST MUTATED DST WILD-TYPE
  R0          45           212
  R1           0             2
  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"
D1169V10, 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
D1169V11, 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(1170) Variable = KIRREL2 MUTATION ANALYSIS
D1170V1, survival
                   sevent
clus2                 0   1
  KIRREL2 MUTATED    12   1
  KIRREL2 WILD-TYPE 270  72
  KIRREL2 MUTATED KIRREL2 WILD-TYPE 
               13               342 
  KIRREL2 MUTATED KIRREL2 WILD-TYPE 
                1                72 
$`KIRREL2 MUTATED`
TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3663 TCGA-AA-3715 TCGA-AA-3831 
       33.53        22.06        19.66         6.97        19.04        17.98 
TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-A010 TCGA-AD-5900 TCGA-CM-4743 TCGA-D5-6540 
       53.00        33.01        34.98         0.07        23.05        16.14 
TCGA-G4-6588 
       26.17 

$`KIRREL2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
       25.02         1.02        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        52.80 

  KIRREL2 MUTATED KIRREL2 WILD-TYPE 
             0.07              0.00 
  KIRREL2 MUTATED KIRREL2 WILD-TYPE 
            53.00            140.38 
  KIRREL2 MUTATED KIRREL2 WILD-TYPE 
           22.060            20.155 
[1] "0.1 - 53.0 (22.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2.4"
D1170V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIRREL2 MUTATED         2        0        3         5         2         0
  KIRREL2 WILD-TYPE      62        1       22       104         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIRREL2 MUTATED           0          0          0          1        0
  KIRREL2 WILD-TYPE        19         10         41         30       35
                   vv
clus                STAGE IVA STAGE IVB
  KIRREL2 MUTATED           0         0
  KIRREL2 WILD-TYPE        13         1
D1170V3, multiclass
            clus
vv           KIRREL2 MUTATED KIRREL2 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 3                22
  STAGE IIA                5               104
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               1                30
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  KIRREL2 MUTATED     0   2   8   3
  KIRREL2 WILD-TYPE   9  66 240  38
D1170V4, multiclass
    clus
vv   KIRREL2 MUTATED KIRREL2 WILD-TYPE
  T1               0                 9
  T2               2                66
  T3               8               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
  KIRREL2 MUTATED    12   1   0
  KIRREL2 WILD-TYPE 208  79  66
D1170V5, multiclass
    clus
vv   KIRREL2 MUTATED KIRREL2 WILD-TYPE
  N0              12               208
  N1               1                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"
D1170V6, binary
                   cls
clus                  0   1
  KIRREL2 MUTATED    11   0
  KIRREL2 WILD-TYPE 272  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KIRREL2 MUTATED     11    0
  KIRREL2 WILD-TYPE  272   48
   clus
vv  KIRREL2 MUTATED KIRREL2 WILD-TYPE
  0              11               272
  1               0                48
[1] 2 2
[1] FALSE
D1170V7, binary
                   cls
clus                  0   1
  KIRREL2 MUTATED     5   8
  KIRREL2 WILD-TYPE 165 189
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KIRREL2 MUTATED      5    8
  KIRREL2 WILD-TYPE  165  189
        clus
vv       KIRREL2 MUTATED KIRREL2 WILD-TYPE
  FEMALE               5               165
  MALE                 8               189
[1] 2 2
[1] FALSE
D1170V8, binary
                   cls
clus                  0   1
  KIRREL2 MUTATED     9   4
  KIRREL2 WILD-TYPE 308  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KIRREL2 MUTATED      9    4
  KIRREL2 WILD-TYPE  308   44
                               clus
vv                              KIRREL2 MUTATED KIRREL2 WILD-TYPE
  COLON ADENOCARCINOMA                        9               308
  COLON MUCINOUS ADENOCARCINOMA               4                44
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  KIRREL2 MUTATED    13   0   0   0
  KIRREL2 WILD-TYPE 244   2  22  21
D1170V9, multiclass
    clus
vv   KIRREL2 MUTATED KIRREL2 WILD-TYPE
  R0              13               244
  R1               0                 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"
D1170V10, 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
D1170V11, 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(1171) Variable = ICAM5 MUTATION ANALYSIS
D1171V1, survival
                 sevent
clus2               0   1
  ICAM5 MUTATED     7   2
  ICAM5 WILD-TYPE 275  71
  ICAM5 MUTATED ICAM5 WILD-TYPE 
              9             346 
  ICAM5 MUTATED ICAM5 WILD-TYPE 
              2              71 
$`ICAM5 MUTATED`
TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3713 TCGA-AZ-6600 TCGA-CM-4746 TCGA-D5-6540 
       22.06         3.02        19.04        12.10        37.02        16.14 
TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 
       45.11        22.09        26.17 

$`ICAM5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        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        51.75        36.72        36.00        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        91.79        46.75        52.80 

  ICAM5 MUTATED ICAM5 WILD-TYPE 
           3.02            0.00 
  ICAM5 MUTATED ICAM5 WILD-TYPE 
          45.11          140.38 
  ICAM5 MUTATED ICAM5 WILD-TYPE 
         22.060          20.155 
[1] "3.0 - 45.1 (22.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.3"
D1171V2, 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       24       106         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        18         10         40         31       33        13
                 vv
clus              STAGE IVB
  ICAM5 MUTATED           0
  ICAM5 WILD-TYPE         1
D1171V3, multiclass
            clus
vv           ICAM5 MUTATED ICAM5 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              3             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               2              33
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ICAM5 MUTATED     0   3   6   1
  ICAM5 WILD-TYPE   9  65 242  40
D1171V4, multiclass
    clus
vv   ICAM5 MUTATED ICAM5 WILD-TYPE
  T1             0               9
  T2             3              65
  T3             6             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
  ICAM5 MUTATED     7   3   0
  ICAM5 WILD-TYPE 213  77  66
D1171V5, multiclass
    clus
vv   ICAM5 MUTATED ICAM5 WILD-TYPE
  N0             7             213
  N1             3              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"
D1171V6, binary
                 cls
clus                0   1
  ICAM5 MUTATED     7   2
  ICAM5 WILD-TYPE 276  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ICAM5 MUTATED      7    2
  ICAM5 WILD-TYPE  276   46
   clus
vv  ICAM5 MUTATED ICAM5 WILD-TYPE
  0             7             276
  1             2              46
[1] 2 2
[1] FALSE
D1171V7, 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
D1171V8, binary
                 cls
clus                0   1
  ICAM5 MUTATED     9   1
  ICAM5 WILD-TYPE 308  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ICAM5 MUTATED      9    1
  ICAM5 WILD-TYPE  308   47
                               clus
vv                              ICAM5 MUTATED ICAM5 WILD-TYPE
  COLON ADENOCARCINOMA                      9             308
  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 249   2  21  21
D1171V9, multiclass
    clus
vv   ICAM5 MUTATED ICAM5 WILD-TYPE
  R0             8             249
  R1             0               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"
D1171V10, 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
D1171V11, 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(1172) Variable = ACCN5 MUTATION ANALYSIS
D1172V1, survival
                 sevent
clus2               0   1
  ACCN5 MUTATED    10   2
  ACCN5 WILD-TYPE 272  71
  ACCN5 MUTATED ACCN5 WILD-TYPE 
             12             343 
  ACCN5 MUTATED ACCN5 WILD-TYPE 
              2              71 
$`ACCN5 MUTATED`
TCGA-AA-3510 TCGA-AA-3681 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6888 TCGA-AU-3779 
       63.98         5.98         4.01        34.98         4.21        14.50 
TCGA-CM-6162 TCGA-D5-6532 TCGA-D5-6536 TCGA-DM-A1HB TCGA-DM-A285 TCGA-G4-6306 
       12.00        18.25        17.85       135.65         6.12        44.68 

$`ACCN5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       47.01        15.02        11.01        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 
        5.79        22.42        27.42        10.88         0.20        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       13.51        11.51        20.19         1.32        43.27        15.12 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  ACCN5 MUTATED ACCN5 WILD-TYPE 
           4.01            0.00 
  ACCN5 MUTATED ACCN5 WILD-TYPE 
         135.65          140.38 
  ACCN5 MUTATED ACCN5 WILD-TYPE 
         16.175          20.980 
[1] "4.0 - 135.7 (16.2)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.4"
D1172V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ACCN5 MUTATED         0        0        1         5         2         0
  ACCN5 WILD-TYPE      64        1       24       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        18         10         38         31       34        13
                 vv
clus              STAGE IVB
  ACCN5 MUTATED           0
  ACCN5 WILD-TYPE         1
D1172V3, multiclass
            clus
vv           ACCN5 MUTATED ACCN5 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              5             104
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             3              38
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ACCN5 MUTATED     0   2   9   2
  ACCN5 WILD-TYPE   9  66 239  39
D1172V4, multiclass
    clus
vv   ACCN5 MUTATED ACCN5 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             9             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   3   1
  ACCN5 WILD-TYPE 212  77  65
D1172V5, multiclass
    clus
vv   ACCN5 MUTATED ACCN5 WILD-TYPE
  N0             8             212
  N1             3              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"
D1172V6, binary
                 cls
clus                0   1
  ACCN5 MUTATED    12   1
  ACCN5 WILD-TYPE 271  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACCN5 MUTATED     12    1
  ACCN5 WILD-TYPE  271   47
   clus
vv  ACCN5 MUTATED ACCN5 WILD-TYPE
  0            12             271
  1             1              47
[1] 2 2
[1] FALSE
D1172V7, 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
D1172V8, binary
                 cls
clus                0   1
  ACCN5 MUTATED    10   3
  ACCN5 WILD-TYPE 307  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACCN5 MUTATED     10    3
  ACCN5 WILD-TYPE  307   45
                               clus
vv                              ACCN5 MUTATED ACCN5 WILD-TYPE
  COLON ADENOCARCINOMA                     10             307
  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 246   2  22  21
D1172V9, multiclass
    clus
vv   ACCN5 MUTATED ACCN5 WILD-TYPE
  R0            11             246
  R1             0               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"
D1172V10, 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
D1172V11, 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(1173) Variable = LUM MUTATION ANALYSIS
D1173V1, survival
               sevent
clus2             0   1
  LUM MUTATED     8   3
  LUM WILD-TYPE 274  70
  LUM MUTATED LUM WILD-TYPE 
           11           344 
  LUM MUTATED LUM WILD-TYPE 
            3            70 
$`LUM MUTATED`
TCGA-AA-3510 TCGA-AA-3548 TCGA-AA-3845 TCGA-AA-A010 TCGA-AA-A01R TCGA-AZ-6600 
       63.98        33.99         0.00        34.98        35.01        12.10 
TCGA-CM-6161 TCGA-D5-6536 TCGA-D5-6538 TCGA-DM-A1HB TCGA-DM-A285 
       15.02        17.85        17.13       135.65         6.12 

$`LUM WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3552 
       26.01        12.99         0.99        14.01        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02        14.93        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       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        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41        49.41         6.77       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       15.12         4.80        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  LUM MUTATED LUM WILD-TYPE 
            0             0 
  LUM MUTATED LUM WILD-TYPE 
       135.65        140.38 
  LUM MUTATED LUM WILD-TYPE 
       17.850        20.235 
[1] "0.0 - 135.7 (17.9)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D1173V2, 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       23       107         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        18         10         39         30       33        13
               vv
clus            STAGE IVB
  LUM MUTATED           0
  LUM WILD-TYPE         1
D1173V3, multiclass
            clus
vv           LUM MUTATED LUM WILD-TYPE
  STAGE I              1            63
  STAGE IA             0             1
  STAGE II             2            23
  STAGE IIA            2           107
  STAGE IIB            1             7
  STAGE IIC            0             1
  STAGE III            1            18
  STAGE IIIA           0            10
  STAGE IIIB           2            39
  STAGE IIIC           1            30
  STAGE IV             2            33
  STAGE IVA            0            13
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  LUM MUTATED     0   1   8   3
  LUM WILD-TYPE   9  67 240  38
D1173V4, multiclass
    clus
vv   LUM MUTATED LUM WILD-TYPE
  T1           0             9
  T2           1            67
  T3           8           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
  LUM MUTATED     6   2   4
  LUM WILD-TYPE 214  78  62
D1173V5, multiclass
    clus
vv   LUM MUTATED LUM WILD-TYPE
  N0           6           214
  N1           2            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"
D1173V6, binary
               cls
clus              0   1
  LUM MUTATED    10   2
  LUM WILD-TYPE 273  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  LUM MUTATED     10    2
  LUM WILD-TYPE  273   46
   clus
vv  LUM MUTATED LUM WILD-TYPE
  0          10           273
  1           2            46
[1] 2 2
[1] FALSE
D1173V7, 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
D1173V8, binary
               cls
clus              0   1
  LUM MUTATED    10   2
  LUM WILD-TYPE 307  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  LUM MUTATED     10    2
  LUM WILD-TYPE  307   46
                               clus
vv                              LUM MUTATED LUM WILD-TYPE
  COLON ADENOCARCINOMA                   10           307
  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 248   2  22  21
D1173V9, multiclass
    clus
vv   LUM MUTATED LUM WILD-TYPE
  R0           9           248
  R1           0             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"
D1173V10, 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
D1173V11, 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(1174) Variable = DNAH6 MUTATION ANALYSIS
D1174V1, survival
                 sevent
clus2               0   1
  DNAH6 MUTATED    18   2
  DNAH6 WILD-TYPE 264  71
  DNAH6 MUTATED DNAH6 WILD-TYPE 
             20             335 
  DNAH6 MUTATED DNAH6 WILD-TYPE 
              2              71 
$`DNAH6 MUTATED`
TCGA-A6-5659 TCGA-A6-6141 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3663 
       30.44         8.38        19.66         3.02        63.98         6.97 
TCGA-AA-3977 TCGA-AD-5900 TCGA-AD-6889 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 
       25.02         0.07        56.55        58.39        49.41         0.33 
TCGA-CA-6718 TCGA-CM-4747 TCGA-CM-6162 TCGA-CM-6171 TCGA-CM-6674 TCGA-D5-6928 
        0.10        25.02        12.00        14.04        12.95        11.64 
TCGA-F4-6703 TCGA-G4-6588 
       35.87        26.17 

$`DNAH6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 
       20.28         7.04         1.02        35.01         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       78.08         6.05        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37         4.21 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07         0.26         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       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        13.38        13.45         6.18         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        91.79        46.75        52.80 

  DNAH6 MUTATED DNAH6 WILD-TYPE 
           0.07            0.00 
  DNAH6 MUTATED DNAH6 WILD-TYPE 
          63.98          140.38 
  DNAH6 MUTATED DNAH6 WILD-TYPE 
          16.85           20.28 
[1] "0.1 - 64.0 (16.9)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "2"  
D1174V2, 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       21       100         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        19         10         40         30       35        12
                 vv
clus              STAGE IVB
  DNAH6 MUTATED           0
  DNAH6 WILD-TYPE         1
D1174V3, multiclass
            clus
vv           DNAH6 MUTATED DNAH6 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               4              21
  STAGE IIA              9             100
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  64 234  39
D1174V4, multiclass
    clus
vv   DNAH6 MUTATED DNAH6 WILD-TYPE
  T1             0               9
  T2             4              64
  T3            14             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
  DNAH6 MUTATED    17   3   0
  DNAH6 WILD-TYPE 203  77  66
D1174V5, multiclass
    clus
vv   DNAH6 MUTATED DNAH6 WILD-TYPE
  N0            17             203
  N1             3              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"
D1174V6, binary
                 cls
clus                0   1
  DNAH6 MUTATED    15   1
  DNAH6 WILD-TYPE 268  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH6 MUTATED     15    1
  DNAH6 WILD-TYPE  268   47
   clus
vv  DNAH6 MUTATED DNAH6 WILD-TYPE
  0            15             268
  1             1              47
[1] 2 2
[1] FALSE
D1174V7, 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
D1174V8, binary
                 cls
clus                0   1
  DNAH6 MUTATED    15   5
  DNAH6 WILD-TYPE 302  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH6 MUTATED     15    5
  DNAH6 WILD-TYPE  302   43
                               clus
vv                              DNAH6 MUTATED DNAH6 WILD-TYPE
  COLON ADENOCARCINOMA                     15             302
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DNAH6 MUTATED    14   0   0   2
  DNAH6 WILD-TYPE 243   2  22  19
D1174V9, multiclass
    clus
vv   DNAH6 MUTATED DNAH6 WILD-TYPE
  R0            14             243
  R1             0               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"
D1174V10, 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
D1174V11, 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(1175) Variable = DCAF6 MUTATION ANALYSIS
D1175V1, survival
                 sevent
clus2               0   1
  DCAF6 MUTATED    12   1
  DCAF6 WILD-TYPE 270  72
  DCAF6 MUTATED DCAF6 WILD-TYPE 
             13             342 
  DCAF6 MUTATED DCAF6 WILD-TYPE 
              1              72 
$`DCAF6 MUTATED`
TCGA-A6-5661 TCGA-AA-3815 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6889 
       33.53        33.04        25.02         4.01        34.98        56.55 
TCGA-AD-6895 TCGA-AY-6197 TCGA-CA-5254 TCGA-CA-6718 TCGA-CM-6163 TCGA-CM-6677 
        0.72        21.44         2.24         0.10        14.04        11.08 
TCGA-D5-6540 
       16.14 

$`DCAF6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
        0.07        21.37         4.21         0.79         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        15.75         0.20        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19         1.94         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.33         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  DCAF6 MUTATED DCAF6 WILD-TYPE 
            0.1             0.0 
  DCAF6 MUTATED DCAF6 WILD-TYPE 
          56.55          140.38 
  DCAF6 MUTATED DCAF6 WILD-TYPE 
         16.140          20.235 
[1] "0.1 - 56.5 (16.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2"  
D1175V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DCAF6 MUTATED         2        0        0         8         2         0
  DCAF6 WILD-TYPE      62        1       25       101         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DCAF6 MUTATED           0          0          0          0        0         0
  DCAF6 WILD-TYPE        19         10         41         31       35        13
                 vv
clus              STAGE IVB
  DCAF6 MUTATED           0
  DCAF6 WILD-TYPE         1
D1175V3, multiclass
            clus
vv           DCAF6 MUTATED DCAF6 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              8             101
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DCAF6 MUTATED     1   2   9   2
  DCAF6 WILD-TYPE   8  66 239  39
D1175V4, multiclass
    clus
vv   DCAF6 MUTATED DCAF6 WILD-TYPE
  T1             1               8
  T2             2              66
  T3             9             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
  DCAF6 MUTATED    13   1   0
  DCAF6 WILD-TYPE 207  79  66
D1175V5, multiclass
    clus
vv   DCAF6 MUTATED DCAF6 WILD-TYPE
  N0            13             207
  N1             1              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"
D1175V6, binary
                 cls
clus                0   1
  DCAF6 MUTATED    11   0
  DCAF6 WILD-TYPE 272  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DCAF6 MUTATED     11    0
  DCAF6 WILD-TYPE  272   48
   clus
vv  DCAF6 MUTATED DCAF6 WILD-TYPE
  0            11             272
  1             0              48
[1] 2 2
[1] FALSE
D1175V7, binary
                 cls
clus                0   1
  DCAF6 MUTATED     6   8
  DCAF6 WILD-TYPE 164 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DCAF6 MUTATED      6    8
  DCAF6 WILD-TYPE  164  189
        clus
vv       DCAF6 MUTATED DCAF6 WILD-TYPE
  FEMALE             6             164
  MALE               8             189
[1] 2 2
[1] FALSE
D1175V8, binary
                 cls
clus                0   1
  DCAF6 MUTATED    12   2
  DCAF6 WILD-TYPE 305  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DCAF6 MUTATED     12    2
  DCAF6 WILD-TYPE  305   46
                               clus
vv                              DCAF6 MUTATED DCAF6 WILD-TYPE
  COLON ADENOCARCINOMA                     12             305
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DCAF6 MUTATED     9   0   0   2
  DCAF6 WILD-TYPE 248   2  22  19
D1175V9, multiclass
    clus
vv   DCAF6 MUTATED DCAF6 WILD-TYPE
  R0             9             248
  R1             0               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"
D1175V10, 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     5
  DCAF6 WILD-TYPE                        18   171
D1175V11, 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                                        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(1176) Variable = SF1 MUTATION ANALYSIS
D1176V1, survival
               sevent
clus2             0   1
  SF1 MUTATED    14   1
  SF1 WILD-TYPE 268  72
  SF1 MUTATED SF1 WILD-TYPE 
           15           340 
  SF1 MUTATED SF1 WILD-TYPE 
            1            72 
$`SF1 MUTATED`
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-6142 TCGA-A6-6653 TCGA-AA-3821 TCGA-AA-3947 
       31.63        29.19        25.08        24.39         1.02        33.01 
TCGA-AA-3977 TCGA-AA-A02Y TCGA-AD-6895 TCGA-AZ-6603 TCGA-CA-6718 TCGA-CM-4743 
       25.02        39.98         0.72        29.56         0.10        23.05 
TCGA-CM-4746 TCGA-CM-5868 TCGA-DM-A1HB 
       37.02        17.03       135.65 

$`SF1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       32.91        30.44        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 
       32.71        27.09        22.52         8.38        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       21.76        24.69        23.87        20.12        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        7.04         3.02         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
        0.99        25.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 
       18.05        31.00         2.01        12.99        24.00        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       41.00        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10       100.01         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.33         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  SF1 MUTATED SF1 WILD-TYPE 
          0.1           0.0 
  SF1 MUTATED SF1 WILD-TYPE 
       135.65        140.38 
  SF1 MUTATED SF1 WILD-TYPE 
        25.08         19.99 
[1] "0.1 - 135.7 (25.1)" "0.0 - 140.4 (20.0)"
[1] "hr=" "3.3"
D1176V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SF1 MUTATED         4        0        1         2         1         0
  SF1 WILD-TYPE      60        1       24       107         7         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SF1 MUTATED           0          0          2          1        0         2
  SF1 WILD-TYPE        19         10         39         30       35        11
               vv
clus            STAGE IVB
  SF1 MUTATED           0
  SF1 WILD-TYPE         1
D1176V3, multiclass
            clus
vv           SF1 MUTATED SF1 WILD-TYPE
  STAGE I              4            60
  STAGE IA             0             1
  STAGE II             1            24
  STAGE IIA            2           107
  STAGE IIB            1             7
  STAGE IIC            0             1
  STAGE III            0            19
  STAGE IIIA           0            10
  STAGE IIIB           2            39
  STAGE IIIC           1            30
  STAGE IV             0            35
  STAGE IVA            2            11
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of 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   6   7   3
  SF1 WILD-TYPE   9  62 241  38
D1176V4, multiclass
    clus
vv   SF1 MUTATED SF1 WILD-TYPE
  T1           0             9
  T2           6            62
  T3           7           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
  SF1 MUTATED     9   6   1
  SF1 WILD-TYPE 211  74  65
D1176V5, multiclass
    clus
vv   SF1 MUTATED SF1 WILD-TYPE
  N0           9           211
  N1           6            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"
D1176V6, binary
               cls
clus              0   1
  SF1 MUTATED    11   2
  SF1 WILD-TYPE 272  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  SF1 MUTATED     11    2
  SF1 WILD-TYPE  272   46
   clus
vv  SF1 MUTATED SF1 WILD-TYPE
  0          11           272
  1           2            46
[1] 2 2
[1] FALSE
D1176V7, binary
               cls
clus              0   1
  SF1 MUTATED     6  10
  SF1 WILD-TYPE 164 187
[1] "tbl2"
               cls
clus            [,1] [,2]
  SF1 MUTATED      6   10
  SF1 WILD-TYPE  164  187
        clus
vv       SF1 MUTATED SF1 WILD-TYPE
  FEMALE           6           164
  MALE            10           187
[1] 2 2
[1] FALSE
D1176V8, binary
               cls
clus              0   1
  SF1 MUTATED    14   2
  SF1 WILD-TYPE 303  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  SF1 MUTATED     14    2
  SF1 WILD-TYPE  303   46
                               clus
vv                              SF1 MUTATED SF1 WILD-TYPE
  COLON ADENOCARCINOMA                   14           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 249   2  22  20
D1176V9, multiclass
    clus
vv   SF1 MUTATED SF1 WILD-TYPE
  R0           8           249
  R1           0             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"
D1176V10, 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                           3     7
  SF1 WILD-TYPE                        16   169
D1176V11, multiclass
                                  clus
vv                                 SF1 MUTATED SF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1             9
  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(1177) Variable = NXF3 MUTATION ANALYSIS
D1177V1, survival
                sevent
clus2              0   1
  NXF3 MUTATED     6   4
  NXF3 WILD-TYPE 276  69
  NXF3 MUTATED NXF3 WILD-TYPE 
            10            345 
  NXF3 MUTATED NXF3 WILD-TYPE 
             4             69 
$`NXF3 MUTATED`
TCGA-A6-6781 TCGA-AA-3821 TCGA-AU-3779 TCGA-AZ-6608 TCGA-CA-6717 TCGA-CK-5912 
       19.66         1.02        14.50         1.94         0.33        49.08 
TCGA-CK-5913 TCGA-CM-5862 TCGA-DM-A1DB TCGA-G4-6317 
       51.32         5.03        44.32        36.00 

$`NXF3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 
       10.06        35.05        33.04         0.99        25.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38         7.50       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       45.11        36.72        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  NXF3 MUTATED NXF3 WILD-TYPE 
          0.33           0.00 
  NXF3 MUTATED NXF3 WILD-TYPE 
         51.32         140.38 
  NXF3 MUTATED NXF3 WILD-TYPE 
         17.08          20.28 
[1] "0.3 - 51.3 (17.1)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "2.2"
D1177V2, 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       25       105         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        19          9         41         29       35        12
                vv
clus             STAGE IVB
  NXF3 MUTATED           0
  NXF3 WILD-TYPE         1
D1177V3, multiclass
            clus
vv           NXF3 MUTATED NXF3 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             4            105
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            1              9
  STAGE IIIB            0             41
  STAGE IIIC            2             29
  STAGE IV              0             35
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  65 242  40
D1177V4, multiclass
    clus
vv   NXF3 MUTATED NXF3 WILD-TYPE
  T1            0              9
  T2            3             65
  T3            6            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
  NXF3 MUTATED     6   3   1
  NXF3 WILD-TYPE 214  77  65
D1177V5, multiclass
    clus
vv   NXF3 MUTATED NXF3 WILD-TYPE
  N0            6            214
  N1            3             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"
D1177V6, binary
                cls
clus               0   1
  NXF3 MUTATED     5   1
  NXF3 WILD-TYPE 278  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  NXF3 MUTATED      5    1
  NXF3 WILD-TYPE  278   47
   clus
vv  NXF3 MUTATED NXF3 WILD-TYPE
  0            5            278
  1            1             47
[1] 2 2
[1] FALSE
D1177V7, 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
D1177V8, binary
                cls
clus               0   1
  NXF3 MUTATED     7   3
  NXF3 WILD-TYPE 310  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  NXF3 MUTATED      7    3
  NXF3 WILD-TYPE  310   45
                               clus
vv                              NXF3 MUTATED NXF3 WILD-TYPE
  COLON ADENOCARCINOMA                     7            310
  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 252   2  22  18
D1177V9, multiclass
    clus
vv   NXF3 MUTATED NXF3 WILD-TYPE
  R0            5            252
  R1            0              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"
D1177V10, 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
D1177V11, 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(1178) Variable = NUP205 MUTATION ANALYSIS
D1178V1, survival
                  sevent
clus2                0   1
  NUP205 MUTATED    18   2
  NUP205 WILD-TYPE 264  71
  NUP205 MUTATED NUP205 WILD-TYPE 
              20              335 
  NUP205 MUTATED NUP205 WILD-TYPE 
               2               71 
$`NUP205 MUTATED`
TCGA-A6-6141 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3667 TCGA-AA-3821 TCGA-AA-3870 
        8.38        63.98         6.97        14.01         1.02        29.98 
TCGA-AA-3947 TCGA-AA-A010 TCGA-AA-A01P TCGA-AD-5900 TCGA-AZ-4315 TCGA-AZ-4682 
       33.01        34.98        38.07         0.07        58.39        22.36 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-6747 TCGA-CM-6162 TCGA-CM-6679 TCGA-D5-6540 
        0.33         0.10         2.93        12.00        10.06        16.14 
TCGA-D5-6927 TCGA-G4-6304 
        9.44        53.62 

$`NUP205 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
        0.99        25.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 
       30.05        53.00        17.03        24.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-5403 
       21.44        17.82         1.41         5.13        83.80        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07         0.26         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        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 
       16.01        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-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 
       19.43       107.67        74.56        65.85        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  NUP205 MUTATED NUP205 WILD-TYPE 
            0.07             0.00 
  NUP205 MUTATED NUP205 WILD-TYPE 
           63.98           140.38 
  NUP205 MUTATED NUP205 WILD-TYPE 
          13.005           20.980 
[1] "0.1 - 64.0 (13.0)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.7"
D1178V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NUP205 MUTATED         4        0        2         9         3         0
  NUP205 WILD-TYPE      60        1       23       100         5         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NUP205 MUTATED           1          0          1          0        1
  NUP205 WILD-TYPE        18         10         40         31       34
                  vv
clus               STAGE IVA STAGE IVB
  NUP205 MUTATED           1         0
  NUP205 WILD-TYPE        12         1
D1178V3, multiclass
            clus
vv           NUP205 MUTATED NUP205 WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               9              100
  STAGE IIB               3                5
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  15   3
  NUP205 WILD-TYPE   9  64 233  38
D1178V4, multiclass
    clus
vv   NUP205 MUTATED NUP205 WILD-TYPE
  T1              0                9
  T2              4               64
  T3             15              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
  NUP205 MUTATED    19   2   1
  NUP205 WILD-TYPE 201  78  65
D1178V5, multiclass
    clus
vv   NUP205 MUTATED NUP205 WILD-TYPE
  N0             19              201
  N1              2               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"
D1178V6, binary
                  cls
clus                 0   1
  NUP205 MUTATED    18   2
  NUP205 WILD-TYPE 265  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUP205 MUTATED     18    2
  NUP205 WILD-TYPE  265   46
   clus
vv  NUP205 MUTATED NUP205 WILD-TYPE
  0             18              265
  1              2               46
[1] 2 2
[1] FALSE
D1178V7, binary
                  cls
clus                 0   1
  NUP205 MUTATED    11  11
  NUP205 WILD-TYPE 159 186
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUP205 MUTATED     11   11
  NUP205 WILD-TYPE  159  186
        clus
vv       NUP205 MUTATED NUP205 WILD-TYPE
  FEMALE             11              159
  MALE               11              186
[1] 2 2
[1] FALSE
D1178V8, binary
                  cls
clus                 0   1
  NUP205 MUTATED    16   6
  NUP205 WILD-TYPE 301  42
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUP205 MUTATED     16    6
  NUP205 WILD-TYPE  301   42
                               clus
vv                              NUP205 MUTATED NUP205 WILD-TYPE
  COLON ADENOCARCINOMA                      16              301
  COLON MUCINOUS ADENOCARCINOMA              6               42
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  NUP205 MUTATED    18   0   0   3
  NUP205 WILD-TYPE 239   2  22  18
D1178V9, multiclass
    clus
vv   NUP205 MUTATED NUP205 WILD-TYPE
  R0             18              239
  R1              0                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"
D1178V10, 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     9
  NUP205 WILD-TYPE                        18   167
D1178V11, 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                                         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(1179) Variable = DUSP7 MUTATION ANALYSIS
D1179V1, survival
                 sevent
clus2               0   1
  DUSP7 MUTATED     5   1
  DUSP7 WILD-TYPE 277  72
  DUSP7 MUTATED DUSP7 WILD-TYPE 
              6             349 
  DUSP7 MUTATED DUSP7 WILD-TYPE 
              1              72 
$`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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
       19.07        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        19.99         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       12.26        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  DUSP7 MUTATED DUSP7 WILD-TYPE 
              0               0 
  DUSP7 MUTATED DUSP7 WILD-TYPE 
          78.08          140.38 
  DUSP7 MUTATED DUSP7 WILD-TYPE 
         19.855          20.280 
[1] "0.0 - 78.1 (19.9)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.6"
D1179V2, 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       23       108         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        19          9         41         30       35        13
                 vv
clus              STAGE IVB
  DUSP7 MUTATED           0
  DUSP7 WILD-TYPE         1
D1179V3, multiclass
            clus
vv           DUSP7 MUTATED DUSP7 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              1             108
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DUSP7 MUTATED     0   1   5   0
  DUSP7 WILD-TYPE   9  67 243  41
D1179V4, multiclass
    clus
vv   DUSP7 MUTATED DUSP7 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             5             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
  DUSP7 MUTATED     4   1   1
  DUSP7 WILD-TYPE 216  79  65
D1179V5, multiclass
    clus
vv   DUSP7 MUTATED DUSP7 WILD-TYPE
  N0             4             216
  N1             1              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"
D1179V6, binary
                 cls
clus                0   1
  DUSP7 MUTATED     5   0
  DUSP7 WILD-TYPE 278  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DUSP7 MUTATED      5    0
  DUSP7 WILD-TYPE  278   48
   clus
vv  DUSP7 MUTATED DUSP7 WILD-TYPE
  0             5             278
  1             0              48
[1] 2 2
[1] FALSE
D1179V7, 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
D1179V8, binary
                 cls
clus                0   1
  DUSP7 MUTATED     4   2
  DUSP7 WILD-TYPE 313  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DUSP7 MUTATED      4    2
  DUSP7 WILD-TYPE  313   46
                               clus
vv                              DUSP7 MUTATED DUSP7 WILD-TYPE
  COLON ADENOCARCINOMA                      4             313
  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 252   2  22  21
D1179V9, multiclass
    clus
vv   DUSP7 MUTATED DUSP7 WILD-TYPE
  R0             5             252
  R1             0               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"
D1179V10, 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
D1179V11, 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(1180) Variable = PAK7 MUTATION ANALYSIS
D1180V1, survival
                sevent
clus2              0   1
  PAK7 MUTATED    13   7
  PAK7 WILD-TYPE 269  66
  PAK7 MUTATED PAK7 WILD-TYPE 
            20            335 
  PAK7 MUTATED PAK7 WILD-TYPE 
             7             66 
$`PAK7 MUTATED`
TCGA-A6-6141 TCGA-AA-3662 TCGA-AA-3815 TCGA-AA-3837 TCGA-AA-A00N TCGA-AA-A010 
        8.38         6.05        33.04        38.99         4.01        34.98 
TCGA-AA-A024 TCGA-AD-6889 TCGA-AZ-4315 TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-5797 
       39.06        56.55        58.39        29.56         3.19         3.29 
TCGA-CK-5912 TCGA-D5-6540 TCGA-D5-6541 TCGA-DM-A285 TCGA-F4-6570 TCGA-F4-6703 
       49.08        16.14        15.58         6.12         6.18        35.87 
TCGA-G4-6307 TCGA-G4-6321 
       55.04        22.09 

$`PAK7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       19.99        13.94        19.99        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        4.21         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 
       12.10       100.01         5.23        11.74         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.06         3.25         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 
        1.35        17.56       102.44        40.34        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         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 
       15.12        17.85         4.80        17.13        12.49         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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-F4-6704 
      117.07        98.24         8.61        13.38        13.45         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       44.68        51.75        45.11        36.72        36.00        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  PAK7 MUTATED PAK7 WILD-TYPE 
          3.19           0.00 
  PAK7 MUTATED PAK7 WILD-TYPE 
         58.39         140.38 
  PAK7 MUTATED PAK7 WILD-TYPE 
        25.825         20.120 
[1] "3.2 - 58.4 (25.8)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.8"
D1180V2, 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       24       100         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        18         10         40         31       32        13
                vv
clus             STAGE IVB
  PAK7 MUTATED           0
  PAK7 WILD-TYPE         1
D1180V3, multiclass
            clus
vv           PAK7 MUTATED PAK7 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             9            100
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              3             32
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PAK7 MUTATED     0   4  12   4
  PAK7 WILD-TYPE   9  64 236  37
D1180V4, multiclass
    clus
vv   PAK7 MUTATED PAK7 WILD-TYPE
  T1            0              9
  T2            4             64
  T3           12            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
  PAK7 MUTATED    14   3   3
  PAK7 WILD-TYPE 206  77  63
D1180V5, multiclass
    clus
vv   PAK7 MUTATED PAK7 WILD-TYPE
  N0           14            206
  N1            3             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"
D1180V6, binary
                cls
clus               0   1
  PAK7 MUTATED    14   3
  PAK7 WILD-TYPE 269  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK7 MUTATED     14    3
  PAK7 WILD-TYPE  269   45
   clus
vv  PAK7 MUTATED PAK7 WILD-TYPE
  0           14            269
  1            3             45
[1] 2 2
[1] FALSE
D1180V7, 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
D1180V8, binary
                cls
clus               0   1
  PAK7 MUTATED    15   5
  PAK7 WILD-TYPE 302  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK7 MUTATED     15    5
  PAK7 WILD-TYPE  302   43
                               clus
vv                              PAK7 MUTATED PAK7 WILD-TYPE
  COLON ADENOCARCINOMA                    15            302
  COLON MUCINOUS ADENOCARCINOMA            5             43
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PAK7 MUTATED    13   0   1   1
  PAK7 WILD-TYPE 244   2  21  20
D1180V9, multiclass
    clus
vv   PAK7 MUTATED PAK7 WILD-TYPE
  R0           13            244
  R1            0              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"
D1180V10, 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
D1180V11, 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(1181) Variable = AFF1 MUTATION ANALYSIS
D1181V1, survival
                sevent
clus2              0   1
  AFF1 MUTATED     7   5
  AFF1 WILD-TYPE 275  68
  AFF1 MUTATED AFF1 WILD-TYPE 
            12            343 
  AFF1 MUTATED AFF1 WILD-TYPE 
             5             68 
$`AFF1 MUTATED`
TCGA-A6-6652 TCGA-AA-3869 TCGA-AA-3977 TCGA-AA-A00N TCGA-AY-6197 TCGA-AZ-6601 
       24.69        27.02        25.02         4.01        21.44       100.01 
TCGA-CA-6717 TCGA-CK-5916 TCGA-CM-6170 TCGA-CM-6677 TCGA-D5-5537 TCGA-G4-6588 
        0.33        21.14        15.02        11.08        45.40        26.17 

$`AFF1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       17.03        24.03        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        61.41        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99         2.93         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        16.01        15.02         5.03        15.02        15.02 
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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 
       52.80 

  AFF1 MUTATED AFF1 WILD-TYPE 
          0.33           0.00 
  AFF1 MUTATED AFF1 WILD-TYPE 
        100.01         140.38 
  AFF1 MUTATED AFF1 WILD-TYPE 
        23.065         20.020 
[1] "0.3 - 100.0 (23.1)" "0.0 - 140.4 (20.0)"
[1] "hr=" "2"  
D1181V2, 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       24       104         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        19         10         41         31       34        12
                vv
clus             STAGE IVB
  AFF1 MUTATED           0
  AFF1 WILD-TYPE         1
D1181V3, multiclass
            clus
vv           AFF1 MUTATED AFF1 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             5            104
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 241  39
D1181V4, multiclass
    clus
vv   AFF1 MUTATED AFF1 WILD-TYPE
  T1            1              8
  T2            2             66
  T3            7            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
  AFF1 MUTATED    10   0   2
  AFF1 WILD-TYPE 210  80  64
D1181V5, multiclass
    clus
vv   AFF1 MUTATED AFF1 WILD-TYPE
  N0           10            210
  N1            0             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"
D1181V6, binary
                cls
clus               0   1
  AFF1 MUTATED     7   2
  AFF1 WILD-TYPE 276  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  AFF1 MUTATED      7    2
  AFF1 WILD-TYPE  276   46
   clus
vv  AFF1 MUTATED AFF1 WILD-TYPE
  0            7            276
  1            2             46
[1] 2 2
[1] FALSE
D1181V7, 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
D1181V8, binary
                cls
clus               0   1
  AFF1 MUTATED    10   2
  AFF1 WILD-TYPE 307  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  AFF1 MUTATED     10    2
  AFF1 WILD-TYPE  307   46
                               clus
vv                              AFF1 MUTATED AFF1 WILD-TYPE
  COLON ADENOCARCINOMA                    10            307
  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 252   2  21  18
D1181V9, multiclass
    clus
vv   AFF1 MUTATED AFF1 WILD-TYPE
  R0            5            252
  R1            0              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"
D1181V10, 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
D1181V11, 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(1182) Variable = ING1 MUTATION ANALYSIS
D1182V1, survival
                sevent
clus2              0   1
  ING1 MUTATED     8   2
  ING1 WILD-TYPE 274  71
  ING1 MUTATED ING1 WILD-TYPE 
            10            345 
  ING1 MUTATED ING1 WILD-TYPE 
             2             71 
$`ING1 MUTATED`
TCGA-A6-2672 TCGA-AA-3502 TCGA-AA-3949 TCGA-AA-A010 TCGA-AA-A01F TCGA-AA-A03F 
       46.65        35.01        26.01        34.98        32.02        18.05 
TCGA-CK-4950 TCGA-DM-A28K TCGA-F4-6570 TCGA-G4-6586 
       40.34        98.24         6.18        35.80 

$`ING1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       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        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 
       14.01         0.92        41.00        39.98        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
        1.35        17.56       102.44        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 
      119.93        35.97        60.79       117.07         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 
       45.11        36.72        36.00        22.09        13.78        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  ING1 MUTATED ING1 WILD-TYPE 
          6.18           0.00 
  ING1 MUTATED ING1 WILD-TYPE 
         98.24         140.38 
  ING1 MUTATED ING1 WILD-TYPE 
        34.995         19.990 
[1] "6.2 - 98.2 (35.0)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1.4"
D1182V2, 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       25       106         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ING1 MUTATED           1          1          3          0        0         0
  ING1 WILD-TYPE        18          9         38         31       35        13
                vv
clus             STAGE IVB
  ING1 MUTATED           0
  ING1 WILD-TYPE         1
D1182V3, multiclass
            clus
vv           ING1 MUTATED ING1 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             3            106
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            1              9
  STAGE IIIB            3             38
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ING1 MUTATED     0   1   8   1
  ING1 WILD-TYPE   9  67 240  40
D1182V4, multiclass
    clus
vv   ING1 MUTATED ING1 WILD-TYPE
  T1            0              9
  T2            1             67
  T3            8            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
  ING1 MUTATED     5   4   1
  ING1 WILD-TYPE 215  76  65
D1182V5, multiclass
    clus
vv   ING1 MUTATED ING1 WILD-TYPE
  N0            5            215
  N1            4             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"
D1182V6, binary
                cls
clus               0   1
  ING1 MUTATED    10   0
  ING1 WILD-TYPE 273  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  ING1 MUTATED     10    0
  ING1 WILD-TYPE  273   48
   clus
vv  ING1 MUTATED ING1 WILD-TYPE
  0           10            273
  1            0             48
[1] 2 2
[1] FALSE
D1182V7, 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
D1182V8, binary
                cls
clus               0   1
  ING1 MUTATED     7   3
  ING1 WILD-TYPE 310  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  ING1 MUTATED      7    3
  ING1 WILD-TYPE  310   45
                               clus
vv                              ING1 MUTATED ING1 WILD-TYPE
  COLON ADENOCARCINOMA                     7            310
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ING1 MUTATED     8   1   0   0
  ING1 WILD-TYPE 249   1  22  21
D1182V9, multiclass
    clus
vv   ING1 MUTATED ING1 WILD-TYPE
  R0            8            249
  R1            1              1
  R2            0             22
  RX            0             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1182V10, 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
D1182V11, 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(1183) Variable = C5ORF42 MUTATION ANALYSIS
D1183V1, survival
                   sevent
clus2                 0   1
  C5ORF42 MUTATED    24   7
  C5ORF42 WILD-TYPE 258  66
  C5ORF42 MUTATED C5ORF42 WILD-TYPE 
               31               324 
  C5ORF42 MUTATED C5ORF42 WILD-TYPE 
                7                66 
$`C5ORF42 MUTATED`
TCGA-A6-3809 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6653 
       32.75        29.19        33.53        22.06         8.38        24.39 
TCGA-AA-3511 TCGA-AA-3664 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3950 
        6.97        54.02        26.99        19.04        19.04        24.00 
TCGA-AA-3966 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01P TCGA-AD-5900 TCGA-AD-6963 
        2.01         4.01        34.98        38.07         0.07        27.42 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CA-6718 
       58.39         1.41        12.10       100.01         0.33         0.10 
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        13.45        55.04 
TCGA-G4-6309 
       51.75 

$`C5ORF42 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 
       31.63        30.44        23.61        22.09        32.71        27.09 
TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 
       22.52        25.08        25.18        24.16        21.76        24.69 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01        63.98         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
        6.97         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
        5.03        85.05        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       26.01         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
        6.77        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6703 
      117.07        98.24         8.61        13.38         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       53.62        44.68        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  C5ORF42 MUTATED C5ORF42 WILD-TYPE 
             0.07              0.00 
  C5ORF42 MUTATED C5ORF42 WILD-TYPE 
           100.01            140.38 
  C5ORF42 MUTATED C5ORF42 WILD-TYPE 
            24.00             20.07 
[1] "0.1 - 100.0 (24.0)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1"  
D1183V2, 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       21        95         5         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C5ORF42 MUTATED           1          0          2          1        3
  C5ORF42 WILD-TYPE        18         10         39         30       32
                   vv
clus                STAGE IVA STAGE IVB
  C5ORF42 MUTATED           0         0
  C5ORF42 WILD-TYPE        13         1
D1183V3, multiclass
            clus
vv           C5ORF42 MUTATED C5ORF42 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 4                21
  STAGE IIA               14                95
  STAGE IIB                3                 5
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               0                10
  STAGE IIIB               2                39
  STAGE IIIC               1                30
  STAGE IV                 3                32
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C5ORF42 MUTATED     0   3  23   6
  C5ORF42 WILD-TYPE   9  65 225  35
D1183V4, multiclass
    clus
vv   C5ORF42 MUTATED C5ORF42 WILD-TYPE
  T1               0                 9
  T2               3                65
  T3              23               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
  C5ORF42 MUTATED    25   4   3
  C5ORF42 WILD-TYPE 195  76  63
D1183V5, multiclass
    clus
vv   C5ORF42 MUTATED C5ORF42 WILD-TYPE
  N0              25               195
  N1               4                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"
D1183V6, binary
                   cls
clus                  0   1
  C5ORF42 MUTATED    25   3
  C5ORF42 WILD-TYPE 258  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF42 MUTATED     25    3
  C5ORF42 WILD-TYPE  258   45
   clus
vv  C5ORF42 MUTATED C5ORF42 WILD-TYPE
  0              25               258
  1               3                45
[1] 2 2
[1] FALSE
D1183V7, 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
D1183V8, binary
                   cls
clus                  0   1
  C5ORF42 MUTATED    25   7
  C5ORF42 WILD-TYPE 292  41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF42 MUTATED     25    7
  C5ORF42 WILD-TYPE  292   41
                               clus
vv                              C5ORF42 MUTATED C5ORF42 WILD-TYPE
  COLON ADENOCARCINOMA                       25               292
  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 238   2  21  17
D1183V9, multiclass
    clus
vv   C5ORF42 MUTATED C5ORF42 WILD-TYPE
  R0              19               238
  R1               0                 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"
D1183V10, 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
D1183V11, 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(1184) Variable = ZNF622 MUTATION ANALYSIS
D1184V1, survival
                  sevent
clus2                0   1
  ZNF622 MUTATED     4   3
  ZNF622 WILD-TYPE 278  70
  ZNF622 MUTATED ZNF622 WILD-TYPE 
               7              348 
  ZNF622 MUTATED ZNF622 WILD-TYPE 
               3               70 
$`ZNF622 MUTATED`
TCGA-AA-3663 TCGA-AA-3715 TCGA-CK-4952 TCGA-CK-5916 TCGA-CM-6679 TCGA-D5-6923 
        6.97        19.04        15.62        21.14        10.06        12.43 
TCGA-DM-A0XD 
       24.43 

$`ZNF622 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
      102.44        40.34        49.08        51.32        21.99         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        11.38        10.26       119.70        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  ZNF622 MUTATED ZNF622 WILD-TYPE 
            6.97             0.00 
  ZNF622 MUTATED ZNF622 WILD-TYPE 
           24.43           140.38 
  ZNF622 MUTATED ZNF622 WILD-TYPE 
           15.62            20.63 
[1] "7.0 - 24.4 (15.6)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "3.2"
D1184V2, 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       23       107         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF622 MUTATED           1          0          0          0        0
  ZNF622 WILD-TYPE        18         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF622 MUTATED           0         0
  ZNF622 WILD-TYPE        13         1
D1184V3, multiclass
            clus
vv           ZNF622 MUTATED ZNF622 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               2              107
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF622 MUTATED     1   1   4   1
  ZNF622 WILD-TYPE   8  67 244  40
D1184V4, multiclass
    clus
vv   ZNF622 MUTATED ZNF622 WILD-TYPE
  T1              1                8
  T2              1               67
  T3              4              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
  ZNF622 MUTATED     6   0   1
  ZNF622 WILD-TYPE 214  80  65
D1184V5, multiclass
    clus
vv   ZNF622 MUTATED ZNF622 WILD-TYPE
  N0              6              214
  N1              0               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"
D1184V6, binary
                  cls
clus                 0   1
  ZNF622 MUTATED     7   0
  ZNF622 WILD-TYPE 276  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF622 MUTATED      7    0
  ZNF622 WILD-TYPE  276   48
   clus
vv  ZNF622 MUTATED ZNF622 WILD-TYPE
  0              7              276
  1              0               48
[1] 2 2
[1] FALSE
D1184V7, 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
D1184V8, binary
                  cls
clus                 0   1
  ZNF622 MUTATED     6   1
  ZNF622 WILD-TYPE 311  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF622 MUTATED      6    1
  ZNF622 WILD-TYPE  311   47
                               clus
vv                              ZNF622 MUTATED ZNF622 WILD-TYPE
  COLON ADENOCARCINOMA                       6              311
  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 253   2  22  19
D1184V9, multiclass
    clus
vv   ZNF622 MUTATED ZNF622 WILD-TYPE
  R0              4              253
  R1              0                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"
D1184V10, 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
D1184V11, 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(1185) Variable = OR8K3 MUTATION ANALYSIS
D1185V1, survival
                 sevent
clus2               0   1
  OR8K3 MUTATED    10   0
  OR8K3 WILD-TYPE 272  73
  OR8K3 MUTATED OR8K3 WILD-TYPE 
             10             345 
  OR8K3 MUTATED OR8K3 WILD-TYPE 
              0              73 
$`OR8K3 MUTATED`
TCGA-A6-6141 TCGA-A6-6780 TCGA-AA-3821 TCGA-AA-A010 TCGA-AU-3779 TCGA-CA-6717 
        8.38        20.12         1.02        34.98        14.50         0.33 
TCGA-CA-6718 TCGA-CK-4948 TCGA-DM-A1HB TCGA-G4-6625 
        0.10       102.44       135.65        91.79 

$`OR8K3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 
       35.05        33.04         0.99        25.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07         0.26         1.35 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6628 
       26.17        46.75        52.80 

  OR8K3 MUTATED OR8K3 WILD-TYPE 
            0.1             0.0 
  OR8K3 MUTATED OR8K3 WILD-TYPE 
         135.65          140.38 
  OR8K3 MUTATED OR8K3 WILD-TYPE 
          17.31           20.28 
[1] "0.1 - 135.7 (17.3)" "0.0 - 140.4 (20.3)"
[1] "hr="     "2.7e+07"
D1185V2, 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       25       103         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR8K3 MUTATED           0          1          1          0        0         0
  OR8K3 WILD-TYPE        19          9         40         31       35        13
                 vv
clus              STAGE IVB
  OR8K3 MUTATED           0
  OR8K3 WILD-TYPE         1
D1185V3, multiclass
            clus
vv           OR8K3 MUTATED OR8K3 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              6             103
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR8K3 MUTATED     0   1   8   1
  OR8K3 WILD-TYPE   9  67 240  40
D1185V4, multiclass
    clus
vv   OR8K3 MUTATED OR8K3 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             8             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
  OR8K3 MUTATED     8   2   0
  OR8K3 WILD-TYPE 212  78  66
D1185V5, multiclass
    clus
vv   OR8K3 MUTATED OR8K3 WILD-TYPE
  N0             8             212
  N1             2              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"
D1185V6, binary
                 cls
clus                0   1
  OR8K3 MUTATED     9   0
  OR8K3 WILD-TYPE 274  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR8K3 MUTATED      9    0
  OR8K3 WILD-TYPE  274   48
   clus
vv  OR8K3 MUTATED OR8K3 WILD-TYPE
  0             9             274
  1             0              48
[1] 2 2
[1] FALSE
D1185V7, 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
D1185V8, binary
                 cls
clus                0   1
  OR8K3 MUTATED     7   3
  OR8K3 WILD-TYPE 310  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR8K3 MUTATED      7    3
  OR8K3 WILD-TYPE  310   45
                               clus
vv                              OR8K3 MUTATED OR8K3 WILD-TYPE
  COLON ADENOCARCINOMA                      7             310
  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 252   2  22  19
D1185V9, multiclass
    clus
vv   OR8K3 MUTATED OR8K3 WILD-TYPE
  R0             5             252
  R1             0               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"
D1185V10, 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
D1185V11, 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(1186) Variable = METT5D1 MUTATION ANALYSIS
D1186V1, survival
                   sevent
clus2                 0   1
  METT5D1 MUTATED     6   0
  METT5D1 WILD-TYPE 276  73
  METT5D1 MUTATED METT5D1 WILD-TYPE 
                6               349 
  METT5D1 MUTATED METT5D1 WILD-TYPE 
                0                73 
$`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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        15.75         0.20        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      131.51         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 
       13.25         0.53        35.41        19.43       107.67        65.85 
TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  METT5D1 MUTATED METT5D1 WILD-TYPE 
             2.01              0.00 
  METT5D1 MUTATED METT5D1 WILD-TYPE 
           139.17            140.38 
  METT5D1 MUTATED METT5D1 WILD-TYPE 
            59.62             20.02 
[1] "2.0 - 139.2 (59.6)" "0.0 - 140.4 (20.0)"
[1] "hr="     "2.7e+07"
D1186V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  METT5D1 MUTATED         0        0        0         4         0         0
  METT5D1 WILD-TYPE      64        1       25       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        19         10         40         30       35
                   vv
clus                STAGE IVA STAGE IVB
  METT5D1 MUTATED           0         0
  METT5D1 WILD-TYPE        13         1
D1186V3, multiclass
            clus
vv           METT5D1 MUTATED METT5D1 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                4               105
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               1                30
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  METT5D1 MUTATED     0   1   5   0
  METT5D1 WILD-TYPE   9  67 243  41
D1186V4, multiclass
    clus
vv   METT5D1 MUTATED METT5D1 WILD-TYPE
  T1               0                 9
  T2               1                67
  T3               5               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
  METT5D1 MUTATED     4   1   1
  METT5D1 WILD-TYPE 216  79  65
D1186V5, multiclass
    clus
vv   METT5D1 MUTATED METT5D1 WILD-TYPE
  N0               4               216
  N1               1                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"
D1186V6, binary
                   cls
clus                  0   1
  METT5D1 MUTATED     5   0
  METT5D1 WILD-TYPE 278  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  METT5D1 MUTATED      5    0
  METT5D1 WILD-TYPE  278   48
   clus
vv  METT5D1 MUTATED METT5D1 WILD-TYPE
  0               5               278
  1               0                48
[1] 2 2
[1] FALSE
D1186V7, 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
D1186V8, binary
                   cls
clus                  0   1
  METT5D1 MUTATED     5   1
  METT5D1 WILD-TYPE 312  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  METT5D1 MUTATED      5    1
  METT5D1 WILD-TYPE  312   47
                               clus
vv                              METT5D1 MUTATED METT5D1 WILD-TYPE
  COLON ADENOCARCINOMA                        5               312
  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 254   2  22  21
D1186V9, multiclass
    clus
vv   METT5D1 MUTATED METT5D1 WILD-TYPE
  R0               3               254
  R1               0                 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"
D1186V10, 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
D1186V11, 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(1187) Variable = ESCO1 MUTATION ANALYSIS
D1187V1, survival
                 sevent
clus2               0   1
  ESCO1 MUTATED    10   2
  ESCO1 WILD-TYPE 272  71
  ESCO1 MUTATED ESCO1 WILD-TYPE 
             12             343 
  ESCO1 MUTATED ESCO1 WILD-TYPE 
              2              71 
$`ESCO1 MUTATED`
TCGA-A6-3809 TCGA-A6-6141 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3697 TCGA-AA-3947 
       32.75         8.38        63.98        29.95        85.05        33.01 
TCGA-AA-3977 TCGA-AD-6889 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-5916 
       25.02        56.55        58.39        49.41         0.33        21.14 

$`ESCO1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 
        5.98        37.05        19.00        36.00         5.03        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 
       18.05        31.00         2.01        12.99        24.00        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        4.21         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32        21.99         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  ESCO1 MUTATED ESCO1 WILD-TYPE 
           0.33            0.00 
  ESCO1 MUTATED ESCO1 WILD-TYPE 
          85.05          140.38 
  ESCO1 MUTATED ESCO1 WILD-TYPE 
          32.88           19.99 
[1] "0.3 - 85.0 (32.9)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1.9"
D1187V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ESCO1 MUTATED         1        0        2         6         2         0
  ESCO1 WILD-TYPE      63        1       23       103         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ESCO1 MUTATED           1          0          0          0        0         0
  ESCO1 WILD-TYPE        18         10         41         31       35        13
                 vv
clus              STAGE IVB
  ESCO1 MUTATED           0
  ESCO1 WILD-TYPE         1
D1187V3, multiclass
            clus
vv           ESCO1 MUTATED ESCO1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              6             103
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ESCO1 MUTATED     1   1   9   2
  ESCO1 WILD-TYPE   8  67 239  39
D1187V4, multiclass
    clus
vv   ESCO1 MUTATED ESCO1 WILD-TYPE
  T1             1               8
  T2             1              67
  T3             9             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
  ESCO1 MUTATED    13   0   0
  ESCO1 WILD-TYPE 207  80  66
D1187V5, multiclass
    clus
vv   ESCO1 MUTATED ESCO1 WILD-TYPE
  N0            13             207
  N1             0              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
  ESCO1 MUTATED    11   0
  ESCO1 WILD-TYPE 272  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESCO1 MUTATED     11    0
  ESCO1 WILD-TYPE  272   48
   clus
vv  ESCO1 MUTATED ESCO1 WILD-TYPE
  0            11             272
  1             0              48
[1] 2 2
[1] FALSE
D1187V7, 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
D1187V8, binary
                 cls
clus                0   1
  ESCO1 MUTATED     9   4
  ESCO1 WILD-TYPE 308  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESCO1 MUTATED      9    4
  ESCO1 WILD-TYPE  308   44
                               clus
vv                              ESCO1 MUTATED ESCO1 WILD-TYPE
  COLON ADENOCARCINOMA                      9             308
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ESCO1 MUTATED     7   0   0   2
  ESCO1 WILD-TYPE 250   2  22  19
D1187V9, multiclass
    clus
vv   ESCO1 MUTATED ESCO1 WILD-TYPE
  R0             7             250
  R1             0               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"
D1187V10, 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
D1187V11, 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(1188) Variable = PTCH2 MUTATION ANALYSIS
D1188V1, survival
                 sevent
clus2               0   1
  PTCH2 MUTATED    14   3
  PTCH2 WILD-TYPE 268  70
  PTCH2 MUTATED PTCH2 WILD-TYPE 
             17             338 
  PTCH2 MUTATED PTCH2 WILD-TYPE 
              3              70 
$`PTCH2 MUTATED`
TCGA-A6-6653 TCGA-AA-3510 TCGA-AA-3660 TCGA-AA-3811 TCGA-AA-3821 TCGA-AA-3947 
       24.39        63.98        78.08        10.06         1.02        33.01 
TCGA-AA-A00E TCGA-AD-6889 TCGA-AU-6004 TCGA-AZ-6601 TCGA-CM-4743 TCGA-CM-5348 
       30.02        56.55        27.09       100.01        23.05        22.98 
TCGA-CM-5861 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6928 TCGA-DM-A1D7 
       15.02        17.13        12.49        11.64        13.32 

$`PTCH2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        19.04        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
        0.99        25.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 
       18.05        31.00         2.01        12.99        24.00        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        19.00        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        4.21         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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-5862 TCGA-CM-5863 
       29.06        22.03        30.08        16.01         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       15.12        17.85         4.80        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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 
       24.43        38.20       130.65        92.75        49.91        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  PTCH2 MUTATED PTCH2 WILD-TYPE 
           1.02            0.00 
  PTCH2 MUTATED PTCH2 WILD-TYPE 
         100.01          140.38 
  PTCH2 MUTATED PTCH2 WILD-TYPE 
          23.05           20.07 
[1] "1.0 - 100.0 (23.1)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.5"
D1188V2, 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       22       103         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PTCH2 MUTATED           1          1          2          0        0         0
  PTCH2 WILD-TYPE        18          9         39         31       35        13
                 vv
clus              STAGE IVB
  PTCH2 MUTATED           0
  PTCH2 WILD-TYPE         1
D1188V3, multiclass
            clus
vv           PTCH2 MUTATED PTCH2 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              6             103
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             1               9
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PTCH2 MUTATED     0   3  13   1
  PTCH2 WILD-TYPE   9  65 235  40
D1188V4, multiclass
    clus
vv   PTCH2 MUTATED PTCH2 WILD-TYPE
  T1             0               9
  T2             3              65
  T3            13             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
  PTCH2 MUTATED    14   1   2
  PTCH2 WILD-TYPE 206  79  64
D1188V5, multiclass
    clus
vv   PTCH2 MUTATED PTCH2 WILD-TYPE
  N0            14             206
  N1             1              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"
D1188V6, binary
                 cls
clus                0   1
  PTCH2 MUTATED    17   0
  PTCH2 WILD-TYPE 266  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTCH2 MUTATED     17    0
  PTCH2 WILD-TYPE  266   48
   clus
vv  PTCH2 MUTATED PTCH2 WILD-TYPE
  0            17             266
  1             0              48
[1] 2 2
[1] FALSE
D1188V7, 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
D1188V8, binary
                 cls
clus                0   1
  PTCH2 MUTATED    14   3
  PTCH2 WILD-TYPE 303  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTCH2 MUTATED     14    3
  PTCH2 WILD-TYPE  303   45
                               clus
vv                              PTCH2 MUTATED PTCH2 WILD-TYPE
  COLON ADENOCARCINOMA                     14             303
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PTCH2 MUTATED    13   0   0   0
  PTCH2 WILD-TYPE 244   2  22  21
D1188V9, multiclass
    clus
vv   PTCH2 MUTATED PTCH2 WILD-TYPE
  R0            13             244
  R1             0               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"
D1188V10, 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
D1188V11, 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(1189) Variable = RARG MUTATION ANALYSIS
D1189V1, survival
                sevent
clus2              0   1
  RARG MUTATED     6   3
  RARG WILD-TYPE 276  70
  RARG MUTATED RARG WILD-TYPE 
             9            346 
  RARG MUTATED RARG WILD-TYPE 
             3             70 
$`RARG MUTATED`
TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3713 TCGA-AA-3968 TCGA-AA-A00J TCGA-AA-A02J 
       13.02         1.02        19.04        21.99        18.05         5.03 
TCGA-AY-6386 TCGA-AZ-6598 TCGA-G4-6307 
       17.82        49.41        55.04 

$`RARG WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        1.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02K 
       37.02        39.06        51.98        39.98         2.01        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 
       16.31         0.95        15.75         0.20        21.44        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 
      107.67        74.56        65.85        53.62        44.68        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  RARG MUTATED RARG WILD-TYPE 
          1.02           0.00 
  RARG MUTATED RARG WILD-TYPE 
         55.04         140.38 
  RARG MUTATED RARG WILD-TYPE 
         18.05          20.63 
[1] "1.0 - 55.0 (18.1)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "1.7"
D1189V2, 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       24       107         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        18         10         38         31       33        13
                vv
clus             STAGE IVB
  RARG MUTATED           0
  RARG WILD-TYPE         1
D1189V3, multiclass
            clus
vv           RARG MUTATED RARG WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             2            107
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            3             38
  STAGE IIIC            0             31
  STAGE IV              2             33
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RARG MUTATED     0   1   8   1
  RARG WILD-TYPE   9  67 240  40
D1189V4, multiclass
    clus
vv   RARG MUTATED RARG WILD-TYPE
  T1            0              9
  T2            1             67
  T3            8            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
  RARG MUTATED     6   3   1
  RARG WILD-TYPE 214  77  65
D1189V5, multiclass
    clus
vv   RARG MUTATED RARG WILD-TYPE
  N0            6            214
  N1            3             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"
D1189V6, binary
                cls
clus               0   1
  RARG MUTATED     7   2
  RARG WILD-TYPE 276  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  RARG MUTATED      7    2
  RARG WILD-TYPE  276   46
   clus
vv  RARG MUTATED RARG WILD-TYPE
  0            7            276
  1            2             46
[1] 2 2
[1] FALSE
D1189V7, 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
D1189V8, binary
                cls
clus               0   1
  RARG MUTATED     8   2
  RARG WILD-TYPE 309  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  RARG MUTATED      8    2
  RARG WILD-TYPE  309   46
                               clus
vv                              RARG MUTATED RARG WILD-TYPE
  COLON ADENOCARCINOMA                     8            309
  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 251   2  20  21
D1189V9, multiclass
    clus
vv   RARG MUTATED RARG WILD-TYPE
  R0            6            251
  R1            0              2
  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"
D1189V10, 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
D1189V11, 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(1190) Variable = PPYR1 MUTATION ANALYSIS
D1190V1, survival
                 sevent
clus2               0   1
  PPYR1 MUTATED     3   1
  PPYR1 WILD-TYPE 279  72
  PPYR1 MUTATED PPYR1 WILD-TYPE 
              4             351 
  PPYR1 MUTATED PPYR1 WILD-TYPE 
              1              72 
$`PPYR1 MUTATED`
TCGA-AU-6004 TCGA-CM-6674 TCGA-G4-6586 TCGA-G4-6626 
       27.09        12.95        35.80        46.75 

$`PPYR1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       26.17        91.79        52.80 

  PPYR1 MUTATED PPYR1 WILD-TYPE 
          12.95            0.00 
  PPYR1 MUTATED PPYR1 WILD-TYPE 
          46.75          140.38 
  PPYR1 MUTATED PPYR1 WILD-TYPE 
         31.445          20.120 
[1] "12.9 - 46.8 (31.4)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.1"
D1190V2, 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       25       105         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        19         10         41         31       35        13
                 vv
clus              STAGE IVB
  PPYR1 MUTATED           0
  PPYR1 WILD-TYPE         1
D1190V3, multiclass
            clus
vv           PPYR1 MUTATED PPYR1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              4             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PPYR1 MUTATED     0   1   4   0
  PPYR1 WILD-TYPE   9  67 244  41
D1190V4, multiclass
    clus
vv   PPYR1 MUTATED PPYR1 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             4             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
  PPYR1 MUTATED     5   0   0
  PPYR1 WILD-TYPE 215  80  66
D1190V5, multiclass
    clus
vv   PPYR1 MUTATED PPYR1 WILD-TYPE
  N0             5             215
  N1             0              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"
D1190V6, binary
                 cls
clus                0   1
  PPYR1 MUTATED     5   0
  PPYR1 WILD-TYPE 278  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPYR1 MUTATED      5    0
  PPYR1 WILD-TYPE  278   48
   clus
vv  PPYR1 MUTATED PPYR1 WILD-TYPE
  0             5             278
  1             0              48
[1] 2 2
[1] FALSE
D1190V7, 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
D1190V8, binary
                 cls
clus                0   1
  PPYR1 MUTATED     5   0
  PPYR1 WILD-TYPE 312  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPYR1 MUTATED      5    0
  PPYR1 WILD-TYPE  312   48
                               clus
vv                              PPYR1 MUTATED PPYR1 WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  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 252   2  22  21
D1190V9, multiclass
    clus
vv   PPYR1 MUTATED PPYR1 WILD-TYPE
  R0             5             252
  R1             0               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"
D1190V10, 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
D1190V11, 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(1191) Variable = ERCC6 MUTATION ANALYSIS
D1191V1, survival
                 sevent
clus2               0   1
  ERCC6 MUTATED    20   6
  ERCC6 WILD-TYPE 262  67
  ERCC6 MUTATED ERCC6 WILD-TYPE 
             26             329 
  ERCC6 MUTATED ERCC6 WILD-TYPE 
              6              67 
$`ERCC6 MUTATED`
TCGA-A6-2676 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6652 TCGA-AA-3496 TCGA-AA-3510 
       42.90        22.06         8.38        24.69         1.02        63.98 
TCGA-AA-3554 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3697 TCGA-AA-3977 TCGA-AA-A00J 
       17.95         6.97         2.01        85.05        25.02        18.05 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6964 TCGA-AY-6197 TCGA-AZ-4315 TCGA-CA-6717 
        4.01        34.98        10.88        21.44        58.39         0.33 
TCGA-CK-5913 TCGA-D5-6540 TCGA-DM-A1D4 TCGA-DM-A28H TCGA-F4-6703 TCGA-F4-6856 
       51.32        16.14        92.75       117.07        35.87        19.43 
TCGA-G4-6303 TCGA-G4-6586 
       65.85        35.80 

$`ERCC6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       32.71        27.09        22.52        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       21.76        24.39        23.87        20.12        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        7.04         3.02        35.01         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
        0.20        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 
       10.26       119.70        24.43        38.20       130.65        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 
        0.53        35.41       107.67        74.56        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        26.17        91.79        46.75        52.80 

  ERCC6 MUTATED ERCC6 WILD-TYPE 
           0.33            0.00 
  ERCC6 MUTATED ERCC6 WILD-TYPE 
         117.07          140.38 
  ERCC6 MUTATED ERCC6 WILD-TYPE 
         23.375          20.020 
[1] "0.3 - 117.1 (23.4)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.2"
D1191V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ERCC6 MUTATED         2        0        4        10         3         0
  ERCC6 WILD-TYPE      62        1       21        99         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ERCC6 MUTATED           2          0          1          1        1         1
  ERCC6 WILD-TYPE        17         10         40         30       34        12
                 vv
clus              STAGE IVB
  ERCC6 MUTATED           0
  ERCC6 WILD-TYPE         1
D1191V3, multiclass
            clus
vv           ERCC6 MUTATED ERCC6 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               4              21
  STAGE IIA             10              99
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  18   6
  ERCC6 WILD-TYPE   9  65 230  35
D1191V4, multiclass
    clus
vv   ERCC6 MUTATED ERCC6 WILD-TYPE
  T1             0               9
  T2             3              65
  T3            18             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   2
  ERCC6 WILD-TYPE 198  77  64
D1191V5, multiclass
    clus
vv   ERCC6 MUTATED ERCC6 WILD-TYPE
  N0            22             198
  N1             3              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"
D1191V6, binary
                 cls
clus                0   1
  ERCC6 MUTATED    21   2
  ERCC6 WILD-TYPE 262  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC6 MUTATED     21    2
  ERCC6 WILD-TYPE  262   46
   clus
vv  ERCC6 MUTATED ERCC6 WILD-TYPE
  0            21             262
  1             2              46
[1] 2 2
[1] FALSE
D1191V7, binary
                 cls
clus                0   1
  ERCC6 MUTATED     9  18
  ERCC6 WILD-TYPE 161 179
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC6 MUTATED      9   18
  ERCC6 WILD-TYPE  161  179
        clus
vv       ERCC6 MUTATED ERCC6 WILD-TYPE
  FEMALE             9             161
  MALE              18             179
[1] 2 2
[1] FALSE
D1191V8, binary
                 cls
clus                0   1
  ERCC6 MUTATED    22   5
  ERCC6 WILD-TYPE 295  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC6 MUTATED     22    5
  ERCC6 WILD-TYPE  295   43
                               clus
vv                              ERCC6 MUTATED ERCC6 WILD-TYPE
  COLON ADENOCARCINOMA                     22             295
  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 238   2  22  19
D1191V9, multiclass
    clus
vv   ERCC6 MUTATED ERCC6 WILD-TYPE
  R0            19             238
  R1             0               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"
D1191V10, 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    13
  ERCC6 WILD-TYPE                        17   163
D1191V11, 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                                       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(1192) Variable = NHLRC2 MUTATION ANALYSIS
D1192V1, survival
                  sevent
clus2                0   1
  NHLRC2 MUTATED     8   0
  NHLRC2 WILD-TYPE 274  73
  NHLRC2 MUTATED NHLRC2 WILD-TYPE 
               8              347 
  NHLRC2 MUTATED NHLRC2 WILD-TYPE 
               0               73 
$`NHLRC2 MUTATED`
TCGA-AA-3510 TCGA-AA-A01R TCGA-AD-6889 TCGA-AD-6965 TCGA-AY-5543 TCGA-CM-4746 
       63.98        35.01        56.55         0.20        15.75        37.02 
TCGA-D5-6536 TCGA-G4-6309 
       17.85        51.75 

$`NHLRC2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-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-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  NHLRC2 MUTATED NHLRC2 WILD-TYPE 
             0.2              0.0 
  NHLRC2 MUTATED NHLRC2 WILD-TYPE 
           63.98           140.38 
  NHLRC2 MUTATED NHLRC2 WILD-TYPE 
          36.015           20.120 
[1] "0.2 - 64.0 (36.0)"  "0.0 - 140.4 (20.1)"
[1] "hr="     "2.6e+07"
D1192V2, 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       24       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NHLRC2 MUTATED           1          0          1          0        0
  NHLRC2 WILD-TYPE        18         10         40         31       35
                  vv
clus               STAGE IVA STAGE IVB
  NHLRC2 MUTATED           1         0
  NHLRC2 WILD-TYPE        12         1
D1192V3, multiclass
            clus
vv           NHLRC2 MUTATED NHLRC2 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               3              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 241  40
D1192V4, multiclass
    clus
vv   NHLRC2 MUTATED NHLRC2 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              7              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
  NHLRC2 MUTATED     5   2   2
  NHLRC2 WILD-TYPE 215  78  64
D1192V5, multiclass
    clus
vv   NHLRC2 MUTATED NHLRC2 WILD-TYPE
  N0              5              215
  N1              2               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
  NHLRC2 MUTATED     7   1
  NHLRC2 WILD-TYPE 276  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NHLRC2 MUTATED      7    1
  NHLRC2 WILD-TYPE  276   47
   clus
vv  NHLRC2 MUTATED NHLRC2 WILD-TYPE
  0              7              276
  1              1               47
[1] 2 2
[1] FALSE
D1192V7, 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
D1192V8, binary
                  cls
clus                 0   1
  NHLRC2 MUTATED     8   1
  NHLRC2 WILD-TYPE 309  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NHLRC2 MUTATED      8    1
  NHLRC2 WILD-TYPE  309   47
                               clus
vv                              NHLRC2 MUTATED NHLRC2 WILD-TYPE
  COLON ADENOCARCINOMA                       8              309
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  NHLRC2 MUTATED     7   0   0   0
  NHLRC2 WILD-TYPE 250   2  22  21
D1192V9, multiclass
    clus
vv   NHLRC2 MUTATED NHLRC2 WILD-TYPE
  R0              7              250
  R1              0                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"
D1192V10, 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
D1192V11, 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(1193) Variable = NRAP MUTATION ANALYSIS
D1193V1, survival
                sevent
clus2              0   1
  NRAP MUTATED    20   4
  NRAP WILD-TYPE 262  69
  NRAP MUTATED NRAP WILD-TYPE 
            24            331 
  NRAP MUTATED NRAP WILD-TYPE 
             4             69 
$`NRAP MUTATED`
TCGA-A6-6141 TCGA-A6-6780 TCGA-AA-3510 TCGA-AA-3811 TCGA-AA-3854 TCGA-AA-A00N 
        8.38        20.12        63.98        10.06        36.03         4.01 
TCGA-AA-A010 TCGA-AD-6889 TCGA-AD-6964 TCGA-AU-3779 TCGA-AU-6004 TCGA-AZ-6606 
       34.98        56.55        10.88        14.50        27.09        11.74 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4952 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-6162 
        0.33         0.10        15.62        30.08        15.02        12.00 
TCGA-D5-6529 TCGA-D5-6930 TCGA-DM-A28E TCGA-F4-6703 TCGA-G4-6586 TCGA-G4-6588 
       20.19         1.51       119.93        35.87        35.80        26.17 

$`NRAP WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        19.04        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
       33.07         0.00        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        4.21         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
        0.20        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07         0.26         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      102.44        40.34        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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        16.01 
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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       19.59        13.51        11.51        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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-A285 TCGA-DM-A28C TCGA-DM-A28F 
      131.51       135.65       139.17         6.12        81.37        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 
       36.72        36.00        22.09        13.78        91.79        46.75 
TCGA-G4-6628 
       52.80 

  NRAP MUTATED NRAP WILD-TYPE 
           0.1            0.0 
  NRAP MUTATED NRAP WILD-TYPE 
        119.93         140.38 
  NRAP MUTATED NRAP WILD-TYPE 
         17.87          20.98 
[1] "0.1 - 119.9 (17.9)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.2"
D1193V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NRAP MUTATED         2        0        1        15         2         0
  NRAP WILD-TYPE      62        1       24        94         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NRAP MUTATED           2          0          1          0        2         0
  NRAP WILD-TYPE        17         10         40         31       33        13
                vv
clus             STAGE IVB
  NRAP MUTATED           0
  NRAP WILD-TYPE         1
D1193V3, multiclass
            clus
vv           NRAP MUTATED NRAP WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA            15             94
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             2             17
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              2             33
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NRAP MUTATED     0   2  18   6
  NRAP WILD-TYPE   9  66 230  35
D1193V4, multiclass
    clus
vv   NRAP MUTATED NRAP WILD-TYPE
  T1            0              9
  T2            2             66
  T3           18            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
  NRAP MUTATED    20   1   5
  NRAP WILD-TYPE 200  79  61
D1193V5, multiclass
    clus
vv   NRAP MUTATED NRAP WILD-TYPE
  N0           20            200
  N1            1             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"
D1193V6, binary
                cls
clus               0   1
  NRAP MUTATED    22   2
  NRAP WILD-TYPE 261  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAP MUTATED     22    2
  NRAP WILD-TYPE  261   46
   clus
vv  NRAP MUTATED NRAP WILD-TYPE
  0           22            261
  1            2             46
[1] 2 2
[1] FALSE
D1193V7, binary
                cls
clus               0   1
  NRAP MUTATED    14  12
  NRAP WILD-TYPE 156 185
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAP MUTATED     14   12
  NRAP WILD-TYPE  156  185
        clus
vv       NRAP MUTATED NRAP WILD-TYPE
  FEMALE           14            156
  MALE             12            185
[1] 2 2
[1] FALSE
D1193V8, binary
                cls
clus               0   1
  NRAP MUTATED    18   8
  NRAP WILD-TYPE 299  40
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAP MUTATED     18    8
  NRAP WILD-TYPE  299   40
                               clus
vv                              NRAP MUTATED NRAP WILD-TYPE
  COLON ADENOCARCINOMA                    18            299
  COLON MUCINOUS ADENOCARCINOMA            8             40
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  NRAP MUTATED    16   0   1   3
  NRAP WILD-TYPE 241   2  21  18
D1193V9, multiclass
    clus
vv   NRAP MUTATED NRAP WILD-TYPE
  R0           16            241
  R1            0              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"
D1193V10, 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    15
  NRAP WILD-TYPE                        18   161
D1193V11, 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                                      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(1194) Variable = FABP2 MUTATION ANALYSIS
D1194V1, survival
                 sevent
clus2               0   1
  FABP2 MUTATED     7   1
  FABP2 WILD-TYPE 275  72
  FABP2 MUTATED FABP2 WILD-TYPE 
              8             347 
  FABP2 MUTATED FABP2 WILD-TYPE 
              1              72 
$`FABP2 MUTATED`
TCGA-A6-6137 TCGA-AA-3977 TCGA-AZ-4315 TCGA-AZ-6599 TCGA-CM-6677 TCGA-D5-5540 
       27.09        25.02        58.39         6.77        11.08        13.51 
TCGA-D5-6540 TCGA-G4-6309 
       16.14        51.75 

$`FABP2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        32.71        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41        49.41        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       12.26        19.59        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  FABP2 MUTATED FABP2 WILD-TYPE 
           6.77            0.00 
  FABP2 MUTATED FABP2 WILD-TYPE 
          58.39          140.38 
  FABP2 MUTATED FABP2 WILD-TYPE 
          20.58           20.19 
[1] "6.8 - 58.4 (20.6)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.8"
D1194V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FABP2 MUTATED         2        0        0         3         0         0
  FABP2 WILD-TYPE      62        1       25       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        19         10         39         31       35        13
                 vv
clus              STAGE IVB
  FABP2 MUTATED           0
  FABP2 WILD-TYPE         1
D1194V3, multiclass
            clus
vv           FABP2 MUTATED FABP2 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              3             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FABP2 MUTATED     0   3   5   0
  FABP2 WILD-TYPE   9  65 243  41
D1194V4, multiclass
    clus
vv   FABP2 MUTATED FABP2 WILD-TYPE
  T1             0               9
  T2             3              65
  T3             5             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
  FABP2 MUTATED     6   2   0
  FABP2 WILD-TYPE 214  78  66
D1194V5, multiclass
    clus
vv   FABP2 MUTATED FABP2 WILD-TYPE
  N0             6             214
  N1             2              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"
D1194V6, binary
                 cls
clus                0   1
  FABP2 MUTATED     6   0
  FABP2 WILD-TYPE 277  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FABP2 MUTATED      6    0
  FABP2 WILD-TYPE  277   48
   clus
vv  FABP2 MUTATED FABP2 WILD-TYPE
  0             6             277
  1             0              48
[1] 2 2
[1] FALSE
D1194V7, binary
                 cls
clus                0   1
  FABP2 MUTATED     2   6
  FABP2 WILD-TYPE 168 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FABP2 MUTATED      2    6
  FABP2 WILD-TYPE  168  191
        clus
vv       FABP2 MUTATED FABP2 WILD-TYPE
  FEMALE             2             168
  MALE               6             191
[1] 2 2
[1] FALSE
D1194V8, binary
                 cls
clus                0   1
  FABP2 MUTATED     7   1
  FABP2 WILD-TYPE 310  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FABP2 MUTATED      7    1
  FABP2 WILD-TYPE  310   47
                               clus
vv                              FABP2 MUTATED FABP2 WILD-TYPE
  COLON ADENOCARCINOMA                      7             310
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  FABP2 MUTATED     5   0   0   0
  FABP2 WILD-TYPE 252   2  22  21
D1194V9, multiclass
    clus
vv   FABP2 MUTATED FABP2 WILD-TYPE
  R0             5             252
  R1             0               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"
D1194V10, 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     6
  FABP2 WILD-TYPE                        18   170
D1194V11, 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                                        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(1195) Variable = KIF16B MUTATION ANALYSIS
D1195V1, survival
                  sevent
clus2                0   1
  KIF16B MUTATED    21   3
  KIF16B WILD-TYPE 261  70
  KIF16B MUTATED KIF16B WILD-TYPE 
              24              331 
  KIF16B MUTATED KIF16B WILD-TYPE 
               3               70 
$`KIF16B MUTATED`
TCGA-A6-6653 TCGA-AA-3663 TCGA-AA-3815 TCGA-AA-3864 TCGA-AA-3949 TCGA-AA-3950 
       24.39         6.97        33.04        53.00        26.01        24.00 
TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00E TCGA-AA-A00N TCGA-AD-6548 TCGA-AY-6196 
        2.01        25.02        30.02         4.01        21.37         0.20 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-CA-5797 TCGA-CA-6717 TCGA-CK-5913 TCGA-CK-5914 
       17.82        58.39         3.29         0.33        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         1.51         6.18 

$`KIF16B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       33.01         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       19.00        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4323 
       27.09        16.31         0.95        15.75        21.44         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 
        3.19         1.94         2.24         3.06         3.25         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        49.08        21.14         2.93         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        16.01         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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85        17.13        12.49        16.14        15.58         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-D5-6931 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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        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        13.38        13.45        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  KIF16B MUTATED KIF16B WILD-TYPE 
             0.2              0.0 
  KIF16B MUTATED KIF16B WILD-TYPE 
           58.39           140.38 
  KIF16B MUTATED KIF16B WILD-TYPE 
           16.42            20.28 
[1] "0.2 - 58.4 (16.4)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.3"
D1195V2, 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       22        98         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIF16B MUTATED           0          0          4          1        0
  KIF16B WILD-TYPE        19         10         37         30       35
                  vv
clus               STAGE IVA STAGE IVB
  KIF16B MUTATED           0         0
  KIF16B WILD-TYPE        13         1
D1195V3, multiclass
            clus
vv           KIF16B MUTATED KIF16B WILD-TYPE
  STAGE I                 5               59
  STAGE IA                0                1
  STAGE II                3               22
  STAGE IIA              11               98
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              4               37
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  KIF16B MUTATED     0   6  18   2
  KIF16B WILD-TYPE   9  62 230  39
D1195V4, multiclass
    clus
vv   KIF16B MUTATED KIF16B WILD-TYPE
  T1              0                9
  T2              6               62
  T3             18              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
  KIF16B MUTATED    21   4   1
  KIF16B WILD-TYPE 199  76  65
D1195V5, multiclass
    clus
vv   KIF16B MUTATED KIF16B WILD-TYPE
  N0             21              199
  N1              4               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"
D1195V6, binary
                  cls
clus                 0   1
  KIF16B MUTATED    20   0
  KIF16B WILD-TYPE 263  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF16B MUTATED     20    0
  KIF16B WILD-TYPE  263   48
   clus
vv  KIF16B MUTATED KIF16B WILD-TYPE
  0             20              263
  1              0               48
[1] 2 2
[1] FALSE
D1195V7, 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
D1195V8, binary
                  cls
clus                 0   1
  KIF16B MUTATED    19   7
  KIF16B WILD-TYPE 298  41
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF16B MUTATED     19    7
  KIF16B WILD-TYPE  298   41
                               clus
vv                              KIF16B MUTATED KIF16B WILD-TYPE
  COLON ADENOCARCINOMA                      19              298
  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 238   2  22  17
D1195V9, multiclass
    clus
vv   KIF16B MUTATED KIF16B WILD-TYPE
  R0             19              238
  R1              0                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"
D1195V10, 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
D1195V11, 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(1196) Variable = TAB3 MUTATION ANALYSIS
D1196V1, survival
                sevent
clus2              0   1
  TAB3 MUTATED     7   2
  TAB3 WILD-TYPE 275  71
  TAB3 MUTATED TAB3 WILD-TYPE 
             9            346 
  TAB3 MUTATED TAB3 WILD-TYPE 
             2             71 
$`TAB3 MUTATED`
TCGA-A6-5662 TCGA-AA-3966 TCGA-AA-A00N TCGA-AA-A01R TCGA-AZ-5403 TCGA-CA-6718 
       23.61         2.01         4.01        35.01        62.79         0.10 
TCGA-CM-5348 TCGA-F4-6807 TCGA-G4-6628 
       22.98        16.24        52.80 

$`TAB3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        33.53        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       29.59        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       35.80        26.17        91.79        46.75 

  TAB3 MUTATED TAB3 WILD-TYPE 
           0.1            0.0 
  TAB3 MUTATED TAB3 WILD-TYPE 
         62.79         140.38 
  TAB3 MUTATED TAB3 WILD-TYPE 
        22.980         20.155 
[1] "0.1 - 62.8 (23.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D1196V2, 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       24       107         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        17         10         40         30       35        12
                vv
clus             STAGE IVB
  TAB3 MUTATED           0
  TAB3 WILD-TYPE         1
D1196V3, multiclass
            clus
vv           TAB3 MUTATED TAB3 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             2            107
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             2             17
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            1             30
  STAGE IV              0             35
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 240  40
D1196V4, multiclass
    clus
vv   TAB3 MUTATED TAB3 WILD-TYPE
  T1            0              9
  T2            1             67
  T3            8            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
  TAB3 MUTATED     5   1   4
  TAB3 WILD-TYPE 215  79  62
D1196V5, multiclass
    clus
vv   TAB3 MUTATED TAB3 WILD-TYPE
  N0            5            215
  N1            1             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"
D1196V6, binary
                cls
clus               0   1
  TAB3 MUTATED     8   1
  TAB3 WILD-TYPE 275  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAB3 MUTATED      8    1
  TAB3 WILD-TYPE  275   47
   clus
vv  TAB3 MUTATED TAB3 WILD-TYPE
  0            8            275
  1            1             47
[1] 2 2
[1] FALSE
D1196V7, 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
D1196V8, binary
                cls
clus               0   1
  TAB3 MUTATED     7   3
  TAB3 WILD-TYPE 310  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAB3 MUTATED      7    3
  TAB3 WILD-TYPE  310   45
                               clus
vv                              TAB3 MUTATED TAB3 WILD-TYPE
  COLON ADENOCARCINOMA                     7            310
  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 251   2  22  20
D1196V9, multiclass
    clus
vv   TAB3 MUTATED TAB3 WILD-TYPE
  R0            6            251
  R1            0              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"
D1196V10, 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
D1196V11, 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(1197) Variable = C16ORF45 MUTATION ANALYSIS
D1197V1, survival
                    sevent
clus2                  0   1
  C16ORF45 MUTATED     5   0
  C16ORF45 WILD-TYPE 277  73
  C16ORF45 MUTATED C16ORF45 WILD-TYPE 
                 5                350 
  C16ORF45 MUTATED C16ORF45 WILD-TYPE 
                 0                 73 
$`C16ORF45 MUTATED`
TCGA-A6-6141 TCGA-AA-3941 TCGA-AA-3982 TCGA-F4-6703 TCGA-G4-6306 
        8.38        24.00        27.02        35.87        44.68 

$`C16ORF45 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  C16ORF45 MUTATED C16ORF45 WILD-TYPE 
              8.38               0.00 
  C16ORF45 MUTATED C16ORF45 WILD-TYPE 
             44.68             140.38 
  C16ORF45 MUTATED C16ORF45 WILD-TYPE 
             27.02              20.07 
[1] "8.4 - 44.7 (27.0)"  "0.0 - 140.4 (20.1)"
[1] "hr="     "9100000"
D1197V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C16ORF45 MUTATED         0        0        0         3         0         0
  C16ORF45 WILD-TYPE      64        1       25       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        19         10         40         31       35
                    vv
clus                 STAGE IVA STAGE IVB
  C16ORF45 MUTATED           1         0
  C16ORF45 WILD-TYPE        12         1
D1197V3, multiclass
            clus
vv           C16ORF45 MUTATED C16ORF45 WILD-TYPE
  STAGE I                   0                 64
  STAGE IA                  0                  1
  STAGE II                  0                 25
  STAGE IIA                 3                106
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                0                 10
  STAGE IIIB                1                 40
  STAGE IIIC                0                 31
  STAGE IV                  0                 35
  STAGE IVA                 1                 12
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 245  40
D1197V4, multiclass
    clus
vv   C16ORF45 MUTATED C16ORF45 WILD-TYPE
  T1                0                  9
  T2                1                 67
  T3                3                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
  C16ORF45 MUTATED     3   2   0
  C16ORF45 WILD-TYPE 217  78  66
D1197V5, multiclass
    clus
vv   C16ORF45 MUTATED C16ORF45 WILD-TYPE
  N0                3                217
  N1                2                 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"
D1197V6, binary
                    cls
clus                   0   1
  C16ORF45 MUTATED     4   1
  C16ORF45 WILD-TYPE 279  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF45 MUTATED      4    1
  C16ORF45 WILD-TYPE  279   47
   clus
vv  C16ORF45 MUTATED C16ORF45 WILD-TYPE
  0                4                279
  1                1                 47
[1] 2 2
[1] FALSE
D1197V7, 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
D1197V8, binary
                    cls
clus                   0   1
  C16ORF45 MUTATED     5   0
  C16ORF45 WILD-TYPE 312  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF45 MUTATED      5    0
  C16ORF45 WILD-TYPE  312   48
                               clus
vv                              C16ORF45 MUTATED C16ORF45 WILD-TYPE
  COLON ADENOCARCINOMA                         5                312
  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 254   2  22  21
D1197V9, multiclass
    clus
vv   C16ORF45 MUTATED C16ORF45 WILD-TYPE
  R0                3                254
  R1                0                  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"
D1197V10, 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
D1197V11, 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(1198) Variable = A1CF MUTATION ANALYSIS
D1198V1, survival
                sevent
clus2              0   1
  A1CF MUTATED     7   0
  A1CF WILD-TYPE 275  73
  A1CF MUTATED A1CF WILD-TYPE 
             7            348 
  A1CF MUTATED A1CF WILD-TYPE 
             0             73 
$`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         0.33        16.01        11.08 
TCGA-G4-6307 
       55.04 

$`A1CF WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  A1CF MUTATED A1CF WILD-TYPE 
          0.33           0.00 
  A1CF MUTATED A1CF WILD-TYPE 
         55.04         140.38 
  A1CF MUTATED A1CF WILD-TYPE 
        25.020         20.155 
[1] "0.3 - 55.0 (25.0)"  "0.0 - 140.4 (20.2)"
[1] "hr="     "9200000"
D1198V2, 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       25       106         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        19         10         40         30       35        13
                vv
clus             STAGE IVB
  A1CF MUTATED           0
  A1CF WILD-TYPE         1
D1198V3, multiclass
            clus
vv           A1CF MUTATED A1CF WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             3            106
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            1             30
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  A1CF MUTATED     0   2   5   1
  A1CF WILD-TYPE   9  66 243  40
D1198V4, multiclass
    clus
vv   A1CF MUTATED A1CF WILD-TYPE
  T1            0              9
  T2            2             66
  T3            5            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
  A1CF MUTATED     6   1   1
  A1CF WILD-TYPE 214  79  65
D1198V5, multiclass
    clus
vv   A1CF MUTATED A1CF WILD-TYPE
  N0            6            214
  N1            1             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"
D1198V6, binary
                cls
clus               0   1
  A1CF MUTATED     7   0
  A1CF WILD-TYPE 276  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  A1CF MUTATED      7    0
  A1CF WILD-TYPE  276   48
   clus
vv  A1CF MUTATED A1CF WILD-TYPE
  0            7            276
  1            0             48
[1] 2 2
[1] FALSE
D1198V7, 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
D1198V8, binary
                cls
clus               0   1
  A1CF MUTATED     6   2
  A1CF WILD-TYPE 311  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  A1CF MUTATED      6    2
  A1CF WILD-TYPE  311   46
                               clus
vv                              A1CF MUTATED A1CF WILD-TYPE
  COLON ADENOCARCINOMA                     6            311
  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 252   2  22  20
D1198V9, multiclass
    clus
vv   A1CF MUTATED A1CF WILD-TYPE
  R0            5            252
  R1            0              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"
D1198V10, 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
D1198V11, 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(1199) Variable = NUPL2 MUTATION ANALYSIS
D1199V1, survival
                 sevent
clus2               0   1
  NUPL2 MUTATED     7   4
  NUPL2 WILD-TYPE 275  69
  NUPL2 MUTATED NUPL2 WILD-TYPE 
             11             344 
  NUPL2 MUTATED NUPL2 WILD-TYPE 
              4              69 
$`NUPL2 MUTATED`
TCGA-AA-3510 TCGA-AA-3815 TCGA-AA-A00E TCGA-AA-A00K TCGA-AA-A010 TCGA-AD-6895 
       63.98        33.04        30.02        18.05        34.98         0.72 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-CK-5916 TCGA-CM-4743 TCGA-DM-A0XF 
       12.10        29.56        21.14        23.05        38.20 

$`NUPL2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       19.00        34.03        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
        0.07        21.37         4.21        56.55         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 
       61.41        49.41         6.77       100.01         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  NUPL2 MUTATED NUPL2 WILD-TYPE 
           0.72            0.00 
  NUPL2 MUTATED NUPL2 WILD-TYPE 
          63.98          140.38 
  NUPL2 MUTATED NUPL2 WILD-TYPE 
         29.560          20.005 
[1] "0.7 - 64.0 (29.6)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1.8"
D1199V2, 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       24       105         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NUPL2 MUTATED           0          0          0          1        1         0
  NUPL2 WILD-TYPE        19         10         41         30       34        13
                 vv
clus              STAGE IVB
  NUPL2 MUTATED           0
  NUPL2 WILD-TYPE         1
D1199V3, multiclass
            clus
vv           NUPL2 MUTATED NUPL2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              4             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NUPL2 MUTATED     1   1   7   2
  NUPL2 WILD-TYPE   8  67 241  39
D1199V4, multiclass
    clus
vv   NUPL2 MUTATED NUPL2 WILD-TYPE
  T1             1               8
  T2             1              67
  T3             7             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
  NUPL2 MUTATED     7   3   1
  NUPL2 WILD-TYPE 213  77  65
D1199V5, multiclass
    clus
vv   NUPL2 MUTATED NUPL2 WILD-TYPE
  N0             7             213
  N1             3              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"
D1199V6, binary
                 cls
clus                0   1
  NUPL2 MUTATED     8   1
  NUPL2 WILD-TYPE 275  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUPL2 MUTATED      8    1
  NUPL2 WILD-TYPE  275   47
   clus
vv  NUPL2 MUTATED NUPL2 WILD-TYPE
  0             8             275
  1             1              47
[1] 2 2
[1] FALSE
D1199V7, 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
D1199V8, binary
                 cls
clus                0   1
  NUPL2 MUTATED    10   1
  NUPL2 WILD-TYPE 307  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUPL2 MUTATED     10    1
  NUPL2 WILD-TYPE  307   47
                               clus
vv                              NUPL2 MUTATED NUPL2 WILD-TYPE
  COLON ADENOCARCINOMA                     10             307
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  NUPL2 MUTATED     6   0   0   1
  NUPL2 WILD-TYPE 251   2  22  20
D1199V9, multiclass
    clus
vv   NUPL2 MUTATED NUPL2 WILD-TYPE
  R0             6             251
  R1             0               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"
D1199V10, 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
D1199V11, 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(1200) Variable = MRPS22 MUTATION ANALYSIS
D1200V1, survival
                  sevent
clus2                0   1
  MRPS22 MUTATED     8   2
  MRPS22 WILD-TYPE 274  71
  MRPS22 MUTATED MRPS22 WILD-TYPE 
              10              345 
  MRPS22 MUTATED MRPS22 WILD-TYPE 
               2               71 
$`MRPS22 MUTATED`
TCGA-A6-5661 TCGA-AA-3977 TCGA-AA-A010 TCGA-AY-6197 TCGA-AZ-6603 TCGA-AZ-6608 
       33.53        25.02        34.98        21.44        29.56         1.94 
TCGA-CM-4743 TCGA-D5-6541 TCGA-DM-A1HB TCGA-G4-6317 
       23.05        15.58       135.65        36.00 

$`MRPS22 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
      100.01         5.23        11.74         3.19         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       45.11        36.72        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  MRPS22 MUTATED MRPS22 WILD-TYPE 
            1.94             0.00 
  MRPS22 MUTATED MRPS22 WILD-TYPE 
          135.65           140.38 
  MRPS22 MUTATED MRPS22 WILD-TYPE 
           27.29            19.99 
[1] "1.9 - 135.7 (27.3)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.2"
D1200V2, 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       25       105         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MRPS22 MUTATED           0          1          1          1        0
  MRPS22 WILD-TYPE        19          9         40         30       35
                  vv
clus               STAGE IVA STAGE IVB
  MRPS22 MUTATED           0         0
  MRPS22 WILD-TYPE        13         1
D1200V3, multiclass
            clus
vv           MRPS22 MUTATED MRPS22 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               4              105
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              1                9
  STAGE IIIB              1               40
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MRPS22 MUTATED     0   3   6   1
  MRPS22 WILD-TYPE   9  65 242  40
D1200V4, multiclass
    clus
vv   MRPS22 MUTATED MRPS22 WILD-TYPE
  T1              0                9
  T2              3               65
  T3              6              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
  MRPS22 MUTATED     6   3   1
  MRPS22 WILD-TYPE 214  77  65
D1200V5, multiclass
    clus
vv   MRPS22 MUTATED MRPS22 WILD-TYPE
  N0              6              214
  N1              3               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"
D1200V6, binary
                  cls
clus                 0   1
  MRPS22 MUTATED     6   0
  MRPS22 WILD-TYPE 277  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPS22 MUTATED      6    0
  MRPS22 WILD-TYPE  277   48
   clus
vv  MRPS22 MUTATED MRPS22 WILD-TYPE
  0              6              277
  1              0               48
[1] 2 2
[1] FALSE
D1200V7, 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
D1200V8, binary
                  cls
clus                 0   1
  MRPS22 MUTATED    10   0
  MRPS22 WILD-TYPE 307  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPS22 MUTATED     10    0
  MRPS22 WILD-TYPE  307   48
                               clus
vv                              MRPS22 MUTATED MRPS22 WILD-TYPE
  COLON ADENOCARCINOMA                      10              307
  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 251   2  22  21
D1200V9, multiclass
    clus
vv   MRPS22 MUTATED MRPS22 WILD-TYPE
  R0              6              251
  R1              0                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"
D1200V10, 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
D1200V11, 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(1201) Variable = STAU1 MUTATION ANALYSIS
D1201V1, survival
                 sevent
clus2               0   1
  STAU1 MUTATED     4   2
  STAU1 WILD-TYPE 278  71
  STAU1 MUTATED STAU1 WILD-TYPE 
              6             349 
  STAU1 MUTATED STAU1 WILD-TYPE 
              2              71 
$`STAU1 MUTATED`
TCGA-AA-3713 TCGA-AY-6386 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-D5-5538 TCGA-D5-6536 
       19.04        17.82       100.01        29.56        12.26        17.85 

$`STAU1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
        6.77        12.10         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        15.12         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  STAU1 MUTATED STAU1 WILD-TYPE 
          12.26            0.00 
  STAU1 MUTATED STAU1 WILD-TYPE 
         100.01          140.38 
  STAU1 MUTATED STAU1 WILD-TYPE 
         18.445          20.280 
[1] "12.3 - 100.0 (18.4)" "0.0 - 140.4 (20.3)" 
[1] "hr=" "1.2"
D1201V2, 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       24       108         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        18         10         39         31       34        13
                 vv
clus              STAGE IVB
  STAU1 MUTATED           0
  STAU1 WILD-TYPE         1
D1201V3, multiclass
            clus
vv           STAU1 MUTATED STAU1 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              1             108
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  STAU1 MUTATED     0   1   6   0
  STAU1 WILD-TYPE   9  67 242  41
D1201V4, multiclass
    clus
vv   STAU1 MUTATED STAU1 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             6             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
  STAU1 MUTATED     3   3   1
  STAU1 WILD-TYPE 217  77  65
D1201V5, multiclass
    clus
vv   STAU1 MUTATED STAU1 WILD-TYPE
  N0             3             217
  N1             3              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"
D1201V6, binary
                 cls
clus                0   1
  STAU1 MUTATED     5   1
  STAU1 WILD-TYPE 278  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAU1 MUTATED      5    1
  STAU1 WILD-TYPE  278   47
   clus
vv  STAU1 MUTATED STAU1 WILD-TYPE
  0             5             278
  1             1              47
[1] 2 2
[1] FALSE
D1201V7, 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
D1201V8, binary
                 cls
clus                0   1
  STAU1 MUTATED     7   0
  STAU1 WILD-TYPE 310  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAU1 MUTATED      7    0
  STAU1 WILD-TYPE  310   48
                               clus
vv                              STAU1 MUTATED STAU1 WILD-TYPE
  COLON ADENOCARCINOMA                      7             310
  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 253   2  21  21
D1201V9, multiclass
    clus
vv   STAU1 MUTATED STAU1 WILD-TYPE
  R0             4             253
  R1             0               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"
D1201V10, 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
D1201V11, 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(1202) Variable = OR4N4 MUTATION ANALYSIS
D1202V1, survival
                 sevent
clus2               0   1
  OR4N4 MUTATED     8   4
  OR4N4 WILD-TYPE 274  69
  OR4N4 MUTATED OR4N4 WILD-TYPE 
             12             343 
  OR4N4 MUTATED OR4N4 WILD-TYPE 
              4              69 
$`OR4N4 MUTATED`
TCGA-A6-6137 TCGA-AA-3655 TCGA-AA-3715 TCGA-AA-A00N TCGA-AA-A010 TCGA-CM-6162 
       27.09        61.02        19.04         4.01        34.98        12.00 
TCGA-CM-6676 TCGA-DM-A0XF TCGA-DM-A1HB TCGA-F4-6460 TCGA-G4-6303 TCGA-G4-6586 
       11.08        38.20       135.65        13.38        65.85        35.80 

$`OR4N4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        32.71        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38        10.26       119.70        24.43       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 
       60.79       117.07        98.24         8.61        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  OR4N4 MUTATED OR4N4 WILD-TYPE 
           4.01            0.00 
  OR4N4 MUTATED OR4N4 WILD-TYPE 
         135.65          140.38 
  OR4N4 MUTATED OR4N4 WILD-TYPE 
         31.035          20.120 
[1] "4.0 - 135.7 (31.0)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.2"
D1202V2, 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       23       108         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        19         10         37         30       34        13
                 vv
clus              STAGE IVB
  OR4N4 MUTATED           0
  OR4N4 WILD-TYPE         1
D1202V3, multiclass
            clus
vv           OR4N4 MUTATED OR4N4 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              1             108
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             4              37
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR4N4 MUTATED     0   1   9   2
  OR4N4 WILD-TYPE   9  67 239  39
D1202V4, multiclass
    clus
vv   OR4N4 MUTATED OR4N4 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             9             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
  OR4N4 MUTATED     6   5   1
  OR4N4 WILD-TYPE 214  75  65
D1202V5, multiclass
    clus
vv   OR4N4 MUTATED OR4N4 WILD-TYPE
  N0             6             214
  N1             5              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"
D1202V6, binary
                 cls
clus                0   1
  OR4N4 MUTATED    11   1
  OR4N4 WILD-TYPE 272  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4N4 MUTATED     11    1
  OR4N4 WILD-TYPE  272   47
   clus
vv  OR4N4 MUTATED OR4N4 WILD-TYPE
  0            11             272
  1             1              47
[1] 2 2
[1] FALSE
D1202V7, 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
D1202V8, binary
                 cls
clus                0   1
  OR4N4 MUTATED     9   3
  OR4N4 WILD-TYPE 308  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4N4 MUTATED      9    3
  OR4N4 WILD-TYPE  308   45
                               clus
vv                              OR4N4 MUTATED OR4N4 WILD-TYPE
  COLON ADENOCARCINOMA                      9             308
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  OR4N4 MUTATED     9   0   0   0
  OR4N4 WILD-TYPE 248   2  22  21
D1202V9, multiclass
    clus
vv   OR4N4 MUTATED OR4N4 WILD-TYPE
  R0             9             248
  R1             0               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"
D1202V10, 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
D1202V11, 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(1203) Variable = ATP12A MUTATION ANALYSIS
D1203V1, survival
                  sevent
clus2                0   1
  ATP12A MUTATED    19   5
  ATP12A WILD-TYPE 263  68
  ATP12A MUTATED ATP12A WILD-TYPE 
              24              331 
  ATP12A MUTATED ATP12A WILD-TYPE 
               5               68 
$`ATP12A MUTATED`
TCGA-A6-5656 TCGA-A6-5661 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3530 TCGA-AA-3543 
       32.91        33.53        19.66         3.02        19.07         0.99 
TCGA-AA-3672 TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 
        0.92        53.00        33.01        25.02         4.01        34.98 
TCGA-AD-6963 TCGA-AY-4071 TCGA-CK-4952 TCGA-CM-4743 TCGA-CM-6161 TCGA-CM-6675 
       27.42         0.95        15.62        23.05        15.02        13.05 
TCGA-D5-6529 TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-F4-6704 TCGA-G4-6307 TCGA-G4-6628 
       20.19        49.91         7.50         1.55        55.04        52.80 

$`ATP12A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3531 
       37.05        36.03         8.05        19.07         0.00        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
       29.00        29.00        26.01        12.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
        6.05         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      102.44        40.34        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93         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        16.01 
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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       19.59        13.51        11.51        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18        35.87        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 
       46.75 

  ATP12A MUTATED ATP12A WILD-TYPE 
            0.92             0.00 
  ATP12A MUTATED ATP12A WILD-TYPE 
           55.04           140.38 
  ATP12A MUTATED ATP12A WILD-TYPE 
          19.925           20.280 
[1] "0.9 - 55.0 (19.9)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.1"
D1203V2, 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       22       105         5         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP12A MUTATED           2          0          1          3        0
  ATP12A WILD-TYPE        17         10         40         28       35
                  vv
clus               STAGE IVA STAGE IVB
  ATP12A MUTATED           0         1
  ATP12A WILD-TYPE        13         0
D1203V3, multiclass
            clus
vv           ATP12A MUTATED ATP12A WILD-TYPE
  STAGE I                 7               57
  STAGE IA                0                1
  STAGE II                3               22
  STAGE IIA               4              105
  STAGE IIB               3                5
  STAGE IIC               0                1
  STAGE III               2               17
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              3               28
  STAGE IV                0               35
  STAGE IVA               0               13
  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  61 236  35
D1203V4, multiclass
    clus
vv   ATP12A MUTATED ATP12A WILD-TYPE
  T1              1                8
  T2              7               61
  T3             12              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
  ATP12A MUTATED    19   3   4
  ATP12A WILD-TYPE 201  77  62
D1203V5, multiclass
    clus
vv   ATP12A MUTATED ATP12A WILD-TYPE
  N0             19              201
  N1              3               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"
D1203V6, binary
                  cls
clus                 0   1
  ATP12A MUTATED    19   1
  ATP12A WILD-TYPE 264  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP12A MUTATED     19    1
  ATP12A WILD-TYPE  264   47
   clus
vv  ATP12A MUTATED ATP12A WILD-TYPE
  0             19              264
  1              1               47
[1] 2 2
[1] FALSE
D1203V7, 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
D1203V8, binary
                  cls
clus                 0   1
  ATP12A MUTATED    18   7
  ATP12A WILD-TYPE 299  41
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP12A MUTATED     18    7
  ATP12A WILD-TYPE  299   41
                               clus
vv                              ATP12A MUTATED ATP12A WILD-TYPE
  COLON ADENOCARCINOMA                      18              299
  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 238   2  22  19
D1203V9, multiclass
    clus
vv   ATP12A MUTATED ATP12A WILD-TYPE
  R0             19              238
  R1              0                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"
D1203V10, 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
D1203V11, 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(1204) Variable = SPATA16 MUTATION ANALYSIS
D1204V1, survival
                   sevent
clus2                 0   1
  SPATA16 MUTATED     8   4
  SPATA16 WILD-TYPE 274  69
  SPATA16 MUTATED SPATA16 WILD-TYPE 
               12               343 
  SPATA16 MUTATED SPATA16 WILD-TYPE 
                4                69 
$`SPATA16 MUTATED`
TCGA-A6-2676 TCGA-A6-3807 TCGA-A6-6651 TCGA-AA-3518 TCGA-AA-3845 TCGA-AA-3966 
       42.90        34.65        21.76         1.02         0.00         2.01 
TCGA-AA-A00N TCGA-AA-A01I TCGA-AD-6889 TCGA-CA-6717 TCGA-DM-A1DB TCGA-G4-6309 
        4.01        31.00        56.55         0.33        44.32        51.75 

$`SPATA16 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       33.34        32.75        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       24.16        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 
        6.97         1.02        13.02        38.99         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02        14.93        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       26.01        24.00         2.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       12.59       140.38         7.50       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  SPATA16 MUTATED SPATA16 WILD-TYPE 
                0                 0 
  SPATA16 MUTATED SPATA16 WILD-TYPE 
            56.55            140.38 
  SPATA16 MUTATED SPATA16 WILD-TYPE 
            26.38             20.12 
[1] "0.0 - 56.5 (26.4)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.8"
D1204V2, 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       25       103         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SPATA16 MUTATED           0          0          2          1        0
  SPATA16 WILD-TYPE        19         10         39         30       35
                   vv
clus                STAGE IVA STAGE IVB
  SPATA16 MUTATED           0         0
  SPATA16 WILD-TYPE        13         1
D1204V3, multiclass
            clus
vv           SPATA16 MUTATED SPATA16 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                6               103
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               2                39
  STAGE IIIC               1                30
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SPATA16 MUTATED     0   1   9   2
  SPATA16 WILD-TYPE   9  67 239  39
D1204V4, multiclass
    clus
vv   SPATA16 MUTATED SPATA16 WILD-TYPE
  T1               0                 9
  T2               1                67
  T3               9               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
  SPATA16 MUTATED     9   2   1
  SPATA16 WILD-TYPE 211  78  65
D1204V5, multiclass
    clus
vv   SPATA16 MUTATED SPATA16 WILD-TYPE
  N0               9               211
  N1               2                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"
D1204V6, binary
                   cls
clus                  0   1
  SPATA16 MUTATED    11   0
  SPATA16 WILD-TYPE 272  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPATA16 MUTATED     11    0
  SPATA16 WILD-TYPE  272   48
   clus
vv  SPATA16 MUTATED SPATA16 WILD-TYPE
  0              11               272
  1               0                48
[1] 2 2
[1] FALSE
D1204V7, 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
D1204V8, binary
                   cls
clus                  0   1
  SPATA16 MUTATED     9   3
  SPATA16 WILD-TYPE 308  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPATA16 MUTATED      9    3
  SPATA16 WILD-TYPE  308   45
                               clus
vv                              SPATA16 MUTATED SPATA16 WILD-TYPE
  COLON ADENOCARCINOMA                        9               308
  COLON MUCINOUS ADENOCARCINOMA               3                45
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SPATA16 MUTATED     7   0   0   1
  SPATA16 WILD-TYPE 250   2  22  20
D1204V9, multiclass
    clus
vv   SPATA16 MUTATED SPATA16 WILD-TYPE
  R0               7               250
  R1               0                 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"
D1204V10, 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
D1204V11, 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(1205) Variable = BFSP1 MUTATION ANALYSIS
D1205V1, survival
                 sevent
clus2               0   1
  BFSP1 MUTATED     4   3
  BFSP1 WILD-TYPE 278  70
  BFSP1 MUTATED BFSP1 WILD-TYPE 
              7             348 
  BFSP1 MUTATED BFSP1 WILD-TYPE 
              3              70 
$`BFSP1 MUTATED`
TCGA-A6-5659 TCGA-A6-6141 TCGA-A6-6654 TCGA-AZ-4616 TCGA-CA-5254 TCGA-DM-A285 
       30.44         8.38        23.87         5.13         2.24         6.12 
TCGA-F4-6570 
        6.18 

$`BFSP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       24.16        21.76        24.69        24.39        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4681 
        0.20        21.44        17.82        58.39         1.41        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        13.38        13.45        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  BFSP1 MUTATED BFSP1 WILD-TYPE 
           2.24            0.00 
  BFSP1 MUTATED BFSP1 WILD-TYPE 
          30.44          140.38 
  BFSP1 MUTATED BFSP1 WILD-TYPE 
           6.18           20.63 
[1] "2.2 - 30.4 (6.2)"   "0.0 - 140.4 (20.6)"
[1] "hr=" "4.3"
D1205V2, 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       25       105         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        19         10         40         31       33        13
                 vv
clus              STAGE IVB
  BFSP1 MUTATED           0
  BFSP1 WILD-TYPE         1
D1205V3, multiclass
            clus
vv           BFSP1 MUTATED BFSP1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              4             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               2              33
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  BFSP1 MUTATED     0   1   7   0
  BFSP1 WILD-TYPE   9  67 241  41
D1205V4, multiclass
    clus
vv   BFSP1 MUTATED BFSP1 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             7             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
  BFSP1 MUTATED     5   1   2
  BFSP1 WILD-TYPE 215  79  64
D1205V5, multiclass
    clus
vv   BFSP1 MUTATED BFSP1 WILD-TYPE
  N0             5             215
  N1             1              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"
D1205V6, binary
                 cls
clus                0   1
  BFSP1 MUTATED     6   2
  BFSP1 WILD-TYPE 277  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BFSP1 MUTATED      6    2
  BFSP1 WILD-TYPE  277   46
   clus
vv  BFSP1 MUTATED BFSP1 WILD-TYPE
  0             6             277
  1             2              46
[1] 2 2
[1] FALSE
D1205V7, 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
D1205V8, binary
                 cls
clus                0   1
  BFSP1 MUTATED     7   1
  BFSP1 WILD-TYPE 310  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BFSP1 MUTATED      7    1
  BFSP1 WILD-TYPE  310   47
                               clus
vv                              BFSP1 MUTATED BFSP1 WILD-TYPE
  COLON ADENOCARCINOMA                      7             310
  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 254   2  22  20
D1205V9, multiclass
    clus
vv   BFSP1 MUTATED BFSP1 WILD-TYPE
  R0             3             254
  R1             0               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"
D1205V10, 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
D1205V11, 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(1206) Variable = NEUROD1 MUTATION ANALYSIS
D1206V1, survival
                   sevent
clus2                 0   1
  NEUROD1 MUTATED     9   0
  NEUROD1 WILD-TYPE 273  73
  NEUROD1 MUTATED NEUROD1 WILD-TYPE 
                9               346 
  NEUROD1 MUTATED NEUROD1 WILD-TYPE 
                0                73 
$`NEUROD1 MUTATED`
TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3713 TCGA-AA-3950 TCGA-AA-A00J TCGA-AZ-4315 
       22.06        63.98        19.04        24.00        18.05        58.39 
TCGA-CM-4752 TCGA-CM-6164 TCGA-CM-6172 
       13.02        29.03        11.01 

$`NEUROD1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        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-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  NEUROD1 MUTATED NEUROD1 WILD-TYPE 
            11.01              0.00 
  NEUROD1 MUTATED NEUROD1 WILD-TYPE 
            63.98            140.38 
  NEUROD1 MUTATED NEUROD1 WILD-TYPE 
           22.060            20.155 
[1] "11.0 - 64.0 (22.1)" "0.0 - 140.4 (20.2)"
[1] "hr="     "2.5e+07"
D1206V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NEUROD1 MUTATED         0        0        1         5         0         0
  NEUROD1 WILD-TYPE      64        1       24       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        19         10         39         31       34
                   vv
clus                STAGE IVA STAGE IVB
  NEUROD1 MUTATED           0         0
  NEUROD1 WILD-TYPE        13         1
D1206V3, multiclass
            clus
vv           NEUROD1 MUTATED NEUROD1 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                5               104
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               2                39
  STAGE IIIC               0                31
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  NEUROD1 MUTATED     0   0   8   1
  NEUROD1 WILD-TYPE   9  68 240  40
D1206V4, multiclass
    clus
vv   NEUROD1 MUTATED NEUROD1 WILD-TYPE
  T1               0                 9
  T2               0                68
  T3               8               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
  NEUROD1 MUTATED     7   2   0
  NEUROD1 WILD-TYPE 213  78  66
D1206V5, multiclass
    clus
vv   NEUROD1 MUTATED NEUROD1 WILD-TYPE
  N0               7               213
  N1               2                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"
D1206V6, binary
                   cls
clus                  0   1
  NEUROD1 MUTATED     8   1
  NEUROD1 WILD-TYPE 275  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NEUROD1 MUTATED      8    1
  NEUROD1 WILD-TYPE  275   47
   clus
vv  NEUROD1 MUTATED NEUROD1 WILD-TYPE
  0               8               275
  1               1                47
[1] 2 2
[1] FALSE
D1206V7, binary
                   cls
clus                  0   1
  NEUROD1 MUTATED     4   5
  NEUROD1 WILD-TYPE 166 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NEUROD1 MUTATED      4    5
  NEUROD1 WILD-TYPE  166  192
        clus
vv       NEUROD1 MUTATED NEUROD1 WILD-TYPE
  FEMALE               4               166
  MALE                 5               192
[1] 2 2
[1] FALSE
D1206V8, binary
                   cls
clus                  0   1
  NEUROD1 MUTATED     7   2
  NEUROD1 WILD-TYPE 310  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NEUROD1 MUTATED      7    2
  NEUROD1 WILD-TYPE  310   46
                               clus
vv                              NEUROD1 MUTATED NEUROD1 WILD-TYPE
  COLON ADENOCARCINOMA                        7               310
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  NEUROD1 MUTATED     8   0   1   0
  NEUROD1 WILD-TYPE 249   2  21  21
D1206V9, multiclass
    clus
vv   NEUROD1 MUTATED NEUROD1 WILD-TYPE
  R0               8               249
  R1               0                 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"
D1206V10, 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     4
  NEUROD1 WILD-TYPE                        18   172
D1206V11, 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                                          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 = CCR8 MUTATION ANALYSIS
D1207V1, survival
                sevent
clus2              0   1
  CCR8 MUTATED     3   4
  CCR8 WILD-TYPE 279  69
  CCR8 MUTATED CCR8 WILD-TYPE 
             7            348 
  CCR8 MUTATED CCR8 WILD-TYPE 
             4             69 
$`CCR8 MUTATED`
TCGA-AA-3555 TCGA-AA-3966 TCGA-AA-A00N TCGA-AZ-6603 TCGA-AZ-6607 TCGA-D5-6924 
       29.95         2.01         4.01        29.56         3.19        14.30 
TCGA-DM-A1D4 
       92.75 

$`CCR8 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        17.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 
       12.10       100.01         5.23        11.74         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  CCR8 MUTATED CCR8 WILD-TYPE 
          2.01           0.00 
  CCR8 MUTATED CCR8 WILD-TYPE 
         92.75         140.38 
  CCR8 MUTATED CCR8 WILD-TYPE 
        14.300         20.235 
[1] "2.0 - 92.8 (14.3)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "3"  
D1207V2, 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       25       105         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        19         10         41         31       34        13
                vv
clus             STAGE IVB
  CCR8 MUTATED           0
  CCR8 WILD-TYPE         1
D1207V3, multiclass
            clus
vv           CCR8 MUTATED CCR8 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             4            105
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CCR8 MUTATED     0   1   4   2
  CCR8 WILD-TYPE   9  67 244  39
D1207V4, multiclass
    clus
vv   CCR8 MUTATED CCR8 WILD-TYPE
  T1            0              9
  T2            1             67
  T3            4            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
  CCR8 MUTATED     5   1   1
  CCR8 WILD-TYPE 215  79  65
D1207V5, multiclass
    clus
vv   CCR8 MUTATED CCR8 WILD-TYPE
  N0            5            215
  N1            1             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"
D1207V6, binary
                cls
clus               0   1
  CCR8 MUTATED     5   1
  CCR8 WILD-TYPE 278  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCR8 MUTATED      5    1
  CCR8 WILD-TYPE  278   47
   clus
vv  CCR8 MUTATED CCR8 WILD-TYPE
  0            5            278
  1            1             47
[1] 2 2
[1] FALSE
D1207V7, 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
D1207V8, binary
                cls
clus               0   1
  CCR8 MUTATED     4   3
  CCR8 WILD-TYPE 313  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCR8 MUTATED      4    3
  CCR8 WILD-TYPE  313   45
                               clus
vv                              CCR8 MUTATED CCR8 WILD-TYPE
  COLON ADENOCARCINOMA                     4            313
  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 254   2  22  21
D1207V9, multiclass
    clus
vv   CCR8 MUTATED CCR8 WILD-TYPE
  R0            3            254
  R1            0              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"
D1207V10, 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
D1207V11, 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(1208) Variable = DHX36 MUTATION ANALYSIS
D1208V1, survival
                 sevent
clus2               0   1
  DHX36 MUTATED     8   4
  DHX36 WILD-TYPE 274  69
  DHX36 MUTATED DHX36 WILD-TYPE 
             12             343 
  DHX36 MUTATED DHX36 WILD-TYPE 
              4              69 
$`DHX36 MUTATED`
TCGA-AA-3516 TCGA-AA-3663 TCGA-AD-6964 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CM-6674 
       13.02         6.97        10.88        58.39        49.41        12.95 
TCGA-D5-6540 TCGA-D5-6928 TCGA-DM-A0XF TCGA-G4-6307 TCGA-G4-6625 TCGA-G4-6628 
       16.14        11.64        38.20        55.04        91.79        52.80 

$`DHX36 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        1.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       10.26       119.70        24.43       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        53.62        44.68        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6626 
       46.75 

  DHX36 MUTATED DHX36 WILD-TYPE 
           6.97            0.00 
  DHX36 MUTATED DHX36 WILD-TYPE 
          91.79          140.38 
  DHX36 MUTATED DHX36 WILD-TYPE 
          27.17           20.19 
[1] "7.0 - 91.8 (27.2)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D1208V2, 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       23       105         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        18         10         40         30       35        13
                 vv
clus              STAGE IVB
  DHX36 MUTATED           0
  DHX36 WILD-TYPE         1
D1208V3, multiclass
            clus
vv           DHX36 MUTATED DHX36 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              4             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DHX36 MUTATED     0   2   9   1
  DHX36 WILD-TYPE   9  66 239  40
D1208V4, multiclass
    clus
vv   DHX36 MUTATED DHX36 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             9             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
  DHX36 MUTATED     8   1   3
  DHX36 WILD-TYPE 212  79  63
D1208V5, multiclass
    clus
vv   DHX36 MUTATED DHX36 WILD-TYPE
  N0             8             212
  N1             1              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"
D1208V6, binary
                 cls
clus                0   1
  DHX36 MUTATED    10   0
  DHX36 WILD-TYPE 273  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX36 MUTATED     10    0
  DHX36 WILD-TYPE  273   48
   clus
vv  DHX36 MUTATED DHX36 WILD-TYPE
  0            10             273
  1             0              48
[1] 2 2
[1] FALSE
D1208V7, 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
D1208V8, binary
                 cls
clus                0   1
  DHX36 MUTATED     8   4
  DHX36 WILD-TYPE 309  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX36 MUTATED      8    4
  DHX36 WILD-TYPE  309   44
                               clus
vv                              DHX36 MUTATED DHX36 WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DHX36 MUTATED     8   0   0   0
  DHX36 WILD-TYPE 249   2  22  21
D1208V9, multiclass
    clus
vv   DHX36 MUTATED DHX36 WILD-TYPE
  R0             8             249
  R1             0               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"
D1208V10, 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
D1208V11, 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(1209) Variable = CACNA1D MUTATION ANALYSIS
D1209V1, survival
                   sevent
clus2                 0   1
  CACNA1D MUTATED    15   6
  CACNA1D WILD-TYPE 267  67
  CACNA1D MUTATED CACNA1D WILD-TYPE 
               21               334 
  CACNA1D MUTATED CACNA1D WILD-TYPE 
                6                67 
$`CACNA1D MUTATED`
TCGA-A6-2676 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-A00K TCGA-AA-A010 TCGA-AA-A01R 
       42.90        20.12        19.66        18.05        34.98        35.01 
TCGA-AD-5900 TCGA-AD-6895 TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-AZ-6598 
        0.07         0.72        27.09        58.39        61.41        49.41 
TCGA-AZ-6601 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5913 TCGA-CK-5916 TCGA-DM-A0XD 
      100.01         0.33         0.10        51.32        21.14        24.43 
TCGA-DM-A1DA TCGA-G4-6309 TCGA-G4-6588 
        7.50        51.75        26.17 

$`CACNA1D WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        4.21        56.55         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       22.36        62.79         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07         0.26         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       40.34        15.62        49.08        21.99         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        91.79        46.75        52.80 

  CACNA1D MUTATED CACNA1D WILD-TYPE 
             0.07              0.00 
  CACNA1D MUTATED CACNA1D WILD-TYPE 
           100.01            140.38 
  CACNA1D MUTATED CACNA1D WILD-TYPE 
            26.17             19.99 
[1] "0.1 - 100.0 (26.2)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.1"
D1209V2, 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       22       101         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CACNA1D MUTATED           1          0          1          2        0
  CACNA1D WILD-TYPE        18         10         40         29       35
                   vv
clus                STAGE IVA STAGE IVB
  CACNA1D MUTATED           0         0
  CACNA1D WILD-TYPE        13         1
D1209V3, multiclass
            clus
vv           CACNA1D MUTATED CACNA1D WILD-TYPE
  STAGE I                  4                60
  STAGE IA                 0                 1
  STAGE II                 3                22
  STAGE IIA                8               101
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               2                29
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CACNA1D MUTATED     2   2  14   4
  CACNA1D WILD-TYPE   7  66 234  37
D1209V4, multiclass
    clus
vv   CACNA1D MUTATED CACNA1D WILD-TYPE
  T1               2                 7
  T2               2                66
  T3              14               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
  CACNA1D MUTATED    17   3   2
  CACNA1D WILD-TYPE 203  77  64
D1209V5, multiclass
    clus
vv   CACNA1D MUTATED CACNA1D WILD-TYPE
  N0              17               203
  N1               3                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"
D1209V6, binary
                   cls
clus                  0   1
  CACNA1D MUTATED    16   0
  CACNA1D WILD-TYPE 267  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CACNA1D MUTATED     16    0
  CACNA1D WILD-TYPE  267   48
   clus
vv  CACNA1D MUTATED CACNA1D WILD-TYPE
  0              16               267
  1               0                48
[1] 2 2
[1] FALSE
D1209V7, 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
D1209V8, binary
                   cls
clus                  0   1
  CACNA1D MUTATED    17   5
  CACNA1D WILD-TYPE 300  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CACNA1D MUTATED     17    5
  CACNA1D WILD-TYPE  300   43
                               clus
vv                              CACNA1D MUTATED CACNA1D WILD-TYPE
  COLON ADENOCARCINOMA                       17               300
  COLON MUCINOUS ADENOCARCINOMA               5                43
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  CACNA1D MUTATED    11   0   0   4
  CACNA1D WILD-TYPE 246   2  22  17
D1209V9, multiclass
    clus
vv   CACNA1D MUTATED CACNA1D WILD-TYPE
  R0              11               246
  R1               0                 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"
D1209V10, 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
D1209V11, 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(1210) Variable = ACTL6B MUTATION ANALYSIS
D1210V1, survival
                  sevent
clus2                0   1
  ACTL6B MUTATED     7   1
  ACTL6B WILD-TYPE 275  72
  ACTL6B MUTATED ACTL6B WILD-TYPE 
               8              347 
  ACTL6B MUTATED ACTL6B WILD-TYPE 
               1               72 
$`ACTL6B MUTATED`
TCGA-A6-4105 TCGA-A6-5665 TCGA-AA-A02O TCGA-CM-5860 TCGA-CM-6170 TCGA-D5-5539 
       14.53        22.06         0.92        16.01        15.02        19.59 
TCGA-D5-6533 TCGA-G4-6321 
        1.32        22.09 

$`ACTL6B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02W TCGA-AA-A02Y 
       39.98         2.01         5.03        14.01        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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-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-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 
       12.26        13.51        11.51        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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       55.04        51.75        45.11        36.72        36.00        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  ACTL6B MUTATED ACTL6B WILD-TYPE 
            0.92             0.00 
  ACTL6B MUTATED ACTL6B WILD-TYPE 
           22.09           140.38 
  ACTL6B MUTATED ACTL6B WILD-TYPE 
          15.515           20.980 
[1] "0.9 - 22.1 (15.5)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1"  
D1210V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ACTL6B MUTATED         1        0        1         3         0         0
  ACTL6B WILD-TYPE      63        1       24       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ACTL6B MUTATED           1          1          1          0        0
  ACTL6B WILD-TYPE        18          9         40         31       35
                  vv
clus               STAGE IVA STAGE IVB
  ACTL6B MUTATED           0         0
  ACTL6B WILD-TYPE        13         1
D1210V3, multiclass
            clus
vv           ACTL6B MUTATED ACTL6B WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               3              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              1                9
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ACTL6B MUTATED     0   2   5   1
  ACTL6B WILD-TYPE   9  66 243  40
D1210V4, multiclass
    clus
vv   ACTL6B MUTATED ACTL6B WILD-TYPE
  T1              0                9
  T2              2               66
  T3              5              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
  ACTL6B MUTATED     6   2   0
  ACTL6B WILD-TYPE 214  78  66
D1210V5, multiclass
    clus
vv   ACTL6B MUTATED ACTL6B WILD-TYPE
  N0              6              214
  N1              2               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"
D1210V6, binary
                  cls
clus                 0   1
  ACTL6B MUTATED     7   0
  ACTL6B WILD-TYPE 276  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACTL6B MUTATED      7    0
  ACTL6B WILD-TYPE  276   48
   clus
vv  ACTL6B MUTATED ACTL6B WILD-TYPE
  0              7              276
  1              0               48
[1] 2 2
[1] FALSE
D1210V7, binary
                  cls
clus                 0   1
  ACTL6B MUTATED     4   4
  ACTL6B WILD-TYPE 166 193
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACTL6B MUTATED      4    4
  ACTL6B WILD-TYPE  166  193
        clus
vv       ACTL6B MUTATED ACTL6B WILD-TYPE
  FEMALE              4              166
  MALE                4              193
[1] 2 2
[1] FALSE
D1210V8, binary
                  cls
clus                 0   1
  ACTL6B MUTATED     7   1
  ACTL6B WILD-TYPE 310  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACTL6B MUTATED      7    1
  ACTL6B WILD-TYPE  310   47
                               clus
vv                              ACTL6B MUTATED ACTL6B WILD-TYPE
  COLON ADENOCARCINOMA                       7              310
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ACTL6B MUTATED     7   0   0   0
  ACTL6B WILD-TYPE 250   2  22  21
D1210V9, multiclass
    clus
vv   ACTL6B MUTATED ACTL6B WILD-TYPE
  R0              7              250
  R1              0                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"
D1210V10, 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
D1210V11, 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(1211) Variable = HERC1 MUTATION ANALYSIS
D1211V1, survival
                 sevent
clus2               0   1
  HERC1 MUTATED    23   7
  HERC1 WILD-TYPE 259  66
  HERC1 MUTATED HERC1 WILD-TYPE 
             30             325 
  HERC1 MUTATED HERC1 WILD-TYPE 
              7              66 
$`HERC1 MUTATED`
TCGA-A6-3809 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6653 TCGA-A6-6780 TCGA-AA-3660 
       32.75        22.06        32.71        24.39        20.12        78.08 
TCGA-AA-3663 TCGA-AA-3710 TCGA-AA-3870 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 
        6.97        26.99        29.98        33.01        24.00         2.01 
TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A02K TCGA-AD-5900 TCGA-AD-6889 
       25.02         4.01        34.98        14.01         0.07        56.55 
TCGA-AD-6895 TCGA-AZ-4315 TCGA-CA-5797 TCGA-CA-6716 TCGA-CK-6751 TCGA-D5-6538 
        0.72        58.39         3.29         0.26       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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 
       21.76        24.69        23.87        19.66        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        3.02         1.02        35.01        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        21.37         4.21         0.79         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 
        3.19         1.94         2.24         3.06         3.25         0.07 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 
        1.32        43.27        15.12        17.85         4.80        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28E TCGA-DM-A28G 
      131.51       135.65       139.17         6.12       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        13.38        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  HERC1 MUTATED HERC1 WILD-TYPE 
           0.07            0.00 
  HERC1 MUTATED HERC1 WILD-TYPE 
         124.27          140.38 
  HERC1 MUTATED HERC1 WILD-TYPE 
         24.705          19.990 
[1] "0.1 - 124.3 (24.7)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.1"
D1211V2, 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       23        96         4         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HERC1 MUTATED           0          0          3          1        2         0
  HERC1 WILD-TYPE        19         10         38         30       33        13
                 vv
clus              STAGE IVB
  HERC1 MUTATED           0
  HERC1 WILD-TYPE         1
D1211V3, multiclass
            clus
vv           HERC1 MUTATED HERC1 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA             13              96
  STAGE IIB              4               4
  STAGE IIC              1               0
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             3              38
  STAGE IIIC             1              30
  STAGE IV               2              33
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HERC1 MUTATED     0   4  21   6
  HERC1 WILD-TYPE   9  64 227  35
D1211V4, multiclass
    clus
vv   HERC1 MUTATED HERC1 WILD-TYPE
  T1             0               9
  T2             4              64
  T3            21             227
  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  77  62
D1211V5, multiclass
    clus
vv   HERC1 MUTATED HERC1 WILD-TYPE
  N0            24             196
  N1             3              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"
D1211V6, binary
                 cls
clus                0   1
  HERC1 MUTATED    24   2
  HERC1 WILD-TYPE 259  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HERC1 MUTATED     24    2
  HERC1 WILD-TYPE  259   46
   clus
vv  HERC1 MUTATED HERC1 WILD-TYPE
  0            24             259
  1             2              46
[1] 2 2
[1] FALSE
D1211V7, 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
D1211V8, binary
                 cls
clus                0   1
  HERC1 MUTATED    23   8
  HERC1 WILD-TYPE 294  40
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HERC1 MUTATED     23    8
  HERC1 WILD-TYPE  294   40
                               clus
vv                              HERC1 MUTATED HERC1 WILD-TYPE
  COLON ADENOCARCINOMA                     23             294
  COLON MUCINOUS ADENOCARCINOMA             8              40
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  HERC1 MUTATED    19   0   1   2
  HERC1 WILD-TYPE 238   2  21  19
D1211V9, multiclass
    clus
vv   HERC1 MUTATED HERC1 WILD-TYPE
  R0            19             238
  R1             0               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"
D1211V10, 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
D1211V11, 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(1212) Variable = MYLK4 MUTATION ANALYSIS
D1212V1, survival
                 sevent
clus2               0   1
  MYLK4 MUTATED    10   1
  MYLK4 WILD-TYPE 272  72
  MYLK4 MUTATED MYLK4 WILD-TYPE 
             11             344 
  MYLK4 MUTATED MYLK4 WILD-TYPE 
              1              72 
$`MYLK4 MUTATED`
TCGA-A6-5662 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3713 TCGA-AA-3815 TCGA-AZ-6601 
       23.61        63.98         6.97        19.04        33.04       100.01 
TCGA-CA-6717 TCGA-CK-5914 TCGA-CM-5860 TCGA-CM-5861 TCGA-D5-6539 
        0.33        21.99        16.01        15.02        12.49 

$`MYLK4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        33.53        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       35.01         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       85.05        26.99        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        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        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        61.41        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  MYLK4 MUTATED MYLK4 WILD-TYPE 
           0.33            0.00 
  MYLK4 MUTATED MYLK4 WILD-TYPE 
         100.01          140.38 
  MYLK4 MUTATED MYLK4 WILD-TYPE 
         19.040          20.235 
[1] "0.3 - 100.0 (19.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "2.7"
D1212V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MYLK4 MUTATED         0        0        3         4         0         0
  MYLK4 WILD-TYPE      64        1       22       105         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MYLK4 MUTATED           0          1          1          0        1         1
  MYLK4 WILD-TYPE        19          9         40         31       34        12
                 vv
clus              STAGE IVB
  MYLK4 MUTATED           0
  MYLK4 WILD-TYPE         1
D1212V3, multiclass
            clus
vv           MYLK4 MUTATED MYLK4 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              4             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  10   1
  MYLK4 WILD-TYPE   9  68 238  40
D1212V4, multiclass
    clus
vv   MYLK4 MUTATED MYLK4 WILD-TYPE
  T1             0               9
  T2             0              68
  T3            10             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     9   1   1
  MYLK4 WILD-TYPE 211  79  65
D1212V5, multiclass
    clus
vv   MYLK4 MUTATED MYLK4 WILD-TYPE
  N0             9             211
  N1             1              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"
D1212V6, binary
                 cls
clus                0   1
  MYLK4 MUTATED     8   2
  MYLK4 WILD-TYPE 275  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYLK4 MUTATED      8    2
  MYLK4 WILD-TYPE  275   46
   clus
vv  MYLK4 MUTATED MYLK4 WILD-TYPE
  0             8             275
  1             2              46
[1] 2 2
[1] FALSE
D1212V7, binary
                 cls
clus                0   1
  MYLK4 MUTATED     3   8
  MYLK4 WILD-TYPE 167 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYLK4 MUTATED      3    8
  MYLK4 WILD-TYPE  167  189
        clus
vv       MYLK4 MUTATED MYLK4 WILD-TYPE
  FEMALE             3             167
  MALE               8             189
[1] 2 2
[1] FALSE
D1212V8, binary
                 cls
clus                0   1
  MYLK4 MUTATED    10   1
  MYLK4 WILD-TYPE 307  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYLK4 MUTATED     10    1
  MYLK4 WILD-TYPE  307   47
                               clus
vv                              MYLK4 MUTATED MYLK4 WILD-TYPE
  COLON ADENOCARCINOMA                     10             307
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MYLK4 MUTATED     6   0   1   2
  MYLK4 WILD-TYPE 251   2  21  19
D1212V9, multiclass
    clus
vv   MYLK4 MUTATED MYLK4 WILD-TYPE
  R0             6             251
  R1             0               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"
D1212V10, 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
D1212V11, 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(1213) Variable = UBE3C MUTATION ANALYSIS
D1213V1, survival
                 sevent
clus2               0   1
  UBE3C MUTATED    14   4
  UBE3C WILD-TYPE 268  69
  UBE3C MUTATED UBE3C WILD-TYPE 
             18             337 
  UBE3C MUTATED UBE3C WILD-TYPE 
              4              69 
$`UBE3C MUTATED`
TCGA-A6-5657 TCGA-A6-5662 TCGA-AA-3715 TCGA-AA-3819 TCGA-AA-3977 TCGA-AA-A00N 
       31.63        23.61        19.04        25.02        25.02         4.01 
TCGA-AA-A010 TCGA-AA-A01I TCGA-AD-5900 TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-5403 
       34.98        31.00         0.07        27.09        58.39        62.79 
TCGA-AZ-6600 TCGA-CA-6717 TCGA-CM-5864 TCGA-DM-A1D9 TCGA-F4-6808 TCGA-G4-6586 
       12.10         0.33        15.02       140.38        33.67        35.80 

$`UBE3C WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 
       32.91        30.44        29.19        33.53        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       33.04         0.99         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.20        14.50        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41        49.41         6.77       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32        12.59         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 
       35.87         1.55        16.31        29.59        16.24        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  UBE3C MUTATED UBE3C WILD-TYPE 
           0.07            0.00 
  UBE3C MUTATED UBE3C WILD-TYPE 
         140.38          139.17 
  UBE3C MUTATED UBE3C WILD-TYPE 
         26.055          19.990 
[1] "0.1 - 140.4 (26.1)" "0.0 - 139.2 (20.0)"
[1] "hr=" "1"  
D1213V2, 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       23       104         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        19         10         40         31       34        12
                 vv
clus              STAGE IVB
  UBE3C MUTATED           0
  UBE3C WILD-TYPE         1
D1213V3, multiclass
            clus
vv           UBE3C MUTATED UBE3C WILD-TYPE
  STAGE I                5              59
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              5             104
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  63 239  38
D1213V4, multiclass
    clus
vv   UBE3C MUTATED UBE3C WILD-TYPE
  T1             1               8
  T2             5              63
  T3             9             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
  UBE3C MUTATED    15   2   1
  UBE3C WILD-TYPE 205  78  65
D1213V5, multiclass
    clus
vv   UBE3C MUTATED UBE3C WILD-TYPE
  N0            15             205
  N1             2              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"
D1213V6, binary
                 cls
clus                0   1
  UBE3C MUTATED    13   2
  UBE3C WILD-TYPE 270  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UBE3C MUTATED     13    2
  UBE3C WILD-TYPE  270   46
   clus
vv  UBE3C MUTATED UBE3C WILD-TYPE
  0            13             270
  1             2              46
[1] 2 2
[1] FALSE
D1213V7, 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
D1213V8, binary
                 cls
clus                0   1
  UBE3C MUTATED    15   3
  UBE3C WILD-TYPE 302  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UBE3C MUTATED     15    3
  UBE3C WILD-TYPE  302   45
                               clus
vv                              UBE3C MUTATED UBE3C WILD-TYPE
  COLON ADENOCARCINOMA                     15             302
  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 245   2  22  20
D1213V9, multiclass
    clus
vv   UBE3C MUTATED UBE3C WILD-TYPE
  R0            12             245
  R1             0               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"
D1213V10, 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
D1213V11, 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(1214) Variable = GFRA4 MUTATION ANALYSIS
D1214V1, survival
                 sevent
clus2               0   1
  GFRA4 MUTATED     3   0
  GFRA4 WILD-TYPE 279  73
  GFRA4 MUTATED GFRA4 WILD-TYPE 
              3             352 
  GFRA4 MUTATED GFRA4 WILD-TYPE 
              0              73 
$`GFRA4 MUTATED`
TCGA-AA-3510 TCGA-AA-3864 TCGA-G4-6304 
       63.98        53.00        53.62 

$`GFRA4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      107.67        74.56        65.85        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  GFRA4 MUTATED GFRA4 WILD-TYPE 
             53               0 
  GFRA4 MUTATED GFRA4 WILD-TYPE 
          63.98          140.38 
  GFRA4 MUTATED GFRA4 WILD-TYPE 
          53.62           20.07 
[1] "53.0 - 64.0 (53.6)" "0.0 - 140.4 (20.1)"
[1] "hr="     "9500000"
D1214V2, 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       23       109         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        19         10         41         31       35        13
                 vv
clus              STAGE IVB
  GFRA4 MUTATED           0
  GFRA4 WILD-TYPE         1
D1214V3, multiclass
            clus
vv           GFRA4 MUTATED GFRA4 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              0             109
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GFRA4 MUTATED     0   0   2   1
  GFRA4 WILD-TYPE   9  68 246  40
D1214V4, multiclass
    clus
vv   GFRA4 MUTATED GFRA4 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             2             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
  GFRA4 MUTATED     3   0   0
  GFRA4 WILD-TYPE 217  80  66
D1214V5, multiclass
    clus
vv   GFRA4 MUTATED GFRA4 WILD-TYPE
  N0             3             217
  N1             0              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"
D1214V6, binary
                 cls
clus                0   1
  GFRA4 MUTATED     3   0
  GFRA4 WILD-TYPE 280  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GFRA4 MUTATED      3    0
  GFRA4 WILD-TYPE  280   48
   clus
vv  GFRA4 MUTATED GFRA4 WILD-TYPE
  0             3             280
  1             0              48
[1] 2 2
[1] FALSE
D1214V7, 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
D1214V8, binary
                 cls
clus                0   1
  GFRA4 MUTATED     3   0
  GFRA4 WILD-TYPE 314  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GFRA4 MUTATED      3    0
  GFRA4 WILD-TYPE  314   48
                               clus
vv                              GFRA4 MUTATED GFRA4 WILD-TYPE
  COLON ADENOCARCINOMA                      3             314
  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 254   2  22  21
D1214V9, multiclass
    clus
vv   GFRA4 MUTATED GFRA4 WILD-TYPE
  R0             3             254
  R1             0               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"
D1214V10, 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
D1214V11, multiclass
[1] "Remove cluster labels:" "GFRA4 MUTATED"         
clus
  GFRA4 MUTATED GFRA4 WILD-TYPE 
              1             205 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-4105 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-A6-5656      TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5660 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-A6-5661      TCGA-A6-5662      TCGA-A6-5664      TCGA-A6-5665 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-A6-5666      TCGA-A6-6137      TCGA-A6-6138      TCGA-A6-6141 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-A6-6142      TCGA-A6-6648      TCGA-A6-6649      TCGA-A6-6651 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-A6-6652      TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-A6-6781      TCGA-A6-6782      TCGA-AD-5900      TCGA-AD-6548 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-AD-6888      TCGA-AD-6889      TCGA-AD-6890      TCGA-AD-6895 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-AD-6899      TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6964 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-AD-6965      TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-AY-4071      TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-AY-6386      TCGA-AZ-4315      TCGA-AZ-4323      TCGA-AZ-4616 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-AZ-4681      TCGA-AZ-4682      TCGA-AZ-5403      TCGA-AZ-5407 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-AZ-6598      TCGA-AZ-6599      TCGA-AZ-6600      TCGA-AZ-6601 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-AZ-6603      TCGA-AZ-6605      TCGA-AZ-6606      TCGA-AZ-6607 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-AZ-6608      TCGA-CA-5254      TCGA-CA-5255      TCGA-CA-5796 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-CA-5797      TCGA-CA-6715      TCGA-CA-6716      TCGA-CA-6717 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-CA-6718      TCGA-CA-6719      TCGA-CK-4947      TCGA-CK-4948 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-CK-4950      TCGA-CK-4952      TCGA-CK-5912      TCGA-CK-5913 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-CK-5914      TCGA-CK-5915      TCGA-CK-5916      TCGA-CK-6746 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-CK-6747      TCGA-CK-6748      TCGA-CK-6751      TCGA-CM-4743 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-CM-4744      TCGA-CM-4746      TCGA-CM-4747      TCGA-CM-4752 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-CM-5341      TCGA-CM-5344      TCGA-CM-5348      TCGA-CM-5349 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-CM-5860      TCGA-CM-5861      TCGA-CM-5862      TCGA-CM-5863 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-CM-5864      TCGA-CM-5868      TCGA-CM-6161      TCGA-CM-6162 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-CM-6163      TCGA-CM-6164      TCGA-CM-6165      TCGA-CM-6166 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-CM-6167      TCGA-CM-6168      TCGA-CM-6169      TCGA-CM-6170 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-CM-6171      TCGA-CM-6172      TCGA-CM-6674      TCGA-CM-6675 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-CM-6676      TCGA-CM-6677      TCGA-CM-6678      TCGA-CM-6679 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-CM-6680      TCGA-D5-5537      TCGA-D5-5538      TCGA-D5-5539 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-D5-5540      TCGA-D5-5541      TCGA-D5-6529      TCGA-D5-6532 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-D5-6533      TCGA-D5-6534      TCGA-D5-6535      TCGA-D5-6536 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-D5-6537      TCGA-D5-6538      TCGA-D5-6539      TCGA-D5-6540 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-D5-6541      TCGA-D5-6898      TCGA-D5-6920      TCGA-D5-6922 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-D5-6923      TCGA-D5-6924      TCGA-D5-6926      TCGA-D5-6927 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-D5-6928      TCGA-D5-6929      TCGA-D5-6930      TCGA-D5-6931 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-D5-6932      TCGA-D5-7000      TCGA-DM-A0X9      TCGA-DM-A0XD 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-DM-A0XF      TCGA-DM-A1D0      TCGA-DM-A1D4      TCGA-DM-A1D6 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-DM-A1D7      TCGA-DM-A1D8      TCGA-DM-A1D9      TCGA-DM-A1DA 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-DM-A1DB      TCGA-DM-A1HA      TCGA-DM-A1HB      TCGA-DM-A282 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-DM-A285      TCGA-DM-A28C      TCGA-DM-A28E      TCGA-DM-A28F 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-DM-A28G      TCGA-DM-A28H      TCGA-DM-A28K      TCGA-F4-6459 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-F4-6460      TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-F4-6704      TCGA-F4-6805      TCGA-F4-6806      TCGA-F4-6807 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-F4-6808      TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-F4-6856      TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-G4-6306      TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-G4-6586      TCGA-G4-6588      TCGA-G4-6625      TCGA-G4-6626 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-G4-6628 
"GFRA4 WILD-TYPE" 

Clustering(1215) Variable = MCM9 MUTATION ANALYSIS
D1215V1, survival
                sevent
clus2              0   1
  MCM9 MUTATED     6   2
  MCM9 WILD-TYPE 276  71
  MCM9 MUTATED MCM9 WILD-TYPE 
             8            347 
  MCM9 MUTATED MCM9 WILD-TYPE 
             2             71 
$`MCM9 MUTATED`
TCGA-AA-3510 TCGA-AA-3662 TCGA-AA-3864 TCGA-AA-A010 TCGA-AZ-5403 TCGA-CA-6717 
       63.98         6.05        53.00        34.98        62.79         0.33 
TCGA-D5-6541 TCGA-F4-6809 
       15.58        13.25 

$`MCM9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       19.99        13.94        19.99        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       29.59        16.24        33.67         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  MCM9 MUTATED MCM9 WILD-TYPE 
          0.33           0.00 
  MCM9 MUTATED MCM9 WILD-TYPE 
         63.98         140.38 
  MCM9 MUTATED MCM9 WILD-TYPE 
         25.28          20.19 
[1] "0.3 - 64.0 (25.3)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D1215V2, 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       22       107         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MCM9 MUTATED           0          0          0          0        1         1
  MCM9 WILD-TYPE        19         10         41         31       34        12
                vv
clus             STAGE IVB
  MCM9 MUTATED           0
  MCM9 WILD-TYPE         1
D1215V3, multiclass
            clus
vv           MCM9 MUTATED MCM9 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              3             22
  STAGE IIA             2            107
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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   6   2
  MCM9 WILD-TYPE   9  68 242  39
D1215V4, multiclass
    clus
vv   MCM9 MUTATED MCM9 WILD-TYPE
  T1            0              9
  T2            0             68
  T3            6            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
  MCM9 MUTATED     6   1   1
  MCM9 WILD-TYPE 214  79  65
D1215V5, multiclass
    clus
vv   MCM9 MUTATED MCM9 WILD-TYPE
  N0            6            214
  N1            1             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"
D1215V6, binary
                cls
clus               0   1
  MCM9 MUTATED     5   2
  MCM9 WILD-TYPE 278  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCM9 MUTATED      5    2
  MCM9 WILD-TYPE  278   46
   clus
vv  MCM9 MUTATED MCM9 WILD-TYPE
  0            5            278
  1            2             46
[1] 2 2
[1] FALSE
D1215V7, binary
                cls
clus               0   1
  MCM9 MUTATED     3   5
  MCM9 WILD-TYPE 167 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCM9 MUTATED      3    5
  MCM9 WILD-TYPE  167  192
        clus
vv       MCM9 MUTATED MCM9 WILD-TYPE
  FEMALE            3            167
  MALE              5            192
[1] 2 2
[1] FALSE
D1215V8, binary
                cls
clus               0   1
  MCM9 MUTATED     7   1
  MCM9 WILD-TYPE 310  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCM9 MUTATED      7    1
  MCM9 WILD-TYPE  310   47
                               clus
vv                              MCM9 MUTATED MCM9 WILD-TYPE
  COLON ADENOCARCINOMA                     7            310
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MCM9 MUTATED     5   0   1   1
  MCM9 WILD-TYPE 252   2  21  20
D1215V9, multiclass
    clus
vv   MCM9 MUTATED MCM9 WILD-TYPE
  R0            5            252
  R1            0              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"
D1215V10, 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     3
  MCM9 WILD-TYPE                        19   173
D1215V11, 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                                       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(1216) Variable = ABCB6 MUTATION ANALYSIS
D1216V1, survival
                 sevent
clus2               0   1
  ABCB6 MUTATED     4   3
  ABCB6 WILD-TYPE 278  70
  ABCB6 MUTATED ABCB6 WILD-TYPE 
              7             348 
  ABCB6 MUTATED ABCB6 WILD-TYPE 
              3              70 
$`ABCB6 MUTATED`
TCGA-AA-3672 TCGA-AA-3696 TCGA-AA-A01Q TCGA-AU-3779 TCGA-AZ-6600 TCGA-AZ-6601 
        0.92         5.03         1.02        14.50        12.10       100.01 
TCGA-D5-6927 
        9.44 

$`ABCB6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
        6.05         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.20        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6603 
       22.36        62.79        61.41        49.41         6.77        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  ABCB6 MUTATED ABCB6 WILD-TYPE 
           0.92            0.00 
  ABCB6 MUTATED ABCB6 WILD-TYPE 
         100.01          140.38 
  ABCB6 MUTATED ABCB6 WILD-TYPE 
           9.44           20.98 
[1] "0.9 - 100.0 (9.4)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "2.5"
D1216V2, 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       23       107         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        18         10         41         31       33        13
                 vv
clus              STAGE IVB
  ABCB6 MUTATED           0
  ABCB6 WILD-TYPE         1
D1216V3, multiclass
            clus
vv           ABCB6 MUTATED ABCB6 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              2             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               2              33
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ABCB6 MUTATED     0   0   6   1
  ABCB6 WILD-TYPE   9  68 242  40
D1216V4, multiclass
    clus
vv   ABCB6 MUTATED ABCB6 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             6             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
  ABCB6 MUTATED     4   3   0
  ABCB6 WILD-TYPE 216  77  66
D1216V5, multiclass
    clus
vv   ABCB6 MUTATED ABCB6 WILD-TYPE
  N0             4             216
  N1             3              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"
D1216V6, binary
                 cls
clus                0   1
  ABCB6 MUTATED     5   2
  ABCB6 WILD-TYPE 278  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCB6 MUTATED      5    2
  ABCB6 WILD-TYPE  278   46
   clus
vv  ABCB6 MUTATED ABCB6 WILD-TYPE
  0             5             278
  1             2              46
[1] 2 2
[1] FALSE
D1216V7, 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
D1216V8, binary
                 cls
clus                0   1
  ABCB6 MUTATED     7   0
  ABCB6 WILD-TYPE 310  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCB6 MUTATED      7    0
  ABCB6 WILD-TYPE  310   48
                               clus
vv                              ABCB6 MUTATED ABCB6 WILD-TYPE
  COLON ADENOCARCINOMA                      7             310
  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 253   2  21  21
D1216V9, multiclass
    clus
vv   ABCB6 MUTATED ABCB6 WILD-TYPE
  R0             4             253
  R1             0               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"
D1216V10, 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
D1216V11, 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(1217) Variable = OR5AK2 MUTATION ANALYSIS
D1217V1, survival
                  sevent
clus2                0   1
  OR5AK2 MUTATED     6   3
  OR5AK2 WILD-TYPE 276  70
  OR5AK2 MUTATED OR5AK2 WILD-TYPE 
               9              346 
  OR5AK2 MUTATED OR5AK2 WILD-TYPE 
               3               70 
$`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         0.10 
TCGA-DM-A1D7 TCGA-DM-A28K TCGA-F4-6808 
       13.32        98.24        33.67 

$`OR5AK2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82        58.39         1.41        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        92.75        49.91        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 
      119.93        35.97        60.79       117.07         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       16.24        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  OR5AK2 MUTATED OR5AK2 WILD-TYPE 
             0.1              0.0 
  OR5AK2 MUTATED OR5AK2 WILD-TYPE 
           98.24           140.38 
  OR5AK2 MUTATED OR5AK2 WILD-TYPE 
          19.040           20.235 
[1] "0.1 - 98.2 (19.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.7"
D1217V2, 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       23       106         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR5AK2 MUTATED           0          0          0          0        1
  OR5AK2 WILD-TYPE        19         10         41         31       34
                  vv
clus               STAGE IVA STAGE IVB
  OR5AK2 MUTATED           0         0
  OR5AK2 WILD-TYPE        13         1
D1217V3, multiclass
            clus
vv           OR5AK2 MUTATED OR5AK2 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               3              106
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  OR5AK2 MUTATED     1   0   6   2
  OR5AK2 WILD-TYPE   8  68 242  39
D1217V4, multiclass
    clus
vv   OR5AK2 MUTATED OR5AK2 WILD-TYPE
  T1              1                8
  T2              0               68
  T3              6              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
  OR5AK2 MUTATED     8   0   1
  OR5AK2 WILD-TYPE 212  80  65
D1217V5, multiclass
    clus
vv   OR5AK2 MUTATED OR5AK2 WILD-TYPE
  N0              8              212
  N1              0               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"
D1217V6, binary
                  cls
clus                 0   1
  OR5AK2 MUTATED     8   1
  OR5AK2 WILD-TYPE 275  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR5AK2 MUTATED      8    1
  OR5AK2 WILD-TYPE  275   47
   clus
vv  OR5AK2 MUTATED OR5AK2 WILD-TYPE
  0              8              275
  1              1               47
[1] 2 2
[1] FALSE
D1217V7, 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
D1217V8, binary
                  cls
clus                 0   1
  OR5AK2 MUTATED     7   2
  OR5AK2 WILD-TYPE 310  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR5AK2 MUTATED      7    2
  OR5AK2 WILD-TYPE  310   46
                               clus
vv                              OR5AK2 MUTATED OR5AK2 WILD-TYPE
  COLON ADENOCARCINOMA                       7              310
  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 252   2  22  20
D1217V9, multiclass
    clus
vv   OR5AK2 MUTATED OR5AK2 WILD-TYPE
  R0              5              252
  R1              0                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"
D1217V10, 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
D1217V11, 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(1218) Variable = IGSF5 MUTATION ANALYSIS
D1218V1, survival
                 sevent
clus2               0   1
  IGSF5 MUTATED     9   4
  IGSF5 WILD-TYPE 273  69
  IGSF5 MUTATED IGSF5 WILD-TYPE 
             13             342 
  IGSF5 MUTATED IGSF5 WILD-TYPE 
              4              69 
$`IGSF5 MUTATED`
TCGA-A6-2676 TCGA-A6-6780 TCGA-AA-3517 TCGA-AA-3542 TCGA-AA-3713 TCGA-AA-3815 
       42.90        20.12        38.99        12.99        19.04        33.04 
TCGA-AA-A00N TCGA-AA-A00R TCGA-AZ-6600 TCGA-CK-5913 TCGA-CM-4746 TCGA-CM-6168 
        4.01         0.99        12.10        51.32        37.02        12.99 
TCGA-F4-6570 
        6.18 

$`IGSF5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        13.02         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 
       19.07        34.03        29.00        29.00        26.01         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       26.99        19.04        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W 
       18.05        38.04        27.02        42.02        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       40.34        15.62        49.08        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-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        13.38        13.45        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  IGSF5 MUTATED IGSF5 WILD-TYPE 
           0.99            0.00 
  IGSF5 MUTATED IGSF5 WILD-TYPE 
          51.32          140.38 
  IGSF5 MUTATED IGSF5 WILD-TYPE 
          19.04           20.63 
[1] "1.0 - 51.3 (19.0)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "1.8"
D1218V2, 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       25       102         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        19         10         41         30       33        13
                 vv
clus              STAGE IVB
  IGSF5 MUTATED           0
  IGSF5 WILD-TYPE         1
D1218V3, multiclass
            clus
vv           IGSF5 MUTATED IGSF5 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              7             102
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               2              33
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  IGSF5 MUTATED     0   2   9   3
  IGSF5 WILD-TYPE   9  66 239  38
D1218V4, multiclass
    clus
vv   IGSF5 MUTATED IGSF5 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             9             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
  IGSF5 MUTATED    12   1   1
  IGSF5 WILD-TYPE 208  79  65
D1218V5, multiclass
    clus
vv   IGSF5 MUTATED IGSF5 WILD-TYPE
  N0            12             208
  N1             1              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"
D1218V6, binary
                 cls
clus                0   1
  IGSF5 MUTATED    10   2
  IGSF5 WILD-TYPE 273  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGSF5 MUTATED     10    2
  IGSF5 WILD-TYPE  273   46
   clus
vv  IGSF5 MUTATED IGSF5 WILD-TYPE
  0            10             273
  1             2              46
[1] 2 2
[1] FALSE
D1218V7, 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
D1218V8, binary
                 cls
clus                0   1
  IGSF5 MUTATED    12   2
  IGSF5 WILD-TYPE 305  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGSF5 MUTATED     12    2
  IGSF5 WILD-TYPE  305   46
                               clus
vv                              IGSF5 MUTATED IGSF5 WILD-TYPE
  COLON ADENOCARCINOMA                     12             305
  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 247   2  21  20
D1218V9, multiclass
    clus
vv   IGSF5 MUTATED IGSF5 WILD-TYPE
  R0            10             247
  R1             0               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"
D1218V10, 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
D1218V11, 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(1219) Variable = PEBP4 MUTATION ANALYSIS
D1219V1, survival
                 sevent
clus2               0   1
  PEBP4 MUTATED     4   2
  PEBP4 WILD-TYPE 278  71
  PEBP4 MUTATED PEBP4 WILD-TYPE 
              6             349 
  PEBP4 MUTATED PEBP4 WILD-TYPE 
              2              71 
$`PEBP4 MUTATED`
TCGA-AA-3663 TCGA-AZ-6599 TCGA-D5-6540 TCGA-D5-6927 TCGA-DM-A1DB TCGA-G4-6306 
        6.97         6.77        16.14         9.44        44.32        44.68 

$`PEBP4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       12.59       140.38         7.50       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  PEBP4 MUTATED PEBP4 WILD-TYPE 
           6.77            0.00 
  PEBP4 MUTATED PEBP4 WILD-TYPE 
          44.68          140.38 
  PEBP4 MUTATED PEBP4 WILD-TYPE 
          12.79           20.28 
[1] "6.8 - 44.7 (12.8)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.9"
D1219V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PEBP4 MUTATED         2        0        1         3         1         0
  PEBP4 WILD-TYPE      62        1       24       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        19         10         41         31       35        13
                 vv
clus              STAGE IVB
  PEBP4 MUTATED           0
  PEBP4 WILD-TYPE         1
D1219V3, multiclass
            clus
vv           PEBP4 MUTATED PEBP4 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              3             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PEBP4 MUTATED     0   3   3   1
  PEBP4 WILD-TYPE   9  65 245  40
D1219V4, multiclass
    clus
vv   PEBP4 MUTATED PEBP4 WILD-TYPE
  T1             0               9
  T2             3              65
  T3             3             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
  PEBP4 MUTATED     7   0   0
  PEBP4 WILD-TYPE 213  80  66
D1219V5, multiclass
    clus
vv   PEBP4 MUTATED PEBP4 WILD-TYPE
  N0             7             213
  N1             0              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"
D1219V6, binary
                 cls
clus                0   1
  PEBP4 MUTATED     5   0
  PEBP4 WILD-TYPE 278  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PEBP4 MUTATED      5    0
  PEBP4 WILD-TYPE  278   48
   clus
vv  PEBP4 MUTATED PEBP4 WILD-TYPE
  0             5             278
  1             0              48
[1] 2 2
[1] FALSE
D1219V7, 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
D1219V8, binary
                 cls
clus                0   1
  PEBP4 MUTATED     6   1
  PEBP4 WILD-TYPE 311  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PEBP4 MUTATED      6    1
  PEBP4 WILD-TYPE  311   47
                               clus
vv                              PEBP4 MUTATED PEBP4 WILD-TYPE
  COLON ADENOCARCINOMA                      6             311
  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 253   2  22  20
D1219V9, multiclass
    clus
vv   PEBP4 MUTATED PEBP4 WILD-TYPE
  R0             4             253
  R1             0               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"
D1219V10, 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
D1219V11, 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(1220) Variable = ATXN7L1 MUTATION ANALYSIS
D1220V1, survival
                   sevent
clus2                 0   1
  ATXN7L1 MUTATED     8   2
  ATXN7L1 WILD-TYPE 274  71
  ATXN7L1 MUTATED ATXN7L1 WILD-TYPE 
               10               345 
  ATXN7L1 MUTATED ATXN7L1 WILD-TYPE 
                2                71 
$`ATXN7L1 MUTATED`
TCGA-A6-6653 TCGA-AA-3492 TCGA-AA-3525 TCGA-AA-3966 TCGA-AD-6889 TCGA-AY-6197 
       24.39         3.02         8.05         2.01        56.55        21.44 
TCGA-AZ-6601 TCGA-CA-6717 TCGA-D5-6540 TCGA-D5-6928 
      100.01         0.33        16.14        11.64 

$`ATXN7L1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 
        9.07        24.03        37.05        36.03        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37         4.21         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       27.09        16.31         0.95        15.75         0.20        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  ATXN7L1 MUTATED ATXN7L1 WILD-TYPE 
             0.33              0.00 
  ATXN7L1 MUTATED ATXN7L1 WILD-TYPE 
           100.01            140.38 
  ATXN7L1 MUTATED ATXN7L1 WILD-TYPE 
            13.89             20.28 
[1] "0.3 - 100.0 (13.9)" "0.0 - 140.4 (20.3)"
[1] "hr=" "1"  
D1220V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATXN7L1 MUTATED         2        0        2         6         0         0
  ATXN7L1 WILD-TYPE      62        1       23       103         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATXN7L1 MUTATED           0          0          1          0        0
  ATXN7L1 WILD-TYPE        19         10         40         31       35
                   vv
clus                STAGE IVA STAGE IVB
  ATXN7L1 MUTATED           0         0
  ATXN7L1 WILD-TYPE        13         1
D1220V3, multiclass
            clus
vv           ATXN7L1 MUTATED ATXN7L1 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 2                23
  STAGE IIA                6               103
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ATXN7L1 MUTATED     0   2   9   0
  ATXN7L1 WILD-TYPE   9  66 239  41
D1220V4, multiclass
    clus
vv   ATXN7L1 MUTATED ATXN7L1 WILD-TYPE
  T1               0                 9
  T2               2                66
  T3               9               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
  ATXN7L1 MUTATED    10   1   0
  ATXN7L1 WILD-TYPE 210  79  66
D1220V5, multiclass
    clus
vv   ATXN7L1 MUTATED ATXN7L1 WILD-TYPE
  N0              10               210
  N1               1                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"
D1220V6, binary
                   cls
clus                  0   1
  ATXN7L1 MUTATED    10   0
  ATXN7L1 WILD-TYPE 273  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ATXN7L1 MUTATED     10    0
  ATXN7L1 WILD-TYPE  273   48
   clus
vv  ATXN7L1 MUTATED ATXN7L1 WILD-TYPE
  0              10               273
  1               0                48
[1] 2 2
[1] FALSE
D1220V7, binary
                   cls
clus                  0   1
  ATXN7L1 MUTATED     3   8
  ATXN7L1 WILD-TYPE 167 189
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ATXN7L1 MUTATED      3    8
  ATXN7L1 WILD-TYPE  167  189
        clus
vv       ATXN7L1 MUTATED ATXN7L1 WILD-TYPE
  FEMALE               3               167
  MALE                 8               189
[1] 2 2
[1] FALSE
D1220V8, binary
                   cls
clus                  0   1
  ATXN7L1 MUTATED     7   4
  ATXN7L1 WILD-TYPE 310  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ATXN7L1 MUTATED      7    4
  ATXN7L1 WILD-TYPE  310   44
                               clus
vv                              ATXN7L1 MUTATED ATXN7L1 WILD-TYPE
  COLON ADENOCARCINOMA                        7               310
  COLON MUCINOUS ADENOCARCINOMA               4                44
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ATXN7L1 MUTATED     6   0   0   1
  ATXN7L1 WILD-TYPE 251   2  22  20
D1220V9, multiclass
    clus
vv   ATXN7L1 MUTATED ATXN7L1 WILD-TYPE
  R0               6               251
  R1               0                 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"
D1220V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATXN7L1 MUTATED                                  0     2
  ATXN7L1 WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ATXN7L1 MUTATED                           0     5
  ATXN7L1 WILD-TYPE                        19   171
D1220V11, multiclass
                                  clus
vv                                 ATXN7L1 MUTATED ATXN7L1 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(1221) Variable = CDK14 MUTATION ANALYSIS
D1221V1, survival
                 sevent
clus2               0   1
  CDK14 MUTATED    11   3
  CDK14 WILD-TYPE 271  70
  CDK14 MUTATED CDK14 WILD-TYPE 
             14             341 
  CDK14 MUTATED CDK14 WILD-TYPE 
              3              70 
$`CDK14 MUTATED`
TCGA-A6-3807 TCGA-A6-5665 TCGA-AA-3667 TCGA-AA-3855 TCGA-AA-A00N TCGA-AA-A02H 
       34.65        22.06        14.01        32.05         4.01         2.01 
TCGA-AZ-5407 TCGA-CA-6718 TCGA-CK-4952 TCGA-CM-4743 TCGA-D5-6532 TCGA-D5-6539 
       61.41         0.10        15.62        23.05        18.25        12.49 
TCGA-G4-6303 TCGA-G4-6588 
       65.85        26.17 

$`CDK14 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 
        0.00        33.07         0.00        36.03         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02K 
       37.02        39.06        51.98        39.98         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.33         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      102.44        40.34        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6540 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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 
       35.41        19.43       107.67        74.56        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        91.79        46.75        52.80 

  CDK14 MUTATED CDK14 WILD-TYPE 
            0.1             0.0 
  CDK14 MUTATED CDK14 WILD-TYPE 
          65.85          140.38 
  CDK14 MUTATED CDK14 WILD-TYPE 
         20.155          20.190 
[1] "0.1 - 65.8 (20.2)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D1221V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CDK14 MUTATED         3        0        0         5         1         0
  CDK14 WILD-TYPE      61        1       25       104         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CDK14 MUTATED           1          1          0          1        2         0
  CDK14 WILD-TYPE        18          9         41         30       33        13
                 vv
clus              STAGE IVB
  CDK14 MUTATED           0
  CDK14 WILD-TYPE         1
D1221V3, multiclass
            clus
vv           CDK14 MUTATED CDK14 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              5             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             1               9
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               2              33
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CDK14 MUTATED     1   2   9   2
  CDK14 WILD-TYPE   8  66 239  39
D1221V4, multiclass
    clus
vv   CDK14 MUTATED CDK14 WILD-TYPE
  T1             1               8
  T2             2              66
  T3             9             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
  CDK14 MUTATED    10   1   3
  CDK14 WILD-TYPE 210  79  63
D1221V5, multiclass
    clus
vv   CDK14 MUTATED CDK14 WILD-TYPE
  N0            10             210
  N1             1              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"
D1221V6, binary
                 cls
clus                0   1
  CDK14 MUTATED    12   2
  CDK14 WILD-TYPE 271  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK14 MUTATED     12    2
  CDK14 WILD-TYPE  271   46
   clus
vv  CDK14 MUTATED CDK14 WILD-TYPE
  0            12             271
  1             2              46
[1] 2 2
[1] FALSE
D1221V7, binary
                 cls
clus                0   1
  CDK14 MUTATED     9   5
  CDK14 WILD-TYPE 161 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK14 MUTATED      9    5
  CDK14 WILD-TYPE  161  192
        clus
vv       CDK14 MUTATED CDK14 WILD-TYPE
  FEMALE             9             161
  MALE               5             192
[1] 2 2
[1] FALSE
D1221V8, binary
                 cls
clus                0   1
  CDK14 MUTATED    12   2
  CDK14 WILD-TYPE 305  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK14 MUTATED     12    2
  CDK14 WILD-TYPE  305   46
                               clus
vv                              CDK14 MUTATED CDK14 WILD-TYPE
  COLON ADENOCARCINOMA                     12             305
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CDK14 MUTATED    10   0   1   2
  CDK14 WILD-TYPE 247   2  21  19
D1221V9, multiclass
    clus
vv   CDK14 MUTATED CDK14 WILD-TYPE
  R0            10             247
  R1             0               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"
D1221V10, 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     9
  CDK14 WILD-TYPE                        19   167
D1221V11, 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                                        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(1222) Variable = CEPT1 MUTATION ANALYSIS
D1222V1, survival
                 sevent
clus2               0   1
  CEPT1 MUTATED     5   0
  CEPT1 WILD-TYPE 277  73
  CEPT1 MUTATED CEPT1 WILD-TYPE 
              5             350 
  CEPT1 MUTATED CEPT1 WILD-TYPE 
              0              73 
$`CEPT1 MUTATED`
TCGA-AA-3877 TCGA-CA-6717 TCGA-CA-6718 TCGA-DM-A1D9 TCGA-G4-6586 
       31.00         0.33         0.10       140.38        35.80 

$`CEPT1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07         0.26         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32        12.59         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  CEPT1 MUTATED CEPT1 WILD-TYPE 
            0.1             0.0 
  CEPT1 MUTATED CEPT1 WILD-TYPE 
         140.38          139.17 
  CEPT1 MUTATED CEPT1 WILD-TYPE 
         31.000          20.155 
[1] "0.1 - 140.4 (31.0)" "0.0 - 139.2 (20.2)"
[1] "hr="     "9300000"
D1222V2, 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       25       105         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        19         10         41         31       35        13
                 vv
clus              STAGE IVB
  CEPT1 MUTATED           0
  CEPT1 WILD-TYPE         1
D1222V3, multiclass
            clus
vv           CEPT1 MUTATED CEPT1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              4             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CEPT1 MUTATED     1   0   4   0
  CEPT1 WILD-TYPE   8  68 244  41
D1222V4, multiclass
    clus
vv   CEPT1 MUTATED CEPT1 WILD-TYPE
  T1             1               8
  T2             0              68
  T3             4             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
  CEPT1 MUTATED     5   0   0
  CEPT1 WILD-TYPE 215  80  66
D1222V5, multiclass
    clus
vv   CEPT1 MUTATED CEPT1 WILD-TYPE
  N0             5             215
  N1             0              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"
D1222V6, binary
                 cls
clus                0   1
  CEPT1 MUTATED     5   0
  CEPT1 WILD-TYPE 278  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CEPT1 MUTATED      5    0
  CEPT1 WILD-TYPE  278   48
   clus
vv  CEPT1 MUTATED CEPT1 WILD-TYPE
  0             5             278
  1             0              48
[1] 2 2
[1] FALSE
D1222V7, 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
D1222V8, binary
                 cls
clus                0   1
  CEPT1 MUTATED     3   2
  CEPT1 WILD-TYPE 314  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CEPT1 MUTATED      3    2
  CEPT1 WILD-TYPE  314   46
                               clus
vv                              CEPT1 MUTATED CEPT1 WILD-TYPE
  COLON ADENOCARCINOMA                      3             314
  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 255   2  22  19
D1222V9, multiclass
    clus
vv   CEPT1 MUTATED CEPT1 WILD-TYPE
  R0             2             255
  R1             0               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"
D1222V10, 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
D1222V11, 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(1223) Variable = OR9Q1 MUTATION ANALYSIS
D1223V1, survival
                 sevent
clus2               0   1
  OR9Q1 MUTATED     4   2
  OR9Q1 WILD-TYPE 278  71
  OR9Q1 MUTATED OR9Q1 WILD-TYPE 
              6             349 
  OR9Q1 MUTATED OR9Q1 WILD-TYPE 
              2              71 
$`OR9Q1 MUTATED`
TCGA-AA-3713 TCGA-AD-6889 TCGA-CK-4952 TCGA-CM-6674 TCGA-DM-A1DB TCGA-F4-6570 
       19.04        56.55        15.62        12.95        44.32         6.18 

$`OR9Q1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        4.21         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      102.44        40.34        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       12.59       140.38         7.50       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        13.38        13.45        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  OR9Q1 MUTATED OR9Q1 WILD-TYPE 
           6.18            0.00 
  OR9Q1 MUTATED OR9Q1 WILD-TYPE 
          56.55          140.38 
  OR9Q1 MUTATED OR9Q1 WILD-TYPE 
          17.33           20.28 
[1] "6.2 - 56.5 (17.3)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.5"
D1223V2, 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       25       105         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR9Q1 MUTATED           1          0          0          0        1         0
  OR9Q1 WILD-TYPE        18         10         41         31       34        13
                 vv
clus              STAGE IVB
  OR9Q1 MUTATED           0
  OR9Q1 WILD-TYPE         1
D1223V3, multiclass
            clus
vv           OR9Q1 MUTATED OR9Q1 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              4             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR9Q1 MUTATED     0   0   5   1
  OR9Q1 WILD-TYPE   9  68 243  40
D1223V4, multiclass
    clus
vv   OR9Q1 MUTATED OR9Q1 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             5             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
  OR9Q1 MUTATED     5   0   1
  OR9Q1 WILD-TYPE 215  80  65
D1223V5, multiclass
    clus
vv   OR9Q1 MUTATED OR9Q1 WILD-TYPE
  N0             5             215
  N1             0              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"
D1223V6, binary
                 cls
clus                0   1
  OR9Q1 MUTATED     5   1
  OR9Q1 WILD-TYPE 278  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR9Q1 MUTATED      5    1
  OR9Q1 WILD-TYPE  278   47
   clus
vv  OR9Q1 MUTATED OR9Q1 WILD-TYPE
  0             5             278
  1             1              47
[1] 2 2
[1] FALSE
D1223V7, 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
D1223V8, binary
                 cls
clus                0   1
  OR9Q1 MUTATED     5   1
  OR9Q1 WILD-TYPE 312  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR9Q1 MUTATED      5    1
  OR9Q1 WILD-TYPE  312   47
                               clus
vv                              OR9Q1 MUTATED OR9Q1 WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  OR9Q1 MUTATED     2   0   1   1
  OR9Q1 WILD-TYPE 255   2  21  20
D1223V9, multiclass
    clus
vv   OR9Q1 MUTATED OR9Q1 WILD-TYPE
  R0             2             255
  R1             0               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"
D1223V10, 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
D1223V11, 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(1224) Variable = ZBTB24 MUTATION ANALYSIS
D1224V1, survival
                  sevent
clus2                0   1
  ZBTB24 MUTATED     7   1
  ZBTB24 WILD-TYPE 275  72
  ZBTB24 MUTATED ZBTB24 WILD-TYPE 
               8              347 
  ZBTB24 MUTATED ZBTB24 WILD-TYPE 
               1               72 
$`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         0.10        14.04        10.06 
TCGA-DM-A0XF TCGA-DM-A1HB 
       38.20       135.65 

$`ZBTB24 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.33         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 
       12.00        11.38        10.26       119.70        24.43       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  ZBTB24 MUTATED ZBTB24 WILD-TYPE 
             0.1              0.0 
  ZBTB24 MUTATED ZBTB24 WILD-TYPE 
          135.65           140.38 
  ZBTB24 MUTATED ZBTB24 WILD-TYPE 
           29.57            20.12 
[1] "0.1 - 135.7 (29.6)" "0.0 - 140.4 (20.1)"
[1] "hr=" "2.2"
D1224V2, 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       24       107         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZBTB24 MUTATED           0          0          2          1        0
  ZBTB24 WILD-TYPE        19         10         39         30       35
                  vv
clus               STAGE IVA STAGE IVB
  ZBTB24 MUTATED           0         0
  ZBTB24 WILD-TYPE        13         1
D1224V3, multiclass
            clus
vv           ZBTB24 MUTATED ZBTB24 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               2              107
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZBTB24 MUTATED     0   1   6   1
  ZBTB24 WILD-TYPE   9  67 242  40
D1224V4, multiclass
    clus
vv   ZBTB24 MUTATED ZBTB24 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              6              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
  ZBTB24 MUTATED     5   2   1
  ZBTB24 WILD-TYPE 215  78  65
D1224V5, multiclass
    clus
vv   ZBTB24 MUTATED ZBTB24 WILD-TYPE
  N0              5              215
  N1              2               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"
D1224V6, binary
                  cls
clus                 0   1
  ZBTB24 MUTATED     8   0
  ZBTB24 WILD-TYPE 275  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB24 MUTATED      8    0
  ZBTB24 WILD-TYPE  275   48
   clus
vv  ZBTB24 MUTATED ZBTB24 WILD-TYPE
  0              8              275
  1              0               48
[1] 2 2
[1] FALSE
D1224V7, 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
D1224V8, binary
                  cls
clus                 0   1
  ZBTB24 MUTATED     7   1
  ZBTB24 WILD-TYPE 310  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB24 MUTATED      7    1
  ZBTB24 WILD-TYPE  310   47
                               clus
vv                              ZBTB24 MUTATED ZBTB24 WILD-TYPE
  COLON ADENOCARCINOMA                       7              310
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZBTB24 MUTATED     4   0   0   1
  ZBTB24 WILD-TYPE 253   2  22  20
D1224V9, multiclass
    clus
vv   ZBTB24 MUTATED ZBTB24 WILD-TYPE
  R0              4              253
  R1              0                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"
D1224V10, 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
D1224V11, 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(1225) Variable = NSUN2 MUTATION ANALYSIS
D1225V1, survival
                 sevent
clus2               0   1
  NSUN2 MUTATED     9   2
  NSUN2 WILD-TYPE 273  71
  NSUN2 MUTATED NSUN2 WILD-TYPE 
             11             344 
  NSUN2 MUTATED NSUN2 WILD-TYPE 
              2              71 
$`NSUN2 MUTATED`
TCGA-A6-5659 TCGA-AA-3685 TCGA-AA-3833 TCGA-AA-3930 TCGA-AD-6964 TCGA-AZ-4315 
       30.44        37.05        15.95         2.01        10.88        58.39 
TCGA-CM-6674 TCGA-D5-5539 TCGA-D5-6541 TCGA-F4-6856 TCGA-G4-6304 
       12.95        19.59        15.58        19.43        53.62 

$`NSUN2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 
       47.01        15.02        11.01         5.98        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3941 
       27.02        29.98        18.05        31.00        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
        0.72         5.79        22.42        27.42         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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-D5-5540 
       11.01        10.06        12.03        45.40        12.26        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        16.14         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 
       33.67        13.25         0.53        35.41       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  NSUN2 MUTATED NSUN2 WILD-TYPE 
           2.01            0.00 
  NSUN2 MUTATED NSUN2 WILD-TYPE 
          58.39          140.38 
  NSUN2 MUTATED NSUN2 WILD-TYPE 
          19.43           20.63 
[1] "2.0 - 58.4 (19.4)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "1.1"
D1225V2, 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       24       105         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        19          9         41         31       34        13
                 vv
clus              STAGE IVB
  NSUN2 MUTATED           0
  NSUN2 WILD-TYPE         1
D1225V3, multiclass
            clus
vv           NSUN2 MUTATED NSUN2 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              4             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NSUN2 MUTATED     0   2   7   2
  NSUN2 WILD-TYPE   9  66 241  39
D1225V4, multiclass
    clus
vv   NSUN2 MUTATED NSUN2 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             7             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
  NSUN2 MUTATED     8   1   2
  NSUN2 WILD-TYPE 212  79  64
D1225V5, multiclass
    clus
vv   NSUN2 MUTATED NSUN2 WILD-TYPE
  N0             8             212
  N1             1              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"
D1225V6, binary
                 cls
clus                0   1
  NSUN2 MUTATED     9   1
  NSUN2 WILD-TYPE 274  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NSUN2 MUTATED      9    1
  NSUN2 WILD-TYPE  274   47
   clus
vv  NSUN2 MUTATED NSUN2 WILD-TYPE
  0             9             274
  1             1              47
[1] 2 2
[1] FALSE
D1225V7, 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
D1225V8, binary
                 cls
clus                0   1
  NSUN2 MUTATED     9   2
  NSUN2 WILD-TYPE 308  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NSUN2 MUTATED      9    2
  NSUN2 WILD-TYPE  308   46
                               clus
vv                              NSUN2 MUTATED NSUN2 WILD-TYPE
  COLON ADENOCARCINOMA                      9             308
  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 248   2  21  21
D1225V9, multiclass
    clus
vv   NSUN2 MUTATED NSUN2 WILD-TYPE
  R0             9             248
  R1             0               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"
D1225V10, 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
D1225V11, 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(1226) Variable = PPP2R5E MUTATION ANALYSIS
D1226V1, survival
                   sevent
clus2                 0   1
  PPP2R5E MUTATED     8   0
  PPP2R5E WILD-TYPE 274  73
  PPP2R5E MUTATED PPP2R5E WILD-TYPE 
                8               347 
  PPP2R5E MUTATED PPP2R5E WILD-TYPE 
                0                73 
$`PPP2R5E MUTATED`
TCGA-A6-5661 TCGA-AA-A00J TCGA-AA-A01Q TCGA-AD-6895 TCGA-CA-6717 TCGA-CM-4746 
       33.53        18.05         1.02         0.72         0.33        37.02 
TCGA-D5-6541 TCGA-DM-A1HB 
       15.58       135.65 

$`PPP2R5E WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  PPP2R5E MUTATED PPP2R5E WILD-TYPE 
             0.33              0.00 
  PPP2R5E MUTATED PPP2R5E WILD-TYPE 
           135.65            140.38 
  PPP2R5E MUTATED PPP2R5E WILD-TYPE 
           16.815            20.280 
[1] "0.3 - 135.7 (16.8)" "0.0 - 140.4 (20.3)"
[1] "hr="     "9300000"
D1226V2, 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       24       106         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PPP2R5E MUTATED           0          0          2          0        0
  PPP2R5E WILD-TYPE        19         10         39         31       35
                   vv
clus                STAGE IVA STAGE IVB
  PPP2R5E MUTATED           0         0
  PPP2R5E WILD-TYPE        13         1
D1226V3, multiclass
            clus
vv           PPP2R5E MUTATED PPP2R5E WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                3               106
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               2                39
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PPP2R5E MUTATED     0   1   6   1
  PPP2R5E WILD-TYPE   9  67 242  40
D1226V4, multiclass
    clus
vv   PPP2R5E MUTATED PPP2R5E WILD-TYPE
  T1               0                 9
  T2               1                67
  T3               6               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
  PPP2R5E MUTATED     5   3   0
  PPP2R5E WILD-TYPE 215  77  66
D1226V5, multiclass
    clus
vv   PPP2R5E MUTATED PPP2R5E WILD-TYPE
  N0               5               215
  N1               3                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"
D1226V6, binary
                   cls
clus                  0   1
  PPP2R5E MUTATED     7   0
  PPP2R5E WILD-TYPE 276  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP2R5E MUTATED      7    0
  PPP2R5E WILD-TYPE  276   48
   clus
vv  PPP2R5E MUTATED PPP2R5E WILD-TYPE
  0               7               276
  1               0                48
[1] 2 2
[1] FALSE
D1226V7, 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
D1226V8, binary
                   cls
clus                  0   1
  PPP2R5E MUTATED     6   2
  PPP2R5E WILD-TYPE 311  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP2R5E MUTATED      6    2
  PPP2R5E WILD-TYPE  311   46
                               clus
vv                              PPP2R5E MUTATED PPP2R5E WILD-TYPE
  COLON ADENOCARCINOMA                        6               311
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  PPP2R5E MUTATED     5   0   0   1
  PPP2R5E WILD-TYPE 252   2  22  20
D1226V9, multiclass
    clus
vv   PPP2R5E MUTATED PPP2R5E WILD-TYPE
  R0               5               252
  R1               0                 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"
D1226V10, 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
D1226V11, 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(1227) Variable = ABCF3 MUTATION ANALYSIS
D1227V1, survival
                 sevent
clus2               0   1
  ABCF3 MUTATED    12   2
  ABCF3 WILD-TYPE 270  71
  ABCF3 MUTATED ABCF3 WILD-TYPE 
             14             341 
  ABCF3 MUTATED ABCF3 WILD-TYPE 
              2              71 
$`ABCF3 MUTATED`
TCGA-A6-6781 TCGA-AA-3815 TCGA-AA-3852 TCGA-AA-A00J TCGA-AD-6889 TCGA-AZ-4315 
       19.66        33.04         0.00        18.05        56.55        58.39 
TCGA-AZ-6601 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-6161 TCGA-CM-6165 TCGA-D5-6535 
      100.01        23.05        37.02        15.02        16.04        15.12 
TCGA-G4-6293 TCGA-G4-6310 
      107.67        45.11 

$`ABCF3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       10.06         0.00        33.07        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37         4.21         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
       21.99        21.14         2.93         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 
       16.01        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.41        19.43        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        51.75        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  ABCF3 MUTATED ABCF3 WILD-TYPE 
              0               0 
  ABCF3 MUTATED ABCF3 WILD-TYPE 
         107.67          140.38 
  ABCF3 MUTATED ABCF3 WILD-TYPE 
         28.045          20.120 
[1] "0.0 - 107.7 (28.0)" "0.0 - 140.4 (20.1)"
[1] "hr=" "2.2"
D1227V2, 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       24       103         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        18         10         38         30       35        13
                 vv
clus              STAGE IVB
  ABCF3 MUTATED           0
  ABCF3 WILD-TYPE         1
D1227V3, multiclass
            clus
vv           ABCF3 MUTATED ABCF3 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              6             103
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             3              38
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ABCF3 MUTATED     0   2  10   3
  ABCF3 WILD-TYPE   9  66 238  38
D1227V4, multiclass
    clus
vv   ABCF3 MUTATED ABCF3 WILD-TYPE
  T1             0               9
  T2             2              66
  T3            10             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
  ABCF3 MUTATED    10   5   0
  ABCF3 WILD-TYPE 210  75  66
D1227V5, multiclass
    clus
vv   ABCF3 MUTATED ABCF3 WILD-TYPE
  N0            10             210
  N1             5              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"
D1227V6, binary
                 cls
clus                0   1
  ABCF3 MUTATED    12   0
  ABCF3 WILD-TYPE 271  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCF3 MUTATED     12    0
  ABCF3 WILD-TYPE  271   48
   clus
vv  ABCF3 MUTATED ABCF3 WILD-TYPE
  0            12             271
  1             0              48
[1] 2 2
[1] FALSE
D1227V7, 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
D1227V8, binary
                 cls
clus                0   1
  ABCF3 MUTATED    12   3
  ABCF3 WILD-TYPE 305  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCF3 MUTATED     12    3
  ABCF3 WILD-TYPE  305   45
                               clus
vv                              ABCF3 MUTATED ABCF3 WILD-TYPE
  COLON ADENOCARCINOMA                     12             305
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ABCF3 MUTATED    11   0   0   2
  ABCF3 WILD-TYPE 246   2  22  19
D1227V9, multiclass
    clus
vv   ABCF3 MUTATED ABCF3 WILD-TYPE
  R0            11             246
  R1             0               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"
D1227V10, 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
D1227V11, 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(1228) Variable = BEX5 MUTATION ANALYSIS
D1228V1, survival
                sevent
clus2              0   1
  BEX5 MUTATED     5   2
  BEX5 WILD-TYPE 277  71
  BEX5 MUTATED BEX5 WILD-TYPE 
             7            348 
  BEX5 MUTATED BEX5 WILD-TYPE 
             2             71 
$`BEX5 MUTATED`
TCGA-AA-3854 TCGA-AA-3966 TCGA-AD-6964 TCGA-CM-5349 TCGA-D5-6541 TCGA-G4-6293 
       36.03         2.01        10.88        30.08        15.58       107.67 
TCGA-G4-6303 
       65.85 

$`BEX5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        16.14         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 
        0.53        35.41        19.43        74.56        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  BEX5 MUTATED BEX5 WILD-TYPE 
          2.01           0.00 
  BEX5 MUTATED BEX5 WILD-TYPE 
        107.67         140.38 
  BEX5 MUTATED BEX5 WILD-TYPE 
        30.080         20.155 
[1] "2.0 - 107.7 (30.1)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D1228V2, 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       25       106         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        18         10         41         31       34        13
                vv
clus             STAGE IVB
  BEX5 MUTATED           0
  BEX5 WILD-TYPE         1
D1228V3, multiclass
            clus
vv           BEX5 MUTATED BEX5 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             3            106
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  BEX5 MUTATED     0   1   5   1
  BEX5 WILD-TYPE   9  67 243  40
D1228V4, multiclass
    clus
vv   BEX5 MUTATED BEX5 WILD-TYPE
  T1            0              9
  T2            1             67
  T3            5            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
  BEX5 MUTATED     4   2   1
  BEX5 WILD-TYPE 216  78  65
D1228V5, multiclass
    clus
vv   BEX5 MUTATED BEX5 WILD-TYPE
  N0            4            216
  N1            2             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"
D1228V6, binary
                cls
clus               0   1
  BEX5 MUTATED     5   1
  BEX5 WILD-TYPE 278  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  BEX5 MUTATED      5    1
  BEX5 WILD-TYPE  278   47
   clus
vv  BEX5 MUTATED BEX5 WILD-TYPE
  0            5            278
  1            1             47
[1] 2 2
[1] FALSE
D1228V7, 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
D1228V8, binary
                cls
clus               0   1
  BEX5 MUTATED     5   2
  BEX5 WILD-TYPE 312  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  BEX5 MUTATED      5    2
  BEX5 WILD-TYPE  312   46
                               clus
vv                              BEX5 MUTATED BEX5 WILD-TYPE
  COLON ADENOCARCINOMA                     5            312
  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 252   2  22  21
D1228V9, multiclass
    clus
vv   BEX5 MUTATED BEX5 WILD-TYPE
  R0            5            252
  R1            0              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"
D1228V10, 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
D1228V11, 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(1229) Variable = GBA2 MUTATION ANALYSIS
D1229V1, survival
                sevent
clus2              0   1
  GBA2 MUTATED    11   3
  GBA2 WILD-TYPE 271  70
  GBA2 MUTATED GBA2 WILD-TYPE 
            14            341 
  GBA2 MUTATED GBA2 WILD-TYPE 
             3             70 
$`GBA2 MUTATED`
TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-3663 TCGA-AA-3715 TCGA-AA-3833 TCGA-AA-3966 
       22.06        20.12         6.97        19.04        15.95         2.01 
TCGA-AA-A00J TCGA-AU-6004 TCGA-AY-6197 TCGA-AZ-6601 TCGA-DM-A1DA TCGA-DM-A28K 
       18.05        27.09        21.44       100.01         7.50        98.24 
TCGA-F4-6460 TCGA-G4-6586 
       13.38        35.80 

$`GBA2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 
        0.99        25.02         1.02        17.98        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       26.01        24.00         2.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       15.75         0.20        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       12.59       140.38        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        26.17        91.79        46.75        52.80 

  GBA2 MUTATED GBA2 WILD-TYPE 
          2.01           0.00 
  GBA2 MUTATED GBA2 WILD-TYPE 
        100.01         140.38 
  GBA2 MUTATED GBA2 WILD-TYPE 
         19.58          20.28 
[1] "2.0 - 100.0 (19.6)" "0.0 - 140.4 (20.3)"
[1] "hr=" "1.1"
D1229V2, 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       22       102         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        19         10         39         30       34        13
                vv
clus             STAGE IVB
  GBA2 MUTATED           0
  GBA2 WILD-TYPE         1
D1229V3, multiclass
            clus
vv           GBA2 MUTATED GBA2 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              3             22
  STAGE IIA             7            102
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            2             39
  STAGE IIIC            1             30
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GBA2 MUTATED     0   1  13   1
  GBA2 WILD-TYPE   9  67 235  40
D1229V4, multiclass
    clus
vv   GBA2 MUTATED GBA2 WILD-TYPE
  T1            0              9
  T2            1             67
  T3           13            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
  GBA2 MUTATED    11   2   2
  GBA2 WILD-TYPE 209  78  64
D1229V5, multiclass
    clus
vv   GBA2 MUTATED GBA2 WILD-TYPE
  N0           11            209
  N1            2             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"
D1229V6, binary
                cls
clus               0   1
  GBA2 MUTATED    12   1
  GBA2 WILD-TYPE 271  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  GBA2 MUTATED     12    1
  GBA2 WILD-TYPE  271   47
   clus
vv  GBA2 MUTATED GBA2 WILD-TYPE
  0           12            271
  1            1             47
[1] 2 2
[1] FALSE
D1229V7, 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
D1229V8, binary
                cls
clus               0   1
  GBA2 MUTATED    11   4
  GBA2 WILD-TYPE 306  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  GBA2 MUTATED     11    4
  GBA2 WILD-TYPE  306   44
                               clus
vv                              GBA2 MUTATED GBA2 WILD-TYPE
  COLON ADENOCARCINOMA                    11            306
  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 248   2  21  21
D1229V9, multiclass
    clus
vv   GBA2 MUTATED GBA2 WILD-TYPE
  R0            9            248
  R1            0              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"
D1229V10, 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
D1229V11, 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(1230) Variable = CYP2C9 MUTATION ANALYSIS
D1230V1, survival
                  sevent
clus2                0   1
  CYP2C9 MUTATED     6   0
  CYP2C9 WILD-TYPE 276  73
  CYP2C9 MUTATED CYP2C9 WILD-TYPE 
               6              349 
  CYP2C9 MUTATED CYP2C9 WILD-TYPE 
               0               73 
$`CYP2C9 MUTATED`
TCGA-AA-3697 TCGA-AA-3947 TCGA-AA-A01Q TCGA-D5-6532 TCGA-G4-6306 TCGA-G4-6588 
       85.05        33.01         1.02        18.25        44.68        26.17 

$`CYP2C9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 
       52.80 

  CYP2C9 MUTATED CYP2C9 WILD-TYPE 
            1.02             0.00 
  CYP2C9 MUTATED CYP2C9 WILD-TYPE 
           85.05           140.38 
  CYP2C9 MUTATED CYP2C9 WILD-TYPE 
           29.59            20.12 
[1] "1.0 - 85.0 (29.6)"  "0.0 - 140.4 (20.1)"
[1] "hr="     "9300000"
D1230V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CYP2C9 MUTATED         0        0        2         4         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           1          0          0          0        0
  CYP2C9 WILD-TYPE        18         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  CYP2C9 MUTATED           0         0
  CYP2C9 WILD-TYPE        13         1
D1230V3, multiclass
            clus
vv           CYP2C9 MUTATED CYP2C9 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               4              105
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CYP2C9 MUTATED     0   1   6   1
  CYP2C9 WILD-TYPE   9  67 242  40
D1230V4, multiclass
    clus
vv   CYP2C9 MUTATED CYP2C9 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              6              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
  CYP2C9 MUTATED     8   0   0
  CYP2C9 WILD-TYPE 212  80  66
D1230V5, multiclass
    clus
vv   CYP2C9 MUTATED CYP2C9 WILD-TYPE
  N0              8              212
  N1              0               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"
D1230V6, binary
                  cls
clus                 0   1
  CYP2C9 MUTATED     8   0
  CYP2C9 WILD-TYPE 275  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP2C9 MUTATED      8    0
  CYP2C9 WILD-TYPE  275   48
   clus
vv  CYP2C9 MUTATED CYP2C9 WILD-TYPE
  0              8              275
  1              0               48
[1] 2 2
[1] FALSE
D1230V7, 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
D1230V8, binary
                  cls
clus                 0   1
  CYP2C9 MUTATED     7   1
  CYP2C9 WILD-TYPE 310  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP2C9 MUTATED      7    1
  CYP2C9 WILD-TYPE  310   47
                               clus
vv                              CYP2C9 MUTATED CYP2C9 WILD-TYPE
  COLON ADENOCARCINOMA                       7              310
  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 249   2  22  21
D1230V9, multiclass
    clus
vv   CYP2C9 MUTATED CYP2C9 WILD-TYPE
  R0              8              249
  R1              0                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"
D1230V10, 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
D1230V11, 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(1231) Variable = SLFN12L MUTATION ANALYSIS
D1231V1, survival
                   sevent
clus2                 0   1
  SLFN12L MUTATED     6   1
  SLFN12L WILD-TYPE 276  72
  SLFN12L MUTATED SLFN12L WILD-TYPE 
                7               348 
  SLFN12L MUTATED SLFN12L WILD-TYPE 
                1                72 
$`SLFN12L MUTATED`
TCGA-AA-3681 TCGA-AA-3811 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4948 
        5.98        10.06        58.39         0.33         0.10       102.44 
TCGA-G4-6315 
       36.72 

$`SLFN12L WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3688 
       50.04        47.01        15.02        11.01        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        0.26         1.35        17.56        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        51.75        45.11        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  SLFN12L MUTATED SLFN12L WILD-TYPE 
              0.1               0.0 
  SLFN12L MUTATED SLFN12L WILD-TYPE 
           102.44            140.38 
  SLFN12L MUTATED SLFN12L WILD-TYPE 
           10.060            20.235 
[1] "0.1 - 102.4 (10.1)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.7"
D1231V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLFN12L MUTATED         0        0        0         3         0         0
  SLFN12L WILD-TYPE      64        1       25       106         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLFN12L MUTATED           2          1          0          0        1
  SLFN12L WILD-TYPE        17          9         41         31       34
                   vv
clus                STAGE IVA STAGE IVB
  SLFN12L MUTATED           0         0
  SLFN12L WILD-TYPE        13         1
D1231V3, multiclass
            clus
vv           SLFN12L MUTATED SLFN12L WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                3               106
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                2                17
  STAGE IIIA               1                 9
  STAGE IIIB               0                41
  STAGE IIIC               0                31
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLFN12L MUTATED     0   0   7   0
  SLFN12L WILD-TYPE   9  68 241  41
D1231V4, multiclass
    clus
vv   SLFN12L MUTATED SLFN12L WILD-TYPE
  T1               0                 9
  T2               0                68
  T3               7               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     3   3   1
  SLFN12L WILD-TYPE 217  77  65
D1231V5, multiclass
    clus
vv   SLFN12L MUTATED SLFN12L WILD-TYPE
  N0               3               217
  N1               3                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"
D1231V6, binary
                   cls
clus                  0   1
  SLFN12L MUTATED     6   1
  SLFN12L WILD-TYPE 277  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLFN12L MUTATED      6    1
  SLFN12L WILD-TYPE  277   47
   clus
vv  SLFN12L MUTATED SLFN12L WILD-TYPE
  0               6               277
  1               1                47
[1] 2 2
[1] FALSE
D1231V7, binary
                   cls
clus                  0   1
  SLFN12L MUTATED     3   4
  SLFN12L WILD-TYPE 167 193
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLFN12L MUTATED      3    4
  SLFN12L WILD-TYPE  167  193
        clus
vv       SLFN12L MUTATED SLFN12L WILD-TYPE
  FEMALE               3               167
  MALE                 4               193
[1] 2 2
[1] FALSE
D1231V8, binary
                   cls
clus                  0   1
  SLFN12L MUTATED     6   1
  SLFN12L WILD-TYPE 311  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLFN12L MUTATED      6    1
  SLFN12L WILD-TYPE  311   47
                               clus
vv                              SLFN12L MUTATED SLFN12L WILD-TYPE
  COLON ADENOCARCINOMA                        6               311
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SLFN12L MUTATED     5   0   0   2
  SLFN12L WILD-TYPE 252   2  22  19
D1231V9, multiclass
    clus
vv   SLFN12L MUTATED SLFN12L WILD-TYPE
  R0               5               252
  R1               0                 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"
D1231V10, 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
D1231V11, 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(1232) Variable = HSPBAP1 MUTATION ANALYSIS
D1232V1, survival
                   sevent
clus2                 0   1
  HSPBAP1 MUTATED     4   3
  HSPBAP1 WILD-TYPE 278  70
  HSPBAP1 MUTATED HSPBAP1 WILD-TYPE 
                7               348 
  HSPBAP1 MUTATED HSPBAP1 WILD-TYPE 
                3                70 
$`HSPBAP1 MUTATED`
TCGA-A6-6142 TCGA-AA-A00N TCGA-AD-6889 TCGA-AZ-6598 TCGA-CK-5913 TCGA-DM-A1HB 
       25.08         4.01        56.55        49.41        51.32       135.65 
TCGA-F4-6459 
        8.61 

$`HSPBAP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  HSPBAP1 MUTATED HSPBAP1 WILD-TYPE 
             4.01              0.00 
  HSPBAP1 MUTATED HSPBAP1 WILD-TYPE 
           135.65            140.38 
  HSPBAP1 MUTATED HSPBAP1 WILD-TYPE 
            49.41             20.07 
[1] "4.0 - 135.7 (49.4)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.2"
D1232V2, 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       24       107         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HSPBAP1 MUTATED           0          0          2          0        0
  HSPBAP1 WILD-TYPE        19         10         39         31       35
                   vv
clus                STAGE IVA STAGE IVB
  HSPBAP1 MUTATED           1         0
  HSPBAP1 WILD-TYPE        12         1
D1232V3, multiclass
            clus
vv           HSPBAP1 MUTATED HSPBAP1 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                2               107
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               2                39
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                1                12
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of 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  68 242  40
D1232V4, multiclass
    clus
vv   HSPBAP1 MUTATED HSPBAP1 WILD-TYPE
  T1               0                 9
  T2               0                68
  T3               6               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
  HSPBAP1 MUTATED     4   2   1
  HSPBAP1 WILD-TYPE 216  78  65
D1232V5, multiclass
    clus
vv   HSPBAP1 MUTATED HSPBAP1 WILD-TYPE
  N0               4               216
  N1               2                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"
D1232V6, binary
                   cls
clus                  0   1
  HSPBAP1 MUTATED     4   1
  HSPBAP1 WILD-TYPE 279  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HSPBAP1 MUTATED      4    1
  HSPBAP1 WILD-TYPE  279   47
   clus
vv  HSPBAP1 MUTATED HSPBAP1 WILD-TYPE
  0               4               279
  1               1                47
[1] 2 2
[1] FALSE
D1232V7, 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
D1232V8, binary
                   cls
clus                  0   1
  HSPBAP1 MUTATED     6   1
  HSPBAP1 WILD-TYPE 311  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HSPBAP1 MUTATED      6    1
  HSPBAP1 WILD-TYPE  311   47
                               clus
vv                              HSPBAP1 MUTATED HSPBAP1 WILD-TYPE
  COLON ADENOCARCINOMA                        6               311
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  HSPBAP1 MUTATED     2   0   0   1
  HSPBAP1 WILD-TYPE 255   2  22  20
D1232V9, multiclass
    clus
vv   HSPBAP1 MUTATED HSPBAP1 WILD-TYPE
  R0               2               255
  R1               0                 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"
D1232V10, 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
D1232V11, 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(1233) Variable = METTL5 MUTATION ANALYSIS
D1233V1, survival
                  sevent
clus2                0   1
  METTL5 MUTATED     4   0
  METTL5 WILD-TYPE 278  73
  METTL5 MUTATED METTL5 WILD-TYPE 
               4              351 
  METTL5 MUTATED METTL5 WILD-TYPE 
               0               73 
$`METTL5 MUTATED`
TCGA-AA-3710 TCGA-AD-6889 TCGA-CM-5860 TCGA-CM-6171 
       26.99        56.55        16.01        14.04 

$`METTL5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        4.21         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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-6172 TCGA-CM-6674 
       14.99        12.99        13.02        15.02        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  METTL5 MUTATED METTL5 WILD-TYPE 
           14.04             0.00 
  METTL5 MUTATED METTL5 WILD-TYPE 
           56.55           140.38 
  METTL5 MUTATED METTL5 WILD-TYPE 
           21.50            20.19 
[1] "14.0 - 56.5 (21.5)" "0.0 - 140.4 (20.2)"
[1] "hr="     "9100000"
D1233V2, 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       25       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  METTL5 MUTATED           1          0          0          0        0
  METTL5 WILD-TYPE        18         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  METTL5 MUTATED           0         0
  METTL5 WILD-TYPE        13         1
D1233V3, multiclass
            clus
vv           METTL5 MUTATED METTL5 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               3              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  METTL5 MUTATED     0   1   4   0
  METTL5 WILD-TYPE   9  67 244  41
D1233V4, multiclass
    clus
vv   METTL5 MUTATED METTL5 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              4              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
  METTL5 MUTATED     4   0   1
  METTL5 WILD-TYPE 216  80  65
D1233V5, multiclass
    clus
vv   METTL5 MUTATED METTL5 WILD-TYPE
  N0              4              216
  N1              0               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"
D1233V6, binary
                  cls
clus                 0   1
  METTL5 MUTATED     5   0
  METTL5 WILD-TYPE 278  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  METTL5 MUTATED      5    0
  METTL5 WILD-TYPE  278   48
   clus
vv  METTL5 MUTATED METTL5 WILD-TYPE
  0              5              278
  1              0               48
[1] 2 2
[1] FALSE
D1233V7, 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
D1233V8, binary
                  cls
clus                 0   1
  METTL5 MUTATED     5   0
  METTL5 WILD-TYPE 312  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  METTL5 MUTATED      5    0
  METTL5 WILD-TYPE  312   48
                               clus
vv                              METTL5 MUTATED METTL5 WILD-TYPE
  COLON ADENOCARCINOMA                       5              312
  COLON MUCINOUS ADENOCARCINOMA              0               48
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  METTL5 MUTATED     4   0   0   0
  METTL5 WILD-TYPE 253   2  22  21
D1233V9, multiclass
    clus
vv   METTL5 MUTATED METTL5 WILD-TYPE
  R0              4              253
  R1              0                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"
D1233V10, 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
D1233V11, 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(1234) Variable = SULT1C4 MUTATION ANALYSIS
D1234V1, survival
                   sevent
clus2                 0   1
  SULT1C4 MUTATED     2   1
  SULT1C4 WILD-TYPE 280  72
  SULT1C4 MUTATED SULT1C4 WILD-TYPE 
                3               352 
  SULT1C4 MUTATED SULT1C4 WILD-TYPE 
                1                72 
$`SULT1C4 MUTATED`
TCGA-AA-3526 TCGA-AA-3555 TCGA-AA-A00N 
       19.07        29.95         4.01 

$`SULT1C4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
        8.05         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        17.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  SULT1C4 MUTATED SULT1C4 WILD-TYPE 
             4.01              0.00 
  SULT1C4 MUTATED SULT1C4 WILD-TYPE 
            29.95            140.38 
  SULT1C4 MUTATED SULT1C4 WILD-TYPE 
           19.070            20.235 
[1] "4.0 - 29.9 (19.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2.4"
D1234V2, 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       25       108         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SULT1C4 MUTATED           0          0          0          0        0
  SULT1C4 WILD-TYPE        19         10         41         31       35
                   vv
clus                STAGE IVA STAGE IVB
  SULT1C4 MUTATED           0         0
  SULT1C4 WILD-TYPE        13         1
D1234V3, multiclass
            clus
vv           SULT1C4 MUTATED SULT1C4 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                1               108
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SULT1C4 MUTATED     0   1   1   1
  SULT1C4 WILD-TYPE   9  67 247  40
D1234V4, multiclass
    clus
vv   SULT1C4 MUTATED SULT1C4 WILD-TYPE
  T1               0                 9
  T2               1                67
  T3               1               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
  SULT1C4 MUTATED     3   0   0
  SULT1C4 WILD-TYPE 217  80  66
D1234V5, multiclass
    clus
vv   SULT1C4 MUTATED SULT1C4 WILD-TYPE
  N0               3               217
  N1               0                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"
D1234V6, binary
                   cls
clus                  0   1
  SULT1C4 MUTATED     3   0
  SULT1C4 WILD-TYPE 280  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SULT1C4 MUTATED      3    0
  SULT1C4 WILD-TYPE  280   48
   clus
vv  SULT1C4 MUTATED SULT1C4 WILD-TYPE
  0               3               280
  1               0                48
[1] 2 2
[1] FALSE
D1234V7, 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
D1234V8, binary
                   cls
clus                  0   1
  SULT1C4 MUTATED     1   2
  SULT1C4 WILD-TYPE 316  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SULT1C4 MUTATED      1    2
  SULT1C4 WILD-TYPE  316   46
                               clus
vv                              SULT1C4 MUTATED SULT1C4 WILD-TYPE
  COLON ADENOCARCINOMA                        1               316
  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 254   2  22  21
D1234V9, multiclass
    clus
vv   SULT1C4 MUTATED SULT1C4 WILD-TYPE
  R0               3               254
  R1               0                 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"
D1234V10, 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
D1234V11, multiclass

Clustering(1235) Variable = COLEC12 MUTATION ANALYSIS
D1235V1, survival
                   sevent
clus2                 0   1
  COLEC12 MUTATED    16   1
  COLEC12 WILD-TYPE 266  72
  COLEC12 MUTATED COLEC12 WILD-TYPE 
               17               338 
  COLEC12 MUTATED COLEC12 WILD-TYPE 
                1                72 
$`COLEC12 MUTATED`
TCGA-A6-3809 TCGA-A6-5661 TCGA-AA-3663 TCGA-AA-3710 TCGA-AA-3831 TCGA-AA-3949 
       32.75        33.53         6.97        26.99        17.98        26.01 
TCGA-AA-3977 TCGA-AA-A010 TCGA-AD-6888 TCGA-AU-6004 TCGA-AZ-4315 TCGA-CA-6717 
       25.02        34.98         4.21        27.09        58.39         0.33 
TCGA-CK-4952 TCGA-CM-5862 TCGA-D5-6928 TCGA-DM-A1HB TCGA-F4-6856 
       15.62         5.03        11.64       135.65        19.43 

$`COLEC12 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
        0.99        25.02         1.02        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 
       39.98        18.05        40.96         0.07        21.37        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.20        14.50        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 
        1.35        17.56       102.44        40.34        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        35.41       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  COLEC12 MUTATED COLEC12 WILD-TYPE 
             0.33              0.00 
  COLEC12 MUTATED COLEC12 WILD-TYPE 
           135.65            140.38 
  COLEC12 MUTATED COLEC12 WILD-TYPE 
           25.020            20.155 
[1] "0.3 - 135.7 (25.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "3.6"
D1235V2, 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       24       103         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  COLEC12 MUTATED           1          0          3          0        0
  COLEC12 WILD-TYPE        18         10         38         31       35
                   vv
clus                STAGE IVA STAGE IVB
  COLEC12 MUTATED           1         0
  COLEC12 WILD-TYPE        12         1
D1235V3, multiclass
            clus
vv           COLEC12 MUTATED COLEC12 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                6               103
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               0                10
  STAGE IIIB               3                38
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                1                12
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  COLEC12 MUTATED     0   4  10   3
  COLEC12 WILD-TYPE   9  64 238  38
D1235V4, multiclass
    clus
vv   COLEC12 MUTATED COLEC12 WILD-TYPE
  T1               0                 9
  T2               4                64
  T3              10               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   3   1
  COLEC12 WILD-TYPE 208  77  65
D1235V5, multiclass
    clus
vv   COLEC12 MUTATED COLEC12 WILD-TYPE
  N0              12               208
  N1               3                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"
D1235V6, binary
                   cls
clus                  0   1
  COLEC12 MUTATED    15   1
  COLEC12 WILD-TYPE 268  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COLEC12 MUTATED     15    1
  COLEC12 WILD-TYPE  268   47
   clus
vv  COLEC12 MUTATED COLEC12 WILD-TYPE
  0              15               268
  1               1                47
[1] 2 2
[1] FALSE
D1235V7, 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
D1235V8, binary
                   cls
clus                  0   1
  COLEC12 MUTATED    11   6
  COLEC12 WILD-TYPE 306  42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COLEC12 MUTATED     11    6
  COLEC12 WILD-TYPE  306   42
                               clus
vv                              COLEC12 MUTATED COLEC12 WILD-TYPE
  COLON ADENOCARCINOMA                       11               306
  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 244   2  22  19
D1235V9, multiclass
    clus
vv   COLEC12 MUTATED COLEC12 WILD-TYPE
  R0              13               244
  R1               0                 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"
D1235V10, 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
D1235V11, 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(1236) Variable = MAOB MUTATION ANALYSIS
D1236V1, survival
                sevent
clus2              0   1
  MAOB MUTATED     6   0
  MAOB WILD-TYPE 276  73
  MAOB MUTATED MAOB WILD-TYPE 
             6            349 
  MAOB MUTATED MAOB WILD-TYPE 
             0             73 
$`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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        15.75         0.20        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14         2.93         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 
       16.01         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       13.05        11.08        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  MAOB MUTATED MAOB WILD-TYPE 
         11.01           0.00 
  MAOB MUTATED MAOB WILD-TYPE 
         24.00         140.38 
  MAOB MUTATED MAOB WILD-TYPE 
         18.23          20.19 
[1] "11.0 - 24.0 (18.2)" "0.0 - 140.4 (20.2)"
[1] "hr="     "9200000"
D1236V2, 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       25       104         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        19         10         41         31       35        12
                vv
clus             STAGE IVB
  MAOB MUTATED           0
  MAOB WILD-TYPE         1
D1236V3, multiclass
            clus
vv           MAOB MUTATED MAOB WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             5            104
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  68 243  40
D1236V4, multiclass
    clus
vv   MAOB MUTATED MAOB WILD-TYPE
  T1            0              9
  T2            0             68
  T3            5            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
  MAOB MUTATED     5   1   0
  MAOB WILD-TYPE 215  79  66
D1236V5, multiclass
    clus
vv   MAOB MUTATED MAOB WILD-TYPE
  N0            5            215
  N1            1             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"
D1236V6, binary
                cls
clus               0   1
  MAOB MUTATED     4   1
  MAOB WILD-TYPE 279  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAOB MUTATED      4    1
  MAOB WILD-TYPE  279   47
   clus
vv  MAOB MUTATED MAOB WILD-TYPE
  0            4            279
  1            1             47
[1] 2 2
[1] FALSE
D1236V7, 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
D1236V8, binary
                cls
clus               0   1
  MAOB MUTATED     5   1
  MAOB WILD-TYPE 312  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAOB MUTATED      5    1
  MAOB WILD-TYPE  312   47
                               clus
vv                              MAOB MUTATED MAOB WILD-TYPE
  COLON ADENOCARCINOMA                     5            312
  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 251   2  22  21
D1236V9, multiclass
    clus
vv   MAOB MUTATED MAOB WILD-TYPE
  R0            6            251
  R1            0              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"
D1236V10, 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
D1236V11, 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(1237) Variable = LPAR6 MUTATION ANALYSIS
D1237V1, survival
                 sevent
clus2               0   1
  LPAR6 MUTATED     5   1
  LPAR6 WILD-TYPE 277  72
  LPAR6 MUTATED LPAR6 WILD-TYPE 
              6             349 
  LPAR6 MUTATED LPAR6 WILD-TYPE 
              1              72 
$`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         0.10        13.02 

$`LPAR6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       15.75         0.20        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.33         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  LPAR6 MUTATED LPAR6 WILD-TYPE 
            0.1             0.0 
  LPAR6 MUTATED LPAR6 WILD-TYPE 
          58.39          140.38 
  LPAR6 MUTATED LPAR6 WILD-TYPE 
          17.23           20.19 
[1] "0.1 - 58.4 (17.2)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1"  
D1237V2, 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       25       105         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        19         10         41         31       35        13
                 vv
clus              STAGE IVB
  LPAR6 MUTATED           0
  LPAR6 WILD-TYPE         1
D1237V3, multiclass
            clus
vv           LPAR6 MUTATED LPAR6 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              4             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LPAR6 MUTATED     0   1   5   1
  LPAR6 WILD-TYPE   9  67 243  40
D1237V4, multiclass
    clus
vv   LPAR6 MUTATED LPAR6 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             5             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
  LPAR6 MUTATED     7   0   0
  LPAR6 WILD-TYPE 213  80  66
D1237V5, multiclass
    clus
vv   LPAR6 MUTATED LPAR6 WILD-TYPE
  N0             7             213
  N1             0              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"
D1237V6, binary
                 cls
clus                0   1
  LPAR6 MUTATED     4   0
  LPAR6 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LPAR6 MUTATED      4    0
  LPAR6 WILD-TYPE  279   48
   clus
vv  LPAR6 MUTATED LPAR6 WILD-TYPE
  0             4             279
  1             0              48
[1] 2 2
[1] FALSE
D1237V7, 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
D1237V8, binary
                 cls
clus                0   1
  LPAR6 MUTATED     6   1
  LPAR6 WILD-TYPE 311  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LPAR6 MUTATED      6    1
  LPAR6 WILD-TYPE  311   47
                               clus
vv                              LPAR6 MUTATED LPAR6 WILD-TYPE
  COLON ADENOCARCINOMA                      6             311
  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 253   2  22  19
D1237V9, multiclass
    clus
vv   LPAR6 MUTATED LPAR6 WILD-TYPE
  R0             4             253
  R1             0               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"
D1237V10, 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
D1237V11, 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(1238) Variable = ARHGEF1 MUTATION ANALYSIS
D1238V1, survival
                   sevent
clus2                 0   1
  ARHGEF1 MUTATED    10   3
  ARHGEF1 WILD-TYPE 272  70
  ARHGEF1 MUTATED ARHGEF1 WILD-TYPE 
               13               342 
  ARHGEF1 MUTATED ARHGEF1 WILD-TYPE 
                3                70 
$`ARHGEF1 MUTATED`
TCGA-A6-5665 TCGA-A6-6141 TCGA-AA-3660 TCGA-AA-3811 TCGA-AA-3815 TCGA-AA-3977 
       22.06         8.38        78.08        10.06        33.04        25.02 
TCGA-AA-3986 TCGA-AD-6889 TCGA-AU-6004 TCGA-CK-5916 TCGA-F4-6570 TCGA-G4-6306 
       19.07        56.55        27.09        21.14         6.18        44.68 
TCGA-G4-6588 
       26.17 

$`ARHGEF1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.09        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 
       85.05        26.99        19.04        19.04        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       24.00        27.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        4.21         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
       40.34        15.62        49.08        51.32        21.99         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       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        13.38        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        52.80 

  ARHGEF1 MUTATED ARHGEF1 WILD-TYPE 
             6.18              0.00 
  ARHGEF1 MUTATED ARHGEF1 WILD-TYPE 
            78.08            140.38 
  ARHGEF1 MUTATED ARHGEF1 WILD-TYPE 
           25.020            20.005 
[1] "6.2 - 78.1 (25.0)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1"  
D1238V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ARHGEF1 MUTATED         3        0        1         7         0         0
  ARHGEF1 WILD-TYPE      61        1       24       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        18         10         41         31       35
                   vv
clus                STAGE IVA STAGE IVB
  ARHGEF1 MUTATED           0         0
  ARHGEF1 WILD-TYPE        13         1
D1238V3, multiclass
            clus
vv           ARHGEF1 MUTATED ARHGEF1 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                7               102
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ARHGEF1 MUTATED     1   4   8   0
  ARHGEF1 WILD-TYPE   8  64 240  41
D1238V4, multiclass
    clus
vv   ARHGEF1 MUTATED ARHGEF1 WILD-TYPE
  T1               1                 8
  T2               4                64
  T3               8               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
  ARHGEF1 MUTATED    12   0   1
  ARHGEF1 WILD-TYPE 208  80  65
D1238V5, multiclass
    clus
vv   ARHGEF1 MUTATED ARHGEF1 WILD-TYPE
  N0              12               208
  N1               0                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"
D1238V6, binary
                   cls
clus                  0   1
  ARHGEF1 MUTATED    12   0
  ARHGEF1 WILD-TYPE 271  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGEF1 MUTATED     12    0
  ARHGEF1 WILD-TYPE  271   48
   clus
vv  ARHGEF1 MUTATED ARHGEF1 WILD-TYPE
  0              12               271
  1               0                48
[1] 2 2
[1] FALSE
D1238V7, 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
D1238V8, binary
                   cls
clus                  0   1
  ARHGEF1 MUTATED    13   0
  ARHGEF1 WILD-TYPE 304  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGEF1 MUTATED     13    0
  ARHGEF1 WILD-TYPE  304   48
                               clus
vv                              ARHGEF1 MUTATED ARHGEF1 WILD-TYPE
  COLON ADENOCARCINOMA                       13               304
  COLON MUCINOUS ADENOCARCINOMA               0                48
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ARHGEF1 MUTATED     9   0   0   1
  ARHGEF1 WILD-TYPE 248   2  22  20
D1238V9, multiclass
    clus
vv   ARHGEF1 MUTATED ARHGEF1 WILD-TYPE
  R0               9               248
  R1               0                 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"
D1238V10, 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
D1238V11, 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(1239) Variable = ANXA11 MUTATION ANALYSIS
D1239V1, survival
                  sevent
clus2                0   1
  ANXA11 MUTATED     5   2
  ANXA11 WILD-TYPE 277  71
  ANXA11 MUTATED ANXA11 WILD-TYPE 
               7              348 
  ANXA11 MUTATED ANXA11 WILD-TYPE 
               2               71 
$`ANXA11 MUTATED`
TCGA-A6-6653 TCGA-AA-3492 TCGA-AA-3516 TCGA-AA-3531 TCGA-AA-A010 TCGA-AZ-4315 
       24.39         3.02        13.02        34.03        34.98        58.39 
TCGA-CM-5861 
       15.02 

$`ANXA11 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       19.07        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  ANXA11 MUTATED ANXA11 WILD-TYPE 
            3.02             0.00 
  ANXA11 MUTATED ANXA11 WILD-TYPE 
           58.39           140.38 
  ANXA11 MUTATED ANXA11 WILD-TYPE 
          24.390           20.155 
[1] "3.0 - 58.4 (24.4)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.4"
D1239V2, 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       24       106         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANXA11 MUTATED           1          0          0          0        0
  ANXA11 WILD-TYPE        18         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  ANXA11 MUTATED           0         0
  ANXA11 WILD-TYPE        13         1
D1239V3, multiclass
            clus
vv           ANXA11 MUTATED ANXA11 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               3              106
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ANXA11 MUTATED     0   1   5   1
  ANXA11 WILD-TYPE   9  67 243  40
D1239V4, multiclass
    clus
vv   ANXA11 MUTATED ANXA11 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              5              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
  ANXA11 MUTATED     6   0   1
  ANXA11 WILD-TYPE 214  80  65
D1239V5, multiclass
    clus
vv   ANXA11 MUTATED ANXA11 WILD-TYPE
  N0              6              214
  N1              0               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"
D1239V6, binary
                  cls
clus                 0   1
  ANXA11 MUTATED     7   0
  ANXA11 WILD-TYPE 276  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANXA11 MUTATED      7    0
  ANXA11 WILD-TYPE  276   48
   clus
vv  ANXA11 MUTATED ANXA11 WILD-TYPE
  0              7              276
  1              0               48
[1] 2 2
[1] FALSE
D1239V7, 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
D1239V8, binary
                  cls
clus                 0   1
  ANXA11 MUTATED     6   1
  ANXA11 WILD-TYPE 311  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANXA11 MUTATED      6    1
  ANXA11 WILD-TYPE  311   47
                               clus
vv                              ANXA11 MUTATED ANXA11 WILD-TYPE
  COLON ADENOCARCINOMA                       6              311
  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 252   2  22  21
D1239V9, multiclass
    clus
vv   ANXA11 MUTATED ANXA11 WILD-TYPE
  R0              5              252
  R1              0                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"
D1239V10, 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
D1239V11, 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(1240) Variable = AKAP7 MUTATION ANALYSIS
D1240V1, survival
                 sevent
clus2               0   1
  AKAP7 MUTATED     5   1
  AKAP7 WILD-TYPE 277  72
  AKAP7 MUTATED AKAP7 WILD-TYPE 
              6             349 
  AKAP7 MUTATED AKAP7 WILD-TYPE 
              1              72 
$`AKAP7 MUTATED`
TCGA-A6-2671 TCGA-A6-5665 TCGA-AA-A010 TCGA-AD-5900 TCGA-CA-6717 TCGA-CK-4948 
       43.76        22.06        34.98         0.07         0.33       102.44 

$`AKAP7 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        0.10         1.35        17.56        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  AKAP7 MUTATED AKAP7 WILD-TYPE 
           0.07            0.00 
  AKAP7 MUTATED AKAP7 WILD-TYPE 
         102.44          140.38 
  AKAP7 MUTATED AKAP7 WILD-TYPE 
          28.52           20.12 
[1] "0.1 - 102.4 (28.5)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.6"
D1240V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AKAP7 MUTATED         1        0        0         2         1         0
  AKAP7 WILD-TYPE      63        1       25       107         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AKAP7 MUTATED           0          1          0          0        1         0
  AKAP7 WILD-TYPE        19          9         41         31       34        13
                 vv
clus              STAGE IVB
  AKAP7 MUTATED           0
  AKAP7 WILD-TYPE         1
D1240V3, multiclass
            clus
vv           AKAP7 MUTATED AKAP7 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              2             107
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  AKAP7 MUTATED     0   1   4   1
  AKAP7 WILD-TYPE   9  67 244  40
D1240V4, multiclass
    clus
vv   AKAP7 MUTATED AKAP7 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             4             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
  AKAP7 MUTATED     4   1   1
  AKAP7 WILD-TYPE 216  79  65
D1240V5, multiclass
    clus
vv   AKAP7 MUTATED AKAP7 WILD-TYPE
  N0             4             216
  N1             1              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"
D1240V6, binary
                 cls
clus                0   1
  AKAP7 MUTATED     4   1
  AKAP7 WILD-TYPE 279  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AKAP7 MUTATED      4    1
  AKAP7 WILD-TYPE  279   47
   clus
vv  AKAP7 MUTATED AKAP7 WILD-TYPE
  0             4             279
  1             1              47
[1] 2 2
[1] FALSE
D1240V7, binary
                 cls
clus                0   1
  AKAP7 MUTATED     3   3
  AKAP7 WILD-TYPE 167 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AKAP7 MUTATED      3    3
  AKAP7 WILD-TYPE  167  194
        clus
vv       AKAP7 MUTATED AKAP7 WILD-TYPE
  FEMALE             3             167
  MALE               3             194
[1] 2 2
[1] FALSE
D1240V8, binary
                 cls
clus                0   1
  AKAP7 MUTATED     4   2
  AKAP7 WILD-TYPE 313  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AKAP7 MUTATED      4    2
  AKAP7 WILD-TYPE  313   46
                               clus
vv                              AKAP7 MUTATED AKAP7 WILD-TYPE
  COLON ADENOCARCINOMA                      4             313
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  AKAP7 MUTATED     5   0   0   1
  AKAP7 WILD-TYPE 252   2  22  20
D1240V9, multiclass
    clus
vv   AKAP7 MUTATED AKAP7 WILD-TYPE
  R0             5             252
  R1             0               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"
D1240V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AKAP7 MUTATED                                  0     1
  AKAP7 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AKAP7 MUTATED                           0     4
  AKAP7 WILD-TYPE                        19   172
D1240V11, multiclass
                                  clus
vv                                 AKAP7 MUTATED AKAP7 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(1241) Variable = USP16 MUTATION ANALYSIS
D1241V1, survival
                 sevent
clus2               0   1
  USP16 MUTATED     7   1
  USP16 WILD-TYPE 275  72
  USP16 MUTATED USP16 WILD-TYPE 
              8             347 
  USP16 MUTATED USP16 WILD-TYPE 
              1              72 
$`USP16 MUTATED`
TCGA-AA-3520 TCGA-AA-3877 TCGA-AA-A00N TCGA-AU-6004 TCGA-AY-5543 TCGA-CA-6717 
       24.03        31.00         4.01        27.09        15.75         0.33 
TCGA-CK-5913 TCGA-D5-5538 
       51.32        12.26 

$`USP16 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       38.99         1.02         9.07        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 
        0.20        14.50        16.31         0.95         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  USP16 MUTATED USP16 WILD-TYPE 
           0.33            0.00 
  USP16 MUTATED USP16 WILD-TYPE 
          51.32          140.38 
  USP16 MUTATED USP16 WILD-TYPE 
          19.89           20.19 
[1] "0.3 - 51.3 (19.9)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.4"
D1241V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  USP16 MUTATED         2        0        1         3         1         0
  USP16 WILD-TYPE      62        1       24       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        19         10         40         31       35        12
                 vv
clus              STAGE IVB
  USP16 MUTATED           0
  USP16 WILD-TYPE         1
D1241V3, multiclass
            clus
vv           USP16 MUTATED USP16 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              3             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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   6   1
  USP16 WILD-TYPE   8  67 242  40
D1241V4, multiclass
    clus
vv   USP16 MUTATED USP16 WILD-TYPE
  T1             1               8
  T2             1              67
  T3             6             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
  USP16 MUTATED     7   2   0
  USP16 WILD-TYPE 213  78  66
D1241V5, multiclass
    clus
vv   USP16 MUTATED USP16 WILD-TYPE
  N0             7             213
  N1             2              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"
D1241V6, binary
                 cls
clus                0   1
  USP16 MUTATED     7   1
  USP16 WILD-TYPE 276  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP16 MUTATED      7    1
  USP16 WILD-TYPE  276   47
   clus
vv  USP16 MUTATED USP16 WILD-TYPE
  0             7             276
  1             1              47
[1] 2 2
[1] FALSE
D1241V7, binary
                 cls
clus                0   1
  USP16 MUTATED     7   2
  USP16 WILD-TYPE 163 195
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP16 MUTATED      7    2
  USP16 WILD-TYPE  163  195
        clus
vv       USP16 MUTATED USP16 WILD-TYPE
  FEMALE             7             163
  MALE               2             195
[1] 2 2
[1] FALSE
D1241V8, binary
                 cls
clus                0   1
  USP16 MUTATED     6   3
  USP16 WILD-TYPE 311  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP16 MUTATED      6    3
  USP16 WILD-TYPE  311   45
                               clus
vv                              USP16 MUTATED USP16 WILD-TYPE
  COLON ADENOCARCINOMA                      6             311
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  USP16 MUTATED     7   0   0   2
  USP16 WILD-TYPE 250   2  22  19
D1241V9, multiclass
    clus
vv   USP16 MUTATED USP16 WILD-TYPE
  R0             7             250
  R1             0               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"
D1241V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  USP16 MUTATED                                  0     1
  USP16 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  USP16 MUTATED                           1     3
  USP16 WILD-TYPE                        18   173
D1241V11, multiclass
                                  clus
vv                                 USP16 MUTATED USP16 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(1242) Variable = GPR161 MUTATION ANALYSIS
D1242V1, survival
                  sevent
clus2                0   1
  GPR161 MUTATED     7   1
  GPR161 WILD-TYPE 275  72
  GPR161 MUTATED GPR161 WILD-TYPE 
               8              347 
  GPR161 MUTATED GPR161 WILD-TYPE 
               1               72 
$`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         0.33         0.10 
TCGA-D5-6930 TCGA-F4-6570 
        1.51         6.18 

$`GPR161 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
        6.05         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.38        13.45        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  GPR161 MUTATED GPR161 WILD-TYPE 
             0.1              0.0 
  GPR161 MUTATED GPR161 WILD-TYPE 
           35.01           140.38 
  GPR161 MUTATED GPR161 WILD-TYPE 
           3.845           20.280 
[1] "0.1 - 35.0 (3.8)"   "0.0 - 140.4 (20.3)"
[1] "hr=" "1.3"
D1242V2, 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       24       104         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPR161 MUTATED           2          0          0          0        0
  GPR161 WILD-TYPE        17         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  GPR161 MUTATED           0         0
  GPR161 WILD-TYPE        13         1
D1242V3, multiclass
            clus
vv           GPR161 MUTATED GPR161 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               5              104
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               2               17
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GPR161 MUTATED     0   0   7   2
  GPR161 WILD-TYPE   9  68 241  39
D1242V4, multiclass
    clus
vv   GPR161 MUTATED GPR161 WILD-TYPE
  T1              0                9
  T2              0               68
  T3              7              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
  GPR161 MUTATED     7   1   1
  GPR161 WILD-TYPE 213  79  65
D1242V5, multiclass
    clus
vv   GPR161 MUTATED GPR161 WILD-TYPE
  N0              7              213
  N1              1               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"
D1242V6, binary
                  cls
clus                 0   1
  GPR161 MUTATED     9   0
  GPR161 WILD-TYPE 274  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR161 MUTATED      9    0
  GPR161 WILD-TYPE  274   48
   clus
vv  GPR161 MUTATED GPR161 WILD-TYPE
  0              9              274
  1              0               48
[1] 2 2
[1] FALSE
D1242V7, 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
D1242V8, binary
                  cls
clus                 0   1
  GPR161 MUTATED     6   3
  GPR161 WILD-TYPE 311  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR161 MUTATED      6    3
  GPR161 WILD-TYPE  311   45
                               clus
vv                              GPR161 MUTATED GPR161 WILD-TYPE
  COLON ADENOCARCINOMA                       6              311
  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 250   2  22  19
D1242V9, multiclass
    clus
vv   GPR161 MUTATED GPR161 WILD-TYPE
  R0              7              250
  R1              0                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"
D1242V10, 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
D1242V11, 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(1243) Variable = AHSA2 MUTATION ANALYSIS
D1243V1, survival
                 sevent
clus2               0   1
  AHSA2 MUTATED     1   2
  AHSA2 WILD-TYPE 281  71
  AHSA2 MUTATED AHSA2 WILD-TYPE 
              3             352 
  AHSA2 MUTATED AHSA2 WILD-TYPE 
              2              71 
$`AHSA2 MUTATED`
TCGA-AZ-6598 TCGA-CK-5912 TCGA-D5-6534 
       49.41        49.08        43.27 

$`AHSA2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
       17.56       102.44        40.34        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         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 
       11.51        20.19        18.25         1.32        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  AHSA2 MUTATED AHSA2 WILD-TYPE 
          43.27            0.00 
  AHSA2 MUTATED AHSA2 WILD-TYPE 
          49.41          140.38 
  AHSA2 MUTATED AHSA2 WILD-TYPE 
          49.08           20.07 
[1] "43.3 - 49.4 (49.1)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.7"
D1243V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AHSA2 MUTATED         1        0        1         1         0         0
  AHSA2 WILD-TYPE      63        1       24       108         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AHSA2 MUTATED           0          0          0          0        0         0
  AHSA2 WILD-TYPE        19         10         41         31       35        13
                 vv
clus              STAGE IVB
  AHSA2 MUTATED           0
  AHSA2 WILD-TYPE         1
D1243V3, multiclass
            clus
vv           AHSA2 MUTATED AHSA2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              1             108
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  AHSA2 MUTATED     0   1   2   0
  AHSA2 WILD-TYPE   9  67 246  41
D1243V4, multiclass
    clus
vv   AHSA2 MUTATED AHSA2 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             2             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
  AHSA2 MUTATED     3   0   0
  AHSA2 WILD-TYPE 217  80  66
D1243V5, multiclass
    clus
vv   AHSA2 MUTATED AHSA2 WILD-TYPE
  N0             3             217
  N1             0              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
  AHSA2 MUTATED     1   0
  AHSA2 WILD-TYPE 282  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AHSA2 MUTATED      1    0
  AHSA2 WILD-TYPE  282   48
   clus
vv  AHSA2 MUTATED AHSA2 WILD-TYPE
  0             1             282
  1             0              48
[1] 2 2
[1] FALSE
D1243V7, binary
                 cls
clus                0   1
  AHSA2 MUTATED     2   1
  AHSA2 WILD-TYPE 168 196
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AHSA2 MUTATED      2    1
  AHSA2 WILD-TYPE  168  196
        clus
vv       AHSA2 MUTATED AHSA2 WILD-TYPE
  FEMALE             2             168
  MALE               1             196
[1] 2 2
[1] FALSE
D1243V8, binary
                 cls
clus                0   1
  AHSA2 MUTATED     2   1
  AHSA2 WILD-TYPE 315  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AHSA2 MUTATED      2    1
  AHSA2 WILD-TYPE  315   47
                               clus
vv                              AHSA2 MUTATED AHSA2 WILD-TYPE
  COLON ADENOCARCINOMA                      2             315
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  AHSA2 MUTATED     1   0   0   1
  AHSA2 WILD-TYPE 256   2  22  20
D1243V9, multiclass
[1] "Remove cluster labels:" "AHSA2 MUTATED"         
clus
  AHSA2 MUTATED AHSA2 WILD-TYPE 
              2             300 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-5657 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-A6-5659      TCGA-A6-5661      TCGA-A6-5665      TCGA-A6-6781 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3489      TCGA-AA-3492      TCGA-AA-3496      TCGA-AA-3502 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3510      TCGA-AA-3511      TCGA-AA-3514      TCGA-AA-3517 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3518      TCGA-AA-3519      TCGA-AA-3520      TCGA-AA-3521 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3522      TCGA-AA-3524      TCGA-AA-3525      TCGA-AA-3526 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3527      TCGA-AA-3529      TCGA-AA-3530      TCGA-AA-3531 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3532      TCGA-AA-3534      TCGA-AA-3538      TCGA-AA-3542 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3543      TCGA-AA-3544      TCGA-AA-3548      TCGA-AA-3549 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3552      TCGA-AA-3553      TCGA-AA-3554      TCGA-AA-3555 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3556      TCGA-AA-3558      TCGA-AA-3560      TCGA-AA-3561 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3562      TCGA-AA-3655      TCGA-AA-3660      TCGA-AA-3662 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3663      TCGA-AA-3664      TCGA-AA-3666      TCGA-AA-3667 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3672      TCGA-AA-3673      TCGA-AA-3678      TCGA-AA-3679 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3680      TCGA-AA-3681      TCGA-AA-3684      TCGA-AA-3685 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3688      TCGA-AA-3692      TCGA-AA-3693      TCGA-AA-3695 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3696      TCGA-AA-3697      TCGA-AA-3710      TCGA-AA-3712 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3713      TCGA-AA-3715      TCGA-AA-3811      TCGA-AA-3812 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3814      TCGA-AA-3815      TCGA-AA-3818      TCGA-AA-3819 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3821      TCGA-AA-3831      TCGA-AA-3833      TCGA-AA-3837 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3842      TCGA-AA-3844      TCGA-AA-3845      TCGA-AA-3846 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3848      TCGA-AA-3850      TCGA-AA-3851      TCGA-AA-3852 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3854      TCGA-AA-3855      TCGA-AA-3856      TCGA-AA-3858 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3860      TCGA-AA-3861      TCGA-AA-3864      TCGA-AA-3866 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3867      TCGA-AA-3869      TCGA-AA-3870      TCGA-AA-3872 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3875      TCGA-AA-3877      TCGA-AA-3930      TCGA-AA-3939 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3941      TCGA-AA-3947      TCGA-AA-3949      TCGA-AA-3950 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3952      TCGA-AA-3955      TCGA-AA-3956      TCGA-AA-3968 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3971      TCGA-AA-3972      TCGA-AA-3973      TCGA-AA-3975 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3976      TCGA-AA-3979      TCGA-AA-3984      TCGA-AA-3986 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3989      TCGA-AA-3994      TCGA-AA-A004      TCGA-AA-A00A 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-A00D      TCGA-AA-A00E      TCGA-AA-A00F      TCGA-AA-A00J 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-A00K      TCGA-AA-A00L      TCGA-AA-A00N      TCGA-AA-A00O 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-A00Q      TCGA-AA-A00R      TCGA-AA-A00U      TCGA-AA-A00W 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-A00Z      TCGA-AA-A010      TCGA-AA-A017      TCGA-AA-A01D 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-A01F      TCGA-AA-A01G      TCGA-AA-A01I      TCGA-AA-A01K 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-A01P      TCGA-AA-A01Q      TCGA-AA-A01R      TCGA-AA-A01S 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-A01T      TCGA-AA-A01V      TCGA-AA-A01X      TCGA-AA-A01Z 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-A022      TCGA-AA-A024      TCGA-AA-A029      TCGA-AA-A02F 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-A02H      TCGA-AA-A02J      TCGA-AA-A02K      TCGA-AA-A02O 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-A02W      TCGA-AA-A02Y      TCGA-AA-A03F      TCGA-AA-A03J 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AD-5900      TCGA-AD-6548      TCGA-AD-6888      TCGA-AU-3779 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AU-6004      TCGA-AY-4070      TCGA-AY-4071      TCGA-AY-5543 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AY-6196      TCGA-AY-6197      TCGA-AY-6386      TCGA-AZ-4315 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AZ-4681      TCGA-AZ-4682      TCGA-CA-5254      TCGA-CA-5255 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-CA-5796      TCGA-CA-5797      TCGA-CA-6715      TCGA-CA-6716 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-CA-6717      TCGA-CA-6718      TCGA-CA-6719      TCGA-CK-4947 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-CK-4948      TCGA-CK-4950      TCGA-CK-4952      TCGA-CK-5913 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-CK-5914      TCGA-CK-5915      TCGA-CK-5916      TCGA-CK-6746 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-CK-6747      TCGA-CK-6748      TCGA-CK-6751      TCGA-CM-4743 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-CM-4744      TCGA-CM-4746      TCGA-CM-4747      TCGA-CM-4752 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-CM-5341      TCGA-CM-5344      TCGA-CM-5348      TCGA-CM-5349 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-CM-5860      TCGA-CM-5861      TCGA-CM-5862      TCGA-CM-5863 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-CM-5864      TCGA-CM-5868      TCGA-CM-6161      TCGA-CM-6162 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-CM-6163      TCGA-CM-6164      TCGA-CM-6165      TCGA-CM-6166 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-CM-6167      TCGA-CM-6168      TCGA-CM-6169      TCGA-CM-6170 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-CM-6171      TCGA-CM-6172      TCGA-CM-6674      TCGA-CM-6675 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-CM-6676      TCGA-CM-6677      TCGA-CM-6678      TCGA-CM-6679 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-CM-6680      TCGA-D5-5537      TCGA-D5-5538      TCGA-D5-5539 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-D5-5540      TCGA-D5-5541      TCGA-D5-6529      TCGA-D5-6532 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-D5-6533      TCGA-D5-6535      TCGA-D5-6536      TCGA-D5-6537 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-D5-6538      TCGA-D5-6539      TCGA-D5-6540      TCGA-D5-6541 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-D5-6898      TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-D5-6924      TCGA-D5-6926      TCGA-D5-6927      TCGA-D5-6928 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-D5-6929      TCGA-D5-6930      TCGA-D5-6931      TCGA-D5-6932 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-D5-7000      TCGA-F4-6459      TCGA-F4-6460      TCGA-F4-6569 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704      TCGA-F4-6805 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808      TCGA-F4-6809 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856      TCGA-G4-6293 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304      TCGA-G4-6306 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310      TCGA-G4-6315 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323      TCGA-G4-6586 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-G4-6588      TCGA-G4-6625      TCGA-G4-6626      TCGA-G4-6628 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
D1243V10, continuous
[1] "Remove cluster labels:" "AHSA2 MUTATED"         
clus
  AHSA2 MUTATED AHSA2 WILD-TYPE 
              2             343 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-4105 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-A6-5656      TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5660 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-A6-5661      TCGA-A6-5662      TCGA-A6-5664      TCGA-A6-5665 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-A6-5666      TCGA-A6-6137      TCGA-A6-6138      TCGA-A6-6141 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-A6-6142      TCGA-A6-6648      TCGA-A6-6649      TCGA-A6-6651 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-A6-6652      TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-A6-6781      TCGA-A6-6782      TCGA-AA-3489      TCGA-AA-3492 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3496      TCGA-AA-3502      TCGA-AA-3510      TCGA-AA-3511 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3514      TCGA-AA-3516      TCGA-AA-3517      TCGA-AA-3518 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3519      TCGA-AA-3520      TCGA-AA-3521      TCGA-AA-3522 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3524      TCGA-AA-3525      TCGA-AA-3526      TCGA-AA-3527 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3529      TCGA-AA-3530      TCGA-AA-3531      TCGA-AA-3532 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3534      TCGA-AA-3538      TCGA-AA-3542      TCGA-AA-3543 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3544      TCGA-AA-3548      TCGA-AA-3549      TCGA-AA-3552 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3553      TCGA-AA-3554      TCGA-AA-3555      TCGA-AA-3556 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3558      TCGA-AA-3560      TCGA-AA-3562      TCGA-AA-3655 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3660      TCGA-AA-3662      TCGA-AA-3663      TCGA-AA-3664 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3666      TCGA-AA-3667      TCGA-AA-3672      TCGA-AA-3673 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3678      TCGA-AA-3679      TCGA-AA-3680      TCGA-AA-3681 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3684      TCGA-AA-3685      TCGA-AA-3688      TCGA-AA-3692 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3693      TCGA-AA-3695      TCGA-AA-3696      TCGA-AA-3697 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3710      TCGA-AA-3712      TCGA-AA-3713      TCGA-AA-3715 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3811      TCGA-AA-3812      TCGA-AA-3814      TCGA-AA-3815 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3818      TCGA-AA-3819      TCGA-AA-3821      TCGA-AA-3831 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3833      TCGA-AA-3837      TCGA-AA-3842      TCGA-AA-3844 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3845      TCGA-AA-3846      TCGA-AA-3848      TCGA-AA-3850 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3851      TCGA-AA-3852      TCGA-AA-3854      TCGA-AA-3855 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3856      TCGA-AA-3858      TCGA-AA-3860      TCGA-AA-3861 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3864      TCGA-AA-3866      TCGA-AA-3867      TCGA-AA-3869 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3870      TCGA-AA-3872      TCGA-AA-3875      TCGA-AA-3877 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3930      TCGA-AA-3939      TCGA-AA-3941      TCGA-AA-3947 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3949      TCGA-AA-3950      TCGA-AA-3952      TCGA-AA-3955 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3956      TCGA-AA-3966      TCGA-AA-3968      TCGA-AA-3971 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3972      TCGA-AA-3973      TCGA-AA-3975      TCGA-AA-3976 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3977      TCGA-AA-3979      TCGA-AA-3980      TCGA-AA-3982 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-3984      TCGA-AA-3986      TCGA-AA-3989      TCGA-AA-3994 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-A004      TCGA-AA-A00A      TCGA-AA-A00D      TCGA-AA-A00E 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-A00F      TCGA-AA-A00J      TCGA-AA-A00K      TCGA-AA-A00L 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-A00N      TCGA-AA-A00O      TCGA-AA-A00Q      TCGA-AA-A00R 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-A00U      TCGA-AA-A00W      TCGA-AA-A00Z      TCGA-AA-A010 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-A017      TCGA-AA-A01D      TCGA-AA-A01F      TCGA-AA-A01G 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-A01I      TCGA-AA-A01K      TCGA-AA-A01P      TCGA-AA-A01Q 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-A01R      TCGA-AA-A01S      TCGA-AA-A01T      TCGA-AA-A01V 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-A01X      TCGA-AA-A01Z      TCGA-AA-A022      TCGA-AA-A024 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-A029      TCGA-AA-A02F      TCGA-AA-A02H      TCGA-AA-A02J 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-A02K      TCGA-AA-A02O      TCGA-AA-A02W      TCGA-AA-A02Y 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AA-A03F      TCGA-AA-A03J      TCGA-AD-5900      TCGA-AD-6548 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AD-6888      TCGA-AD-6889      TCGA-AD-6890      TCGA-AD-6895 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AD-6899      TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6964 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AD-6965      TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AY-4071      TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AY-6386      TCGA-AZ-4323      TCGA-AZ-4616      TCGA-AZ-4682 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AZ-5403      TCGA-AZ-5407      TCGA-AZ-6599      TCGA-AZ-6600 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AZ-6601      TCGA-AZ-6603      TCGA-AZ-6605      TCGA-AZ-6606 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-AZ-6607      TCGA-AZ-6608      TCGA-CK-4947      TCGA-CK-4948 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-CK-4950      TCGA-CK-4952      TCGA-CM-4743      TCGA-CM-4744 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-CM-4746      TCGA-CM-4747      TCGA-CM-4752      TCGA-CM-5341 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-CM-5344      TCGA-CM-5348      TCGA-CM-5349      TCGA-CM-5860 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-CM-5861      TCGA-CM-5862      TCGA-CM-5863      TCGA-CM-5864 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-CM-5868      TCGA-CM-6161      TCGA-CM-6162      TCGA-CM-6163 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-CM-6164      TCGA-CM-6165      TCGA-CM-6166      TCGA-CM-6167 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-CM-6168      TCGA-CM-6169      TCGA-CM-6170      TCGA-CM-6171 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-CM-6172      TCGA-CM-6674      TCGA-CM-6675      TCGA-CM-6676 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-CM-6677      TCGA-CM-6678      TCGA-CM-6679      TCGA-CM-6680 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-D5-5537      TCGA-D5-5538      TCGA-D5-5539      TCGA-D5-5540 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-D5-5541      TCGA-D5-6529      TCGA-D5-6532      TCGA-D5-6533 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-D5-6535      TCGA-D5-6536      TCGA-D5-6537      TCGA-D5-6538 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-D5-6539      TCGA-D5-6540      TCGA-D5-6541      TCGA-D5-6898 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923      TCGA-D5-6924 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-D5-6926      TCGA-D5-6927      TCGA-D5-6928      TCGA-D5-6929 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-D5-6930      TCGA-D5-6931      TCGA-D5-6932      TCGA-D5-7000 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-DM-A0X9      TCGA-DM-A0XD      TCGA-DM-A0XF      TCGA-DM-A1D0 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-DM-A1D4      TCGA-DM-A1D6      TCGA-DM-A1D7      TCGA-DM-A1D8 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-DM-A1D9      TCGA-DM-A1DA      TCGA-DM-A1DB      TCGA-DM-A1HA 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-DM-A1HB      TCGA-DM-A282      TCGA-DM-A285      TCGA-DM-A28C 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-DM-A28E      TCGA-DM-A28F      TCGA-DM-A28G      TCGA-DM-A28H 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-DM-A28K      TCGA-F4-6459      TCGA-F4-6460      TCGA-F4-6569 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704      TCGA-F4-6806 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-F4-6807      TCGA-F4-6808      TCGA-F4-6809      TCGA-F4-6854 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-F4-6855      TCGA-F4-6856      TCGA-G4-6293      TCGA-G4-6299 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-G4-6303      TCGA-G4-6304      TCGA-G4-6306      TCGA-G4-6307 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-G4-6309      TCGA-G4-6310      TCGA-G4-6315      TCGA-G4-6317 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-G4-6321      TCGA-G4-6323      TCGA-G4-6586      TCGA-G4-6588 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
     TCGA-G4-6625      TCGA-G4-6626      TCGA-G4-6628 
"AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" "AHSA2 WILD-TYPE" 
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AHSA2 MUTATED                                  0     0
  AHSA2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AHSA2 MUTATED                           0     3
  AHSA2 WILD-TYPE                        19   173
D1243V11, multiclass
                                  clus
vv                                 AHSA2 MUTATED AHSA2 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(1244) Variable = FAM167B MUTATION ANALYSIS
D1244V1, survival
                   sevent
clus2                 0   1
  FAM167B MUTATED     2   1
  FAM167B WILD-TYPE 280  72
  FAM167B MUTATED FAM167B WILD-TYPE 
                3               352 
  FAM167B MUTATED FAM167B WILD-TYPE 
                1                72 
$`FAM167B MUTATED`
TCGA-A6-6780 TCGA-CK-4952 TCGA-DM-A1D7 
       20.12        15.62        13.32 

$`FAM167B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       102.44        40.34        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  FAM167B MUTATED FAM167B WILD-TYPE 
            13.32              0.00 
  FAM167B MUTATED FAM167B WILD-TYPE 
            20.12            140.38 
  FAM167B MUTATED FAM167B WILD-TYPE 
            15.62             20.63 
[1] "13.3 - 20.1 (15.6)" "0.0 - 140.4 (20.6)"
[1] "hr=" "2.2"
D1244V2, 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       25       106         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM167B MUTATED           1          0          0          0        0
  FAM167B WILD-TYPE        18         10         41         31       35
                   vv
clus                STAGE IVA STAGE IVB
  FAM167B MUTATED           0         0
  FAM167B WILD-TYPE        13         1
D1244V3, multiclass
            clus
vv           FAM167B MUTATED FAM167B WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                3               106
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  FAM167B MUTATED     0   0   3   1
  FAM167B WILD-TYPE   9  68 245  40
D1244V4, multiclass
    clus
vv   FAM167B MUTATED FAM167B WILD-TYPE
  T1               0                 9
  T2               0                68
  T3               3               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
  FAM167B MUTATED     3   0   1
  FAM167B WILD-TYPE 217  80  65
D1244V5, multiclass
    clus
vv   FAM167B MUTATED FAM167B WILD-TYPE
  N0               3               217
  N1               0                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"
D1244V6, binary
                   cls
clus                  0   1
  FAM167B MUTATED     3   0
  FAM167B WILD-TYPE 280  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM167B MUTATED      3    0
  FAM167B WILD-TYPE  280   48
   clus
vv  FAM167B MUTATED FAM167B WILD-TYPE
  0               3               280
  1               0                48
[1] 2 2
[1] FALSE
D1244V7, 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
D1244V8, binary
                   cls
clus                  0   1
  FAM167B MUTATED     2   2
  FAM167B WILD-TYPE 315  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM167B MUTATED      2    2
  FAM167B WILD-TYPE  315   46
                               clus
vv                              FAM167B MUTATED FAM167B WILD-TYPE
  COLON ADENOCARCINOMA                        2               315
  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 256   2  22  20
D1244V9, multiclass
[1] "Remove cluster labels:" "FAM167B MUTATED"       
clus
  FAM167B MUTATED FAM167B WILD-TYPE 
                2               300 
       TCGA-A6-2671        TCGA-A6-2672        TCGA-A6-2674        TCGA-A6-2676 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-A6-2677        TCGA-A6-2678        TCGA-A6-2683        TCGA-A6-3807 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-A6-3808        TCGA-A6-3809        TCGA-A6-3810        TCGA-A6-5657 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-A6-5659        TCGA-A6-5661        TCGA-A6-5665        TCGA-A6-6781 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3489        TCGA-AA-3492        TCGA-AA-3496        TCGA-AA-3502 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3510        TCGA-AA-3511        TCGA-AA-3514        TCGA-AA-3517 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3518        TCGA-AA-3519        TCGA-AA-3520        TCGA-AA-3521 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3522        TCGA-AA-3524        TCGA-AA-3525        TCGA-AA-3526 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3527        TCGA-AA-3529        TCGA-AA-3530        TCGA-AA-3531 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3532        TCGA-AA-3534        TCGA-AA-3538        TCGA-AA-3542 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3543        TCGA-AA-3544        TCGA-AA-3548        TCGA-AA-3549 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3552        TCGA-AA-3553        TCGA-AA-3554        TCGA-AA-3555 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3556        TCGA-AA-3558        TCGA-AA-3560        TCGA-AA-3561 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3562        TCGA-AA-3655        TCGA-AA-3660        TCGA-AA-3662 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3663        TCGA-AA-3664        TCGA-AA-3666        TCGA-AA-3667 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3672        TCGA-AA-3673        TCGA-AA-3678        TCGA-AA-3679 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3680        TCGA-AA-3681        TCGA-AA-3684        TCGA-AA-3685 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3688        TCGA-AA-3692        TCGA-AA-3693        TCGA-AA-3695 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3696        TCGA-AA-3697        TCGA-AA-3710        TCGA-AA-3712 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3713        TCGA-AA-3715        TCGA-AA-3811        TCGA-AA-3812 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3814        TCGA-AA-3815        TCGA-AA-3818        TCGA-AA-3819 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3821        TCGA-AA-3831        TCGA-AA-3833        TCGA-AA-3837 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3842        TCGA-AA-3844        TCGA-AA-3845        TCGA-AA-3846 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3848        TCGA-AA-3850        TCGA-AA-3851        TCGA-AA-3852 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3854        TCGA-AA-3855        TCGA-AA-3856        TCGA-AA-3858 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3860        TCGA-AA-3861        TCGA-AA-3864        TCGA-AA-3866 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3867        TCGA-AA-3869        TCGA-AA-3870        TCGA-AA-3872 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3875        TCGA-AA-3877        TCGA-AA-3930        TCGA-AA-3939 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3941        TCGA-AA-3947        TCGA-AA-3949        TCGA-AA-3950 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3952        TCGA-AA-3955        TCGA-AA-3956        TCGA-AA-3968 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3971        TCGA-AA-3972        TCGA-AA-3973        TCGA-AA-3975 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3976        TCGA-AA-3979        TCGA-AA-3986        TCGA-AA-3989 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3994        TCGA-AA-A004        TCGA-AA-A00A        TCGA-AA-A00D 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-A00E        TCGA-AA-A00F        TCGA-AA-A00J        TCGA-AA-A00K 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-A00L        TCGA-AA-A00N        TCGA-AA-A00O        TCGA-AA-A00Q 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-A00R        TCGA-AA-A00U        TCGA-AA-A00W        TCGA-AA-A00Z 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-A010        TCGA-AA-A017        TCGA-AA-A01D        TCGA-AA-A01F 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-A01G        TCGA-AA-A01I        TCGA-AA-A01K        TCGA-AA-A01P 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-A01Q        TCGA-AA-A01R        TCGA-AA-A01S        TCGA-AA-A01T 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-A01V        TCGA-AA-A01X        TCGA-AA-A01Z        TCGA-AA-A022 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-A024        TCGA-AA-A029        TCGA-AA-A02F        TCGA-AA-A02H 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-A02J        TCGA-AA-A02K        TCGA-AA-A02O        TCGA-AA-A02W 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-A02Y        TCGA-AA-A03F        TCGA-AA-A03J        TCGA-AD-5900 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AD-6548        TCGA-AD-6888        TCGA-AU-3779        TCGA-AU-6004 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AY-4070        TCGA-AY-4071        TCGA-AY-5543        TCGA-AY-6196 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AY-6197        TCGA-AY-6386        TCGA-AZ-4315        TCGA-AZ-4681 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AZ-4682        TCGA-CA-5254        TCGA-CA-5255        TCGA-CA-5796 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-CA-5797        TCGA-CA-6715        TCGA-CA-6716        TCGA-CA-6717 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-CA-6718        TCGA-CA-6719        TCGA-CK-4947        TCGA-CK-4948 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-CK-4950        TCGA-CK-5912        TCGA-CK-5913        TCGA-CK-5914 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-CK-5915        TCGA-CK-5916        TCGA-CK-6746        TCGA-CK-6747 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-CK-6748        TCGA-CK-6751        TCGA-CM-4743        TCGA-CM-4744 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-CM-4746        TCGA-CM-4747        TCGA-CM-4752        TCGA-CM-5341 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-CM-5344        TCGA-CM-5348        TCGA-CM-5349        TCGA-CM-5860 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-CM-5861        TCGA-CM-5862        TCGA-CM-5863        TCGA-CM-5864 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-CM-5868        TCGA-CM-6161        TCGA-CM-6162        TCGA-CM-6163 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-CM-6164        TCGA-CM-6165        TCGA-CM-6166        TCGA-CM-6167 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-CM-6168        TCGA-CM-6169        TCGA-CM-6170        TCGA-CM-6171 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-CM-6172        TCGA-CM-6674        TCGA-CM-6675        TCGA-CM-6676 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-CM-6677        TCGA-CM-6678        TCGA-CM-6679        TCGA-CM-6680 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-D5-5537        TCGA-D5-5538        TCGA-D5-5539        TCGA-D5-5540 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-D5-5541        TCGA-D5-6529        TCGA-D5-6532        TCGA-D5-6533 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-D5-6534        TCGA-D5-6535        TCGA-D5-6536        TCGA-D5-6537 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-D5-6538        TCGA-D5-6539        TCGA-D5-6540        TCGA-D5-6541 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-D5-6898        TCGA-D5-6920        TCGA-D5-6922        TCGA-D5-6923 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-D5-6924        TCGA-D5-6926        TCGA-D5-6927        TCGA-D5-6928 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-D5-6929        TCGA-D5-6930        TCGA-D5-6931        TCGA-D5-6932 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-D5-7000        TCGA-F4-6459        TCGA-F4-6460        TCGA-F4-6569 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-F4-6570        TCGA-F4-6703        TCGA-F4-6704        TCGA-F4-6805 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-F4-6806        TCGA-F4-6807        TCGA-F4-6808        TCGA-F4-6809 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-F4-6854        TCGA-F4-6855        TCGA-F4-6856        TCGA-G4-6293 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-G4-6299        TCGA-G4-6303        TCGA-G4-6304        TCGA-G4-6306 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-G4-6307        TCGA-G4-6309        TCGA-G4-6310        TCGA-G4-6315 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-G4-6317        TCGA-G4-6321        TCGA-G4-6323        TCGA-G4-6586 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-G4-6588        TCGA-G4-6625        TCGA-G4-6626        TCGA-G4-6628 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
D1244V10, 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
D1244V11, 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(1245) Variable = MST1R MUTATION ANALYSIS
D1245V1, survival
                 sevent
clus2               0   1
  MST1R MUTATED    11   3
  MST1R WILD-TYPE 271  70
  MST1R MUTATED MST1R WILD-TYPE 
             14             341 
  MST1R MUTATED MST1R WILD-TYPE 
              3              70 
$`MST1R MUTATED`
TCGA-A6-6138 TCGA-AA-3845 TCGA-AD-5900 TCGA-AY-6196 TCGA-AZ-6607 TCGA-CK-4952 
       22.52         0.00         0.07         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 
       19.43        36.72 

$`MST1R WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        32.71        27.09         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
       17.98        15.95        38.99        37.02        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 
      100.01        29.56         5.23        11.74         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 
        0.10         1.35        17.56       102.44        40.34        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 
       51.32        21.99        21.14         2.93         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-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        16.01         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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-A0XF 
        1.51        12.00        11.38        10.26       119.70        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.41       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        51.75        45.11        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  MST1R MUTATED MST1R WILD-TYPE 
              0               0 
  MST1R MUTATED MST1R WILD-TYPE 
         124.27          140.38 
  MST1R MUTATED MST1R WILD-TYPE 
          14.53           20.98 
[1] "0.0 - 124.3 (14.5)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.3"
D1245V2, 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       25       104         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MST1R MUTATED           1          0          0          1        2         0
  MST1R WILD-TYPE        18         10         41         30       33        13
                 vv
clus              STAGE IVB
  MST1R MUTATED           0
  MST1R WILD-TYPE         1
D1245V3, multiclass
            clus
vv           MST1R MUTATED MST1R WILD-TYPE
  STAGE I                5              59
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              5             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               2              33
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MST1R MUTATED     0   5   7   2
  MST1R WILD-TYPE   9  63 241  39
D1245V4, multiclass
    clus
vv   MST1R MUTATED MST1R WILD-TYPE
  T1             0               9
  T2             5              63
  T3             7             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
  MST1R MUTATED    10   1   3
  MST1R WILD-TYPE 210  79  63
D1245V5, multiclass
    clus
vv   MST1R MUTATED MST1R WILD-TYPE
  N0            10             210
  N1             1              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"
D1245V6, binary
                 cls
clus                0   1
  MST1R MUTATED     9   2
  MST1R WILD-TYPE 274  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MST1R MUTATED      9    2
  MST1R WILD-TYPE  274   46
   clus
vv  MST1R MUTATED MST1R WILD-TYPE
  0             9             274
  1             2              46
[1] 2 2
[1] FALSE
D1245V7, 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
D1245V8, binary
                 cls
clus                0   1
  MST1R MUTATED     8   6
  MST1R WILD-TYPE 309  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MST1R MUTATED      8    6
  MST1R WILD-TYPE  309   42
                               clus
vv                              MST1R MUTATED MST1R WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  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 248   2  22  19
D1245V9, multiclass
    clus
vv   MST1R MUTATED MST1R WILD-TYPE
  R0             9             248
  R1             0               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"
D1245V10, 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
D1245V11, 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(1246) Variable = MAP2K4 MUTATION ANALYSIS
D1246V1, survival
                  sevent
clus2                0   1
  MAP2K4 MUTATED    20   8
  MAP2K4 WILD-TYPE 262  65
  MAP2K4 MUTATED MAP2K4 WILD-TYPE 
              28              327 
  MAP2K4 MUTATED MAP2K4 WILD-TYPE 
               8               65 
$`MAP2K4 MUTATED`
TCGA-A6-5666 TCGA-A6-6141 TCGA-AA-3492 TCGA-AA-3672 TCGA-AA-3845 TCGA-AA-3861 
       32.71         8.38         3.02         0.92         0.00        30.05 
TCGA-AA-3864 TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3986 TCGA-AA-A00N TCGA-AA-A010 
       53.00         2.01         2.01        19.07         4.01        34.98 
TCGA-AD-6548 TCGA-AD-6899 TCGA-AD-6901 TCGA-AY-6196 TCGA-AZ-6598 TCGA-CA-6716 
       21.37         5.79        22.42         0.20        49.41         0.26 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CM-6171 TCGA-CM-6172 
        0.10        17.56       102.44        15.62        14.04        11.01 
TCGA-D5-6535 TCGA-D5-6539 TCGA-DM-A1DA TCGA-G4-6628 
       15.12        12.49         7.50        52.80 

$`MAP2K4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.09        22.06        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02        14.93        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 
        4.21        56.55         0.79         0.72        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6719 
        3.06         3.25         3.29         0.07         0.33         1.35 
TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       40.34        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 
       43.27        17.85         4.80        17.13        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       26.17        91.79        46.75 

  MAP2K4 MUTATED MAP2K4 WILD-TYPE 
               0                0 
  MAP2K4 MUTATED MAP2K4 WILD-TYPE 
          102.44           140.38 
  MAP2K4 MUTATED MAP2K4 WILD-TYPE 
          13.265           21.140 
[1] "0.0 - 102.4 (13.3)" "0.0 - 140.4 (21.1)"
[1] "hr=" "1.8"
D1246V2, 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       22       102         5         0
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAP2K4 MUTATED           2          2          2          4        0
  MAP2K4 WILD-TYPE        17          8         39         27       35
                  vv
clus               STAGE IVA STAGE IVB
  MAP2K4 MUTATED           1         0
  MAP2K4 WILD-TYPE        12         1
D1246V3, multiclass
            clus
vv           MAP2K4 MUTATED MAP2K4 WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                3               22
  STAGE IIA               7              102
  STAGE IIB               3                5
  STAGE IIC               1                0
  STAGE III               2               17
  STAGE IIIA              2                8
  STAGE IIIB              2               39
  STAGE IIIC              4               27
  STAGE IV                0               35
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  64 229  34
D1246V4, multiclass
    clus
vv   MAP2K4 MUTATED MAP2K4 WILD-TYPE
  T1              0                9
  T2              4               64
  T3             19              229
  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  75  61
D1246V5, multiclass
    clus
vv   MAP2K4 MUTATED MAP2K4 WILD-TYPE
  N0             20              200
  N1              5               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"
D1246V6, binary
                  cls
clus                 0   1
  MAP2K4 MUTATED    24   0
  MAP2K4 WILD-TYPE 259  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP2K4 MUTATED     24    0
  MAP2K4 WILD-TYPE  259   48
   clus
vv  MAP2K4 MUTATED MAP2K4 WILD-TYPE
  0             24              259
  1              0               48
[1] 2 2
[1] FALSE
D1246V7, 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
D1246V8, binary
                  cls
clus                 0   1
  MAP2K4 MUTATED    25   5
  MAP2K4 WILD-TYPE 292  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP2K4 MUTATED     25    5
  MAP2K4 WILD-TYPE  292   43
                               clus
vv                              MAP2K4 MUTATED MAP2K4 WILD-TYPE
  COLON ADENOCARCINOMA                      25              292
  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 240   2  22  15
D1246V9, multiclass
    clus
vv   MAP2K4 MUTATED MAP2K4 WILD-TYPE
  R0             17              240
  R1              0                2
  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"
D1246V10, 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
D1246V11, 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(1247) Variable = SCYL2 MUTATION ANALYSIS
D1247V1, survival
                 sevent
clus2               0   1
  SCYL2 MUTATED    13   2
  SCYL2 WILD-TYPE 269  71
  SCYL2 MUTATED SCYL2 WILD-TYPE 
             15             340 
  SCYL2 MUTATED SCYL2 WILD-TYPE 
              2              71 
$`SCYL2 MUTATED`
TCGA-A6-5661 TCGA-A6-5665 TCGA-AA-3663 TCGA-AA-3977 TCGA-AA-A02K TCGA-AD-5900 
       33.53        22.06         6.97        25.02        14.01         0.07 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-CA-6718 TCGA-CM-4744 TCGA-CM-5863 TCGA-D5-6926 
       21.44        58.39         0.10        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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        15.75         0.20        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.33         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 
        2.93         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        16.01 
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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6932 
       12.43        14.30         9.44        11.64         1.51        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       35.97       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  SCYL2 MUTATED SCYL2 WILD-TYPE 
           0.07            0.00 
  SCYL2 MUTATED SCYL2 WILD-TYPE 
          60.79          140.38 
  SCYL2 MUTATED SCYL2 WILD-TYPE 
          15.02           20.63 
[1] "0.1 - 60.8 (15.0)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "1.3"
D1247V2, 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       24       102         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SCYL2 MUTATED           0          1          1          1        2         0
  SCYL2 WILD-TYPE        19          9         40         30       33        13
                 vv
clus              STAGE IVB
  SCYL2 MUTATED           0
  SCYL2 WILD-TYPE         1
D1247V3, multiclass
            clus
vv           SCYL2 MUTATED SCYL2 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              7             102
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             1              40
  STAGE IIIC             1              30
  STAGE IV               2              33
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SCYL2 MUTATED     0   3  10   3
  SCYL2 WILD-TYPE   9  65 238  38
D1247V4, multiclass
    clus
vv   SCYL2 MUTATED SCYL2 WILD-TYPE
  T1             0               9
  T2             3              65
  T3            10             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
  SCYL2 MUTATED    11   3   2
  SCYL2 WILD-TYPE 209  77  64
D1247V5, multiclass
    clus
vv   SCYL2 MUTATED SCYL2 WILD-TYPE
  N0            11             209
  N1             3              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"
D1247V6, binary
                 cls
clus                0   1
  SCYL2 MUTATED    11   2
  SCYL2 WILD-TYPE 272  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCYL2 MUTATED     11    2
  SCYL2 WILD-TYPE  272   46
   clus
vv  SCYL2 MUTATED SCYL2 WILD-TYPE
  0            11             272
  1             2              46
[1] 2 2
[1] FALSE
D1247V7, 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
D1247V8, binary
                 cls
clus                0   1
  SCYL2 MUTATED    14   2
  SCYL2 WILD-TYPE 303  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCYL2 MUTATED     14    2
  SCYL2 WILD-TYPE  303   46
                               clus
vv                              SCYL2 MUTATED SCYL2 WILD-TYPE
  COLON ADENOCARCINOMA                     14             303
  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 245   2  21  20
D1247V9, multiclass
    clus
vv   SCYL2 MUTATED SCYL2 WILD-TYPE
  R0            12             245
  R1             0               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"
D1247V10, 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
D1247V11, 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(1248) Variable = NSF MUTATION ANALYSIS
D1248V1, survival
               sevent
clus2             0   1
  NSF MUTATED     4   0
  NSF WILD-TYPE 278  73
  NSF MUTATED NSF WILD-TYPE 
            4           351 
  NSF MUTATED NSF WILD-TYPE 
            0            73 
$`NSF MUTATED`
TCGA-AA-A01R TCGA-CA-5255 TCGA-CM-6676 TCGA-D5-6930 
       35.01         3.06        11.08         1.51 

$`NSF WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19         1.94         2.24         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  NSF MUTATED NSF WILD-TYPE 
         1.51          0.00 
  NSF MUTATED NSF WILD-TYPE 
        35.01        140.38 
  NSF MUTATED NSF WILD-TYPE 
         7.07         20.28 
[1] "1.5 - 35.0 (7.1)"   "0.0 - 140.4 (20.3)"
[1] "hr="     "3300000"
D1248V2, 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       25       107         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        18         10         41         31       35        13
               vv
clus            STAGE IVB
  NSF MUTATED           0
  NSF WILD-TYPE         1
D1248V3, multiclass
            clus
vv           NSF MUTATED NSF WILD-TYPE
  STAGE I              1            63
  STAGE IA             0             1
  STAGE II             0            25
  STAGE IIA            2           107
  STAGE IIB            0             8
  STAGE IIC            0             1
  STAGE III            1            18
  STAGE IIIA           0            10
  STAGE IIIB           0            41
  STAGE IIIC           0            31
  STAGE IV             0            35
  STAGE IVA            0            13
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  NSF MUTATED     0   1   3   0
  NSF WILD-TYPE   9  67 245  41
D1248V4, multiclass
    clus
vv   NSF MUTATED NSF WILD-TYPE
  T1           0             9
  T2           1            67
  T3           3           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
  NSF MUTATED     3   0   1
  NSF WILD-TYPE 217  80  65
D1248V5, multiclass
    clus
vv   NSF MUTATED NSF WILD-TYPE
  N0           3           217
  N1           0            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"
D1248V6, binary
               cls
clus              0   1
  NSF MUTATED     4   0
  NSF WILD-TYPE 279  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  NSF MUTATED      4    0
  NSF WILD-TYPE  279   48
   clus
vv  NSF MUTATED NSF WILD-TYPE
  0           4           279
  1           0            48
[1] 2 2
[1] FALSE
D1248V7, 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
D1248V8, binary
               cls
clus              0   1
  NSF MUTATED     2   2
  NSF WILD-TYPE 315  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  NSF MUTATED      2    2
  NSF WILD-TYPE  315   46
                               clus
vv                              NSF MUTATED NSF WILD-TYPE
  COLON ADENOCARCINOMA                    2           315
  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 254   2  22  20
D1248V9, multiclass
    clus
vv   NSF MUTATED NSF WILD-TYPE
  R0           3           254
  R1           0             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"
D1248V10, 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
D1248V11, 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(1249) Variable = PCDH20 MUTATION ANALYSIS
D1249V1, survival
                  sevent
clus2                0   1
  PCDH20 MUTATED    13   7
  PCDH20 WILD-TYPE 269  66
  PCDH20 MUTATED PCDH20 WILD-TYPE 
              20              335 
  PCDH20 MUTATED PCDH20 WILD-TYPE 
               7               66 
$`PCDH20 MUTATED`
TCGA-A6-6649 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3672 TCGA-AA-3850 TCGA-AA-3947 
       24.16        20.28         3.02         0.92         0.00        33.01 
TCGA-AA-3977 TCGA-AA-A010 TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6718 
       25.02        34.98        27.09        58.39        49.41         0.10 
TCGA-CK-5913 TCGA-CM-5864 TCGA-D5-5537 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-G4-6293 
       51.32        15.02        45.40        12.59         7.50       107.67 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

$`PCDH20 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.12        19.66         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 
       37.02        14.93         0.00        17.03        10.06        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 
       18.05        31.00         2.01        12.99        24.00        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        35.41        19.43        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       22.09        13.78        35.80        26.17        91.79 

  PCDH20 MUTATED PCDH20 WILD-TYPE 
               0                0 
  PCDH20 MUTATED PCDH20 WILD-TYPE 
          107.67           140.38 
  PCDH20 MUTATED PCDH20 WILD-TYPE 
          26.055           19.990 
[1] "0.0 - 107.7 (26.1)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.4"
D1249V2, 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       22       104         5         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PCDH20 MUTATED           2          0          1          1        0
  PCDH20 WILD-TYPE        17         10         40         30       35
                  vv
clus               STAGE IVA STAGE IVB
  PCDH20 MUTATED           0         0
  PCDH20 WILD-TYPE        13         1
D1249V3, multiclass
            clus
vv           PCDH20 MUTATED PCDH20 WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                3               22
  STAGE IIA               5              104
  STAGE IIB               3                5
  STAGE IIC               0                1
  STAGE III               2               17
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PCDH20 MUTATED     0   5  13   3
  PCDH20 WILD-TYPE   9  63 235  38
D1249V4, multiclass
    clus
vv   PCDH20 MUTATED PCDH20 WILD-TYPE
  T1              0                9
  T2              5               63
  T3             13              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
  PCDH20 MUTATED    15   4   2
  PCDH20 WILD-TYPE 205  76  64
D1249V5, multiclass
    clus
vv   PCDH20 MUTATED PCDH20 WILD-TYPE
  N0             15              205
  N1              4               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"
D1249V6, binary
                  cls
clus                 0   1
  PCDH20 MUTATED    15   0
  PCDH20 WILD-TYPE 268  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH20 MUTATED     15    0
  PCDH20 WILD-TYPE  268   48
   clus
vv  PCDH20 MUTATED PCDH20 WILD-TYPE
  0             15              268
  1              0               48
[1] 2 2
[1] FALSE
D1249V7, 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
D1249V8, binary
                  cls
clus                 0   1
  PCDH20 MUTATED    20   1
  PCDH20 WILD-TYPE 297  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH20 MUTATED     20    1
  PCDH20 WILD-TYPE  297   47
                               clus
vv                              PCDH20 MUTATED PCDH20 WILD-TYPE
  COLON ADENOCARCINOMA                      20              297
  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 245   2  22  18
D1249V9, multiclass
    clus
vv   PCDH20 MUTATED PCDH20 WILD-TYPE
  R0             12              245
  R1              0                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"
D1249V10, 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
D1249V11, 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(1250) Variable = ATF2 MUTATION ANALYSIS
D1250V1, survival
                sevent
clus2              0   1
  ATF2 MUTATED     4   2
  ATF2 WILD-TYPE 278  71
  ATF2 MUTATED ATF2 WILD-TYPE 
             6            349 
  ATF2 MUTATED ATF2 WILD-TYPE 
             2             71 
$`ATF2 MUTATED`
TCGA-AA-3496 TCGA-AA-A02K TCGA-CA-6716 TCGA-CA-6718 TCGA-D5-5539 TCGA-DM-A1DB 
        1.02        14.01         0.26         0.10        19.59        44.32 

$`ATF2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W 
       51.98        39.98         2.01         5.03         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07         0.33         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  ATF2 MUTATED ATF2 WILD-TYPE 
           0.1            0.0 
  ATF2 MUTATED ATF2 WILD-TYPE 
         44.32         140.38 
  ATF2 MUTATED ATF2 WILD-TYPE 
         7.515         20.980 
[1] "0.1 - 44.3 (7.5)"   "0.0 - 140.4 (21.0)"
[1] "hr=" "2.9"
D1250V2, 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       24       106         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        19          9         41         31       34        13
                vv
clus             STAGE IVB
  ATF2 MUTATED           0
  ATF2 WILD-TYPE         1
D1250V3, multiclass
            clus
vv           ATF2 MUTATED ATF2 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             3            106
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            1              9
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ATF2 MUTATED     0   0   5   1
  ATF2 WILD-TYPE   9  68 243  40
D1250V4, multiclass
    clus
vv   ATF2 MUTATED ATF2 WILD-TYPE
  T1            0              9
  T2            0             68
  T3            5            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
  ATF2 MUTATED     4   1   1
  ATF2 WILD-TYPE 216  79  65
D1250V5, multiclass
    clus
vv   ATF2 MUTATED ATF2 WILD-TYPE
  N0            4            216
  N1            1             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"
D1250V6, binary
                cls
clus               0   1
  ATF2 MUTATED     5   1
  ATF2 WILD-TYPE 278  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATF2 MUTATED      5    1
  ATF2 WILD-TYPE  278   47
   clus
vv  ATF2 MUTATED ATF2 WILD-TYPE
  0            5            278
  1            1             47
[1] 2 2
[1] FALSE
D1250V7, 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
D1250V8, binary
                cls
clus               0   1
  ATF2 MUTATED     5   1
  ATF2 WILD-TYPE 312  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATF2 MUTATED      5    1
  ATF2 WILD-TYPE  312   47
                               clus
vv                              ATF2 MUTATED ATF2 WILD-TYPE
  COLON ADENOCARCINOMA                     5            312
  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 255   2  21  19
D1250V9, multiclass
    clus
vv   ATF2 MUTATED ATF2 WILD-TYPE
  R0            2            255
  R1            0              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"
D1250V10, 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
D1250V11, 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(1251) Variable = NUFIP1 MUTATION ANALYSIS
D1251V1, survival
                  sevent
clus2                0   1
  NUFIP1 MUTATED     7   0
  NUFIP1 WILD-TYPE 275  73
  NUFIP1 MUTATED NUFIP1 WILD-TYPE 
               7              348 
  NUFIP1 MUTATED NUFIP1 WILD-TYPE 
               0               73 
$`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         0.33 
TCGA-CK-5913 
       51.32 

$`NUFIP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  NUFIP1 MUTATED NUFIP1 WILD-TYPE 
            0.33             0.00 
  NUFIP1 MUTATED NUFIP1 WILD-TYPE 
           63.98           140.38 
  NUFIP1 MUTATED NUFIP1 WILD-TYPE 
          34.980           20.105 
[1] "0.3 - 64.0 (35.0)"  "0.0 - 140.4 (20.1)"
[1] "hr="     "2.6e+07"
D1251V2, 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       22       105         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NUFIP1 MUTATED           0          0          0          0        0
  NUFIP1 WILD-TYPE        19         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  NUFIP1 MUTATED           0         0
  NUFIP1 WILD-TYPE        13         1
D1251V3, multiclass
            clus
vv           NUFIP1 MUTATED NUFIP1 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                3               22
  STAGE IIA               4              105
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  NUFIP1 MUTATED     0   0   6   2
  NUFIP1 WILD-TYPE   9  68 242  39
D1251V4, multiclass
    clus
vv   NUFIP1 MUTATED NUFIP1 WILD-TYPE
  T1              0                9
  T2              0               68
  T3              6              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
  NUFIP1 MUTATED     8   0   0
  NUFIP1 WILD-TYPE 212  80  66
D1251V5, multiclass
    clus
vv   NUFIP1 MUTATED NUFIP1 WILD-TYPE
  N0              8              212
  N1              0               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"
D1251V6, binary
                  cls
clus                 0   1
  NUFIP1 MUTATED     6   0
  NUFIP1 WILD-TYPE 277  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUFIP1 MUTATED      6    0
  NUFIP1 WILD-TYPE  277   48
   clus
vv  NUFIP1 MUTATED NUFIP1 WILD-TYPE
  0              6              277
  1              0               48
[1] 2 2
[1] FALSE
D1251V7, 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
D1251V8, binary
                  cls
clus                 0   1
  NUFIP1 MUTATED     6   2
  NUFIP1 WILD-TYPE 311  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUFIP1 MUTATED      6    2
  NUFIP1 WILD-TYPE  311   46
                               clus
vv                              NUFIP1 MUTATED NUFIP1 WILD-TYPE
  COLON ADENOCARCINOMA                       6              311
  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 252   2  22  19
D1251V9, multiclass
    clus
vv   NUFIP1 MUTATED NUFIP1 WILD-TYPE
  R0              5              252
  R1              0                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"
D1251V10, 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
D1251V11, 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(1252) Variable = HEPH MUTATION ANALYSIS
D1252V1, survival
                sevent
clus2              0   1
  HEPH MUTATED    13   2
  HEPH WILD-TYPE 269  71
  HEPH MUTATED HEPH WILD-TYPE 
            15            340 
  HEPH MUTATED HEPH WILD-TYPE 
             2             71 
$`HEPH MUTATED`
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-AA-3655 TCGA-AA-A00N TCGA-AZ-4315 
       31.63        30.44        33.53        61.02         4.01        58.39 
TCGA-CK-4952 TCGA-CM-4743 TCGA-CM-5861 TCGA-D5-5538 TCGA-D5-5541 TCGA-DM-A1D8 
       15.62        23.05        15.02        12.26        11.51        12.59 
TCGA-DM-A28H TCGA-F4-6856 TCGA-G4-6321 
      117.07        19.43        22.09 

$`HEPH WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       32.91        29.19        23.61        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 
        1.35        17.56       102.44        40.34        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
       21.99        21.14         2.93         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        16.01         5.03        15.02        15.02        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        13.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 
       38.20       130.65        92.75        49.91        13.32       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-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 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 
       51.75        45.11        36.72        36.00        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  HEPH MUTATED HEPH WILD-TYPE 
          4.01           0.00 
  HEPH MUTATED HEPH WILD-TYPE 
        117.07         140.38 
  HEPH MUTATED HEPH WILD-TYPE 
        22.090         20.155 
[1] "4.0 - 117.1 (22.1)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.9"
D1252V2, 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       24       105         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HEPH MUTATED           2          0          3          1        0         0
  HEPH WILD-TYPE        17         10         38         30       35        13
                vv
clus             STAGE IVB
  HEPH MUTATED           0
  HEPH WILD-TYPE         1
D1252V3, multiclass
            clus
vv           HEPH MUTATED HEPH WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             4            105
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             2             17
  STAGE IIIA            0             10
  STAGE IIIB            3             38
  STAGE IIIC            1             30
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  HEPH MUTATED     0   3  10   2
  HEPH WILD-TYPE   9  65 238  39
D1252V4, multiclass
    clus
vv   HEPH MUTATED HEPH WILD-TYPE
  T1            0              9
  T2            3             65
  T3           10            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
  HEPH MUTATED     8   5   2
  HEPH WILD-TYPE 212  75  64
D1252V5, multiclass
    clus
vv   HEPH MUTATED HEPH WILD-TYPE
  N0            8            212
  N1            5             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"
D1252V6, binary
                cls
clus               0   1
  HEPH MUTATED    13   0
  HEPH WILD-TYPE 270  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  HEPH MUTATED     13    0
  HEPH WILD-TYPE  270   48
   clus
vv  HEPH MUTATED HEPH WILD-TYPE
  0           13            270
  1            0             48
[1] 2 2
[1] FALSE
D1252V7, 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
D1252V8, binary
                cls
clus               0   1
  HEPH MUTATED    12   3
  HEPH WILD-TYPE 305  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  HEPH MUTATED     12    3
  HEPH WILD-TYPE  305   45
                               clus
vv                              HEPH MUTATED HEPH WILD-TYPE
  COLON ADENOCARCINOMA                    12            305
  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 245   2  22  20
D1252V9, multiclass
    clus
vv   HEPH MUTATED HEPH WILD-TYPE
  R0           12            245
  R1            0              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"
D1252V10, 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
D1252V11, 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(1253) Variable = ALAS1 MUTATION ANALYSIS
D1253V1, survival
                 sevent
clus2               0   1
  ALAS1 MUTATED     7   0
  ALAS1 WILD-TYPE 275  73
  ALAS1 MUTATED ALAS1 WILD-TYPE 
              7             348 
  ALAS1 MUTATED ALAS1 WILD-TYPE 
              0              73 
$`ALAS1 MUTATED`
TCGA-AA-3821 TCGA-AA-3977 TCGA-AA-A010 TCGA-CK-5913 TCGA-D5-5538 TCGA-D5-6930 
        1.02        25.02        34.98        51.32        12.26         1.51 
TCGA-G4-6588 
       26.17 

$`ALAS1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       40.34        15.62        49.08        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        52.80 

  ALAS1 MUTATED ALAS1 WILD-TYPE 
           1.02            0.00 
  ALAS1 MUTATED ALAS1 WILD-TYPE 
          51.32          140.38 
  ALAS1 MUTATED ALAS1 WILD-TYPE 
         25.020          20.155 
[1] "1.0 - 51.3 (25.0)"  "0.0 - 140.4 (20.2)"
[1] "hr="     "9200000"
D1253V2, 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       24       106         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        19         10         40         31       35        13
                 vv
clus              STAGE IVB
  ALAS1 MUTATED           0
  ALAS1 WILD-TYPE         1
D1253V3, multiclass
            clus
vv           ALAS1 MUTATED ALAS1 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              3             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ALAS1 MUTATED     0   3   4   2
  ALAS1 WILD-TYPE   9  65 244  39
D1253V4, multiclass
    clus
vv   ALAS1 MUTATED ALAS1 WILD-TYPE
  T1             0               9
  T2             3              65
  T3             4             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
  ALAS1 MUTATED     8   1   0
  ALAS1 WILD-TYPE 212  79  66
D1253V5, multiclass
    clus
vv   ALAS1 MUTATED ALAS1 WILD-TYPE
  N0             8             212
  N1             1              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"
D1253V6, binary
                 cls
clus                0   1
  ALAS1 MUTATED     6   0
  ALAS1 WILD-TYPE 277  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALAS1 MUTATED      6    0
  ALAS1 WILD-TYPE  277   48
   clus
vv  ALAS1 MUTATED ALAS1 WILD-TYPE
  0             6             277
  1             0              48
[1] 2 2
[1] FALSE
D1253V7, 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
D1253V8, binary
                 cls
clus                0   1
  ALAS1 MUTATED     7   2
  ALAS1 WILD-TYPE 310  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALAS1 MUTATED      7    2
  ALAS1 WILD-TYPE  310   46
                               clus
vv                              ALAS1 MUTATED ALAS1 WILD-TYPE
  COLON ADENOCARCINOMA                      7             310
  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 251   2  22  19
D1253V9, multiclass
    clus
vv   ALAS1 MUTATED ALAS1 WILD-TYPE
  R0             6             251
  R1             0               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"
D1253V10, 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
D1253V11, 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(1254) Variable = KIAA0564 MUTATION ANALYSIS
D1254V1, survival
                    sevent
clus2                  0   1
  KIAA0564 MUTATED    18   3
  KIAA0564 WILD-TYPE 264  70
  KIAA0564 MUTATED KIAA0564 WILD-TYPE 
                21                334 
  KIAA0564 MUTATED KIAA0564 WILD-TYPE 
                 3                 70 
$`KIAA0564 MUTATED`
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3525 
       24.39        20.12        19.66        20.28         3.02         8.05 
TCGA-AA-3554 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6889 TCGA-AY-6197 
       17.95        25.02         4.01        34.98        56.55        21.44 
TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-6171 TCGA-D5-6540 TCGA-DM-A1DB 
       58.39         0.33         0.10        14.04        16.14        44.32 
TCGA-DM-A1HA TCGA-G4-6588 TCGA-G4-6628 
      131.51        26.17        52.80 

$`KIAA0564 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        7.04         1.02        35.01        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
       36.03        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37         4.21         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       27.09        16.31         0.95        15.75         0.20        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07         0.26         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
      140.38         7.50       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       13.78        35.80        91.79        46.75 

  KIAA0564 MUTATED KIAA0564 WILD-TYPE 
               0.1                0.0 
  KIAA0564 MUTATED KIAA0564 WILD-TYPE 
            131.51             140.38 
  KIAA0564 MUTATED KIAA0564 WILD-TYPE 
            20.280             20.105 
[1] "0.1 - 131.5 (20.3)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.6"
D1254V2, 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       24        99         5         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0564 MUTATED           0          0          1          2        0
  KIAA0564 WILD-TYPE        19         10         40         29       35
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA0564 MUTATED           0         0
  KIAA0564 WILD-TYPE        13         1
D1254V3, multiclass
            clus
vv           KIAA0564 MUTATED KIAA0564 WILD-TYPE
  STAGE I                   4                 60
  STAGE IA                  0                  1
  STAGE II                  1                 24
  STAGE IIA                10                 99
  STAGE IIB                 3                  5
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                0                 10
  STAGE IIIB                1                 40
  STAGE IIIC                2                 29
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA0564 MUTATED     0   5  13   4
  KIAA0564 WILD-TYPE   9  63 235  37
D1254V4, multiclass
    clus
vv   KIAA0564 MUTATED KIAA0564 WILD-TYPE
  T1                0                  9
  T2                5                 63
  T3               13                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
  KIAA0564 MUTATED    19   2   1
  KIAA0564 WILD-TYPE 201  78  65
D1254V5, multiclass
    clus
vv   KIAA0564 MUTATED KIAA0564 WILD-TYPE
  N0               19                201
  N1                2                 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"
D1254V6, binary
                    cls
clus                   0   1
  KIAA0564 MUTATED    17   0
  KIAA0564 WILD-TYPE 266  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0564 MUTATED     17    0
  KIAA0564 WILD-TYPE  266   48
   clus
vv  KIAA0564 MUTATED KIAA0564 WILD-TYPE
  0               17                266
  1                0                 48
[1] 2 2
[1] FALSE
D1254V7, 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
D1254V8, binary
                    cls
clus                   0   1
  KIAA0564 MUTATED    17   5
  KIAA0564 WILD-TYPE 300  43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0564 MUTATED     17    5
  KIAA0564 WILD-TYPE  300   43
                               clus
vv                              KIAA0564 MUTATED KIAA0564 WILD-TYPE
  COLON ADENOCARCINOMA                        17                300
  COLON MUCINOUS ADENOCARCINOMA                5                 43
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  KIAA0564 MUTATED    13   0   0   2
  KIAA0564 WILD-TYPE 244   2  22  19
D1254V9, multiclass
    clus
vv   KIAA0564 MUTATED KIAA0564 WILD-TYPE
  R0               13                244
  R1                0                  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"
D1254V10, 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
D1254V11, 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(1255) Variable = PDGFC MUTATION ANALYSIS
D1255V1, survival
                 sevent
clus2               0   1
  PDGFC MUTATED     7   2
  PDGFC WILD-TYPE 275  71
  PDGFC MUTATED PDGFC WILD-TYPE 
              9             346 
  PDGFC MUTATED PDGFC WILD-TYPE 
              2              71 
$`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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
       58.39         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 
      107.67        74.56        65.85        53.62        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  PDGFC MUTATED PDGFC WILD-TYPE 
           1.41            0.00 
  PDGFC MUTATED PDGFC WILD-TYPE 
          44.68          140.38 
  PDGFC MUTATED PDGFC WILD-TYPE 
         22.060          20.155 
[1] "1.4 - 44.7 (22.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.3"
D1255V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PDGFC MUTATED         0        0        0         4         1         0
  PDGFC WILD-TYPE      64        1       25       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        19         10         41         30       33        13
                 vv
clus              STAGE IVB
  PDGFC MUTATED           0
  PDGFC WILD-TYPE         1
D1255V3, multiclass
            clus
vv           PDGFC MUTATED PDGFC WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              4             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               2              33
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PDGFC MUTATED     0   1   4   4
  PDGFC WILD-TYPE   9  67 244  37
D1255V4, multiclass
    clus
vv   PDGFC MUTATED PDGFC WILD-TYPE
  T1             0               9
  T2             1              67
  T3             4             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
  PDGFC MUTATED     6   1   2
  PDGFC WILD-TYPE 214  79  64
D1255V5, multiclass
    clus
vv   PDGFC MUTATED PDGFC WILD-TYPE
  N0             6             214
  N1             1              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"
D1255V6, binary
                 cls
clus                0   1
  PDGFC MUTATED     5   2
  PDGFC WILD-TYPE 278  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDGFC MUTATED      5    2
  PDGFC WILD-TYPE  278   46
   clus
vv  PDGFC MUTATED PDGFC WILD-TYPE
  0             5             278
  1             2              46
[1] 2 2
[1] FALSE
D1255V7, 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
D1255V8, binary
                 cls
clus                0   1
  PDGFC MUTATED     8   1
  PDGFC WILD-TYPE 309  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDGFC MUTATED      8    1
  PDGFC WILD-TYPE  309   47
                               clus
vv                              PDGFC MUTATED PDGFC WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  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 251   2  21  21
D1255V9, multiclass
    clus
vv   PDGFC MUTATED PDGFC WILD-TYPE
  R0             6             251
  R1             0               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"
D1255V10, 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
D1255V11, 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(1256) Variable = MSLNL MUTATION ANALYSIS
D1256V1, survival
                 sevent
clus2               0   1
  MSLNL MUTATED     6   0
  MSLNL WILD-TYPE 276  73
  MSLNL MUTATED MSLNL WILD-TYPE 
              6             349 
  MSLNL MUTATED MSLNL WILD-TYPE 
              0              73 
$`MSLNL MUTATED`
TCGA-AD-6889 TCGA-CM-6162 TCGA-D5-6927 TCGA-D5-6928 TCGA-DM-A28E TCGA-G4-6586 
       56.55        12.00         9.44        11.64       119.93        35.80 

$`MSLNL WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        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        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
      139.17         6.12        81.37        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  MSLNL MUTATED MSLNL WILD-TYPE 
           9.44            0.00 
  MSLNL MUTATED MSLNL WILD-TYPE 
         119.93          140.38 
  MSLNL MUTATED MSLNL WILD-TYPE 
          23.90           20.19 
[1] "9.4 - 119.9 (23.9)" "0.0 - 140.4 (20.2)"
[1] "hr="     "9400000"
D1256V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MSLNL MUTATED         0        0        0         5         0         0
  MSLNL WILD-TYPE      64        1       25       104         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MSLNL MUTATED           0          0          1          0        0         0
  MSLNL WILD-TYPE        19         10         40         31       35        13
                 vv
clus              STAGE IVB
  MSLNL MUTATED           0
  MSLNL WILD-TYPE         1
D1256V3, multiclass
            clus
vv           MSLNL MUTATED MSLNL WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              5             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MSLNL MUTATED     0   0   6   0
  MSLNL WILD-TYPE   9  68 242  41
D1256V4, multiclass
    clus
vv   MSLNL MUTATED MSLNL WILD-TYPE
  T1             0               9
  T2             0              68
  T3             6             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
  MSLNL MUTATED     5   1   0
  MSLNL WILD-TYPE 215  79  66
D1256V5, multiclass
    clus
vv   MSLNL MUTATED MSLNL WILD-TYPE
  N0             5             215
  N1             1              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"
D1256V6, binary
                 cls
clus                0   1
  MSLNL MUTATED     6   0
  MSLNL WILD-TYPE 277  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MSLNL MUTATED      6    0
  MSLNL WILD-TYPE  277   48
   clus
vv  MSLNL MUTATED MSLNL WILD-TYPE
  0             6             277
  1             0              48
[1] 2 2
[1] FALSE
D1256V7, binary
                 cls
clus                0   1
  MSLNL MUTATED     3   3
  MSLNL WILD-TYPE 167 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MSLNL MUTATED      3    3
  MSLNL WILD-TYPE  167  194
        clus
vv       MSLNL MUTATED MSLNL WILD-TYPE
  FEMALE             3             167
  MALE               3             194
[1] 2 2
[1] FALSE
D1256V8, binary
                 cls
clus                0   1
  MSLNL MUTATED     4   2
  MSLNL WILD-TYPE 313  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MSLNL MUTATED      4    2
  MSLNL WILD-TYPE  313   46
                               clus
vv                              MSLNL MUTATED MSLNL WILD-TYPE
  COLON ADENOCARCINOMA                      4             313
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MSLNL MUTATED     4   0   0   0
  MSLNL WILD-TYPE 253   2  22  21
D1256V9, multiclass
    clus
vv   MSLNL MUTATED MSLNL WILD-TYPE
  R0             4             253
  R1             0               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"
D1256V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MSLNL MUTATED                                  0     1
  MSLNL WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MSLNL MUTATED                           0     5
  MSLNL WILD-TYPE                        19   171
D1256V11, multiclass
                                  clus
vv                                 MSLNL MUTATED MSLNL 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(1257) Variable = SENP8 MUTATION ANALYSIS
D1257V1, survival
                 sevent
clus2               0   1
  SENP8 MUTATED     3   0
  SENP8 WILD-TYPE 279  73
  SENP8 MUTATED SENP8 WILD-TYPE 
              3             352 
  SENP8 MUTATED SENP8 WILD-TYPE 
              0              73 
$`SENP8 MUTATED`
TCGA-A6-6780 TCGA-A6-6781 TCGA-CM-6674 
       20.12        19.66        12.95 

$`SENP8 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       23.87        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  SENP8 MUTATED SENP8 WILD-TYPE 
          12.95            0.00 
  SENP8 MUTATED SENP8 WILD-TYPE 
          20.12          140.38 
  SENP8 MUTATED SENP8 WILD-TYPE 
          19.66           20.63 
[1] "12.9 - 20.1 (19.7)" "0.0 - 140.4 (20.6)"
[1] "hr="     "3300000"
D1257V2, 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       25       107         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        19         10         41         30       35        13
                 vv
clus              STAGE IVB
  SENP8 MUTATED           0
  SENP8 WILD-TYPE         1
D1257V3, multiclass
            clus
vv           SENP8 MUTATED SENP8 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              2             107
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SENP8 MUTATED     0   0   2   2
  SENP8 WILD-TYPE   9  68 246  39
D1257V4, multiclass
    clus
vv   SENP8 MUTATED SENP8 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             2             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
  SENP8 MUTATED     3   1   0
  SENP8 WILD-TYPE 217  79  66
D1257V5, multiclass
    clus
vv   SENP8 MUTATED SENP8 WILD-TYPE
  N0             3             217
  N1             1              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"
D1257V6, binary
                 cls
clus                0   1
  SENP8 MUTATED     1   0
  SENP8 WILD-TYPE 282  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SENP8 MUTATED      1    0
  SENP8 WILD-TYPE  282   48
   clus
vv  SENP8 MUTATED SENP8 WILD-TYPE
  0             1             282
  1             0              48
[1] 2 2
[1] FALSE
D1257V7, 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
D1257V8, binary
                 cls
clus                0   1
  SENP8 MUTATED     2   2
  SENP8 WILD-TYPE 315  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SENP8 MUTATED      2    2
  SENP8 WILD-TYPE  315   46
                               clus
vv                              SENP8 MUTATED SENP8 WILD-TYPE
  COLON ADENOCARCINOMA                      2             315
  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 255   2  22  20
D1257V9, multiclass
    clus
vv   SENP8 MUTATED SENP8 WILD-TYPE
  R0             2             255
  R1             0               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"
D1257V10, 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
D1257V11, 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(1258) Variable = STK11 MUTATION ANALYSIS
D1258V1, survival
                 sevent
clus2               0   1
  STK11 MUTATED    25   6
  STK11 WILD-TYPE 257  67
  STK11 MUTATED STK11 WILD-TYPE 
             31             324 
  STK11 MUTATED STK11 WILD-TYPE 
              6              67 
$`STK11 MUTATED`
TCGA-A6-4105 TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3660 TCGA-AA-3662 
       14.53        22.06         3.02         1.02        78.08         6.05 
TCGA-AA-3713 TCGA-AD-6895 TCGA-AU-3779 TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-5407 
       19.04         0.72        14.50        15.75        21.44        61.41 
TCGA-AZ-6601 TCGA-CA-6719 TCGA-CK-4950 TCGA-CM-4743 TCGA-CM-4752 TCGA-CM-5344 
      100.01         1.35        40.34        23.05        13.02        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-6533 TCGA-D5-6923 
       22.98        30.08        45.40        19.59         1.32        12.43 
TCGA-DM-A0XF TCGA-DM-A282 TCGA-G4-6293 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6586 
       38.20       139.17       107.67        45.11        36.72        35.80 
TCGA-G4-6626 
       46.75 

$`STK11 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       19.66        20.28         7.04        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       61.02         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        4.21        56.55         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 
       10.88         0.20        27.09        16.31         0.95         0.20 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       62.79        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 
        3.29         0.07         0.26         0.33         0.10        17.56 
TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      102.44        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        13.51        11.51        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 
       12.00        11.38        10.26       119.70        24.43       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       135.65         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       36.00        22.09        13.78        26.17        91.79        52.80 

  STK11 MUTATED STK11 WILD-TYPE 
           0.72            0.00 
  STK11 MUTATED STK11 WILD-TYPE 
         139.17          140.38 
  STK11 MUTATED STK11 WILD-TYPE 
         22.060          20.005 
[1] "0.7 - 139.2 (22.1)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.4"
D1258V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  STK11 MUTATED         3        0        4        12         0         0
  STK11 WILD-TYPE      61        1       21        97         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  STK11 MUTATED           1          2          4          1        3         1
  STK11 WILD-TYPE        18          8         37         30       32        12
                 vv
clus              STAGE IVB
  STK11 MUTATED           0
  STK11 WILD-TYPE         1
D1258V3, multiclass
            clus
vv           STK11 MUTATED STK11 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               4              21
  STAGE IIA             12              97
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             2               8
  STAGE IIIB             4              37
  STAGE IIIC             1              30
  STAGE IV               3              32
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  27   2
  STK11 WILD-TYPE   8  66 221  39
D1258V4, multiclass
    clus
vv   STK11 MUTATED STK11 WILD-TYPE
  T1             1               8
  T2             2              66
  T3            27             221
  T4             2              39
[1] 4 2
[1] TRUE
[1] "dimension 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    20   9   3
  STK11 WILD-TYPE 200  71  63
D1258V5, multiclass
    clus
vv   STK11 MUTATED STK11 WILD-TYPE
  N0            20             200
  N1             9              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"
D1258V6, binary
                 cls
clus                0   1
  STK11 MUTATED    24   4
  STK11 WILD-TYPE 259  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK11 MUTATED     24    4
  STK11 WILD-TYPE  259   44
   clus
vv  STK11 MUTATED STK11 WILD-TYPE
  0            24             259
  1             4              44
[1] 2 2
[1] FALSE
D1258V7, binary
                 cls
clus                0   1
  STK11 MUTATED    16  16
  STK11 WILD-TYPE 154 181
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK11 MUTATED     16   16
  STK11 WILD-TYPE  154  181
        clus
vv       STK11 MUTATED STK11 WILD-TYPE
  FEMALE            16             154
  MALE              16             181
[1] 2 2
[1] FALSE
D1258V8, binary
                 cls
clus                0   1
  STK11 MUTATED    30   2
  STK11 WILD-TYPE 287  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK11 MUTATED     30    2
  STK11 WILD-TYPE  287   46
                               clus
vv                              STK11 MUTATED STK11 WILD-TYPE
  COLON ADENOCARCINOMA                     30             287
  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 237   1  20  18
D1258V9, multiclass
    clus
vv   STK11 MUTATED STK11 WILD-TYPE
  R0            20             237
  R1             1               1
  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"
D1258V10, 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
D1258V11, 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(1259) Variable = BRD4 MUTATION ANALYSIS
D1259V1, survival
                sevent
clus2              0   1
  BRD4 MUTATED    18   1
  BRD4 WILD-TYPE 264  72
  BRD4 MUTATED BRD4 WILD-TYPE 
            19            336 
  BRD4 MUTATED BRD4 WILD-TYPE 
             1             72 
$`BRD4 MUTATED`
TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3815 
       20.12        19.66        63.98        26.99        35.05        33.04 
TCGA-AA-3864 TCGA-AA-3949 TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6895 TCGA-CM-4752 
       53.00        26.01         0.07        56.55         0.72        13.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-6171 TCGA-D5-6539 TCGA-D5-6928 TCGA-DM-A1D9 
       15.02         5.03        14.04        12.49        11.64       140.38 
TCGA-G4-6628 
       52.80 

$`BRD4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       23.87        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3818 TCGA-AA-3819 
       85.05        19.04        19.04        10.06         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       39.98        18.05        40.96        21.37         4.21         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 

  BRD4 MUTATED BRD4 WILD-TYPE 
          0.07           0.00 
  BRD4 MUTATED BRD4 WILD-TYPE 
        140.38         139.17 
  BRD4 MUTATED BRD4 WILD-TYPE 
        20.120         20.235 
[1] "0.1 - 140.4 (20.1)" "0.0 - 139.2 (20.2)"
[1] "hr=" "4.9"
D1259V2, 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       23       100         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BRD4 MUTATED           1          1          1          1        0         1
  BRD4 WILD-TYPE        18          9         40         30       35        12
                vv
clus             STAGE IVB
  BRD4 MUTATED           0
  BRD4 WILD-TYPE         1
D1259V3, multiclass
            clus
vv           BRD4 MUTATED BRD4 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             9            100
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            1              9
  STAGE IIIB            1             40
  STAGE IIIC            1             30
  STAGE IV              0             35
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  65 232  40
D1259V4, multiclass
    clus
vv   BRD4 MUTATED BRD4 WILD-TYPE
  T1            0              9
  T2            3             65
  T3           16            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
  BRD4 MUTATED    15   4   1
  BRD4 WILD-TYPE 205  76  65
D1259V5, multiclass
    clus
vv   BRD4 MUTATED BRD4 WILD-TYPE
  N0           15            205
  N1            4             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"
D1259V6, binary
                cls
clus               0   1
  BRD4 MUTATED    15   1
  BRD4 WILD-TYPE 268  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD4 MUTATED     15    1
  BRD4 WILD-TYPE  268   47
   clus
vv  BRD4 MUTATED BRD4 WILD-TYPE
  0           15            268
  1            1             47
[1] 2 2
[1] FALSE
D1259V7, 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
D1259V8, binary
                cls
clus               0   1
  BRD4 MUTATED    15   5
  BRD4 WILD-TYPE 302  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD4 MUTATED     15    5
  BRD4 WILD-TYPE  302   43
                               clus
vv                              BRD4 MUTATED BRD4 WILD-TYPE
  COLON ADENOCARCINOMA                    15            302
  COLON MUCINOUS ADENOCARCINOMA            5             43
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  BRD4 MUTATED    16   0   0   0
  BRD4 WILD-TYPE 241   2  22  21
D1259V9, multiclass
    clus
vv   BRD4 MUTATED BRD4 WILD-TYPE
  R0           16            241
  R1            0              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"
D1259V10, 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
D1259V11, 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(1260) Variable = IGFN1 MUTATION ANALYSIS
D1260V1, survival
                 sevent
clus2               0   1
  IGFN1 MUTATED    13   2
  IGFN1 WILD-TYPE 269  71
  IGFN1 MUTATED IGFN1 WILD-TYPE 
             15             340 
  IGFN1 MUTATED IGFN1 WILD-TYPE 
              2              71 
$`IGFN1 MUTATED`
TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3811 TCGA-AA-3815 TCGA-AA-A00E TCGA-AD-6889 
       22.06         3.02        10.06        33.04        30.02        56.55 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4743 TCGA-CM-6171 TCGA-D5-6533 TCGA-DM-A28K 
        0.33         0.10        23.05        14.04         1.32        98.24 
TCGA-G4-6293 TCGA-G4-6323 TCGA-G4-6588 
      107.67        13.78        26.17 

$`IGFN1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        19.04        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F 
        7.96        27.02        13.94        38.04        19.00        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37         4.21         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07         0.26         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14         2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51        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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.41        19.43        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        91.79        46.75        52.80 

  IGFN1 MUTATED IGFN1 WILD-TYPE 
            0.1             0.0 
  IGFN1 MUTATED IGFN1 WILD-TYPE 
         107.67          140.38 
  IGFN1 MUTATED IGFN1 WILD-TYPE 
         22.060          20.155 
[1] "0.1 - 107.7 (22.1)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.8"
D1260V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IGFN1 MUTATED         1        1        1         9         0         0
  IGFN1 WILD-TYPE      63        0       24       100         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IGFN1 MUTATED           2          0          1          0        0         0
  IGFN1 WILD-TYPE        17         10         40         31       35        13
                 vv
clus              STAGE IVB
  IGFN1 MUTATED           0
  IGFN1 WILD-TYPE         1
D1260V3, multiclass
            clus
vv           IGFN1 MUTATED IGFN1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               1               0
  STAGE II               1              24
  STAGE IIA              9             100
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  IGFN1 MUTATED     0   1  12   1
  IGFN1 WILD-TYPE   9  67 236  40
D1260V4, multiclass
    clus
vv   IGFN1 MUTATED IGFN1 WILD-TYPE
  T1             0               9
  T2             1              67
  T3            12             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    13   1   1
  IGFN1 WILD-TYPE 207  79  65
D1260V5, multiclass
    clus
vv   IGFN1 MUTATED IGFN1 WILD-TYPE
  N0            13             207
  N1             1              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"
D1260V6, binary
                 cls
clus                0   1
  IGFN1 MUTATED    14   0
  IGFN1 WILD-TYPE 269  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGFN1 MUTATED     14    0
  IGFN1 WILD-TYPE  269   48
   clus
vv  IGFN1 MUTATED IGFN1 WILD-TYPE
  0            14             269
  1             0              48
[1] 2 2
[1] FALSE
D1260V7, binary
                 cls
clus                0   1
  IGFN1 MUTATED     8   7
  IGFN1 WILD-TYPE 162 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGFN1 MUTATED      8    7
  IGFN1 WILD-TYPE  162  190
        clus
vv       IGFN1 MUTATED IGFN1 WILD-TYPE
  FEMALE             8             162
  MALE               7             190
[1] 2 2
[1] FALSE
D1260V8, binary
                 cls
clus                0   1
  IGFN1 MUTATED    13   2
  IGFN1 WILD-TYPE 304  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGFN1 MUTATED     13    2
  IGFN1 WILD-TYPE  304   46
                               clus
vv                              IGFN1 MUTATED IGFN1 WILD-TYPE
  COLON ADENOCARCINOMA                     13             304
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  IGFN1 MUTATED    11   0   0   2
  IGFN1 WILD-TYPE 246   2  22  19
D1260V9, multiclass
    clus
vv   IGFN1 MUTATED IGFN1 WILD-TYPE
  R0            11             246
  R1             0               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"
D1260V10, 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
D1260V11, 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(1261) Variable = TOP2A MUTATION ANALYSIS
D1261V1, survival
                 sevent
clus2               0   1
  TOP2A MUTATED    15   1
  TOP2A WILD-TYPE 267  72
  TOP2A MUTATED TOP2A WILD-TYPE 
             16             339 
  TOP2A MUTATED TOP2A WILD-TYPE 
              1              72 
$`TOP2A MUTATED`
TCGA-A6-5665 TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3697 
       22.06         1.02        63.98         6.97         0.92        85.05 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AU-6004 TCGA-AY-6386 TCGA-CA-6718 TCGA-CK-5913 
        0.79         0.72        27.09        17.82         0.10        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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 
       37.05        19.00        36.00         5.03        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       21.37         4.21        56.55         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.33         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  TOP2A MUTATED TOP2A WILD-TYPE 
            0.1             0.0 
  TOP2A MUTATED TOP2A WILD-TYPE 
          85.05          140.38 
  TOP2A MUTATED TOP2A WILD-TYPE 
          12.77           20.98 
[1] "0.1 - 85.0 (12.8)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "2.9"
D1261V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TOP2A MUTATED         2        0        3         5         0         0
  TOP2A WILD-TYPE      62        1       22       104         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TOP2A MUTATED           2          1          1          0        0         0
  TOP2A WILD-TYPE        17          9         40         31       35        13
                 vv
clus              STAGE IVB
  TOP2A MUTATED           1
  TOP2A WILD-TYPE         0
D1261V3, multiclass
            clus
vv           TOP2A MUTATED TOP2A WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              5             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             1               9
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  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  66 234  41
D1261V4, multiclass
    clus
vv   TOP2A MUTATED TOP2A WILD-TYPE
  T1             1               8
  T2             2              66
  T3            14             234
  T4             0              41
[1] 4 2
[1] TRUE
[1] "dimension 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  77  65
D1261V5, multiclass
    clus
vv   TOP2A MUTATED TOP2A WILD-TYPE
  N0            13             207
  N1             3              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"
D1261V6, binary
                 cls
clus                0   1
  TOP2A MUTATED    13   1
  TOP2A WILD-TYPE 270  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TOP2A MUTATED     13    1
  TOP2A WILD-TYPE  270   47
   clus
vv  TOP2A MUTATED TOP2A WILD-TYPE
  0            13             270
  1             1              47
[1] 2 2
[1] FALSE
D1261V7, 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
D1261V8, binary
                 cls
clus                0   1
  TOP2A MUTATED    17   0
  TOP2A WILD-TYPE 300  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TOP2A MUTATED     17    0
  TOP2A WILD-TYPE  300   48
                               clus
vv                              TOP2A MUTATED TOP2A WILD-TYPE
  COLON ADENOCARCINOMA                     17             300
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TOP2A MUTATED    13   0   0   2
  TOP2A WILD-TYPE 244   2  22  19
D1261V9, multiclass
    clus
vv   TOP2A MUTATED TOP2A WILD-TYPE
  R0            13             244
  R1             0               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"
D1261V10, 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
D1261V11, 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(1262) Variable = MARCH5 MUTATION ANALYSIS
D1262V1, survival
                  sevent
clus2                0   1
  MARCH5 MUTATED     5   1
  MARCH5 WILD-TYPE 277  72
  MARCH5 MUTATED MARCH5 WILD-TYPE 
               6              349 
  MARCH5 MUTATED MARCH5 WILD-TYPE 
               1               72 
$`MARCH5 MUTATED`
TCGA-A6-2672 TCGA-AA-3950 TCGA-AZ-6608 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-6168 
       46.65        24.00         1.94         2.93         2.01        12.99 

$`MARCH5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  MARCH5 MUTATED MARCH5 WILD-TYPE 
            1.94             0.00 
  MARCH5 MUTATED MARCH5 WILD-TYPE 
           46.65           140.38 
  MARCH5 MUTATED MARCH5 WILD-TYPE 
            7.96            20.28 
[1] "1.9 - 46.6 (8.0)"   "0.0 - 140.4 (20.3)"
[1] "hr=" "1.3"
D1262V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MARCH5 MUTATED         0        0        0         3         0         0
  MARCH5 WILD-TYPE      64        1       25       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MARCH5 MUTATED           0          1          1          0        1
  MARCH5 WILD-TYPE        19          9         40         31       34
                  vv
clus               STAGE IVA STAGE IVB
  MARCH5 MUTATED           0         0
  MARCH5 WILD-TYPE        13         1
D1262V3, multiclass
            clus
vv           MARCH5 MUTATED MARCH5 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               3              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              1                9
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MARCH5 MUTATED     0   1   5   0
  MARCH5 WILD-TYPE   9  67 243  41
D1262V4, multiclass
    clus
vv   MARCH5 MUTATED MARCH5 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              5              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
  MARCH5 MUTATED     3   3   0
  MARCH5 WILD-TYPE 217  77  66
D1262V5, multiclass
    clus
vv   MARCH5 MUTATED MARCH5 WILD-TYPE
  N0              3              217
  N1              3               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"
D1262V6, binary
                  cls
clus                 0   1
  MARCH5 MUTATED     4   1
  MARCH5 WILD-TYPE 279  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MARCH5 MUTATED      4    1
  MARCH5 WILD-TYPE  279   47
   clus
vv  MARCH5 MUTATED MARCH5 WILD-TYPE
  0              4              279
  1              1               47
[1] 2 2
[1] FALSE
D1262V7, binary
                  cls
clus                 0   1
  MARCH5 MUTATED     6   0
  MARCH5 WILD-TYPE 164 197
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MARCH5 MUTATED      6    0
  MARCH5 WILD-TYPE  164  197
        clus
vv       MARCH5 MUTATED MARCH5 WILD-TYPE
  FEMALE              6              164
  MALE                0              197
[1] 2 2
[1] FALSE
D1262V8, binary
                  cls
clus                 0   1
  MARCH5 MUTATED     4   2
  MARCH5 WILD-TYPE 313  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MARCH5 MUTATED      4    2
  MARCH5 WILD-TYPE  313   46
                               clus
vv                              MARCH5 MUTATED MARCH5 WILD-TYPE
  COLON ADENOCARCINOMA                       4              313
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  MARCH5 MUTATED     3   0   0   2
  MARCH5 WILD-TYPE 254   2  22  19
D1262V9, multiclass
    clus
vv   MARCH5 MUTATED MARCH5 WILD-TYPE
  R0              3              254
  R1              0                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"
D1262V10, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MARCH5 MUTATED                                  0     0
  MARCH5 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MARCH5 MUTATED                           1     4
  MARCH5 WILD-TYPE                        18   172
D1262V11, multiclass
                                  clus
vv                                 MARCH5 MUTATED MARCH5 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(1263) Variable = SBDS MUTATION ANALYSIS
D1263V1, survival
                sevent
clus2              0   1
  SBDS MUTATED     2   1
  SBDS WILD-TYPE 280  72
  SBDS MUTATED SBDS WILD-TYPE 
             3            352 
  SBDS MUTATED SBDS WILD-TYPE 
             1             72 
$`SBDS MUTATED`
TCGA-AA-3660 TCGA-D5-6926 TCGA-G4-6303 
       78.08         9.04        65.85 

$`SBDS WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        61.02         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      107.67        74.56        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  SBDS MUTATED SBDS WILD-TYPE 
          9.04           0.00 
  SBDS MUTATED SBDS WILD-TYPE 
         78.08         140.38 
  SBDS MUTATED SBDS WILD-TYPE 
        65.850         20.155 
[1] "9.0 - 78.1 (65.8)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.3"
D1263V2, 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       24       109         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SBDS MUTATED           0          1          0          0        1         0
  SBDS WILD-TYPE        19          9         41         31       34        13
                vv
clus             STAGE IVB
  SBDS MUTATED           0
  SBDS WILD-TYPE         1
D1263V3, multiclass
            clus
vv           SBDS MUTATED SBDS WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             0            109
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            1              9
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SBDS MUTATED     0   0   2   1
  SBDS WILD-TYPE   9  68 246  40
D1263V4, multiclass
    clus
vv   SBDS MUTATED SBDS WILD-TYPE
  T1            0              9
  T2            0             68
  T3            2            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
  SBDS MUTATED     1   2   0
  SBDS WILD-TYPE 219  78  66
D1263V5, multiclass
    clus
vv   SBDS MUTATED SBDS WILD-TYPE
  N0            1            219
  N1            2             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"
D1263V6, binary
                cls
clus               0   1
  SBDS MUTATED     2   1
  SBDS WILD-TYPE 281  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  SBDS MUTATED      2    1
  SBDS WILD-TYPE  281   47
   clus
vv  SBDS MUTATED SBDS WILD-TYPE
  0            2            281
  1            1             47
[1] 2 2
[1] FALSE
D1263V7, 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
D1263V8, binary
                cls
clus               0   1
  SBDS MUTATED     3   0
  SBDS WILD-TYPE 314  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  SBDS MUTATED      3    0
  SBDS WILD-TYPE  314   48
                               clus
vv                              SBDS MUTATED SBDS WILD-TYPE
  COLON ADENOCARCINOMA                     3            314
  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 254   2  22  21
D1263V9, multiclass
    clus
vv   SBDS MUTATED SBDS WILD-TYPE
  R0            3            254
  R1            0              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"
D1263V10, 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
D1263V11, multiclass
[1] "Remove cluster labels:" "SBDS MUTATED"          
clus
  SBDS MUTATED SBDS WILD-TYPE 
             2            204 
    TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810     TCGA-A6-4105 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-A6-5656     TCGA-A6-5657     TCGA-A6-5659     TCGA-A6-5660 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-A6-5661     TCGA-A6-5662     TCGA-A6-5664     TCGA-A6-5665 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-A6-5666     TCGA-A6-6137     TCGA-A6-6138     TCGA-A6-6141 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-A6-6142     TCGA-A6-6648     TCGA-A6-6649     TCGA-A6-6651 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-A6-6652     TCGA-A6-6653     TCGA-A6-6654     TCGA-A6-6780 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-A6-6781     TCGA-A6-6782     TCGA-AD-5900     TCGA-AD-6548 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-AD-6888     TCGA-AD-6889     TCGA-AD-6890     TCGA-AD-6895 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-AD-6899     TCGA-AD-6901     TCGA-AD-6963     TCGA-AD-6964 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-AD-6965     TCGA-AU-3779     TCGA-AU-6004     TCGA-AY-4070 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-AY-4071     TCGA-AY-5543     TCGA-AY-6196     TCGA-AY-6197 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-AY-6386     TCGA-AZ-4315     TCGA-AZ-4323     TCGA-AZ-4616 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-AZ-4681     TCGA-AZ-4682     TCGA-AZ-5403     TCGA-AZ-5407 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-AZ-6598     TCGA-AZ-6599     TCGA-AZ-6600     TCGA-AZ-6601 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-AZ-6603     TCGA-AZ-6605     TCGA-AZ-6606     TCGA-AZ-6607 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-AZ-6608     TCGA-CA-5254     TCGA-CA-5255     TCGA-CA-5796 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-CA-5797     TCGA-CA-6715     TCGA-CA-6716     TCGA-CA-6717 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-CA-6718     TCGA-CA-6719     TCGA-CK-4947     TCGA-CK-4948 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-CK-4950     TCGA-CK-4952     TCGA-CK-5912     TCGA-CK-5913 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-CK-5914     TCGA-CK-5915     TCGA-CK-5916     TCGA-CK-6746 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-CK-6747     TCGA-CK-6748     TCGA-CK-6751     TCGA-CM-4743 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-CM-4744     TCGA-CM-4746     TCGA-CM-4747     TCGA-CM-4752 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-CM-5341     TCGA-CM-5344     TCGA-CM-5348     TCGA-CM-5349 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-CM-5860     TCGA-CM-5861     TCGA-CM-5862     TCGA-CM-5863 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-CM-5864     TCGA-CM-5868     TCGA-CM-6161     TCGA-CM-6162 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-CM-6163     TCGA-CM-6164     TCGA-CM-6165     TCGA-CM-6166 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-CM-6167     TCGA-CM-6168     TCGA-CM-6169     TCGA-CM-6170 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-CM-6171     TCGA-CM-6172     TCGA-CM-6674     TCGA-CM-6675 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-CM-6676     TCGA-CM-6677     TCGA-CM-6678     TCGA-CM-6679 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-CM-6680     TCGA-D5-5537     TCGA-D5-5538     TCGA-D5-5539 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-D5-5540     TCGA-D5-5541     TCGA-D5-6529     TCGA-D5-6532 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-D5-6533     TCGA-D5-6534     TCGA-D5-6535     TCGA-D5-6536 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-D5-6537     TCGA-D5-6538     TCGA-D5-6539     TCGA-D5-6540 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-D5-6541     TCGA-D5-6898     TCGA-D5-6920     TCGA-D5-6922 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-D5-6923     TCGA-D5-6924     TCGA-D5-6927     TCGA-D5-6928 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-D5-6929     TCGA-D5-6930     TCGA-D5-6931     TCGA-D5-6932 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-D5-7000     TCGA-DM-A0X9     TCGA-DM-A0XD     TCGA-DM-A0XF 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-DM-A1D0     TCGA-DM-A1D4     TCGA-DM-A1D6     TCGA-DM-A1D7 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-DM-A1D8     TCGA-DM-A1D9     TCGA-DM-A1DA     TCGA-DM-A1DB 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-DM-A1HA     TCGA-DM-A1HB     TCGA-DM-A282     TCGA-DM-A285 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-DM-A28C     TCGA-DM-A28E     TCGA-DM-A28F     TCGA-DM-A28G 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-DM-A28H     TCGA-DM-A28K     TCGA-F4-6459     TCGA-F4-6460 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-F4-6569     TCGA-F4-6570     TCGA-F4-6703     TCGA-F4-6704 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-F4-6805     TCGA-F4-6806     TCGA-F4-6807     TCGA-F4-6808 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-F4-6809     TCGA-F4-6854     TCGA-F4-6855     TCGA-F4-6856 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-G4-6293     TCGA-G4-6299     TCGA-G4-6304     TCGA-G4-6306 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-G4-6307     TCGA-G4-6309     TCGA-G4-6310     TCGA-G4-6315 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-G4-6317     TCGA-G4-6321     TCGA-G4-6323     TCGA-G4-6586 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-G4-6588     TCGA-G4-6625     TCGA-G4-6626     TCGA-G4-6628 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 

Clustering(1264) Variable = SYNGR4 MUTATION ANALYSIS
D1264V1, survival
                  sevent
clus2                0   1
  SYNGR4 MUTATED     4   1
  SYNGR4 WILD-TYPE 278  72
  SYNGR4 MUTATED SYNGR4 WILD-TYPE 
               5              350 
  SYNGR4 MUTATED SYNGR4 WILD-TYPE 
               1               72 
$`SYNGR4 MUTATED`
TCGA-A6-6781 TCGA-AA-A00N TCGA-AD-5900 TCGA-AZ-4315 TCGA-D5-5539 
       19.66         4.01         0.07        58.39        19.59 

$`SYNGR4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  SYNGR4 MUTATED SYNGR4 WILD-TYPE 
            0.07             0.00 
  SYNGR4 MUTATED SYNGR4 WILD-TYPE 
           58.39           140.38 
  SYNGR4 MUTATED SYNGR4 WILD-TYPE 
           19.59            20.63 
[1] "0.1 - 58.4 (19.6)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "1.2"
D1264V2, 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       24       108         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SYNGR4 MUTATED           0          1          0          1        0
  SYNGR4 WILD-TYPE        19          9         41         30       35
                  vv
clus               STAGE IVA STAGE IVB
  SYNGR4 MUTATED           0         0
  SYNGR4 WILD-TYPE        13         1
D1264V3, multiclass
            clus
vv           SYNGR4 MUTATED SYNGR4 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               1              108
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              1                9
  STAGE IIIB              0               41
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SYNGR4 MUTATED     0   1   3   2
  SYNGR4 WILD-TYPE   9  67 245  39
D1264V4, multiclass
    clus
vv   SYNGR4 MUTATED SYNGR4 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              3              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
  SYNGR4 MUTATED     4   2   0
  SYNGR4 WILD-TYPE 216  78  66
D1264V5, multiclass
    clus
vv   SYNGR4 MUTATED SYNGR4 WILD-TYPE
  N0              4              216
  N1              2               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"
D1264V6, binary
                  cls
clus                 0   1
  SYNGR4 MUTATED     4   0
  SYNGR4 WILD-TYPE 279  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SYNGR4 MUTATED      4    0
  SYNGR4 WILD-TYPE  279   48
   clus
vv  SYNGR4 MUTATED SYNGR4 WILD-TYPE
  0              4              279
  1              0               48
[1] 2 2
[1] FALSE
D1264V7, 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
D1264V8, binary
                  cls
clus                 0   1
  SYNGR4 MUTATED     2   4
  SYNGR4 WILD-TYPE 315  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SYNGR4 MUTATED      2    4
  SYNGR4 WILD-TYPE  315   44
                               clus
vv                              SYNGR4 MUTATED SYNGR4 WILD-TYPE
  COLON ADENOCARCINOMA                       2              315
  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 251   2  22  21
D1264V9, multiclass
    clus
vv   SYNGR4 MUTATED SYNGR4 WILD-TYPE
  R0              6              251
  R1              0                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"
D1264V10, 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
D1264V11, 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(1265) Variable = USP1 MUTATION ANALYSIS
D1265V1, survival
                sevent
clus2              0   1
  USP1 MUTATED     8   1
  USP1 WILD-TYPE 274  72
  USP1 MUTATED USP1 WILD-TYPE 
             9            346 
  USP1 MUTATED USP1 WILD-TYPE 
             1             72 
$`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         0.33         0.10        12.00 
TCGA-CM-6171 TCGA-D5-6927 TCGA-F4-6570 
       14.04         9.44         6.18 

$`USP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       15.75        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.26         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  USP1 MUTATED USP1 WILD-TYPE 
           0.1            0.0 
  USP1 MUTATED USP1 WILD-TYPE 
         63.98         140.38 
  USP1 MUTATED USP1 WILD-TYPE 
          9.44          20.98 
[1] "0.1 - 64.0 (9.4)"   "0.0 - 140.4 (21.0)"
[1] "hr=" "1.2"
D1265V2, 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       24       104         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        19         10         40         30       35        13
                vv
clus             STAGE IVB
  USP1 MUTATED           0
  USP1 WILD-TYPE         1
D1265V3, multiclass
            clus
vv           USP1 MUTATED USP1 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             5            104
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            1             30
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  USP1 MUTATED     0   1   8   0
  USP1 WILD-TYPE   9  67 240  41
D1265V4, multiclass
    clus
vv   USP1 MUTATED USP1 WILD-TYPE
  T1            0              9
  T2            1             67
  T3            8            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
  USP1 MUTATED     7   1   1
  USP1 WILD-TYPE 213  79  65
D1265V5, multiclass
    clus
vv   USP1 MUTATED USP1 WILD-TYPE
  N0            7            213
  N1            1             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"
D1265V6, binary
                cls
clus               0   1
  USP1 MUTATED     8   0
  USP1 WILD-TYPE 275  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  USP1 MUTATED      8    0
  USP1 WILD-TYPE  275   48
   clus
vv  USP1 MUTATED USP1 WILD-TYPE
  0            8            275
  1            0             48
[1] 2 2
[1] FALSE
D1265V7, 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
D1265V8, binary
                cls
clus               0   1
  USP1 MUTATED     6   3
  USP1 WILD-TYPE 311  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  USP1 MUTATED      6    3
  USP1 WILD-TYPE  311   45
                               clus
vv                              USP1 MUTATED USP1 WILD-TYPE
  COLON ADENOCARCINOMA                     6            311
  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 250   2  22  19
D1265V9, multiclass
    clus
vv   USP1 MUTATED USP1 WILD-TYPE
  R0            7            250
  R1            0              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"
D1265V10, 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
D1265V11, 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(1266) Variable = VANGL1 MUTATION ANALYSIS
D1266V1, survival
                  sevent
clus2                0   1
  VANGL1 MUTATED     6   3
  VANGL1 WILD-TYPE 276  70
  VANGL1 MUTATED VANGL1 WILD-TYPE 
               9              346 
  VANGL1 MUTATED VANGL1 WILD-TYPE 
               3               70 
$`VANGL1 MUTATED`
TCGA-AA-3715 TCGA-AA-A00J TCGA-AZ-6600 TCGA-AZ-6601 TCGA-CM-4746 TCGA-CM-4752 
       19.04        18.05        12.10       100.01        37.02        13.02 
TCGA-D5-6535 TCGA-DM-A28H TCGA-G4-6588 
       15.12       117.07        26.17 

$`VANGL1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
        6.77        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
      119.93        35.97        60.79        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        91.79        46.75        52.80 

  VANGL1 MUTATED VANGL1 WILD-TYPE 
            12.1              0.0 
  VANGL1 MUTATED VANGL1 WILD-TYPE 
          117.07           140.38 
  VANGL1 MUTATED VANGL1 WILD-TYPE 
          19.040           20.235 
[1] "12.1 - 117.1 (19.0)" "0.0 - 140.4 (20.2)" 
[1] "hr=" "1.1"
D1266V2, 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       23       107         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  VANGL1 MUTATED           1          0          2          1        1
  VANGL1 WILD-TYPE        18         10         39         30       34
                  vv
clus               STAGE IVA STAGE IVB
  VANGL1 MUTATED           0         0
  VANGL1 WILD-TYPE        13         1
D1266V3, multiclass
            clus
vv           VANGL1 MUTATED VANGL1 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               2              107
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              1               30
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  VANGL1 MUTATED     0   1   7   2
  VANGL1 WILD-TYPE   9  67 241  39
D1266V4, multiclass
    clus
vv   VANGL1 MUTATED VANGL1 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              7              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
  VANGL1 MUTATED     5   3   2
  VANGL1 WILD-TYPE 215  77  64
D1266V5, multiclass
    clus
vv   VANGL1 MUTATED VANGL1 WILD-TYPE
  N0              5              215
  N1              3               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"
D1266V6, binary
                  cls
clus                 0   1
  VANGL1 MUTATED     8   1
  VANGL1 WILD-TYPE 275  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VANGL1 MUTATED      8    1
  VANGL1 WILD-TYPE  275   47
   clus
vv  VANGL1 MUTATED VANGL1 WILD-TYPE
  0              8              275
  1              1               47
[1] 2 2
[1] FALSE
D1266V7, 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
D1266V8, binary
                  cls
clus                 0   1
  VANGL1 MUTATED     9   1
  VANGL1 WILD-TYPE 308  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VANGL1 MUTATED      9    1
  VANGL1 WILD-TYPE  308   47
                               clus
vv                              VANGL1 MUTATED VANGL1 WILD-TYPE
  COLON ADENOCARCINOMA                       9              308
  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 251   2  22  20
D1266V9, multiclass
    clus
vv   VANGL1 MUTATED VANGL1 WILD-TYPE
  R0              6              251
  R1              0                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"
D1266V10, 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
D1266V11, 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(1267) Variable = C10ORF119 MUTATION ANALYSIS
D1267V1, survival
                     sevent
clus2                   0   1
  C10ORF119 MUTATED     6   2
  C10ORF119 WILD-TYPE 276  71
  C10ORF119 MUTATED C10ORF119 WILD-TYPE 
                  8                 347 
  C10ORF119 MUTATED C10ORF119 WILD-TYPE 
                  2                  71 
$`C10ORF119 MUTATED`
TCGA-A6-6780 TCGA-AA-3660 TCGA-AA-A010 TCGA-AD-6964 TCGA-AZ-4315 TCGA-CM-5344 
       20.12        78.08        34.98        10.88        58.39        22.03 
TCGA-DM-A1D4 TCGA-G4-6628 
       92.75        52.80 

$`C10ORF119 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        61.02         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       13.78        35.80        26.17        91.79        46.75 

  C10ORF119 MUTATED C10ORF119 WILD-TYPE 
              10.88                0.00 
  C10ORF119 MUTATED C10ORF119 WILD-TYPE 
              92.75              140.38 
  C10ORF119 MUTATED C10ORF119 WILD-TYPE 
              43.89               19.99 
[1] "10.9 - 92.8 (43.9)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.5"
D1267V2, 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       24       105         7         1
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C10ORF119 MUTATED           0          0          1          0        0
  C10ORF119 WILD-TYPE        19         10         40         31       35
                     vv
clus                  STAGE IVA STAGE IVB
  C10ORF119 MUTATED           0         0
  C10ORF119 WILD-TYPE        13         1
D1267V3, multiclass
            clus
vv           C10ORF119 MUTATED C10ORF119 WILD-TYPE
  STAGE I                    1                  63
  STAGE IA                   0                   1
  STAGE II                   1                  24
  STAGE IIA                  4                 105
  STAGE IIB                  1                   7
  STAGE IIC                  0                   1
  STAGE III                  0                  19
  STAGE IIIA                 0                  10
  STAGE IIIB                 1                  40
  STAGE IIIC                 0                  31
  STAGE IV                   0                  35
  STAGE IVA                  0                  13
  STAGE IVB                  0                   1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2  T3  T4
  C10ORF119 MUTATED     0   1   6   2
  C10ORF119 WILD-TYPE   9  67 242  39
D1267V4, multiclass
    clus
vv   C10ORF119 MUTATED C10ORF119 WILD-TYPE
  T1                 0                   9
  T2                 1                  67
  T3                 6                 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
  C10ORF119 MUTATED     7   1   1
  C10ORF119 WILD-TYPE 213  79  65
D1267V5, multiclass
    clus
vv   C10ORF119 MUTATED C10ORF119 WILD-TYPE
  N0                 7                 213
  N1                 1                  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"
D1267V6, binary
                     cls
clus                    0   1
  C10ORF119 MUTATED     7   0
  C10ORF119 WILD-TYPE 276  48
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C10ORF119 MUTATED      7    0
  C10ORF119 WILD-TYPE  276   48
   clus
vv  C10ORF119 MUTATED C10ORF119 WILD-TYPE
  0                 7                 276
  1                 0                  48
[1] 2 2
[1] FALSE
D1267V7, 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
D1267V8, binary
                     cls
clus                    0   1
  C10ORF119 MUTATED     8   1
  C10ORF119 WILD-TYPE 309  47
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C10ORF119 MUTATED      8    1
  C10ORF119 WILD-TYPE  309   47
                               clus
vv                              C10ORF119 MUTATED C10ORF119 WILD-TYPE
  COLON ADENOCARCINOMA                          8                 309
  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 251   2  22  21
D1267V9, multiclass
    clus
vv   C10ORF119 MUTATED C10ORF119 WILD-TYPE
  R0                 6                 251
  R1                 0                   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"
D1267V10, 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
D1267V11, 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(1268) Variable = FBXO38 MUTATION ANALYSIS
D1268V1, survival
                  sevent
clus2                0   1
  FBXO38 MUTATED    12   5
  FBXO38 WILD-TYPE 270  68
  FBXO38 MUTATED FBXO38 WILD-TYPE 
              17              338 
  FBXO38 MUTATED FBXO38 WILD-TYPE 
               5               68 
$`FBXO38 MUTATED`
TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3554 TCGA-AA-3666 TCGA-AA-3713 TCGA-AA-3811 
       22.06        19.66        17.95         2.01        19.04        10.06 
TCGA-AA-A00N TCGA-AD-6963 TCGA-AD-6964 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 
        4.01        27.42        10.88        58.39         0.33         0.10 
TCGA-CK-4952 TCGA-CK-5916 TCGA-CM-6168 TCGA-D5-6533 TCGA-DM-A28K 
       15.62        21.14        12.99         1.32        98.24 

$`FBXO38 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       26.99        19.04        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 
        1.35        17.56       102.44        40.34        49.08        51.32 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
      117.07         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  FBXO38 MUTATED FBXO38 WILD-TYPE 
             0.1              0.0 
  FBXO38 MUTATED FBXO38 WILD-TYPE 
           98.24           140.38 
  FBXO38 MUTATED FBXO38 WILD-TYPE 
          15.620           20.995 
[1] "0.1 - 98.2 (15.6)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.8"
D1268V2, 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       25       102         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FBXO38 MUTATED           3          0          1          1        1
  FBXO38 WILD-TYPE        16         10         40         30       34
                  vv
clus               STAGE IVA STAGE IVB
  FBXO38 MUTATED           0         0
  FBXO38 WILD-TYPE        13         1
D1268V3, multiclass
            clus
vv           FBXO38 MUTATED FBXO38 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               7              102
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               3               16
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              1               30
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FBXO38 MUTATED     1   0  11   6
  FBXO38 WILD-TYPE   8  68 237  35
D1268V4, multiclass
    clus
vv   FBXO38 MUTATED FBXO38 WILD-TYPE
  T1              1                8
  T2              0               68
  T3             11              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
  FBXO38 MUTATED    13   2   3
  FBXO38 WILD-TYPE 207  78  63
D1268V5, multiclass
    clus
vv   FBXO38 MUTATED FBXO38 WILD-TYPE
  N0             13              207
  N1              2               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"
D1268V6, binary
                  cls
clus                 0   1
  FBXO38 MUTATED    13   1
  FBXO38 WILD-TYPE 270  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO38 MUTATED     13    1
  FBXO38 WILD-TYPE  270   47
   clus
vv  FBXO38 MUTATED FBXO38 WILD-TYPE
  0             13              270
  1              1               47
[1] 2 2
[1] FALSE
D1268V7, 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
D1268V8, binary
                  cls
clus                 0   1
  FBXO38 MUTATED    13   5
  FBXO38 WILD-TYPE 304  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO38 MUTATED     13    5
  FBXO38 WILD-TYPE  304   43
                               clus
vv                              FBXO38 MUTATED FBXO38 WILD-TYPE
  COLON ADENOCARCINOMA                      13              304
  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 248   2  21  16
D1268V9, multiclass
    clus
vv   FBXO38 MUTATED FBXO38 WILD-TYPE
  R0              9              248
  R1              0                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"
D1268V10, 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
D1268V11, 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(1269) Variable = CD47 MUTATION ANALYSIS
D1269V1, survival
                sevent
clus2              0   1
  CD47 MUTATED     6   0
  CD47 WILD-TYPE 276  73
  CD47 MUTATED CD47 WILD-TYPE 
             6            349 
  CD47 MUTATED CD47 WILD-TYPE 
             0             73 
$`CD47 MUTATED`
TCGA-AA-3947 TCGA-AA-A010 TCGA-CA-6717 TCGA-CK-4952 TCGA-CM-5868 TCGA-D5-6541 
       33.01        34.98         0.33        15.62        17.03        15.58 

$`CD47 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       40.34        49.08        51.32        21.99        21.14         2.93 
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        16.01 
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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        16.14         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  CD47 MUTATED CD47 WILD-TYPE 
          0.33           0.00 
  CD47 MUTATED CD47 WILD-TYPE 
         34.98         140.38 
  CD47 MUTATED CD47 WILD-TYPE 
        16.325         20.280 
[1] "0.3 - 35.0 (16.3)"  "0.0 - 140.4 (20.3)"
[1] "hr="     "9100000"
D1269V2, 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       24       107         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CD47 MUTATED           2          0          0          0        0         1
  CD47 WILD-TYPE        17         10         41         31       35        12
                vv
clus             STAGE IVB
  CD47 MUTATED           0
  CD47 WILD-TYPE         1
D1269V3, multiclass
            clus
vv           CD47 MUTATED CD47 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             2            107
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             2             17
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  68 245  36
D1269V4, multiclass
    clus
vv   CD47 MUTATED CD47 WILD-TYPE
  T1            0              9
  T2            0             68
  T3            3            245
  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  79  64
D1269V5, multiclass
    clus
vv   CD47 MUTATED CD47 WILD-TYPE
  N0            5            215
  N1            1             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"
D1269V6, binary
                cls
clus               0   1
  CD47 MUTATED     7   1
  CD47 WILD-TYPE 276  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD47 MUTATED      7    1
  CD47 WILD-TYPE  276   47
   clus
vv  CD47 MUTATED CD47 WILD-TYPE
  0            7            276
  1            1             47
[1] 2 2
[1] FALSE
D1269V7, 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
D1269V8, binary
                cls
clus               0   1
  CD47 MUTATED     5   3
  CD47 WILD-TYPE 312  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD47 MUTATED      5    3
  CD47 WILD-TYPE  312   45
                               clus
vv                              CD47 MUTATED CD47 WILD-TYPE
  COLON ADENOCARCINOMA                     5            312
  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 251   2  22  19
D1269V9, multiclass
    clus
vv   CD47 MUTATED CD47 WILD-TYPE
  R0            6            251
  R1            0              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"
D1269V10, 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
D1269V11, 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(1270) Variable = FAM199X MUTATION ANALYSIS
D1270V1, survival
                   sevent
clus2                 0   1
  FAM199X MUTATED     6   4
  FAM199X WILD-TYPE 276  69
  FAM199X MUTATED FAM199X WILD-TYPE 
               10               345 
  FAM199X MUTATED FAM199X WILD-TYPE 
                4                69 
$`FAM199X MUTATED`
TCGA-AA-3866 TCGA-AA-3877 TCGA-AZ-6599 TCGA-CM-6162 TCGA-CM-6169 TCGA-D5-6928 
       17.03        31.00         6.77        12.00        13.02        11.64 
TCGA-DM-A1DA TCGA-DM-A285 TCGA-F4-6459 TCGA-G4-6307 
        7.50         6.12         8.61        55.04 

$`FAM199X WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       53.00        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-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        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        53.62        44.68        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  FAM199X MUTATED FAM199X WILD-TYPE 
             6.12              0.00 
  FAM199X MUTATED FAM199X WILD-TYPE 
            55.04            140.38 
  FAM199X MUTATED FAM199X WILD-TYPE 
            11.82             20.98 
[1] "6.1 - 55.0 (11.8)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "2.7"
D1270V2, 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       25       107         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM199X MUTATED           0          0          3          1        1
  FAM199X WILD-TYPE        19         10         38         30       34
                   vv
clus                STAGE IVA STAGE IVB
  FAM199X MUTATED           0         0
  FAM199X WILD-TYPE        13         1
D1270V3, multiclass
            clus
vv           FAM199X MUTATED FAM199X WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                2               107
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               3                38
  STAGE IIIC               1                30
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  FAM199X MUTATED     1   2   7   0
  FAM199X WILD-TYPE   8  66 241  41
D1270V4, multiclass
    clus
vv   FAM199X MUTATED FAM199X WILD-TYPE
  T1               1                 8
  T2               2                66
  T3               7               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
  FAM199X MUTATED     5   2   3
  FAM199X WILD-TYPE 215  78  63
D1270V5, multiclass
    clus
vv   FAM199X MUTATED FAM199X WILD-TYPE
  N0               5               215
  N1               2                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"
D1270V6, binary
                   cls
clus                  0   1
  FAM199X MUTATED     8   1
  FAM199X WILD-TYPE 275  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM199X MUTATED      8    1
  FAM199X WILD-TYPE  275   47
   clus
vv  FAM199X MUTATED FAM199X WILD-TYPE
  0               8               275
  1               1                47
[1] 2 2
[1] FALSE
D1270V7, 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
D1270V8, binary
                   cls
clus                  0   1
  FAM199X MUTATED     6   4
  FAM199X WILD-TYPE 311  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM199X MUTATED      6    4
  FAM199X WILD-TYPE  311   44
                               clus
vv                              FAM199X MUTATED FAM199X WILD-TYPE
  COLON ADENOCARCINOMA                        6               311
  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 250   2  22  21
D1270V9, multiclass
    clus
vv   FAM199X MUTATED FAM199X WILD-TYPE
  R0               7               250
  R1               0                 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"
D1270V10, 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
D1270V11, 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(1271) Variable = DPP8 MUTATION ANALYSIS
D1271V1, survival
                sevent
clus2              0   1
  DPP8 MUTATED    10   2
  DPP8 WILD-TYPE 272  71
  DPP8 MUTATED DPP8 WILD-TYPE 
            12            343 
  DPP8 MUTATED DPP8 WILD-TYPE 
             2             71 
$`DPP8 MUTATED`
TCGA-AA-3510 TCGA-AA-3715 TCGA-AA-3864 TCGA-AA-3949 TCGA-AA-3977 TCGA-AA-A010 
       63.98        19.04        53.00        26.01        25.02        34.98 
TCGA-AA-A01S TCGA-AA-A03J TCGA-AD-5900 TCGA-AZ-6598 TCGA-CM-6162 TCGA-G4-6304 
        1.02        40.96         0.07        49.41        12.00        53.62 

$`DPP8 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
       35.01        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       41.00        39.98        18.05        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  DPP8 MUTATED DPP8 WILD-TYPE 
          0.07           0.00 
  DPP8 MUTATED DPP8 WILD-TYPE 
         63.98         140.38 
  DPP8 MUTATED DPP8 WILD-TYPE 
        30.495         20.020 
[1] "0.1 - 64.0 (30.5)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1.6"
D1271V2, 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       21       108         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        18         10         39         31       35        13
                vv
clus             STAGE IVB
  DPP8 MUTATED           0
  DPP8 WILD-TYPE         1
D1271V3, multiclass
            clus
vv           DPP8 MUTATED DPP8 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              4             21
  STAGE IIA             1            108
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            2             39
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  DPP8 MUTATED     0   3   8   2
  DPP8 WILD-TYPE   9  65 240  39
D1271V4, multiclass
    clus
vv   DPP8 MUTATED DPP8 WILD-TYPE
  T1            0              9
  T2            3             65
  T3            8            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
  DPP8 MUTATED    10   3   0
  DPP8 WILD-TYPE 210  77  66
D1271V5, multiclass
    clus
vv   DPP8 MUTATED DPP8 WILD-TYPE
  N0           10            210
  N1            3             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"
D1271V6, binary
                cls
clus               0   1
  DPP8 MUTATED    10   0
  DPP8 WILD-TYPE 273  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  DPP8 MUTATED     10    0
  DPP8 WILD-TYPE  273   48
   clus
vv  DPP8 MUTATED DPP8 WILD-TYPE
  0           10            273
  1            0             48
[1] 2 2
[1] FALSE
D1271V7, 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
D1271V8, binary
                cls
clus               0   1
  DPP8 MUTATED    10   3
  DPP8 WILD-TYPE 307  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  DPP8 MUTATED     10    3
  DPP8 WILD-TYPE  307   45
                               clus
vv                              DPP8 MUTATED DPP8 WILD-TYPE
  COLON ADENOCARCINOMA                    10            307
  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 246   2  22  21
D1271V9, multiclass
    clus
vv   DPP8 MUTATED DPP8 WILD-TYPE
  R0           11            246
  R1            0              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"
D1271V10, 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
D1271V11, 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(1272) Variable = TRIM45 MUTATION ANALYSIS
D1272V1, survival
                  sevent
clus2                0   1
  TRIM45 MUTATED    12   2
  TRIM45 WILD-TYPE 270  71
  TRIM45 MUTATED TRIM45 WILD-TYPE 
              14              341 
  TRIM45 MUTATED TRIM45 WILD-TYPE 
               2               71 
$`TRIM45 MUTATED`
TCGA-A6-2672 TCGA-A6-6780 TCGA-AA-3518 TCGA-AA-3811 TCGA-AA-3864 TCGA-AA-A00J 
       46.65        20.12         1.02        10.06        53.00        18.05 
TCGA-AD-6895 TCGA-CA-6717 TCGA-CM-4743 TCGA-CM-5349 TCGA-CM-5861 TCGA-DM-A28K 
        0.72         0.33        23.05        30.08        15.02        98.24 
TCGA-F4-6570 TCGA-G4-6588 
        6.18        26.17 

$`TRIM45 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 
       63.98         6.97         1.02        13.02        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        19.04        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21        56.55         0.79         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14         2.93         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        16.01 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        13.38        13.45        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        91.79        46.75        52.80 

  TRIM45 MUTATED TRIM45 WILD-TYPE 
            0.33             0.00 
  TRIM45 MUTATED TRIM45 WILD-TYPE 
           98.24           140.38 
  TRIM45 MUTATED TRIM45 WILD-TYPE 
          19.085           20.280 
[1] "0.3 - 98.2 (19.1)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.4"
D1272V2, 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       24       100         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRIM45 MUTATED           1          0          2          0        0
  TRIM45 WILD-TYPE        18         10         39         31       35
                  vv
clus               STAGE IVA STAGE IVB
  TRIM45 MUTATED           0         0
  TRIM45 WILD-TYPE        13         1
D1272V3, multiclass
            clus
vv           TRIM45 MUTATED TRIM45 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               9              100
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TRIM45 MUTATED     0   0  13   1
  TRIM45 WILD-TYPE   9  68 235  40
D1272V4, multiclass
    clus
vv   TRIM45 MUTATED TRIM45 WILD-TYPE
  T1              0                9
  T2              0               68
  T3             13              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
  TRIM45 MUTATED    10   3   1
  TRIM45 WILD-TYPE 210  77  65
D1272V5, multiclass
    clus
vv   TRIM45 MUTATED TRIM45 WILD-TYPE
  N0             10              210
  N1              3               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"
D1272V6, binary
                  cls
clus                 0   1
  TRIM45 MUTATED    12   0
  TRIM45 WILD-TYPE 271  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM45 MUTATED     12    0
  TRIM45 WILD-TYPE  271   48
   clus
vv  TRIM45 MUTATED TRIM45 WILD-TYPE
  0             12              271
  1              0               48
[1] 2 2
[1] FALSE
D1272V7, 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
D1272V8, binary
                  cls
clus                 0   1
  TRIM45 MUTATED    10   4
  TRIM45 WILD-TYPE 307  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM45 MUTATED     10    4
  TRIM45 WILD-TYPE  307   44
                               clus
vv                              TRIM45 MUTATED TRIM45 WILD-TYPE
  COLON ADENOCARCINOMA                      10              307
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TRIM45 MUTATED    10   0   0   1
  TRIM45 WILD-TYPE 247   2  22  20
D1272V9, multiclass
    clus
vv   TRIM45 MUTATED TRIM45 WILD-TYPE
  R0             10              247
  R1              0                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"
D1272V10, 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
D1272V11, 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(1273) Variable = KRTAP12-3 MUTATION ANALYSIS
D1273V1, survival
                     sevent
clus2                   0   1
  KRTAP12-3 MUTATED     2   1
  KRTAP12-3 WILD-TYPE 280  72
  KRTAP12-3 MUTATED KRTAP12-3 WILD-TYPE 
                  3                 352 
  KRTAP12-3 MUTATED KRTAP12-3 WILD-TYPE 
                  1                  72 
$`KRTAP12-3 MUTATED`
TCGA-AZ-6599 TCGA-D5-6931 TCGA-G4-6586 
        6.77        12.00        35.80 

$`KRTAP12-3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41        49.41        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  KRTAP12-3 MUTATED KRTAP12-3 WILD-TYPE 
               6.77                0.00 
  KRTAP12-3 MUTATED KRTAP12-3 WILD-TYPE 
              35.80              140.38 
  KRTAP12-3 MUTATED KRTAP12-3 WILD-TYPE 
             12.000              20.235 
[1] "6.8 - 35.8 (12.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2.5"
D1273V2, 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       25       108         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        19         10         41         30       35
                     vv
clus                  STAGE IVA STAGE IVB
  KRTAP12-3 MUTATED           0         0
  KRTAP12-3 WILD-TYPE        13         1
D1273V3, multiclass
            clus
vv           KRTAP12-3 MUTATED KRTAP12-3 WILD-TYPE
  STAGE I                    1                  63
  STAGE IA                   0                   1
  STAGE II                   0                  25
  STAGE IIA                  1                 108
  STAGE IIB                  0                   8
  STAGE IIC                  0                   1
  STAGE III                  0                  19
  STAGE IIIA                 0                  10
  STAGE IIIB                 0                  41
  STAGE IIIC                 1                  30
  STAGE IV                   0                  35
  STAGE IVA                  0                  13
  STAGE IVB                  0                   1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2  T3  T4
  KRTAP12-3 MUTATED     0   1   1   1
  KRTAP12-3 WILD-TYPE   9  67 247  40
D1273V4, multiclass
    clus
vv   KRTAP12-3 MUTATED KRTAP12-3 WILD-TYPE
  T1                 0                   9
  T2                 1                  67
  T3                 1                 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
  KRTAP12-3 MUTATED     2   0   1
  KRTAP12-3 WILD-TYPE 218  80  65
D1273V5, multiclass
    clus
vv   KRTAP12-3 MUTATED KRTAP12-3 WILD-TYPE
  N0                 2                 218
  N1                 0                  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"
D1273V6, binary
                     cls
clus                    0   1
  KRTAP12-3 MUTATED     2   0
  KRTAP12-3 WILD-TYPE 281  48
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KRTAP12-3 MUTATED      2    0
  KRTAP12-3 WILD-TYPE  281   48
   clus
vv  KRTAP12-3 MUTATED KRTAP12-3 WILD-TYPE
  0                 2                 281
  1                 0                  48
[1] 2 2
[1] FALSE
D1273V7, 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
D1273V8, binary
                     cls
clus                    0   1
  KRTAP12-3 MUTATED     3   0
  KRTAP12-3 WILD-TYPE 314  48
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KRTAP12-3 MUTATED      3    0
  KRTAP12-3 WILD-TYPE  314   48
                               clus
vv                              KRTAP12-3 MUTATED KRTAP12-3 WILD-TYPE
  COLON ADENOCARCINOMA                          3                 314
  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 255   2  22  21
D1273V9, multiclass
[1] "Remove cluster labels:" "KRTAP12-3 MUTATED"     
clus
  KRTAP12-3 MUTATED KRTAP12-3 WILD-TYPE 
                  2                 300 
         TCGA-A6-2671          TCGA-A6-2672          TCGA-A6-2674 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-A6-2676          TCGA-A6-2677          TCGA-A6-2678 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-A6-2683          TCGA-A6-3807          TCGA-A6-3808 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-A6-3809          TCGA-A6-3810          TCGA-A6-5657 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-A6-5659          TCGA-A6-5661          TCGA-A6-5665 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-A6-6781          TCGA-AA-3489          TCGA-AA-3492 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3496          TCGA-AA-3502          TCGA-AA-3510 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3511          TCGA-AA-3514          TCGA-AA-3517 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3518          TCGA-AA-3519          TCGA-AA-3520 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3521          TCGA-AA-3522          TCGA-AA-3524 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3525          TCGA-AA-3526          TCGA-AA-3527 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3529          TCGA-AA-3530          TCGA-AA-3531 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3532          TCGA-AA-3534          TCGA-AA-3538 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3542          TCGA-AA-3543          TCGA-AA-3544 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3548          TCGA-AA-3549          TCGA-AA-3552 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3553          TCGA-AA-3554          TCGA-AA-3555 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3556          TCGA-AA-3558          TCGA-AA-3560 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3561          TCGA-AA-3562          TCGA-AA-3655 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3660          TCGA-AA-3662          TCGA-AA-3663 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3664          TCGA-AA-3666          TCGA-AA-3667 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3672          TCGA-AA-3673          TCGA-AA-3678 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3679          TCGA-AA-3680          TCGA-AA-3681 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3684          TCGA-AA-3685          TCGA-AA-3688 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3692          TCGA-AA-3693          TCGA-AA-3695 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3696          TCGA-AA-3697          TCGA-AA-3710 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3712          TCGA-AA-3713          TCGA-AA-3715 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3811          TCGA-AA-3812          TCGA-AA-3814 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3815          TCGA-AA-3818          TCGA-AA-3819 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3821          TCGA-AA-3831          TCGA-AA-3833 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3837          TCGA-AA-3842          TCGA-AA-3844 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3845          TCGA-AA-3846          TCGA-AA-3848 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3850          TCGA-AA-3851          TCGA-AA-3852 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3854          TCGA-AA-3855          TCGA-AA-3856 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3858          TCGA-AA-3860          TCGA-AA-3861 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3864          TCGA-AA-3866          TCGA-AA-3867 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3869          TCGA-AA-3870          TCGA-AA-3872 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3875          TCGA-AA-3877          TCGA-AA-3930 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3939          TCGA-AA-3941          TCGA-AA-3947 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3949          TCGA-AA-3950          TCGA-AA-3952 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3955          TCGA-AA-3956          TCGA-AA-3968 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3971          TCGA-AA-3972          TCGA-AA-3973 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3975          TCGA-AA-3976          TCGA-AA-3979 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3984          TCGA-AA-3986          TCGA-AA-3989 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3994          TCGA-AA-A004          TCGA-AA-A00A 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-A00D          TCGA-AA-A00E          TCGA-AA-A00F 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-A00J          TCGA-AA-A00K          TCGA-AA-A00L 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-A00N          TCGA-AA-A00O          TCGA-AA-A00Q 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-A00R          TCGA-AA-A00U          TCGA-AA-A00W 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-A00Z          TCGA-AA-A010          TCGA-AA-A017 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-A01D          TCGA-AA-A01F          TCGA-AA-A01G 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-A01I          TCGA-AA-A01K          TCGA-AA-A01P 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-A01Q          TCGA-AA-A01R          TCGA-AA-A01S 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-A01T          TCGA-AA-A01V          TCGA-AA-A01X 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-A01Z          TCGA-AA-A022          TCGA-AA-A024 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-A029          TCGA-AA-A02F          TCGA-AA-A02H 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-A02J          TCGA-AA-A02K          TCGA-AA-A02O 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-A02W          TCGA-AA-A02Y          TCGA-AA-A03F 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-A03J          TCGA-AD-5900          TCGA-AD-6548 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AD-6888          TCGA-AU-3779          TCGA-AU-6004 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AY-4070          TCGA-AY-4071          TCGA-AY-5543 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AY-6196          TCGA-AY-6197          TCGA-AY-6386 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AZ-4315          TCGA-AZ-4681          TCGA-AZ-4682 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-CA-5254          TCGA-CA-5255          TCGA-CA-5796 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-CA-5797          TCGA-CA-6715          TCGA-CA-6716 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-CA-6717          TCGA-CA-6718          TCGA-CA-6719 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-CK-4947          TCGA-CK-4948          TCGA-CK-4950 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-CK-4952          TCGA-CK-5912          TCGA-CK-5913 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-CK-5914          TCGA-CK-5915          TCGA-CK-5916 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-CK-6746          TCGA-CK-6747          TCGA-CK-6748 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-CK-6751          TCGA-CM-4743          TCGA-CM-4744 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-CM-4746          TCGA-CM-4747          TCGA-CM-4752 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-CM-5341          TCGA-CM-5344          TCGA-CM-5348 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-CM-5349          TCGA-CM-5860          TCGA-CM-5861 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-CM-5862          TCGA-CM-5863          TCGA-CM-5864 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-CM-5868          TCGA-CM-6161          TCGA-CM-6162 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-CM-6163          TCGA-CM-6164          TCGA-CM-6165 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-CM-6166          TCGA-CM-6167          TCGA-CM-6168 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-CM-6169          TCGA-CM-6170          TCGA-CM-6171 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-CM-6172          TCGA-CM-6674          TCGA-CM-6675 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-CM-6676          TCGA-CM-6677          TCGA-CM-6678 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-CM-6679          TCGA-CM-6680          TCGA-D5-5537 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-D5-5538          TCGA-D5-5539          TCGA-D5-5540 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-D5-5541          TCGA-D5-6529          TCGA-D5-6532 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-D5-6533          TCGA-D5-6534          TCGA-D5-6535 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-D5-6536          TCGA-D5-6537          TCGA-D5-6538 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-D5-6539          TCGA-D5-6540          TCGA-D5-6541 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-D5-6898          TCGA-D5-6920          TCGA-D5-6922 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-D5-6923          TCGA-D5-6924          TCGA-D5-6926 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-D5-6927          TCGA-D5-6928          TCGA-D5-6929 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-D5-6930          TCGA-D5-6932          TCGA-D5-7000 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-F4-6459          TCGA-F4-6460          TCGA-F4-6569 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-F4-6570          TCGA-F4-6703          TCGA-F4-6704 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-F4-6805          TCGA-F4-6806          TCGA-F4-6807 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-F4-6808          TCGA-F4-6809          TCGA-F4-6854 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-F4-6855          TCGA-F4-6856          TCGA-G4-6293 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-G4-6299          TCGA-G4-6303          TCGA-G4-6304 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-G4-6306          TCGA-G4-6307          TCGA-G4-6309 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-G4-6310          TCGA-G4-6315          TCGA-G4-6317 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-G4-6321          TCGA-G4-6323          TCGA-G4-6588 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-G4-6625          TCGA-G4-6626          TCGA-G4-6628 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
D1273V10, 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
D1273V11, 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(1274) Variable = KIF13A MUTATION ANALYSIS
D1274V1, survival
                  sevent
clus2                0   1
  KIF13A MUTATED    17   3
  KIF13A WILD-TYPE 265  70
  KIF13A MUTATED KIF13A WILD-TYPE 
              20              335 
  KIF13A MUTATED KIF13A WILD-TYPE 
               3               70 
$`KIF13A MUTATED`
TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3680 TCGA-AA-3688 TCGA-AA-3713 TCGA-AA-3966 
       22.06        19.66        11.01        19.00        19.04         2.01 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A02O TCGA-AD-5900 TCGA-AY-6197 TCGA-CA-6717 
        4.01        34.98         0.92         0.07        21.44         0.33 
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         1.51 
TCGA-D5-6932 TCGA-DM-A1HB 
       11.38       135.65 

$`KIF13A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
       15.02         5.98        37.05        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       26.01        24.00         2.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02W TCGA-AA-A02Y 
       39.98         2.01         5.03        14.01        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99         2.93         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        16.01         5.03        15.02        15.02        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        12.26        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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-D5-7000 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-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  KIF13A MUTATED KIF13A WILD-TYPE 
            0.07             0.00 
  KIF13A MUTATED KIF13A WILD-TYPE 
          135.65           140.38 
  KIF13A MUTATED KIF13A WILD-TYPE 
           17.01            21.01 
[1] "0.1 - 135.7 (17.0)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.1"
D1274V2, 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       24       100         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIF13A MUTATED           0          2          1          1        3
  KIF13A WILD-TYPE        19          8         40         30       32
                  vv
clus               STAGE IVA STAGE IVB
  KIF13A MUTATED           0         0
  KIF13A WILD-TYPE        13         1
D1274V3, multiclass
            clus
vv           KIF13A MUTATED KIF13A WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               9              100
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              2                8
  STAGE IIIB              1               40
  STAGE IIIC              1               30
  STAGE IV                3               32
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  KIF13A MUTATED     1   1  15   4
  KIF13A WILD-TYPE   8  67 233  37
D1274V4, multiclass
    clus
vv   KIF13A MUTATED KIF13A WILD-TYPE
  T1              1                8
  T2              1               67
  T3             15              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
  KIF13A MUTATED    15   5   1
  KIF13A WILD-TYPE 205  75  65
D1274V5, multiclass
    clus
vv   KIF13A MUTATED KIF13A WILD-TYPE
  N0             15              205
  N1              5               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"
D1274V6, binary
                  cls
clus                 0   1
  KIF13A MUTATED    14   3
  KIF13A WILD-TYPE 269  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF13A MUTATED     14    3
  KIF13A WILD-TYPE  269   45
   clus
vv  KIF13A MUTATED KIF13A WILD-TYPE
  0             14              269
  1              3               45
[1] 2 2
[1] FALSE
D1274V7, 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
D1274V8, binary
                  cls
clus                 0   1
  KIF13A MUTATED    14   7
  KIF13A WILD-TYPE 303  41
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF13A MUTATED     14    7
  KIF13A WILD-TYPE  303   41
                               clus
vv                              KIF13A MUTATED KIF13A WILD-TYPE
  COLON ADENOCARCINOMA                      14              303
  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 244   2  19  18
D1274V9, multiclass
    clus
vv   KIF13A MUTATED KIF13A WILD-TYPE
  R0             13              244
  R1              0                2
  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"
D1274V10, 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
D1274V11, 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(1275) Variable = PTPRR MUTATION ANALYSIS
D1275V1, survival
                 sevent
clus2               0   1
  PTPRR MUTATED     7   3
  PTPRR WILD-TYPE 275  70
  PTPRR MUTATED PTPRR WILD-TYPE 
             10             345 
  PTPRR MUTATED PTPRR WILD-TYPE 
              3              70 
$`PTPRR MUTATED`
TCGA-A6-6141 TCGA-AA-3663 TCGA-AA-3845 TCGA-AZ-4315 TCGA-AZ-6599 TCGA-AZ-6601 
        8.38         6.97         0.00        58.39         6.77       100.01 
TCGA-CM-4743 TCGA-CM-6162 TCGA-CM-6171 TCGA-D5-6538 
       23.05        12.00        14.04        17.13 

$`PTPRR WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02        14.93        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 
       22.36        62.79        61.41        49.41        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        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-6172 
       21.99        14.99        12.99        13.02        15.02        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        12.49        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  PTPRR MUTATED PTPRR WILD-TYPE 
              0               0 
  PTPRR MUTATED PTPRR WILD-TYPE 
         100.01          140.38 
  PTPRR MUTATED PTPRR WILD-TYPE 
          13.02           20.98 
[1] "0.0 - 100.0 (13.0)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.4"
D1275V2, 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       23       105         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        19         10         39         31       35        13
                 vv
clus              STAGE IVB
  PTPRR MUTATED           0
  PTPRR WILD-TYPE         1
D1275V3, multiclass
            clus
vv           PTPRR MUTATED PTPRR WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              4             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PTPRR MUTATED     0   2   8   0
  PTPRR WILD-TYPE   9  66 240  41
D1275V4, multiclass
    clus
vv   PTPRR MUTATED PTPRR WILD-TYPE
  T1             0               9
  T2             2              66
  T3             8             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
  PTPRR MUTATED     8   1   1
  PTPRR WILD-TYPE 212  79  65
D1275V5, multiclass
    clus
vv   PTPRR MUTATED PTPRR WILD-TYPE
  N0             8             212
  N1             1              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"
D1275V6, binary
                 cls
clus                0   1
  PTPRR MUTATED     9   0
  PTPRR WILD-TYPE 274  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRR MUTATED      9    0
  PTPRR WILD-TYPE  274   48
   clus
vv  PTPRR MUTATED PTPRR WILD-TYPE
  0             9             274
  1             0              48
[1] 2 2
[1] FALSE
D1275V7, 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
D1275V8, binary
                 cls
clus                0   1
  PTPRR MUTATED     9   1
  PTPRR WILD-TYPE 308  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRR MUTATED      9    1
  PTPRR WILD-TYPE  308   47
                               clus
vv                              PTPRR MUTATED PTPRR WILD-TYPE
  COLON ADENOCARCINOMA                      9             308
  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 250   2  22  21
D1275V9, multiclass
    clus
vv   PTPRR MUTATED PTPRR WILD-TYPE
  R0             7             250
  R1             0               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"
D1275V10, 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
D1275V11, 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(1276) Variable = CIZ1 MUTATION ANALYSIS
D1276V1, survival
                sevent
clus2              0   1
  CIZ1 MUTATED    12   2
  CIZ1 WILD-TYPE 270  71
  CIZ1 MUTATED CIZ1 WILD-TYPE 
            14            341 
  CIZ1 MUTATED CIZ1 WILD-TYPE 
             2             71 
$`CIZ1 MUTATED`
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6653 TCGA-AA-3542 TCGA-AA-3558 TCGA-AA-3715 
       22.06        32.71        24.39        12.99        20.98        19.04 
TCGA-AA-3877 TCGA-AA-3980 TCGA-AA-3982 TCGA-AD-5900 TCGA-AY-5543 TCGA-AZ-6598 
       31.00        27.02        27.02         0.07        15.75        49.41 
TCGA-CK-6751 TCGA-CM-6162 
      124.27        12.00 

$`CIZ1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.09        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       24.16        21.76        24.69        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 
       19.07        34.03        29.00        29.00        26.01         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       29.95        23.01        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-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-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 
       51.32        21.99        21.14         2.93         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        16.01        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  CIZ1 MUTATED CIZ1 WILD-TYPE 
          0.07           0.00 
  CIZ1 MUTATED CIZ1 WILD-TYPE 
        124.27         140.38 
  CIZ1 MUTATED CIZ1 WILD-TYPE 
        23.225         20.020 
[1] "0.1 - 124.3 (23.2)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.6"
D1276V2, 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       22       108         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        19         10         39         30       35        12
                vv
clus             STAGE IVB
  CIZ1 MUTATED           0
  CIZ1 WILD-TYPE         1
D1276V3, multiclass
            clus
vv           CIZ1 MUTATED CIZ1 WILD-TYPE
  STAGE I               6             58
  STAGE IA              0              1
  STAGE II              3             22
  STAGE IIA             1            108
  STAGE IIB             0              8
  STAGE IIC             1              0
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            2             39
  STAGE IIIC            1             30
  STAGE IV              0             35
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  63 241  39
D1276V4, multiclass
    clus
vv   CIZ1 MUTATED CIZ1 WILD-TYPE
  T1            1              8
  T2            5             63
  T3            7            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
  CIZ1 MUTATED    11   3   1
  CIZ1 WILD-TYPE 209  77  65
D1276V5, multiclass
    clus
vv   CIZ1 MUTATED CIZ1 WILD-TYPE
  N0           11            209
  N1            3             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"
D1276V6, binary
                cls
clus               0   1
  CIZ1 MUTATED    11   1
  CIZ1 WILD-TYPE 272  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  CIZ1 MUTATED     11    1
  CIZ1 WILD-TYPE  272   47
   clus
vv  CIZ1 MUTATED CIZ1 WILD-TYPE
  0           11            272
  1            1             47
[1] 2 2
[1] FALSE
D1276V7, 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
D1276V8, binary
                cls
clus               0   1
  CIZ1 MUTATED    11   4
  CIZ1 WILD-TYPE 306  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  CIZ1 MUTATED     11    4
  CIZ1 WILD-TYPE  306   44
                               clus
vv                              CIZ1 MUTATED CIZ1 WILD-TYPE
  COLON ADENOCARCINOMA                    11            306
  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 249   2  21  20
D1276V9, multiclass
    clus
vv   CIZ1 MUTATED CIZ1 WILD-TYPE
  R0            8            249
  R1            0              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"
D1276V10, 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
D1276V11, 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(1277) Variable = TBX4 MUTATION ANALYSIS
D1277V1, survival
                sevent
clus2              0   1
  TBX4 MUTATED     8   3
  TBX4 WILD-TYPE 274  70
  TBX4 MUTATED TBX4 WILD-TYPE 
            11            344 
  TBX4 MUTATED TBX4 WILD-TYPE 
             3             70 
$`TBX4 MUTATED`
TCGA-A6-5661 TCGA-A6-6653 TCGA-AA-3492 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-A00N 
       33.53        24.39         3.02        53.00        31.00         4.01 
TCGA-AA-A010 TCGA-AZ-5407 TCGA-AZ-6601 TCGA-CA-5254 TCGA-CA-6718 
       34.98        61.41       100.01         2.24         0.10 

$`TBX4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 
        1.41         5.13        83.80        22.36        62.79        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        1.94         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.33         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  TBX4 MUTATED TBX4 WILD-TYPE 
           0.1            0.0 
  TBX4 MUTATED TBX4 WILD-TYPE 
        100.01         140.38 
  TBX4 MUTATED TBX4 WILD-TYPE 
         31.00          20.07 
[1] "0.1 - 100.0 (31.0)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.1"
D1277V2, 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       22       106         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        19         10         41         31       35        13
                vv
clus             STAGE IVB
  TBX4 MUTATED           0
  TBX4 WILD-TYPE         1
D1277V3, multiclass
            clus
vv           TBX4 MUTATED TBX4 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              3             22
  STAGE IIA             3            106
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TBX4 MUTATED     2   1   6   2
  TBX4 WILD-TYPE   7  67 242  39
D1277V4, multiclass
    clus
vv   TBX4 MUTATED TBX4 WILD-TYPE
  T1            2              7
  T2            1             67
  T3            6            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
  TBX4 MUTATED    11   0   0
  TBX4 WILD-TYPE 209  80  66
D1277V5, multiclass
    clus
vv   TBX4 MUTATED TBX4 WILD-TYPE
  N0           11            209
  N1            0             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"
D1277V6, binary
                cls
clus               0   1
  TBX4 MUTATED    11   0
  TBX4 WILD-TYPE 272  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  TBX4 MUTATED     11    0
  TBX4 WILD-TYPE  272   48
   clus
vv  TBX4 MUTATED TBX4 WILD-TYPE
  0           11            272
  1            0             48
[1] 2 2
[1] FALSE
D1277V7, 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
D1277V8, binary
                cls
clus               0   1
  TBX4 MUTATED     9   2
  TBX4 WILD-TYPE 308  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  TBX4 MUTATED      9    2
  TBX4 WILD-TYPE  308   46
                               clus
vv                              TBX4 MUTATED TBX4 WILD-TYPE
  COLON ADENOCARCINOMA                     9            308
  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 251   2  22  19
D1277V9, multiclass
    clus
vv   TBX4 MUTATED TBX4 WILD-TYPE
  R0            6            251
  R1            0              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"
D1277V10, 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
D1277V11, 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(1278) Variable = LPGAT1 MUTATION ANALYSIS
D1278V1, survival
                  sevent
clus2                0   1
  LPGAT1 MUTATED     3   0
  LPGAT1 WILD-TYPE 279  73
  LPGAT1 MUTATED LPGAT1 WILD-TYPE 
               3              352 
  LPGAT1 MUTATED LPGAT1 WILD-TYPE 
               0               73 
$`LPGAT1 MUTATED`
TCGA-D5-5540 TCGA-D5-6533 TCGA-G4-6628 
       13.51         1.32        52.80 

$`LPGAT1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 
       19.59        11.51        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       35.80        26.17        91.79        46.75 

  LPGAT1 MUTATED LPGAT1 WILD-TYPE 
            1.32             0.00 
  LPGAT1 MUTATED LPGAT1 WILD-TYPE 
           52.80           140.38 
  LPGAT1 MUTATED LPGAT1 WILD-TYPE 
          13.510           20.235 
[1] "1.3 - 52.8 (13.5)"  "0.0 - 140.4 (20.2)"
[1] "hr="     "3300000"
D1278V2, 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       25       108         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LPGAT1 MUTATED           0          0          1          0        0
  LPGAT1 WILD-TYPE        19         10         40         31       35
                  vv
clus               STAGE IVA STAGE IVB
  LPGAT1 MUTATED           0         0
  LPGAT1 WILD-TYPE        13         1
D1278V3, multiclass
            clus
vv           LPGAT1 MUTATED LPGAT1 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               1              108
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  LPGAT1 MUTATED     0   1   1   1
  LPGAT1 WILD-TYPE   9  67 247  40
D1278V4, multiclass
    clus
vv   LPGAT1 MUTATED LPGAT1 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              1              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
  LPGAT1 MUTATED     3   0   0
  LPGAT1 WILD-TYPE 217  80  66
D1278V5, multiclass
    clus
vv   LPGAT1 MUTATED LPGAT1 WILD-TYPE
  N0              3              217
  N1              0               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"
D1278V6, binary
                  cls
clus                 0   1
  LPGAT1 MUTATED     3   0
  LPGAT1 WILD-TYPE 280  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LPGAT1 MUTATED      3    0
  LPGAT1 WILD-TYPE  280   48
   clus
vv  LPGAT1 MUTATED LPGAT1 WILD-TYPE
  0              3              280
  1              0               48
[1] 2 2
[1] FALSE
D1278V7, 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
D1278V8, binary
                  cls
clus                 0   1
  LPGAT1 MUTATED     3   0
  LPGAT1 WILD-TYPE 314  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LPGAT1 MUTATED      3    0
  LPGAT1 WILD-TYPE  314   48
                               clus
vv                              LPGAT1 MUTATED LPGAT1 WILD-TYPE
  COLON ADENOCARCINOMA                       3              314
  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 254   2  22  21
D1278V9, multiclass
    clus
vv   LPGAT1 MUTATED LPGAT1 WILD-TYPE
  R0              3              254
  R1              0                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"
D1278V10, 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
D1278V11, 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(1279) Variable = PROM1 MUTATION ANALYSIS
D1279V1, survival
                 sevent
clus2               0   1
  PROM1 MUTATED    10   2
  PROM1 WILD-TYPE 272  71
  PROM1 MUTATED PROM1 WILD-TYPE 
             12             343 
  PROM1 MUTATED PROM1 WILD-TYPE 
              2              71 
$`PROM1 MUTATED`
TCGA-A6-6653 TCGA-AA-3864 TCGA-AA-A010 TCGA-AD-6964 TCGA-AZ-6608 TCGA-CM-6163 
       24.39        53.00        34.98        10.88         1.94        14.04 
TCGA-CM-6171 TCGA-CM-6172 TCGA-D5-6532 TCGA-D5-6930 TCGA-DM-A28H TCGA-G4-6588 
       14.04        11.01        18.25         1.51       117.07        26.17 

$`PROM1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
      100.01        29.56         5.23        11.74         3.19         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       15.02        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       11.51        20.19         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 
       52.80 

  PROM1 MUTATED PROM1 WILD-TYPE 
           1.51            0.00 
  PROM1 MUTATED PROM1 WILD-TYPE 
         117.07          140.38 
  PROM1 MUTATED PROM1 WILD-TYPE 
         16.145          20.280 
[1] "1.5 - 117.1 (16.1)" "0.0 - 140.4 (20.3)"
[1] "hr=" "1.3"
D1279V2, 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       24       106         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        19          9         40         30       35        13
                 vv
clus              STAGE IVB
  PROM1 MUTATED           0
  PROM1 WILD-TYPE         1
D1279V3, multiclass
            clus
vv           PROM1 MUTATED PROM1 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              3             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             1              40
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PROM1 MUTATED     1   3   6   2
  PROM1 WILD-TYPE   8  65 242  39
D1279V4, multiclass
    clus
vv   PROM1 MUTATED PROM1 WILD-TYPE
  T1             1               8
  T2             3              65
  T3             6             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
  PROM1 MUTATED     8   2   2
  PROM1 WILD-TYPE 212  78  64
D1279V5, multiclass
    clus
vv   PROM1 MUTATED PROM1 WILD-TYPE
  N0             8             212
  N1             2              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"
D1279V6, binary
                 cls
clus                0   1
  PROM1 MUTATED    11   0
  PROM1 WILD-TYPE 272  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PROM1 MUTATED     11    0
  PROM1 WILD-TYPE  272   48
   clus
vv  PROM1 MUTATED PROM1 WILD-TYPE
  0            11             272
  1             0              48
[1] 2 2
[1] FALSE
D1279V7, 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
D1279V8, binary
                 cls
clus                0   1
  PROM1 MUTATED    11   1
  PROM1 WILD-TYPE 306  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PROM1 MUTATED     11    1
  PROM1 WILD-TYPE  306   47
                               clus
vv                              PROM1 MUTATED PROM1 WILD-TYPE
  COLON ADENOCARCINOMA                     11             306
  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 249   2  22  21
D1279V9, multiclass
    clus
vv   PROM1 MUTATED PROM1 WILD-TYPE
  R0             8             249
  R1             0               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"
D1279V10, 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
D1279V11, 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(1280) Variable = AP4B1 MUTATION ANALYSIS
D1280V1, survival
                 sevent
clus2               0   1
  AP4B1 MUTATED    10   1
  AP4B1 WILD-TYPE 272  72
  AP4B1 MUTATED AP4B1 WILD-TYPE 
             11             344 
  AP4B1 MUTATED AP4B1 WILD-TYPE 
              1              72 
$`AP4B1 MUTATED`
TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-3510 TCGA-AA-3713 TCGA-AA-3977 TCGA-AA-A010 
       22.06        20.12        63.98        19.04        25.02        34.98 
TCGA-CK-4952 TCGA-CM-5344 TCGA-D5-6532 TCGA-DM-A1DB TCGA-F4-6703 
       15.62        22.03        18.25        44.32        35.87 

$`AP4B1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 
        1.35        17.56       102.44        40.34        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       11.51        20.19         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32        12.59       140.38         7.50       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  AP4B1 MUTATED AP4B1 WILD-TYPE 
          15.62            0.00 
  AP4B1 MUTATED AP4B1 WILD-TYPE 
          63.98          140.38 
  AP4B1 MUTATED AP4B1 WILD-TYPE 
         22.060          20.005 
[1] "15.6 - 64.0 (22.1)" "0.0 - 140.4 (20.0)"
[1] "hr=" "2.6"
D1280V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AP4B1 MUTATED         0        0        1         5         1         0
  AP4B1 WILD-TYPE      64        1       24       104         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AP4B1 MUTATED           1          0          1          0        1         0
  AP4B1 WILD-TYPE        18         10         40         31       34        13
                 vv
clus              STAGE IVB
  AP4B1 MUTATED           0
  AP4B1 WILD-TYPE         1
D1280V3, multiclass
            clus
vv           AP4B1 MUTATED AP4B1 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              5             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  AP4B1 MUTATED     0   1   8   2
  AP4B1 WILD-TYPE   9  67 240  39
D1280V4, multiclass
    clus
vv   AP4B1 MUTATED AP4B1 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             8             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     9   1   1
  AP4B1 WILD-TYPE 211  79  65
D1280V5, multiclass
    clus
vv   AP4B1 MUTATED AP4B1 WILD-TYPE
  N0             9             211
  N1             1              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"
D1280V6, binary
                 cls
clus                0   1
  AP4B1 MUTATED     8   1
  AP4B1 WILD-TYPE 275  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP4B1 MUTATED      8    1
  AP4B1 WILD-TYPE  275   47
   clus
vv  AP4B1 MUTATED AP4B1 WILD-TYPE
  0             8             275
  1             1              47
[1] 2 2
[1] FALSE
D1280V7, binary
                 cls
clus                0   1
  AP4B1 MUTATED     4   7
  AP4B1 WILD-TYPE 166 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP4B1 MUTATED      4    7
  AP4B1 WILD-TYPE  166  190
        clus
vv       AP4B1 MUTATED AP4B1 WILD-TYPE
  FEMALE             4             166
  MALE               7             190
[1] 2 2
[1] FALSE
D1280V8, binary
                 cls
clus                0   1
  AP4B1 MUTATED     9   2
  AP4B1 WILD-TYPE 308  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP4B1 MUTATED      9    2
  AP4B1 WILD-TYPE  308   46
                               clus
vv                              AP4B1 MUTATED AP4B1 WILD-TYPE
  COLON ADENOCARCINOMA                      9             308
  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 251   2  21  20
D1280V9, multiclass
    clus
vv   AP4B1 MUTATED AP4B1 WILD-TYPE
  R0             6             251
  R1             0               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"
D1280V10, 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     7
  AP4B1 WILD-TYPE                        19   169
D1280V11, 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                                        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(1281) Variable = BTBD11 MUTATION ANALYSIS
D1281V1, survival
                  sevent
clus2                0   1
  BTBD11 MUTATED    13   7
  BTBD11 WILD-TYPE 269  66
  BTBD11 MUTATED BTBD11 WILD-TYPE 
              20              335 
  BTBD11 MUTATED BTBD11 WILD-TYPE 
               7               66 
$`BTBD11 MUTATED`
TCGA-A6-2676 TCGA-A6-6780 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3525 TCGA-AA-3555 
       42.90        20.12         3.02        63.98         8.05        29.95 
TCGA-AA-3663 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3952 TCGA-AA-3977 TCGA-AZ-4315 
        6.97        19.04        19.04         2.01        25.02        58.39 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5916 TCGA-CM-4743 
      100.01         1.94         0.33         0.10        21.14        23.05 
TCGA-CM-5864 TCGA-CM-6674 
       15.02        12.95 

$`BTBD11 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       19.66        20.28         7.04         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       37.05        36.03        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 
       33.99        21.01        13.02        24.00        17.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
       36.00         5.03        85.05        26.99        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01        24.00        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41        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         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07         0.26         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        51.32        21.99         2.93         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        16.01        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  BTBD11 MUTATED BTBD11 WILD-TYPE 
             0.1              0.0 
  BTBD11 MUTATED BTBD11 WILD-TYPE 
          100.01           140.38 
  BTBD11 MUTATED BTBD11 WILD-TYPE 
           19.04            20.98 
[1] "0.1 - 100.0 (19.0)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.9"
D1281V2, 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       20       101         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BTBD11 MUTATED           0          1          1          1        1
  BTBD11 WILD-TYPE        19          9         40         30       34
                  vv
clus               STAGE IVA STAGE IVB
  BTBD11 MUTATED           0         0
  BTBD11 WILD-TYPE        13         1
D1281V3, multiclass
            clus
vv           BTBD11 MUTATED BTBD11 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                5               20
  STAGE IIA               8              101
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              1                9
  STAGE IIIB              1               40
  STAGE IIIC              1               30
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  BTBD11 MUTATED     1   3  16   1
  BTBD11 WILD-TYPE   8  65 232  40
D1281V4, multiclass
    clus
vv   BTBD11 MUTATED BTBD11 WILD-TYPE
  T1              1                8
  T2              3               65
  T3             16              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   1
  BTBD11 WILD-TYPE 202  78  65
D1281V5, multiclass
    clus
vv   BTBD11 MUTATED BTBD11 WILD-TYPE
  N0             18              202
  N1              2               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"
D1281V6, binary
                  cls
clus                 0   1
  BTBD11 MUTATED    18   1
  BTBD11 WILD-TYPE 265  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTBD11 MUTATED     18    1
  BTBD11 WILD-TYPE  265   47
   clus
vv  BTBD11 MUTATED BTBD11 WILD-TYPE
  0             18              265
  1              1               47
[1] 2 2
[1] FALSE
D1281V7, binary
                  cls
clus                 0   1
  BTBD11 MUTATED     6  15
  BTBD11 WILD-TYPE 164 182
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTBD11 MUTATED      6   15
  BTBD11 WILD-TYPE  164  182
        clus
vv       BTBD11 MUTATED BTBD11 WILD-TYPE
  FEMALE              6              164
  MALE               15              182
[1] 2 2
[1] FALSE
D1281V8, binary
                  cls
clus                 0   1
  BTBD11 MUTATED    18   3
  BTBD11 WILD-TYPE 299  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTBD11 MUTATED     18    3
  BTBD11 WILD-TYPE  299   45
                               clus
vv                              BTBD11 MUTATED BTBD11 WILD-TYPE
  COLON ADENOCARCINOMA                      18              299
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  BTBD11 MUTATED    13   0   1   3
  BTBD11 WILD-TYPE 244   2  21  18
D1281V9, multiclass
    clus
vv   BTBD11 MUTATED BTBD11 WILD-TYPE
  R0             13              244
  R1              0                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"
D1281V10, 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
D1281V11, 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(1282) Variable = CALB2 MUTATION ANALYSIS
D1282V1, survival
                 sevent
clus2               0   1
  CALB2 MUTATED     3   1
  CALB2 WILD-TYPE 279  72
  CALB2 MUTATED CALB2 WILD-TYPE 
              4             351 
  CALB2 MUTATED CALB2 WILD-TYPE 
              1              72 
$`CALB2 MUTATED`
TCGA-AA-3966 TCGA-AD-5900 TCGA-AZ-6606 TCGA-G4-6628 
        2.01         0.07        11.74        52.80 

$`CALB2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 
        6.77        12.10       100.01        29.56         5.23         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       26.17        91.79        46.75 

  CALB2 MUTATED CALB2 WILD-TYPE 
           0.07            0.00 
  CALB2 MUTATED CALB2 WILD-TYPE 
          52.80          140.38 
  CALB2 MUTATED CALB2 WILD-TYPE 
          6.875          20.280 
[1] "0.1 - 52.8 (6.9)"   "0.0 - 140.4 (20.3)"
[1] "hr=" "1.6"
D1282V2, 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       25       108         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        19         10         41         31       34        13
                 vv
clus              STAGE IVB
  CALB2 MUTATED           0
  CALB2 WILD-TYPE         1
D1282V3, multiclass
            clus
vv           CALB2 MUTATED CALB2 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              1             108
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CALB2 MUTATED     0   2   1   1
  CALB2 WILD-TYPE   9  66 247  40
D1282V4, multiclass
    clus
vv   CALB2 MUTATED CALB2 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             1             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
  CALB2 MUTATED     3   0   1
  CALB2 WILD-TYPE 217  80  65
D1282V5, multiclass
    clus
vv   CALB2 MUTATED CALB2 WILD-TYPE
  N0             3             217
  N1             0              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"
D1282V6, binary
                 cls
clus                0   1
  CALB2 MUTATED     2   1
  CALB2 WILD-TYPE 281  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CALB2 MUTATED      2    1
  CALB2 WILD-TYPE  281   47
   clus
vv  CALB2 MUTATED CALB2 WILD-TYPE
  0             2             281
  1             1              47
[1] 2 2
[1] FALSE
D1282V7, 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
D1282V8, binary
                 cls
clus                0   1
  CALB2 MUTATED     2   2
  CALB2 WILD-TYPE 315  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CALB2 MUTATED      2    2
  CALB2 WILD-TYPE  315   46
                               clus
vv                              CALB2 MUTATED CALB2 WILD-TYPE
  COLON ADENOCARCINOMA                      2             315
  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 255   2  22  21
D1282V9, multiclass
[1] "Remove cluster labels:" "CALB2 MUTATED"         
clus
  CALB2 MUTATED CALB2 WILD-TYPE 
              2             300 
     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-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-5657 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-A6-5659      TCGA-A6-5661      TCGA-A6-5665      TCGA-A6-6781 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-3489      TCGA-AA-3492      TCGA-AA-3496      TCGA-AA-3502 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-3510      TCGA-AA-3511      TCGA-AA-3514      TCGA-AA-3517 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-3518      TCGA-AA-3519      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-3526 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-3527      TCGA-AA-3529      TCGA-AA-3530      TCGA-AA-3531 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-3532      TCGA-AA-3534      TCGA-AA-3538      TCGA-AA-3542 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-3543      TCGA-AA-3544      TCGA-AA-3548      TCGA-AA-3549 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-3552      TCGA-AA-3553      TCGA-AA-3554      TCGA-AA-3555 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-3556      TCGA-AA-3558      TCGA-AA-3560      TCGA-AA-3561 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-3562      TCGA-AA-3655      TCGA-AA-3660      TCGA-AA-3662 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-3663      TCGA-AA-3664      TCGA-AA-3666      TCGA-AA-3667 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-3672      TCGA-AA-3673      TCGA-AA-3678      TCGA-AA-3679 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-3680      TCGA-AA-3681      TCGA-AA-3684      TCGA-AA-3685 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-3688      TCGA-AA-3692      TCGA-AA-3693      TCGA-AA-3695 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-3696      TCGA-AA-3697      TCGA-AA-3710      TCGA-AA-3712 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-3713      TCGA-AA-3715      TCGA-AA-3811      TCGA-AA-3812 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-3814      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-3844      TCGA-AA-3845      TCGA-AA-3846 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-3848      TCGA-AA-3850      TCGA-AA-3851      TCGA-AA-3852 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-3854      TCGA-AA-3855      TCGA-AA-3856      TCGA-AA-3858 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-3860      TCGA-AA-3861      TCGA-AA-3864      TCGA-AA-3866 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-3867      TCGA-AA-3869      TCGA-AA-3870      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-3939 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-3941      TCGA-AA-3947      TCGA-AA-3949      TCGA-AA-3950 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-3952      TCGA-AA-3955      TCGA-AA-3956      TCGA-AA-3968 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-3971      TCGA-AA-3972      TCGA-AA-3973      TCGA-AA-3975 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-3976      TCGA-AA-3979      TCGA-AA-3984      TCGA-AA-3986 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-3989      TCGA-AA-3994      TCGA-AA-A004      TCGA-AA-A00A 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-A00D      TCGA-AA-A00E      TCGA-AA-A00F      TCGA-AA-A00J 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-A00K      TCGA-AA-A00L      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-A00Z      TCGA-AA-A010      TCGA-AA-A017      TCGA-AA-A01D 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-A01F      TCGA-AA-A01G      TCGA-AA-A01I      TCGA-AA-A01K 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-A01P      TCGA-AA-A01Q      TCGA-AA-A01R      TCGA-AA-A01S 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-A01T      TCGA-AA-A01V      TCGA-AA-A01X      TCGA-AA-A01Z 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-A022      TCGA-AA-A024      TCGA-AA-A029      TCGA-AA-A02F 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-A02H      TCGA-AA-A02J      TCGA-AA-A02K      TCGA-AA-A02O 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AA-A02W      TCGA-AA-A02Y      TCGA-AA-A03F      TCGA-AA-A03J 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AD-6548      TCGA-AD-6888      TCGA-AU-3779      TCGA-AU-6004 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AY-4070      TCGA-AY-4071      TCGA-AY-5543      TCGA-AY-6196 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AY-6197      TCGA-AY-6386      TCGA-AZ-4315      TCGA-AZ-4681 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-AZ-4682      TCGA-CA-5254      TCGA-CA-5255      TCGA-CA-5796 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-CA-5797      TCGA-CA-6715      TCGA-CA-6716      TCGA-CA-6717 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-CA-6718      TCGA-CA-6719      TCGA-CK-4947      TCGA-CK-4948 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-CK-4950      TCGA-CK-4952      TCGA-CK-5912      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-G4-6310 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
     TCGA-G4-6586      TCGA-G4-6588      TCGA-G4-6625      TCGA-G4-6626 
"CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" "CALB2 WILD-TYPE" 
D1282V10, 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
D1282V11, 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(1283) Variable = COL4A6 MUTATION ANALYSIS
D1283V1, survival
                  sevent
clus2                0   1
  COL4A6 MUTATED    17   3
  COL4A6 WILD-TYPE 265  70
  COL4A6 MUTATED COL4A6 WILD-TYPE 
              20              335 
  COL4A6 MUTATED COL4A6 WILD-TYPE 
               3               70 
$`COL4A6 MUTATED`
TCGA-A6-5661 TCGA-A6-5666 TCGA-AA-3542 TCGA-AA-3672 TCGA-AA-3846 TCGA-AA-A00K 
       33.53        32.71        12.99         0.92        17.03        18.05 
TCGA-AA-A00N TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A01K TCGA-AA-A01Q TCGA-AD-5900 
        4.01        21.99        34.98        31.00         1.02         0.07 
TCGA-AZ-4323 TCGA-CA-6717 TCGA-CK-5913 TCGA-CK-5914 TCGA-CM-5349 TCGA-CM-6162 
        1.41         0.33        51.32        21.99        30.08        12.00 
TCGA-DM-A0XD TCGA-F4-6807 
       24.43        16.24 

$`COL4A6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02        14.93         0.00        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       14.99        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
       58.39         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5916 TCGA-CK-6747 
      102.44        40.34        15.62        49.08        21.14         2.93 
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        16.01        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        11.38        10.26       119.70        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       29.59        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  COL4A6 MUTATED COL4A6 WILD-TYPE 
            0.07             0.00 
  COL4A6 MUTATED COL4A6 WILD-TYPE 
           51.32           140.38 
  COL4A6 MUTATED COL4A6 WILD-TYPE 
           17.54            20.28 
[1] "0.1 - 51.3 (17.5)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1"  
D1283V2, 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       24       100         6         0
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  COL4A6 MUTATED           1          0          2          3        1
  COL4A6 WILD-TYPE        18         10         39         28       34
                  vv
clus               STAGE IVA STAGE IVB
  COL4A6 MUTATED           0         0
  COL4A6 WILD-TYPE        13         1
D1283V3, multiclass
            clus
vv           COL4A6 MUTATED COL4A6 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               9              100
  STAGE IIB               2                6
  STAGE IIC               1                0
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              3               28
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  COL4A6 MUTATED     0   1  16   4
  COL4A6 WILD-TYPE   9  67 232  37
D1283V4, multiclass
    clus
vv   COL4A6 MUTATED COL4A6 WILD-TYPE
  T1              0                9
  T2              1               67
  T3             16              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
  COL4A6 MUTATED    14   3   4
  COL4A6 WILD-TYPE 206  77  62
D1283V5, multiclass
    clus
vv   COL4A6 MUTATED COL4A6 WILD-TYPE
  N0             14              206
  N1              3               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"
D1283V6, binary
                  cls
clus                 0   1
  COL4A6 MUTATED    17   1
  COL4A6 WILD-TYPE 266  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL4A6 MUTATED     17    1
  COL4A6 WILD-TYPE  266   47
   clus
vv  COL4A6 MUTATED COL4A6 WILD-TYPE
  0             17              266
  1              1               47
[1] 2 2
[1] FALSE
D1283V7, 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
D1283V8, binary
                  cls
clus                 0   1
  COL4A6 MUTATED    17   4
  COL4A6 WILD-TYPE 300  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL4A6 MUTATED     17    4
  COL4A6 WILD-TYPE  300   44
                               clus
vv                              COL4A6 MUTATED COL4A6 WILD-TYPE
  COLON ADENOCARCINOMA                      17              300
  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 242   2  22  18
D1283V9, multiclass
    clus
vv   COL4A6 MUTATED COL4A6 WILD-TYPE
  R0             15              242
  R1              0                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"
D1283V10, 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
D1283V11, 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(1284) Variable = PAK1 MUTATION ANALYSIS
D1284V1, survival
                sevent
clus2              0   1
  PAK1 MUTATED     8   0
  PAK1 WILD-TYPE 274  73
  PAK1 MUTATED PAK1 WILD-TYPE 
             8            347 
  PAK1 MUTATED PAK1 WILD-TYPE 
             0             73 
$`PAK1 MUTATED`
TCGA-AA-3947 TCGA-AA-A010 TCGA-AZ-4315 TCGA-CA-6717 TCGA-D5-6539 TCGA-DM-A28H 
       33.01        34.98        58.39         0.33        12.49       117.07 
TCGA-G4-6588 TCGA-G4-6628 
       26.17        52.80 

$`PAK1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K 
        6.12        81.37       119.93        35.97        60.79        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        91.79        46.75 

  PAK1 MUTATED PAK1 WILD-TYPE 
          0.33           0.00 
  PAK1 MUTATED PAK1 WILD-TYPE 
        117.07         140.38 
  PAK1 MUTATED PAK1 WILD-TYPE 
        33.995         20.020 
[1] "0.3 - 117.1 (34.0)" "0.0 - 140.4 (20.0)"
[1] "hr="     "2.6e+07"
D1284V2, 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       24       105         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PAK1 MUTATED           0          1          0          1        0         0
  PAK1 WILD-TYPE        19          9         41         30       35        13
                vv
clus             STAGE IVB
  PAK1 MUTATED           0
  PAK1 WILD-TYPE         1
D1284V3, multiclass
            clus
vv           PAK1 MUTATED PAK1 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             4            105
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            1              9
  STAGE IIIB            0             41
  STAGE IIIC            1             30
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PAK1 MUTATED     0   1   6   3
  PAK1 WILD-TYPE   9  67 242  38
D1284V4, multiclass
    clus
vv   PAK1 MUTATED PAK1 WILD-TYPE
  T1            0              9
  T2            1             67
  T3            6            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
  PAK1 MUTATED     9   0   1
  PAK1 WILD-TYPE 211  80  65
D1284V5, multiclass
    clus
vv   PAK1 MUTATED PAK1 WILD-TYPE
  N0            9            211
  N1            0             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"
D1284V6, binary
                cls
clus               0   1
  PAK1 MUTATED    10   0
  PAK1 WILD-TYPE 273  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK1 MUTATED     10    0
  PAK1 WILD-TYPE  273   48
   clus
vv  PAK1 MUTATED PAK1 WILD-TYPE
  0           10            273
  1            0             48
[1] 2 2
[1] FALSE
D1284V7, 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
D1284V8, binary
                cls
clus               0   1
  PAK1 MUTATED     8   2
  PAK1 WILD-TYPE 309  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK1 MUTATED      8    2
  PAK1 WILD-TYPE  309   46
                               clus
vv                              PAK1 MUTATED PAK1 WILD-TYPE
  COLON ADENOCARCINOMA                     8            309
  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 249   2  22  20
D1284V9, multiclass
    clus
vv   PAK1 MUTATED PAK1 WILD-TYPE
  R0            8            249
  R1            0              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"
D1284V10, 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
D1284V11, 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(1285) Variable = NXPH1 MUTATION ANALYSIS
D1285V1, survival
                 sevent
clus2               0   1
  NXPH1 MUTATED     7   1
  NXPH1 WILD-TYPE 275  72
  NXPH1 MUTATED NXPH1 WILD-TYPE 
              8             347 
  NXPH1 MUTATED NXPH1 WILD-TYPE 
              1              72 
$`NXPH1 MUTATED`
TCGA-A6-6141 TCGA-A6-6649 TCGA-AA-3861 TCGA-AA-A00N TCGA-AA-A010 TCGA-D5-6541 
        8.38        24.16        30.05         4.01        34.98        15.58 
TCGA-G4-6309 TCGA-G4-6628 
       51.75        52.80 

$`NXPH1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.18        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        16.14         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       13.78        35.80        26.17        91.79        46.75 

  NXPH1 MUTATED NXPH1 WILD-TYPE 
           4.01            0.00 
  NXPH1 MUTATED NXPH1 WILD-TYPE 
          52.80          140.38 
  NXPH1 MUTATED NXPH1 WILD-TYPE 
         27.105          20.120 
[1] "4.0 - 52.8 (27.1)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.9"
D1285V2, 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       25       106         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        19         10         39         31       35        13
                 vv
clus              STAGE IVB
  NXPH1 MUTATED           0
  NXPH1 WILD-TYPE         1
D1285V3, multiclass
            clus
vv           NXPH1 MUTATED NXPH1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              3             106
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NXPH1 MUTATED     0   1   5   2
  NXPH1 WILD-TYPE   9  67 243  39
D1285V4, multiclass
    clus
vv   NXPH1 MUTATED NXPH1 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             5             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
  NXPH1 MUTATED     6   2   0
  NXPH1 WILD-TYPE 214  78  66
D1285V5, multiclass
    clus
vv   NXPH1 MUTATED NXPH1 WILD-TYPE
  N0             6             214
  N1             2              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"
D1285V6, binary
                 cls
clus                0   1
  NXPH1 MUTATED     8   0
  NXPH1 WILD-TYPE 275  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NXPH1 MUTATED      8    0
  NXPH1 WILD-TYPE  275   48
   clus
vv  NXPH1 MUTATED NXPH1 WILD-TYPE
  0             8             275
  1             0              48
[1] 2 2
[1] FALSE
D1285V7, 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
D1285V8, binary
                 cls
clus                0   1
  NXPH1 MUTATED     7   1
  NXPH1 WILD-TYPE 310  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NXPH1 MUTATED      7    1
  NXPH1 WILD-TYPE  310   47
                               clus
vv                              NXPH1 MUTATED NXPH1 WILD-TYPE
  COLON ADENOCARCINOMA                      7             310
  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 251   2  22  21
D1285V9, multiclass
    clus
vv   NXPH1 MUTATED NXPH1 WILD-TYPE
  R0             6             251
  R1             0               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"
D1285V10, 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
D1285V11, 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(1286) Variable = CXXC5 MUTATION ANALYSIS
D1286V1, survival
                 sevent
clus2               0   1
  CXXC5 MUTATED     4   1
  CXXC5 WILD-TYPE 278  72
  CXXC5 MUTATED CXXC5 WILD-TYPE 
              5             350 
  CXXC5 MUTATED CXXC5 WILD-TYPE 
              1              72 
$`CXXC5 MUTATED`
TCGA-A6-6780 TCGA-AA-3673 TCGA-AD-6899 TCGA-CM-5861 TCGA-CM-6674 
       20.12        50.04         5.79        15.02        12.95 

$`CXXC5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3678 
        6.97        54.02         2.01        14.01         0.92        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         0.72        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  CXXC5 MUTATED CXXC5 WILD-TYPE 
           5.79            0.00 
  CXXC5 MUTATED CXXC5 WILD-TYPE 
          50.04          140.38 
  CXXC5 MUTATED CXXC5 WILD-TYPE 
          15.02           20.63 
[1] "5.8 - 50.0 (15.0)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "1"  
D1286V2, 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       24       106         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        19         10         41         30       35        13
                 vv
clus              STAGE IVB
  CXXC5 MUTATED           0
  CXXC5 WILD-TYPE         1
D1286V3, multiclass
            clus
vv           CXXC5 MUTATED CXXC5 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              3             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CXXC5 MUTATED     0   0   4   2
  CXXC5 WILD-TYPE   9  68 244  39
D1286V4, multiclass
    clus
vv   CXXC5 MUTATED CXXC5 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             4             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
  CXXC5 MUTATED     5   0   1
  CXXC5 WILD-TYPE 215  80  65
D1286V5, multiclass
    clus
vv   CXXC5 MUTATED CXXC5 WILD-TYPE
  N0             5             215
  N1             0              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"
D1286V6, binary
                 cls
clus                0   1
  CXXC5 MUTATED     3   0
  CXXC5 WILD-TYPE 280  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CXXC5 MUTATED      3    0
  CXXC5 WILD-TYPE  280   48
   clus
vv  CXXC5 MUTATED CXXC5 WILD-TYPE
  0             3             280
  1             0              48
[1] 2 2
[1] FALSE
D1286V7, 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
D1286V8, binary
                 cls
clus                0   1
  CXXC5 MUTATED     4   2
  CXXC5 WILD-TYPE 313  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CXXC5 MUTATED      4    2
  CXXC5 WILD-TYPE  313   46
                               clus
vv                              CXXC5 MUTATED CXXC5 WILD-TYPE
  COLON ADENOCARCINOMA                      4             313
  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 254   2  22  20
D1286V9, multiclass
    clus
vv   CXXC5 MUTATED CXXC5 WILD-TYPE
  R0             3             254
  R1             0               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"
D1286V10, 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
D1286V11, 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(1287) Variable = POLQ MUTATION ANALYSIS
D1287V1, survival
                sevent
clus2              0   1
  POLQ MUTATED    23   5
  POLQ WILD-TYPE 259  68
  POLQ MUTATED POLQ WILD-TYPE 
            28            327 
  POLQ MUTATED POLQ WILD-TYPE 
             5             68 
$`POLQ MUTATED`
TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3518 TCGA-AA-3672 TCGA-AA-3713 
       20.12        19.66        63.98         1.02         0.92        19.04 
TCGA-AA-3947 TCGA-AA-3971 TCGA-AA-3977 TCGA-AA-A010 TCGA-AD-6889 TCGA-AZ-5403 
       33.01        16.08        25.02        34.98        56.55        62.79 
TCGA-AZ-6598 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 
       49.41         0.33         0.10       124.27        23.05        37.02 
TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6675 TCGA-D5-6537 TCGA-D5-6540 TCGA-DM-A1D4 
       15.02        12.00        13.05         4.80        16.14        92.75 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6303 TCGA-G4-6628 
       35.41        19.43        65.85        52.80 

$`POLQ WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       23.87        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 
        6.97         1.02        13.02        38.99         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 
        2.01        20.98        34.03         2.01        21.99        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37         4.21         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07         0.26         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
        2.93         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        16.01         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-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       11.01        12.95        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20       130.65        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      107.67        74.56        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       26.17        91.79        46.75 

  POLQ MUTATED POLQ WILD-TYPE 
           0.1            0.0 
  POLQ MUTATED POLQ WILD-TYPE 
        124.27         140.38 
  POLQ MUTATED POLQ WILD-TYPE 
        21.585         20.190 
[1] "0.1 - 124.3 (21.6)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.5"
D1287V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  POLQ MUTATED         5        0        3        10         2         0
  POLQ WILD-TYPE      59        1       22        99         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        17         10         39         30       33        13
                vv
clus             STAGE IVB
  POLQ MUTATED           1
  POLQ WILD-TYPE         0
D1287V3, multiclass
            clus
vv           POLQ MUTATED POLQ WILD-TYPE
  STAGE I               5             59
  STAGE IA              0              1
  STAGE II              3             22
  STAGE IIA            10             99
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             2             17
  STAGE IIIA            0             10
  STAGE IIIB            2             39
  STAGE IIIC            1             30
  STAGE IV              2             33
  STAGE IVA             0             13
  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  20   3
  POLQ WILD-TYPE   9  62 228  38
D1287V4, multiclass
    clus
vv   POLQ MUTATED POLQ WILD-TYPE
  T1            0              9
  T2            6             62
  T3           20            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    22   6   1
  POLQ WILD-TYPE 198  74  65
D1287V5, multiclass
    clus
vv   POLQ MUTATED POLQ WILD-TYPE
  N0           22            198
  N1            6             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"
D1287V6, binary
                cls
clus               0   1
  POLQ MUTATED    19   3
  POLQ WILD-TYPE 264  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  POLQ MUTATED     19    3
  POLQ WILD-TYPE  264   45
   clus
vv  POLQ MUTATED POLQ WILD-TYPE
  0           19            264
  1            3             45
[1] 2 2
[1] FALSE
D1287V7, binary
                cls
clus               0   1
  POLQ MUTATED    11  18
  POLQ WILD-TYPE 159 179
[1] "tbl2"
                cls
clus             [,1] [,2]
  POLQ MUTATED     11   18
  POLQ WILD-TYPE  159  179
        clus
vv       POLQ MUTATED POLQ WILD-TYPE
  FEMALE           11            159
  MALE             18            179
[1] 2 2
[1] FALSE
D1287V8, binary
                cls
clus               0   1
  POLQ MUTATED    21   8
  POLQ WILD-TYPE 296  40
[1] "tbl2"
                cls
clus             [,1] [,2]
  POLQ MUTATED     21    8
  POLQ WILD-TYPE  296   40
                               clus
vv                              POLQ MUTATED POLQ WILD-TYPE
  COLON ADENOCARCINOMA                    21            296
  COLON MUCINOUS ADENOCARCINOMA            8             40
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  POLQ MUTATED    19   0   1   3
  POLQ WILD-TYPE 238   2  21  18
D1287V9, multiclass
    clus
vv   POLQ MUTATED POLQ WILD-TYPE
  R0           19            238
  R1            0              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"
D1287V10, 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    15
  POLQ WILD-TYPE                        17   161
D1287V11, 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                                      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(1288) Variable = DSC2 MUTATION ANALYSIS
D1288V1, survival
                sevent
clus2              0   1
  DSC2 MUTATED    11   3
  DSC2 WILD-TYPE 271  70
  DSC2 MUTATED DSC2 WILD-TYPE 
            14            341 
  DSC2 MUTATED DSC2 WILD-TYPE 
             3             70 
$`DSC2 MUTATED`
TCGA-A6-2672 TCGA-A6-5666 TCGA-A6-6142 TCGA-AA-3662 TCGA-AA-A00N TCGA-AZ-4315 
       46.65        32.71        25.08         6.05         4.01        58.39 
TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4746 TCGA-CM-6161 
       49.41       100.01         0.33         0.10        37.02        15.02 
TCGA-D5-6540 TCGA-DM-A0X9 
       16.14       119.70 

$`DSC2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 
       22.06        27.09        22.52         8.38        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       61.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07         0.26         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38        10.26        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  DSC2 MUTATED DSC2 WILD-TYPE 
           0.1            0.0 
  DSC2 MUTATED DSC2 WILD-TYPE 
        119.70         140.38 
  DSC2 MUTATED DSC2 WILD-TYPE 
        28.895         20.120 
[1] "0.1 - 119.7 (28.9)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.4"
D1288V2, 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       23       105         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        19         10         40         31       34        12
                vv
clus             STAGE IVB
  DSC2 MUTATED           0
  DSC2 WILD-TYPE         1
D1288V3, multiclass
            clus
vv           DSC2 MUTATED DSC2 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             4            105
  STAGE IIB             1              7
  STAGE IIC             1              0
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  65 240  38
D1288V4, multiclass
    clus
vv   DSC2 MUTATED DSC2 WILD-TYPE
  T1            0              9
  T2            3             65
  T3            8            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
  DSC2 MUTATED    11   2   1
  DSC2 WILD-TYPE 209  78  65
D1288V5, multiclass
    clus
vv   DSC2 MUTATED DSC2 WILD-TYPE
  N0           11            209
  N1            2             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"
D1288V6, binary
                cls
clus               0   1
  DSC2 MUTATED    11   2
  DSC2 WILD-TYPE 272  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSC2 MUTATED     11    2
  DSC2 WILD-TYPE  272   46
   clus
vv  DSC2 MUTATED DSC2 WILD-TYPE
  0           11            272
  1            2             46
[1] 2 2
[1] FALSE
D1288V7, 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
D1288V8, binary
                cls
clus               0   1
  DSC2 MUTATED    11   3
  DSC2 WILD-TYPE 306  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSC2 MUTATED     11    3
  DSC2 WILD-TYPE  306   45
                               clus
vv                              DSC2 MUTATED DSC2 WILD-TYPE
  COLON ADENOCARCINOMA                    11            306
  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 251   2  21  19
D1288V9, multiclass
    clus
vv   DSC2 MUTATED DSC2 WILD-TYPE
  R0            6            251
  R1            0              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"
D1288V10, 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
D1288V11, 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(1289) Variable = CCDC110 MUTATION ANALYSIS
D1289V1, survival
                   sevent
clus2                 0   1
  CCDC110 MUTATED     7   4
  CCDC110 WILD-TYPE 275  69
  CCDC110 MUTATED CCDC110 WILD-TYPE 
               11               344 
  CCDC110 MUTATED CCDC110 WILD-TYPE 
                4                69 
$`CCDC110 MUTATED`
TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3680 TCGA-AA-3977 TCGA-AA-A010 TCGA-AZ-6598 
       22.06        63.98        11.01        25.02        34.98        49.41 
TCGA-AZ-6601 TCGA-CA-6717 TCGA-CM-5861 TCGA-D5-6926 TCGA-F4-6570 
      100.01         0.33        15.02         9.04         6.18 

$`CCDC110 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       15.02         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       62.79        61.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 
       12.39        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-A0X9 
       13.41         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       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        13.38        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  CCDC110 MUTATED CCDC110 WILD-TYPE 
             0.33              0.00 
  CCDC110 MUTATED CCDC110 WILD-TYPE 
           100.01            140.38 
  CCDC110 MUTATED CCDC110 WILD-TYPE 
           22.060            20.155 
[1] "0.3 - 100.0 (22.1)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.4"
D1289V2, 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       22       104         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC110 MUTATED           0          1          0          0        1
  CCDC110 WILD-TYPE        19          9         41         31       34
                   vv
clus                STAGE IVA STAGE IVB
  CCDC110 MUTATED           0         0
  CCDC110 WILD-TYPE        13         1
D1289V3, multiclass
            clus
vv           CCDC110 MUTATED CCDC110 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 3                22
  STAGE IIA                5               104
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               1                 9
  STAGE IIIB               0                41
  STAGE IIIC               0                31
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CCDC110 MUTATED     0   1   8   4
  CCDC110 WILD-TYPE   9  67 240  37
D1289V4, multiclass
    clus
vv   CCDC110 MUTATED CCDC110 WILD-TYPE
  T1               0                 9
  T2               1                67
  T3               8               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
  CCDC110 MUTATED    11   1   1
  CCDC110 WILD-TYPE 209  79  65
D1289V5, multiclass
    clus
vv   CCDC110 MUTATED CCDC110 WILD-TYPE
  N0              11               209
  N1               1                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"
D1289V6, binary
                   cls
clus                  0   1
  CCDC110 MUTATED     9   1
  CCDC110 WILD-TYPE 274  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC110 MUTATED      9    1
  CCDC110 WILD-TYPE  274   47
   clus
vv  CCDC110 MUTATED CCDC110 WILD-TYPE
  0               9               274
  1               1                47
[1] 2 2
[1] FALSE
D1289V7, 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
D1289V8, binary
                   cls
clus                  0   1
  CCDC110 MUTATED    12   1
  CCDC110 WILD-TYPE 305  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC110 MUTATED     12    1
  CCDC110 WILD-TYPE  305   47
                               clus
vv                              CCDC110 MUTATED CCDC110 WILD-TYPE
  COLON ADENOCARCINOMA                       12               305
  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 250   2  21  19
D1289V9, multiclass
    clus
vv   CCDC110 MUTATED CCDC110 WILD-TYPE
  R0               7               250
  R1               0                 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"
D1289V10, 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
D1289V11, 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(1290) Variable = KIAA1919 MUTATION ANALYSIS
D1290V1, survival
                    sevent
clus2                  0   1
  KIAA1919 MUTATED     7   2
  KIAA1919 WILD-TYPE 275  71
  KIAA1919 MUTATED KIAA1919 WILD-TYPE 
                 9                346 
  KIAA1919 MUTATED KIAA1919 WILD-TYPE 
                 2                 71 
$`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         0.33         0.10         2.93 
TCGA-CM-6171 TCGA-D5-6927 TCGA-F4-6570 
       14.04         9.44         6.18 

$`KIAA1919 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.26         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 
       49.08        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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  KIAA1919 MUTATED KIAA1919 WILD-TYPE 
               0.1                0.0 
  KIAA1919 MUTATED KIAA1919 WILD-TYPE 
             58.39             140.38 
  KIAA1919 MUTATED KIAA1919 WILD-TYPE 
              9.44              20.63 
[1] "0.1 - 58.4 (9.4)"   "0.0 - 140.4 (20.6)"
[1] "hr=" "1.5"
D1290V2, 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       25       103         6         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1919 MUTATED           0          0          0          0        0
  KIAA1919 WILD-TYPE        19         10         41         31       35
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA1919 MUTATED           0         0
  KIAA1919 WILD-TYPE        13         1
D1290V3, multiclass
            clus
vv           KIAA1919 MUTATED KIAA1919 WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  0                 25
  STAGE IIA                 6                103
  STAGE IIB                 2                  6
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                0                 10
  STAGE IIIB                0                 41
  STAGE IIIC                0                 31
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA1919 MUTATED     0   1   6   2
  KIAA1919 WILD-TYPE   9  67 242  39
D1290V4, multiclass
    clus
vv   KIAA1919 MUTATED KIAA1919 WILD-TYPE
  T1                0                  9
  T2                1                 67
  T3                6                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
  KIAA1919 MUTATED     9   0   0
  KIAA1919 WILD-TYPE 211  80  66
D1290V5, multiclass
    clus
vv   KIAA1919 MUTATED KIAA1919 WILD-TYPE
  N0                9                211
  N1                0                 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"
D1290V6, binary
                    cls
clus                   0   1
  KIAA1919 MUTATED     8   0
  KIAA1919 WILD-TYPE 275  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1919 MUTATED      8    0
  KIAA1919 WILD-TYPE  275   48
   clus
vv  KIAA1919 MUTATED KIAA1919 WILD-TYPE
  0                8                275
  1                0                 48
[1] 2 2
[1] FALSE
D1290V7, 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
D1290V8, binary
                    cls
clus                   0   1
  KIAA1919 MUTATED     8   1
  KIAA1919 WILD-TYPE 309  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1919 MUTATED      8    1
  KIAA1919 WILD-TYPE  309   47
                               clus
vv                              KIAA1919 MUTATED KIAA1919 WILD-TYPE
  COLON ADENOCARCINOMA                         8                309
  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 251   2  22  18
D1290V9, multiclass
    clus
vv   KIAA1919 MUTATED KIAA1919 WILD-TYPE
  R0                6                251
  R1                0                  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"
D1290V10, 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
D1290V11, 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(1291) Variable = CCNH MUTATION ANALYSIS
D1291V1, survival
                sevent
clus2              0   1
  CCNH MUTATED     6   1
  CCNH WILD-TYPE 276  72
  CCNH MUTATED CCNH WILD-TYPE 
             7            348 
  CCNH MUTATED CCNH WILD-TYPE 
             1             72 
$`CCNH MUTATED`
TCGA-AA-3977 TCGA-AA-A00R TCGA-CM-6168 TCGA-D5-6536 TCGA-F4-6569 TCGA-G4-6626 
       25.02         0.99        12.99        17.85        13.45        46.75 
TCGA-G4-6628 
       52.80 

$`CCNH WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W 
       38.04         4.01        27.02        42.02        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 
       20.19        18.25         1.32        43.27        15.12         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6703 
      117.07        98.24         8.61        13.38         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 

  CCNH MUTATED CCNH WILD-TYPE 
          0.99           0.00 
  CCNH MUTATED CCNH WILD-TYPE 
         52.80         140.38 
  CCNH MUTATED CCNH WILD-TYPE 
        17.850         20.235 
[1] "1.0 - 52.8 (17.9)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.5"
D1291V2, 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       25       106         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        19         10         41         31       35        13
                vv
clus             STAGE IVB
  CCNH MUTATED           0
  CCNH WILD-TYPE         1
D1291V3, multiclass
            clus
vv           CCNH MUTATED CCNH WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             3            106
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CCNH MUTATED     0   4   3   0
  CCNH WILD-TYPE   9  64 245  41
D1291V4, multiclass
    clus
vv   CCNH MUTATED CCNH WILD-TYPE
  T1            0              9
  T2            4             64
  T3            3            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
  CCNH MUTATED     7   0   0
  CCNH WILD-TYPE 213  80  66
D1291V5, multiclass
    clus
vv   CCNH MUTATED CCNH WILD-TYPE
  N0            7            213
  N1            0             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"
D1291V6, binary
                cls
clus               0   1
  CCNH MUTATED     6   0
  CCNH WILD-TYPE 277  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCNH MUTATED      6    0
  CCNH WILD-TYPE  277   48
   clus
vv  CCNH MUTATED CCNH WILD-TYPE
  0            6            277
  1            0             48
[1] 2 2
[1] FALSE
D1291V7, 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
D1291V8, binary
                cls
clus               0   1
  CCNH MUTATED     7   0
  CCNH WILD-TYPE 310  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCNH MUTATED      7    0
  CCNH WILD-TYPE  310   48
                               clus
vv                              CCNH MUTATED CCNH WILD-TYPE
  COLON ADENOCARCINOMA                     7            310
  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 251   2  22  21
D1291V9, multiclass
    clus
vv   CCNH MUTATED CCNH WILD-TYPE
  R0            6            251
  R1            0              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"
D1291V10, 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
D1291V11, 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(1292) Variable = TRERF1 MUTATION ANALYSIS
D1292V1, survival
                  sevent
clus2                0   1
  TRERF1 MUTATED    12   6
  TRERF1 WILD-TYPE 270  67
  TRERF1 MUTATED TRERF1 WILD-TYPE 
              18              337 
  TRERF1 MUTATED TRERF1 WILD-TYPE 
               6               67 
$`TRERF1 MUTATED`
TCGA-A6-2676 TCGA-A6-5666 TCGA-A6-6648 TCGA-AA-3492 TCGA-AA-3516 TCGA-AA-3663 
       42.90        32.71        25.18         3.02        13.02         6.97 
TCGA-AA-3672 TCGA-AA-3681 TCGA-AA-3811 TCGA-AA-3815 TCGA-AA-3977 TCGA-AZ-6598 
        0.92         5.98        10.06        33.04        25.02        49.41 
TCGA-CA-6717 TCGA-CK-5916 TCGA-D5-6533 TCGA-D5-6928 TCGA-F4-6703 TCGA-G4-6304 
        0.33        21.14         1.32        11.64        35.87        53.62 

$`TRERF1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6649 
       22.06        27.09        22.52         8.38        25.08        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
        1.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       78.08         6.05        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       47.01        15.02        11.01        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        19.04        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       11.51        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-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  TRERF1 MUTATED TRERF1 WILD-TYPE 
            0.33             0.00 
  TRERF1 MUTATED TRERF1 WILD-TYPE 
           53.62           140.38 
  TRERF1 MUTATED TRERF1 WILD-TYPE 
           17.08            20.19 
[1] "0.3 - 53.6 (17.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2.1"
D1292V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TRERF1 MUTATED         1        0        3         5         2         1
  TRERF1 WILD-TYPE      63        1       22       104         6         0
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRERF1 MUTATED           4          0          1          0        1
  TRERF1 WILD-TYPE        15         10         40         31       34
                  vv
clus               STAGE IVA STAGE IVB
  TRERF1 MUTATED           1         0
  TRERF1 WILD-TYPE        12         1
D1292V3, multiclass
            clus
vv           TRERF1 MUTATED TRERF1 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                3               22
  STAGE IIA               5              104
  STAGE IIB               2                6
  STAGE IIC               1                0
  STAGE III               4               15
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TRERF1 MUTATED     1   1  14   4
  TRERF1 WILD-TYPE   8  67 234  37
D1292V4, multiclass
    clus
vv   TRERF1 MUTATED TRERF1 WILD-TYPE
  T1              1                8
  T2              1               67
  T3             14              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
  TRERF1 MUTATED    15   2   3
  TRERF1 WILD-TYPE 205  78  63
D1292V5, multiclass
    clus
vv   TRERF1 MUTATED TRERF1 WILD-TYPE
  N0             15              205
  N1              2               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"
D1292V6, binary
                  cls
clus                 0   1
  TRERF1 MUTATED    16   2
  TRERF1 WILD-TYPE 267  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRERF1 MUTATED     16    2
  TRERF1 WILD-TYPE  267   46
   clus
vv  TRERF1 MUTATED TRERF1 WILD-TYPE
  0             16              267
  1              2               46
[1] 2 2
[1] FALSE
D1292V7, binary
                  cls
clus                 0   1
  TRERF1 MUTATED    13   7
  TRERF1 WILD-TYPE 157 190
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRERF1 MUTATED     13    7
  TRERF1 WILD-TYPE  157  190
        clus
vv       TRERF1 MUTATED TRERF1 WILD-TYPE
  FEMALE             13              157
  MALE                7              190
[1] 2 2
[1] FALSE
D1292V8, binary
                  cls
clus                 0   1
  TRERF1 MUTATED    17   3
  TRERF1 WILD-TYPE 300  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRERF1 MUTATED     17    3
  TRERF1 WILD-TYPE  300   45
                               clus
vv                              TRERF1 MUTATED TRERF1 WILD-TYPE
  COLON ADENOCARCINOMA                      17              300
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TRERF1 MUTATED    12   0   1   2
  TRERF1 WILD-TYPE 245   2  21  19
D1292V9, multiclass
    clus
vv   TRERF1 MUTATED TRERF1 WILD-TYPE
  R0             12              245
  R1              0                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"
D1292V10, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRERF1 MUTATED                                  0     1
  TRERF1 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TRERF1 MUTATED                           0     9
  TRERF1 WILD-TYPE                        19   167
D1292V11, multiclass
                                  clus
vv                                 TRERF1 MUTATED TRERF1 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(1293) Variable = CACHD1 MUTATION ANALYSIS
D1293V1, survival
                  sevent
clus2                0   1
  CACHD1 MUTATED    17   3
  CACHD1 WILD-TYPE 265  70
  CACHD1 MUTATED CACHD1 WILD-TYPE 
              20              335 
  CACHD1 MUTATED CACHD1 WILD-TYPE 
               3               70 
$`CACHD1 MUTATED`
TCGA-A6-2672 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6781 TCGA-AA-3516 
       46.65        22.06         8.38        25.18        19.66        13.02 
TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01I 
       24.00         2.01        25.02         4.01        34.98        31.00 
TCGA-AU-3779 TCGA-AZ-4315 TCGA-CA-6718 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-6162 
       14.50        58.39         0.10        30.08         5.03        12.00 
TCGA-D5-6538 TCGA-G4-6586 
       17.13        35.80 

$`CACHD1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6651 
       32.71        27.09        22.52        25.08        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 
       24.69        24.39        23.87        20.12        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        3.02         1.02        35.01        63.98         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        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        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.33         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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        16.01 
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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12        17.85         4.80        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        26.17        91.79        46.75        52.80 

  CACHD1 MUTATED CACHD1 WILD-TYPE 
             0.1              0.0 
  CACHD1 MUTATED CACHD1 WILD-TYPE 
           58.39           140.38 
  CACHD1 MUTATED CACHD1 WILD-TYPE 
           20.86            20.19 
[1] "0.1 - 58.4 (20.9)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D1293V2, 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       25        99         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CACHD1 MUTATED           1          0          3          1        0
  CACHD1 WILD-TYPE        18         10         38         30       35
                  vv
clus               STAGE IVA STAGE IVB
  CACHD1 MUTATED           2         0
  CACHD1 WILD-TYPE        11         1
D1293V3, multiclass
            clus
vv           CACHD1 MUTATED CACHD1 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA              10               99
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              3               38
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               2               11
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 232  38
D1293V4, multiclass
    clus
vv   CACHD1 MUTATED CACHD1 WILD-TYPE
  T1              0                9
  T2              2               66
  T3             16              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
  CACHD1 MUTATED    15   4   2
  CACHD1 WILD-TYPE 205  76  64
D1293V5, multiclass
    clus
vv   CACHD1 MUTATED CACHD1 WILD-TYPE
  N0             15              205
  N1              4               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"
D1293V6, binary
                  cls
clus                 0   1
  CACHD1 MUTATED    17   2
  CACHD1 WILD-TYPE 266  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CACHD1 MUTATED     17    2
  CACHD1 WILD-TYPE  266   46
   clus
vv  CACHD1 MUTATED CACHD1 WILD-TYPE
  0             17              266
  1              2               46
[1] 2 2
[1] FALSE
D1293V7, 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
D1293V8, binary
                  cls
clus                 0   1
  CACHD1 MUTATED    15   6
  CACHD1 WILD-TYPE 302  42
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CACHD1 MUTATED     15    6
  CACHD1 WILD-TYPE  302   42
                               clus
vv                              CACHD1 MUTATED CACHD1 WILD-TYPE
  COLON ADENOCARCINOMA                      15              302
  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 242   2  22  20
D1293V9, multiclass
    clus
vv   CACHD1 MUTATED CACHD1 WILD-TYPE
  R0             15              242
  R1              0                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"
D1293V10, 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
D1293V11, 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(1294) Variable = PRKCQ MUTATION ANALYSIS
D1294V1, survival
                 sevent
clus2               0   1
  PRKCQ MUTATED    12   3
  PRKCQ WILD-TYPE 270  70
  PRKCQ MUTATED PRKCQ WILD-TYPE 
             15             340 
  PRKCQ MUTATED PRKCQ WILD-TYPE 
              3              70 
$`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        15.75 
TCGA-AZ-6600 TCGA-CA-6717 TCGA-CM-5344 TCGA-CM-6674 TCGA-D5-6930 TCGA-DM-A28G 
       12.10         0.33        22.03        12.95         1.51        60.79 
TCGA-DM-A28H TCGA-F4-6704 TCGA-G4-6307 
      117.07         1.55        55.04 

$`PRKCQ WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-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-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41        49.41         6.77       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28K TCGA-F4-6459 
        6.12        81.37       119.93        35.97        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 
       13.38        13.45         6.18        35.87        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 
      107.67        74.56        65.85        53.62        44.68        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  PRKCQ MUTATED PRKCQ WILD-TYPE 
           0.33            0.00 
  PRKCQ MUTATED PRKCQ WILD-TYPE 
         117.07          140.38 
  PRKCQ MUTATED PRKCQ WILD-TYPE 
         22.030          20.155 
[1] "0.3 - 117.1 (22.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D1294V2, 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       25       104         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        19         10         39         29       34        11
                 vv
clus              STAGE IVB
  PRKCQ MUTATED           0
  PRKCQ WILD-TYPE         1
D1294V3, multiclass
            clus
vv           PRKCQ MUTATED PRKCQ WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              5             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             2              29
  STAGE IV               1              34
  STAGE IVA              2              11
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 237  39
D1294V4, multiclass
    clus
vv   PRKCQ MUTATED PRKCQ WILD-TYPE
  T1             1               8
  T2             1              67
  T3            11             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
  PRKCQ MUTATED     9   4   2
  PRKCQ WILD-TYPE 211  76  64
D1294V5, multiclass
    clus
vv   PRKCQ MUTATED PRKCQ WILD-TYPE
  N0             9             211
  N1             4              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"
D1294V6, binary
                 cls
clus                0   1
  PRKCQ MUTATED    10   3
  PRKCQ WILD-TYPE 273  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCQ MUTATED     10    3
  PRKCQ WILD-TYPE  273   45
   clus
vv  PRKCQ MUTATED PRKCQ WILD-TYPE
  0            10             273
  1             3              45
[1] 2 2
[1] FALSE
D1294V7, 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
D1294V8, binary
                 cls
clus                0   1
  PRKCQ MUTATED    10   5
  PRKCQ WILD-TYPE 307  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCQ MUTATED     10    5
  PRKCQ WILD-TYPE  307   43
                               clus
vv                              PRKCQ MUTATED PRKCQ WILD-TYPE
  COLON ADENOCARCINOMA                     10             307
  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 248   2  22  20
D1294V9, multiclass
    clus
vv   PRKCQ MUTATED PRKCQ WILD-TYPE
  R0             9             248
  R1             0               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"
D1294V10, 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
D1294V11, 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(1295) Variable = DNAJC11 MUTATION ANALYSIS
D1295V1, survival
                   sevent
clus2                 0   1
  DNAJC11 MUTATED     7   1
  DNAJC11 WILD-TYPE 275  72
  DNAJC11 MUTATED DNAJC11 WILD-TYPE 
                8               347 
  DNAJC11 MUTATED DNAJC11 WILD-TYPE 
                1                72 
$`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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-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        13.38        13.45        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  DNAJC11 MUTATED DNAJC11 WILD-TYPE 
             2.01              0.00 
  DNAJC11 MUTATED DNAJC11 WILD-TYPE 
            55.04            140.38 
  DNAJC11 MUTATED DNAJC11 WILD-TYPE 
            18.23             20.19 
[1] "2.0 - 55.0 (18.2)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.4"
D1295V2, 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       25       104         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DNAJC11 MUTATED           1          0          1          0        1
  DNAJC11 WILD-TYPE        18         10         40         31       34
                   vv
clus                STAGE IVA STAGE IVB
  DNAJC11 MUTATED           0         0
  DNAJC11 WILD-TYPE        13         1
D1295V3, multiclass
            clus
vv           DNAJC11 MUTATED DNAJC11 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                5               104
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               0                31
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  DNAJC11 MUTATED     0   1   8   0
  DNAJC11 WILD-TYPE   9  67 240  41
D1295V4, multiclass
    clus
vv   DNAJC11 MUTATED DNAJC11 WILD-TYPE
  T1               0                 9
  T2               1                67
  T3               8               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
  DNAJC11 MUTATED     6   2   1
  DNAJC11 WILD-TYPE 214  78  65
D1295V5, multiclass
    clus
vv   DNAJC11 MUTATED DNAJC11 WILD-TYPE
  N0               6               214
  N1               2                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"
D1295V6, binary
                   cls
clus                  0   1
  DNAJC11 MUTATED     7   1
  DNAJC11 WILD-TYPE 276  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DNAJC11 MUTATED      7    1
  DNAJC11 WILD-TYPE  276   47
   clus
vv  DNAJC11 MUTATED DNAJC11 WILD-TYPE
  0               7               276
  1               1                47
[1] 2 2
[1] FALSE
D1295V7, 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
D1295V8, binary
                   cls
clus                  0   1
  DNAJC11 MUTATED     6   3
  DNAJC11 WILD-TYPE 311  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DNAJC11 MUTATED      6    3
  DNAJC11 WILD-TYPE  311   45
                               clus
vv                              DNAJC11 MUTATED DNAJC11 WILD-TYPE
  COLON ADENOCARCINOMA                        6               311
  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 249   2  22  21
D1295V9, multiclass
    clus
vv   DNAJC11 MUTATED DNAJC11 WILD-TYPE
  R0               8               249
  R1               0                 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"
D1295V10, 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
D1295V11, 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(1296) Variable = FOXA2 MUTATION ANALYSIS
D1296V1, survival
                 sevent
clus2               0   1
  FOXA2 MUTATED     5   0
  FOXA2 WILD-TYPE 277  73
  FOXA2 MUTATED FOXA2 WILD-TYPE 
              5             350 
  FOXA2 MUTATED FOXA2 WILD-TYPE 
              0              73 
$`FOXA2 MUTATED`
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3844 TCGA-D5-5539 TCGA-DM-A282 
       78.08         6.97        14.93        19.59       139.17 

$`FOXA2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        61.02         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  FOXA2 MUTATED FOXA2 WILD-TYPE 
           6.97            0.00 
  FOXA2 MUTATED FOXA2 WILD-TYPE 
         139.17          140.38 
  FOXA2 MUTATED FOXA2 WILD-TYPE 
         19.590          20.235 
[1] "7.0 - 139.2 (19.6)" "0.0 - 140.4 (20.2)"
[1] "hr="     "9500000"
D1296V2, 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       23       108         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        19          9         41         30       35        13
                 vv
clus              STAGE IVB
  FOXA2 MUTATED           0
  FOXA2 WILD-TYPE         1
D1296V3, multiclass
            clus
vv           FOXA2 MUTATED FOXA2 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              1             108
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FOXA2 MUTATED     0   0   5   1
  FOXA2 WILD-TYPE   9  68 243  40
D1296V4, multiclass
    clus
vv   FOXA2 MUTATED FOXA2 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             5             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
  FOXA2 MUTATED     4   1   1
  FOXA2 WILD-TYPE 216  79  65
D1296V5, multiclass
    clus
vv   FOXA2 MUTATED FOXA2 WILD-TYPE
  N0             4             216
  N1             1              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"
D1296V6, binary
                 cls
clus                0   1
  FOXA2 MUTATED     5   0
  FOXA2 WILD-TYPE 278  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXA2 MUTATED      5    0
  FOXA2 WILD-TYPE  278   48
   clus
vv  FOXA2 MUTATED FOXA2 WILD-TYPE
  0             5             278
  1             0              48
[1] 2 2
[1] FALSE
D1296V7, 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
D1296V8, binary
                 cls
clus                0   1
  FOXA2 MUTATED     5   1
  FOXA2 WILD-TYPE 312  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXA2 MUTATED      5    1
  FOXA2 WILD-TYPE  312   47
                               clus
vv                              FOXA2 MUTATED FOXA2 WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  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 253   2  22  20
D1296V9, multiclass
    clus
vv   FOXA2 MUTATED FOXA2 WILD-TYPE
  R0             4             253
  R1             0               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"
D1296V10, 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
D1296V11, 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(1297) Variable = ZNF14 MUTATION ANALYSIS
D1297V1, survival
                 sevent
clus2               0   1
  ZNF14 MUTATED    10   2
  ZNF14 WILD-TYPE 272  71
  ZNF14 MUTATED ZNF14 WILD-TYPE 
             12             343 
  ZNF14 MUTATED ZNF14 WILD-TYPE 
              2              71 
$`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 
       61.41         0.33         0.10        16.01        12.49        14.30 

$`ZNF14 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.09        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07         0.26         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  ZNF14 MUTATED ZNF14 WILD-TYPE 
            0.1             0.0 
  ZNF14 MUTATED ZNF14 WILD-TYPE 
          61.41          140.38 
  ZNF14 MUTATED ZNF14 WILD-TYPE 
         15.155          20.280 
[1] "0.1 - 61.4 (15.2)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.1"
D1297V2, 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       25       102         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ZNF14 MUTATED           1          1          0          0        0         0
  ZNF14 WILD-TYPE        18          9         41         31       35        13
                 vv
clus              STAGE IVB
  ZNF14 MUTATED           0
  ZNF14 WILD-TYPE         1
D1297V3, multiclass
            clus
vv           ZNF14 MUTATED ZNF14 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              7             102
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             1               9
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ZNF14 MUTATED     1   1   9   2
  ZNF14 WILD-TYPE   8  67 239  39
D1297V4, multiclass
    clus
vv   ZNF14 MUTATED ZNF14 WILD-TYPE
  T1             1               8
  T2             1              67
  T3             9             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
  ZNF14 MUTATED    12   1   0
  ZNF14 WILD-TYPE 208  79  66
D1297V5, multiclass
    clus
vv   ZNF14 MUTATED ZNF14 WILD-TYPE
  N0            12             208
  N1             1              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"
D1297V6, binary
                 cls
clus                0   1
  ZNF14 MUTATED    12   0
  ZNF14 WILD-TYPE 271  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF14 MUTATED     12    0
  ZNF14 WILD-TYPE  271   48
   clus
vv  ZNF14 MUTATED ZNF14 WILD-TYPE
  0            12             271
  1             0              48
[1] 2 2
[1] FALSE
D1297V7, 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
D1297V8, binary
                 cls
clus                0   1
  ZNF14 MUTATED    11   2
  ZNF14 WILD-TYPE 306  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF14 MUTATED     11    2
  ZNF14 WILD-TYPE  306   46
                               clus
vv                              ZNF14 MUTATED ZNF14 WILD-TYPE
  COLON ADENOCARCINOMA                     11             306
  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 250   2  22  18
D1297V9, multiclass
    clus
vv   ZNF14 MUTATED ZNF14 WILD-TYPE
  R0             7             250
  R1             0               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"
D1297V10, 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
D1297V11, 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(1298) Variable = FLNB MUTATION ANALYSIS
D1298V1, survival
                sevent
clus2              0   1
  FLNB MUTATED    22   5
  FLNB WILD-TYPE 260  68
  FLNB MUTATED FLNB WILD-TYPE 
            27            328 
  FLNB MUTATED FLNB WILD-TYPE 
             5             68 
$`FLNB MUTATED`
TCGA-A6-5661 TCGA-A6-6138 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3492 
       33.53        22.52        24.39        20.12        19.66         3.02 
TCGA-AA-3516 TCGA-AA-3663 TCGA-AA-3713 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-A00A 
       13.02         6.97        19.04        53.00        31.00        38.04 
TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01T 
       18.05         4.01        34.98         1.02        35.01        33.04 
TCGA-AD-6889 TCGA-AU-6004 TCGA-AY-6197 TCGA-CA-6717 TCGA-CK-5916 TCGA-CM-4746 
       56.55        27.09        21.44         0.33        21.14        37.02 
TCGA-D5-6920 TCGA-DM-A1D4 TCGA-G4-6588 
       12.39        92.75        26.17 

$`FLNB WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 
       24.16        21.76        24.69        23.87        20.28         7.04 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        1.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K 
       27.02        13.94        19.00        30.02        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       31.00        38.07         1.02        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       15.75         0.20        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        51.32        21.99         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        91.79        46.75        52.80 

  FLNB MUTATED FLNB WILD-TYPE 
          0.33           0.00 
  FLNB MUTATED FLNB WILD-TYPE 
         92.75         140.38 
  FLNB MUTATED FLNB WILD-TYPE 
         22.52          19.99 
[1] "0.3 - 92.8 (22.5)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1.1"
D1298V2, 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       20       100         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        16         10         40         30       34        13
                vv
clus             STAGE IVB
  FLNB MUTATED           0
  FLNB WILD-TYPE         1
D1298V3, multiclass
            clus
vv           FLNB MUTATED FLNB WILD-TYPE
  STAGE I               6             58
  STAGE IA              0              1
  STAGE II              5             20
  STAGE IIA             9            100
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             3             16
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            1             30
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  FLNB MUTATED     2   4  17   5
  FLNB WILD-TYPE   7  64 231  36
D1298V4, multiclass
    clus
vv   FLNB MUTATED FLNB WILD-TYPE
  T1            2              7
  T2            4             64
  T3           17            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
  FLNB MUTATED    23   3   2
  FLNB WILD-TYPE 197  77  64
D1298V5, multiclass
    clus
vv   FLNB MUTATED FLNB WILD-TYPE
  N0           23            197
  N1            3             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"
D1298V6, binary
                cls
clus               0   1
  FLNB MUTATED    24   1
  FLNB WILD-TYPE 259  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLNB MUTATED     24    1
  FLNB WILD-TYPE  259   47
   clus
vv  FLNB MUTATED FLNB WILD-TYPE
  0           24            259
  1            1             47
[1] 2 2
[1] FALSE
D1298V7, 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
D1298V8, binary
                cls
clus               0   1
  FLNB MUTATED    20   8
  FLNB WILD-TYPE 297  40
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLNB MUTATED     20    8
  FLNB WILD-TYPE  297   40
                               clus
vv                              FLNB MUTATED FLNB WILD-TYPE
  COLON ADENOCARCINOMA                    20            297
  COLON MUCINOUS ADENOCARCINOMA            8             40
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  FLNB MUTATED    19   0   1   2
  FLNB WILD-TYPE 238   2  21  19
D1298V9, multiclass
    clus
vv   FLNB MUTATED FLNB WILD-TYPE
  R0           19            238
  R1            0              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"
D1298V10, 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
D1298V11, 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(1299) Variable = DUSP9 MUTATION ANALYSIS
D1299V1, survival
                 sevent
clus2               0   1
  DUSP9 MUTATED     8   1
  DUSP9 WILD-TYPE 274  72
  DUSP9 MUTATED DUSP9 WILD-TYPE 
              9             346 
  DUSP9 MUTATED DUSP9 WILD-TYPE 
              1              72 
$`DUSP9 MUTATED`
TCGA-A6-6652 TCGA-A6-6782 TCGA-AA-3655 TCGA-AA-3821 TCGA-CM-4743 TCGA-D5-6534 
       24.69        20.28        61.02         1.02        23.05        43.27 
TCGA-D5-6930 TCGA-G4-6303 TCGA-G4-6588 
        1.51        65.85        26.17 

$`DUSP9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       33.04         0.99        25.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       19.43       107.67        74.56        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        91.79        46.75        52.80 

  DUSP9 MUTATED DUSP9 WILD-TYPE 
           1.02            0.00 
  DUSP9 MUTATED DUSP9 WILD-TYPE 
          65.85          140.38 
  DUSP9 MUTATED DUSP9 WILD-TYPE 
         24.690          20.005 
[1] "1.0 - 65.8 (24.7)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "2.2"
D1299V2, 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       24       105         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        19         10         41         31       34        12
                 vv
clus              STAGE IVB
  DUSP9 MUTATED           0
  DUSP9 WILD-TYPE         1
D1299V3, multiclass
            clus
vv           DUSP9 MUTATED DUSP9 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              4             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 241  40
D1299V4, multiclass
    clus
vv   DUSP9 MUTATED DUSP9 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             7             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
  DUSP9 MUTATED     8   1   0
  DUSP9 WILD-TYPE 212  79  66
D1299V5, multiclass
    clus
vv   DUSP9 MUTATED DUSP9 WILD-TYPE
  N0             8             212
  N1             1              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"
D1299V6, binary
                 cls
clus                0   1
  DUSP9 MUTATED     6   2
  DUSP9 WILD-TYPE 277  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DUSP9 MUTATED      6    2
  DUSP9 WILD-TYPE  277   46
   clus
vv  DUSP9 MUTATED DUSP9 WILD-TYPE
  0             6             277
  1             2              46
[1] 2 2
[1] FALSE
D1299V7, 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
D1299V8, binary
                 cls
clus                0   1
  DUSP9 MUTATED     6   3
  DUSP9 WILD-TYPE 311  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DUSP9 MUTATED      6    3
  DUSP9 WILD-TYPE  311   45
                               clus
vv                              DUSP9 MUTATED DUSP9 WILD-TYPE
  COLON ADENOCARCINOMA                      6             311
  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 250   2  22  21
D1299V9, multiclass
    clus
vv   DUSP9 MUTATED DUSP9 WILD-TYPE
  R0             7             250
  R1             0               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"
D1299V10, 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
D1299V11, 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(1300) Variable = PCDH9 MUTATION ANALYSIS
D1300V1, survival
                 sevent
clus2               0   1
  PCDH9 MUTATED    32   6
  PCDH9 WILD-TYPE 250  67
  PCDH9 MUTATED PCDH9 WILD-TYPE 
             38             317 
  PCDH9 MUTATED PCDH9 WILD-TYPE 
              6              67 
$`PCDH9 MUTATED`
TCGA-A6-6141 TCGA-AA-3510 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3555 TCGA-AA-3679 
        8.38        63.98        29.00        12.99        29.95        15.02 
TCGA-AA-3715 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3831 TCGA-AA-3842 TCGA-AA-3939 
       19.04        33.04         0.99        17.98        37.02        12.99 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A00U TCGA-AA-A010 
       34.03         2.01        25.02         4.01        17.03        34.98 
TCGA-AA-A01K TCGA-AD-6895 TCGA-AU-6004 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-5403 
       31.00         0.72        27.09        21.44        58.39        62.79 
TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-5254 TCGA-CA-6715 TCGA-CA-6717 TCGA-CM-4743 
       49.41       100.01         2.24         0.07         0.33        23.05 
TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-6166 TCGA-CM-6171 TCGA-D5-6538 TCGA-D5-6898 
       13.02        22.03        21.99        14.04        17.13         7.53 
TCGA-G4-6293 TCGA-G4-6586 
      107.67        35.80 

$`PCDH9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3543 
        0.00        19.07        34.03        29.00        26.01         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
        0.92        50.04        47.01        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3833 TCGA-AA-3837 
       10.06        35.05        25.02         1.02        15.95        38.99 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05        31.00         2.01        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       24.00         2.01        20.98        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        4.21        56.55         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
        0.20        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       61.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 
        3.19         1.94         3.06         3.25         3.29         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.41        19.43        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        26.17        91.79        46.75        52.80 

  PCDH9 MUTATED PCDH9 WILD-TYPE 
           0.07            0.00 
  PCDH9 MUTATED PCDH9 WILD-TYPE 
         107.67          140.38 
  PCDH9 MUTATED PCDH9 WILD-TYPE 
         21.715          20.120 
[1] "0.1 - 107.7 (21.7)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.4"
D1300V2, 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       20        93         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PCDH9 MUTATED           1          1          4          2        1         0
  PCDH9 WILD-TYPE        18          9         37         29       34        13
                 vv
clus              STAGE IVB
  PCDH9 MUTATED           0
  PCDH9 WILD-TYPE         1
D1300V3, multiclass
            clus
vv           PCDH9 MUTATED PCDH9 WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               5              20
  STAGE IIA             16              93
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             1               9
  STAGE IIIB             4              37
  STAGE IIIC             2              29
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PCDH9 MUTATED     0   6  30   2
  PCDH9 WILD-TYPE   9  62 218  39
D1300V4, multiclass
    clus
vv   PCDH9 MUTATED PCDH9 WILD-TYPE
  T1             0               9
  T2             6              62
  T3            30             218
  T4             2              39
[1] 4 2
[1] TRUE
[1] "dimension 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  74  62
D1300V5, multiclass
    clus
vv   PCDH9 MUTATED PCDH9 WILD-TYPE
  N0            28             192
  N1             6              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"
D1300V6, binary
                 cls
clus                0   1
  PCDH9 MUTATED    32   1
  PCDH9 WILD-TYPE 251  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCDH9 MUTATED     32    1
  PCDH9 WILD-TYPE  251   47
   clus
vv  PCDH9 MUTATED PCDH9 WILD-TYPE
  0            32             251
  1             1              47
[1] 2 2
[1] FALSE
D1300V7, 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
D1300V8, binary
                 cls
clus                0   1
  PCDH9 MUTATED    34   4
  PCDH9 WILD-TYPE 283  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCDH9 MUTATED     34    4
  PCDH9 WILD-TYPE  283   44
                               clus
vv                              PCDH9 MUTATED PCDH9 WILD-TYPE
  COLON ADENOCARCINOMA                     34             283
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PCDH9 MUTATED    27   0   1   3
  PCDH9 WILD-TYPE 230   2  21  18
D1300V9, multiclass
    clus
vv   PCDH9 MUTATED PCDH9 WILD-TYPE
  R0            27             230
  R1             0               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"
D1300V10, 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
D1300V11, 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(1301) Variable = MAP2 MUTATION ANALYSIS
D1301V1, survival
                sevent
clus2              0   1
  MAP2 MUTATED    27   8
  MAP2 WILD-TYPE 255  65
  MAP2 MUTATED MAP2 WILD-TYPE 
            35            320 
  MAP2 MUTATED MAP2 WILD-TYPE 
             8             65 
$`MAP2 MUTATED`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-5660 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3492 
       43.76        46.65        29.19        22.06        19.66         3.02 
TCGA-AA-3510 TCGA-AA-3518 TCGA-AA-3525 TCGA-AA-3663 TCGA-AA-3818 TCGA-AA-3819 
       63.98         1.02         8.05         6.97         0.99        25.02 
TCGA-AA-3852 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3980 TCGA-AA-A00J TCGA-AA-A00N 
        0.00        26.01        24.00        27.02        18.05         4.01 
TCGA-AA-A010 TCGA-AA-A01Z TCGA-AD-5900 TCGA-AD-6964 TCGA-AD-6965 TCGA-AZ-4315 
       34.98        37.02         0.07        10.88         0.20        58.39 
TCGA-AZ-6601 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4950 TCGA-CM-6167 TCGA-CM-6171 
      100.01         0.33         0.10        40.34        14.99        14.04 
TCGA-CM-6676 TCGA-D5-5540 TCGA-F4-6570 TCGA-F4-6856 TCGA-G4-6323 
       11.08        13.51         6.18        19.43        13.78 

$`MAP2 WILD-TYPE`
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       43.76        42.90        24.33        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       33.34        32.75        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 
       30.44        33.53        23.61        22.09        32.71        27.09 
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 
       22.52         8.38        25.08        25.18        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 
       24.69        24.39        23.87        20.12        20.28         7.04 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 
        9.07        24.03        37.05        36.03        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3854 
        0.00        17.03        10.06         0.00        33.07        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3952 TCGA-AA-3955 
        2.01        12.99        24.00        33.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        25.02        24.00        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 TCGA-AA-A029 
        1.02        33.04        35.01        26.01        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AU-3779 
        0.79         0.72         5.79        22.42        27.42        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07         0.26         1.35        17.56       102.44 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        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-6677 
       13.02        15.02        11.01        12.95        13.05        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 
       33.67        13.25         0.53        35.41       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.72        36.00        22.09        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  MAP2 MUTATED MAP2 WILD-TYPE 
             0              0 
  MAP2 MUTATED MAP2 WILD-TYPE 
        100.01         140.38 
  MAP2 MUTATED MAP2 WILD-TYPE 
        14.990         20.995 
[1] "0.0 - 100.0 (15.0)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.3"
D1301V2, 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       20        97         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MAP2 MUTATED           0          1          4          3        1         0
  MAP2 WILD-TYPE        19          9         37         28       34        13
                vv
clus             STAGE IVB
  MAP2 MUTATED           0
  MAP2 WILD-TYPE         1
D1301V3, multiclass
            clus
vv           MAP2 MUTATED MAP2 WILD-TYPE
  STAGE I               5             59
  STAGE IA              1              0
  STAGE II              5             20
  STAGE IIA            12             97
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            1              9
  STAGE IIIB            4             37
  STAGE IIIC            3             28
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MAP2 MUTATED     0   5  24   6
  MAP2 WILD-TYPE   9  63 224  35
D1301V4, multiclass
    clus
vv   MAP2 MUTATED MAP2 WILD-TYPE
  T1            0              9
  T2            5             63
  T3           24            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
  MAP2 MUTATED    25   6   5
  MAP2 WILD-TYPE 195  74  61
D1301V5, multiclass
    clus
vv   MAP2 MUTATED MAP2 WILD-TYPE
  N0           25            195
  N1            6             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"
D1301V6, binary
                cls
clus               0   1
  MAP2 MUTATED    30   1
  MAP2 WILD-TYPE 253  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAP2 MUTATED     30    1
  MAP2 WILD-TYPE  253   47
   clus
vv  MAP2 MUTATED MAP2 WILD-TYPE
  0           30            253
  1            1             47
[1] 2 2
[1] FALSE
D1301V7, 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
D1301V8, binary
                cls
clus               0   1
  MAP2 MUTATED    27   9
  MAP2 WILD-TYPE 290  39
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAP2 MUTATED     27    9
  MAP2 WILD-TYPE  290   39
                               clus
vv                              MAP2 MUTATED MAP2 WILD-TYPE
  COLON ADENOCARCINOMA                    27            290
  COLON MUCINOUS ADENOCARCINOMA            9             39
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MAP2 MUTATED    28   1   0   2
  MAP2 WILD-TYPE 229   1  22  19
D1301V9, multiclass
    clus
vv   MAP2 MUTATED MAP2 WILD-TYPE
  R0           28            229
  R1            1              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"
D1301V10, 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
D1301V11, 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(1302) Variable = TRAF2 MUTATION ANALYSIS
D1302V1, survival
                 sevent
clus2               0   1
  TRAF2 MUTATED     6   1
  TRAF2 WILD-TYPE 276  72
  TRAF2 MUTATED TRAF2 WILD-TYPE 
              7             348 
  TRAF2 MUTATED TRAF2 WILD-TYPE 
              1              72 
$`TRAF2 MUTATED`
TCGA-AA-3502 TCGA-AA-3662 TCGA-AA-3715 TCGA-AY-6386 TCGA-AZ-5407 TCGA-CA-6718 
       35.01         6.05        19.04        17.82        61.41         0.10 
TCGA-D5-6540 
       16.14 

$`TRAF2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       19.99        13.94        19.99        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  TRAF2 MUTATED TRAF2 WILD-TYPE 
            0.1             0.0 
  TRAF2 MUTATED TRAF2 WILD-TYPE 
          61.41          140.38 
  TRAF2 MUTATED TRAF2 WILD-TYPE 
          17.82           20.63 
[1] "0.1 - 61.4 (17.8)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "1.3"
D1302V2, 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       24       108         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        19         10         40         31       34        13
                 vv
clus              STAGE IVB
  TRAF2 MUTATED           0
  TRAF2 WILD-TYPE         1
D1302V3, multiclass
            clus
vv           TRAF2 MUTATED TRAF2 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              1             108
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TRAF2 MUTATED     1   2   3   1
  TRAF2 WILD-TYPE   8  66 245  40
D1302V4, multiclass
    clus
vv   TRAF2 MUTATED TRAF2 WILD-TYPE
  T1             1               8
  T2             2              66
  T3             3             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
  TRAF2 MUTATED     5   1   1
  TRAF2 WILD-TYPE 215  79  65
D1302V5, multiclass
    clus
vv   TRAF2 MUTATED TRAF2 WILD-TYPE
  N0             5             215
  N1             1              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"
D1302V6, binary
                 cls
clus                0   1
  TRAF2 MUTATED     6   1
  TRAF2 WILD-TYPE 277  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRAF2 MUTATED      6    1
  TRAF2 WILD-TYPE  277   47
   clus
vv  TRAF2 MUTATED TRAF2 WILD-TYPE
  0             6             277
  1             1              47
[1] 2 2
[1] FALSE
D1302V7, 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
D1302V8, binary
                 cls
clus                0   1
  TRAF2 MUTATED     6   1
  TRAF2 WILD-TYPE 311  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRAF2 MUTATED      6    1
  TRAF2 WILD-TYPE  311   47
                               clus
vv                              TRAF2 MUTATED TRAF2 WILD-TYPE
  COLON ADENOCARCINOMA                      6             311
  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 253   2  21  20
D1302V9, multiclass
    clus
vv   TRAF2 MUTATED TRAF2 WILD-TYPE
  R0             4             253
  R1             0               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"
D1302V10, 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
D1302V11, 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(1303) Variable = ZNF711 MUTATION ANALYSIS
D1303V1, survival
                  sevent
clus2                0   1
  ZNF711 MUTATED     7   2
  ZNF711 WILD-TYPE 275  71
  ZNF711 MUTATED ZNF711 WILD-TYPE 
               9              346 
  ZNF711 MUTATED ZNF711 WILD-TYPE 
               2               71 
$`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        11.51 
TCGA-D5-6539 TCGA-D5-6928 TCGA-F4-6570 
       12.49        11.64         6.18 

$`ZNF711 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        32.71        27.09         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 
       43.27        15.12        17.85         4.80        17.13        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  ZNF711 MUTATED ZNF711 WILD-TYPE 
            1.02             0.00 
  ZNF711 MUTATED ZNF711 WILD-TYPE 
           27.09           140.38 
  ZNF711 MUTATED ZNF711 WILD-TYPE 
           11.64            20.63 
[1] "1.0 - 27.1 (11.6)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "2"  
D1303V2, 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       23       107         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF711 MUTATED           0          1          2          0        1
  ZNF711 WILD-TYPE        19          9         39         31       34
                  vv
clus               STAGE IVA STAGE IVB
  ZNF711 MUTATED           0         0
  ZNF711 WILD-TYPE        13         1
D1303V3, multiclass
            clus
vv           ZNF711 MUTATED ZNF711 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               2              107
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              1                9
  STAGE IIIB              2               39
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF711 MUTATED     0   2   7   1
  ZNF711 WILD-TYPE   9  66 241  40
D1303V4, multiclass
    clus
vv   ZNF711 MUTATED ZNF711 WILD-TYPE
  T1              0                9
  T2              2               66
  T3              7              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
  ZNF711 MUTATED     7   2   1
  ZNF711 WILD-TYPE 213  78  65
D1303V5, multiclass
    clus
vv   ZNF711 MUTATED ZNF711 WILD-TYPE
  N0              7              213
  N1              2               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"
D1303V6, binary
                  cls
clus                 0   1
  ZNF711 MUTATED     8   1
  ZNF711 WILD-TYPE 275  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF711 MUTATED      8    1
  ZNF711 WILD-TYPE  275   47
   clus
vv  ZNF711 MUTATED ZNF711 WILD-TYPE
  0              8              275
  1              1               47
[1] 2 2
[1] FALSE
D1303V7, 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
D1303V8, binary
                  cls
clus                 0   1
  ZNF711 MUTATED     9   1
  ZNF711 WILD-TYPE 308  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF711 MUTATED      9    1
  ZNF711 WILD-TYPE  308   47
                               clus
vv                              ZNF711 MUTATED ZNF711 WILD-TYPE
  COLON ADENOCARCINOMA                       9              308
  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 250   2  21  21
D1303V9, multiclass
    clus
vv   ZNF711 MUTATED ZNF711 WILD-TYPE
  R0              7              250
  R1              0                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"
D1303V10, 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
D1303V11, 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(1304) Variable = SYNJ1 MUTATION ANALYSIS
D1304V1, survival
                 sevent
clus2               0   1
  SYNJ1 MUTATED    12   3
  SYNJ1 WILD-TYPE 270  70
  SYNJ1 MUTATED SYNJ1 WILD-TYPE 
             15             340 
  SYNJ1 MUTATED SYNJ1 WILD-TYPE 
              3              70 
$`SYNJ1 MUTATED`
TCGA-AA-3492 TCGA-AA-3555 TCGA-AA-3672 TCGA-AA-3710 TCGA-AA-3977 TCGA-AA-A010 
        3.02        29.95         0.92        26.99        25.02        34.98 
TCGA-AD-6895 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-5860 
        0.72        49.41        12.10         0.33         0.10        16.01 
TCGA-CM-6161 TCGA-CM-6168 TCGA-G4-6628 
       15.02        12.99        52.80 

$`SYNJ1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        17.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21        56.55         0.79         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.26         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       35.80        26.17        91.79        46.75 

  SYNJ1 MUTATED SYNJ1 WILD-TYPE 
            0.1             0.0 
  SYNJ1 MUTATED SYNJ1 WILD-TYPE 
          52.80          140.38 
  SYNJ1 MUTATED SYNJ1 WILD-TYPE 
          15.02           20.63 
[1] "0.1 - 52.8 (15.0)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "1.3"
D1304V2, 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       23       102         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SYNJ1 MUTATED           1          0          0          0        1         0
  SYNJ1 WILD-TYPE        18         10         41         31       34        13
                 vv
clus              STAGE IVB
  SYNJ1 MUTATED           0
  SYNJ1 WILD-TYPE         1
D1304V3, multiclass
            clus
vv           SYNJ1 MUTATED SYNJ1 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              7             102
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SYNJ1 MUTATED     0   3  11   2
  SYNJ1 WILD-TYPE   9  65 237  39
D1304V4, multiclass
    clus
vv   SYNJ1 MUTATED SYNJ1 WILD-TYPE
  T1             0               9
  T2             3              65
  T3            11             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
  SYNJ1 MUTATED    13   3   0
  SYNJ1 WILD-TYPE 207  77  66
D1304V5, multiclass
    clus
vv   SYNJ1 MUTATED SYNJ1 WILD-TYPE
  N0            13             207
  N1             3              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"
D1304V6, binary
                 cls
clus                0   1
  SYNJ1 MUTATED    12   1
  SYNJ1 WILD-TYPE 271  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYNJ1 MUTATED     12    1
  SYNJ1 WILD-TYPE  271   47
   clus
vv  SYNJ1 MUTATED SYNJ1 WILD-TYPE
  0            12             271
  1             1              47
[1] 2 2
[1] FALSE
D1304V7, 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
D1304V8, binary
                 cls
clus                0   1
  SYNJ1 MUTATED    14   2
  SYNJ1 WILD-TYPE 303  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYNJ1 MUTATED     14    2
  SYNJ1 WILD-TYPE  303   46
                               clus
vv                              SYNJ1 MUTATED SYNJ1 WILD-TYPE
  COLON ADENOCARCINOMA                     14             303
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SYNJ1 MUTATED    10   0   0   2
  SYNJ1 WILD-TYPE 247   2  22  19
D1304V9, multiclass
    clus
vv   SYNJ1 MUTATED SYNJ1 WILD-TYPE
  R0            10             247
  R1             0               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"
D1304V10, 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
D1304V11, 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(1305) Variable = BTBD3 MUTATION ANALYSIS
D1305V1, survival
                 sevent
clus2               0   1
  BTBD3 MUTATED    10   2
  BTBD3 WILD-TYPE 272  71
  BTBD3 MUTATED BTBD3 WILD-TYPE 
             12             343 
  BTBD3 MUTATED BTBD3 WILD-TYPE 
              2              71 
$`BTBD3 MUTATED`
TCGA-A6-5661 TCGA-A6-6137 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-A00N TCGA-AU-6004 
       33.53        27.09         6.05         6.97         4.01        27.09 
TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CM-6162 TCGA-D5-6541 TCGA-G4-6315 TCGA-G4-6321 
       58.39        49.41        12.00        15.58        36.72        22.09 

$`BTBD3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       13.94        19.99        61.02        78.08        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        16.14         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  BTBD3 MUTATED BTBD3 WILD-TYPE 
           4.01            0.00 
  BTBD3 MUTATED BTBD3 WILD-TYPE 
          58.39          140.38 
  BTBD3 MUTATED BTBD3 WILD-TYPE 
          24.59           20.12 
[1] "4.0 - 58.4 (24.6)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.2"
D1305V2, 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       22       106         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        18         10         39         31       33        13
                 vv
clus              STAGE IVB
  BTBD3 MUTATED           0
  BTBD3 WILD-TYPE         1
D1305V3, multiclass
            clus
vv           BTBD3 MUTATED BTBD3 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              3             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               2              33
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  BTBD3 MUTATED     0   2   8   3
  BTBD3 WILD-TYPE   9  66 240  38
D1305V4, multiclass
    clus
vv   BTBD3 MUTATED BTBD3 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             8             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
  BTBD3 MUTATED     8   4   1
  BTBD3 WILD-TYPE 212  76  65
D1305V5, multiclass
    clus
vv   BTBD3 MUTATED BTBD3 WILD-TYPE
  N0             8             212
  N1             4              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"
D1305V6, binary
                 cls
clus                0   1
  BTBD3 MUTATED     9   2
  BTBD3 WILD-TYPE 274  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTBD3 MUTATED      9    2
  BTBD3 WILD-TYPE  274   46
   clus
vv  BTBD3 MUTATED BTBD3 WILD-TYPE
  0             9             274
  1             2              46
[1] 2 2
[1] FALSE
D1305V7, 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
D1305V8, binary
                 cls
clus                0   1
  BTBD3 MUTATED    11   2
  BTBD3 WILD-TYPE 306  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTBD3 MUTATED     11    2
  BTBD3 WILD-TYPE  306   46
                               clus
vv                              BTBD3 MUTATED BTBD3 WILD-TYPE
  COLON ADENOCARCINOMA                     11             306
  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 247   2  21  21
D1305V9, multiclass
    clus
vv   BTBD3 MUTATED BTBD3 WILD-TYPE
  R0            10             247
  R1             0               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"
D1305V10, 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
D1305V11, 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(1306) Variable = MAGOHB MUTATION ANALYSIS
D1306V1, survival
                  sevent
clus2                0   1
  MAGOHB MUTATED     2   1
  MAGOHB WILD-TYPE 280  72
  MAGOHB MUTATED MAGOHB WILD-TYPE 
               3              352 
  MAGOHB MUTATED MAGOHB WILD-TYPE 
               1               72 
$`MAGOHB MUTATED`
TCGA-AY-6196 TCGA-AZ-6605 TCGA-F4-6569 
        0.20         5.23        13.45 

$`MAGOHB WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        15.75        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 
       49.41         6.77        12.10       100.01        29.56        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  MAGOHB MUTATED MAGOHB WILD-TYPE 
             0.2              0.0 
  MAGOHB MUTATED MAGOHB WILD-TYPE 
           13.45           140.38 
  MAGOHB MUTATED MAGOHB WILD-TYPE 
            5.23            20.63 
[1] "0.2 - 13.4 (5.2)"   "0.0 - 140.4 (20.6)"
[1] "hr=" "4.8"
D1306V2, 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       25       109         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAGOHB MUTATED           0          0          1          1        0
  MAGOHB WILD-TYPE        19         10         40         30       35
                  vv
clus               STAGE IVA STAGE IVB
  MAGOHB MUTATED           0         0
  MAGOHB WILD-TYPE        13         1
D1306V3, multiclass
            clus
vv           MAGOHB MUTATED MAGOHB WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               0              109
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MAGOHB MUTATED     0   1   1   1
  MAGOHB WILD-TYPE   9  67 247  40
D1306V4, multiclass
    clus
vv   MAGOHB MUTATED MAGOHB WILD-TYPE
  T1              0                9
  T2              1               67
  T3              1              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
  MAGOHB MUTATED     1   1   1
  MAGOHB WILD-TYPE 219  79  65
D1306V5, multiclass
    clus
vv   MAGOHB MUTATED MAGOHB WILD-TYPE
  N0              1              219
  N1              1               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"
D1306V6, binary
                  cls
clus                 0   1
  MAGOHB MUTATED     2   0
  MAGOHB WILD-TYPE 281  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGOHB MUTATED      2    0
  MAGOHB WILD-TYPE  281   48
   clus
vv  MAGOHB MUTATED MAGOHB WILD-TYPE
  0              2              281
  1              0               48
[1] 2 2
[1] FALSE
D1306V7, 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
D1306V8, binary
                  cls
clus                 0   1
  MAGOHB MUTATED     2   1
  MAGOHB WILD-TYPE 315  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGOHB MUTATED      2    1
  MAGOHB WILD-TYPE  315   47
                               clus
vv                              MAGOHB MUTATED MAGOHB WILD-TYPE
  COLON ADENOCARCINOMA                       2              315
  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 255   2  22  21
D1306V9, multiclass
[1] "Remove cluster labels:" "MAGOHB MUTATED"        
clus
  MAGOHB MUTATED MAGOHB WILD-TYPE 
               2              300 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-A6-2677       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-3496       TCGA-AA-3502 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-3510       TCGA-AA-3511       TCGA-AA-3514       TCGA-AA-3517 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-3518       TCGA-AA-3519       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-3526 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-3527       TCGA-AA-3529       TCGA-AA-3530       TCGA-AA-3531 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-3532       TCGA-AA-3534       TCGA-AA-3538       TCGA-AA-3542 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-3543       TCGA-AA-3544       TCGA-AA-3548       TCGA-AA-3549 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-3552       TCGA-AA-3553       TCGA-AA-3554       TCGA-AA-3555 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-3556       TCGA-AA-3558       TCGA-AA-3560       TCGA-AA-3561 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-3562       TCGA-AA-3655       TCGA-AA-3660       TCGA-AA-3662 
"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-3672       TCGA-AA-3673       TCGA-AA-3678       TCGA-AA-3679 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-3680       TCGA-AA-3681       TCGA-AA-3684       TCGA-AA-3685 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-3688       TCGA-AA-3692       TCGA-AA-3693       TCGA-AA-3695 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-3696       TCGA-AA-3697       TCGA-AA-3710       TCGA-AA-3712 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-3713       TCGA-AA-3715       TCGA-AA-3811       TCGA-AA-3812 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-3814       TCGA-AA-3815       TCGA-AA-3818       TCGA-AA-3819 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-3821       TCGA-AA-3831       TCGA-AA-3833       TCGA-AA-3837 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-3842       TCGA-AA-3844       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-3860       TCGA-AA-3861       TCGA-AA-3864       TCGA-AA-3866 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-3867       TCGA-AA-3869       TCGA-AA-3870       TCGA-AA-3872 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-3875       TCGA-AA-3877       TCGA-AA-3930       TCGA-AA-3939 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-3941       TCGA-AA-3947       TCGA-AA-3949       TCGA-AA-3950 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-3952       TCGA-AA-3955       TCGA-AA-3956       TCGA-AA-3968 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-3971       TCGA-AA-3972       TCGA-AA-3973       TCGA-AA-3975 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-3976       TCGA-AA-3979       TCGA-AA-3984       TCGA-AA-3986 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-3989       TCGA-AA-3994       TCGA-AA-A004       TCGA-AA-A00A 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-A00D       TCGA-AA-A00E       TCGA-AA-A00F       TCGA-AA-A00J 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-A00K       TCGA-AA-A00L       TCGA-AA-A00N       TCGA-AA-A00O 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-A00Q       TCGA-AA-A00R       TCGA-AA-A00U       TCGA-AA-A00W 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-A00Z       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-A024       TCGA-AA-A029       TCGA-AA-A02F 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-A02H       TCGA-AA-A02J       TCGA-AA-A02K       TCGA-AA-A02O 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AA-A02W       TCGA-AA-A02Y       TCGA-AA-A03F       TCGA-AA-A03J 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AD-5900       TCGA-AD-6548       TCGA-AD-6888       TCGA-AU-3779 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AU-6004       TCGA-AY-4070       TCGA-AY-4071       TCGA-AY-5543 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AY-6197       TCGA-AY-6386       TCGA-AZ-4315       TCGA-AZ-4681 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-AZ-4682       TCGA-CA-5254       TCGA-CA-5255       TCGA-CA-5796 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-CA-5797       TCGA-CA-6715       TCGA-CA-6716       TCGA-CA-6717 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-CA-6718       TCGA-CA-6719       TCGA-CK-4947       TCGA-CK-4948 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-CK-4950       TCGA-CK-4952       TCGA-CK-5912       TCGA-CK-5913 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-CK-5914       TCGA-CK-5915       TCGA-CK-5916       TCGA-CK-6746 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-CK-6747       TCGA-CK-6748       TCGA-CK-6751       TCGA-CM-4743 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-CM-4744       TCGA-CM-4746       TCGA-CM-4747       TCGA-CM-4752 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-CM-5341       TCGA-CM-5344       TCGA-CM-5348       TCGA-CM-5349 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-CM-5860       TCGA-CM-5861       TCGA-CM-5862       TCGA-CM-5863 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-CM-5864       TCGA-CM-5868       TCGA-CM-6161       TCGA-CM-6162 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-CM-6163       TCGA-CM-6164       TCGA-CM-6165       TCGA-CM-6166 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-CM-6167       TCGA-CM-6168       TCGA-CM-6169       TCGA-CM-6170 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-CM-6171       TCGA-CM-6172       TCGA-CM-6674       TCGA-CM-6675 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-CM-6676       TCGA-CM-6677       TCGA-CM-6678       TCGA-CM-6679 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-CM-6680       TCGA-D5-5537       TCGA-D5-5538       TCGA-D5-5539 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-D5-5540       TCGA-D5-5541       TCGA-D5-6529       TCGA-D5-6532 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-D5-6533       TCGA-D5-6534       TCGA-D5-6535       TCGA-D5-6536 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-D5-6537       TCGA-D5-6538       TCGA-D5-6539       TCGA-D5-6540 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-D5-6541       TCGA-D5-6898       TCGA-D5-6920       TCGA-D5-6922 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-D5-6923       TCGA-D5-6924       TCGA-D5-6926       TCGA-D5-6927 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-D5-6928       TCGA-D5-6929       TCGA-D5-6930       TCGA-D5-6931 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-D5-6932       TCGA-D5-7000       TCGA-F4-6459       TCGA-F4-6460 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704       TCGA-F4-6805 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808       TCGA-F4-6809 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856       TCGA-G4-6293 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304       TCGA-G4-6306 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310       TCGA-G4-6315 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323       TCGA-G4-6586 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
      TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628 
"MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" "MAGOHB WILD-TYPE" 
D1306V10, 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
D1306V11, 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(1307) Variable = CDH24 MUTATION ANALYSIS
D1307V1, survival
                 sevent
clus2               0   1
  CDH24 MUTATED     9   2
  CDH24 WILD-TYPE 273  71
  CDH24 MUTATED CDH24 WILD-TYPE 
             11             344 
  CDH24 MUTATED CDH24 WILD-TYPE 
              2              71 
$`CDH24 MUTATED`
TCGA-A6-4105 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3710 TCGA-AA-3713 
       14.53        22.06        19.66         3.02        26.99        19.04 
TCGA-AA-3966 TCGA-AA-A00U TCGA-AA-A010 TCGA-AY-6386 TCGA-CK-6747 
        2.01        17.03        34.98        17.82         2.93 

$`CDH24 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00W 
       38.04         4.01        27.02        42.02         0.99        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 
       15.62        49.08        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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  CDH24 MUTATED CDH24 WILD-TYPE 
           2.01            0.00 
  CDH24 MUTATED CDH24 WILD-TYPE 
          34.98          140.38 
  CDH24 MUTATED CDH24 WILD-TYPE 
          17.82           20.98 
[1] "2.0 - 35.0 (17.8)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.4"
D1307V2, 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       24       104         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CDH24 MUTATED           0          0          2          1        1         0
  CDH24 WILD-TYPE        19         10         39         30       34        13
                 vv
clus              STAGE IVB
  CDH24 MUTATED           0
  CDH24 WILD-TYPE         1
D1307V3, multiclass
            clus
vv           CDH24 MUTATED CDH24 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              5             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CDH24 MUTATED     0   0   9   2
  CDH24 WILD-TYPE   9  68 239  39
D1307V4, multiclass
    clus
vv   CDH24 MUTATED CDH24 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             9             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   3   0
  CDH24 WILD-TYPE 212  77  66
D1307V5, multiclass
    clus
vv   CDH24 MUTATED CDH24 WILD-TYPE
  N0             8             212
  N1             3              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"
D1307V6, binary
                 cls
clus                0   1
  CDH24 MUTATED     8   1
  CDH24 WILD-TYPE 275  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH24 MUTATED      8    1
  CDH24 WILD-TYPE  275   47
   clus
vv  CDH24 MUTATED CDH24 WILD-TYPE
  0             8             275
  1             1              47
[1] 2 2
[1] FALSE
D1307V7, binary
                 cls
clus                0   1
  CDH24 MUTATED     7   4
  CDH24 WILD-TYPE 163 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH24 MUTATED      7    4
  CDH24 WILD-TYPE  163  193
        clus
vv       CDH24 MUTATED CDH24 WILD-TYPE
  FEMALE             7             163
  MALE               4             193
[1] 2 2
[1] FALSE
D1307V8, binary
                 cls
clus                0   1
  CDH24 MUTATED     9   2
  CDH24 WILD-TYPE 308  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH24 MUTATED      9    2
  CDH24 WILD-TYPE  308   46
                               clus
vv                              CDH24 MUTATED CDH24 WILD-TYPE
  COLON ADENOCARCINOMA                      9             308
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CDH24 MUTATED     7   0   1   1
  CDH24 WILD-TYPE 250   2  21  20
D1307V9, multiclass
    clus
vv   CDH24 MUTATED CDH24 WILD-TYPE
  R0             7             250
  R1             0               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"
D1307V10, 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
D1307V11, 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(1308) Variable = DIAPH3 MUTATION ANALYSIS
D1308V1, survival
                  sevent
clus2                0   1
  DIAPH3 MUTATED    13   2
  DIAPH3 WILD-TYPE 269  71
  DIAPH3 MUTATED DIAPH3 WILD-TYPE 
              15              340 
  DIAPH3 MUTATED DIAPH3 WILD-TYPE 
               2               71 
$`DIAPH3 MUTATED`
TCGA-A6-6780 TCGA-AA-3489 TCGA-AA-3662 TCGA-AA-3977 TCGA-AD-6899 TCGA-CA-6717 
       20.12         7.04         6.05        25.02         5.79         0.33 
TCGA-CK-5913 TCGA-CM-4743 TCGA-CM-6171 TCGA-CM-6674 TCGA-D5-6929 TCGA-F4-6855 
       51.32        23.05        14.04        12.95        13.41        35.41 
TCGA-G4-6293 TCGA-G4-6306 TCGA-G4-6310 
      107.67        44.68        45.11 

$`DIAPH3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       23.87        19.66        20.28         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        0.72        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 
        0.53        19.43        74.56        65.85        53.62        55.04 
TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       51.75        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  DIAPH3 MUTATED DIAPH3 WILD-TYPE 
            0.33             0.00 
  DIAPH3 MUTATED DIAPH3 WILD-TYPE 
          107.67           140.38 
  DIAPH3 MUTATED DIAPH3 WILD-TYPE 
          20.120           20.235 
[1] "0.3 - 107.7 (20.1)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.7"
D1308V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DIAPH3 MUTATED         1        0        1         8         0         0
  DIAPH3 WILD-TYPE      63        1       24       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        18         10         40         30       33
                  vv
clus               STAGE IVA STAGE IVB
  DIAPH3 MUTATED           0         0
  DIAPH3 WILD-TYPE        13         1
D1308V3, multiclass
            clus
vv           DIAPH3 MUTATED DIAPH3 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               8              101
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              1               30
  STAGE IV                2               33
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  DIAPH3 MUTATED     0   3  11   2
  DIAPH3 WILD-TYPE   9  65 237  39
D1308V4, multiclass
    clus
vv   DIAPH3 MUTATED DIAPH3 WILD-TYPE
  T1              0                9
  T2              3               65
  T3             11              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
  DIAPH3 MUTATED    11   3   2
  DIAPH3 WILD-TYPE 209  77  64
D1308V5, multiclass
    clus
vv   DIAPH3 MUTATED DIAPH3 WILD-TYPE
  N0             11              209
  N1              3               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"
D1308V6, binary
                  cls
clus                 0   1
  DIAPH3 MUTATED    10   2
  DIAPH3 WILD-TYPE 273  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DIAPH3 MUTATED     10    2
  DIAPH3 WILD-TYPE  273   46
   clus
vv  DIAPH3 MUTATED DIAPH3 WILD-TYPE
  0             10              273
  1              2               46
[1] 2 2
[1] FALSE
D1308V7, 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
D1308V8, binary
                  cls
clus                 0   1
  DIAPH3 MUTATED    13   3
  DIAPH3 WILD-TYPE 304  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DIAPH3 MUTATED     13    3
  DIAPH3 WILD-TYPE  304   45
                               clus
vv                              DIAPH3 MUTATED DIAPH3 WILD-TYPE
  COLON ADENOCARCINOMA                      13              304
  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 247   2  21  19
D1308V9, multiclass
    clus
vv   DIAPH3 MUTATED DIAPH3 WILD-TYPE
  R0             10              247
  R1              0                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"
D1308V10, 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
D1308V11, 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(1309) Variable = BTF3L4 MUTATION ANALYSIS
D1309V1, survival
                  sevent
clus2                0   1
  BTF3L4 MUTATED     2   3
  BTF3L4 WILD-TYPE 280  70
  BTF3L4 MUTATED BTF3L4 WILD-TYPE 
               5              350 
  BTF3L4 MUTATED BTF3L4 WILD-TYPE 
               3               70 
$`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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  BTF3L4 MUTATED BTF3L4 WILD-TYPE 
            1.94             0.00 
  BTF3L4 MUTATED BTF3L4 WILD-TYPE 
           23.05           140.38 
  BTF3L4 MUTATED BTF3L4 WILD-TYPE 
          12.490           20.235 
[1] "1.9 - 23.1 (12.5)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "5.3"
D1309V2, 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       25       108         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BTF3L4 MUTATED           0          2          0          0        0
  BTF3L4 WILD-TYPE        19          8         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  BTF3L4 MUTATED           0         0
  BTF3L4 WILD-TYPE        13         1
D1309V3, multiclass
            clus
vv           BTF3L4 MUTATED BTF3L4 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               1              108
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              2                8
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  BTF3L4 MUTATED     1   1   2   1
  BTF3L4 WILD-TYPE   8  67 246  40
D1309V4, multiclass
    clus
vv   BTF3L4 MUTATED BTF3L4 WILD-TYPE
  T1              1                8
  T2              1               67
  T3              2              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
  BTF3L4 MUTATED     3   1   1
  BTF3L4 WILD-TYPE 217  79  65
D1309V5, multiclass
    clus
vv   BTF3L4 MUTATED BTF3L4 WILD-TYPE
  N0              3              217
  N1              1               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"
D1309V6, binary
                  cls
clus                 0   1
  BTF3L4 MUTATED     4   0
  BTF3L4 WILD-TYPE 279  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTF3L4 MUTATED      4    0
  BTF3L4 WILD-TYPE  279   48
   clus
vv  BTF3L4 MUTATED BTF3L4 WILD-TYPE
  0              4              279
  1              0               48
[1] 2 2
[1] FALSE
D1309V7, 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
D1309V8, binary
                  cls
clus                 0   1
  BTF3L4 MUTATED     5   0
  BTF3L4 WILD-TYPE 312  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTF3L4 MUTATED      5    0
  BTF3L4 WILD-TYPE  312   48
                               clus
vv                              BTF3L4 MUTATED BTF3L4 WILD-TYPE
  COLON ADENOCARCINOMA                       5              312
  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 255   2  22  20
D1309V9, multiclass
    clus
vv   BTF3L4 MUTATED BTF3L4 WILD-TYPE
  R0              2              255
  R1              0                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"
D1309V10, 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
D1309V11, 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(1310) Variable = ADAMTS16 MUTATION ANALYSIS
D1310V1, survival
                    sevent
clus2                  0   1
  ADAMTS16 MUTATED    22   7
  ADAMTS16 WILD-TYPE 260  66
  ADAMTS16 MUTATED ADAMTS16 WILD-TYPE 
                29                326 
  ADAMTS16 MUTATED ADAMTS16 WILD-TYPE 
                 7                 66 
$`ADAMTS16 MUTATED`
TCGA-A6-5666 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3815 TCGA-AA-3854 TCGA-AA-3939 
       32.71        35.01        63.98        33.04        36.03        12.99 
TCGA-AA-3955 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01I TCGA-AY-4071 
       20.98        25.02         4.01        34.98        31.00         0.95 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6600 TCGA-CA-6719 TCGA-CK-4952 TCGA-CK-5916 
       21.44        58.39        12.10         1.35        15.62        21.14 
TCGA-CM-4743 TCGA-CM-5348 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6171 TCGA-D5-6537 
       23.05        22.98        12.00        16.04        14.04         4.80 
TCGA-DM-A28C TCGA-DM-A28H TCGA-G4-6303 TCGA-G4-6588 TCGA-G4-6628 
       81.37       117.07        65.85        26.17        52.80 

$`ADAMTS16 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
       33.07         0.00        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05        31.00         2.01        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01P 
       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        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 
       27.09        16.31        15.75         0.20        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.33         0.10        17.56       102.44        40.34 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32        21.99         2.93         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-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        16.01        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 
       17.03        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        15.12        17.85        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
      119.93        35.97        60.79        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      107.67        74.56        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 
       91.79        46.75 

  ADAMTS16 MUTATED ADAMTS16 WILD-TYPE 
              0.95               0.00 
  ADAMTS16 MUTATED ADAMTS16 WILD-TYPE 
            117.07             140.38 
  ADAMTS16 MUTATED ADAMTS16 WILD-TYPE 
            23.050             19.825 
[1] "0.9 - 117.1 (23.1)" "0.0 - 140.4 (19.8)"
[1] "hr=" "1"  
D1310V2, 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       24        99         6         0
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ADAMTS16 MUTATED           1          0          4          1        2
  ADAMTS16 WILD-TYPE        18         10         37         30       33
                    vv
clus                 STAGE IVA STAGE IVB
  ADAMTS16 MUTATED           0         0
  ADAMTS16 WILD-TYPE        13         1
D1310V3, multiclass
            clus
vv           ADAMTS16 MUTATED ADAMTS16 WILD-TYPE
  STAGE I                   7                 57
  STAGE IA                  0                  1
  STAGE II                  1                 24
  STAGE IIA                10                 99
  STAGE IIB                 2                  6
  STAGE IIC                 1                  0
  STAGE III                 1                 18
  STAGE IIIA                0                 10
  STAGE IIIB                4                 37
  STAGE IIIC                1                 30
  STAGE IV                  2                 33
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  ADAMTS16 MUTATED     2   7  16   5
  ADAMTS16 WILD-TYPE   7  61 232  36
D1310V4, multiclass
    clus
vv   ADAMTS16 MUTATED ADAMTS16 WILD-TYPE
  T1                2                  7
  T2                7                 61
  T3               16                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
  ADAMTS16 MUTATED    22   5   3
  ADAMTS16 WILD-TYPE 198  75  63
D1310V5, multiclass
    clus
vv   ADAMTS16 MUTATED ADAMTS16 WILD-TYPE
  N0               22                198
  N1                5                 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"
D1310V6, binary
                    cls
clus                   0   1
  ADAMTS16 MUTATED    24   2
  ADAMTS16 WILD-TYPE 259  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ADAMTS16 MUTATED     24    2
  ADAMTS16 WILD-TYPE  259   46
   clus
vv  ADAMTS16 MUTATED ADAMTS16 WILD-TYPE
  0               24                259
  1                2                 46
[1] 2 2
[1] FALSE
D1310V7, 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
D1310V8, binary
                    cls
clus                   0   1
  ADAMTS16 MUTATED    25   4
  ADAMTS16 WILD-TYPE 292  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ADAMTS16 MUTATED     25    4
  ADAMTS16 WILD-TYPE  292   44
                               clus
vv                              ADAMTS16 MUTATED ADAMTS16 WILD-TYPE
  COLON ADENOCARCINOMA                        25                292
  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 235   2  22  18
D1310V9, multiclass
    clus
vv   ADAMTS16 MUTATED ADAMTS16 WILD-TYPE
  R0               22                235
  R1                0                  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"
D1310V10, 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
D1310V11, 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(1311) Variable = LAMB4 MUTATION ANALYSIS
D1311V1, survival
                 sevent
clus2               0   1
  LAMB4 MUTATED    19   6
  LAMB4 WILD-TYPE 263  67
  LAMB4 MUTATED LAMB4 WILD-TYPE 
             25             330 
  LAMB4 MUTATED LAMB4 WILD-TYPE 
              6              67 
$`LAMB4 MUTATED`
TCGA-AA-3492 TCGA-AA-3555 TCGA-AA-3655 TCGA-AA-3681 TCGA-AA-3710 TCGA-AA-3815 
        3.02        29.95        61.02         5.98        26.99        33.04 
TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3950 TCGA-AA-3968 TCGA-AA-A00N TCGA-AA-A024 
       53.00        31.00        24.00        21.99         4.01        39.06 
TCGA-AD-6963 TCGA-AY-6386 TCGA-AZ-6600 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-5344 
       27.42        17.82        12.10         0.33         0.10        22.03 
TCGA-D5-5539 TCGA-D5-6926 TCGA-D5-6929 TCGA-DM-A0XF TCGA-F4-6459 TCGA-F4-6807 
       19.59         9.04        13.41        38.20         8.61        16.24 
TCGA-G4-6628 
       52.80 

$`LAMB4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        17.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
       11.01        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       19.04        19.04        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       37.02        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.26         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        24.43       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
      117.07        98.24        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
        1.55        16.31        29.59        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 

  LAMB4 MUTATED LAMB4 WILD-TYPE 
            0.1             0.0 
  LAMB4 MUTATED LAMB4 WILD-TYPE 
          61.02          140.38 
  LAMB4 MUTATED LAMB4 WILD-TYPE 
         21.990          20.155 
[1] "0.1 - 61.0 (22.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.3"
D1311V2, 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       21       102         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LAMB4 MUTATED           1          2          3          2        2         0
  LAMB4 WILD-TYPE        18          8         38         29       33        13
                 vv
clus              STAGE IVB
  LAMB4 MUTATED           0
  LAMB4 WILD-TYPE         1
D1311V3, multiclass
            clus
vv           LAMB4 MUTATED LAMB4 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               4              21
  STAGE IIA              7             102
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             2               8
  STAGE IIIB             3              38
  STAGE IIIC             2              29
  STAGE IV               2              33
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LAMB4 MUTATED     1   2  20   3
  LAMB4 WILD-TYPE   8  66 228  38
D1311V4, multiclass
    clus
vv   LAMB4 MUTATED LAMB4 WILD-TYPE
  T1             1               8
  T2             2              66
  T3            20             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
  LAMB4 MUTATED    16   7   3
  LAMB4 WILD-TYPE 204  73  63
D1311V5, multiclass
    clus
vv   LAMB4 MUTATED LAMB4 WILD-TYPE
  N0            16             204
  N1             7              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"
D1311V6, binary
                 cls
clus                0   1
  LAMB4 MUTATED    23   2
  LAMB4 WILD-TYPE 260  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LAMB4 MUTATED     23    2
  LAMB4 WILD-TYPE  260   46
   clus
vv  LAMB4 MUTATED LAMB4 WILD-TYPE
  0            23             260
  1             2              46
[1] 2 2
[1] FALSE
D1311V7, 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
D1311V8, binary
                 cls
clus                0   1
  LAMB4 MUTATED    18   8
  LAMB4 WILD-TYPE 299  40
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LAMB4 MUTATED     18    8
  LAMB4 WILD-TYPE  299   40
                               clus
vv                              LAMB4 MUTATED LAMB4 WILD-TYPE
  COLON ADENOCARCINOMA                     18             299
  COLON MUCINOUS ADENOCARCINOMA             8              40
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  LAMB4 MUTATED    21   0   0   2
  LAMB4 WILD-TYPE 236   2  22  19
D1311V9, multiclass
    clus
vv   LAMB4 MUTATED LAMB4 WILD-TYPE
  R0            21             236
  R1             0               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"
D1311V10, 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
D1311V11, 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(1312) Variable = BTNL3 MUTATION ANALYSIS
D1312V1, survival
                 sevent
clus2               0   1
  BTNL3 MUTATED     7   0
  BTNL3 WILD-TYPE 275  73
  BTNL3 MUTATED BTNL3 WILD-TYPE 
              7             348 
  BTNL3 MUTATED BTNL3 WILD-TYPE 
              0              73 
$`BTNL3 MUTATED`
TCGA-A6-5665 TCGA-A6-6781 TCGA-CA-6717 TCGA-CM-4743 TCGA-CM-5861 TCGA-G4-6586 
       22.06        19.66         0.33        23.05        15.02        35.80 
TCGA-G4-6588 
       26.17 

$`BTNL3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93         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        16.01 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       36.00        22.09        13.78        91.79        46.75        52.80 

  BTNL3 MUTATED BTNL3 WILD-TYPE 
           0.33            0.00 
  BTNL3 MUTATED BTNL3 WILD-TYPE 
          35.80          140.38 
  BTNL3 MUTATED BTNL3 WILD-TYPE 
         22.060          20.155 
[1] "0.3 - 35.8 (22.1)"  "0.0 - 140.4 (20.2)"
[1] "hr="     "9200000"
D1312V2, 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       25       103         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        19         10         41         30       35        13
                 vv
clus              STAGE IVB
  BTNL3 MUTATED           0
  BTNL3 WILD-TYPE         1
D1312V3, multiclass
            clus
vv           BTNL3 MUTATED BTNL3 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              6             103
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  BTNL3 MUTATED     0   0   6   1
  BTNL3 WILD-TYPE   9  68 242  40
D1312V4, multiclass
    clus
vv   BTNL3 MUTATED BTNL3 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             6             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
  BTNL3 MUTATED     6   1   0
  BTNL3 WILD-TYPE 214  79  66
D1312V5, multiclass
    clus
vv   BTNL3 MUTATED BTNL3 WILD-TYPE
  N0             6             214
  N1             1              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"
D1312V6, binary
                 cls
clus                0   1
  BTNL3 MUTATED     6   0
  BTNL3 WILD-TYPE 277  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTNL3 MUTATED      6    0
  BTNL3 WILD-TYPE  277   48
   clus
vv  BTNL3 MUTATED BTNL3 WILD-TYPE
  0             6             277
  1             0              48
[1] 2 2
[1] FALSE
D1312V7, 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
D1312V8, binary
                 cls
clus                0   1
  BTNL3 MUTATED     5   2
  BTNL3 WILD-TYPE 312  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTNL3 MUTATED      5    2
  BTNL3 WILD-TYPE  312   46
                               clus
vv                              BTNL3 MUTATED BTNL3 WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  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 251   2  22  20
D1312V9, multiclass
    clus
vv   BTNL3 MUTATED BTNL3 WILD-TYPE
  R0             6             251
  R1             0               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"
D1312V10, 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
D1312V11, 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(1313) Variable = CLVS1 MUTATION ANALYSIS
D1313V1, survival
                 sevent
clus2               0   1
  CLVS1 MUTATED     8   1
  CLVS1 WILD-TYPE 274  72
  CLVS1 MUTATED CLVS1 WILD-TYPE 
              9             346 
  CLVS1 MUTATED CLVS1 WILD-TYPE 
              1              72 
$`CLVS1 MUTATED`
TCGA-A6-5666 TCGA-AA-3510 TCGA-AA-3864 TCGA-AA-A01Z TCGA-CA-6717 TCGA-CM-6168 
       32.71        63.98        53.00        37.02         0.33        12.99 
TCGA-CM-6676 TCGA-D5-6532 TCGA-DM-A1D8 
       11.08        18.25        12.59 

$`CLVS1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-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-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       35.01        26.01        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       13.51        11.51        20.19         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  CLVS1 MUTATED CLVS1 WILD-TYPE 
           0.33            0.00 
  CLVS1 MUTATED CLVS1 WILD-TYPE 
          63.98          140.38 
  CLVS1 MUTATED CLVS1 WILD-TYPE 
         18.250          20.235 
[1] "0.3 - 64.0 (18.2)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2"  
D1313V2, 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       22       106         8         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CLVS1 MUTATED           0          0          0          0        0         0
  CLVS1 WILD-TYPE        19         10         41         31       35        13
                 vv
clus              STAGE IVB
  CLVS1 MUTATED           0
  CLVS1 WILD-TYPE         1
D1313V3, multiclass
            clus
vv           CLVS1 MUTATED CLVS1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              3             106
  STAGE IIB              0               8
  STAGE IIC              1               0
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CLVS1 MUTATED     0   1   7   1
  CLVS1 WILD-TYPE   9  67 241  40
D1313V4, multiclass
    clus
vv   CLVS1 MUTATED CLVS1 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             7             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   0
  CLVS1 WILD-TYPE 212  79  66
D1313V5, multiclass
    clus
vv   CLVS1 MUTATED CLVS1 WILD-TYPE
  N0             8             212
  N1             1              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"
D1313V6, binary
                 cls
clus                0   1
  CLVS1 MUTATED     8   0
  CLVS1 WILD-TYPE 275  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLVS1 MUTATED      8    0
  CLVS1 WILD-TYPE  275   48
   clus
vv  CLVS1 MUTATED CLVS1 WILD-TYPE
  0             8             275
  1             0              48
[1] 2 2
[1] FALSE
D1313V7, binary
                 cls
clus                0   1
  CLVS1 MUTATED     2   7
  CLVS1 WILD-TYPE 168 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLVS1 MUTATED      2    7
  CLVS1 WILD-TYPE  168  190
        clus
vv       CLVS1 MUTATED CLVS1 WILD-TYPE
  FEMALE             2             168
  MALE               7             190
[1] 2 2
[1] FALSE
D1313V8, binary
                 cls
clus                0   1
  CLVS1 MUTATED     8   1
  CLVS1 WILD-TYPE 309  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLVS1 MUTATED      8    1
  CLVS1 WILD-TYPE  309   47
                               clus
vv                              CLVS1 MUTATED CLVS1 WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CLVS1 MUTATED     6   0   0   1
  CLVS1 WILD-TYPE 251   2  22  20
D1313V9, multiclass
    clus
vv   CLVS1 MUTATED CLVS1 WILD-TYPE
  R0             6             251
  R1             0               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"
D1313V10, 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
D1313V11, 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(1314) Variable = C4ORF29 MUTATION ANALYSIS
D1314V1, survival
                   sevent
clus2                 0   1
  C4ORF29 MUTATED     4   1
  C4ORF29 WILD-TYPE 278  72
  C4ORF29 MUTATED C4ORF29 WILD-TYPE 
                5               350 
  C4ORF29 MUTATED C4ORF29 WILD-TYPE 
                1                72 
$`C4ORF29 MUTATED`
TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3811 TCGA-G4-6628 
       22.06        19.66        63.98        10.06        52.80 

$`C4ORF29 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        19.04        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 
       91.79        46.75 

  C4ORF29 MUTATED C4ORF29 WILD-TYPE 
            10.06              0.00 
  C4ORF29 MUTATED C4ORF29 WILD-TYPE 
            63.98            140.38 
  C4ORF29 MUTATED C4ORF29 WILD-TYPE 
           22.060            20.155 
[1] "10.1 - 64.0 (22.1)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.5"
D1314V2, 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       24       108         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C4ORF29 MUTATED           1          0          0          1        0
  C4ORF29 WILD-TYPE        18         10         41         30       35
                   vv
clus                STAGE IVA STAGE IVB
  C4ORF29 MUTATED           0         0
  C4ORF29 WILD-TYPE        13         1
D1314V3, multiclass
            clus
vv           C4ORF29 MUTATED C4ORF29 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                1               108
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               1                30
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C4ORF29 MUTATED     0   1   3   1
  C4ORF29 WILD-TYPE   9  67 245  40
D1314V4, multiclass
    clus
vv   C4ORF29 MUTATED C4ORF29 WILD-TYPE
  T1               0                 9
  T2               1                67
  T3               3               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
  C4ORF29 MUTATED     3   1   1
  C4ORF29 WILD-TYPE 217  79  65
D1314V5, multiclass
    clus
vv   C4ORF29 MUTATED C4ORF29 WILD-TYPE
  N0               3               217
  N1               1                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"
D1314V6, binary
                   cls
clus                  0   1
  C4ORF29 MUTATED     4   0
  C4ORF29 WILD-TYPE 279  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C4ORF29 MUTATED      4    0
  C4ORF29 WILD-TYPE  279   48
   clus
vv  C4ORF29 MUTATED C4ORF29 WILD-TYPE
  0               4               279
  1               0                48
[1] 2 2
[1] FALSE
D1314V7, 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
D1314V8, binary
                   cls
clus                  0   1
  C4ORF29 MUTATED     4   1
  C4ORF29 WILD-TYPE 313  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C4ORF29 MUTATED      4    1
  C4ORF29 WILD-TYPE  313   47
                               clus
vv                              C4ORF29 MUTATED C4ORF29 WILD-TYPE
  COLON ADENOCARCINOMA                        4               313
  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 252   2  22  21
D1314V9, multiclass
    clus
vv   C4ORF29 MUTATED C4ORF29 WILD-TYPE
  R0               5               252
  R1               0                 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"
D1314V10, 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
D1314V11, 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(1315) Variable = CMTM2 MUTATION ANALYSIS
D1315V1, survival
                 sevent
clus2               0   1
  CMTM2 MUTATED     3   0
  CMTM2 WILD-TYPE 279  73
  CMTM2 MUTATED CMTM2 WILD-TYPE 
              3             352 
  CMTM2 MUTATED CMTM2 WILD-TYPE 
              0              73 
$`CMTM2 MUTATED`
TCGA-AA-3833 TCGA-CM-5860 TCGA-G4-6588 
       15.95        16.01        26.17 

$`CMTM2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
        1.02        17.98        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        91.79        46.75        52.80 

  CMTM2 MUTATED CMTM2 WILD-TYPE 
          15.95            0.00 
  CMTM2 MUTATED CMTM2 WILD-TYPE 
          26.17          140.38 
  CMTM2 MUTATED CMTM2 WILD-TYPE 
         16.010          20.235 
[1] "15.9 - 26.2 (16.0)" "0.0 - 140.4 (20.2)"
[1] "hr="     "3300000"
D1315V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CMTM2 MUTATED         0        0        1         3         0         0
  CMTM2 WILD-TYPE      64        1       24       106         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CMTM2 MUTATED           0          0          0          0        0         0
  CMTM2 WILD-TYPE        19         10         41         31       35        13
                 vv
clus              STAGE IVB
  CMTM2 MUTATED           0
  CMTM2 WILD-TYPE         1
D1315V3, multiclass
            clus
vv           CMTM2 MUTATED CMTM2 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              3             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CMTM2 MUTATED     0   0   3   1
  CMTM2 WILD-TYPE   9  68 245  40
D1315V4, multiclass
    clus
vv   CMTM2 MUTATED CMTM2 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             3             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
  CMTM2 MUTATED     4   0   0
  CMTM2 WILD-TYPE 216  80  66
D1315V5, multiclass
    clus
vv   CMTM2 MUTATED CMTM2 WILD-TYPE
  N0             4             216
  N1             0              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"
D1315V6, binary
                 cls
clus                0   1
  CMTM2 MUTATED     4   0
  CMTM2 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CMTM2 MUTATED      4    0
  CMTM2 WILD-TYPE  279   48
   clus
vv  CMTM2 MUTATED CMTM2 WILD-TYPE
  0             4             279
  1             0              48
[1] 2 2
[1] FALSE
D1315V7, binary
                 cls
clus                0   1
  CMTM2 MUTATED     3   1
  CMTM2 WILD-TYPE 167 196
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CMTM2 MUTATED      3    1
  CMTM2 WILD-TYPE  167  196
        clus
vv       CMTM2 MUTATED CMTM2 WILD-TYPE
  FEMALE             3             167
  MALE               1             196
[1] 2 2
[1] FALSE
D1315V8, binary
                 cls
clus                0   1
  CMTM2 MUTATED     4   0
  CMTM2 WILD-TYPE 313  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CMTM2 MUTATED      4    0
  CMTM2 WILD-TYPE  313   48
                               clus
vv                              CMTM2 MUTATED CMTM2 WILD-TYPE
  COLON ADENOCARCINOMA                      4             313
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CMTM2 MUTATED     4   0   0   0
  CMTM2 WILD-TYPE 253   2  22  21
D1315V9, multiclass
    clus
vv   CMTM2 MUTATED CMTM2 WILD-TYPE
  R0             4             253
  R1             0               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"
D1315V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CMTM2 MUTATED                                  0     0
  CMTM2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CMTM2 MUTATED                           0     2
  CMTM2 WILD-TYPE                        19   174
D1315V11, multiclass
[1] "Remove cluster labels:" "CMTM2 MUTATED"         
clus
  CMTM2 MUTATED CMTM2 WILD-TYPE 
              2             204 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-4105 
"CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" 
     TCGA-A6-5656      TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5660 
"CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" 
     TCGA-A6-5661      TCGA-A6-5662      TCGA-A6-5664      TCGA-A6-5665 
"CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" 
     TCGA-A6-5666      TCGA-A6-6137      TCGA-A6-6138      TCGA-A6-6141 
"CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" 
     TCGA-A6-6142      TCGA-A6-6648      TCGA-A6-6649      TCGA-A6-6651 
"CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" 
     TCGA-A6-6652      TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780 
"CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" 
     TCGA-A6-6781      TCGA-A6-6782      TCGA-AD-5900      TCGA-AD-6548 
"CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" 
     TCGA-AD-6888      TCGA-AD-6889      TCGA-AD-6890      TCGA-AD-6895 
"CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" 
     TCGA-AD-6899      TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6964 
"CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" 
     TCGA-AD-6965      TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070 
"CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" 
     TCGA-AY-4071      TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197 
"CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" 
     TCGA-AY-6386      TCGA-AZ-4315      TCGA-AZ-4323      TCGA-AZ-4616 
"CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" 
     TCGA-AZ-4681      TCGA-AZ-4682      TCGA-AZ-5403      TCGA-AZ-5407 
"CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" 
     TCGA-AZ-6598      TCGA-AZ-6599      TCGA-AZ-6600      TCGA-AZ-6601 
"CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" 
     TCGA-AZ-6603      TCGA-AZ-6605      TCGA-AZ-6606      TCGA-AZ-6607 
"CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" 
     TCGA-AZ-6608      TCGA-CA-5254      TCGA-CA-5255      TCGA-CA-5796 
"CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" 
     TCGA-CA-5797      TCGA-CA-6715      TCGA-CA-6716      TCGA-CA-6717 
"CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" 
     TCGA-CA-6718      TCGA-CA-6719      TCGA-CK-4947      TCGA-CK-4948 
"CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" 
     TCGA-CK-4950      TCGA-CK-4952      TCGA-CK-5912      TCGA-CK-5913 
"CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" 
     TCGA-CK-5914      TCGA-CK-5915      TCGA-CK-5916      TCGA-CK-6746 
"CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" 
     TCGA-CK-6747      TCGA-CK-6748      TCGA-CK-6751      TCGA-CM-4743 
"CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" 
     TCGA-CM-4744      TCGA-CM-4746      TCGA-CM-4747      TCGA-CM-4752 
"CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" 
     TCGA-CM-5341      TCGA-CM-5344      TCGA-CM-5348      TCGA-CM-5349 
"CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" 
     TCGA-CM-5861      TCGA-CM-5862      TCGA-CM-5863      TCGA-CM-5864 
"CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" 
     TCGA-CM-5868      TCGA-CM-6161      TCGA-CM-6162      TCGA-CM-6163 
"CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" 
     TCGA-CM-6164      TCGA-CM-6165      TCGA-CM-6166      TCGA-CM-6167 
"CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" 
     TCGA-CM-6168      TCGA-CM-6169      TCGA-CM-6170      TCGA-CM-6171 
"CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" 
     TCGA-CM-6172      TCGA-CM-6674      TCGA-CM-6675      TCGA-CM-6676 
"CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" 
     TCGA-CM-6677      TCGA-CM-6678      TCGA-CM-6679      TCGA-CM-6680 
"CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" 
     TCGA-D5-5537      TCGA-D5-5538      TCGA-D5-5539      TCGA-D5-5540 
"CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" 
     TCGA-D5-5541      TCGA-D5-6529      TCGA-D5-6532      TCGA-D5-6533 
"CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" 
     TCGA-D5-6534      TCGA-D5-6535      TCGA-D5-6536      TCGA-D5-6537 
"CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" 
     TCGA-D5-6538      TCGA-D5-6539      TCGA-D5-6540      TCGA-D5-6541 
"CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" 
     TCGA-D5-6898      TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923 
"CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" 
     TCGA-D5-6924      TCGA-D5-6926      TCGA-D5-6927      TCGA-D5-6928 
"CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" 
     TCGA-D5-6929      TCGA-D5-6930      TCGA-D5-6931      TCGA-D5-6932 
"CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" 
     TCGA-D5-7000      TCGA-DM-A0X9      TCGA-DM-A0XD      TCGA-DM-A0XF 
"CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" 
     TCGA-DM-A1D0      TCGA-DM-A1D4      TCGA-DM-A1D6      TCGA-DM-A1D7 
"CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" 
     TCGA-DM-A1D8      TCGA-DM-A1D9      TCGA-DM-A1DA      TCGA-DM-A1DB 
"CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" 
     TCGA-DM-A1HA      TCGA-DM-A1HB      TCGA-DM-A282      TCGA-DM-A285 
"CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" 
     TCGA-DM-A28C      TCGA-DM-A28E      TCGA-DM-A28F      TCGA-DM-A28G 
"CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" 
     TCGA-DM-A28H      TCGA-DM-A28K      TCGA-F4-6459      TCGA-F4-6460 
"CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" 
     TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704 
"CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" 
     TCGA-F4-6805      TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808 
"CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" 
     TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856 
"CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" 
     TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304 
"CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" 
     TCGA-G4-6306      TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310 
"CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" 
     TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323 
"CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" 
     TCGA-G4-6586      TCGA-G4-6625      TCGA-G4-6626      TCGA-G4-6628 
"CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" "CMTM2 WILD-TYPE" 

Clustering(1316) Variable = PSMA2 MUTATION ANALYSIS
D1316V1, survival
                 sevent
clus2               0   1
  PSMA2 MUTATED     4   2
  PSMA2 WILD-TYPE 278  71
  PSMA2 MUTATED PSMA2 WILD-TYPE 
              6             349 
  PSMA2 MUTATED PSMA2 WILD-TYPE 
              2              71 
$`PSMA2 MUTATED`
TCGA-AA-3492 TCGA-AA-A00A TCGA-AD-6895 TCGA-CK-4950 TCGA-F4-6570 TCGA-G4-6321 
        3.02        38.04         0.72        40.34         6.18        22.09 

$`PSMA2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       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        13.38        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  PSMA2 MUTATED PSMA2 WILD-TYPE 
           0.72            0.00 
  PSMA2 MUTATED PSMA2 WILD-TYPE 
          40.34          140.38 
  PSMA2 MUTATED PSMA2 WILD-TYPE 
         14.135          20.190 
[1] "0.7 - 40.3 (14.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2.5"
D1316V2, 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       24       107         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PSMA2 MUTATED           1          1          0          0        0         0
  PSMA2 WILD-TYPE        18          9         41         31       35        13
                 vv
clus              STAGE IVB
  PSMA2 MUTATED           0
  PSMA2 WILD-TYPE         1
D1316V3, multiclass
            clus
vv           PSMA2 MUTATED PSMA2 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              2             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             1               9
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PSMA2 MUTATED     0   1   5   0
  PSMA2 WILD-TYPE   9  67 243  41
D1316V4, multiclass
    clus
vv   PSMA2 MUTATED PSMA2 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             5             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
  PSMA2 MUTATED     3   3   0
  PSMA2 WILD-TYPE 217  77  66
D1316V5, multiclass
    clus
vv   PSMA2 MUTATED PSMA2 WILD-TYPE
  N0             3             217
  N1             3              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"
D1316V6, binary
                 cls
clus                0   1
  PSMA2 MUTATED     4   0
  PSMA2 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSMA2 MUTATED      4    0
  PSMA2 WILD-TYPE  279   48
   clus
vv  PSMA2 MUTATED PSMA2 WILD-TYPE
  0             4             279
  1             0              48
[1] 2 2
[1] FALSE
D1316V7, 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
D1316V8, binary
                 cls
clus                0   1
  PSMA2 MUTATED     6   0
  PSMA2 WILD-TYPE 311  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSMA2 MUTATED      6    0
  PSMA2 WILD-TYPE  311   48
                               clus
vv                              PSMA2 MUTATED PSMA2 WILD-TYPE
  COLON ADENOCARCINOMA                      6             311
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PSMA2 MUTATED     4   1   0   0
  PSMA2 WILD-TYPE 253   1  22  21
D1316V9, multiclass
    clus
vv   PSMA2 MUTATED PSMA2 WILD-TYPE
  R0             4             253
  R1             1               1
  R2             0              22
  RX             0              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1316V10, 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
D1316V11, 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(1317) Variable = AIM2 MUTATION ANALYSIS
D1317V1, survival
                sevent
clus2              0   1
  AIM2 MUTATED     7   2
  AIM2 WILD-TYPE 275  71
  AIM2 MUTATED AIM2 WILD-TYPE 
             9            346 
  AIM2 MUTATED AIM2 WILD-TYPE 
             2             71 
$`AIM2 MUTATED`
TCGA-A6-6780 TCGA-AA-3510 TCGA-AA-A010 TCGA-AD-6964 TCGA-AZ-4315 TCGA-AZ-6601 
       20.12        63.98        34.98        10.88        58.39       100.01 
TCGA-CM-4744 TCGA-CM-5864 TCGA-G4-6304 
       20.02        15.02        53.62 

$`AIM2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        61.41        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        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-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      107.67        74.56        65.85        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  AIM2 MUTATED AIM2 WILD-TYPE 
         10.88           0.00 
  AIM2 MUTATED AIM2 WILD-TYPE 
        100.01         140.38 
  AIM2 MUTATED AIM2 WILD-TYPE 
         34.98          20.09 
[1] "10.9 - 100.0 (35.0)" "0.0 - 140.4 (20.1)" 
[1] "hr=" "1.6"
D1317V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AIM2 MUTATED         2        0        2         2         2         0
  AIM2 WILD-TYPE      62        1       23       107         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AIM2 MUTATED           0          0          0          0        0         0
  AIM2 WILD-TYPE        19         10         41         31       35        13
                vv
clus             STAGE IVB
  AIM2 MUTATED           0
  AIM2 WILD-TYPE         1
D1317V3, multiclass
            clus
vv           AIM2 MUTATED AIM2 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             2            107
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  AIM2 MUTATED     0   2   4   3
  AIM2 WILD-TYPE   9  66 244  38
D1317V4, multiclass
    clus
vv   AIM2 MUTATED AIM2 WILD-TYPE
  T1            0              9
  T2            2             66
  T3            4            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
  AIM2 MUTATED     8   0   1
  AIM2 WILD-TYPE 212  80  65
D1317V5, multiclass
    clus
vv   AIM2 MUTATED AIM2 WILD-TYPE
  N0            8            212
  N1            0             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"
D1317V6, binary
                cls
clus               0   1
  AIM2 MUTATED     7   0
  AIM2 WILD-TYPE 276  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  AIM2 MUTATED      7    0
  AIM2 WILD-TYPE  276   48
   clus
vv  AIM2 MUTATED AIM2 WILD-TYPE
  0            7            276
  1            0             48
[1] 2 2
[1] FALSE
D1317V7, binary
                cls
clus               0   1
  AIM2 MUTATED     2   7
  AIM2 WILD-TYPE 168 190
[1] "tbl2"
                cls
clus             [,1] [,2]
  AIM2 MUTATED      2    7
  AIM2 WILD-TYPE  168  190
        clus
vv       AIM2 MUTATED AIM2 WILD-TYPE
  FEMALE            2            168
  MALE              7            190
[1] 2 2
[1] FALSE
D1317V8, binary
                cls
clus               0   1
  AIM2 MUTATED     8   1
  AIM2 WILD-TYPE 309  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  AIM2 MUTATED      8    1
  AIM2 WILD-TYPE  309   47
                               clus
vv                              AIM2 MUTATED AIM2 WILD-TYPE
  COLON ADENOCARCINOMA                     8            309
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  AIM2 MUTATED     6   0   0   0
  AIM2 WILD-TYPE 251   2  22  21
D1317V9, multiclass
    clus
vv   AIM2 MUTATED AIM2 WILD-TYPE
  R0            6            251
  R1            0              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"
D1317V10, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AIM2 MUTATED                                  0     0
  AIM2 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  AIM2 MUTATED                           0     7
  AIM2 WILD-TYPE                        19   169
D1317V11, multiclass
                                  clus
vv                                 AIM2 MUTATED AIM2 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(1318) Variable = DLGAP3 MUTATION ANALYSIS
D1318V1, survival
                  sevent
clus2                0   1
  DLGAP3 MUTATED    14   1
  DLGAP3 WILD-TYPE 268  72
  DLGAP3 MUTATED DLGAP3 WILD-TYPE 
              15              340 
  DLGAP3 MUTATED DLGAP3 WILD-TYPE 
               1               72 
$`DLGAP3 MUTATED`
TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3815 TCGA-AA-A010 TCGA-AA-A01Q 
       22.06        63.98         6.97        33.04        34.98         1.02 
TCGA-AD-6889 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4952 TCGA-CK-5913 
       56.55        49.41         0.33         0.10        15.62        51.32 
TCGA-CM-5861 TCGA-D5-6529 TCGA-D5-6928 
       15.02        20.19        11.64 

$`DLGAP3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        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        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07         0.26         1.35        17.56       102.44        40.34 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        21.99        21.14         2.93         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        16.01         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       13.51        11.51        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  DLGAP3 MUTATED DLGAP3 WILD-TYPE 
             0.1              0.0 
  DLGAP3 MUTATED DLGAP3 WILD-TYPE 
           63.98           140.38 
  DLGAP3 MUTATED DLGAP3 WILD-TYPE 
           20.19            20.20 
[1] "0.1 - 64.0 (20.2)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "3.3"
D1318V2, 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       21        99         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DLGAP3 MUTATED           1          0          0          0        0
  DLGAP3 WILD-TYPE        18         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  DLGAP3 MUTATED           0         0
  DLGAP3 WILD-TYPE        13         1
D1318V3, multiclass
            clus
vv           DLGAP3 MUTATED DLGAP3 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                4               21
  STAGE IIA              10               99
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  DLGAP3 MUTATED     0   0  14   2
  DLGAP3 WILD-TYPE   9  68 234  39
D1318V4, multiclass
    clus
vv   DLGAP3 MUTATED DLGAP3 WILD-TYPE
  T1              0                9
  T2              0               68
  T3             14              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
  DLGAP3 MUTATED    15   0   1
  DLGAP3 WILD-TYPE 205  80  65
D1318V5, multiclass
    clus
vv   DLGAP3 MUTATED DLGAP3 WILD-TYPE
  N0             15              205
  N1              0               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"
D1318V6, binary
                  cls
clus                 0   1
  DLGAP3 MUTATED    14   0
  DLGAP3 WILD-TYPE 269  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DLGAP3 MUTATED     14    0
  DLGAP3 WILD-TYPE  269   48
   clus
vv  DLGAP3 MUTATED DLGAP3 WILD-TYPE
  0             14              269
  1              0               48
[1] 2 2
[1] FALSE
D1318V7, 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
D1318V8, binary
                  cls
clus                 0   1
  DLGAP3 MUTATED    13   3
  DLGAP3 WILD-TYPE 304  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DLGAP3 MUTATED     13    3
  DLGAP3 WILD-TYPE  304   45
                               clus
vv                              DLGAP3 MUTATED DLGAP3 WILD-TYPE
  COLON ADENOCARCINOMA                      13              304
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  DLGAP3 MUTATED    10   0   0   4
  DLGAP3 WILD-TYPE 247   2  22  17
D1318V9, multiclass
    clus
vv   DLGAP3 MUTATED DLGAP3 WILD-TYPE
  R0             10              247
  R1              0                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"
D1318V10, 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
D1318V11, 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(1319) Variable = RFXAP MUTATION ANALYSIS
D1319V1, survival
                 sevent
clus2               0   1
  RFXAP MUTATED     3   2
  RFXAP WILD-TYPE 279  71
  RFXAP MUTATED RFXAP WILD-TYPE 
              5             350 
  RFXAP MUTATED RFXAP WILD-TYPE 
              2              71 
$`RFXAP MUTATED`
TCGA-A6-5660 TCGA-AA-3529 TCGA-AZ-6600 TCGA-CA-6717 TCGA-D5-6927 
       29.19         0.00        12.10         0.33         9.44 

$`RFXAP WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
       19.07        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  RFXAP MUTATED RFXAP WILD-TYPE 
              0               0 
  RFXAP MUTATED RFXAP WILD-TYPE 
          29.19          140.38 
  RFXAP MUTATED RFXAP WILD-TYPE 
           9.44           20.63 
[1] "0.0 - 29.2 (9.4)"   "0.0 - 140.4 (20.6)"
[1] "hr=" "4.8"
D1319V2, 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       25       107         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RFXAP MUTATED           0          0          0          2        1         0
  RFXAP WILD-TYPE        19         10         41         29       34        13
                 vv
clus              STAGE IVB
  RFXAP MUTATED           0
  RFXAP WILD-TYPE         1
D1319V3, multiclass
            clus
vv           RFXAP MUTATED RFXAP WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              2             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             2              29
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RFXAP MUTATED     0   0   4   1
  RFXAP WILD-TYPE   9  68 244  40
D1319V4, multiclass
    clus
vv   RFXAP MUTATED RFXAP WILD-TYPE
  T1             0               9
  T2             0              68
  T3             4             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   1   2
  RFXAP WILD-TYPE 218  79  64
D1319V5, multiclass
    clus
vv   RFXAP MUTATED RFXAP WILD-TYPE
  N0             2             218
  N1             1              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"
D1319V6, binary
                 cls
clus                0   1
  RFXAP MUTATED     4   1
  RFXAP WILD-TYPE 279  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RFXAP MUTATED      4    1
  RFXAP WILD-TYPE  279   47
   clus
vv  RFXAP MUTATED RFXAP WILD-TYPE
  0             4             279
  1             1              47
[1] 2 2
[1] FALSE
D1319V7, binary
                 cls
clus                0   1
  RFXAP MUTATED     1   4
  RFXAP WILD-TYPE 169 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RFXAP MUTATED      1    4
  RFXAP WILD-TYPE  169  193
        clus
vv       RFXAP MUTATED RFXAP WILD-TYPE
  FEMALE             1             169
  MALE               4             193
[1] 2 2
[1] FALSE
D1319V8, binary
                 cls
clus                0   1
  RFXAP MUTATED     4   1
  RFXAP WILD-TYPE 313  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RFXAP MUTATED      4    1
  RFXAP WILD-TYPE  313   47
                               clus
vv                              RFXAP MUTATED RFXAP WILD-TYPE
  COLON ADENOCARCINOMA                      4             313
  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 255   2  22  20
D1319V9, multiclass
    clus
vv   RFXAP MUTATED RFXAP WILD-TYPE
  R0             2             255
  R1             0               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"
D1319V10, 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     1
  RFXAP WILD-TYPE                        17   175
D1319V11, 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                                        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(1320) Variable = NCL MUTATION ANALYSIS
D1320V1, survival
               sevent
clus2             0   1
  NCL MUTATED     6   4
  NCL WILD-TYPE 276  69
  NCL MUTATED NCL WILD-TYPE 
           10           345 
  NCL MUTATED NCL WILD-TYPE 
            4            69 
$`NCL MUTATED`
TCGA-AA-3697 TCGA-AA-3845 TCGA-AA-A00N TCGA-AD-6889 TCGA-AD-6964 TCGA-AU-3779 
       85.05         0.00         4.01        56.55        10.88        14.50 
TCGA-AZ-6608 TCGA-CM-5341 TCGA-CM-6674 TCGA-DM-A28H 
        1.94        29.06        12.95       117.07 

$`NCL WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
       17.98        15.95        38.99        37.02        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37         4.21         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 
        0.72         5.79        22.42        27.42         0.20        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  NCL MUTATED NCL WILD-TYPE 
            0             0 
  NCL MUTATED NCL WILD-TYPE 
       117.07        140.38 
  NCL MUTATED NCL WILD-TYPE 
       13.725        20.280 
[1] "0.0 - 117.1 (13.7)" "0.0 - 140.4 (20.3)"
[1] "hr=" "1.6"
D1320V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NCL MUTATED         0        0        0         4         1         0
  NCL WILD-TYPE      64        1       25       105         7         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NCL MUTATED           1          2          0          1        0         0
  NCL WILD-TYPE        18          8         41         30       35        13
               vv
clus            STAGE IVB
  NCL MUTATED           0
  NCL WILD-TYPE         1
D1320V3, multiclass
            clus
vv           NCL MUTATED NCL WILD-TYPE
  STAGE I              0            64
  STAGE IA             0             1
  STAGE II             0            25
  STAGE IIA            4           105
  STAGE IIB            1             7
  STAGE IIC            0             1
  STAGE III            1            18
  STAGE IIIA           2             8
  STAGE IIIB           0            41
  STAGE IIIC           1            30
  STAGE IV             0            35
  STAGE IVA            0            13
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  NCL MUTATED     0   2   6   2
  NCL WILD-TYPE   9  66 242  39
D1320V4, multiclass
    clus
vv   NCL MUTATED NCL WILD-TYPE
  T1           0             9
  T2           2            66
  T3           6           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
  NCL MUTATED     6   2   2
  NCL WILD-TYPE 214  78  64
D1320V5, multiclass
    clus
vv   NCL MUTATED NCL WILD-TYPE
  N0           6           214
  N1           2            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"
D1320V6, binary
               cls
clus              0   1
  NCL MUTATED     9   0
  NCL WILD-TYPE 274  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  NCL MUTATED      9    0
  NCL WILD-TYPE  274   48
   clus
vv  NCL MUTATED NCL WILD-TYPE
  0           9           274
  1           0            48
[1] 2 2
[1] FALSE
D1320V7, 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
D1320V8, binary
               cls
clus              0   1
  NCL MUTATED     9   1
  NCL WILD-TYPE 308  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  NCL MUTATED      9    1
  NCL WILD-TYPE  308   47
                               clus
vv                              NCL MUTATED NCL WILD-TYPE
  COLON ADENOCARCINOMA                    9           308
  COLON MUCINOUS ADENOCARCINOMA           1            47
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  NCL MUTATED     6   0   0   0
  NCL WILD-TYPE 251   2  22  21
D1320V9, multiclass
    clus
vv   NCL MUTATED NCL WILD-TYPE
  R0           6           251
  R1           0             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"
D1320V10, 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
D1320V11, 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(1321) Variable = PACS2 MUTATION ANALYSIS
D1321V1, survival
                 sevent
clus2               0   1
  PACS2 MUTATED     4   1
  PACS2 WILD-TYPE 278  72
  PACS2 MUTATED PACS2 WILD-TYPE 
              5             350 
  PACS2 MUTATED PACS2 WILD-TYPE 
              1              72 
$`PACS2 MUTATED`
TCGA-AD-5900 TCGA-CK-5913 TCGA-CK-6747 TCGA-CM-6674 TCGA-F4-6570 
        0.07        51.32         2.93        12.95         6.18 

$`PACS2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
       17.56       102.44        40.34        15.62        49.08        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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       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        13.38        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  PACS2 MUTATED PACS2 WILD-TYPE 
           0.07            0.00 
  PACS2 MUTATED PACS2 WILD-TYPE 
          51.32          140.38 
  PACS2 MUTATED PACS2 WILD-TYPE 
           6.18           20.63 
[1] "0.1 - 51.3 (6.2)"   "0.0 - 140.4 (20.6)"
[1] "hr=" "1.4"
D1321V2, 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       25       105         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        19         10         41         31       35        13
                 vv
clus              STAGE IVB
  PACS2 MUTATED           0
  PACS2 WILD-TYPE         1
D1321V3, multiclass
            clus
vv           PACS2 MUTATED PACS2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              4             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PACS2 MUTATED     0   1   4   0
  PACS2 WILD-TYPE   9  67 244  41
D1321V4, multiclass
    clus
vv   PACS2 MUTATED PACS2 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             4             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
  PACS2 MUTATED     5   0   0
  PACS2 WILD-TYPE 215  80  66
D1321V5, multiclass
    clus
vv   PACS2 MUTATED PACS2 WILD-TYPE
  N0             5             215
  N1             0              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"
D1321V6, binary
                 cls
clus                0   1
  PACS2 MUTATED     2   0
  PACS2 WILD-TYPE 281  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PACS2 MUTATED      2    0
  PACS2 WILD-TYPE  281   48
   clus
vv  PACS2 MUTATED PACS2 WILD-TYPE
  0             2             281
  1             0              48
[1] 2 2
[1] FALSE
D1321V7, 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
D1321V8, binary
                 cls
clus                0   1
  PACS2 MUTATED     4   1
  PACS2 WILD-TYPE 313  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PACS2 MUTATED      4    1
  PACS2 WILD-TYPE  313   47
                               clus
vv                              PACS2 MUTATED PACS2 WILD-TYPE
  COLON ADENOCARCINOMA                      4             313
  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 254   2  22  19
D1321V9, multiclass
    clus
vv   PACS2 MUTATED PACS2 WILD-TYPE
  R0             3             254
  R1             0               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"
D1321V10, 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
D1321V11, 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(1322) Variable = GNA11 MUTATION ANALYSIS
D1322V1, survival
                 sevent
clus2               0   1
  GNA11 MUTATED     7   0
  GNA11 WILD-TYPE 275  73
  GNA11 MUTATED GNA11 WILD-TYPE 
              7             348 
  GNA11 MUTATED GNA11 WILD-TYPE 
              0              73 
$`GNA11 MUTATED`
TCGA-A6-5661 TCGA-A6-6141 TCGA-A6-6654 TCGA-A6-6780 TCGA-AA-3526 TCGA-AU-6004 
       33.53         8.38        23.87        20.12        19.07        27.09 
TCGA-D5-6536 
       17.85 

$`GNA11 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6781 TCGA-A6-6782 
       24.16        21.76        24.69        24.39        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        7.04         3.02         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       37.05        36.03         8.05         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  GNA11 MUTATED GNA11 WILD-TYPE 
           8.38            0.00 
  GNA11 MUTATED GNA11 WILD-TYPE 
          33.53          140.38 
  GNA11 MUTATED GNA11 WILD-TYPE 
         20.120          20.235 
[1] "8.4 - 33.5 (20.1)"  "0.0 - 140.4 (20.2)"
[1] "hr="     "9200000"
D1322V2, 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       25       105         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        19         10         40         31       35        13
                 vv
clus              STAGE IVB
  GNA11 MUTATED           0
  GNA11 WILD-TYPE         1
D1322V3, multiclass
            clus
vv           GNA11 MUTATED GNA11 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              4             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GNA11 MUTATED     0   2   5   0
  GNA11 WILD-TYPE   9  66 243  41
D1322V4, multiclass
    clus
vv   GNA11 MUTATED GNA11 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             5             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
  GNA11 MUTATED     6   1   0
  GNA11 WILD-TYPE 214  79  66
D1322V5, multiclass
    clus
vv   GNA11 MUTATED GNA11 WILD-TYPE
  N0             6             214
  N1             1              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
  GNA11 MUTATED     6   0
  GNA11 WILD-TYPE 277  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNA11 MUTATED      6    0
  GNA11 WILD-TYPE  277   48
   clus
vv  GNA11 MUTATED GNA11 WILD-TYPE
  0             6             277
  1             0              48
[1] 2 2
[1] FALSE
D1322V7, 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
D1322V8, binary
                 cls
clus                0   1
  GNA11 MUTATED     6   1
  GNA11 WILD-TYPE 311  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNA11 MUTATED      6    1
  GNA11 WILD-TYPE  311   47
                               clus
vv                              GNA11 MUTATED GNA11 WILD-TYPE
  COLON ADENOCARCINOMA                      6             311
  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 253   2  22  21
D1322V9, multiclass
    clus
vv   GNA11 MUTATED GNA11 WILD-TYPE
  R0             4             253
  R1             0               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"
D1322V10, 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
D1322V11, 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(1323) Variable = MED13 MUTATION ANALYSIS
D1323V1, survival
                 sevent
clus2               0   1
  MED13 MUTATED    16   3
  MED13 WILD-TYPE 266  70
  MED13 MUTATED MED13 WILD-TYPE 
             19             336 
  MED13 MUTATED MED13 WILD-TYPE 
              3              70 
$`MED13 MUTATED`
TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3710 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-A00N 
       24.39        19.66        26.99        53.00        31.00         4.01 
TCGA-AA-A010 TCGA-AD-6895 TCGA-AY-5543 TCGA-CA-6717 TCGA-CK-5913 TCGA-CM-4746 
       34.98         0.72        15.75         0.33        51.32        37.02 
TCGA-CM-5341 TCGA-D5-6928 TCGA-D5-6932 TCGA-F4-6570 TCGA-F4-6856 TCGA-G4-6588 
       29.06        11.64        11.38         6.18        19.43        26.17 
TCGA-G4-6626 
       46.75 

$`MED13 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        4.21        56.55         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        35.41       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 
       36.00        22.09        13.78        35.80        91.79        52.80 

  MED13 MUTATED MED13 WILD-TYPE 
           0.33            0.00 
  MED13 MUTATED MED13 WILD-TYPE 
          53.00          140.38 
  MED13 MUTATED MED13 WILD-TYPE 
         24.390          20.155 
[1] "0.3 - 53.0 (24.4)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D1323V2, 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       24       101         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MED13 MUTATED           0          1          0          1        0         1
  MED13 WILD-TYPE        19          9         41         30       35        12
                 vv
clus              STAGE IVB
  MED13 MUTATED           0
  MED13 WILD-TYPE         1
D1323V3, multiclass
            clus
vv           MED13 MUTATED MED13 WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              8             101
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  64 237  37
D1323V4, multiclass
    clus
vv   MED13 MUTATED MED13 WILD-TYPE
  T1             1               8
  T2             4              64
  T3            11             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
  MED13 MUTATED    16   4   0
  MED13 WILD-TYPE 204  76  66
D1323V5, multiclass
    clus
vv   MED13 MUTATED MED13 WILD-TYPE
  N0            16             204
  N1             4              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"
D1323V6, binary
                 cls
clus                0   1
  MED13 MUTATED    15   1
  MED13 WILD-TYPE 268  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED13 MUTATED     15    1
  MED13 WILD-TYPE  268   47
   clus
vv  MED13 MUTATED MED13 WILD-TYPE
  0            15             268
  1             1              47
[1] 2 2
[1] FALSE
D1323V7, 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
D1323V8, binary
                 cls
clus                0   1
  MED13 MUTATED    14   6
  MED13 WILD-TYPE 303  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED13 MUTATED     14    6
  MED13 WILD-TYPE  303   42
                               clus
vv                              MED13 MUTATED MED13 WILD-TYPE
  COLON ADENOCARCINOMA                     14             303
  COLON MUCINOUS ADENOCARCINOMA             6              42
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MED13 MUTATED    15   0   0   3
  MED13 WILD-TYPE 242   2  22  18
D1323V9, multiclass
    clus
vv   MED13 MUTATED MED13 WILD-TYPE
  R0            15             242
  R1             0               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"
D1323V10, 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
D1323V11, 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(1324) Variable = TNNI3K MUTATION ANALYSIS
D1324V1, survival
                  sevent
clus2                0   1
  TNNI3K MUTATED     8   2
  TNNI3K WILD-TYPE 274  71
  TNNI3K MUTATED TNNI3K WILD-TYPE 
              10              345 
  TNNI3K MUTATED TNNI3K WILD-TYPE 
               2               71 
$`TNNI3K MUTATED`
TCGA-A6-2672 TCGA-A6-5665 TCGA-A6-6137 TCGA-AA-3510 TCGA-AA-3667 TCGA-AA-3672 
       46.65        22.06        27.09        63.98        14.01         0.92 
TCGA-AA-3696 TCGA-AA-3833 TCGA-AA-A00N TCGA-AA-A00R 
        5.03        15.95         4.01         0.99 

$`TNNI3K WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       32.71        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       17.98        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       27.02        42.02        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  TNNI3K MUTATED TNNI3K WILD-TYPE 
            0.92             0.00 
  TNNI3K MUTATED TNNI3K WILD-TYPE 
           63.98           140.38 
  TNNI3K MUTATED TNNI3K WILD-TYPE 
           14.98            20.28 
[1] "0.9 - 64.0 (15.0)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.2"
D1324V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TNNI3K MUTATED         2        0        1         2         1         0
  TNNI3K WILD-TYPE      62        1       24       107         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TNNI3K MUTATED           1          0          2          0        2
  TNNI3K WILD-TYPE        18         10         39         31       33
                  vv
clus               STAGE IVA STAGE IVB
  TNNI3K MUTATED           0         0
  TNNI3K WILD-TYPE        13         1
D1324V3, multiclass
            clus
vv           TNNI3K MUTATED TNNI3K WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               2              107
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              0               31
  STAGE IV                2               33
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TNNI3K MUTATED     0   2   8   1
  TNNI3K WILD-TYPE   9  66 240  40
D1324V4, multiclass
    clus
vv   TNNI3K MUTATED TNNI3K WILD-TYPE
  T1              0                9
  T2              2               66
  T3              8              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
  TNNI3K MUTATED     6   4   1
  TNNI3K WILD-TYPE 214  76  65
D1324V5, multiclass
    clus
vv   TNNI3K MUTATED TNNI3K WILD-TYPE
  N0              6              214
  N1              4               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"
D1324V6, binary
                  cls
clus                 0   1
  TNNI3K MUTATED     9   2
  TNNI3K WILD-TYPE 274  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNNI3K MUTATED      9    2
  TNNI3K WILD-TYPE  274   46
   clus
vv  TNNI3K MUTATED TNNI3K WILD-TYPE
  0              9              274
  1              2               46
[1] 2 2
[1] FALSE
D1324V7, binary
                  cls
clus                 0   1
  TNNI3K MUTATED     8   3
  TNNI3K WILD-TYPE 162 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNNI3K MUTATED      8    3
  TNNI3K WILD-TYPE  162  194
        clus
vv       TNNI3K MUTATED TNNI3K WILD-TYPE
  FEMALE              8              162
  MALE                3              194
[1] 2 2
[1] FALSE
D1324V8, binary
                  cls
clus                 0   1
  TNNI3K MUTATED    10   1
  TNNI3K WILD-TYPE 307  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNNI3K MUTATED     10    1
  TNNI3K WILD-TYPE  307   47
                               clus
vv                              TNNI3K MUTATED TNNI3K WILD-TYPE
  COLON ADENOCARCINOMA                      10              307
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TNNI3K MUTATED     8   0   2   0
  TNNI3K WILD-TYPE 249   2  20  21
D1324V9, multiclass
    clus
vv   TNNI3K MUTATED TNNI3K WILD-TYPE
  R0              8              249
  R1              0                2
  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"
D1324V10, 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                           0     3
  TNNI3K WILD-TYPE                        19   173
D1324V11, multiclass
                                  clus
vv                                 TNNI3K MUTATED TNNI3K 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(1325) Variable = FAM70A MUTATION ANALYSIS
D1325V1, survival
                  sevent
clus2                0   1
  FAM70A MUTATED     5   2
  FAM70A WILD-TYPE 277  71
  FAM70A MUTATED FAM70A WILD-TYPE 
               7              348 
  FAM70A MUTATED FAM70A WILD-TYPE 
               2               71 
$`FAM70A MUTATED`
TCGA-AA-3660 TCGA-AA-A00N TCGA-AD-6889 TCGA-AZ-4315 TCGA-CA-6717 TCGA-D5-6537 
       78.08         4.01        56.55        58.39         0.33         4.80 
TCGA-G4-6317 
       36.00 

$`FAM70A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        61.02         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        15.12        17.85        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 
       44.68        55.04        51.75        45.11        36.72        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  FAM70A MUTATED FAM70A WILD-TYPE 
            0.33             0.00 
  FAM70A MUTATED FAM70A WILD-TYPE 
           78.08           140.38 
  FAM70A MUTATED FAM70A WILD-TYPE 
          36.000           20.155 
[1] "0.3 - 78.1 (36.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D1325V2, 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       24       106         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM70A MUTATED           0          0          1          1        0
  FAM70A WILD-TYPE        19         10         40         30       35
                  vv
clus               STAGE IVA STAGE IVB
  FAM70A MUTATED           0         0
  FAM70A WILD-TYPE        13         1
D1325V3, multiclass
            clus
vv           FAM70A MUTATED FAM70A WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               3              106
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FAM70A MUTATED     0   0   6   1
  FAM70A WILD-TYPE   9  68 242  40
D1325V4, multiclass
    clus
vv   FAM70A MUTATED FAM70A WILD-TYPE
  T1              0                9
  T2              0               68
  T3              6              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
  FAM70A MUTATED     5   1   1
  FAM70A WILD-TYPE 215  79  65
D1325V5, multiclass
    clus
vv   FAM70A MUTATED FAM70A WILD-TYPE
  N0              5              215
  N1              1               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"
D1325V6, binary
                  cls
clus                 0   1
  FAM70A MUTATED     5   0
  FAM70A WILD-TYPE 278  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM70A MUTATED      5    0
  FAM70A WILD-TYPE  278   48
   clus
vv  FAM70A MUTATED FAM70A WILD-TYPE
  0              5              278
  1              0               48
[1] 2 2
[1] FALSE
D1325V7, 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
D1325V8, binary
                  cls
clus                 0   1
  FAM70A MUTATED     5   2
  FAM70A WILD-TYPE 312  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM70A MUTATED      5    2
  FAM70A WILD-TYPE  312   46
                               clus
vv                              FAM70A MUTATED FAM70A WILD-TYPE
  COLON ADENOCARCINOMA                       5              312
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  FAM70A MUTATED     5   0   0   1
  FAM70A WILD-TYPE 252   2  22  20
D1325V9, multiclass
    clus
vv   FAM70A MUTATED FAM70A WILD-TYPE
  R0              5              252
  R1              0                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"
D1325V10, 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
D1325V11, 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(1326) Variable = TMPRSS5 MUTATION ANALYSIS
D1326V1, survival
                   sevent
clus2                 0   1
  TMPRSS5 MUTATED     5   2
  TMPRSS5 WILD-TYPE 277  71
  TMPRSS5 MUTATED TMPRSS5 WILD-TYPE 
                7               348 
  TMPRSS5 MUTATED TMPRSS5 WILD-TYPE 
                2                71 
$`TMPRSS5 MUTATED`
TCGA-A6-6141 TCGA-AA-3715 TCGA-AA-3977 TCGA-AU-6004 TCGA-AZ-6598 TCGA-CM-5860 
        8.38        19.04        25.02        27.09        49.41        16.01 
TCGA-CM-6162 
       12.00 

$`TMPRSS5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.20        14.50        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  TMPRSS5 MUTATED TMPRSS5 WILD-TYPE 
             8.38              0.00 
  TMPRSS5 MUTATED TMPRSS5 WILD-TYPE 
            49.41            140.38 
  TMPRSS5 MUTATED TMPRSS5 WILD-TYPE 
           19.040            20.235 
[1] "8.4 - 49.4 (19.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.5"
D1326V2, 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       23       107         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMPRSS5 MUTATED           0          0          1          0        0
  TMPRSS5 WILD-TYPE        19         10         40         31       35
                   vv
clus                STAGE IVA STAGE IVB
  TMPRSS5 MUTATED           0         0
  TMPRSS5 WILD-TYPE        13         1
D1326V3, multiclass
            clus
vv           TMPRSS5 MUTATED TMPRSS5 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 2                23
  STAGE IIA                2               107
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TMPRSS5 MUTATED     0   2   5   0
  TMPRSS5 WILD-TYPE   9  66 243  41
D1326V4, multiclass
    clus
vv   TMPRSS5 MUTATED TMPRSS5 WILD-TYPE
  T1               0                 9
  T2               2                66
  T3               5               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
  TMPRSS5 MUTATED     6   1   0
  TMPRSS5 WILD-TYPE 214  79  66
D1326V5, multiclass
    clus
vv   TMPRSS5 MUTATED TMPRSS5 WILD-TYPE
  N0               6               214
  N1               1                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"
D1326V6, binary
                   cls
clus                  0   1
  TMPRSS5 MUTATED     5   0
  TMPRSS5 WILD-TYPE 278  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMPRSS5 MUTATED      5    0
  TMPRSS5 WILD-TYPE  278   48
   clus
vv  TMPRSS5 MUTATED TMPRSS5 WILD-TYPE
  0               5               278
  1               0                48
[1] 2 2
[1] FALSE
D1326V7, 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
D1326V8, binary
                   cls
clus                  0   1
  TMPRSS5 MUTATED     6   1
  TMPRSS5 WILD-TYPE 311  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMPRSS5 MUTATED      6    1
  TMPRSS5 WILD-TYPE  311   47
                               clus
vv                              TMPRSS5 MUTATED TMPRSS5 WILD-TYPE
  COLON ADENOCARCINOMA                        6               311
  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 253   2  22  21
D1326V9, multiclass
    clus
vv   TMPRSS5 MUTATED TMPRSS5 WILD-TYPE
  R0               4               253
  R1               0                 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"
D1326V10, 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
D1326V11, 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(1327) Variable = DMXL2 MUTATION ANALYSIS
D1327V1, survival
                 sevent
clus2               0   1
  DMXL2 MUTATED    24   7
  DMXL2 WILD-TYPE 258  66
  DMXL2 MUTATED DMXL2 WILD-TYPE 
             31             324 
  DMXL2 MUTATED DMXL2 WILD-TYPE 
              7              66 
$`DMXL2 MUTATED`
TCGA-A6-2676 TCGA-A6-3809 TCGA-A6-5665 TCGA-A6-6782 TCGA-AA-3496 TCGA-AA-3510 
       42.90        32.75        22.06        20.28         1.02        63.98 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3662 TCGA-AA-3713 TCGA-AA-3833 TCGA-AA-3842 
       17.95        29.95         6.05        19.04        15.95        37.02 
TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-5900 
       53.00        27.02        25.02         4.01        34.98         0.07 
TCGA-AY-6197 TCGA-AZ-4323 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5916 
       21.44         1.41       100.01         0.33         0.10        21.14 
TCGA-CM-6674 TCGA-D5-6928 TCGA-DM-A28E TCGA-F4-6460 TCGA-G4-6293 TCGA-G4-6303 
       12.95        11.64       119.93        13.38       107.67        65.85 
TCGA-G4-6588 
       26.17 

$`DMXL2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       34.65        33.34        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       30.44        29.19        33.53        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        7.04         3.02        35.01         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       21.01        13.02        24.00        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3844 
        0.99        25.02         1.02        17.98        38.99        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       17.03        24.03        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        15.75         0.20        17.82        58.39 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.26         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32        21.99         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28F 
      131.51       135.65       139.17         6.12        81.37        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 
       60.79       117.07        98.24         8.61        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6304 
       13.25         0.53        35.41        19.43        74.56        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        52.80 

  DMXL2 MUTATED DMXL2 WILD-TYPE 
           0.07            0.00 
  DMXL2 MUTATED DMXL2 WILD-TYPE 
         119.93          140.38 
  DMXL2 MUTATED DMXL2 WILD-TYPE 
         21.440          20.005 
[1] "0.1 - 119.9 (21.4)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.1"
D1327V2, 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       21        97         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        18          9         40         31       30        13
                 vv
clus              STAGE IVB
  DMXL2 MUTATED           0
  DMXL2 WILD-TYPE         1
D1327V3, multiclass
            clus
vv           DMXL2 MUTATED DMXL2 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               4              21
  STAGE IIA             12              97
  STAGE IIB              6               2
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             1               9
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               5              30
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DMXL2 MUTATED     1   3  20   9
  DMXL2 WILD-TYPE   8  65 228  32
D1327V4, multiclass
    clus
vv   DMXL2 MUTATED DMXL2 WILD-TYPE
  T1             1               8
  T2             3              65
  T3            20             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
  DMXL2 MUTATED    26   4   3
  DMXL2 WILD-TYPE 194  76  63
D1327V5, multiclass
    clus
vv   DMXL2 MUTATED DMXL2 WILD-TYPE
  N0            26             194
  N1             4              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"
D1327V6, binary
                 cls
clus                0   1
  DMXL2 MUTATED    23   5
  DMXL2 WILD-TYPE 260  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DMXL2 MUTATED     23    5
  DMXL2 WILD-TYPE  260   43
   clus
vv  DMXL2 MUTATED DMXL2 WILD-TYPE
  0            23             260
  1             5              43
[1] 2 2
[1] FALSE
D1327V7, 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
D1327V8, binary
                 cls
clus                0   1
  DMXL2 MUTATED    27   6
  DMXL2 WILD-TYPE 290  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DMXL2 MUTATED     27    6
  DMXL2 WILD-TYPE  290   42
                               clus
vv                              DMXL2 MUTATED DMXL2 WILD-TYPE
  COLON ADENOCARCINOMA                     27             290
  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 236   2  19  17
D1327V9, multiclass
    clus
vv   DMXL2 MUTATED DMXL2 WILD-TYPE
  R0            21             236
  R1             0               2
  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"
D1327V10, 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
D1327V11, 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(1328) Variable = MED12L MUTATION ANALYSIS
D1328V1, survival
                  sevent
clus2                0   1
  MED12L MUTATED    24   3
  MED12L WILD-TYPE 258  70
  MED12L MUTATED MED12L WILD-TYPE 
              27              328 
  MED12L MUTATED MED12L WILD-TYPE 
               3               70 
$`MED12L MUTATED`
TCGA-A6-4105 TCGA-A6-5659 TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3531 TCGA-AA-3543 
       14.53        30.44         1.02        63.98        34.03         0.99 
TCGA-AA-3555 TCGA-AA-3713 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3977 TCGA-AA-3986 
       29.95        19.04        26.01        24.00        25.02        19.07 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q TCGA-AD-5900 TCGA-AD-6895 TCGA-AY-5543 
        4.01        34.98         1.02         0.07         0.72        15.75 
TCGA-AZ-4315 TCGA-AZ-4681 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-5913 TCGA-D5-6920 
       58.39        83.80        49.41         0.33        51.32        12.39 
TCGA-D5-6928 TCGA-F4-6807 TCGA-G4-6586 
       11.64        16.24        35.80 

$`MED12L WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3511 
       19.66        20.28         7.04         3.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
       29.00        29.00        26.01        12.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        17.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       12.99        24.00        33.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       26.01        24.00        27.02        27.02         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37         4.21        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       27.09        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-6599 
        1.41         5.13        22.36        62.79        61.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 
       12.49        16.14        15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       29.59        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  MED12L MUTATED MED12L WILD-TYPE 
            0.07             0.00 
  MED12L MUTATED MED12L WILD-TYPE 
           83.80           140.38 
  MED12L MUTATED MED12L WILD-TYPE 
          19.070           20.235 
[1] "0.1 - 83.8 (19.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.9"
D1328V2, 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       21        97         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MED12L MUTATED           0          0          1          1        1
  MED12L WILD-TYPE        19         10         40         30       34
                  vv
clus               STAGE IVA STAGE IVB
  MED12L MUTATED           1         0
  MED12L WILD-TYPE        12         1
D1328V3, multiclass
            clus
vv           MED12L MUTATED MED12L WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                4               21
  STAGE IIA              12               97
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              1               30
  STAGE IV                1               34
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  63 227  39
D1328V4, multiclass
    clus
vv   MED12L MUTATED MED12L WILD-TYPE
  T1              0                9
  T2              5               63
  T3             21              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
  MED12L MUTATED    24   3   1
  MED12L WILD-TYPE 196  77  65
D1328V5, multiclass
    clus
vv   MED12L MUTATED MED12L WILD-TYPE
  N0             24              196
  N1              3               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"
D1328V6, binary
                  cls
clus                 0   1
  MED12L MUTATED    21   2
  MED12L WILD-TYPE 262  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MED12L MUTATED     21    2
  MED12L WILD-TYPE  262   46
   clus
vv  MED12L MUTATED MED12L WILD-TYPE
  0             21              262
  1              2               46
[1] 2 2
[1] FALSE
D1328V7, 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
D1328V8, binary
                  cls
clus                 0   1
  MED12L MUTATED    20   8
  MED12L WILD-TYPE 297  40
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MED12L MUTATED     20    8
  MED12L WILD-TYPE  297   40
                               clus
vv                              MED12L MUTATED MED12L WILD-TYPE
  COLON ADENOCARCINOMA                      20              297
  COLON MUCINOUS ADENOCARCINOMA              8               40
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  MED12L MUTATED    21   0   1   2
  MED12L WILD-TYPE 236   2  21  19
D1328V9, multiclass
    clus
vv   MED12L MUTATED MED12L WILD-TYPE
  R0             21              236
  R1              0                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"
D1328V10, 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
D1328V11, 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(1329) Variable = ATP6V0A4 MUTATION ANALYSIS
D1329V1, survival
                    sevent
clus2                  0   1
  ATP6V0A4 MUTATED     7   2
  ATP6V0A4 WILD-TYPE 275  71
  ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE 
                 9                346 
  ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE 
                 2                 71 
$`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         0.33 
TCGA-CA-6718 TCGA-CK-4950 TCGA-D5-7000 
        0.10        40.34        10.26 

$`ATP6V0A4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.20        14.50        16.31         0.95        15.75         0.20 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07         0.26         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       102.44        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE 
               0.1                0.0 
  ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE 
             40.34             140.38 
  ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE 
            19.040             20.235 
[1] "0.1 - 40.3 (19.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.7"
D1329V2, 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       24       105         5         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP6V0A4 MUTATED           0          1          0          0        0
  ATP6V0A4 WILD-TYPE        19          9         41         31       35
                    vv
clus                 STAGE IVA STAGE IVB
  ATP6V0A4 MUTATED           0         0
  ATP6V0A4 WILD-TYPE        13         1
D1329V3, multiclass
            clus
vv           ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE
  STAGE I                   2                 62
  STAGE IA                  0                  1
  STAGE II                  1                 24
  STAGE IIA                 4                105
  STAGE IIB                 3                  5
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                1                  9
  STAGE IIIB                0                 41
  STAGE IIIC                0                 31
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  ATP6V0A4 MUTATED     0   2   6   3
  ATP6V0A4 WILD-TYPE   9  66 242  38
D1329V4, multiclass
    clus
vv   ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE
  T1                0                  9
  T2                2                 66
  T3                6                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
  ATP6V0A4 MUTATED    10   1   0
  ATP6V0A4 WILD-TYPE 210  79  66
D1329V5, multiclass
    clus
vv   ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE
  N0               10                210
  N1                1                 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"
D1329V6, binary
                    cls
clus                   0   1
  ATP6V0A4 MUTATED     9   0
  ATP6V0A4 WILD-TYPE 274  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ATP6V0A4 MUTATED      9    0
  ATP6V0A4 WILD-TYPE  274   48
   clus
vv  ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE
  0                9                274
  1                0                 48
[1] 2 2
[1] FALSE
D1329V7, 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
D1329V8, binary
                    cls
clus                   0   1
  ATP6V0A4 MUTATED     8   3
  ATP6V0A4 WILD-TYPE 309  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ATP6V0A4 MUTATED      8    3
  ATP6V0A4 WILD-TYPE  309   45
                               clus
vv                              ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE
  COLON ADENOCARCINOMA                         8                309
  COLON MUCINOUS ADENOCARCINOMA                3                 45
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  ATP6V0A4 MUTATED     7   1   0   3
  ATP6V0A4 WILD-TYPE 250   1  22  18
D1329V9, multiclass
    clus
vv   ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE
  R0                7                250
  R1                1                  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"
D1329V10, 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
D1329V11, 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(1330) Variable = TMSB15B MUTATION ANALYSIS
D1330V1, survival
                   sevent
clus2                 0   1
  TMSB15B MUTATED     1   2
  TMSB15B WILD-TYPE 281  71
  TMSB15B MUTATED TMSB15B WILD-TYPE 
                3               352 
  TMSB15B MUTATED TMSB15B WILD-TYPE 
                2                71 
$`TMSB15B MUTATED`
TCGA-D5-6540 TCGA-DM-A285 TCGA-F4-6459 
       16.14         6.12         8.61 

$`TMSB15B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        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        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  TMSB15B MUTATED TMSB15B WILD-TYPE 
             6.12              0.00 
  TMSB15B MUTATED TMSB15B WILD-TYPE 
            16.14            140.38 
  TMSB15B MUTATED TMSB15B WILD-TYPE 
             8.61             20.63 
[1] "6.1 - 16.1 (8.6)"   "0.0 - 140.4 (20.6)"
[1] "hr=" "6.7"
D1330V2, 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       25       109         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMSB15B MUTATED           0          0          1          0        1
  TMSB15B WILD-TYPE        19         10         40         31       34
                   vv
clus                STAGE IVA STAGE IVB
  TMSB15B MUTATED           0         0
  TMSB15B WILD-TYPE        13         1
D1330V3, multiclass
            clus
vv           TMSB15B MUTATED TMSB15B WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                0               109
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               0                31
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TMSB15B MUTATED     0   1   2   0
  TMSB15B WILD-TYPE   9  67 246  41
D1330V4, multiclass
    clus
vv   TMSB15B MUTATED TMSB15B WILD-TYPE
  T1               0                 9
  T2               1                67
  T3               2               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
  TMSB15B MUTATED     1   0   2
  TMSB15B WILD-TYPE 219  80  64
D1330V5, multiclass
    clus
vv   TMSB15B MUTATED TMSB15B WILD-TYPE
  N0               1               219
  N1               0                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"
D1330V6, binary
                   cls
clus                  0   1
  TMSB15B MUTATED     2   1
  TMSB15B WILD-TYPE 281  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMSB15B MUTATED      2    1
  TMSB15B WILD-TYPE  281   47
   clus
vv  TMSB15B MUTATED TMSB15B WILD-TYPE
  0               2               281
  1               1                47
[1] 2 2
[1] FALSE
D1330V7, 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
D1330V8, binary
                   cls
clus                  0   1
  TMSB15B MUTATED     1   2
  TMSB15B WILD-TYPE 316  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMSB15B MUTATED      1    2
  TMSB15B WILD-TYPE  316   46
                               clus
vv                              TMSB15B MUTATED TMSB15B WILD-TYPE
  COLON ADENOCARCINOMA                        1               316
  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 255   2  22  21
D1330V9, multiclass
[1] "Remove cluster labels:" "TMSB15B MUTATED"       
clus
  TMSB15B MUTATED TMSB15B WILD-TYPE 
                2               300 
       TCGA-A6-2671        TCGA-A6-2672        TCGA-A6-2674        TCGA-A6-2676 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-A6-2677        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-3496        TCGA-AA-3502 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-3510        TCGA-AA-3511        TCGA-AA-3514        TCGA-AA-3517 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-3518        TCGA-AA-3519        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-3526 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-3527        TCGA-AA-3529        TCGA-AA-3530        TCGA-AA-3531 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-3532        TCGA-AA-3534        TCGA-AA-3538        TCGA-AA-3542 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-3543        TCGA-AA-3544        TCGA-AA-3548        TCGA-AA-3549 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-3552        TCGA-AA-3553        TCGA-AA-3554        TCGA-AA-3555 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-3556        TCGA-AA-3558        TCGA-AA-3560        TCGA-AA-3561 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-3562        TCGA-AA-3655        TCGA-AA-3660        TCGA-AA-3662 
"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-3672        TCGA-AA-3673        TCGA-AA-3678        TCGA-AA-3679 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-3680        TCGA-AA-3681        TCGA-AA-3684        TCGA-AA-3685 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-3688        TCGA-AA-3692        TCGA-AA-3693        TCGA-AA-3695 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-3696        TCGA-AA-3697        TCGA-AA-3710        TCGA-AA-3712 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-3713        TCGA-AA-3715        TCGA-AA-3811        TCGA-AA-3812 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-3814        TCGA-AA-3815        TCGA-AA-3818        TCGA-AA-3819 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-3821        TCGA-AA-3831        TCGA-AA-3833        TCGA-AA-3837 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-3842        TCGA-AA-3844        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-3860        TCGA-AA-3861        TCGA-AA-3864        TCGA-AA-3866 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-3867        TCGA-AA-3869        TCGA-AA-3870        TCGA-AA-3872 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-3875        TCGA-AA-3877        TCGA-AA-3930        TCGA-AA-3939 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-3941        TCGA-AA-3947        TCGA-AA-3949        TCGA-AA-3950 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-3952        TCGA-AA-3955        TCGA-AA-3956        TCGA-AA-3968 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-3971        TCGA-AA-3972        TCGA-AA-3973        TCGA-AA-3975 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-3976        TCGA-AA-3979        TCGA-AA-3984        TCGA-AA-3986 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-3989        TCGA-AA-3994        TCGA-AA-A004        TCGA-AA-A00A 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-A00D        TCGA-AA-A00E        TCGA-AA-A00F        TCGA-AA-A00J 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-A00K        TCGA-AA-A00L        TCGA-AA-A00N        TCGA-AA-A00O 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-A00Q        TCGA-AA-A00R        TCGA-AA-A00U        TCGA-AA-A00W 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-A00Z        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-A024        TCGA-AA-A029        TCGA-AA-A02F 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-A02H        TCGA-AA-A02J        TCGA-AA-A02K        TCGA-AA-A02O 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AA-A02W        TCGA-AA-A02Y        TCGA-AA-A03F        TCGA-AA-A03J 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AD-5900        TCGA-AD-6548        TCGA-AD-6888        TCGA-AU-3779 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AU-6004        TCGA-AY-4070        TCGA-AY-4071        TCGA-AY-5543 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AY-6196        TCGA-AY-6197        TCGA-AY-6386        TCGA-AZ-4315 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-AZ-4681        TCGA-AZ-4682        TCGA-CA-5254        TCGA-CA-5255 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-CA-5796        TCGA-CA-5797        TCGA-CA-6715        TCGA-CA-6716 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-CA-6717        TCGA-CA-6718        TCGA-CA-6719        TCGA-CK-4947 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-CK-4948        TCGA-CK-4950        TCGA-CK-4952        TCGA-CK-5912 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-CK-5913        TCGA-CK-5914        TCGA-CK-5915        TCGA-CK-5916 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-CK-6746        TCGA-CK-6747        TCGA-CK-6748        TCGA-CK-6751 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-CM-4743        TCGA-CM-4744        TCGA-CM-4746        TCGA-CM-4747 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-CM-4752        TCGA-CM-5341        TCGA-CM-5344        TCGA-CM-5348 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-CM-5349        TCGA-CM-5860        TCGA-CM-5861        TCGA-CM-5862 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-CM-5863        TCGA-CM-5864        TCGA-CM-5868        TCGA-CM-6161 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-CM-6162        TCGA-CM-6163        TCGA-CM-6164        TCGA-CM-6165 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-CM-6166        TCGA-CM-6167        TCGA-CM-6168        TCGA-CM-6169 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-CM-6170        TCGA-CM-6171        TCGA-CM-6172        TCGA-CM-6674 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-CM-6675        TCGA-CM-6676        TCGA-CM-6677        TCGA-CM-6678 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-CM-6679        TCGA-CM-6680        TCGA-D5-5537        TCGA-D5-5538 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-D5-5539        TCGA-D5-5540        TCGA-D5-5541        TCGA-D5-6529 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-D5-6532        TCGA-D5-6533        TCGA-D5-6534        TCGA-D5-6535 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-D5-6536        TCGA-D5-6537        TCGA-D5-6538        TCGA-D5-6539 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-D5-6541        TCGA-D5-6898        TCGA-D5-6920        TCGA-D5-6922 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-D5-6923        TCGA-D5-6924        TCGA-D5-6926        TCGA-D5-6927 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-D5-6928        TCGA-D5-6929        TCGA-D5-6930        TCGA-D5-6931 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-D5-6932        TCGA-D5-7000        TCGA-F4-6460        TCGA-F4-6569 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-F4-6570        TCGA-F4-6703        TCGA-F4-6704        TCGA-F4-6805 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-F4-6806        TCGA-F4-6807        TCGA-F4-6808        TCGA-F4-6809 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-F4-6854        TCGA-F4-6855        TCGA-F4-6856        TCGA-G4-6293 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-G4-6299        TCGA-G4-6303        TCGA-G4-6304        TCGA-G4-6306 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-G4-6307        TCGA-G4-6309        TCGA-G4-6310        TCGA-G4-6315 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-G4-6317        TCGA-G4-6321        TCGA-G4-6323        TCGA-G4-6586 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
       TCGA-G4-6588        TCGA-G4-6625        TCGA-G4-6626        TCGA-G4-6628 
"TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" "TMSB15B WILD-TYPE" 
D1330V10, 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
D1330V11, 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(1331) Variable = TRIP12 MUTATION ANALYSIS
D1331V1, survival
                  sevent
clus2                0   1
  TRIP12 MUTATED    22   5
  TRIP12 WILD-TYPE 260  68
  TRIP12 MUTATED TRIP12 WILD-TYPE 
              27              328 
  TRIP12 MUTATED TRIP12 WILD-TYPE 
               5               68 
$`TRIP12 MUTATED`
TCGA-A6-3808 TCGA-A6-5661 TCGA-A6-6141 TCGA-A6-6654 TCGA-A6-6781 TCGA-AA-3492 
       33.34        33.53         8.38        23.87        19.66         3.02 
TCGA-AA-3845 TCGA-AA-3877 TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00N 
        0.00        31.00        24.00         2.01        25.02         4.01 
TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-6889 TCGA-AD-6895 TCGA-AU-3779 TCGA-AU-6004 
       34.98        35.01        56.55         0.72        14.50        27.09 
TCGA-AZ-4315 TCGA-CK-4952 TCGA-D5-6538 TCGA-DM-A0XD TCGA-DM-A1D8 TCGA-DM-A1HB 
       58.39        15.62        17.13        24.43        12.59       135.65 
TCGA-F4-6703 TCGA-G4-6586 TCGA-G4-6588 
       35.87        35.80        26.17 

$`TRIP12 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       32.71        27.09        22.52        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 
       21.76        24.69        24.39        20.12        20.28         7.04 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       102.44        40.34        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 
        8.61        13.38        13.45         6.18         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        91.79        46.75        52.80 

  TRIP12 MUTATED TRIP12 WILD-TYPE 
               0                0 
  TRIP12 MUTATED TRIP12 WILD-TYPE 
          135.65           140.38 
  TRIP12 MUTATED TRIP12 WILD-TYPE 
          24.430           20.005 
[1] "0.0 - 135.7 (24.4)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.1"
D1331V2, 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       24        95         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRIP12 MUTATED           2          0          3          1        0
  TRIP12 WILD-TYPE        17         10         38         30       35
                  vv
clus               STAGE IVA STAGE IVB
  TRIP12 MUTATED           0         0
  TRIP12 WILD-TYPE        13         1
D1331V3, multiclass
            clus
vv           TRIP12 MUTATED TRIP12 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA              14               95
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               2               17
  STAGE IIIA              0               10
  STAGE IIIB              3               38
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TRIP12 MUTATED     1   2  21   4
  TRIP12 WILD-TYPE   8  66 227  37
D1331V4, multiclass
    clus
vv   TRIP12 MUTATED TRIP12 WILD-TYPE
  T1              1                8
  T2              2               66
  T3             21              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
  TRIP12 MUTATED    20   5   3
  TRIP12 WILD-TYPE 200  75  63
D1331V5, multiclass
    clus
vv   TRIP12 MUTATED TRIP12 WILD-TYPE
  N0             20              200
  N1              5               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"
D1331V6, binary
                  cls
clus                 0   1
  TRIP12 MUTATED    24   0
  TRIP12 WILD-TYPE 259  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIP12 MUTATED     24    0
  TRIP12 WILD-TYPE  259   48
   clus
vv  TRIP12 MUTATED TRIP12 WILD-TYPE
  0             24              259
  1              0               48
[1] 2 2
[1] FALSE
D1331V7, 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
D1331V8, binary
                  cls
clus                 0   1
  TRIP12 MUTATED    21   7
  TRIP12 WILD-TYPE 296  41
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIP12 MUTATED     21    7
  TRIP12 WILD-TYPE  296   41
                               clus
vv                              TRIP12 MUTATED TRIP12 WILD-TYPE
  COLON ADENOCARCINOMA                      21              296
  COLON MUCINOUS ADENOCARCINOMA              7               41
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TRIP12 MUTATED    18   0   0   1
  TRIP12 WILD-TYPE 239   2  22  20
D1331V9, multiclass
    clus
vv   TRIP12 MUTATED TRIP12 WILD-TYPE
  R0             18              239
  R1              0                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"
D1331V10, 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
D1331V11, 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(1332) Variable = STAT5B MUTATION ANALYSIS
D1332V1, survival
                  sevent
clus2                0   1
  STAT5B MUTATED    10   2
  STAT5B WILD-TYPE 272  71
  STAT5B MUTATED STAT5B WILD-TYPE 
              12              343 
  STAT5B MUTATED STAT5B WILD-TYPE 
               2               71 
$`STAT5B MUTATED`
TCGA-A6-3809 TCGA-A6-6653 TCGA-A6-6780 TCGA-AA-3815 TCGA-AA-3950 TCGA-AA-A00N 
       32.75        24.39        20.12        33.04        24.00         4.01 
TCGA-AA-A010 TCGA-AU-6004 TCGA-AY-6196 TCGA-CA-6717 TCGA-G4-6303 TCGA-G4-6628 
       34.98        27.09         0.20         0.33        65.85        52.80 

$`STAT5B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6781 
       25.18        24.16        21.76        24.69        23.87        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       15.75        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 
       46.75 

  STAT5B MUTATED STAT5B WILD-TYPE 
             0.2              0.0 
  STAT5B MUTATED STAT5B WILD-TYPE 
           65.85           140.38 
  STAT5B MUTATED STAT5B WILD-TYPE 
           25.74            19.99 
[1] "0.2 - 65.8 (25.7)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1.3"
D1332V2, 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       25       105         5         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  STAT5B MUTATED           0          0          0          1        1
  STAT5B WILD-TYPE        19         10         41         30       34
                  vv
clus               STAGE IVA STAGE IVB
  STAT5B MUTATED           0         0
  STAT5B WILD-TYPE        13         1
D1332V3, multiclass
            clus
vv           STAT5B MUTATED STAT5B WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               4              105
  STAGE IIB               3                5
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              1               30
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  STAT5B MUTATED     0   3   6   3
  STAT5B WILD-TYPE   9  65 242  38
D1332V4, multiclass
    clus
vv   STAT5B MUTATED STAT5B WILD-TYPE
  T1              0                9
  T2              3               65
  T3              6              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
  STAT5B MUTATED    10   1   1
  STAT5B WILD-TYPE 210  79  65
D1332V5, multiclass
    clus
vv   STAT5B MUTATED STAT5B WILD-TYPE
  N0             10              210
  N1              1               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"
D1332V6, binary
                  cls
clus                 0   1
  STAT5B MUTATED     9   1
  STAT5B WILD-TYPE 274  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STAT5B MUTATED      9    1
  STAT5B WILD-TYPE  274   47
   clus
vv  STAT5B MUTATED STAT5B WILD-TYPE
  0              9              274
  1              1               47
[1] 2 2
[1] FALSE
D1332V7, 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
D1332V8, binary
                  cls
clus                 0   1
  STAT5B MUTATED     6   6
  STAT5B WILD-TYPE 311  42
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STAT5B MUTATED      6    6
  STAT5B WILD-TYPE  311   42
                               clus
vv                              STAT5B MUTATED STAT5B WILD-TYPE
  COLON ADENOCARCINOMA                       6              311
  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 248   2  22  20
D1332V9, multiclass
    clus
vv   STAT5B MUTATED STAT5B WILD-TYPE
  R0              9              248
  R1              0                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"
D1332V10, 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
D1332V11, 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(1333) Variable = PLCG2 MUTATION ANALYSIS
D1333V1, survival
                 sevent
clus2               0   1
  PLCG2 MUTATED    14   4
  PLCG2 WILD-TYPE 268  69
  PLCG2 MUTATED PLCG2 WILD-TYPE 
             18             337 
  PLCG2 MUTATED PLCG2 WILD-TYPE 
              4              69 
$`PLCG2 MUTATED`
TCGA-A6-6138 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3662 TCGA-AA-3715 TCGA-AA-3812 
       22.52         3.02        63.98         6.05        19.04        35.05 
TCGA-AA-3855 TCGA-AA-3947 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01P TCGA-AZ-4315 
       32.05        33.01         4.01        34.98        38.07        58.39 
TCGA-CA-6717 TCGA-CM-6164 TCGA-CM-6171 TCGA-D5-6930 TCGA-G4-6586 TCGA-G4-6588 
        0.33        29.03        14.04         1.51        35.80        26.17 

$`PLCG2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        32.71        27.09         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       26.99        19.04        10.06        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       36.03         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       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        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        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-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 
       36.72        36.00        22.09        13.78        91.79        46.75 
TCGA-G4-6628 
       52.80 

  PLCG2 MUTATED PLCG2 WILD-TYPE 
           0.33            0.00 
  PLCG2 MUTATED PLCG2 WILD-TYPE 
          63.98          140.38 
  PLCG2 MUTATED PLCG2 WILD-TYPE 
          27.60           20.02 
[1] "0.3 - 64.0 (27.6)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1.2"
D1333V2, 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       22       102         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        18         10         41         31       34        13
                 vv
clus              STAGE IVB
  PLCG2 MUTATED           0
  PLCG2 WILD-TYPE         1
D1333V3, multiclass
            clus
vv           PLCG2 MUTATED PLCG2 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              7             102
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PLCG2 MUTATED     0   3  11   4
  PLCG2 WILD-TYPE   9  65 237  37
D1333V4, multiclass
    clus
vv   PLCG2 MUTATED PLCG2 WILD-TYPE
  T1             0               9
  T2             3              65
  T3            11             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
  PLCG2 MUTATED    16   1   1
  PLCG2 WILD-TYPE 204  79  65
D1333V5, multiclass
    clus
vv   PLCG2 MUTATED PLCG2 WILD-TYPE
  N0            16             204
  N1             1              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"
D1333V6, binary
                 cls
clus                0   1
  PLCG2 MUTATED    17   1
  PLCG2 WILD-TYPE 266  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLCG2 MUTATED     17    1
  PLCG2 WILD-TYPE  266   47
   clus
vv  PLCG2 MUTATED PLCG2 WILD-TYPE
  0            17             266
  1             1              47
[1] 2 2
[1] FALSE
D1333V7, 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
D1333V8, binary
                 cls
clus                0   1
  PLCG2 MUTATED    14   4
  PLCG2 WILD-TYPE 303  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLCG2 MUTATED     14    4
  PLCG2 WILD-TYPE  303   44
                               clus
vv                              PLCG2 MUTATED PLCG2 WILD-TYPE
  COLON ADENOCARCINOMA                     14             303
  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 242   2  21  20
D1333V9, multiclass
    clus
vv   PLCG2 MUTATED PLCG2 WILD-TYPE
  R0            15             242
  R1             0               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"
D1333V10, 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
D1333V11, 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(1334) Variable = PTPRB MUTATION ANALYSIS
D1334V1, survival
                 sevent
clus2               0   1
  PTPRB MUTATED    15   2
  PTPRB WILD-TYPE 267  71
  PTPRB MUTATED PTPRB WILD-TYPE 
             17             338 
  PTPRB MUTATED PTPRB WILD-TYPE 
              2              71 
$`PTPRB MUTATED`
TCGA-A6-5659 TCGA-A6-6653 TCGA-AA-3510 TCGA-AA-3713 TCGA-AA-3845 TCGA-AA-3864 
       30.44        24.39        63.98        19.04         0.00        53.00 
TCGA-AA-3949 TCGA-AU-6004 TCGA-AY-6196 TCGA-CA-6717 TCGA-CM-4743 TCGA-D5-6928 
       26.01        27.09         0.20         0.33        23.05        11.64 
TCGA-D5-6930 TCGA-DM-A1D0 TCGA-DM-A1DB TCGA-G4-6293 TCGA-G4-6586 
        1.51       130.65        44.32       107.67        35.80 

$`PTPRB WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02        14.93        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        33.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       15.75        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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-A1D4 
       11.38        10.26       119.70        24.43        38.20        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38         7.50       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 
       33.67        13.25         0.53        35.41        19.43        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  PTPRB MUTATED PTPRB WILD-TYPE 
              0               0 
  PTPRB MUTATED PTPRB WILD-TYPE 
         130.65          140.38 
  PTPRB MUTATED PTPRB WILD-TYPE 
         26.010          20.005 
[1] "0.0 - 130.7 (26.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "2.4"
D1334V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PTPRB MUTATED         4        0        2         9         0         0
  PTPRB WILD-TYPE      60        1       23       100         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        18         10         40         30       34        13
                 vv
clus              STAGE IVB
  PTPRB MUTATED           0
  PTPRB WILD-TYPE         1
D1334V3, multiclass
            clus
vv           PTPRB MUTATED PTPRB WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              9             100
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PTPRB MUTATED     0   4  15   0
  PTPRB WILD-TYPE   9  64 233  41
D1334V4, multiclass
    clus
vv   PTPRB MUTATED PTPRB WILD-TYPE
  T1             0               9
  T2             4              64
  T3            15             233
  T4             0              41
[1] 4 2
[1] TRUE
[1] "dimension 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    16   2   1
  PTPRB WILD-TYPE 204  78  65
D1334V5, multiclass
    clus
vv   PTPRB MUTATED PTPRB WILD-TYPE
  N0            16             204
  N1             2              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"
D1334V6, binary
                 cls
clus                0   1
  PTPRB MUTATED    16   1
  PTPRB WILD-TYPE 267  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRB MUTATED     16    1
  PTPRB WILD-TYPE  267   47
   clus
vv  PTPRB MUTATED PTPRB WILD-TYPE
  0            16             267
  1             1              47
[1] 2 2
[1] FALSE
D1334V7, binary
                 cls
clus                0   1
  PTPRB MUTATED     7  12
  PTPRB WILD-TYPE 163 185
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRB MUTATED      7   12
  PTPRB WILD-TYPE  163  185
        clus
vv       PTPRB MUTATED PTPRB WILD-TYPE
  FEMALE             7             163
  MALE              12             185
[1] 2 2
[1] FALSE
D1334V8, binary
                 cls
clus                0   1
  PTPRB MUTATED    14   5
  PTPRB WILD-TYPE 303  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRB MUTATED     14    5
  PTPRB WILD-TYPE  303   43
                               clus
vv                              PTPRB MUTATED PTPRB WILD-TYPE
  COLON ADENOCARCINOMA                     14             303
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PTPRB MUTATED    13   0   1   2
  PTPRB WILD-TYPE 244   2  21  19
D1334V9, multiclass
    clus
vv   PTPRB MUTATED PTPRB WILD-TYPE
  R0            13             244
  R1             0               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"
D1334V10, 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    12
  PTPRB WILD-TYPE                        19   164
D1334V11, 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                                       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(1335) Variable = PRPH2 MUTATION ANALYSIS
D1335V1, survival
                 sevent
clus2               0   1
  PRPH2 MUTATED     7   2
  PRPH2 WILD-TYPE 275  71
  PRPH2 MUTATED PRPH2 WILD-TYPE 
              9             346 
  PRPH2 MUTATED PRPH2 WILD-TYPE 
              2              71 
$`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         0.10         9.04 
TCGA-DM-A1DB TCGA-G4-6306 TCGA-G4-6307 
       44.32        44.68        55.04 

$`PRPH2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        1.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03        14.01        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.33         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6309 
       19.43       107.67        74.56        65.85        53.62        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  PRPH2 MUTATED PRPH2 WILD-TYPE 
            0.1             0.0 
  PRPH2 MUTATED PRPH2 WILD-TYPE 
          55.04          140.38 
  PRPH2 MUTATED PRPH2 WILD-TYPE 
         25.020          20.155 
[1] "0.1 - 55.0 (25.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D1335V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PRPH2 MUTATED         0        0        1         3         1         0
  PRPH2 WILD-TYPE      64        1       24       106         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PRPH2 MUTATED           2          1          1          0        0         0
  PRPH2 WILD-TYPE        17          9         40         31       35        13
                 vv
clus              STAGE IVB
  PRPH2 MUTATED           0
  PRPH2 WILD-TYPE         1
D1335V3, multiclass
            clus
vv           PRPH2 MUTATED PRPH2 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              3             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             1               9
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PRPH2 MUTATED     0   2   6   2
  PRPH2 WILD-TYPE   9  66 242  39
D1335V4, multiclass
    clus
vv   PRPH2 MUTATED PRPH2 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             6             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
  PRPH2 MUTATED     6   2   2
  PRPH2 WILD-TYPE 214  78  64
D1335V5, multiclass
    clus
vv   PRPH2 MUTATED PRPH2 WILD-TYPE
  N0             6             214
  N1             2              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
  PRPH2 MUTATED     9   0
  PRPH2 WILD-TYPE 274  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRPH2 MUTATED      9    0
  PRPH2 WILD-TYPE  274   48
   clus
vv  PRPH2 MUTATED PRPH2 WILD-TYPE
  0             9             274
  1             0              48
[1] 2 2
[1] FALSE
D1335V7, 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
D1335V8, binary
                 cls
clus                0   1
  PRPH2 MUTATED     8   2
  PRPH2 WILD-TYPE 309  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRPH2 MUTATED      8    2
  PRPH2 WILD-TYPE  309   46
                               clus
vv                              PRPH2 MUTATED PRPH2 WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  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 251   2  22  20
D1335V9, multiclass
    clus
vv   PRPH2 MUTATED PRPH2 WILD-TYPE
  R0             6             251
  R1             0               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"
D1335V10, 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
D1335V11, 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(1336) Variable = ATAD1 MUTATION ANALYSIS
D1336V1, survival
                 sevent
clus2               0   1
  ATAD1 MUTATED     6   2
  ATAD1 WILD-TYPE 276  71
  ATAD1 MUTATED ATAD1 WILD-TYPE 
              8             347 
  ATAD1 MUTATED ATAD1 WILD-TYPE 
              2              71 
$`ATAD1 MUTATED`
TCGA-AA-3947 TCGA-AD-6895 TCGA-AZ-4315 TCGA-CK-5916 TCGA-CM-4743 TCGA-CM-6168 
       33.01         0.72        58.39        21.14        23.05        12.99 
TCGA-D5-6920 TCGA-DM-A28F 
       12.39        35.97 

$`ATAD1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        4.21        56.55         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
       40.34        15.62        49.08        51.32        21.99         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
      119.93        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  ATAD1 MUTATED ATAD1 WILD-TYPE 
           0.72            0.00 
  ATAD1 MUTATED ATAD1 WILD-TYPE 
          58.39          140.38 
  ATAD1 MUTATED ATAD1 WILD-TYPE 
         22.095          20.120 
[1] "0.7 - 58.4 (22.1)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.3"
D1336V2, 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       25       105         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ATAD1 MUTATED           0          0          1          0        0         0
  ATAD1 WILD-TYPE        19         10         40         31       35        13
                 vv
clus              STAGE IVB
  ATAD1 MUTATED           0
  ATAD1 WILD-TYPE         1
D1336V3, multiclass
            clus
vv           ATAD1 MUTATED ATAD1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              4             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ATAD1 MUTATED     1   0   6   1
  ATAD1 WILD-TYPE   8  68 242  40
D1336V4, multiclass
    clus
vv   ATAD1 MUTATED ATAD1 WILD-TYPE
  T1             1               8
  T2             0              68
  T3             6             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
  ATAD1 MUTATED     6   2   0
  ATAD1 WILD-TYPE 214  78  66
D1336V5, multiclass
    clus
vv   ATAD1 MUTATED ATAD1 WILD-TYPE
  N0             6             214
  N1             2              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"
D1336V6, binary
                 cls
clus                0   1
  ATAD1 MUTATED     7   0
  ATAD1 WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATAD1 MUTATED      7    0
  ATAD1 WILD-TYPE  276   48
   clus
vv  ATAD1 MUTATED ATAD1 WILD-TYPE
  0             7             276
  1             0              48
[1] 2 2
[1] FALSE
D1336V7, 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
D1336V8, binary
                 cls
clus                0   1
  ATAD1 MUTATED     7   1
  ATAD1 WILD-TYPE 310  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATAD1 MUTATED      7    1
  ATAD1 WILD-TYPE  310   47
                               clus
vv                              ATAD1 MUTATED ATAD1 WILD-TYPE
  COLON ADENOCARCINOMA                      7             310
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ATAD1 MUTATED     5   0   0   1
  ATAD1 WILD-TYPE 252   2  22  20
D1336V9, multiclass
    clus
vv   ATAD1 MUTATED ATAD1 WILD-TYPE
  R0             5             252
  R1             0               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"
D1336V10, 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
D1336V11, 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(1337) Variable = EFCAB4B MUTATION ANALYSIS
D1337V1, survival
                   sevent
clus2                 0   1
  EFCAB4B MUTATED     4   1
  EFCAB4B WILD-TYPE 278  72
  EFCAB4B MUTATED EFCAB4B WILD-TYPE 
                5               350 
  EFCAB4B MUTATED EFCAB4B WILD-TYPE 
                1                72 
$`EFCAB4B MUTATED`
TCGA-AA-3821 TCGA-CA-5796 TCGA-CK-4950 TCGA-CM-6171 TCGA-F4-6459 
        1.02         3.25        40.34        14.04         8.61 

$`EFCAB4B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5797 
       11.74         3.19         1.94         2.24         3.06         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      102.44        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
      117.07        98.24        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  EFCAB4B MUTATED EFCAB4B WILD-TYPE 
             1.02              0.00 
  EFCAB4B MUTATED EFCAB4B WILD-TYPE 
            40.34            140.38 
  EFCAB4B MUTATED EFCAB4B WILD-TYPE 
             8.61             20.63 
[1] "1.0 - 40.3 (8.6)"   "0.0 - 140.4 (20.6)"
[1] "hr=" "1.7"
D1337V2, 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       25       108         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EFCAB4B MUTATED           0          1          1          0        0
  EFCAB4B WILD-TYPE        19          9         40         31       35
                   vv
clus                STAGE IVA STAGE IVB
  EFCAB4B MUTATED           0         0
  EFCAB4B WILD-TYPE        13         1
D1337V3, multiclass
            clus
vv           EFCAB4B MUTATED EFCAB4B WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                1               108
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               1                 9
  STAGE IIIB               1                40
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  EFCAB4B MUTATED     0   2   3   0
  EFCAB4B WILD-TYPE   9  66 245  41
D1337V4, multiclass
    clus
vv   EFCAB4B MUTATED EFCAB4B WILD-TYPE
  T1               0                 9
  T2               2                66
  T3               3               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
  EFCAB4B MUTATED     3   1   1
  EFCAB4B WILD-TYPE 217  79  65
D1337V5, multiclass
    clus
vv   EFCAB4B MUTATED EFCAB4B WILD-TYPE
  N0               3               217
  N1               1                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"
D1337V6, binary
                   cls
clus                  0   1
  EFCAB4B MUTATED     5   0
  EFCAB4B WILD-TYPE 278  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EFCAB4B MUTATED      5    0
  EFCAB4B WILD-TYPE  278   48
   clus
vv  EFCAB4B MUTATED EFCAB4B WILD-TYPE
  0               5               278
  1               0                48
[1] 2 2
[1] FALSE
D1337V7, 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
D1337V8, binary
                   cls
clus                  0   1
  EFCAB4B MUTATED     3   2
  EFCAB4B WILD-TYPE 314  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EFCAB4B MUTATED      3    2
  EFCAB4B WILD-TYPE  314   46
                               clus
vv                              EFCAB4B MUTATED EFCAB4B WILD-TYPE
  COLON ADENOCARCINOMA                        3               314
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  EFCAB4B MUTATED     4   1   0   0
  EFCAB4B WILD-TYPE 253   1  22  21
D1337V9, multiclass
    clus
vv   EFCAB4B MUTATED EFCAB4B WILD-TYPE
  R0               4               253
  R1               1                 1
  R2               0                22
  RX               0                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1337V10, 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
D1337V11, 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(1338) Variable = ZNF41 MUTATION ANALYSIS
D1338V1, survival
                 sevent
clus2               0   1
  ZNF41 MUTATED     8   1
  ZNF41 WILD-TYPE 274  72
  ZNF41 MUTATED ZNF41 WILD-TYPE 
              9             346 
  ZNF41 MUTATED ZNF41 WILD-TYPE 
              1              72 
$`ZNF41 MUTATED`
TCGA-AA-3549 TCGA-AA-3939 TCGA-AA-A010 TCGA-AZ-6598 TCGA-CK-4947 TCGA-CK-6747 
       21.01        12.99        34.98        49.41        17.56         2.93 
TCGA-CM-4752 TCGA-D5-6532 TCGA-D5-6533 
       13.02        18.25         1.32 

$`ZNF41 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.33         0.10         1.35       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32        21.99        21.14         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       13.51        11.51        20.19        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  ZNF41 MUTATED ZNF41 WILD-TYPE 
           1.32            0.00 
  ZNF41 MUTATED ZNF41 WILD-TYPE 
          49.41          140.38 
  ZNF41 MUTATED ZNF41 WILD-TYPE 
          17.56           20.63 
[1] "1.3 - 49.4 (17.6)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "1.5"
D1338V2, 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       24       105         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ZNF41 MUTATED           0          0          1          0        0         1
  ZNF41 WILD-TYPE        19         10         40         31       35        12
                 vv
clus              STAGE IVB
  ZNF41 MUTATED           0
  ZNF41 WILD-TYPE         1
D1338V3, multiclass
            clus
vv           ZNF41 MUTATED ZNF41 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              4             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 243  38
D1338V4, multiclass
    clus
vv   ZNF41 MUTATED ZNF41 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             5             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
  ZNF41 MUTATED     8   1   0
  ZNF41 WILD-TYPE 212  79  66
D1338V5, multiclass
    clus
vv   ZNF41 MUTATED ZNF41 WILD-TYPE
  N0             8             212
  N1             1              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"
D1338V6, binary
                 cls
clus                0   1
  ZNF41 MUTATED     7   0
  ZNF41 WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF41 MUTATED      7    0
  ZNF41 WILD-TYPE  276   48
   clus
vv  ZNF41 MUTATED ZNF41 WILD-TYPE
  0             7             276
  1             0              48
[1] 2 2
[1] FALSE
D1338V7, 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
D1338V8, binary
                 cls
clus                0   1
  ZNF41 MUTATED     9   0
  ZNF41 WILD-TYPE 308  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF41 MUTATED      9    0
  ZNF41 WILD-TYPE  308   48
                               clus
vv                              ZNF41 MUTATED ZNF41 WILD-TYPE
  COLON ADENOCARCINOMA                      9             308
  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 251   2  22  19
D1338V9, multiclass
    clus
vv   ZNF41 MUTATED ZNF41 WILD-TYPE
  R0             6             251
  R1             0               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"
D1338V10, 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
D1338V11, 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(1339) Variable = ZNF295 MUTATION ANALYSIS
D1339V1, survival
                  sevent
clus2                0   1
  ZNF295 MUTATED     7   2
  ZNF295 WILD-TYPE 275  71
  ZNF295 MUTATED ZNF295 WILD-TYPE 
               9              346 
  ZNF295 MUTATED ZNF295 WILD-TYPE 
               2               71 
$`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        19.43 

$`ZNF295 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 
       10.06         0.00        33.07         0.00        36.03         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        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        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41        49.41        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 
        9.04         9.44        11.64        13.41         1.51        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 
       16.24        33.67        13.25         0.53        35.41       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  ZNF295 MUTATED ZNF295 WILD-TYPE 
            6.77             0.00 
  ZNF295 MUTATED ZNF295 WILD-TYPE 
           42.90           140.38 
  ZNF295 MUTATED ZNF295 WILD-TYPE 
          25.020           20.155 
[1] "6.8 - 42.9 (25.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D1339V2, 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       25       107         6         0
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF295 MUTATED           0          0          0          1        0
  ZNF295 WILD-TYPE        19         10         41         30       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF295 MUTATED           0         0
  ZNF295 WILD-TYPE        13         1
D1339V3, multiclass
            clus
vv           ZNF295 MUTATED ZNF295 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               2              107
  STAGE IIB               2                6
  STAGE IIC               1                0
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF295 MUTATED     0   4   2   4
  ZNF295 WILD-TYPE   9  64 246  37
D1339V4, multiclass
    clus
vv   ZNF295 MUTATED ZNF295 WILD-TYPE
  T1              0                9
  T2              4               64
  T3              2              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
  ZNF295 MUTATED     9   0   1
  ZNF295 WILD-TYPE 211  80  65
D1339V5, multiclass
    clus
vv   ZNF295 MUTATED ZNF295 WILD-TYPE
  N0              9              211
  N1              0               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"
D1339V6, binary
                  cls
clus                 0   1
  ZNF295 MUTATED     8   0
  ZNF295 WILD-TYPE 275  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF295 MUTATED      8    0
  ZNF295 WILD-TYPE  275   48
   clus
vv  ZNF295 MUTATED ZNF295 WILD-TYPE
  0              8              275
  1              0               48
[1] 2 2
[1] FALSE
D1339V7, 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
D1339V8, binary
                  cls
clus                 0   1
  ZNF295 MUTATED     9   1
  ZNF295 WILD-TYPE 308  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF295 MUTATED      9    1
  ZNF295 WILD-TYPE  308   47
                               clus
vv                              ZNF295 MUTATED ZNF295 WILD-TYPE
  COLON ADENOCARCINOMA                       9              308
  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 250   2  22  21
D1339V9, multiclass
    clus
vv   ZNF295 MUTATED ZNF295 WILD-TYPE
  R0              7              250
  R1              0                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"
D1339V10, 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
D1339V11, 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(1340) Variable = ZNF512 MUTATION ANALYSIS
D1340V1, survival
                  sevent
clus2                0   1
  ZNF512 MUTATED     2   1
  ZNF512 WILD-TYPE 280  72
  ZNF512 MUTATED ZNF512 WILD-TYPE 
               3              352 
  ZNF512 MUTATED ZNF512 WILD-TYPE 
               1               72 
$`ZNF512 MUTATED`
TCGA-AD-6963 TCGA-AZ-6600 TCGA-G4-6315 
       27.42        12.10        36.72 

$`ZNF512 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       51.75        45.11        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  ZNF512 MUTATED ZNF512 WILD-TYPE 
            12.1              0.0 
  ZNF512 MUTATED ZNF512 WILD-TYPE 
           36.72           140.38 
  ZNF512 MUTATED ZNF512 WILD-TYPE 
          27.420           20.155 
[1] "12.1 - 36.7 (27.4)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.8"
D1340V2, 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       25       109         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF512 MUTATED           0          0          0          0        2
  ZNF512 WILD-TYPE        19         10         41         31       33
                  vv
clus               STAGE IVA STAGE IVB
  ZNF512 MUTATED           0         0
  ZNF512 WILD-TYPE        13         1
D1340V3, multiclass
[1] "Remove cluster labels:" "ZNF512 MUTATED"        
clus
  ZNF512 MUTATED ZNF512 WILD-TYPE 
               2              356 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-4105 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-A6-5661       TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5665 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-A6-5666       TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-A6-6142       TCGA-A6-6648       TCGA-A6-6649       TCGA-A6-6651 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-A6-6652       TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-A6-6781       TCGA-A6-6782       TCGA-AA-3489       TCGA-AA-3492 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3496       TCGA-AA-3502       TCGA-AA-3510       TCGA-AA-3511 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3514       TCGA-AA-3516       TCGA-AA-3517       TCGA-AA-3518 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3519       TCGA-AA-3520       TCGA-AA-3521       TCGA-AA-3522 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3524       TCGA-AA-3525       TCGA-AA-3526       TCGA-AA-3527 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3529       TCGA-AA-3530       TCGA-AA-3531       TCGA-AA-3532 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3534       TCGA-AA-3538       TCGA-AA-3542       TCGA-AA-3543 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3544       TCGA-AA-3548       TCGA-AA-3549       TCGA-AA-3552 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3553       TCGA-AA-3554       TCGA-AA-3555       TCGA-AA-3556 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3558       TCGA-AA-3560       TCGA-AA-3561       TCGA-AA-3562 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3655       TCGA-AA-3660       TCGA-AA-3662       TCGA-AA-3663 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3664       TCGA-AA-3666       TCGA-AA-3667       TCGA-AA-3672 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3673       TCGA-AA-3678       TCGA-AA-3679       TCGA-AA-3680 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3681       TCGA-AA-3684       TCGA-AA-3685       TCGA-AA-3688 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3692       TCGA-AA-3693       TCGA-AA-3695       TCGA-AA-3696 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3697       TCGA-AA-3710       TCGA-AA-3712       TCGA-AA-3713 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3715       TCGA-AA-3811       TCGA-AA-3812       TCGA-AA-3814 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3815       TCGA-AA-3818       TCGA-AA-3819       TCGA-AA-3821 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3831       TCGA-AA-3833       TCGA-AA-3837       TCGA-AA-3842 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3844       TCGA-AA-3845       TCGA-AA-3846       TCGA-AA-3848 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3850       TCGA-AA-3851       TCGA-AA-3852       TCGA-AA-3854 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3855       TCGA-AA-3856       TCGA-AA-3858       TCGA-AA-3860 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3861       TCGA-AA-3864       TCGA-AA-3866       TCGA-AA-3867 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3869       TCGA-AA-3870       TCGA-AA-3872       TCGA-AA-3875 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3877       TCGA-AA-3930       TCGA-AA-3939       TCGA-AA-3941 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3947       TCGA-AA-3949       TCGA-AA-3950       TCGA-AA-3952 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3955       TCGA-AA-3956       TCGA-AA-3966       TCGA-AA-3968 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3971       TCGA-AA-3972       TCGA-AA-3973       TCGA-AA-3975 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3976       TCGA-AA-3979       TCGA-AA-3980       TCGA-AA-3982 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3984       TCGA-AA-3986       TCGA-AA-3989       TCGA-AA-3994 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-A004       TCGA-AA-A00A       TCGA-AA-A00D       TCGA-AA-A00E 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-A00F       TCGA-AA-A00J       TCGA-AA-A00K       TCGA-AA-A00L 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-A00N       TCGA-AA-A00O       TCGA-AA-A00Q       TCGA-AA-A00R 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-A00U       TCGA-AA-A00W       TCGA-AA-A00Z       TCGA-AA-A010 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-A017       TCGA-AA-A01D       TCGA-AA-A01F       TCGA-AA-A01G 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-A01I       TCGA-AA-A01K       TCGA-AA-A01P       TCGA-AA-A01Q 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-A01R       TCGA-AA-A01S       TCGA-AA-A01T       TCGA-AA-A01V 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-A01X       TCGA-AA-A01Z       TCGA-AA-A022       TCGA-AA-A024 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-A029       TCGA-AA-A02F       TCGA-AA-A02H       TCGA-AA-A02J 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-A02K       TCGA-AA-A02O       TCGA-AA-A02W       TCGA-AA-A02Y 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-A03F       TCGA-AA-A03J       TCGA-AD-5900       TCGA-AD-6548 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AD-6888       TCGA-AD-6889       TCGA-AD-6899       TCGA-AU-3779 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AU-6004       TCGA-AY-4070       TCGA-AY-4071       TCGA-AY-5543 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386       TCGA-AZ-4315 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4681       TCGA-AZ-4682 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AZ-5403       TCGA-AZ-5407       TCGA-AZ-6598       TCGA-AZ-6599 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AZ-6601       TCGA-AZ-6605       TCGA-AZ-6606       TCGA-AZ-6607 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AZ-6608       TCGA-CA-5254       TCGA-CA-5255       TCGA-CA-5796 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CA-5797       TCGA-CA-6715       TCGA-CA-6716       TCGA-CA-6717 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CA-6718       TCGA-CA-6719       TCGA-CK-4947       TCGA-CK-4948 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CK-4950       TCGA-CK-4952       TCGA-CK-5912       TCGA-CK-5913 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CK-5914       TCGA-CK-5915       TCGA-CK-5916       TCGA-CK-6746 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CK-6747       TCGA-CK-6748       TCGA-CK-6751       TCGA-CM-4743 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CM-4744       TCGA-CM-4746       TCGA-CM-4747       TCGA-CM-4752 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CM-5341       TCGA-CM-5344       TCGA-CM-5348       TCGA-CM-5349 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CM-5860       TCGA-CM-5861       TCGA-CM-5862       TCGA-CM-5863 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CM-5864       TCGA-CM-5868       TCGA-CM-6161       TCGA-CM-6162 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CM-6163       TCGA-CM-6164       TCGA-CM-6165       TCGA-CM-6166 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CM-6167       TCGA-CM-6168       TCGA-CM-6169       TCGA-CM-6170 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CM-6171       TCGA-CM-6172       TCGA-CM-6674       TCGA-CM-6675 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CM-6676       TCGA-CM-6677       TCGA-CM-6678       TCGA-CM-6679 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CM-6680       TCGA-D5-5537       TCGA-D5-5538       TCGA-D5-5539 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-D5-5540       TCGA-D5-5541       TCGA-D5-6529       TCGA-D5-6532 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-D5-6533       TCGA-D5-6534       TCGA-D5-6535       TCGA-D5-6536 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-D5-6537       TCGA-D5-6538       TCGA-D5-6539       TCGA-D5-6540 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-D5-6541       TCGA-D5-6898       TCGA-D5-6920       TCGA-D5-6922 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-D5-6923       TCGA-D5-6924       TCGA-D5-6926       TCGA-D5-6927 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-D5-6928       TCGA-D5-6929       TCGA-D5-6930       TCGA-D5-6931 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-D5-6932       TCGA-D5-7000       TCGA-DM-A0X9       TCGA-DM-A0XD 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-DM-A0XF       TCGA-DM-A1D0       TCGA-DM-A1D4       TCGA-DM-A1D6 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-DM-A1D7       TCGA-DM-A1D9       TCGA-DM-A1DA       TCGA-DM-A1DB 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-DM-A1HA       TCGA-DM-A1HB       TCGA-DM-A282       TCGA-DM-A285 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-DM-A28C       TCGA-DM-A28E       TCGA-DM-A28F       TCGA-DM-A28G 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-DM-A28H       TCGA-DM-A28K       TCGA-F4-6459       TCGA-F4-6460 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-F4-6569       TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-F4-6805       TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-F4-6809       TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-G4-6293       TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-G4-6306       TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323       TCGA-G4-6586 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
                  vv
clus                T1  T2  T3  T4
  ZNF512 MUTATED     0   0   2   1
  ZNF512 WILD-TYPE   9  68 246  40
D1340V4, multiclass
    clus
vv   ZNF512 MUTATED ZNF512 WILD-TYPE
  T1              0                9
  T2              0               68
  T3              2              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
  ZNF512 MUTATED     1   2   0
  ZNF512 WILD-TYPE 219  78  66
D1340V5, multiclass
    clus
vv   ZNF512 MUTATED ZNF512 WILD-TYPE
  N0              1              219
  N1              2               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"
D1340V6, binary
                  cls
clus                 0   1
  ZNF512 MUTATED     0   2
  ZNF512 WILD-TYPE 283  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF512 MUTATED      0    2
  ZNF512 WILD-TYPE  283   46
   clus
vv  ZNF512 MUTATED ZNF512 WILD-TYPE
  0              0              283
  1              2               46
[1] 2 2
[1] FALSE
D1340V7, 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
D1340V8, binary
                  cls
clus                 0   1
  ZNF512 MUTATED     3   0
  ZNF512 WILD-TYPE 314  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF512 MUTATED      3    0
  ZNF512 WILD-TYPE  314   48
                               clus
vv                              ZNF512 MUTATED ZNF512 WILD-TYPE
  COLON ADENOCARCINOMA                       3              314
  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 256   2  22  21
D1340V9, multiclass
[1] "Remove cluster labels:" "ZNF512 MUTATED"        
clus
  ZNF512 MUTATED ZNF512 WILD-TYPE 
               1              301 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-5657 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-A6-5659       TCGA-A6-5661       TCGA-A6-5665       TCGA-A6-6781 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3489       TCGA-AA-3492       TCGA-AA-3496       TCGA-AA-3502 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3510       TCGA-AA-3511       TCGA-AA-3514       TCGA-AA-3517 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3518       TCGA-AA-3519       TCGA-AA-3520       TCGA-AA-3521 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3522       TCGA-AA-3524       TCGA-AA-3525       TCGA-AA-3526 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3527       TCGA-AA-3529       TCGA-AA-3530       TCGA-AA-3531 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3532       TCGA-AA-3534       TCGA-AA-3538       TCGA-AA-3542 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3543       TCGA-AA-3544       TCGA-AA-3548       TCGA-AA-3549 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3552       TCGA-AA-3553       TCGA-AA-3554       TCGA-AA-3555 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3556       TCGA-AA-3558       TCGA-AA-3560       TCGA-AA-3561 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3562       TCGA-AA-3655       TCGA-AA-3660       TCGA-AA-3662 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3663       TCGA-AA-3664       TCGA-AA-3666       TCGA-AA-3667 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3672       TCGA-AA-3673       TCGA-AA-3678       TCGA-AA-3679 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3680       TCGA-AA-3681       TCGA-AA-3684       TCGA-AA-3685 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3688       TCGA-AA-3692       TCGA-AA-3693       TCGA-AA-3695 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3696       TCGA-AA-3697       TCGA-AA-3710       TCGA-AA-3712 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3713       TCGA-AA-3715       TCGA-AA-3811       TCGA-AA-3812 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3814       TCGA-AA-3815       TCGA-AA-3818       TCGA-AA-3819 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3821       TCGA-AA-3831       TCGA-AA-3833       TCGA-AA-3837 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3842       TCGA-AA-3844       TCGA-AA-3845       TCGA-AA-3846 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3848       TCGA-AA-3850       TCGA-AA-3851       TCGA-AA-3852 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3854       TCGA-AA-3855       TCGA-AA-3856       TCGA-AA-3858 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3860       TCGA-AA-3861       TCGA-AA-3864       TCGA-AA-3866 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3867       TCGA-AA-3869       TCGA-AA-3870       TCGA-AA-3872 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3875       TCGA-AA-3877       TCGA-AA-3930       TCGA-AA-3939 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3941       TCGA-AA-3947       TCGA-AA-3949       TCGA-AA-3950 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3952       TCGA-AA-3955       TCGA-AA-3956       TCGA-AA-3968 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3971       TCGA-AA-3972       TCGA-AA-3973       TCGA-AA-3975 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3976       TCGA-AA-3979       TCGA-AA-3984       TCGA-AA-3986 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3989       TCGA-AA-3994       TCGA-AA-A004       TCGA-AA-A00A 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-A00D       TCGA-AA-A00E       TCGA-AA-A00F       TCGA-AA-A00J 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-A00K       TCGA-AA-A00L       TCGA-AA-A00N       TCGA-AA-A00O 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-A00Q       TCGA-AA-A00R       TCGA-AA-A00U       TCGA-AA-A00W 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-A00Z       TCGA-AA-A010       TCGA-AA-A017       TCGA-AA-A01D 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-A01F       TCGA-AA-A01G       TCGA-AA-A01I       TCGA-AA-A01K 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-A01P       TCGA-AA-A01Q       TCGA-AA-A01R       TCGA-AA-A01S 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-A01T       TCGA-AA-A01V       TCGA-AA-A01X       TCGA-AA-A01Z 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-A022       TCGA-AA-A024       TCGA-AA-A029       TCGA-AA-A02F 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-A02H       TCGA-AA-A02J       TCGA-AA-A02K       TCGA-AA-A02O 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-A02W       TCGA-AA-A02Y       TCGA-AA-A03F       TCGA-AA-A03J 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AD-5900       TCGA-AD-6548       TCGA-AD-6888       TCGA-AU-3779 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AU-6004       TCGA-AY-4070       TCGA-AY-4071       TCGA-AY-5543 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386       TCGA-AZ-4315 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AZ-4681       TCGA-AZ-4682       TCGA-CA-5254       TCGA-CA-5255 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CA-5796       TCGA-CA-5797       TCGA-CA-6715       TCGA-CA-6716 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CA-6717       TCGA-CA-6718       TCGA-CA-6719       TCGA-CK-4947 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CK-4948       TCGA-CK-4950       TCGA-CK-4952       TCGA-CK-5912 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CK-5913       TCGA-CK-5914       TCGA-CK-5915       TCGA-CK-5916 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CK-6746       TCGA-CK-6747       TCGA-CK-6748       TCGA-CK-6751 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CM-4743       TCGA-CM-4744       TCGA-CM-4746       TCGA-CM-4747 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CM-4752       TCGA-CM-5341       TCGA-CM-5344       TCGA-CM-5348 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CM-5349       TCGA-CM-5860       TCGA-CM-5861       TCGA-CM-5862 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CM-5863       TCGA-CM-5864       TCGA-CM-5868       TCGA-CM-6161 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CM-6162       TCGA-CM-6163       TCGA-CM-6164       TCGA-CM-6165 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CM-6166       TCGA-CM-6167       TCGA-CM-6168       TCGA-CM-6169 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CM-6170       TCGA-CM-6171       TCGA-CM-6172       TCGA-CM-6674 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CM-6675       TCGA-CM-6676       TCGA-CM-6677       TCGA-CM-6678 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CM-6679       TCGA-CM-6680       TCGA-D5-5537       TCGA-D5-5538 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-D5-5539       TCGA-D5-5540       TCGA-D5-5541       TCGA-D5-6529 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-D5-6532       TCGA-D5-6533       TCGA-D5-6534       TCGA-D5-6535 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-D5-6536       TCGA-D5-6537       TCGA-D5-6538       TCGA-D5-6539 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-D5-6540       TCGA-D5-6541       TCGA-D5-6898       TCGA-D5-6920 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-D5-6922       TCGA-D5-6923       TCGA-D5-6924       TCGA-D5-6926 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-D5-6927       TCGA-D5-6928       TCGA-D5-6929       TCGA-D5-6930 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-D5-6931       TCGA-D5-6932       TCGA-D5-7000       TCGA-F4-6459 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-F4-6460       TCGA-F4-6569       TCGA-F4-6570       TCGA-F4-6703 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-F4-6704       TCGA-F4-6805       TCGA-F4-6806       TCGA-F4-6807 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-F4-6808       TCGA-F4-6809       TCGA-F4-6854       TCGA-F4-6855 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-F4-6856       TCGA-G4-6293       TCGA-G4-6299       TCGA-G4-6303 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-G4-6304       TCGA-G4-6306       TCGA-G4-6307       TCGA-G4-6309 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-G4-6310       TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-G4-6586       TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-G4-6628 
"ZNF512 WILD-TYPE" 
D1340V10, 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
D1340V11, 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(1341) Variable = NCOA5 MUTATION ANALYSIS
D1341V1, survival
                 sevent
clus2               0   1
  NCOA5 MUTATED     9   2
  NCOA5 WILD-TYPE 273  71
  NCOA5 MUTATED NCOA5 WILD-TYPE 
             11             344 
  NCOA5 MUTATED NCOA5 WILD-TYPE 
              2              71 
$`NCOA5 MUTATED`
TCGA-AA-3655 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A02O 
       61.02        31.00        33.01        25.02         4.01         0.92 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-CM-4743 TCGA-CM-6674 TCGA-G4-6293 
       61.41        49.41        23.05        12.95       107.67 

$`NCOA5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
       14.01        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14         2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        35.41        19.43        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  NCOA5 MUTATED NCOA5 WILD-TYPE 
           0.92            0.00 
  NCOA5 MUTATED NCOA5 WILD-TYPE 
         107.67          140.38 
  NCOA5 MUTATED NCOA5 WILD-TYPE 
         31.000          20.005 
[1] "0.9 - 107.7 (31.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.7"
D1341V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NCOA5 MUTATED         2        0        3         2         2         0
  NCOA5 WILD-TYPE      62        1       22       107         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NCOA5 MUTATED           1          0          0          0        0         0
  NCOA5 WILD-TYPE        18         10         41         31       35        13
                 vv
clus              STAGE IVB
  NCOA5 MUTATED           0
  NCOA5 WILD-TYPE         1
D1341V3, multiclass
            clus
vv           NCOA5 MUTATED NCOA5 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              2             107
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NCOA5 MUTATED     2   1   6   2
  NCOA5 WILD-TYPE   7  67 242  39
D1341V4, multiclass
    clus
vv   NCOA5 MUTATED NCOA5 WILD-TYPE
  T1             2               7
  T2             1              67
  T3             6             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
  NCOA5 MUTATED    10   1   0
  NCOA5 WILD-TYPE 210  79  66
D1341V5, multiclass
    clus
vv   NCOA5 MUTATED NCOA5 WILD-TYPE
  N0            10             210
  N1             1              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
  NCOA5 MUTATED     9   0
  NCOA5 WILD-TYPE 274  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA5 MUTATED      9    0
  NCOA5 WILD-TYPE  274   48
   clus
vv  NCOA5 MUTATED NCOA5 WILD-TYPE
  0             9             274
  1             0              48
[1] 2 2
[1] FALSE
D1341V7, binary
                 cls
clus                0   1
  NCOA5 MUTATED     5   6
  NCOA5 WILD-TYPE 165 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA5 MUTATED      5    6
  NCOA5 WILD-TYPE  165  191
        clus
vv       NCOA5 MUTATED NCOA5 WILD-TYPE
  FEMALE             5             165
  MALE               6             191
[1] 2 2
[1] FALSE
D1341V8, binary
                 cls
clus                0   1
  NCOA5 MUTATED     8   3
  NCOA5 WILD-TYPE 309  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA5 MUTATED      8    3
  NCOA5 WILD-TYPE  309   45
                               clus
vv                              NCOA5 MUTATED NCOA5 WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  NCOA5 MUTATED     8   0   0   0
  NCOA5 WILD-TYPE 249   2  22  21
D1341V9, multiclass
    clus
vv   NCOA5 MUTATED NCOA5 WILD-TYPE
  R0             8             249
  R1             0               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"
D1341V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NCOA5 MUTATED                                  0     0
  NCOA5 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NCOA5 MUTATED                           0     5
  NCOA5 WILD-TYPE                        19   171
D1341V11, multiclass
                                  clus
vv                                 NCOA5 MUTATED NCOA5 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(1342) Variable = ZHX2 MUTATION ANALYSIS
D1342V1, survival
                sevent
clus2              0   1
  ZHX2 MUTATED    14   1
  ZHX2 WILD-TYPE 268  72
  ZHX2 MUTATED ZHX2 WILD-TYPE 
            15            340 
  ZHX2 MUTATED ZHX2 WILD-TYPE 
             1             72 
$`ZHX2 MUTATED`
TCGA-A6-2672 TCGA-A6-5661 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3976 
       46.65        33.53         3.02        63.98         6.97        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-A00A TCGA-AA-A00R TCGA-AA-A010 TCGA-AU-6004 
       25.02        24.00        38.04         0.99        34.98        27.09 
TCGA-CA-6717 TCGA-CM-6162 TCGA-DM-A1HB 
        0.33        12.00       135.65 

$`ZHX2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       19.66        20.28         7.04         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.05        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
       21.99        16.08        50.99        13.05        34.06        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D 
       27.02        19.07         7.96        27.02        13.94        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       27.02        42.02        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  ZHX2 MUTATED ZHX2 WILD-TYPE 
          0.33           0.00 
  ZHX2 MUTATED ZHX2 WILD-TYPE 
        135.65         140.38 
  ZHX2 MUTATED ZHX2 WILD-TYPE 
        26.010         20.005 
[1] "0.3 - 135.7 (26.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "3.6"
D1342V2, 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       21       105         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        19          9         38         31       35        13
                vv
clus             STAGE IVB
  ZHX2 MUTATED           0
  ZHX2 WILD-TYPE         1
D1342V3, multiclass
            clus
vv           ZHX2 MUTATED ZHX2 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              4             21
  STAGE IIA             4            105
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            1              9
  STAGE IIIB            3             38
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ZHX2 MUTATED     0   4  10   3
  ZHX2 WILD-TYPE   9  64 238  38
D1342V4, multiclass
    clus
vv   ZHX2 MUTATED ZHX2 WILD-TYPE
  T1            0              9
  T2            4             64
  T3           10            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
  ZHX2 MUTATED    13   4   0
  ZHX2 WILD-TYPE 207  76  66
D1342V5, multiclass
    clus
vv   ZHX2 MUTATED ZHX2 WILD-TYPE
  N0           13            207
  N1            4             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"
D1342V6, binary
                cls
clus               0   1
  ZHX2 MUTATED    15   0
  ZHX2 WILD-TYPE 268  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZHX2 MUTATED     15    0
  ZHX2 WILD-TYPE  268   48
   clus
vv  ZHX2 MUTATED ZHX2 WILD-TYPE
  0           15            268
  1            0             48
[1] 2 2
[1] FALSE
D1342V7, 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
D1342V8, binary
                cls
clus               0   1
  ZHX2 MUTATED    15   2
  ZHX2 WILD-TYPE 302  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZHX2 MUTATED     15    2
  ZHX2 WILD-TYPE  302   46
                               clus
vv                              ZHX2 MUTATED ZHX2 WILD-TYPE
  COLON ADENOCARCINOMA                    15            302
  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 244   2  22  19
D1342V9, multiclass
    clus
vv   ZHX2 MUTATED ZHX2 WILD-TYPE
  R0           13            244
  R1            0              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"
D1342V10, 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
D1342V11, 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(1343) Variable = SKIV2L2 MUTATION ANALYSIS
D1343V1, survival
                   sevent
clus2                 0   1
  SKIV2L2 MUTATED     4   7
  SKIV2L2 WILD-TYPE 278  66
  SKIV2L2 MUTATED SKIV2L2 WILD-TYPE 
               11               344 
  SKIV2L2 MUTATED SKIV2L2 WILD-TYPE 
                7                66 
$`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 
       11.51        24.43        35.97        13.38         6.18 

$`SKIV2L2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.20        14.50        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        51.32        21.99         2.93         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        16.01        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       19.59        13.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38        10.26       119.70        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6703 
       60.79       117.07        98.24         8.61        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  SKIV2L2 MUTATED SKIV2L2 WILD-TYPE 
             3.02              0.00 
  SKIV2L2 MUTATED SKIV2L2 WILD-TYPE 
            35.97            140.38 
  SKIV2L2 MUTATED SKIV2L2 WILD-TYPE 
            13.38             20.63 
[1] "3.0 - 36.0 (13.4)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "5.5"
D1343V2, 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       24       107         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SKIV2L2 MUTATED           0          0          4          0        0
  SKIV2L2 WILD-TYPE        19         10         37         31       35
                   vv
clus                STAGE IVA STAGE IVB
  SKIV2L2 MUTATED           1         0
  SKIV2L2 WILD-TYPE        12         1
D1343V3, multiclass
            clus
vv           SKIV2L2 MUTATED SKIV2L2 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                2               107
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               4                37
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                1                12
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 241  39
D1343V4, multiclass
    clus
vv   SKIV2L2 MUTATED SKIV2L2 WILD-TYPE
  T1               1                 8
  T2               1                67
  T3               7               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
  SKIV2L2 MUTATED     6   5   0
  SKIV2L2 WILD-TYPE 214  75  66
D1343V5, multiclass
    clus
vv   SKIV2L2 MUTATED SKIV2L2 WILD-TYPE
  N0               6               214
  N1               5                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"
D1343V6, binary
                   cls
clus                  0   1
  SKIV2L2 MUTATED    10   1
  SKIV2L2 WILD-TYPE 273  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SKIV2L2 MUTATED     10    1
  SKIV2L2 WILD-TYPE  273   47
   clus
vv  SKIV2L2 MUTATED SKIV2L2 WILD-TYPE
  0              10               273
  1               1                47
[1] 2 2
[1] FALSE
D1343V7, 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
D1343V8, binary
                   cls
clus                  0   1
  SKIV2L2 MUTATED     9   2
  SKIV2L2 WILD-TYPE 308  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SKIV2L2 MUTATED      9    2
  SKIV2L2 WILD-TYPE  308   46
                               clus
vv                              SKIV2L2 MUTATED SKIV2L2 WILD-TYPE
  COLON ADENOCARCINOMA                        9               308
  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 249   2  22  20
D1343V9, multiclass
    clus
vv   SKIV2L2 MUTATED SKIV2L2 WILD-TYPE
  R0               8               249
  R1               0                 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"
D1343V10, 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
D1343V11, 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(1344) Variable = MYO3A MUTATION ANALYSIS
D1344V1, survival
                 sevent
clus2               0   1
  MYO3A MUTATED    29   7
  MYO3A WILD-TYPE 253  66
  MYO3A MUTATED MYO3A WILD-TYPE 
             36             319 
  MYO3A MUTATED MYO3A WILD-TYPE 
              7              66 
$`MYO3A MUTATED`
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5661 TCGA-A6-6138 TCGA-A6-6652 TCGA-A6-6780 
       32.75        36.53        33.53        22.52        24.69        20.12 
TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3811 TCGA-AA-3947 TCGA-AA-3966 
       19.66        63.98         6.97        10.06        33.01         2.01 
TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q TCGA-AD-6889 TCGA-AD-6899 
       25.02         4.01        34.98         1.02        56.55         5.79 
TCGA-AZ-4315 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4948 TCGA-CM-4743 
       58.39       100.01         0.33         0.10       102.44        23.05 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5861 TCGA-CM-6161 TCGA-CM-6163 TCGA-D5-6535 
       22.03        22.98        15.02        15.02        14.04        15.12 
TCGA-D5-6537 TCGA-DM-A28G TCGA-F4-6806 TCGA-F4-6808 TCGA-G4-6588 TCGA-G4-6626 
        4.80        60.79        29.59        33.67        26.17        46.75 

$`MYO3A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       16.57        34.65        33.34        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       30.44        29.19        23.61        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 
       27.09         8.38        25.08        25.18        24.16        21.76 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       24.39        23.87        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        19.04        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       26.01        24.00         2.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37         4.21         0.79         0.72 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 
        0.07         0.26         1.35        17.56        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01         5.03        15.02        15.02        17.03 
TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       12.00        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
        1.32        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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
      119.93        35.97       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 
       13.45         6.18        35.87         1.55        16.31        16.24 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6628 
       52.80 

  MYO3A MUTATED MYO3A WILD-TYPE 
            0.1             0.0 
  MYO3A MUTATED MYO3A WILD-TYPE 
         102.44          140.38 
  MYO3A MUTATED MYO3A WILD-TYPE 
         23.015          19.990 
[1] "0.1 - 102.4 (23.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.2"
D1344V2, 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       21        96         4         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MYO3A MUTATED           1          1          4          2        0         1
  MYO3A WILD-TYPE        18          9         37         29       35        12
                 vv
clus              STAGE IVB
  MYO3A MUTATED           0
  MYO3A WILD-TYPE         1
D1344V3, multiclass
            clus
vv           MYO3A MUTATED MYO3A WILD-TYPE
  STAGE I                6              58
  STAGE IA               0               1
  STAGE II               4              21
  STAGE IIA             13              96
  STAGE IIB              4               4
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             1               9
  STAGE IIIB             4              37
  STAGE IIIC             2              29
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  63 224  35
D1344V4, multiclass
    clus
vv   MYO3A MUTATED MYO3A WILD-TYPE
  T1             2               7
  T2             5              63
  T3            24             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
  MYO3A MUTATED    29   6   2
  MYO3A WILD-TYPE 191  74  64
D1344V5, multiclass
    clus
vv   MYO3A MUTATED MYO3A WILD-TYPE
  N0            29             191
  N1             6              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"
D1344V6, binary
                 cls
clus                0   1
  MYO3A MUTATED    29   1
  MYO3A WILD-TYPE 254  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYO3A MUTATED     29    1
  MYO3A WILD-TYPE  254   47
   clus
vv  MYO3A MUTATED MYO3A WILD-TYPE
  0            29             254
  1             1              47
[1] 2 2
[1] FALSE
D1344V7, 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
D1344V8, binary
                 cls
clus                0   1
  MYO3A MUTATED    29   8
  MYO3A WILD-TYPE 288  40
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYO3A MUTATED     29    8
  MYO3A WILD-TYPE  288   40
                               clus
vv                              MYO3A MUTATED MYO3A WILD-TYPE
  COLON ADENOCARCINOMA                     29             288
  COLON MUCINOUS ADENOCARCINOMA             8              40
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MYO3A MUTATED    24   0   0   4
  MYO3A WILD-TYPE 233   2  22  17
D1344V9, multiclass
    clus
vv   MYO3A MUTATED MYO3A WILD-TYPE
  R0            24             233
  R1             0               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"
D1344V10, 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
D1344V11, 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(1345) Variable = APOBEC4 MUTATION ANALYSIS
D1345V1, survival
                   sevent
clus2                 0   1
  APOBEC4 MUTATED     7   0
  APOBEC4 WILD-TYPE 275  73
  APOBEC4 MUTATED APOBEC4 WILD-TYPE 
                7               348 
  APOBEC4 MUTATED APOBEC4 WILD-TYPE 
                0                73 
$`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         0.33         0.10 
TCGA-G4-6309 
       51.75 

$`APOBEC4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        17.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  APOBEC4 MUTATED APOBEC4 WILD-TYPE 
              0.1               0.0 
  APOBEC4 MUTATED APOBEC4 WILD-TYPE 
            51.75            140.38 
  APOBEC4 MUTATED APOBEC4 WILD-TYPE 
            29.95             20.07 
[1] "0.1 - 51.8 (29.9)"  "0.0 - 140.4 (20.1)"
[1] "hr="     "9200000"
D1345V2, 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       25       104         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  APOBEC4 MUTATED           0          0          1          0        0
  APOBEC4 WILD-TYPE        19         10         40         31       35
                   vv
clus                STAGE IVA STAGE IVB
  APOBEC4 MUTATED           0         0
  APOBEC4 WILD-TYPE        13         1
D1345V3, multiclass
            clus
vv           APOBEC4 MUTATED APOBEC4 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                5               104
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  APOBEC4 MUTATED     0   0   6   1
  APOBEC4 WILD-TYPE   9  68 242  40
D1345V4, multiclass
    clus
vv   APOBEC4 MUTATED APOBEC4 WILD-TYPE
  T1               0                 9
  T2               0                68
  T3               6               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
  APOBEC4 MUTATED     6   1   0
  APOBEC4 WILD-TYPE 214  79  66
D1345V5, multiclass
    clus
vv   APOBEC4 MUTATED APOBEC4 WILD-TYPE
  N0               6               214
  N1               1                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"
D1345V6, binary
                   cls
clus                  0   1
  APOBEC4 MUTATED     7   0
  APOBEC4 WILD-TYPE 276  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  APOBEC4 MUTATED      7    0
  APOBEC4 WILD-TYPE  276   48
   clus
vv  APOBEC4 MUTATED APOBEC4 WILD-TYPE
  0               7               276
  1               0                48
[1] 2 2
[1] FALSE
D1345V7, 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
D1345V8, binary
                   cls
clus                  0   1
  APOBEC4 MUTATED     5   2
  APOBEC4 WILD-TYPE 312  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  APOBEC4 MUTATED      5    2
  APOBEC4 WILD-TYPE  312   46
                               clus
vv                              APOBEC4 MUTATED APOBEC4 WILD-TYPE
  COLON ADENOCARCINOMA                        5               312
  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 252   2  22  19
D1345V9, multiclass
    clus
vv   APOBEC4 MUTATED APOBEC4 WILD-TYPE
  R0               5               252
  R1               0                 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"
D1345V10, 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
D1345V11, 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(1346) Variable = ACAN MUTATION ANALYSIS
D1346V1, survival
                sevent
clus2              0   1
  ACAN MUTATED    19   7
  ACAN WILD-TYPE 263  66
  ACAN MUTATED ACAN WILD-TYPE 
            26            329 
  ACAN MUTATED ACAN WILD-TYPE 
             7             66 
$`ACAN MUTATED`
TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3672 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       22.06         3.02         0.92        26.99        19.04        19.04 
TCGA-AA-3854 TCGA-AA-3861 TCGA-AA-3930 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-5900 
       36.03        30.05         2.01         4.01        34.98         0.07 
TCGA-AD-6965 TCGA-AZ-4616 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4952 
        0.20         5.13       100.01         0.33         0.10        15.62 
TCGA-CM-4746 TCGA-CM-5348 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6541 
       37.02        22.98        43.27        17.85         4.80        15.58 
TCGA-D5-6931 TCGA-G4-6588 
       12.00        26.17 

$`ACAN WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       85.05        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3939 
       24.03        27.02        29.98        18.05        31.00        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        10.88        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        1.41        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 
        0.26         1.35        17.56       102.44        40.34        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6538 
       11.51        20.19        18.25         1.32        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         1.51 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        91.79        46.75        52.80 

  ACAN MUTATED ACAN WILD-TYPE 
          0.07           0.00 
  ACAN MUTATED ACAN WILD-TYPE 
        100.01         140.38 
  ACAN MUTATED ACAN WILD-TYPE 
        16.735         20.980 
[1] "0.1 - 100.0 (16.7)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.9"
D1346V2, 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       22        99         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ACAN MUTATED           2          0          2          1        3         0
  ACAN WILD-TYPE        17         10         39         30       32        13
                vv
clus             STAGE IVB
  ACAN MUTATED           0
  ACAN WILD-TYPE         1
D1346V3, multiclass
            clus
vv           ACAN MUTATED ACAN WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              3             22
  STAGE IIA            10             99
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             2             17
  STAGE IIIA            0             10
  STAGE IIIB            2             39
  STAGE IIIC            1             30
  STAGE IV              3             32
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ACAN MUTATED     0   3  19   5
  ACAN WILD-TYPE   9  65 229  36
D1346V4, multiclass
    clus
vv   ACAN MUTATED ACAN WILD-TYPE
  T1            0              9
  T2            3             65
  T3           19            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
  ACAN MUTATED    19   3   5
  ACAN WILD-TYPE 201  77  61
D1346V5, multiclass
    clus
vv   ACAN MUTATED ACAN WILD-TYPE
  N0           19            201
  N1            3             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"
D1346V6, binary
                cls
clus               0   1
  ACAN MUTATED    21   3
  ACAN WILD-TYPE 262  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  ACAN MUTATED     21    3
  ACAN WILD-TYPE  262   45
   clus
vv  ACAN MUTATED ACAN WILD-TYPE
  0           21            262
  1            3             45
[1] 2 2
[1] FALSE
D1346V7, 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
D1346V8, binary
                cls
clus               0   1
  ACAN MUTATED    21   6
  ACAN WILD-TYPE 296  42
[1] "tbl2"
                cls
clus             [,1] [,2]
  ACAN MUTATED     21    6
  ACAN WILD-TYPE  296   42
                               clus
vv                              ACAN MUTATED ACAN WILD-TYPE
  COLON ADENOCARCINOMA                    21            296
  COLON MUCINOUS ADENOCARCINOMA            6             42
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ACAN MUTATED    19   0   2   3
  ACAN WILD-TYPE 238   2  20  18
D1346V9, multiclass
    clus
vv   ACAN MUTATED ACAN WILD-TYPE
  R0           19            238
  R1            0              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"
D1346V10, 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
D1346V11, 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(1347) Variable = SLC16A5 MUTATION ANALYSIS
D1347V1, survival
                   sevent
clus2                 0   1
  SLC16A5 MUTATED     8   1
  SLC16A5 WILD-TYPE 274  72
  SLC16A5 MUTATED SLC16A5 WILD-TYPE 
                9               346 
  SLC16A5 MUTATED SLC16A5 WILD-TYPE 
                1                72 
$`SLC16A5 MUTATED`
TCGA-A6-6651 TCGA-AA-3517 TCGA-AA-3672 TCGA-AA-3815 TCGA-AA-3977 TCGA-CA-6717 
       21.76        38.99         0.92        33.04        25.02         0.33 
TCGA-D5-5539 TCGA-F4-6808 TCGA-G4-6626 
       19.59        33.67        46.75 

$`SLC16A5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        24.16        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        13.02         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       29.59        16.24        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       35.80        26.17        91.79        52.80 

  SLC16A5 MUTATED SLC16A5 WILD-TYPE 
             0.33              0.00 
  SLC16A5 MUTATED SLC16A5 WILD-TYPE 
            46.75            140.38 
  SLC16A5 MUTATED SLC16A5 WILD-TYPE 
            25.02             20.07 
[1] "0.3 - 46.8 (25.0)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.7"
D1347V2, 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       24       105         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC16A5 MUTATED           1          1          1          0        0
  SLC16A5 WILD-TYPE        18          9         40         31       35
                   vv
clus                STAGE IVA STAGE IVB
  SLC16A5 MUTATED           0         0
  SLC16A5 WILD-TYPE        13         1
D1347V3, multiclass
            clus
vv           SLC16A5 MUTATED SLC16A5 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                4               105
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               1                 9
  STAGE IIIB               1                40
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC16A5 MUTATED     1   1   7   1
  SLC16A5 WILD-TYPE   8  67 241  40
D1347V4, multiclass
    clus
vv   SLC16A5 MUTATED SLC16A5 WILD-TYPE
  T1               1                 8
  T2               1                67
  T3               7               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
  SLC16A5 MUTATED     7   3   0
  SLC16A5 WILD-TYPE 213  77  66
D1347V5, multiclass
    clus
vv   SLC16A5 MUTATED SLC16A5 WILD-TYPE
  N0               7               213
  N1               3                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"
D1347V6, binary
                   cls
clus                  0   1
  SLC16A5 MUTATED     8   0
  SLC16A5 WILD-TYPE 275  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC16A5 MUTATED      8    0
  SLC16A5 WILD-TYPE  275   48
   clus
vv  SLC16A5 MUTATED SLC16A5 WILD-TYPE
  0               8               275
  1               0                48
[1] 2 2
[1] FALSE
D1347V7, 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
D1347V8, binary
                   cls
clus                  0   1
  SLC16A5 MUTATED     8   2
  SLC16A5 WILD-TYPE 309  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC16A5 MUTATED      8    2
  SLC16A5 WILD-TYPE  309   46
                               clus
vv                              SLC16A5 MUTATED SLC16A5 WILD-TYPE
  COLON ADENOCARCINOMA                        8               309
  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 250   2  22  20
D1347V9, multiclass
    clus
vv   SLC16A5 MUTATED SLC16A5 WILD-TYPE
  R0               7               250
  R1               0                 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"
D1347V10, 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
D1347V11, 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(1348) Variable = FBXO40 MUTATION ANALYSIS
D1348V1, survival
                  sevent
clus2                0   1
  FBXO40 MUTATED    14   2
  FBXO40 WILD-TYPE 268  71
  FBXO40 MUTATED FBXO40 WILD-TYPE 
              16              339 
  FBXO40 MUTATED FBXO40 WILD-TYPE 
               2               71 
$`FBXO40 MUTATED`
TCGA-A6-5666 TCGA-AA-3543 TCGA-AA-3663 TCGA-AA-3710 TCGA-AA-A00R TCGA-AA-A010 
       32.71         0.99         6.97        26.99         0.99        34.98 
TCGA-AU-6004 TCGA-AY-6197 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-6718 TCGA-CM-6164 
       27.09        21.44        49.41       100.01         0.10        29.03 
TCGA-CM-6169 TCGA-CM-6170 TCGA-D5-6930 TCGA-G4-6588 
       13.02        15.02         1.51        26.17 

$`FBXO40 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       26.01        12.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
       42.02        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        15.75         0.20        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13        83.80        22.36        62.79        61.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.33         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  FBXO40 MUTATED FBXO40 WILD-TYPE 
             0.1              0.0 
  FBXO40 MUTATED FBXO40 WILD-TYPE 
          100.01           140.38 
  FBXO40 MUTATED FBXO40 WILD-TYPE 
          23.805           20.120 
[1] "0.1 - 100.0 (23.8)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.6"
D1348V2, 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       22       102         7         0
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FBXO40 MUTATED           0          0          0          0        0
  FBXO40 WILD-TYPE        19         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  FBXO40 MUTATED           0         0
  FBXO40 WILD-TYPE        13         1
D1348V3, multiclass
            clus
vv           FBXO40 MUTATED FBXO40 WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                3               22
  STAGE IIA               7              102
  STAGE IIB               1                7
  STAGE IIC               1                0
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FBXO40 MUTATED     0   4  10   2
  FBXO40 WILD-TYPE   9  64 238  39
D1348V4, multiclass
    clus
vv   FBXO40 MUTATED FBXO40 WILD-TYPE
  T1              0                9
  T2              4               64
  T3             10              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
  FBXO40 MUTATED    16   0   0
  FBXO40 WILD-TYPE 204  80  66
D1348V5, multiclass
    clus
vv   FBXO40 MUTATED FBXO40 WILD-TYPE
  N0             16              204
  N1              0               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"
D1348V6, binary
                  cls
clus                 0   1
  FBXO40 MUTATED    14   0
  FBXO40 WILD-TYPE 269  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO40 MUTATED     14    0
  FBXO40 WILD-TYPE  269   48
   clus
vv  FBXO40 MUTATED FBXO40 WILD-TYPE
  0             14              269
  1              0               48
[1] 2 2
[1] FALSE
D1348V7, 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
D1348V8, binary
                  cls
clus                 0   1
  FBXO40 MUTATED    14   2
  FBXO40 WILD-TYPE 303  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO40 MUTATED     14    2
  FBXO40 WILD-TYPE  303   46
                               clus
vv                              FBXO40 MUTATED FBXO40 WILD-TYPE
  COLON ADENOCARCINOMA                      14              303
  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 245   2  22  20
D1348V9, multiclass
    clus
vv   FBXO40 MUTATED FBXO40 WILD-TYPE
  R0             12              245
  R1              0                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"
D1348V10, 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
D1348V11, 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(1349) Variable = GRK5 MUTATION ANALYSIS
D1349V1, survival
                sevent
clus2              0   1
  GRK5 MUTATED     8   3
  GRK5 WILD-TYPE 274  70
  GRK5 MUTATED GRK5 WILD-TYPE 
            11            344 
  GRK5 MUTATED GRK5 WILD-TYPE 
             3             70 
$`GRK5 MUTATED`
TCGA-A6-6651 TCGA-AA-3692 TCGA-AA-3848 TCGA-AA-3950 TCGA-AA-3994 TCGA-AU-6004 
       21.76        36.00        10.06        24.00        27.02        27.09 
TCGA-CA-5254 TCGA-CM-5344 TCGA-CM-5862 TCGA-D5-6930 TCGA-G4-6293 
        2.24        22.03         5.03         1.51       107.67 

$`GRK5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        24.16        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
        7.96        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19         1.94         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        16.01        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        35.41        19.43        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  GRK5 MUTATED GRK5 WILD-TYPE 
          1.51           0.00 
  GRK5 MUTATED GRK5 WILD-TYPE 
        107.67         140.38 
  GRK5 MUTATED GRK5 WILD-TYPE 
         22.03          20.07 
[1] "1.5 - 107.7 (22.0)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.4"
D1349V2, 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       25       106         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        18         10         38         30       34        12
                vv
clus             STAGE IVB
  GRK5 MUTATED           0
  GRK5 WILD-TYPE         1
D1349V3, multiclass
            clus
vv           GRK5 MUTATED GRK5 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             3            106
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            3             38
  STAGE IIIC            1             30
  STAGE IV              1             34
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 238  41
D1349V4, multiclass
    clus
vv   GRK5 MUTATED GRK5 WILD-TYPE
  T1            0              9
  T2            1             67
  T3           10            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
  GRK5 MUTATED     4   5   2
  GRK5 WILD-TYPE 216  75  64
D1349V5, multiclass
    clus
vv   GRK5 MUTATED GRK5 WILD-TYPE
  N0            4            216
  N1            5             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"
D1349V6, binary
                cls
clus               0   1
  GRK5 MUTATED     8   2
  GRK5 WILD-TYPE 275  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRK5 MUTATED      8    2
  GRK5 WILD-TYPE  275   46
   clus
vv  GRK5 MUTATED GRK5 WILD-TYPE
  0            8            275
  1            2             46
[1] 2 2
[1] FALSE
D1349V7, 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
D1349V8, binary
                cls
clus               0   1
  GRK5 MUTATED     7   4
  GRK5 WILD-TYPE 310  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRK5 MUTATED      7    4
  GRK5 WILD-TYPE  310   44
                               clus
vv                              GRK5 MUTATED GRK5 WILD-TYPE
  COLON ADENOCARCINOMA                     7            310
  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 249   2  21  20
D1349V9, multiclass
    clus
vv   GRK5 MUTATED GRK5 WILD-TYPE
  R0            8            249
  R1            0              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"
D1349V10, 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
D1349V11, 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(1350) Variable = PTPN13 MUTATION ANALYSIS
D1350V1, survival
                  sevent
clus2                0   1
  PTPN13 MUTATED    17   5
  PTPN13 WILD-TYPE 265  68
  PTPN13 MUTATED PTPN13 WILD-TYPE 
              22              333 
  PTPN13 MUTATED PTPN13 WILD-TYPE 
               5               68 
$`PTPN13 MUTATED`
TCGA-A6-5661 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3947 
       33.53         3.02        63.98        85.05        19.04        33.01 
TCGA-AA-3955 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01P TCGA-AA-A02H TCGA-AZ-4315 
       20.98         4.01        34.98        38.07         2.01        58.39 
TCGA-CA-6717 TCGA-CM-5349 TCGA-CM-6171 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        0.33        30.08        14.04        13.41         1.51        12.00 
TCGA-D5-7000 TCGA-DM-A0XD TCGA-G4-6323 TCGA-G4-6588 
       10.26        24.43        13.78        26.17 

$`PTPN13 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 
       18.05        31.00         2.01        12.99        24.00        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02J 
       26.01        37.02        39.06        51.98        39.98         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 
       51.75        45.11        36.72        36.00        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  PTPN13 MUTATED PTPN13 WILD-TYPE 
            0.33             0.00 
  PTPN13 MUTATED PTPN13 WILD-TYPE 
           85.05           140.38 
  PTPN13 MUTATED PTPN13 WILD-TYPE 
           20.01            20.19 
[1] "0.3 - 85.0 (20.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D1350V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PTPN13 MUTATED         2        1        2         7         3         0
  PTPN13 WILD-TYPE      62        0       23       102         5         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PTPN13 MUTATED           2          0          1          1        3
  PTPN13 WILD-TYPE        17         10         40         30       32
                  vv
clus               STAGE IVA STAGE IVB
  PTPN13 MUTATED           0         0
  PTPN13 WILD-TYPE        13         1
D1350V3, multiclass
            clus
vv           PTPN13 MUTATED PTPN13 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                1                0
  STAGE II                2               23
  STAGE IIA               7              102
  STAGE IIB               3                5
  STAGE IIC               0                1
  STAGE III               2               17
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              1               30
  STAGE IV                3               32
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PTPN13 MUTATED     0   3  14   4
  PTPN13 WILD-TYPE   9  65 234  37
D1350V4, multiclass
    clus
vv   PTPN13 MUTATED PTPN13 WILD-TYPE
  T1              0                9
  T2              3               65
  T3             14              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
  PTPN13 MUTATED    17   2   3
  PTPN13 WILD-TYPE 203  78  63
D1350V5, multiclass
    clus
vv   PTPN13 MUTATED PTPN13 WILD-TYPE
  N0             17              203
  N1              2               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"
D1350V6, binary
                  cls
clus                 0   1
  PTPN13 MUTATED    18   3
  PTPN13 WILD-TYPE 265  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN13 MUTATED     18    3
  PTPN13 WILD-TYPE  265   45
   clus
vv  PTPN13 MUTATED PTPN13 WILD-TYPE
  0             18              265
  1              3               45
[1] 2 2
[1] FALSE
D1350V7, 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
D1350V8, binary
                  cls
clus                 0   1
  PTPN13 MUTATED    17   5
  PTPN13 WILD-TYPE 300  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN13 MUTATED     17    5
  PTPN13 WILD-TYPE  300   43
                               clus
vv                              PTPN13 MUTATED PTPN13 WILD-TYPE
  COLON ADENOCARCINOMA                      17              300
  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 239   2  20  20
D1350V9, multiclass
    clus
vv   PTPN13 MUTATED PTPN13 WILD-TYPE
  R0             18              239
  R1              0                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"
D1350V10, 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
D1350V11, 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(1351) Variable = JAK1 MUTATION ANALYSIS
D1351V1, survival
                sevent
clus2              0   1
  JAK1 MUTATED    16   2
  JAK1 WILD-TYPE 266  71
  JAK1 MUTATED JAK1 WILD-TYPE 
            18            337 
  JAK1 MUTATED JAK1 WILD-TYPE 
             2             71 
$`JAK1 MUTATED`
TCGA-A6-5657 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3710 TCGA-AA-3977 TCGA-AA-A01P 
       31.63        22.06        19.66        26.99        25.02        38.07 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AY-6196 TCGA-AY-6197 TCGA-CA-6717 TCGA-CK-4948 
        0.72        10.88         0.20        21.44         0.33       102.44 
TCGA-CK-4952 TCGA-CM-4743 TCGA-CM-6171 TCGA-D5-6928 TCGA-G4-6586 TCGA-G4-6628 
       15.62        23.05        14.04        11.64        35.80        52.80 

$`JAK1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        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        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21        56.55         0.79         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       15.75        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 
        0.10         1.35        17.56        40.34        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        26.17        91.79 
TCGA-G4-6626 
       46.75 

  JAK1 MUTATED JAK1 WILD-TYPE 
           0.2            0.0 
  JAK1 MUTATED JAK1 WILD-TYPE 
        102.44         140.38 
  JAK1 MUTATED JAK1 WILD-TYPE 
         21.75          20.12 
[1] "0.2 - 102.4 (21.8)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.8"
D1351V2, 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       25       102         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  JAK1 MUTATED           2          1          1          2        0         0
  JAK1 WILD-TYPE        17          9         40         29       35        13
                vv
clus             STAGE IVB
  JAK1 MUTATED           0
  JAK1 WILD-TYPE         1
D1351V3, multiclass
            clus
vv           JAK1 MUTATED JAK1 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             7            102
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             2             17
  STAGE IIIA            1              9
  STAGE IIIB            1             40
  STAGE IIIC            2             29
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  JAK1 MUTATED     0   3  12   3
  JAK1 WILD-TYPE   9  65 236  38
D1351V4, multiclass
    clus
vv   JAK1 MUTATED JAK1 WILD-TYPE
  T1            0              9
  T2            3             65
  T3           12            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
  JAK1 MUTATED    10   5   3
  JAK1 WILD-TYPE 210  75  63
D1351V5, multiclass
    clus
vv   JAK1 MUTATED JAK1 WILD-TYPE
  N0           10            210
  N1            5             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"
D1351V6, binary
                cls
clus               0   1
  JAK1 MUTATED    12   0
  JAK1 WILD-TYPE 271  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  JAK1 MUTATED     12    0
  JAK1 WILD-TYPE  271   48
   clus
vv  JAK1 MUTATED JAK1 WILD-TYPE
  0           12            271
  1            0             48
[1] 2 2
[1] FALSE
D1351V7, 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
D1351V8, binary
                cls
clus               0   1
  JAK1 MUTATED    13   5
  JAK1 WILD-TYPE 304  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  JAK1 MUTATED     13    5
  JAK1 WILD-TYPE  304   43
                               clus
vv                              JAK1 MUTATED JAK1 WILD-TYPE
  COLON ADENOCARCINOMA                    13            304
  COLON MUCINOUS ADENOCARCINOMA            5             43
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  JAK1 MUTATED    13   0   0   2
  JAK1 WILD-TYPE 244   2  22  19
D1351V9, multiclass
    clus
vv   JAK1 MUTATED JAK1 WILD-TYPE
  R0           13            244
  R1            0              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"
D1351V10, 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
D1351V11, 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(1352) Variable = C14ORF105 MUTATION ANALYSIS
D1352V1, survival
                     sevent
clus2                   0   1
  C14ORF105 MUTATED     3   0
  C14ORF105 WILD-TYPE 279  73
  C14ORF105 MUTATED C14ORF105 WILD-TYPE 
                  3                 352 
  C14ORF105 MUTATED C14ORF105 WILD-TYPE 
                  0                  73 
$`C14ORF105 MUTATED`
TCGA-AA-3977 TCGA-AA-A010 TCGA-D5-6928 
       25.02        34.98        11.64 

$`C14ORF105 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  C14ORF105 MUTATED C14ORF105 WILD-TYPE 
              11.64                0.00 
  C14ORF105 MUTATED C14ORF105 WILD-TYPE 
              34.98              140.38 
  C14ORF105 MUTATED C14ORF105 WILD-TYPE 
             25.020              20.155 
[1] "11.6 - 35.0 (25.0)" "0.0 - 140.4 (20.2)"
[1] "hr="     "3300000"
D1352V2, 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       25       108         7         1
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C14ORF105 MUTATED           0          0          0          0        0
  C14ORF105 WILD-TYPE        19         10         41         31       35
                     vv
clus                  STAGE IVA STAGE IVB
  C14ORF105 MUTATED           0         0
  C14ORF105 WILD-TYPE        13         1
D1352V3, multiclass
[1] "Remove cluster labels:" "C14ORF105 MUTATED"     
clus
  C14ORF105 MUTATED C14ORF105 WILD-TYPE 
                  2                 356 
         TCGA-A6-2671          TCGA-A6-2672          TCGA-A6-2674 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-2676          TCGA-A6-2677          TCGA-A6-2678 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-2683          TCGA-A6-3807          TCGA-A6-3808 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-3809          TCGA-A6-3810          TCGA-A6-4105 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-5656          TCGA-A6-5657          TCGA-A6-5659 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-5660          TCGA-A6-5661          TCGA-A6-5662 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-5664          TCGA-A6-5665          TCGA-A6-5666 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-6137          TCGA-A6-6138          TCGA-A6-6141 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-6142          TCGA-A6-6648          TCGA-A6-6649 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-6651          TCGA-A6-6652          TCGA-A6-6653 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-6654          TCGA-A6-6780          TCGA-A6-6781 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-6782          TCGA-AA-3489          TCGA-AA-3492 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3496          TCGA-AA-3502          TCGA-AA-3510 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3511          TCGA-AA-3514          TCGA-AA-3516 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3517          TCGA-AA-3518          TCGA-AA-3519 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3520          TCGA-AA-3521          TCGA-AA-3522 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3524          TCGA-AA-3525          TCGA-AA-3526 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3527          TCGA-AA-3529          TCGA-AA-3530 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3531          TCGA-AA-3532          TCGA-AA-3534 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3538          TCGA-AA-3542          TCGA-AA-3543 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3544          TCGA-AA-3548          TCGA-AA-3549 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3552          TCGA-AA-3553          TCGA-AA-3554 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3555          TCGA-AA-3556          TCGA-AA-3558 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3560          TCGA-AA-3561          TCGA-AA-3562 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3655          TCGA-AA-3660          TCGA-AA-3662 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3663          TCGA-AA-3664          TCGA-AA-3666 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3667          TCGA-AA-3672          TCGA-AA-3673 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3678          TCGA-AA-3679          TCGA-AA-3680 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3681          TCGA-AA-3684          TCGA-AA-3685 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3688          TCGA-AA-3692          TCGA-AA-3693 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3695          TCGA-AA-3696          TCGA-AA-3697 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3710          TCGA-AA-3712          TCGA-AA-3713 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3715          TCGA-AA-3811          TCGA-AA-3812 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3814          TCGA-AA-3815          TCGA-AA-3818 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3819          TCGA-AA-3821          TCGA-AA-3831 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3833          TCGA-AA-3837          TCGA-AA-3842 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3844          TCGA-AA-3845          TCGA-AA-3846 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3848          TCGA-AA-3850          TCGA-AA-3851 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3852          TCGA-AA-3854          TCGA-AA-3855 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3856          TCGA-AA-3858          TCGA-AA-3860 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3861          TCGA-AA-3864          TCGA-AA-3866 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3867          TCGA-AA-3869          TCGA-AA-3870 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3872          TCGA-AA-3875          TCGA-AA-3877 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3930          TCGA-AA-3939          TCGA-AA-3941 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3947          TCGA-AA-3949          TCGA-AA-3950 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3952          TCGA-AA-3955          TCGA-AA-3956 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3966          TCGA-AA-3968          TCGA-AA-3971 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3972          TCGA-AA-3973          TCGA-AA-3975 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3976          TCGA-AA-3979          TCGA-AA-3980 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3982          TCGA-AA-3984          TCGA-AA-3986 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3989          TCGA-AA-3994          TCGA-AA-A004 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A00A          TCGA-AA-A00D          TCGA-AA-A00E 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A00F          TCGA-AA-A00J          TCGA-AA-A00K 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A00L          TCGA-AA-A00N          TCGA-AA-A00O 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A00Q          TCGA-AA-A00R          TCGA-AA-A00U 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A00W          TCGA-AA-A00Z          TCGA-AA-A017 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A01D          TCGA-AA-A01F          TCGA-AA-A01G 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A01I          TCGA-AA-A01K          TCGA-AA-A01P 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A01Q          TCGA-AA-A01R          TCGA-AA-A01S 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A01T          TCGA-AA-A01V          TCGA-AA-A01X 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A01Z          TCGA-AA-A022          TCGA-AA-A024 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A029          TCGA-AA-A02F          TCGA-AA-A02H 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A02J          TCGA-AA-A02K          TCGA-AA-A02O 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A02W          TCGA-AA-A02Y          TCGA-AA-A03F 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A03J          TCGA-AD-5900          TCGA-AD-6548 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AD-6888          TCGA-AD-6889          TCGA-AD-6899 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AU-3779          TCGA-AU-6004          TCGA-AY-4070 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AY-4071          TCGA-AY-5543          TCGA-AY-6196 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AY-6197          TCGA-AY-6386          TCGA-AZ-4315 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AZ-4323          TCGA-AZ-4616          TCGA-AZ-4681 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AZ-4682          TCGA-AZ-5403          TCGA-AZ-5407 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AZ-6598          TCGA-AZ-6599          TCGA-AZ-6600 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AZ-6601          TCGA-AZ-6605          TCGA-AZ-6606 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AZ-6607          TCGA-AZ-6608          TCGA-CA-5254 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CA-5255          TCGA-CA-5796          TCGA-CA-5797 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CA-6715          TCGA-CA-6716          TCGA-CA-6717 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CA-6718          TCGA-CA-6719          TCGA-CK-4947 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CK-4948          TCGA-CK-4950          TCGA-CK-4952 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CK-5912          TCGA-CK-5913          TCGA-CK-5914 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CK-5915          TCGA-CK-5916          TCGA-CK-6746 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CK-6747          TCGA-CK-6748          TCGA-CK-6751 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-4743          TCGA-CM-4744          TCGA-CM-4746 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-4747          TCGA-CM-4752          TCGA-CM-5341 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-5344          TCGA-CM-5348          TCGA-CM-5349 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-5860          TCGA-CM-5861          TCGA-CM-5862 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-5863          TCGA-CM-5864          TCGA-CM-5868 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-6161          TCGA-CM-6162          TCGA-CM-6163 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-6164          TCGA-CM-6165          TCGA-CM-6166 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-6167          TCGA-CM-6168          TCGA-CM-6169 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-6170          TCGA-CM-6171          TCGA-CM-6172 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-6674          TCGA-CM-6675          TCGA-CM-6676 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-6677          TCGA-CM-6678          TCGA-CM-6679 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-6680          TCGA-D5-5537          TCGA-D5-5538 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-5539          TCGA-D5-5540          TCGA-D5-5541 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6529          TCGA-D5-6532          TCGA-D5-6533 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6534          TCGA-D5-6535          TCGA-D5-6536 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6537          TCGA-D5-6538          TCGA-D5-6539 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6540          TCGA-D5-6541          TCGA-D5-6898 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6920          TCGA-D5-6922          TCGA-D5-6923 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6924          TCGA-D5-6926          TCGA-D5-6927 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6929          TCGA-D5-6930          TCGA-D5-6931 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6932          TCGA-D5-7000          TCGA-DM-A0X9 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-DM-A0XD          TCGA-DM-A0XF          TCGA-DM-A1D0 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-DM-A1D4          TCGA-DM-A1D6          TCGA-DM-A1D7 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-DM-A1D9          TCGA-DM-A1DA          TCGA-DM-A1DB 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-DM-A1HA          TCGA-DM-A1HB          TCGA-DM-A282 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-DM-A285          TCGA-DM-A28C          TCGA-DM-A28E 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-DM-A28F          TCGA-DM-A28G          TCGA-DM-A28H 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-DM-A28K          TCGA-F4-6459          TCGA-F4-6460 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-F4-6569          TCGA-F4-6570          TCGA-F4-6703 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-F4-6704          TCGA-F4-6805          TCGA-F4-6806 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-F4-6807          TCGA-F4-6808          TCGA-F4-6809 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-F4-6854          TCGA-F4-6855          TCGA-F4-6856 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-G4-6293          TCGA-G4-6299          TCGA-G4-6303 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-G4-6304          TCGA-G4-6306          TCGA-G4-6307 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-G4-6309          TCGA-G4-6310          TCGA-G4-6315 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-G4-6317          TCGA-G4-6321          TCGA-G4-6323 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-G4-6586          TCGA-G4-6588          TCGA-G4-6625 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-G4-6626          TCGA-G4-6628 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
                     vv
clus                   T1  T2  T3  T4
  C14ORF105 MUTATED     0   1   1   1
  C14ORF105 WILD-TYPE   9  67 247  40
D1352V4, multiclass
    clus
vv   C14ORF105 MUTATED C14ORF105 WILD-TYPE
  T1                 0                   9
  T2                 1                  67
  T3                 1                 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
  C14ORF105 MUTATED     3   0   0
  C14ORF105 WILD-TYPE 217  80  66
D1352V5, multiclass
    clus
vv   C14ORF105 MUTATED C14ORF105 WILD-TYPE
  N0                 3                 217
  N1                 0                  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"
D1352V6, binary
                     cls
clus                    0   1
  C14ORF105 MUTATED     2   0
  C14ORF105 WILD-TYPE 281  48
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF105 MUTATED      2    0
  C14ORF105 WILD-TYPE  281   48
   clus
vv  C14ORF105 MUTATED C14ORF105 WILD-TYPE
  0                 2                 281
  1                 0                  48
[1] 2 2
[1] FALSE
D1352V7, 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
D1352V8, binary
                     cls
clus                    0   1
  C14ORF105 MUTATED     2   1
  C14ORF105 WILD-TYPE 315  47
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF105 MUTATED      2    1
  C14ORF105 WILD-TYPE  315   47
                               clus
vv                              C14ORF105 MUTATED C14ORF105 WILD-TYPE
  COLON ADENOCARCINOMA                          2                 315
  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 255   2  22  21
D1352V9, multiclass
[1] "Remove cluster labels:" "C14ORF105 MUTATED"     
clus
  C14ORF105 MUTATED C14ORF105 WILD-TYPE 
                  2                 300 
         TCGA-A6-2671          TCGA-A6-2672          TCGA-A6-2674 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-2676          TCGA-A6-2677          TCGA-A6-2678 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-2683          TCGA-A6-3807          TCGA-A6-3808 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-3809          TCGA-A6-3810          TCGA-A6-5657 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-5659          TCGA-A6-5661          TCGA-A6-5665 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-6781          TCGA-AA-3489          TCGA-AA-3492 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3496          TCGA-AA-3502          TCGA-AA-3510 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3511          TCGA-AA-3514          TCGA-AA-3517 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3518          TCGA-AA-3519          TCGA-AA-3520 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3521          TCGA-AA-3522          TCGA-AA-3524 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3525          TCGA-AA-3526          TCGA-AA-3527 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3529          TCGA-AA-3530          TCGA-AA-3531 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3532          TCGA-AA-3534          TCGA-AA-3538 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3542          TCGA-AA-3543          TCGA-AA-3544 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3548          TCGA-AA-3549          TCGA-AA-3552 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3553          TCGA-AA-3554          TCGA-AA-3555 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3556          TCGA-AA-3558          TCGA-AA-3560 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3561          TCGA-AA-3562          TCGA-AA-3655 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3660          TCGA-AA-3662          TCGA-AA-3663 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3664          TCGA-AA-3666          TCGA-AA-3667 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3672          TCGA-AA-3673          TCGA-AA-3678 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3679          TCGA-AA-3680          TCGA-AA-3681 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3684          TCGA-AA-3685          TCGA-AA-3688 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3692          TCGA-AA-3693          TCGA-AA-3695 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3696          TCGA-AA-3697          TCGA-AA-3710 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3712          TCGA-AA-3713          TCGA-AA-3715 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3811          TCGA-AA-3812          TCGA-AA-3814 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3815          TCGA-AA-3818          TCGA-AA-3819 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3821          TCGA-AA-3831          TCGA-AA-3833 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3837          TCGA-AA-3842          TCGA-AA-3844 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3845          TCGA-AA-3846          TCGA-AA-3848 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3850          TCGA-AA-3851          TCGA-AA-3852 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3854          TCGA-AA-3855          TCGA-AA-3856 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3858          TCGA-AA-3860          TCGA-AA-3861 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3864          TCGA-AA-3866          TCGA-AA-3867 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3869          TCGA-AA-3870          TCGA-AA-3872 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3875          TCGA-AA-3877          TCGA-AA-3930 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3939          TCGA-AA-3941          TCGA-AA-3947 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3949          TCGA-AA-3950          TCGA-AA-3952 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3955          TCGA-AA-3956          TCGA-AA-3968 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3971          TCGA-AA-3972          TCGA-AA-3973 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3975          TCGA-AA-3976          TCGA-AA-3979 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3984          TCGA-AA-3986          TCGA-AA-3989 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3994          TCGA-AA-A004          TCGA-AA-A00A 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A00D          TCGA-AA-A00E          TCGA-AA-A00F 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A00J          TCGA-AA-A00K          TCGA-AA-A00L 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A00N          TCGA-AA-A00O          TCGA-AA-A00Q 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A00R          TCGA-AA-A00U          TCGA-AA-A00W 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A00Z          TCGA-AA-A017          TCGA-AA-A01D 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A01F          TCGA-AA-A01G          TCGA-AA-A01I 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A01K          TCGA-AA-A01P          TCGA-AA-A01Q 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A01R          TCGA-AA-A01S          TCGA-AA-A01T 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A01V          TCGA-AA-A01X          TCGA-AA-A01Z 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A022          TCGA-AA-A024          TCGA-AA-A029 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A02F          TCGA-AA-A02H          TCGA-AA-A02J 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A02K          TCGA-AA-A02O          TCGA-AA-A02W 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A02Y          TCGA-AA-A03F          TCGA-AA-A03J 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AD-5900          TCGA-AD-6548          TCGA-AD-6888 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AU-3779          TCGA-AU-6004          TCGA-AY-4070 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AY-4071          TCGA-AY-5543          TCGA-AY-6196 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AY-6197          TCGA-AY-6386          TCGA-AZ-4315 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AZ-4681          TCGA-AZ-4682          TCGA-CA-5254 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CA-5255          TCGA-CA-5796          TCGA-CA-5797 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CA-6715          TCGA-CA-6716          TCGA-CA-6717 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CA-6718          TCGA-CA-6719          TCGA-CK-4947 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CK-4948          TCGA-CK-4950          TCGA-CK-4952 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CK-5912          TCGA-CK-5913          TCGA-CK-5914 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CK-5915          TCGA-CK-5916          TCGA-CK-6746 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CK-6747          TCGA-CK-6748          TCGA-CK-6751 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-4743          TCGA-CM-4744          TCGA-CM-4746 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-4747          TCGA-CM-4752          TCGA-CM-5341 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-5344          TCGA-CM-5348          TCGA-CM-5349 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-5860          TCGA-CM-5861          TCGA-CM-5862 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-5863          TCGA-CM-5864          TCGA-CM-5868 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-6161          TCGA-CM-6162          TCGA-CM-6163 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-6164          TCGA-CM-6165          TCGA-CM-6166 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-6167          TCGA-CM-6168          TCGA-CM-6169 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-6170          TCGA-CM-6171          TCGA-CM-6172 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-6674          TCGA-CM-6675          TCGA-CM-6676 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-6677          TCGA-CM-6678          TCGA-CM-6679 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-6680          TCGA-D5-5537          TCGA-D5-5538 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-5539          TCGA-D5-5540          TCGA-D5-5541 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6529          TCGA-D5-6532          TCGA-D5-6533 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6534          TCGA-D5-6535          TCGA-D5-6536 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6537          TCGA-D5-6538          TCGA-D5-6539 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6540          TCGA-D5-6541          TCGA-D5-6898 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6920          TCGA-D5-6922          TCGA-D5-6923 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6924          TCGA-D5-6926          TCGA-D5-6927 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6929          TCGA-D5-6930          TCGA-D5-6931 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6932          TCGA-D5-7000          TCGA-F4-6459 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-F4-6460          TCGA-F4-6569          TCGA-F4-6570 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-F4-6703          TCGA-F4-6704          TCGA-F4-6805 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-F4-6806          TCGA-F4-6807          TCGA-F4-6808 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-F4-6809          TCGA-F4-6854          TCGA-F4-6855 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-F4-6856          TCGA-G4-6293          TCGA-G4-6299 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-G4-6303          TCGA-G4-6304          TCGA-G4-6306 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-G4-6307          TCGA-G4-6309          TCGA-G4-6310 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-G4-6315          TCGA-G4-6317          TCGA-G4-6321 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-G4-6323          TCGA-G4-6586          TCGA-G4-6588 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-G4-6625          TCGA-G4-6626          TCGA-G4-6628 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
D1352V10, 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
D1352V11, multiclass
[1] "Remove cluster labels:" "C14ORF105 MUTATED"     
clus
  C14ORF105 MUTATED C14ORF105 WILD-TYPE 
                  1                 205 
         TCGA-A6-2671          TCGA-A6-2672          TCGA-A6-2674 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-2676          TCGA-A6-2677          TCGA-A6-2678 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-2683          TCGA-A6-3807          TCGA-A6-3808 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-3809          TCGA-A6-3810          TCGA-A6-4105 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-5656          TCGA-A6-5657          TCGA-A6-5659 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-5660          TCGA-A6-5661          TCGA-A6-5662 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-5664          TCGA-A6-5665          TCGA-A6-5666 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-6137          TCGA-A6-6138          TCGA-A6-6141 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-6142          TCGA-A6-6648          TCGA-A6-6649 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-6651          TCGA-A6-6652          TCGA-A6-6653 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-6654          TCGA-A6-6780          TCGA-A6-6781 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-6782          TCGA-AD-5900          TCGA-AD-6548 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AD-6888          TCGA-AD-6889          TCGA-AD-6890 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AD-6895          TCGA-AD-6899          TCGA-AD-6901 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AD-6963          TCGA-AD-6964          TCGA-AD-6965 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AU-3779          TCGA-AU-6004          TCGA-AY-4070 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AY-4071          TCGA-AY-5543          TCGA-AY-6196 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AY-6197          TCGA-AY-6386          TCGA-AZ-4315 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AZ-4323          TCGA-AZ-4616          TCGA-AZ-4681 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AZ-4682          TCGA-AZ-5403          TCGA-AZ-5407 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AZ-6598          TCGA-AZ-6599          TCGA-AZ-6600 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AZ-6601          TCGA-AZ-6603          TCGA-AZ-6605 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AZ-6606          TCGA-AZ-6607          TCGA-AZ-6608 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CA-5254          TCGA-CA-5255          TCGA-CA-5796 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CA-5797          TCGA-CA-6715          TCGA-CA-6716 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CA-6717          TCGA-CA-6718          TCGA-CA-6719 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CK-4947          TCGA-CK-4948          TCGA-CK-4950 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CK-4952          TCGA-CK-5912          TCGA-CK-5913 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CK-5914          TCGA-CK-5915          TCGA-CK-5916 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CK-6746          TCGA-CK-6747          TCGA-CK-6748 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CK-6751          TCGA-CM-4743          TCGA-CM-4744 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-4746          TCGA-CM-4747          TCGA-CM-4752 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-5341          TCGA-CM-5344          TCGA-CM-5348 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-5349          TCGA-CM-5860          TCGA-CM-5861 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-5862          TCGA-CM-5863          TCGA-CM-5864 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-5868          TCGA-CM-6161          TCGA-CM-6162 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-6163          TCGA-CM-6164          TCGA-CM-6165 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-6166          TCGA-CM-6167          TCGA-CM-6168 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-6169          TCGA-CM-6170          TCGA-CM-6171 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-6172          TCGA-CM-6674          TCGA-CM-6675 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-6676          TCGA-CM-6677          TCGA-CM-6678 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-6679          TCGA-CM-6680          TCGA-D5-5537 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-5538          TCGA-D5-5539          TCGA-D5-5540 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-5541          TCGA-D5-6529          TCGA-D5-6532 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6533          TCGA-D5-6534          TCGA-D5-6535 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6536          TCGA-D5-6537          TCGA-D5-6538 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6539          TCGA-D5-6540          TCGA-D5-6541 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6898          TCGA-D5-6920          TCGA-D5-6922 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6923          TCGA-D5-6924          TCGA-D5-6926 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6927          TCGA-D5-6929          TCGA-D5-6930 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6931          TCGA-D5-6932          TCGA-D5-7000 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-DM-A0X9          TCGA-DM-A0XD          TCGA-DM-A0XF 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-DM-A1D0          TCGA-DM-A1D4          TCGA-DM-A1D6 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-DM-A1D7          TCGA-DM-A1D8          TCGA-DM-A1D9 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-DM-A1DA          TCGA-DM-A1DB          TCGA-DM-A1HA 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-DM-A1HB          TCGA-DM-A282          TCGA-DM-A285 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-DM-A28C          TCGA-DM-A28E          TCGA-DM-A28F 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-DM-A28G          TCGA-DM-A28H          TCGA-DM-A28K 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-F4-6459          TCGA-F4-6460          TCGA-F4-6569 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-F4-6570          TCGA-F4-6703          TCGA-F4-6704 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-F4-6805          TCGA-F4-6806          TCGA-F4-6807 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-F4-6808          TCGA-F4-6809          TCGA-F4-6854 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-F4-6855          TCGA-F4-6856          TCGA-G4-6293 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-G4-6299          TCGA-G4-6303          TCGA-G4-6304 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-G4-6306          TCGA-G4-6307          TCGA-G4-6309 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-G4-6310          TCGA-G4-6315          TCGA-G4-6317 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-G4-6321          TCGA-G4-6323          TCGA-G4-6586 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-G4-6588          TCGA-G4-6625          TCGA-G4-6626 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-G4-6628 
"C14ORF105 WILD-TYPE" 

Clustering(1353) Variable = C9ORF102 MUTATION ANALYSIS
D1353V1, survival
                    sevent
clus2                  0   1
  C9ORF102 MUTATED     7   0
  C9ORF102 WILD-TYPE 275  73
  C9ORF102 MUTATED C9ORF102 WILD-TYPE 
                 7                348 
  C9ORF102 MUTATED C9ORF102 WILD-TYPE 
                 0                 73 
$`C9ORF102 MUTATED`
TCGA-A6-3808 TCGA-A6-6780 TCGA-AA-3977 TCGA-AA-A010 TCGA-AD-5900 TCGA-AD-6895 
       33.34        20.12        25.02        34.98         0.07         0.72 
TCGA-CM-6167 
       14.99 

$`C9ORF102 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
       40.96        21.37         4.21        56.55         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  C9ORF102 MUTATED C9ORF102 WILD-TYPE 
              0.07               0.00 
  C9ORF102 MUTATED C9ORF102 WILD-TYPE 
             34.98             140.38 
  C9ORF102 MUTATED C9ORF102 WILD-TYPE 
            20.120             20.235 
[1] "0.1 - 35.0 (20.1)"  "0.0 - 140.4 (20.2)"
[1] "hr="     "9100000"
D1353V2, 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       25       106         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C9ORF102 MUTATED           0          0          0          1        0
  C9ORF102 WILD-TYPE        19         10         41         30       35
                    vv
clus                 STAGE IVA STAGE IVB
  C9ORF102 MUTATED           0         0
  C9ORF102 WILD-TYPE        13         1
D1353V3, multiclass
            clus
vv           C9ORF102 MUTATED C9ORF102 WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  0                 25
  STAGE IIA                 3                106
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                0                 10
  STAGE IIIB                0                 41
  STAGE IIIC                1                 30
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C9ORF102 MUTATED     0   2   5   1
  C9ORF102 WILD-TYPE   9  66 243  40
D1353V4, multiclass
    clus
vv   C9ORF102 MUTATED C9ORF102 WILD-TYPE
  T1                0                  9
  T2                2                 66
  T3                5                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
  C9ORF102 MUTATED     6   1   1
  C9ORF102 WILD-TYPE 214  79  65
D1353V5, multiclass
    clus
vv   C9ORF102 MUTATED C9ORF102 WILD-TYPE
  N0                6                214
  N1                1                 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"
D1353V6, binary
                    cls
clus                   0   1
  C9ORF102 MUTATED     4   0
  C9ORF102 WILD-TYPE 279  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF102 MUTATED      4    0
  C9ORF102 WILD-TYPE  279   48
   clus
vv  C9ORF102 MUTATED C9ORF102 WILD-TYPE
  0                4                279
  1                0                 48
[1] 2 2
[1] FALSE
D1353V7, 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
D1353V8, binary
                    cls
clus                   0   1
  C9ORF102 MUTATED     6   2
  C9ORF102 WILD-TYPE 311  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF102 MUTATED      6    2
  C9ORF102 WILD-TYPE  311   46
                               clus
vv                              C9ORF102 MUTATED C9ORF102 WILD-TYPE
  COLON ADENOCARCINOMA                         6                311
  COLON MUCINOUS ADENOCARCINOMA                2                 46
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C9ORF102 MUTATED     5   0   0   0
  C9ORF102 WILD-TYPE 252   2  22  21
D1353V9, multiclass
    clus
vv   C9ORF102 MUTATED C9ORF102 WILD-TYPE
  R0                5                252
  R1                0                  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"
D1353V10, 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
D1353V11, 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(1354) Variable = OR11H12 MUTATION ANALYSIS
D1354V1, survival
                   sevent
clus2                 0   1
  OR11H12 MUTATED     3   0
  OR11H12 WILD-TYPE 279  73
  OR11H12 MUTATED OR11H12 WILD-TYPE 
                3               352 
  OR11H12 MUTATED OR11H12 WILD-TYPE 
                0                73 
$`OR11H12 MUTATED`
TCGA-AU-3779 TCGA-D5-6535 TCGA-G4-6628 
       14.50        15.12        52.80 

$`OR11H12 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       35.80        26.17        91.79        46.75 

  OR11H12 MUTATED OR11H12 WILD-TYPE 
             14.5               0.0 
  OR11H12 MUTATED OR11H12 WILD-TYPE 
            52.80            140.38 
  OR11H12 MUTATED OR11H12 WILD-TYPE 
           15.120            20.235 
[1] "14.5 - 52.8 (15.1)" "0.0 - 140.4 (20.2)"
[1] "hr="     "9100000"
D1354V2, 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       25       108         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR11H12 MUTATED           0          0          1          0        0
  OR11H12 WILD-TYPE        19         10         40         31       35
                   vv
clus                STAGE IVA STAGE IVB
  OR11H12 MUTATED           0         0
  OR11H12 WILD-TYPE        13         1
D1354V3, multiclass
            clus
vv           OR11H12 MUTATED OR11H12 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                1               108
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  OR11H12 MUTATED     0   1   2   0
  OR11H12 WILD-TYPE   9  67 246  41
D1354V4, multiclass
    clus
vv   OR11H12 MUTATED OR11H12 WILD-TYPE
  T1               0                 9
  T2               1                67
  T3               2               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
  OR11H12 MUTATED     2   1   0
  OR11H12 WILD-TYPE 218  79  66
D1354V5, multiclass
    clus
vv   OR11H12 MUTATED OR11H12 WILD-TYPE
  N0               2               218
  N1               1                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"
D1354V6, binary
                   cls
clus                  0   1
  OR11H12 MUTATED     2   0
  OR11H12 WILD-TYPE 281  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  OR11H12 MUTATED      2    0
  OR11H12 WILD-TYPE  281   48
   clus
vv  OR11H12 MUTATED OR11H12 WILD-TYPE
  0               2               281
  1               0                48
[1] 2 2
[1] FALSE
D1354V7, 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
D1354V8, binary
                   cls
clus                  0   1
  OR11H12 MUTATED     3   0
  OR11H12 WILD-TYPE 314  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  OR11H12 MUTATED      3    0
  OR11H12 WILD-TYPE  314   48
                               clus
vv                              OR11H12 MUTATED OR11H12 WILD-TYPE
  COLON ADENOCARCINOMA                        3               314
  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 255   2  22  20
D1354V9, multiclass
    clus
vv   OR11H12 MUTATED OR11H12 WILD-TYPE
  R0               2               255
  R1               0                 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"
D1354V10, 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
D1354V11, 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(1355) Variable = STYK1 MUTATION ANALYSIS
D1355V1, survival
                 sevent
clus2               0   1
  STYK1 MUTATED     4   3
  STYK1 WILD-TYPE 278  70
  STYK1 MUTATED STYK1 WILD-TYPE 
              7             348 
  STYK1 MUTATED STYK1 WILD-TYPE 
              3              70 
$`STYK1 MUTATED`
TCGA-AA-A01R TCGA-AD-6964 TCGA-AZ-6608 TCGA-D5-6537 TCGA-D5-6538 TCGA-G4-6307 
       35.01        10.88         1.94         4.80        17.13        55.04 
TCGA-G4-6588 
       26.17 

$`STYK1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        52.80 

  STYK1 MUTATED STYK1 WILD-TYPE 
           1.94            0.00 
  STYK1 MUTATED STYK1 WILD-TYPE 
          55.04          140.38 
  STYK1 MUTATED STYK1 WILD-TYPE 
         17.130          20.235 
[1] "1.9 - 55.0 (17.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2.5"
D1355V2, 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       25       108         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        18          9         38         31       35        13
                 vv
clus              STAGE IVB
  STYK1 MUTATED           0
  STYK1 WILD-TYPE         1
D1355V3, multiclass
            clus
vv           STYK1 MUTATED STYK1 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              1             108
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             1               9
  STAGE IIIB             3              38
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  STYK1 MUTATED     0   1   5   1
  STYK1 WILD-TYPE   9  67 243  40
D1355V4, multiclass
    clus
vv   STYK1 MUTATED STYK1 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             5             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
  STYK1 MUTATED     1   3   3
  STYK1 WILD-TYPE 219  77  63
D1355V5, multiclass
    clus
vv   STYK1 MUTATED STYK1 WILD-TYPE
  N0             1             219
  N1             3              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"
D1355V6, binary
                 cls
clus                0   1
  STYK1 MUTATED     5   0
  STYK1 WILD-TYPE 278  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STYK1 MUTATED      5    0
  STYK1 WILD-TYPE  278   48
   clus
vv  STYK1 MUTATED STYK1 WILD-TYPE
  0             5             278
  1             0              48
[1] 2 2
[1] FALSE
D1355V7, 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
D1355V8, binary
                 cls
clus                0   1
  STYK1 MUTATED     6   1
  STYK1 WILD-TYPE 311  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STYK1 MUTATED      6    1
  STYK1 WILD-TYPE  311   47
                               clus
vv                              STYK1 MUTATED STYK1 WILD-TYPE
  COLON ADENOCARCINOMA                      6             311
  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 252   2  22  21
D1355V9, multiclass
    clus
vv   STYK1 MUTATED STYK1 WILD-TYPE
  R0             5             252
  R1             0               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"
D1355V10, 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
D1355V11, 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(1356) Variable = TTC13 MUTATION ANALYSIS
D1356V1, survival
                 sevent
clus2               0   1
  TTC13 MUTATED     6   3
  TTC13 WILD-TYPE 276  70
  TTC13 MUTATED TTC13 WILD-TYPE 
              9             346 
  TTC13 MUTATED TTC13 WILD-TYPE 
              3              70 
$`TTC13 MUTATED`
TCGA-AA-3555 TCGA-AA-3811 TCGA-AA-A00N TCGA-AA-A01R TCGA-AZ-6599 TCGA-CA-5255 
       29.95        10.06         4.01        35.01         6.77         3.06 
TCGA-CK-5913 TCGA-CM-4744 TCGA-G4-6628 
       51.32        20.02        52.80 

$`TTC13 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        17.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41        49.41        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       35.80        26.17        91.79        46.75 

  TTC13 MUTATED TTC13 WILD-TYPE 
           3.06            0.00 
  TTC13 MUTATED TTC13 WILD-TYPE 
          52.80          140.38 
  TTC13 MUTATED TTC13 WILD-TYPE 
         20.020          20.235 
[1] "3.1 - 52.8 (20.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.7"
D1356V2, 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       25       106         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        17         10         41         31       35        13
                 vv
clus              STAGE IVB
  TTC13 MUTATED           0
  TTC13 WILD-TYPE         1
D1356V3, multiclass
            clus
vv           TTC13 MUTATED TTC13 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              3             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TTC13 MUTATED     0   3   5   1
  TTC13 WILD-TYPE   9  65 243  40
D1356V4, multiclass
    clus
vv   TTC13 MUTATED TTC13 WILD-TYPE
  T1             0               9
  T2             3              65
  T3             5             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
  TTC13 MUTATED     7   0   2
  TTC13 WILD-TYPE 213  80  64
D1356V5, multiclass
    clus
vv   TTC13 MUTATED TTC13 WILD-TYPE
  N0             7             213
  N1             0              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"
D1356V6, binary
                 cls
clus                0   1
  TTC13 MUTATED     7   0
  TTC13 WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TTC13 MUTATED      7    0
  TTC13 WILD-TYPE  276   48
   clus
vv  TTC13 MUTATED TTC13 WILD-TYPE
  0             7             276
  1             0              48
[1] 2 2
[1] FALSE
D1356V7, 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
D1356V8, binary
                 cls
clus                0   1
  TTC13 MUTATED     6   3
  TTC13 WILD-TYPE 311  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TTC13 MUTATED      6    3
  TTC13 WILD-TYPE  311   45
                               clus
vv                              TTC13 MUTATED TTC13 WILD-TYPE
  COLON ADENOCARCINOMA                      6             311
  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 251   2  22  19
D1356V9, multiclass
    clus
vv   TTC13 MUTATED TTC13 WILD-TYPE
  R0             6             251
  R1             0               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"
D1356V10, 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
D1356V11, 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(1357) Variable = OR2F2 MUTATION ANALYSIS
D1357V1, survival
                 sevent
clus2               0   1
  OR2F2 MUTATED     5   2
  OR2F2 WILD-TYPE 277  71
  OR2F2 MUTATED OR2F2 WILD-TYPE 
              7             348 
  OR2F2 MUTATED OR2F2 WILD-TYPE 
              2              71 
$`OR2F2 MUTATED`
TCGA-AA-3877 TCGA-AA-3966 TCGA-AZ-6601 TCGA-CA-6717 TCGA-D5-6930 TCGA-DM-A1HA 
       31.00         2.01       100.01         0.33         1.51       131.51 
TCGA-F4-6809 
       13.25 

$`OR2F2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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-A1HB TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 
       16.31        29.59        16.24        33.67         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  OR2F2 MUTATED OR2F2 WILD-TYPE 
           0.33            0.00 
  OR2F2 MUTATED OR2F2 WILD-TYPE 
         131.51          140.38 
  OR2F2 MUTATED OR2F2 WILD-TYPE 
         13.250          20.235 
[1] "0.3 - 131.5 (13.2)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1"  
D1357V2, 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       24       106         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        19         10         41         30       35        12
                 vv
clus              STAGE IVB
  OR2F2 MUTATED           0
  OR2F2 WILD-TYPE         1
D1357V3, multiclass
            clus
vv           OR2F2 MUTATED OR2F2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              3             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  68 242  41
D1357V4, multiclass
    clus
vv   OR2F2 MUTATED OR2F2 WILD-TYPE
  T1             1               8
  T2             0              68
  T3             6             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
  OR2F2 MUTATED     5   1   1
  OR2F2 WILD-TYPE 215  79  65
D1357V5, multiclass
    clus
vv   OR2F2 MUTATED OR2F2 WILD-TYPE
  N0             5             215
  N1             1              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"
D1357V6, binary
                 cls
clus                0   1
  OR2F2 MUTATED     6   1
  OR2F2 WILD-TYPE 277  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2F2 MUTATED      6    1
  OR2F2 WILD-TYPE  277   47
   clus
vv  OR2F2 MUTATED OR2F2 WILD-TYPE
  0             6             277
  1             1              47
[1] 2 2
[1] FALSE
D1357V7, 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
D1357V8, binary
                 cls
clus                0   1
  OR2F2 MUTATED     3   4
  OR2F2 WILD-TYPE 314  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2F2 MUTATED      3    4
  OR2F2 WILD-TYPE  314   44
                               clus
vv                              OR2F2 MUTATED OR2F2 WILD-TYPE
  COLON ADENOCARCINOMA                      3             314
  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 254   2  22  20
D1357V9, multiclass
    clus
vv   OR2F2 MUTATED OR2F2 WILD-TYPE
  R0             3             254
  R1             0               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"
D1357V10, 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
D1357V11, 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(1358) Variable = GCC2 MUTATION ANALYSIS
D1358V1, survival
                sevent
clus2              0   1
  GCC2 MUTATED    10   0
  GCC2 WILD-TYPE 272  73
  GCC2 MUTATED GCC2 WILD-TYPE 
            10            345 
  GCC2 MUTATED GCC2 WILD-TYPE 
             0             73 
$`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         0.07 
TCGA-AY-6196 TCGA-CA-6717 TCGA-CM-6674 TCGA-F4-6569 
        0.20         0.33        12.95        13.45 

$`GCC2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 
       35.05        33.04         0.99        25.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        15.75        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 
       60.79       117.07        98.24         8.61        13.38         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  GCC2 MUTATED GCC2 WILD-TYPE 
          0.07           0.00 
  GCC2 MUTATED GCC2 WILD-TYPE 
         34.98         140.38 
  GCC2 MUTATED GCC2 WILD-TYPE 
         6.985         20.980 
[1] "0.1 - 35.0 (7.0)"   "0.0 - 140.4 (21.0)"
[1] "hr="     "9100000"
D1358V2, 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       24       107         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        19         10         41         30       34        13
                vv
clus             STAGE IVB
  GCC2 MUTATED           0
  GCC2 WILD-TYPE         1
D1358V3, multiclass
            clus
vv           GCC2 MUTATED GCC2 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             2            107
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            1             30
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GCC2 MUTATED     0   4   5   1
  GCC2 WILD-TYPE   9  64 243  40
D1358V4, multiclass
    clus
vv   GCC2 MUTATED GCC2 WILD-TYPE
  T1            0              9
  T2            4             64
  T3            5            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
  GCC2 MUTATED     9   0   1
  GCC2 WILD-TYPE 211  80  65
D1358V5, multiclass
    clus
vv   GCC2 MUTATED GCC2 WILD-TYPE
  N0            9            211
  N1            0             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"
D1358V6, binary
                cls
clus               0   1
  GCC2 MUTATED     6   1
  GCC2 WILD-TYPE 277  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  GCC2 MUTATED      6    1
  GCC2 WILD-TYPE  277   47
   clus
vv  GCC2 MUTATED GCC2 WILD-TYPE
  0            6            277
  1            1             47
[1] 2 2
[1] FALSE
D1358V7, 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
D1358V8, binary
                cls
clus               0   1
  GCC2 MUTATED     6   4
  GCC2 WILD-TYPE 311  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  GCC2 MUTATED      6    4
  GCC2 WILD-TYPE  311   44
                               clus
vv                              GCC2 MUTATED GCC2 WILD-TYPE
  COLON ADENOCARCINOMA                     6            311
  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 250   2  21  20
D1358V9, multiclass
    clus
vv   GCC2 MUTATED GCC2 WILD-TYPE
  R0            7            250
  R1            0              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"
D1358V10, 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
D1358V11, 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(1359) Variable = ZMIZ1 MUTATION ANALYSIS
D1359V1, survival
                 sevent
clus2               0   1
  ZMIZ1 MUTATED     8   1
  ZMIZ1 WILD-TYPE 274  72
  ZMIZ1 MUTATED ZMIZ1 WILD-TYPE 
              9             346 
  ZMIZ1 MUTATED ZMIZ1 WILD-TYPE 
              1              72 
$`ZMIZ1 MUTATED`
TCGA-A6-2676 TCGA-AA-3663 TCGA-AA-3977 TCGA-AY-6386 TCGA-D5-6533 TCGA-D5-6928 
       42.90         6.97        25.02        17.82         1.32        11.64 
TCGA-DM-A1HB TCGA-G4-6317 TCGA-G4-6586 
      135.65        36.00        35.80 

$`ZMIZ1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 
       55.04        51.75        45.11        36.72        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  ZMIZ1 MUTATED ZMIZ1 WILD-TYPE 
           1.32            0.00 
  ZMIZ1 MUTATED ZMIZ1 WILD-TYPE 
         135.65          140.38 
  ZMIZ1 MUTATED ZMIZ1 WILD-TYPE 
         25.020          20.155 
[1] "1.3 - 135.7 (25.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "2.2"
D1359V2, 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       24       107         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ZMIZ1 MUTATED           0          0          3          1        0         0
  ZMIZ1 WILD-TYPE        19         10         38         30       35        13
                 vv
clus              STAGE IVB
  ZMIZ1 MUTATED           0
  ZMIZ1 WILD-TYPE         1
D1359V3, multiclass
            clus
vv           ZMIZ1 MUTATED ZMIZ1 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              2             107
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             3              38
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ZMIZ1 MUTATED     0   1   6   2
  ZMIZ1 WILD-TYPE   9  67 242  39
D1359V4, multiclass
    clus
vv   ZMIZ1 MUTATED ZMIZ1 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             6             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
  ZMIZ1 MUTATED     6   2   1
  ZMIZ1 WILD-TYPE 214  78  65
D1359V5, multiclass
    clus
vv   ZMIZ1 MUTATED ZMIZ1 WILD-TYPE
  N0             6             214
  N1             2              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"
D1359V6, binary
                 cls
clus                0   1
  ZMIZ1 MUTATED     7   0
  ZMIZ1 WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMIZ1 MUTATED      7    0
  ZMIZ1 WILD-TYPE  276   48
   clus
vv  ZMIZ1 MUTATED ZMIZ1 WILD-TYPE
  0             7             276
  1             0              48
[1] 2 2
[1] FALSE
D1359V7, 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
D1359V8, binary
                 cls
clus                0   1
  ZMIZ1 MUTATED     8   1
  ZMIZ1 WILD-TYPE 309  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMIZ1 MUTATED      8    1
  ZMIZ1 WILD-TYPE  309   47
                               clus
vv                              ZMIZ1 MUTATED ZMIZ1 WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  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 250   2  22  21
D1359V9, multiclass
    clus
vv   ZMIZ1 MUTATED ZMIZ1 WILD-TYPE
  R0             7             250
  R1             0               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"
D1359V10, 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
D1359V11, 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(1360) Variable = CCDC19 MUTATION ANALYSIS
D1360V1, survival
                  sevent
clus2                0   1
  CCDC19 MUTATED    12   2
  CCDC19 WILD-TYPE 270  71
  CCDC19 MUTATED CCDC19 WILD-TYPE 
              14              341 
  CCDC19 MUTATED CCDC19 WILD-TYPE 
               2               71 
$`CCDC19 MUTATED`
TCGA-A6-6141 TCGA-A6-6781 TCGA-AA-A00E TCGA-AA-A010 TCGA-AA-A01F TCGA-AZ-4315 
        8.38        19.66        30.02        34.98        32.02        58.39 
TCGA-AZ-6598 TCGA-CA-6717 TCGA-CA-6718 TCGA-D5-6928 TCGA-D5-7000 TCGA-DM-A1HB 
       49.41         0.33         0.10        11.64        10.26       135.65 
TCGA-G4-6303 TCGA-G4-6628 
       65.85        52.80 

$`CCDC19 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-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        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07         0.26         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 
       35.41        19.43       107.67        74.56        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       13.78        35.80        26.17        91.79        46.75 

  CCDC19 MUTATED CCDC19 WILD-TYPE 
             0.1              0.0 
  CCDC19 MUTATED CCDC19 WILD-TYPE 
          135.65           140.38 
  CCDC19 MUTATED CCDC19 WILD-TYPE 
           31.02            20.12 
[1] "0.1 - 135.7 (31.0)" "0.0 - 140.4 (20.1)"
[1] "hr=" "2"  
D1360V2, 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       24       102         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC19 MUTATED           0          0          2          1        1
  CCDC19 WILD-TYPE        19         10         39         30       34
                  vv
clus               STAGE IVA STAGE IVB
  CCDC19 MUTATED           0         0
  CCDC19 WILD-TYPE        13         1
D1360V3, multiclass
            clus
vv           CCDC19 MUTATED CCDC19 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               7              102
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              1               30
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CCDC19 MUTATED     0   2  11   2
  CCDC19 WILD-TYPE   9  66 237  39
D1360V4, multiclass
    clus
vv   CCDC19 MUTATED CCDC19 WILD-TYPE
  T1              0                9
  T2              2               66
  T3             11              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
  CCDC19 MUTATED    11   4   0
  CCDC19 WILD-TYPE 209  76  66
D1360V5, multiclass
    clus
vv   CCDC19 MUTATED CCDC19 WILD-TYPE
  N0             11              209
  N1              4               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"
D1360V6, binary
                  cls
clus                 0   1
  CCDC19 MUTATED    12   1
  CCDC19 WILD-TYPE 271  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC19 MUTATED     12    1
  CCDC19 WILD-TYPE  271   47
   clus
vv  CCDC19 MUTATED CCDC19 WILD-TYPE
  0             12              271
  1              1               47
[1] 2 2
[1] FALSE
D1360V7, 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
D1360V8, binary
                  cls
clus                 0   1
  CCDC19 MUTATED    11   4
  CCDC19 WILD-TYPE 306  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC19 MUTATED     11    4
  CCDC19 WILD-TYPE  306   44
                               clus
vv                              CCDC19 MUTATED CCDC19 WILD-TYPE
  COLON ADENOCARCINOMA                      11              306
  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 247   2  22  19
D1360V9, multiclass
    clus
vv   CCDC19 MUTATED CCDC19 WILD-TYPE
  R0             10              247
  R1              0                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"
D1360V10, 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
D1360V11, 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(1361) Variable = AGFG2 MUTATION ANALYSIS
D1361V1, survival
                 sevent
clus2               0   1
  AGFG2 MUTATED     6   3
  AGFG2 WILD-TYPE 276  70
  AGFG2 MUTATED AGFG2 WILD-TYPE 
              9             346 
  AGFG2 MUTATED AGFG2 WILD-TYPE 
              3              70 
$`AGFG2 MUTATED`
TCGA-AA-3492 TCGA-AA-3518 TCGA-AA-3663 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3947 
        3.02         1.02         6.97        19.04        19.04        33.01 
TCGA-AZ-6601 TCGA-CA-6717 TCGA-G4-6586 
      100.01         0.33        35.80 

$`AGFG2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       85.05        26.99        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 
       18.05        31.00         2.01        12.99        24.00        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  AGFG2 MUTATED AGFG2 WILD-TYPE 
           0.33            0.00 
  AGFG2 MUTATED AGFG2 WILD-TYPE 
         100.01          140.38 
  AGFG2 MUTATED AGFG2 WILD-TYPE 
          19.04           20.63 
[1] "0.3 - 100.0 (19.0)" "0.0 - 140.4 (20.6)"
[1] "hr=" "1.8"
D1361V2, 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       21       106         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        19         10         41         31       34        13
                 vv
clus              STAGE IVB
  AGFG2 MUTATED           0
  AGFG2 WILD-TYPE         1
D1361V3, multiclass
            clus
vv           AGFG2 MUTATED AGFG2 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               4              21
  STAGE IIA              3             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  AGFG2 MUTATED     0   0   8   1
  AGFG2 WILD-TYPE   9  68 240  40
D1361V4, multiclass
    clus
vv   AGFG2 MUTATED AGFG2 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             8             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
  AGFG2 MUTATED     9   0   0
  AGFG2 WILD-TYPE 211  80  66
D1361V5, multiclass
    clus
vv   AGFG2 MUTATED AGFG2 WILD-TYPE
  N0             9             211
  N1             0              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"
D1361V6, binary
                 cls
clus                0   1
  AGFG2 MUTATED     8   1
  AGFG2 WILD-TYPE 275  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGFG2 MUTATED      8    1
  AGFG2 WILD-TYPE  275   47
   clus
vv  AGFG2 MUTATED AGFG2 WILD-TYPE
  0             8             275
  1             1              47
[1] 2 2
[1] FALSE
D1361V7, 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
D1361V8, binary
                 cls
clus                0   1
  AGFG2 MUTATED     7   2
  AGFG2 WILD-TYPE 310  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGFG2 MUTATED      7    2
  AGFG2 WILD-TYPE  310   46
                               clus
vv                              AGFG2 MUTATED AGFG2 WILD-TYPE
  COLON ADENOCARCINOMA                      7             310
  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 251   2  21  20
D1361V9, multiclass
    clus
vv   AGFG2 MUTATED AGFG2 WILD-TYPE
  R0             6             251
  R1             0               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"
D1361V10, 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
D1361V11, 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(1362) Variable = BATF3 MUTATION ANALYSIS
D1362V1, survival
                 sevent
clus2               0   1
  BATF3 MUTATED     2   1
  BATF3 WILD-TYPE 280  72
  BATF3 MUTATED BATF3 WILD-TYPE 
              3             352 
  BATF3 MUTATED BATF3 WILD-TYPE 
              1              72 
$`BATF3 MUTATED`
TCGA-AA-3818 TCGA-AZ-4315 TCGA-CM-4743 
        0.99        58.39        23.05 

$`BATF3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3819 TCGA-AA-3821 
       19.04        10.06        35.05        33.04        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14         2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  BATF3 MUTATED BATF3 WILD-TYPE 
           0.99            0.00 
  BATF3 MUTATED BATF3 WILD-TYPE 
          58.39          140.38 
  BATF3 MUTATED BATF3 WILD-TYPE 
         23.050          20.155 
[1] "1.0 - 58.4 (23.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.5"
D1362V2, 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       25       106         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        19         10         41         31       35        13
                 vv
clus              STAGE IVB
  BATF3 MUTATED           0
  BATF3 WILD-TYPE         1
D1362V3, multiclass
            clus
vv           BATF3 MUTATED BATF3 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              3             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  BATF3 MUTATED     0   0   3   1
  BATF3 WILD-TYPE   9  68 245  40
D1362V4, multiclass
    clus
vv   BATF3 MUTATED BATF3 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             3             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
  BATF3 MUTATED     4   0   0
  BATF3 WILD-TYPE 216  80  66
D1362V5, multiclass
    clus
vv   BATF3 MUTATED BATF3 WILD-TYPE
  N0             4             216
  N1             0              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"
D1362V6, binary
                 cls
clus                0   1
  BATF3 MUTATED     3   0
  BATF3 WILD-TYPE 280  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BATF3 MUTATED      3    0
  BATF3 WILD-TYPE  280   48
   clus
vv  BATF3 MUTATED BATF3 WILD-TYPE
  0             3             280
  1             0              48
[1] 2 2
[1] FALSE
D1362V7, 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
D1362V8, binary
                 cls
clus                0   1
  BATF3 MUTATED     4   0
  BATF3 WILD-TYPE 313  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BATF3 MUTATED      4    0
  BATF3 WILD-TYPE  313   48
                               clus
vv                              BATF3 MUTATED BATF3 WILD-TYPE
  COLON ADENOCARCINOMA                      4             313
  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 254   2  22  20
D1362V9, multiclass
    clus
vv   BATF3 MUTATED BATF3 WILD-TYPE
  R0             3             254
  R1             0               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"
D1362V10, continuous
[1] "Remove cluster labels:" "BATF3 MUTATED"         
clus
  BATF3 MUTATED BATF3 WILD-TYPE 
              2             343 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-4105 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-A6-5656      TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5660 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-A6-5661      TCGA-A6-5662      TCGA-A6-5664      TCGA-A6-5665 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-A6-5666      TCGA-A6-6137      TCGA-A6-6138      TCGA-A6-6141 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-A6-6142      TCGA-A6-6648      TCGA-A6-6649      TCGA-A6-6651 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-A6-6652      TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-A6-6781      TCGA-A6-6782      TCGA-AA-3489      TCGA-AA-3492 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3496      TCGA-AA-3502      TCGA-AA-3510      TCGA-AA-3511 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3514      TCGA-AA-3516      TCGA-AA-3517      TCGA-AA-3518 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3519      TCGA-AA-3520      TCGA-AA-3521      TCGA-AA-3522 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3524      TCGA-AA-3525      TCGA-AA-3526      TCGA-AA-3527 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3529      TCGA-AA-3530      TCGA-AA-3531      TCGA-AA-3532 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3534      TCGA-AA-3538      TCGA-AA-3542      TCGA-AA-3543 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3544      TCGA-AA-3548      TCGA-AA-3549      TCGA-AA-3552 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3553      TCGA-AA-3554      TCGA-AA-3555      TCGA-AA-3556 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3558      TCGA-AA-3560      TCGA-AA-3562      TCGA-AA-3655 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3660      TCGA-AA-3662      TCGA-AA-3663      TCGA-AA-3664 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3666      TCGA-AA-3667      TCGA-AA-3672      TCGA-AA-3673 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3678      TCGA-AA-3679      TCGA-AA-3680      TCGA-AA-3681 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3684      TCGA-AA-3685      TCGA-AA-3688      TCGA-AA-3692 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3693      TCGA-AA-3695      TCGA-AA-3696      TCGA-AA-3697 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3710      TCGA-AA-3712      TCGA-AA-3713      TCGA-AA-3715 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3811      TCGA-AA-3812      TCGA-AA-3814      TCGA-AA-3815 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3819      TCGA-AA-3821      TCGA-AA-3831      TCGA-AA-3833 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3837      TCGA-AA-3842      TCGA-AA-3844      TCGA-AA-3845 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3846      TCGA-AA-3848      TCGA-AA-3850      TCGA-AA-3851 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3852      TCGA-AA-3854      TCGA-AA-3855      TCGA-AA-3856 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3858      TCGA-AA-3860      TCGA-AA-3861      TCGA-AA-3864 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3866      TCGA-AA-3867      TCGA-AA-3869      TCGA-AA-3870 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3872      TCGA-AA-3875      TCGA-AA-3877      TCGA-AA-3930 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3939      TCGA-AA-3941      TCGA-AA-3947      TCGA-AA-3949 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3950      TCGA-AA-3952      TCGA-AA-3955      TCGA-AA-3956 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3966      TCGA-AA-3968      TCGA-AA-3971      TCGA-AA-3972 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3973      TCGA-AA-3975      TCGA-AA-3976      TCGA-AA-3977 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3979      TCGA-AA-3980      TCGA-AA-3982      TCGA-AA-3984 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3986      TCGA-AA-3989      TCGA-AA-3994      TCGA-AA-A004 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-A00A      TCGA-AA-A00D      TCGA-AA-A00E      TCGA-AA-A00F 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-A00J      TCGA-AA-A00K      TCGA-AA-A00L      TCGA-AA-A00N 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-A00O      TCGA-AA-A00Q      TCGA-AA-A00R      TCGA-AA-A00U 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-A00W      TCGA-AA-A00Z      TCGA-AA-A010      TCGA-AA-A017 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-A01D      TCGA-AA-A01F      TCGA-AA-A01G      TCGA-AA-A01I 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-A01K      TCGA-AA-A01P      TCGA-AA-A01Q      TCGA-AA-A01R 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-A01S      TCGA-AA-A01T      TCGA-AA-A01V      TCGA-AA-A01X 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-A01Z      TCGA-AA-A022      TCGA-AA-A024      TCGA-AA-A029 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-A02F      TCGA-AA-A02H      TCGA-AA-A02J      TCGA-AA-A02K 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-A02O      TCGA-AA-A02W      TCGA-AA-A02Y      TCGA-AA-A03F 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-A03J      TCGA-AD-5900      TCGA-AD-6548      TCGA-AD-6888 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AD-6889      TCGA-AD-6890      TCGA-AD-6895      TCGA-AD-6899 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6964      TCGA-AD-6965 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070      TCGA-AY-4071 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197      TCGA-AY-6386 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AZ-4323      TCGA-AZ-4616      TCGA-AZ-4682      TCGA-AZ-5403 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AZ-5407      TCGA-AZ-6598      TCGA-AZ-6599      TCGA-AZ-6600 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AZ-6601      TCGA-AZ-6603      TCGA-AZ-6605      TCGA-AZ-6606 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AZ-6607      TCGA-AZ-6608      TCGA-CK-4947      TCGA-CK-4948 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-CK-4950      TCGA-CK-4952      TCGA-CM-4744      TCGA-CM-4746 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-CM-4747      TCGA-CM-4752      TCGA-CM-5341      TCGA-CM-5344 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-CM-5348      TCGA-CM-5349      TCGA-CM-5860      TCGA-CM-5861 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-CM-5862      TCGA-CM-5863      TCGA-CM-5864      TCGA-CM-5868 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-CM-6161      TCGA-CM-6162      TCGA-CM-6163      TCGA-CM-6164 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-CM-6165      TCGA-CM-6166      TCGA-CM-6167      TCGA-CM-6168 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-CM-6169      TCGA-CM-6170      TCGA-CM-6171      TCGA-CM-6172 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-CM-6674      TCGA-CM-6675      TCGA-CM-6676      TCGA-CM-6677 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-CM-6678      TCGA-CM-6679      TCGA-CM-6680      TCGA-D5-5537 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-D5-5538      TCGA-D5-5539      TCGA-D5-5540      TCGA-D5-5541 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-D5-6529      TCGA-D5-6532      TCGA-D5-6533      TCGA-D5-6534 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-D5-6535      TCGA-D5-6536      TCGA-D5-6537      TCGA-D5-6538 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-D5-6539      TCGA-D5-6540      TCGA-D5-6541      TCGA-D5-6898 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923      TCGA-D5-6924 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-D5-6926      TCGA-D5-6927      TCGA-D5-6928      TCGA-D5-6929 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-D5-6930      TCGA-D5-6931      TCGA-D5-6932      TCGA-D5-7000 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-DM-A0X9      TCGA-DM-A0XD      TCGA-DM-A0XF      TCGA-DM-A1D0 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-DM-A1D4      TCGA-DM-A1D6      TCGA-DM-A1D7      TCGA-DM-A1D8 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-DM-A1D9      TCGA-DM-A1DA      TCGA-DM-A1DB      TCGA-DM-A1HA 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-DM-A1HB      TCGA-DM-A282      TCGA-DM-A285      TCGA-DM-A28C 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-DM-A28E      TCGA-DM-A28F      TCGA-DM-A28G      TCGA-DM-A28H 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-DM-A28K      TCGA-F4-6459      TCGA-F4-6460      TCGA-F4-6569 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704      TCGA-F4-6806 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-F4-6807      TCGA-F4-6808      TCGA-F4-6809      TCGA-F4-6854 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-F4-6855      TCGA-F4-6856      TCGA-G4-6293      TCGA-G4-6299 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-G4-6303      TCGA-G4-6304      TCGA-G4-6306      TCGA-G4-6307 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-G4-6309      TCGA-G4-6310      TCGA-G4-6315      TCGA-G4-6317 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-G4-6321      TCGA-G4-6323      TCGA-G4-6586      TCGA-G4-6588 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-G4-6625      TCGA-G4-6626      TCGA-G4-6628 
"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
D1362V11, 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(1363) Variable = ZNF124 MUTATION ANALYSIS
D1363V1, survival
                  sevent
clus2                0   1
  ZNF124 MUTATED     7   1
  ZNF124 WILD-TYPE 275  72
  ZNF124 MUTATED ZNF124 WILD-TYPE 
               8              347 
  ZNF124 MUTATED ZNF124 WILD-TYPE 
               1               72 
$`ZNF124 MUTATED`
TCGA-A6-3809 TCGA-A6-5665 TCGA-AA-A00N TCGA-AD-6889 TCGA-AU-6004 TCGA-AZ-4315 
       32.75        22.06         4.01        56.55        27.09        58.39 
TCGA-CA-6717 TCGA-CM-4743 
        0.33        23.05 

$`ZNF124 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37         4.21         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  ZNF124 MUTATED ZNF124 WILD-TYPE 
            0.33             0.00 
  ZNF124 MUTATED ZNF124 WILD-TYPE 
           58.39           140.38 
  ZNF124 MUTATED ZNF124 WILD-TYPE 
           25.07            20.02 
[1] "0.3 - 58.4 (25.1)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1.8"
D1363V2, 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       25       104         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF124 MUTATED           0          0          0          0        0
  ZNF124 WILD-TYPE        19         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF124 MUTATED           0         0
  ZNF124 WILD-TYPE        13         1
D1363V3, multiclass
            clus
vv           ZNF124 MUTATED ZNF124 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               5              104
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF124 MUTATED     0   1   5   2
  ZNF124 WILD-TYPE   9  67 243  39
D1363V4, multiclass
    clus
vv   ZNF124 MUTATED ZNF124 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              5              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
  ZNF124 MUTATED     8   0   0
  ZNF124 WILD-TYPE 212  80  66
D1363V5, multiclass
    clus
vv   ZNF124 MUTATED ZNF124 WILD-TYPE
  N0              8              212
  N1              0               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"
D1363V6, binary
                  cls
clus                 0   1
  ZNF124 MUTATED     8   0
  ZNF124 WILD-TYPE 275  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF124 MUTATED      8    0
  ZNF124 WILD-TYPE  275   48
   clus
vv  ZNF124 MUTATED ZNF124 WILD-TYPE
  0              8              275
  1              0               48
[1] 2 2
[1] FALSE
D1363V7, 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
D1363V8, binary
                  cls
clus                 0   1
  ZNF124 MUTATED     5   3
  ZNF124 WILD-TYPE 312  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF124 MUTATED      5    3
  ZNF124 WILD-TYPE  312   45
                               clus
vv                              ZNF124 MUTATED ZNF124 WILD-TYPE
  COLON ADENOCARCINOMA                       5              312
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF124 MUTATED     6   0   0   1
  ZNF124 WILD-TYPE 251   2  22  20
D1363V9, multiclass
    clus
vv   ZNF124 MUTATED ZNF124 WILD-TYPE
  R0              6              251
  R1              0                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"
D1363V10, 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
D1363V11, 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(1364) Variable = TBCA MUTATION ANALYSIS
D1364V1, survival
                sevent
clus2              0   1
  TBCA MUTATED     4   0
  TBCA WILD-TYPE 278  73
  TBCA MUTATED TBCA WILD-TYPE 
             4            351 
  TBCA MUTATED TBCA WILD-TYPE 
             0             73 
$`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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       15.75        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  TBCA MUTATED TBCA WILD-TYPE 
           0.2            0.0 
  TBCA MUTATED TBCA WILD-TYPE 
         34.98         140.38 
  TBCA MUTATED TBCA WILD-TYPE 
        31.545         20.120 
[1] "0.2 - 35.0 (31.5)"  "0.0 - 140.4 (20.1)"
[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       25       108         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        19         10         41         30       35        13
                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             25
  STAGE IIA             1            108
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            1             30
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TBCA MUTATED     0   0   2   2
  TBCA WILD-TYPE   9  68 246  39
D1364V4, multiclass
    clus
vv   TBCA MUTATED TBCA WILD-TYPE
  T1            0              9
  T2            0             68
  T3            2            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
  TBCA MUTATED     3   0   1
  TBCA WILD-TYPE 217  80  65
D1364V5, multiclass
    clus
vv   TBCA MUTATED TBCA WILD-TYPE
  N0            3            217
  N1            0             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"
D1364V6, binary
                cls
clus               0   1
  TBCA MUTATED     3   0
  TBCA WILD-TYPE 280  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  TBCA MUTATED      3    0
  TBCA WILD-TYPE  280   48
   clus
vv  TBCA MUTATED TBCA WILD-TYPE
  0            3            280
  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     2   2
  TBCA WILD-TYPE 315  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  TBCA MUTATED      2    2
  TBCA WILD-TYPE  315   46
                               clus
vv                              TBCA MUTATED TBCA WILD-TYPE
  COLON ADENOCARCINOMA                     2            315
  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 253   2  22  21
D1364V9, multiclass
    clus
vv   TBCA MUTATED TBCA WILD-TYPE
  R0            4            253
  R1            0              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"
D1364V10, 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
D1364V11, multiclass
[1] "Remove cluster labels:" "TBCA MUTATED"          
clus
  TBCA MUTATED TBCA WILD-TYPE 
             2            204 
    TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810     TCGA-A6-4105 
"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-A6-6649     TCGA-A6-6651 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-A6-6652     TCGA-A6-6653     TCGA-A6-6654     TCGA-A6-6780 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-A6-6781     TCGA-A6-6782     TCGA-AD-5900     TCGA-AD-6548 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-AD-6888     TCGA-AD-6889     TCGA-AD-6890     TCGA-AD-6895 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-AD-6899     TCGA-AD-6901     TCGA-AD-6963     TCGA-AD-6964 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-AD-6965     TCGA-AU-3779     TCGA-AU-6004     TCGA-AY-4070 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-AY-4071     TCGA-AY-5543     TCGA-AY-6197     TCGA-AY-6386 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-AZ-4315     TCGA-AZ-4323     TCGA-AZ-4616     TCGA-AZ-4681 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-AZ-4682     TCGA-AZ-5403     TCGA-AZ-5407     TCGA-AZ-6598 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-AZ-6599     TCGA-AZ-6600     TCGA-AZ-6601     TCGA-AZ-6603 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-AZ-6605     TCGA-AZ-6606     TCGA-AZ-6607     TCGA-AZ-6608 
"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-5912     TCGA-CK-5913     TCGA-CK-5914 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-CK-5915     TCGA-CK-5916     TCGA-CK-6746     TCGA-CK-6747 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-CK-6748     TCGA-CK-6751     TCGA-CM-4743     TCGA-CM-4744 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-CM-4746     TCGA-CM-4747     TCGA-CM-4752     TCGA-CM-5341 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-CM-5344     TCGA-CM-5348     TCGA-CM-5860     TCGA-CM-5861 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-CM-5862     TCGA-CM-5863     TCGA-CM-5864     TCGA-CM-5868 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-CM-6161     TCGA-CM-6162     TCGA-CM-6163     TCGA-CM-6164 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-CM-6165     TCGA-CM-6166     TCGA-CM-6167     TCGA-CM-6168 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-CM-6169     TCGA-CM-6170     TCGA-CM-6171     TCGA-CM-6172 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-CM-6674     TCGA-CM-6675     TCGA-CM-6676     TCGA-CM-6677 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-CM-6678     TCGA-CM-6679     TCGA-CM-6680     TCGA-D5-5537 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-D5-5538     TCGA-D5-5539     TCGA-D5-5540     TCGA-D5-5541 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-D5-6529     TCGA-D5-6532     TCGA-D5-6533     TCGA-D5-6534 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-D5-6535     TCGA-D5-6536     TCGA-D5-6537     TCGA-D5-6538 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-D5-6539     TCGA-D5-6540     TCGA-D5-6541     TCGA-D5-6898 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-D5-6920     TCGA-D5-6922     TCGA-D5-6923     TCGA-D5-6924 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-D5-6926     TCGA-D5-6927     TCGA-D5-6928     TCGA-D5-6929 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-D5-6930     TCGA-D5-6931     TCGA-D5-6932     TCGA-D5-7000 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-DM-A0X9     TCGA-DM-A0XD     TCGA-DM-A0XF     TCGA-DM-A1D0 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-DM-A1D4     TCGA-DM-A1D6     TCGA-DM-A1D7     TCGA-DM-A1D8 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-DM-A1D9     TCGA-DM-A1DA     TCGA-DM-A1DB     TCGA-DM-A1HA 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-DM-A1HB     TCGA-DM-A282     TCGA-DM-A285     TCGA-DM-A28C 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-DM-A28E     TCGA-DM-A28F     TCGA-DM-A28G     TCGA-DM-A28H 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-DM-A28K     TCGA-F4-6459     TCGA-F4-6460     TCGA-F4-6569 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-F4-6570     TCGA-F4-6703     TCGA-F4-6704     TCGA-F4-6805 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-F4-6806     TCGA-F4-6807     TCGA-F4-6808     TCGA-F4-6809 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-F4-6854     TCGA-F4-6855     TCGA-F4-6856     TCGA-G4-6293 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-G4-6299     TCGA-G4-6303     TCGA-G4-6304     TCGA-G4-6306 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-G4-6307     TCGA-G4-6309     TCGA-G4-6310     TCGA-G4-6315 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-G4-6317     TCGA-G4-6321     TCGA-G4-6323     TCGA-G4-6586 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 
    TCGA-G4-6588     TCGA-G4-6625     TCGA-G4-6626     TCGA-G4-6628 
"TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" "TBCA WILD-TYPE" 

Clustering(1365) Variable = LRRC6 MUTATION ANALYSIS
D1365V1, survival
                 sevent
clus2               0   1
  LRRC6 MUTATED     2   1
  LRRC6 WILD-TYPE 280  72
  LRRC6 MUTATED LRRC6 WILD-TYPE 
              3             352 
  LRRC6 MUTATED LRRC6 WILD-TYPE 
              1              72 
$`LRRC6 MUTATED`
TCGA-A6-6142 TCGA-AZ-6607 TCGA-F4-6808 
       25.08         3.19        33.67 

$`LRRC6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       16.24        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  LRRC6 MUTATED LRRC6 WILD-TYPE 
           3.19            0.00 
  LRRC6 MUTATED LRRC6 WILD-TYPE 
          33.67          140.38 
  LRRC6 MUTATED LRRC6 WILD-TYPE 
         25.080          20.155 
[1] "3.2 - 33.7 (25.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2.2"
D1365V2, 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       25       109         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        19         10         41         31       34        12
                 vv
clus              STAGE IVB
  LRRC6 MUTATED           0
  LRRC6 WILD-TYPE         1
D1365V3, multiclass
            clus
vv           LRRC6 MUTATED LRRC6 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              0             109
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  68 247  40
D1365V4, multiclass
    clus
vv   LRRC6 MUTATED LRRC6 WILD-TYPE
  T1             1               8
  T2             0              68
  T3             1             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
  LRRC6 MUTATED     1   1   1
  LRRC6 WILD-TYPE 219  79  65
D1365V5, multiclass
    clus
vv   LRRC6 MUTATED LRRC6 WILD-TYPE
  N0             1             219
  N1             1              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"
D1365V6, binary
                 cls
clus                0   1
  LRRC6 MUTATED     1   2
  LRRC6 WILD-TYPE 282  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRRC6 MUTATED      1    2
  LRRC6 WILD-TYPE  282   46
   clus
vv  LRRC6 MUTATED LRRC6 WILD-TYPE
  0             1             282
  1             2              46
[1] 2 2
[1] FALSE
D1365V7, 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
D1365V8, binary
                 cls
clus                0   1
  LRRC6 MUTATED     3   0
  LRRC6 WILD-TYPE 314  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRRC6 MUTATED      3    0
  LRRC6 WILD-TYPE  314   48
                               clus
vv                              LRRC6 MUTATED LRRC6 WILD-TYPE
  COLON ADENOCARCINOMA                      3             314
  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 256   2  22  21
D1365V9, multiclass
[1] "Remove cluster labels:" "LRRC6 MUTATED"         
clus
  LRRC6 MUTATED LRRC6 WILD-TYPE 
              1             301 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-5657 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-A6-5659      TCGA-A6-5661      TCGA-A6-5665      TCGA-A6-6781 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3489      TCGA-AA-3492      TCGA-AA-3496      TCGA-AA-3502 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3510      TCGA-AA-3511      TCGA-AA-3514      TCGA-AA-3517 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3518      TCGA-AA-3519      TCGA-AA-3520      TCGA-AA-3521 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3522      TCGA-AA-3524      TCGA-AA-3525      TCGA-AA-3526 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3527      TCGA-AA-3529      TCGA-AA-3530      TCGA-AA-3531 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3532      TCGA-AA-3534      TCGA-AA-3538      TCGA-AA-3542 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3543      TCGA-AA-3544      TCGA-AA-3548      TCGA-AA-3549 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3552      TCGA-AA-3553      TCGA-AA-3554      TCGA-AA-3555 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3556      TCGA-AA-3558      TCGA-AA-3560      TCGA-AA-3561 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3562      TCGA-AA-3655      TCGA-AA-3660      TCGA-AA-3662 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3663      TCGA-AA-3664      TCGA-AA-3666      TCGA-AA-3667 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3672      TCGA-AA-3673      TCGA-AA-3678      TCGA-AA-3679 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3680      TCGA-AA-3681      TCGA-AA-3684      TCGA-AA-3685 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3688      TCGA-AA-3692      TCGA-AA-3693      TCGA-AA-3695 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3696      TCGA-AA-3697      TCGA-AA-3710      TCGA-AA-3712 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3713      TCGA-AA-3715      TCGA-AA-3811      TCGA-AA-3812 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3814      TCGA-AA-3815      TCGA-AA-3818      TCGA-AA-3819 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3821      TCGA-AA-3831      TCGA-AA-3833      TCGA-AA-3837 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3842      TCGA-AA-3844      TCGA-AA-3845      TCGA-AA-3846 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3848      TCGA-AA-3850      TCGA-AA-3851      TCGA-AA-3852 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3854      TCGA-AA-3855      TCGA-AA-3856      TCGA-AA-3858 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3860      TCGA-AA-3861      TCGA-AA-3864      TCGA-AA-3866 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3867      TCGA-AA-3869      TCGA-AA-3870      TCGA-AA-3872 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3875      TCGA-AA-3877      TCGA-AA-3930      TCGA-AA-3939 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3941      TCGA-AA-3947      TCGA-AA-3949      TCGA-AA-3950 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3952      TCGA-AA-3955      TCGA-AA-3956      TCGA-AA-3968 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3971      TCGA-AA-3972      TCGA-AA-3973      TCGA-AA-3975 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3976      TCGA-AA-3979      TCGA-AA-3984      TCGA-AA-3986 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3989      TCGA-AA-3994      TCGA-AA-A004      TCGA-AA-A00A 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-A00D      TCGA-AA-A00E      TCGA-AA-A00F      TCGA-AA-A00J 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-A00K      TCGA-AA-A00L      TCGA-AA-A00N      TCGA-AA-A00O 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-A00Q      TCGA-AA-A00R      TCGA-AA-A00U      TCGA-AA-A00W 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-A00Z      TCGA-AA-A010      TCGA-AA-A017      TCGA-AA-A01D 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-A01F      TCGA-AA-A01G      TCGA-AA-A01I      TCGA-AA-A01K 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-A01P      TCGA-AA-A01Q      TCGA-AA-A01R      TCGA-AA-A01S 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-A01T      TCGA-AA-A01V      TCGA-AA-A01X      TCGA-AA-A01Z 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-A022      TCGA-AA-A024      TCGA-AA-A029      TCGA-AA-A02F 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-A02H      TCGA-AA-A02J      TCGA-AA-A02K      TCGA-AA-A02O 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-A02W      TCGA-AA-A02Y      TCGA-AA-A03F      TCGA-AA-A03J 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AD-5900      TCGA-AD-6548      TCGA-AD-6888      TCGA-AU-3779 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AU-6004      TCGA-AY-4070      TCGA-AY-4071      TCGA-AY-5543 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AY-6196      TCGA-AY-6197      TCGA-AY-6386      TCGA-AZ-4315 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AZ-4681      TCGA-AZ-4682      TCGA-CA-5254      TCGA-CA-5255 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-CA-5796      TCGA-CA-5797      TCGA-CA-6715      TCGA-CA-6716 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-CA-6717      TCGA-CA-6718      TCGA-CA-6719      TCGA-CK-4947 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-CK-4948      TCGA-CK-4950      TCGA-CK-4952      TCGA-CK-5912 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-CK-5913      TCGA-CK-5914      TCGA-CK-5915      TCGA-CK-5916 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-CK-6746      TCGA-CK-6747      TCGA-CK-6748      TCGA-CK-6751 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-CM-4743      TCGA-CM-4744      TCGA-CM-4746      TCGA-CM-4747 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-CM-4752      TCGA-CM-5341      TCGA-CM-5344      TCGA-CM-5348 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-CM-5349      TCGA-CM-5860      TCGA-CM-5861      TCGA-CM-5862 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-CM-5863      TCGA-CM-5864      TCGA-CM-5868      TCGA-CM-6161 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-CM-6162      TCGA-CM-6163      TCGA-CM-6164      TCGA-CM-6165 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-CM-6166      TCGA-CM-6167      TCGA-CM-6168      TCGA-CM-6169 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-CM-6170      TCGA-CM-6171      TCGA-CM-6172      TCGA-CM-6674 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-CM-6675      TCGA-CM-6676      TCGA-CM-6677      TCGA-CM-6678 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-CM-6679      TCGA-CM-6680      TCGA-D5-5537      TCGA-D5-5538 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-D5-5539      TCGA-D5-5540      TCGA-D5-5541      TCGA-D5-6529 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-D5-6532      TCGA-D5-6533      TCGA-D5-6534      TCGA-D5-6535 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-D5-6536      TCGA-D5-6537      TCGA-D5-6538      TCGA-D5-6539 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-D5-6540      TCGA-D5-6541      TCGA-D5-6898      TCGA-D5-6920 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-D5-6922      TCGA-D5-6923      TCGA-D5-6924      TCGA-D5-6926 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-D5-6927      TCGA-D5-6928      TCGA-D5-6929      TCGA-D5-6930 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-D5-6931      TCGA-D5-6932      TCGA-D5-7000      TCGA-F4-6459 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-F4-6460      TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-F4-6704      TCGA-F4-6805      TCGA-F4-6806      TCGA-F4-6807 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-G4-6306      TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-G4-6586      TCGA-G4-6588      TCGA-G4-6625      TCGA-G4-6626 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-G4-6628 
"LRRC6 WILD-TYPE" 
D1365V10, 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
D1365V11, 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(1366) Variable = NLRP13 MUTATION ANALYSIS
D1366V1, survival
                  sevent
clus2                0   1
  NLRP13 MUTATED    21   3
  NLRP13 WILD-TYPE 261  70
  NLRP13 MUTATED NLRP13 WILD-TYPE 
              24              331 
  NLRP13 MUTATED NLRP13 WILD-TYPE 
               3               70 
$`NLRP13 MUTATED`
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3525 TCGA-AA-3860 
       32.71        27.09        19.66        63.98         8.05        31.07 
TCGA-AA-3877 TCGA-AA-3950 TCGA-AA-A010 TCGA-AA-A01K TCGA-AD-6890 TCGA-AD-6899 
       31.00        24.00        34.98        31.00         0.79         5.79 
TCGA-AY-6196 TCGA-AZ-4315 TCGA-AZ-5403 TCGA-CA-6717 TCGA-CM-5344 TCGA-CM-5861 
        0.20        58.39        62.79         0.33        22.03        15.02 
TCGA-D5-6541 TCGA-D5-6930 TCGA-DM-A1DB TCGA-G4-6299 TCGA-G4-6309 TCGA-G4-6586 
       15.58         1.51        44.32        74.56        51.75        35.80 

$`NLRP13 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.09        22.06        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       37.05        36.03        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 
        0.00        36.03        32.05         0.99        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 
       40.96         0.07        21.37         4.21        56.55         0.72 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        15.75        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13        83.80        22.36        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  NLRP13 MUTATED NLRP13 WILD-TYPE 
             0.2              0.0 
  NLRP13 MUTATED NLRP13 WILD-TYPE 
           74.56           140.38 
  NLRP13 MUTATED NLRP13 WILD-TYPE 
          29.045           19.990 
[1] "0.2 - 74.6 (29.0)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1.9"
D1366V2, 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       23       100         7         0
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NLRP13 MUTATED           1          0          5          5        1
  NLRP13 WILD-TYPE        18         10         36         26       34
                  vv
clus               STAGE IVA STAGE IVB
  NLRP13 MUTATED           0         0
  NLRP13 WILD-TYPE        13         1
D1366V3, multiclass
            clus
vv           NLRP13 MUTATED NLRP13 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               9              100
  STAGE IIB               1                7
  STAGE IIC               1                0
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              5               36
  STAGE IIIC              5               26
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  NLRP13 MUTATED     2   0  21   4
  NLRP13 WILD-TYPE   7  68 227  37
D1366V4, multiclass
    clus
vv   NLRP13 MUTATED NLRP13 WILD-TYPE
  T1              2                7
  T2              0               68
  T3             21              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
  NLRP13 MUTATED    15   6   6
  NLRP13 WILD-TYPE 205  74  60
D1366V5, multiclass
    clus
vv   NLRP13 MUTATED NLRP13 WILD-TYPE
  N0             15              205
  N1              6               74
  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"
D1366V6, binary
                  cls
clus                 0   1
  NLRP13 MUTATED    21   1
  NLRP13 WILD-TYPE 262  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NLRP13 MUTATED     21    1
  NLRP13 WILD-TYPE  262   47
   clus
vv  NLRP13 MUTATED NLRP13 WILD-TYPE
  0             21              262
  1              1               47
[1] 2 2
[1] FALSE
D1366V7, 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
D1366V8, binary
                  cls
clus                 0   1
  NLRP13 MUTATED    20   7
  NLRP13 WILD-TYPE 297  41
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NLRP13 MUTATED     20    7
  NLRP13 WILD-TYPE  297   41
                               clus
vv                              NLRP13 MUTATED NLRP13 WILD-TYPE
  COLON ADENOCARCINOMA                      20              297
  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 238   2  21  20
D1366V9, multiclass
    clus
vv   NLRP13 MUTATED NLRP13 WILD-TYPE
  R0             19              238
  R1              0                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"
D1366V10, 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
D1366V11, 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(1367) Variable = TMEM62 MUTATION ANALYSIS
D1367V1, survival
                  sevent
clus2                0   1
  TMEM62 MUTATED     3   2
  TMEM62 WILD-TYPE 279  71
  TMEM62 MUTATED TMEM62 WILD-TYPE 
               5              350 
  TMEM62 MUTATED TMEM62 WILD-TYPE 
               2               71 
$`TMEM62 MUTATED`
TCGA-AA-3864 TCGA-AZ-6608 TCGA-CA-6717 TCGA-DM-A28C TCGA-DM-A28K 
       53.00         1.94         0.33        81.37        98.24 

$`TMEM62 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      135.65       139.17         6.12       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
      117.07         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  TMEM62 MUTATED TMEM62 WILD-TYPE 
            0.33             0.00 
  TMEM62 MUTATED TMEM62 WILD-TYPE 
           98.24           140.38 
  TMEM62 MUTATED TMEM62 WILD-TYPE 
          53.000           20.155 
[1] "0.3 - 98.2 (53.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D1367V2, 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       24       105         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM62 MUTATED           0          1          0          0        0
  TMEM62 WILD-TYPE        19          9         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  TMEM62 MUTATED           0         0
  TMEM62 WILD-TYPE        13         1
D1367V3, multiclass
            clus
vv           TMEM62 MUTATED TMEM62 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               4              105
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              1                9
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TMEM62 MUTATED     0   1   5   0
  TMEM62 WILD-TYPE   9  67 243  41
D1367V4, multiclass
    clus
vv   TMEM62 MUTATED TMEM62 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              5              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
  TMEM62 MUTATED     5   1   0
  TMEM62 WILD-TYPE 215  79  66
D1367V5, multiclass
    clus
vv   TMEM62 MUTATED TMEM62 WILD-TYPE
  N0              5              215
  N1              1               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
  TMEM62 MUTATED     6   0
  TMEM62 WILD-TYPE 277  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM62 MUTATED      6    0
  TMEM62 WILD-TYPE  277   48
   clus
vv  TMEM62 MUTATED TMEM62 WILD-TYPE
  0              6              277
  1              0               48
[1] 2 2
[1] FALSE
D1367V7, 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
D1367V8, binary
                  cls
clus                 0   1
  TMEM62 MUTATED     4   2
  TMEM62 WILD-TYPE 313  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM62 MUTATED      4    2
  TMEM62 WILD-TYPE  313   46
                               clus
vv                              TMEM62 MUTATED TMEM62 WILD-TYPE
  COLON ADENOCARCINOMA                       4              313
  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 255   2  22  20
D1367V9, multiclass
    clus
vv   TMEM62 MUTATED TMEM62 WILD-TYPE
  R0              2              255
  R1              0                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"
D1367V10, 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
D1367V11, 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(1368) Variable = ZNF385B MUTATION ANALYSIS
D1368V1, survival
                   sevent
clus2                 0   1
  ZNF385B MUTATED     4   3
  ZNF385B WILD-TYPE 278  70
  ZNF385B MUTATED ZNF385B WILD-TYPE 
                7               348 
  ZNF385B MUTATED ZNF385B WILD-TYPE 
                3                70 
$`ZNF385B MUTATED`
TCGA-AA-3952 TCGA-AD-6899 TCGA-AY-6197 TCGA-AZ-4315 TCGA-D5-6529 TCGA-DM-A28G 
        2.01         5.79        21.44        58.39        20.19        60.79 
TCGA-G4-6321 
       22.09 

$`ZNF385B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-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-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 
        4.21        56.55         0.79         0.72        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       15.75         0.20        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K 
        6.12        81.37       119.93        35.97       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  ZNF385B MUTATED ZNF385B WILD-TYPE 
             2.01              0.00 
  ZNF385B MUTATED ZNF385B WILD-TYPE 
            60.79            140.38 
  ZNF385B MUTATED ZNF385B WILD-TYPE 
            21.44             20.07 
[1] "2.0 - 60.8 (21.4)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.9"
D1368V2, 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       25       105         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF385B MUTATED           1          0          0          2        0
  ZNF385B WILD-TYPE        18         10         41         29       35
                   vv
clus                STAGE IVA STAGE IVB
  ZNF385B MUTATED           0         0
  ZNF385B WILD-TYPE        13         1
D1368V3, multiclass
            clus
vv           ZNF385B MUTATED ZNF385B WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                4               105
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               2                29
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ZNF385B MUTATED     0   1   5   1
  ZNF385B WILD-TYPE   9  67 243  40
D1368V4, multiclass
    clus
vv   ZNF385B MUTATED ZNF385B WILD-TYPE
  T1               0                 9
  T2               1                67
  T3               5               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
  ZNF385B MUTATED     4   1   2
  ZNF385B WILD-TYPE 216  79  64
D1368V5, multiclass
    clus
vv   ZNF385B MUTATED ZNF385B WILD-TYPE
  N0               4               216
  N1               1                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"
D1368V6, binary
                   cls
clus                  0   1
  ZNF385B MUTATED     4   0
  ZNF385B WILD-TYPE 279  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF385B MUTATED      4    0
  ZNF385B WILD-TYPE  279   48
   clus
vv  ZNF385B MUTATED ZNF385B WILD-TYPE
  0               4               279
  1               0                48
[1] 2 2
[1] FALSE
D1368V7, 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
D1368V8, binary
                   cls
clus                  0   1
  ZNF385B MUTATED     6   1
  ZNF385B WILD-TYPE 311  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF385B MUTATED      6    1
  ZNF385B WILD-TYPE  311   47
                               clus
vv                              ZNF385B MUTATED ZNF385B WILD-TYPE
  COLON ADENOCARCINOMA                        6               311
  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 252   2  22  21
D1368V9, multiclass
    clus
vv   ZNF385B MUTATED ZNF385B WILD-TYPE
  R0               5               252
  R1               0                 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"
D1368V10, 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
D1368V11, 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(1369) Variable = SAFB MUTATION ANALYSIS
D1369V1, survival
                sevent
clus2              0   1
  SAFB MUTATED    12   1
  SAFB WILD-TYPE 270  72
  SAFB MUTATED SAFB WILD-TYPE 
            13            342 
  SAFB MUTATED SAFB WILD-TYPE 
             1             72 
$`SAFB MUTATED`
TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3663 TCGA-AA-3833 TCGA-AA-3950 
       33.53        22.06        19.66         6.97        15.95        24.00 
TCGA-AA-3973 TCGA-AZ-6608 TCGA-CA-6717 TCGA-CM-4743 TCGA-CM-6161 TCGA-D5-6930 
       13.05         1.94         0.33        23.05        15.02         1.51 
TCGA-G4-6293 
      107.67 

$`SAFB WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 
        0.99        25.02         1.02        17.98        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       16.08        50.99        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93         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        16.01 
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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.41        19.43        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  SAFB MUTATED SAFB WILD-TYPE 
          0.33           0.00 
  SAFB MUTATED SAFB WILD-TYPE 
        107.67         140.38 
  SAFB MUTATED SAFB WILD-TYPE 
         15.95          20.63 
[1] "0.3 - 107.7 (15.9)" "0.0 - 140.4 (20.6)"
[1] "hr=" "2.3"
D1369V2, 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       24       101         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        18          9         41         30       34        13
                vv
clus             STAGE IVB
  SAFB MUTATED           0
  SAFB WILD-TYPE         1
D1369V3, multiclass
            clus
vv           SAFB MUTATED SAFB WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             8            101
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            1              9
  STAGE IIIB            0             41
  STAGE IIIC            1             30
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SAFB MUTATED     0   2  10   2
  SAFB WILD-TYPE   9  66 238  39
D1369V4, multiclass
    clus
vv   SAFB MUTATED SAFB WILD-TYPE
  T1            0              9
  T2            2             66
  T3           10            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
  SAFB MUTATED    10   4   0
  SAFB WILD-TYPE 210  76  66
D1369V5, multiclass
    clus
vv   SAFB MUTATED SAFB WILD-TYPE
  N0           10            210
  N1            4             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"
D1369V6, binary
                cls
clus               0   1
  SAFB MUTATED    12   1
  SAFB WILD-TYPE 271  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  SAFB MUTATED     12    1
  SAFB WILD-TYPE  271   47
   clus
vv  SAFB MUTATED SAFB WILD-TYPE
  0           12            271
  1            1             47
[1] 2 2
[1] FALSE
D1369V7, 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
D1369V8, binary
                cls
clus               0   1
  SAFB MUTATED    10   4
  SAFB WILD-TYPE 307  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  SAFB MUTATED     10    4
  SAFB WILD-TYPE  307   44
                               clus
vv                              SAFB MUTATED SAFB WILD-TYPE
  COLON ADENOCARCINOMA                    10            307
  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 246   2  21  20
D1369V9, multiclass
    clus
vv   SAFB MUTATED SAFB WILD-TYPE
  R0           11            246
  R1            0              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"
D1369V10, 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
D1369V11, 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(1370) Variable = C7ORF60 MUTATION ANALYSIS
D1370V1, survival
                   sevent
clus2                 0   1
  C7ORF60 MUTATED     5   1
  C7ORF60 WILD-TYPE 277  72
  C7ORF60 MUTATED C7ORF60 WILD-TYPE 
                6               349 
  C7ORF60 MUTATED C7ORF60 WILD-TYPE 
                1                72 
$`C7ORF60 MUTATED`
TCGA-A6-6137 TCGA-A6-6651 TCGA-AZ-4315 TCGA-AZ-4616 TCGA-CM-6161 TCGA-G4-6323 
       27.09        21.76        58.39         5.13        15.02        13.78 

$`C7ORF60 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        32.71        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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-4681 
       15.75         0.20        21.44        17.82         1.41        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  C7ORF60 MUTATED C7ORF60 WILD-TYPE 
             5.13              0.00 
  C7ORF60 MUTATED C7ORF60 WILD-TYPE 
            58.39            140.38 
  C7ORF60 MUTATED C7ORF60 WILD-TYPE 
            18.39             20.19 
[1] "5.1 - 58.4 (18.4)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D1370V2, 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       25       108         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C7ORF60 MUTATED           0          0          2          0        1
  C7ORF60 WILD-TYPE        19         10         39         31       34
                   vv
clus                STAGE IVA STAGE IVB
  C7ORF60 MUTATED           0         0
  C7ORF60 WILD-TYPE        13         1
D1370V3, multiclass
            clus
vv           C7ORF60 MUTATED C7ORF60 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 1                 0
  STAGE II                 0                25
  STAGE IIA                1               108
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               2                39
  STAGE IIIC               0                31
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C7ORF60 MUTATED     0   1   4   0
  C7ORF60 WILD-TYPE   9  67 244  41
D1370V4, multiclass
    clus
vv   C7ORF60 MUTATED C7ORF60 WILD-TYPE
  T1               0                 9
  T2               1                67
  T3               4               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
  C7ORF60 MUTATED     3   2   1
  C7ORF60 WILD-TYPE 217  78  65
D1370V5, multiclass
    clus
vv   C7ORF60 MUTATED C7ORF60 WILD-TYPE
  N0               3               217
  N1               2                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"
D1370V6, binary
                   cls
clus                  0   1
  C7ORF60 MUTATED     3   1
  C7ORF60 WILD-TYPE 280  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF60 MUTATED      3    1
  C7ORF60 WILD-TYPE  280   47
   clus
vv  C7ORF60 MUTATED C7ORF60 WILD-TYPE
  0               3               280
  1               1                47
[1] 2 2
[1] FALSE
D1370V7, 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
D1370V8, binary
                   cls
clus                  0   1
  C7ORF60 MUTATED     6   0
  C7ORF60 WILD-TYPE 311  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF60 MUTATED      6    0
  C7ORF60 WILD-TYPE  311   48
                               clus
vv                              C7ORF60 MUTATED C7ORF60 WILD-TYPE
  COLON ADENOCARCINOMA                        6               311
  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 254   2  22  21
D1370V9, multiclass
    clus
vv   C7ORF60 MUTATED C7ORF60 WILD-TYPE
  R0               3               254
  R1               0                 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"
D1370V10, 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
D1370V11, 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(1371) Variable = ZNF585B MUTATION ANALYSIS
D1371V1, survival
                   sevent
clus2                 0   1
  ZNF585B MUTATED     5   2
  ZNF585B WILD-TYPE 277  71
  ZNF585B MUTATED ZNF585B WILD-TYPE 
                7               348 
  ZNF585B MUTATED ZNF585B WILD-TYPE 
                2                71 
$`ZNF585B MUTATED`
TCGA-AA-3715 TCGA-AA-A010 TCGA-AD-6895 TCGA-CK-6747 TCGA-D5-6923 TCGA-F4-6460 
       19.04        34.98         0.72         2.93        12.43        13.38 
TCGA-F4-6570 
        6.18 

$`ZNF585B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       98.24         8.61        13.45        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  ZNF585B MUTATED ZNF585B WILD-TYPE 
             0.72              0.00 
  ZNF585B MUTATED ZNF585B WILD-TYPE 
            34.98            140.38 
  ZNF585B MUTATED ZNF585B WILD-TYPE 
            12.43             20.98 
[1] "0.7 - 35.0 (12.4)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "2.7"
D1371V2, 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       24       107         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF585B MUTATED           0          0          1          0        0
  ZNF585B WILD-TYPE        19         10         40         31       35
                   vv
clus                STAGE IVA STAGE IVB
  ZNF585B MUTATED           0         0
  ZNF585B WILD-TYPE        13         1
D1371V3, multiclass
            clus
vv           ZNF585B MUTATED ZNF585B WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                2               107
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ZNF585B MUTATED     0   1   5   1
  ZNF585B WILD-TYPE   9  67 243  40
D1371V4, multiclass
    clus
vv   ZNF585B MUTATED ZNF585B WILD-TYPE
  T1               0                 9
  T2               1                67
  T3               5               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
  ZNF585B MUTATED     5   2   0
  ZNF585B WILD-TYPE 215  78  66
D1371V5, multiclass
    clus
vv   ZNF585B MUTATED ZNF585B WILD-TYPE
  N0               5               215
  N1               2                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"
D1371V6, binary
                   cls
clus                  0   1
  ZNF585B MUTATED     5   0
  ZNF585B WILD-TYPE 278  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF585B MUTATED      5    0
  ZNF585B WILD-TYPE  278   48
   clus
vv  ZNF585B MUTATED ZNF585B WILD-TYPE
  0               5               278
  1               0                48
[1] 2 2
[1] FALSE
D1371V7, 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
D1371V8, binary
                   cls
clus                  0   1
  ZNF585B MUTATED     7   0
  ZNF585B WILD-TYPE 310  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF585B MUTATED      7    0
  ZNF585B WILD-TYPE  310   48
                               clus
vv                              ZNF585B MUTATED ZNF585B WILD-TYPE
  COLON ADENOCARCINOMA                        7               310
  COLON MUCINOUS ADENOCARCINOMA               0                48
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ZNF585B MUTATED     5   0   0   1
  ZNF585B WILD-TYPE 252   2  22  20
D1371V9, multiclass
    clus
vv   ZNF585B MUTATED ZNF585B WILD-TYPE
  R0               5               252
  R1               0                 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"
D1371V10, 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
D1371V11, 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(1372) Variable = FAM151A MUTATION ANALYSIS
D1372V1, survival
                   sevent
clus2                 0   1
  FAM151A MUTATED     4   2
  FAM151A WILD-TYPE 278  71
  FAM151A MUTATED FAM151A WILD-TYPE 
                6               349 
  FAM151A MUTATED FAM151A WILD-TYPE 
                2                71 
$`FAM151A MUTATED`
TCGA-A6-6780 TCGA-AA-3811 TCGA-AZ-6601 TCGA-CA-6717 TCGA-D5-6540 TCGA-F4-6856 
       20.12        10.06       100.01         0.33        16.14        19.43 

$`FAM151A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        35.41       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  FAM151A MUTATED FAM151A WILD-TYPE 
             0.33              0.00 
  FAM151A MUTATED FAM151A WILD-TYPE 
           100.01            140.38 
  FAM151A MUTATED FAM151A WILD-TYPE 
           17.785            20.980 
[1] "0.3 - 100.0 (17.8)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.4"
D1372V2, 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       24       107         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM151A MUTATED           1          0          0          0        0
  FAM151A WILD-TYPE        18         10         41         31       35
                   vv
clus                STAGE IVA STAGE IVB
  FAM151A MUTATED           0         0
  FAM151A WILD-TYPE        13         1
D1372V3, multiclass
            clus
vv           FAM151A MUTATED FAM151A WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                2               107
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  FAM151A MUTATED     0   2   4   0
  FAM151A WILD-TYPE   9  66 244  41
D1372V4, multiclass
    clus
vv   FAM151A MUTATED FAM151A WILD-TYPE
  T1               0                 9
  T2               2                66
  T3               4               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
  FAM151A MUTATED     5   0   1
  FAM151A WILD-TYPE 215  80  65
D1372V5, multiclass
    clus
vv   FAM151A MUTATED FAM151A WILD-TYPE
  N0               5               215
  N1               0                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"
D1372V6, binary
                   cls
clus                  0   1
  FAM151A MUTATED     5   0
  FAM151A WILD-TYPE 278  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM151A MUTATED      5    0
  FAM151A WILD-TYPE  278   48
   clus
vv  FAM151A MUTATED FAM151A WILD-TYPE
  0               5               278
  1               0                48
[1] 2 2
[1] FALSE
D1372V7, 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
D1372V8, binary
                   cls
clus                  0   1
  FAM151A MUTATED     2   4
  FAM151A WILD-TYPE 315  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM151A MUTATED      2    4
  FAM151A WILD-TYPE  315   44
                               clus
vv                              FAM151A MUTATED FAM151A WILD-TYPE
  COLON ADENOCARCINOMA                        2               315
  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 254   2  22  20
D1372V9, multiclass
    clus
vv   FAM151A MUTATED FAM151A WILD-TYPE
  R0               3               254
  R1               0                 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"
D1372V10, 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
D1372V11, 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(1373) Variable = CDK5RAP2 MUTATION ANALYSIS
D1373V1, survival
                    sevent
clus2                  0   1
  CDK5RAP2 MUTATED    21   1
  CDK5RAP2 WILD-TYPE 261  72
  CDK5RAP2 MUTATED CDK5RAP2 WILD-TYPE 
                22                333 
  CDK5RAP2 MUTATED CDK5RAP2 WILD-TYPE 
                 1                 72 
$`CDK5RAP2 MUTATED`
TCGA-A6-5659 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6653 TCGA-AA-3510 TCGA-AA-3977 
       30.44        22.06        32.71        24.39        63.98        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-5900 TCGA-AD-6889 TCGA-AU-6004 TCGA-AZ-4315 
        4.01        34.98         0.07        56.55        27.09        58.39 
TCGA-AZ-5407 TCGA-CA-5797 TCGA-CA-6717 TCGA-CM-5861 TCGA-CM-6168 TCGA-CM-6674 
       61.41         3.29         0.33        15.02        12.99        12.95 
TCGA-D5-6930 TCGA-G4-6293 TCGA-G4-6586 TCGA-G4-6628 
        1.51       107.67        35.80        52.80 

$`CDK5RAP2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       21.76        24.69        23.87        20.12        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 
        7.04         3.02         1.02        35.01         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       39.98        18.05        40.96        21.37         4.21         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-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-6675 TCGA-CM-6676 
       13.02        15.02        14.04        11.01        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       19.43        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       26.17        91.79        46.75 

  CDK5RAP2 MUTATED CDK5RAP2 WILD-TYPE 
              0.07               0.00 
  CDK5RAP2 MUTATED CDK5RAP2 WILD-TYPE 
            107.67             140.38 
  CDK5RAP2 MUTATED CDK5RAP2 WILD-TYPE 
            26.055             19.990 
[1] "0.1 - 107.7 (26.1)" "0.0 - 140.4 (20.0)"
[1] "hr=" "5.8"
D1373V2, 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       23        99         6         0
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CDK5RAP2 MUTATED           1          0          0          0        0
  CDK5RAP2 WILD-TYPE        18         10         41         31       35
                    vv
clus                 STAGE IVA STAGE IVB
  CDK5RAP2 MUTATED           0         0
  CDK5RAP2 WILD-TYPE        13         1
D1373V3, multiclass
            clus
vv           CDK5RAP2 MUTATED CDK5RAP2 WILD-TYPE
  STAGE I                   6                 58
  STAGE IA                  0                  1
  STAGE II                  2                 23
  STAGE IIA                10                 99
  STAGE IIB                 2                  6
  STAGE IIC                 1                  0
  STAGE III                 1                 18
  STAGE IIIA                0                 10
  STAGE IIIB                0                 41
  STAGE IIIC                0                 31
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  CDK5RAP2 MUTATED     1   6  12   4
  CDK5RAP2 WILD-TYPE   8  62 236  37
D1373V4, multiclass
    clus
vv   CDK5RAP2 MUTATED CDK5RAP2 WILD-TYPE
  T1                1                  8
  T2                6                 62
  T3               12                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
  CDK5RAP2 MUTATED    22   1   0
  CDK5RAP2 WILD-TYPE 198  79  66
D1373V5, multiclass
    clus
vv   CDK5RAP2 MUTATED CDK5RAP2 WILD-TYPE
  N0               22                198
  N1                1                 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"
D1373V6, binary
                    cls
clus                   0   1
  CDK5RAP2 MUTATED    21   0
  CDK5RAP2 WILD-TYPE 262  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CDK5RAP2 MUTATED     21    0
  CDK5RAP2 WILD-TYPE  262   48
   clus
vv  CDK5RAP2 MUTATED CDK5RAP2 WILD-TYPE
  0               21                262
  1                0                 48
[1] 2 2
[1] FALSE
D1373V7, 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
D1373V8, binary
                    cls
clus                   0   1
  CDK5RAP2 MUTATED    19   4
  CDK5RAP2 WILD-TYPE 298  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CDK5RAP2 MUTATED     19    4
  CDK5RAP2 WILD-TYPE  298   44
                               clus
vv                              CDK5RAP2 MUTATED CDK5RAP2 WILD-TYPE
  COLON ADENOCARCINOMA                        19                298
  COLON MUCINOUS ADENOCARCINOMA                4                 44
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  CDK5RAP2 MUTATED    17   0   0   1
  CDK5RAP2 WILD-TYPE 240   2  22  20
D1373V9, multiclass
    clus
vv   CDK5RAP2 MUTATED CDK5RAP2 WILD-TYPE
  R0               17                240
  R1                0                  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"
D1373V10, 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
D1373V11, 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(1374) Variable = BRSK1 MUTATION ANALYSIS
D1374V1, survival
                 sevent
clus2               0   1
  BRSK1 MUTATED    10   6
  BRSK1 WILD-TYPE 272  67
  BRSK1 MUTATED BRSK1 WILD-TYPE 
             16             339 
  BRSK1 MUTATED BRSK1 WILD-TYPE 
              6              67 
$`BRSK1 MUTATED`
TCGA-AA-3492 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
        3.02         6.05         6.97        26.99        19.04        10.06 
TCGA-AA-3821 TCGA-AA-3848 TCGA-AA-3977 TCGA-AA-A00J TCGA-AZ-6598 TCGA-AZ-6599 
        1.02        10.06        25.02        18.05        49.41         6.77 
TCGA-CM-6676 TCGA-D5-6536 TCGA-G4-6307 TCGA-G4-6588 
       11.08        17.85        55.04        26.17 

$`BRSK1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       19.99        13.94        19.99        61.02        78.08        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       85.05        19.04        35.05        33.04         0.99        25.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       17.03         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       22.36        62.79        61.41        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 
      107.67        74.56        65.85        53.62        44.68        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  BRSK1 MUTATED BRSK1 WILD-TYPE 
           1.02            0.00 
  BRSK1 MUTATED BRSK1 WILD-TYPE 
          55.04          140.38 
  BRSK1 MUTATED BRSK1 WILD-TYPE 
         14.465          20.980 
[1] "1.0 - 55.0 (14.5)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "2.5"
D1374V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BRSK1 MUTATED         3        0        4         3         0         0
  BRSK1 WILD-TYPE      61        1       21       106         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BRSK1 MUTATED           1          0          2          1        1         0
  BRSK1 WILD-TYPE        18         10         39         30       34        13
                 vv
clus              STAGE IVB
  BRSK1 MUTATED           0
  BRSK1 WILD-TYPE         1
D1374V3, multiclass
            clus
vv           BRSK1 MUTATED BRSK1 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               4              21
  STAGE IIA              3             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  BRSK1 MUTATED     0   4  10   2
  BRSK1 WILD-TYPE   9  64 238  39
D1374V4, multiclass
    clus
vv   BRSK1 MUTATED BRSK1 WILD-TYPE
  T1             0               9
  T2             4              64
  T3            10             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
  BRSK1 MUTATED    11   2   3
  BRSK1 WILD-TYPE 209  78  63
D1374V5, multiclass
    clus
vv   BRSK1 MUTATED BRSK1 WILD-TYPE
  N0            11             209
  N1             2              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"
D1374V6, binary
                 cls
clus                0   1
  BRSK1 MUTATED    12   1
  BRSK1 WILD-TYPE 271  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRSK1 MUTATED     12    1
  BRSK1 WILD-TYPE  271   47
   clus
vv  BRSK1 MUTATED BRSK1 WILD-TYPE
  0            12             271
  1             1              47
[1] 2 2
[1] FALSE
D1374V7, binary
                 cls
clus                0   1
  BRSK1 MUTATED     9   7
  BRSK1 WILD-TYPE 161 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRSK1 MUTATED      9    7
  BRSK1 WILD-TYPE  161  190
        clus
vv       BRSK1 MUTATED BRSK1 WILD-TYPE
  FEMALE             9             161
  MALE               7             190
[1] 2 2
[1] FALSE
D1374V8, binary
                 cls
clus                0   1
  BRSK1 MUTATED    14   2
  BRSK1 WILD-TYPE 303  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRSK1 MUTATED     14    2
  BRSK1 WILD-TYPE  303   46
                               clus
vv                              BRSK1 MUTATED BRSK1 WILD-TYPE
  COLON ADENOCARCINOMA                     14             303
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  BRSK1 MUTATED    12   0   1   0
  BRSK1 WILD-TYPE 245   2  21  21
D1374V9, multiclass
    clus
vv   BRSK1 MUTATED BRSK1 WILD-TYPE
  R0            12             245
  R1             0               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"
D1374V10, 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     6
  BRSK1 WILD-TYPE                        19   170
D1374V11, 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                                        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(1375) Variable = IRGQ MUTATION ANALYSIS
D1375V1, survival
                sevent
clus2              0   1
  IRGQ MUTATED     3   0
  IRGQ WILD-TYPE 279  73
  IRGQ MUTATED IRGQ WILD-TYPE 
             3            352 
  IRGQ MUTATED IRGQ WILD-TYPE 
             0             73 
$`IRGQ MUTATED`
TCGA-A6-6653 TCGA-AA-3672 TCGA-G4-6588 
       24.39         0.92        26.17 

$`IRGQ WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        91.79        46.75        52.80 

  IRGQ MUTATED IRGQ WILD-TYPE 
          0.92           0.00 
  IRGQ MUTATED IRGQ WILD-TYPE 
         26.17         140.38 
  IRGQ MUTATED IRGQ WILD-TYPE 
        24.390         20.155 
[1] "0.9 - 26.2 (24.4)"  "0.0 - 140.4 (20.2)"
[1] "hr="     "3300000"
D1375V2, 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       25       108         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        18         10         41         31       35        13
                vv
clus             STAGE IVB
  IRGQ MUTATED           0
  IRGQ WILD-TYPE         1
D1375V3, multiclass
            clus
vv           IRGQ MUTATED IRGQ WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             1            108
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  IRGQ MUTATED     0   1   2   0
  IRGQ WILD-TYPE   9  67 246  41
D1375V4, multiclass
    clus
vv   IRGQ MUTATED IRGQ WILD-TYPE
  T1            0              9
  T2            1             67
  T3            2            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
  IRGQ MUTATED     2   1   0
  IRGQ WILD-TYPE 218  79  66
D1375V5, multiclass
    clus
vv   IRGQ MUTATED IRGQ WILD-TYPE
  N0            2            218
  N1            1             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"
D1375V6, binary
                cls
clus               0   1
  IRGQ MUTATED     3   0
  IRGQ WILD-TYPE 280  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRGQ MUTATED      3    0
  IRGQ WILD-TYPE  280   48
   clus
vv  IRGQ MUTATED IRGQ WILD-TYPE
  0            3            280
  1            0             48
[1] 2 2
[1] FALSE
D1375V7, 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
D1375V8, binary
                cls
clus               0   1
  IRGQ MUTATED     3   0
  IRGQ WILD-TYPE 314  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRGQ MUTATED      3    0
  IRGQ WILD-TYPE  314   48
                               clus
vv                              IRGQ MUTATED IRGQ WILD-TYPE
  COLON ADENOCARCINOMA                     3            314
  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 255   2  22  21
D1375V9, multiclass
[1] "Remove cluster labels:" "IRGQ MUTATED"          
clus
  IRGQ MUTATED IRGQ WILD-TYPE 
             2            300 
    TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-A6-2677     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-A6-5657 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-A6-5659     TCGA-A6-5661     TCGA-A6-5665     TCGA-A6-6781 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-3489     TCGA-AA-3492     TCGA-AA-3496     TCGA-AA-3502 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-3510     TCGA-AA-3511     TCGA-AA-3514     TCGA-AA-3517 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-3518     TCGA-AA-3519     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-3526 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-3527     TCGA-AA-3529     TCGA-AA-3530     TCGA-AA-3531 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-3532     TCGA-AA-3534     TCGA-AA-3538     TCGA-AA-3542 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-3543     TCGA-AA-3544     TCGA-AA-3548     TCGA-AA-3549 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-3552     TCGA-AA-3553     TCGA-AA-3554     TCGA-AA-3555 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-3556     TCGA-AA-3558     TCGA-AA-3560     TCGA-AA-3561 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-3562     TCGA-AA-3655     TCGA-AA-3660     TCGA-AA-3662 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-3663     TCGA-AA-3664     TCGA-AA-3666     TCGA-AA-3667 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-3673     TCGA-AA-3678     TCGA-AA-3679     TCGA-AA-3680 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-3681     TCGA-AA-3684     TCGA-AA-3685     TCGA-AA-3688 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-3692     TCGA-AA-3693     TCGA-AA-3695     TCGA-AA-3696 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-3697     TCGA-AA-3710     TCGA-AA-3712     TCGA-AA-3713 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-3715     TCGA-AA-3811     TCGA-AA-3812     TCGA-AA-3814 
"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-3844     TCGA-AA-3845     TCGA-AA-3846     TCGA-AA-3848 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-3850     TCGA-AA-3851     TCGA-AA-3852     TCGA-AA-3854 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-3855     TCGA-AA-3856     TCGA-AA-3858     TCGA-AA-3860 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-3861     TCGA-AA-3864     TCGA-AA-3866     TCGA-AA-3867 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-3869     TCGA-AA-3870     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-3939     TCGA-AA-3941 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-3947     TCGA-AA-3949     TCGA-AA-3950     TCGA-AA-3952 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-3955     TCGA-AA-3956     TCGA-AA-3968     TCGA-AA-3971 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-3972     TCGA-AA-3973     TCGA-AA-3975     TCGA-AA-3976 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-3979     TCGA-AA-3984     TCGA-AA-3986     TCGA-AA-3989 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-3994     TCGA-AA-A004     TCGA-AA-A00A     TCGA-AA-A00D 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-A00E     TCGA-AA-A00F     TCGA-AA-A00J     TCGA-AA-A00K 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-A00L     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-A00Z 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-A010     TCGA-AA-A017     TCGA-AA-A01D     TCGA-AA-A01F 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-A01G     TCGA-AA-A01I     TCGA-AA-A01K     TCGA-AA-A01P 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-A01Q     TCGA-AA-A01R     TCGA-AA-A01S     TCGA-AA-A01T 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-A01V     TCGA-AA-A01X     TCGA-AA-A01Z     TCGA-AA-A022 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-A024     TCGA-AA-A029     TCGA-AA-A02F     TCGA-AA-A02H 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-A02J     TCGA-AA-A02K     TCGA-AA-A02O     TCGA-AA-A02W 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AA-A02Y     TCGA-AA-A03F     TCGA-AA-A03J     TCGA-AD-5900 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AD-6548     TCGA-AD-6888     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-4681 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AZ-4682     TCGA-CA-5254     TCGA-CA-5255     TCGA-CA-5796 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-CA-5797     TCGA-CA-6715     TCGA-CA-6716     TCGA-CA-6717 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-CA-6718     TCGA-CA-6719     TCGA-CK-4947     TCGA-CK-4948 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-CK-4950     TCGA-CK-4952     TCGA-CK-5912     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-G4-6310 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-G4-6315     TCGA-G4-6317     TCGA-G4-6321     TCGA-G4-6323 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-G4-6586     TCGA-G4-6625     TCGA-G4-6626     TCGA-G4-6628 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
D1375V10, 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
D1375V11, multiclass
[1] "Remove cluster labels:" "IRGQ MUTATED"          
clus
  IRGQ MUTATED IRGQ WILD-TYPE 
             2            204 
    TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-A6-2677     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-A6-4105 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-A6-5656     TCGA-A6-5657     TCGA-A6-5659     TCGA-A6-5660 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-A6-5661     TCGA-A6-5662     TCGA-A6-5664     TCGA-A6-5665 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-A6-5666     TCGA-A6-6137     TCGA-A6-6138     TCGA-A6-6141 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-A6-6142     TCGA-A6-6648     TCGA-A6-6649     TCGA-A6-6651 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-A6-6652     TCGA-A6-6654     TCGA-A6-6780     TCGA-A6-6781 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-A6-6782     TCGA-AD-5900     TCGA-AD-6548     TCGA-AD-6888 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AD-6889     TCGA-AD-6890     TCGA-AD-6895     TCGA-AD-6899 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AD-6901     TCGA-AD-6963     TCGA-AD-6964     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-4323     TCGA-AZ-4616     TCGA-AZ-4681 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AZ-4682     TCGA-AZ-5403     TCGA-AZ-5407     TCGA-AZ-6598 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-AZ-6599     TCGA-AZ-6600     TCGA-AZ-6601     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-AZ-6608 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-CA-5254     TCGA-CA-5255     TCGA-CA-5796     TCGA-CA-5797 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-CA-6715     TCGA-CA-6716     TCGA-CA-6717     TCGA-CA-6718 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-CA-6719     TCGA-CK-4947     TCGA-CK-4948     TCGA-CK-4950 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-CK-4952     TCGA-CK-5912     TCGA-CK-5913     TCGA-CK-5914 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-CK-5915     TCGA-CK-5916     TCGA-CK-6746     TCGA-CK-6747 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-CK-6748     TCGA-CK-6751     TCGA-CM-4743     TCGA-CM-4744 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-CM-4746     TCGA-CM-4747     TCGA-CM-4752     TCGA-CM-5341 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-CM-5344     TCGA-CM-5348     TCGA-CM-5349     TCGA-CM-5860 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-CM-5861     TCGA-CM-5862     TCGA-CM-5863     TCGA-CM-5864 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-CM-5868     TCGA-CM-6161     TCGA-CM-6162     TCGA-CM-6163 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-CM-6164     TCGA-CM-6165     TCGA-CM-6166     TCGA-CM-6167 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-CM-6168     TCGA-CM-6169     TCGA-CM-6170     TCGA-CM-6171 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-CM-6172     TCGA-CM-6674     TCGA-CM-6675     TCGA-CM-6676 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-CM-6677     TCGA-CM-6678     TCGA-CM-6679     TCGA-CM-6680 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-D5-5537     TCGA-D5-5538     TCGA-D5-5539     TCGA-D5-5540 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-D5-5541     TCGA-D5-6529     TCGA-D5-6532     TCGA-D5-6533 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-D5-6534     TCGA-D5-6535     TCGA-D5-6536     TCGA-D5-6537 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-D5-6538     TCGA-D5-6539     TCGA-D5-6540     TCGA-D5-6541 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-D5-6898     TCGA-D5-6920     TCGA-D5-6922     TCGA-D5-6923 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-D5-6924     TCGA-D5-6926     TCGA-D5-6927     TCGA-D5-6928 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-D5-6929     TCGA-D5-6930     TCGA-D5-6931     TCGA-D5-6932 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-D5-7000     TCGA-DM-A0X9     TCGA-DM-A0XD     TCGA-DM-A0XF 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-DM-A1D0     TCGA-DM-A1D4     TCGA-DM-A1D6     TCGA-DM-A1D7 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-DM-A1D8     TCGA-DM-A1D9     TCGA-DM-A1DA     TCGA-DM-A1DB 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-DM-A1HA     TCGA-DM-A1HB     TCGA-DM-A282     TCGA-DM-A285 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-DM-A28C     TCGA-DM-A28E     TCGA-DM-A28F     TCGA-DM-A28G 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-DM-A28H     TCGA-DM-A28K     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-G4-6310 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-G4-6315     TCGA-G4-6317     TCGA-G4-6321     TCGA-G4-6323 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 
    TCGA-G4-6586     TCGA-G4-6625     TCGA-G4-6626     TCGA-G4-6628 
"IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" "IRGQ WILD-TYPE" 

Clustering(1376) Variable = POPDC3 MUTATION ANALYSIS
D1376V1, survival
                  sevent
clus2                0   1
  POPDC3 MUTATED     4   1
  POPDC3 WILD-TYPE 278  72
  POPDC3 MUTATED POPDC3 WILD-TYPE 
               5              350 
  POPDC3 MUTATED POPDC3 WILD-TYPE 
               1               72 
$`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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        17.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41        49.41        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  POPDC3 MUTATED POPDC3 WILD-TYPE 
            6.77             0.00 
  POPDC3 MUTATED POPDC3 WILD-TYPE 
           78.08           140.38 
  POPDC3 MUTATED POPDC3 WILD-TYPE 
          29.950           20.155 
[1] "6.8 - 78.1 (29.9)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D1376V2, 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       24       106         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  POPDC3 MUTATED           0          0          0          0        0
  POPDC3 WILD-TYPE        19         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  POPDC3 MUTATED           0         0
  POPDC3 WILD-TYPE        13         1
D1376V3, multiclass
            clus
vv           POPDC3 MUTATED POPDC3 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               3              106
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  POPDC3 MUTATED     0   1   4   1
  POPDC3 WILD-TYPE   9  67 244  40
D1376V4, multiclass
    clus
vv   POPDC3 MUTATED POPDC3 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              4              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
  POPDC3 MUTATED     6   0   0
  POPDC3 WILD-TYPE 214  80  66
D1376V5, multiclass
    clus
vv   POPDC3 MUTATED POPDC3 WILD-TYPE
  N0              6              214
  N1              0               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"
D1376V6, binary
                  cls
clus                 0   1
  POPDC3 MUTATED     5   0
  POPDC3 WILD-TYPE 278  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POPDC3 MUTATED      5    0
  POPDC3 WILD-TYPE  278   48
   clus
vv  POPDC3 MUTATED POPDC3 WILD-TYPE
  0              5              278
  1              0               48
[1] 2 2
[1] FALSE
D1376V7, 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
D1376V8, binary
                  cls
clus                 0   1
  POPDC3 MUTATED     5   1
  POPDC3 WILD-TYPE 312  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POPDC3 MUTATED      5    1
  POPDC3 WILD-TYPE  312   47
                               clus
vv                              POPDC3 MUTATED POPDC3 WILD-TYPE
  COLON ADENOCARCINOMA                       5              312
  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 253   2  22  21
D1376V9, multiclass
    clus
vv   POPDC3 MUTATED POPDC3 WILD-TYPE
  R0              4              253
  R1              0                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"
D1376V10, 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
D1376V11, multiclass
[1] "Remove cluster labels:" "POPDC3 MUTATED"        
clus
  POPDC3 MUTATED POPDC3 WILD-TYPE 
               2              204 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-4105 
"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-A6-6649       TCGA-A6-6651       TCGA-A6-6652 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780       TCGA-A6-6781 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-A6-6782       TCGA-AD-5900       TCGA-AD-6548       TCGA-AD-6888 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-AD-6889       TCGA-AD-6890       TCGA-AD-6895       TCGA-AD-6899 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6964       TCGA-AD-6965 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070       TCGA-AY-4071 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-AZ-4315       TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4681 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-AZ-4682       TCGA-AZ-5403       TCGA-AZ-5407       TCGA-AZ-6598 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-AZ-6600       TCGA-AZ-6601       TCGA-AZ-6603       TCGA-AZ-6605 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-AZ-6606       TCGA-AZ-6607       TCGA-AZ-6608       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-5912       TCGA-CK-5913       TCGA-CK-5914       TCGA-CK-5915 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-CK-5916       TCGA-CK-6746       TCGA-CK-6747       TCGA-CK-6748 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-CK-6751       TCGA-CM-4743       TCGA-CM-4744       TCGA-CM-4746 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341       TCGA-CM-5344 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860       TCGA-CM-5861 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864       TCGA-CM-5868 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163       TCGA-CM-6164 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167       TCGA-CM-6168 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171       TCGA-CM-6172 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676       TCGA-CM-6677 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680       TCGA-D5-5537 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540       TCGA-D5-5541 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533       TCGA-D5-6534 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537       TCGA-D5-6538 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541       TCGA-D5-6898 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923       TCGA-D5-6924 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928       TCGA-D5-6929 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932       TCGA-D5-7000 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-DM-A0X9       TCGA-DM-A0XD       TCGA-DM-A0XF       TCGA-DM-A1D0 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-DM-A1D4       TCGA-DM-A1D6       TCGA-DM-A1D7       TCGA-DM-A1D8 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-DM-A1D9       TCGA-DM-A1DA       TCGA-DM-A1DB       TCGA-DM-A1HA 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-DM-A1HB       TCGA-DM-A282       TCGA-DM-A285       TCGA-DM-A28C 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-DM-A28E       TCGA-DM-A28F       TCGA-DM-A28G       TCGA-DM-A28H 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-DM-A28K       TCGA-F4-6459       TCGA-F4-6460       TCGA-F4-6569 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704       TCGA-F4-6805 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808       TCGA-F4-6809 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856       TCGA-G4-6293 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304       TCGA-G4-6306 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310       TCGA-G4-6315 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323       TCGA-G4-6586 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 
      TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628 
"POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" "POPDC3 WILD-TYPE" 

Clustering(1377) Variable = SLC22A10 MUTATION ANALYSIS
D1377V1, survival
                    sevent
clus2                  0   1
  SLC22A10 MUTATED    15   0
  SLC22A10 WILD-TYPE 267  73
  SLC22A10 MUTATED SLC22A10 WILD-TYPE 
                15                340 
  SLC22A10 MUTATED SLC22A10 WILD-TYPE 
                 0                 73 
$`SLC22A10 MUTATED`
TCGA-A6-6653 TCGA-AA-3812 TCGA-AA-3877 TCGA-AA-3950 TCGA-AA-A010 TCGA-AD-6889 
       24.39        35.05        31.00        24.00        34.98        56.55 
TCGA-AU-6004 TCGA-AY-6196 TCGA-CA-6717 TCGA-CK-4950 TCGA-CM-4744 TCGA-CM-5348 
       27.09         0.20         0.33        40.34        20.02        22.98 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 
       15.02        12.00        16.04 

$`SLC22A10 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        18.05         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37         4.21         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        15.75        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.03        30.08        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 
       15.02        15.02        17.03        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-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  SLC22A10 MUTATED SLC22A10 WILD-TYPE 
               0.2                0.0 
  SLC22A10 MUTATED SLC22A10 WILD-TYPE 
             56.55             140.38 
  SLC22A10 MUTATED SLC22A10 WILD-TYPE 
            24.000             20.055 
[1] "0.2 - 56.5 (24.0)"  "0.0 - 140.4 (20.1)"
[1] "hr="     "2.6e+07"
D1377V2, 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       25       104         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC22A10 MUTATED           0          1          2          1        0
  SLC22A10 WILD-TYPE        19          9         39         30       35
                    vv
clus                 STAGE IVA STAGE IVB
  SLC22A10 MUTATED           0         0
  SLC22A10 WILD-TYPE        13         1
D1377V3, multiclass
            clus
vv           SLC22A10 MUTATED SLC22A10 WILD-TYPE
  STAGE I                   5                 59
  STAGE IA                  0                  1
  STAGE II                  0                 25
  STAGE IIA                 5                104
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                1                  9
  STAGE IIIB                2                 39
  STAGE IIIC                1                 30
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  SLC22A10 MUTATED     1   4   9   1
  SLC22A10 WILD-TYPE   8  64 239  40
D1377V4, multiclass
    clus
vv   SLC22A10 MUTATED SLC22A10 WILD-TYPE
  T1                1                  8
  T2                4                 64
  T3                9                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
  SLC22A10 MUTATED    11   3   1
  SLC22A10 WILD-TYPE 209  77  65
D1377V5, multiclass
    clus
vv   SLC22A10 MUTATED SLC22A10 WILD-TYPE
  N0               11                209
  N1                3                 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"
D1377V6, binary
                    cls
clus                   0   1
  SLC22A10 MUTATED    14   0
  SLC22A10 WILD-TYPE 269  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC22A10 MUTATED     14    0
  SLC22A10 WILD-TYPE  269   48
   clus
vv  SLC22A10 MUTATED SLC22A10 WILD-TYPE
  0               14                269
  1                0                 48
[1] 2 2
[1] FALSE
D1377V7, 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
D1377V8, binary
                    cls
clus                   0   1
  SLC22A10 MUTATED    10   5
  SLC22A10 WILD-TYPE 307  43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC22A10 MUTATED     10    5
  SLC22A10 WILD-TYPE  307   43
                               clus
vv                              SLC22A10 MUTATED SLC22A10 WILD-TYPE
  COLON ADENOCARCINOMA                        10                307
  COLON MUCINOUS ADENOCARCINOMA                5                 43
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  SLC22A10 MUTATED    11   1   0   1
  SLC22A10 WILD-TYPE 246   1  22  20
D1377V9, multiclass
    clus
vv   SLC22A10 MUTATED SLC22A10 WILD-TYPE
  R0               11                246
  R1                1                  1
  R2                0                 22
  RX                1                 20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1377V10, 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
D1377V11, 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(1378) Variable = FKTN MUTATION ANALYSIS
D1378V1, survival
                sevent
clus2              0   1
  FKTN MUTATED     6   1
  FKTN WILD-TYPE 276  72
  FKTN MUTATED FKTN WILD-TYPE 
             7            348 
  FKTN MUTATED FKTN WILD-TYPE 
             1             72 
$`FKTN MUTATED`
TCGA-AA-3811 TCGA-AA-3950 TCGA-AA-A010 TCGA-AZ-4315 TCGA-D5-5540 TCGA-DM-A1HB 
       10.06        24.00        34.98        58.39        13.51       135.65 
TCGA-G4-6586 
       35.80 

$`FKTN WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        26.17        91.79        46.75        52.80 

  FKTN MUTATED FKTN WILD-TYPE 
         10.06           0.00 
  FKTN MUTATED FKTN WILD-TYPE 
        135.65         140.38 
  FKTN MUTATED FKTN WILD-TYPE 
         34.98          20.07 
[1] "10.1 - 135.7 (35.0)" "0.0 - 140.4 (20.1)" 
[1] "hr=" "2.2"
D1378V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FKTN MUTATED         0        0        0         4         1         0
  FKTN WILD-TYPE      64        1       25       105         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FKTN MUTATED           1          0          1          0        0         0
  FKTN WILD-TYPE        18         10         40         31       35        13
                vv
clus             STAGE IVB
  FKTN MUTATED           0
  FKTN WILD-TYPE         1
D1378V3, multiclass
            clus
vv           FKTN MUTATED FKTN WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             4            105
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  FKTN MUTATED     0   0   6   1
  FKTN WILD-TYPE   9  68 242  40
D1378V4, multiclass
    clus
vv   FKTN MUTATED FKTN WILD-TYPE
  T1            0              9
  T2            0             68
  T3            6            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
  FKTN MUTATED     5   1   1
  FKTN WILD-TYPE 215  79  65
D1378V5, multiclass
    clus
vv   FKTN MUTATED FKTN WILD-TYPE
  N0            5            215
  N1            1             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"
D1378V6, binary
                cls
clus               0   1
  FKTN MUTATED     7   0
  FKTN WILD-TYPE 276  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  FKTN MUTATED      7    0
  FKTN WILD-TYPE  276   48
   clus
vv  FKTN MUTATED FKTN WILD-TYPE
  0            7            276
  1            0             48
[1] 2 2
[1] FALSE
D1378V7, binary
                cls
clus               0   1
  FKTN MUTATED     4   3
  FKTN WILD-TYPE 166 194
[1] "tbl2"
                cls
clus             [,1] [,2]
  FKTN MUTATED      4    3
  FKTN WILD-TYPE  166  194
        clus
vv       FKTN MUTATED FKTN WILD-TYPE
  FEMALE            4            166
  MALE              3            194
[1] 2 2
[1] FALSE
D1378V8, binary
                cls
clus               0   1
  FKTN MUTATED     6   1
  FKTN WILD-TYPE 311  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  FKTN MUTATED      6    1
  FKTN WILD-TYPE  311   47
                               clus
vv                              FKTN MUTATED FKTN WILD-TYPE
  COLON ADENOCARCINOMA                     6            311
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  FKTN MUTATED     6   0   0   0
  FKTN WILD-TYPE 251   2  22  21
D1378V9, multiclass
    clus
vv   FKTN MUTATED FKTN WILD-TYPE
  R0            6            251
  R1            0              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"
D1378V10, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FKTN MUTATED                                  0     0
  FKTN WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  FKTN MUTATED                           0     4
  FKTN WILD-TYPE                        19   172
D1378V11, multiclass
                                  clus
vv                                 FKTN MUTATED FKTN 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 = ENPP3 MUTATION ANALYSIS
D1379V1, survival
                 sevent
clus2               0   1
  ENPP3 MUTATED     6   3
  ENPP3 WILD-TYPE 276  70
  ENPP3 MUTATED ENPP3 WILD-TYPE 
              9             346 
  ENPP3 MUTATED ENPP3 WILD-TYPE 
              3              70 
$`ENPP3 MUTATED`
TCGA-AA-3555 TCGA-AA-3713 TCGA-AA-A00N TCGA-AD-6964 TCGA-AZ-6598 TCGA-CA-6717 
       29.95        19.04         4.01        10.88        49.41         0.33 
TCGA-CM-5344 TCGA-D5-6928 TCGA-DM-A1HB 
       22.03        11.64       135.65 

$`ENPP3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        17.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  ENPP3 MUTATED ENPP3 WILD-TYPE 
           0.33            0.00 
  ENPP3 MUTATED ENPP3 WILD-TYPE 
         135.65          140.38 
  ENPP3 MUTATED ENPP3 WILD-TYPE 
         19.040          20.235 
[1] "0.3 - 135.7 (19.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.5"
D1379V2, 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       24       106         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        19         10         39         31       34        13
                 vv
clus              STAGE IVB
  ENPP3 MUTATED           0
  ENPP3 WILD-TYPE         1
D1379V3, multiclass
            clus
vv           ENPP3 MUTATED ENPP3 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              3             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ENPP3 MUTATED     0   0   7   2
  ENPP3 WILD-TYPE   9  68 241  39
D1379V4, multiclass
    clus
vv   ENPP3 MUTATED ENPP3 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             7             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
  ENPP3 MUTATED     6   2   1
  ENPP3 WILD-TYPE 214  78  65
D1379V5, multiclass
    clus
vv   ENPP3 MUTATED ENPP3 WILD-TYPE
  N0             6             214
  N1             2              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"
D1379V6, binary
                 cls
clus                0   1
  ENPP3 MUTATED     6   1
  ENPP3 WILD-TYPE 277  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ENPP3 MUTATED      6    1
  ENPP3 WILD-TYPE  277   47
   clus
vv  ENPP3 MUTATED ENPP3 WILD-TYPE
  0             6             277
  1             1              47
[1] 2 2
[1] FALSE
D1379V7, 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
D1379V8, binary
                 cls
clus                0   1
  ENPP3 MUTATED     5   4
  ENPP3 WILD-TYPE 312  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ENPP3 MUTATED      5    4
  ENPP3 WILD-TYPE  312   44
                               clus
vv                              ENPP3 MUTATED ENPP3 WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  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 253   2  21  20
D1379V9, multiclass
    clus
vv   ENPP3 MUTATED ENPP3 WILD-TYPE
  R0             4             253
  R1             0               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"
D1379V10, 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
D1379V11, 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(1380) Variable = MYH9 MUTATION ANALYSIS
D1380V1, survival
                sevent
clus2              0   1
  MYH9 MUTATED    24   6
  MYH9 WILD-TYPE 258  67
  MYH9 MUTATED MYH9 WILD-TYPE 
            30            325 
  MYH9 MUTATED MYH9 WILD-TYPE 
             6             67 
$`MYH9 MUTATED`
TCGA-A6-2676 TCGA-A6-4105 TCGA-A6-5665 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       42.90        14.53        22.06        24.69        24.39        20.12 
TCGA-AA-3525 TCGA-AA-3663 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3877 TCGA-AA-3977 
        8.05         6.97        19.04        19.04        31.00        25.02 
TCGA-AA-A00E TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-5900 TCGA-AD-6895 TCGA-AD-6964 
       30.02        34.98        35.01         0.07         0.72        10.88 
TCGA-AU-6004 TCGA-AZ-6598 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-5861 TCGA-CM-5868 
       27.09        49.41        23.05        37.02        15.02        17.03 
TCGA-CM-6171 TCGA-D5-6535 TCGA-D5-6540 TCGA-DM-A1DA TCGA-F4-6856 TCGA-G4-6628 
       14.04        15.12        16.14         7.50        19.43        52.80 

$`MYH9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 
       34.65        33.34        32.75        36.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       30.44        29.19        33.53        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       21.76        23.87        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.03        85.05        26.99        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        19.00        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37         4.21        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
        5.79        22.42        27.42         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4747 
       21.14         2.93         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        16.01 
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-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32        12.59       140.38        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        35.41       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 
       46.75 

  MYH9 MUTATED MYH9 WILD-TYPE 
          0.07           0.00 
  MYH9 MUTATED MYH9 WILD-TYPE 
         52.80         140.38 
  MYH9 MUTATED MYH9 WILD-TYPE 
        19.775         20.280 
[1] "0.1 - 52.8 (19.8)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.1"
D1380V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MYH9 MUTATED         9        0        3         6         3         0
  MYH9 WILD-TYPE      55        1       22       103         5         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MYH9 MUTATED           1          0          2          1        1         2
  MYH9 WILD-TYPE        18         10         39         30       34        11
                vv
clus             STAGE IVB
  MYH9 MUTATED           0
  MYH9 WILD-TYPE         1
D1380V3, multiclass
            clus
vv           MYH9 MUTATED MYH9 WILD-TYPE
  STAGE I               9             55
  STAGE IA              0              1
  STAGE II              3             22
  STAGE IIA             6            103
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            2             39
  STAGE IIIC            1             30
  STAGE IV              1             34
  STAGE IVA             2             11
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MYH9 MUTATED     1   9  16   5
  MYH9 WILD-TYPE   8  59 232  36
D1380V4, multiclass
    clus
vv   MYH9 MUTATED MYH9 WILD-TYPE
  T1            1              8
  T2            9             59
  T3           16            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
  MYH9 MUTATED    24   4   3
  MYH9 WILD-TYPE 196  76  63
D1380V5, multiclass
    clus
vv   MYH9 MUTATED MYH9 WILD-TYPE
  N0           24            196
  N1            4             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"
D1380V6, binary
                cls
clus               0   1
  MYH9 MUTATED    20   3
  MYH9 WILD-TYPE 263  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYH9 MUTATED     20    3
  MYH9 WILD-TYPE  263   45
   clus
vv  MYH9 MUTATED MYH9 WILD-TYPE
  0           20            263
  1            3             45
[1] 2 2
[1] FALSE
D1380V7, binary
                cls
clus               0   1
  MYH9 MUTATED    12  19
  MYH9 WILD-TYPE 158 178
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYH9 MUTATED     12   19
  MYH9 WILD-TYPE  158  178
        clus
vv       MYH9 MUTATED MYH9 WILD-TYPE
  FEMALE           12            158
  MALE             19            178
[1] 2 2
[1] FALSE
D1380V8, binary
                cls
clus               0   1
  MYH9 MUTATED    25   6
  MYH9 WILD-TYPE 292  42
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYH9 MUTATED     25    6
  MYH9 WILD-TYPE  292   42
                               clus
vv                              MYH9 MUTATED MYH9 WILD-TYPE
  COLON ADENOCARCINOMA                    25            292
  COLON MUCINOUS ADENOCARCINOMA            6             42
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MYH9 MUTATED    19   0   1   2
  MYH9 WILD-TYPE 238   2  21  19
D1380V9, multiclass
    clus
vv   MYH9 MUTATED MYH9 WILD-TYPE
  R0           19            238
  R1            0              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"
D1380V10, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MYH9 MUTATED                                  0     0
  MYH9 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MYH9 MUTATED                           2    20
  MYH9 WILD-TYPE                        17   156
D1380V11, multiclass
                                  clus
vv                                 MYH9 MUTATED MYH9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             10
  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(1381) Variable = ZNF643 MUTATION ANALYSIS
D1381V1, survival
                  sevent
clus2                0   1
  ZNF643 MUTATED     6   2
  ZNF643 WILD-TYPE 276  71
  ZNF643 MUTATED ZNF643 WILD-TYPE 
               8              347 
  ZNF643 MUTATED ZNF643 WILD-TYPE 
               2               71 
$`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 
       13.45        46.75 

$`ZNF643 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.33         0.10         1.35       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-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        13.38         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        52.80 

  ZNF643 MUTATED ZNF643 WILD-TYPE 
            4.01             0.00 
  ZNF643 MUTATED ZNF643 WILD-TYPE 
           85.05           140.38 
  ZNF643 MUTATED ZNF643 WILD-TYPE 
           26.27            20.19 
[1] "4.0 - 85.0 (26.3)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D1381V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF643 MUTATED         1        0        0         3         2         0
  ZNF643 WILD-TYPE      63        1       25       106         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF643 MUTATED           1          0          1          0        0
  ZNF643 WILD-TYPE        18         10         40         31       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF643 MUTATED           1         0
  ZNF643 WILD-TYPE        12         1
D1381V3, multiclass
            clus
vv           ZNF643 MUTATED ZNF643 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               3              106
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 243  38
D1381V4, multiclass
    clus
vv   ZNF643 MUTATED ZNF643 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              5              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
  ZNF643 MUTATED     7   2   0
  ZNF643 WILD-TYPE 213  78  66
D1381V5, multiclass
    clus
vv   ZNF643 MUTATED ZNF643 WILD-TYPE
  N0              7              213
  N1              2               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"
D1381V6, binary
                  cls
clus                 0   1
  ZNF643 MUTATED     8   0
  ZNF643 WILD-TYPE 275  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF643 MUTATED      8    0
  ZNF643 WILD-TYPE  275   48
   clus
vv  ZNF643 MUTATED ZNF643 WILD-TYPE
  0              8              275
  1              0               48
[1] 2 2
[1] FALSE
D1381V7, 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
D1381V8, binary
                  cls
clus                 0   1
  ZNF643 MUTATED     8   1
  ZNF643 WILD-TYPE 309  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF643 MUTATED      8    1
  ZNF643 WILD-TYPE  309   47
                               clus
vv                              ZNF643 MUTATED ZNF643 WILD-TYPE
  COLON ADENOCARCINOMA                       8              309
  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 250   2  22  19
D1381V9, multiclass
    clus
vv   ZNF643 MUTATED ZNF643 WILD-TYPE
  R0              7              250
  R1              0                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"
D1381V10, 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
D1381V11, 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(1382) Variable = SLC45A2 MUTATION ANALYSIS
D1382V1, survival
                   sevent
clus2                 0   1
  SLC45A2 MUTATED     7   2
  SLC45A2 WILD-TYPE 275  71
  SLC45A2 MUTATED SLC45A2 WILD-TYPE 
                9               346 
  SLC45A2 MUTATED SLC45A2 WILD-TYPE 
                2                71 
$`SLC45A2 MUTATED`
TCGA-A6-5661 TCGA-AA-3544 TCGA-AA-3666 TCGA-AA-A00D TCGA-AD-6899 TCGA-CK-4948 
       33.53        14.01         2.01        19.00         5.79       102.44 
TCGA-D5-6529 TCGA-D5-6541 TCGA-G4-6588 
       20.19        15.58        26.17 

$`SLC45A2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       26.01        12.99         0.99        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E 
       19.07         7.96        27.02        13.94        38.04        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        0.72        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        0.10         1.35        17.56        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       19.59        13.51        11.51        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        91.79        46.75        52.80 

  SLC45A2 MUTATED SLC45A2 WILD-TYPE 
             2.01              0.00 
  SLC45A2 MUTATED SLC45A2 WILD-TYPE 
           102.44            140.38 
  SLC45A2 MUTATED SLC45A2 WILD-TYPE 
            19.00             20.63 
[1] "2.0 - 102.4 (19.0)" "0.0 - 140.4 (20.6)"
[1] "hr=" "1"  
D1382V2, 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       25       105         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC45A2 MUTATED           1          1          0          1        0
  SLC45A2 WILD-TYPE        18          9         41         30       35
                   vv
clus                STAGE IVA STAGE IVB
  SLC45A2 MUTATED           0         0
  SLC45A2 WILD-TYPE        13         1
D1382V3, multiclass
            clus
vv           SLC45A2 MUTATED SLC45A2 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                4               105
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               1                 9
  STAGE IIIB               0                41
  STAGE IIIC               1                30
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC45A2 MUTATED     0   2   6   1
  SLC45A2 WILD-TYPE   9  66 242  40
D1382V4, multiclass
    clus
vv   SLC45A2 MUTATED SLC45A2 WILD-TYPE
  T1               0                 9
  T2               2                66
  T3               6               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
  SLC45A2 MUTATED     6   2   1
  SLC45A2 WILD-TYPE 214  78  65
D1382V5, multiclass
    clus
vv   SLC45A2 MUTATED SLC45A2 WILD-TYPE
  N0               6               214
  N1               2                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"
D1382V6, binary
                   cls
clus                  0   1
  SLC45A2 MUTATED     8   0
  SLC45A2 WILD-TYPE 275  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC45A2 MUTATED      8    0
  SLC45A2 WILD-TYPE  275   48
   clus
vv  SLC45A2 MUTATED SLC45A2 WILD-TYPE
  0               8               275
  1               0                48
[1] 2 2
[1] FALSE
D1382V7, 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
D1382V8, binary
                   cls
clus                  0   1
  SLC45A2 MUTATED     8   1
  SLC45A2 WILD-TYPE 309  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC45A2 MUTATED      8    1
  SLC45A2 WILD-TYPE  309   47
                               clus
vv                              SLC45A2 MUTATED SLC45A2 WILD-TYPE
  COLON ADENOCARCINOMA                        8               309
  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 249   2  22  21
D1382V9, multiclass
    clus
vv   SLC45A2 MUTATED SLC45A2 WILD-TYPE
  R0               8               249
  R1               0                 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"
D1382V10, 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
D1382V11, 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(1383) Variable = ERN1 MUTATION ANALYSIS
D1383V1, survival
                sevent
clus2              0   1
  ERN1 MUTATED     2   1
  ERN1 WILD-TYPE 280  72
  ERN1 MUTATED ERN1 WILD-TYPE 
             3            352 
  ERN1 MUTATED ERN1 WILD-TYPE 
             1             72 
$`ERN1 MUTATED`
TCGA-AA-3968 TCGA-AZ-6601 TCGA-CM-5860 
       21.99       100.01        16.01 

$`ERN1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 
       24.00         2.01        20.98        34.03         2.01        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  ERN1 MUTATED ERN1 WILD-TYPE 
         16.01           0.00 
  ERN1 MUTATED ERN1 WILD-TYPE 
        100.01         140.38 
  ERN1 MUTATED ERN1 WILD-TYPE 
        21.990         20.155 
[1] "16.0 - 100.0 (22.0)" "0.0 - 140.4 (20.2)" 
[1] "hr=" "1.1"
D1383V2, 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       24       108         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        19         10         41         31       35        13
                vv
clus             STAGE IVB
  ERN1 MUTATED           0
  ERN1 WILD-TYPE         1
D1383V3, multiclass
            clus
vv           ERN1 MUTATED ERN1 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             1            108
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ERN1 MUTATED     0   1   2   0
  ERN1 WILD-TYPE   9  67 246  41
D1383V4, multiclass
    clus
vv   ERN1 MUTATED ERN1 WILD-TYPE
  T1            0              9
  T2            1             67
  T3            2            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
  ERN1 MUTATED     3   0   0
  ERN1 WILD-TYPE 217  80  66
D1383V5, multiclass
    clus
vv   ERN1 MUTATED ERN1 WILD-TYPE
  N0            3            217
  N1            0             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"
D1383V6, binary
                cls
clus               0   1
  ERN1 MUTATED     3   0
  ERN1 WILD-TYPE 280  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  ERN1 MUTATED      3    0
  ERN1 WILD-TYPE  280   48
   clus
vv  ERN1 MUTATED ERN1 WILD-TYPE
  0            3            280
  1            0             48
[1] 2 2
[1] FALSE
D1383V7, 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
D1383V8, binary
                cls
clus               0   1
  ERN1 MUTATED     3   0
  ERN1 WILD-TYPE 314  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  ERN1 MUTATED      3    0
  ERN1 WILD-TYPE  314   48
                               clus
vv                              ERN1 MUTATED ERN1 WILD-TYPE
  COLON ADENOCARCINOMA                     3            314
  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 255   2  22  21
D1383V9, multiclass
[1] "Remove cluster labels:" "ERN1 MUTATED"          
clus
  ERN1 MUTATED ERN1 WILD-TYPE 
             2            300 
    TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810     TCGA-A6-5657 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-A6-5659     TCGA-A6-5661     TCGA-A6-5665     TCGA-A6-6781 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3489     TCGA-AA-3492     TCGA-AA-3496     TCGA-AA-3502 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3510     TCGA-AA-3511     TCGA-AA-3514     TCGA-AA-3517 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3518     TCGA-AA-3519     TCGA-AA-3520     TCGA-AA-3521 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3522     TCGA-AA-3524     TCGA-AA-3525     TCGA-AA-3526 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3527     TCGA-AA-3529     TCGA-AA-3530     TCGA-AA-3531 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3532     TCGA-AA-3534     TCGA-AA-3538     TCGA-AA-3542 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3543     TCGA-AA-3544     TCGA-AA-3548     TCGA-AA-3549 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3552     TCGA-AA-3553     TCGA-AA-3554     TCGA-AA-3555 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3556     TCGA-AA-3558     TCGA-AA-3560     TCGA-AA-3561 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3562     TCGA-AA-3655     TCGA-AA-3660     TCGA-AA-3662 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3663     TCGA-AA-3664     TCGA-AA-3666     TCGA-AA-3667 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3672     TCGA-AA-3673     TCGA-AA-3678     TCGA-AA-3679 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3680     TCGA-AA-3681     TCGA-AA-3684     TCGA-AA-3685 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3688     TCGA-AA-3692     TCGA-AA-3693     TCGA-AA-3695 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3696     TCGA-AA-3697     TCGA-AA-3710     TCGA-AA-3712 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3713     TCGA-AA-3715     TCGA-AA-3811     TCGA-AA-3812 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3814     TCGA-AA-3815     TCGA-AA-3818     TCGA-AA-3819 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3821     TCGA-AA-3831     TCGA-AA-3833     TCGA-AA-3837 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3842     TCGA-AA-3844     TCGA-AA-3845     TCGA-AA-3846 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3848     TCGA-AA-3850     TCGA-AA-3851     TCGA-AA-3852 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3854     TCGA-AA-3855     TCGA-AA-3856     TCGA-AA-3858 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3860     TCGA-AA-3861     TCGA-AA-3864     TCGA-AA-3866 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3867     TCGA-AA-3869     TCGA-AA-3870     TCGA-AA-3872 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3875     TCGA-AA-3877     TCGA-AA-3930     TCGA-AA-3939 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3941     TCGA-AA-3947     TCGA-AA-3949     TCGA-AA-3950 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3952     TCGA-AA-3955     TCGA-AA-3956     TCGA-AA-3971 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3972     TCGA-AA-3973     TCGA-AA-3975     TCGA-AA-3976 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3979     TCGA-AA-3984     TCGA-AA-3986     TCGA-AA-3989 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3994     TCGA-AA-A004     TCGA-AA-A00A     TCGA-AA-A00D 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-A00E     TCGA-AA-A00F     TCGA-AA-A00J     TCGA-AA-A00K 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-A00L     TCGA-AA-A00N     TCGA-AA-A00O     TCGA-AA-A00Q 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-A00R     TCGA-AA-A00U     TCGA-AA-A00W     TCGA-AA-A00Z 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-A010     TCGA-AA-A017     TCGA-AA-A01D     TCGA-AA-A01F 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-A01G     TCGA-AA-A01I     TCGA-AA-A01K     TCGA-AA-A01P 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-A01Q     TCGA-AA-A01R     TCGA-AA-A01S     TCGA-AA-A01T 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-A01V     TCGA-AA-A01X     TCGA-AA-A01Z     TCGA-AA-A022 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-A024     TCGA-AA-A029     TCGA-AA-A02F     TCGA-AA-A02H 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-A02J     TCGA-AA-A02K     TCGA-AA-A02O     TCGA-AA-A02W 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-A02Y     TCGA-AA-A03F     TCGA-AA-A03J     TCGA-AD-5900 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AD-6548     TCGA-AD-6888     TCGA-AU-3779     TCGA-AU-6004 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AY-4070     TCGA-AY-4071     TCGA-AY-5543     TCGA-AY-6196 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AY-6197     TCGA-AY-6386     TCGA-AZ-4315     TCGA-AZ-4681 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AZ-4682     TCGA-CA-5254     TCGA-CA-5255     TCGA-CA-5796 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CA-5797     TCGA-CA-6715     TCGA-CA-6716     TCGA-CA-6717 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CA-6718     TCGA-CA-6719     TCGA-CK-4947     TCGA-CK-4948 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CK-4950     TCGA-CK-4952     TCGA-CK-5912     TCGA-CK-5913 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CK-5914     TCGA-CK-5915     TCGA-CK-5916     TCGA-CK-6746 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CK-6747     TCGA-CK-6748     TCGA-CK-6751     TCGA-CM-4743 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CM-4744     TCGA-CM-4746     TCGA-CM-4747     TCGA-CM-4752 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CM-5341     TCGA-CM-5344     TCGA-CM-5348     TCGA-CM-5349 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CM-5861     TCGA-CM-5862     TCGA-CM-5863     TCGA-CM-5864 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CM-5868     TCGA-CM-6161     TCGA-CM-6162     TCGA-CM-6163 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CM-6164     TCGA-CM-6165     TCGA-CM-6166     TCGA-CM-6167 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CM-6168     TCGA-CM-6169     TCGA-CM-6170     TCGA-CM-6171 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CM-6172     TCGA-CM-6674     TCGA-CM-6675     TCGA-CM-6676 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CM-6677     TCGA-CM-6678     TCGA-CM-6679     TCGA-CM-6680 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-D5-5537     TCGA-D5-5538     TCGA-D5-5539     TCGA-D5-5540 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-D5-5541     TCGA-D5-6529     TCGA-D5-6532     TCGA-D5-6533 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-D5-6534     TCGA-D5-6535     TCGA-D5-6536     TCGA-D5-6537 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-D5-6538     TCGA-D5-6539     TCGA-D5-6540     TCGA-D5-6541 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-D5-6898     TCGA-D5-6920     TCGA-D5-6922     TCGA-D5-6923 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-D5-6924     TCGA-D5-6926     TCGA-D5-6927     TCGA-D5-6928 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-D5-6929     TCGA-D5-6930     TCGA-D5-6931     TCGA-D5-6932 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-D5-7000     TCGA-F4-6459     TCGA-F4-6460     TCGA-F4-6569 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-F4-6570     TCGA-F4-6703     TCGA-F4-6704     TCGA-F4-6805 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-F4-6806     TCGA-F4-6807     TCGA-F4-6808     TCGA-F4-6809 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-F4-6854     TCGA-F4-6855     TCGA-F4-6856     TCGA-G4-6293 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-G4-6299     TCGA-G4-6303     TCGA-G4-6304     TCGA-G4-6306 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-G4-6307     TCGA-G4-6309     TCGA-G4-6310     TCGA-G4-6315 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-G4-6317     TCGA-G4-6321     TCGA-G4-6323     TCGA-G4-6586 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-G4-6588     TCGA-G4-6625     TCGA-G4-6626     TCGA-G4-6628 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
D1383V10, 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
D1383V11, multiclass
[1] "Remove cluster labels:" "ERN1 MUTATED"          
clus
  ERN1 MUTATED ERN1 WILD-TYPE 
             2            204 
    TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810     TCGA-A6-4105 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-A6-5656     TCGA-A6-5657     TCGA-A6-5659     TCGA-A6-5660 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-A6-5661     TCGA-A6-5662     TCGA-A6-5664     TCGA-A6-5665 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-A6-5666     TCGA-A6-6137     TCGA-A6-6138     TCGA-A6-6141 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-A6-6142     TCGA-A6-6648     TCGA-A6-6649     TCGA-A6-6651 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-A6-6652     TCGA-A6-6653     TCGA-A6-6654     TCGA-A6-6780 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-A6-6781     TCGA-A6-6782     TCGA-AD-5900     TCGA-AD-6548 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AD-6888     TCGA-AD-6889     TCGA-AD-6890     TCGA-AD-6895 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AD-6899     TCGA-AD-6901     TCGA-AD-6963     TCGA-AD-6964 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AD-6965     TCGA-AU-3779     TCGA-AU-6004     TCGA-AY-4070 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AY-4071     TCGA-AY-5543     TCGA-AY-6196     TCGA-AY-6197 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AY-6386     TCGA-AZ-4315     TCGA-AZ-4323     TCGA-AZ-4616 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AZ-4681     TCGA-AZ-4682     TCGA-AZ-5403     TCGA-AZ-5407 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AZ-6598     TCGA-AZ-6599     TCGA-AZ-6600     TCGA-AZ-6603 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AZ-6605     TCGA-AZ-6606     TCGA-AZ-6607     TCGA-AZ-6608 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CA-5254     TCGA-CA-5255     TCGA-CA-5796     TCGA-CA-5797 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CA-6715     TCGA-CA-6716     TCGA-CA-6717     TCGA-CA-6718 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CA-6719     TCGA-CK-4947     TCGA-CK-4948     TCGA-CK-4950 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CK-4952     TCGA-CK-5912     TCGA-CK-5913     TCGA-CK-5914 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CK-5915     TCGA-CK-5916     TCGA-CK-6746     TCGA-CK-6747 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CK-6748     TCGA-CK-6751     TCGA-CM-4743     TCGA-CM-4744 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CM-4746     TCGA-CM-4747     TCGA-CM-4752     TCGA-CM-5341 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CM-5344     TCGA-CM-5348     TCGA-CM-5349     TCGA-CM-5861 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CM-5862     TCGA-CM-5863     TCGA-CM-5864     TCGA-CM-5868 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CM-6161     TCGA-CM-6162     TCGA-CM-6163     TCGA-CM-6164 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CM-6165     TCGA-CM-6166     TCGA-CM-6167     TCGA-CM-6168 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CM-6169     TCGA-CM-6170     TCGA-CM-6171     TCGA-CM-6172 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CM-6674     TCGA-CM-6675     TCGA-CM-6676     TCGA-CM-6677 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CM-6678     TCGA-CM-6679     TCGA-CM-6680     TCGA-D5-5537 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-D5-5538     TCGA-D5-5539     TCGA-D5-5540     TCGA-D5-5541 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-D5-6529     TCGA-D5-6532     TCGA-D5-6533     TCGA-D5-6534 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-D5-6535     TCGA-D5-6536     TCGA-D5-6537     TCGA-D5-6538 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-D5-6539     TCGA-D5-6540     TCGA-D5-6541     TCGA-D5-6898 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-D5-6920     TCGA-D5-6922     TCGA-D5-6923     TCGA-D5-6924 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-D5-6926     TCGA-D5-6927     TCGA-D5-6928     TCGA-D5-6929 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-D5-6930     TCGA-D5-6931     TCGA-D5-6932     TCGA-D5-7000 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-DM-A0X9     TCGA-DM-A0XD     TCGA-DM-A0XF     TCGA-DM-A1D0 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-DM-A1D4     TCGA-DM-A1D6     TCGA-DM-A1D7     TCGA-DM-A1D8 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-DM-A1D9     TCGA-DM-A1DA     TCGA-DM-A1DB     TCGA-DM-A1HA 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-DM-A1HB     TCGA-DM-A282     TCGA-DM-A285     TCGA-DM-A28C 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-DM-A28E     TCGA-DM-A28F     TCGA-DM-A28G     TCGA-DM-A28H 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-DM-A28K     TCGA-F4-6459     TCGA-F4-6460     TCGA-F4-6569 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-F4-6570     TCGA-F4-6703     TCGA-F4-6704     TCGA-F4-6805 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-F4-6806     TCGA-F4-6807     TCGA-F4-6808     TCGA-F4-6809 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-F4-6854     TCGA-F4-6855     TCGA-F4-6856     TCGA-G4-6293 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-G4-6299     TCGA-G4-6303     TCGA-G4-6304     TCGA-G4-6306 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-G4-6307     TCGA-G4-6309     TCGA-G4-6310     TCGA-G4-6315 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-G4-6317     TCGA-G4-6321     TCGA-G4-6323     TCGA-G4-6586 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-G4-6588     TCGA-G4-6625     TCGA-G4-6626     TCGA-G4-6628 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 

Clustering(1384) Variable = DPF3 MUTATION ANALYSIS
D1384V1, survival
                sevent
clus2              0   1
  DPF3 MUTATED     5   1
  DPF3 WILD-TYPE 277  72
  DPF3 MUTATED DPF3 WILD-TYPE 
             6            349 
  DPF3 MUTATED DPF3 WILD-TYPE 
             1             72 
$`DPF3 MUTATED`
TCGA-AA-3492 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-A010 TCGA-AD-5900 TCGA-CM-6674 
        3.02        61.02         6.97        34.98         0.07        12.95 

$`DPF3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       19.99        13.94        19.99        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  DPF3 MUTATED DPF3 WILD-TYPE 
          0.07           0.00 
  DPF3 MUTATED DPF3 WILD-TYPE 
         61.02         140.38 
  DPF3 MUTATED DPF3 WILD-TYPE 
          9.96          20.28 
[1] "0.1 - 61.0 (10.0)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1"  
D1384V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DPF3 MUTATED         1        0        3         1         1         0
  DPF3 WILD-TYPE      63        1       22       108         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        19         10         41         31       35        13
                vv
clus             STAGE IVB
  DPF3 MUTATED           0
  DPF3 WILD-TYPE         1
D1384V3, multiclass
            clus
vv           DPF3 MUTATED DPF3 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              3             22
  STAGE IIA             1            108
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  DPF3 MUTATED     0   1   4   1
  DPF3 WILD-TYPE   9  67 244  40
D1384V4, multiclass
    clus
vv   DPF3 MUTATED DPF3 WILD-TYPE
  T1            0              9
  T2            1             67
  T3            4            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
  DPF3 MUTATED     6   0   0
  DPF3 WILD-TYPE 214  80  66
D1384V5, multiclass
    clus
vv   DPF3 MUTATED DPF3 WILD-TYPE
  N0            6            214
  N1            0             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"
D1384V6, binary
                cls
clus               0   1
  DPF3 MUTATED     5   0
  DPF3 WILD-TYPE 278  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  DPF3 MUTATED      5    0
  DPF3 WILD-TYPE  278   48
   clus
vv  DPF3 MUTATED DPF3 WILD-TYPE
  0            5            278
  1            0             48
[1] 2 2
[1] FALSE
D1384V7, binary
                cls
clus               0   1
  DPF3 MUTATED     2   4
  DPF3 WILD-TYPE 168 193
[1] "tbl2"
                cls
clus             [,1] [,2]
  DPF3 MUTATED      2    4
  DPF3 WILD-TYPE  168  193
        clus
vv       DPF3 MUTATED DPF3 WILD-TYPE
  FEMALE            2            168
  MALE              4            193
[1] 2 2
[1] FALSE
D1384V8, binary
                cls
clus               0   1
  DPF3 MUTATED     5   1
  DPF3 WILD-TYPE 312  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  DPF3 MUTATED      5    1
  DPF3 WILD-TYPE  312   47
                               clus
vv                              DPF3 MUTATED DPF3 WILD-TYPE
  COLON ADENOCARCINOMA                     5            312
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  DPF3 MUTATED     6   0   0   0
  DPF3 WILD-TYPE 251   2  22  21
D1384V9, multiclass
    clus
vv   DPF3 MUTATED DPF3 WILD-TYPE
  R0            6            251
  R1            0              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"
D1384V10, 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
D1384V11, multiclass
[1] "Remove cluster labels:" "DPF3 MUTATED"          
clus
  DPF3 MUTATED DPF3 WILD-TYPE 
             2            204 
    TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810     TCGA-A6-4105 
"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-A6-6649     TCGA-A6-6651 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-A6-6652     TCGA-A6-6653     TCGA-A6-6654     TCGA-A6-6780 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-A6-6781     TCGA-A6-6782     TCGA-AD-6548     TCGA-AD-6888 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-AD-6889     TCGA-AD-6890     TCGA-AD-6895     TCGA-AD-6899 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-AD-6901     TCGA-AD-6963     TCGA-AD-6964     TCGA-AD-6965 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-AU-3779     TCGA-AU-6004     TCGA-AY-4070     TCGA-AY-4071 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-AY-5543     TCGA-AY-6196     TCGA-AY-6197     TCGA-AY-6386 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-AZ-4315     TCGA-AZ-4323     TCGA-AZ-4616     TCGA-AZ-4681 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-AZ-4682     TCGA-AZ-5403     TCGA-AZ-5407     TCGA-AZ-6598 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-AZ-6599     TCGA-AZ-6600     TCGA-AZ-6601     TCGA-AZ-6603 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-AZ-6605     TCGA-AZ-6606     TCGA-AZ-6607     TCGA-AZ-6608 
"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-5912     TCGA-CK-5913     TCGA-CK-5914 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-CK-5915     TCGA-CK-5916     TCGA-CK-6746     TCGA-CK-6747 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-CK-6748     TCGA-CK-6751     TCGA-CM-4743     TCGA-CM-4744 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-CM-4746     TCGA-CM-4747     TCGA-CM-4752     TCGA-CM-5341 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-CM-5344     TCGA-CM-5348     TCGA-CM-5349     TCGA-CM-5860 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-CM-5861     TCGA-CM-5862     TCGA-CM-5863     TCGA-CM-5864 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-CM-5868     TCGA-CM-6161     TCGA-CM-6162     TCGA-CM-6163 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-CM-6164     TCGA-CM-6165     TCGA-CM-6166     TCGA-CM-6167 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-CM-6168     TCGA-CM-6169     TCGA-CM-6170     TCGA-CM-6171 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-CM-6172     TCGA-CM-6675     TCGA-CM-6676     TCGA-CM-6677 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-CM-6678     TCGA-CM-6679     TCGA-CM-6680     TCGA-D5-5537 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-D5-5538     TCGA-D5-5539     TCGA-D5-5540     TCGA-D5-5541 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-D5-6529     TCGA-D5-6532     TCGA-D5-6533     TCGA-D5-6534 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-D5-6535     TCGA-D5-6536     TCGA-D5-6537     TCGA-D5-6538 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-D5-6539     TCGA-D5-6540     TCGA-D5-6541     TCGA-D5-6898 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-D5-6920     TCGA-D5-6922     TCGA-D5-6923     TCGA-D5-6924 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-D5-6926     TCGA-D5-6927     TCGA-D5-6928     TCGA-D5-6929 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-D5-6930     TCGA-D5-6931     TCGA-D5-6932     TCGA-D5-7000 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-DM-A0X9     TCGA-DM-A0XD     TCGA-DM-A0XF     TCGA-DM-A1D0 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-DM-A1D4     TCGA-DM-A1D6     TCGA-DM-A1D7     TCGA-DM-A1D8 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-DM-A1D9     TCGA-DM-A1DA     TCGA-DM-A1DB     TCGA-DM-A1HA 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-DM-A1HB     TCGA-DM-A282     TCGA-DM-A285     TCGA-DM-A28C 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-DM-A28E     TCGA-DM-A28F     TCGA-DM-A28G     TCGA-DM-A28H 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-DM-A28K     TCGA-F4-6459     TCGA-F4-6460     TCGA-F4-6569 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-F4-6570     TCGA-F4-6703     TCGA-F4-6704     TCGA-F4-6805 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-F4-6806     TCGA-F4-6807     TCGA-F4-6808     TCGA-F4-6809 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-F4-6854     TCGA-F4-6855     TCGA-F4-6856     TCGA-G4-6293 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-G4-6299     TCGA-G4-6303     TCGA-G4-6304     TCGA-G4-6306 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-G4-6307     TCGA-G4-6309     TCGA-G4-6310     TCGA-G4-6315 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-G4-6317     TCGA-G4-6321     TCGA-G4-6323     TCGA-G4-6586 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 
    TCGA-G4-6588     TCGA-G4-6625     TCGA-G4-6626     TCGA-G4-6628 
"DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" "DPF3 WILD-TYPE" 

Clustering(1385) Variable = TRPC1 MUTATION ANALYSIS
D1385V1, survival
                 sevent
clus2               0   1
  TRPC1 MUTATED     8   3
  TRPC1 WILD-TYPE 274  70
  TRPC1 MUTATED TRPC1 WILD-TYPE 
             11             344 
  TRPC1 MUTATED TRPC1 WILD-TYPE 
              3              70 
$`TRPC1 MUTATED`
TCGA-AA-3511 TCGA-AA-3877 TCGA-AA-A00A TCGA-AA-A010 TCGA-AD-6895 TCGA-AZ-6607 
        6.97        31.00        38.04        34.98         0.72         3.19 
TCGA-CA-6717 TCGA-CA-6718 TCGA-D5-5538 TCGA-DM-A1D7 TCGA-F4-6570 
        0.33         0.10        12.26        13.32         6.18 

$`TRPC1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01        63.98         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D 
       27.02        19.07         7.96        27.02        13.94        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07         0.26         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      117.07        98.24         8.61        13.38        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  TRPC1 MUTATED TRPC1 WILD-TYPE 
            0.1             0.0 
  TRPC1 MUTATED TRPC1 WILD-TYPE 
          38.04          140.38 
  TRPC1 MUTATED TRPC1 WILD-TYPE 
           6.97           20.98 
[1] "0.1 - 38.0 (7.0)"   "0.0 - 140.4 (21.0)"
[1] "hr=" "2.7"
D1385V2, 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       24       103         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TRPC1 MUTATED           0          0          1          0        1         0
  TRPC1 WILD-TYPE        19         10         40         31       34        13
                 vv
clus              STAGE IVB
  TRPC1 MUTATED           0
  TRPC1 WILD-TYPE         1
D1385V3, multiclass
            clus
vv           TRPC1 MUTATED TRPC1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              6             103
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TRPC1 MUTATED     1   0   8   4
  TRPC1 WILD-TYPE   8  68 240  37
D1385V4, multiclass
    clus
vv   TRPC1 MUTATED TRPC1 WILD-TYPE
  T1             1               8
  T2             0              68
  T3             8             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
  TRPC1 MUTATED    10   2   1
  TRPC1 WILD-TYPE 210  78  65
D1385V5, multiclass
    clus
vv   TRPC1 MUTATED TRPC1 WILD-TYPE
  N0            10             210
  N1             2              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"
D1385V6, binary
                 cls
clus                0   1
  TRPC1 MUTATED    10   1
  TRPC1 WILD-TYPE 273  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPC1 MUTATED     10    1
  TRPC1 WILD-TYPE  273   47
   clus
vv  TRPC1 MUTATED TRPC1 WILD-TYPE
  0            10             273
  1             1              47
[1] 2 2
[1] FALSE
D1385V7, 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
D1385V8, binary
                 cls
clus                0   1
  TRPC1 MUTATED    11   2
  TRPC1 WILD-TYPE 306  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPC1 MUTATED     11    2
  TRPC1 WILD-TYPE  306   46
                               clus
vv                              TRPC1 MUTATED TRPC1 WILD-TYPE
  COLON ADENOCARCINOMA                     11             306
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TRPC1 MUTATED     7   0   0   3
  TRPC1 WILD-TYPE 250   2  22  18
D1385V9, multiclass
    clus
vv   TRPC1 MUTATED TRPC1 WILD-TYPE
  R0             7             250
  R1             0               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"
D1385V10, 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
D1385V11, 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(1386) Variable = FSTL4 MUTATION ANALYSIS
D1386V1, survival
                 sevent
clus2               0   1
  FSTL4 MUTATED    14   1
  FSTL4 WILD-TYPE 268  72
  FSTL4 MUTATED FSTL4 WILD-TYPE 
             15             340 
  FSTL4 MUTATED FSTL4 WILD-TYPE 
              1              72 
$`FSTL4 MUTATED`
TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3986 TCGA-AD-6964 
       22.06        63.98         6.97         0.92        19.07        10.88 
TCGA-AU-6004 TCGA-AY-6197 TCGA-CA-6718 TCGA-CM-5860 TCGA-CM-5861 TCGA-D5-6536 
       27.09        21.44         0.10        16.01        15.02        17.85 
TCGA-D5-6540 TCGA-D5-6541 TCGA-DM-A1HB 
       16.14        15.58       135.65 

$`FSTL4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       26.01        25.02        24.00        27.02        27.02         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
        5.79        22.42        27.42         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        15.75         0.20        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.33         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        15.12         4.80        17.13        12.49 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  FSTL4 MUTATED FSTL4 WILD-TYPE 
            0.1             0.0 
  FSTL4 MUTATED FSTL4 WILD-TYPE 
         135.65          140.38 
  FSTL4 MUTATED FSTL4 WILD-TYPE 
          16.14           20.98 
[1] "0.1 - 135.7 (16.1)" "0.0 - 140.4 (21.0)"
[1] "hr=" "3.1"
D1386V2, 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       23       102         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        18         10         40         31       35        13
                 vv
clus              STAGE IVB
  FSTL4 MUTATED           0
  FSTL4 WILD-TYPE         1
D1386V3, multiclass
            clus
vv           FSTL4 MUTATED FSTL4 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              7             102
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FSTL4 MUTATED     0   3  11   1
  FSTL4 WILD-TYPE   9  65 237  40
D1386V4, multiclass
    clus
vv   FSTL4 MUTATED FSTL4 WILD-TYPE
  T1             0               9
  T2             3              65
  T3            11             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
  FSTL4 MUTATED    12   2   1
  FSTL4 WILD-TYPE 208  78  65
D1386V5, multiclass
    clus
vv   FSTL4 MUTATED FSTL4 WILD-TYPE
  N0            12             208
  N1             2              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"
D1386V6, binary
                 cls
clus                0   1
  FSTL4 MUTATED    13   0
  FSTL4 WILD-TYPE 270  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FSTL4 MUTATED     13    0
  FSTL4 WILD-TYPE  270   48
   clus
vv  FSTL4 MUTATED FSTL4 WILD-TYPE
  0            13             270
  1             0              48
[1] 2 2
[1] FALSE
D1386V7, 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
D1386V8, binary
                 cls
clus                0   1
  FSTL4 MUTATED    14   1
  FSTL4 WILD-TYPE 303  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FSTL4 MUTATED     14    1
  FSTL4 WILD-TYPE  303   47
                               clus
vv                              FSTL4 MUTATED FSTL4 WILD-TYPE
  COLON ADENOCARCINOMA                     14             303
  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 245   2  22  20
D1386V9, multiclass
    clus
vv   FSTL4 MUTATED FSTL4 WILD-TYPE
  R0            12             245
  R1             0               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"
D1386V10, 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
D1386V11, 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(1387) Variable = SETX MUTATION ANALYSIS
D1387V1, survival
                sevent
clus2              0   1
  SETX MUTATED    18   5
  SETX WILD-TYPE 264  68
  SETX MUTATED SETX WILD-TYPE 
            23            332 
  SETX MUTATED SETX WILD-TYPE 
             5             68 
$`SETX MUTATED`
TCGA-A6-5665 TCGA-A6-6782 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3848 TCGA-AA-3966 
       22.06        20.28        63.98         6.97        10.06         2.01 
TCGA-AA-3977 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A02O TCGA-AD-6889 
       25.02        18.05         4.01        34.98         0.92        56.55 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5916 
       21.44        58.39        49.41         0.33         0.10        21.14 
TCGA-CM-4744 TCGA-CM-6162 TCGA-CM-6172 TCGA-F4-6570 TCGA-F4-6854 
       20.02        12.00        11.01         6.18         0.53 

$`SETX WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3851 
       37.02        14.93         0.00        17.03         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       26.01        24.00         2.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03        14.01        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37         4.21         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        15.75         0.20        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13        83.80        22.36        62.79        61.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.26         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32        21.99         2.93         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        16.01        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       13.25        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  SETX MUTATED SETX WILD-TYPE 
           0.1            0.0 
  SETX MUTATED SETX WILD-TYPE 
         63.98         140.38 
  SETX MUTATED SETX WILD-TYPE 
         18.05          20.98 
[1] "0.1 - 64.0 (18.1)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.3"
D1387V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SETX MUTATED         2        0        4        10         4         0
  SETX WILD-TYPE      62        1       21        99         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        19         10         38         30       35        13
                vv
clus             STAGE IVB
  SETX MUTATED           0
  SETX WILD-TYPE         1
D1387V3, multiclass
            clus
vv           SETX MUTATED SETX WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              4             21
  STAGE IIA            10             99
  STAGE IIB             4              4
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            3             38
  STAGE IIIC            1             30
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SETX MUTATED     1   2  17   5
  SETX WILD-TYPE   8  66 231  36
D1387V4, multiclass
    clus
vv   SETX MUTATED SETX WILD-TYPE
  T1            1              8
  T2            2             66
  T3           17            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    21   3   1
  SETX WILD-TYPE 199  77  65
D1387V5, multiclass
    clus
vv   SETX MUTATED SETX WILD-TYPE
  N0           21            199
  N1            3             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"
D1387V6, binary
                cls
clus               0   1
  SETX MUTATED    20   0
  SETX WILD-TYPE 263  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  SETX MUTATED     20    0
  SETX WILD-TYPE  263   48
   clus
vv  SETX MUTATED SETX WILD-TYPE
  0           20            263
  1            0             48
[1] 2 2
[1] FALSE
D1387V7, binary
                cls
clus               0   1
  SETX MUTATED    12  13
  SETX WILD-TYPE 158 184
[1] "tbl2"
                cls
clus             [,1] [,2]
  SETX MUTATED     12   13
  SETX WILD-TYPE  158  184
        clus
vv       SETX MUTATED SETX WILD-TYPE
  FEMALE           12            158
  MALE             13            184
[1] 2 2
[1] FALSE
D1387V8, binary
                cls
clus               0   1
  SETX MUTATED    20   5
  SETX WILD-TYPE 297  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  SETX MUTATED     20    5
  SETX WILD-TYPE  297   43
                               clus
vv                              SETX MUTATED SETX WILD-TYPE
  COLON ADENOCARCINOMA                    20            297
  COLON MUCINOUS ADENOCARCINOMA            5             43
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SETX MUTATED    16   0   0   4
  SETX WILD-TYPE 241   2  22  17
D1387V9, multiclass
    clus
vv   SETX MUTATED SETX WILD-TYPE
  R0           16            241
  R1            0              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"
D1387V10, 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
D1387V11, 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(1388) Variable = SLC44A1 MUTATION ANALYSIS
D1388V1, survival
                   sevent
clus2                 0   1
  SLC44A1 MUTATED     7   1
  SLC44A1 WILD-TYPE 275  72
  SLC44A1 MUTATED SLC44A1 WILD-TYPE 
                8               347 
  SLC44A1 MUTATED SLC44A1 WILD-TYPE 
                1                72 
$`SLC44A1 MUTATED`
TCGA-AA-3821 TCGA-AA-3844 TCGA-AD-6964 TCGA-AY-6386 TCGA-CA-6717 TCGA-CM-4743 
        1.02        14.93        10.88        17.82         0.33        23.05 
TCGA-D5-6535 TCGA-G4-6323 
       15.12        13.78 

$`SLC44A1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 
       17.98        15.95        38.99        37.02         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  SLC44A1 MUTATED SLC44A1 WILD-TYPE 
             0.33              0.00 
  SLC44A1 MUTATED SLC44A1 WILD-TYPE 
            23.05            140.38 
  SLC44A1 MUTATED SLC44A1 WILD-TYPE 
           14.355            20.980 
[1] "0.3 - 23.1 (14.4)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.1"
D1388V2, 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       25       106         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC44A1 MUTATED           0          0          2          1        0
  SLC44A1 WILD-TYPE        19         10         39         30       35
                   vv
clus                STAGE IVA STAGE IVB
  SLC44A1 MUTATED           0         0
  SLC44A1 WILD-TYPE        13         1
D1388V3, multiclass
            clus
vv           SLC44A1 MUTATED SLC44A1 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 1                 0
  STAGE II                 0                25
  STAGE IIA                3               106
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               2                39
  STAGE IIIC               1                30
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC44A1 MUTATED     0   1   6   1
  SLC44A1 WILD-TYPE   9  67 242  40
D1388V4, multiclass
    clus
vv   SLC44A1 MUTATED SLC44A1 WILD-TYPE
  T1               0                 9
  T2               1                67
  T3               6               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
  SLC44A1 MUTATED     5   2   2
  SLC44A1 WILD-TYPE 215  78  64
D1388V5, multiclass
    clus
vv   SLC44A1 MUTATED SLC44A1 WILD-TYPE
  N0               5               215
  N1               2                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"
D1388V6, binary
                   cls
clus                  0   1
  SLC44A1 MUTATED     6   0
  SLC44A1 WILD-TYPE 277  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC44A1 MUTATED      6    0
  SLC44A1 WILD-TYPE  277   48
   clus
vv  SLC44A1 MUTATED SLC44A1 WILD-TYPE
  0               6               277
  1               0                48
[1] 2 2
[1] FALSE
D1388V7, 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
D1388V8, binary
                   cls
clus                  0   1
  SLC44A1 MUTATED     7   2
  SLC44A1 WILD-TYPE 310  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC44A1 MUTATED      7    2
  SLC44A1 WILD-TYPE  310   46
                               clus
vv                              SLC44A1 MUTATED SLC44A1 WILD-TYPE
  COLON ADENOCARCINOMA                        7               310
  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 251   2  22  19
D1388V9, multiclass
    clus
vv   SLC44A1 MUTATED SLC44A1 WILD-TYPE
  R0               6               251
  R1               0                 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"
D1388V10, 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
D1388V11, 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(1389) Variable = SYT2 MUTATION ANALYSIS
D1389V1, survival
                sevent
clus2              0   1
  SYT2 MUTATED     5   3
  SYT2 WILD-TYPE 277  70
  SYT2 MUTATED SYT2 WILD-TYPE 
             8            347 
  SYT2 MUTATED SYT2 WILD-TYPE 
             3             70 
$`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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
      100.01        29.56         5.23         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 
      119.93        35.97        60.79       117.07         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  SYT2 MUTATED SYT2 WILD-TYPE 
          1.02           0.00 
  SYT2 MUTATED SYT2 WILD-TYPE 
         98.24         140.38 
  SYT2 MUTATED SYT2 WILD-TYPE 
         14.58          20.28 
[1] "1.0 - 98.2 (14.6)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.7"
D1389V2, 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       23       107         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        19         10         41         31       34        13
                vv
clus             STAGE IVB
  SYT2 MUTATED           0
  SYT2 WILD-TYPE         1
D1389V3, multiclass
            clus
vv           SYT2 MUTATED SYT2 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             2            107
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SYT2 MUTATED     0   1   4   3
  SYT2 WILD-TYPE   9  67 244  38
D1389V4, multiclass
    clus
vv   SYT2 MUTATED SYT2 WILD-TYPE
  T1            0              9
  T2            1             67
  T3            4            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
  SYT2 MUTATED     7   0   1
  SYT2 WILD-TYPE 213  80  65
D1389V5, multiclass
    clus
vv   SYT2 MUTATED SYT2 WILD-TYPE
  N0            7            213
  N1            0             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"
D1389V6, binary
                cls
clus               0   1
  SYT2 MUTATED     6   1
  SYT2 WILD-TYPE 277  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  SYT2 MUTATED      6    1
  SYT2 WILD-TYPE  277   47
   clus
vv  SYT2 MUTATED SYT2 WILD-TYPE
  0            6            277
  1            1             47
[1] 2 2
[1] FALSE
D1389V7, 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
D1389V8, binary
                cls
clus               0   1
  SYT2 MUTATED     5   3
  SYT2 WILD-TYPE 312  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  SYT2 MUTATED      5    3
  SYT2 WILD-TYPE  312   45
                               clus
vv                              SYT2 MUTATED SYT2 WILD-TYPE
  COLON ADENOCARCINOMA                     5            312
  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 252   2  22  21
D1389V9, multiclass
    clus
vv   SYT2 MUTATED SYT2 WILD-TYPE
  R0            5            252
  R1            0              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"
D1389V10, 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
D1389V11, 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(1390) Variable = LCN9 MUTATION ANALYSIS
D1390V1, survival
                sevent
clus2              0   1
  LCN9 MUTATED     2   1
  LCN9 WILD-TYPE 280  72
  LCN9 MUTATED LCN9 WILD-TYPE 
             3            352 
  LCN9 MUTATED LCN9 WILD-TYPE 
             1             72 
$`LCN9 MUTATED`
TCGA-AZ-6608 TCGA-CK-4950 TCGA-D5-6534 
        1.94        40.34        43.27 

$`LCN9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       102.44        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 
       11.51        20.19        18.25         1.32        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  LCN9 MUTATED LCN9 WILD-TYPE 
          1.94           0.00 
  LCN9 MUTATED LCN9 WILD-TYPE 
         43.27         140.38 
  LCN9 MUTATED LCN9 WILD-TYPE 
        40.340         20.155 
[1] "1.9 - 43.3 (40.3)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.6"
D1390V2, 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       25       107         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LCN9 MUTATED           0          2          0          0        0         0
  LCN9 WILD-TYPE        19          8         41         31       35        13
                vv
clus             STAGE IVB
  LCN9 MUTATED           0
  LCN9 WILD-TYPE         1
D1390V3, multiclass
            clus
vv           LCN9 MUTATED LCN9 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             2            107
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            2              8
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  LCN9 MUTATED     0   1   3   0
  LCN9 WILD-TYPE   9  67 245  41
D1390V4, multiclass
    clus
vv   LCN9 MUTATED LCN9 WILD-TYPE
  T1            0              9
  T2            1             67
  T3            3            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
  LCN9 MUTATED     2   2   0
  LCN9 WILD-TYPE 218  78  66
D1390V5, multiclass
    clus
vv   LCN9 MUTATED LCN9 WILD-TYPE
  N0            2            218
  N1            2             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"
D1390V6, binary
                cls
clus               0   1
  LCN9 MUTATED     4   0
  LCN9 WILD-TYPE 279  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  LCN9 MUTATED      4    0
  LCN9 WILD-TYPE  279   48
   clus
vv  LCN9 MUTATED LCN9 WILD-TYPE
  0            4            279
  1            0             48
[1] 2 2
[1] FALSE
D1390V7, 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
D1390V8, binary
                cls
clus               0   1
  LCN9 MUTATED     3   1
  LCN9 WILD-TYPE 314  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  LCN9 MUTATED      3    1
  LCN9 WILD-TYPE  314   47
                               clus
vv                              LCN9 MUTATED LCN9 WILD-TYPE
  COLON ADENOCARCINOMA                     3            314
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  LCN9 MUTATED     2   1   0   0
  LCN9 WILD-TYPE 255   1  22  21
D1390V9, multiclass
    clus
vv   LCN9 MUTATED LCN9 WILD-TYPE
  R0            2            255
  R1            1              1
  R2            0             22
  RX            0             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1390V10, 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
D1390V11, 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(1391) Variable = DDHD2 MUTATION ANALYSIS
D1391V1, survival
                 sevent
clus2               0   1
  DDHD2 MUTATED     6   3
  DDHD2 WILD-TYPE 276  70
  DDHD2 MUTATED DDHD2 WILD-TYPE 
              9             346 
  DDHD2 MUTATED DDHD2 WILD-TYPE 
              3              70 
$`DDHD2 MUTATED`
TCGA-A6-6781 TCGA-AA-3555 TCGA-AA-3715 TCGA-AA-3947 TCGA-AZ-6599 TCGA-CK-5913 
       19.66        29.95        19.04        33.01         6.77        51.32 
TCGA-CM-6161 TCGA-D5-6923 TCGA-G4-6626 
       15.02        12.43        46.75 

$`DDHD2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        17.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41        49.41        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        21.99        21.14         2.93         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        16.01        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 
       15.58         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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       35.80        26.17        91.79        52.80 

  DDHD2 MUTATED DDHD2 WILD-TYPE 
           6.77            0.00 
  DDHD2 MUTATED DDHD2 WILD-TYPE 
          51.32          140.38 
  DDHD2 MUTATED DDHD2 WILD-TYPE 
         19.660          20.235 
[1] "6.8 - 51.3 (19.7)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.6"
D1391V2, 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       24       106         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        19         10         41         30       35        13
                 vv
clus              STAGE IVB
  DDHD2 MUTATED           0
  DDHD2 WILD-TYPE         1
D1391V3, multiclass
            clus
vv           DDHD2 MUTATED DDHD2 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              3             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DDHD2 MUTATED     0   3   4   2
  DDHD2 WILD-TYPE   9  65 244  39
D1391V4, multiclass
    clus
vv   DDHD2 MUTATED DDHD2 WILD-TYPE
  T1             0               9
  T2             3              65
  T3             4             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
  DDHD2 MUTATED     8   1   0
  DDHD2 WILD-TYPE 212  79  66
D1391V5, multiclass
    clus
vv   DDHD2 MUTATED DDHD2 WILD-TYPE
  N0             8             212
  N1             1              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"
D1391V6, binary
                 cls
clus                0   1
  DDHD2 MUTATED     6   0
  DDHD2 WILD-TYPE 277  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDHD2 MUTATED      6    0
  DDHD2 WILD-TYPE  277   48
   clus
vv  DDHD2 MUTATED DDHD2 WILD-TYPE
  0             6             277
  1             0              48
[1] 2 2
[1] FALSE
D1391V7, 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
D1391V8, binary
                 cls
clus                0   1
  DDHD2 MUTATED     6   3
  DDHD2 WILD-TYPE 311  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDHD2 MUTATED      6    3
  DDHD2 WILD-TYPE  311   45
                               clus
vv                              DDHD2 MUTATED DDHD2 WILD-TYPE
  COLON ADENOCARCINOMA                      6             311
  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 250   2  22  20
D1391V9, multiclass
    clus
vv   DDHD2 MUTATED DDHD2 WILD-TYPE
  R0             7             250
  R1             0               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"
D1391V10, 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
D1391V11, 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(1392) Variable = RBM15B MUTATION ANALYSIS
D1392V1, survival
                  sevent
clus2                0   1
  RBM15B MUTATED     7   1
  RBM15B WILD-TYPE 275  72
  RBM15B MUTATED RBM15B WILD-TYPE 
               8              347 
  RBM15B MUTATED RBM15B WILD-TYPE 
               1               72 
$`RBM15B MUTATED`
TCGA-A6-5661 TCGA-A6-6653 TCGA-AA-3492 TCGA-AA-3864 TCGA-AA-A00K TCGA-AD-5900 
       33.53        24.39         3.02        53.00        18.05         0.07 
TCGA-CA-6718 TCGA-CM-6678 
        0.10        11.01 

$`RBM15B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.33         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  RBM15B MUTATED RBM15B WILD-TYPE 
            0.07             0.00 
  RBM15B MUTATED RBM15B WILD-TYPE 
           53.00           140.38 
  RBM15B MUTATED RBM15B WILD-TYPE 
           14.53            20.28 
[1] "0.1 - 53.0 (14.5)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.2"
D1392V2, 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       23       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RBM15B MUTATED           0          0          0          0        0
  RBM15B WILD-TYPE        19         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  RBM15B MUTATED           1         0
  RBM15B WILD-TYPE        12         1
D1392V3, multiclass
            clus
vv           RBM15B MUTATED RBM15B WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               3              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 243  40
D1392V4, multiclass
    clus
vv   RBM15B MUTATED RBM15B WILD-TYPE
  T1              0                9
  T2              2               66
  T3              5              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
  RBM15B MUTATED     7   1   0
  RBM15B WILD-TYPE 213  79  66
D1392V5, multiclass
    clus
vv   RBM15B MUTATED RBM15B WILD-TYPE
  N0              7              213
  N1              1               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"
D1392V6, binary
                  cls
clus                 0   1
  RBM15B MUTATED     6   1
  RBM15B WILD-TYPE 277  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RBM15B MUTATED      6    1
  RBM15B WILD-TYPE  277   47
   clus
vv  RBM15B MUTATED RBM15B WILD-TYPE
  0              6              277
  1              1               47
[1] 2 2
[1] FALSE
D1392V7, 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
D1392V8, binary
                  cls
clus                 0   1
  RBM15B MUTATED     7   1
  RBM15B WILD-TYPE 310  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RBM15B MUTATED      7    1
  RBM15B WILD-TYPE  310   47
                               clus
vv                              RBM15B MUTATED RBM15B WILD-TYPE
  COLON ADENOCARCINOMA                       7              310
  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 251   2  22  20
D1392V9, multiclass
    clus
vv   RBM15B MUTATED RBM15B WILD-TYPE
  R0              6              251
  R1              0                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"
D1392V10, 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
D1392V11, 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(1393) Variable = DCLRE1C MUTATION ANALYSIS
D1393V1, survival
                   sevent
clus2                 0   1
  DCLRE1C MUTATED     6   2
  DCLRE1C WILD-TYPE 276  71
  DCLRE1C MUTATED DCLRE1C WILD-TYPE 
                8               347 
  DCLRE1C MUTATED DCLRE1C WILD-TYPE 
                2                71 
$`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         0.33 
TCGA-CK-6747 TCGA-D5-5540 
        2.93        13.51 

$`DCLRE1C WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.12        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  DCLRE1C MUTATED DCLRE1C WILD-TYPE 
             0.33              0.00 
  DCLRE1C MUTATED DCLRE1C WILD-TYPE 
            49.41            140.38 
  DCLRE1C MUTATED DCLRE1C WILD-TYPE 
           16.585            20.280 
[1] "0.3 - 49.4 (16.6)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.7"
D1393V2, 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       22       105         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DCLRE1C MUTATED           0          0          0          1        0
  DCLRE1C WILD-TYPE        19         10         41         30       35
                   vv
clus                STAGE IVA STAGE IVB
  DCLRE1C MUTATED           0         0
  DCLRE1C WILD-TYPE        13         1
D1393V3, multiclass
            clus
vv           DCLRE1C MUTATED DCLRE1C WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 3                22
  STAGE IIA                4               105
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               1                30
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  DCLRE1C MUTATED     0   0   6   3
  DCLRE1C WILD-TYPE   9  68 242  38
D1393V4, multiclass
    clus
vv   DCLRE1C MUTATED DCLRE1C WILD-TYPE
  T1               0                 9
  T2               0                68
  T3               6               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
  DCLRE1C MUTATED     8   1   0
  DCLRE1C WILD-TYPE 212  79  66
D1393V5, multiclass
    clus
vv   DCLRE1C MUTATED DCLRE1C WILD-TYPE
  N0               8               212
  N1               1                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"
D1393V6, binary
                   cls
clus                  0   1
  DCLRE1C MUTATED     6   0
  DCLRE1C WILD-TYPE 277  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DCLRE1C MUTATED      6    0
  DCLRE1C WILD-TYPE  277   48
   clus
vv  DCLRE1C MUTATED DCLRE1C WILD-TYPE
  0               6               277
  1               0                48
[1] 2 2
[1] FALSE
D1393V7, 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
D1393V8, binary
                   cls
clus                  0   1
  DCLRE1C MUTATED     6   3
  DCLRE1C WILD-TYPE 311  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DCLRE1C MUTATED      6    3
  DCLRE1C WILD-TYPE  311   45
                               clus
vv                              DCLRE1C MUTATED DCLRE1C WILD-TYPE
  COLON ADENOCARCINOMA                        6               311
  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 251   2  22  19
D1393V9, multiclass
    clus
vv   DCLRE1C MUTATED DCLRE1C WILD-TYPE
  R0               6               251
  R1               0                 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"
D1393V10, 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
D1393V11, 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(1394) Variable = TAF4 MUTATION ANALYSIS
D1394V1, survival
                sevent
clus2              0   1
  TAF4 MUTATED     4   4
  TAF4 WILD-TYPE 278  69
  TAF4 MUTATED TAF4 WILD-TYPE 
             8            347 
  TAF4 MUTATED TAF4 WILD-TYPE 
             4             69 
$`TAF4 MUTATED`
TCGA-AA-3492 TCGA-AA-3660 TCGA-AA-3692 TCGA-AA-3811 TCGA-AA-3977 TCGA-AZ-4682 
        3.02        78.08        36.00        10.06        25.02        22.36 
TCGA-CM-6169 TCGA-G4-6309 
       13.02        51.75 

$`TAF4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        61.02         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3696 
       15.02        11.01         5.98        37.05        19.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        19.04        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-5403 
       17.82        58.39         1.41         5.13        83.80        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  TAF4 MUTATED TAF4 WILD-TYPE 
          3.02           0.00 
  TAF4 MUTATED TAF4 WILD-TYPE 
         78.08         140.38 
  TAF4 MUTATED TAF4 WILD-TYPE 
         23.69          20.12 
[1] "3.0 - 78.1 (23.7)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "2.1"
D1394V2, 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       22       108         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        18         10         40         31       34        12
                vv
clus             STAGE IVB
  TAF4 MUTATED           0
  TAF4 WILD-TYPE         1
D1394V3, multiclass
            clus
vv           TAF4 MUTATED TAF4 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              3             22
  STAGE IIA             1            108
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 241  40
D1394V4, multiclass
    clus
vv   TAF4 MUTATED TAF4 WILD-TYPE
  T1            0              9
  T2            1             67
  T3            7            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
  TAF4 MUTATED     6   1   2
  TAF4 WILD-TYPE 214  79  64
D1394V5, multiclass
    clus
vv   TAF4 MUTATED TAF4 WILD-TYPE
  N0            6            214
  N1            1             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"
D1394V6, binary
                cls
clus               0   1
  TAF4 MUTATED     6   2
  TAF4 WILD-TYPE 277  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF4 MUTATED      6    2
  TAF4 WILD-TYPE  277   46
   clus
vv  TAF4 MUTATED TAF4 WILD-TYPE
  0            6            277
  1            2             46
[1] 2 2
[1] FALSE
D1394V7, 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
D1394V8, binary
                cls
clus               0   1
  TAF4 MUTATED     8   1
  TAF4 WILD-TYPE 309  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF4 MUTATED      8    1
  TAF4 WILD-TYPE  309   47
                               clus
vv                              TAF4 MUTATED TAF4 WILD-TYPE
  COLON ADENOCARCINOMA                     8            309
  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 250   2  21  21
D1394V9, multiclass
    clus
vv   TAF4 MUTATED TAF4 WILD-TYPE
  R0            7            250
  R1            0              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"
D1394V10, 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
D1394V11, 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(1395) Variable = IFITM5 MUTATION ANALYSIS
D1395V1, survival
                  sevent
clus2                0   1
  IFITM5 MUTATED     2   1
  IFITM5 WILD-TYPE 280  72
  IFITM5 MUTATED IFITM5 WILD-TYPE 
               3              352 
  IFITM5 MUTATED IFITM5 WILD-TYPE 
               1               72 
$`IFITM5 MUTATED`
TCGA-A6-6653 TCGA-AA-3492 TCGA-D5-6922 
       24.39         3.02        10.13 

$`IFITM5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  IFITM5 MUTATED IFITM5 WILD-TYPE 
            3.02             0.00 
  IFITM5 MUTATED IFITM5 WILD-TYPE 
           24.39           140.38 
  IFITM5 MUTATED IFITM5 WILD-TYPE 
          10.130           20.235 
[1] "3.0 - 24.4 (10.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "3.1"
D1395V2, 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       24       109         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IFITM5 MUTATED           0          1          0          0        0
  IFITM5 WILD-TYPE        19          9         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  IFITM5 MUTATED           0         0
  IFITM5 WILD-TYPE        13         1
D1395V3, multiclass
            clus
vv           IFITM5 MUTATED IFITM5 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               0              109
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              1                9
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  IFITM5 MUTATED     0   1   2   0
  IFITM5 WILD-TYPE   9  67 246  41
D1395V4, multiclass
    clus
vv   IFITM5 MUTATED IFITM5 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              2              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
  IFITM5 MUTATED     2   1   0
  IFITM5 WILD-TYPE 218  79  66
D1395V5, multiclass
    clus
vv   IFITM5 MUTATED IFITM5 WILD-TYPE
  N0              2              218
  N1              1               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"
D1395V6, binary
                  cls
clus                 0   1
  IFITM5 MUTATED     3   0
  IFITM5 WILD-TYPE 280  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFITM5 MUTATED      3    0
  IFITM5 WILD-TYPE  280   48
   clus
vv  IFITM5 MUTATED IFITM5 WILD-TYPE
  0              3              280
  1              0               48
[1] 2 2
[1] FALSE
D1395V7, 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
D1395V8, binary
                  cls
clus                 0   1
  IFITM5 MUTATED     3   0
  IFITM5 WILD-TYPE 314  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFITM5 MUTATED      3    0
  IFITM5 WILD-TYPE  314   48
                               clus
vv                              IFITM5 MUTATED IFITM5 WILD-TYPE
  COLON ADENOCARCINOMA                       3              314
  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 255   2  22  21
D1395V9, multiclass
[1] "Remove cluster labels:" "IFITM5 MUTATED"        
clus
  IFITM5 MUTATED IFITM5 WILD-TYPE 
               2              300 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-5657 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-A6-5659       TCGA-A6-5661       TCGA-A6-5665       TCGA-A6-6781 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3489       TCGA-AA-3496       TCGA-AA-3502       TCGA-AA-3510 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3511       TCGA-AA-3514       TCGA-AA-3517       TCGA-AA-3518 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3519       TCGA-AA-3520       TCGA-AA-3521       TCGA-AA-3522 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3524       TCGA-AA-3525       TCGA-AA-3526       TCGA-AA-3527 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3529       TCGA-AA-3530       TCGA-AA-3531       TCGA-AA-3532 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3534       TCGA-AA-3538       TCGA-AA-3542       TCGA-AA-3543 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3544       TCGA-AA-3548       TCGA-AA-3549       TCGA-AA-3552 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3553       TCGA-AA-3554       TCGA-AA-3555       TCGA-AA-3556 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3558       TCGA-AA-3560       TCGA-AA-3561       TCGA-AA-3562 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3655       TCGA-AA-3660       TCGA-AA-3662       TCGA-AA-3663 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3664       TCGA-AA-3666       TCGA-AA-3667       TCGA-AA-3672 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3673       TCGA-AA-3678       TCGA-AA-3679       TCGA-AA-3680 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3681       TCGA-AA-3684       TCGA-AA-3685       TCGA-AA-3688 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3692       TCGA-AA-3693       TCGA-AA-3695       TCGA-AA-3696 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3697       TCGA-AA-3710       TCGA-AA-3712       TCGA-AA-3713 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3715       TCGA-AA-3811       TCGA-AA-3812       TCGA-AA-3814 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3815       TCGA-AA-3818       TCGA-AA-3819       TCGA-AA-3821 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3831       TCGA-AA-3833       TCGA-AA-3837       TCGA-AA-3842 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3844       TCGA-AA-3845       TCGA-AA-3846       TCGA-AA-3848 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3850       TCGA-AA-3851       TCGA-AA-3852       TCGA-AA-3854 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3855       TCGA-AA-3856       TCGA-AA-3858       TCGA-AA-3860 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3861       TCGA-AA-3864       TCGA-AA-3866       TCGA-AA-3867 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3869       TCGA-AA-3870       TCGA-AA-3872       TCGA-AA-3875 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3877       TCGA-AA-3930       TCGA-AA-3939       TCGA-AA-3941 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3947       TCGA-AA-3949       TCGA-AA-3950       TCGA-AA-3952 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3955       TCGA-AA-3956       TCGA-AA-3968       TCGA-AA-3971 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3972       TCGA-AA-3973       TCGA-AA-3975       TCGA-AA-3976 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3979       TCGA-AA-3984       TCGA-AA-3986       TCGA-AA-3989 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3994       TCGA-AA-A004       TCGA-AA-A00A       TCGA-AA-A00D 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-A00E       TCGA-AA-A00F       TCGA-AA-A00J       TCGA-AA-A00K 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-A00L       TCGA-AA-A00N       TCGA-AA-A00O       TCGA-AA-A00Q 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-A00R       TCGA-AA-A00U       TCGA-AA-A00W       TCGA-AA-A00Z 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-A010       TCGA-AA-A017       TCGA-AA-A01D       TCGA-AA-A01F 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-A01G       TCGA-AA-A01I       TCGA-AA-A01K       TCGA-AA-A01P 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-A01Q       TCGA-AA-A01R       TCGA-AA-A01S       TCGA-AA-A01T 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-A01V       TCGA-AA-A01X       TCGA-AA-A01Z       TCGA-AA-A022 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-A024       TCGA-AA-A029       TCGA-AA-A02F       TCGA-AA-A02H 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-A02J       TCGA-AA-A02K       TCGA-AA-A02O       TCGA-AA-A02W 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-A02Y       TCGA-AA-A03F       TCGA-AA-A03J       TCGA-AD-5900 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AD-6548       TCGA-AD-6888       TCGA-AU-3779       TCGA-AU-6004 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AY-4070       TCGA-AY-4071       TCGA-AY-5543       TCGA-AY-6196 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AY-6197       TCGA-AY-6386       TCGA-AZ-4315       TCGA-AZ-4681 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AZ-4682       TCGA-CA-5254       TCGA-CA-5255       TCGA-CA-5796 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CA-5797       TCGA-CA-6715       TCGA-CA-6716       TCGA-CA-6717 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CA-6718       TCGA-CA-6719       TCGA-CK-4947       TCGA-CK-4948 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CK-4950       TCGA-CK-4952       TCGA-CK-5912       TCGA-CK-5913 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CK-5914       TCGA-CK-5915       TCGA-CK-5916       TCGA-CK-6746 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CK-6747       TCGA-CK-6748       TCGA-CK-6751       TCGA-CM-4743 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CM-4744       TCGA-CM-4746       TCGA-CM-4747       TCGA-CM-4752 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CM-5341       TCGA-CM-5344       TCGA-CM-5348       TCGA-CM-5349 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CM-5860       TCGA-CM-5861       TCGA-CM-5862       TCGA-CM-5863 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CM-5864       TCGA-CM-5868       TCGA-CM-6161       TCGA-CM-6162 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CM-6163       TCGA-CM-6164       TCGA-CM-6165       TCGA-CM-6166 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CM-6167       TCGA-CM-6168       TCGA-CM-6169       TCGA-CM-6170 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CM-6171       TCGA-CM-6172       TCGA-CM-6674       TCGA-CM-6675 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CM-6676       TCGA-CM-6677       TCGA-CM-6678       TCGA-CM-6679 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CM-6680       TCGA-D5-5537       TCGA-D5-5538       TCGA-D5-5539 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-D5-5540       TCGA-D5-5541       TCGA-D5-6529       TCGA-D5-6532 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-D5-6533       TCGA-D5-6534       TCGA-D5-6535       TCGA-D5-6536 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-D5-6537       TCGA-D5-6538       TCGA-D5-6539       TCGA-D5-6540 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-D5-6541       TCGA-D5-6898       TCGA-D5-6920       TCGA-D5-6923 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-D5-6924       TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-D5-6929       TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-D5-7000       TCGA-F4-6459       TCGA-F4-6460       TCGA-F4-6569 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704       TCGA-F4-6805 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808       TCGA-F4-6809 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856       TCGA-G4-6293 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304       TCGA-G4-6306 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310       TCGA-G4-6315 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323       TCGA-G4-6586 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
D1395V10, 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
D1395V11, multiclass
[1] "Remove cluster labels:" "IFITM5 MUTATED"        
clus
  IFITM5 MUTATED IFITM5 WILD-TYPE 
               2              204 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-4105 
"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-A6-6649       TCGA-A6-6651 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-A6-6652       TCGA-A6-6654       TCGA-A6-6780       TCGA-A6-6781 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-A6-6782       TCGA-AD-5900       TCGA-AD-6548       TCGA-AD-6888 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AD-6889       TCGA-AD-6890       TCGA-AD-6895       TCGA-AD-6899 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6964       TCGA-AD-6965 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070       TCGA-AY-4071 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AZ-4315       TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4681 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AZ-4682       TCGA-AZ-5403       TCGA-AZ-5407       TCGA-AZ-6598 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AZ-6599       TCGA-AZ-6600       TCGA-AZ-6601       TCGA-AZ-6603 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AZ-6605       TCGA-AZ-6606       TCGA-AZ-6607       TCGA-AZ-6608 
"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-5912       TCGA-CK-5913       TCGA-CK-5914 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CK-5915       TCGA-CK-5916       TCGA-CK-6746       TCGA-CK-6747 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CK-6748       TCGA-CK-6751       TCGA-CM-4743       TCGA-CM-4744 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CM-4746       TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CM-5344       TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CM-5861       TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CM-5868       TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CM-6164       TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CM-6168       TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CM-6172       TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CM-6677       TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-D5-5537       TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-D5-5541       TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-D5-6534       TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-D5-6538       TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-D5-6898       TCGA-D5-6920       TCGA-D5-6923       TCGA-D5-6924 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928       TCGA-D5-6929 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932       TCGA-D5-7000 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-DM-A0X9       TCGA-DM-A0XD       TCGA-DM-A0XF       TCGA-DM-A1D0 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-DM-A1D4       TCGA-DM-A1D6       TCGA-DM-A1D7       TCGA-DM-A1D8 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-DM-A1D9       TCGA-DM-A1DA       TCGA-DM-A1DB       TCGA-DM-A1HA 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-DM-A1HB       TCGA-DM-A282       TCGA-DM-A285       TCGA-DM-A28C 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-DM-A28E       TCGA-DM-A28F       TCGA-DM-A28G       TCGA-DM-A28H 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-DM-A28K       TCGA-F4-6459       TCGA-F4-6460       TCGA-F4-6569 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704       TCGA-F4-6805 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808       TCGA-F4-6809 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856       TCGA-G4-6293 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304       TCGA-G4-6306 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310       TCGA-G4-6315 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323       TCGA-G4-6586 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 

Clustering(1396) Variable = ESRP2 MUTATION ANALYSIS
D1396V1, survival
                 sevent
clus2               0   1
  ESRP2 MUTATED     7   2
  ESRP2 WILD-TYPE 275  71
  ESRP2 MUTATED ESRP2 WILD-TYPE 
              9             346 
  ESRP2 MUTATED ESRP2 WILD-TYPE 
              2              71 
$`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         0.10 
TCGA-CM-5344 TCGA-D5-6536 TCGA-DM-A1D9 
       22.03        17.85       140.38 

$`ESRP2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         0.72         5.79        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32        12.59         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  ESRP2 MUTATED ESRP2 WILD-TYPE 
            0.1             0.0 
  ESRP2 MUTATED ESRP2 WILD-TYPE 
         140.38          139.17 
  ESRP2 MUTATED ESRP2 WILD-TYPE 
          22.36           20.07 
[1] "0.1 - 140.4 (22.4)" "0.0 - 139.2 (20.1)"
[1] "hr=" "1"  
D1396V2, 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       24       105         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        19         10         40         31       35        12
                 vv
clus              STAGE IVB
  ESRP2 MUTATED           0
  ESRP2 WILD-TYPE         1
D1396V3, multiclass
            clus
vv           ESRP2 MUTATED ESRP2 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              4             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  68 240  40
D1396V4, multiclass
    clus
vv   ESRP2 MUTATED ESRP2 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             8             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
  ESRP2 MUTATED     8   1   0
  ESRP2 WILD-TYPE 212  79  66
D1396V5, multiclass
    clus
vv   ESRP2 MUTATED ESRP2 WILD-TYPE
  N0             8             212
  N1             1              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
  ESRP2 MUTATED     7   1
  ESRP2 WILD-TYPE 276  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESRP2 MUTATED      7    1
  ESRP2 WILD-TYPE  276   47
   clus
vv  ESRP2 MUTATED ESRP2 WILD-TYPE
  0             7             276
  1             1              47
[1] 2 2
[1] FALSE
D1396V7, 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
D1396V8, binary
                 cls
clus                0   1
  ESRP2 MUTATED     9   0
  ESRP2 WILD-TYPE 308  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESRP2 MUTATED      9    0
  ESRP2 WILD-TYPE  308   48
                               clus
vv                              ESRP2 MUTATED ESRP2 WILD-TYPE
  COLON ADENOCARCINOMA                      9             308
  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 251   2  22  20
D1396V9, multiclass
    clus
vv   ESRP2 MUTATED ESRP2 WILD-TYPE
  R0             6             251
  R1             0               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"
D1396V10, 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
D1396V11, 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(1397) Variable = FRY MUTATION ANALYSIS
D1397V1, survival
               sevent
clus2             0   1
  FRY MUTATED    31   7
  FRY WILD-TYPE 251  66
  FRY MUTATED FRY WILD-TYPE 
           38           317 
  FRY MUTATED FRY WILD-TYPE 
            7            66 
$`FRY MUTATED`
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-4105 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6141 
       33.34        32.75        14.53        33.53        22.06         8.38 
TCGA-AA-3492 TCGA-AA-3663 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3977 
        3.02         6.97        53.00        31.00        33.01        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A02O TCGA-AA-A03F 
        4.01        34.98        38.07        35.01         0.92        18.05 
TCGA-AD-5900 TCGA-AU-6004 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 
        0.07        27.09        21.44        58.39        49.41         0.33 
TCGA-CA-6718 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-6168 
        0.10        37.02        25.02        16.01        15.02        12.99 
TCGA-D5-6538 TCGA-DM-A0X9 TCGA-DM-A1DA TCGA-F4-6703 TCGA-F4-6806 TCGA-F4-6855 
       17.13       119.70         7.50        35.87        29.59        35.41 
TCGA-G4-6307 TCGA-G4-6628 
       55.04        52.80 

$`FRY WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       16.57        34.65        36.53        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       29.19        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       27.02        29.98        18.05         2.01        12.99        24.00 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-6548 
        5.03        14.01        41.00        39.98        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       15.75         0.20        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07         0.26         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12        17.85         4.80        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38        10.26        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        6.18         1.55        16.31        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       13.78        35.80        26.17        91.79        46.75 

  FRY MUTATED FRY WILD-TYPE 
         0.07          0.00 
  FRY MUTATED FRY WILD-TYPE 
       119.70        140.38 
  FRY MUTATED FRY WILD-TYPE 
       26.055        19.990 
[1] "0.1 - 119.7 (26.1)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.2"
D1397V2, 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       20        94         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        16         10         39         30       35        12
               vv
clus            STAGE IVB
  FRY MUTATED           0
  FRY WILD-TYPE         1
D1397V3, multiclass
            clus
vv           FRY MUTATED FRY WILD-TYPE
  STAGE I              6            58
  STAGE IA             0             1
  STAGE II             5            20
  STAGE IIA           15            94
  STAGE IIB            4             4
  STAGE IIC            0             1
  STAGE III            3            16
  STAGE IIIA           0            10
  STAGE IIIB           2            39
  STAGE IIIC           1            30
  STAGE IV             0            35
  STAGE IVA            1            12
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of 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  62 222  36
D1397V4, multiclass
    clus
vv   FRY MUTATED FRY WILD-TYPE
  T1           1             8
  T2           6            62
  T3          26           222
  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  77  62
D1397V5, multiclass
    clus
vv   FRY MUTATED FRY WILD-TYPE
  N0          31           189
  N1           3            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"
D1397V6, binary
               cls
clus              0   1
  FRY MUTATED    33   1
  FRY WILD-TYPE 250  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  FRY MUTATED     33    1
  FRY WILD-TYPE  250   47
   clus
vv  FRY MUTATED FRY WILD-TYPE
  0          33           250
  1           1            47
[1] 2 2
[1] FALSE
D1397V7, 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
D1397V8, binary
               cls
clus              0   1
  FRY MUTATED    30   8
  FRY WILD-TYPE 287  40
[1] "tbl2"
               cls
clus            [,1] [,2]
  FRY MUTATED     30    8
  FRY WILD-TYPE  287   40
                               clus
vv                              FRY MUTATED FRY WILD-TYPE
  COLON ADENOCARCINOMA                   30           287
  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 227   2  22  19
D1397V9, multiclass
    clus
vv   FRY MUTATED FRY WILD-TYPE
  R0          30           227
  R1           0             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"
D1397V10, 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
D1397V11, 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(1398) Variable = CTCFL MUTATION ANALYSIS
D1398V1, survival
                 sevent
clus2               0   1
  CTCFL MUTATED    11   3
  CTCFL WILD-TYPE 271  70
  CTCFL MUTATED CTCFL WILD-TYPE 
             14             341 
  CTCFL MUTATED CTCFL WILD-TYPE 
              3              70 
$`CTCFL MUTATED`
TCGA-A6-6141 TCGA-AA-3672 TCGA-AA-3815 TCGA-AA-3833 TCGA-AA-3977 TCGA-AA-A00N 
        8.38         0.92        33.04        15.95        25.02         4.01 
TCGA-AA-A01R TCGA-AY-6196 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-6171 TCGA-D5-5537 
       35.01         0.20         0.33         0.10        14.04        45.40 
TCGA-DM-A1DB TCGA-G4-6323 
       44.32        13.78 

$`CTCFL WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 
       35.05         0.99        25.02         1.02        17.98        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        15.75        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07         0.26         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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-D5-5538 
       11.08        11.08        11.01        10.06        12.03        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  CTCFL MUTATED CTCFL WILD-TYPE 
            0.1             0.0 
  CTCFL MUTATED CTCFL WILD-TYPE 
          45.40          140.38 
  CTCFL MUTATED CTCFL WILD-TYPE 
          13.91           20.98 
[1] "0.1 - 45.4 (13.9)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.6"
D1398V2, 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       25       101         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        17         10         41         30       35        13
                 vv
clus              STAGE IVB
  CTCFL MUTATED           0
  CTCFL WILD-TYPE         1
D1398V3, multiclass
            clus
vv           CTCFL MUTATED CTCFL WILD-TYPE
  STAGE I                1              63
  STAGE IA               1               0
  STAGE II               0              25
  STAGE IIA              8             101
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CTCFL MUTATED     0   2  11   1
  CTCFL WILD-TYPE   9  66 237  40
D1398V4, multiclass
    clus
vv   CTCFL MUTATED CTCFL WILD-TYPE
  T1             0               9
  T2             2              66
  T3            11             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
  CTCFL MUTATED    11   1   3
  CTCFL WILD-TYPE 209  79  63
D1398V5, multiclass
    clus
vv   CTCFL MUTATED CTCFL WILD-TYPE
  N0            11             209
  N1             1              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"
D1398V6, binary
                 cls
clus                0   1
  CTCFL MUTATED    11   0
  CTCFL WILD-TYPE 272  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CTCFL MUTATED     11    0
  CTCFL WILD-TYPE  272   48
   clus
vv  CTCFL MUTATED CTCFL WILD-TYPE
  0            11             272
  1             0              48
[1] 2 2
[1] FALSE
D1398V7, 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
D1398V8, binary
                 cls
clus                0   1
  CTCFL MUTATED    11   4
  CTCFL WILD-TYPE 306  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CTCFL MUTATED     11    4
  CTCFL WILD-TYPE  306   44
                               clus
vv                              CTCFL MUTATED CTCFL WILD-TYPE
  COLON ADENOCARCINOMA                     11             306
  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 248   2  22  18
D1398V9, multiclass
    clus
vv   CTCFL MUTATED CTCFL WILD-TYPE
  R0             9             248
  R1             0               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"
D1398V10, 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
D1398V11, 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(1399) Variable = HIST1H2BC MUTATION ANALYSIS
D1399V1, survival
                     sevent
clus2                   0   1
  HIST1H2BC MUTATED     4   0
  HIST1H2BC WILD-TYPE 278  73
  HIST1H2BC MUTATED HIST1H2BC WILD-TYPE 
                  4                 351 
  HIST1H2BC MUTATED HIST1H2BC WILD-TYPE 
                  0                  73 
$`HIST1H2BC MUTATED`
TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-A010 TCGA-G4-6299 
       22.06        63.98        34.98        74.56 

$`HIST1H2BC WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  HIST1H2BC MUTATED HIST1H2BC WILD-TYPE 
              22.06                0.00 
  HIST1H2BC MUTATED HIST1H2BC WILD-TYPE 
              74.56              140.38 
  HIST1H2BC MUTATED HIST1H2BC WILD-TYPE 
              49.48               20.02 
[1] "22.1 - 74.6 (49.5)" "0.0 - 140.4 (20.0)"
[1] "hr="     "9400000"
D1399V2, 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       24       108         7         1
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HIST1H2BC MUTATED           0          0          0          1        0
  HIST1H2BC WILD-TYPE        19         10         41         30       35
                     vv
clus                  STAGE IVA STAGE IVB
  HIST1H2BC MUTATED           0         0
  HIST1H2BC WILD-TYPE        13         1
D1399V3, multiclass
            clus
vv           HIST1H2BC MUTATED HIST1H2BC WILD-TYPE
  STAGE I                    0                  64
  STAGE IA                   0                   1
  STAGE II                   1                  24
  STAGE IIA                  1                 108
  STAGE IIB                  1                   7
  STAGE IIC                  0                   1
  STAGE III                  0                  19
  STAGE IIIA                 0                  10
  STAGE IIIB                 0                  41
  STAGE IIIC                 1                  30
  STAGE IV                   0                  35
  STAGE IVA                  0                  13
  STAGE IVB                  0                   1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2  T3  T4
  HIST1H2BC MUTATED     0   0   3   1
  HIST1H2BC WILD-TYPE   9  68 245  40
D1399V4, multiclass
    clus
vv   HIST1H2BC MUTATED HIST1H2BC WILD-TYPE
  T1                 0                   9
  T2                 0                  68
  T3                 3                 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
  HIST1H2BC MUTATED     3   0   1
  HIST1H2BC WILD-TYPE 217  80  65
D1399V5, multiclass
    clus
vv   HIST1H2BC MUTATED HIST1H2BC WILD-TYPE
  N0                 3                 217
  N1                 0                  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"
D1399V6, binary
                     cls
clus                    0   1
  HIST1H2BC MUTATED     4   0
  HIST1H2BC WILD-TYPE 279  48
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  HIST1H2BC MUTATED      4    0
  HIST1H2BC WILD-TYPE  279   48
   clus
vv  HIST1H2BC MUTATED HIST1H2BC WILD-TYPE
  0                 4                 279
  1                 0                  48
[1] 2 2
[1] FALSE
D1399V7, 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
D1399V8, binary
                     cls
clus                    0   1
  HIST1H2BC MUTATED     4   0
  HIST1H2BC WILD-TYPE 313  48
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  HIST1H2BC MUTATED      4    0
  HIST1H2BC WILD-TYPE  313   48
                               clus
vv                              HIST1H2BC MUTATED HIST1H2BC WILD-TYPE
  COLON ADENOCARCINOMA                          4                 313
  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 253   2  22  21
D1399V9, multiclass
    clus
vv   HIST1H2BC MUTATED HIST1H2BC WILD-TYPE
  R0                 4                 253
  R1                 0                   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"
D1399V10, 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
D1399V11, multiclass
[1] "Remove cluster labels:" "HIST1H2BC MUTATED"     
clus
  HIST1H2BC MUTATED HIST1H2BC WILD-TYPE 
                  2                 204 
         TCGA-A6-2671          TCGA-A6-2672          TCGA-A6-2674 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-A6-2676          TCGA-A6-2677          TCGA-A6-2678 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-A6-2683          TCGA-A6-3807          TCGA-A6-3808 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-A6-3809          TCGA-A6-3810          TCGA-A6-4105 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-A6-5656          TCGA-A6-5657          TCGA-A6-5659 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-A6-5660          TCGA-A6-5661          TCGA-A6-5662 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-A6-5664          TCGA-A6-5666          TCGA-A6-6137 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-A6-6138          TCGA-A6-6141          TCGA-A6-6142 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-A6-6648          TCGA-A6-6649          TCGA-A6-6651 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-A6-6652          TCGA-A6-6653          TCGA-A6-6654 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-A6-6780          TCGA-A6-6781          TCGA-A6-6782 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-AD-5900          TCGA-AD-6548          TCGA-AD-6888 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-AD-6889          TCGA-AD-6890          TCGA-AD-6895 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-AD-6899          TCGA-AD-6901          TCGA-AD-6963 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-AD-6964          TCGA-AD-6965          TCGA-AU-3779 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-AU-6004          TCGA-AY-4070          TCGA-AY-4071 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-AY-5543          TCGA-AY-6196          TCGA-AY-6197 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-AY-6386          TCGA-AZ-4315          TCGA-AZ-4323 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-AZ-4616          TCGA-AZ-4681          TCGA-AZ-4682 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-AZ-5403          TCGA-AZ-5407          TCGA-AZ-6598 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-AZ-6599          TCGA-AZ-6600          TCGA-AZ-6601 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-AZ-6603          TCGA-AZ-6605          TCGA-AZ-6606 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-AZ-6607          TCGA-AZ-6608          TCGA-CA-5254 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CA-5255          TCGA-CA-5796          TCGA-CA-5797 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CA-6715          TCGA-CA-6716          TCGA-CA-6717 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CA-6718          TCGA-CA-6719          TCGA-CK-4947 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CK-4948          TCGA-CK-4950          TCGA-CK-4952 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CK-5912          TCGA-CK-5913          TCGA-CK-5914 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CK-5915          TCGA-CK-5916          TCGA-CK-6746 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CK-6747          TCGA-CK-6748          TCGA-CK-6751 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CM-4743          TCGA-CM-4744          TCGA-CM-4746 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CM-4747          TCGA-CM-4752          TCGA-CM-5341 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CM-5344          TCGA-CM-5348          TCGA-CM-5349 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CM-5860          TCGA-CM-5861          TCGA-CM-5862 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CM-5863          TCGA-CM-5864          TCGA-CM-5868 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CM-6161          TCGA-CM-6162          TCGA-CM-6163 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CM-6164          TCGA-CM-6165          TCGA-CM-6166 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CM-6167          TCGA-CM-6168          TCGA-CM-6169 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CM-6170          TCGA-CM-6171          TCGA-CM-6172 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CM-6674          TCGA-CM-6675          TCGA-CM-6676 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CM-6677          TCGA-CM-6678          TCGA-CM-6679 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CM-6680          TCGA-D5-5537          TCGA-D5-5538 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-D5-5539          TCGA-D5-5540          TCGA-D5-5541 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-D5-6529          TCGA-D5-6532          TCGA-D5-6533 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-D5-6534          TCGA-D5-6535          TCGA-D5-6536 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-D5-6537          TCGA-D5-6538          TCGA-D5-6539 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-D5-6540          TCGA-D5-6541          TCGA-D5-6898 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-D5-6920          TCGA-D5-6922          TCGA-D5-6923 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-D5-6924          TCGA-D5-6926          TCGA-D5-6927 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-D5-6928          TCGA-D5-6929          TCGA-D5-6930 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-D5-6931          TCGA-D5-6932          TCGA-D5-7000 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-DM-A0X9          TCGA-DM-A0XD          TCGA-DM-A0XF 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-DM-A1D0          TCGA-DM-A1D4          TCGA-DM-A1D6 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-DM-A1D7          TCGA-DM-A1D8          TCGA-DM-A1D9 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-DM-A1DA          TCGA-DM-A1DB          TCGA-DM-A1HA 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-DM-A1HB          TCGA-DM-A282          TCGA-DM-A285 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-DM-A28C          TCGA-DM-A28E          TCGA-DM-A28F 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-DM-A28G          TCGA-DM-A28H          TCGA-DM-A28K 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-F4-6459          TCGA-F4-6460          TCGA-F4-6569 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-F4-6570          TCGA-F4-6703          TCGA-F4-6704 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-F4-6805          TCGA-F4-6806          TCGA-F4-6807 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-F4-6808          TCGA-F4-6809          TCGA-F4-6854 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-F4-6855          TCGA-F4-6856          TCGA-G4-6293 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-G4-6303          TCGA-G4-6304          TCGA-G4-6306 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-G4-6307          TCGA-G4-6309          TCGA-G4-6310 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-G4-6315          TCGA-G4-6317          TCGA-G4-6321 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-G4-6323          TCGA-G4-6586          TCGA-G4-6588 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-G4-6625          TCGA-G4-6626          TCGA-G4-6628 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 

Clustering(1400) Variable = CNOT10 MUTATION ANALYSIS
D1400V1, survival
                  sevent
clus2                0   1
  CNOT10 MUTATED     6   3
  CNOT10 WILD-TYPE 276  70
  CNOT10 MUTATED CNOT10 WILD-TYPE 
               9              346 
  CNOT10 MUTATED CNOT10 WILD-TYPE 
               3               70 
$`CNOT10 MUTATED`
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R TCGA-AZ-4315 TCGA-AZ-4616 TCGA-AZ-6601 
        4.01        34.98        35.01        58.39         5.13       100.01 
TCGA-CA-6717 TCGA-G4-6317 TCGA-G4-6586 
        0.33        36.00        35.80 

$`CNOT10 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4681 TCGA-AZ-4682 
        0.20        21.44        17.82         1.41        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        61.41        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 
       55.04        51.75        45.11        36.72        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  CNOT10 MUTATED CNOT10 WILD-TYPE 
            0.33             0.00 
  CNOT10 MUTATED CNOT10 WILD-TYPE 
          100.01           140.38 
  CNOT10 MUTATED CNOT10 WILD-TYPE 
           35.01            20.07 
[1] "0.3 - 100.0 (35.0)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.3"
D1400V2, 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       24       106         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CNOT10 MUTATED           1          0          0          1        1
  CNOT10 WILD-TYPE        18         10         41         30       34
                  vv
clus               STAGE IVA STAGE IVB
  CNOT10 MUTATED           0         0
  CNOT10 WILD-TYPE        13         1
D1400V3, multiclass
            clus
vv           CNOT10 MUTATED CNOT10 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               3              106
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              1               30
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CNOT10 MUTATED     0   0   7   2
  CNOT10 WILD-TYPE   9  68 241  39
D1400V4, multiclass
    clus
vv   CNOT10 MUTATED CNOT10 WILD-TYPE
  T1              0                9
  T2              0               68
  T3              7              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
  CNOT10 MUTATED     6   0   3
  CNOT10 WILD-TYPE 214  80  63
D1400V5, multiclass
    clus
vv   CNOT10 MUTATED CNOT10 WILD-TYPE
  N0              6              214
  N1              0               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"
D1400V6, binary
                  cls
clus                 0   1
  CNOT10 MUTATED     7   1
  CNOT10 WILD-TYPE 276  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CNOT10 MUTATED      7    1
  CNOT10 WILD-TYPE  276   47
   clus
vv  CNOT10 MUTATED CNOT10 WILD-TYPE
  0              7              276
  1              1               47
[1] 2 2
[1] FALSE
D1400V7, 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
D1400V8, binary
                  cls
clus                 0   1
  CNOT10 MUTATED     6   3
  CNOT10 WILD-TYPE 311  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CNOT10 MUTATED      6    3
  CNOT10 WILD-TYPE  311   45
                               clus
vv                              CNOT10 MUTATED CNOT10 WILD-TYPE
  COLON ADENOCARCINOMA                       6              311
  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 251   2  22  20
D1400V9, multiclass
    clus
vv   CNOT10 MUTATED CNOT10 WILD-TYPE
  R0              6              251
  R1              0                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"
D1400V10, 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
D1400V11, 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(1401) Variable = GUCY1A3 MUTATION ANALYSIS
D1401V1, survival
                   sevent
clus2                 0   1
  GUCY1A3 MUTATED    17   5
  GUCY1A3 WILD-TYPE 265  68
  GUCY1A3 MUTATED GUCY1A3 WILD-TYPE 
               22               333 
  GUCY1A3 MUTATED GUCY1A3 WILD-TYPE 
                5                68 
$`GUCY1A3 MUTATED`
TCGA-A6-5661 TCGA-A6-5666 TCGA-A6-6141 TCGA-A6-6651 TCGA-AA-3663 TCGA-AA-3666 
       33.53        32.71         8.38        21.76         6.97         2.01 
TCGA-AA-3673 TCGA-AA-3811 TCGA-AA-3851 TCGA-AA-3947 TCGA-AA-3977 TCGA-AA-A00N 
       50.04        10.06        33.07        33.01        25.02         4.01 
TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01R TCGA-AD-6889 TCGA-CA-6717 TCGA-CM-5861 
       34.98        10.98        35.01        56.55         0.33        15.02 
TCGA-D5-6533 TCGA-DM-A0X9 TCGA-DM-A1DA TCGA-G4-6315 
        1.32       119.70         7.50        36.72 

$`GUCY1A3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       22.06        27.09        22.52        25.08        25.18        24.16 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        7.04         3.02         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 
       61.02        78.08         6.05        54.02        14.01         0.92 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       10.06         0.00         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        21.99        15.02        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07         1.02         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37         4.21         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 
       19.59        13.51        11.51        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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38        10.26        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       45.11        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  GUCY1A3 MUTATED GUCY1A3 WILD-TYPE 
             0.33              0.00 
  GUCY1A3 MUTATED GUCY1A3 WILD-TYPE 
           119.70            140.38 
  GUCY1A3 MUTATED GUCY1A3 WILD-TYPE 
            23.39             20.12 
[1] "0.3 - 119.7 (23.4)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.2"
D1401V2, 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       23       102         5         0
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GUCY1A3 MUTATED           3          0          2          2        1
  GUCY1A3 WILD-TYPE        16         10         39         29       34
                   vv
clus                STAGE IVA STAGE IVB
  GUCY1A3 MUTATED           0         0
  GUCY1A3 WILD-TYPE        13         1
D1401V3, multiclass
            clus
vv           GUCY1A3 MUTATED GUCY1A3 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 2                23
  STAGE IIA                7               102
  STAGE IIB                3                 5
  STAGE IIC                1                 0
  STAGE III                3                16
  STAGE IIIA               0                10
  STAGE IIIB               2                39
  STAGE IIIC               2                29
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  GUCY1A3 MUTATED     0   1  16   5
  GUCY1A3 WILD-TYPE   9  67 232  36
D1401V4, multiclass
    clus
vv   GUCY1A3 MUTATED GUCY1A3 WILD-TYPE
  T1               0                 9
  T2               1                67
  T3              16               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
  GUCY1A3 MUTATED    15   3   4
  GUCY1A3 WILD-TYPE 205  77  62
D1401V5, multiclass
    clus
vv   GUCY1A3 MUTATED GUCY1A3 WILD-TYPE
  N0              15               205
  N1               3                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"
D1401V6, binary
                   cls
clus                  0   1
  GUCY1A3 MUTATED    19   1
  GUCY1A3 WILD-TYPE 264  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GUCY1A3 MUTATED     19    1
  GUCY1A3 WILD-TYPE  264   47
   clus
vv  GUCY1A3 MUTATED GUCY1A3 WILD-TYPE
  0              19               264
  1               1                47
[1] 2 2
[1] FALSE
D1401V7, 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
D1401V8, binary
                   cls
clus                  0   1
  GUCY1A3 MUTATED    17   5
  GUCY1A3 WILD-TYPE 300  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GUCY1A3 MUTATED     17    5
  GUCY1A3 WILD-TYPE  300   43
                               clus
vv                              GUCY1A3 MUTATED GUCY1A3 WILD-TYPE
  COLON ADENOCARCINOMA                       17               300
  COLON MUCINOUS ADENOCARCINOMA               5                43
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  GUCY1A3 MUTATED    14   0   0   1
  GUCY1A3 WILD-TYPE 243   2  22  20
D1401V9, multiclass
    clus
vv   GUCY1A3 MUTATED GUCY1A3 WILD-TYPE
  R0              14               243
  R1               0                 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"
D1401V10, 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
D1401V11, 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(1402) Variable = CENPJ MUTATION ANALYSIS
D1402V1, survival
                 sevent
clus2               0   1
  CENPJ MUTATED    14   5
  CENPJ WILD-TYPE 268  68
  CENPJ MUTATED CENPJ WILD-TYPE 
             19             336 
  CENPJ MUTATED CENPJ WILD-TYPE 
              5              68 
$`CENPJ MUTATED`
TCGA-A6-6141 TCGA-A6-6651 TCGA-A6-6781 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3715 
        8.38        21.76        19.66         6.97         0.92        19.04 
TCGA-AA-3851 TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 
       33.07         4.01        34.98        58.39         0.33         0.10 
TCGA-CM-6171 TCGA-D5-6537 TCGA-F4-6570 TCGA-G4-6303 TCGA-G4-6321 TCGA-G4-6323 
       14.04         4.80         6.18        65.85        22.09        13.78 
TCGA-G4-6628 
       52.80 

$`CENPJ WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 
        0.00        17.03        10.06         0.00         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.72        36.00        35.80        26.17        91.79        46.75 

  CENPJ MUTATED CENPJ WILD-TYPE 
            0.1             0.0 
  CENPJ MUTATED CENPJ WILD-TYPE 
          65.85          140.38 
  CENPJ MUTATED CENPJ WILD-TYPE 
          14.04           20.98 
[1] "0.1 - 65.8 (14.0)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.6"
D1402V2, 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       22       102         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        17         10         39         30       34        13
                 vv
clus              STAGE IVB
  CENPJ MUTATED           0
  CENPJ WILD-TYPE         1
D1402V3, multiclass
            clus
vv           CENPJ MUTATED CENPJ WILD-TYPE
  STAGE I                2              62
  STAGE IA               1               0
  STAGE II               3              22
  STAGE IIA              7             102
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CENPJ MUTATED     0   3  13   4
  CENPJ WILD-TYPE   9  65 235  37
D1402V4, multiclass
    clus
vv   CENPJ MUTATED CENPJ WILD-TYPE
  T1             0               9
  T2             3              65
  T3            13             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
  CENPJ MUTATED    15   6   0
  CENPJ WILD-TYPE 205  74  66
D1402V5, multiclass
    clus
vv   CENPJ MUTATED CENPJ WILD-TYPE
  N0            15             205
  N1             6              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"
D1402V6, binary
                 cls
clus                0   1
  CENPJ MUTATED    15   1
  CENPJ WILD-TYPE 268  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CENPJ MUTATED     15    1
  CENPJ WILD-TYPE  268   47
   clus
vv  CENPJ MUTATED CENPJ WILD-TYPE
  0            15             268
  1             1              47
[1] 2 2
[1] FALSE
D1402V7, 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
D1402V8, binary
                 cls
clus                0   1
  CENPJ MUTATED    18   3
  CENPJ WILD-TYPE 299  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CENPJ MUTATED     18    3
  CENPJ WILD-TYPE  299   45
                               clus
vv                              CENPJ MUTATED CENPJ WILD-TYPE
  COLON ADENOCARCINOMA                     18             299
  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 240   2  22  19
D1402V9, multiclass
    clus
vv   CENPJ MUTATED CENPJ WILD-TYPE
  R0            17             240
  R1             0               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"
D1402V10, 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
D1402V11, 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(1403) Variable = BAZ1B MUTATION ANALYSIS
D1403V1, survival
                 sevent
clus2               0   1
  BAZ1B MUTATED    15   5
  BAZ1B WILD-TYPE 267  68
  BAZ1B MUTATED BAZ1B WILD-TYPE 
             20             335 
  BAZ1B MUTATED BAZ1B WILD-TYPE 
              5              68 
$`BAZ1B MUTATED`
TCGA-AA-3663 TCGA-AA-3713 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-A00A TCGA-AA-A00N 
        6.97        19.04         2.01        33.01        38.04         4.01 
TCGA-AD-5900 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-6162 
        0.07        49.41       100.01         0.33         0.10        12.00 
TCGA-CM-6171 TCGA-D5-6532 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6926 TCGA-D5-6930 
       14.04        18.25        16.14         7.53         9.04         1.51 
TCGA-DM-A1D6 TCGA-G4-6588 
       49.91        26.17 

$`BAZ1B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3939 
       24.03        27.02        29.98        18.05        31.00        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
        7.96        27.02        13.94        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.26         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       13.51        11.51        20.19         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6920 
       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-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        91.79        46.75        52.80 

  BAZ1B MUTATED BAZ1B WILD-TYPE 
           0.07            0.00 
  BAZ1B MUTATED BAZ1B WILD-TYPE 
         100.01          140.38 
  BAZ1B MUTATED BAZ1B WILD-TYPE 
          13.02           21.01 
[1] "0.1 - 100.0 (13.0)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.5"
D1403V2, 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       22       101         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BAZ1B MUTATED           0          1          1          0        2         0
  BAZ1B WILD-TYPE        19          9         40         31       33        13
                 vv
clus              STAGE IVB
  BAZ1B MUTATED           0
  BAZ1B WILD-TYPE         1
D1403V3, multiclass
            clus
vv           BAZ1B MUTATED BAZ1B WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              8             101
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               2              33
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  BAZ1B MUTATED     0   4  14   3
  BAZ1B WILD-TYPE   9  64 234  38
D1403V4, multiclass
    clus
vv   BAZ1B MUTATED BAZ1B WILD-TYPE
  T1             0               9
  T2             4              64
  T3            14             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
  BAZ1B MUTATED    18   2   1
  BAZ1B WILD-TYPE 202  78  65
D1403V5, multiclass
    clus
vv   BAZ1B MUTATED BAZ1B WILD-TYPE
  N0            18             202
  N1             2              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"
D1403V6, binary
                 cls
clus                0   1
  BAZ1B MUTATED    17   2
  BAZ1B WILD-TYPE 266  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BAZ1B MUTATED     17    2
  BAZ1B WILD-TYPE  266   46
   clus
vv  BAZ1B MUTATED BAZ1B WILD-TYPE
  0            17             266
  1             2              46
[1] 2 2
[1] FALSE
D1403V7, 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
D1403V8, binary
                 cls
clus                0   1
  BAZ1B MUTATED    13   8
  BAZ1B WILD-TYPE 304  40
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BAZ1B MUTATED     13    8
  BAZ1B WILD-TYPE  304   40
                               clus
vv                              BAZ1B MUTATED BAZ1B WILD-TYPE
  COLON ADENOCARCINOMA                     13             304
  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 243   2  20  19
D1403V9, multiclass
    clus
vv   BAZ1B MUTATED BAZ1B WILD-TYPE
  R0            14             243
  R1             0               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"
D1403V10, 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
D1403V11, 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(1404) Variable = ESR1 MUTATION ANALYSIS
D1404V1, survival
                sevent
clus2              0   1
  ESR1 MUTATED    15   3
  ESR1 WILD-TYPE 267  70
  ESR1 MUTATED ESR1 WILD-TYPE 
            18            337 
  ESR1 MUTATED ESR1 WILD-TYPE 
             3             70 
$`ESR1 MUTATED`
TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3525 TCGA-AA-3858 TCGA-AA-3947 
       22.06        19.66         3.02         8.05        31.07        33.01 
TCGA-AA-3949 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q 
       26.01        25.02        27.02         4.01        34.98         1.02 
TCGA-AZ-6601 TCGA-CM-4743 TCGA-CM-5861 TCGA-F4-6569 TCGA-G4-6315 TCGA-G4-6588 
      100.01        23.05        15.02        13.45        36.72        26.17 

$`ESR1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.12        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       24.03        37.05        36.03        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3860 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3950 
       18.05        31.00         2.01        12.99        24.00        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
       21.99        21.14         2.93         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        16.01         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 
       60.79       117.07        98.24         8.61        13.38         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 
       52.80 

  ESR1 MUTATED ESR1 WILD-TYPE 
          1.02           0.00 
  ESR1 MUTATED ESR1 WILD-TYPE 
        100.01         140.38 
  ESR1 MUTATED ESR1 WILD-TYPE 
        24.035         20.020 
[1] "1.0 - 100.0 (24.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.2"
D1404V2, 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       21       105         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        19         10         38         30       34        13
                vv
clus             STAGE IVB
  ESR1 MUTATED           0
  ESR1 WILD-TYPE         1
D1404V3, multiclass
            clus
vv           ESR1 MUTATED ESR1 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              4             21
  STAGE IIA             4            105
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            3             38
  STAGE IIIC            1             30
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ESR1 MUTATED     0   3  11   5
  ESR1 WILD-TYPE   9  65 237  36
D1404V4, multiclass
    clus
vv   ESR1 MUTATED ESR1 WILD-TYPE
  T1            0              9
  T2            3             65
  T3           11            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
  ESR1 MUTATED    14   5   0
  ESR1 WILD-TYPE 206  75  66
D1404V5, multiclass
    clus
vv   ESR1 MUTATED ESR1 WILD-TYPE
  N0           14            206
  N1            5             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"
D1404V6, binary
                cls
clus               0   1
  ESR1 MUTATED    16   1
  ESR1 WILD-TYPE 267  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  ESR1 MUTATED     16    1
  ESR1 WILD-TYPE  267   47
   clus
vv  ESR1 MUTATED ESR1 WILD-TYPE
  0           16            267
  1            1             47
[1] 2 2
[1] FALSE
D1404V7, 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
D1404V8, binary
                cls
clus               0   1
  ESR1 MUTATED    15   4
  ESR1 WILD-TYPE 302  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  ESR1 MUTATED     15    4
  ESR1 WILD-TYPE  302   44
                               clus
vv                              ESR1 MUTATED ESR1 WILD-TYPE
  COLON ADENOCARCINOMA                    15            302
  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 241   2  22  21
D1404V9, multiclass
    clus
vv   ESR1 MUTATED ESR1 WILD-TYPE
  R0           16            241
  R1            0              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"
D1404V10, 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
D1404V11, 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(1405) Variable = LPIN2 MUTATION ANALYSIS
D1405V1, survival
                 sevent
clus2               0   1
  LPIN2 MUTATED     7   1
  LPIN2 WILD-TYPE 275  72
  LPIN2 MUTATED LPIN2 WILD-TYPE 
              8             347 
  LPIN2 MUTATED LPIN2 WILD-TYPE 
              1              72 
$`LPIN2 MUTATED`
TCGA-AA-A010 TCGA-AA-A02J TCGA-AZ-4315 TCGA-CK-4948 TCGA-D5-6922 TCGA-F4-6703 
       34.98         5.03        58.39       102.44        10.13        35.87 
TCGA-F4-6856 TCGA-G4-6586 
       19.43        35.80 

$`LPIN2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       51.98        39.98         2.01        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 
        0.26         0.33         0.10         1.35        17.56        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        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        13.38        13.45         6.18         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.41       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        26.17        91.79        46.75        52.80 

  LPIN2 MUTATED LPIN2 WILD-TYPE 
           5.03            0.00 
  LPIN2 MUTATED LPIN2 WILD-TYPE 
         102.44          140.38 
  LPIN2 MUTATED LPIN2 WILD-TYPE 
          35.39           20.12 
[1] "5.0 - 102.4 (35.4)" "0.0 - 140.4 (20.1)"
[1] "hr=" "2.3"
D1405V2, 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       25       105         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LPIN2 MUTATED           0          2          0          0        1         0
  LPIN2 WILD-TYPE        19          8         41         31       34        13
                 vv
clus              STAGE IVB
  LPIN2 MUTATED           0
  LPIN2 WILD-TYPE         1
D1405V3, multiclass
            clus
vv           LPIN2 MUTATED LPIN2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              4             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             2               8
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LPIN2 MUTATED     0   1   7   1
  LPIN2 WILD-TYPE   9  67 241  40
D1405V4, multiclass
    clus
vv   LPIN2 MUTATED LPIN2 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             7             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
  LPIN2 MUTATED     7   2   0
  LPIN2 WILD-TYPE 213  78  66
D1405V5, multiclass
    clus
vv   LPIN2 MUTATED LPIN2 WILD-TYPE
  N0             7             213
  N1             2              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"
D1405V6, binary
                 cls
clus                0   1
  LPIN2 MUTATED     8   1
  LPIN2 WILD-TYPE 275  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LPIN2 MUTATED      8    1
  LPIN2 WILD-TYPE  275   47
   clus
vv  LPIN2 MUTATED LPIN2 WILD-TYPE
  0             8             275
  1             1              47
[1] 2 2
[1] FALSE
D1405V7, 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
D1405V8, binary
                 cls
clus                0   1
  LPIN2 MUTATED     8   1
  LPIN2 WILD-TYPE 309  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LPIN2 MUTATED      8    1
  LPIN2 WILD-TYPE  309   47
                               clus
vv                              LPIN2 MUTATED LPIN2 WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  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 249   2  21  21
D1405V9, multiclass
    clus
vv   LPIN2 MUTATED LPIN2 WILD-TYPE
  R0             8             249
  R1             0               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"
D1405V10, 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
D1405V11, 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(1406) Variable = TEX2 MUTATION ANALYSIS
D1406V1, survival
                sevent
clus2              0   1
  TEX2 MUTATED    11   1
  TEX2 WILD-TYPE 271  72
  TEX2 MUTATED TEX2 WILD-TYPE 
            12            343 
  TEX2 MUTATED TEX2 WILD-TYPE 
             1             72 
$`TEX2 MUTATED`
TCGA-AA-3522 TCGA-AA-A010 TCGA-AD-6889 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6601 
       37.05        34.98        56.55        21.44        58.39       100.01 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4950 TCGA-CM-4744 TCGA-CM-5861 TCGA-G4-6588 
        0.33         0.10        40.34        20.02        15.02        26.17 

$`TEX2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 
       38.99         1.02         9.07        24.03        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
        0.20        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        61.41        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07         0.26         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      102.44        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 
        2.93         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        16.01 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 
       52.80 

  TEX2 MUTATED TEX2 WILD-TYPE 
           0.1            0.0 
  TEX2 MUTATED TEX2 WILD-TYPE 
        100.01         140.38 
  TEX2 MUTATED TEX2 WILD-TYPE 
        30.575         19.990 
[1] "0.1 - 100.0 (30.6)" "0.0 - 140.4 (20.0)"
[1] "hr=" "3.3"
D1406V2, 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       24       101         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TEX2 MUTATED           0          1          0          0        0         0
  TEX2 WILD-TYPE        19          9         41         31       35        13
                vv
clus             STAGE IVB
  TEX2 MUTATED           0
  TEX2 WILD-TYPE         1
D1406V3, multiclass
            clus
vv           TEX2 MUTATED TEX2 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             8            101
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            1              9
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TEX2 MUTATED     0   1  10   1
  TEX2 WILD-TYPE   9  67 238  40
D1406V4, multiclass
    clus
vv   TEX2 MUTATED TEX2 WILD-TYPE
  T1            0              9
  T2            1             67
  T3           10            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
  TEX2 MUTATED    11   1   0
  TEX2 WILD-TYPE 209  79  66
D1406V5, multiclass
    clus
vv   TEX2 MUTATED TEX2 WILD-TYPE
  N0           11            209
  N1            1             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"
D1406V6, binary
                cls
clus               0   1
  TEX2 MUTATED    11   0
  TEX2 WILD-TYPE 272  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  TEX2 MUTATED     11    0
  TEX2 WILD-TYPE  272   48
   clus
vv  TEX2 MUTATED TEX2 WILD-TYPE
  0           11            272
  1            0             48
[1] 2 2
[1] FALSE
D1406V7, 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
D1406V8, binary
                cls
clus               0   1
  TEX2 MUTATED    11   1
  TEX2 WILD-TYPE 306  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  TEX2 MUTATED     11    1
  TEX2 WILD-TYPE  306   47
                               clus
vv                              TEX2 MUTATED TEX2 WILD-TYPE
  COLON ADENOCARCINOMA                    11            306
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TEX2 MUTATED     7   1   0   2
  TEX2 WILD-TYPE 250   1  22  19
D1406V9, multiclass
    clus
vv   TEX2 MUTATED TEX2 WILD-TYPE
  R0            7            250
  R1            1              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"
D1406V10, 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
D1406V11, 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(1407) Variable = ANKRD26 MUTATION ANALYSIS
D1407V1, survival
                   sevent
clus2                 0   1
  ANKRD26 MUTATED    16   2
  ANKRD26 WILD-TYPE 266  71
  ANKRD26 MUTATED ANKRD26 WILD-TYPE 
               18               337 
  ANKRD26 MUTATED ANKRD26 WILD-TYPE 
                2                71 
$`ANKRD26 MUTATED`
TCGA-A6-3809 TCGA-A6-5659 TCGA-AA-3663 TCGA-AA-3710 TCGA-AA-3977 TCGA-AA-A00N 
       32.75        30.44         6.97        26.99        25.02         4.01 
TCGA-AA-A010 TCGA-AD-6889 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CK-6748 TCGA-CM-4744 
       34.98        56.55        58.39         0.33         2.01        20.02 
TCGA-CM-5860 TCGA-CM-6162 TCGA-D5-5539 TCGA-DM-A1D4 TCGA-DM-A28K TCGA-G4-6588 
       16.01        12.00        19.59        92.75        98.24        26.17 

$`ANKRD26 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        4.21         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        12.26        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        24.43        38.20       130.65        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
      117.07         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 
       52.80 

  ANKRD26 MUTATED ANKRD26 WILD-TYPE 
             0.33              0.00 
  ANKRD26 MUTATED ANKRD26 WILD-TYPE 
            98.24            140.38 
  ANKRD26 MUTATED ANKRD26 WILD-TYPE 
           25.595            20.120 
[1] "0.3 - 98.2 (25.6)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "2.3"
D1407V2, 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       24       101         5         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANKRD26 MUTATED           0          1          1          0        1
  ANKRD26 WILD-TYPE        19          9         40         31       34
                   vv
clus                STAGE IVA STAGE IVB
  ANKRD26 MUTATED           0         0
  ANKRD26 WILD-TYPE        13         1
D1407V3, multiclass
            clus
vv           ANKRD26 MUTATED ANKRD26 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                8               101
  STAGE IIB                3                 5
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               1                 9
  STAGE IIIB               1                40
  STAGE IIIC               0                31
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ANKRD26 MUTATED     0   4  12   3
  ANKRD26 WILD-TYPE   9  64 236  38
D1407V4, multiclass
    clus
vv   ANKRD26 MUTATED ANKRD26 WILD-TYPE
  T1               0                 9
  T2               4                64
  T3              12               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
  ANKRD26 MUTATED    16   3   0
  ANKRD26 WILD-TYPE 204  77  66
D1407V5, multiclass
    clus
vv   ANKRD26 MUTATED ANKRD26 WILD-TYPE
  N0              16               204
  N1               3                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"
D1407V6, binary
                   cls
clus                  0   1
  ANKRD26 MUTATED    16   1
  ANKRD26 WILD-TYPE 267  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD26 MUTATED     16    1
  ANKRD26 WILD-TYPE  267   47
   clus
vv  ANKRD26 MUTATED ANKRD26 WILD-TYPE
  0              16               267
  1               1                47
[1] 2 2
[1] FALSE
D1407V7, 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
D1407V8, binary
                   cls
clus                  0   1
  ANKRD26 MUTATED    12   7
  ANKRD26 WILD-TYPE 305  41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD26 MUTATED     12    7
  ANKRD26 WILD-TYPE  305   41
                               clus
vv                              ANKRD26 MUTATED ANKRD26 WILD-TYPE
  COLON ADENOCARCINOMA                       12               305
  COLON MUCINOUS ADENOCARCINOMA               7                41
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ANKRD26 MUTATED    12   0   0   3
  ANKRD26 WILD-TYPE 245   2  22  18
D1407V9, multiclass
    clus
vv   ANKRD26 MUTATED ANKRD26 WILD-TYPE
  R0              12               245
  R1               0                 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"
D1407V10, 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
D1407V11, 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(1408) Variable = SLC8A3 MUTATION ANALYSIS
D1408V1, survival
                  sevent
clus2                0   1
  SLC8A3 MUTATED    11   0
  SLC8A3 WILD-TYPE 271  73
  SLC8A3 MUTATED SLC8A3 WILD-TYPE 
              11              344 
  SLC8A3 MUTATED SLC8A3 WILD-TYPE 
               0               73 
$`SLC8A3 MUTATED`
TCGA-A6-2672 TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3518 TCGA-AA-3522 TCGA-AA-3864 
       46.65        22.06        63.98         1.02        37.05        53.00 
TCGA-AA-3968 TCGA-AZ-4315 TCGA-CM-6172 TCGA-D5-6928 TCGA-G4-6299 
       21.99        58.39        11.01        11.64        74.56 

$`SLC8A3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 
        6.97         1.02        13.02        38.99         9.07        24.03 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 
       24.00         2.01        20.98        34.03         2.01        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 
       13.25         0.53        35.41        19.43       107.67        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  SLC8A3 MUTATED SLC8A3 WILD-TYPE 
            1.02             0.00 
  SLC8A3 MUTATED SLC8A3 WILD-TYPE 
           74.56           140.38 
  SLC8A3 MUTATED SLC8A3 WILD-TYPE 
          37.050           20.005 
[1] "1.0 - 74.6 (37.0)"  "0.0 - 140.4 (20.0)"
[1] "hr="     "2.7e+07"
D1408V2, 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       23       104         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC8A3 MUTATED           0          0          2          1        0
  SLC8A3 WILD-TYPE        19         10         39         30       35
                  vv
clus               STAGE IVA STAGE IVB
  SLC8A3 MUTATED           0         0
  SLC8A3 WILD-TYPE        13         1
D1408V3, multiclass
            clus
vv           SLC8A3 MUTATED SLC8A3 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               5              104
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SLC8A3 MUTATED     0   1  10   0
  SLC8A3 WILD-TYPE   9  67 238  41
D1408V4, multiclass
    clus
vv   SLC8A3 MUTATED SLC8A3 WILD-TYPE
  T1              0                9
  T2              1               67
  T3             10              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
  SLC8A3 MUTATED     8   2   1
  SLC8A3 WILD-TYPE 212  78  65
D1408V5, multiclass
    clus
vv   SLC8A3 MUTATED SLC8A3 WILD-TYPE
  N0              8              212
  N1              2               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"
D1408V6, binary
                  cls
clus                 0   1
  SLC8A3 MUTATED    11   0
  SLC8A3 WILD-TYPE 272  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC8A3 MUTATED     11    0
  SLC8A3 WILD-TYPE  272   48
   clus
vv  SLC8A3 MUTATED SLC8A3 WILD-TYPE
  0             11              272
  1              0               48
[1] 2 2
[1] FALSE
D1408V7, binary
                  cls
clus                 0   1
  SLC8A3 MUTATED     5   6
  SLC8A3 WILD-TYPE 165 191
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC8A3 MUTATED      5    6
  SLC8A3 WILD-TYPE  165  191
        clus
vv       SLC8A3 MUTATED SLC8A3 WILD-TYPE
  FEMALE              5              165
  MALE                6              191
[1] 2 2
[1] FALSE
D1408V8, binary
                  cls
clus                 0   1
  SLC8A3 MUTATED    10   1
  SLC8A3 WILD-TYPE 307  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC8A3 MUTATED     10    1
  SLC8A3 WILD-TYPE  307   47
                               clus
vv                              SLC8A3 MUTATED SLC8A3 WILD-TYPE
  COLON ADENOCARCINOMA                      10              307
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SLC8A3 MUTATED    11   0   0   0
  SLC8A3 WILD-TYPE 246   2  22  21
D1408V9, multiclass
    clus
vv   SLC8A3 MUTATED SLC8A3 WILD-TYPE
  R0             11              246
  R1              0                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"
D1408V10, 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     6
  SLC8A3 WILD-TYPE                        19   170
D1408V11, 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                                         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(1409) Variable = OR6K2 MUTATION ANALYSIS
D1409V1, survival
                 sevent
clus2               0   1
  OR6K2 MUTATED    12   2
  OR6K2 WILD-TYPE 270  71
  OR6K2 MUTATED OR6K2 WILD-TYPE 
             14             341 
  OR6K2 MUTATED OR6K2 WILD-TYPE 
              2              71 
$`OR6K2 MUTATED`
TCGA-A6-3809 TCGA-AA-3554 TCGA-AA-3663 TCGA-AA-3989 TCGA-AA-A00N TCGA-AD-5900 
       32.75        17.95         6.97         7.96         4.01         0.07 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-CA-6718 TCGA-D5-6920 TCGA-DM-A0X9 TCGA-F4-6856 
       21.44        58.39         0.10        12.39       119.70        19.43 
TCGA-G4-6586 TCGA-G4-6588 
       35.80        26.17 

$`OR6K2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       19.07        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        15.75         0.20        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.33         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         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-A0XD 
       13.41         1.51        12.00        11.38        10.26        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        35.41       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        91.79        46.75        52.80 

  OR6K2 MUTATED OR6K2 WILD-TYPE 
           0.07            0.00 
  OR6K2 MUTATED OR6K2 WILD-TYPE 
         119.70          140.38 
  OR6K2 MUTATED OR6K2 WILD-TYPE 
          18.69           20.28 
[1] "0.1 - 119.7 (18.7)" "0.0 - 140.4 (20.3)"
[1] "hr=" "1.4"
D1409V2, 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       24       101         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        19         10         41         31       34        13
                 vv
clus              STAGE IVB
  OR6K2 MUTATED           0
  OR6K2 WILD-TYPE         1
D1409V3, multiclass
            clus
vv           OR6K2 MUTATED OR6K2 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              8             101
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR6K2 MUTATED     0   2  10   2
  OR6K2 WILD-TYPE   9  66 238  39
D1409V4, multiclass
    clus
vv   OR6K2 MUTATED OR6K2 WILD-TYPE
  T1             0               9
  T2             2              66
  T3            10             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
  OR6K2 MUTATED    13   0   1
  OR6K2 WILD-TYPE 207  80  65
D1409V5, multiclass
    clus
vv   OR6K2 MUTATED OR6K2 WILD-TYPE
  N0            13             207
  N1             0              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"
D1409V6, binary
                 cls
clus                0   1
  OR6K2 MUTATED    11   1
  OR6K2 WILD-TYPE 272  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR6K2 MUTATED     11    1
  OR6K2 WILD-TYPE  272   47
   clus
vv  OR6K2 MUTATED OR6K2 WILD-TYPE
  0            11             272
  1             1              47
[1] 2 2
[1] FALSE
D1409V7, 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
D1409V8, binary
                 cls
clus                0   1
  OR6K2 MUTATED    10   4
  OR6K2 WILD-TYPE 307  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR6K2 MUTATED     10    4
  OR6K2 WILD-TYPE  307   44
                               clus
vv                              OR6K2 MUTATED OR6K2 WILD-TYPE
  COLON ADENOCARCINOMA                     10             307
  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 246   2  21  20
D1409V9, multiclass
    clus
vv   OR6K2 MUTATED OR6K2 WILD-TYPE
  R0            11             246
  R1             0               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"
D1409V10, 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
D1409V11, 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(1410) Variable = CASP10 MUTATION ANALYSIS
D1410V1, survival
                  sevent
clus2                0   1
  CASP10 MUTATED     6   0
  CASP10 WILD-TYPE 276  73
  CASP10 MUTATED CASP10 WILD-TYPE 
               6              349 
  CASP10 MUTATED CASP10 WILD-TYPE 
               0               73 
$`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         0.33        15.02       107.67 

$`CASP10 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        13.02         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        35.41        19.43        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  CASP10 MUTATED CASP10 WILD-TYPE 
            0.33             0.00 
  CASP10 MUTATED CASP10 WILD-TYPE 
          107.67           140.38 
  CASP10 MUTATED CASP10 WILD-TYPE 
          33.305           20.120 
[1] "0.3 - 107.7 (33.3)" "0.0 - 140.4 (20.1)"
[1] "hr="     "9300000"
D1410V2, 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       25       106         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CASP10 MUTATED           2          0          1          0        0
  CASP10 WILD-TYPE        17         10         40         31       35
                  vv
clus               STAGE IVA STAGE IVB
  CASP10 MUTATED           0         0
  CASP10 WILD-TYPE        13         1
D1410V3, multiclass
            clus
vv           CASP10 MUTATED CASP10 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               3              106
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               2               17
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CASP10 MUTATED     0   0   6   1
  CASP10 WILD-TYPE   9  68 242  40
D1410V4, multiclass
    clus
vv   CASP10 MUTATED CASP10 WILD-TYPE
  T1              0                9
  T2              0               68
  T3              6              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
  CASP10 MUTATED     4   2   1
  CASP10 WILD-TYPE 216  78  65
D1410V5, multiclass
    clus
vv   CASP10 MUTATED CASP10 WILD-TYPE
  N0              4              216
  N1              2               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"
D1410V6, binary
                  cls
clus                 0   1
  CASP10 MUTATED     7   0
  CASP10 WILD-TYPE 276  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CASP10 MUTATED      7    0
  CASP10 WILD-TYPE  276   48
   clus
vv  CASP10 MUTATED CASP10 WILD-TYPE
  0              7              276
  1              0               48
[1] 2 2
[1] FALSE
D1410V7, 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
D1410V8, binary
                  cls
clus                 0   1
  CASP10 MUTATED     6   1
  CASP10 WILD-TYPE 311  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CASP10 MUTATED      6    1
  CASP10 WILD-TYPE  311   47
                               clus
vv                              CASP10 MUTATED CASP10 WILD-TYPE
  COLON ADENOCARCINOMA                       6              311
  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 251   2  22  20
D1410V9, multiclass
    clus
vv   CASP10 MUTATED CASP10 WILD-TYPE
  R0              6              251
  R1              0                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"
D1410V10, 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
D1410V11, 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(1411) Variable = PLCL2 MUTATION ANALYSIS
D1411V1, survival
                 sevent
clus2               0   1
  PLCL2 MUTATED    14   5
  PLCL2 WILD-TYPE 268  68
  PLCL2 MUTATED PLCL2 WILD-TYPE 
             19             336 
  PLCL2 MUTATED PLCL2 WILD-TYPE 
              5              68 
$`PLCL2 MUTATED`
TCGA-AA-3955 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A01Q TCGA-AA-A01R TCGA-AD-6901 
       20.98        25.02         4.01         1.02        35.01        22.42 
TCGA-AZ-4315 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CA-6718 
       58.39        62.79        49.41       100.01         0.33         0.10 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CM-4746 TCGA-CM-5348 TCGA-CM-6171 TCGA-D5-6931 
       17.56        40.34        37.02        22.98        14.04        12.00 
TCGA-G4-6588 
       26.17 

$`PLCL2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       31.00        38.07         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6599 
        1.41         5.13        83.80        22.36        61.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
        1.35       102.44        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        52.80 

  PLCL2 MUTATED PLCL2 WILD-TYPE 
            0.1             0.0 
  PLCL2 MUTATED PLCL2 WILD-TYPE 
         100.01          140.38 
  PLCL2 MUTATED PLCL2 WILD-TYPE 
         22.980          20.005 
[1] "0.1 - 100.0 (23.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.1"
D1411V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PLCL2 MUTATED         2        0        4         4         1         0
  PLCL2 WILD-TYPE      62        1       21       105         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PLCL2 MUTATED           1          1          2          1        0         1
  PLCL2 WILD-TYPE        18          9         39         30       35        12
                 vv
clus              STAGE IVB
  PLCL2 MUTATED           0
  PLCL2 WILD-TYPE         1
D1411V3, multiclass
            clus
vv           PLCL2 MUTATED PLCL2 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               4              21
  STAGE IIA              4             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             1               9
  STAGE IIIB             2              39
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PLCL2 MUTATED     0   4  12   3
  PLCL2 WILD-TYPE   9  64 236  38
D1411V4, multiclass
    clus
vv   PLCL2 MUTATED PLCL2 WILD-TYPE
  T1             0               9
  T2             4              64
  T3            12             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
  PLCL2 MUTATED    13   3   3
  PLCL2 WILD-TYPE 207  77  63
D1411V5, multiclass
    clus
vv   PLCL2 MUTATED PLCL2 WILD-TYPE
  N0            13             207
  N1             3              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"
D1411V6, binary
                 cls
clus                0   1
  PLCL2 MUTATED    15   0
  PLCL2 WILD-TYPE 268  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLCL2 MUTATED     15    0
  PLCL2 WILD-TYPE  268   48
   clus
vv  PLCL2 MUTATED PLCL2 WILD-TYPE
  0            15             268
  1             0              48
[1] 2 2
[1] FALSE
D1411V7, binary
                 cls
clus                0   1
  PLCL2 MUTATED     6  13
  PLCL2 WILD-TYPE 164 184
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLCL2 MUTATED      6   13
  PLCL2 WILD-TYPE  164  184
        clus
vv       PLCL2 MUTATED PLCL2 WILD-TYPE
  FEMALE             6             164
  MALE              13             184
[1] 2 2
[1] FALSE
D1411V8, binary
                 cls
clus                0   1
  PLCL2 MUTATED    16   3
  PLCL2 WILD-TYPE 301  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLCL2 MUTATED     16    3
  PLCL2 WILD-TYPE  301   45
                               clus
vv                              PLCL2 MUTATED PLCL2 WILD-TYPE
  COLON ADENOCARCINOMA                     16             301
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PLCL2 MUTATED    10   1   0   3
  PLCL2 WILD-TYPE 247   1  22  18
D1411V9, multiclass
    clus
vv   PLCL2 MUTATED PLCL2 WILD-TYPE
  R0            10             247
  R1             1               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"
D1411V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PLCL2 MUTATED                                  0     2
  PLCL2 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PLCL2 MUTATED                           2    10
  PLCL2 WILD-TYPE                        17   166
D1411V11, multiclass
                                  clus
vv                                 PLCL2 MUTATED PLCL2 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(1412) Variable = ADAM30 MUTATION ANALYSIS
D1412V1, survival
                  sevent
clus2                0   1
  ADAM30 MUTATED     7   1
  ADAM30 WILD-TYPE 275  72
  ADAM30 MUTATED ADAM30 WILD-TYPE 
               8              347 
  ADAM30 MUTATED ADAM30 WILD-TYPE 
               1               72 
$`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        19.43 

$`ADAM30 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 
       10.06        35.05        33.04         0.99        25.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        18.05         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        92.75        49.91        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  ADAM30 MUTATED ADAM30 WILD-TYPE 
            1.02             0.00 
  ADAM30 MUTATED ADAM30 WILD-TYPE 
           33.53           140.38 
  ADAM30 MUTATED ADAM30 WILD-TYPE 
          16.375           20.280 
[1] "1.0 - 33.5 (16.4)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.2"
D1412V2, 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       25       105         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ADAM30 MUTATED           0          0          0          0        0
  ADAM30 WILD-TYPE        19         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  ADAM30 MUTATED           0         0
  ADAM30 WILD-TYPE        13         1
D1412V3, multiclass
            clus
vv           ADAM30 MUTATED ADAM30 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               4              105
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ADAM30 MUTATED     1   3   4   0
  ADAM30 WILD-TYPE   8  65 244  41
D1412V4, multiclass
    clus
vv   ADAM30 MUTATED ADAM30 WILD-TYPE
  T1              1                8
  T2              3               65
  T3              4              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
  ADAM30 MUTATED     8   0   0
  ADAM30 WILD-TYPE 212  80  66
D1412V5, multiclass
    clus
vv   ADAM30 MUTATED ADAM30 WILD-TYPE
  N0              8              212
  N1              0               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"
D1412V6, binary
                  cls
clus                 0   1
  ADAM30 MUTATED     7   0
  ADAM30 WILD-TYPE 276  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM30 MUTATED      7    0
  ADAM30 WILD-TYPE  276   48
   clus
vv  ADAM30 MUTATED ADAM30 WILD-TYPE
  0              7              276
  1              0               48
[1] 2 2
[1] FALSE
D1412V7, 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
D1412V8, binary
                  cls
clus                 0   1
  ADAM30 MUTATED     4   4
  ADAM30 WILD-TYPE 313  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM30 MUTATED      4    4
  ADAM30 WILD-TYPE  313   44
                               clus
vv                              ADAM30 MUTATED ADAM30 WILD-TYPE
  COLON ADENOCARCINOMA                       4              313
  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 251   2  22  21
D1412V9, multiclass
    clus
vv   ADAM30 MUTATED ADAM30 WILD-TYPE
  R0              6              251
  R1              0                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"
D1412V10, 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
D1412V11, 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(1413) Variable = MICAL1 MUTATION ANALYSIS
D1413V1, survival
                  sevent
clus2                0   1
  MICAL1 MUTATED     8   0
  MICAL1 WILD-TYPE 274  73
  MICAL1 MUTATED MICAL1 WILD-TYPE 
               8              347 
  MICAL1 MUTATED MICAL1 WILD-TYPE 
               0               73 
$`MICAL1 MUTATED`
TCGA-A6-6141 TCGA-A6-6653 TCGA-AA-3663 TCGA-AA-3821 TCGA-AD-6889 TCGA-AU-6004 
        8.38        24.39         6.97         1.02        56.55        27.09 
TCGA-CM-6162 TCGA-D5-6927 
       12.00         9.44 

$`MICAL1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       33.04         0.99        25.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37         4.21         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  MICAL1 MUTATED MICAL1 WILD-TYPE 
            1.02             0.00 
  MICAL1 MUTATED MICAL1 WILD-TYPE 
           56.55           140.38 
  MICAL1 MUTATED MICAL1 WILD-TYPE 
           10.72            20.28 
[1] "1.0 - 56.5 (10.7)"  "0.0 - 140.4 (20.3)"
[1] "hr="     "9200000"
D1413V2, 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       23       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MICAL1 MUTATED           0          0          1          0        0
  MICAL1 WILD-TYPE        19         10         40         31       35
                  vv
clus               STAGE IVA STAGE IVB
  MICAL1 MUTATED           0         0
  MICAL1 WILD-TYPE        13         1
D1413V3, multiclass
            clus
vv           MICAL1 MUTATED MICAL1 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               3              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MICAL1 MUTATED     0   3   5   1
  MICAL1 WILD-TYPE   9  65 243  40
D1413V4, multiclass
    clus
vv   MICAL1 MUTATED MICAL1 WILD-TYPE
  T1              0                9
  T2              3               65
  T3              5              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
  MICAL1 MUTATED     8   1   0
  MICAL1 WILD-TYPE 212  79  66
D1413V5, multiclass
    clus
vv   MICAL1 MUTATED MICAL1 WILD-TYPE
  N0              8              212
  N1              1               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"
D1413V6, binary
                  cls
clus                 0   1
  MICAL1 MUTATED     9   0
  MICAL1 WILD-TYPE 274  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MICAL1 MUTATED      9    0
  MICAL1 WILD-TYPE  274   48
   clus
vv  MICAL1 MUTATED MICAL1 WILD-TYPE
  0              9              274
  1              0               48
[1] 2 2
[1] FALSE
D1413V7, 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
D1413V8, binary
                  cls
clus                 0   1
  MICAL1 MUTATED     7   2
  MICAL1 WILD-TYPE 310  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MICAL1 MUTATED      7    2
  MICAL1 WILD-TYPE  310   46
                               clus
vv                              MICAL1 MUTATED MICAL1 WILD-TYPE
  COLON ADENOCARCINOMA                       7              310
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  MICAL1 MUTATED     6   0   0   0
  MICAL1 WILD-TYPE 251   2  22  21
D1413V9, multiclass
    clus
vv   MICAL1 MUTATED MICAL1 WILD-TYPE
  R0              6              251
  R1              0                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"
D1413V10, 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
D1413V11, 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(1414) Variable = SUPT3H MUTATION ANALYSIS
D1414V1, survival
                  sevent
clus2                0   1
  SUPT3H MUTATED     6   2
  SUPT3H WILD-TYPE 276  71
  SUPT3H MUTATED SUPT3H WILD-TYPE 
               8              347 
  SUPT3H MUTATED SUPT3H WILD-TYPE 
               2               71 
$`SUPT3H MUTATED`
TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3950 TCGA-AA-A010 TCGA-AZ-6599 TCGA-CA-6719 
       63.98        13.02        24.00        34.98         6.77         1.35 
TCGA-CM-6674 TCGA-F4-6854 
       12.95         0.53 

$`SUPT3H WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        1.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41        49.41        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        0.10        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6855 TCGA-F4-6856 
       29.59        16.24        33.67        13.25        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  SUPT3H MUTATED SUPT3H WILD-TYPE 
            0.53             0.00 
  SUPT3H MUTATED SUPT3H WILD-TYPE 
           63.98           140.38 
  SUPT3H MUTATED SUPT3H WILD-TYPE 
          12.985           20.280 
[1] "0.5 - 64.0 (13.0)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.5"
D1414V2, 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       24       104         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SUPT3H MUTATED           2          0          0          0        0
  SUPT3H WILD-TYPE        17         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  SUPT3H MUTATED           0         0
  SUPT3H WILD-TYPE        13         1
D1414V3, multiclass
            clus
vv           SUPT3H MUTATED SUPT3H WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               5              104
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               2               17
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SUPT3H MUTATED     0   1   8   2
  SUPT3H WILD-TYPE   9  67 240  39
D1414V4, multiclass
    clus
vv   SUPT3H MUTATED SUPT3H WILD-TYPE
  T1              0                9
  T2              1               67
  T3              8              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
  SUPT3H MUTATED     9   0   2
  SUPT3H WILD-TYPE 211  80  64
D1414V5, multiclass
    clus
vv   SUPT3H MUTATED SUPT3H WILD-TYPE
  N0              9              211
  N1              0               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"
D1414V6, binary
                  cls
clus                 0   1
  SUPT3H MUTATED     9   0
  SUPT3H WILD-TYPE 274  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SUPT3H MUTATED      9    0
  SUPT3H WILD-TYPE  274   48
   clus
vv  SUPT3H MUTATED SUPT3H WILD-TYPE
  0              9              274
  1              0               48
[1] 2 2
[1] FALSE
D1414V7, 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
D1414V8, binary
                  cls
clus                 0   1
  SUPT3H MUTATED     9   2
  SUPT3H WILD-TYPE 308  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SUPT3H MUTATED      9    2
  SUPT3H WILD-TYPE  308   46
                               clus
vv                              SUPT3H MUTATED SUPT3H WILD-TYPE
  COLON ADENOCARCINOMA                       9              308
  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 250   2  22  19
D1414V9, multiclass
    clus
vv   SUPT3H MUTATED SUPT3H WILD-TYPE
  R0              7              250
  R1              0                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"
D1414V10, 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
D1414V11, 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(1415) Variable = TMPRSS15 MUTATION ANALYSIS
D1415V1, survival
                    sevent
clus2                  0   1
  TMPRSS15 MUTATED    14   4
  TMPRSS15 WILD-TYPE 268  69
  TMPRSS15 MUTATED TMPRSS15 WILD-TYPE 
                18                337 
  TMPRSS15 MUTATED TMPRSS15 WILD-TYPE 
                 4                 69 
$`TMPRSS15 MUTATED`
TCGA-A6-6137 TCGA-AA-3715 TCGA-AA-3864 TCGA-AA-A010 TCGA-AD-6888 TCGA-AY-6386 
       27.09        19.04        53.00        34.98         4.21        17.82 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-CA-5797 TCGA-CA-6718 TCGA-CK-6748 TCGA-CM-4746 
       49.41         6.77         3.29         0.10         2.01        37.02 
TCGA-CM-4752 TCGA-CM-6166 TCGA-D5-6536 TCGA-D5-6931 TCGA-DM-A28F TCGA-G4-6309 
       13.02        21.99        17.85        12.00        35.97        51.75 

$`TMPRSS15 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        32.71        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       61.41        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 
        3.19         1.94         2.24         3.06         3.25         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.33         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
      139.17         6.12        81.37       119.93        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  TMPRSS15 MUTATED TMPRSS15 WILD-TYPE 
               0.1                0.0 
  TMPRSS15 MUTATED TMPRSS15 WILD-TYPE 
             53.00             140.38 
  TMPRSS15 MUTATED TMPRSS15 WILD-TYPE 
            18.445             20.280 
[1] "0.1 - 53.0 (18.4)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.2"
D1415V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TMPRSS15 MUTATED         3        0        3         4         1         0
  TMPRSS15 WILD-TYPE      61        1       22       105         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMPRSS15 MUTATED           0          0          5          1        1
  TMPRSS15 WILD-TYPE        19         10         36         30       34
                    vv
clus                 STAGE IVA STAGE IVB
  TMPRSS15 MUTATED           0         0
  TMPRSS15 WILD-TYPE        13         1
D1415V3, multiclass
            clus
vv           TMPRSS15 MUTATED TMPRSS15 WILD-TYPE
  STAGE I                   3                 61
  STAGE IA                  0                  1
  STAGE II                  3                 22
  STAGE IIA                 4                105
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                0                 10
  STAGE IIIB                5                 36
  STAGE IIIC                1                 30
  STAGE IV                  1                 34
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  TMPRSS15 MUTATED     0   4  12   2
  TMPRSS15 WILD-TYPE   9  64 236  39
D1415V4, multiclass
    clus
vv   TMPRSS15 MUTATED TMPRSS15 WILD-TYPE
  T1                0                  9
  T2                4                 64
  T3               12                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
  TMPRSS15 MUTATED    11   5   1
  TMPRSS15 WILD-TYPE 209  75  65
D1415V5, multiclass
    clus
vv   TMPRSS15 MUTATED TMPRSS15 WILD-TYPE
  N0               11                209
  N1                5                 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"
D1415V6, binary
                    cls
clus                   0   1
  TMPRSS15 MUTATED    15   1
  TMPRSS15 WILD-TYPE 268  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMPRSS15 MUTATED     15    1
  TMPRSS15 WILD-TYPE  268   47
   clus
vv  TMPRSS15 MUTATED TMPRSS15 WILD-TYPE
  0               15                268
  1                1                 47
[1] 2 2
[1] FALSE
D1415V7, binary
                    cls
clus                   0   1
  TMPRSS15 MUTATED     6  12
  TMPRSS15 WILD-TYPE 164 185
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMPRSS15 MUTATED      6   12
  TMPRSS15 WILD-TYPE  164  185
        clus
vv       TMPRSS15 MUTATED TMPRSS15 WILD-TYPE
  FEMALE                6                164
  MALE                 12                185
[1] 2 2
[1] FALSE
D1415V8, binary
                    cls
clus                   0   1
  TMPRSS15 MUTATED    17   1
  TMPRSS15 WILD-TYPE 300  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMPRSS15 MUTATED     17    1
  TMPRSS15 WILD-TYPE  300   47
                               clus
vv                              TMPRSS15 MUTATED TMPRSS15 WILD-TYPE
  COLON ADENOCARCINOMA                        17                300
  COLON MUCINOUS ADENOCARCINOMA                1                 47
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  TMPRSS15 MUTATED    12   0   0   2
  TMPRSS15 WILD-TYPE 245   2  22  19
D1415V9, multiclass
    clus
vv   TMPRSS15 MUTATED TMPRSS15 WILD-TYPE
  R0               12                245
  R1                0                  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"
D1415V10, 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
D1415V11, 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(1416) Variable = RNF219 MUTATION ANALYSIS
D1416V1, survival
                  sevent
clus2                0   1
  RNF219 MUTATED    13   1
  RNF219 WILD-TYPE 269  72
  RNF219 MUTATED RNF219 WILD-TYPE 
              14              341 
  RNF219 MUTATED RNF219 WILD-TYPE 
               1               72 
$`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         0.33 
TCGA-CA-6718 TCGA-CM-5861 TCGA-D5-5539 TCGA-D5-6540 TCGA-D5-6923 TCGA-D5-6928 
        0.10        15.02        19.59        16.14        12.43        11.64 
TCGA-G4-6309 TCGA-G4-6323 
       51.75        13.78 

$`RNF219 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        27.09        16.31         0.95        15.75 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07         0.26         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01         5.03        15.02        15.02 
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        12.26        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 
       10.13        14.30         9.04         9.44        13.41         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        45.11        36.72        36.00        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  RNF219 MUTATED RNF219 WILD-TYPE 
             0.1              0.0 
  RNF219 MUTATED RNF219 WILD-TYPE 
           51.75           140.38 
  RNF219 MUTATED RNF219 WILD-TYPE 
           14.14            21.01 
[1] "0.1 - 51.8 (14.1)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "2.2"
D1416V2, 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       23       104         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RNF219 MUTATED           0          1          1          2        0
  RNF219 WILD-TYPE        19          9         40         29       35
                  vv
clus               STAGE IVA STAGE IVB
  RNF219 MUTATED           0         0
  RNF219 WILD-TYPE        13         1
D1416V3, multiclass
            clus
vv           RNF219 MUTATED RNF219 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                1                0
  STAGE II                2               23
  STAGE IIA               5              104
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              1                9
  STAGE IIIB              1               40
  STAGE IIIC              2               29
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  RNF219 MUTATED     0   2  11   0
  RNF219 WILD-TYPE   9  66 237  41
D1416V4, multiclass
    clus
vv   RNF219 MUTATED RNF219 WILD-TYPE
  T1              0                9
  T2              2               66
  T3             11              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
  RNF219 MUTATED    10   2   2
  RNF219 WILD-TYPE 210  78  64
D1416V5, multiclass
    clus
vv   RNF219 MUTATED RNF219 WILD-TYPE
  N0             10              210
  N1              2               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"
D1416V6, binary
                  cls
clus                 0   1
  RNF219 MUTATED    11   0
  RNF219 WILD-TYPE 272  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF219 MUTATED     11    0
  RNF219 WILD-TYPE  272   48
   clus
vv  RNF219 MUTATED RNF219 WILD-TYPE
  0             11              272
  1              0               48
[1] 2 2
[1] FALSE
D1416V7, 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
D1416V8, binary
                  cls
clus                 0   1
  RNF219 MUTATED     9   5
  RNF219 WILD-TYPE 308  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF219 MUTATED      9    5
  RNF219 WILD-TYPE  308   43
                               clus
vv                              RNF219 MUTATED RNF219 WILD-TYPE
  COLON ADENOCARCINOMA                       9              308
  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 247   2  22  19
D1416V9, multiclass
    clus
vv   RNF219 MUTATED RNF219 WILD-TYPE
  R0             10              247
  R1              0                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"
D1416V10, 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
D1416V11, 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(1417) Variable = SSRP1 MUTATION ANALYSIS
D1417V1, survival
                 sevent
clus2               0   1
  SSRP1 MUTATED    11   1
  SSRP1 WILD-TYPE 271  72
  SSRP1 MUTATED SSRP1 WILD-TYPE 
             12             343 
  SSRP1 MUTATED SSRP1 WILD-TYPE 
              1              72 
$`SSRP1 MUTATED`
TCGA-A6-6653 TCGA-AA-3663 TCGA-AA-3966 TCGA-AD-6964 TCGA-AU-6004 TCGA-CM-6162 
       24.39         6.97         2.01        10.88        27.09        12.00 
TCGA-CM-6166 TCGA-CM-6674 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6323 TCGA-G4-6628 
       21.99        12.95        53.62        55.04        13.78        52.80 

$`SSRP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 
      107.67        74.56        65.85        44.68        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.72        36.00        22.09        35.80        26.17        91.79 
TCGA-G4-6626 
       46.75 

  SSRP1 MUTATED SSRP1 WILD-TYPE 
           2.01            0.00 
  SSRP1 MUTATED SSRP1 WILD-TYPE 
          55.04          140.38 
  SSRP1 MUTATED SSRP1 WILD-TYPE 
         17.885          20.190 
[1] "2.0 - 55.0 (17.9)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2.6"
D1417V2, 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       24       107         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        18         10         39         31       35        13
                 vv
clus              STAGE IVB
  SSRP1 MUTATED           0
  SSRP1 WILD-TYPE         1
D1417V3, multiclass
            clus
vv           SSRP1 MUTATED SSRP1 WILD-TYPE
  STAGE I                4              60
  STAGE IA               1               0
  STAGE II               1              24
  STAGE IIA              2             107
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SSRP1 MUTATED     0   4   6   2
  SSRP1 WILD-TYPE   9  64 242  39
D1417V4, multiclass
    clus
vv   SSRP1 MUTATED SSRP1 WILD-TYPE
  T1             0               9
  T2             4              64
  T3             6             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
  SSRP1 MUTATED     9   2   2
  SSRP1 WILD-TYPE 211  78  64
D1417V5, multiclass
    clus
vv   SSRP1 MUTATED SSRP1 WILD-TYPE
  N0             9             211
  N1             2              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"
D1417V6, binary
                 cls
clus                0   1
  SSRP1 MUTATED    11   0
  SSRP1 WILD-TYPE 272  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SSRP1 MUTATED     11    0
  SSRP1 WILD-TYPE  272   48
   clus
vv  SSRP1 MUTATED SSRP1 WILD-TYPE
  0            11             272
  1             0              48
[1] 2 2
[1] FALSE
D1417V7, 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
D1417V8, binary
                 cls
clus                0   1
  SSRP1 MUTATED    11   2
  SSRP1 WILD-TYPE 306  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SSRP1 MUTATED     11    2
  SSRP1 WILD-TYPE  306   46
                               clus
vv                              SSRP1 MUTATED SSRP1 WILD-TYPE
  COLON ADENOCARCINOMA                     11             306
  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 247   2  22  21
D1417V9, multiclass
    clus
vv   SSRP1 MUTATED SSRP1 WILD-TYPE
  R0            10             247
  R1             0               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"
D1417V10, 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
D1417V11, 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(1418) Variable = IKBKE MUTATION ANALYSIS
D1418V1, survival
                 sevent
clus2               0   1
  IKBKE MUTATED     3   3
  IKBKE WILD-TYPE 279  70
  IKBKE MUTATED IKBKE WILD-TYPE 
              6             349 
  IKBKE MUTATED IKBKE WILD-TYPE 
              3              70 
$`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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       12.59         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 
        0.53        35.41        19.43       107.67        74.56        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  IKBKE MUTATED IKBKE WILD-TYPE 
           3.02            0.00 
  IKBKE MUTATED IKBKE WILD-TYPE 
         140.38          139.17 
  IKBKE MUTATED IKBKE WILD-TYPE 
          42.21           20.02 
[1] "3.0 - 140.4 (42.2)" "0.0 - 139.2 (20.0)"
[1] "hr=" "1.3"
D1418V2, 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       23       106         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        18         10         41         31       34        13
                 vv
clus              STAGE IVB
  IKBKE MUTATED           0
  IKBKE WILD-TYPE         1
D1418V3, multiclass
            clus
vv           IKBKE MUTATED IKBKE WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              3             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  IKBKE MUTATED     0   0   7   0
  IKBKE WILD-TYPE   9  68 241  41
D1418V4, multiclass
    clus
vv   IKBKE MUTATED IKBKE WILD-TYPE
  T1             0               9
  T2             0              68
  T3             7             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
  IKBKE MUTATED     5   1   1
  IKBKE WILD-TYPE 215  79  65
D1418V5, multiclass
    clus
vv   IKBKE MUTATED IKBKE WILD-TYPE
  N0             5             215
  N1             1              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"
D1418V6, binary
                 cls
clus                0   1
  IKBKE MUTATED     4   1
  IKBKE WILD-TYPE 279  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IKBKE MUTATED      4    1
  IKBKE WILD-TYPE  279   47
   clus
vv  IKBKE MUTATED IKBKE WILD-TYPE
  0             4             279
  1             1              47
[1] 2 2
[1] FALSE
D1418V7, 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
D1418V8, binary
                 cls
clus                0   1
  IKBKE MUTATED     6   1
  IKBKE WILD-TYPE 311  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IKBKE MUTATED      6    1
  IKBKE WILD-TYPE  311   47
                               clus
vv                              IKBKE MUTATED IKBKE WILD-TYPE
  COLON ADENOCARCINOMA                      6             311
  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 252   2  22  21
D1418V9, multiclass
    clus
vv   IKBKE MUTATED IKBKE WILD-TYPE
  R0             5             252
  R1             0               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"
D1418V10, 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
D1418V11, 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(1419) Variable = EHHADH MUTATION ANALYSIS
D1419V1, survival
                  sevent
clus2                0   1
  EHHADH MUTATED    10   3
  EHHADH WILD-TYPE 272  70
  EHHADH MUTATED EHHADH WILD-TYPE 
              13              342 
  EHHADH MUTATED EHHADH WILD-TYPE 
               3               70 
$`EHHADH MUTATED`
TCGA-AA-3815 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6895 TCGA-AD-6899 TCGA-AZ-6598 
       33.04         4.01        34.98         0.72         5.79        49.41 
TCGA-CA-6717 TCGA-CK-5913 TCGA-CM-4746 TCGA-CM-4752 TCGA-CM-6167 TCGA-D5-6536 
        0.33        51.32        37.02        13.02        14.99        17.85 
TCGA-F4-6704 
        1.55 

$`EHHADH WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        0.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
       17.56       102.44        40.34        15.62        49.08        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         2.01       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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        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-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        15.12         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 
        8.61        13.38        13.45         6.18        35.87        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  EHHADH MUTATED EHHADH WILD-TYPE 
            0.33             0.00 
  EHHADH MUTATED EHHADH WILD-TYPE 
           51.32           140.38 
  EHHADH MUTATED EHHADH WILD-TYPE 
           14.99            20.63 
[1] "0.3 - 51.3 (15.0)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "1.4"
D1419V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EHHADH MUTATED         1        0        1         5         2         0
  EHHADH WILD-TYPE      63        1       24       104         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EHHADH MUTATED           0          0          0          3        0
  EHHADH WILD-TYPE        19         10         41         28       35
                  vv
clus               STAGE IVA STAGE IVB
  EHHADH MUTATED           0         0
  EHHADH WILD-TYPE        13         1
D1419V3, multiclass
            clus
vv           EHHADH MUTATED EHHADH WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               5              104
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              3               28
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  EHHADH MUTATED     0   1   9   3
  EHHADH WILD-TYPE   9  67 239  38
D1419V4, multiclass
    clus
vv   EHHADH MUTATED EHHADH WILD-TYPE
  T1              0                9
  T2              1               67
  T3              9              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
  EHHADH MUTATED     9   1   3
  EHHADH WILD-TYPE 211  79  63
D1419V5, multiclass
    clus
vv   EHHADH MUTATED EHHADH WILD-TYPE
  N0              9              211
  N1              1               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"
D1419V6, binary
                  cls
clus                 0   1
  EHHADH MUTATED     8   0
  EHHADH WILD-TYPE 275  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EHHADH MUTATED      8    0
  EHHADH WILD-TYPE  275   48
   clus
vv  EHHADH MUTATED EHHADH WILD-TYPE
  0              8              275
  1              0               48
[1] 2 2
[1] FALSE
D1419V7, binary
                  cls
clus                 0   1
  EHHADH MUTATED     5   8
  EHHADH WILD-TYPE 165 189
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EHHADH MUTATED      5    8
  EHHADH WILD-TYPE  165  189
        clus
vv       EHHADH MUTATED EHHADH WILD-TYPE
  FEMALE              5              165
  MALE                8              189
[1] 2 2
[1] FALSE
D1419V8, binary
                  cls
clus                 0   1
  EHHADH MUTATED     9   4
  EHHADH WILD-TYPE 308  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EHHADH MUTATED      9    4
  EHHADH WILD-TYPE  308   44
                               clus
vv                              EHHADH MUTATED EHHADH WILD-TYPE
  COLON ADENOCARCINOMA                       9              308
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  EHHADH MUTATED     8   0   0   2
  EHHADH WILD-TYPE 249   2  22  19
D1419V9, multiclass
    clus
vv   EHHADH MUTATED EHHADH WILD-TYPE
  R0              8              249
  R1              0                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"
D1419V10, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EHHADH MUTATED                                  1     1
  EHHADH WILD-TYPE                                0     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  EHHADH MUTATED                           3     5
  EHHADH WILD-TYPE                        16   171
D1419V11, multiclass
                                  clus
vv                                 EHHADH MUTATED EHHADH WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              1                0
  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(1420) Variable = ZNF564 MUTATION ANALYSIS
D1420V1, survival
                  sevent
clus2                0   1
  ZNF564 MUTATED     7   2
  ZNF564 WILD-TYPE 275  71
  ZNF564 MUTATED ZNF564 WILD-TYPE 
               9              346 
  ZNF564 MUTATED ZNF564 WILD-TYPE 
               2               71 
$`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         0.33         0.10 
TCGA-CK-4952 TCGA-CM-5864 TCGA-DM-A1D6 
       15.62        15.02        49.91 

$`ZNF564 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 
        1.35        17.56       102.44        40.34        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        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-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  ZNF564 MUTATED ZNF564 WILD-TYPE 
             0.1              0.0 
  ZNF564 MUTATED ZNF564 WILD-TYPE 
           53.00           140.38 
  ZNF564 MUTATED ZNF564 WILD-TYPE 
           15.02            20.63 
[1] "0.1 - 53.0 (15.0)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "1.3"
D1420V2, 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       23       105         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF564 MUTATED           1          0          0          0        0
  ZNF564 WILD-TYPE        18         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF564 MUTATED           0         0
  ZNF564 WILD-TYPE        13         1
D1420V3, multiclass
            clus
vv           ZNF564 MUTATED ZNF564 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               4              105
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF564 MUTATED     0   1   6   3
  ZNF564 WILD-TYPE   9  67 242  38
D1420V4, multiclass
    clus
vv   ZNF564 MUTATED ZNF564 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              6              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
  ZNF564 MUTATED     9   0   1
  ZNF564 WILD-TYPE 211  80  65
D1420V5, multiclass
    clus
vv   ZNF564 MUTATED ZNF564 WILD-TYPE
  N0              9              211
  N1              0               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"
D1420V6, binary
                  cls
clus                 0   1
  ZNF564 MUTATED    10   0
  ZNF564 WILD-TYPE 273  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF564 MUTATED     10    0
  ZNF564 WILD-TYPE  273   48
   clus
vv  ZNF564 MUTATED ZNF564 WILD-TYPE
  0             10              273
  1              0               48
[1] 2 2
[1] FALSE
D1420V7, 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
D1420V8, binary
                  cls
clus                 0   1
  ZNF564 MUTATED     6   4
  ZNF564 WILD-TYPE 311  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF564 MUTATED      6    4
  ZNF564 WILD-TYPE  311   44
                               clus
vv                              ZNF564 MUTATED ZNF564 WILD-TYPE
  COLON ADENOCARCINOMA                       6              311
  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 251   2  22  18
D1420V9, multiclass
    clus
vv   ZNF564 MUTATED ZNF564 WILD-TYPE
  R0              6              251
  R1              0                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"
D1420V10, 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
D1420V11, 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(1421) Variable = ARHGEF38 MUTATION ANALYSIS
D1421V1, survival
                    sevent
clus2                  0   1
  ARHGEF38 MUTATED     3   1
  ARHGEF38 WILD-TYPE 279  72
  ARHGEF38 MUTATED ARHGEF38 WILD-TYPE 
                 4                351 
  ARHGEF38 MUTATED ARHGEF38 WILD-TYPE 
                 1                 72 
$`ARHGEF38 MUTATED`
TCGA-AA-3663 TCGA-AA-3952 TCGA-CM-5349 TCGA-G4-6586 
        6.97         2.01        30.08        35.80 

$`ARHGEF38 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 
       45.11        36.72        36.00        22.09        13.78        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  ARHGEF38 MUTATED ARHGEF38 WILD-TYPE 
              2.01               0.00 
  ARHGEF38 MUTATED ARHGEF38 WILD-TYPE 
             35.80             140.38 
  ARHGEF38 MUTATED ARHGEF38 WILD-TYPE 
            18.525             20.190 
[1] "2.0 - 35.8 (18.5)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.9"
D1421V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ARHGEF38 MUTATED         0        0        1         2         0         0
  ARHGEF38 WILD-TYPE      64        1       24       107         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARHGEF38 MUTATED           0          0          0          1        0
  ARHGEF38 WILD-TYPE        19         10         41         30       35
                    vv
clus                 STAGE IVA STAGE IVB
  ARHGEF38 MUTATED           0         0
  ARHGEF38 WILD-TYPE        13         1
D1421V3, multiclass
            clus
vv           ARHGEF38 MUTATED ARHGEF38 WILD-TYPE
  STAGE I                   0                 64
  STAGE IA                  0                  1
  STAGE II                  1                 24
  STAGE IIA                 2                107
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                0                 10
  STAGE IIIB                0                 41
  STAGE IIIC                1                 30
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  ARHGEF38 MUTATED     0   0   4   0
  ARHGEF38 WILD-TYPE   9  68 244  41
D1421V4, multiclass
    clus
vv   ARHGEF38 MUTATED ARHGEF38 WILD-TYPE
  T1                0                  9
  T2                0                 68
  T3                4                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
  ARHGEF38 MUTATED     3   0   1
  ARHGEF38 WILD-TYPE 217  80  65
D1421V5, multiclass
    clus
vv   ARHGEF38 MUTATED ARHGEF38 WILD-TYPE
  N0                3                217
  N1                0                 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"
D1421V6, binary
                    cls
clus                   0   1
  ARHGEF38 MUTATED     4   0
  ARHGEF38 WILD-TYPE 279  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGEF38 MUTATED      4    0
  ARHGEF38 WILD-TYPE  279   48
   clus
vv  ARHGEF38 MUTATED ARHGEF38 WILD-TYPE
  0                4                279
  1                0                 48
[1] 2 2
[1] FALSE
D1421V7, binary
                    cls
clus                   0   1
  ARHGEF38 MUTATED     2   2
  ARHGEF38 WILD-TYPE 168 195
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGEF38 MUTATED      2    2
  ARHGEF38 WILD-TYPE  168  195
        clus
vv       ARHGEF38 MUTATED ARHGEF38 WILD-TYPE
  FEMALE                2                168
  MALE                  2                195
[1] 2 2
[1] FALSE
D1421V8, binary
                    cls
clus                   0   1
  ARHGEF38 MUTATED     4   0
  ARHGEF38 WILD-TYPE 313  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGEF38 MUTATED      4    0
  ARHGEF38 WILD-TYPE  313   48
                               clus
vv                              ARHGEF38 MUTATED ARHGEF38 WILD-TYPE
  COLON ADENOCARCINOMA                         4                313
  COLON MUCINOUS ADENOCARCINOMA                0                 48
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  ARHGEF38 MUTATED     4   0   0   0
  ARHGEF38 WILD-TYPE 253   2  22  21
D1421V9, multiclass
    clus
vv   ARHGEF38 MUTATED ARHGEF38 WILD-TYPE
  R0                4                253
  R1                0                  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"
D1421V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARHGEF38 MUTATED                                  0     0
  ARHGEF38 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  ARHGEF38 MUTATED                           0     2
  ARHGEF38 WILD-TYPE                        19   174
D1421V11, multiclass
[1] "Remove cluster labels:" "ARHGEF38 MUTATED"      
clus
  ARHGEF38 MUTATED ARHGEF38 WILD-TYPE 
                 2                204 
        TCGA-A6-2671         TCGA-A6-2672         TCGA-A6-2674 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-A6-2676         TCGA-A6-2677         TCGA-A6-2678 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-A6-2683         TCGA-A6-3807         TCGA-A6-3808 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-A6-3809         TCGA-A6-3810         TCGA-A6-4105 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-A6-5656         TCGA-A6-5657         TCGA-A6-5659 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-A6-5660         TCGA-A6-5661         TCGA-A6-5662 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-A6-5664         TCGA-A6-5665         TCGA-A6-5666 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-A6-6137         TCGA-A6-6138         TCGA-A6-6141 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-A6-6142         TCGA-A6-6648         TCGA-A6-6649 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-A6-6651         TCGA-A6-6652         TCGA-A6-6653 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-A6-6654         TCGA-A6-6780         TCGA-A6-6781 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-A6-6782         TCGA-AD-5900         TCGA-AD-6548 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-AD-6888         TCGA-AD-6889         TCGA-AD-6890 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-AD-6895         TCGA-AD-6899         TCGA-AD-6901 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-AD-6963         TCGA-AD-6964         TCGA-AD-6965 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-AU-3779         TCGA-AU-6004         TCGA-AY-4070 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-AY-4071         TCGA-AY-5543         TCGA-AY-6196 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-AY-6197         TCGA-AY-6386         TCGA-AZ-4315 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-AZ-4323         TCGA-AZ-4616         TCGA-AZ-4681 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-AZ-4682         TCGA-AZ-5403         TCGA-AZ-5407 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-AZ-6598         TCGA-AZ-6599         TCGA-AZ-6600 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-AZ-6601         TCGA-AZ-6603         TCGA-AZ-6605 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-AZ-6606         TCGA-AZ-6607         TCGA-AZ-6608 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-CA-5254         TCGA-CA-5255         TCGA-CA-5796 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-CA-5797         TCGA-CA-6715         TCGA-CA-6716 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-CA-6717         TCGA-CA-6718         TCGA-CA-6719 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-CK-4947         TCGA-CK-4948         TCGA-CK-4950 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-CK-4952         TCGA-CK-5912         TCGA-CK-5913 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-CK-5914         TCGA-CK-5915         TCGA-CK-5916 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-CK-6746         TCGA-CK-6747         TCGA-CK-6748 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-CK-6751         TCGA-CM-4743         TCGA-CM-4744 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-CM-4746         TCGA-CM-4747         TCGA-CM-4752 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-CM-5341         TCGA-CM-5344         TCGA-CM-5348 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-CM-5860         TCGA-CM-5861         TCGA-CM-5862 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-CM-5863         TCGA-CM-5864         TCGA-CM-5868 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-CM-6161         TCGA-CM-6162         TCGA-CM-6163 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-CM-6164         TCGA-CM-6165         TCGA-CM-6166 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-CM-6167         TCGA-CM-6168         TCGA-CM-6169 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-CM-6170         TCGA-CM-6171         TCGA-CM-6172 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-CM-6674         TCGA-CM-6675         TCGA-CM-6676 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-CM-6677         TCGA-CM-6678         TCGA-CM-6679 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-CM-6680         TCGA-D5-5537         TCGA-D5-5538 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-D5-5539         TCGA-D5-5540         TCGA-D5-5541 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-D5-6529         TCGA-D5-6532         TCGA-D5-6533 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-D5-6534         TCGA-D5-6535         TCGA-D5-6536 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-D5-6537         TCGA-D5-6538         TCGA-D5-6539 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-D5-6540         TCGA-D5-6541         TCGA-D5-6898 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-D5-6920         TCGA-D5-6922         TCGA-D5-6923 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-D5-6924         TCGA-D5-6926         TCGA-D5-6927 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-D5-6928         TCGA-D5-6929         TCGA-D5-6930 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-D5-6931         TCGA-D5-6932         TCGA-D5-7000 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-DM-A0X9         TCGA-DM-A0XD         TCGA-DM-A0XF 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-DM-A1D0         TCGA-DM-A1D4         TCGA-DM-A1D6 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-DM-A1D7         TCGA-DM-A1D8         TCGA-DM-A1D9 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-DM-A1DA         TCGA-DM-A1DB         TCGA-DM-A1HA 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-DM-A1HB         TCGA-DM-A282         TCGA-DM-A285 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-DM-A28C         TCGA-DM-A28E         TCGA-DM-A28F 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-DM-A28G         TCGA-DM-A28H         TCGA-DM-A28K 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-F4-6459         TCGA-F4-6460         TCGA-F4-6569 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-F4-6570         TCGA-F4-6703         TCGA-F4-6704 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-F4-6805         TCGA-F4-6806         TCGA-F4-6807 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-F4-6808         TCGA-F4-6809         TCGA-F4-6854 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-F4-6855         TCGA-F4-6856         TCGA-G4-6293 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-G4-6299         TCGA-G4-6303         TCGA-G4-6304 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-G4-6306         TCGA-G4-6307         TCGA-G4-6309 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-G4-6310         TCGA-G4-6315         TCGA-G4-6317 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-G4-6321         TCGA-G4-6323         TCGA-G4-6588 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 
        TCGA-G4-6625         TCGA-G4-6626         TCGA-G4-6628 
"ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" "ARHGEF38 WILD-TYPE" 

Clustering(1422) Variable = PNPLA5 MUTATION ANALYSIS
D1422V1, survival
                  sevent
clus2                0   1
  PNPLA5 MUTATED     7   1
  PNPLA5 WILD-TYPE 275  72
  PNPLA5 MUTATED PNPLA5 WILD-TYPE 
               8              347 
  PNPLA5 MUTATED PNPLA5 WILD-TYPE 
               1               72 
$`PNPLA5 MUTATED`
TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3877 TCGA-AU-6004 TCGA-CA-5254 TCGA-CK-5913 
        3.02        63.98        31.00        27.09         2.24        51.32 
TCGA-G4-6586 TCGA-G4-6628 
       35.80        52.80 

$`PNPLA5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        18.05         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.20        14.50        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        26.17        91.79        46.75 

  PNPLA5 MUTATED PNPLA5 WILD-TYPE 
            2.24             0.00 
  PNPLA5 MUTATED PNPLA5 WILD-TYPE 
           63.98           140.38 
  PNPLA5 MUTATED PNPLA5 WILD-TYPE 
           33.40            20.02 
[1] "2.2 - 64.0 (33.4)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "2.2"
D1422V2, 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       23       106         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PNPLA5 MUTATED           0          0          0          0        1
  PNPLA5 WILD-TYPE        19         10         41         31       34
                  vv
clus               STAGE IVA STAGE IVB
  PNPLA5 MUTATED           0         0
  PNPLA5 WILD-TYPE        13         1
D1422V3, multiclass
            clus
vv           PNPLA5 MUTATED PNPLA5 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               3              106
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PNPLA5 MUTATED     1   2   6   1
  PNPLA5 WILD-TYPE   8  66 242  40
D1422V4, multiclass
    clus
vv   PNPLA5 MUTATED PNPLA5 WILD-TYPE
  T1              1                8
  T2              2               66
  T3              6              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
  PNPLA5 MUTATED     9   0   1
  PNPLA5 WILD-TYPE 211  80  65
D1422V5, multiclass
    clus
vv   PNPLA5 MUTATED PNPLA5 WILD-TYPE
  N0              9              211
  N1              0               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"
D1422V6, binary
                  cls
clus                 0   1
  PNPLA5 MUTATED     7   1
  PNPLA5 WILD-TYPE 276  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PNPLA5 MUTATED      7    1
  PNPLA5 WILD-TYPE  276   47
   clus
vv  PNPLA5 MUTATED PNPLA5 WILD-TYPE
  0              7              276
  1              1               47
[1] 2 2
[1] FALSE
D1422V7, 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
D1422V8, binary
                  cls
clus                 0   1
  PNPLA5 MUTATED     9   1
  PNPLA5 WILD-TYPE 308  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PNPLA5 MUTATED      9    1
  PNPLA5 WILD-TYPE  308   47
                               clus
vv                              PNPLA5 MUTATED PNPLA5 WILD-TYPE
  COLON ADENOCARCINOMA                       9              308
  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 251   2  21  18
D1422V9, multiclass
    clus
vv   PNPLA5 MUTATED PNPLA5 WILD-TYPE
  R0              6              251
  R1              0                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"
D1422V10, 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
D1422V11, 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(1423) Variable = C1ORF85 MUTATION ANALYSIS
D1423V1, survival
                   sevent
clus2                 0   1
  C1ORF85 MUTATED     7   0
  C1ORF85 WILD-TYPE 275  73
  C1ORF85 MUTATED C1ORF85 WILD-TYPE 
                7               348 
  C1ORF85 MUTATED C1ORF85 WILD-TYPE 
                0                73 
$`C1ORF85 MUTATED`
TCGA-AD-5900 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CM-5860 TCGA-DM-A282 TCGA-G4-6588 
        0.07        58.39         0.33        16.01       139.17        26.17 
TCGA-G4-6628 
       52.80 

$`C1ORF85 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 

  C1ORF85 MUTATED C1ORF85 WILD-TYPE 
             0.07              0.00 
  C1ORF85 MUTATED C1ORF85 WILD-TYPE 
           139.17            140.38 
  C1ORF85 MUTATED C1ORF85 WILD-TYPE 
           26.170            20.155 
[1] "0.1 - 139.2 (26.2)" "0.0 - 140.4 (20.2)"
[1] "hr="     "2.6e+07"
D1423V2, 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       25       104         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C1ORF85 MUTATED           0          0          0          0        0
  C1ORF85 WILD-TYPE        19         10         41         31       35
                   vv
clus                STAGE IVA STAGE IVB
  C1ORF85 MUTATED           0         0
  C1ORF85 WILD-TYPE        13         1
D1423V3, multiclass
            clus
vv           C1ORF85 MUTATED C1ORF85 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                5               104
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C1ORF85 MUTATED     0   2   5   0
  C1ORF85 WILD-TYPE   9  66 243  41
D1423V4, multiclass
    clus
vv   C1ORF85 MUTATED C1ORF85 WILD-TYPE
  T1               0                 9
  T2               2                66
  T3               5               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
  C1ORF85 MUTATED     7   0   0
  C1ORF85 WILD-TYPE 213  80  66
D1423V5, multiclass
    clus
vv   C1ORF85 MUTATED C1ORF85 WILD-TYPE
  N0               7               213
  N1               0                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
  C1ORF85 MUTATED     6   0
  C1ORF85 WILD-TYPE 277  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1ORF85 MUTATED      6    0
  C1ORF85 WILD-TYPE  277   48
   clus
vv  C1ORF85 MUTATED C1ORF85 WILD-TYPE
  0               6               277
  1               0                48
[1] 2 2
[1] FALSE
D1423V7, 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
D1423V8, binary
                   cls
clus                  0   1
  C1ORF85 MUTATED     5   2
  C1ORF85 WILD-TYPE 312  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1ORF85 MUTATED      5    2
  C1ORF85 WILD-TYPE  312   46
                               clus
vv                              C1ORF85 MUTATED C1ORF85 WILD-TYPE
  COLON ADENOCARCINOMA                        5               312
  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 252   2  22  20
D1423V9, multiclass
    clus
vv   C1ORF85 MUTATED C1ORF85 WILD-TYPE
  R0               5               252
  R1               0                 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"
D1423V10, 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
D1423V11, 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(1424) Variable = PANK3 MUTATION ANALYSIS
D1424V1, survival
                 sevent
clus2               0   1
  PANK3 MUTATED     5   1
  PANK3 WILD-TYPE 277  72
  PANK3 MUTATED PANK3 WILD-TYPE 
              6             349 
  PANK3 MUTATED PANK3 WILD-TYPE 
              1              72 
$`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-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       12.00        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
      140.38        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  PANK3 MUTATED PANK3 WILD-TYPE 
            7.5             0.0 
  PANK3 MUTATED PANK3 WILD-TYPE 
          46.65          140.38 
  PANK3 MUTATED PANK3 WILD-TYPE 
          31.56           20.12 
[1] "7.5 - 46.6 (31.6)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.2"
D1424V2, 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       25       107         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        19         10         40         30       35        13
                 vv
clus              STAGE IVB
  PANK3 MUTATED           0
  PANK3 WILD-TYPE         1
D1424V3, multiclass
            clus
vv           PANK3 MUTATED PANK3 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              2             107
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PANK3 MUTATED     1   0   4   1
  PANK3 WILD-TYPE   8  68 244  40
D1424V4, multiclass
    clus
vv   PANK3 MUTATED PANK3 WILD-TYPE
  T1             1               8
  T2             0              68
  T3             4             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
  PANK3 MUTATED     4   1   1
  PANK3 WILD-TYPE 216  79  65
D1424V5, multiclass
    clus
vv   PANK3 MUTATED PANK3 WILD-TYPE
  N0             4             216
  N1             1              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"
D1424V6, binary
                 cls
clus                0   1
  PANK3 MUTATED     6   0
  PANK3 WILD-TYPE 277  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PANK3 MUTATED      6    0
  PANK3 WILD-TYPE  277   48
   clus
vv  PANK3 MUTATED PANK3 WILD-TYPE
  0             6             277
  1             0              48
[1] 2 2
[1] FALSE
D1424V7, 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
D1424V8, binary
                 cls
clus                0   1
  PANK3 MUTATED     6   0
  PANK3 WILD-TYPE 311  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PANK3 MUTATED      6    0
  PANK3 WILD-TYPE  311   48
                               clus
vv                              PANK3 MUTATED PANK3 WILD-TYPE
  COLON ADENOCARCINOMA                      6             311
  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 252   2  22  21
D1424V9, multiclass
    clus
vv   PANK3 MUTATED PANK3 WILD-TYPE
  R0             5             252
  R1             0               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"
D1424V10, 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
D1424V11, 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(1425) Variable = CHRM3 MUTATION ANALYSIS
D1425V1, survival
                 sevent
clus2               0   1
  CHRM3 MUTATED     8   5
  CHRM3 WILD-TYPE 274  68
  CHRM3 MUTATED CHRM3 WILD-TYPE 
             13             342 
  CHRM3 MUTATED CHRM3 WILD-TYPE 
              5              68 
$`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        61.41         0.33 
TCGA-CA-6718 TCGA-CM-5349 TCGA-CM-6166 TCGA-D5-6931 TCGA-DM-A1D6 TCGA-F4-6570 
        0.10        30.08        21.99        12.00        49.91         6.18 
TCGA-G4-6303 
       65.85 

$`CHRM3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         0.72         5.79        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07         0.26         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43        38.20       130.65        92.75        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        13.38        13.45        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 
       35.41        19.43       107.67        74.56        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  CHRM3 MUTATED CHRM3 WILD-TYPE 
            0.1             0.0 
  CHRM3 MUTATED CHRM3 WILD-TYPE 
          65.85          140.38 
  CHRM3 MUTATED CHRM3 WILD-TYPE 
          22.42           20.07 
[1] "0.1 - 65.8 (22.4)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.7"
D1425V2, 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       24       104         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        18         10         41         30       34        13
                 vv
clus              STAGE IVB
  CHRM3 MUTATED           0
  CHRM3 WILD-TYPE         1
D1425V3, multiclass
            clus
vv           CHRM3 MUTATED CHRM3 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              5             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CHRM3 MUTATED     1   1   9   2
  CHRM3 WILD-TYPE   8  67 239  39
D1425V4, multiclass
    clus
vv   CHRM3 MUTATED CHRM3 WILD-TYPE
  T1             1               8
  T2             1              67
  T3             9             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
  CHRM3 MUTATED    10   1   2
  CHRM3 WILD-TYPE 210  79  64
D1425V5, multiclass
    clus
vv   CHRM3 MUTATED CHRM3 WILD-TYPE
  N0            10             210
  N1             1              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"
D1425V6, binary
                 cls
clus                0   1
  CHRM3 MUTATED    11   1
  CHRM3 WILD-TYPE 272  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHRM3 MUTATED     11    1
  CHRM3 WILD-TYPE  272   47
   clus
vv  CHRM3 MUTATED CHRM3 WILD-TYPE
  0            11             272
  1             1              47
[1] 2 2
[1] FALSE
D1425V7, 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
D1425V8, binary
                 cls
clus                0   1
  CHRM3 MUTATED     9   4
  CHRM3 WILD-TYPE 308  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHRM3 MUTATED      9    4
  CHRM3 WILD-TYPE  308   44
                               clus
vv                              CHRM3 MUTATED CHRM3 WILD-TYPE
  COLON ADENOCARCINOMA                      9             308
  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 249   2  22  19
D1425V9, multiclass
    clus
vv   CHRM3 MUTATED CHRM3 WILD-TYPE
  R0             8             249
  R1             0               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"
D1425V10, 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
D1425V11, 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(1426) Variable = GFRAL MUTATION ANALYSIS
D1426V1, survival
                 sevent
clus2               0   1
  GFRAL MUTATED     3   1
  GFRAL WILD-TYPE 279  72
  GFRAL MUTATED GFRAL WILD-TYPE 
              4             351 
  GFRAL MUTATED GFRAL WILD-TYPE 
              1              72 
$`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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        16.14         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  GFRAL MUTATED GFRAL WILD-TYPE 
           6.97            0.00 
  GFRAL MUTATED GFRAL WILD-TYPE 
          63.98          140.38 
  GFRAL MUTATED GFRAL WILD-TYPE 
          13.84           20.28 
[1] "7.0 - 64.0 (13.8)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.1"
D1426V2, 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       23       108         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        19         10         41         31       34        13
                 vv
clus              STAGE IVB
  GFRAL MUTATED           0
  GFRAL WILD-TYPE         1
D1426V3, multiclass
            clus
vv           GFRAL MUTATED GFRAL WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              1             108
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GFRAL MUTATED     0   0   3   1
  GFRAL WILD-TYPE   9  68 245  40
D1426V4, multiclass
    clus
vv   GFRAL MUTATED GFRAL WILD-TYPE
  T1             0               9
  T2             0              68
  T3             3             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
  GFRAL MUTATED     3   1   0
  GFRAL WILD-TYPE 217  79  66
D1426V5, multiclass
    clus
vv   GFRAL MUTATED GFRAL WILD-TYPE
  N0             3             217
  N1             1              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"
D1426V6, binary
                 cls
clus                0   1
  GFRAL MUTATED     3   1
  GFRAL WILD-TYPE 280  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GFRAL MUTATED      3    1
  GFRAL WILD-TYPE  280   47
   clus
vv  GFRAL MUTATED GFRAL WILD-TYPE
  0             3             280
  1             1              47
[1] 2 2
[1] FALSE
D1426V7, 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
D1426V8, binary
                 cls
clus                0   1
  GFRAL MUTATED     4   0
  GFRAL WILD-TYPE 313  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GFRAL MUTATED      4    0
  GFRAL WILD-TYPE  313   48
                               clus
vv                              GFRAL MUTATED GFRAL WILD-TYPE
  COLON ADENOCARCINOMA                      4             313
  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 254   2  22  21
D1426V9, multiclass
    clus
vv   GFRAL MUTATED GFRAL WILD-TYPE
  R0             3             254
  R1             0               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"
D1426V10, 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
D1426V11, multiclass
[1] "Remove cluster labels:" "GFRAL MUTATED"         
clus
  GFRAL MUTATED GFRAL WILD-TYPE 
              2             204 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-4105 
"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-A6-6649      TCGA-A6-6651 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-A6-6652      TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-A6-6781      TCGA-A6-6782      TCGA-AD-5900      TCGA-AD-6548 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-AD-6888      TCGA-AD-6889      TCGA-AD-6890      TCGA-AD-6895 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-AD-6899      TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6964 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-AD-6965      TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-AY-4071      TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-AY-6386      TCGA-AZ-4315      TCGA-AZ-4323      TCGA-AZ-4616 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-AZ-4681      TCGA-AZ-4682      TCGA-AZ-5403      TCGA-AZ-5407 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-AZ-6598      TCGA-AZ-6599      TCGA-AZ-6601      TCGA-AZ-6603 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-AZ-6605      TCGA-AZ-6606      TCGA-AZ-6607      TCGA-AZ-6608 
"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-5912      TCGA-CK-5913      TCGA-CK-5914 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-CK-5915      TCGA-CK-5916      TCGA-CK-6746      TCGA-CK-6747 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-CK-6748      TCGA-CK-6751      TCGA-CM-4743      TCGA-CM-4744 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-CM-4746      TCGA-CM-4747      TCGA-CM-4752      TCGA-CM-5341 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-CM-5344      TCGA-CM-5348      TCGA-CM-5349      TCGA-CM-5860 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-CM-5861      TCGA-CM-5862      TCGA-CM-5863      TCGA-CM-5864 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-CM-5868      TCGA-CM-6161      TCGA-CM-6162      TCGA-CM-6163 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-CM-6164      TCGA-CM-6165      TCGA-CM-6166      TCGA-CM-6167 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-CM-6168      TCGA-CM-6169      TCGA-CM-6170      TCGA-CM-6171 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-CM-6172      TCGA-CM-6674      TCGA-CM-6675      TCGA-CM-6676 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-CM-6677      TCGA-CM-6678      TCGA-CM-6679      TCGA-CM-6680 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-D5-5537      TCGA-D5-5538      TCGA-D5-5539      TCGA-D5-5540 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-D5-5541      TCGA-D5-6529      TCGA-D5-6532      TCGA-D5-6533 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-D5-6534      TCGA-D5-6535      TCGA-D5-6536      TCGA-D5-6537 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-D5-6538      TCGA-D5-6539      TCGA-D5-6540      TCGA-D5-6898 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923      TCGA-D5-6924 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-D5-6926      TCGA-D5-6927      TCGA-D5-6928      TCGA-D5-6929 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-D5-6930      TCGA-D5-6931      TCGA-D5-6932      TCGA-D5-7000 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-DM-A0X9      TCGA-DM-A0XD      TCGA-DM-A0XF      TCGA-DM-A1D0 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-DM-A1D4      TCGA-DM-A1D6      TCGA-DM-A1D7      TCGA-DM-A1D8 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-DM-A1D9      TCGA-DM-A1DA      TCGA-DM-A1DB      TCGA-DM-A1HA 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-DM-A1HB      TCGA-DM-A282      TCGA-DM-A285      TCGA-DM-A28C 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-DM-A28E      TCGA-DM-A28F      TCGA-DM-A28G      TCGA-DM-A28H 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-DM-A28K      TCGA-F4-6459      TCGA-F4-6460      TCGA-F4-6569 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704      TCGA-F4-6805 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808      TCGA-F4-6809 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856      TCGA-G4-6293 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304      TCGA-G4-6306 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310      TCGA-G4-6315 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323      TCGA-G4-6586 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-G4-6588      TCGA-G4-6625      TCGA-G4-6626      TCGA-G4-6628 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 

Clustering(1427) Variable = CCDC6 MUTATION ANALYSIS
D1427V1, survival
                 sevent
clus2               0   1
  CCDC6 MUTATED    11   0
  CCDC6 WILD-TYPE 271  73
  CCDC6 MUTATED CCDC6 WILD-TYPE 
             11             344 
  CCDC6 MUTATED CCDC6 WILD-TYPE 
              0              73 
$`CCDC6 MUTATED`
TCGA-A6-6138 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3947 TCGA-AY-6386 TCGA-CM-4743 
       22.52        63.98         1.02        33.01        17.82        23.05 
TCGA-CM-6168 TCGA-CM-6674 TCGA-D5-6538 TCGA-G4-6304 TCGA-G4-6586 
       12.99        12.95        17.13        53.62        35.80 

$`CCDC6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        32.71        27.09         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       35.01         6.97        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  CCDC6 MUTATED CCDC6 WILD-TYPE 
           1.02            0.00 
  CCDC6 MUTATED CCDC6 WILD-TYPE 
          63.98          140.38 
  CCDC6 MUTATED CCDC6 WILD-TYPE 
         22.520          20.155 
[1] "1.0 - 64.0 (22.5)"  "0.0 - 140.4 (20.2)"
[1] "hr="     "2.6e+07"
D1427V2, 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       24       105         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        19         10         39         31       35        13
                 vv
clus              STAGE IVB
  CCDC6 MUTATED           0
  CCDC6 WILD-TYPE         1
D1427V3, multiclass
            clus
vv           CCDC6 MUTATED CCDC6 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              4             105
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CCDC6 MUTATED     0   2   7   2
  CCDC6 WILD-TYPE   9  66 241  39
D1427V4, multiclass
    clus
vv   CCDC6 MUTATED CCDC6 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             7             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
  CCDC6 MUTATED     9   1   1
  CCDC6 WILD-TYPE 211  79  65
D1427V5, multiclass
    clus
vv   CCDC6 MUTATED CCDC6 WILD-TYPE
  N0             9             211
  N1             1              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"
D1427V6, binary
                 cls
clus                0   1
  CCDC6 MUTATED    11   0
  CCDC6 WILD-TYPE 272  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCDC6 MUTATED     11    0
  CCDC6 WILD-TYPE  272   48
   clus
vv  CCDC6 MUTATED CCDC6 WILD-TYPE
  0            11             272
  1             0              48
[1] 2 2
[1] FALSE
D1427V7, 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
D1427V8, binary
                 cls
clus                0   1
  CCDC6 MUTATED    10   1
  CCDC6 WILD-TYPE 307  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCDC6 MUTATED     10    1
  CCDC6 WILD-TYPE  307   47
                               clus
vv                              CCDC6 MUTATED CCDC6 WILD-TYPE
  COLON ADENOCARCINOMA                     10             307
  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 247   2  22  21
D1427V9, multiclass
    clus
vv   CCDC6 MUTATED CCDC6 WILD-TYPE
  R0            10             247
  R1             0               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"
D1427V10, 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
D1427V11, 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(1428) Variable = CHRND MUTATION ANALYSIS
D1428V1, survival
                 sevent
clus2               0   1
  CHRND MUTATED     9   4
  CHRND WILD-TYPE 273  69
  CHRND MUTATED CHRND WILD-TYPE 
             13             342 
  CHRND MUTATED CHRND WILD-TYPE 
              4              69 
$`CHRND MUTATED`
TCGA-A6-6781 TCGA-AA-3713 TCGA-AA-3949 TCGA-AA-A00J TCGA-AA-A00N TCGA-AD-6964 
       19.66        19.04        26.01        18.05         4.01        10.88 
TCGA-AU-3779 TCGA-AZ-6601 TCGA-CA-6716 TCGA-CK-6751 TCGA-CM-5861 TCGA-CM-5868 
       14.50       100.01         0.26       124.27        15.02        17.03 
TCGA-DM-A1DA 
        7.50 

$`CHRND WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 
        5.79        22.42        27.42         0.20        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93         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        16.01 
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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  CHRND MUTATED CHRND WILD-TYPE 
           0.26            0.00 
  CHRND MUTATED CHRND WILD-TYPE 
         124.27          140.38 
  CHRND MUTATED CHRND WILD-TYPE 
         17.030          20.995 
[1] "0.3 - 124.3 (17.0)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.4"
D1428V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CHRND MUTATED         1        0        1         3         1         0
  CHRND WILD-TYPE      63        1       24       106         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CHRND MUTATED           0          0          2          2        1         1
  CHRND WILD-TYPE        19         10         39         29       34        12
                 vv
clus              STAGE IVB
  CHRND MUTATED           0
  CHRND WILD-TYPE         1
D1428V3, multiclass
            clus
vv           CHRND MUTATED CHRND WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              3             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             2              29
  STAGE IV               1              34
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CHRND MUTATED     0   1   7   5
  CHRND WILD-TYPE   9  67 241  36
D1428V4, multiclass
    clus
vv   CHRND MUTATED CHRND WILD-TYPE
  T1             0               9
  T2             1              67
  T3             7             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
  CHRND MUTATED     7   4   2
  CHRND WILD-TYPE 213  76  64
D1428V5, multiclass
    clus
vv   CHRND MUTATED CHRND WILD-TYPE
  N0             7             213
  N1             4              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"
D1428V6, binary
                 cls
clus                0   1
  CHRND MUTATED     8   2
  CHRND WILD-TYPE 275  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHRND MUTATED      8    2
  CHRND WILD-TYPE  275   46
   clus
vv  CHRND MUTATED CHRND WILD-TYPE
  0             8             275
  1             2              46
[1] 2 2
[1] FALSE
D1428V7, binary
                 cls
clus                0   1
  CHRND MUTATED     6   7
  CHRND WILD-TYPE 164 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHRND MUTATED      6    7
  CHRND WILD-TYPE  164  190
        clus
vv       CHRND MUTATED CHRND WILD-TYPE
  FEMALE             6             164
  MALE               7             190
[1] 2 2
[1] FALSE
D1428V8, binary
                 cls
clus                0   1
  CHRND MUTATED     8   5
  CHRND WILD-TYPE 309  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHRND MUTATED      8    5
  CHRND WILD-TYPE  309   43
                               clus
vv                              CHRND MUTATED CHRND WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CHRND MUTATED     7   0   1   2
  CHRND WILD-TYPE 250   2  21  19
D1428V9, multiclass
    clus
vv   CHRND MUTATED CHRND WILD-TYPE
  R0             7             250
  R1             0               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"
D1428V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CHRND MUTATED                                  0     1
  CHRND WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CHRND MUTATED                           0     8
  CHRND WILD-TYPE                        19   168
D1428V11, multiclass
                                  clus
vv                                 CHRND MUTATED CHRND 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(1429) Variable = WDR45L MUTATION ANALYSIS
D1429V1, survival
                  sevent
clus2                0   1
  WDR45L MUTATED     5   1
  WDR45L WILD-TYPE 277  72
  WDR45L MUTATED WDR45L WILD-TYPE 
               6              349 
  WDR45L MUTATED WDR45L WILD-TYPE 
               1               72 
$`WDR45L MUTATED`
TCGA-AA-3660 TCGA-AD-6895 TCGA-CA-6718 TCGA-D5-6532 TCGA-D5-6930 TCGA-G4-6626 
       78.08         0.72         0.10        18.25         1.51        46.75 

$`WDR45L WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        61.02         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        4.21        56.55         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.33         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6628 
       52.80 

  WDR45L MUTATED WDR45L WILD-TYPE 
             0.1              0.0 
  WDR45L MUTATED WDR45L WILD-TYPE 
           78.08           140.38 
  WDR45L MUTATED WDR45L WILD-TYPE 
            9.88            20.28 
[1] "0.1 - 78.1 (9.9)"   "0.0 - 140.4 (20.3)"
[1] "hr=" "1.2"
D1429V2, 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       23       105         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  WDR45L MUTATED           0          0          0          0        0
  WDR45L WILD-TYPE        19         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  WDR45L MUTATED           0         0
  WDR45L WILD-TYPE        13         1
D1429V3, multiclass
            clus
vv           WDR45L MUTATED WDR45L WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               4              105
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  WDR45L MUTATED     0   0   6   1
  WDR45L WILD-TYPE   9  68 242  40
D1429V4, multiclass
    clus
vv   WDR45L MUTATED WDR45L WILD-TYPE
  T1              0                9
  T2              0               68
  T3              6              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
  WDR45L MUTATED     6   1   0
  WDR45L WILD-TYPE 214  79  66
D1429V5, multiclass
    clus
vv   WDR45L MUTATED WDR45L WILD-TYPE
  N0              6              214
  N1              1               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"
D1429V6, binary
                  cls
clus                 0   1
  WDR45L MUTATED     6   0
  WDR45L WILD-TYPE 277  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  WDR45L MUTATED      6    0
  WDR45L WILD-TYPE  277   48
   clus
vv  WDR45L MUTATED WDR45L WILD-TYPE
  0              6              277
  1              0               48
[1] 2 2
[1] FALSE
D1429V7, 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
D1429V8, binary
                  cls
clus                 0   1
  WDR45L MUTATED     6   1
  WDR45L WILD-TYPE 311  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  WDR45L MUTATED      6    1
  WDR45L WILD-TYPE  311   47
                               clus
vv                              WDR45L MUTATED WDR45L WILD-TYPE
  COLON ADENOCARCINOMA                       6              311
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  WDR45L MUTATED     5   0   0   1
  WDR45L WILD-TYPE 252   2  22  20
D1429V9, multiclass
    clus
vv   WDR45L MUTATED WDR45L WILD-TYPE
  R0              5              252
  R1              0                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"
D1429V10, 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
D1429V11, 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(1430) Variable = VEPH1 MUTATION ANALYSIS
D1430V1, survival
                 sevent
clus2               0   1
  VEPH1 MUTATED    13   3
  VEPH1 WILD-TYPE 269  70
  VEPH1 MUTATED VEPH1 WILD-TYPE 
             16             339 
  VEPH1 MUTATED VEPH1 WILD-TYPE 
              3              70 
$`VEPH1 MUTATED`
TCGA-A6-6653 TCGA-A6-6780 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3715 TCGA-AA-3815 
       24.39        20.12        17.95        29.95        19.04        33.04 
TCGA-AA-3845 TCGA-AA-A010 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4743 TCGA-CM-6674 
        0.00        34.98         0.33         0.10        23.05        12.95 
TCGA-D5-6533 TCGA-D5-6928 TCGA-DM-A28C TCGA-G4-6309 
        1.32        11.64        81.37        51.75 

$`VEPH1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       24.00        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       26.99        19.04        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07         0.26         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 
       19.59        13.51        11.51        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-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44        13.41         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28E TCGA-DM-A28F 
      131.51       135.65       139.17         6.12       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       74.56        65.85        53.62        44.68        55.04        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  VEPH1 MUTATED VEPH1 WILD-TYPE 
              0               0 
  VEPH1 MUTATED VEPH1 WILD-TYPE 
          81.37          140.38 
  VEPH1 MUTATED VEPH1 WILD-TYPE 
          19.58           20.28 
[1] "0.0 - 81.4 (19.6)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1"  
D1430V2, 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       24        98         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  VEPH1 MUTATED           0          0          2          0        0         0
  VEPH1 WILD-TYPE        19         10         39         31       35        13
                 vv
clus              STAGE IVB
  VEPH1 MUTATED           0
  VEPH1 WILD-TYPE         1
D1430V3, multiclass
            clus
vv           VEPH1 MUTATED VEPH1 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA             11              98
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  VEPH1 MUTATED     0   2  13   2
  VEPH1 WILD-TYPE   9  66 235  39
D1430V4, multiclass
    clus
vv   VEPH1 MUTATED VEPH1 WILD-TYPE
  T1             0               9
  T2             2              66
  T3            13             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
  VEPH1 MUTATED    16   1   0
  VEPH1 WILD-TYPE 204  79  66
D1430V5, multiclass
    clus
vv   VEPH1 MUTATED VEPH1 WILD-TYPE
  N0            16             204
  N1             1              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"
D1430V6, binary
                 cls
clus                0   1
  VEPH1 MUTATED    15   0
  VEPH1 WILD-TYPE 268  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VEPH1 MUTATED     15    0
  VEPH1 WILD-TYPE  268   48
   clus
vv  VEPH1 MUTATED VEPH1 WILD-TYPE
  0            15             268
  1             0              48
[1] 2 2
[1] FALSE
D1430V7, 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
D1430V8, binary
                 cls
clus                0   1
  VEPH1 MUTATED    13   4
  VEPH1 WILD-TYPE 304  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VEPH1 MUTATED     13    4
  VEPH1 WILD-TYPE  304   44
                               clus
vv                              VEPH1 MUTATED VEPH1 WILD-TYPE
  COLON ADENOCARCINOMA                     13             304
  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 246   2  22  18
D1430V9, multiclass
    clus
vv   VEPH1 MUTATED VEPH1 WILD-TYPE
  R0            11             246
  R1             0               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"
D1430V10, 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
D1430V11, 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(1431) Variable = SUSD5 MUTATION ANALYSIS
D1431V1, survival
                 sevent
clus2               0   1
  SUSD5 MUTATED     7   1
  SUSD5 WILD-TYPE 275  72
  SUSD5 MUTATED SUSD5 WILD-TYPE 
              8             347 
  SUSD5 MUTATED SUSD5 WILD-TYPE 
              1              72 
$`SUSD5 MUTATED`
TCGA-AA-3511 TCGA-AA-3664 TCGA-AA-A03J TCGA-AZ-6598 TCGA-CA-6717 TCGA-CA-6718 
        6.97        54.02        40.96        49.41         0.33         0.10 
TCGA-CM-4752 TCGA-F4-6703 
       13.02        35.87 

$`SUSD5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01        63.98         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
        6.97         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.38        13.45         6.18         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  SUSD5 MUTATED SUSD5 WILD-TYPE 
            0.1             0.0 
  SUSD5 MUTATED SUSD5 WILD-TYPE 
          54.02          140.38 
  SUSD5 MUTATED SUSD5 WILD-TYPE 
         24.445          20.190 
[1] "0.1 - 54.0 (24.4)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.7"
D1431V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SUSD5 MUTATED         1        0        3         5         0         0
  SUSD5 WILD-TYPE      63        1       22       104         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SUSD5 MUTATED           0          0          0          0        0         0
  SUSD5 WILD-TYPE        19         10         41         31       35        13
                 vv
clus              STAGE IVB
  SUSD5 MUTATED           0
  SUSD5 WILD-TYPE         1
D1431V3, multiclass
            clus
vv           SUSD5 MUTATED SUSD5 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              5             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SUSD5 MUTATED     0   1   7   1
  SUSD5 WILD-TYPE   9  67 241  40
D1431V4, multiclass
    clus
vv   SUSD5 MUTATED SUSD5 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             7             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
  SUSD5 MUTATED     9   0   0
  SUSD5 WILD-TYPE 211  80  66
D1431V5, multiclass
    clus
vv   SUSD5 MUTATED SUSD5 WILD-TYPE
  N0             9             211
  N1             0              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"
D1431V6, binary
                 cls
clus                0   1
  SUSD5 MUTATED     8   0
  SUSD5 WILD-TYPE 275  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SUSD5 MUTATED      8    0
  SUSD5 WILD-TYPE  275   48
   clus
vv  SUSD5 MUTATED SUSD5 WILD-TYPE
  0             8             275
  1             0              48
[1] 2 2
[1] FALSE
D1431V7, binary
                 cls
clus                0   1
  SUSD5 MUTATED     4   5
  SUSD5 WILD-TYPE 166 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SUSD5 MUTATED      4    5
  SUSD5 WILD-TYPE  166  192
        clus
vv       SUSD5 MUTATED SUSD5 WILD-TYPE
  FEMALE             4             166
  MALE               5             192
[1] 2 2
[1] FALSE
D1431V8, binary
                 cls
clus                0   1
  SUSD5 MUTATED     8   1
  SUSD5 WILD-TYPE 309  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SUSD5 MUTATED      8    1
  SUSD5 WILD-TYPE  309   47
                               clus
vv                              SUSD5 MUTATED SUSD5 WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SUSD5 MUTATED     6   0   0   2
  SUSD5 WILD-TYPE 251   2  22  19
D1431V9, multiclass
    clus
vv   SUSD5 MUTATED SUSD5 WILD-TYPE
  R0             6             251
  R1             0               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"
D1431V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SUSD5 MUTATED                                  0     2
  SUSD5 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SUSD5 MUTATED                           1     2
  SUSD5 WILD-TYPE                        18   174
D1431V11, multiclass
                                  clus
vv                                 SUSD5 MUTATED SUSD5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               8
  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(1432) Variable = C20ORF43 MUTATION ANALYSIS
D1432V1, survival
                    sevent
clus2                  0   1
  C20ORF43 MUTATED     3   0
  C20ORF43 WILD-TYPE 279  73
  C20ORF43 MUTATED C20ORF43 WILD-TYPE 
                 3                352 
  C20ORF43 MUTATED C20ORF43 WILD-TYPE 
                 0                 73 
$`C20ORF43 MUTATED`
TCGA-AA-3510 TCGA-AY-6196 TCGA-CK-4947 
       63.98         0.20        17.56 

$`C20ORF43 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        15.75        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 
        0.07         0.26         0.33         0.10         1.35       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  C20ORF43 MUTATED C20ORF43 WILD-TYPE 
               0.2                0.0 
  C20ORF43 MUTATED C20ORF43 WILD-TYPE 
             63.98             140.38 
  C20ORF43 MUTATED C20ORF43 WILD-TYPE 
            17.560             20.235 
[1] "0.2 - 64.0 (17.6)"  "0.0 - 140.4 (20.2)"
[1] "hr="     "9100000"
D1432V2, 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       24       109         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C20ORF43 MUTATED           0          0          0          1        0
  C20ORF43 WILD-TYPE        19         10         41         30       35
                    vv
clus                 STAGE IVA STAGE IVB
  C20ORF43 MUTATED           1         0
  C20ORF43 WILD-TYPE        12         1
D1432V3, multiclass
            clus
vv           C20ORF43 MUTATED C20ORF43 WILD-TYPE
  STAGE I                   0                 64
  STAGE IA                  0                  1
  STAGE II                  1                 24
  STAGE IIA                 0                109
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                0                 10
  STAGE IIIB                0                 41
  STAGE IIIC                1                 30
  STAGE IV                  0                 35
  STAGE IVA                 1                 12
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of 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  68 246  40
D1432V4, multiclass
    clus
vv   C20ORF43 MUTATED C20ORF43 WILD-TYPE
  T1                0                  9
  T2                0                 68
  T3                2                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
  C20ORF43 MUTATED     1   1   1
  C20ORF43 WILD-TYPE 219  79  65
D1432V5, multiclass
    clus
vv   C20ORF43 MUTATED C20ORF43 WILD-TYPE
  N0                1                219
  N1                1                 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"
D1432V6, binary
                    cls
clus                   0   1
  C20ORF43 MUTATED     2   0
  C20ORF43 WILD-TYPE 281  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C20ORF43 MUTATED      2    0
  C20ORF43 WILD-TYPE  281   48
   clus
vv  C20ORF43 MUTATED C20ORF43 WILD-TYPE
  0                2                281
  1                0                 48
[1] 2 2
[1] FALSE
D1432V7, 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
D1432V8, binary
                    cls
clus                   0   1
  C20ORF43 MUTATED     2   1
  C20ORF43 WILD-TYPE 315  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C20ORF43 MUTATED      2    1
  C20ORF43 WILD-TYPE  315   47
                               clus
vv                              C20ORF43 MUTATED C20ORF43 WILD-TYPE
  COLON ADENOCARCINOMA                         2                315
  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 255   2  22  20
D1432V9, multiclass
    clus
vv   C20ORF43 MUTATED C20ORF43 WILD-TYPE
  R0                2                255
  R1                0                  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"
D1432V10, 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
D1432V11, multiclass
[1] "Remove cluster labels:" "C20ORF43 MUTATED"      
clus
  C20ORF43 MUTATED C20ORF43 WILD-TYPE 
                 2                204 
        TCGA-A6-2671         TCGA-A6-2672         TCGA-A6-2674 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-A6-2676         TCGA-A6-2677         TCGA-A6-2678 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-A6-2683         TCGA-A6-3807         TCGA-A6-3808 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-A6-3809         TCGA-A6-3810         TCGA-A6-4105 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-A6-5656         TCGA-A6-5657         TCGA-A6-5659 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-A6-5660         TCGA-A6-5661         TCGA-A6-5662 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-A6-5664         TCGA-A6-5665         TCGA-A6-5666 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-A6-6137         TCGA-A6-6138         TCGA-A6-6141 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-A6-6142         TCGA-A6-6648         TCGA-A6-6649 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-A6-6651         TCGA-A6-6652         TCGA-A6-6653 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-A6-6654         TCGA-A6-6780         TCGA-A6-6781 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-A6-6782         TCGA-AD-5900         TCGA-AD-6548 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-AD-6888         TCGA-AD-6889         TCGA-AD-6890 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-AD-6895         TCGA-AD-6899         TCGA-AD-6901 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-AD-6963         TCGA-AD-6964         TCGA-AD-6965 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-AU-3779         TCGA-AU-6004         TCGA-AY-4070 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-AY-4071         TCGA-AY-5543         TCGA-AY-6197 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-AY-6386         TCGA-AZ-4315         TCGA-AZ-4323 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-AZ-4616         TCGA-AZ-4681         TCGA-AZ-4682 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-AZ-5403         TCGA-AZ-5407         TCGA-AZ-6598 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-AZ-6599         TCGA-AZ-6600         TCGA-AZ-6601 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-AZ-6603         TCGA-AZ-6605         TCGA-AZ-6606 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-AZ-6607         TCGA-AZ-6608         TCGA-CA-5254 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CA-5255         TCGA-CA-5796         TCGA-CA-5797 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CA-6715         TCGA-CA-6716         TCGA-CA-6717 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CA-6718         TCGA-CA-6719         TCGA-CK-4948 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CK-4950         TCGA-CK-4952         TCGA-CK-5912 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CK-5913         TCGA-CK-5914         TCGA-CK-5915 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CK-5916         TCGA-CK-6746         TCGA-CK-6747 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CK-6748         TCGA-CK-6751         TCGA-CM-4743 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CM-4744         TCGA-CM-4746         TCGA-CM-4747 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CM-4752         TCGA-CM-5341         TCGA-CM-5344 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CM-5348         TCGA-CM-5349         TCGA-CM-5860 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CM-5861         TCGA-CM-5862         TCGA-CM-5863 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CM-5864         TCGA-CM-5868         TCGA-CM-6161 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CM-6162         TCGA-CM-6163         TCGA-CM-6164 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CM-6165         TCGA-CM-6166         TCGA-CM-6167 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CM-6168         TCGA-CM-6169         TCGA-CM-6170 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CM-6171         TCGA-CM-6172         TCGA-CM-6674 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CM-6675         TCGA-CM-6676         TCGA-CM-6677 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CM-6678         TCGA-CM-6679         TCGA-CM-6680 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-D5-5537         TCGA-D5-5538         TCGA-D5-5539 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-D5-5540         TCGA-D5-5541         TCGA-D5-6529 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-D5-6532         TCGA-D5-6533         TCGA-D5-6534 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-D5-6535         TCGA-D5-6536         TCGA-D5-6537 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-D5-6538         TCGA-D5-6539         TCGA-D5-6540 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-D5-6541         TCGA-D5-6898         TCGA-D5-6920 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-D5-6922         TCGA-D5-6923         TCGA-D5-6924 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-D5-6926         TCGA-D5-6927         TCGA-D5-6928 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-D5-6929         TCGA-D5-6930         TCGA-D5-6931 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-D5-6932         TCGA-D5-7000         TCGA-DM-A0X9 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-DM-A0XD         TCGA-DM-A0XF         TCGA-DM-A1D0 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-DM-A1D4         TCGA-DM-A1D6         TCGA-DM-A1D7 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-DM-A1D8         TCGA-DM-A1D9         TCGA-DM-A1DA 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-DM-A1DB         TCGA-DM-A1HA         TCGA-DM-A1HB 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-DM-A282         TCGA-DM-A285         TCGA-DM-A28C 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-DM-A28E         TCGA-DM-A28F         TCGA-DM-A28G 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-DM-A28H         TCGA-DM-A28K         TCGA-F4-6459 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-F4-6460         TCGA-F4-6569         TCGA-F4-6570 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-F4-6703         TCGA-F4-6704         TCGA-F4-6805 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-F4-6806         TCGA-F4-6807         TCGA-F4-6808 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-F4-6809         TCGA-F4-6854         TCGA-F4-6855 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-F4-6856         TCGA-G4-6293         TCGA-G4-6299 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-G4-6303         TCGA-G4-6304         TCGA-G4-6306 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-G4-6307         TCGA-G4-6309         TCGA-G4-6310 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-G4-6315         TCGA-G4-6317         TCGA-G4-6321 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-G4-6323         TCGA-G4-6586         TCGA-G4-6588 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-G4-6625         TCGA-G4-6626         TCGA-G4-6628 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 

Clustering(1433) Variable = HIST4H4 MUTATION ANALYSIS
D1433V1, survival
                   sevent
clus2                 0   1
  HIST4H4 MUTATED     3   0
  HIST4H4 WILD-TYPE 279  73
  HIST4H4 MUTATED HIST4H4 WILD-TYPE 
                3               352 
  HIST4H4 MUTATED HIST4H4 WILD-TYPE 
                0                73 
$`HIST4H4 MUTATED`
TCGA-AA-3713 TCGA-AY-5543 TCGA-CK-4950 
       19.04        15.75        40.34 

$`HIST4H4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      102.44        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  HIST4H4 MUTATED HIST4H4 WILD-TYPE 
            15.75              0.00 
  HIST4H4 MUTATED HIST4H4 WILD-TYPE 
            40.34            140.38 
  HIST4H4 MUTATED HIST4H4 WILD-TYPE 
           19.040            20.235 
[1] "15.8 - 40.3 (19.0)" "0.0 - 140.4 (20.2)"
[1] "hr="     "3300000"
D1433V2, 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       25       109         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HIST4H4 MUTATED           0          1          0          0        1
  HIST4H4 WILD-TYPE        19          9         41         31       34
                   vv
clus                STAGE IVA STAGE IVB
  HIST4H4 MUTATED           1         0
  HIST4H4 WILD-TYPE        12         1
D1433V3, multiclass
            clus
vv           HIST4H4 MUTATED HIST4H4 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                0               109
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               1                 9
  STAGE IIIB               0                41
  STAGE IIIC               0                31
  STAGE IV                 1                34
  STAGE IVA                1                12
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of 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  68 245  41
D1433V4, multiclass
    clus
vv   HIST4H4 MUTATED HIST4H4 WILD-TYPE
  T1               0                 9
  T2               0                68
  T3               3               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
  HIST4H4 MUTATED     1   2   0
  HIST4H4 WILD-TYPE 219  78  66
D1433V5, multiclass
    clus
vv   HIST4H4 MUTATED HIST4H4 WILD-TYPE
  N0               1               219
  N1               2                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"
D1433V6, binary
                   cls
clus                  0   1
  HIST4H4 MUTATED     1   2
  HIST4H4 WILD-TYPE 282  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HIST4H4 MUTATED      1    2
  HIST4H4 WILD-TYPE  282   46
   clus
vv  HIST4H4 MUTATED HIST4H4 WILD-TYPE
  0               1               282
  1               2                46
[1] 2 2
[1] FALSE
D1433V7, 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
D1433V8, binary
                   cls
clus                  0   1
  HIST4H4 MUTATED     3   0
  HIST4H4 WILD-TYPE 314  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HIST4H4 MUTATED      3    0
  HIST4H4 WILD-TYPE  314   48
                               clus
vv                              HIST4H4 MUTATED HIST4H4 WILD-TYPE
  COLON ADENOCARCINOMA                        3               314
  COLON MUCINOUS ADENOCARCINOMA               0                48
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  HIST4H4 MUTATED     1   1   1   0
  HIST4H4 WILD-TYPE 256   1  21  21
D1433V9, multiclass
    clus
vv   HIST4H4 MUTATED HIST4H4 WILD-TYPE
  R0               1               256
  R1               1                 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"
D1433V10, 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
D1433V11, multiclass
[1] "Remove cluster labels:" "HIST4H4 MUTATED"       
clus
  HIST4H4 MUTATED HIST4H4 WILD-TYPE 
                2               204 
       TCGA-A6-2671        TCGA-A6-2672        TCGA-A6-2674        TCGA-A6-2676 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-A6-2677        TCGA-A6-2678        TCGA-A6-2683        TCGA-A6-3807 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-A6-3808        TCGA-A6-3809        TCGA-A6-3810        TCGA-A6-4105 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-A6-5656        TCGA-A6-5657        TCGA-A6-5659        TCGA-A6-5660 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-A6-5661        TCGA-A6-5662        TCGA-A6-5664        TCGA-A6-5665 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-A6-5666        TCGA-A6-6137        TCGA-A6-6138        TCGA-A6-6141 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-A6-6142        TCGA-A6-6648        TCGA-A6-6649        TCGA-A6-6651 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-A6-6652        TCGA-A6-6653        TCGA-A6-6654        TCGA-A6-6780 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-A6-6781        TCGA-A6-6782        TCGA-AD-5900        TCGA-AD-6548 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-AD-6888        TCGA-AD-6889        TCGA-AD-6890        TCGA-AD-6895 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-AD-6899        TCGA-AD-6901        TCGA-AD-6963        TCGA-AD-6964 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-AD-6965        TCGA-AU-3779        TCGA-AU-6004        TCGA-AY-4070 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-AY-4071        TCGA-AY-6196        TCGA-AY-6197        TCGA-AY-6386 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-AZ-4315        TCGA-AZ-4323        TCGA-AZ-4616        TCGA-AZ-4681 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-AZ-4682        TCGA-AZ-5403        TCGA-AZ-5407        TCGA-AZ-6598 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-AZ-6599        TCGA-AZ-6600        TCGA-AZ-6601        TCGA-AZ-6603 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-AZ-6605        TCGA-AZ-6606        TCGA-AZ-6607        TCGA-AZ-6608 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-CA-5254        TCGA-CA-5255        TCGA-CA-5796        TCGA-CA-5797 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-CA-6715        TCGA-CA-6716        TCGA-CA-6717        TCGA-CA-6718 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-CA-6719        TCGA-CK-4947        TCGA-CK-4948        TCGA-CK-4952 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-CK-5912        TCGA-CK-5913        TCGA-CK-5914        TCGA-CK-5915 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-CK-5916        TCGA-CK-6746        TCGA-CK-6747        TCGA-CK-6748 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-CK-6751        TCGA-CM-4743        TCGA-CM-4744        TCGA-CM-4746 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-CM-4747        TCGA-CM-4752        TCGA-CM-5341        TCGA-CM-5344 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-CM-5348        TCGA-CM-5349        TCGA-CM-5860        TCGA-CM-5861 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-CM-5862        TCGA-CM-5863        TCGA-CM-5864        TCGA-CM-5868 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-CM-6161        TCGA-CM-6162        TCGA-CM-6163        TCGA-CM-6164 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-CM-6165        TCGA-CM-6166        TCGA-CM-6167        TCGA-CM-6168 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-CM-6169        TCGA-CM-6170        TCGA-CM-6171        TCGA-CM-6172 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-CM-6674        TCGA-CM-6675        TCGA-CM-6676        TCGA-CM-6677 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-CM-6678        TCGA-CM-6679        TCGA-CM-6680        TCGA-D5-5537 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-D5-5538        TCGA-D5-5539        TCGA-D5-5540        TCGA-D5-5541 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-D5-6529        TCGA-D5-6532        TCGA-D5-6533        TCGA-D5-6534 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-D5-6535        TCGA-D5-6536        TCGA-D5-6537        TCGA-D5-6538 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-D5-6539        TCGA-D5-6540        TCGA-D5-6541        TCGA-D5-6898 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-D5-6920        TCGA-D5-6922        TCGA-D5-6923        TCGA-D5-6924 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-D5-6926        TCGA-D5-6927        TCGA-D5-6928        TCGA-D5-6929 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-D5-6930        TCGA-D5-6931        TCGA-D5-6932        TCGA-D5-7000 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-DM-A0X9        TCGA-DM-A0XD        TCGA-DM-A0XF        TCGA-DM-A1D0 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-DM-A1D4        TCGA-DM-A1D6        TCGA-DM-A1D7        TCGA-DM-A1D8 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-DM-A1D9        TCGA-DM-A1DA        TCGA-DM-A1DB        TCGA-DM-A1HA 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-DM-A1HB        TCGA-DM-A282        TCGA-DM-A285        TCGA-DM-A28C 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-DM-A28E        TCGA-DM-A28F        TCGA-DM-A28G        TCGA-DM-A28H 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-DM-A28K        TCGA-F4-6459        TCGA-F4-6460        TCGA-F4-6569 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-F4-6570        TCGA-F4-6703        TCGA-F4-6704        TCGA-F4-6805 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-F4-6806        TCGA-F4-6807        TCGA-F4-6808        TCGA-F4-6809 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-F4-6854        TCGA-F4-6855        TCGA-F4-6856        TCGA-G4-6293 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-G4-6299        TCGA-G4-6303        TCGA-G4-6304        TCGA-G4-6306 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-G4-6307        TCGA-G4-6309        TCGA-G4-6310        TCGA-G4-6315 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-G4-6317        TCGA-G4-6321        TCGA-G4-6323        TCGA-G4-6586 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-G4-6588        TCGA-G4-6625        TCGA-G4-6626        TCGA-G4-6628 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 

Clustering(1434) Variable = MDN1 MUTATION ANALYSIS
D1434V1, survival
                sevent
clus2              0   1
  MDN1 MUTATED    39  11
  MDN1 WILD-TYPE 243  62
  MDN1 MUTATED MDN1 WILD-TYPE 
            50            305 
  MDN1 MUTATED MDN1 WILD-TYPE 
            11             62 
$`MDN1 MUTATED`
TCGA-A6-2676 TCGA-A6-4105 TCGA-A6-5665 TCGA-A6-6653 TCGA-A6-6780 TCGA-AA-3510 
       42.90        14.53        22.06        24.39        20.12        63.98 
TCGA-AA-3516 TCGA-AA-3555 TCGA-AA-3655 TCGA-AA-3672 TCGA-AA-3685 TCGA-AA-3697 
       13.02        29.95        61.02         0.92        37.05        85.05 
TCGA-AA-3715 TCGA-AA-3815 TCGA-AA-3821 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3855 
       19.04        33.04         1.02        37.02         0.00        32.05 
TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3977 TCGA-AA-A004 TCGA-AA-A00J 
       31.00        33.01        26.01        25.02        13.94        18.05 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6963 TCGA-AY-4070 
        4.01        34.98         4.21        56.55        27.42        16.31 
TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4950 
       58.39        49.41        12.10         0.33         0.10        40.34 
TCGA-CK-5916 TCGA-CM-5349 TCGA-CM-6162 TCGA-CM-6168 TCGA-CM-6680 TCGA-DM-A1HB 
       21.14        30.08        12.00        12.99        12.03       135.65 
TCGA-DM-A28C TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6317 
       81.37        19.43       107.67        74.56        53.62        36.00 
TCGA-G4-6588 TCGA-G4-6628 
       26.17        52.80 

$`MDN1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 
       34.65        33.34        32.75        36.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       30.44        29.19        33.53        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 
       21.76        24.69        23.87        19.66        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02         1.02        35.01         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        17.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 
        5.98        19.00        36.00         5.03        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 
       10.06        35.05         0.99        25.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       38.99        14.93        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
        0.00        36.03         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
        2.01        12.99        24.00        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
        7.96        27.02        38.04        19.00        30.02        34.03 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6890 
       39.98        18.05        40.96         0.07        21.37         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        0.72         5.79        22.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       27.09         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 
        0.26         1.35        17.56       102.44        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99         2.93         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        16.01        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-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-D5-5537 
       13.05        11.08        11.08        11.01        10.06        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        91.79        46.75 

  MDN1 MUTATED MDN1 WILD-TYPE 
             0              0 
  MDN1 MUTATED MDN1 WILD-TYPE 
        135.65         140.38 
  MDN1 MUTATED MDN1 WILD-TYPE 
        26.795         19.070 
[1] "0.0 - 135.7 (26.8)" "0.0 - 140.4 (19.1)"
[1] "hr=" "1.2"
D1434V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MDN1 MUTATED         7        0        6        16         5         0
  MDN1 WILD-TYPE      57        1       19        93         3         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MDN1 MUTATED           4          2          6          3        1         0
  MDN1 WILD-TYPE        15          8         35         28       34        13
                vv
clus             STAGE IVB
  MDN1 MUTATED           0
  MDN1 WILD-TYPE         1
D1434V3, multiclass
            clus
vv           MDN1 MUTATED MDN1 WILD-TYPE
  STAGE I               7             57
  STAGE IA              0              1
  STAGE II              6             19
  STAGE IIA            16             93
  STAGE IIB             5              3
  STAGE IIC             0              1
  STAGE III             4             15
  STAGE IIIA            2              8
  STAGE IIIB            6             35
  STAGE IIIC            3             28
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MDN1 MUTATED     2   8  34   8
  MDN1 WILD-TYPE   7  60 214  33
D1434V4, multiclass
    clus
vv   MDN1 MUTATED MDN1 WILD-TYPE
  T1            2              7
  T2            8             60
  T3           34            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
  MDN1 MUTATED    37   9   5
  MDN1 WILD-TYPE 183  71  61
D1434V5, multiclass
    clus
vv   MDN1 MUTATED MDN1 WILD-TYPE
  N0           37            183
  N1            9             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"
D1434V6, binary
                cls
clus               0   1
  MDN1 MUTATED    46   1
  MDN1 WILD-TYPE 237  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  MDN1 MUTATED     46    1
  MDN1 WILD-TYPE  237   47
   clus
vv  MDN1 MUTATED MDN1 WILD-TYPE
  0           46            237
  1            1             47
[1] 2 2
[1] FALSE
D1434V7, binary
                cls
clus               0   1
  MDN1 MUTATED    26  26
  MDN1 WILD-TYPE 144 171
[1] "tbl2"
                cls
clus             [,1] [,2]
  MDN1 MUTATED     26   26
  MDN1 WILD-TYPE  144  171
        clus
vv       MDN1 MUTATED MDN1 WILD-TYPE
  FEMALE           26            144
  MALE             26            171
[1] 2 2
[1] FALSE
D1434V8, binary
                cls
clus               0   1
  MDN1 MUTATED    40  12
  MDN1 WILD-TYPE 277  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  MDN1 MUTATED     40   12
  MDN1 WILD-TYPE  277   36
                               clus
vv                              MDN1 MUTATED MDN1 WILD-TYPE
  COLON ADENOCARCINOMA                    40            277
  COLON MUCINOUS ADENOCARCINOMA           12             36
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MDN1 MUTATED    36   2   0   3
  MDN1 WILD-TYPE 221   0  22  18
D1434V9, multiclass
    clus
vv   MDN1 MUTATED MDN1 WILD-TYPE
  R0           36            221
  R1            2              0
  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"
D1434V10, 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
D1434V11, 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(1435) Variable = PAK2 MUTATION ANALYSIS
D1435V1, survival
                sevent
clus2              0   1
  PAK2 MUTATED     9   1
  PAK2 WILD-TYPE 273  72
  PAK2 MUTATED PAK2 WILD-TYPE 
            10            345 
  PAK2 MUTATED PAK2 WILD-TYPE 
             1             72 
$`PAK2 MUTATED`
TCGA-A6-2672 TCGA-A6-6781 TCGA-CK-4948 TCGA-CM-4752 TCGA-CM-5868 TCGA-CM-6171 
       46.65        19.66       102.44        13.02        17.03        14.04 
TCGA-D5-6931 TCGA-F4-6570 TCGA-G4-6293 TCGA-G4-6586 
       12.00         6.18       107.67        35.80 

$`PAK2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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        16.01 
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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.38        13.45        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 
       45.11        36.72        36.00        22.09        13.78        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  PAK2 MUTATED PAK2 WILD-TYPE 
          6.18           0.00 
  PAK2 MUTATED PAK2 WILD-TYPE 
        107.67         140.38 
  PAK2 MUTATED PAK2 WILD-TYPE 
        18.345         20.280 
[1] "6.2 - 107.7 (18.3)" "0.0 - 140.4 (20.3)"
[1] "hr=" "3.1"
D1435V2, 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       25       106         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PAK2 MUTATED           1          1          1          2        0         1
  PAK2 WILD-TYPE        18          9         40         29       35        12
                vv
clus             STAGE IVB
  PAK2 MUTATED           0
  PAK2 WILD-TYPE         1
D1435V3, multiclass
            clus
vv           PAK2 MUTATED PAK2 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             3            106
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            1              9
  STAGE IIIB            1             40
  STAGE IIIC            2             29
  STAGE IV              0             35
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 242  38
D1435V4, multiclass
    clus
vv   PAK2 MUTATED PAK2 WILD-TYPE
  T1            0              9
  T2            1             67
  T3            6            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
  PAK2 MUTATED     4   5   1
  PAK2 WILD-TYPE 216  75  65
D1435V5, multiclass
    clus
vv   PAK2 MUTATED PAK2 WILD-TYPE
  N0            4            216
  N1            5             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"
D1435V6, binary
                cls
clus               0   1
  PAK2 MUTATED     8   1
  PAK2 WILD-TYPE 275  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK2 MUTATED      8    1
  PAK2 WILD-TYPE  275   47
   clus
vv  PAK2 MUTATED PAK2 WILD-TYPE
  0            8            275
  1            1             47
[1] 2 2
[1] FALSE
D1435V7, 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
D1435V8, binary
                cls
clus               0   1
  PAK2 MUTATED     9   1
  PAK2 WILD-TYPE 308  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK2 MUTATED      9    1
  PAK2 WILD-TYPE  308   47
                               clus
vv                              PAK2 MUTATED PAK2 WILD-TYPE
  COLON ADENOCARCINOMA                     9            308
  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 247   2  22  21
D1435V9, multiclass
    clus
vv   PAK2 MUTATED PAK2 WILD-TYPE
  R0           10            247
  R1            0              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"
D1435V10, 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
D1435V11, 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(1436) Variable = MBP MUTATION ANALYSIS
D1436V1, survival
               sevent
clus2             0   1
  MBP MUTATED     5   1
  MBP WILD-TYPE 277  72
  MBP MUTATED MBP WILD-TYPE 
            6           349 
  MBP MUTATED MBP WILD-TYPE 
            1            72 
$`MBP MUTATED`
TCGA-A6-2672 TCGA-AA-3833 TCGA-AA-A010 TCGA-AZ-6598 TCGA-CM-4743 TCGA-CM-6674 
       46.65        15.95        34.98        49.41        23.05        12.95 

$`MBP WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       17.98        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  MBP MUTATED MBP WILD-TYPE 
        12.95          0.00 
  MBP MUTATED MBP WILD-TYPE 
        49.41        140.38 
  MBP MUTATED MBP WILD-TYPE 
       29.015        20.120 
[1] "12.9 - 49.4 (29.0)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.5"
D1436V2, 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       24       106         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        19         10         40         31       35        13
               vv
clus            STAGE IVB
  MBP MUTATED           0
  MBP WILD-TYPE         1
D1436V3, multiclass
            clus
vv           MBP MUTATED MBP WILD-TYPE
  STAGE I              0            64
  STAGE IA             0             1
  STAGE II             1            24
  STAGE IIA            3           106
  STAGE IIB            1             7
  STAGE IIC            0             1
  STAGE III            0            19
  STAGE IIIA           0            10
  STAGE IIIB           1            40
  STAGE IIIC           0            31
  STAGE IV             0            35
  STAGE IVA            0            13
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  MBP MUTATED     0   0   5   1
  MBP WILD-TYPE   9  68 243  40
D1436V4, multiclass
    clus
vv   MBP MUTATED MBP WILD-TYPE
  T1           0             9
  T2           0            68
  T3           5           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
  MBP MUTATED     5   1   0
  MBP WILD-TYPE 215  79  66
D1436V5, multiclass
    clus
vv   MBP MUTATED MBP WILD-TYPE
  N0           5           215
  N1           1            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"
D1436V6, binary
               cls
clus              0   1
  MBP MUTATED     5   0
  MBP WILD-TYPE 278  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  MBP MUTATED      5    0
  MBP WILD-TYPE  278   48
   clus
vv  MBP MUTATED MBP WILD-TYPE
  0           5           278
  1           0            48
[1] 2 2
[1] FALSE
D1436V7, 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
D1436V8, binary
               cls
clus              0   1
  MBP MUTATED     6   0
  MBP WILD-TYPE 311  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  MBP MUTATED      6    0
  MBP WILD-TYPE  311   48
                               clus
vv                              MBP MUTATED MBP WILD-TYPE
  COLON ADENOCARCINOMA                    6           311
  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 252   2  22  21
D1436V9, multiclass
    clus
vv   MBP MUTATED MBP WILD-TYPE
  R0           5           252
  R1           0             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"
D1436V10, 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
D1436V11, 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(1437) Variable = CSF3R MUTATION ANALYSIS
D1437V1, survival
                 sevent
clus2               0   1
  CSF3R MUTATED     8   6
  CSF3R WILD-TYPE 274  67
  CSF3R MUTATED CSF3R WILD-TYPE 
             14             341 
  CSF3R MUTATED CSF3R WILD-TYPE 
              6              67 
$`CSF3R MUTATED`
TCGA-AA-3516 TCGA-AA-3552 TCGA-AA-3864 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 
       13.02        13.02        53.00        18.05         4.01        34.98 
TCGA-AA-A01P TCGA-AD-5900 TCGA-CK-5913 TCGA-CM-4743 TCGA-CM-5861 TCGA-D5-6540 
       38.07         0.07        51.32        23.05        15.02        16.14 
TCGA-DM-A1DA TCGA-F4-6570 
        7.50         6.18 

$`CSF3R WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        1.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 
      102.44        40.34        15.62        49.08        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93         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        16.01 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.38        13.45        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  CSF3R MUTATED CSF3R WILD-TYPE 
           0.07            0.00 
  CSF3R MUTATED CSF3R WILD-TYPE 
          53.00          140.38 
  CSF3R MUTATED CSF3R WILD-TYPE 
          15.58           20.98 
[1] "0.1 - 53.0 (15.6)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "2.5"
D1437V2, 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       24       105         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        17         10         40         29       35        13
                 vv
clus              STAGE IVB
  CSF3R MUTATED           0
  CSF3R WILD-TYPE         1
D1437V3, multiclass
            clus
vv           CSF3R MUTATED CSF3R WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              4             105
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             2              29
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CSF3R MUTATED     0   2   9   3
  CSF3R WILD-TYPE   9  66 239  38
D1437V4, multiclass
    clus
vv   CSF3R MUTATED CSF3R WILD-TYPE
  T1             0               9
  T2             2              66
  T3             9             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
  CSF3R MUTATED     9   2   3
  CSF3R WILD-TYPE 211  78  63
D1437V5, multiclass
    clus
vv   CSF3R MUTATED CSF3R WILD-TYPE
  N0             9             211
  N1             2              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"
D1437V6, binary
                 cls
clus                0   1
  CSF3R MUTATED    12   0
  CSF3R WILD-TYPE 271  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CSF3R MUTATED     12    0
  CSF3R WILD-TYPE  271   48
   clus
vv  CSF3R MUTATED CSF3R WILD-TYPE
  0            12             271
  1             0              48
[1] 2 2
[1] FALSE
D1437V7, 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
D1437V8, binary
                 cls
clus                0   1
  CSF3R MUTATED     9   5
  CSF3R WILD-TYPE 308  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CSF3R MUTATED      9    5
  CSF3R WILD-TYPE  308   43
                               clus
vv                              CSF3R MUTATED CSF3R WILD-TYPE
  COLON ADENOCARCINOMA                      9             308
  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 246   2  22  20
D1437V9, multiclass
    clus
vv   CSF3R MUTATED CSF3R WILD-TYPE
  R0            11             246
  R1             0               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"
D1437V10, 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
D1437V11, 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(1438) Variable = ZNF615 MUTATION ANALYSIS
D1438V1, survival
                  sevent
clus2                0   1
  ZNF615 MUTATED    11   5
  ZNF615 WILD-TYPE 271  68
  ZNF615 MUTATED ZNF615 WILD-TYPE 
              16              339 
  ZNF615 MUTATED ZNF615 WILD-TYPE 
               5               68 
$`ZNF615 MUTATED`
TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AY-5543 TCGA-AZ-4315 TCGA-AZ-6598 
       25.02         4.01        34.98        15.75        58.39        49.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4744 TCGA-D5-5539 
        6.77       100.01         0.33         0.10        20.02        19.59 
TCGA-D5-6928 TCGA-DM-A1D4 TCGA-DM-A1HB TCGA-G4-6586 
       11.64        92.75       135.65        35.80 

$`ZNF615 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 
        0.20        14.50        27.09        16.31         0.95         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       62.79        61.41        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07         0.26         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 
       45.11        36.72        36.00        22.09        13.78        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  ZNF615 MUTATED ZNF615 WILD-TYPE 
             0.1              0.0 
  ZNF615 MUTATED ZNF615 WILD-TYPE 
          135.65           140.38 
  ZNF615 MUTATED ZNF615 WILD-TYPE 
           22.52            20.19 
[1] "0.1 - 135.7 (22.5)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D1438V2, 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       23       102         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF615 MUTATED           0          1          1          0        0
  ZNF615 WILD-TYPE        19          9         40         31       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF615 MUTATED           1         0
  ZNF615 WILD-TYPE        12         1
D1438V3, multiclass
            clus
vv           ZNF615 MUTATED ZNF615 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               7              102
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              1                9
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  65 236  39
D1438V4, multiclass
    clus
vv   ZNF615 MUTATED ZNF615 WILD-TYPE
  T1              0                9
  T2              3               65
  T3             12              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
  ZNF615 MUTATED    14   3   0
  ZNF615 WILD-TYPE 206  77  66
D1438V5, multiclass
    clus
vv   ZNF615 MUTATED ZNF615 WILD-TYPE
  N0             14              206
  N1              3               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"
D1438V6, binary
                  cls
clus                 0   1
  ZNF615 MUTATED    13   1
  ZNF615 WILD-TYPE 270  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF615 MUTATED     13    1
  ZNF615 WILD-TYPE  270   47
   clus
vv  ZNF615 MUTATED ZNF615 WILD-TYPE
  0             13              270
  1              1               47
[1] 2 2
[1] FALSE
D1438V7, 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
D1438V8, binary
                  cls
clus                 0   1
  ZNF615 MUTATED    13   4
  ZNF615 WILD-TYPE 304  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF615 MUTATED     13    4
  ZNF615 WILD-TYPE  304   44
                               clus
vv                              ZNF615 MUTATED ZNF615 WILD-TYPE
  COLON ADENOCARCINOMA                      13              304
  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 248   2  22  19
D1438V9, multiclass
    clus
vv   ZNF615 MUTATED ZNF615 WILD-TYPE
  R0              9              248
  R1              0                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"
D1438V10, 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
D1438V11, 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(1439) Variable = MMAA MUTATION ANALYSIS
D1439V1, survival
                sevent
clus2              0   1
  MMAA MUTATED     7   2
  MMAA WILD-TYPE 275  71
  MMAA MUTATED MMAA WILD-TYPE 
             9            346 
  MMAA MUTATED MMAA WILD-TYPE 
             2             71 
$`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 
        0.33        29.06        30.08 

$`MMAA WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  MMAA MUTATED MMAA WILD-TYPE 
          0.33           0.00 
  MMAA MUTATED MMAA WILD-TYPE 
         58.39         140.38 
  MMAA MUTATED MMAA WILD-TYPE 
         8.380         20.585 
[1] "0.3 - 58.4 (8.4)"   "0.0 - 140.4 (20.6)"
[1] "hr=" "1.5"
D1439V2, 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       24       105         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        19          9         41         31       34        13
                vv
clus             STAGE IVB
  MMAA MUTATED           0
  MMAA WILD-TYPE         1
D1439V3, multiclass
            clus
vv           MMAA MUTATED MMAA WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             4            105
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            1              9
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MMAA MUTATED     0   1   5   3
  MMAA WILD-TYPE   9  67 243  38
D1439V4, multiclass
    clus
vv   MMAA MUTATED MMAA WILD-TYPE
  T1            0              9
  T2            1             67
  T3            5            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
  MMAA MUTATED     7   1   1
  MMAA WILD-TYPE 213  79  65
D1439V5, multiclass
    clus
vv   MMAA MUTATED MMAA WILD-TYPE
  N0            7            213
  N1            1             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"
D1439V6, binary
                cls
clus               0   1
  MMAA MUTATED     7   1
  MMAA WILD-TYPE 276  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMAA MUTATED      7    1
  MMAA WILD-TYPE  276   47
   clus
vv  MMAA MUTATED MMAA WILD-TYPE
  0            7            276
  1            1             47
[1] 2 2
[1] FALSE
D1439V7, 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
D1439V8, binary
                cls
clus               0   1
  MMAA MUTATED     7   2
  MMAA WILD-TYPE 310  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMAA MUTATED      7    2
  MMAA WILD-TYPE  310   46
                               clus
vv                              MMAA MUTATED MMAA WILD-TYPE
  COLON ADENOCARCINOMA                     7            310
  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 252   2  22  20
D1439V9, multiclass
    clus
vv   MMAA MUTATED MMAA WILD-TYPE
  R0            5            252
  R1            0              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"
D1439V10, 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
D1439V11, 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(1440) Variable = MAP7 MUTATION ANALYSIS
D1440V1, survival
                sevent
clus2              0   1
  MAP7 MUTATED    10   0
  MAP7 WILD-TYPE 272  73
  MAP7 MUTATED MAP7 WILD-TYPE 
            10            345 
  MAP7 MUTATED MAP7 WILD-TYPE 
             0             73 
$`MAP7 MUTATED`
TCGA-A6-6653 TCGA-AA-3543 TCGA-AA-3555 TCGA-AA-3949 TCGA-AA-3966 TCGA-AA-A010 
       24.39         0.99        29.95        26.01         2.01        34.98 
TCGA-AA-A01Q TCGA-AD-6889 TCGA-CA-6718 TCGA-D5-6540 
        1.02        56.55         0.10        16.14 

$`MAP7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       26.01        12.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        24.00         2.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        4.21         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.33         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  MAP7 MUTATED MAP7 WILD-TYPE 
           0.1            0.0 
  MAP7 MUTATED MAP7 WILD-TYPE 
         56.55         140.38 
  MAP7 MUTATED MAP7 WILD-TYPE 
        20.265         20.190 
[1] "0.1 - 56.5 (20.3)"  "0.0 - 140.4 (20.2)"
[1] "hr="     "9200000"
D1440V2, 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       24       104         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        19         10         40         31       35        13
                vv
clus             STAGE IVB
  MAP7 MUTATED           0
  MAP7 WILD-TYPE         1
D1440V3, multiclass
            clus
vv           MAP7 MUTATED MAP7 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             5            104
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MAP7 MUTATED     0   3   7   1
  MAP7 WILD-TYPE   9  65 241  40
D1440V4, multiclass
    clus
vv   MAP7 MUTATED MAP7 WILD-TYPE
  T1            0              9
  T2            3             65
  T3            7            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
  MAP7 MUTATED    10   1   0
  MAP7 WILD-TYPE 210  79  66
D1440V5, multiclass
    clus
vv   MAP7 MUTATED MAP7 WILD-TYPE
  N0           10            210
  N1            1             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"
D1440V6, binary
                cls
clus               0   1
  MAP7 MUTATED    11   0
  MAP7 WILD-TYPE 272  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAP7 MUTATED     11    0
  MAP7 WILD-TYPE  272   48
   clus
vv  MAP7 MUTATED MAP7 WILD-TYPE
  0           11            272
  1            0             48
[1] 2 2
[1] FALSE
D1440V7, 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
D1440V8, binary
                cls
clus               0   1
  MAP7 MUTATED     6   5
  MAP7 WILD-TYPE 311  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAP7 MUTATED      6    5
  MAP7 WILD-TYPE  311   43
                               clus
vv                              MAP7 MUTATED MAP7 WILD-TYPE
  COLON ADENOCARCINOMA                     6            311
  COLON MUCINOUS ADENOCARCINOMA            5             43
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MAP7 MUTATED     7   0   0   1
  MAP7 WILD-TYPE 250   2  22  20
D1440V9, multiclass
    clus
vv   MAP7 MUTATED MAP7 WILD-TYPE
  R0            7            250
  R1            0              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"
D1440V10, 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
D1440V11, 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(1441) Variable = ZNF167 MUTATION ANALYSIS
D1441V1, survival
                  sevent
clus2                0   1
  ZNF167 MUTATED    11   5
  ZNF167 WILD-TYPE 271  68
  ZNF167 MUTATED ZNF167 WILD-TYPE 
              16              339 
  ZNF167 MUTATED ZNF167 WILD-TYPE 
               5               68 
$`ZNF167 MUTATED`
TCGA-A6-6141 TCGA-AA-3510 TCGA-AA-3696 TCGA-AA-3715 TCGA-AA-3979 TCGA-AA-A00N 
        8.38        63.98         5.03        19.04        24.00         4.01 
TCGA-AA-A010 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CA-6718 
       34.98        10.88        83.80       100.01         0.33         0.10 
TCGA-CM-6171 TCGA-D5-6923 TCGA-D5-6929 TCGA-G4-6586 
       14.04        12.43        13.41        35.80 

$`ZNF167 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        25.02        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       15.75         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        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 
       15.58         7.53        12.39        10.13        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 
       45.11        36.72        36.00        22.09        13.78        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  ZNF167 MUTATED ZNF167 WILD-TYPE 
             0.1              0.0 
  ZNF167 MUTATED ZNF167 WILD-TYPE 
          100.01           140.38 
  ZNF167 MUTATED ZNF167 WILD-TYPE 
          13.725           20.980 
[1] "0.1 - 100.0 (13.7)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.5"
D1441V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF167 MUTATED         2        0        3         7         2         0
  ZNF167 WILD-TYPE      62        1       22       102         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF167 MUTATED           0          0          0          0        2
  ZNF167 WILD-TYPE        19         10         41         31       33
                  vv
clus               STAGE IVA STAGE IVB
  ZNF167 MUTATED           0         0
  ZNF167 WILD-TYPE        13         1
D1441V3, multiclass
            clus
vv           ZNF167 MUTATED ZNF167 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                3               22
  STAGE IIA               7              102
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                2               33
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF167 MUTATED     0   2  12   3
  ZNF167 WILD-TYPE   9  66 236  38
D1441V4, multiclass
    clus
vv   ZNF167 MUTATED ZNF167 WILD-TYPE
  T1              0                9
  T2              2               66
  T3             12              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
  ZNF167 MUTATED    14   2   1
  ZNF167 WILD-TYPE 206  78  65
D1441V5, multiclass
    clus
vv   ZNF167 MUTATED ZNF167 WILD-TYPE
  N0             14              206
  N1              2               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"
D1441V6, binary
                  cls
clus                 0   1
  ZNF167 MUTATED    14   2
  ZNF167 WILD-TYPE 269  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF167 MUTATED     14    2
  ZNF167 WILD-TYPE  269   46
   clus
vv  ZNF167 MUTATED ZNF167 WILD-TYPE
  0             14              269
  1              2               46
[1] 2 2
[1] FALSE
D1441V7, binary
                  cls
clus                 0   1
  ZNF167 MUTATED     7  10
  ZNF167 WILD-TYPE 163 187
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF167 MUTATED      7   10
  ZNF167 WILD-TYPE  163  187
        clus
vv       ZNF167 MUTATED ZNF167 WILD-TYPE
  FEMALE              7              163
  MALE               10              187
[1] 2 2
[1] FALSE
D1441V8, binary
                  cls
clus                 0   1
  ZNF167 MUTATED    15   2
  ZNF167 WILD-TYPE 302  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF167 MUTATED     15    2
  ZNF167 WILD-TYPE  302   46
                               clus
vv                              ZNF167 MUTATED ZNF167 WILD-TYPE
  COLON ADENOCARCINOMA                      15              302
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF167 MUTATED    11   0   1   2
  ZNF167 WILD-TYPE 246   2  21  19
D1441V9, multiclass
    clus
vv   ZNF167 MUTATED ZNF167 WILD-TYPE
  R0             11              246
  R1              0                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"
D1441V10, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF167 MUTATED                                  0     2
  ZNF167 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF167 MUTATED                           1     7
  ZNF167 WILD-TYPE                        18   169
D1441V11, multiclass
                                  clus
vv                                 ZNF167 MUTATED ZNF167 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(1442) Variable = LRRN3 MUTATION ANALYSIS
D1442V1, survival
                 sevent
clus2               0   1
  LRRN3 MUTATED    16   4
  LRRN3 WILD-TYPE 266  69
  LRRN3 MUTATED LRRN3 WILD-TYPE 
             20             335 
  LRRN3 MUTATED LRRN3 WILD-TYPE 
              4              69 
$`LRRN3 MUTATED`
TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-5666 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3672 
       34.65        32.75        32.71         3.02        63.98         0.92 
TCGA-AA-3715 TCGA-AA-3941 TCGA-AA-A00E TCGA-AA-A00R TCGA-AA-A01P TCGA-AA-A01R 
       19.04        24.00        30.02         0.99        38.07        35.01 
TCGA-AZ-4315 TCGA-CM-4743 TCGA-CM-6165 TCGA-CM-6676 TCGA-D5-6930 TCGA-F4-6570 
       58.39        23.05        16.04        11.08         1.51         6.18 
TCGA-G4-6293 TCGA-G4-6628 
      107.67        52.80 

$`LRRN3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       16.57        33.34        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 
       20.28         7.04         1.02        35.01         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       27.02        42.02        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       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        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
       21.99        21.14         2.93         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        16.01        15.02         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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        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        13.38        13.45        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.41        19.43        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       13.78        35.80        26.17        91.79        46.75 

  LRRN3 MUTATED LRRN3 WILD-TYPE 
           0.92            0.00 
  LRRN3 MUTATED LRRN3 WILD-TYPE 
         107.67          140.38 
  LRRN3 MUTATED LRRN3 WILD-TYPE 
          27.01           20.02 
[1] "0.9 - 107.7 (27.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.2"
D1442V2, 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       22       103         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        15         10         41         30       34        12
                 vv
clus              STAGE IVB
  LRRN3 MUTATED           0
  LRRN3 WILD-TYPE         1
D1442V3, multiclass
            clus
vv           LRRN3 MUTATED LRRN3 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              6             103
  STAGE IIB              1               7
  STAGE IIC              1               0
  STAGE III              4              15
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  65 234  37
D1442V4, multiclass
    clus
vv   LRRN3 MUTATED LRRN3 WILD-TYPE
  T1             0               9
  T2             3              65
  T3            14             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
  LRRN3 MUTATED    14   4   3
  LRRN3 WILD-TYPE 206  76  63
D1442V5, multiclass
    clus
vv   LRRN3 MUTATED LRRN3 WILD-TYPE
  N0            14             206
  N1             4              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"
D1442V6, binary
                 cls
clus                0   1
  LRRN3 MUTATED    19   2
  LRRN3 WILD-TYPE 264  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRRN3 MUTATED     19    2
  LRRN3 WILD-TYPE  264   46
   clus
vv  LRRN3 MUTATED LRRN3 WILD-TYPE
  0            19             264
  1             2              46
[1] 2 2
[1] FALSE
D1442V7, 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
D1442V8, binary
                 cls
clus                0   1
  LRRN3 MUTATED    18   3
  LRRN3 WILD-TYPE 299  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRRN3 MUTATED     18    3
  LRRN3 WILD-TYPE  299   45
                               clus
vv                              LRRN3 MUTATED LRRN3 WILD-TYPE
  COLON ADENOCARCINOMA                     18             299
  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 238   2  21  21
D1442V9, multiclass
    clus
vv   LRRN3 MUTATED LRRN3 WILD-TYPE
  R0            19             238
  R1             0               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"
D1442V10, 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
D1442V11, 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(1443) Variable = HMG20A MUTATION ANALYSIS
D1443V1, survival
                  sevent
clus2                0   1
  HMG20A MUTATED     8   3
  HMG20A WILD-TYPE 274  70
  HMG20A MUTATED HMG20A WILD-TYPE 
              11              344 
  HMG20A MUTATED HMG20A WILD-TYPE 
               3               70 
$`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-6172 TCGA-DM-A1D8 
        0.33        40.34        21.14        11.01        12.59 

$`HMG20A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02        14.93        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       102.44        15.62        49.08        51.32        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  HMG20A MUTATED HMG20A WILD-TYPE 
               0                0 
  HMG20A MUTATED HMG20A WILD-TYPE 
           58.39           140.38 
  HMG20A MUTATED HMG20A WILD-TYPE 
          21.140           20.155 
[1] "0.0 - 58.4 (21.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.7"
D1443V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HMG20A MUTATED         3        0        0         4         1         0
  HMG20A WILD-TYPE      61        1       25       105         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HMG20A MUTATED           0          1          1          0        0
  HMG20A WILD-TYPE        19          9         40         31       35
                  vv
clus               STAGE IVA STAGE IVB
  HMG20A MUTATED           0         0
  HMG20A WILD-TYPE        13         1
D1443V3, multiclass
            clus
vv           HMG20A MUTATED HMG20A WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               4              105
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              1                9
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  HMG20A MUTATED     1   2   7   1
  HMG20A WILD-TYPE   8  66 241  40
D1443V4, multiclass
    clus
vv   HMG20A MUTATED HMG20A WILD-TYPE
  T1              1                8
  T2              2               66
  T3              7              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
  HMG20A MUTATED     8   3   0
  HMG20A WILD-TYPE 212  77  66
D1443V5, multiclass
    clus
vv   HMG20A MUTATED HMG20A WILD-TYPE
  N0              8              212
  N1              3               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"
D1443V6, binary
                  cls
clus                 0   1
  HMG20A MUTATED    10   0
  HMG20A WILD-TYPE 273  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HMG20A MUTATED     10    0
  HMG20A WILD-TYPE  273   48
   clus
vv  HMG20A MUTATED HMG20A WILD-TYPE
  0             10              273
  1              0               48
[1] 2 2
[1] FALSE
D1443V7, binary
                  cls
clus                 0   1
  HMG20A MUTATED     8   3
  HMG20A WILD-TYPE 162 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HMG20A MUTATED      8    3
  HMG20A WILD-TYPE  162  194
        clus
vv       HMG20A MUTATED HMG20A WILD-TYPE
  FEMALE              8              162
  MALE                3              194
[1] 2 2
[1] FALSE
D1443V8, binary
                  cls
clus                 0   1
  HMG20A MUTATED    10   1
  HMG20A WILD-TYPE 307  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HMG20A MUTATED     10    1
  HMG20A WILD-TYPE  307   47
                               clus
vv                              HMG20A MUTATED HMG20A WILD-TYPE
  COLON ADENOCARCINOMA                      10              307
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  HMG20A MUTATED     6   1   0   2
  HMG20A WILD-TYPE 251   1  22  19
D1443V9, multiclass
    clus
vv   HMG20A MUTATED HMG20A WILD-TYPE
  R0              6              251
  R1              1                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"
D1443V10, 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                           2     4
  HMG20A WILD-TYPE                        17   172
D1443V11, multiclass
                                  clus
vv                                 HMG20A MUTATED HMG20A 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(1444) Variable = CCDC111 MUTATION ANALYSIS
D1444V1, survival
                   sevent
clus2                 0   1
  CCDC111 MUTATED     5   2
  CCDC111 WILD-TYPE 277  71
  CCDC111 MUTATED CCDC111 WILD-TYPE 
                7               348 
  CCDC111 MUTATED CCDC111 WILD-TYPE 
                2                71 
$`CCDC111 MUTATED`
TCGA-AA-3660 TCGA-AA-A010 TCGA-AD-6889 TCGA-AD-6899 TCGA-AZ-4315 TCGA-CM-6168 
       78.08        34.98        56.55         5.79        58.39        12.99 
TCGA-DM-A0XD 
       24.43 

$`CCDC111 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        61.02         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         0.72        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        11.38        10.26       119.70        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  CCDC111 MUTATED CCDC111 WILD-TYPE 
             5.79              0.00 
  CCDC111 MUTATED CCDC111 WILD-TYPE 
            78.08            140.38 
  CCDC111 MUTATED CCDC111 WILD-TYPE 
            34.98             20.07 
[1] "5.8 - 78.1 (35.0)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.1"
D1444V2, 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       24       105         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC111 MUTATED           0          0          0          1        0
  CCDC111 WILD-TYPE        19         10         41         30       35
                   vv
clus                STAGE IVA STAGE IVB
  CCDC111 MUTATED           0         0
  CCDC111 WILD-TYPE        13         1
D1444V3, multiclass
            clus
vv           CCDC111 MUTATED CCDC111 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                4               105
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               1                30
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CCDC111 MUTATED     0   0   5   2
  CCDC111 WILD-TYPE   9  68 243  39
D1444V4, multiclass
    clus
vv   CCDC111 MUTATED CCDC111 WILD-TYPE
  T1               0                 9
  T2               0                68
  T3               5               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
  CCDC111 MUTATED     6   0   1
  CCDC111 WILD-TYPE 214  80  65
D1444V5, multiclass
    clus
vv   CCDC111 MUTATED CCDC111 WILD-TYPE
  N0               6               214
  N1               0                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"
D1444V6, binary
                   cls
clus                  0   1
  CCDC111 MUTATED     6   0
  CCDC111 WILD-TYPE 277  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC111 MUTATED      6    0
  CCDC111 WILD-TYPE  277   48
   clus
vv  CCDC111 MUTATED CCDC111 WILD-TYPE
  0               6               277
  1               0                48
[1] 2 2
[1] FALSE
D1444V7, 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
D1444V8, binary
                   cls
clus                  0   1
  CCDC111 MUTATED     6   1
  CCDC111 WILD-TYPE 311  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC111 MUTATED      6    1
  CCDC111 WILD-TYPE  311   47
                               clus
vv                              CCDC111 MUTATED CCDC111 WILD-TYPE
  COLON ADENOCARCINOMA                        6               311
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  CCDC111 MUTATED     4   0   0   0
  CCDC111 WILD-TYPE 253   2  22  21
D1444V9, multiclass
    clus
vv   CCDC111 MUTATED CCDC111 WILD-TYPE
  R0               4               253
  R1               0                 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"
D1444V10, 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
D1444V11, 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(1445) Variable = ZNF235 MUTATION ANALYSIS
D1445V1, survival
                  sevent
clus2                0   1
  ZNF235 MUTATED     6   2
  ZNF235 WILD-TYPE 276  71
  ZNF235 MUTATED ZNF235 WILD-TYPE 
               8              347 
  ZNF235 MUTATED ZNF235 WILD-TYPE 
               2               71 
$`ZNF235 MUTATED`
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3844 TCGA-CM-5344 
        3.02         1.02        36.00        19.04        14.93        22.03 
TCGA-CM-5349 TCGA-F4-6807 
       30.08        16.24 

$`ZNF235 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3502 
       23.87        20.12        19.66        20.28         7.04        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3696 
       15.02        11.01         5.98        37.05        19.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       29.06        22.98        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       29.59        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  ZNF235 MUTATED ZNF235 WILD-TYPE 
            1.02             0.00 
  ZNF235 MUTATED ZNF235 WILD-TYPE 
           36.00           140.38 
  ZNF235 MUTATED ZNF235 WILD-TYPE 
           17.64            20.28 
[1] "1.0 - 36.0 (17.6)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.8"
D1445V2, 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       23       107         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF235 MUTATED           0          0          1          2        2
  ZNF235 WILD-TYPE        19         10         40         29       33
                  vv
clus               STAGE IVA STAGE IVB
  ZNF235 MUTATED           0         0
  ZNF235 WILD-TYPE        13         1
D1445V3, multiclass
            clus
vv           ZNF235 MUTATED ZNF235 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               2              107
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              2               29
  STAGE IV                2               33
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF235 MUTATED     0   0   9   0
  ZNF235 WILD-TYPE   9  68 239  41
D1445V4, multiclass
    clus
vv   ZNF235 MUTATED ZNF235 WILD-TYPE
  T1              0                9
  T2              0               68
  T3              9              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
  ZNF235 MUTATED     5   1   3
  ZNF235 WILD-TYPE 215  79  63
D1445V5, multiclass
    clus
vv   ZNF235 MUTATED ZNF235 WILD-TYPE
  N0              5              215
  N1              1               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
  ZNF235 MUTATED     7   2
  ZNF235 WILD-TYPE 276  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF235 MUTATED      7    2
  ZNF235 WILD-TYPE  276   46
   clus
vv  ZNF235 MUTATED ZNF235 WILD-TYPE
  0              7              276
  1              2               46
[1] 2 2
[1] FALSE
D1445V7, 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
D1445V8, binary
                  cls
clus                 0   1
  ZNF235 MUTATED     8   1
  ZNF235 WILD-TYPE 309  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF235 MUTATED      8    1
  ZNF235 WILD-TYPE  309   47
                               clus
vv                              ZNF235 MUTATED ZNF235 WILD-TYPE
  COLON ADENOCARCINOMA                       8              309
  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 250   2  20  21
D1445V9, multiclass
    clus
vv   ZNF235 MUTATED ZNF235 WILD-TYPE
  R0              7              250
  R1              0                2
  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"
D1445V10, 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
D1445V11, 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(1446) Variable = ZNF286B MUTATION ANALYSIS
D1446V1, survival
                   sevent
clus2                 0   1
  ZNF286B MUTATED     4   1
  ZNF286B WILD-TYPE 278  72
  ZNF286B MUTATED ZNF286B WILD-TYPE 
                5               350 
  ZNF286B MUTATED ZNF286B WILD-TYPE 
                1                72 
$`ZNF286B MUTATED`
TCGA-A6-5662 TCGA-AA-3510 TCGA-AZ-4315 TCGA-CA-6717 TCGA-F4-6570 
       23.61        63.98        58.39         0.33         6.18 

$`ZNF286B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        33.53        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       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        13.38        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  ZNF286B MUTATED ZNF286B WILD-TYPE 
             0.33              0.00 
  ZNF286B MUTATED ZNF286B WILD-TYPE 
            63.98            140.38 
  ZNF286B MUTATED ZNF286B WILD-TYPE 
           23.610            20.155 
[1] "0.3 - 64.0 (23.6)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.3"
D1446V2, 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       24       106         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF286B MUTATED           0          0          0          0        0
  ZNF286B WILD-TYPE        19         10         41         31       35
                   vv
clus                STAGE IVA STAGE IVB
  ZNF286B MUTATED           1         0
  ZNF286B WILD-TYPE        12         1
D1446V3, multiclass
            clus
vv           ZNF286B MUTATED ZNF286B WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                3               106
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                1                12
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of 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  68 243  41
D1446V4, multiclass
    clus
vv   ZNF286B MUTATED ZNF286B WILD-TYPE
  T1               0                 9
  T2               0                68
  T3               5               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
  ZNF286B MUTATED     4   0   1
  ZNF286B WILD-TYPE 216  80  65
D1446V5, multiclass
    clus
vv   ZNF286B MUTATED ZNF286B WILD-TYPE
  N0               4               216
  N1               0                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"
D1446V6, binary
                   cls
clus                  0   1
  ZNF286B MUTATED     4   1
  ZNF286B WILD-TYPE 279  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF286B MUTATED      4    1
  ZNF286B WILD-TYPE  279   47
   clus
vv  ZNF286B MUTATED ZNF286B WILD-TYPE
  0               4               279
  1               1                47
[1] 2 2
[1] FALSE
D1446V7, 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
D1446V8, binary
                   cls
clus                  0   1
  ZNF286B MUTATED     4   1
  ZNF286B WILD-TYPE 313  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF286B MUTATED      4    1
  ZNF286B WILD-TYPE  313   47
                               clus
vv                              ZNF286B MUTATED ZNF286B WILD-TYPE
  COLON ADENOCARCINOMA                        4               313
  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 254   2  22  20
D1446V9, multiclass
    clus
vv   ZNF286B MUTATED ZNF286B WILD-TYPE
  R0               3               254
  R1               0                 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"
D1446V10, 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
D1446V11, 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(1447) Variable = TIFAB MUTATION ANALYSIS
D1447V1, survival
                 sevent
clus2               0   1
  TIFAB MUTATED     2   0
  TIFAB WILD-TYPE 280  73
  TIFAB MUTATED TIFAB WILD-TYPE 
              2             353 
  TIFAB MUTATED TIFAB WILD-TYPE 
              0              73 
$`TIFAB MUTATED`
TCGA-AZ-4315 TCGA-F4-6856 
       58.39        19.43 

$`TIFAB WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  TIFAB MUTATED TIFAB WILD-TYPE 
          19.43            0.00 
  TIFAB MUTATED TIFAB WILD-TYPE 
          58.39          140.38 
  TIFAB MUTATED TIFAB WILD-TYPE 
          38.91           20.19 
[1] "19.4 - 58.4 (38.9)" "0.0 - 140.4 (20.2)"
[1] "Remove cluster labels:" "TIFAB MUTATED"         
D1447V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TIFAB MUTATED         1        0        0         1         1         0
  TIFAB WILD-TYPE      63        1       25       108         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TIFAB MUTATED           0          0          0          0        0         0
  TIFAB WILD-TYPE        19         10         41         31       35        13
                 vv
clus              STAGE IVB
  TIFAB MUTATED           0
  TIFAB WILD-TYPE         1
D1447V3, multiclass
            clus
vv           TIFAB MUTATED TIFAB WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              1             108
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TIFAB MUTATED     0   1   1   1
  TIFAB WILD-TYPE   9  67 247  40
D1447V4, multiclass
    clus
vv   TIFAB MUTATED TIFAB WILD-TYPE
  T1             0               9
  T2             1              67
  T3             1             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
  TIFAB MUTATED     3   0   0
  TIFAB WILD-TYPE 217  80  66
D1447V5, multiclass
    clus
vv   TIFAB MUTATED TIFAB WILD-TYPE
  N0             3             217
  N1             0              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"
D1447V6, binary
                 cls
clus                0   1
  TIFAB MUTATED     2   0
  TIFAB WILD-TYPE 281  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TIFAB MUTATED      2    0
  TIFAB WILD-TYPE  281   48
   clus
vv  TIFAB MUTATED TIFAB WILD-TYPE
  0             2             281
  1             0              48
[1] 2 2
[1] FALSE
D1447V7, binary
                 cls
clus                0   1
  TIFAB MUTATED     1   2
  TIFAB WILD-TYPE 169 195
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TIFAB MUTATED      1    2
  TIFAB WILD-TYPE  169  195
        clus
vv       TIFAB MUTATED TIFAB WILD-TYPE
  FEMALE             1             169
  MALE               2             195
[1] 2 2
[1] FALSE
D1447V8, binary
                 cls
clus                0   1
  TIFAB MUTATED     2   1
  TIFAB WILD-TYPE 315  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TIFAB MUTATED      2    1
  TIFAB WILD-TYPE  315   47
                               clus
vv                              TIFAB MUTATED TIFAB WILD-TYPE
  COLON ADENOCARCINOMA                      2             315
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TIFAB MUTATED     2   0   0   1
  TIFAB WILD-TYPE 255   2  22  20
D1447V9, multiclass
    clus
vv   TIFAB MUTATED TIFAB WILD-TYPE
  R0             2             255
  R1             0               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"
D1447V10, continuous
[1] "Remove cluster labels:" "TIFAB MUTATED"         
clus
  TIFAB MUTATED TIFAB WILD-TYPE 
              1             344 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-4105 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-A6-5656      TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5660 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-A6-5661      TCGA-A6-5662      TCGA-A6-5664      TCGA-A6-5665 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-A6-5666      TCGA-A6-6137      TCGA-A6-6138      TCGA-A6-6141 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-A6-6142      TCGA-A6-6648      TCGA-A6-6649      TCGA-A6-6651 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-A6-6652      TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-A6-6781      TCGA-A6-6782      TCGA-AA-3489      TCGA-AA-3492 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-AA-3496      TCGA-AA-3502      TCGA-AA-3510      TCGA-AA-3511 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-AA-3514      TCGA-AA-3516      TCGA-AA-3517      TCGA-AA-3518 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-AA-3519      TCGA-AA-3520      TCGA-AA-3521      TCGA-AA-3522 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-AA-3524      TCGA-AA-3525      TCGA-AA-3526      TCGA-AA-3527 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-AA-3529      TCGA-AA-3530      TCGA-AA-3531      TCGA-AA-3532 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-AA-3534      TCGA-AA-3538      TCGA-AA-3542      TCGA-AA-3543 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-AA-3544      TCGA-AA-3548      TCGA-AA-3549      TCGA-AA-3552 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-AA-3553      TCGA-AA-3554      TCGA-AA-3555      TCGA-AA-3556 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-AA-3558      TCGA-AA-3560      TCGA-AA-3562      TCGA-AA-3655 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-AA-3660      TCGA-AA-3662      TCGA-AA-3663      TCGA-AA-3664 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-AA-3666      TCGA-AA-3667      TCGA-AA-3672      TCGA-AA-3673 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-AA-3678      TCGA-AA-3679      TCGA-AA-3680      TCGA-AA-3681 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-AA-3684      TCGA-AA-3685      TCGA-AA-3688      TCGA-AA-3692 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-AA-3693      TCGA-AA-3695      TCGA-AA-3696      TCGA-AA-3697 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-AA-3710      TCGA-AA-3712      TCGA-AA-3713      TCGA-AA-3715 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-AA-3811      TCGA-AA-3812      TCGA-AA-3814      TCGA-AA-3815 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-AA-3818      TCGA-AA-3819      TCGA-AA-3821      TCGA-AA-3831 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-AA-3833      TCGA-AA-3837      TCGA-AA-3842      TCGA-AA-3844 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-AA-3845      TCGA-AA-3846      TCGA-AA-3848      TCGA-AA-3850 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-AA-3851      TCGA-AA-3852      TCGA-AA-3854      TCGA-AA-3855 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-AA-3856      TCGA-AA-3858      TCGA-AA-3860      TCGA-AA-3861 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-AA-3864      TCGA-AA-3866      TCGA-AA-3867      TCGA-AA-3869 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-AA-3870      TCGA-AA-3872      TCGA-AA-3875      TCGA-AA-3877 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-AA-3930      TCGA-AA-3939      TCGA-AA-3941      TCGA-AA-3947 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-AA-3949      TCGA-AA-3950      TCGA-AA-3952      TCGA-AA-3955 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-AA-3956      TCGA-AA-3966      TCGA-AA-3968      TCGA-AA-3971 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-AA-3972      TCGA-AA-3973      TCGA-AA-3975      TCGA-AA-3976 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-AA-3977      TCGA-AA-3979      TCGA-AA-3980      TCGA-AA-3982 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-AA-3984      TCGA-AA-3986      TCGA-AA-3989      TCGA-AA-3994 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-AA-A004      TCGA-AA-A00A      TCGA-AA-A00D      TCGA-AA-A00E 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-AA-A00F      TCGA-AA-A00J      TCGA-AA-A00K      TCGA-AA-A00L 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-AA-A00N      TCGA-AA-A00O      TCGA-AA-A00Q      TCGA-AA-A00R 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-AA-A00U      TCGA-AA-A00W      TCGA-AA-A00Z      TCGA-AA-A010 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-AA-A017      TCGA-AA-A01D      TCGA-AA-A01F      TCGA-AA-A01G 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-AA-A01I      TCGA-AA-A01K      TCGA-AA-A01P      TCGA-AA-A01Q 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-AA-A01R      TCGA-AA-A01S      TCGA-AA-A01T      TCGA-AA-A01V 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-AA-A01X      TCGA-AA-A01Z      TCGA-AA-A022      TCGA-AA-A024 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-AA-A029      TCGA-AA-A02F      TCGA-AA-A02H      TCGA-AA-A02J 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-AA-A02K      TCGA-AA-A02O      TCGA-AA-A02W      TCGA-AA-A02Y 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-AA-A03F      TCGA-AA-A03J      TCGA-AD-5900      TCGA-AD-6548 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-AD-6888      TCGA-AD-6889      TCGA-AD-6890      TCGA-AD-6895 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-AD-6899      TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6964 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-AD-6965      TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-AY-4071      TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-AY-6386      TCGA-AZ-4323      TCGA-AZ-4616      TCGA-AZ-4682 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-AZ-5403      TCGA-AZ-5407      TCGA-AZ-6598      TCGA-AZ-6599 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-AZ-6600      TCGA-AZ-6601      TCGA-AZ-6603      TCGA-AZ-6605 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-AZ-6606      TCGA-AZ-6607      TCGA-AZ-6608      TCGA-CK-4947 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-CK-4948      TCGA-CK-4950      TCGA-CK-4952      TCGA-CM-4743 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-CM-4744      TCGA-CM-4746      TCGA-CM-4747      TCGA-CM-4752 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-CM-5341      TCGA-CM-5344      TCGA-CM-5348      TCGA-CM-5349 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-CM-5860      TCGA-CM-5861      TCGA-CM-5862      TCGA-CM-5863 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-CM-5864      TCGA-CM-5868      TCGA-CM-6161      TCGA-CM-6162 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-CM-6163      TCGA-CM-6164      TCGA-CM-6165      TCGA-CM-6166 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-CM-6167      TCGA-CM-6168      TCGA-CM-6169      TCGA-CM-6170 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-CM-6171      TCGA-CM-6172      TCGA-CM-6674      TCGA-CM-6675 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-CM-6676      TCGA-CM-6677      TCGA-CM-6678      TCGA-CM-6679 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-CM-6680      TCGA-D5-5537      TCGA-D5-5538      TCGA-D5-5539 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-D5-5540      TCGA-D5-5541      TCGA-D5-6529      TCGA-D5-6532 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-D5-6533      TCGA-D5-6534      TCGA-D5-6535      TCGA-D5-6536 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-D5-6537      TCGA-D5-6538      TCGA-D5-6539      TCGA-D5-6540 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-D5-6541      TCGA-D5-6898      TCGA-D5-6920      TCGA-D5-6922 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-D5-6923      TCGA-D5-6924      TCGA-D5-6926      TCGA-D5-6927 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-D5-6928      TCGA-D5-6929      TCGA-D5-6930      TCGA-D5-6931 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-D5-6932      TCGA-D5-7000      TCGA-DM-A0X9      TCGA-DM-A0XD 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-DM-A0XF      TCGA-DM-A1D0      TCGA-DM-A1D4      TCGA-DM-A1D6 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-DM-A1D7      TCGA-DM-A1D8      TCGA-DM-A1D9      TCGA-DM-A1DA 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-DM-A1DB      TCGA-DM-A1HA      TCGA-DM-A1HB      TCGA-DM-A282 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-DM-A285      TCGA-DM-A28C      TCGA-DM-A28E      TCGA-DM-A28F 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-DM-A28G      TCGA-DM-A28H      TCGA-DM-A28K      TCGA-F4-6459 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-F4-6460      TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-F4-6704      TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855      TCGA-G4-6293 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304      TCGA-G4-6306 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310      TCGA-G4-6315 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323      TCGA-G4-6586 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
     TCGA-G4-6588      TCGA-G4-6625      TCGA-G4-6626      TCGA-G4-6628 
"TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" "TIFAB WILD-TYPE" 
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TIFAB MUTATED                                  0     0
  TIFAB WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TIFAB MUTATED                           0     3
  TIFAB WILD-TYPE                        19   173
D1447V11, multiclass
                                  clus
vv                                 TIFAB MUTATED TIFAB 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(1448) Variable = CPO MUTATION ANALYSIS
D1448V1, survival
               sevent
clus2             0   1
  CPO MUTATED     5   2
  CPO WILD-TYPE 277  71
  CPO MUTATED CPO WILD-TYPE 
            7           348 
  CPO MUTATED CPO WILD-TYPE 
            2            71 
$`CPO MUTATED`
TCGA-A6-5660 TCGA-A6-6782 TCGA-AA-3666 TCGA-AZ-4315 TCGA-AZ-6606 TCGA-CK-4950 
       29.19        20.28         2.01        58.39        11.74        40.34 
TCGA-G4-6628 
       52.80 

$`CPO WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
      100.01        29.56         5.23         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 
        0.10         1.35        17.56       102.44        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 

  CPO MUTATED CPO WILD-TYPE 
         2.01          0.00 
  CPO MUTATED CPO WILD-TYPE 
        58.39        140.38 
  CPO MUTATED CPO WILD-TYPE 
        29.19         20.07 
[1] "2.0 - 58.4 (29.2)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.2"
D1448V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CPO MUTATED         1        0        0         2         1         0
  CPO WILD-TYPE      63        1       25       107         7         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CPO MUTATED           1          1          0          1        1         0
  CPO WILD-TYPE        18          9         41         30       34        13
               vv
clus            STAGE IVB
  CPO MUTATED           0
  CPO WILD-TYPE         1
D1448V3, multiclass
            clus
vv           CPO MUTATED CPO WILD-TYPE
  STAGE I              1            63
  STAGE IA             0             1
  STAGE II             0            25
  STAGE IIA            2           107
  STAGE IIB            1             7
  STAGE IIC            0             1
  STAGE III            1            18
  STAGE IIIA           1             9
  STAGE IIIB           0            41
  STAGE IIIC           1            30
  STAGE IV             1            34
  STAGE IVA            0            13
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  CPO MUTATED     0   1   5   2
  CPO WILD-TYPE   9  67 243  39
D1448V4, multiclass
    clus
vv   CPO MUTATED CPO WILD-TYPE
  T1           0             9
  T2           1            67
  T3           5           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
  CPO MUTATED     4   2   2
  CPO WILD-TYPE 216  78  64
D1448V5, multiclass
    clus
vv   CPO MUTATED CPO WILD-TYPE
  N0           4           216
  N1           2            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"
D1448V6, binary
               cls
clus              0   1
  CPO MUTATED     6   1
  CPO WILD-TYPE 277  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  CPO MUTATED      6    1
  CPO WILD-TYPE  277   47
   clus
vv  CPO MUTATED CPO WILD-TYPE
  0           6           277
  1           1            47
[1] 2 2
[1] FALSE
D1448V7, binary
               cls
clus              0   1
  CPO MUTATED     2   6
  CPO WILD-TYPE 168 191
[1] "tbl2"
               cls
clus            [,1] [,2]
  CPO MUTATED      2    6
  CPO WILD-TYPE  168  191
        clus
vv       CPO MUTATED CPO WILD-TYPE
  FEMALE           2           168
  MALE             6           191
[1] 2 2
[1] FALSE
D1448V8, binary
               cls
clus              0   1
  CPO MUTATED     8   0
  CPO WILD-TYPE 309  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  CPO MUTATED      8    0
  CPO WILD-TYPE  309   48
                               clus
vv                              CPO MUTATED CPO WILD-TYPE
  COLON ADENOCARCINOMA                    8           309
  COLON MUCINOUS ADENOCARCINOMA           0            48
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  CPO MUTATED     4   1   0   0
  CPO WILD-TYPE 253   1  22  21
D1448V9, multiclass
    clus
vv   CPO MUTATED CPO WILD-TYPE
  R0           4           253
  R1           1             1
  R2           0            22
  RX           0            21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1448V10, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CPO MUTATED                                  0     0
  CPO WILD-TYPE                                1    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  CPO MUTATED                           2     4
  CPO WILD-TYPE                        17   172
D1448V11, multiclass
                                  clus
vv                                 CPO MUTATED CPO 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(1449) Variable = SLC26A7 MUTATION ANALYSIS
D1449V1, survival
                   sevent
clus2                 0   1
  SLC26A7 MUTATED    12   4
  SLC26A7 WILD-TYPE 270  69
  SLC26A7 MUTATED SLC26A7 WILD-TYPE 
               16               339 
  SLC26A7 MUTATED SLC26A7 WILD-TYPE 
                4                69 
$`SLC26A7 MUTATED`
TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3811 TCGA-AA-3979 TCGA-AA-A00J TCGA-AA-A00N 
       22.06        63.98        10.06        24.00        18.05         4.01 
TCGA-AA-A010 TCGA-AA-A01G TCGA-AA-A02J TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 
       34.98        12.00         5.03        58.39        49.41         0.33 
TCGA-CA-6718 TCGA-D5-6541 TCGA-DM-A1HB TCGA-F4-6856 
        0.10        15.58       135.65        19.43 

$`SLC26A7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        19.04        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        25.02        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
       39.98         2.01        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07         0.26         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 
       33.67        13.25         0.53        35.41       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  SLC26A7 MUTATED SLC26A7 WILD-TYPE 
              0.1               0.0 
  SLC26A7 MUTATED SLC26A7 WILD-TYPE 
           135.65            140.38 
  SLC26A7 MUTATED SLC26A7 WILD-TYPE 
            18.74             20.28 
[1] "0.1 - 135.7 (18.7)" "0.0 - 140.4 (20.3)"
[1] "hr=" "1.1"
D1449V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC26A7 MUTATED         1        0        2         7         2         0
  SLC26A7 WILD-TYPE      63        1       23       102         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC26A7 MUTATED           1          0          2          0        1
  SLC26A7 WILD-TYPE        18         10         39         31       34
                   vv
clus                STAGE IVA STAGE IVB
  SLC26A7 MUTATED           0         0
  SLC26A7 WILD-TYPE        13         1
D1449V3, multiclass
            clus
vv           SLC26A7 MUTATED SLC26A7 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 2                23
  STAGE IIA                7               102
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               0                10
  STAGE IIIB               2                39
  STAGE IIIC               0                31
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC26A7 MUTATED     0   1  12   3
  SLC26A7 WILD-TYPE   9  67 236  38
D1449V4, multiclass
    clus
vv   SLC26A7 MUTATED SLC26A7 WILD-TYPE
  T1               0                 9
  T2               1                67
  T3              12               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    13   2   1
  SLC26A7 WILD-TYPE 207  78  65
D1449V5, multiclass
    clus
vv   SLC26A7 MUTATED SLC26A7 WILD-TYPE
  N0              13               207
  N1               2                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"
D1449V6, binary
                   cls
clus                  0   1
  SLC26A7 MUTATED    14   1
  SLC26A7 WILD-TYPE 269  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC26A7 MUTATED     14    1
  SLC26A7 WILD-TYPE  269   47
   clus
vv  SLC26A7 MUTATED SLC26A7 WILD-TYPE
  0              14               269
  1               1                47
[1] 2 2
[1] FALSE
D1449V7, binary
                   cls
clus                  0   1
  SLC26A7 MUTATED     5  11
  SLC26A7 WILD-TYPE 165 186
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC26A7 MUTATED      5   11
  SLC26A7 WILD-TYPE  165  186
        clus
vv       SLC26A7 MUTATED SLC26A7 WILD-TYPE
  FEMALE               5               165
  MALE                11               186
[1] 2 2
[1] FALSE
D1449V8, binary
                   cls
clus                  0   1
  SLC26A7 MUTATED    11   5
  SLC26A7 WILD-TYPE 306  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC26A7 MUTATED     11    5
  SLC26A7 WILD-TYPE  306   43
                               clus
vv                              SLC26A7 MUTATED SLC26A7 WILD-TYPE
  COLON ADENOCARCINOMA                       11               306
  COLON MUCINOUS ADENOCARCINOMA               5                43
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SLC26A7 MUTATED    11   0   1   2
  SLC26A7 WILD-TYPE 246   2  21  19
D1449V9, multiclass
    clus
vv   SLC26A7 MUTATED SLC26A7 WILD-TYPE
  R0              11               246
  R1               0                 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"
D1449V10, 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
D1449V11, 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(1450) Variable = HECW2 MUTATION ANALYSIS
D1450V1, survival
                 sevent
clus2               0   1
  HECW2 MUTATED    20   6
  HECW2 WILD-TYPE 262  67
  HECW2 MUTATED HECW2 WILD-TYPE 
             26             329 
  HECW2 MUTATED HECW2 WILD-TYPE 
              6              67 
$`HECW2 MUTATED`
TCGA-A6-2672 TCGA-A6-5656 TCGA-A6-5660 TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3672 
       46.65        32.91        29.19        63.98        13.02         0.92 
TCGA-AA-3854 TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A02Y 
       36.03        25.02        19.07         4.01        34.98        39.98 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6895 TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-5403 
        0.07        56.55         0.72        27.09        58.39        62.79 
TCGA-AZ-6601 TCGA-CA-6717 TCGA-CK-5916 TCGA-CM-6674 TCGA-D5-6922 TCGA-D5-6924 
      100.01         0.33        21.14        12.95        10.13        14.30 
TCGA-G4-6307 TCGA-G4-6626 
       55.04        46.75 

$`HECW2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5657 
       34.65        33.34        32.75        36.53        14.53        31.63 
TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       30.44        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
        1.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       27.02         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
       14.01         0.92        41.00        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        4.21         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.20        14.50        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       12.43         9.04         9.44        11.64        13.41         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        52.80 

  HECW2 MUTATED HECW2 WILD-TYPE 
           0.07            0.00 
  HECW2 MUTATED HECW2 WILD-TYPE 
         100.01          140.38 
  HECW2 MUTATED HECW2 WILD-TYPE 
          28.14           19.99 
[1] "0.1 - 100.0 (28.1)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.1"
D1450V2, 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       22       103         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HECW2 MUTATED           3          1          2          1        0         0
  HECW2 WILD-TYPE        16          9         39         30       35        13
                 vv
clus              STAGE IVB
  HECW2 MUTATED           0
  HECW2 WILD-TYPE         1
D1450V3, multiclass
            clus
vv           HECW2 MUTATED HECW2 WILD-TYPE
  STAGE I                7              57
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              6             103
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              3              16
  STAGE IIIA             1               9
  STAGE IIIB             2              39
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HECW2 MUTATED     1   7  17   3
  HECW2 WILD-TYPE   8  61 231  38
D1450V4, multiclass
    clus
vv   HECW2 MUTATED HECW2 WILD-TYPE
  T1             1               8
  T2             7              61
  T3            17             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
  HECW2 MUTATED    20   5   3
  HECW2 WILD-TYPE 200  75  63
D1450V5, multiclass
    clus
vv   HECW2 MUTATED HECW2 WILD-TYPE
  N0            20             200
  N1             5              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"
D1450V6, binary
                 cls
clus                0   1
  HECW2 MUTATED    23   0
  HECW2 WILD-TYPE 260  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HECW2 MUTATED     23    0
  HECW2 WILD-TYPE  260   48
   clus
vv  HECW2 MUTATED HECW2 WILD-TYPE
  0            23             260
  1             0              48
[1] 2 2
[1] FALSE
D1450V7, 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
D1450V8, binary
                 cls
clus                0   1
  HECW2 MUTATED    23   5
  HECW2 WILD-TYPE 294  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HECW2 MUTATED     23    5
  HECW2 WILD-TYPE  294   43
                               clus
vv                              HECW2 MUTATED HECW2 WILD-TYPE
  COLON ADENOCARCINOMA                     23             294
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  HECW2 MUTATED    17   0   0   3
  HECW2 WILD-TYPE 240   2  22  18
D1450V9, multiclass
    clus
vv   HECW2 MUTATED HECW2 WILD-TYPE
  R0            17             240
  R1             0               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"
D1450V10, 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
D1450V11, 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(1451) Variable = GOLIM4 MUTATION ANALYSIS
D1451V1, survival
                  sevent
clus2                0   1
  GOLIM4 MUTATED     6   3
  GOLIM4 WILD-TYPE 276  70
  GOLIM4 MUTATED GOLIM4 WILD-TYPE 
               9              346 
  GOLIM4 MUTATED GOLIM4 WILD-TYPE 
               3               70 
$`GOLIM4 MUTATED`
TCGA-A6-3810 TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3710 TCGA-AA-A00J TCGA-AA-A00N 
       36.53        63.98        13.02        26.99        18.05         4.01 
TCGA-AA-A010 TCGA-AZ-6601 TCGA-DM-A1HB 
       34.98       100.01       135.65 

$`GOLIM4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       35.01         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  GOLIM4 MUTATED GOLIM4 WILD-TYPE 
            4.01             0.00 
  GOLIM4 MUTATED GOLIM4 WILD-TYPE 
          135.65           140.38 
  GOLIM4 MUTATED GOLIM4 WILD-TYPE 
           34.98            20.07 
[1] "4.0 - 135.7 (35.0)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.1"
D1451V2, 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       23       107         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GOLIM4 MUTATED           1          0          2          0        0
  GOLIM4 WILD-TYPE        18         10         39         31       35
                  vv
clus               STAGE IVA STAGE IVB
  GOLIM4 MUTATED           0         0
  GOLIM4 WILD-TYPE        13         1
D1451V3, multiclass
            clus
vv           GOLIM4 MUTATED GOLIM4 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               2              107
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GOLIM4 MUTATED     0   0   6   3
  GOLIM4 WILD-TYPE   9  68 242  38
D1451V4, multiclass
    clus
vv   GOLIM4 MUTATED GOLIM4 WILD-TYPE
  T1              0                9
  T2              0               68
  T3              6              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
  GOLIM4 MUTATED     6   2   1
  GOLIM4 WILD-TYPE 214  78  65
D1451V5, multiclass
    clus
vv   GOLIM4 MUTATED GOLIM4 WILD-TYPE
  N0              6              214
  N1              2               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"
D1451V6, binary
                  cls
clus                 0   1
  GOLIM4 MUTATED     9   0
  GOLIM4 WILD-TYPE 274  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GOLIM4 MUTATED      9    0
  GOLIM4 WILD-TYPE  274   48
   clus
vv  GOLIM4 MUTATED GOLIM4 WILD-TYPE
  0              9              274
  1              0               48
[1] 2 2
[1] FALSE
D1451V7, 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
D1451V8, binary
                  cls
clus                 0   1
  GOLIM4 MUTATED     6   3
  GOLIM4 WILD-TYPE 311  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GOLIM4 MUTATED      6    3
  GOLIM4 WILD-TYPE  311   45
                               clus
vv                              GOLIM4 MUTATED GOLIM4 WILD-TYPE
  COLON ADENOCARCINOMA                       6              311
  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 251   2  22  21
D1451V9, multiclass
    clus
vv   GOLIM4 MUTATED GOLIM4 WILD-TYPE
  R0              6              251
  R1              0                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"
D1451V10, 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
D1451V11, 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(1452) Variable = STK40 MUTATION ANALYSIS
D1452V1, survival
                 sevent
clus2               0   1
  STK40 MUTATED     7   0
  STK40 WILD-TYPE 275  73
  STK40 MUTATED STK40 WILD-TYPE 
              7             348 
  STK40 MUTATED STK40 WILD-TYPE 
              0              73 
$`STK40 MUTATED`
TCGA-AA-3525 TCGA-AA-3864 TCGA-AA-3949 TCGA-CK-4947 TCGA-D5-6533 TCGA-F4-6569 
        8.05        53.00        26.01        17.56         1.32        13.45 
TCGA-G4-6321 
       22.09 

$`STK40 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.33         0.10         1.35       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        13.38         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  STK40 MUTATED STK40 WILD-TYPE 
           1.32            0.00 
  STK40 MUTATED STK40 WILD-TYPE 
          53.00          140.38 
  STK40 MUTATED STK40 WILD-TYPE 
         17.560          20.235 
[1] "1.3 - 53.0 (17.6)"  "0.0 - 140.4 (20.2)"
[1] "hr="     "9200000"
D1452V2, 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       24       109         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  STK40 MUTATED           1          0          3          0        0         1
  STK40 WILD-TYPE        18         10         38         31       35        12
                 vv
clus              STAGE IVB
  STK40 MUTATED           0
  STK40 WILD-TYPE         1
D1452V3, multiclass
            clus
vv           STK40 MUTATED STK40 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              0             109
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             3              38
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 245  39
D1452V4, multiclass
    clus
vv   STK40 MUTATED STK40 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             3             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
  STK40 MUTATED     3   4   0
  STK40 WILD-TYPE 217  76  66
D1452V5, multiclass
    clus
vv   STK40 MUTATED STK40 WILD-TYPE
  N0             3             217
  N1             4              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"
D1452V6, binary
                 cls
clus                0   1
  STK40 MUTATED     6   0
  STK40 WILD-TYPE 277  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK40 MUTATED      6    0
  STK40 WILD-TYPE  277   48
   clus
vv  STK40 MUTATED STK40 WILD-TYPE
  0             6             277
  1             0              48
[1] 2 2
[1] FALSE
D1452V7, 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
D1452V8, binary
                 cls
clus                0   1
  STK40 MUTATED     6   1
  STK40 WILD-TYPE 311  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK40 MUTATED      6    1
  STK40 WILD-TYPE  311   47
                               clus
vv                              STK40 MUTATED STK40 WILD-TYPE
  COLON ADENOCARCINOMA                      6             311
  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 251   2  22  20
D1452V9, multiclass
    clus
vv   STK40 MUTATED STK40 WILD-TYPE
  R0             6             251
  R1             0               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"
D1452V10, 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
D1452V11, 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(1453) Variable = APBB1IP MUTATION ANALYSIS
D1453V1, survival
                   sevent
clus2                 0   1
  APBB1IP MUTATED    12   5
  APBB1IP WILD-TYPE 270  68
  APBB1IP MUTATED APBB1IP WILD-TYPE 
               17               338 
  APBB1IP MUTATED APBB1IP WILD-TYPE 
                5                68 
$`APBB1IP MUTATED`
TCGA-A6-4105 TCGA-AA-3510 TCGA-AA-3697 TCGA-AA-3877 TCGA-AA-3994 TCGA-AA-A00N 
       14.53        63.98        85.05        31.00        27.02         4.01 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AD-6965 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-CM-5344 
        0.72        10.88         0.20        61.41         6.77        22.03 
TCGA-D5-6534 TCGA-DM-A28E TCGA-F4-6570 TCGA-F4-6807 TCGA-G4-6628 
       43.27       119.93         6.18        16.24        52.80 

$`APBB1IP WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       27.02        29.98        18.05         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
        7.96        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21        56.55         0.79         5.79        22.42 
TCGA-AD-6963 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       27.42        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 
       83.80        22.36        62.79        49.41        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 
       13.45        35.87         1.55        16.31        29.59        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 
       91.79        46.75 

  APBB1IP MUTATED APBB1IP WILD-TYPE 
              0.2               0.0 
  APBB1IP MUTATED APBB1IP WILD-TYPE 
           119.93            140.38 
  APBB1IP MUTATED APBB1IP WILD-TYPE 
           22.030            20.155 
[1] "0.2 - 119.9 (22.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D1453V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  APBB1IP MUTATED         4        0        1         5         1         0
  APBB1IP WILD-TYPE      60        1       24       104         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  APBB1IP MUTATED           1          0          2          1        0
  APBB1IP WILD-TYPE        18         10         39         30       35
                   vv
clus                STAGE IVA STAGE IVB
  APBB1IP MUTATED           0         0
  APBB1IP WILD-TYPE        13         1
D1453V3, multiclass
            clus
vv           APBB1IP MUTATED APBB1IP WILD-TYPE
  STAGE I                  4                60
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                5               104
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               0                10
  STAGE IIIB               2                39
  STAGE IIIC               1                30
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  APBB1IP MUTATED     2   2  11   3
  APBB1IP WILD-TYPE   7  66 237  38
D1453V4, multiclass
    clus
vv   APBB1IP MUTATED APBB1IP WILD-TYPE
  T1               2                 7
  T2               2                66
  T3              11               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
  APBB1IP MUTATED    12   3   3
  APBB1IP WILD-TYPE 208  77  63
D1453V5, multiclass
    clus
vv   APBB1IP MUTATED APBB1IP WILD-TYPE
  N0              12               208
  N1               3                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"
D1453V6, binary
                   cls
clus                  0   1
  APBB1IP MUTATED    14   0
  APBB1IP WILD-TYPE 269  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  APBB1IP MUTATED     14    0
  APBB1IP WILD-TYPE  269   48
   clus
vv  APBB1IP MUTATED APBB1IP WILD-TYPE
  0              14               269
  1               0                48
[1] 2 2
[1] FALSE
D1453V7, 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
D1453V8, binary
                   cls
clus                  0   1
  APBB1IP MUTATED    14   4
  APBB1IP WILD-TYPE 303  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  APBB1IP MUTATED     14    4
  APBB1IP WILD-TYPE  303   44
                               clus
vv                              APBB1IP MUTATED APBB1IP WILD-TYPE
  COLON ADENOCARCINOMA                       14               303
  COLON MUCINOUS ADENOCARCINOMA               4                44
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  APBB1IP MUTATED    11   0   0   0
  APBB1IP WILD-TYPE 246   2  22  21
D1453V9, multiclass
    clus
vv   APBB1IP MUTATED APBB1IP WILD-TYPE
  R0              11               246
  R1               0                 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"
D1453V10, 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
D1453V11, 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(1454) Variable = ZNF232 MUTATION ANALYSIS
D1454V1, survival
                  sevent
clus2                0   1
  ZNF232 MUTATED     3   1
  ZNF232 WILD-TYPE 279  72
  ZNF232 MUTATED ZNF232 WILD-TYPE 
               4              351 
  ZNF232 MUTATED ZNF232 WILD-TYPE 
               1               72 
$`ZNF232 MUTATED`
TCGA-AZ-4315 TCGA-F4-6459 TCGA-G4-6586 TCGA-G4-6588 
       58.39         8.61        35.80        26.17 

$`ZNF232 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 
      119.93        35.97        60.79       117.07        98.24        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  ZNF232 MUTATED ZNF232 WILD-TYPE 
            8.61             0.00 
  ZNF232 MUTATED ZNF232 WILD-TYPE 
           58.39           140.38 
  ZNF232 MUTATED ZNF232 WILD-TYPE 
          30.985           20.120 
[1] "8.6 - 58.4 (31.0)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1"  
D1454V2, 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       25       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF232 MUTATED           0          0          1          0        0
  ZNF232 WILD-TYPE        19         10         40         31       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF232 MUTATED           0         0
  ZNF232 WILD-TYPE        13         1
D1454V3, multiclass
            clus
vv           ZNF232 MUTATED ZNF232 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               3              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF232 MUTATED     0   0   4   0
  ZNF232 WILD-TYPE   9  68 244  41
D1454V4, multiclass
    clus
vv   ZNF232 MUTATED ZNF232 WILD-TYPE
  T1              0                9
  T2              0               68
  T3              4              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
  ZNF232 MUTATED     3   0   1
  ZNF232 WILD-TYPE 217  80  65
D1454V5, multiclass
    clus
vv   ZNF232 MUTATED ZNF232 WILD-TYPE
  N0              3              217
  N1              0               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"
D1454V6, binary
                  cls
clus                 0   1
  ZNF232 MUTATED     4   0
  ZNF232 WILD-TYPE 279  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF232 MUTATED      4    0
  ZNF232 WILD-TYPE  279   48
   clus
vv  ZNF232 MUTATED ZNF232 WILD-TYPE
  0              4              279
  1              0               48
[1] 2 2
[1] FALSE
D1454V7, 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
D1454V8, binary
                  cls
clus                 0   1
  ZNF232 MUTATED     4   0
  ZNF232 WILD-TYPE 313  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF232 MUTATED      4    0
  ZNF232 WILD-TYPE  313   48
                               clus
vv                              ZNF232 MUTATED ZNF232 WILD-TYPE
  COLON ADENOCARCINOMA                       4              313
  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 253   2  22  21
D1454V9, multiclass
    clus
vv   ZNF232 MUTATED ZNF232 WILD-TYPE
  R0              4              253
  R1              0                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"
D1454V10, 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
D1454V11, 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(1455) Variable = RNF38 MUTATION ANALYSIS
D1455V1, survival
                 sevent
clus2               0   1
  RNF38 MUTATED     3   1
  RNF38 WILD-TYPE 279  72
  RNF38 MUTATED RNF38 WILD-TYPE 
              4             351 
  RNF38 MUTATED RNF38 WILD-TYPE 
              1              72 
$`RNF38 MUTATED`
TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-A010 TCGA-F4-6570 
       22.06        19.66        34.98         6.18 

$`RNF38 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  RNF38 MUTATED RNF38 WILD-TYPE 
           6.18            0.00 
  RNF38 MUTATED RNF38 WILD-TYPE 
          34.98          140.38 
  RNF38 MUTATED RNF38 WILD-TYPE 
          20.86           20.19 
[1] "6.2 - 35.0 (20.9)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.6"
D1455V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RNF38 MUTATED         0        0        0         2         1         0
  RNF38 WILD-TYPE      64        1       25       107         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        19         10         41         30       35        13
                 vv
clus              STAGE IVB
  RNF38 MUTATED           0
  RNF38 WILD-TYPE         1
D1455V3, multiclass
            clus
vv           RNF38 MUTATED RNF38 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              2             107
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RNF38 MUTATED     0   0   2   2
  RNF38 WILD-TYPE   9  68 246  39
D1455V4, multiclass
    clus
vv   RNF38 MUTATED RNF38 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             2             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
  RNF38 MUTATED     3   1   0
  RNF38 WILD-TYPE 217  79  66
D1455V5, multiclass
    clus
vv   RNF38 MUTATED RNF38 WILD-TYPE
  N0             3             217
  N1             1              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"
D1455V6, binary
                 cls
clus                0   1
  RNF38 MUTATED     3   0
  RNF38 WILD-TYPE 280  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF38 MUTATED      3    0
  RNF38 WILD-TYPE  280   48
   clus
vv  RNF38 MUTATED RNF38 WILD-TYPE
  0             3             280
  1             0              48
[1] 2 2
[1] FALSE
D1455V7, binary
                 cls
clus                0   1
  RNF38 MUTATED     3   1
  RNF38 WILD-TYPE 167 196
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF38 MUTATED      3    1
  RNF38 WILD-TYPE  167  196
        clus
vv       RNF38 MUTATED RNF38 WILD-TYPE
  FEMALE             3             167
  MALE               1             196
[1] 2 2
[1] FALSE
D1455V8, binary
                 cls
clus                0   1
  RNF38 MUTATED     3   1
  RNF38 WILD-TYPE 314  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF38 MUTATED      3    1
  RNF38 WILD-TYPE  314   47
                               clus
vv                              RNF38 MUTATED RNF38 WILD-TYPE
  COLON ADENOCARCINOMA                      3             314
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RNF38 MUTATED     4   0   0   0
  RNF38 WILD-TYPE 253   2  22  21
D1455V9, multiclass
    clus
vv   RNF38 MUTATED RNF38 WILD-TYPE
  R0             4             253
  R1             0               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"
D1455V10, 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     3
  RNF38 WILD-TYPE                        19   173
D1455V11, 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                                        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(1456) Variable = CTR9 MUTATION ANALYSIS
D1456V1, survival
                sevent
clus2              0   1
  CTR9 MUTATED    14   3
  CTR9 WILD-TYPE 268  70
  CTR9 MUTATED CTR9 WILD-TYPE 
            17            338 
  CTR9 MUTATED CTR9 WILD-TYPE 
             3             70 
$`CTR9 MUTATED`
TCGA-A6-5665 TCGA-A6-6137 TCGA-AA-3663 TCGA-AA-3864 TCGA-AA-3966 TCGA-AA-3971 
       22.06        27.09         6.97        53.00         2.01        16.08 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-6601 TCGA-CA-5254 TCGA-CA-6717 
        4.01        34.98        58.39       100.01         2.24         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CM-6168 TCGA-DM-A1D4 TCGA-G4-6628 
        0.10         1.35        12.99        92.75        52.80 

$`CTR9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.09        32.71        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       21.99        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CK-4947 
        3.06         3.25         3.29         0.07         0.26        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        24.43        38.20       130.65        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 
       91.79        46.75 

  CTR9 MUTATED CTR9 WILD-TYPE 
           0.1            0.0 
  CTR9 MUTATED CTR9 WILD-TYPE 
        100.01         140.38 
  CTR9 MUTATED CTR9 WILD-TYPE 
        16.080         20.235 
[1] "0.1 - 100.0 (16.1)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.4"
D1456V2, 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       22       100         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        18         10         40         31       35        13
                vv
clus             STAGE IVB
  CTR9 MUTATED           0
  CTR9 WILD-TYPE         1
D1456V3, multiclass
            clus
vv           CTR9 MUTATED CTR9 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              3             22
  STAGE IIA             9            100
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CTR9 MUTATED     0   1  14   2
  CTR9 WILD-TYPE   9  67 234  39
D1456V4, multiclass
    clus
vv   CTR9 MUTATED CTR9 WILD-TYPE
  T1            0              9
  T2            1             67
  T3           14            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
  CTR9 MUTATED    15   2   0
  CTR9 WILD-TYPE 205  78  66
D1456V5, multiclass
    clus
vv   CTR9 MUTATED CTR9 WILD-TYPE
  N0           15            205
  N1            2             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"
D1456V6, binary
                cls
clus               0   1
  CTR9 MUTATED    17   0
  CTR9 WILD-TYPE 266  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTR9 MUTATED     17    0
  CTR9 WILD-TYPE  266   48
   clus
vv  CTR9 MUTATED CTR9 WILD-TYPE
  0           17            266
  1            0             48
[1] 2 2
[1] FALSE
D1456V7, 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
D1456V8, binary
                cls
clus               0   1
  CTR9 MUTATED    14   3
  CTR9 WILD-TYPE 303  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTR9 MUTATED     14    3
  CTR9 WILD-TYPE  303   45
                               clus
vv                              CTR9 MUTATED CTR9 WILD-TYPE
  COLON ADENOCARCINOMA                    14            303
  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 248   2  22  17
D1456V9, multiclass
    clus
vv   CTR9 MUTATED CTR9 WILD-TYPE
  R0            9            248
  R1            0              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"
D1456V10, 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
D1456V11, 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(1457) Variable = FAM175A MUTATION ANALYSIS
D1457V1, survival
                   sevent
clus2                 0   1
  FAM175A MUTATED     6   2
  FAM175A WILD-TYPE 276  71
  FAM175A MUTATED FAM175A WILD-TYPE 
                8               347 
  FAM175A MUTATED FAM175A WILD-TYPE 
                2                71 
$`FAM175A MUTATED`
TCGA-A6-5664 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q TCGA-AZ-6599 TCGA-DM-A28E 
       22.09         4.01        34.98         1.02         6.77       119.93 
TCGA-G4-6309 TCGA-G4-6586 
       51.75        35.80 

$`FAM175A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41        49.41        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
        6.12        81.37        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        26.17        91.79        46.75        52.80 

  FAM175A MUTATED FAM175A WILD-TYPE 
             1.02              0.00 
  FAM175A MUTATED FAM175A WILD-TYPE 
           119.93            140.38 
  FAM175A MUTATED FAM175A WILD-TYPE 
           28.535            20.120 
[1] "1.0 - 119.9 (28.5)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1"  
D1457V2, 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       24       107         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM175A MUTATED           0          0          1          1        0
  FAM175A WILD-TYPE        19         10         40         30       35
                   vv
clus                STAGE IVA STAGE IVB
  FAM175A MUTATED           0         0
  FAM175A WILD-TYPE        13         1
D1457V3, multiclass
            clus
vv           FAM175A MUTATED FAM175A WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                2               107
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               1                30
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  FAM175A MUTATED     0   1   4   3
  FAM175A WILD-TYPE   9  67 244  38
D1457V4, multiclass
    clus
vv   FAM175A MUTATED FAM175A WILD-TYPE
  T1               0                 9
  T2               1                67
  T3               4               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
  FAM175A MUTATED     6   1   1
  FAM175A WILD-TYPE 214  79  65
D1457V5, multiclass
    clus
vv   FAM175A MUTATED FAM175A WILD-TYPE
  N0               6               214
  N1               1                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"
D1457V6, binary
                   cls
clus                  0   1
  FAM175A MUTATED     6   0
  FAM175A WILD-TYPE 277  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM175A MUTATED      6    0
  FAM175A WILD-TYPE  277   48
   clus
vv  FAM175A MUTATED FAM175A WILD-TYPE
  0               6               277
  1               0                48
[1] 2 2
[1] FALSE
D1457V7, 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
D1457V8, binary
                   cls
clus                  0   1
  FAM175A MUTATED     7   1
  FAM175A WILD-TYPE 310  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM175A MUTATED      7    1
  FAM175A WILD-TYPE  310   47
                               clus
vv                              FAM175A MUTATED FAM175A WILD-TYPE
  COLON ADENOCARCINOMA                        7               310
  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 252   2  22  21
D1457V9, multiclass
    clus
vv   FAM175A MUTATED FAM175A WILD-TYPE
  R0               5               252
  R1               0                 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"
D1457V10, 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
D1457V11, 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(1458) Variable = KIAA0528 MUTATION ANALYSIS
D1458V1, survival
                    sevent
clus2                  0   1
  KIAA0528 MUTATED    11   3
  KIAA0528 WILD-TYPE 271  70
  KIAA0528 MUTATED KIAA0528 WILD-TYPE 
                14                341 
  KIAA0528 MUTATED KIAA0528 WILD-TYPE 
                 3                 70 
$`KIAA0528 MUTATED`
TCGA-AA-3510 TCGA-AA-3543 TCGA-AA-3663 TCGA-AA-3956 TCGA-AA-3977 TCGA-AA-A010 
       63.98         0.99         6.97        34.03        25.02        34.98 
TCGA-AA-A02K TCGA-AD-6964 TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-6601 TCGA-CM-5861 
       14.01        10.88        27.09        58.39       100.01        15.02 
TCGA-CM-6165 TCGA-CM-6166 
       16.04        21.99 

$`KIAA0528 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       26.01        12.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       39.06        51.98        39.98         2.01         5.03         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       27.42         0.20        14.50        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01         5.03 
TCGA-CM-5863 TCGA-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-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       29.03        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  KIAA0528 MUTATED KIAA0528 WILD-TYPE 
              0.99               0.00 
  KIAA0528 MUTATED KIAA0528 WILD-TYPE 
            100.01             140.38 
  KIAA0528 MUTATED KIAA0528 WILD-TYPE 
            23.505             20.120 
[1] "1.0 - 100.0 (23.5)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.2"
D1458V2, 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       22       105         6         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0528 MUTATED           0          0          0          0        1
  KIAA0528 WILD-TYPE        19         10         41         31       34
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA0528 MUTATED           0         0
  KIAA0528 WILD-TYPE        13         1
D1458V3, multiclass
            clus
vv           KIAA0528 MUTATED KIAA0528 WILD-TYPE
  STAGE I                   3                 61
  STAGE IA                  0                  1
  STAGE II                  3                 22
  STAGE IIA                 4                105
  STAGE IIB                 2                  6
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                0                 10
  STAGE IIIB                0                 41
  STAGE IIIC                0                 31
  STAGE IV                  1                 34
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA0528 MUTATED     0   4   7   4
  KIAA0528 WILD-TYPE   9  64 241  37
D1458V4, multiclass
    clus
vv   KIAA0528 MUTATED KIAA0528 WILD-TYPE
  T1                0                  9
  T2                4                 64
  T3                7                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
  KIAA0528 MUTATED    13   0   2
  KIAA0528 WILD-TYPE 207  80  64
D1458V5, multiclass
    clus
vv   KIAA0528 MUTATED KIAA0528 WILD-TYPE
  N0               13                207
  N1                0                 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"
D1458V6, binary
                    cls
clus                   0   1
  KIAA0528 MUTATED    11   1
  KIAA0528 WILD-TYPE 272  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0528 MUTATED     11    1
  KIAA0528 WILD-TYPE  272   47
   clus
vv  KIAA0528 MUTATED KIAA0528 WILD-TYPE
  0               11                272
  1                1                 47
[1] 2 2
[1] FALSE
D1458V7, 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
D1458V8, binary
                    cls
clus                   0   1
  KIAA0528 MUTATED    14   1
  KIAA0528 WILD-TYPE 303  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0528 MUTATED     14    1
  KIAA0528 WILD-TYPE  303   47
                               clus
vv                              KIAA0528 MUTATED KIAA0528 WILD-TYPE
  COLON ADENOCARCINOMA                        14                303
  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 247   2  21  20
D1458V9, multiclass
    clus
vv   KIAA0528 MUTATED KIAA0528 WILD-TYPE
  R0               10                247
  R1                0                  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"
D1458V10, 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
D1458V11, 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(1459) Variable = FGD4 MUTATION ANALYSIS
D1459V1, survival
                sevent
clus2              0   1
  FGD4 MUTATED     4   0
  FGD4 WILD-TYPE 278  73
  FGD4 MUTATED FGD4 WILD-TYPE 
             4            351 
  FGD4 MUTATED FGD4 WILD-TYPE 
             0             73 
$`FGD4 MUTATED`
TCGA-CM-4746 TCGA-D5-6533 TCGA-F4-6703 TCGA-G4-6306 
       37.02         1.32        35.87        44.68 

$`FGD4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 
       13.51        11.51        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45         6.18         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        53.62        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  FGD4 MUTATED FGD4 WILD-TYPE 
          1.32           0.00 
  FGD4 MUTATED FGD4 WILD-TYPE 
         44.68         140.38 
  FGD4 MUTATED FGD4 WILD-TYPE 
        36.445         20.120 
[1] "1.3 - 44.7 (36.4)"  "0.0 - 140.4 (20.1)"
[1] "hr="     "9100000"
D1459V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FGD4 MUTATED         1        0        0         3         0         0
  FGD4 WILD-TYPE      63        1       25       106         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FGD4 MUTATED           0          0          1          0        0         0
  FGD4 WILD-TYPE        19         10         40         31       35        13
                vv
clus             STAGE IVB
  FGD4 MUTATED           0
  FGD4 WILD-TYPE         1
D1459V3, multiclass
            clus
vv           FGD4 MUTATED FGD4 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             3            106
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  FGD4 MUTATED     0   2   2   1
  FGD4 WILD-TYPE   9  66 246  40
D1459V4, multiclass
    clus
vv   FGD4 MUTATED FGD4 WILD-TYPE
  T1            0              9
  T2            2             66
  T3            2            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
  FGD4 MUTATED     5   0   0
  FGD4 WILD-TYPE 215  80  66
D1459V5, multiclass
    clus
vv   FGD4 MUTATED FGD4 WILD-TYPE
  N0            5            215
  N1            0             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"
D1459V6, binary
                cls
clus               0   1
  FGD4 MUTATED     5   0
  FGD4 WILD-TYPE 278  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  FGD4 MUTATED      5    0
  FGD4 WILD-TYPE  278   48
   clus
vv  FGD4 MUTATED FGD4 WILD-TYPE
  0            5            278
  1            0             48
[1] 2 2
[1] FALSE
D1459V7, 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
D1459V8, binary
                cls
clus               0   1
  FGD4 MUTATED     5   0
  FGD4 WILD-TYPE 312  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  FGD4 MUTATED      5    0
  FGD4 WILD-TYPE  312   48
                               clus
vv                              FGD4 MUTATED FGD4 WILD-TYPE
  COLON ADENOCARCINOMA                     5            312
  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 252   2  22  21
D1459V9, multiclass
    clus
vv   FGD4 MUTATED FGD4 WILD-TYPE
  R0            5            252
  R1            0              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"
D1459V10, 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
D1459V11, 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(1460) Variable = IRF6 MUTATION ANALYSIS
D1460V1, survival
                sevent
clus2              0   1
  IRF6 MUTATED     3   3
  IRF6 WILD-TYPE 279  70
  IRF6 MUTATED IRF6 WILD-TYPE 
             6            349 
  IRF6 MUTATED IRF6 WILD-TYPE 
             3             70 
$`IRF6 MUTATED`
TCGA-A6-6141 TCGA-AA-3510 TCGA-AA-3715 TCGA-AA-A00N TCGA-D5-5538 TCGA-DM-A1DA 
        8.38        63.98        19.04         4.01        12.26         7.50 

$`IRF6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
      140.38        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  IRF6 MUTATED IRF6 WILD-TYPE 
          4.01           0.00 
  IRF6 MUTATED IRF6 WILD-TYPE 
         63.98         140.38 
  IRF6 MUTATED IRF6 WILD-TYPE 
         10.32          20.98 
[1] "4.0 - 64.0 (10.3)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "2.9"
D1460V2, 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       23       108         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        19         10         40         30       35        13
                vv
clus             STAGE IVB
  IRF6 MUTATED           0
  IRF6 WILD-TYPE         1
D1460V3, multiclass
            clus
vv           IRF6 MUTATED IRF6 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             1            108
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            1             30
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  IRF6 MUTATED     0   0   5   1
  IRF6 WILD-TYPE   9  68 243  40
D1460V4, multiclass
    clus
vv   IRF6 MUTATED IRF6 WILD-TYPE
  T1            0              9
  T2            0             68
  T3            5            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
  IRF6 MUTATED     4   1   1
  IRF6 WILD-TYPE 216  79  65
D1460V5, multiclass
    clus
vv   IRF6 MUTATED IRF6 WILD-TYPE
  N0            4            216
  N1            1             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"
D1460V6, binary
                cls
clus               0   1
  IRF6 MUTATED     6   0
  IRF6 WILD-TYPE 277  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRF6 MUTATED      6    0
  IRF6 WILD-TYPE  277   48
   clus
vv  IRF6 MUTATED IRF6 WILD-TYPE
  0            6            277
  1            0             48
[1] 2 2
[1] FALSE
D1460V7, 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
D1460V8, binary
                cls
clus               0   1
  IRF6 MUTATED     5   1
  IRF6 WILD-TYPE 312  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRF6 MUTATED      5    1
  IRF6 WILD-TYPE  312   47
                               clus
vv                              IRF6 MUTATED IRF6 WILD-TYPE
  COLON ADENOCARCINOMA                     5            312
  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 253   2  22  21
D1460V9, multiclass
    clus
vv   IRF6 MUTATED IRF6 WILD-TYPE
  R0            4            253
  R1            0              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"
D1460V10, 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
D1460V11, 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(1461) Variable = FANCD2 MUTATION ANALYSIS
D1461V1, survival
                  sevent
clus2                0   1
  FANCD2 MUTATED     8   5
  FANCD2 WILD-TYPE 274  68
  FANCD2 MUTATED FANCD2 WILD-TYPE 
              13              342 
  FANCD2 MUTATED FANCD2 WILD-TYPE 
               5               68 
$`FANCD2 MUTATED`
TCGA-AA-3663 TCGA-AA-3715 TCGA-AA-3845 TCGA-AA-3947 TCGA-AA-A00J TCGA-AA-A00N 
        6.97        19.04         0.00        33.01        18.05         4.01 
TCGA-AA-A02F TCGA-AD-6964 TCGA-AZ-6600 TCGA-CK-4950 TCGA-D5-6532 TCGA-G4-6299 
       39.98        10.88        12.10        40.34        18.25        74.56 
TCGA-G4-6588 
       26.17 

$`FANCD2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02        14.93        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       39.06        51.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 
        0.53        35.41        19.43       107.67        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        52.80 

  FANCD2 MUTATED FANCD2 WILD-TYPE 
               0                0 
  FANCD2 MUTATED FANCD2 WILD-TYPE 
           74.56           140.38 
  FANCD2 MUTATED FANCD2 WILD-TYPE 
           18.25            20.63 
[1] "0.0 - 74.6 (18.2)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "2.1"
D1461V2, 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       23       105         5         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FANCD2 MUTATED           0          1          1          1        2
  FANCD2 WILD-TYPE        19          9         40         30       33
                  vv
clus               STAGE IVA STAGE IVB
  FANCD2 MUTATED           0         0
  FANCD2 WILD-TYPE        13         1
D1461V3, multiclass
            clus
vv           FANCD2 MUTATED FANCD2 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               4              105
  STAGE IIB               3                5
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              1                9
  STAGE IIIB              1               40
  STAGE IIIC              1               30
  STAGE IV                2               33
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FANCD2 MUTATED     0   0   9   6
  FANCD2 WILD-TYPE   9  68 239  35
D1461V4, multiclass
    clus
vv   FANCD2 MUTATED FANCD2 WILD-TYPE
  T1              0                9
  T2              0               68
  T3              9              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
  FANCD2 MUTATED     9   4   2
  FANCD2 WILD-TYPE 211  76  64
D1461V5, multiclass
    clus
vv   FANCD2 MUTATED FANCD2 WILD-TYPE
  N0              9              211
  N1              4               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"
D1461V6, binary
                  cls
clus                 0   1
  FANCD2 MUTATED    11   2
  FANCD2 WILD-TYPE 272  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FANCD2 MUTATED     11    2
  FANCD2 WILD-TYPE  272   46
   clus
vv  FANCD2 MUTATED FANCD2 WILD-TYPE
  0             11              272
  1              2               46
[1] 2 2
[1] FALSE
D1461V7, 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
D1461V8, binary
                  cls
clus                 0   1
  FANCD2 MUTATED    12   3
  FANCD2 WILD-TYPE 305  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FANCD2 MUTATED     12    3
  FANCD2 WILD-TYPE  305   45
                               clus
vv                              FANCD2 MUTATED FANCD2 WILD-TYPE
  COLON ADENOCARCINOMA                      12              305
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  FANCD2 MUTATED    10   1   1   1
  FANCD2 WILD-TYPE 247   1  21  20
D1461V9, multiclass
    clus
vv   FANCD2 MUTATED FANCD2 WILD-TYPE
  R0             10              247
  R1              1                1
  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"
D1461V10, 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
D1461V11, 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(1462) Variable = PSMD11 MUTATION ANALYSIS
D1462V1, survival
                  sevent
clus2                0   1
  PSMD11 MUTATED     6   2
  PSMD11 WILD-TYPE 276  71
  PSMD11 MUTATED PSMD11 WILD-TYPE 
               8              347 
  PSMD11 MUTATED PSMD11 WILD-TYPE 
               2               71 
$`PSMD11 MUTATED`
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-5900 TCGA-AY-5543 TCGA-CM-6161 
        4.01        34.98        35.01         0.07        15.75        15.02 
TCGA-CM-6162 TCGA-DM-A1D8 
       12.00        12.59 

$`PSMD11 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-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-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        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-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        49.91        13.32       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  PSMD11 MUTATED PSMD11 WILD-TYPE 
            0.07             0.00 
  PSMD11 MUTATED PSMD11 WILD-TYPE 
           35.01           140.38 
  PSMD11 MUTATED PSMD11 WILD-TYPE 
          13.805           20.980 
[1] "0.1 - 35.0 (13.8)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "2"  
D1462V2, 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       25       109         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PSMD11 MUTATED           1          0          1          0        0
  PSMD11 WILD-TYPE        18         10         40         31       35
                  vv
clus               STAGE IVA STAGE IVB
  PSMD11 MUTATED           1         0
  PSMD11 WILD-TYPE        12         1
D1462V3, multiclass
            clus
vv           PSMD11 MUTATED PSMD11 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               0              109
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 244  39
D1462V4, multiclass
    clus
vv   PSMD11 MUTATED PSMD11 WILD-TYPE
  T1              0                9
  T2              2               66
  T3              4              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
  PSMD11 MUTATED     4   3   1
  PSMD11 WILD-TYPE 216  77  65
D1462V5, multiclass
    clus
vv   PSMD11 MUTATED PSMD11 WILD-TYPE
  N0              4              216
  N1              3               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"
D1462V6, binary
                  cls
clus                 0   1
  PSMD11 MUTATED     5   1
  PSMD11 WILD-TYPE 278  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PSMD11 MUTATED      5    1
  PSMD11 WILD-TYPE  278   47
   clus
vv  PSMD11 MUTATED PSMD11 WILD-TYPE
  0              5              278
  1              1               47
[1] 2 2
[1] FALSE
D1462V7, 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
D1462V8, binary
                  cls
clus                 0   1
  PSMD11 MUTATED     4   4
  PSMD11 WILD-TYPE 313  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PSMD11 MUTATED      4    4
  PSMD11 WILD-TYPE  313   44
                               clus
vv                              PSMD11 MUTATED PSMD11 WILD-TYPE
  COLON ADENOCARCINOMA                       4              313
  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 250   2  22  21
D1462V9, multiclass
    clus
vv   PSMD11 MUTATED PSMD11 WILD-TYPE
  R0              7              250
  R1              0                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"
D1462V10, 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
D1462V11, 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(1463) Variable = MTOR MUTATION ANALYSIS
D1463V1, survival
                sevent
clus2              0   1
  MTOR MUTATED    26   7
  MTOR WILD-TYPE 256  66
  MTOR MUTATED MTOR WILD-TYPE 
            33            322 
  MTOR MUTATED MTOR WILD-TYPE 
             7             66 
$`MTOR MUTATED`
TCGA-A6-4105 TCGA-A6-5666 TCGA-A6-6141 TCGA-A6-6781 TCGA-AA-3555 TCGA-AA-3663 
       14.53        32.71         8.38        19.66        29.95         6.97 
TCGA-AA-3666 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3821 TCGA-AA-3854 TCGA-AA-3867 
        2.01        26.99        19.04         1.02        36.03        24.03 
TCGA-AA-3877 TCGA-AA-3949 TCGA-AA-3956 TCGA-AA-3980 TCGA-AA-A00K TCGA-AA-A010 
       31.00        26.01        34.03        27.02        18.05        34.98 
TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-6716 
       27.09        15.75        21.44        49.41       100.01         0.26 
TCGA-CM-4752 TCGA-DM-A1D4 TCGA-DM-A282 TCGA-DM-A28K TCGA-F4-6570 TCGA-F4-6806 
       13.02        92.75       139.17        98.24         6.18        29.59 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6586 
       55.04        51.75        35.80 

$`MTOR WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       22.06        27.09        22.52        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 
       21.76        24.69        24.39        23.87        20.12        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        7.04         3.02         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
       78.08         6.05        54.02        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
       36.00         5.03        85.05        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       33.04         0.99        25.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
       33.07         0.00        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        53.00        17.03        27.02        29.98        18.05 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        25.02        24.00        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95         0.20        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       135.65         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
       60.79       117.07         8.61        13.38        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
        1.55        16.31        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       44.68        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  MTOR MUTATED MTOR WILD-TYPE 
          0.26           0.00 
  MTOR MUTATED MTOR WILD-TYPE 
        139.17         140.38 
  MTOR MUTATED MTOR WILD-TYPE 
         27.02          19.79 
[1] "0.3 - 139.2 (27.0)" "0.0 - 140.4 (19.8)"
[1] "hr=" "1.3"
D1463V2, 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       21        94         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        18         10         38         30       34        12
                vv
clus             STAGE IVB
  MTOR MUTATED           0
  MTOR WILD-TYPE         1
D1463V3, multiclass
            clus
vv           MTOR MUTATED MTOR WILD-TYPE
  STAGE I               6             58
  STAGE IA              0              1
  STAGE II              4             21
  STAGE IIA            15             94
  STAGE IIB             1              7
  STAGE IIC             1              0
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            3             38
  STAGE IIIC            1             30
  STAGE IV              1             34
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  63 223  38
D1463V4, multiclass
    clus
vv   MTOR MUTATED MTOR WILD-TYPE
  T1            1              8
  T2            5             63
  T3           25            223
  T4            3             38
[1] 4 2
[1] TRUE
[1] "dimension 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  74  65
D1463V5, multiclass
    clus
vv   MTOR MUTATED MTOR WILD-TYPE
  N0           27            193
  N1            6             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"
D1463V6, binary
                cls
clus               0   1
  MTOR MUTATED    29   2
  MTOR WILD-TYPE 254  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTOR MUTATED     29    2
  MTOR WILD-TYPE  254   46
   clus
vv  MTOR MUTATED MTOR WILD-TYPE
  0           29            254
  1            2             46
[1] 2 2
[1] FALSE
D1463V7, 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
D1463V8, binary
                cls
clus               0   1
  MTOR MUTATED    27   7
  MTOR WILD-TYPE 290  41
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTOR MUTATED     27    7
  MTOR WILD-TYPE  290   41
                               clus
vv                              MTOR MUTATED MTOR WILD-TYPE
  COLON ADENOCARCINOMA                    27            290
  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 234   2  21  20
D1463V9, multiclass
    clus
vv   MTOR MUTATED MTOR WILD-TYPE
  R0           23            234
  R1            0              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"
D1463V10, 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
D1463V11, 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(1464) Variable = RNF10 MUTATION ANALYSIS
D1464V1, survival
                 sevent
clus2               0   1
  RNF10 MUTATED    12   1
  RNF10 WILD-TYPE 270  72
  RNF10 MUTATED RNF10 WILD-TYPE 
             13             342 
  RNF10 MUTATED RNF10 WILD-TYPE 
              1              72 
$`RNF10 MUTATED`
TCGA-AA-3510 TCGA-AA-3554 TCGA-AA-3815 TCGA-AA-3864 TCGA-AA-3950 TCGA-AA-A00U 
       63.98        17.95        33.04        53.00        24.00        17.03 
TCGA-AZ-4315 TCGA-CA-6717 TCGA-CM-4744 TCGA-CM-5348 TCGA-DM-A0XD TCGA-DM-A1D9 
       58.39         0.33        20.02        22.98        24.43       140.38 
TCGA-G4-6321 
       22.09 

$`RNF10 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 
       21.14         2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  RNF10 MUTATED RNF10 WILD-TYPE 
           0.33            0.00 
  RNF10 MUTATED RNF10 WILD-TYPE 
         140.38          139.17 
  RNF10 MUTATED RNF10 WILD-TYPE 
          24.00           19.99 
[1] "0.3 - 140.4 (24.0)" "0.0 - 139.2 (20.0)"
[1] "hr=" "3.9"
D1464V2, 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       23       102         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        18         10         39         31       35        13
                 vv
clus              STAGE IVB
  RNF10 MUTATED           0
  RNF10 WILD-TYPE         1
D1464V3, multiclass
            clus
vv           RNF10 MUTATED RNF10 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              7             102
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RNF10 MUTATED     0   2  11   0
  RNF10 WILD-TYPE   9  66 237  41
D1464V4, multiclass
    clus
vv   RNF10 MUTATED RNF10 WILD-TYPE
  T1             0               9
  T2             2              66
  T3            11             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
  RNF10 MUTATED    10   3   0
  RNF10 WILD-TYPE 210  77  66
D1464V5, multiclass
    clus
vv   RNF10 MUTATED RNF10 WILD-TYPE
  N0            10             210
  N1             3              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"
D1464V6, binary
                 cls
clus                0   1
  RNF10 MUTATED    12   0
  RNF10 WILD-TYPE 271  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF10 MUTATED     12    0
  RNF10 WILD-TYPE  271   48
   clus
vv  RNF10 MUTATED RNF10 WILD-TYPE
  0            12             271
  1             0              48
[1] 2 2
[1] FALSE
D1464V7, 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
D1464V8, binary
                 cls
clus                0   1
  RNF10 MUTATED    11   2
  RNF10 WILD-TYPE 306  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF10 MUTATED     11    2
  RNF10 WILD-TYPE  306   46
                               clus
vv                              RNF10 MUTATED RNF10 WILD-TYPE
  COLON ADENOCARCINOMA                     11             306
  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 247   2  22  20
D1464V9, multiclass
    clus
vv   RNF10 MUTATED RNF10 WILD-TYPE
  R0            10             247
  R1             0               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"
D1464V10, 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
D1464V11, 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(1465) Variable = KMO MUTATION ANALYSIS
D1465V1, survival
               sevent
clus2             0   1
  KMO MUTATED     8   3
  KMO WILD-TYPE 274  70
  KMO MUTATED KMO WILD-TYPE 
           11           344 
  KMO MUTATED KMO WILD-TYPE 
            3            70 
$`KMO MUTATED`
TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3877 TCGA-AA-A00N TCGA-AD-6964 
        3.02        63.98         6.97        31.00         4.01        10.88 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5914 TCGA-CM-5861 TCGA-CM-6677 
        0.33         0.10        21.99        15.02        11.08 

$`KMO WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       35.01         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       27.02        29.98        18.05         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07         0.26         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 
      102.44        40.34        15.62        49.08        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  KMO MUTATED KMO WILD-TYPE 
          0.1           0.0 
  KMO MUTATED KMO WILD-TYPE 
        63.98        140.38 
  KMO MUTATED KMO WILD-TYPE 
        10.88         20.98 
[1] "0.1 - 64.0 (10.9)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "2.1"
D1465V2, 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       22       104         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        19         10         40         31       35        13
               vv
clus            STAGE IVB
  KMO MUTATED           0
  KMO WILD-TYPE         1
D1465V3, multiclass
            clus
vv           KMO MUTATED KMO WILD-TYPE
  STAGE I              1            63
  STAGE IA             0             1
  STAGE II             3            22
  STAGE IIA            5           104
  STAGE IIB            1             7
  STAGE IIC            0             1
  STAGE III            0            19
  STAGE IIIA           0            10
  STAGE IIIB           1            40
  STAGE IIIC           0            31
  STAGE IV             0            35
  STAGE IVA            0            13
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  KMO MUTATED     1   0   8   3
  KMO WILD-TYPE   8  68 240  38
D1465V4, multiclass
    clus
vv   KMO MUTATED KMO WILD-TYPE
  T1           1             8
  T2           0            68
  T3           8           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
  KMO MUTATED    10   1   1
  KMO WILD-TYPE 210  79  65
D1465V5, multiclass
    clus
vv   KMO MUTATED KMO WILD-TYPE
  N0          10           210
  N1           1            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
  KMO MUTATED    10   0
  KMO WILD-TYPE 273  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  KMO MUTATED     10    0
  KMO WILD-TYPE  273   48
   clus
vv  KMO MUTATED KMO WILD-TYPE
  0          10           273
  1           0            48
[1] 2 2
[1] FALSE
D1465V7, 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
D1465V8, binary
               cls
clus              0   1
  KMO MUTATED     9   3
  KMO WILD-TYPE 308  45
[1] "tbl2"
               cls
clus            [,1] [,2]
  KMO MUTATED      9    3
  KMO WILD-TYPE  308   45
                               clus
vv                              KMO MUTATED KMO WILD-TYPE
  COLON ADENOCARCINOMA                    9           308
  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 249   2  22  18
D1465V9, multiclass
    clus
vv   KMO MUTATED KMO WILD-TYPE
  R0           8           249
  R1           0             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"
D1465V10, 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
D1465V11, 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(1466) Variable = CREB3 MUTATION ANALYSIS
D1466V1, survival
                 sevent
clus2               0   1
  CREB3 MUTATED     4   1
  CREB3 WILD-TYPE 278  72
  CREB3 MUTATED CREB3 WILD-TYPE 
              5             350 
  CREB3 MUTATED CREB3 WILD-TYPE 
              1              72 
$`CREB3 MUTATED`
TCGA-AA-3516 TCGA-AA-3672 TCGA-AD-6965 TCGA-AZ-4315 TCGA-D5-6535 
       13.02         0.92         0.20        58.39        15.12 

$`CREB3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        1.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        43.27        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  CREB3 MUTATED CREB3 WILD-TYPE 
            0.2             0.0 
  CREB3 MUTATED CREB3 WILD-TYPE 
          58.39          140.38 
  CREB3 MUTATED CREB3 WILD-TYPE 
          13.02           20.63 
[1] "0.2 - 58.4 (13.0)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "1.3"
D1466V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CREB3 MUTATED         0        0        0         1         0         0
  CREB3 WILD-TYPE      64        1       25       108         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CREB3 MUTATED           2          0          1          0        0         0
  CREB3 WILD-TYPE        17         10         40         31       35        13
                 vv
clus              STAGE IVB
  CREB3 MUTATED           0
  CREB3 WILD-TYPE         1
D1466V3, multiclass
            clus
vv           CREB3 MUTATED CREB3 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              1             108
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CREB3 MUTATED     0   0   4   1
  CREB3 WILD-TYPE   9  68 244  40
D1466V4, multiclass
    clus
vv   CREB3 MUTATED CREB3 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             4             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
  CREB3 MUTATED     1   2   2
  CREB3 WILD-TYPE 219  78  64
D1466V5, multiclass
    clus
vv   CREB3 MUTATED CREB3 WILD-TYPE
  N0             1             219
  N1             2              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"
D1466V6, binary
                 cls
clus                0   1
  CREB3 MUTATED     3   0
  CREB3 WILD-TYPE 280  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CREB3 MUTATED      3    0
  CREB3 WILD-TYPE  280   48
   clus
vv  CREB3 MUTATED CREB3 WILD-TYPE
  0             3             280
  1             0              48
[1] 2 2
[1] FALSE
D1466V7, binary
                 cls
clus                0   1
  CREB3 MUTATED     3   2
  CREB3 WILD-TYPE 167 195
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CREB3 MUTATED      3    2
  CREB3 WILD-TYPE  167  195
        clus
vv       CREB3 MUTATED CREB3 WILD-TYPE
  FEMALE             3             167
  MALE               2             195
[1] 2 2
[1] FALSE
D1466V8, binary
                 cls
clus                0   1
  CREB3 MUTATED     4   1
  CREB3 WILD-TYPE 313  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CREB3 MUTATED      4    1
  CREB3 WILD-TYPE  313   47
                               clus
vv                              CREB3 MUTATED CREB3 WILD-TYPE
  COLON ADENOCARCINOMA                      4             313
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CREB3 MUTATED     2   0   0   1
  CREB3 WILD-TYPE 255   2  22  20
D1466V9, multiclass
    clus
vv   CREB3 MUTATED CREB3 WILD-TYPE
  R0             2             255
  R1             0               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"
D1466V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CREB3 MUTATED                                  0     0
  CREB3 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CREB3 MUTATED                           0     3
  CREB3 WILD-TYPE                        19   173
D1466V11, multiclass
                                  clus
vv                                 CREB3 MUTATED CREB3 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 = MTIF2 MUTATION ANALYSIS
D1467V1, survival
                 sevent
clus2               0   1
  MTIF2 MUTATED     9   0
  MTIF2 WILD-TYPE 273  73
  MTIF2 MUTATED MTIF2 WILD-TYPE 
              9             346 
  MTIF2 MUTATED MTIF2 WILD-TYPE 
              0              73 
$`MTIF2 MUTATED`
TCGA-AA-3966 TCGA-AA-A010 TCGA-AA-A01R TCGA-CA-6717 TCGA-CA-6719 TCGA-CM-5861 
        2.01        34.98        35.01         0.33         1.35        15.02 
TCGA-D5-5538 TCGA-D5-6927 TCGA-G4-6628 
       12.26         9.44        52.80 

$`MTIF2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.26         0.10        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01         5.03 
TCGA-CM-5863 TCGA-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 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       35.80        26.17        91.79        46.75 

  MTIF2 MUTATED MTIF2 WILD-TYPE 
           0.33            0.00 
  MTIF2 MUTATED MTIF2 WILD-TYPE 
          52.80          140.38 
  MTIF2 MUTATED MTIF2 WILD-TYPE 
          12.26           20.63 
[1] "0.3 - 52.8 (12.3)"  "0.0 - 140.4 (20.6)"
[1] "hr="     "9200000"
D1467V2, 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       25       104         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        18         10         40         31       35        13
                 vv
clus              STAGE IVB
  MTIF2 MUTATED           0
  MTIF2 WILD-TYPE         1
D1467V3, multiclass
            clus
vv           MTIF2 MUTATED MTIF2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              5             104
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MTIF2 MUTATED     0   1   7   1
  MTIF2 WILD-TYPE   9  67 241  40
D1467V4, multiclass
    clus
vv   MTIF2 MUTATED MTIF2 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             7             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
  MTIF2 MUTATED     7   1   1
  MTIF2 WILD-TYPE 213  79  65
D1467V5, multiclass
    clus
vv   MTIF2 MUTATED MTIF2 WILD-TYPE
  N0             7             213
  N1             1              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"
D1467V6, binary
                 cls
clus                0   1
  MTIF2 MUTATED     9   0
  MTIF2 WILD-TYPE 274  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTIF2 MUTATED      9    0
  MTIF2 WILD-TYPE  274   48
   clus
vv  MTIF2 MUTATED MTIF2 WILD-TYPE
  0             9             274
  1             0              48
[1] 2 2
[1] FALSE
D1467V7, 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
D1467V8, binary
                 cls
clus                0   1
  MTIF2 MUTATED     6   3
  MTIF2 WILD-TYPE 311  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTIF2 MUTATED      6    3
  MTIF2 WILD-TYPE  311   45
                               clus
vv                              MTIF2 MUTATED MTIF2 WILD-TYPE
  COLON ADENOCARCINOMA                      6             311
  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 251   2  22  19
D1467V9, multiclass
    clus
vv   MTIF2 MUTATED MTIF2 WILD-TYPE
  R0             6             251
  R1             0               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"
D1467V10, 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
D1467V11, 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(1468) Variable = MAP3K13 MUTATION ANALYSIS
D1468V1, survival
                   sevent
clus2                 0   1
  MAP3K13 MUTATED    13   5
  MAP3K13 WILD-TYPE 269  68
  MAP3K13 MUTATED MAP3K13 WILD-TYPE 
               18               337 
  MAP3K13 MUTATED MAP3K13 WILD-TYPE 
                5                68 
$`MAP3K13 MUTATED`
TCGA-A6-6141 TCGA-A6-6653 TCGA-AA-3811 TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-3949 
        8.38        24.39        10.06        53.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-6599 TCGA-AZ-6606 
       24.00        25.02         4.01        34.98         6.77        11.74 
TCGA-CM-4746 TCGA-CM-6170 TCGA-CM-6680 TCGA-DM-A1D9 TCGA-F4-6570 TCGA-G4-6586 
       37.02        15.02        12.03       140.38         6.18        35.80 

$`MAP3K13 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        19.04        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41        49.41        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32        12.59         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      117.07        98.24         8.61        13.38        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  MAP3K13 MUTATED MAP3K13 WILD-TYPE 
             4.01              0.00 
  MAP3K13 MUTATED MAP3K13 WILD-TYPE 
           140.38            139.17 
  MAP3K13 MUTATED MAP3K13 WILD-TYPE 
           24.195            20.120 
[1] "4.0 - 140.4 (24.2)" "0.0 - 139.2 (20.1)"
[1] "hr=" "1.4"
D1468V2, 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       24       104         5         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAP3K13 MUTATED           1          0          2          0        1
  MAP3K13 WILD-TYPE        18         10         39         31       34
                   vv
clus                STAGE IVA STAGE IVB
  MAP3K13 MUTATED           0         0
  MAP3K13 WILD-TYPE        13         1
D1468V3, multiclass
            clus
vv           MAP3K13 MUTATED MAP3K13 WILD-TYPE
  STAGE I                  4                60
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                5               104
  STAGE IIB                3                 5
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               0                10
  STAGE IIIB               2                39
  STAGE IIIC               0                31
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  MAP3K13 MUTATED     0   5   9   4
  MAP3K13 WILD-TYPE   9  63 239  37
D1468V4, multiclass
    clus
vv   MAP3K13 MUTATED MAP3K13 WILD-TYPE
  T1               0                 9
  T2               5                63
  T3               9               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
  MAP3K13 MUTATED    14   1   3
  MAP3K13 WILD-TYPE 206  79  63
D1468V5, multiclass
    clus
vv   MAP3K13 MUTATED MAP3K13 WILD-TYPE
  N0              14               206
  N1               1                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"
D1468V6, binary
                   cls
clus                  0   1
  MAP3K13 MUTATED    15   1
  MAP3K13 WILD-TYPE 268  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MAP3K13 MUTATED     15    1
  MAP3K13 WILD-TYPE  268   47
   clus
vv  MAP3K13 MUTATED MAP3K13 WILD-TYPE
  0              15               268
  1               1                47
[1] 2 2
[1] FALSE
D1468V7, 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
D1468V8, binary
                   cls
clus                  0   1
  MAP3K13 MUTATED    14   4
  MAP3K13 WILD-TYPE 303  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MAP3K13 MUTATED     14    4
  MAP3K13 WILD-TYPE  303   44
                               clus
vv                              MAP3K13 MUTATED MAP3K13 WILD-TYPE
  COLON ADENOCARCINOMA                       14               303
  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 245   2  22  21
D1468V9, multiclass
    clus
vv   MAP3K13 MUTATED MAP3K13 WILD-TYPE
  R0              12               245
  R1               0                 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"
D1468V10, 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
D1468V11, 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(1469) Variable = SETD7 MUTATION ANALYSIS
D1469V1, survival
                 sevent
clus2               0   1
  SETD7 MUTATED     6   1
  SETD7 WILD-TYPE 276  72
  SETD7 MUTATED SETD7 WILD-TYPE 
              7             348 
  SETD7 MUTATED SETD7 WILD-TYPE 
              1              72 
$`SETD7 MUTATED`
TCGA-AA-3558 TCGA-AA-3663 TCGA-AA-3877 TCGA-AD-6964 TCGA-AZ-4315 TCGA-CK-4952 
       20.98         6.97        31.00        10.88        58.39        15.62 
TCGA-D5-6928 
       11.64 

$`SETD7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        18.05         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 
        0.10         1.35        17.56       102.44        40.34        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  SETD7 MUTATED SETD7 WILD-TYPE 
           6.97            0.00 
  SETD7 MUTATED SETD7 WILD-TYPE 
          58.39          140.38 
  SETD7 MUTATED SETD7 WILD-TYPE 
         15.620          20.235 
[1] "7.0 - 58.4 (15.6)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.3"
D1469V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SETD7 MUTATED         2        0        1         2         0         0
  SETD7 WILD-TYPE      62        1       24       107         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SETD7 MUTATED           1          0          0          0        0         0
  SETD7 WILD-TYPE        18         10         41         31       35        13
                 vv
clus              STAGE IVB
  SETD7 MUTATED           0
  SETD7 WILD-TYPE         1
D1469V3, multiclass
            clus
vv           SETD7 MUTATED SETD7 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              2             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SETD7 MUTATED     1   1   3   2
  SETD7 WILD-TYPE   8  67 245  39
D1469V4, multiclass
    clus
vv   SETD7 MUTATED SETD7 WILD-TYPE
  T1             1               8
  T2             1              67
  T3             3             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
  SETD7 MUTATED     5   0   2
  SETD7 WILD-TYPE 215  80  64
D1469V5, multiclass
    clus
vv   SETD7 MUTATED SETD7 WILD-TYPE
  N0             5             215
  N1             0              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"
D1469V6, binary
                 cls
clus                0   1
  SETD7 MUTATED     6   0
  SETD7 WILD-TYPE 277  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD7 MUTATED      6    0
  SETD7 WILD-TYPE  277   48
   clus
vv  SETD7 MUTATED SETD7 WILD-TYPE
  0             6             277
  1             0              48
[1] 2 2
[1] FALSE
D1469V7, binary
                 cls
clus                0   1
  SETD7 MUTATED     2   5
  SETD7 WILD-TYPE 168 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD7 MUTATED      2    5
  SETD7 WILD-TYPE  168  192
        clus
vv       SETD7 MUTATED SETD7 WILD-TYPE
  FEMALE             2             168
  MALE               5             192
[1] 2 2
[1] FALSE
D1469V8, binary
                 cls
clus                0   1
  SETD7 MUTATED     4   3
  SETD7 WILD-TYPE 313  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD7 MUTATED      4    3
  SETD7 WILD-TYPE  313   45
                               clus
vv                              SETD7 MUTATED SETD7 WILD-TYPE
  COLON ADENOCARCINOMA                      4             313
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SETD7 MUTATED     4   0   1   1
  SETD7 WILD-TYPE 253   2  21  20
D1469V9, multiclass
    clus
vv   SETD7 MUTATED SETD7 WILD-TYPE
  R0             4             253
  R1             0               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"
D1469V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SETD7 MUTATED                                  0     0
  SETD7 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SETD7 MUTATED                           0     4
  SETD7 WILD-TYPE                        19   172
D1469V11, multiclass
                                  clus
vv                                 SETD7 MUTATED SETD7 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(1470) Variable = MYST3 MUTATION ANALYSIS
D1470V1, survival
                 sevent
clus2               0   1
  MYST3 MUTATED    18   6
  MYST3 WILD-TYPE 264  67
  MYST3 MUTATED MYST3 WILD-TYPE 
             24             331 
  MYST3 MUTATED MYST3 WILD-TYPE 
              6              67 
$`MYST3 MUTATED`
TCGA-A6-5661 TCGA-A6-5665 TCGA-AA-3525 TCGA-AA-3663 TCGA-AA-3710 TCGA-AA-3949 
       33.53        22.06         8.05         6.97        26.99        26.01 
TCGA-AA-3977 TCGA-AA-3989 TCGA-AA-A00A TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q 
       25.02         7.96        38.04         4.01        34.98         1.02 
TCGA-AD-6889 TCGA-AZ-4315 TCGA-AZ-4682 TCGA-AZ-6598 TCGA-AZ-6607 TCGA-CA-6717 
       56.55        58.39        22.36        49.41         3.19         0.33 
TCGA-CM-4743 TCGA-CM-6171 TCGA-DM-A28E TCGA-G4-6303 TCGA-G4-6315 TCGA-G4-6625 
       23.05        14.04       119.93        65.85        36.72        91.79 

$`MYST3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 
        9.07        24.03        37.05        36.03        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D 
       27.02        27.02        19.07        27.02        13.94        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        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        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
        5.13        83.80        62.79        61.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 
      100.01        29.56         5.23        11.74         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28F 
      131.51       135.65       139.17         6.12        81.37        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        26.17        46.75 
TCGA-G4-6628 
       52.80 

  MYST3 MUTATED MYST3 WILD-TYPE 
           0.33            0.00 
  MYST3 MUTATED MYST3 WILD-TYPE 
         119.93          140.38 
  MYST3 MUTATED MYST3 WILD-TYPE 
         25.515          19.990 
[1] "0.3 - 119.9 (25.5)" "0.0 - 140.4 (20.0)"
[1] "hr=" "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       22        99         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        19         10         39         31       31        12
                 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              22
  STAGE IIA             10              99
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               4              31
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 229  38
D1470V4, multiclass
    clus
vv   MYST3 MUTATED MYST3 WILD-TYPE
  T1             0               9
  T2             2              66
  T3            19             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
  MYST3 MUTATED    18   4   2
  MYST3 WILD-TYPE 202  76  64
D1470V5, multiclass
    clus
vv   MYST3 MUTATED MYST3 WILD-TYPE
  N0            18             202
  N1             4              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"
D1470V6, binary
                 cls
clus                0   1
  MYST3 MUTATED    17   5
  MYST3 WILD-TYPE 266  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYST3 MUTATED     17    5
  MYST3 WILD-TYPE  266   43
   clus
vv  MYST3 MUTATED MYST3 WILD-TYPE
  0            17             266
  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   3
  MYST3 WILD-TYPE 296  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYST3 MUTATED     21    3
  MYST3 WILD-TYPE  296   45
                               clus
vv                              MYST3 MUTATED MYST3 WILD-TYPE
  COLON ADENOCARCINOMA                     21             296
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MYST3 MUTATED    17   0   1   1
  MYST3 WILD-TYPE 240   2  21  20
D1470V9, multiclass
    clus
vv   MYST3 MUTATED MYST3 WILD-TYPE
  R0            17             240
  R1             0               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"
D1470V10, 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
D1470V11, 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 = ETV1 MUTATION ANALYSIS
D1471V1, survival
                sevent
clus2              0   1
  ETV1 MUTATED     9   3
  ETV1 WILD-TYPE 273  70
  ETV1 MUTATED ETV1 WILD-TYPE 
            12            343 
  ETV1 MUTATED ETV1 WILD-TYPE 
             3             70 
$`ETV1 MUTATED`
TCGA-A6-5661 TCGA-A6-6654 TCGA-AA-3715 TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-6598 
       33.53        23.87        19.04         4.01        34.98        49.41 
TCGA-CA-6717 TCGA-CM-6677 TCGA-D5-6536 TCGA-D5-6926 TCGA-G4-6304 TCGA-G4-6628 
        0.33        11.08        17.85         9.04        53.62        52.80 

$`ETV1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 
       12.39        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-A0X9 
       13.41         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 
       46.75 

  ETV1 MUTATED ETV1 WILD-TYPE 
          0.33           0.00 
  ETV1 MUTATED ETV1 WILD-TYPE 
         53.62         140.38 
  ETV1 MUTATED ETV1 WILD-TYPE 
        21.455         20.190 
[1] "0.3 - 53.6 (21.5)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D1471V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ETV1 MUTATED         1        0        2         5         3         0
  ETV1 WILD-TYPE      63        1       23       104         5         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ETV1 MUTATED           0          1          1          0        0         0
  ETV1 WILD-TYPE        19          9         40         31       35        13
                vv
clus             STAGE IVB
  ETV1 MUTATED           0
  ETV1 WILD-TYPE         1
D1471V3, multiclass
            clus
vv           ETV1 MUTATED ETV1 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             5            104
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            1              9
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ETV1 MUTATED     0   1   8   4
  ETV1 WILD-TYPE   9  67 240  37
D1471V4, multiclass
    clus
vv   ETV1 MUTATED ETV1 WILD-TYPE
  T1            0              9
  T2            1             67
  T3            8            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
  ETV1 MUTATED    11   2   0
  ETV1 WILD-TYPE 209  78  66
D1471V5, multiclass
    clus
vv   ETV1 MUTATED ETV1 WILD-TYPE
  N0           11            209
  N1            2             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"
D1471V6, binary
                cls
clus               0   1
  ETV1 MUTATED    12   0
  ETV1 WILD-TYPE 271  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  ETV1 MUTATED     12    0
  ETV1 WILD-TYPE  271   48
   clus
vv  ETV1 MUTATED ETV1 WILD-TYPE
  0           12            271
  1            0             48
[1] 2 2
[1] FALSE
D1471V7, binary
                cls
clus               0   1
  ETV1 MUTATED     7   6
  ETV1 WILD-TYPE 163 191
[1] "tbl2"
                cls
clus             [,1] [,2]
  ETV1 MUTATED      7    6
  ETV1 WILD-TYPE  163  191
        clus
vv       ETV1 MUTATED ETV1 WILD-TYPE
  FEMALE            7            163
  MALE              6            191
[1] 2 2
[1] FALSE
D1471V8, binary
                cls
clus               0   1
  ETV1 MUTATED    11   2
  ETV1 WILD-TYPE 306  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  ETV1 MUTATED     11    2
  ETV1 WILD-TYPE  306   46
                               clus
vv                              ETV1 MUTATED ETV1 WILD-TYPE
  COLON ADENOCARCINOMA                    11            306
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ETV1 MUTATED    10   0   0   1
  ETV1 WILD-TYPE 247   2  22  20
D1471V9, multiclass
    clus
vv   ETV1 MUTATED ETV1 WILD-TYPE
  R0           10            247
  R1            0              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"
D1471V10, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ETV1 MUTATED                                  0     1
  ETV1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ETV1 MUTATED                           1     7
  ETV1 WILD-TYPE                        18   169
D1471V11, multiclass
                                  clus
vv                                 ETV1 MUTATED ETV1 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(1472) Variable = WWC3 MUTATION ANALYSIS
D1472V1, survival
                sevent
clus2              0   1
  WWC3 MUTATED    16   5
  WWC3 WILD-TYPE 266  68
  WWC3 MUTATED WWC3 WILD-TYPE 
            21            334 
  WWC3 MUTATED WWC3 WILD-TYPE 
             5             68 
$`WWC3 MUTATED`
TCGA-AA-3510 TCGA-AA-3833 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3950 TCGA-AA-A00N 
       63.98        15.95        53.00        31.00        24.00         4.01 
TCGA-AD-5900 TCGA-AZ-6608 TCGA-CA-5797 TCGA-CK-4947 TCGA-CK-5913 TCGA-CM-6171 
        0.07         1.94         3.29        17.56        51.32        14.04 
TCGA-DM-A1DA TCGA-DM-A1HB TCGA-F4-6570 TCGA-F4-6808 TCGA-G4-6304 TCGA-G4-6309 
        7.50       135.65         6.18        33.67        53.62        51.75 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 
       35.80        26.17        46.75 

$`WWC3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       17.98        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       27.02        29.98        18.05         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 
       11.74         3.19         2.24         3.06         3.25         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.33         0.10         1.35       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       65.85        44.68        55.04        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6628 
       22.09        13.78        91.79        52.80 

  WWC3 MUTATED WWC3 WILD-TYPE 
          0.07           0.00 
  WWC3 MUTATED WWC3 WILD-TYPE 
        135.65         140.38 
  WWC3 MUTATED WWC3 WILD-TYPE 
         26.17          20.07 
[1] "0.1 - 135.7 (26.2)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.1"
D1472V2, 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       23       100         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  WWC3 MUTATED           0          1          2          1        0         1
  WWC3 WILD-TYPE        19          9         39         30       35        12
                vv
clus             STAGE IVB
  WWC3 MUTATED           0
  WWC3 WILD-TYPE         1
D1472V3, multiclass
            clus
vv           WWC3 MUTATED WWC3 WILD-TYPE
  STAGE I               4             60
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             9            100
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            1              9
  STAGE IIIB            2             39
  STAGE IIIC            1             30
  STAGE IV              0             35
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  65 234  38
D1472V4, multiclass
    clus
vv   WWC3 MUTATED WWC3 WILD-TYPE
  T1            2              7
  T2            3             65
  T3           14            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
  WWC3 MUTATED    17   4   1
  WWC3 WILD-TYPE 203  76  65
D1472V5, multiclass
    clus
vv   WWC3 MUTATED WWC3 WILD-TYPE
  N0           17            203
  N1            4             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"
D1472V6, binary
                cls
clus               0   1
  WWC3 MUTATED    20   0
  WWC3 WILD-TYPE 263  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  WWC3 MUTATED     20    0
  WWC3 WILD-TYPE  263   48
   clus
vv  WWC3 MUTATED WWC3 WILD-TYPE
  0           20            263
  1            0             48
[1] 2 2
[1] FALSE
D1472V7, 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
D1472V8, binary
                cls
clus               0   1
  WWC3 MUTATED    18   4
  WWC3 WILD-TYPE 299  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  WWC3 MUTATED     18    4
  WWC3 WILD-TYPE  299   44
                               clus
vv                              WWC3 MUTATED WWC3 WILD-TYPE
  COLON ADENOCARCINOMA                    18            299
  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 240   2  22  19
D1472V9, multiclass
    clus
vv   WWC3 MUTATED WWC3 WILD-TYPE
  R0           17            240
  R1            0              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"
D1472V10, 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
D1472V11, 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(1473) Variable = SMC3 MUTATION ANALYSIS
D1473V1, survival
                sevent
clus2              0   1
  SMC3 MUTATED     7   3
  SMC3 WILD-TYPE 275  70
  SMC3 MUTATED SMC3 WILD-TYPE 
            10            345 
  SMC3 MUTATED SMC3 WILD-TYPE 
             3             70 
$`SMC3 MUTATED`
TCGA-A6-5661 TCGA-AA-A010 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-5403 
       33.53        34.98         0.79         0.72        10.88        62.79 
TCGA-CA-6717 TCGA-CA-6718 TCGA-D5-6533 TCGA-DM-A1D8 
        0.33         0.10         1.32        12.59 

$`SMC3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       56.55         5.79        22.42        27.42         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07         0.26         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       11.51        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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  SMC3 MUTATED SMC3 WILD-TYPE 
           0.1            0.0 
  SMC3 MUTATED SMC3 WILD-TYPE 
         62.79         140.38 
  SMC3 MUTATED SMC3 WILD-TYPE 
          6.10          20.98 
[1] "0.1 - 62.8 (6.1)"   "0.0 - 140.4 (21.0)"
[1] "hr=" "2.4"
D1473V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SMC3 MUTATED         0        0        1         3         1         0
  SMC3 WILD-TYPE      64        1       24       106         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SMC3 MUTATED           0          0          1          0        0         0
  SMC3 WILD-TYPE        19         10         40         31       35        13
                vv
clus             STAGE IVB
  SMC3 MUTATED           0
  SMC3 WILD-TYPE         1
D1473V3, multiclass
            clus
vv           SMC3 MUTATED SMC3 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             3            106
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SMC3 MUTATED     1   0   6   3
  SMC3 WILD-TYPE   8  68 242  38
D1473V4, multiclass
    clus
vv   SMC3 MUTATED SMC3 WILD-TYPE
  T1            1              8
  T2            0             68
  T3            6            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
  SMC3 MUTATED     7   2   1
  SMC3 WILD-TYPE 213  78  65
D1473V5, multiclass
    clus
vv   SMC3 MUTATED SMC3 WILD-TYPE
  N0            7            213
  N1            2             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"
D1473V6, binary
                cls
clus               0   1
  SMC3 MUTATED     5   0
  SMC3 WILD-TYPE 278  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMC3 MUTATED      5    0
  SMC3 WILD-TYPE  278   48
   clus
vv  SMC3 MUTATED SMC3 WILD-TYPE
  0            5            278
  1            0             48
[1] 2 2
[1] FALSE
D1473V7, binary
                cls
clus               0   1
  SMC3 MUTATED     4   6
  SMC3 WILD-TYPE 166 191
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMC3 MUTATED      4    6
  SMC3 WILD-TYPE  166  191
        clus
vv       SMC3 MUTATED SMC3 WILD-TYPE
  FEMALE            4            166
  MALE              6            191
[1] 2 2
[1] FALSE
D1473V8, binary
                cls
clus               0   1
  SMC3 MUTATED     9   1
  SMC3 WILD-TYPE 308  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMC3 MUTATED      9    1
  SMC3 WILD-TYPE  308   47
                               clus
vv                              SMC3 MUTATED SMC3 WILD-TYPE
  COLON ADENOCARCINOMA                     9            308
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SMC3 MUTATED     3   0   0   2
  SMC3 WILD-TYPE 254   2  22  19
D1473V9, multiclass
    clus
vv   SMC3 MUTATED SMC3 WILD-TYPE
  R0            3            254
  R1            0              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"
D1473V10, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SMC3 MUTATED                                  0     2
  SMC3 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SMC3 MUTATED                           1     6
  SMC3 WILD-TYPE                        18   170
D1473V11, multiclass
                                  clus
vv                                 SMC3 MUTATED SMC3 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(1474) Variable = ANKRD40 MUTATION ANALYSIS
D1474V1, survival
                   sevent
clus2                 0   1
  ANKRD40 MUTATED     5   3
  ANKRD40 WILD-TYPE 277  70
  ANKRD40 MUTATED ANKRD40 WILD-TYPE 
                8               347 
  ANKRD40 MUTATED ANKRD40 WILD-TYPE 
                3                70 
$`ANKRD40 MUTATED`
TCGA-AA-3492 TCGA-AA-3811 TCGA-AA-3821 TCGA-AA-3968 TCGA-AD-5900 TCGA-AY-6197 
        3.02        10.06         1.02        21.99         0.07        21.44 
TCGA-AZ-6598 TCGA-G4-6628 
       49.41        52.80 

$`ANKRD40 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 
       35.05        33.04         0.99        25.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       27.09        16.31         0.95        15.75         0.20        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       13.78        35.80        26.17        91.79        46.75 

  ANKRD40 MUTATED ANKRD40 WILD-TYPE 
             0.07              0.00 
  ANKRD40 MUTATED ANKRD40 WILD-TYPE 
            52.80            140.38 
  ANKRD40 MUTATED ANKRD40 WILD-TYPE 
            15.75             20.19 
[1] "0.1 - 52.8 (15.8)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2.2"
D1474V2, 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       23       108         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANKRD40 MUTATED           1          0          0          0        0
  ANKRD40 WILD-TYPE        18         10         41         31       35
                   vv
clus                STAGE IVA STAGE IVB
  ANKRD40 MUTATED           0         0
  ANKRD40 WILD-TYPE        13         1
D1474V3, multiclass
            clus
vv           ANKRD40 MUTATED ANKRD40 WILD-TYPE
  STAGE I                  4                60
  STAGE IA                 0                 1
  STAGE II                 2                23
  STAGE IIA                1               108
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ANKRD40 MUTATED     0   4   4   0
  ANKRD40 WILD-TYPE   9  64 244  41
D1474V4, multiclass
    clus
vv   ANKRD40 MUTATED ANKRD40 WILD-TYPE
  T1               0                 9
  T2               4                64
  T3               4               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
  ANKRD40 MUTATED     7   0   1
  ANKRD40 WILD-TYPE 213  80  65
D1474V5, multiclass
    clus
vv   ANKRD40 MUTATED ANKRD40 WILD-TYPE
  N0               7               213
  N1               0                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"
D1474V6, binary
                   cls
clus                  0   1
  ANKRD40 MUTATED     5   0
  ANKRD40 WILD-TYPE 278  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD40 MUTATED      5    0
  ANKRD40 WILD-TYPE  278   48
   clus
vv  ANKRD40 MUTATED ANKRD40 WILD-TYPE
  0               5               278
  1               0                48
[1] 2 2
[1] FALSE
D1474V7, 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
D1474V8, binary
                   cls
clus                  0   1
  ANKRD40 MUTATED     6   2
  ANKRD40 WILD-TYPE 311  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD40 MUTATED      6    2
  ANKRD40 WILD-TYPE  311   46
                               clus
vv                              ANKRD40 MUTATED ANKRD40 WILD-TYPE
  COLON ADENOCARCINOMA                        6               311
  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 250   2  22  21
D1474V9, multiclass
    clus
vv   ANKRD40 MUTATED ANKRD40 WILD-TYPE
  R0               7               250
  R1               0                 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"
D1474V10, 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
D1474V11, 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(1475) Variable = STAT3 MUTATION ANALYSIS
D1475V1, survival
                 sevent
clus2               0   1
  STAT3 MUTATED     8   1
  STAT3 WILD-TYPE 274  72
  STAT3 MUTATED STAT3 WILD-TYPE 
              9             346 
  STAT3 MUTATED STAT3 WILD-TYPE 
              1              72 
$`STAT3 MUTATED`
TCGA-AA-3510 TCGA-AA-A010 TCGA-AD-5900 TCGA-AU-3779 TCGA-D5-6532 TCGA-D5-6536 
       63.98        34.98         0.07        14.50        18.25        17.85 
TCGA-DM-A1HA TCGA-F4-6570 TCGA-G4-6628 
      131.51         6.18        52.80 

$`STAT3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.20        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        15.12         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.38        13.45        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       35.80        26.17        91.79        46.75 

  STAT3 MUTATED STAT3 WILD-TYPE 
           0.07            0.00 
  STAT3 MUTATED STAT3 WILD-TYPE 
         131.51          140.38 
  STAT3 MUTATED STAT3 WILD-TYPE 
         18.250          20.235 
[1] "0.1 - 131.5 (18.2)" "0.0 - 140.4 (20.2)"
[1] "hr=" "2.7"
D1475V2, 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       24       105         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        19         10         41         30       35        13
                 vv
clus              STAGE IVB
  STAT3 MUTATED           0
  STAT3 WILD-TYPE         1
D1475V3, multiclass
            clus
vv           STAT3 MUTATED STAT3 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              4             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  STAT3 MUTATED     0   2   6   1
  STAT3 WILD-TYPE   9  66 242  40
D1475V4, multiclass
    clus
vv   STAT3 MUTATED STAT3 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             6             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
  STAT3 MUTATED     8   0   1
  STAT3 WILD-TYPE 212  80  65
D1475V5, multiclass
    clus
vv   STAT3 MUTATED STAT3 WILD-TYPE
  N0             8             212
  N1             0              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"
D1475V6, binary
                 cls
clus                0   1
  STAT3 MUTATED     8   0
  STAT3 WILD-TYPE 275  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAT3 MUTATED      8    0
  STAT3 WILD-TYPE  275   48
   clus
vv  STAT3 MUTATED STAT3 WILD-TYPE
  0             8             275
  1             0              48
[1] 2 2
[1] FALSE
D1475V7, 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
D1475V8, binary
                 cls
clus                0   1
  STAT3 MUTATED     8   1
  STAT3 WILD-TYPE 309  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAT3 MUTATED      8    1
  STAT3 WILD-TYPE  309   47
                               clus
vv                              STAT3 MUTATED STAT3 WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  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 249   2  22  21
D1475V9, multiclass
    clus
vv   STAT3 MUTATED STAT3 WILD-TYPE
  R0             8             249
  R1             0               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"
D1475V10, 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
D1475V11, 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(1476) Variable = WFDC10B MUTATION ANALYSIS
D1476V1, survival
                   sevent
clus2                 0   1
  WFDC10B MUTATED     4   1
  WFDC10B WILD-TYPE 278  72
  WFDC10B MUTATED WFDC10B WILD-TYPE 
                5               350 
  WFDC10B MUTATED WFDC10B WILD-TYPE 
                1                72 
$`WFDC10B MUTATED`
TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-F4-6459 TCGA-G4-6588 
       11.01        13.05        11.08         8.61        26.17 

$`WFDC10B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79       117.07        98.24        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  WFDC10B MUTATED WFDC10B WILD-TYPE 
             8.61              0.00 
  WFDC10B MUTATED WFDC10B WILD-TYPE 
            26.17            140.38 
  WFDC10B MUTATED WFDC10B WILD-TYPE 
            11.08             20.63 
[1] "8.6 - 26.2 (11.1)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "1.6"
D1476V2, 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       25       108         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  WFDC10B MUTATED           0          0          2          0        0
  WFDC10B WILD-TYPE        19         10         39         31       35
                   vv
clus                STAGE IVA STAGE IVB
  WFDC10B MUTATED           0         1
  WFDC10B WILD-TYPE        13         0
D1476V3, multiclass
            clus
vv           WFDC10B MUTATED WFDC10B WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                1               108
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               2                39
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  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  67 244  41
D1476V4, multiclass
    clus
vv   WFDC10B MUTATED WFDC10B WILD-TYPE
  T1               0                 9
  T2               1                67
  T3               4               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
  WFDC10B MUTATED     2   1   2
  WFDC10B WILD-TYPE 218  79  64
D1476V5, multiclass
    clus
vv   WFDC10B MUTATED WFDC10B WILD-TYPE
  N0               2               218
  N1               1                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"
D1476V6, binary
                   cls
clus                  0   1
  WFDC10B MUTATED     4   1
  WFDC10B WILD-TYPE 279  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  WFDC10B MUTATED      4    1
  WFDC10B WILD-TYPE  279   47
   clus
vv  WFDC10B MUTATED WFDC10B WILD-TYPE
  0               4               279
  1               1                47
[1] 2 2
[1] FALSE
D1476V7, 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
D1476V8, binary
                   cls
clus                  0   1
  WFDC10B MUTATED     5   0
  WFDC10B WILD-TYPE 312  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  WFDC10B MUTATED      5    0
  WFDC10B WILD-TYPE  312   48
                               clus
vv                              WFDC10B MUTATED WFDC10B WILD-TYPE
  COLON ADENOCARCINOMA                        5               312
  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 252   2  22  21
D1476V9, multiclass
    clus
vv   WFDC10B MUTATED WFDC10B WILD-TYPE
  R0               5               252
  R1               0                 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"
D1476V10, 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
D1476V11, 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(1477) Variable = OR10T2 MUTATION ANALYSIS
D1477V1, survival
                  sevent
clus2                0   1
  OR10T2 MUTATED     6   2
  OR10T2 WILD-TYPE 276  71
  OR10T2 MUTATED OR10T2 WILD-TYPE 
               8              347 
  OR10T2 MUTATED OR10T2 WILD-TYPE 
               2               71 
$`OR10T2 MUTATED`
TCGA-AA-3492 TCGA-AA-3542 TCGA-AA-3713 TCGA-AA-3977 TCGA-CA-6717 TCGA-CM-6163 
        3.02        12.99        19.04        25.02         0.33        14.04 
TCGA-D5-6536 TCGA-DM-A0XF 
       17.85        38.20 

$`OR10T2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       26.01         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38        10.26       119.70        24.43       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  OR10T2 MUTATED OR10T2 WILD-TYPE 
            0.33             0.00 
  OR10T2 MUTATED OR10T2 WILD-TYPE 
           38.20           140.38 
  OR10T2 MUTATED OR10T2 WILD-TYPE 
          15.945           20.980 
[1] "0.3 - 38.2 (15.9)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.8"
D1477V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR10T2 MUTATED         1        0        1         2         0         0
  OR10T2 WILD-TYPE      63        1       24       107         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR10T2 MUTATED           0          0          0          2        1
  OR10T2 WILD-TYPE        19         10         41         29       34
                  vv
clus               STAGE IVA STAGE IVB
  OR10T2 MUTATED           0         0
  OR10T2 WILD-TYPE        13         1
D1477V3, multiclass
            clus
vv           OR10T2 MUTATED OR10T2 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               2              107
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              2               29
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  OR10T2 MUTATED     1   1   6   0
  OR10T2 WILD-TYPE   8  67 242  41
D1477V4, multiclass
    clus
vv   OR10T2 MUTATED OR10T2 WILD-TYPE
  T1              1                8
  T2              1               67
  T3              6              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
  OR10T2 MUTATED     6   0   2
  OR10T2 WILD-TYPE 214  80  64
D1477V5, multiclass
    clus
vv   OR10T2 MUTATED OR10T2 WILD-TYPE
  N0              6              214
  N1              0               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"
D1477V6, binary
                  cls
clus                 0   1
  OR10T2 MUTATED     6   1
  OR10T2 WILD-TYPE 277  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR10T2 MUTATED      6    1
  OR10T2 WILD-TYPE  277   47
   clus
vv  OR10T2 MUTATED OR10T2 WILD-TYPE
  0              6              277
  1              1               47
[1] 2 2
[1] FALSE
D1477V7, binary
                  cls
clus                 0   1
  OR10T2 MUTATED     2   6
  OR10T2 WILD-TYPE 168 191
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR10T2 MUTATED      2    6
  OR10T2 WILD-TYPE  168  191
        clus
vv       OR10T2 MUTATED OR10T2 WILD-TYPE
  FEMALE              2              168
  MALE                6              191
[1] 2 2
[1] FALSE
D1477V8, binary
                  cls
clus                 0   1
  OR10T2 MUTATED     6   2
  OR10T2 WILD-TYPE 311  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR10T2 MUTATED      6    2
  OR10T2 WILD-TYPE  311   46
                               clus
vv                              OR10T2 MUTATED OR10T2 WILD-TYPE
  COLON ADENOCARCINOMA                       6              311
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  OR10T2 MUTATED     4   0   1   1
  OR10T2 WILD-TYPE 253   2  21  20
D1477V9, multiclass
    clus
vv   OR10T2 MUTATED OR10T2 WILD-TYPE
  R0              4              253
  R1              0                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"
D1477V10, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR10T2 MUTATED                                  0     1
  OR10T2 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  OR10T2 MUTATED                           0     3
  OR10T2 WILD-TYPE                        19   173
D1477V11, multiclass
                                  clus
vv                                 OR10T2 MUTATED OR10T2 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(1478) Variable = KIAA0415 MUTATION ANALYSIS
D1478V1, survival
                    sevent
clus2                  0   1
  KIAA0415 MUTATED    10   2
  KIAA0415 WILD-TYPE 272  71
  KIAA0415 MUTATED KIAA0415 WILD-TYPE 
                12                343 
  KIAA0415 MUTATED KIAA0415 WILD-TYPE 
                 2                 71 
$`KIAA0415 MUTATED`
TCGA-A6-6653 TCGA-AA-3663 TCGA-AA-3811 TCGA-AD-6889 TCGA-AD-6895 TCGA-AY-6197 
       24.39         6.97        10.06        56.55         0.72        21.44 
TCGA-CA-6717 TCGA-CK-5916 TCGA-CM-6674 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6628 
        0.33        21.14        12.95        53.62        51.75        52.80 

$`KIAA0415 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        19.04        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37         4.21         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       27.09        16.31         0.95        15.75         0.20        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       74.56        65.85        44.68        55.04        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 
       46.75 

  KIAA0415 MUTATED KIAA0415 WILD-TYPE 
              0.33               0.00 
  KIAA0415 MUTATED KIAA0415 WILD-TYPE 
             56.55             140.38 
  KIAA0415 MUTATED KIAA0415 WILD-TYPE 
             21.29              20.12 
[1] "0.3 - 56.5 (21.3)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.4"
D1478V2, 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       24       105         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0415 MUTATED           1          0          1          0        0
  KIAA0415 WILD-TYPE        18         10         40         31       35
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA0415 MUTATED           0         0
  KIAA0415 WILD-TYPE        13         1
D1478V3, multiclass
            clus
vv           KIAA0415 MUTATED KIAA0415 WILD-TYPE
  STAGE I                   3                 61
  STAGE IA                  0                  1
  STAGE II                  1                 24
  STAGE IIA                 4                105
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 1                 18
  STAGE IIIA                0                 10
  STAGE IIIB                1                 40
  STAGE IIIC                0                 31
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA0415 MUTATED     1   2   8   1
  KIAA0415 WILD-TYPE   8  66 240  40
D1478V4, multiclass
    clus
vv   KIAA0415 MUTATED KIAA0415 WILD-TYPE
  T1                1                  8
  T2                2                 66
  T3                8                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
  KIAA0415 MUTATED     9   2   1
  KIAA0415 WILD-TYPE 211  78  65
D1478V5, multiclass
    clus
vv   KIAA0415 MUTATED KIAA0415 WILD-TYPE
  N0                9                211
  N1                2                 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"
D1478V6, binary
                    cls
clus                   0   1
  KIAA0415 MUTATED    10   0
  KIAA0415 WILD-TYPE 273  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0415 MUTATED     10    0
  KIAA0415 WILD-TYPE  273   48
   clus
vv  KIAA0415 MUTATED KIAA0415 WILD-TYPE
  0               10                273
  1                0                 48
[1] 2 2
[1] FALSE
D1478V7, 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
D1478V8, binary
                    cls
clus                   0   1
  KIAA0415 MUTATED    11   1
  KIAA0415 WILD-TYPE 306  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0415 MUTATED     11    1
  KIAA0415 WILD-TYPE  306   47
                               clus
vv                              KIAA0415 MUTATED KIAA0415 WILD-TYPE
  COLON ADENOCARCINOMA                        11                306
  COLON MUCINOUS ADENOCARCINOMA                1                 47
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  KIAA0415 MUTATED     7   0   0   2
  KIAA0415 WILD-TYPE 250   2  22  19
D1478V9, multiclass
    clus
vv   KIAA0415 MUTATED KIAA0415 WILD-TYPE
  R0                7                250
  R1                0                  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"
D1478V10, 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
D1478V11, 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(1479) Variable = CD79A MUTATION ANALYSIS
D1479V1, survival
                 sevent
clus2               0   1
  CD79A MUTATED     5   1
  CD79A WILD-TYPE 277  72
  CD79A MUTATED CD79A WILD-TYPE 
              6             349 
  CD79A MUTATED CD79A WILD-TYPE 
              1              72 
$`CD79A MUTATED`
TCGA-A6-2676 TCGA-AA-3864 TCGA-AA-3947 TCGA-CM-4743 TCGA-CM-6169 TCGA-CM-6680 
       42.90        53.00        33.01        23.05        13.02        12.03 

$`CD79A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-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-D5-5537 TCGA-D5-5538 
       11.08        11.08        11.01        10.06        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  CD79A MUTATED CD79A WILD-TYPE 
          12.03            0.00 
  CD79A MUTATED CD79A WILD-TYPE 
          53.00          140.38 
  CD79A MUTATED CD79A WILD-TYPE 
          28.03           20.12 
[1] "12.0 - 53.0 (28.0)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.4"
D1479V2, 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       24       107         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        19         10         40         31       35        13
                 vv
clus              STAGE IVB
  CD79A MUTATED           0
  CD79A WILD-TYPE         1
D1479V3, multiclass
            clus
vv           CD79A MUTATED CD79A WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              2             107
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CD79A MUTATED     0   0   4   2
  CD79A WILD-TYPE   9  68 244  39
D1479V4, multiclass
    clus
vv   CD79A MUTATED CD79A WILD-TYPE
  T1             0               9
  T2             0              68
  T3             4             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
  CD79A MUTATED     5   0   1
  CD79A WILD-TYPE 215  80  65
D1479V5, multiclass
    clus
vv   CD79A MUTATED CD79A WILD-TYPE
  N0             5             215
  N1             0              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"
D1479V6, binary
                 cls
clus                0   1
  CD79A MUTATED     6   0
  CD79A WILD-TYPE 277  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD79A MUTATED      6    0
  CD79A WILD-TYPE  277   48
   clus
vv  CD79A MUTATED CD79A WILD-TYPE
  0             6             277
  1             0              48
[1] 2 2
[1] FALSE
D1479V7, 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
D1479V8, binary
                 cls
clus                0   1
  CD79A MUTATED     5   1
  CD79A WILD-TYPE 312  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD79A MUTATED      5    1
  CD79A WILD-TYPE  312   47
                               clus
vv                              CD79A MUTATED CD79A WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  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 251   2  22  21
D1479V9, multiclass
    clus
vv   CD79A MUTATED CD79A WILD-TYPE
  R0             6             251
  R1             0               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"
D1479V10, 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
D1479V11, 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(1480) Variable = HCFC1R1 MUTATION ANALYSIS
D1480V1, survival
                   sevent
clus2                 0   1
  HCFC1R1 MUTATED     3   2
  HCFC1R1 WILD-TYPE 279  71
  HCFC1R1 MUTATED HCFC1R1 WILD-TYPE 
                5               350 
  HCFC1R1 MUTATED HCFC1R1 WILD-TYPE 
                2                71 
$`HCFC1R1 MUTATED`
TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3845 TCGA-DM-A1D7 TCGA-G4-6586 
       22.06        19.66         0.00        13.32        35.80 

$`HCFC1R1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02        14.93        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  HCFC1R1 MUTATED HCFC1R1 WILD-TYPE 
                0                 0 
  HCFC1R1 MUTATED HCFC1R1 WILD-TYPE 
            35.80            140.38 
  HCFC1R1 MUTATED HCFC1R1 WILD-TYPE 
           19.660            20.235 
[1] "0.0 - 35.8 (19.7)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2.9"
D1480V2, 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       25       105         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HCFC1R1 MUTATED           0          0          0          1        0
  HCFC1R1 WILD-TYPE        19         10         41         30       35
                   vv
clus                STAGE IVA STAGE IVB
  HCFC1R1 MUTATED           0         0
  HCFC1R1 WILD-TYPE        13         1
D1480V3, multiclass
            clus
vv           HCFC1R1 MUTATED HCFC1R1 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                4               105
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               1                30
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  HCFC1R1 MUTATED     0   0   4   1
  HCFC1R1 WILD-TYPE   9  68 244  40
D1480V4, multiclass
    clus
vv   HCFC1R1 MUTATED HCFC1R1 WILD-TYPE
  T1               0                 9
  T2               0                68
  T3               4               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
  HCFC1R1 MUTATED     4   1   0
  HCFC1R1 WILD-TYPE 216  79  66
D1480V5, multiclass
    clus
vv   HCFC1R1 MUTATED HCFC1R1 WILD-TYPE
  N0               4               216
  N1               1                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"
D1480V6, binary
                   cls
clus                  0   1
  HCFC1R1 MUTATED     4   0
  HCFC1R1 WILD-TYPE 279  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HCFC1R1 MUTATED      4    0
  HCFC1R1 WILD-TYPE  279   48
   clus
vv  HCFC1R1 MUTATED HCFC1R1 WILD-TYPE
  0               4               279
  1               0                48
[1] 2 2
[1] FALSE
D1480V7, 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
D1480V8, binary
                   cls
clus                  0   1
  HCFC1R1 MUTATED     4   1
  HCFC1R1 WILD-TYPE 313  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HCFC1R1 MUTATED      4    1
  HCFC1R1 WILD-TYPE  313   47
                               clus
vv                              HCFC1R1 MUTATED HCFC1R1 WILD-TYPE
  COLON ADENOCARCINOMA                        4               313
  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 253   2  22  21
D1480V9, multiclass
    clus
vv   HCFC1R1 MUTATED HCFC1R1 WILD-TYPE
  R0               4               253
  R1               0                 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"
D1480V10, 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
D1480V11, 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(1481) Variable = GPR113 MUTATION ANALYSIS
D1481V1, survival
                  sevent
clus2                0   1
  GPR113 MUTATED    12   1
  GPR113 WILD-TYPE 270  72
  GPR113 MUTATED GPR113 WILD-TYPE 
              13              342 
  GPR113 MUTATED GPR113 WILD-TYPE 
               1               72 
$`GPR113 MUTATED`
TCGA-A6-5661 TCGA-AA-3510 TCGA-AA-3519 TCGA-AA-3663 TCGA-AA-3710 TCGA-AA-3877 
       33.53        63.98         9.07         6.97        26.99        31.00 
TCGA-AA-3966 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CK-4952 TCGA-CM-4743 TCGA-D5-6532 
        2.01       100.01         0.33        15.62        23.05        18.25 
TCGA-D5-6928 
       11.64 

$`GPR113 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       40.34        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  GPR113 MUTATED GPR113 WILD-TYPE 
            0.33             0.00 
  GPR113 MUTATED GPR113 WILD-TYPE 
          100.01           140.38 
  GPR113 MUTATED GPR113 WILD-TYPE 
          18.250           20.235 
[1] "0.3 - 100.0 (18.2)" "0.0 - 140.4 (20.2)"
[1] "hr=" "2.9"
D1481V2, 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       22       102         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPR113 MUTATED           2          0          0          0        0
  GPR113 WILD-TYPE        17         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  GPR113 MUTATED           0         0
  GPR113 WILD-TYPE        13         1
D1481V3, multiclass
            clus
vv           GPR113 MUTATED GPR113 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                3               22
  STAGE IIA               7              102
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               2               17
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GPR113 MUTATED     1   0  11   2
  GPR113 WILD-TYPE   8  68 237  39
D1481V4, multiclass
    clus
vv   GPR113 MUTATED GPR113 WILD-TYPE
  T1              1                8
  T2              0               68
  T3             11              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
  GPR113 MUTATED    12   1   1
  GPR113 WILD-TYPE 208  79  65
D1481V5, multiclass
    clus
vv   GPR113 MUTATED GPR113 WILD-TYPE
  N0             12              208
  N1              1               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"
D1481V6, binary
                  cls
clus                 0   1
  GPR113 MUTATED    13   0
  GPR113 WILD-TYPE 270  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR113 MUTATED     13    0
  GPR113 WILD-TYPE  270   48
   clus
vv  GPR113 MUTATED GPR113 WILD-TYPE
  0             13              270
  1              0               48
[1] 2 2
[1] FALSE
D1481V7, 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
D1481V8, binary
                  cls
clus                 0   1
  GPR113 MUTATED     9   5
  GPR113 WILD-TYPE 308  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR113 MUTATED      9    5
  GPR113 WILD-TYPE  308   43
                               clus
vv                              GPR113 MUTATED GPR113 WILD-TYPE
  COLON ADENOCARCINOMA                       9              308
  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 248   2  22  18
D1481V9, multiclass
    clus
vv   GPR113 MUTATED GPR113 WILD-TYPE
  R0              9              248
  R1              0                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"
D1481V10, 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
D1481V11, 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(1482) Variable = HIST1H4L MUTATION ANALYSIS
D1482V1, survival
                    sevent
clus2                  0   1
  HIST1H4L MUTATED     3   3
  HIST1H4L WILD-TYPE 279  70
  HIST1H4L MUTATED HIST1H4L WILD-TYPE 
                 6                349 
  HIST1H4L MUTATED HIST1H4L WILD-TYPE 
                 3                 70 
$`HIST1H4L MUTATED`
TCGA-A6-6142 TCGA-AA-3715 TCGA-CK-5916 TCGA-CM-6170 TCGA-DM-A1D6 TCGA-G4-6586 
       25.08        19.04        21.14        15.02        49.91        35.80 

$`HIST1H4L WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43        38.20       130.65        92.75        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  HIST1H4L MUTATED HIST1H4L WILD-TYPE 
             15.02               0.00 
  HIST1H4L MUTATED HIST1H4L WILD-TYPE 
             49.91             140.38 
  HIST1H4L MUTATED HIST1H4L WILD-TYPE 
             23.11              20.12 
[1] "15.0 - 49.9 (23.1)" "0.0 - 140.4 (20.1)"
[1] "hr=" "2.3"
D1482V2, 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       24       107         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HIST1H4L MUTATED           0          0          0          0        0
  HIST1H4L WILD-TYPE        19         10         41         31       35
                    vv
clus                 STAGE IVA STAGE IVB
  HIST1H4L MUTATED           1         0
  HIST1H4L WILD-TYPE        12         1
D1482V3, multiclass
            clus
vv           HIST1H4L MUTATED HIST1H4L WILD-TYPE
  STAGE I                   2                 62
  STAGE IA                  0                  1
  STAGE II                  1                 24
  STAGE IIA                 2                107
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                0                 10
  STAGE IIIB                0                 41
  STAGE IIIC                0                 31
  STAGE IV                  0                 35
  STAGE IVA                 1                 12
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 244  41
D1482V4, multiclass
    clus
vv   HIST1H4L MUTATED HIST1H4L WILD-TYPE
  T1                1                  8
  T2                1                 67
  T3                4                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
  HIST1H4L MUTATED     5   1   0
  HIST1H4L WILD-TYPE 215  79  66
D1482V5, multiclass
    clus
vv   HIST1H4L MUTATED HIST1H4L WILD-TYPE
  N0                5                215
  N1                1                 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"
D1482V6, binary
                    cls
clus                   0   1
  HIST1H4L MUTATED     5   1
  HIST1H4L WILD-TYPE 278  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H4L MUTATED      5    1
  HIST1H4L WILD-TYPE  278   47
   clus
vv  HIST1H4L MUTATED HIST1H4L WILD-TYPE
  0                5                278
  1                1                 47
[1] 2 2
[1] FALSE
D1482V7, 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
D1482V8, binary
                    cls
clus                   0   1
  HIST1H4L MUTATED     5   1
  HIST1H4L WILD-TYPE 312  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H4L MUTATED      5    1
  HIST1H4L WILD-TYPE  312   47
                               clus
vv                              HIST1H4L MUTATED HIST1H4L WILD-TYPE
  COLON ADENOCARCINOMA                         5                312
  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 254   2  22  20
D1482V9, multiclass
    clus
vv   HIST1H4L MUTATED HIST1H4L WILD-TYPE
  R0                3                254
  R1                0                  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"
D1482V10, 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
D1482V11, 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(1483) Variable = GRIN2B MUTATION ANALYSIS
D1483V1, survival
                  sevent
clus2                0   1
  GRIN2B MUTATED    17   8
  GRIN2B WILD-TYPE 265  65
  GRIN2B MUTATED GRIN2B WILD-TYPE 
              25              330 
  GRIN2B MUTATED GRIN2B WILD-TYPE 
               8               65 
$`GRIN2B MUTATED`
TCGA-A6-5661 TCGA-AA-3492 TCGA-AA-3511 TCGA-AA-3660 TCGA-AA-3833 TCGA-AA-3977 
       33.53         3.02         6.97        78.08        15.95        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q TCGA-AD-6901 TCGA-AD-6964 TCGA-AU-3779 
        4.01        34.98         1.02        22.42        10.88        14.50 
TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4950 TCGA-CK-4952 
       49.41       100.01         0.33         0.10        40.34        15.62 
TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6931 TCGA-DM-A1D4 TCGA-DM-A28G 
       16.14        12.39        10.13        12.00        92.75        60.79 
TCGA-G4-6586 
       35.80 

$`GRIN2B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 
        0.99        25.02         1.02        17.98        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 
        0.79         0.72         5.79        27.42         0.20        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       61.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-5912 
        0.07         0.26         1.35        17.56       102.44        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 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         1.51        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43        38.20       130.65        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K 
        6.12        81.37       119.93        35.97       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        26.17        91.79        46.75        52.80 

  GRIN2B MUTATED GRIN2B WILD-TYPE 
             0.1              0.0 
  GRIN2B MUTATED GRIN2B WILD-TYPE 
          100.01           140.38 
  GRIN2B MUTATED GRIN2B WILD-TYPE 
           15.95            20.63 
[1] "0.1 - 100.0 (15.9)" "0.0 - 140.4 (20.6)"
[1] "hr=" "1.5"
D1483V2, 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       18       100         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GRIN2B MUTATED           1          2          0          1        0
  GRIN2B WILD-TYPE        18          8         41         30       35
                  vv
clus               STAGE IVA STAGE IVB
  GRIN2B MUTATED           0         0
  GRIN2B WILD-TYPE        13         1
D1483V3, multiclass
            clus
vv           GRIN2B MUTATED GRIN2B WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                7               18
  STAGE IIA               9              100
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              2                8
  STAGE IIIB              0               41
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GRIN2B MUTATED     0   2  17   7
  GRIN2B WILD-TYPE   9  66 231  34
D1483V4, multiclass
    clus
vv   GRIN2B MUTATED GRIN2B WILD-TYPE
  T1              0                9
  T2              2               66
  T3             17              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
  GRIN2B MUTATED    21   2   3
  GRIN2B WILD-TYPE 199  78  63
D1483V5, multiclass
    clus
vv   GRIN2B MUTATED GRIN2B WILD-TYPE
  N0             21              199
  N1              2               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"
D1483V6, binary
                  cls
clus                 0   1
  GRIN2B MUTATED    22   0
  GRIN2B WILD-TYPE 261  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GRIN2B MUTATED     22    0
  GRIN2B WILD-TYPE  261   48
   clus
vv  GRIN2B MUTATED GRIN2B WILD-TYPE
  0             22              261
  1              0               48
[1] 2 2
[1] FALSE
D1483V7, 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
D1483V8, binary
                  cls
clus                 0   1
  GRIN2B MUTATED    22   4
  GRIN2B WILD-TYPE 295  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GRIN2B MUTATED     22    4
  GRIN2B WILD-TYPE  295   44
                               clus
vv                              GRIN2B MUTATED GRIN2B WILD-TYPE
  COLON ADENOCARCINOMA                      22              295
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  GRIN2B MUTATED    15   1   0   3
  GRIN2B WILD-TYPE 242   1  22  18
D1483V9, multiclass
    clus
vv   GRIN2B MUTATED GRIN2B WILD-TYPE
  R0             15              242
  R1              1                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"
D1483V10, 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
D1483V11, 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(1484) Variable = PON3 MUTATION ANALYSIS
D1484V1, survival
                sevent
clus2              0   1
  PON3 MUTATED     8   2
  PON3 WILD-TYPE 274  71
  PON3 MUTATED PON3 WILD-TYPE 
            10            345 
  PON3 MUTATED PON3 WILD-TYPE 
             2             71 
$`PON3 MUTATED`
TCGA-A6-5659 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3715 TCGA-AA-3971 TCGA-CA-6717 
       30.44        63.98         6.97        19.04        16.08         0.33 
TCGA-CA-6718 TCGA-CK-5916 TCGA-G4-6588 TCGA-G4-6628 
        0.10        21.14        26.17        52.80 

$`PON3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       35.01         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
        2.01        21.99        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07         0.26         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       35.80        91.79        46.75 

  PON3 MUTATED PON3 WILD-TYPE 
           0.1            0.0 
  PON3 MUTATED PON3 WILD-TYPE 
         63.98         140.38 
  PON3 MUTATED PON3 WILD-TYPE 
         20.09          20.19 
[1] "0.1 - 64.0 (20.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1"  
D1484V2, 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       22       106         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        18         10         41         31       35        13
                vv
clus             STAGE IVB
  PON3 MUTATED           0
  PON3 WILD-TYPE         1
D1484V3, multiclass
            clus
vv           PON3 MUTATED PON3 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              3             22
  STAGE IIA             3            106
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PON3 MUTATED     1   2   6   1
  PON3 WILD-TYPE   8  66 242  40
D1484V4, multiclass
    clus
vv   PON3 MUTATED PON3 WILD-TYPE
  T1            1              8
  T2            2             66
  T3            6            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
  PON3 MUTATED     9   1   0
  PON3 WILD-TYPE 211  79  66
D1484V5, multiclass
    clus
vv   PON3 MUTATED PON3 WILD-TYPE
  N0            9            211
  N1            1             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"
D1484V6, binary
                cls
clus               0   1
  PON3 MUTATED    10   0
  PON3 WILD-TYPE 273  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  PON3 MUTATED     10    0
  PON3 WILD-TYPE  273   48
   clus
vv  PON3 MUTATED PON3 WILD-TYPE
  0           10            273
  1            0             48
[1] 2 2
[1] FALSE
D1484V7, 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
D1484V8, binary
                cls
clus               0   1
  PON3 MUTATED     9   1
  PON3 WILD-TYPE 308  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  PON3 MUTATED      9    1
  PON3 WILD-TYPE  308   47
                               clus
vv                              PON3 MUTATED PON3 WILD-TYPE
  COLON ADENOCARCINOMA                     9            308
  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 250   2  22  18
D1484V9, multiclass
    clus
vv   PON3 MUTATED PON3 WILD-TYPE
  R0            7            250
  R1            0              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"
D1484V10, 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
D1484V11, 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(1485) Variable = LGR4 MUTATION ANALYSIS
D1485V1, survival
                sevent
clus2              0   1
  LGR4 MUTATED    12   1
  LGR4 WILD-TYPE 270  72
  LGR4 MUTATED LGR4 WILD-TYPE 
            13            342 
  LGR4 MUTATED LGR4 WILD-TYPE 
             1             72 
$`LGR4 MUTATED`
TCGA-A6-5661 TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3713 TCGA-AA-3837 TCGA-AA-3977 
       33.53        22.06        63.98        19.04        38.99        25.02 
TCGA-AA-A01R TCGA-AY-6197 TCGA-AZ-4315 TCGA-CM-6162 TCGA-CM-6171 TCGA-F4-6570 
       35.01        21.44        58.39        12.00        14.04         6.18 
TCGA-G4-6628 
       52.80 

$`LGR4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3842 
        0.99        25.02         1.02        17.98        15.95        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        15.75         0.20        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        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        13.38        13.45        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 

  LGR4 MUTATED LGR4 WILD-TYPE 
          6.18           0.00 
  LGR4 MUTATED LGR4 WILD-TYPE 
         63.98         140.38 
  LGR4 MUTATED LGR4 WILD-TYPE 
        25.020         20.005 
[1] "6.2 - 64.0 (25.0)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "3.3"
D1485V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LGR4 MUTATED         2        0        1         7         0         0
  LGR4 WILD-TYPE      62        1       24       102         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LGR4 MUTATED           1          0          1          0        1         0
  LGR4 WILD-TYPE        18         10         40         31       34        13
                vv
clus             STAGE IVB
  LGR4 MUTATED           0
  LGR4 WILD-TYPE         1
D1485V3, multiclass
            clus
vv           LGR4 MUTATED LGR4 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             7            102
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  LGR4 MUTATED     0   3  11   0
  LGR4 WILD-TYPE   9  65 237  41
D1485V4, multiclass
    clus
vv   LGR4 MUTATED LGR4 WILD-TYPE
  T1            0              9
  T2            3             65
  T3           11            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
  LGR4 MUTATED    12   1   1
  LGR4 WILD-TYPE 208  79  65
D1485V5, multiclass
    clus
vv   LGR4 MUTATED LGR4 WILD-TYPE
  N0           12            208
  N1            1             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"
D1485V6, binary
                cls
clus               0   1
  LGR4 MUTATED    11   1
  LGR4 WILD-TYPE 272  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  LGR4 MUTATED     11    1
  LGR4 WILD-TYPE  272   47
   clus
vv  LGR4 MUTATED LGR4 WILD-TYPE
  0           11            272
  1            1             47
[1] 2 2
[1] FALSE
D1485V7, binary
                cls
clus               0   1
  LGR4 MUTATED     6   8
  LGR4 WILD-TYPE 164 189
[1] "tbl2"
                cls
clus             [,1] [,2]
  LGR4 MUTATED      6    8
  LGR4 WILD-TYPE  164  189
        clus
vv       LGR4 MUTATED LGR4 WILD-TYPE
  FEMALE            6            164
  MALE              8            189
[1] 2 2
[1] FALSE
D1485V8, binary
                cls
clus               0   1
  LGR4 MUTATED    11   3
  LGR4 WILD-TYPE 306  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  LGR4 MUTATED     11    3
  LGR4 WILD-TYPE  306   45
                               clus
vv                              LGR4 MUTATED LGR4 WILD-TYPE
  COLON ADENOCARCINOMA                    11            306
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  LGR4 MUTATED    12   0   1   0
  LGR4 WILD-TYPE 245   2  21  21
D1485V9, multiclass
    clus
vv   LGR4 MUTATED LGR4 WILD-TYPE
  R0           12            245
  R1            0              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"
D1485V10, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LGR4 MUTATED                                  0     0
  LGR4 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  LGR4 MUTATED                           1     7
  LGR4 WILD-TYPE                        18   169
D1485V11, multiclass
                                  clus
vv                                 LGR4 MUTATED LGR4 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(1486) Variable = MC3R MUTATION ANALYSIS
D1486V1, survival
                sevent
clus2              0   1
  MC3R MUTATED    10   3
  MC3R WILD-TYPE 272  70
  MC3R MUTATED MC3R WILD-TYPE 
            13            342 
  MC3R MUTATED MC3R WILD-TYPE 
             3             70 
$`MC3R MUTATED`
TCGA-AA-A010 TCGA-AY-6196 TCGA-CK-5914 TCGA-CM-4743 TCGA-CM-6163 TCGA-CM-6166 
       34.98         0.20        21.99        23.05        14.04        21.99 
TCGA-CM-6679 TCGA-DM-A1D4 TCGA-DM-A1DB TCGA-F4-6808 TCGA-G4-6303 TCGA-G4-6304 
       10.06        92.75        44.32        33.67        65.85        53.62 
TCGA-G4-6586 
       35.80 

$`MC3R WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        15.75        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 
      102.44        40.34        15.62        49.08        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       12.00        29.03        16.04        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.01        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38         7.50       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        26.17        91.79        46.75        52.80 

  MC3R MUTATED MC3R WILD-TYPE 
           0.2            0.0 
  MC3R MUTATED MC3R WILD-TYPE 
         92.75         140.38 
  MC3R MUTATED MC3R WILD-TYPE 
         33.67          19.99 
[1] "0.2 - 92.8 (33.7)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1.2"
D1486V2, 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       25       104         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        19         10         40         30       34        13
                vv
clus             STAGE IVB
  MC3R MUTATED           0
  MC3R WILD-TYPE         1
D1486V3, multiclass
            clus
vv           MC3R MUTATED MC3R WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             5            104
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            1             30
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MC3R MUTATED     2   1   8   2
  MC3R WILD-TYPE   7  67 240  39
D1486V4, multiclass
    clus
vv   MC3R MUTATED MC3R WILD-TYPE
  T1            2              7
  T2            1             67
  T3            8            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
  MC3R MUTATED    10   2   1
  MC3R WILD-TYPE 210  78  65
D1486V5, multiclass
    clus
vv   MC3R MUTATED MC3R WILD-TYPE
  N0           10            210
  N1            2             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"
D1486V6, binary
                cls
clus               0   1
  MC3R MUTATED    10   1
  MC3R WILD-TYPE 273  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  MC3R MUTATED     10    1
  MC3R WILD-TYPE  273   47
   clus
vv  MC3R MUTATED MC3R WILD-TYPE
  0           10            273
  1            1             47
[1] 2 2
[1] FALSE
D1486V7, 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
D1486V8, binary
                cls
clus               0   1
  MC3R MUTATED    12   1
  MC3R WILD-TYPE 305  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  MC3R MUTATED     12    1
  MC3R WILD-TYPE  305   47
                               clus
vv                              MC3R MUTATED MC3R WILD-TYPE
  COLON ADENOCARCINOMA                    12            305
  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 247   2  22  20
D1486V9, multiclass
    clus
vv   MC3R MUTATED MC3R WILD-TYPE
  R0           10            247
  R1            0              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"
D1486V10, 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
D1486V11, 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(1487) Variable = IDI1 MUTATION ANALYSIS
D1487V1, survival
                sevent
clus2              0   1
  IDI1 MUTATED     1   2
  IDI1 WILD-TYPE 281  71
  IDI1 MUTATED IDI1 WILD-TYPE 
             3            352 
  IDI1 MUTATED IDI1 WILD-TYPE 
             2             71 
$`IDI1 MUTATED`
TCGA-AZ-6598 TCGA-F4-6570 TCGA-G4-6304 
       49.41         6.18        53.62 

$`IDI1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.38        13.45        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      107.67        74.56        65.85        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  IDI1 MUTATED IDI1 WILD-TYPE 
          6.18           0.00 
  IDI1 MUTATED IDI1 WILD-TYPE 
         53.62         140.38 
  IDI1 MUTATED IDI1 WILD-TYPE 
        49.410         20.155 
[1] "6.2 - 53.6 (49.4)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2.1"
D1487V2, 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       24       107         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        19         10         41         31       35        13
                vv
clus             STAGE IVB
  IDI1 MUTATED           0
  IDI1 WILD-TYPE         1
D1487V3, multiclass
            clus
vv           IDI1 MUTATED IDI1 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             2            107
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  IDI1 MUTATED     0   0   3   1
  IDI1 WILD-TYPE   9  68 245  40
D1487V4, multiclass
    clus
vv   IDI1 MUTATED IDI1 WILD-TYPE
  T1            0              9
  T2            0             68
  T3            3            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
  IDI1 MUTATED     4   0   0
  IDI1 WILD-TYPE 216  80  66
D1487V5, multiclass
    clus
vv   IDI1 MUTATED IDI1 WILD-TYPE
  N0            4            216
  N1            0             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"
D1487V6, binary
                cls
clus               0   1
  IDI1 MUTATED     3   0
  IDI1 WILD-TYPE 280  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDI1 MUTATED      3    0
  IDI1 WILD-TYPE  280   48
   clus
vv  IDI1 MUTATED IDI1 WILD-TYPE
  0            3            280
  1            0             48
[1] 2 2
[1] FALSE
D1487V7, 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
D1487V8, binary
                cls
clus               0   1
  IDI1 MUTATED     4   0
  IDI1 WILD-TYPE 313  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDI1 MUTATED      4    0
  IDI1 WILD-TYPE  313   48
                               clus
vv                              IDI1 MUTATED IDI1 WILD-TYPE
  COLON ADENOCARCINOMA                     4            313
  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 254   2  22  21
D1487V9, multiclass
    clus
vv   IDI1 MUTATED IDI1 WILD-TYPE
  R0            3            254
  R1            0              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"
D1487V10, 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
D1487V11, 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(1488) Variable = CCDC14 MUTATION ANALYSIS
D1488V1, survival
                  sevent
clus2                0   1
  CCDC14 MUTATED     7   4
  CCDC14 WILD-TYPE 275  69
  CCDC14 MUTATED CCDC14 WILD-TYPE 
              11              344 
  CCDC14 MUTATED CCDC14 WILD-TYPE 
               4               69 
$`CCDC14 MUTATED`
TCGA-A6-5659 TCGA-AA-3510 TCGA-AA-3713 TCGA-AA-3845 TCGA-AA-3977 TCGA-AA-A00N 
       30.44        63.98        19.04         0.00        25.02         4.01 
TCGA-AD-6964 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-F4-6570 
       10.88        58.39         0.33         0.10         6.18 

$`CCDC14 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       38.99        37.02        14.93        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07         0.26         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       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        13.38        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  CCDC14 MUTATED CCDC14 WILD-TYPE 
               0                0 
  CCDC14 MUTATED CCDC14 WILD-TYPE 
           63.98           140.38 
  CCDC14 MUTATED CCDC14 WILD-TYPE 
           10.88            20.63 
[1] "0.0 - 64.0 (10.9)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "2.2"
D1488V2, 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       24       104         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC14 MUTATED           0          0          0          0        1
  CCDC14 WILD-TYPE        19         10         41         31       34
                  vv
clus               STAGE IVA STAGE IVB
  CCDC14 MUTATED           0         0
  CCDC14 WILD-TYPE        13         1
D1488V3, multiclass
            clus
vv           CCDC14 MUTATED CCDC14 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               5              104
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CCDC14 MUTATED     0   2   7   2
  CCDC14 WILD-TYPE   9  66 241  39
D1488V4, multiclass
    clus
vv   CCDC14 MUTATED CCDC14 WILD-TYPE
  T1              0                9
  T2              2               66
  T3              7              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
  CCDC14 MUTATED    10   0   1
  CCDC14 WILD-TYPE 210  80  65
D1488V5, multiclass
    clus
vv   CCDC14 MUTATED CCDC14 WILD-TYPE
  N0             10              210
  N1              0               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"
D1488V6, binary
                  cls
clus                 0   1
  CCDC14 MUTATED     8   1
  CCDC14 WILD-TYPE 275  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC14 MUTATED      8    1
  CCDC14 WILD-TYPE  275   47
   clus
vv  CCDC14 MUTATED CCDC14 WILD-TYPE
  0              8              275
  1              1               47
[1] 2 2
[1] FALSE
D1488V7, 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
D1488V8, binary
                  cls
clus                 0   1
  CCDC14 MUTATED     9   2
  CCDC14 WILD-TYPE 308  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC14 MUTATED      9    2
  CCDC14 WILD-TYPE  308   46
                               clus
vv                              CCDC14 MUTATED CCDC14 WILD-TYPE
  COLON ADENOCARCINOMA                       9              308
  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 251   2  21  19
D1488V9, multiclass
    clus
vv   CCDC14 MUTATED CCDC14 WILD-TYPE
  R0              6              251
  R1              0                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"
D1488V10, 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
D1488V11, 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(1489) Variable = KLF12 MUTATION ANALYSIS
D1489V1, survival
                 sevent
clus2               0   1
  KLF12 MUTATED     3   0
  KLF12 WILD-TYPE 279  73
  KLF12 MUTATED KLF12 WILD-TYPE 
              3             352 
  KLF12 MUTATED KLF12 WILD-TYPE 
              0              73 
$`KLF12 MUTATED`
TCGA-AA-3949 TCGA-CA-5797 TCGA-G4-6321 
       26.01         3.29        22.09 

$`KLF12 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        33.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 
       51.75        45.11        36.72        36.00        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  KLF12 MUTATED KLF12 WILD-TYPE 
           3.29            0.00 
  KLF12 MUTATED KLF12 WILD-TYPE 
          26.01          140.38 
  KLF12 MUTATED KLF12 WILD-TYPE 
         22.090          20.155 
[1] "3.3 - 26.0 (22.1)"  "0.0 - 140.4 (20.2)"
[1] "hr="     "3300000"
D1489V2, 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       25       108         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        18         10         40         31       35        13
                 vv
clus              STAGE IVB
  KLF12 MUTATED           0
  KLF12 WILD-TYPE         1
D1489V3, multiclass
            clus
vv           KLF12 MUTATED KLF12 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              1             108
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KLF12 MUTATED     0   1   2   0
  KLF12 WILD-TYPE   9  67 246  41
D1489V4, multiclass
    clus
vv   KLF12 MUTATED KLF12 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             2             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
  KLF12 MUTATED     1   2   0
  KLF12 WILD-TYPE 219  78  66
D1489V5, multiclass
    clus
vv   KLF12 MUTATED KLF12 WILD-TYPE
  N0             1             219
  N1             2              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"
D1489V6, binary
                 cls
clus                0   1
  KLF12 MUTATED     2   0
  KLF12 WILD-TYPE 281  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLF12 MUTATED      2    0
  KLF12 WILD-TYPE  281   48
   clus
vv  KLF12 MUTATED KLF12 WILD-TYPE
  0             2             281
  1             0              48
[1] 2 2
[1] FALSE
D1489V7, 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
D1489V8, binary
                 cls
clus                0   1
  KLF12 MUTATED     2   1
  KLF12 WILD-TYPE 315  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLF12 MUTATED      2    1
  KLF12 WILD-TYPE  315   47
                               clus
vv                              KLF12 MUTATED KLF12 WILD-TYPE
  COLON ADENOCARCINOMA                      2             315
  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 254   2  22  21
D1489V9, multiclass
    clus
vv   KLF12 MUTATED KLF12 WILD-TYPE
  R0             3             254
  R1             0               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"
D1489V10, continuous
[1] "Remove cluster labels:" "KLF12 MUTATED"         
clus
  KLF12 MUTATED KLF12 WILD-TYPE 
              2             343 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-A6-2677      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-A6-4105 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-A6-5656      TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5660 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-A6-5661      TCGA-A6-5662      TCGA-A6-5664      TCGA-A6-5665 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-A6-5666      TCGA-A6-6137      TCGA-A6-6138      TCGA-A6-6141 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-A6-6142      TCGA-A6-6648      TCGA-A6-6649      TCGA-A6-6651 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-A6-6652      TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-A6-6781      TCGA-A6-6782      TCGA-AA-3489      TCGA-AA-3492 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3496      TCGA-AA-3502      TCGA-AA-3510      TCGA-AA-3511 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3514      TCGA-AA-3516      TCGA-AA-3517      TCGA-AA-3518 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3519      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-3526      TCGA-AA-3527 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3529      TCGA-AA-3530      TCGA-AA-3531      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-3543 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3544      TCGA-AA-3548      TCGA-AA-3549      TCGA-AA-3552 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3553      TCGA-AA-3554      TCGA-AA-3555      TCGA-AA-3556 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3558      TCGA-AA-3560      TCGA-AA-3562      TCGA-AA-3655 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3660      TCGA-AA-3662      TCGA-AA-3663      TCGA-AA-3664 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3666      TCGA-AA-3667      TCGA-AA-3672      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-3688      TCGA-AA-3692 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3693      TCGA-AA-3695      TCGA-AA-3696      TCGA-AA-3697 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3710      TCGA-AA-3712      TCGA-AA-3713      TCGA-AA-3715 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3811      TCGA-AA-3812      TCGA-AA-3814      TCGA-AA-3815 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3818      TCGA-AA-3819      TCGA-AA-3821      TCGA-AA-3831 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3833      TCGA-AA-3837      TCGA-AA-3842      TCGA-AA-3844 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3845      TCGA-AA-3846      TCGA-AA-3848      TCGA-AA-3850 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3851      TCGA-AA-3852      TCGA-AA-3854      TCGA-AA-3855 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3856      TCGA-AA-3858      TCGA-AA-3860      TCGA-AA-3861 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3864      TCGA-AA-3866      TCGA-AA-3867      TCGA-AA-3869 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3870      TCGA-AA-3872      TCGA-AA-3875      TCGA-AA-3877 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3930      TCGA-AA-3939      TCGA-AA-3941      TCGA-AA-3947 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3950      TCGA-AA-3952      TCGA-AA-3955      TCGA-AA-3956 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3966      TCGA-AA-3968      TCGA-AA-3971      TCGA-AA-3972 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3973      TCGA-AA-3975      TCGA-AA-3976      TCGA-AA-3977 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3979      TCGA-AA-3980      TCGA-AA-3982      TCGA-AA-3984 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-3986      TCGA-AA-3989      TCGA-AA-3994      TCGA-AA-A004 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-A00A      TCGA-AA-A00D      TCGA-AA-A00E      TCGA-AA-A00F 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-A00J      TCGA-AA-A00K      TCGA-AA-A00L      TCGA-AA-A00N 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-A00O      TCGA-AA-A00Q      TCGA-AA-A00R      TCGA-AA-A00U 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-A00W      TCGA-AA-A00Z      TCGA-AA-A010      TCGA-AA-A017 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-A01D      TCGA-AA-A01F      TCGA-AA-A01G      TCGA-AA-A01I 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-A01K      TCGA-AA-A01P      TCGA-AA-A01Q      TCGA-AA-A01R 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-A01S      TCGA-AA-A01T      TCGA-AA-A01V      TCGA-AA-A01X 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AA-A01Z      TCGA-AA-A022      TCGA-AA-A024      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-6548      TCGA-AD-6888 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AD-6889      TCGA-AD-6890      TCGA-AD-6895      TCGA-AD-6899 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6964      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-6601      TCGA-AZ-6603      TCGA-AZ-6605      TCGA-AZ-6606 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AZ-6607      TCGA-AZ-6608      TCGA-CK-4947      TCGA-CK-4948 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-CK-4950      TCGA-CK-4952      TCGA-CM-4743      TCGA-CM-4744 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-CM-4746      TCGA-CM-4747      TCGA-CM-4752      TCGA-CM-5341 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-CM-5344      TCGA-CM-5348      TCGA-CM-5349      TCGA-CM-5860 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-CM-5861      TCGA-CM-5862      TCGA-CM-5863      TCGA-CM-5864 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-CM-5868      TCGA-CM-6161      TCGA-CM-6162      TCGA-CM-6163 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-CM-6164      TCGA-CM-6165      TCGA-CM-6166      TCGA-CM-6167 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-CM-6168      TCGA-CM-6169      TCGA-CM-6170      TCGA-CM-6171 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-CM-6172      TCGA-CM-6674      TCGA-CM-6675      TCGA-CM-6676 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-CM-6677      TCGA-CM-6678      TCGA-CM-6679      TCGA-CM-6680 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-D5-5537      TCGA-D5-5538      TCGA-D5-5539      TCGA-D5-5540 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-D5-5541      TCGA-D5-6529      TCGA-D5-6532      TCGA-D5-6533 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-D5-6534      TCGA-D5-6535      TCGA-D5-6536      TCGA-D5-6537 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-D5-6538      TCGA-D5-6539      TCGA-D5-6540      TCGA-D5-6541 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-D5-6898      TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-D5-6924      TCGA-D5-6926      TCGA-D5-6927      TCGA-D5-6928 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-D5-6929      TCGA-D5-6930      TCGA-D5-6931      TCGA-D5-6932 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-D5-7000      TCGA-DM-A0X9      TCGA-DM-A0XD      TCGA-DM-A0XF 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-DM-A1D0      TCGA-DM-A1D4      TCGA-DM-A1D6      TCGA-DM-A1D7 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-DM-A1D8      TCGA-DM-A1D9      TCGA-DM-A1DA      TCGA-DM-A1DB 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-DM-A1HA      TCGA-DM-A1HB      TCGA-DM-A282      TCGA-DM-A285 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-DM-A28C      TCGA-DM-A28E      TCGA-DM-A28F      TCGA-DM-A28G 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-DM-A28H      TCGA-DM-A28K      TCGA-F4-6459      TCGA-F4-6460 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808      TCGA-F4-6809 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856      TCGA-G4-6293 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304      TCGA-G4-6306 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310      TCGA-G4-6315 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-G4-6317      TCGA-G4-6323      TCGA-G4-6586      TCGA-G4-6588 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-G4-6625      TCGA-G4-6626      TCGA-G4-6628 
"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
D1489V11, multiclass
[1] "Remove cluster labels:" "KLF12 MUTATED"         
clus
  KLF12 MUTATED KLF12 WILD-TYPE 
              2             204 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-A6-2677      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-A6-4105 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-A6-5656      TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5660 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-A6-5661      TCGA-A6-5662      TCGA-A6-5664      TCGA-A6-5665 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-A6-5666      TCGA-A6-6137      TCGA-A6-6138      TCGA-A6-6141 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-A6-6142      TCGA-A6-6648      TCGA-A6-6649      TCGA-A6-6651 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-A6-6652      TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-A6-6781      TCGA-A6-6782      TCGA-AD-5900      TCGA-AD-6548 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AD-6888      TCGA-AD-6889      TCGA-AD-6890      TCGA-AD-6895 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AD-6899      TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6964 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AD-6965      TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AY-4071      TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AY-6386      TCGA-AZ-4315      TCGA-AZ-4323      TCGA-AZ-4616 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AZ-4681      TCGA-AZ-4682      TCGA-AZ-5403      TCGA-AZ-5407 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-AZ-6598      TCGA-AZ-6599      TCGA-AZ-6600      TCGA-AZ-6601 
"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-AZ-6608      TCGA-CA-5254      TCGA-CA-5255      TCGA-CA-5796 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-CA-6715      TCGA-CA-6716      TCGA-CA-6717      TCGA-CA-6718 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-CA-6719      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-CK-5912      TCGA-CK-5913      TCGA-CK-5914 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-CK-5915      TCGA-CK-5916      TCGA-CK-6746      TCGA-CK-6747 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-CK-6748      TCGA-CK-6751      TCGA-CM-4743      TCGA-CM-4744 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-CM-4746      TCGA-CM-4747      TCGA-CM-4752      TCGA-CM-5341 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-CM-5344      TCGA-CM-5348      TCGA-CM-5349      TCGA-CM-5860 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-CM-5861      TCGA-CM-5862      TCGA-CM-5863      TCGA-CM-5864 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-CM-5868      TCGA-CM-6161      TCGA-CM-6162      TCGA-CM-6163 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-CM-6164      TCGA-CM-6165      TCGA-CM-6166      TCGA-CM-6167 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-CM-6168      TCGA-CM-6169      TCGA-CM-6170      TCGA-CM-6171 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-CM-6172      TCGA-CM-6674      TCGA-CM-6675      TCGA-CM-6676 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-CM-6677      TCGA-CM-6678      TCGA-CM-6679      TCGA-CM-6680 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-D5-5537      TCGA-D5-5538      TCGA-D5-5539      TCGA-D5-5540 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-D5-5541      TCGA-D5-6529      TCGA-D5-6532      TCGA-D5-6533 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-D5-6534      TCGA-D5-6535      TCGA-D5-6536      TCGA-D5-6537 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-D5-6538      TCGA-D5-6539      TCGA-D5-6540      TCGA-D5-6541 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-D5-6898      TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-D5-6924      TCGA-D5-6926      TCGA-D5-6927      TCGA-D5-6928 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-D5-6929      TCGA-D5-6930      TCGA-D5-6931      TCGA-D5-6932 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-D5-7000      TCGA-DM-A0X9      TCGA-DM-A0XD      TCGA-DM-A0XF 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-DM-A1D0      TCGA-DM-A1D4      TCGA-DM-A1D6      TCGA-DM-A1D7 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-DM-A1D8      TCGA-DM-A1D9      TCGA-DM-A1DA      TCGA-DM-A1DB 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-DM-A1HA      TCGA-DM-A1HB      TCGA-DM-A282      TCGA-DM-A285 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-DM-A28C      TCGA-DM-A28E      TCGA-DM-A28F      TCGA-DM-A28G 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-DM-A28H      TCGA-DM-A28K      TCGA-F4-6459      TCGA-F4-6460 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-F4-6805      TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-G4-6306      TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6323      TCGA-G4-6586 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 
     TCGA-G4-6588      TCGA-G4-6625      TCGA-G4-6626      TCGA-G4-6628 
"KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" "KLF12 WILD-TYPE" 

Clustering(1490) Variable = ZNF556 MUTATION ANALYSIS
D1490V1, survival
                  sevent
clus2                0   1
  ZNF556 MUTATED     5   0
  ZNF556 WILD-TYPE 277  73
  ZNF556 MUTATED ZNF556 WILD-TYPE 
               5              350 
  ZNF556 MUTATED ZNF556 WILD-TYPE 
               0               73 
$`ZNF556 MUTATED`
TCGA-AA-3555 TCGA-AA-3815 TCGA-AA-A01Q TCGA-CA-6717 TCGA-CA-6718 
       29.95        33.04         1.02         0.33         0.10 

$`ZNF556 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        17.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.26         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  ZNF556 MUTATED ZNF556 WILD-TYPE 
             0.1              0.0 
  ZNF556 MUTATED ZNF556 WILD-TYPE 
           33.04           140.38 
  ZNF556 MUTATED ZNF556 WILD-TYPE 
           1.020           20.235 
[1] "0.1 - 33.0 (1.0)"   "0.0 - 140.4 (20.2)"
[1] "hr="     "3300000"
D1490V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF556 MUTATED         0        0        1         5         0         0
  ZNF556 WILD-TYPE      64        1       24       104         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF556 MUTATED           0          0          0          0        0
  ZNF556 WILD-TYPE        19         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF556 MUTATED           0         0
  ZNF556 WILD-TYPE        13         1
D1490V3, multiclass
            clus
vv           ZNF556 MUTATED ZNF556 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               5              104
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF556 MUTATED     0   0   6   0
  ZNF556 WILD-TYPE   9  68 242  41
D1490V4, multiclass
    clus
vv   ZNF556 MUTATED ZNF556 WILD-TYPE
  T1              0                9
  T2              0               68
  T3              6              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
  ZNF556 MUTATED     6   0   0
  ZNF556 WILD-TYPE 214  80  66
D1490V5, multiclass
    clus
vv   ZNF556 MUTATED ZNF556 WILD-TYPE
  N0              6              214
  N1              0               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"
D1490V6, binary
                  cls
clus                 0   1
  ZNF556 MUTATED     6   0
  ZNF556 WILD-TYPE 277  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF556 MUTATED      6    0
  ZNF556 WILD-TYPE  277   48
   clus
vv  ZNF556 MUTATED ZNF556 WILD-TYPE
  0              6              277
  1              0               48
[1] 2 2
[1] FALSE
D1490V7, binary
                  cls
clus                 0   1
  ZNF556 MUTATED     4   2
  ZNF556 WILD-TYPE 166 195
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF556 MUTATED      4    2
  ZNF556 WILD-TYPE  166  195
        clus
vv       ZNF556 MUTATED ZNF556 WILD-TYPE
  FEMALE              4              166
  MALE                2              195
[1] 2 2
[1] FALSE
D1490V8, binary
                  cls
clus                 0   1
  ZNF556 MUTATED     4   2
  ZNF556 WILD-TYPE 313  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF556 MUTATED      4    2
  ZNF556 WILD-TYPE  313   46
                               clus
vv                              ZNF556 MUTATED ZNF556 WILD-TYPE
  COLON ADENOCARCINOMA                       4              313
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF556 MUTATED     4   0   0   2
  ZNF556 WILD-TYPE 253   2  22  19
D1490V9, multiclass
    clus
vv   ZNF556 MUTATED ZNF556 WILD-TYPE
  R0              4              253
  R1              0                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"
D1490V10, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF556 MUTATED                                  0     2
  ZNF556 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF556 MUTATED                           0     0
  ZNF556 WILD-TYPE                        19   176
D1490V11, multiclass
[1] "Remove cluster labels:" "ZNF556 MUTATED"        
clus
  ZNF556 MUTATED ZNF556 WILD-TYPE 
               2              204 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-4105 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-A6-5661       TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5665 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-A6-5666       TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-A6-6142       TCGA-A6-6648       TCGA-A6-6649       TCGA-A6-6651 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-A6-6652       TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-A6-6781       TCGA-A6-6782       TCGA-AD-5900       TCGA-AD-6548 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-AD-6888       TCGA-AD-6889       TCGA-AD-6890       TCGA-AD-6895 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-AD-6899       TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6964 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-AD-6965       TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-AY-4071       TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-AY-6386       TCGA-AZ-4315       TCGA-AZ-4323       TCGA-AZ-4616 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-AZ-4681       TCGA-AZ-4682       TCGA-AZ-5403       TCGA-AZ-5407 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-AZ-6598       TCGA-AZ-6599       TCGA-AZ-6600       TCGA-AZ-6601 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-AZ-6603       TCGA-AZ-6605       TCGA-AZ-6606       TCGA-AZ-6607 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-AZ-6608       TCGA-CA-5254       TCGA-CA-5255       TCGA-CA-5796 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-CA-5797       TCGA-CA-6715       TCGA-CA-6716       TCGA-CA-6719 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-CK-4947       TCGA-CK-4948       TCGA-CK-4950       TCGA-CK-4952 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-CK-5912       TCGA-CK-5913       TCGA-CK-5914       TCGA-CK-5915 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-CK-5916       TCGA-CK-6746       TCGA-CK-6747       TCGA-CK-6748 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-CK-6751       TCGA-CM-4743       TCGA-CM-4744       TCGA-CM-4746 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341       TCGA-CM-5344 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860       TCGA-CM-5861 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864       TCGA-CM-5868 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163       TCGA-CM-6164 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167       TCGA-CM-6168 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171       TCGA-CM-6172 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676       TCGA-CM-6677 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680       TCGA-D5-5537 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540       TCGA-D5-5541 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533       TCGA-D5-6534 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537       TCGA-D5-6538 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541       TCGA-D5-6898 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923       TCGA-D5-6924 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928       TCGA-D5-6929 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932       TCGA-D5-7000 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-DM-A0X9       TCGA-DM-A0XD       TCGA-DM-A0XF       TCGA-DM-A1D0 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-DM-A1D4       TCGA-DM-A1D6       TCGA-DM-A1D7       TCGA-DM-A1D8 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-DM-A1D9       TCGA-DM-A1DA       TCGA-DM-A1DB       TCGA-DM-A1HA 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-DM-A1HB       TCGA-DM-A282       TCGA-DM-A285       TCGA-DM-A28C 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-DM-A28E       TCGA-DM-A28F       TCGA-DM-A28G       TCGA-DM-A28H 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-DM-A28K       TCGA-F4-6459       TCGA-F4-6460       TCGA-F4-6569 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704       TCGA-F4-6805 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808       TCGA-F4-6809 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856       TCGA-G4-6293 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304       TCGA-G4-6306 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310       TCGA-G4-6315 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323       TCGA-G4-6586 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 

Clustering(1491) Variable = PROKR2 MUTATION ANALYSIS
D1491V1, survival
                  sevent
clus2                0   1
  PROKR2 MUTATED     7   1
  PROKR2 WILD-TYPE 275  72
  PROKR2 MUTATED PROKR2 WILD-TYPE 
               8              347 
  PROKR2 MUTATED PROKR2 WILD-TYPE 
               1               72 
$`PROKR2 MUTATED`
TCGA-A6-6653 TCGA-AA-3510 TCGA-AA-3655 TCGA-AZ-4315 TCGA-AZ-6600 TCGA-CM-6679 
       24.39        63.98        61.02        58.39        12.10        10.06 
TCGA-D5-6898 TCGA-G4-6310 
        7.53        45.11 

$`PROKR2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 
       22.36        62.79        61.41        49.41         6.77       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       16.14        15.58        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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        51.75        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  PROKR2 MUTATED PROKR2 WILD-TYPE 
            7.53             0.00 
  PROKR2 MUTATED PROKR2 WILD-TYPE 
           63.98           140.38 
  PROKR2 MUTATED PROKR2 WILD-TYPE 
           34.75            20.12 
[1] "7.5 - 64.0 (34.8)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "2.4"
D1491V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PROKR2 MUTATED         2        0        2         3         0         0
  PROKR2 WILD-TYPE      62        1       23       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PROKR2 MUTATED           0          0          1          0        1
  PROKR2 WILD-TYPE        19         10         40         31       34
                  vv
clus               STAGE IVA STAGE IVB
  PROKR2 MUTATED           0         0
  PROKR2 WILD-TYPE        13         1
D1491V3, multiclass
            clus
vv           PROKR2 MUTATED PROKR2 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               3              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PROKR2 MUTATED     0   2   6   1
  PROKR2 WILD-TYPE   9  66 242  40
D1491V4, multiclass
    clus
vv   PROKR2 MUTATED PROKR2 WILD-TYPE
  T1              0                9
  T2              2               66
  T3              6              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
  PROKR2 MUTATED     7   2   0
  PROKR2 WILD-TYPE 213  78  66
D1491V5, multiclass
    clus
vv   PROKR2 MUTATED PROKR2 WILD-TYPE
  N0              7              213
  N1              2               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"
D1491V6, binary
                  cls
clus                 0   1
  PROKR2 MUTATED     8   1
  PROKR2 WILD-TYPE 275  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PROKR2 MUTATED      8    1
  PROKR2 WILD-TYPE  275   47
   clus
vv  PROKR2 MUTATED PROKR2 WILD-TYPE
  0              8              275
  1              1               47
[1] 2 2
[1] FALSE
D1491V7, binary
                  cls
clus                 0   1
  PROKR2 MUTATED     2   7
  PROKR2 WILD-TYPE 168 190
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PROKR2 MUTATED      2    7
  PROKR2 WILD-TYPE  168  190
        clus
vv       PROKR2 MUTATED PROKR2 WILD-TYPE
  FEMALE              2              168
  MALE                7              190
[1] 2 2
[1] FALSE
D1491V8, binary
                  cls
clus                 0   1
  PROKR2 MUTATED     9   0
  PROKR2 WILD-TYPE 308  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PROKR2 MUTATED      9    0
  PROKR2 WILD-TYPE  308   48
                               clus
vv                              PROKR2 MUTATED PROKR2 WILD-TYPE
  COLON ADENOCARCINOMA                       9              308
  COLON MUCINOUS ADENOCARCINOMA              0               48
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PROKR2 MUTATED     7   0   0   0
  PROKR2 WILD-TYPE 250   2  22  21
D1491V9, multiclass
    clus
vv   PROKR2 MUTATED PROKR2 WILD-TYPE
  R0              7              250
  R1              0                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"
D1491V10, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PROKR2 MUTATED                                  0     0
  PROKR2 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PROKR2 MUTATED                           1     5
  PROKR2 WILD-TYPE                        18   171
D1491V11, multiclass
                                  clus
vv                                 PROKR2 MUTATED PROKR2 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(1492) Variable = ACTN1 MUTATION ANALYSIS
D1492V1, survival
                 sevent
clus2               0   1
  ACTN1 MUTATED     9   0
  ACTN1 WILD-TYPE 273  73
  ACTN1 MUTATED ACTN1 WILD-TYPE 
              9             346 
  ACTN1 MUTATED ACTN1 WILD-TYPE 
              0              73 
$`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 
        0.33        13.41        33.67 

$`ACTN1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       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        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        15.75        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       16.24        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  ACTN1 MUTATED ACTN1 WILD-TYPE 
            0.2             0.0 
  ACTN1 MUTATED ACTN1 WILD-TYPE 
          63.98          140.38 
  ACTN1 MUTATED ACTN1 WILD-TYPE 
         33.670          20.155 
[1] "0.2 - 64.0 (33.7)"  "0.0 - 140.4 (20.2)"
[1] "hr="     "2.5e+07"
D1492V2, 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       23       108         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        18         10         41         29       34        13
                 vv
clus              STAGE IVB
  ACTN1 MUTATED           0
  ACTN1 WILD-TYPE         1
D1492V3, multiclass
            clus
vv           ACTN1 MUTATED ACTN1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              1             108
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             2              29
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ACTN1 MUTATED     1   0   6   2
  ACTN1 WILD-TYPE   8  68 242  39
D1492V4, multiclass
    clus
vv   ACTN1 MUTATED ACTN1 WILD-TYPE
  T1             1               8
  T2             0              68
  T3             6             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
  ACTN1 MUTATED     5   2   2
  ACTN1 WILD-TYPE 215  78  64
D1492V5, multiclass
    clus
vv   ACTN1 MUTATED ACTN1 WILD-TYPE
  N0             5             215
  N1             2              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"
D1492V6, binary
                 cls
clus                0   1
  ACTN1 MUTATED     6   1
  ACTN1 WILD-TYPE 277  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACTN1 MUTATED      6    1
  ACTN1 WILD-TYPE  277   47
   clus
vv  ACTN1 MUTATED ACTN1 WILD-TYPE
  0             6             277
  1             1              47
[1] 2 2
[1] FALSE
D1492V7, 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
D1492V8, binary
                 cls
clus                0   1
  ACTN1 MUTATED     5   4
  ACTN1 WILD-TYPE 312  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACTN1 MUTATED      5    4
  ACTN1 WILD-TYPE  312   44
                               clus
vv                              ACTN1 MUTATED ACTN1 WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  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 249   2  22  20
D1492V9, multiclass
    clus
vv   ACTN1 MUTATED ACTN1 WILD-TYPE
  R0             8             249
  R1             0               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"
D1492V10, 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
D1492V11, 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(1493) Variable = KIAA2018 MUTATION ANALYSIS
D1493V1, survival
                    sevent
clus2                  0   1
  KIAA2018 MUTATED    17   3
  KIAA2018 WILD-TYPE 265  70
  KIAA2018 MUTATED KIAA2018 WILD-TYPE 
                20                335 
  KIAA2018 MUTATED KIAA2018 WILD-TYPE 
                 3                 70 
$`KIAA2018 MUTATED`
TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3815 
       22.06        63.98         6.97         5.98        37.05        33.04 
TCGA-AA-3864 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-6601 
       53.00        25.02         4.01        34.98        58.39       100.01 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CM-5861 TCGA-CM-6171 TCGA-D5-6928 
        0.33         0.10         1.35        15.02        14.04        11.64 
TCGA-D5-6930 TCGA-F4-6570 
        1.51         6.18 

$`KIAA2018 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       11.01        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       19.04        19.04        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        61.41        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CK-4947 TCGA-CK-4948 
        3.25         3.29         0.07         0.26        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.38        13.45        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  KIAA2018 MUTATED KIAA2018 WILD-TYPE 
               0.1                0.0 
  KIAA2018 MUTATED KIAA2018 WILD-TYPE 
            100.01             140.38 
  KIAA2018 MUTATED KIAA2018 WILD-TYPE 
             14.53              20.28 
[1] "0.1 - 100.0 (14.5)" "0.0 - 140.4 (20.3)"
[1] "hr=" "1.4"
D1493V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIAA2018 MUTATED         1        0        5        11         2         0
  KIAA2018 WILD-TYPE      63        1       20        98         6         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA2018 MUTATED           1          0          0          0        0
  KIAA2018 WILD-TYPE        18         10         41         31       35
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA2018 MUTATED           0         0
  KIAA2018 WILD-TYPE        13         1
D1493V3, multiclass
            clus
vv           KIAA2018 MUTATED KIAA2018 WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  5                 20
  STAGE IIA                11                 98
  STAGE IIB                 2                  6
  STAGE IIC                 0                  1
  STAGE III                 1                 18
  STAGE IIIA                0                 10
  STAGE IIIB                0                 41
  STAGE IIIC                0                 31
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA2018 MUTATED     0   2  17   2
  KIAA2018 WILD-TYPE   9  66 231  39
D1493V4, multiclass
    clus
vv   KIAA2018 MUTATED KIAA2018 WILD-TYPE
  T1                0                  9
  T2                2                 66
  T3               17                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
  KIAA2018 MUTATED    20   1   0
  KIAA2018 WILD-TYPE 200  79  66
D1493V5, multiclass
    clus
vv   KIAA2018 MUTATED KIAA2018 WILD-TYPE
  N0               20                200
  N1                1                 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
  KIAA2018 MUTATED    20   0
  KIAA2018 WILD-TYPE 263  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA2018 MUTATED     20    0
  KIAA2018 WILD-TYPE  263   48
   clus
vv  KIAA2018 MUTATED KIAA2018 WILD-TYPE
  0               20                263
  1                0                 48
[1] 2 2
[1] FALSE
D1493V7, binary
                    cls
clus                   0   1
  KIAA2018 MUTATED     8  13
  KIAA2018 WILD-TYPE 162 184
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA2018 MUTATED      8   13
  KIAA2018 WILD-TYPE  162  184
        clus
vv       KIAA2018 MUTATED KIAA2018 WILD-TYPE
  FEMALE                8                162
  MALE                 13                184
[1] 2 2
[1] FALSE
D1493V8, binary
                    cls
clus                   0   1
  KIAA2018 MUTATED    17   4
  KIAA2018 WILD-TYPE 300  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA2018 MUTATED     17    4
  KIAA2018 WILD-TYPE  300   44
                               clus
vv                              KIAA2018 MUTATED KIAA2018 WILD-TYPE
  COLON ADENOCARCINOMA                        17                300
  COLON MUCINOUS ADENOCARCINOMA                4                 44
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  KIAA2018 MUTATED    16   0   0   3
  KIAA2018 WILD-TYPE 241   2  22  18
D1493V9, multiclass
    clus
vv   KIAA2018 MUTATED KIAA2018 WILD-TYPE
  R0               16                241
  R1                0                  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"
D1493V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIAA2018 MUTATED                                  0     3
  KIAA2018 WILD-TYPE                                1     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  KIAA2018 MUTATED                           0     8
  KIAA2018 WILD-TYPE                        19   168
D1493V11, multiclass
                                  clus
vv                                 KIAA2018 MUTATED KIAA2018 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(1494) Variable = CCT4 MUTATION ANALYSIS
D1494V1, survival
                sevent
clus2              0   1
  CCT4 MUTATED    11   0
  CCT4 WILD-TYPE 271  73
  CCT4 MUTATED CCT4 WILD-TYPE 
            11            344 
  CCT4 MUTATED CCT4 WILD-TYPE 
             0             73 
$`CCT4 MUTATED`
TCGA-A6-6780 TCGA-AA-3496 TCGA-AA-3713 TCGA-AA-3950 TCGA-AD-6895 TCGA-CM-5341 
       20.12         1.02        19.04        24.00         0.72        29.06 
TCGA-D5-5538 TCGA-D5-6536 TCGA-D5-6538 TCGA-G4-6310 TCGA-G4-6628 
       12.26        17.85        17.13        45.11        52.80 

$`CCT4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       23.87        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       15.12         4.80        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 
       91.79        46.75 

  CCT4 MUTATED CCT4 WILD-TYPE 
          0.72           0.00 
  CCT4 MUTATED CCT4 WILD-TYPE 
         52.80         140.38 
  CCT4 MUTATED CCT4 WILD-TYPE 
         19.04          20.63 
[1] "0.7 - 52.8 (19.0)"  "0.0 - 140.4 (20.6)"
[1] "hr="     "2.5e+07"
D1494V2, 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       24       105         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CCT4 MUTATED           0          1          3          0        1         0
  CCT4 WILD-TYPE        19          9         38         31       34        13
                vv
clus             STAGE IVB
  CCT4 MUTATED           0
  CCT4 WILD-TYPE         1
D1494V3, multiclass
            clus
vv           CCT4 MUTATED CCT4 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             4            105
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            1              9
  STAGE IIIB            3             38
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CCT4 MUTATED     0   2  10   0
  CCT4 WILD-TYPE   9  66 238  41
D1494V4, multiclass
    clus
vv   CCT4 MUTATED CCT4 WILD-TYPE
  T1            0              9
  T2            2             66
  T3           10            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
  CCT4 MUTATED     7   4   1
  CCT4 WILD-TYPE 213  76  65
D1494V5, multiclass
    clus
vv   CCT4 MUTATED CCT4 WILD-TYPE
  N0            7            213
  N1            4             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"
D1494V6, binary
                cls
clus               0   1
  CCT4 MUTATED     9   1
  CCT4 WILD-TYPE 274  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCT4 MUTATED      9    1
  CCT4 WILD-TYPE  274   47
   clus
vv  CCT4 MUTATED CCT4 WILD-TYPE
  0            9            274
  1            1             47
[1] 2 2
[1] FALSE
D1494V7, 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
D1494V8, binary
                cls
clus               0   1
  CCT4 MUTATED    10   2
  CCT4 WILD-TYPE 307  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCT4 MUTATED     10    2
  CCT4 WILD-TYPE  307   46
                               clus
vv                              CCT4 MUTATED CCT4 WILD-TYPE
  COLON ADENOCARCINOMA                    10            307
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CCT4 MUTATED     9   0   1   0
  CCT4 WILD-TYPE 248   2  21  21
D1494V9, multiclass
    clus
vv   CCT4 MUTATED CCT4 WILD-TYPE
  R0            9            248
  R1            0              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"
D1494V10, 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
D1494V11, 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(1495) Variable = IFLTD1 MUTATION ANALYSIS
D1495V1, survival
                  sevent
clus2                0   1
  IFLTD1 MUTATED    12   0
  IFLTD1 WILD-TYPE 270  73
  IFLTD1 MUTATED IFLTD1 WILD-TYPE 
              12              343 
  IFLTD1 MUTATED IFLTD1 WILD-TYPE 
               0               73 
$`IFLTD1 MUTATED`
TCGA-A6-5660 TCGA-A6-5665 TCGA-AA-3524 TCGA-AA-3710 TCGA-AA-3864 TCGA-AA-3977 
       29.19        22.06        36.03        26.99        53.00        25.02 
TCGA-AY-6386 TCGA-CA-6717 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-6171 TCGA-CM-6675 
       17.82         0.33        30.08        15.02        14.04        13.05 

$`IFLTD1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
        9.07        24.03        37.05         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 
       16.31         0.95        15.75         0.20        21.44        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       16.01         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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-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-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  IFLTD1 MUTATED IFLTD1 WILD-TYPE 
            0.33             0.00 
  IFLTD1 MUTATED IFLTD1 WILD-TYPE 
           53.00           140.38 
  IFLTD1 MUTATED IFLTD1 WILD-TYPE 
           23.54            20.12 
[1] "0.3 - 53.0 (23.5)"  "0.0 - 140.4 (20.1)"
[1] "hr="     "2.6e+07"
D1495V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IFLTD1 MUTATED         1        0        2         5         0         0
  IFLTD1 WILD-TYPE      63        1       23       104         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IFLTD1 MUTATED           1          0          1          1        0
  IFLTD1 WILD-TYPE        18         10         40         30       35
                  vv
clus               STAGE IVA STAGE IVB
  IFLTD1 MUTATED           0         1
  IFLTD1 WILD-TYPE        13         0
D1495V3, multiclass
            clus
vv           IFLTD1 MUTATED IFLTD1 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               5              104
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  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   2  11   0
  IFLTD1 WILD-TYPE   9  66 237  41
D1495V4, multiclass
    clus
vv   IFLTD1 MUTATED IFLTD1 WILD-TYPE
  T1              0                9
  T2              2               66
  T3             11              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
  IFLTD1 MUTATED     9   1   3
  IFLTD1 WILD-TYPE 211  79  63
D1495V5, multiclass
    clus
vv   IFLTD1 MUTATED IFLTD1 WILD-TYPE
  N0              9              211
  N1              1               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"
D1495V6, binary
                  cls
clus                 0   1
  IFLTD1 MUTATED    11   1
  IFLTD1 WILD-TYPE 272  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFLTD1 MUTATED     11    1
  IFLTD1 WILD-TYPE  272   47
   clus
vv  IFLTD1 MUTATED IFLTD1 WILD-TYPE
  0             11              272
  1              1               47
[1] 2 2
[1] FALSE
D1495V7, binary
                  cls
clus                 0   1
  IFLTD1 MUTATED     6   7
  IFLTD1 WILD-TYPE 164 190
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFLTD1 MUTATED      6    7
  IFLTD1 WILD-TYPE  164  190
        clus
vv       IFLTD1 MUTATED IFLTD1 WILD-TYPE
  FEMALE              6              164
  MALE                7              190
[1] 2 2
[1] FALSE
D1495V8, binary
                  cls
clus                 0   1
  IFLTD1 MUTATED    12   1
  IFLTD1 WILD-TYPE 305  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFLTD1 MUTATED     12    1
  IFLTD1 WILD-TYPE  305   47
                               clus
vv                              IFLTD1 MUTATED IFLTD1 WILD-TYPE
  COLON ADENOCARCINOMA                      12              305
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  IFLTD1 MUTATED    10   0   0   1
  IFLTD1 WILD-TYPE 247   2  22  20
D1495V9, multiclass
    clus
vv   IFLTD1 MUTATED IFLTD1 WILD-TYPE
  R0             10              247
  R1              0                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"
D1495V10, 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     4
  IFLTD1 WILD-TYPE                        16   172
D1495V11, 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                                         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(1496) Variable = IL18R1 MUTATION ANALYSIS
D1496V1, survival
                  sevent
clus2                0   1
  IL18R1 MUTATED    11   2
  IL18R1 WILD-TYPE 271  71
  IL18R1 MUTATED IL18R1 WILD-TYPE 
              13              342 
  IL18R1 MUTATED IL18R1 WILD-TYPE 
               2               71 
$`IL18R1 MUTATED`
TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3672 TCGA-AA-3815 TCGA-AA-3877 
        3.02        63.98        13.02         0.92        33.04        31.00 
TCGA-AA-3955 TCGA-AA-3971 TCGA-AA-A010 TCGA-AA-A02O TCGA-CK-6751 TCGA-F4-6703 
       20.98        16.08        34.98         0.92       124.27        35.87 
TCGA-G4-6306 
       44.68 

$`IL18R1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       35.01         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 
       24.00         2.01        34.03         2.01        21.99        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03        14.01        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        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        13.38        13.45         6.18         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  IL18R1 MUTATED IL18R1 WILD-TYPE 
            0.92             0.00 
  IL18R1 MUTATED IL18R1 WILD-TYPE 
          124.27           140.38 
  IL18R1 MUTATED IL18R1 WILD-TYPE 
           31.00            20.07 
[1] "0.9 - 124.3 (31.0)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.6"
D1496V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IL18R1 MUTATED         2        0        3         3         1         0
  IL18R1 WILD-TYPE      62        1       22       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        16         10         40         31       35
                  vv
clus               STAGE IVA STAGE IVB
  IL18R1 MUTATED           0         0
  IL18R1 WILD-TYPE        13         1
D1496V3, multiclass
            clus
vv           IL18R1 MUTATED IL18R1 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                3               22
  STAGE IIA               3              106
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               3               16
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  IL18R1 MUTATED     1   3   8   1
  IL18R1 WILD-TYPE   8  65 240  40
D1496V4, multiclass
    clus
vv   IL18R1 MUTATED IL18R1 WILD-TYPE
  T1              1                8
  T2              3               65
  T3              8              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
  IL18R1 MUTATED     9   2   2
  IL18R1 WILD-TYPE 211  78  64
D1496V5, multiclass
    clus
vv   IL18R1 MUTATED IL18R1 WILD-TYPE
  N0              9              211
  N1              2               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"
D1496V6, binary
                  cls
clus                 0   1
  IL18R1 MUTATED    12   0
  IL18R1 WILD-TYPE 271  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IL18R1 MUTATED     12    0
  IL18R1 WILD-TYPE  271   48
   clus
vv  IL18R1 MUTATED IL18R1 WILD-TYPE
  0             12              271
  1              0               48
[1] 2 2
[1] FALSE
D1496V7, 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
D1496V8, binary
                  cls
clus                 0   1
  IL18R1 MUTATED    10   3
  IL18R1 WILD-TYPE 307  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IL18R1 MUTATED     10    3
  IL18R1 WILD-TYPE  307   45
                               clus
vv                              IL18R1 MUTATED IL18R1 WILD-TYPE
  COLON ADENOCARCINOMA                      10              307
  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 246   2  22  20
D1496V9, multiclass
    clus
vv   IL18R1 MUTATED IL18R1 WILD-TYPE
  R0             11              246
  R1              0                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"
D1496V10, 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
D1496V11, 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(1497) Variable = TRIM25 MUTATION ANALYSIS
D1497V1, survival
                  sevent
clus2                0   1
  TRIM25 MUTATED     1   3
  TRIM25 WILD-TYPE 281  70
  TRIM25 MUTATED TRIM25 WILD-TYPE 
               4              351 
  TRIM25 MUTATED TRIM25 WILD-TYPE 
               3               70 
$`TRIM25 MUTATED`
TCGA-AA-3492 TCGA-AA-3715 TCGA-CM-6678 TCGA-D5-6537 
        3.02        19.04        11.01         4.80 

$`TRIM25 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  TRIM25 MUTATED TRIM25 WILD-TYPE 
            3.02             0.00 
  TRIM25 MUTATED TRIM25 WILD-TYPE 
           19.04           140.38 
  TRIM25 MUTATED TRIM25 WILD-TYPE 
           7.905           20.980 
[1] "3.0 - 19.0 (7.9)"   "0.0 - 140.4 (21.0)"
[1] "hr=" "8.8"
D1497V2, 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       23       109         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRIM25 MUTATED           0          0          1          0        0
  TRIM25 WILD-TYPE        19         10         40         31       35
                  vv
clus               STAGE IVA STAGE IVB
  TRIM25 MUTATED           1         0
  TRIM25 WILD-TYPE        12         1
D1497V3, multiclass
            clus
vv           TRIM25 MUTATED TRIM25 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               0              109
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  68 245  40
D1497V4, multiclass
    clus
vv   TRIM25 MUTATED TRIM25 WILD-TYPE
  T1              0                9
  T2              0               68
  T3              3              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
  TRIM25 MUTATED     2   2   0
  TRIM25 WILD-TYPE 218  78  66
D1497V5, multiclass
    clus
vv   TRIM25 MUTATED TRIM25 WILD-TYPE
  N0              2              218
  N1              2               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"
D1497V6, binary
                  cls
clus                 0   1
  TRIM25 MUTATED     2   1
  TRIM25 WILD-TYPE 281  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM25 MUTATED      2    1
  TRIM25 WILD-TYPE  281   47
   clus
vv  TRIM25 MUTATED TRIM25 WILD-TYPE
  0              2              281
  1              1               47
[1] 2 2
[1] FALSE
D1497V7, 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
D1497V8, binary
                  cls
clus                 0   1
  TRIM25 MUTATED     4   0
  TRIM25 WILD-TYPE 313  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM25 MUTATED      4    0
  TRIM25 WILD-TYPE  313   48
                               clus
vv                              TRIM25 MUTATED TRIM25 WILD-TYPE
  COLON ADENOCARCINOMA                       4              313
  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 253   2  22  21
D1497V9, multiclass
    clus
vv   TRIM25 MUTATED TRIM25 WILD-TYPE
  R0              4              253
  R1              0                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"
D1497V10, 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
D1497V11, multiclass
[1] "Remove cluster labels:" "TRIM25 MUTATED"        
clus
  TRIM25 MUTATED TRIM25 WILD-TYPE 
               2              204 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-4105 
"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-A6-6649       TCGA-A6-6651 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-A6-6652       TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-A6-6781       TCGA-A6-6782       TCGA-AD-5900       TCGA-AD-6548 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-AD-6888       TCGA-AD-6889       TCGA-AD-6890       TCGA-AD-6895 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-AD-6899       TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6964 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-AD-6965       TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-AY-4071       TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-AY-6386       TCGA-AZ-4315       TCGA-AZ-4323       TCGA-AZ-4616 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-AZ-4681       TCGA-AZ-4682       TCGA-AZ-5403       TCGA-AZ-5407 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-AZ-6598       TCGA-AZ-6599       TCGA-AZ-6600       TCGA-AZ-6601 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-AZ-6603       TCGA-AZ-6605       TCGA-AZ-6606       TCGA-AZ-6607 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-AZ-6608       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-5912       TCGA-CK-5913 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-CK-5914       TCGA-CK-5915       TCGA-CK-5916       TCGA-CK-6746 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-CK-6747       TCGA-CK-6748       TCGA-CK-6751       TCGA-CM-4743 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-CM-4744       TCGA-CM-4746       TCGA-CM-4747       TCGA-CM-4752 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-CM-5341       TCGA-CM-5344       TCGA-CM-5348       TCGA-CM-5349 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-CM-5860       TCGA-CM-5861       TCGA-CM-5862       TCGA-CM-5863 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-CM-5864       TCGA-CM-5868       TCGA-CM-6161       TCGA-CM-6162 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-CM-6163       TCGA-CM-6164       TCGA-CM-6165       TCGA-CM-6166 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-CM-6167       TCGA-CM-6168       TCGA-CM-6169       TCGA-CM-6170 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-CM-6171       TCGA-CM-6172       TCGA-CM-6674       TCGA-CM-6675 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-CM-6676       TCGA-CM-6677       TCGA-CM-6679       TCGA-CM-6680 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-D5-5537       TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-D5-5541       TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-D5-6534       TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6538 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541       TCGA-D5-6898 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923       TCGA-D5-6924 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928       TCGA-D5-6929 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932       TCGA-D5-7000 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-DM-A0X9       TCGA-DM-A0XD       TCGA-DM-A0XF       TCGA-DM-A1D0 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-DM-A1D4       TCGA-DM-A1D6       TCGA-DM-A1D7       TCGA-DM-A1D8 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-DM-A1D9       TCGA-DM-A1DA       TCGA-DM-A1DB       TCGA-DM-A1HA 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-DM-A1HB       TCGA-DM-A282       TCGA-DM-A285       TCGA-DM-A28C 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-DM-A28E       TCGA-DM-A28F       TCGA-DM-A28G       TCGA-DM-A28H 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-DM-A28K       TCGA-F4-6459       TCGA-F4-6460       TCGA-F4-6569 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704       TCGA-F4-6805 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808       TCGA-F4-6809 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856       TCGA-G4-6293 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304       TCGA-G4-6306 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310       TCGA-G4-6315 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323       TCGA-G4-6586 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 
      TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628 
"TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" "TRIM25 WILD-TYPE" 

Clustering(1498) Variable = DONSON MUTATION ANALYSIS
D1498V1, survival
                  sevent
clus2                0   1
  DONSON MUTATED     2   2
  DONSON WILD-TYPE 280  71
  DONSON MUTATED DONSON WILD-TYPE 
               4              351 
  DONSON MUTATED DONSON WILD-TYPE 
               2               71 
$`DONSON MUTATED`
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-DM-A1D9 TCGA-G4-6588 
       49.41         6.77       140.38        26.17 

$`DONSON WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       61.41        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32        12.59         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  DONSON MUTATED DONSON WILD-TYPE 
            6.77             0.00 
  DONSON MUTATED DONSON WILD-TYPE 
          140.38           139.17 
  DONSON MUTATED DONSON WILD-TYPE 
           37.79            20.12 
[1] "6.8 - 140.4 (37.8)" "0.0 - 139.2 (20.1)"
[1] "hr=" "1.3"
D1498V2, 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       24       107         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DONSON MUTATED           0          0          0          0        0
  DONSON WILD-TYPE        19         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  DONSON MUTATED           0         0
  DONSON WILD-TYPE        13         1
D1498V3, multiclass
            clus
vv           DONSON MUTATED DONSON WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               2              107
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  DONSON MUTATED     0   1   3   0
  DONSON WILD-TYPE   9  67 245  41
D1498V4, multiclass
    clus
vv   DONSON MUTATED DONSON WILD-TYPE
  T1              0                9
  T2              1               67
  T3              3              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
  DONSON MUTATED     4   0   0
  DONSON WILD-TYPE 216  80  66
D1498V5, multiclass
    clus
vv   DONSON MUTATED DONSON WILD-TYPE
  N0              4              216
  N1              0               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"
D1498V6, binary
                  cls
clus                 0   1
  DONSON MUTATED     2   0
  DONSON WILD-TYPE 281  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DONSON MUTATED      2    0
  DONSON WILD-TYPE  281   48
   clus
vv  DONSON MUTATED DONSON WILD-TYPE
  0              2              281
  1              0               48
[1] 2 2
[1] FALSE
D1498V7, 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
D1498V8, binary
                  cls
clus                 0   1
  DONSON MUTATED     4   0
  DONSON WILD-TYPE 313  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DONSON MUTATED      4    0
  DONSON WILD-TYPE  313   48
                               clus
vv                              DONSON MUTATED DONSON WILD-TYPE
  COLON ADENOCARCINOMA                       4              313
  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 256   2  22  21
D1498V9, multiclass
[1] "Remove cluster labels:" "DONSON MUTATED"        
clus
  DONSON MUTATED DONSON WILD-TYPE 
               1              301 
      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-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-5657 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-A6-5659       TCGA-A6-5661       TCGA-A6-5665       TCGA-A6-6781 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-3489       TCGA-AA-3492       TCGA-AA-3496       TCGA-AA-3502 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-3510       TCGA-AA-3511       TCGA-AA-3514       TCGA-AA-3517 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-3518       TCGA-AA-3519       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-3526 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-3527       TCGA-AA-3529       TCGA-AA-3530       TCGA-AA-3531 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-3532       TCGA-AA-3534       TCGA-AA-3538       TCGA-AA-3542 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-3543       TCGA-AA-3544       TCGA-AA-3548       TCGA-AA-3549 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-3552       TCGA-AA-3553       TCGA-AA-3554       TCGA-AA-3555 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-3556       TCGA-AA-3558       TCGA-AA-3560       TCGA-AA-3561 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-3562       TCGA-AA-3655       TCGA-AA-3660       TCGA-AA-3662 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-3663       TCGA-AA-3664       TCGA-AA-3666       TCGA-AA-3667 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-3672       TCGA-AA-3673       TCGA-AA-3678       TCGA-AA-3679 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-3680       TCGA-AA-3681       TCGA-AA-3684       TCGA-AA-3685 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-3688       TCGA-AA-3692       TCGA-AA-3693       TCGA-AA-3695 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-3696       TCGA-AA-3697       TCGA-AA-3710       TCGA-AA-3712 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-3713       TCGA-AA-3715       TCGA-AA-3811       TCGA-AA-3812 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-3814       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-3844       TCGA-AA-3845       TCGA-AA-3846 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-3848       TCGA-AA-3850       TCGA-AA-3851       TCGA-AA-3852 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-3854       TCGA-AA-3855       TCGA-AA-3856       TCGA-AA-3858 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-3860       TCGA-AA-3861       TCGA-AA-3864       TCGA-AA-3866 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-3867       TCGA-AA-3869       TCGA-AA-3870       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-3939 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-3941       TCGA-AA-3947       TCGA-AA-3949       TCGA-AA-3950 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-3952       TCGA-AA-3955       TCGA-AA-3956       TCGA-AA-3968 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-3971       TCGA-AA-3972       TCGA-AA-3973       TCGA-AA-3975 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-3976       TCGA-AA-3979       TCGA-AA-3984       TCGA-AA-3986 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-3989       TCGA-AA-3994       TCGA-AA-A004       TCGA-AA-A00A 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-A00D       TCGA-AA-A00E       TCGA-AA-A00F       TCGA-AA-A00J 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-A00K       TCGA-AA-A00L       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-A00Z       TCGA-AA-A010       TCGA-AA-A017       TCGA-AA-A01D 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-A01F       TCGA-AA-A01G       TCGA-AA-A01I       TCGA-AA-A01K 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-A01P       TCGA-AA-A01Q       TCGA-AA-A01R       TCGA-AA-A01S 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-A01T       TCGA-AA-A01V       TCGA-AA-A01X       TCGA-AA-A01Z 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-A022       TCGA-AA-A024       TCGA-AA-A029       TCGA-AA-A02F 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-A02H       TCGA-AA-A02J       TCGA-AA-A02K       TCGA-AA-A02O 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AA-A02W       TCGA-AA-A02Y       TCGA-AA-A03F       TCGA-AA-A03J 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AD-5900       TCGA-AD-6548       TCGA-AD-6888       TCGA-AU-3779 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AU-6004       TCGA-AY-4070       TCGA-AY-4071       TCGA-AY-5543 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386       TCGA-AZ-4315 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-AZ-4681       TCGA-AZ-4682       TCGA-CA-5254       TCGA-CA-5255 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-CA-5796       TCGA-CA-5797       TCGA-CA-6715       TCGA-CA-6716 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-CA-6717       TCGA-CA-6718       TCGA-CA-6719       TCGA-CK-4947 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-CK-4948       TCGA-CK-4950       TCGA-CK-4952       TCGA-CK-5912 
"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-G4-6310       TCGA-G4-6315       TCGA-G4-6317       TCGA-G4-6321 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-G4-6323       TCGA-G4-6586       TCGA-G4-6625       TCGA-G4-6626 
"DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" "DONSON WILD-TYPE" 
      TCGA-G4-6628 
"DONSON WILD-TYPE" 
D1498V10, 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
D1498V11, 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(1499) Variable = CALCOCO2 MUTATION ANALYSIS
D1499V1, survival
                    sevent
clus2                  0   1
  CALCOCO2 MUTATED     5   1
  CALCOCO2 WILD-TYPE 277  72
  CALCOCO2 MUTATED CALCOCO2 WILD-TYPE 
                 6                349 
  CALCOCO2 MUTATED CALCOCO2 WILD-TYPE 
                 1                 72 
$`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         0.33        16.01        36.72 

$`CALCOCO2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       19.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 
       53.62        44.68        55.04        51.75        45.11        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  CALCOCO2 MUTATED CALCOCO2 WILD-TYPE 
              0.33               0.00 
  CALCOCO2 MUTATED CALCOCO2 WILD-TYPE 
             36.72             140.38 
  CALCOCO2 MUTATED CALCOCO2 WILD-TYPE 
            18.545             20.280 
[1] "0.3 - 36.7 (18.5)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1"  
D1499V2, 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       25       107         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CALCOCO2 MUTATED           0          0          1          0        3
  CALCOCO2 WILD-TYPE        19         10         40         31       32
                    vv
clus                 STAGE IVA STAGE IVB
  CALCOCO2 MUTATED           0         0
  CALCOCO2 WILD-TYPE        13         1
D1499V3, multiclass
            clus
vv           CALCOCO2 MUTATED CALCOCO2 WILD-TYPE
  STAGE I                   0                 64
  STAGE IA                  0                  1
  STAGE II                  0                 25
  STAGE IIA                 2                107
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                0                 10
  STAGE IIIB                1                 40
  STAGE IIIC                0                 31
  STAGE IV                  3                 32
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  CALCOCO2 MUTATED     0   0   5   2
  CALCOCO2 WILD-TYPE   9  68 243  39
D1499V4, multiclass
    clus
vv   CALCOCO2 MUTATED CALCOCO2 WILD-TYPE
  T1                0                  9
  T2                0                 68
  T3                5                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
  CALCOCO2 MUTATED     4   2   1
  CALCOCO2 WILD-TYPE 216  78  65
D1499V5, multiclass
    clus
vv   CALCOCO2 MUTATED CALCOCO2 WILD-TYPE
  N0                4                216
  N1                2                 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"
D1499V6, binary
                    cls
clus                   0   1
  CALCOCO2 MUTATED     3   3
  CALCOCO2 WILD-TYPE 280  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CALCOCO2 MUTATED      3    3
  CALCOCO2 WILD-TYPE  280   45
   clus
vv  CALCOCO2 MUTATED CALCOCO2 WILD-TYPE
  0                3                280
  1                3                 45
[1] 2 2
[1] FALSE
D1499V7, 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
D1499V8, binary
                    cls
clus                   0   1
  CALCOCO2 MUTATED     4   3
  CALCOCO2 WILD-TYPE 313  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CALCOCO2 MUTATED      4    3
  CALCOCO2 WILD-TYPE  313   45
                               clus
vv                              CALCOCO2 MUTATED CALCOCO2 WILD-TYPE
  COLON ADENOCARCINOMA                         4                313
  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 254   2  20  19
D1499V9, multiclass
    clus
vv   CALCOCO2 MUTATED CALCOCO2 WILD-TYPE
  R0                3                254
  R1                0                  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"
D1499V10, 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
D1499V11, 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(1500) Variable = CBX8 MUTATION ANALYSIS
D1500V1, survival
                sevent
clus2              0   1
  CBX8 MUTATED     9   2
  CBX8 WILD-TYPE 273  71
  CBX8 MUTATED CBX8 WILD-TYPE 
            11            344 
  CBX8 MUTATED CBX8 WILD-TYPE 
             2             71 
$`CBX8 MUTATED`
TCGA-A6-5665 TCGA-AA-3660 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3947 TCGA-AA-3986 
       22.06        78.08        19.04        10.06        33.01        19.07 
TCGA-AA-A010 TCGA-AY-6197 TCGA-CM-6171 TCGA-D5-6540 TCGA-F4-6570 
       34.98        21.44        14.04        16.14         6.18 

$`CBX8 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        61.02         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 
        5.03        85.05        26.99        19.04        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       25.02        24.00        27.02        27.02         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        15.75         0.20        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       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        13.38        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  CBX8 MUTATED CBX8 WILD-TYPE 
          6.18           0.00 
  CBX8 MUTATED CBX8 WILD-TYPE 
         78.08         140.38 
  CBX8 MUTATED CBX8 WILD-TYPE 
        19.070         20.235 
[1] "6.2 - 78.1 (19.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D1500V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CBX8 MUTATED         3        0        1         3         2         0
  CBX8 WILD-TYPE      61        1       24       106         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CBX8 MUTATED           1          0          0          0        1         0
  CBX8 WILD-TYPE        18         10         41         31       34        13
                vv
clus             STAGE IVB
  CBX8 MUTATED           0
  CBX8 WILD-TYPE         1
D1500V3, multiclass
            clus
vv           CBX8 MUTATED CBX8 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             3            106
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CBX8 MUTATED     0   3   6   2
  CBX8 WILD-TYPE   9  65 242  39
D1500V4, multiclass
    clus
vv   CBX8 MUTATED CBX8 WILD-TYPE
  T1            0              9
  T2            3             65
  T3            6            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
  CBX8 MUTATED    10   0   1
  CBX8 WILD-TYPE 210  80  65
D1500V5, multiclass
    clus
vv   CBX8 MUTATED CBX8 WILD-TYPE
  N0           10            210
  N1            0             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"
D1500V6, binary
                cls
clus               0   1
  CBX8 MUTATED     9   1
  CBX8 WILD-TYPE 274  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  CBX8 MUTATED      9    1
  CBX8 WILD-TYPE  274   47
   clus
vv  CBX8 MUTATED CBX8 WILD-TYPE
  0            9            274
  1            1             47
[1] 2 2
[1] FALSE
D1500V7, binary
                cls
clus               0   1
  CBX8 MUTATED     7   4
  CBX8 WILD-TYPE 163 193
[1] "tbl2"
                cls
clus             [,1] [,2]
  CBX8 MUTATED      7    4
  CBX8 WILD-TYPE  163  193
        clus
vv       CBX8 MUTATED CBX8 WILD-TYPE
  FEMALE            7            163
  MALE              4            193
[1] 2 2
[1] FALSE
D1500V8, binary
                cls
clus               0   1
  CBX8 MUTATED     9   2
  CBX8 WILD-TYPE 308  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  CBX8 MUTATED      9    2
  CBX8 WILD-TYPE  308   46
                               clus
vv                              CBX8 MUTATED CBX8 WILD-TYPE
  COLON ADENOCARCINOMA                     9            308
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CBX8 MUTATED    10   0   1   0
  CBX8 WILD-TYPE 247   2  21  21
D1500V9, multiclass
    clus
vv   CBX8 MUTATED CBX8 WILD-TYPE
  R0           10            247
  R1            0              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"
D1500V10, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CBX8 MUTATED                                  0     0
  CBX8 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CBX8 MUTATED                           0     5
  CBX8 WILD-TYPE                        19   171
D1500V11, multiclass
                                  clus
vv                                 CBX8 MUTATED CBX8 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(1501) Variable = C6ORF150 MUTATION ANALYSIS
D1501V1, survival
                    sevent
clus2                  0   1
  C6ORF150 MUTATED     8   1
  C6ORF150 WILD-TYPE 274  72
  C6ORF150 MUTATED C6ORF150 WILD-TYPE 
                 9                346 
  C6ORF150 MUTATED C6ORF150 WILD-TYPE 
                 1                 72 
$`C6ORF150 MUTATED`
TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3864 TCGA-AA-A00A TCGA-AA-A010 TCGA-AU-6004 
        1.02        63.98        53.00        38.04        34.98        27.09 
TCGA-AZ-6601 TCGA-CM-5349 TCGA-D5-5538 
      100.01        30.08        12.26 

$`C6ORF150 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E 
       19.07         7.96        27.02        13.94        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  C6ORF150 MUTATED C6ORF150 WILD-TYPE 
              1.02               0.00 
  C6ORF150 MUTATED C6ORF150 WILD-TYPE 
            100.01             140.38 
  C6ORF150 MUTATED C6ORF150 WILD-TYPE 
            34.980             20.005 
[1] "1.0 - 100.0 (35.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "2.9"
D1501V2, 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       21       107         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C6ORF150 MUTATED           0          0          1          0        0
  C6ORF150 WILD-TYPE        19         10         40         31       35
                    vv
clus                 STAGE IVA STAGE IVB
  C6ORF150 MUTATED           0         0
  C6ORF150 WILD-TYPE        13         1
D1501V3, multiclass
            clus
vv           C6ORF150 MUTATED C6ORF150 WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  4                 21
  STAGE IIA                 2                107
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                0                 10
  STAGE IIIB                1                 40
  STAGE IIIC                0                 31
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C6ORF150 MUTATED     0   1   7   1
  C6ORF150 WILD-TYPE   9  67 241  40
D1501V4, multiclass
    clus
vv   C6ORF150 MUTATED C6ORF150 WILD-TYPE
  T1                0                  9
  T2                1                 67
  T3                7                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
  C6ORF150 MUTATED     8   1   0
  C6ORF150 WILD-TYPE 212  79  66
D1501V5, multiclass
    clus
vv   C6ORF150 MUTATED C6ORF150 WILD-TYPE
  N0                8                212
  N1                1                 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"
D1501V6, binary
                    cls
clus                   0   1
  C6ORF150 MUTATED     9   0
  C6ORF150 WILD-TYPE 274  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF150 MUTATED      9    0
  C6ORF150 WILD-TYPE  274   48
   clus
vv  C6ORF150 MUTATED C6ORF150 WILD-TYPE
  0                9                274
  1                0                 48
[1] 2 2
[1] FALSE
D1501V7, 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
D1501V8, binary
                    cls
clus                   0   1
  C6ORF150 MUTATED     9   0
  C6ORF150 WILD-TYPE 308  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF150 MUTATED      9    0
  C6ORF150 WILD-TYPE  308   48
                               clus
vv                              C6ORF150 MUTATED C6ORF150 WILD-TYPE
  COLON ADENOCARCINOMA                         9                308
  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 249   2  22  21
D1501V9, multiclass
    clus
vv   C6ORF150 MUTATED C6ORF150 WILD-TYPE
  R0                8                249
  R1                0                  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"
D1501V10, 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
D1501V11, 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(1502) Variable = CDS2 MUTATION ANALYSIS
D1502V1, survival
                sevent
clus2              0   1
  CDS2 MUTATED     7   1
  CDS2 WILD-TYPE 275  72
  CDS2 MUTATED CDS2 WILD-TYPE 
             8            347 
  CDS2 MUTATED CDS2 WILD-TYPE 
             1             72 
$`CDS2 MUTATED`
TCGA-AA-3492 TCGA-AA-3525 TCGA-AA-3555 TCGA-AA-3710 TCGA-AA-A010 TCGA-CM-5861 
        3.02         8.05        29.95        26.99        34.98        15.02 
TCGA-CM-5868 TCGA-G4-6628 
       17.03        52.80 

$`CDS2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 
        1.02         9.07        24.03        37.05        36.03        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01         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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       13.78        35.80        26.17        91.79        46.75 

  CDS2 MUTATED CDS2 WILD-TYPE 
          3.02           0.00 
  CDS2 MUTATED CDS2 WILD-TYPE 
         52.80         140.38 
  CDS2 MUTATED CDS2 WILD-TYPE 
         22.01          20.19 
[1] "3.0 - 52.8 (22.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.5"
D1502V2, 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       24       106         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        19         10         40         31       35        12
                vv
clus             STAGE IVB
  CDS2 MUTATED           0
  CDS2 WILD-TYPE         1
D1502V3, multiclass
            clus
vv           CDS2 MUTATED CDS2 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             3            106
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 243  38
D1502V4, multiclass
    clus
vv   CDS2 MUTATED CDS2 WILD-TYPE
  T1            0              9
  T2            1             67
  T3            5            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
  CDS2 MUTATED     7   2   0
  CDS2 WILD-TYPE 213  78  66
D1502V5, multiclass
    clus
vv   CDS2 MUTATED CDS2 WILD-TYPE
  N0            7            213
  N1            2             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"
D1502V6, binary
                cls
clus               0   1
  CDS2 MUTATED     7   1
  CDS2 WILD-TYPE 276  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDS2 MUTATED      7    1
  CDS2 WILD-TYPE  276   47
   clus
vv  CDS2 MUTATED CDS2 WILD-TYPE
  0            7            276
  1            1             47
[1] 2 2
[1] FALSE
D1502V7, 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
D1502V8, binary
                cls
clus               0   1
  CDS2 MUTATED     8   1
  CDS2 WILD-TYPE 309  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDS2 MUTATED      8    1
  CDS2 WILD-TYPE  309   47
                               clus
vv                              CDS2 MUTATED CDS2 WILD-TYPE
  COLON ADENOCARCINOMA                     8            309
  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 249   2  22  20
D1502V9, multiclass
    clus
vv   CDS2 MUTATED CDS2 WILD-TYPE
  R0            8            249
  R1            0              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"
D1502V10, 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
D1502V11, 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(1503) Variable = IDE MUTATION ANALYSIS
D1503V1, survival
               sevent
clus2             0   1
  IDE MUTATED     8   1
  IDE WILD-TYPE 274  72
  IDE MUTATED IDE WILD-TYPE 
            9           346 
  IDE MUTATED IDE WILD-TYPE 
            1            72 
$`IDE MUTATED`
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3982 TCGA-AA-A010 
        3.02         1.02        85.05        14.93        27.02        34.98 
TCGA-AD-6890 TCGA-CM-5861 TCGA-D5-6932 
        0.79        15.02        11.38 

$`IDE WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3502 
       23.87        20.12        19.66        20.28         7.04        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       38.99        37.02         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3986 TCGA-AA-3989 
       26.01        25.02        24.00        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21        56.55         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  IDE MUTATED IDE WILD-TYPE 
         0.79          0.00 
  IDE MUTATED IDE WILD-TYPE 
        85.05        140.38 
  IDE MUTATED IDE WILD-TYPE 
        14.93         20.63 
[1] "0.8 - 85.0 (14.9)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "1.6"
D1503V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IDE MUTATED         0        0        2         3         1         0
  IDE WILD-TYPE      64        1       23       106         7         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IDE MUTATED           1          0          1          1        0         0
  IDE WILD-TYPE        18         10         40         30       35        13
               vv
clus            STAGE IVB
  IDE MUTATED           0
  IDE WILD-TYPE         1
D1503V3, multiclass
            clus
vv           IDE MUTATED IDE WILD-TYPE
  STAGE I              0            64
  STAGE IA             0             1
  STAGE II             2            23
  STAGE IIA            3           106
  STAGE IIB            1             7
  STAGE IIC            0             1
  STAGE III            1            18
  STAGE IIIA           0            10
  STAGE IIIB           1            40
  STAGE IIIC           1            30
  STAGE IV             0            35
  STAGE IVA            0            13
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  IDE MUTATED     1   0   8   1
  IDE WILD-TYPE   8  68 240  40
D1503V4, multiclass
    clus
vv   IDE MUTATED IDE WILD-TYPE
  T1           1             8
  T2           0            68
  T3           8           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
  IDE MUTATED     8   1   1
  IDE WILD-TYPE 212  79  65
D1503V5, multiclass
    clus
vv   IDE MUTATED IDE WILD-TYPE
  N0           8           212
  N1           1            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"
D1503V6, binary
               cls
clus              0   1
  IDE MUTATED     9   0
  IDE WILD-TYPE 274  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  IDE MUTATED      9    0
  IDE WILD-TYPE  274   48
   clus
vv  IDE MUTATED IDE WILD-TYPE
  0           9           274
  1           0            48
[1] 2 2
[1] FALSE
D1503V7, 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
D1503V8, binary
               cls
clus              0   1
  IDE MUTATED    10   0
  IDE WILD-TYPE 307  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  IDE MUTATED     10    0
  IDE WILD-TYPE  307   48
                               clus
vv                              IDE MUTATED IDE WILD-TYPE
  COLON ADENOCARCINOMA                   10           307
  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 249   2  22  21
D1503V9, multiclass
    clus
vv   IDE MUTATED IDE WILD-TYPE
  R0           8           249
  R1           0             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"
D1503V10, 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
D1503V11, 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(1504) Variable = ARID5A MUTATION ANALYSIS
D1504V1, survival
                  sevent
clus2                0   1
  ARID5A MUTATED     6   1
  ARID5A WILD-TYPE 276  72
  ARID5A MUTATED ARID5A WILD-TYPE 
               7              348 
  ARID5A MUTATED ARID5A WILD-TYPE 
               1               72 
$`ARID5A MUTATED`
TCGA-AA-3502 TCGA-AD-5900 TCGA-AZ-6601 TCGA-CA-6715 TCGA-CM-4743 TCGA-CM-5861 
       35.01         0.07       100.01         0.07        23.05        15.02 
TCGA-G4-6628 
       52.80 

$`ARID5A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 
        1.94         2.24         3.06         3.25         3.29         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 

  ARID5A MUTATED ARID5A WILD-TYPE 
            0.07             0.00 
  ARID5A MUTATED ARID5A WILD-TYPE 
          100.01           140.38 
  ARID5A MUTATED ARID5A WILD-TYPE 
          23.050           20.155 
[1] "0.1 - 100.0 (23.1)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.9"
D1504V2, 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       24       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARID5A MUTATED           0          0          1          0        0
  ARID5A WILD-TYPE        19         10         40         31       35
                  vv
clus               STAGE IVA STAGE IVB
  ARID5A MUTATED           0         0
  ARID5A WILD-TYPE        13         1
D1504V3, multiclass
            clus
vv           ARID5A MUTATED ARID5A WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               3              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ARID5A MUTATED     0   3   5   0
  ARID5A WILD-TYPE   9  65 243  41
D1504V4, multiclass
    clus
vv   ARID5A MUTATED ARID5A WILD-TYPE
  T1              0                9
  T2              3               65
  T3              5              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
  ARID5A MUTATED     7   1   0
  ARID5A WILD-TYPE 213  79  66
D1504V5, multiclass
    clus
vv   ARID5A MUTATED ARID5A WILD-TYPE
  N0              7              213
  N1              1               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"
D1504V6, binary
                  cls
clus                 0   1
  ARID5A MUTATED     7   0
  ARID5A WILD-TYPE 276  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID5A MUTATED      7    0
  ARID5A WILD-TYPE  276   48
   clus
vv  ARID5A MUTATED ARID5A WILD-TYPE
  0              7              276
  1              0               48
[1] 2 2
[1] FALSE
D1504V7, 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
D1504V8, binary
                  cls
clus                 0   1
  ARID5A MUTATED     7   1
  ARID5A WILD-TYPE 310  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID5A MUTATED      7    1
  ARID5A WILD-TYPE  310   47
                               clus
vv                              ARID5A MUTATED ARID5A WILD-TYPE
  COLON ADENOCARCINOMA                       7              310
  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 251   2  22  20
D1504V9, multiclass
    clus
vv   ARID5A MUTATED ARID5A WILD-TYPE
  R0              6              251
  R1              0                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"
D1504V10, 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
D1504V11, 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(1505) Variable = CHD5 MUTATION ANALYSIS
D1505V1, survival
                sevent
clus2              0   1
  CHD5 MUTATED    20   4
  CHD5 WILD-TYPE 262  69
  CHD5 MUTATED CHD5 WILD-TYPE 
            24            331 
  CHD5 MUTATED CHD5 WILD-TYPE 
             4             69 
$`CHD5 MUTATED`
TCGA-A6-5665 TCGA-A6-6141 TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3554 TCGA-AA-3672 
       22.06         8.38        63.98        13.02        17.95         0.92 
TCGA-AA-3710 TCGA-AA-3815 TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-3977 TCGA-AD-6964 
       26.99        33.04        53.00        33.01        25.02        10.88 
TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-4950 TCGA-CK-5916 
       27.09        58.39        49.41         0.33        40.34        21.14 
TCGA-CM-4746 TCGA-CM-5868 TCGA-F4-6703 TCGA-F4-6808 TCGA-G4-6293 TCGA-G4-6307 
       37.02        17.03        35.87        33.67       107.67        55.04 

$`CHD5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.09        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        6.97         1.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3555 
       14.01        33.99        21.01        13.02        24.00        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
        5.79        22.42        27.42         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13        83.80        22.36        62.79        61.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 
        0.26         0.10         1.35        17.56       102.44        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32        21.99         2.93         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        16.01        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45         6.18         1.55        16.31        29.59        16.24 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        35.41        19.43        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  CHD5 MUTATED CHD5 WILD-TYPE 
          0.33           0.00 
  CHD5 MUTATED CHD5 WILD-TYPE 
        107.67         140.38 
  CHD5 MUTATED CHD5 WILD-TYPE 
         30.05          19.66 
[1] "0.3 - 107.7 (30.0)" "0.0 - 140.4 (19.7)"
[1] "hr=" "1.6"
D1505V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CHD5 MUTATED         4        0        4         9         1         0
  CHD5 WILD-TYPE      60        1       21       100         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CHD5 MUTATED           3          1          1          0        0         1
  CHD5 WILD-TYPE        16          9         40         31       35        12
                vv
clus             STAGE IVB
  CHD5 MUTATED           0
  CHD5 WILD-TYPE         1
D1505V3, multiclass
            clus
vv           CHD5 MUTATED CHD5 WILD-TYPE
  STAGE I               4             60
  STAGE IA              0              1
  STAGE II              4             21
  STAGE IIA             9            100
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             3             16
  STAGE IIIA            1              9
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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   3  17   4
  CHD5 WILD-TYPE   7  65 231  37
D1505V4, multiclass
    clus
vv   CHD5 MUTATED CHD5 WILD-TYPE
  T1            2              7
  T2            3             65
  T3           17            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    19   5   2
  CHD5 WILD-TYPE 201  75  64
D1505V5, multiclass
    clus
vv   CHD5 MUTATED CHD5 WILD-TYPE
  N0           19            201
  N1            5             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"
D1505V6, binary
                cls
clus               0   1
  CHD5 MUTATED    22   1
  CHD5 WILD-TYPE 261  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD5 MUTATED     22    1
  CHD5 WILD-TYPE  261   47
   clus
vv  CHD5 MUTATED CHD5 WILD-TYPE
  0           22            261
  1            1             47
[1] 2 2
[1] FALSE
D1505V7, binary
                cls
clus               0   1
  CHD5 MUTATED    17   9
  CHD5 WILD-TYPE 153 188
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD5 MUTATED     17    9
  CHD5 WILD-TYPE  153  188
        clus
vv       CHD5 MUTATED CHD5 WILD-TYPE
  FEMALE           17            153
  MALE              9            188
[1] 2 2
[1] FALSE
D1505V8, binary
                cls
clus               0   1
  CHD5 MUTATED    23   3
  CHD5 WILD-TYPE 294  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD5 MUTATED     23    3
  CHD5 WILD-TYPE  294   45
                               clus
vv                              CHD5 MUTATED CHD5 WILD-TYPE
  COLON ADENOCARCINOMA                    23            294
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CHD5 MUTATED    18   1   0   2
  CHD5 WILD-TYPE 239   1  22  19
D1505V9, multiclass
    clus
vv   CHD5 MUTATED CHD5 WILD-TYPE
  R0           18            239
  R1            1              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"
D1505V10, 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    11
  CHD5 WILD-TYPE                        16   165
D1505V11, 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                                      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(1506) Variable = DNAJC18 MUTATION ANALYSIS
D1506V1, survival
                   sevent
clus2                 0   1
  DNAJC18 MUTATED     6   1
  DNAJC18 WILD-TYPE 276  72
  DNAJC18 MUTATED DNAJC18 WILD-TYPE 
                7               348 
  DNAJC18 MUTATED DNAJC18 WILD-TYPE 
                1                72 
$`DNAJC18 MUTATED`
TCGA-A6-5662 TCGA-AA-A00N TCGA-AZ-4315 TCGA-CK-5913 TCGA-CM-5860 TCGA-D5-5540 
       23.61         4.01        58.39        51.32        16.01        13.51 
TCGA-G4-6628 
       52.80 

$`DNAJC18 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        33.53        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       40.34        15.62        49.08        21.99        21.14         2.93 
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 
       12.26        19.59        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 

  DNAJC18 MUTATED DNAJC18 WILD-TYPE 
             4.01              0.00 
  DNAJC18 MUTATED DNAJC18 WILD-TYPE 
            58.39            140.38 
  DNAJC18 MUTATED DNAJC18 WILD-TYPE 
           23.610            20.155 
[1] "4.0 - 58.4 (23.6)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2"  
D1506V2, 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       25       105         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DNAJC18 MUTATED           0          0          0          0        0
  DNAJC18 WILD-TYPE        19         10         41         31       35
                   vv
clus                STAGE IVA STAGE IVB
  DNAJC18 MUTATED           1         0
  DNAJC18 WILD-TYPE        12         1
D1506V3, multiclass
            clus
vv           DNAJC18 MUTATED DNAJC18 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                4               105
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                1                12
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 243  40
D1506V4, multiclass
    clus
vv   DNAJC18 MUTATED DNAJC18 WILD-TYPE
  T1               0                 9
  T2               1                67
  T3               5               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
  DNAJC18 MUTATED     6   0   1
  DNAJC18 WILD-TYPE 214  80  65
D1506V5, multiclass
    clus
vv   DNAJC18 MUTATED DNAJC18 WILD-TYPE
  N0               6               214
  N1               0                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"
D1506V6, binary
                   cls
clus                  0   1
  DNAJC18 MUTATED     5   1
  DNAJC18 WILD-TYPE 278  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DNAJC18 MUTATED      5    1
  DNAJC18 WILD-TYPE  278   47
   clus
vv  DNAJC18 MUTATED DNAJC18 WILD-TYPE
  0               5               278
  1               1                47
[1] 2 2
[1] FALSE
D1506V7, 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
D1506V8, binary
                   cls
clus                  0   1
  DNAJC18 MUTATED     6   1
  DNAJC18 WILD-TYPE 311  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DNAJC18 MUTATED      6    1
  DNAJC18 WILD-TYPE  311   47
                               clus
vv                              DNAJC18 MUTATED DNAJC18 WILD-TYPE
  COLON ADENOCARCINOMA                        6               311
  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 252   2  22  20
D1506V9, multiclass
    clus
vv   DNAJC18 MUTATED DNAJC18 WILD-TYPE
  R0               5               252
  R1               0                 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"
D1506V10, 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
D1506V11, 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(1507) Variable = CXCR7 MUTATION ANALYSIS
D1507V1, survival
                 sevent
clus2               0   1
  CXCR7 MUTATED    11   4
  CXCR7 WILD-TYPE 271  69
  CXCR7 MUTATED CXCR7 WILD-TYPE 
             15             340 
  CXCR7 MUTATED CXCR7 WILD-TYPE 
              4              69 
$`CXCR7 MUTATED`
TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3522 TCGA-AA-3663 TCGA-AA-3692 TCGA-AU-3779 
       20.12        19.66        37.05         6.97        36.00        14.50 
TCGA-AY-6196 TCGA-AZ-6598 TCGA-CK-5912 TCGA-CM-5344 TCGA-CM-6170 TCGA-D5-6927 
        0.20        49.41        49.08        22.03        15.02         9.44 
TCGA-G4-6303 TCGA-G4-6586 TCGA-G4-6588 
       65.85        35.80        26.17 

$`CXCR7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       23.87        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
        9.07        24.03        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
        5.98        37.05        19.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 
        5.79        22.42        27.42        10.88         0.20        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        15.75        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      102.44        40.34        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 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 
       35.41        19.43       107.67        74.56        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        91.79        46.75        52.80 

  CXCR7 MUTATED CXCR7 WILD-TYPE 
            0.2             0.0 
  CXCR7 MUTATED CXCR7 WILD-TYPE 
          65.85          140.38 
  CXCR7 MUTATED CXCR7 WILD-TYPE 
         22.030          20.105 
[1] "0.2 - 65.8 (22.0)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.2"
D1507V2, 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       22       101         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        19         10         40         29       32        13
                 vv
clus              STAGE IVB
  CXCR7 MUTATED           0
  CXCR7 WILD-TYPE         1
D1507V3, multiclass
            clus
vv           CXCR7 MUTATED CXCR7 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              8             101
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             2              29
  STAGE IV               3              32
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CXCR7 MUTATED     0   2  15   2
  CXCR7 WILD-TYPE   9  66 233  39
D1507V4, multiclass
    clus
vv   CXCR7 MUTATED CXCR7 WILD-TYPE
  T1             0               9
  T2             2              66
  T3            15             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
  CXCR7 MUTATED    13   3   3
  CXCR7 WILD-TYPE 207  77  63
D1507V5, multiclass
    clus
vv   CXCR7 MUTATED CXCR7 WILD-TYPE
  N0            13             207
  N1             3              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"
D1507V6, binary
                 cls
clus                0   1
  CXCR7 MUTATED    11   3
  CXCR7 WILD-TYPE 272  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CXCR7 MUTATED     11    3
  CXCR7 WILD-TYPE  272   45
   clus
vv  CXCR7 MUTATED CXCR7 WILD-TYPE
  0            11             272
  1             3              45
[1] 2 2
[1] FALSE
D1507V7, 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
D1507V8, binary
                 cls
clus                0   1
  CXCR7 MUTATED    15   4
  CXCR7 WILD-TYPE 302  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CXCR7 MUTATED     15    4
  CXCR7 WILD-TYPE  302   44
                               clus
vv                              CXCR7 MUTATED CXCR7 WILD-TYPE
  COLON ADENOCARCINOMA                     15             302
  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 243   2  20  20
D1507V9, multiclass
    clus
vv   CXCR7 MUTATED CXCR7 WILD-TYPE
  R0            14             243
  R1             0               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"
D1507V10, 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
D1507V11, 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(1508) Variable = LEMD1 MUTATION ANALYSIS
D1508V1, survival
                 sevent
clus2               0   1
  LEMD1 MUTATED     3   0
  LEMD1 WILD-TYPE 279  73
  LEMD1 MUTATED LEMD1 WILD-TYPE 
              3             352 
  LEMD1 MUTATED LEMD1 WILD-TYPE 
              0              73 
$`LEMD1 MUTATED`
TCGA-A6-5665 TCGA-AD-6895 TCGA-G4-6588 
       22.06         0.72        26.17 

$`LEMD1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        4.21        56.55         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        91.79        46.75        52.80 

  LEMD1 MUTATED LEMD1 WILD-TYPE 
           0.72            0.00 
  LEMD1 MUTATED LEMD1 WILD-TYPE 
          26.17          140.38 
  LEMD1 MUTATED LEMD1 WILD-TYPE 
         22.060          20.155 
[1] "0.7 - 26.2 (22.1)"  "0.0 - 140.4 (20.2)"
[1] "hr="     "3300000"
D1508V2, 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       25       107         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LEMD1 MUTATED           0          0          0          0        0         0
  LEMD1 WILD-TYPE        19         10         41         31       35        13
                 vv
clus              STAGE IVB
  LEMD1 MUTATED           0
  LEMD1 WILD-TYPE         1
D1508V3, multiclass
[1] "Remove cluster labels:" "LEMD1 MUTATED"         
clus
  LEMD1 MUTATED LEMD1 WILD-TYPE 
              2             356 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-4105 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-A6-5656      TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5660 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-A6-5661      TCGA-A6-5662      TCGA-A6-5664      TCGA-A6-5666 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-A6-6137      TCGA-A6-6138      TCGA-A6-6141      TCGA-A6-6142 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-A6-6648      TCGA-A6-6649      TCGA-A6-6651      TCGA-A6-6652 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780      TCGA-A6-6781 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-A6-6782      TCGA-AA-3489      TCGA-AA-3492      TCGA-AA-3496 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3502      TCGA-AA-3510      TCGA-AA-3511      TCGA-AA-3514 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3516      TCGA-AA-3517      TCGA-AA-3518      TCGA-AA-3519 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3520      TCGA-AA-3521      TCGA-AA-3522      TCGA-AA-3524 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3525      TCGA-AA-3526      TCGA-AA-3527      TCGA-AA-3529 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3530      TCGA-AA-3531      TCGA-AA-3532      TCGA-AA-3534 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3538      TCGA-AA-3542      TCGA-AA-3543      TCGA-AA-3544 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3548      TCGA-AA-3549      TCGA-AA-3552      TCGA-AA-3553 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3554      TCGA-AA-3555      TCGA-AA-3556      TCGA-AA-3558 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3560      TCGA-AA-3561      TCGA-AA-3562      TCGA-AA-3655 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3660      TCGA-AA-3662      TCGA-AA-3663      TCGA-AA-3664 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3666      TCGA-AA-3667      TCGA-AA-3672      TCGA-AA-3673 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3678      TCGA-AA-3679      TCGA-AA-3680      TCGA-AA-3681 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3684      TCGA-AA-3685      TCGA-AA-3688      TCGA-AA-3692 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3693      TCGA-AA-3695      TCGA-AA-3696      TCGA-AA-3697 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3710      TCGA-AA-3712      TCGA-AA-3713      TCGA-AA-3715 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3811      TCGA-AA-3812      TCGA-AA-3814      TCGA-AA-3815 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3818      TCGA-AA-3819      TCGA-AA-3821      TCGA-AA-3831 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3833      TCGA-AA-3837      TCGA-AA-3842      TCGA-AA-3844 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3845      TCGA-AA-3846      TCGA-AA-3848      TCGA-AA-3850 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3851      TCGA-AA-3852      TCGA-AA-3854      TCGA-AA-3855 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3856      TCGA-AA-3858      TCGA-AA-3860      TCGA-AA-3861 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3864      TCGA-AA-3866      TCGA-AA-3867      TCGA-AA-3869 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3870      TCGA-AA-3872      TCGA-AA-3875      TCGA-AA-3877 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3930      TCGA-AA-3939      TCGA-AA-3941      TCGA-AA-3947 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3949      TCGA-AA-3950      TCGA-AA-3952      TCGA-AA-3955 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3956      TCGA-AA-3966      TCGA-AA-3968      TCGA-AA-3971 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3972      TCGA-AA-3973      TCGA-AA-3975      TCGA-AA-3976 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3979      TCGA-AA-3980      TCGA-AA-3982      TCGA-AA-3984 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3986      TCGA-AA-3989      TCGA-AA-3994      TCGA-AA-A004 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-A00A      TCGA-AA-A00D      TCGA-AA-A00E      TCGA-AA-A00F 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-A00J      TCGA-AA-A00K      TCGA-AA-A00L      TCGA-AA-A00N 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-A00O      TCGA-AA-A00Q      TCGA-AA-A00R      TCGA-AA-A00U 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-A00W      TCGA-AA-A00Z      TCGA-AA-A010      TCGA-AA-A017 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-A01D      TCGA-AA-A01F      TCGA-AA-A01G      TCGA-AA-A01I 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-A01K      TCGA-AA-A01P      TCGA-AA-A01Q      TCGA-AA-A01R 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-A01S      TCGA-AA-A01T      TCGA-AA-A01V      TCGA-AA-A01X 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-A01Z      TCGA-AA-A022      TCGA-AA-A024      TCGA-AA-A029 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-A02F      TCGA-AA-A02H      TCGA-AA-A02J      TCGA-AA-A02K 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-A02O      TCGA-AA-A02W      TCGA-AA-A02Y      TCGA-AA-A03F 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-A03J      TCGA-AD-5900      TCGA-AD-6548      TCGA-AD-6888 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AD-6889      TCGA-AD-6899      TCGA-AU-3779      TCGA-AU-6004 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AY-4070      TCGA-AY-4071      TCGA-AY-5543      TCGA-AY-6196 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AY-6197      TCGA-AY-6386      TCGA-AZ-4315      TCGA-AZ-4323 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AZ-4616      TCGA-AZ-4681      TCGA-AZ-4682      TCGA-AZ-5403 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AZ-5407      TCGA-AZ-6598      TCGA-AZ-6599      TCGA-AZ-6600 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AZ-6601      TCGA-AZ-6605      TCGA-AZ-6606      TCGA-AZ-6607 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AZ-6608      TCGA-CA-5254      TCGA-CA-5255      TCGA-CA-5796 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CA-5797      TCGA-CA-6715      TCGA-CA-6716      TCGA-CA-6717 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CA-6718      TCGA-CA-6719      TCGA-CK-4947      TCGA-CK-4948 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CK-4950      TCGA-CK-4952      TCGA-CK-5912      TCGA-CK-5913 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CK-5914      TCGA-CK-5915      TCGA-CK-5916      TCGA-CK-6746 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CK-6747      TCGA-CK-6748      TCGA-CK-6751      TCGA-CM-4743 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CM-4744      TCGA-CM-4746      TCGA-CM-4747      TCGA-CM-4752 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CM-5341      TCGA-CM-5344      TCGA-CM-5348      TCGA-CM-5349 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CM-5860      TCGA-CM-5861      TCGA-CM-5862      TCGA-CM-5863 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CM-5864      TCGA-CM-5868      TCGA-CM-6161      TCGA-CM-6162 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CM-6163      TCGA-CM-6164      TCGA-CM-6165      TCGA-CM-6166 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CM-6167      TCGA-CM-6168      TCGA-CM-6169      TCGA-CM-6170 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CM-6171      TCGA-CM-6172      TCGA-CM-6674      TCGA-CM-6675 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CM-6676      TCGA-CM-6677      TCGA-CM-6678      TCGA-CM-6679 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CM-6680      TCGA-D5-5537      TCGA-D5-5538      TCGA-D5-5539 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-D5-5540      TCGA-D5-5541      TCGA-D5-6529      TCGA-D5-6532 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-D5-6533      TCGA-D5-6534      TCGA-D5-6535      TCGA-D5-6536 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-D5-6537      TCGA-D5-6538      TCGA-D5-6539      TCGA-D5-6540 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-D5-6541      TCGA-D5-6898      TCGA-D5-6920      TCGA-D5-6922 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-D5-6923      TCGA-D5-6924      TCGA-D5-6926      TCGA-D5-6927 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-D5-6928      TCGA-D5-6929      TCGA-D5-6930      TCGA-D5-6931 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-D5-6932      TCGA-D5-7000      TCGA-DM-A0X9      TCGA-DM-A0XD 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-DM-A0XF      TCGA-DM-A1D0      TCGA-DM-A1D4      TCGA-DM-A1D6 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-DM-A1D7      TCGA-DM-A1D9      TCGA-DM-A1DA      TCGA-DM-A1DB 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-DM-A1HA      TCGA-DM-A1HB      TCGA-DM-A282      TCGA-DM-A285 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-DM-A28C      TCGA-DM-A28E      TCGA-DM-A28F      TCGA-DM-A28G 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-DM-A28H      TCGA-DM-A28K      TCGA-F4-6459      TCGA-F4-6460 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-F4-6805      TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-G4-6306      TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-G4-6586      TCGA-G4-6625      TCGA-G4-6626      TCGA-G4-6628 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
                 vv
clus               T1  T2  T3  T4
  LEMD1 MUTATED     0   0   3   0
  LEMD1 WILD-TYPE   9  68 245  41
D1508V4, multiclass
    clus
vv   LEMD1 MUTATED LEMD1 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             3             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
  LEMD1 MUTATED     2   1   0
  LEMD1 WILD-TYPE 218  79  66
D1508V5, multiclass
    clus
vv   LEMD1 MUTATED LEMD1 WILD-TYPE
  N0             2             218
  N1             1              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
  LEMD1 MUTATED     2   0
  LEMD1 WILD-TYPE 281  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LEMD1 MUTATED      2    0
  LEMD1 WILD-TYPE  281   48
   clus
vv  LEMD1 MUTATED LEMD1 WILD-TYPE
  0             2             281
  1             0              48
[1] 2 2
[1] FALSE
D1508V7, 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
D1508V8, binary
                 cls
clus                0   1
  LEMD1 MUTATED     3   0
  LEMD1 WILD-TYPE 314  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LEMD1 MUTATED      3    0
  LEMD1 WILD-TYPE  314   48
                               clus
vv                              LEMD1 MUTATED LEMD1 WILD-TYPE
  COLON ADENOCARCINOMA                      3             314
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  LEMD1 MUTATED     2   0   0   0
  LEMD1 WILD-TYPE 255   2  22  21
D1508V9, multiclass
[1] "Remove cluster labels:" "LEMD1 MUTATED"         
clus
  LEMD1 MUTATED LEMD1 WILD-TYPE 
              2             300 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-5657 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-A6-5659      TCGA-A6-5661      TCGA-A6-6781      TCGA-AA-3489 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3492      TCGA-AA-3496      TCGA-AA-3502      TCGA-AA-3510 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3511      TCGA-AA-3514      TCGA-AA-3517      TCGA-AA-3518 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3519      TCGA-AA-3520      TCGA-AA-3521      TCGA-AA-3522 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3524      TCGA-AA-3525      TCGA-AA-3526      TCGA-AA-3527 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3529      TCGA-AA-3530      TCGA-AA-3531      TCGA-AA-3532 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3534      TCGA-AA-3538      TCGA-AA-3542      TCGA-AA-3543 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3544      TCGA-AA-3548      TCGA-AA-3549      TCGA-AA-3552 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3553      TCGA-AA-3554      TCGA-AA-3555      TCGA-AA-3556 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3558      TCGA-AA-3560      TCGA-AA-3561      TCGA-AA-3562 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3655      TCGA-AA-3660      TCGA-AA-3662      TCGA-AA-3663 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3664      TCGA-AA-3666      TCGA-AA-3667      TCGA-AA-3672 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3673      TCGA-AA-3678      TCGA-AA-3679      TCGA-AA-3680 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3681      TCGA-AA-3684      TCGA-AA-3685      TCGA-AA-3688 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3692      TCGA-AA-3693      TCGA-AA-3695      TCGA-AA-3696 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3697      TCGA-AA-3710      TCGA-AA-3712      TCGA-AA-3713 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3715      TCGA-AA-3811      TCGA-AA-3812      TCGA-AA-3814 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3815      TCGA-AA-3818      TCGA-AA-3819      TCGA-AA-3821 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3831      TCGA-AA-3833      TCGA-AA-3837      TCGA-AA-3842 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3844      TCGA-AA-3845      TCGA-AA-3846      TCGA-AA-3848 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3850      TCGA-AA-3851      TCGA-AA-3852      TCGA-AA-3854 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3855      TCGA-AA-3856      TCGA-AA-3858      TCGA-AA-3860 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3861      TCGA-AA-3864      TCGA-AA-3866      TCGA-AA-3867 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3869      TCGA-AA-3870      TCGA-AA-3872      TCGA-AA-3875 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3877      TCGA-AA-3930      TCGA-AA-3939      TCGA-AA-3941 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3947      TCGA-AA-3949      TCGA-AA-3950      TCGA-AA-3952 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3955      TCGA-AA-3956      TCGA-AA-3968      TCGA-AA-3971 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3972      TCGA-AA-3973      TCGA-AA-3975      TCGA-AA-3976 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3979      TCGA-AA-3984      TCGA-AA-3986      TCGA-AA-3989 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3994      TCGA-AA-A004      TCGA-AA-A00A      TCGA-AA-A00D 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-A00E      TCGA-AA-A00F      TCGA-AA-A00J      TCGA-AA-A00K 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-A00L      TCGA-AA-A00N      TCGA-AA-A00O      TCGA-AA-A00Q 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-A00R      TCGA-AA-A00U      TCGA-AA-A00W      TCGA-AA-A00Z 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-A010      TCGA-AA-A017      TCGA-AA-A01D      TCGA-AA-A01F 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-A01G      TCGA-AA-A01I      TCGA-AA-A01K      TCGA-AA-A01P 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-A01Q      TCGA-AA-A01R      TCGA-AA-A01S      TCGA-AA-A01T 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-A01V      TCGA-AA-A01X      TCGA-AA-A01Z      TCGA-AA-A022 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-A024      TCGA-AA-A029      TCGA-AA-A02F      TCGA-AA-A02H 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-A02J      TCGA-AA-A02K      TCGA-AA-A02O      TCGA-AA-A02W 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-A02Y      TCGA-AA-A03F      TCGA-AA-A03J      TCGA-AD-5900 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AD-6548      TCGA-AD-6888      TCGA-AU-3779      TCGA-AU-6004 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AY-4070      TCGA-AY-4071      TCGA-AY-5543      TCGA-AY-6196 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AY-6197      TCGA-AY-6386      TCGA-AZ-4315      TCGA-AZ-4681 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AZ-4682      TCGA-CA-5254      TCGA-CA-5255      TCGA-CA-5796 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CA-5797      TCGA-CA-6715      TCGA-CA-6716      TCGA-CA-6717 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CA-6718      TCGA-CA-6719      TCGA-CK-4947      TCGA-CK-4948 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CK-4950      TCGA-CK-4952      TCGA-CK-5912      TCGA-CK-5913 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CK-5914      TCGA-CK-5915      TCGA-CK-5916      TCGA-CK-6746 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CK-6747      TCGA-CK-6748      TCGA-CK-6751      TCGA-CM-4743 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CM-4744      TCGA-CM-4746      TCGA-CM-4747      TCGA-CM-4752 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CM-5341      TCGA-CM-5344      TCGA-CM-5348      TCGA-CM-5349 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CM-5860      TCGA-CM-5861      TCGA-CM-5862      TCGA-CM-5863 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CM-5864      TCGA-CM-5868      TCGA-CM-6161      TCGA-CM-6162 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CM-6163      TCGA-CM-6164      TCGA-CM-6165      TCGA-CM-6166 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CM-6167      TCGA-CM-6168      TCGA-CM-6169      TCGA-CM-6170 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CM-6171      TCGA-CM-6172      TCGA-CM-6674      TCGA-CM-6675 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CM-6676      TCGA-CM-6677      TCGA-CM-6678      TCGA-CM-6679 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CM-6680      TCGA-D5-5537      TCGA-D5-5538      TCGA-D5-5539 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-D5-5540      TCGA-D5-5541      TCGA-D5-6529      TCGA-D5-6532 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-D5-6533      TCGA-D5-6534      TCGA-D5-6535      TCGA-D5-6536 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-D5-6537      TCGA-D5-6538      TCGA-D5-6539      TCGA-D5-6540 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-D5-6541      TCGA-D5-6898      TCGA-D5-6920      TCGA-D5-6922 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-D5-6923      TCGA-D5-6924      TCGA-D5-6926      TCGA-D5-6927 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-D5-6928      TCGA-D5-6929      TCGA-D5-6930      TCGA-D5-6931 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-D5-6932      TCGA-D5-7000      TCGA-F4-6459      TCGA-F4-6460 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-F4-6805      TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-G4-6306      TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-G4-6586      TCGA-G4-6625      TCGA-G4-6626      TCGA-G4-6628 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
D1508V10, 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
D1508V11, 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(1509) Variable = FUT8 MUTATION ANALYSIS
D1509V1, survival
                sevent
clus2              0   1
  FUT8 MUTATED     9   1
  FUT8 WILD-TYPE 273  72
  FUT8 MUTATED FUT8 WILD-TYPE 
            10            345 
  FUT8 MUTATED FUT8 WILD-TYPE 
             1             72 
$`FUT8 MUTATED`
TCGA-A6-5660 TCGA-A6-5666 TCGA-AA-3555 TCGA-AA-3713 TCGA-AD-5900 TCGA-AZ-6599 
       29.19        32.71        29.95        19.04         0.07         6.77 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-6163 TCGA-CM-6164 
        0.33         0.10        14.04        29.03 

$`FUT8 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41        49.41        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07         0.26         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       17.03        15.02        12.00        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  FUT8 MUTATED FUT8 WILD-TYPE 
          0.07           0.00 
  FUT8 MUTATED FUT8 WILD-TYPE 
         32.71         140.38 
  FUT8 MUTATED FUT8 WILD-TYPE 
         16.54          20.28 
[1] "0.1 - 32.7 (16.5)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.3"
D1509V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FUT8 MUTATED         3        0        0         4         0         1
  FUT8 WILD-TYPE      61        1       25       105         8         0
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FUT8 MUTATED           0          0          0          1        1         0
  FUT8 WILD-TYPE        19         10         41         30       34        13
                vv
clus             STAGE IVB
  FUT8 MUTATED           0
  FUT8 WILD-TYPE         1
D1509V3, multiclass
            clus
vv           FUT8 MUTATED FUT8 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             4            105
  STAGE IIB             0              8
  STAGE IIC             1              0
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            1             30
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  FUT8 MUTATED     1   2   6   1
  FUT8 WILD-TYPE   8  66 242  40
D1509V4, multiclass
    clus
vv   FUT8 MUTATED FUT8 WILD-TYPE
  T1            1              8
  T2            2             66
  T3            6            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
  FUT8 MUTATED     9   0   1
  FUT8 WILD-TYPE 211  80  65
D1509V5, multiclass
    clus
vv   FUT8 MUTATED FUT8 WILD-TYPE
  N0            9            211
  N1            0             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"
D1509V6, binary
                cls
clus               0   1
  FUT8 MUTATED     7   1
  FUT8 WILD-TYPE 276  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  FUT8 MUTATED      7    1
  FUT8 WILD-TYPE  276   47
   clus
vv  FUT8 MUTATED FUT8 WILD-TYPE
  0            7            276
  1            1             47
[1] 2 2
[1] FALSE
D1509V7, binary
                cls
clus               0   1
  FUT8 MUTATED     2   8
  FUT8 WILD-TYPE 168 189
[1] "tbl2"
                cls
clus             [,1] [,2]
  FUT8 MUTATED      2    8
  FUT8 WILD-TYPE  168  189
        clus
vv       FUT8 MUTATED FUT8 WILD-TYPE
  FEMALE            2            168
  MALE              8            189
[1] 2 2
[1] FALSE
D1509V8, binary
                cls
clus               0   1
  FUT8 MUTATED     7   3
  FUT8 WILD-TYPE 310  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  FUT8 MUTATED      7    3
  FUT8 WILD-TYPE  310   45
                               clus
vv                              FUT8 MUTATED FUT8 WILD-TYPE
  COLON ADENOCARCINOMA                     7            310
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  FUT8 MUTATED     4   0   1   2
  FUT8 WILD-TYPE 253   2  21  19
D1509V9, multiclass
    clus
vv   FUT8 MUTATED FUT8 WILD-TYPE
  R0            4            253
  R1            0              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"
D1509V10, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FUT8 MUTATED                                  0     2
  FUT8 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  FUT8 MUTATED                           1     5
  FUT8 WILD-TYPE                        18   171
D1509V11, multiclass
                                  clus
vv                                 FUT8 MUTATED FUT8 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(1510) Variable = ANKRD12 MUTATION ANALYSIS
D1510V1, survival
                   sevent
clus2                 0   1
  ANKRD12 MUTATED    17   3
  ANKRD12 WILD-TYPE 265  70
  ANKRD12 MUTATED ANKRD12 WILD-TYPE 
               20               335 
  ANKRD12 MUTATED ANKRD12 WILD-TYPE 
                3                70 
$`ANKRD12 MUTATED`
TCGA-A6-2676 TCGA-AA-3502 TCGA-AA-3532 TCGA-AA-3713 TCGA-AA-3815 TCGA-AA-3864 
       42.90        35.01        29.00        19.04        33.04        53.00 
TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A00U TCGA-AA-A010 TCGA-AD-5900 TCGA-AU-6004 
       25.02         4.01        17.03        34.98         0.07        27.09 
TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-5861 TCGA-D5-6540 TCGA-DM-A1HB 
       58.39         0.33         0.10        15.02        16.14       135.65 
TCGA-DM-A285 TCGA-F4-6856 
        6.12        19.43 

$`ANKRD12 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
        0.00        19.07        34.03        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       85.05        26.99        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A00Z 
       38.04        27.02        42.02         0.99        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07         0.26         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       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 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  ANKRD12 MUTATED ANKRD12 WILD-TYPE 
             0.07              0.00 
  ANKRD12 MUTATED ANKRD12 WILD-TYPE 
           135.65            140.38 
  ANKRD12 MUTATED ANKRD12 WILD-TYPE 
           22.225            20.190 
[1] "0.1 - 135.7 (22.2)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.4"
D1510V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ANKRD12 MUTATED         5        0        1         7         4         0
  ANKRD12 WILD-TYPE      59        1       24       102         4         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANKRD12 MUTATED           1          0          2          0        2
  ANKRD12 WILD-TYPE        18         10         39         31       33
                   vv
clus                STAGE IVA STAGE IVB
  ANKRD12 MUTATED           0         0
  ANKRD12 WILD-TYPE        13         1
D1510V3, multiclass
            clus
vv           ANKRD12 MUTATED ANKRD12 WILD-TYPE
  STAGE I                  5                59
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                7               102
  STAGE IIB                4                 4
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               0                10
  STAGE IIIB               2                39
  STAGE IIIC               0                31
  STAGE IV                 2                33
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ANKRD12 MUTATED     0   6  13   4
  ANKRD12 WILD-TYPE   9  62 235  37
D1510V4, multiclass
    clus
vv   ANKRD12 MUTATED ANKRD12 WILD-TYPE
  T1               0                 9
  T2               6                62
  T3              13               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
  ANKRD12 MUTATED    19   2   2
  ANKRD12 WILD-TYPE 201  78  64
D1510V5, multiclass
    clus
vv   ANKRD12 MUTATED ANKRD12 WILD-TYPE
  N0              19               201
  N1               2                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"
D1510V6, binary
                   cls
clus                  0   1
  ANKRD12 MUTATED    18   2
  ANKRD12 WILD-TYPE 265  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD12 MUTATED     18    2
  ANKRD12 WILD-TYPE  265   46
   clus
vv  ANKRD12 MUTATED ANKRD12 WILD-TYPE
  0              18               265
  1               2                46
[1] 2 2
[1] FALSE
D1510V7, binary
                   cls
clus                  0   1
  ANKRD12 MUTATED     8  15
  ANKRD12 WILD-TYPE 162 182
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD12 MUTATED      8   15
  ANKRD12 WILD-TYPE  162  182
        clus
vv       ANKRD12 MUTATED ANKRD12 WILD-TYPE
  FEMALE               8               162
  MALE                15               182
[1] 2 2
[1] FALSE
D1510V8, binary
                   cls
clus                  0   1
  ANKRD12 MUTATED    17   6
  ANKRD12 WILD-TYPE 300  42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD12 MUTATED     17    6
  ANKRD12 WILD-TYPE  300   42
                               clus
vv                              ANKRD12 MUTATED ANKRD12 WILD-TYPE
  COLON ADENOCARCINOMA                       17               300
  COLON MUCINOUS ADENOCARCINOMA               6                42
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ANKRD12 MUTATED    16   0   1   3
  ANKRD12 WILD-TYPE 241   2  21  18
D1510V9, multiclass
    clus
vv   ANKRD12 MUTATED ANKRD12 WILD-TYPE
  R0              16               241
  R1               0                 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"
D1510V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ANKRD12 MUTATED                                  0     2
  ANKRD12 WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ANKRD12 MUTATED                           0    10
  ANKRD12 WILD-TYPE                        19   166
D1510V11, multiclass
                                  clus
vv                                 ANKRD12 MUTATED ANKRD12 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(1511) Variable = FSCB MUTATION ANALYSIS
D1511V1, survival
                sevent
clus2              0   1
  FSCB MUTATED    14   6
  FSCB WILD-TYPE 268  67
  FSCB MUTATED FSCB WILD-TYPE 
            20            335 
  FSCB MUTATED FSCB WILD-TYPE 
             6             67 
$`FSCB MUTATED`
TCGA-A6-5661 TCGA-AA-3555 TCGA-AA-3663 TCGA-AA-3715 TCGA-AA-3968 TCGA-AA-3977 
       33.53        29.95         6.97        19.04        21.99        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6964 TCGA-AY-5543 TCGA-AZ-4616 TCGA-AZ-6601 
        4.01        34.98        10.88        15.75         5.13       100.01 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CM-4752 TCGA-CM-5862 TCGA-CM-6166 TCGA-D5-6932 
        0.26         0.33        13.02         5.03        21.99        11.38 
TCGA-DM-A1HB TCGA-G4-6299 
      135.65        74.56 

$`FSCB WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        17.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
        2.01        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 
        0.20        14.50        27.09        16.31         0.95         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82        58.39         1.41        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        61.41        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       16.01        15.02        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 
       12.00        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       19.43       107.67        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  FSCB MUTATED FSCB WILD-TYPE 
          0.26           0.00 
  FSCB MUTATED FSCB WILD-TYPE 
        135.65         140.38 
  FSCB MUTATED FSCB WILD-TYPE 
        17.395         20.280 
[1] "0.3 - 135.7 (17.4)" "0.0 - 140.4 (20.3)"
[1] "hr=" "1.4"
D1511V2, 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       22       103         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        19         10         40         30       34        11
                vv
clus             STAGE IVB
  FSCB MUTATED           0
  FSCB WILD-TYPE         1
D1511V3, multiclass
            clus
vv           FSCB MUTATED FSCB WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              3             22
  STAGE IIA             6            103
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            1             30
  STAGE IV              1             34
  STAGE IVA             2             11
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  65 234  38
D1511V4, multiclass
    clus
vv   FSCB MUTATED FSCB WILD-TYPE
  T1            0              9
  T2            3             65
  T3           14            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
  FSCB MUTATED    14   3   3
  FSCB WILD-TYPE 206  77  63
D1511V5, multiclass
    clus
vv   FSCB MUTATED FSCB WILD-TYPE
  N0           14            206
  N1            3             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"
D1511V6, binary
                cls
clus               0   1
  FSCB MUTATED    15   3
  FSCB WILD-TYPE 268  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  FSCB MUTATED     15    3
  FSCB WILD-TYPE  268   45
   clus
vv  FSCB MUTATED FSCB WILD-TYPE
  0           15            268
  1            3             45
[1] 2 2
[1] FALSE
D1511V7, 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
D1511V8, binary
                cls
clus               0   1
  FSCB MUTATED    17   3
  FSCB WILD-TYPE 300  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  FSCB MUTATED     17    3
  FSCB WILD-TYPE  300   45
                               clus
vv                              FSCB MUTATED FSCB WILD-TYPE
  COLON ADENOCARCINOMA                    17            300
  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 244   2  22  19
D1511V9, multiclass
    clus
vv   FSCB MUTATED FSCB WILD-TYPE
  R0           13            244
  R1            0              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"
D1511V10, 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
D1511V11, 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(1512) Variable = SLC9A2 MUTATION ANALYSIS
D1512V1, survival
                  sevent
clus2                0   1
  SLC9A2 MUTATED     8   1
  SLC9A2 WILD-TYPE 274  72
  SLC9A2 MUTATED SLC9A2 WILD-TYPE 
               9              346 
  SLC9A2 MUTATED SLC9A2 WILD-TYPE 
               1               72 
$`SLC9A2 MUTATED`
TCGA-AA-3821 TCGA-AA-3949 TCGA-AD-6889 TCGA-AZ-4315 TCGA-AZ-6607 TCGA-CA-6717 
        1.02        26.01        56.55        58.39         3.19         0.33 
TCGA-CK-4950 TCGA-CM-5861 TCGA-F4-6807 
       40.34        15.02        16.24 

$`SLC9A2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 
      100.01        29.56         5.23        11.74         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
        1.35        17.56       102.44        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  SLC9A2 MUTATED SLC9A2 WILD-TYPE 
            0.33             0.00 
  SLC9A2 MUTATED SLC9A2 WILD-TYPE 
           58.39           140.38 
  SLC9A2 MUTATED SLC9A2 WILD-TYPE 
          16.240           20.235 
[1] "0.3 - 58.4 (16.2)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.8"
D1512V2, 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       25       105         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC9A2 MUTATED           0          1          1          1        1
  SLC9A2 WILD-TYPE        19          9         40         30       34
                  vv
clus               STAGE IVA STAGE IVB
  SLC9A2 MUTATED           0         0
  SLC9A2 WILD-TYPE        13         1
D1512V3, multiclass
            clus
vv           SLC9A2 MUTATED SLC9A2 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               4              105
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              1                9
  STAGE IIIB              1               40
  STAGE IIIC              1               30
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SLC9A2 MUTATED     0   1   7   2
  SLC9A2 WILD-TYPE   9  67 241  39
D1512V4, multiclass
    clus
vv   SLC9A2 MUTATED SLC9A2 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              7              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
  SLC9A2 MUTATED     6   2   2
  SLC9A2 WILD-TYPE 214  78  64
D1512V5, multiclass
    clus
vv   SLC9A2 MUTATED SLC9A2 WILD-TYPE
  N0              6              214
  N1              2               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"
D1512V6, binary
                  cls
clus                 0   1
  SLC9A2 MUTATED     8   1
  SLC9A2 WILD-TYPE 275  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC9A2 MUTATED      8    1
  SLC9A2 WILD-TYPE  275   47
   clus
vv  SLC9A2 MUTATED SLC9A2 WILD-TYPE
  0              8              275
  1              1               47
[1] 2 2
[1] FALSE
D1512V7, 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
D1512V8, binary
                  cls
clus                 0   1
  SLC9A2 MUTATED     7   3
  SLC9A2 WILD-TYPE 310  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC9A2 MUTATED      7    3
  SLC9A2 WILD-TYPE  310   45
                               clus
vv                              SLC9A2 MUTATED SLC9A2 WILD-TYPE
  COLON ADENOCARCINOMA                       7              310
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SLC9A2 MUTATED     5   1   0   2
  SLC9A2 WILD-TYPE 252   1  22  19
D1512V9, multiclass
    clus
vv   SLC9A2 MUTATED SLC9A2 WILD-TYPE
  R0              5              252
  R1              1                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"
D1512V10, 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
D1512V11, 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(1513) Variable = CASP5 MUTATION ANALYSIS
D1513V1, survival
                 sevent
clus2               0   1
  CASP5 MUTATED     8   4
  CASP5 WILD-TYPE 274  69
  CASP5 MUTATED CASP5 WILD-TYPE 
             12             343 
  CASP5 MUTATED CASP5 WILD-TYPE 
              4              69 
$`CASP5 MUTATED`
TCGA-A6-5662 TCGA-AA-3510 TCGA-AA-3833 TCGA-AA-3977 TCGA-AA-A00N TCGA-AD-6895 
       23.61        63.98        15.95        25.02         4.01         0.72 
TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6608 TCGA-CM-6676 TCGA-D5-6927 TCGA-G4-6588 
       62.79        49.41         1.94        11.08         9.44        26.17 

$`CASP5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        33.53        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
        0.07        21.37         4.21        56.55         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 
       58.39         1.41         5.13        83.80        22.36        61.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 
       52.80 

  CASP5 MUTATED CASP5 WILD-TYPE 
           0.72            0.00 
  CASP5 MUTATED CASP5 WILD-TYPE 
          63.98          140.38 
  CASP5 MUTATED CASP5 WILD-TYPE 
          19.78           20.19 
[1] "0.7 - 64.0 (19.8)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.6"
D1513V2, 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       22       105         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CASP5 MUTATED           0          1          0          0        0         1
  CASP5 WILD-TYPE        19          9         41         31       35        12
                 vv
clus              STAGE IVB
  CASP5 MUTATED           0
  CASP5 WILD-TYPE         1
D1513V3, multiclass
            clus
vv           CASP5 MUTATED CASP5 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              4             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  65 239  40
D1513V4, multiclass
    clus
vv   CASP5 MUTATED CASP5 WILD-TYPE
  T1             0               9
  T2             3              65
  T3             9             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
  CASP5 MUTATED    10   2   1
  CASP5 WILD-TYPE 210  78  65
D1513V5, multiclass
    clus
vv   CASP5 MUTATED CASP5 WILD-TYPE
  N0            10             210
  N1             2              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
  CASP5 MUTATED     8   1
  CASP5 WILD-TYPE 275  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP5 MUTATED      8    1
  CASP5 WILD-TYPE  275   47
   clus
vv  CASP5 MUTATED CASP5 WILD-TYPE
  0             8             275
  1             1              47
[1] 2 2
[1] FALSE
D1513V7, 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
D1513V8, binary
                 cls
clus                0   1
  CASP5 MUTATED    12   1
  CASP5 WILD-TYPE 305  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP5 MUTATED     12    1
  CASP5 WILD-TYPE  305   47
                               clus
vv                              CASP5 MUTATED CASP5 WILD-TYPE
  COLON ADENOCARCINOMA                     12             305
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CASP5 MUTATED     7   0   0   0
  CASP5 WILD-TYPE 250   2  22  21
D1513V9, multiclass
    clus
vv   CASP5 MUTATED CASP5 WILD-TYPE
  R0             7             250
  R1             0               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"
D1513V10, 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
D1513V11, 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(1514) Variable = TOMM70A MUTATION ANALYSIS
D1514V1, survival
                   sevent
clus2                 0   1
  TOMM70A MUTATED     9   1
  TOMM70A WILD-TYPE 273  72
  TOMM70A MUTATED TOMM70A WILD-TYPE 
               10               345 
  TOMM70A MUTATED TOMM70A WILD-TYPE 
                1                72 
$`TOMM70A MUTATED`
TCGA-AA-3554 TCGA-AA-3815 TCGA-AA-A010 TCGA-AA-A01R TCGA-AZ-4315 TCGA-AZ-6599 
       17.95        33.04        34.98        35.01        58.39         6.77 
TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6625 TCGA-G4-6628 
       74.56        53.62        91.79        52.80 

$`TOMM70A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41        49.41        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 
       35.41        19.43       107.67        65.85        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 
       35.80        26.17        46.75 

  TOMM70A MUTATED TOMM70A WILD-TYPE 
             6.77              0.00 
  TOMM70A MUTATED TOMM70A WILD-TYPE 
            91.79            140.38 
  TOMM70A MUTATED TOMM70A WILD-TYPE 
           43.905            19.990 
[1] "6.8 - 91.8 (43.9)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "3.7"
D1514V2, 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       25       105         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TOMM70A MUTATED           1          0          0          1        0
  TOMM70A WILD-TYPE        18         10         41         30       35
                   vv
clus                STAGE IVA STAGE IVB
  TOMM70A MUTATED           0         0
  TOMM70A WILD-TYPE        13         1
D1514V3, multiclass
            clus
vv           TOMM70A MUTATED TOMM70A WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                4               105
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               1                30
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TOMM70A MUTATED     0   2   6   2
  TOMM70A WILD-TYPE   9  66 242  39
D1514V4, multiclass
    clus
vv   TOMM70A MUTATED TOMM70A WILD-TYPE
  T1               0                 9
  T2               2                66
  T3               6               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
  TOMM70A MUTATED     8   0   2
  TOMM70A WILD-TYPE 212  80  64
D1514V5, multiclass
    clus
vv   TOMM70A MUTATED TOMM70A WILD-TYPE
  N0               8               212
  N1               0                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"
D1514V6, binary
                   cls
clus                  0   1
  TOMM70A MUTATED     9   0
  TOMM70A WILD-TYPE 274  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TOMM70A MUTATED      9    0
  TOMM70A WILD-TYPE  274   48
   clus
vv  TOMM70A MUTATED TOMM70A WILD-TYPE
  0               9               274
  1               0                48
[1] 2 2
[1] FALSE
D1514V7, 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
D1514V8, binary
                   cls
clus                  0   1
  TOMM70A MUTATED     9   1
  TOMM70A WILD-TYPE 308  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TOMM70A MUTATED      9    1
  TOMM70A WILD-TYPE  308   47
                               clus
vv                              TOMM70A MUTATED TOMM70A WILD-TYPE
  COLON ADENOCARCINOMA                        9               308
  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 248   2  22  21
D1514V9, multiclass
    clus
vv   TOMM70A MUTATED TOMM70A WILD-TYPE
  R0               9               248
  R1               0                 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"
D1514V10, 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
D1514V11, 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(1515) Variable = GPX6 MUTATION ANALYSIS
D1515V1, survival
                sevent
clus2              0   1
  GPX6 MUTATED     4   3
  GPX6 WILD-TYPE 278  70
  GPX6 MUTATED GPX6 WILD-TYPE 
             7            348 
  GPX6 MUTATED GPX6 WILD-TYPE 
             3             70 
$`GPX6 MUTATED`
TCGA-A6-6649 TCGA-AA-3510 TCGA-AA-3845 TCGA-AA-A010 TCGA-CK-5914 TCGA-DM-A1DB 
       24.16        63.98         0.00        34.98        21.99        44.32 
TCGA-G4-6303 
       65.85 

$`GPX6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02        14.93        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        51.32        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 
       35.41        19.43       107.67        74.56        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  GPX6 MUTATED GPX6 WILD-TYPE 
             0              0 
  GPX6 MUTATED GPX6 WILD-TYPE 
         65.85         140.38 
  GPX6 MUTATED GPX6 WILD-TYPE 
        34.980         20.005 
[1] "0.0 - 65.8 (35.0)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1.5"
D1515V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GPX6 MUTATED         0        0        1         2         2         0
  GPX6 WILD-TYPE      64        1       24       107         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        19         10         39         31       34        13
                vv
clus             STAGE IVB
  GPX6 MUTATED           0
  GPX6 WILD-TYPE         1
D1515V3, multiclass
            clus
vv           GPX6 MUTATED GPX6 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             2            107
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            2             39
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GPX6 MUTATED     0   0   6   2
  GPX6 WILD-TYPE   9  68 242  39
D1515V4, multiclass
    clus
vv   GPX6 MUTATED GPX6 WILD-TYPE
  T1            0              9
  T2            0             68
  T3            6            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
  GPX6 MUTATED     5   3   0
  GPX6 WILD-TYPE 215  77  66
D1515V5, multiclass
    clus
vv   GPX6 MUTATED GPX6 WILD-TYPE
  N0            5            215
  N1            3             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"
D1515V6, binary
                cls
clus               0   1
  GPX6 MUTATED     5   1
  GPX6 WILD-TYPE 278  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPX6 MUTATED      5    1
  GPX6 WILD-TYPE  278   47
   clus
vv  GPX6 MUTATED GPX6 WILD-TYPE
  0            5            278
  1            1             47
[1] 2 2
[1] FALSE
D1515V7, binary
                cls
clus               0   1
  GPX6 MUTATED     4   4
  GPX6 WILD-TYPE 166 193
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPX6 MUTATED      4    4
  GPX6 WILD-TYPE  166  193
        clus
vv       GPX6 MUTATED GPX6 WILD-TYPE
  FEMALE            4            166
  MALE              4            193
[1] 2 2
[1] FALSE
D1515V8, binary
                cls
clus               0   1
  GPX6 MUTATED     8   0
  GPX6 WILD-TYPE 309  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPX6 MUTATED      8    0
  GPX6 WILD-TYPE  309   48
                               clus
vv                              GPX6 MUTATED GPX6 WILD-TYPE
  COLON ADENOCARCINOMA                     8            309
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  GPX6 MUTATED     4   0   0   2
  GPX6 WILD-TYPE 253   2  22  19
D1515V9, multiclass
    clus
vv   GPX6 MUTATED GPX6 WILD-TYPE
  R0            4            253
  R1            0              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"
D1515V10, 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     5
  GPX6 WILD-TYPE                        19   171
D1515V11, 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                                       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(1516) Variable = OR5H1 MUTATION ANALYSIS
D1516V1, survival
                 sevent
clus2               0   1
  OR5H1 MUTATED     7   2
  OR5H1 WILD-TYPE 275  71
  OR5H1 MUTATED OR5H1 WILD-TYPE 
              9             346 
  OR5H1 MUTATED OR5H1 WILD-TYPE 
              2              71 
$`OR5H1 MUTATED`
TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5666 TCGA-AA-3949 TCGA-AA-A01Q TCGA-AD-6889 
       30.44        33.53        32.71        26.01         1.02        56.55 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-D5-6541 
       49.41        12.10        15.58 

$`OR5H1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       32.91        31.63        29.19        23.61        22.09        22.06 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       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        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37         4.21         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       61.41         6.77       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        16.14         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  OR5H1 MUTATED OR5H1 WILD-TYPE 
           1.02            0.00 
  OR5H1 MUTATED OR5H1 WILD-TYPE 
          56.55          140.38 
  OR5H1 MUTATED OR5H1 WILD-TYPE 
          30.44           20.07 
[1] "1.0 - 56.5 (30.4)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1"  
D1516V2, 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       23       105         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        19         10         40         31       34        13
                 vv
clus              STAGE IVB
  OR5H1 MUTATED           0
  OR5H1 WILD-TYPE         1
D1516V3, multiclass
            clus
vv           OR5H1 MUTATED OR5H1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              4             105
  STAGE IIB              0               8
  STAGE IIC              1               0
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR5H1 MUTATED     0   1   7   2
  OR5H1 WILD-TYPE   9  67 241  39
D1516V4, multiclass
    clus
vv   OR5H1 MUTATED OR5H1 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             7             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
  OR5H1 MUTATED     8   2   0
  OR5H1 WILD-TYPE 212  78  66
D1516V5, multiclass
    clus
vv   OR5H1 MUTATED OR5H1 WILD-TYPE
  N0             8             212
  N1             2              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"
D1516V6, binary
                 cls
clus                0   1
  OR5H1 MUTATED     8   1
  OR5H1 WILD-TYPE 275  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5H1 MUTATED      8    1
  OR5H1 WILD-TYPE  275   47
   clus
vv  OR5H1 MUTATED OR5H1 WILD-TYPE
  0             8             275
  1             1              47
[1] 2 2
[1] FALSE
D1516V7, 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
D1516V8, binary
                 cls
clus                0   1
  OR5H1 MUTATED     9   1
  OR5H1 WILD-TYPE 308  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5H1 MUTATED      9    1
  OR5H1 WILD-TYPE  308   47
                               clus
vv                              OR5H1 MUTATED OR5H1 WILD-TYPE
  COLON ADENOCARCINOMA                      9             308
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  OR5H1 MUTATED     6   0   0   0
  OR5H1 WILD-TYPE 251   2  22  21
D1516V9, multiclass
    clus
vv   OR5H1 MUTATED OR5H1 WILD-TYPE
  R0             6             251
  R1             0               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"
D1516V10, 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
D1516V11, 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(1517) Variable = ESYT1 MUTATION ANALYSIS
D1517V1, survival
                 sevent
clus2               0   1
  ESYT1 MUTATED     6   2
  ESYT1 WILD-TYPE 276  71
  ESYT1 MUTATED ESYT1 WILD-TYPE 
              8             347 
  ESYT1 MUTATED ESYT1 WILD-TYPE 
              2              71 
$`ESYT1 MUTATED`
TCGA-A6-6653 TCGA-A6-6780 TCGA-AA-3864 TCGA-AD-6965 TCGA-AY-5543 TCGA-CK-5913 
       24.39        20.12        53.00         0.20        15.75        51.32 
TCGA-DM-A1DA TCGA-F4-6809 
        7.50        13.25 

$`ESYT1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-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-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       29.59        16.24        33.67         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  ESYT1 MUTATED ESYT1 WILD-TYPE 
            0.2             0.0 
  ESYT1 MUTATED ESYT1 WILD-TYPE 
          53.00          140.38 
  ESYT1 MUTATED ESYT1 WILD-TYPE 
         17.935          20.280 
[1] "0.2 - 53.0 (17.9)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.2"
D1517V2, 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       24       107         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ESYT1 MUTATED           0          0          0          1        0         2
  ESYT1 WILD-TYPE        19         10         41         30       35        11
                 vv
clus              STAGE IVB
  ESYT1 MUTATED           0
  ESYT1 WILD-TYPE         1
D1517V3, multiclass
            clus
vv           ESYT1 MUTATED ESYT1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              2             107
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              2              11
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 242  39
D1517V4, multiclass
    clus
vv   ESYT1 MUTATED ESYT1 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             6             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
  ESYT1 MUTATED     5   2   2
  ESYT1 WILD-TYPE 215  78  64
D1517V5, multiclass
    clus
vv   ESYT1 MUTATED ESYT1 WILD-TYPE
  N0             5             215
  N1             2              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"
D1517V6, binary
                 cls
clus                0   1
  ESYT1 MUTATED     3   2
  ESYT1 WILD-TYPE 280  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESYT1 MUTATED      3    2
  ESYT1 WILD-TYPE  280   46
   clus
vv  ESYT1 MUTATED ESYT1 WILD-TYPE
  0             3             280
  1             2              46
[1] 2 2
[1] FALSE
D1517V7, 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
D1517V8, binary
                 cls
clus                0   1
  ESYT1 MUTATED     8   1
  ESYT1 WILD-TYPE 309  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESYT1 MUTATED      8    1
  ESYT1 WILD-TYPE  309   47
                               clus
vv                              ESYT1 MUTATED ESYT1 WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ESYT1 MUTATED     3   0   0   2
  ESYT1 WILD-TYPE 254   2  22  19
D1517V9, multiclass
    clus
vv   ESYT1 MUTATED ESYT1 WILD-TYPE
  R0             3             254
  R1             0               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"
D1517V10, 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
D1517V11, 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(1518) Variable = TSPAN7 MUTATION ANALYSIS
D1518V1, survival
                  sevent
clus2                0   1
  TSPAN7 MUTATED     6   2
  TSPAN7 WILD-TYPE 276  71
  TSPAN7 MUTATED TSPAN7 WILD-TYPE 
               8              347 
  TSPAN7 MUTATED TSPAN7 WILD-TYPE 
               2               71 
$`TSPAN7 MUTATED`
TCGA-A6-5661 TCGA-A6-6654 TCGA-AA-3492 TCGA-AA-3966 TCGA-AD-5900 TCGA-AU-6004 
       33.53        23.87         3.02         2.01         0.07        27.09 
TCGA-D5-6930 TCGA-DM-A285 
        1.51         6.12 

$`TSPAN7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  TSPAN7 MUTATED TSPAN7 WILD-TYPE 
            0.07             0.00 
  TSPAN7 MUTATED TSPAN7 WILD-TYPE 
           33.53           140.38 
  TSPAN7 MUTATED TSPAN7 WILD-TYPE 
            4.57            20.28 
[1] "0.1 - 33.5 (4.6)"   "0.0 - 140.4 (20.3)"
[1] "hr=" "2.6"
D1518V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TSPAN7 MUTATED         2        0        1         3         0         0
  TSPAN7 WILD-TYPE      62        1       24       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TSPAN7 MUTATED           0          0          1          0        1
  TSPAN7 WILD-TYPE        19         10         40         31       34
                  vv
clus               STAGE IVA STAGE IVB
  TSPAN7 MUTATED           0         0
  TSPAN7 WILD-TYPE        13         1
D1518V3, multiclass
            clus
vv           TSPAN7 MUTATED TSPAN7 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               3              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TSPAN7 MUTATED     0   2   6   0
  TSPAN7 WILD-TYPE   9  66 242  41
D1518V4, multiclass
    clus
vv   TSPAN7 MUTATED TSPAN7 WILD-TYPE
  T1              0                9
  T2              2               66
  T3              6              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     6   1   1
  TSPAN7 WILD-TYPE 214  79  65
D1518V5, multiclass
    clus
vv   TSPAN7 MUTATED TSPAN7 WILD-TYPE
  N0              6              214
  N1              1               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"
D1518V6, binary
                  cls
clus                 0   1
  TSPAN7 MUTATED     6   1
  TSPAN7 WILD-TYPE 277  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TSPAN7 MUTATED      6    1
  TSPAN7 WILD-TYPE  277   47
   clus
vv  TSPAN7 MUTATED TSPAN7 WILD-TYPE
  0              6              277
  1              1               47
[1] 2 2
[1] FALSE
D1518V7, binary
                  cls
clus                 0   1
  TSPAN7 MUTATED     6   2
  TSPAN7 WILD-TYPE 164 195
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TSPAN7 MUTATED      6    2
  TSPAN7 WILD-TYPE  164  195
        clus
vv       TSPAN7 MUTATED TSPAN7 WILD-TYPE
  FEMALE              6              164
  MALE                2              195
[1] 2 2
[1] FALSE
D1518V8, binary
                  cls
clus                 0   1
  TSPAN7 MUTATED     4   4
  TSPAN7 WILD-TYPE 313  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TSPAN7 MUTATED      4    4
  TSPAN7 WILD-TYPE  313   44
                               clus
vv                              TSPAN7 MUTATED TSPAN7 WILD-TYPE
  COLON ADENOCARCINOMA                       4              313
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TSPAN7 MUTATED     5   0   0   0
  TSPAN7 WILD-TYPE 252   2  22  21
D1518V9, multiclass
    clus
vv   TSPAN7 MUTATED TSPAN7 WILD-TYPE
  R0              5              252
  R1              0                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"
D1518V10, 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
D1518V11, 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(1519) Variable = OR4N2 MUTATION ANALYSIS
D1519V1, survival
                 sevent
clus2               0   1
  OR4N2 MUTATED     6   4
  OR4N2 WILD-TYPE 276  69
  OR4N2 MUTATED OR4N2 WILD-TYPE 
             10             345 
  OR4N2 MUTATED OR4N2 WILD-TYPE 
              4              69 
$`OR4N2 MUTATED`
TCGA-AA-3715 TCGA-AA-3858 TCGA-AZ-4315 TCGA-CK-4952 TCGA-D5-6537 TCGA-D5-6931 
       19.04        31.07        58.39        15.62         4.80        12.00 
TCGA-DM-A1D4 TCGA-F4-6570 TCGA-G4-6309 TCGA-G4-6586 
       92.75         6.18        51.75        35.80 

$`OR4N2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
       32.05         0.99        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       40.34        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 
       18.25         1.32        43.27        15.12        17.85        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.38        13.45        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 
       45.11        36.72        36.00        22.09        13.78        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  OR4N2 MUTATED OR4N2 WILD-TYPE 
            4.8             0.0 
  OR4N2 MUTATED OR4N2 WILD-TYPE 
          92.75          140.38 
  OR4N2 MUTATED OR4N2 WILD-TYPE 
         25.055          20.190 
[1] "4.8 - 92.8 (25.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.5"
D1519V2, 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       24       105         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR4N2 MUTATED           1          0          2          1        0         0
  OR4N2 WILD-TYPE        18         10         39         30       35        13
                 vv
clus              STAGE IVB
  OR4N2 MUTATED           0
  OR4N2 WILD-TYPE         1
D1519V3, multiclass
            clus
vv           OR4N2 MUTATED OR4N2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              4             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR4N2 MUTATED     0   1   7   2
  OR4N2 WILD-TYPE   9  67 241  39
D1519V4, multiclass
    clus
vv   OR4N2 MUTATED OR4N2 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             7             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
  OR4N2 MUTATED     6   2   2
  OR4N2 WILD-TYPE 214  78  64
D1519V5, multiclass
    clus
vv   OR4N2 MUTATED OR4N2 WILD-TYPE
  N0             6             214
  N1             2              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"
D1519V6, binary
                 cls
clus                0   1
  OR4N2 MUTATED     9   0
  OR4N2 WILD-TYPE 274  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4N2 MUTATED      9    0
  OR4N2 WILD-TYPE  274   48
   clus
vv  OR4N2 MUTATED OR4N2 WILD-TYPE
  0             9             274
  1             0              48
[1] 2 2
[1] FALSE
D1519V7, 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
D1519V8, binary
                 cls
clus                0   1
  OR4N2 MUTATED     9   1
  OR4N2 WILD-TYPE 308  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4N2 MUTATED      9    1
  OR4N2 WILD-TYPE  308   47
                               clus
vv                              OR4N2 MUTATED OR4N2 WILD-TYPE
  COLON ADENOCARCINOMA                      9             308
  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 249   2  22  20
D1519V9, multiclass
    clus
vv   OR4N2 MUTATED OR4N2 WILD-TYPE
  R0             8             249
  R1             0               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"
D1519V10, 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
D1519V11, 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(1520) Variable = OXA1L MUTATION ANALYSIS
D1520V1, survival
                 sevent
clus2               0   1
  OXA1L MUTATED     3   2
  OXA1L WILD-TYPE 279  71
  OXA1L MUTATED OXA1L WILD-TYPE 
              5             350 
  OXA1L MUTATED OXA1L WILD-TYPE 
              2              71 
$`OXA1L MUTATED`
TCGA-AA-3715 TCGA-AA-3947 TCGA-AD-6963 TCGA-AZ-6598 TCGA-G4-6315 
       19.04        33.01        27.42        49.41        36.72 

$`OXA1L WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 
       56.55         0.79         0.72         5.79        22.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  OXA1L MUTATED OXA1L WILD-TYPE 
          19.04            0.00 
  OXA1L MUTATED OXA1L WILD-TYPE 
          49.41          140.38 
  OXA1L MUTATED OXA1L WILD-TYPE 
          33.01           20.07 
[1] "19.0 - 49.4 (33.0)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.6"
D1520V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OXA1L MUTATED         0        0        2         0         1         0
  OXA1L WILD-TYPE      64        1       23       109         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OXA1L MUTATED           0          0          0          0        1         0
  OXA1L WILD-TYPE        19         10         41         31       34        13
                 vv
clus              STAGE IVB
  OXA1L MUTATED           0
  OXA1L WILD-TYPE         1
D1520V3, multiclass
            clus
vv           OXA1L MUTATED OXA1L WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              0             109
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OXA1L MUTATED     0   0   4   1
  OXA1L WILD-TYPE   9  68 244  40
D1520V4, multiclass
    clus
vv   OXA1L MUTATED OXA1L WILD-TYPE
  T1             0               9
  T2             0              68
  T3             4             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
  OXA1L MUTATED     4   1   0
  OXA1L WILD-TYPE 216  79  66
D1520V5, multiclass
    clus
vv   OXA1L MUTATED OXA1L WILD-TYPE
  N0             4             216
  N1             1              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"
D1520V6, binary
                 cls
clus                0   1
  OXA1L MUTATED     2   1
  OXA1L WILD-TYPE 281  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OXA1L MUTATED      2    1
  OXA1L WILD-TYPE  281   47
   clus
vv  OXA1L MUTATED OXA1L WILD-TYPE
  0             2             281
  1             1              47
[1] 2 2
[1] FALSE
D1520V7, binary
                 cls
clus                0   1
  OXA1L MUTATED     2   3
  OXA1L WILD-TYPE 168 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OXA1L MUTATED      2    3
  OXA1L WILD-TYPE  168  194
        clus
vv       OXA1L MUTATED OXA1L WILD-TYPE
  FEMALE             2             168
  MALE               3             194
[1] 2 2
[1] FALSE
D1520V8, binary
                 cls
clus                0   1
  OXA1L MUTATED     4   1
  OXA1L WILD-TYPE 313  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OXA1L MUTATED      4    1
  OXA1L WILD-TYPE  313   47
                               clus
vv                              OXA1L MUTATED OXA1L WILD-TYPE
  COLON ADENOCARCINOMA                      4             313
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  OXA1L MUTATED     3   0   0   0
  OXA1L WILD-TYPE 254   2  22  21
D1520V9, multiclass
    clus
vv   OXA1L MUTATED OXA1L WILD-TYPE
  R0             3             254
  R1             0               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"
D1520V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OXA1L MUTATED                                  0     0
  OXA1L WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OXA1L MUTATED                           0     3
  OXA1L WILD-TYPE                        19   173
D1520V11, multiclass
                                  clus
vv                                 OXA1L MUTATED OXA1L 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(1521) Variable = DLGAP5 MUTATION ANALYSIS
D1521V1, survival
                  sevent
clus2                0   1
  DLGAP5 MUTATED     5   3
  DLGAP5 WILD-TYPE 277  70
  DLGAP5 MUTATED DLGAP5 WILD-TYPE 
               8              347 
  DLGAP5 MUTATED DLGAP5 WILD-TYPE 
               3               70 
$`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         0.33        21.99        13.02 
TCGA-D5-6537 TCGA-G4-6315 
        4.80        36.72 

$`DLGAP5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10       100.01         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        51.32        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12        17.85        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        51.75        45.11        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  DLGAP5 MUTATED DLGAP5 WILD-TYPE 
            0.33             0.00 
  DLGAP5 MUTATED DLGAP5 WILD-TYPE 
           58.39           140.38 
  DLGAP5 MUTATED DLGAP5 WILD-TYPE 
          20.515           20.190 
[1] "0.3 - 58.4 (20.5)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2.1"
D1521V2, 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       24       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DLGAP5 MUTATED           0          0          2          0        1
  DLGAP5 WILD-TYPE        19         10         39         31       34
                  vv
clus               STAGE IVA STAGE IVB
  DLGAP5 MUTATED           0         0
  DLGAP5 WILD-TYPE        13         1
D1521V3, multiclass
            clus
vv           DLGAP5 MUTATED DLGAP5 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               3              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  DLGAP5 MUTATED     0   1   7   0
  DLGAP5 WILD-TYPE   9  67 241  41
D1521V4, multiclass
    clus
vv   DLGAP5 MUTATED DLGAP5 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              7              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
  DLGAP5 MUTATED     4   4   0
  DLGAP5 WILD-TYPE 216  76  66
D1521V5, multiclass
    clus
vv   DLGAP5 MUTATED DLGAP5 WILD-TYPE
  N0              4              216
  N1              4               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"
D1521V6, binary
                  cls
clus                 0   1
  DLGAP5 MUTATED     4   1
  DLGAP5 WILD-TYPE 279  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DLGAP5 MUTATED      4    1
  DLGAP5 WILD-TYPE  279   47
   clus
vv  DLGAP5 MUTATED DLGAP5 WILD-TYPE
  0              4              279
  1              1               47
[1] 2 2
[1] FALSE
D1521V7, 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
D1521V8, binary
                  cls
clus                 0   1
  DLGAP5 MUTATED     7   1
  DLGAP5 WILD-TYPE 310  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DLGAP5 MUTATED      7    1
  DLGAP5 WILD-TYPE  310   47
                               clus
vv                              DLGAP5 MUTATED DLGAP5 WILD-TYPE
  COLON ADENOCARCINOMA                       7              310
  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 252   2  22  19
D1521V9, multiclass
    clus
vv   DLGAP5 MUTATED DLGAP5 WILD-TYPE
  R0              5              252
  R1              0                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"
D1521V10, 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
D1521V11, 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(1522) Variable = NKTR MUTATION ANALYSIS
D1522V1, survival
                sevent
clus2              0   1
  NKTR MUTATED     8   5
  NKTR WILD-TYPE 274  68
  NKTR MUTATED NKTR WILD-TYPE 
            13            342 
  NKTR MUTATED NKTR WILD-TYPE 
             5             68 
$`NKTR MUTATED`
TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3815 TCGA-AA-3864 TCGA-AA-A00E 
        3.02        63.98         6.97        33.04        53.00        30.02 
TCGA-AA-A00Z TCGA-AD-6889 TCGA-AZ-6601 TCGA-D5-6532 TCGA-DM-A1D8 TCGA-DM-A28F 
       21.99        56.55       100.01        18.25        12.59        35.97 
TCGA-G4-6626 
       46.75 

$`NKTR WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J 
       27.02        13.94        38.04        19.00        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        4.21         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
        6.12        81.37       119.93        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       22.09        13.78        35.80        26.17        91.79        52.80 

  NKTR MUTATED NKTR WILD-TYPE 
          3.02           0.00 
  NKTR MUTATED NKTR WILD-TYPE 
        100.01         140.38 
  NKTR MUTATED NKTR WILD-TYPE 
        33.040         20.005 
[1] "3.0 - 100.0 (33.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.3"
D1522V2, 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       20       103         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        19         10         40         31       35        13
                vv
clus             STAGE IVB
  NKTR MUTATED           0
  NKTR WILD-TYPE         1
D1522V3, multiclass
            clus
vv           NKTR MUTATED NKTR WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              5             20
  STAGE IIA             6            103
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NKTR MUTATED     0   0  13   0
  NKTR WILD-TYPE   9  68 235  41
D1522V4, multiclass
    clus
vv   NKTR MUTATED NKTR WILD-TYPE
  T1            0              9
  T2            0             68
  T3           13            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
  NKTR MUTATED    11   2   0
  NKTR WILD-TYPE 209  78  66
D1522V5, multiclass
    clus
vv   NKTR MUTATED NKTR WILD-TYPE
  N0           11            209
  N1            2             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"
D1522V6, binary
                cls
clus               0   1
  NKTR MUTATED    12   0
  NKTR WILD-TYPE 271  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  NKTR MUTATED     12    0
  NKTR WILD-TYPE  271   48
   clus
vv  NKTR MUTATED NKTR WILD-TYPE
  0           12            271
  1            0             48
[1] 2 2
[1] FALSE
D1522V7, 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
D1522V8, binary
                cls
clus               0   1
  NKTR MUTATED    13   0
  NKTR WILD-TYPE 304  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  NKTR MUTATED     13    0
  NKTR WILD-TYPE  304   48
                               clus
vv                              NKTR MUTATED NKTR WILD-TYPE
  COLON ADENOCARCINOMA                    13            304
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  NKTR MUTATED     9   0   0   0
  NKTR WILD-TYPE 248   2  22  21
D1522V9, multiclass
    clus
vv   NKTR MUTATED NKTR WILD-TYPE
  R0            9            248
  R1            0              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"
D1522V10, 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
D1522V11, 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(1523) Variable = TTLL13 MUTATION ANALYSIS
D1523V1, survival
                  sevent
clus2                0   1
  TTLL13 MUTATED     5   0
  TTLL13 WILD-TYPE 277  73
  TTLL13 MUTATED TTLL13 WILD-TYPE 
               5              350 
  TTLL13 MUTATED TTLL13 WILD-TYPE 
               0               73 
$`TTLL13 MUTATED`
TCGA-A6-5661 TCGA-AA-3713 TCGA-AA-3815 TCGA-AA-3947 TCGA-CA-6717 
       33.53        19.04        33.04        33.01         0.33 

$`TTLL13 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  TTLL13 MUTATED TTLL13 WILD-TYPE 
            0.33             0.00 
  TTLL13 MUTATED TTLL13 WILD-TYPE 
           33.53           140.38 
  TTLL13 MUTATED TTLL13 WILD-TYPE 
          33.010           20.155 
[1] "0.3 - 33.5 (33.0)"  "0.0 - 140.4 (20.2)"
[1] "hr="     "9100000"
D1523V2, 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       25       106         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TTLL13 MUTATED           0          0          0          0        1
  TTLL13 WILD-TYPE        19         10         41         31       34
                  vv
clus               STAGE IVA STAGE IVB
  TTLL13 MUTATED           0         0
  TTLL13 WILD-TYPE        13         1
D1523V3, multiclass
            clus
vv           TTLL13 MUTATED TTLL13 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               3              106
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TTLL13 MUTATED     0   0   4   1
  TTLL13 WILD-TYPE   9  68 244  40
D1523V4, multiclass
    clus
vv   TTLL13 MUTATED TTLL13 WILD-TYPE
  T1              0                9
  T2              0               68
  T3              4              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
  TTLL13 MUTATED     5   0   0
  TTLL13 WILD-TYPE 215  80  66
D1523V5, multiclass
    clus
vv   TTLL13 MUTATED TTLL13 WILD-TYPE
  N0              5              215
  N1              0               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
  TTLL13 MUTATED     4   1
  TTLL13 WILD-TYPE 279  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TTLL13 MUTATED      4    1
  TTLL13 WILD-TYPE  279   47
   clus
vv  TTLL13 MUTATED TTLL13 WILD-TYPE
  0              4              279
  1              1               47
[1] 2 2
[1] FALSE
D1523V7, 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
D1523V8, binary
                  cls
clus                 0   1
  TTLL13 MUTATED     3   2
  TTLL13 WILD-TYPE 314  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TTLL13 MUTATED      3    2
  TTLL13 WILD-TYPE  314   46
                               clus
vv                              TTLL13 MUTATED TTLL13 WILD-TYPE
  COLON ADENOCARCINOMA                       3              314
  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 254   2  21  20
D1523V9, multiclass
    clus
vv   TTLL13 MUTATED TTLL13 WILD-TYPE
  R0              3              254
  R1              0                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"
D1523V10, 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
D1523V11, multiclass
[1] "Remove cluster labels:" "TTLL13 MUTATED"        
clus
  TTLL13 MUTATED TTLL13 WILD-TYPE 
               2              204 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-4105 
"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-A6-6649       TCGA-A6-6651       TCGA-A6-6652 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780       TCGA-A6-6781 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-A6-6782       TCGA-AD-5900       TCGA-AD-6548       TCGA-AD-6888 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-AD-6889       TCGA-AD-6890       TCGA-AD-6895       TCGA-AD-6899 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6964       TCGA-AD-6965 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070       TCGA-AY-4071 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-AZ-4315       TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4681 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-AZ-4682       TCGA-AZ-5403       TCGA-AZ-5407       TCGA-AZ-6598 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-AZ-6599       TCGA-AZ-6600       TCGA-AZ-6601       TCGA-AZ-6603 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-AZ-6605       TCGA-AZ-6606       TCGA-AZ-6607       TCGA-AZ-6608 
"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-5912       TCGA-CK-5913       TCGA-CK-5914       TCGA-CK-5915 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-CK-5916       TCGA-CK-6746       TCGA-CK-6747       TCGA-CK-6748 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-CK-6751       TCGA-CM-4743       TCGA-CM-4744       TCGA-CM-4746 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341       TCGA-CM-5344 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860       TCGA-CM-5861 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864       TCGA-CM-5868 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163       TCGA-CM-6164 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167       TCGA-CM-6168 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171       TCGA-CM-6172 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676       TCGA-CM-6677 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680       TCGA-D5-5537 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540       TCGA-D5-5541 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533       TCGA-D5-6534 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537       TCGA-D5-6538 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541       TCGA-D5-6898 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923       TCGA-D5-6924 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928       TCGA-D5-6929 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932       TCGA-D5-7000 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-DM-A0X9       TCGA-DM-A0XD       TCGA-DM-A0XF       TCGA-DM-A1D0 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-DM-A1D4       TCGA-DM-A1D6       TCGA-DM-A1D7       TCGA-DM-A1D8 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-DM-A1D9       TCGA-DM-A1DA       TCGA-DM-A1DB       TCGA-DM-A1HA 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-DM-A1HB       TCGA-DM-A282       TCGA-DM-A285       TCGA-DM-A28C 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-DM-A28E       TCGA-DM-A28F       TCGA-DM-A28G       TCGA-DM-A28H 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-DM-A28K       TCGA-F4-6459       TCGA-F4-6460       TCGA-F4-6569 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704       TCGA-F4-6805 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808       TCGA-F4-6809 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856       TCGA-G4-6293 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304       TCGA-G4-6306 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310       TCGA-G4-6315 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323       TCGA-G4-6586 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 
      TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628 
"TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" "TTLL13 WILD-TYPE" 

Clustering(1524) Variable = VPS52 MUTATION ANALYSIS
D1524V1, survival
                 sevent
clus2               0   1
  VPS52 MUTATED     5   5
  VPS52 WILD-TYPE 277  68
  VPS52 MUTATED VPS52 WILD-TYPE 
             10             345 
  VPS52 MUTATED VPS52 WILD-TYPE 
              5              68 
$`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 
        0.33        23.05        15.02        46.75 

$`VPS52 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        18.05         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       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        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
       29.56        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
       21.99        21.14         2.93         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        16.01         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       26.17        91.79        52.80 

  VPS52 MUTATED VPS52 WILD-TYPE 
           0.33            0.00 
  VPS52 MUTATED VPS52 WILD-TYPE 
          46.75          140.38 
  VPS52 MUTATED VPS52 WILD-TYPE 
          13.00           20.28 
[1] "0.3 - 46.8 (13.0)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "3.7"
D1524V2, 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       24       103         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        19         10         40         30       35        13
                 vv
clus              STAGE IVB
  VPS52 MUTATED           0
  VPS52 WILD-TYPE         1
D1524V3, multiclass
            clus
vv           VPS52 MUTATED VPS52 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              6             103
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  VPS52 MUTATED     1   0   8   2
  VPS52 WILD-TYPE   8  68 240  39
D1524V4, multiclass
    clus
vv   VPS52 MUTATED VPS52 WILD-TYPE
  T1             1               8
  T2             0              68
  T3             8             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
  VPS52 MUTATED     9   1   1
  VPS52 WILD-TYPE 211  79  65
D1524V5, multiclass
    clus
vv   VPS52 MUTATED VPS52 WILD-TYPE
  N0             9             211
  N1             1              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"
D1524V6, binary
                 cls
clus                0   1
  VPS52 MUTATED    11   0
  VPS52 WILD-TYPE 272  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VPS52 MUTATED     11    0
  VPS52 WILD-TYPE  272   48
   clus
vv  VPS52 MUTATED VPS52 WILD-TYPE
  0            11             272
  1             0              48
[1] 2 2
[1] FALSE
D1524V7, 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
D1524V8, binary
                 cls
clus                0   1
  VPS52 MUTATED     7   4
  VPS52 WILD-TYPE 310  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VPS52 MUTATED      7    4
  VPS52 WILD-TYPE  310   44
                               clus
vv                              VPS52 MUTATED VPS52 WILD-TYPE
  COLON ADENOCARCINOMA                      7             310
  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 248   2  22  20
D1524V9, multiclass
    clus
vv   VPS52 MUTATED VPS52 WILD-TYPE
  R0             9             248
  R1             0               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"
D1524V10, 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
D1524V11, 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(1525) Variable = CDHR5 MUTATION ANALYSIS
D1525V1, survival
                 sevent
clus2               0   1
  CDHR5 MUTATED    10   1
  CDHR5 WILD-TYPE 272  72
  CDHR5 MUTATED CDHR5 WILD-TYPE 
             11             344 
  CDHR5 MUTATED CDHR5 WILD-TYPE 
              1              72 
$`CDHR5 MUTATED`
TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3815 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3950 
       24.39        19.66        33.04        53.00        31.00        24.00 
TCGA-AA-3968 TCGA-AA-A03F TCGA-AY-6197 TCGA-DM-A0X9 TCGA-G4-6586 
       21.99        18.05        21.44       119.70        35.80 

$`CDHR5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 
       26.01         2.01        20.98        34.03         2.01        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  CDHR5 MUTATED CDHR5 WILD-TYPE 
          18.05            0.00 
  CDHR5 MUTATED CDHR5 WILD-TYPE 
         119.70          140.38 
  CDHR5 MUTATED CDHR5 WILD-TYPE 
          24.39           19.99 
[1] "18.1 - 119.7 (24.4)" "0.0 - 140.4 (20.0)" 
[1] "hr=" "3.1"
D1525V2, 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       24       104         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        18         10         41         30       35        13
                 vv
clus              STAGE IVB
  CDHR5 MUTATED           0
  CDHR5 WILD-TYPE         1
D1525V3, multiclass
            clus
vv           CDHR5 MUTATED CDHR5 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              5             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CDHR5 MUTATED     1   2   7   1
  CDHR5 WILD-TYPE   8  66 241  40
D1525V4, multiclass
    clus
vv   CDHR5 MUTATED CDHR5 WILD-TYPE
  T1             1               8
  T2             2              66
  T3             7             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
  CDHR5 MUTATED     9   1   1
  CDHR5 WILD-TYPE 211  79  65
D1525V5, multiclass
    clus
vv   CDHR5 MUTATED CDHR5 WILD-TYPE
  N0             9             211
  N1             1              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"
D1525V6, binary
                 cls
clus                0   1
  CDHR5 MUTATED     9   0
  CDHR5 WILD-TYPE 274  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDHR5 MUTATED      9    0
  CDHR5 WILD-TYPE  274   48
   clus
vv  CDHR5 MUTATED CDHR5 WILD-TYPE
  0             9             274
  1             0              48
[1] 2 2
[1] FALSE
D1525V7, 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
D1525V8, binary
                 cls
clus                0   1
  CDHR5 MUTATED     7   4
  CDHR5 WILD-TYPE 310  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDHR5 MUTATED      7    4
  CDHR5 WILD-TYPE  310   44
                               clus
vv                              CDHR5 MUTATED CDHR5 WILD-TYPE
  COLON ADENOCARCINOMA                      7             310
  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 248   2  22  21
D1525V9, multiclass
    clus
vv   CDHR5 MUTATED CDHR5 WILD-TYPE
  R0             9             248
  R1             0               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"
D1525V10, 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
D1525V11, 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(1526) Variable = AVPR1A MUTATION ANALYSIS
D1526V1, survival
                  sevent
clus2                0   1
  AVPR1A MUTATED     9   1
  AVPR1A WILD-TYPE 273  72
  AVPR1A MUTATED AVPR1A WILD-TYPE 
              10              345 
  AVPR1A MUTATED AVPR1A WILD-TYPE 
               1               72 
$`AVPR1A MUTATED`
TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-3663 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-A010 
       22.06        20.12         6.97        19.04        19.04        34.98 
TCGA-CA-6717 TCGA-CM-6162 TCGA-D5-6927 TCGA-G4-6628 
        0.33        12.00         9.44        52.80 

$`AVPR1A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       85.05        26.99        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       26.17        91.79        46.75 

  AVPR1A MUTATED AVPR1A WILD-TYPE 
            0.33             0.00 
  AVPR1A MUTATED AVPR1A WILD-TYPE 
           52.80           140.38 
  AVPR1A MUTATED AVPR1A WILD-TYPE 
           19.04            20.98 
[1] "0.3 - 52.8 (19.0)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.7"
D1526V2, 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       22       105         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AVPR1A MUTATED           0          0          1          0        1
  AVPR1A WILD-TYPE        19         10         40         31       34
                  vv
clus               STAGE IVA STAGE IVB
  AVPR1A MUTATED           0         0
  AVPR1A WILD-TYPE        13         1
D1526V3, multiclass
            clus
vv           AVPR1A MUTATED AVPR1A WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                3               22
  STAGE IIA               4              105
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  AVPR1A MUTATED     0   1   8   2
  AVPR1A WILD-TYPE   9  67 240  39
D1526V4, multiclass
    clus
vv   AVPR1A MUTATED AVPR1A WILD-TYPE
  T1              0                9
  T2              1               67
  T3              8              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
  AVPR1A MUTATED    10   1   0
  AVPR1A WILD-TYPE 210  79  66
D1526V5, multiclass
    clus
vv   AVPR1A MUTATED AVPR1A WILD-TYPE
  N0             10              210
  N1              1               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"
D1526V6, binary
                  cls
clus                 0   1
  AVPR1A MUTATED     9   1
  AVPR1A WILD-TYPE 274  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AVPR1A MUTATED      9    1
  AVPR1A WILD-TYPE  274   47
   clus
vv  AVPR1A MUTATED AVPR1A WILD-TYPE
  0              9              274
  1              1               47
[1] 2 2
[1] FALSE
D1526V7, 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
D1526V8, binary
                  cls
clus                 0   1
  AVPR1A MUTATED     8   3
  AVPR1A WILD-TYPE 309  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AVPR1A MUTATED      8    3
  AVPR1A WILD-TYPE  309   45
                               clus
vv                              AVPR1A MUTATED AVPR1A WILD-TYPE
  COLON ADENOCARCINOMA                       8              309
  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 249   2  21  20
D1526V9, multiclass
    clus
vv   AVPR1A MUTATED AVPR1A WILD-TYPE
  R0              8              249
  R1              0                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"
D1526V10, 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
D1526V11, 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(1527) Variable = GRIN2A MUTATION ANALYSIS
D1527V1, survival
                  sevent
clus2                0   1
  GRIN2A MUTATED    33   7
  GRIN2A WILD-TYPE 249  66
  GRIN2A MUTATED GRIN2A WILD-TYPE 
              40              315 
  GRIN2A MUTATED GRIN2A WILD-TYPE 
               7               66 
$`GRIN2A MUTATED`
TCGA-A6-5664 TCGA-AA-3510 TCGA-AA-3530 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 
       22.09        63.98        19.07         6.05         0.92        19.00 
TCGA-AA-3715 TCGA-AA-3833 TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-A00E 
       19.04        15.95        13.05        25.02        27.02        30.02 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       38.04         4.01        34.98        38.07         1.02        35.01 
TCGA-AD-6889 TCGA-AY-6386 TCGA-AZ-4681 TCGA-AZ-5403 TCGA-CA-6716 TCGA-CA-6717 
       56.55        17.82        83.80        62.79         0.26         0.33 
TCGA-CA-6718 TCGA-CK-4952 TCGA-CM-5344 TCGA-CM-6165 TCGA-CM-6169 TCGA-CM-6172 
        0.10        15.62        22.03        16.04        13.02        11.01 
TCGA-D5-5539 TCGA-D5-6532 TCGA-D5-6537 TCGA-D5-6928 TCGA-DM-A1DB TCGA-DM-A1HB 
       19.59        18.25         4.80        11.64        44.32       135.65 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        46.75        52.80 

$`GRIN2A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
        0.00        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       37.05        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       17.98        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3986 TCGA-AA-3989 
       34.06        26.01        24.00        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J 
       27.02        13.94        38.04        19.00        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       18.05        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        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        15.75         0.20        21.44        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        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6719 
        2.24         3.06         3.25         3.29         0.07         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       102.44        40.34        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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 
       16.01        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-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       12.99        15.02        14.04        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       13.51        11.51        20.19         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
       12.59       140.38         7.50       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 
       22.09        13.78        91.79 

  GRIN2A MUTATED GRIN2A WILD-TYPE 
             0.1              0.0 
  GRIN2A MUTATED GRIN2A WILD-TYPE 
          135.65           140.38 
  GRIN2A MUTATED GRIN2A WILD-TYPE 
           19.33            20.28 
[1] "0.1 - 135.7 (19.3)" "0.0 - 140.4 (20.3)"
[1] "hr=" "1.3"
D1527V2, 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       21        93         5         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GRIN2A MUTATED           4          1          6          1        3
  GRIN2A WILD-TYPE        15          9         35         30       32
                  vv
clus               STAGE IVA STAGE IVB
  GRIN2A MUTATED           0         0
  GRIN2A WILD-TYPE        13         1
D1527V3, multiclass
            clus
vv           GRIN2A MUTATED GRIN2A WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                4               21
  STAGE IIA              16               93
  STAGE IIB               3                5
  STAGE IIC               0                1
  STAGE III               4               15
  STAGE IIIA              1                9
  STAGE IIIB              6               35
  STAGE IIIC              1               30
  STAGE IV                3               32
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GRIN2A MUTATED     0   3  31   7
  GRIN2A WILD-TYPE   9  65 217  34
D1527V4, multiclass
    clus
vv   GRIN2A MUTATED GRIN2A WILD-TYPE
  T1              0                9
  T2              3               65
  T3             31              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
  GRIN2A MUTATED    26  11   4
  GRIN2A WILD-TYPE 194  69  62
D1527V5, multiclass
    clus
vv   GRIN2A MUTATED GRIN2A WILD-TYPE
  N0             26              194
  N1             11               69
  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"
D1527V6, binary
                  cls
clus                 0   1
  GRIN2A MUTATED    33   3
  GRIN2A WILD-TYPE 250  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GRIN2A MUTATED     33    3
  GRIN2A WILD-TYPE  250   45
   clus
vv  GRIN2A MUTATED GRIN2A WILD-TYPE
  0             33              250
  1              3               45
[1] 2 2
[1] FALSE
D1527V7, 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
D1527V8, binary
                  cls
clus                 0   1
  GRIN2A MUTATED    35   6
  GRIN2A WILD-TYPE 282  42
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GRIN2A MUTATED     35    6
  GRIN2A WILD-TYPE  282   42
                               clus
vv                              GRIN2A MUTATED GRIN2A WILD-TYPE
  COLON ADENOCARCINOMA                      35              282
  COLON MUCINOUS ADENOCARCINOMA              6               42
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  GRIN2A MUTATED    26   0   3   5
  GRIN2A WILD-TYPE 231   2  19  16
D1527V9, multiclass
    clus
vv   GRIN2A MUTATED GRIN2A WILD-TYPE
  R0             26              231
  R1              0                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"
D1527V10, 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
D1527V11, 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(1528) Variable = MFRP MUTATION ANALYSIS
D1528V1, survival
                sevent
clus2              0   1
  MFRP MUTATED     9   2
  MFRP WILD-TYPE 273  71
  MFRP MUTATED MFRP WILD-TYPE 
            11            344 
  MFRP MUTATED MFRP WILD-TYPE 
             2             71 
$`MFRP MUTATED`
TCGA-A6-5665 TCGA-AA-3489 TCGA-AA-3833 TCGA-AA-3989 TCGA-AD-6889 TCGA-AU-6004 
       22.06         7.04        15.95         7.96        56.55        27.09 
TCGA-CA-6717 TCGA-CK-5913 TCGA-CK-6751 TCGA-CM-6162 TCGA-F4-6856 
        0.33        51.32       124.27        12.00        19.43 

$`MFRP WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       19.07        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37         4.21         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
       17.56       102.44        40.34        15.62        49.08        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14         2.93         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 
       16.01        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        35.41       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  MFRP MUTATED MFRP WILD-TYPE 
          0.33           0.00 
  MFRP MUTATED MFRP WILD-TYPE 
        124.27         140.38 
  MFRP MUTATED MFRP WILD-TYPE 
        19.430         20.235 
[1] "0.3 - 124.3 (19.4)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.4"
D1528V2, 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       24       104         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        19         10         40         31       34        13
                vv
clus             STAGE IVB
  MFRP MUTATED           0
  MFRP WILD-TYPE         1
D1528V3, multiclass
            clus
vv           MFRP MUTATED MFRP WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             5            104
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MFRP MUTATED     0   3   8   0
  MFRP WILD-TYPE   9  65 240  41
D1528V4, multiclass
    clus
vv   MFRP MUTATED MFRP WILD-TYPE
  T1            0              9
  T2            3             65
  T3            8            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
  MFRP MUTATED     9   1   1
  MFRP WILD-TYPE 211  79  65
D1528V5, multiclass
    clus
vv   MFRP MUTATED MFRP WILD-TYPE
  N0            9            211
  N1            1             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"
D1528V6, binary
                cls
clus               0   1
  MFRP MUTATED     8   1
  MFRP WILD-TYPE 275  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  MFRP MUTATED      8    1
  MFRP WILD-TYPE  275   47
   clus
vv  MFRP MUTATED MFRP WILD-TYPE
  0            8            275
  1            1             47
[1] 2 2
[1] FALSE
D1528V7, 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
D1528V8, binary
                cls
clus               0   1
  MFRP MUTATED     7   4
  MFRP WILD-TYPE 310  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  MFRP MUTATED      7    4
  MFRP WILD-TYPE  310   44
                               clus
vv                              MFRP MUTATED MFRP WILD-TYPE
  COLON ADENOCARCINOMA                     7            310
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MFRP MUTATED     6   0   1   3
  MFRP WILD-TYPE 251   2  21  18
D1528V9, multiclass
    clus
vv   MFRP MUTATED MFRP WILD-TYPE
  R0            6            251
  R1            0              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"
D1528V10, 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
D1528V11, 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(1529) Variable = WIPI2 MUTATION ANALYSIS
D1529V1, survival
                 sevent
clus2               0   1
  WIPI2 MUTATED     9   1
  WIPI2 WILD-TYPE 273  72
  WIPI2 MUTATED WIPI2 WILD-TYPE 
             10             345 
  WIPI2 MUTATED WIPI2 WILD-TYPE 
              1              72 
$`WIPI2 MUTATED`
TCGA-A6-5659 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6780 TCGA-AA-3510 TCGA-AA-3554 
       30.44        32.71        22.52        20.12        63.98        17.95 
TCGA-AA-3831 TCGA-AZ-6598 TCGA-F4-6856 TCGA-G4-6306 
       17.98        49.41        19.43        44.68 

$`WIPI2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       22.06        27.09         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 
       21.76        24.69        24.39        23.87        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 
        7.04         3.02         1.02        35.01         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3556 
       33.99        21.01        13.02        24.00        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
        1.02        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 
       16.24        33.67        13.25         0.53        35.41       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        53.62        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  WIPI2 MUTATED WIPI2 WILD-TYPE 
          17.95            0.00 
  WIPI2 MUTATED WIPI2 WILD-TYPE 
          63.98          140.38 
  WIPI2 MUTATED WIPI2 WILD-TYPE 
          26.48           20.02 
[1] "17.9 - 64.0 (26.5)" "0.0 - 140.4 (20.0)"
[1] "hr=" "2.7"
D1529V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  WIPI2 MUTATED         3        0        2         4         0         1
  WIPI2 WILD-TYPE      61        1       23       105         8         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  WIPI2 MUTATED           0          0          0          0        0         0
  WIPI2 WILD-TYPE        19         10         41         31       35        13
                 vv
clus              STAGE IVB
  WIPI2 MUTATED           0
  WIPI2 WILD-TYPE         1
D1529V3, multiclass
            clus
vv           WIPI2 MUTATED WIPI2 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              4             105
  STAGE IIB              0               8
  STAGE IIC              1               0
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  WIPI2 MUTATED     0   4   5   1
  WIPI2 WILD-TYPE   9  64 243  40
D1529V4, multiclass
    clus
vv   WIPI2 MUTATED WIPI2 WILD-TYPE
  T1             0               9
  T2             4              64
  T3             5             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
  WIPI2 MUTATED    10   0   0
  WIPI2 WILD-TYPE 210  80  66
D1529V5, multiclass
    clus
vv   WIPI2 MUTATED WIPI2 WILD-TYPE
  N0            10             210
  N1             0              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"
D1529V6, binary
                 cls
clus                0   1
  WIPI2 MUTATED     8   0
  WIPI2 WILD-TYPE 275  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WIPI2 MUTATED      8    0
  WIPI2 WILD-TYPE  275   48
   clus
vv  WIPI2 MUTATED WIPI2 WILD-TYPE
  0             8             275
  1             0              48
[1] 2 2
[1] FALSE
D1529V7, binary
                 cls
clus                0   1
  WIPI2 MUTATED     2   8
  WIPI2 WILD-TYPE 168 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WIPI2 MUTATED      2    8
  WIPI2 WILD-TYPE  168  189
        clus
vv       WIPI2 MUTATED WIPI2 WILD-TYPE
  FEMALE             2             168
  MALE               8             189
[1] 2 2
[1] FALSE
D1529V8, binary
                 cls
clus                0   1
  WIPI2 MUTATED     8   2
  WIPI2 WILD-TYPE 309  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WIPI2 MUTATED      8    2
  WIPI2 WILD-TYPE  309   46
                               clus
vv                              WIPI2 MUTATED WIPI2 WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  WIPI2 MUTATED     6   0   0   0
  WIPI2 WILD-TYPE 251   2  22  21
D1529V9, multiclass
    clus
vv   WIPI2 MUTATED WIPI2 WILD-TYPE
  R0             6             251
  R1             0               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"
D1529V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  WIPI2 MUTATED                                  0     0
  WIPI2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  WIPI2 MUTATED                           0     7
  WIPI2 WILD-TYPE                        19   169
D1529V11, multiclass
                                  clus
vv                                 WIPI2 MUTATED WIPI2 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(1530) Variable = C9ORF125 MUTATION ANALYSIS
D1530V1, survival
                    sevent
clus2                  0   1
  C9ORF125 MUTATED     9   3
  C9ORF125 WILD-TYPE 273  70
  C9ORF125 MUTATED C9ORF125 WILD-TYPE 
                12                343 
  C9ORF125 MUTATED C9ORF125 WILD-TYPE 
                 3                 70 
$`C9ORF125 MUTATED`
TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3516 TCGA-AA-3710 TCGA-AA-A00A TCGA-AA-A00E 
       22.06         3.02        13.02        26.99        38.04        30.02 
TCGA-AD-6895 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-D5-6930 TCGA-DM-A1HB TCGA-G4-6588 
        0.72        58.39        49.41         1.51       135.65        26.17 

$`C9ORF125 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J 
        7.96        27.02        13.94        19.00        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21        56.55         0.79         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13        83.80        22.36        62.79        61.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 
       52.80 

  C9ORF125 MUTATED C9ORF125 WILD-TYPE 
              0.72               0.00 
  C9ORF125 MUTATED C9ORF125 WILD-TYPE 
            135.65             140.38 
  C9ORF125 MUTATED C9ORF125 WILD-TYPE 
             26.58              20.02 
[1] "0.7 - 135.7 (26.6)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1"  
D1530V2, 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       23       102         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C9ORF125 MUTATED           1          0          1          0        0
  C9ORF125 WILD-TYPE        18         10         40         31       35
                    vv
clus                 STAGE IVA STAGE IVB
  C9ORF125 MUTATED           0         0
  C9ORF125 WILD-TYPE        13         1
D1530V3, multiclass
            clus
vv           C9ORF125 MUTATED C9ORF125 WILD-TYPE
  STAGE I                   0                 64
  STAGE IA                  0                  1
  STAGE II                  2                 23
  STAGE IIA                 7                102
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 1                 18
  STAGE IIIA                0                 10
  STAGE IIIB                1                 40
  STAGE IIIC                0                 31
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C9ORF125 MUTATED     0   0  12   0
  C9ORF125 WILD-TYPE   9  68 236  41
D1530V4, multiclass
    clus
vv   C9ORF125 MUTATED C9ORF125 WILD-TYPE
  T1                0                  9
  T2                0                 68
  T3               12                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
  C9ORF125 MUTATED     9   2   1
  C9ORF125 WILD-TYPE 211  78  65
D1530V5, multiclass
    clus
vv   C9ORF125 MUTATED C9ORF125 WILD-TYPE
  N0                9                211
  N1                2                 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"
D1530V6, binary
                    cls
clus                   0   1
  C9ORF125 MUTATED    10   0
  C9ORF125 WILD-TYPE 273  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF125 MUTATED     10    0
  C9ORF125 WILD-TYPE  273   48
   clus
vv  C9ORF125 MUTATED C9ORF125 WILD-TYPE
  0               10                273
  1                0                 48
[1] 2 2
[1] FALSE
D1530V7, 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
D1530V8, binary
                    cls
clus                   0   1
  C9ORF125 MUTATED    10   2
  C9ORF125 WILD-TYPE 307  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF125 MUTATED     10    2
  C9ORF125 WILD-TYPE  307   46
                               clus
vv                              C9ORF125 MUTATED C9ORF125 WILD-TYPE
  COLON ADENOCARCINOMA                        10                307
  COLON MUCINOUS ADENOCARCINOMA                2                 46
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C9ORF125 MUTATED     8   0   0   0
  C9ORF125 WILD-TYPE 249   2  22  21
D1530V9, multiclass
    clus
vv   C9ORF125 MUTATED C9ORF125 WILD-TYPE
  R0                8                249
  R1                0                  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"
D1530V10, 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
D1530V11, 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(1531) Variable = PISD MUTATION ANALYSIS
D1531V1, survival
                sevent
clus2              0   1
  PISD MUTATED     3   2
  PISD WILD-TYPE 279  71
  PISD MUTATED PISD WILD-TYPE 
             5            350 
  PISD MUTATED PISD WILD-TYPE 
             2             71 
$`PISD MUTATED`
TCGA-AZ-5403 TCGA-AZ-6601 TCGA-CM-6171 TCGA-G4-6307 TCGA-G4-6321 
       62.79       100.01        14.04        55.04        22.09 

$`PISD WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 
       58.39         1.41         5.13        83.80        22.36        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        53.62        44.68        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.72        36.00        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  PISD MUTATED PISD WILD-TYPE 
         14.04           0.00 
  PISD MUTATED PISD WILD-TYPE 
        100.01         140.38 
  PISD MUTATED PISD WILD-TYPE 
         55.04          20.07 
[1] "14.0 - 100.0 (55.0)" "0.0 - 140.4 (20.1)" 
[1] "hr=" "1.1"
D1531V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PISD MUTATED         1        0        2         0         0         0
  PISD WILD-TYPE      63        1       23       109         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        18         10         40         31       35        13
                vv
clus             STAGE IVB
  PISD MUTATED           0
  PISD WILD-TYPE         1
D1531V3, multiclass
            clus
vv           PISD MUTATED PISD WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             0            109
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PISD MUTATED     0   2   3   0
  PISD WILD-TYPE   9  66 245  41
D1531V4, multiclass
    clus
vv   PISD MUTATED PISD WILD-TYPE
  T1            0              9
  T2            2             66
  T3            3            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
  PISD MUTATED     3   2   0
  PISD WILD-TYPE 217  78  66
D1531V5, multiclass
    clus
vv   PISD MUTATED PISD WILD-TYPE
  N0            3            217
  N1            2             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"
D1531V6, binary
                cls
clus               0   1
  PISD MUTATED     3   0
  PISD WILD-TYPE 280  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  PISD MUTATED      3    0
  PISD WILD-TYPE  280   48
   clus
vv  PISD MUTATED PISD WILD-TYPE
  0            3            280
  1            0             48
[1] 2 2
[1] FALSE
D1531V7, binary
                cls
clus               0   1
  PISD MUTATED     3   2
  PISD WILD-TYPE 167 195
[1] "tbl2"
                cls
clus             [,1] [,2]
  PISD MUTATED      3    2
  PISD WILD-TYPE  167  195
        clus
vv       PISD MUTATED PISD WILD-TYPE
  FEMALE            3            167
  MALE              2            195
[1] 2 2
[1] FALSE
D1531V8, binary
                cls
clus               0   1
  PISD MUTATED     5   0
  PISD WILD-TYPE 312  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  PISD MUTATED      5    0
  PISD WILD-TYPE  312   48
                               clus
vv                              PISD MUTATED PISD WILD-TYPE
  COLON ADENOCARCINOMA                     5            312
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PISD MUTATED     3   0   0   0
  PISD WILD-TYPE 254   2  22  21
D1531V9, multiclass
    clus
vv   PISD MUTATED PISD WILD-TYPE
  R0            3            254
  R1            0              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"
D1531V10, 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     5
  PISD WILD-TYPE                        19   171
D1531V11, 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                                       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(1532) Variable = DYM MUTATION ANALYSIS
D1532V1, survival
               sevent
clus2             0   1
  DYM MUTATED     8   2
  DYM WILD-TYPE 274  71
  DYM MUTATED DYM WILD-TYPE 
           10           345 
  DYM MUTATED DYM WILD-TYPE 
            2            71 
$`DYM MUTATED`
TCGA-A6-5665 TCGA-A6-6649 TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-4315 
       22.06        24.16        18.05         4.01        34.98        58.39 
TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-5914 TCGA-G4-6304 
       49.41         0.33        21.99        53.62 

$`DYM WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.18        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00O 
       19.00        30.02        34.03        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 
      102.44        40.34        15.62        49.08        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  DYM MUTATED DYM WILD-TYPE 
         0.33          0.00 
  DYM MUTATED DYM WILD-TYPE 
        58.39        140.38 
  DYM MUTATED DYM WILD-TYPE 
        23.11         20.02 
[1] "0.3 - 58.4 (23.1)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1.2"
D1532V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DYM MUTATED         0        0        1         4         3         0
  DYM WILD-TYPE      64        1       24       105         5         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DYM MUTATED           0          0          2          0        0         0
  DYM WILD-TYPE        19         10         39         31       35        13
               vv
clus            STAGE IVB
  DYM MUTATED           0
  DYM WILD-TYPE         1
D1532V3, multiclass
            clus
vv           DYM MUTATED DYM WILD-TYPE
  STAGE I              0            64
  STAGE IA             0             1
  STAGE II             1            24
  STAGE IIA            4           105
  STAGE IIB            3             5
  STAGE IIC            0             1
  STAGE III            0            19
  STAGE IIIA           0            10
  STAGE IIIB           2            39
  STAGE IIIC           0            31
  STAGE IV             0            35
  STAGE IVA            0            13
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  DYM MUTATED     0   0   7   3
  DYM WILD-TYPE   9  68 241  38
D1532V4, multiclass
    clus
vv   DYM MUTATED DYM WILD-TYPE
  T1           0             9
  T2           0            68
  T3           7           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
  DYM MUTATED     8   2   0
  DYM WILD-TYPE 212  78  66
D1532V5, multiclass
    clus
vv   DYM MUTATED DYM WILD-TYPE
  N0           8           212
  N1           2            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"
D1532V6, binary
               cls
clus              0   1
  DYM MUTATED     8   0
  DYM WILD-TYPE 275  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  DYM MUTATED      8    0
  DYM WILD-TYPE  275   48
   clus
vv  DYM MUTATED DYM WILD-TYPE
  0           8           275
  1           0            48
[1] 2 2
[1] FALSE
D1532V7, binary
               cls
clus              0   1
  DYM MUTATED     4   6
  DYM WILD-TYPE 166 191
[1] "tbl2"
               cls
clus            [,1] [,2]
  DYM MUTATED      4    6
  DYM WILD-TYPE  166  191
        clus
vv       DYM MUTATED DYM WILD-TYPE
  FEMALE           4           166
  MALE             6           191
[1] 2 2
[1] FALSE
D1532V8, binary
               cls
clus              0   1
  DYM MUTATED     8   2
  DYM WILD-TYPE 309  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  DYM MUTATED      8    2
  DYM WILD-TYPE  309   46
                               clus
vv                              DYM MUTATED DYM WILD-TYPE
  COLON ADENOCARCINOMA                    8           309
  COLON MUCINOUS ADENOCARCINOMA           2            46
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  DYM MUTATED     6   0   0   2
  DYM WILD-TYPE 251   2  22  19
D1532V9, multiclass
    clus
vv   DYM MUTATED DYM WILD-TYPE
  R0           6           251
  R1           0             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"
D1532V10, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DYM MUTATED                                  0     1
  DYM WILD-TYPE                                1     9
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  DYM MUTATED                           0     6
  DYM WILD-TYPE                        19   170
D1532V11, multiclass
                                  clus
vv                                 DYM MUTATED DYM 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(1533) Variable = MFSD4 MUTATION ANALYSIS
D1533V1, survival
                 sevent
clus2               0   1
  MFSD4 MUTATED     6   0
  MFSD4 WILD-TYPE 276  73
  MFSD4 MUTATED MFSD4 WILD-TYPE 
              6             349 
  MFSD4 MUTATED MFSD4 WILD-TYPE 
              0              73 
$`MFSD4 MUTATED`
TCGA-AA-3520 TCGA-AA-A00U TCGA-AD-6889 TCGA-AZ-4315 TCGA-CA-6716 TCGA-CA-6717 
       24.03        17.03        56.55        58.39         0.26         0.33 

$`MFSD4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       38.99         1.02         9.07        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00W 
       38.04         4.01        27.02        42.02         0.99        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6718 
        2.24         3.06         3.25         3.29         0.07         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  MFSD4 MUTATED MFSD4 WILD-TYPE 
           0.26            0.00 
  MFSD4 MUTATED MFSD4 WILD-TYPE 
          58.39          140.38 
  MFSD4 MUTATED MFSD4 WILD-TYPE 
          20.53           20.19 
[1] "0.3 - 58.4 (20.5)"  "0.0 - 140.4 (20.2)"
[1] "hr="     "9300000"
D1533V2, 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       24       105         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        19         10         40         31       35        13
                 vv
clus              STAGE IVB
  MFSD4 MUTATED           0
  MFSD4 WILD-TYPE         1
D1533V3, multiclass
            clus
vv           MFSD4 MUTATED MFSD4 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              4             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MFSD4 MUTATED     0   0   6   0
  MFSD4 WILD-TYPE   9  68 242  41
D1533V4, multiclass
    clus
vv   MFSD4 MUTATED MFSD4 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             6             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
  MFSD4 MUTATED     5   1   0
  MFSD4 WILD-TYPE 215  79  66
D1533V5, multiclass
    clus
vv   MFSD4 MUTATED MFSD4 WILD-TYPE
  N0             5             215
  N1             1              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"
D1533V6, binary
                 cls
clus                0   1
  MFSD4 MUTATED     6   0
  MFSD4 WILD-TYPE 277  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MFSD4 MUTATED      6    0
  MFSD4 WILD-TYPE  277   48
   clus
vv  MFSD4 MUTATED MFSD4 WILD-TYPE
  0             6             277
  1             0              48
[1] 2 2
[1] FALSE
D1533V7, 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
D1533V8, binary
                 cls
clus                0   1
  MFSD4 MUTATED     5   1
  MFSD4 WILD-TYPE 312  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MFSD4 MUTATED      5    1
  MFSD4 WILD-TYPE  312   47
                               clus
vv                              MFSD4 MUTATED MFSD4 WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MFSD4 MUTATED     3   0   0   2
  MFSD4 WILD-TYPE 254   2  22  19
D1533V9, multiclass
    clus
vv   MFSD4 MUTATED MFSD4 WILD-TYPE
  R0             3             254
  R1             0               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"
D1533V10, 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
D1533V11, 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(1534) Variable = MORC1 MUTATION ANALYSIS
D1534V1, survival
                 sevent
clus2               0   1
  MORC1 MUTATED    11   1
  MORC1 WILD-TYPE 271  72
  MORC1 MUTATED MORC1 WILD-TYPE 
             12             343 
  MORC1 MUTATED MORC1 WILD-TYPE 
              1              72 
$`MORC1 MUTATED`
TCGA-A6-2676 TCGA-AA-3538 TCGA-AA-A00A TCGA-AA-A010 TCGA-AZ-4315 TCGA-CA-5797 
       42.90        26.01        38.04        34.98        58.39         3.29 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4752 TCGA-CM-5868 TCGA-D5-6533 TCGA-G4-6588 
        0.33         0.10        13.02        17.03         1.32        26.17 

$`MORC1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D 
       27.02        19.07         7.96        27.02        13.94        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.06         3.25         0.07         0.26         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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 
       16.01        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        12.26        19.59        13.51        11.51        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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 
       52.80 

  MORC1 MUTATED MORC1 WILD-TYPE 
            0.1             0.0 
  MORC1 MUTATED MORC1 WILD-TYPE 
          58.39          140.38 
  MORC1 MUTATED MORC1 WILD-TYPE 
          21.52           20.19 
[1] "0.1 - 58.4 (21.5)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2"  
D1534V2, 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       25       101         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MORC1 MUTATED           0          0          1          0        0         1
  MORC1 WILD-TYPE        19         10         40         31       35        12
                 vv
clus              STAGE IVB
  MORC1 MUTATED           0
  MORC1 WILD-TYPE         1
D1534V3, multiclass
            clus
vv           MORC1 MUTATED MORC1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              8             101
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 240  37
D1534V4, multiclass
    clus
vv   MORC1 MUTATED MORC1 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             8             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
  MORC1 MUTATED    12   1   0
  MORC1 WILD-TYPE 208  79  66
D1534V5, multiclass
    clus
vv   MORC1 MUTATED MORC1 WILD-TYPE
  N0            12             208
  N1             1              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"
D1534V6, binary
                 cls
clus                0   1
  MORC1 MUTATED    12   1
  MORC1 WILD-TYPE 271  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MORC1 MUTATED     12    1
  MORC1 WILD-TYPE  271   47
   clus
vv  MORC1 MUTATED MORC1 WILD-TYPE
  0            12             271
  1             1              47
[1] 2 2
[1] FALSE
D1534V7, 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
D1534V8, binary
                 cls
clus                0   1
  MORC1 MUTATED    12   1
  MORC1 WILD-TYPE 305  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MORC1 MUTATED     12    1
  MORC1 WILD-TYPE  305   47
                               clus
vv                              MORC1 MUTATED MORC1 WILD-TYPE
  COLON ADENOCARCINOMA                     12             305
  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 246   2  22  19
D1534V9, multiclass
    clus
vv   MORC1 MUTATED MORC1 WILD-TYPE
  R0            11             246
  R1             0               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"
D1534V10, 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
D1534V11, 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(1535) Variable = OR7D4 MUTATION ANALYSIS
D1535V1, survival
                 sevent
clus2               0   1
  OR7D4 MUTATED     7   1
  OR7D4 WILD-TYPE 275  72
  OR7D4 MUTATED OR7D4 WILD-TYPE 
              8             347 
  OR7D4 MUTATED OR7D4 WILD-TYPE 
              1              72 
$`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         0.33         2.93        16.01 
TCGA-DM-A282 TCGA-F4-6460 
      139.17        13.38 

$`OR7D4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
        1.02        35.01         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02        14.93        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 
       15.62        49.08        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-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       135.65         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  OR7D4 MUTATED OR7D4 WILD-TYPE 
              0               0 
  OR7D4 MUTATED OR7D4 WILD-TYPE 
         139.17          140.38 
  OR7D4 MUTATED OR7D4 WILD-TYPE 
         10.175          20.980 
[1] "0.0 - 139.2 (10.2)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.8"
D1535V2, 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       23       104         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        19         10         40         31       35        13
                 vv
clus              STAGE IVB
  OR7D4 MUTATED           0
  OR7D4 WILD-TYPE         1
D1535V3, multiclass
            clus
vv           OR7D4 MUTATED OR7D4 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              5             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR7D4 MUTATED     0   1   7   1
  OR7D4 WILD-TYPE   9  67 241  40
D1535V4, multiclass
    clus
vv   OR7D4 MUTATED OR7D4 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             7             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
  OR7D4 MUTATED     8   1   0
  OR7D4 WILD-TYPE 212  79  66
D1535V5, multiclass
    clus
vv   OR7D4 MUTATED OR7D4 WILD-TYPE
  N0             8             212
  N1             1              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"
D1535V6, binary
                 cls
clus                0   1
  OR7D4 MUTATED     7   0
  OR7D4 WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR7D4 MUTATED      7    0
  OR7D4 WILD-TYPE  276   48
   clus
vv  OR7D4 MUTATED OR7D4 WILD-TYPE
  0             7             276
  1             0              48
[1] 2 2
[1] FALSE
D1535V7, 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
D1535V8, binary
                 cls
clus                0   1
  OR7D4 MUTATED     8   1
  OR7D4 WILD-TYPE 309  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR7D4 MUTATED      8    1
  OR7D4 WILD-TYPE  309   47
                               clus
vv                              OR7D4 MUTATED OR7D4 WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  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 252   2  22  18
D1535V9, multiclass
    clus
vv   OR7D4 MUTATED OR7D4 WILD-TYPE
  R0             5             252
  R1             0               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"
D1535V10, 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
D1535V11, 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(1536) Variable = ST6GALNAC3 MUTATION ANALYSIS
D1536V1, survival
                      sevent
clus2                    0   1
  ST6GALNAC3 MUTATED    10   2
  ST6GALNAC3 WILD-TYPE 272  71
  ST6GALNAC3 MUTATED ST6GALNAC3 WILD-TYPE 
                  12                  343 
  ST6GALNAC3 MUTATED ST6GALNAC3 WILD-TYPE 
                   2                   71 
$`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         0.33 
TCGA-CA-6718 TCGA-CM-5348 TCGA-CM-6167 TCGA-CM-6674 TCGA-D5-6532 TCGA-D5-6540 
        0.10        22.98        14.99        12.95        18.25        16.14 

$`ST6GALNAC3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6648 
       22.09        32.71        27.09        22.52         8.38        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       24.16        21.76        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       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        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07         0.26         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  ST6GALNAC3 MUTATED ST6GALNAC3 WILD-TYPE 
                 0.1                  0.0 
  ST6GALNAC3 MUTATED ST6GALNAC3 WILD-TYPE 
               38.07               140.38 
  ST6GALNAC3 MUTATED ST6GALNAC3 WILD-TYPE 
              17.195               20.280 
[1] "0.1 - 38.1 (17.2)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.2"
D1536V2, 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       25       104         7         1
                      vv
clus                   STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ST6GALNAC3 MUTATED           1          0          1          1        0
  ST6GALNAC3 WILD-TYPE        18         10         40         30       35
                      vv
clus                   STAGE IVA STAGE IVB
  ST6GALNAC3 MUTATED           2         0
  ST6GALNAC3 WILD-TYPE        11         1
D1536V3, multiclass
            clus
vv           ST6GALNAC3 MUTATED ST6GALNAC3 WILD-TYPE
  STAGE I                     1                   63
  STAGE IA                    0                    1
  STAGE II                    0                   25
  STAGE IIA                   5                  104
  STAGE IIB                   1                    7
  STAGE IIC                   0                    1
  STAGE III                   1                   18
  STAGE IIIA                  0                   10
  STAGE IIIB                  1                   40
  STAGE IIIC                  1                   30
  STAGE IV                    0                   35
  STAGE IVA                   2                   11
  STAGE IVB                   0                    1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 238  40
D1536V4, multiclass
    clus
vv   ST6GALNAC3 MUTATED ST6GALNAC3 WILD-TYPE
  T1                  0                    9
  T2                  1                   67
  T3                 10                  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
  ST6GALNAC3 MUTATED     8   3   1
  ST6GALNAC3 WILD-TYPE 212  77  65
D1536V5, multiclass
    clus
vv   ST6GALNAC3 MUTATED ST6GALNAC3 WILD-TYPE
  N0                  8                  212
  N1                  3                   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"
D1536V6, binary
                      cls
clus                     0   1
  ST6GALNAC3 MUTATED    10   2
  ST6GALNAC3 WILD-TYPE 273  46
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  ST6GALNAC3 MUTATED     10    2
  ST6GALNAC3 WILD-TYPE  273   46
   clus
vv  ST6GALNAC3 MUTATED ST6GALNAC3 WILD-TYPE
  0                 10                  273
  1                  2                   46
[1] 2 2
[1] FALSE
D1536V7, 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
D1536V8, binary
                      cls
clus                     0   1
  ST6GALNAC3 MUTATED     9   3
  ST6GALNAC3 WILD-TYPE 308  45
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  ST6GALNAC3 MUTATED      9    3
  ST6GALNAC3 WILD-TYPE  308   45
                               clus
vv                              ST6GALNAC3 MUTATED ST6GALNAC3 WILD-TYPE
  COLON ADENOCARCINOMA                           9                  308
  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 249   2  22  19
D1536V9, multiclass
    clus
vv   ST6GALNAC3 MUTATED ST6GALNAC3 WILD-TYPE
  R0                  8                  249
  R1                  0                    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"
D1536V10, 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
D1536V11, 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(1537) Variable = CCDC18 MUTATION ANALYSIS
D1537V1, survival
                  sevent
clus2                0   1
  CCDC18 MUTATED     8   2
  CCDC18 WILD-TYPE 274  71
  CCDC18 MUTATED CCDC18 WILD-TYPE 
              10              345 
  CCDC18 MUTATED CCDC18 WILD-TYPE 
               2               71 
$`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         0.33        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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        61.02         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         0.72        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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-6678 
       14.04        11.01        12.95        13.05        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      135.65       139.17         6.12       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  CCDC18 MUTATED CCDC18 WILD-TYPE 
            0.33             0.00 
  CCDC18 MUTATED CCDC18 WILD-TYPE 
           81.37           140.38 
  CCDC18 MUTATED CCDC18 WILD-TYPE 
           22.52            20.12 
[1] "0.3 - 81.4 (22.5)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.2"
D1537V2, 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       24       104         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC18 MUTATED           0          0          0          1        1
  CCDC18 WILD-TYPE        19         10         41         30       34
                  vv
clus               STAGE IVA STAGE IVB
  CCDC18 MUTATED           0         0
  CCDC18 WILD-TYPE        13         1
D1537V3, multiclass
            clus
vv           CCDC18 MUTATED CCDC18 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               5              104
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              1               30
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CCDC18 MUTATED     0   2   7   2
  CCDC18 WILD-TYPE   9  66 241  39
D1537V4, multiclass
    clus
vv   CCDC18 MUTATED CCDC18 WILD-TYPE
  T1              0                9
  T2              2               66
  T3              7              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
  CCDC18 MUTATED     9   1   1
  CCDC18 WILD-TYPE 211  79  65
D1537V5, multiclass
    clus
vv   CCDC18 MUTATED CCDC18 WILD-TYPE
  N0              9              211
  N1              1               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"
D1537V6, binary
                  cls
clus                 0   1
  CCDC18 MUTATED     8   1
  CCDC18 WILD-TYPE 275  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC18 MUTATED      8    1
  CCDC18 WILD-TYPE  275   47
   clus
vv  CCDC18 MUTATED CCDC18 WILD-TYPE
  0              8              275
  1              1               47
[1] 2 2
[1] FALSE
D1537V7, 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
D1537V8, binary
                  cls
clus                 0   1
  CCDC18 MUTATED     9   2
  CCDC18 WILD-TYPE 308  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC18 MUTATED      9    2
  CCDC18 WILD-TYPE  308   46
                               clus
vv                              CCDC18 MUTATED CCDC18 WILD-TYPE
  COLON ADENOCARCINOMA                       9              308
  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 250   2  22  20
D1537V9, multiclass
    clus
vv   CCDC18 MUTATED CCDC18 WILD-TYPE
  R0              7              250
  R1              0                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"
D1537V10, 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
D1537V11, 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(1538) Variable = CLDN17 MUTATION ANALYSIS
D1538V1, survival
                  sevent
clus2                0   1
  CLDN17 MUTATED    10   3
  CLDN17 WILD-TYPE 272  70
  CLDN17 MUTATED CLDN17 WILD-TYPE 
              13              342 
  CLDN17 MUTATED CLDN17 WILD-TYPE 
               3               70 
$`CLDN17 MUTATED`
TCGA-AA-3543 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q TCGA-AD-6964 
        0.99        18.05         4.01        34.98         1.02        10.88 
TCGA-AZ-4315 TCGA-AZ-4616 TCGA-CA-6717 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 
       58.39         5.13         0.33         1.32        43.27        17.85 
TCGA-D5-6538 
       17.13 

$`CLDN17 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01        12.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       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        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        1.41        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 
       20.19        18.25        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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  CLDN17 MUTATED CLDN17 WILD-TYPE 
            0.33             0.00 
  CLDN17 MUTATED CLDN17 WILD-TYPE 
           58.39           140.38 
  CLDN17 MUTATED CLDN17 WILD-TYPE 
          10.880           20.995 
[1] "0.3 - 58.4 (10.9)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.8"
D1538V2, 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       24       105         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CLDN17 MUTATED           0          0          3          0        1
  CLDN17 WILD-TYPE        19         10         38         31       34
                  vv
clus               STAGE IVA STAGE IVB
  CLDN17 MUTATED           0         0
  CLDN17 WILD-TYPE        13         1
D1538V3, multiclass
            clus
vv           CLDN17 MUTATED CLDN17 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               4              105
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              3               38
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CLDN17 MUTATED     0   1   7   5
  CLDN17 WILD-TYPE   9  67 241  36
D1538V4, multiclass
    clus
vv   CLDN17 MUTATED CLDN17 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              7              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
  CLDN17 MUTATED     9   1   3
  CLDN17 WILD-TYPE 211  79  63
D1538V5, multiclass
    clus
vv   CLDN17 MUTATED CLDN17 WILD-TYPE
  N0              9              211
  N1              1               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"
D1538V6, binary
                  cls
clus                 0   1
  CLDN17 MUTATED    11   1
  CLDN17 WILD-TYPE 272  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLDN17 MUTATED     11    1
  CLDN17 WILD-TYPE  272   47
   clus
vv  CLDN17 MUTATED CLDN17 WILD-TYPE
  0             11              272
  1              1               47
[1] 2 2
[1] FALSE
D1538V7, 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
D1538V8, binary
                  cls
clus                 0   1
  CLDN17 MUTATED     8   5
  CLDN17 WILD-TYPE 309  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLDN17 MUTATED      8    5
  CLDN17 WILD-TYPE  309   43
                               clus
vv                              CLDN17 MUTATED CLDN17 WILD-TYPE
  COLON ADENOCARCINOMA                       8              309
  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 247   2  22  20
D1538V9, multiclass
    clus
vv   CLDN17 MUTATED CLDN17 WILD-TYPE
  R0             10              247
  R1              0                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"
D1538V10, 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
D1538V11, 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(1539) Variable = ENGASE MUTATION ANALYSIS
D1539V1, survival
                  sevent
clus2                0   1
  ENGASE MUTATED     3   1
  ENGASE WILD-TYPE 279  72
  ENGASE MUTATED ENGASE WILD-TYPE 
               4              351 
  ENGASE MUTATED ENGASE WILD-TYPE 
               1               72 
$`ENGASE MUTATED`
TCGA-A6-6781 TCGA-AA-3815 TCGA-AD-6964 TCGA-CM-6171 
       19.66        33.04        10.88        14.04 

$`ENGASE WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  ENGASE MUTATED ENGASE WILD-TYPE 
           10.88             0.00 
  ENGASE MUTATED ENGASE WILD-TYPE 
           33.04           140.38 
  ENGASE MUTATED ENGASE WILD-TYPE 
           16.85            20.28 
[1] "10.9 - 33.0 (16.9)" "0.0 - 140.4 (20.3)"
[1] "hr=" "1.6"
D1539V2, 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       25       108         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ENGASE MUTATED           0          0          0          1        0
  ENGASE WILD-TYPE        19         10         41         30       35
                  vv
clus               STAGE IVA STAGE IVB
  ENGASE MUTATED           0         0
  ENGASE WILD-TYPE        13         1
D1539V3, multiclass
            clus
vv           ENGASE MUTATED ENGASE WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               1              108
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ENGASE MUTATED     0   1   1   2
  ENGASE WILD-TYPE   9  67 247  39
D1539V4, multiclass
    clus
vv   ENGASE MUTATED ENGASE WILD-TYPE
  T1              0                9
  T2              1               67
  T3              1              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
  ENGASE MUTATED     2   1   1
  ENGASE WILD-TYPE 218  79  65
D1539V5, multiclass
    clus
vv   ENGASE MUTATED ENGASE WILD-TYPE
  N0              2              218
  N1              1               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"
D1539V6, binary
                  cls
clus                 0   1
  ENGASE MUTATED     2   0
  ENGASE WILD-TYPE 281  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ENGASE MUTATED      2    0
  ENGASE WILD-TYPE  281   48
   clus
vv  ENGASE MUTATED ENGASE WILD-TYPE
  0              2              281
  1              0               48
[1] 2 2
[1] FALSE
D1539V7, 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
D1539V8, binary
                  cls
clus                 0   1
  ENGASE MUTATED     3   1
  ENGASE WILD-TYPE 314  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ENGASE MUTATED      3    1
  ENGASE WILD-TYPE  314   47
                               clus
vv                              ENGASE MUTATED ENGASE WILD-TYPE
  COLON ADENOCARCINOMA                       3              314
  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 254   2  22  21
D1539V9, multiclass
    clus
vv   ENGASE MUTATED ENGASE WILD-TYPE
  R0              3              254
  R1              0                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"
D1539V10, 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
D1539V11, 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(1540) Variable = TAPBP MUTATION ANALYSIS
D1540V1, survival
                 sevent
clus2               0   1
  TAPBP MUTATED     3   1
  TAPBP WILD-TYPE 279  72
  TAPBP MUTATED TAPBP WILD-TYPE 
              4             351 
  TAPBP MUTATED TAPBP WILD-TYPE 
              1              72 
$`TAPBP MUTATED`
TCGA-AA-3833 TCGA-AA-A00J TCGA-AA-A010 TCGA-CM-5862 
       15.95        18.05        34.98         5.03 

$`TAPBP WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
        1.02        17.98        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  TAPBP MUTATED TAPBP WILD-TYPE 
           5.03            0.00 
  TAPBP MUTATED TAPBP WILD-TYPE 
          34.98          140.38 
  TAPBP MUTATED TAPBP WILD-TYPE 
          17.00           20.28 
[1] "5.0 - 35.0 (17.0)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.7"
D1540V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TAPBP MUTATED         0        0        0         1         1         0
  TAPBP WILD-TYPE      64        1       25       108         7         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        19         10         40         31       35        12
                 vv
clus              STAGE IVB
  TAPBP MUTATED           0
  TAPBP WILD-TYPE         1
D1540V3, multiclass
            clus
vv           TAPBP MUTATED TAPBP WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              1             108
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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   2
  TAPBP WILD-TYPE   9  68 246  39
D1540V4, multiclass
    clus
vv   TAPBP MUTATED TAPBP WILD-TYPE
  T1             0               9
  T2             0              68
  T3             2             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
  TAPBP MUTATED     2   2   0
  TAPBP WILD-TYPE 218  78  66
D1540V5, multiclass
    clus
vv   TAPBP MUTATED TAPBP WILD-TYPE
  N0             2             218
  N1             2              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"
D1540V6, binary
                 cls
clus                0   1
  TAPBP MUTATED     3   1
  TAPBP WILD-TYPE 280  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAPBP MUTATED      3    1
  TAPBP WILD-TYPE  280   47
   clus
vv  TAPBP MUTATED TAPBP WILD-TYPE
  0             3             280
  1             1              47
[1] 2 2
[1] FALSE
D1540V7, binary
                 cls
clus                0   1
  TAPBP MUTATED     2   2
  TAPBP WILD-TYPE 168 195
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAPBP MUTATED      2    2
  TAPBP WILD-TYPE  168  195
        clus
vv       TAPBP MUTATED TAPBP WILD-TYPE
  FEMALE             2             168
  MALE               2             195
[1] 2 2
[1] FALSE
D1540V8, binary
                 cls
clus                0   1
  TAPBP MUTATED     3   1
  TAPBP WILD-TYPE 314  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAPBP MUTATED      3    1
  TAPBP WILD-TYPE  314   47
                               clus
vv                              TAPBP MUTATED TAPBP WILD-TYPE
  COLON ADENOCARCINOMA                      3             314
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TAPBP MUTATED     4   0   0   0
  TAPBP WILD-TYPE 253   2  22  21
D1540V9, multiclass
    clus
vv   TAPBP MUTATED TAPBP WILD-TYPE
  R0             4             253
  R1             0               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"
D1540V10, 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
D1540V11, multiclass
[1] "Remove cluster labels:" "TAPBP MUTATED"         
clus
  TAPBP MUTATED TAPBP WILD-TYPE 
              1             205 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-4105 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-A6-5656      TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5660 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-A6-5661      TCGA-A6-5662      TCGA-A6-5664      TCGA-A6-5665 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-A6-5666      TCGA-A6-6137      TCGA-A6-6138      TCGA-A6-6141 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-A6-6142      TCGA-A6-6648      TCGA-A6-6649      TCGA-A6-6651 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-A6-6652      TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-A6-6781      TCGA-A6-6782      TCGA-AD-5900      TCGA-AD-6548 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-AD-6888      TCGA-AD-6889      TCGA-AD-6890      TCGA-AD-6895 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-AD-6899      TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6964 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-AD-6965      TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-AY-4071      TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-AY-6386      TCGA-AZ-4315      TCGA-AZ-4323      TCGA-AZ-4616 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-AZ-4681      TCGA-AZ-4682      TCGA-AZ-5403      TCGA-AZ-5407 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-AZ-6598      TCGA-AZ-6599      TCGA-AZ-6600      TCGA-AZ-6601 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-AZ-6603      TCGA-AZ-6605      TCGA-AZ-6606      TCGA-AZ-6607 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-AZ-6608      TCGA-CA-5254      TCGA-CA-5255      TCGA-CA-5796 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-CA-5797      TCGA-CA-6715      TCGA-CA-6716      TCGA-CA-6717 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-CA-6718      TCGA-CA-6719      TCGA-CK-4947      TCGA-CK-4948 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-CK-4950      TCGA-CK-4952      TCGA-CK-5912      TCGA-CK-5913 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-CK-5914      TCGA-CK-5915      TCGA-CK-5916      TCGA-CK-6746 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-CK-6747      TCGA-CK-6748      TCGA-CK-6751      TCGA-CM-4743 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-CM-4744      TCGA-CM-4746      TCGA-CM-4747      TCGA-CM-4752 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-CM-5341      TCGA-CM-5344      TCGA-CM-5348      TCGA-CM-5349 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-CM-5860      TCGA-CM-5861      TCGA-CM-5863      TCGA-CM-5864 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-CM-5868      TCGA-CM-6161      TCGA-CM-6162      TCGA-CM-6163 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-CM-6164      TCGA-CM-6165      TCGA-CM-6166      TCGA-CM-6167 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-CM-6168      TCGA-CM-6169      TCGA-CM-6170      TCGA-CM-6171 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-CM-6172      TCGA-CM-6674      TCGA-CM-6675      TCGA-CM-6676 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-CM-6677      TCGA-CM-6678      TCGA-CM-6679      TCGA-CM-6680 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-D5-5537      TCGA-D5-5538      TCGA-D5-5539      TCGA-D5-5540 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-D5-5541      TCGA-D5-6529      TCGA-D5-6532      TCGA-D5-6533 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-D5-6534      TCGA-D5-6535      TCGA-D5-6536      TCGA-D5-6537 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-D5-6538      TCGA-D5-6539      TCGA-D5-6540      TCGA-D5-6541 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-D5-6898      TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-D5-6924      TCGA-D5-6926      TCGA-D5-6927      TCGA-D5-6928 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-D5-6929      TCGA-D5-6930      TCGA-D5-6931      TCGA-D5-6932 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-D5-7000      TCGA-DM-A0X9      TCGA-DM-A0XD      TCGA-DM-A0XF 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-DM-A1D0      TCGA-DM-A1D4      TCGA-DM-A1D6      TCGA-DM-A1D7 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-DM-A1D8      TCGA-DM-A1D9      TCGA-DM-A1DA      TCGA-DM-A1DB 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-DM-A1HA      TCGA-DM-A1HB      TCGA-DM-A282      TCGA-DM-A285 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-DM-A28C      TCGA-DM-A28E      TCGA-DM-A28F      TCGA-DM-A28G 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-DM-A28H      TCGA-DM-A28K      TCGA-F4-6459      TCGA-F4-6460 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-F4-6805      TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-G4-6306      TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-G4-6586      TCGA-G4-6588      TCGA-G4-6625      TCGA-G4-6626 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-G4-6628 
"TAPBP WILD-TYPE" 

Clustering(1541) Variable = CAPZA3 MUTATION ANALYSIS
D1541V1, survival
                  sevent
clus2                0   1
  CAPZA3 MUTATED     8   1
  CAPZA3 WILD-TYPE 274  72
  CAPZA3 MUTATED CAPZA3 WILD-TYPE 
               9              346 
  CAPZA3 MUTATED CAPZA3 WILD-TYPE 
               1               72 
$`CAPZA3 MUTATED`
TCGA-A6-6141 TCGA-AA-3555 TCGA-AA-3950 TCGA-AA-3989 TCGA-AZ-4315 TCGA-CM-5349 
        8.38        29.95        24.00         7.96        58.39        30.08 
TCGA-D5-6535 TCGA-G4-6304 TCGA-G4-6628 
       15.12        53.62        52.80 

$`CAPZA3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        17.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       19.07        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 
       19.43       107.67        74.56        65.85        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       35.80        26.17        91.79        46.75 

  CAPZA3 MUTATED CAPZA3 WILD-TYPE 
            7.96             0.00 
  CAPZA3 MUTATED CAPZA3 WILD-TYPE 
           58.39           140.38 
  CAPZA3 MUTATED CAPZA3 WILD-TYPE 
           29.95            20.07 
[1] "8.0 - 58.4 (29.9)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "2.4"
D1541V2, 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       25       104         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CAPZA3 MUTATED           0          0          1          0        1
  CAPZA3 WILD-TYPE        19         10         40         31       34
                  vv
clus               STAGE IVA STAGE IVB
  CAPZA3 MUTATED           0         0
  CAPZA3 WILD-TYPE        13         1
D1541V3, multiclass
            clus
vv           CAPZA3 MUTATED CAPZA3 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               5              104
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CAPZA3 MUTATED     0   1   7   1
  CAPZA3 WILD-TYPE   9  67 241  40
D1541V4, multiclass
    clus
vv   CAPZA3 MUTATED CAPZA3 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              7              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
  CAPZA3 MUTATED     7   1   1
  CAPZA3 WILD-TYPE 213  79  65
D1541V5, multiclass
    clus
vv   CAPZA3 MUTATED CAPZA3 WILD-TYPE
  N0              7              213
  N1              1               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"
D1541V6, binary
                  cls
clus                 0   1
  CAPZA3 MUTATED     7   1
  CAPZA3 WILD-TYPE 276  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CAPZA3 MUTATED      7    1
  CAPZA3 WILD-TYPE  276   47
   clus
vv  CAPZA3 MUTATED CAPZA3 WILD-TYPE
  0              7              276
  1              1               47
[1] 2 2
[1] FALSE
D1541V7, 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
D1541V8, binary
                  cls
clus                 0   1
  CAPZA3 MUTATED     7   2
  CAPZA3 WILD-TYPE 310  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CAPZA3 MUTATED      7    2
  CAPZA3 WILD-TYPE  310   46
                               clus
vv                              CAPZA3 MUTATED CAPZA3 WILD-TYPE
  COLON ADENOCARCINOMA                       7              310
  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 251   2  21  20
D1541V9, multiclass
    clus
vv   CAPZA3 MUTATED CAPZA3 WILD-TYPE
  R0              6              251
  R1              0                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"
D1541V10, 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
D1541V11, 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(1542) Variable = BEND2 MUTATION ANALYSIS
D1542V1, survival
                 sevent
clus2               0   1
  BEND2 MUTATED    18   3
  BEND2 WILD-TYPE 264  70
  BEND2 MUTATED BEND2 WILD-TYPE 
             21             334 
  BEND2 MUTATED BEND2 WILD-TYPE 
              3              70 
$`BEND2 MUTATED`
TCGA-A6-3809 TCGA-A6-5666 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3666 TCGA-AA-3710 
       32.75        32.71         1.02        13.02         2.01        26.99 
TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-A00J TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6603 
       31.00        33.01        18.05        21.44        58.39        29.56 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5914 TCGA-CM-5348 TCGA-CM-6162 TCGA-D5-5540 
        0.33         0.10        21.99        22.98        12.00        13.51 
TCGA-D5-6931 TCGA-DM-A28E TCGA-G4-6306 
       12.00       119.93        44.68 

$`BEND2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
       63.98         6.97        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 
       61.02        78.08         6.05         6.97        54.02        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 
       37.05        19.00        36.00         5.03        85.05        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
        0.20        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07         0.26         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 
      102.44        40.34        15.62        49.08        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-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-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       12.26        19.59        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 
      107.67        74.56        65.85        53.62        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  BEND2 MUTATED BEND2 WILD-TYPE 
            0.1             0.0 
  BEND2 MUTATED BEND2 WILD-TYPE 
         119.93          140.38 
  BEND2 MUTATED BEND2 WILD-TYPE 
          21.99           20.07 
[1] "0.1 - 119.9 (22.0)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.4"
D1542V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BEND2 MUTATED         2        0        0         9         2         1
  BEND2 WILD-TYPE      62        1       25       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        16         10         37         30       35        13
                 vv
clus              STAGE IVB
  BEND2 MUTATED           0
  BEND2 WILD-TYPE         1
D1542V3, multiclass
            clus
vv           BEND2 MUTATED BEND2 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              9             100
  STAGE IIB              2               6
  STAGE IIC              1               0
  STAGE III              3              16
  STAGE IIIA             0              10
  STAGE IIIB             4              37
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  BEND2 MUTATED     1   3  14   5
  BEND2 WILD-TYPE   8  65 234  36
D1542V4, multiclass
    clus
vv   BEND2 MUTATED BEND2 WILD-TYPE
  T1             1               8
  T2             3              65
  T3            14             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
  BEND2 MUTATED    14   6   3
  BEND2 WILD-TYPE 206  74  63
D1542V5, multiclass
    clus
vv   BEND2 MUTATED BEND2 WILD-TYPE
  N0            14             206
  N1             6              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"
D1542V6, binary
                 cls
clus                0   1
  BEND2 MUTATED    20   0
  BEND2 WILD-TYPE 263  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BEND2 MUTATED     20    0
  BEND2 WILD-TYPE  263   48
   clus
vv  BEND2 MUTATED BEND2 WILD-TYPE
  0            20             263
  1             0              48
[1] 2 2
[1] FALSE
D1542V7, 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
D1542V8, binary
                 cls
clus                0   1
  BEND2 MUTATED    16   7
  BEND2 WILD-TYPE 301  41
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BEND2 MUTATED     16    7
  BEND2 WILD-TYPE  301   41
                               clus
vv                              BEND2 MUTATED BEND2 WILD-TYPE
  COLON ADENOCARCINOMA                     16             301
  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 241   2  22  18
D1542V9, multiclass
    clus
vv   BEND2 MUTATED BEND2 WILD-TYPE
  R0            16             241
  R1             0               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"
D1542V10, 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
D1542V11, 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(1543) Variable = PIWIL1 MUTATION ANALYSIS
D1543V1, survival
                  sevent
clus2                0   1
  PIWIL1 MUTATED    19   2
  PIWIL1 WILD-TYPE 263  71
  PIWIL1 MUTATED PIWIL1 WILD-TYPE 
              21              334 
  PIWIL1 MUTATED PIWIL1 WILD-TYPE 
               2               71 
$`PIWIL1 MUTATED`
TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-6141 TCGA-A6-6651 TCGA-A6-6653 TCGA-AA-3492 
       30.44        33.53         8.38        21.76        24.39         3.02 
TCGA-AA-3821 TCGA-AA-3977 TCGA-AA-A010 TCGA-AD-6548 TCGA-AD-6890 TCGA-AZ-6600 
        1.02        25.02        34.98        21.37         0.79        12.10 
TCGA-CA-5796 TCGA-CA-6716 TCGA-CA-6717 TCGA-CK-4947 TCGA-CM-4746 TCGA-D5-5539 
        3.25         0.26         0.33        17.56        37.02        19.59 
TCGA-D5-6532 TCGA-D5-6927 TCGA-D5-6930 
       18.25         9.44         1.51 

$`PIWIL1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       32.91        31.63        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       32.71        27.09        22.52        25.08        25.18        24.16 
TCGA-A6-6652 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-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 
       18.05        40.96         0.07         4.21        56.55         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41        49.41         6.77       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 
        3.29         0.07         0.10         1.35       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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-D5-6533 TCGA-D5-6534 
       12.26        13.51        11.51        20.19         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  PIWIL1 MUTATED PIWIL1 WILD-TYPE 
            0.26             0.00 
  PIWIL1 MUTATED PIWIL1 WILD-TYPE 
           37.02           140.38 
  PIWIL1 MUTATED PIWIL1 WILD-TYPE 
           17.56            20.98 
[1] "0.3 - 37.0 (17.6)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.3"
D1543V2, 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       23       101         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PIWIL1 MUTATED           0          1          1          0        1
  PIWIL1 WILD-TYPE        19          9         40         31       34
                  vv
clus               STAGE IVA STAGE IVB
  PIWIL1 MUTATED           1         0
  PIWIL1 WILD-TYPE        12         1
D1543V3, multiclass
            clus
vv           PIWIL1 MUTATED PIWIL1 WILD-TYPE
  STAGE I                 5               59
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               8              101
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              1                9
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  62 237  37
D1543V4, multiclass
    clus
vv   PIWIL1 MUTATED PIWIL1 WILD-TYPE
  T1              1                8
  T2              6               62
  T3             11              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
  PIWIL1 MUTATED    18   4   0
  PIWIL1 WILD-TYPE 202  76  66
D1543V5, multiclass
    clus
vv   PIWIL1 MUTATED PIWIL1 WILD-TYPE
  N0             18              202
  N1              4               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"
D1543V6, binary
                  cls
clus                 0   1
  PIWIL1 MUTATED    18   1
  PIWIL1 WILD-TYPE 265  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIWIL1 MUTATED     18    1
  PIWIL1 WILD-TYPE  265   47
   clus
vv  PIWIL1 MUTATED PIWIL1 WILD-TYPE
  0             18              265
  1              1               47
[1] 2 2
[1] FALSE
D1543V7, 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
D1543V8, binary
                  cls
clus                 0   1
  PIWIL1 MUTATED    17   5
  PIWIL1 WILD-TYPE 300  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIWIL1 MUTATED     17    5
  PIWIL1 WILD-TYPE  300   43
                               clus
vv                              PIWIL1 MUTATED PIWIL1 WILD-TYPE
  COLON ADENOCARCINOMA                      17              300
  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 244   2  22  18
D1543V9, multiclass
    clus
vv   PIWIL1 MUTATED PIWIL1 WILD-TYPE
  R0             13              244
  R1              0                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"
D1543V10, 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
D1543V11, 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(1544) Variable = SLC14A1 MUTATION ANALYSIS
D1544V1, survival
                   sevent
clus2                 0   1
  SLC14A1 MUTATED     8   2
  SLC14A1 WILD-TYPE 274  71
  SLC14A1 MUTATED SLC14A1 WILD-TYPE 
               10               345 
  SLC14A1 MUTATED SLC14A1 WILD-TYPE 
                2                71 
$`SLC14A1 MUTATED`
TCGA-AA-3950 TCGA-AA-3968 TCGA-AD-6895 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 
       24.00        21.99         0.72        58.39        49.41         0.33 
TCGA-CM-6163 TCGA-DM-A1D7 TCGA-DM-A28H TCGA-F4-6460 
       14.04        13.32       117.07        13.38 

$`SLC14A1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03         2.01        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 
       15.02        15.02        17.03        15.02        12.00        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        49.91        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 
       35.97        60.79        98.24         8.61        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  SLC14A1 MUTATED SLC14A1 WILD-TYPE 
             0.33              0.00 
  SLC14A1 MUTATED SLC14A1 WILD-TYPE 
           117.07            140.38 
  SLC14A1 MUTATED SLC14A1 WILD-TYPE 
           18.015            20.190 
[1] "0.3 - 117.1 (18.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.3"
D1544V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC14A1 MUTATED         2        0        1         4         0         0
  SLC14A1 WILD-TYPE      62        1       24       105         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC14A1 MUTATED           0          0          1          1        0
  SLC14A1 WILD-TYPE        19         10         40         30       35
                   vv
clus                STAGE IVA STAGE IVB
  SLC14A1 MUTATED           0         0
  SLC14A1 WILD-TYPE        13         1
D1544V3, multiclass
            clus
vv           SLC14A1 MUTATED SLC14A1 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                4               105
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               1                30
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC14A1 MUTATED     1   1   8   0
  SLC14A1 WILD-TYPE   8  67 240  41
D1544V4, multiclass
    clus
vv   SLC14A1 MUTATED SLC14A1 WILD-TYPE
  T1               1                 8
  T2               1                67
  T3               8               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
  SLC14A1 MUTATED     7   2   1
  SLC14A1 WILD-TYPE 213  78  65
D1544V5, multiclass
    clus
vv   SLC14A1 MUTATED SLC14A1 WILD-TYPE
  N0               7               213
  N1               2                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"
D1544V6, binary
                   cls
clus                  0   1
  SLC14A1 MUTATED     8   0
  SLC14A1 WILD-TYPE 275  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC14A1 MUTATED      8    0
  SLC14A1 WILD-TYPE  275   48
   clus
vv  SLC14A1 MUTATED SLC14A1 WILD-TYPE
  0               8               275
  1               0                48
[1] 2 2
[1] FALSE
D1544V7, binary
                   cls
clus                  0   1
  SLC14A1 MUTATED     4   6
  SLC14A1 WILD-TYPE 166 191
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC14A1 MUTATED      4    6
  SLC14A1 WILD-TYPE  166  191
        clus
vv       SLC14A1 MUTATED SLC14A1 WILD-TYPE
  FEMALE               4               166
  MALE                 6               191
[1] 2 2
[1] FALSE
D1544V8, binary
                   cls
clus                  0   1
  SLC14A1 MUTATED     8   2
  SLC14A1 WILD-TYPE 309  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC14A1 MUTATED      8    2
  SLC14A1 WILD-TYPE  309   46
                               clus
vv                              SLC14A1 MUTATED SLC14A1 WILD-TYPE
  COLON ADENOCARCINOMA                        8               309
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SLC14A1 MUTATED     5   0   0   1
  SLC14A1 WILD-TYPE 252   2  22  20
D1544V9, multiclass
    clus
vv   SLC14A1 MUTATED SLC14A1 WILD-TYPE
  R0               5               252
  R1               0                 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"
D1544V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC14A1 MUTATED                                  0     1
  SLC14A1 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC14A1 MUTATED                           0     7
  SLC14A1 WILD-TYPE                        19   169
D1544V11, multiclass
                                  clus
vv                                 SLC14A1 MUTATED SLC14A1 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(1545) Variable = RIMS2 MUTATION ANALYSIS
D1545V1, survival
                 sevent
clus2               0   1
  RIMS2 MUTATED    27   8
  RIMS2 WILD-TYPE 255  65
  RIMS2 MUTATED RIMS2 WILD-TYPE 
             35             320 
  RIMS2 MUTATED RIMS2 WILD-TYPE 
              8              65 
$`RIMS2 MUTATED`
TCGA-A6-5660 TCGA-A6-6141 TCGA-AA-3672 TCGA-AA-3680 TCGA-AA-3819 TCGA-AA-3821 
       29.19         8.38         0.92        11.01        25.02         1.02 
TCGA-AA-3930 TCGA-AA-3949 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A024 
        2.01        26.01        25.02         4.01        34.98        39.06 
TCGA-AD-6964 TCGA-AU-3779 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 
       10.88        14.50        58.39        61.41        49.41        12.10 
TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4952 TCGA-CM-4747 
        0.07         0.33         0.10        17.56        15.62        25.02 
TCGA-CM-6674 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6928 
       12.95         1.32        15.12        16.14        15.58        11.64 
TCGA-DM-A28G TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6323 TCGA-G4-6588 
       60.79        55.04        51.75        13.78        26.17 

$`RIMS2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        0.99        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 
       31.00        12.99        24.00        33.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       37.02        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42         0.20        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 
       83.80        22.36        62.79         6.77       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 
        3.25         3.29         0.26         1.35       102.44        40.34 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6536 
       13.51        11.51        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
       81.37       119.93        35.97       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 
       45.11        36.72        36.00        22.09        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  RIMS2 MUTATED RIMS2 WILD-TYPE 
           0.07            0.00 
  RIMS2 MUTATED RIMS2 WILD-TYPE 
          61.41          140.38 
  RIMS2 MUTATED RIMS2 WILD-TYPE 
         15.580          20.995 
[1] "0.1 - 61.4 (15.6)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.3"
D1545V2, 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       23        97         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RIMS2 MUTATED           2          0          6          1        3         2
  RIMS2 WILD-TYPE        17         10         35         30       32        11
                 vv
clus              STAGE IVB
  RIMS2 MUTATED           0
  RIMS2 WILD-TYPE         1
D1545V3, multiclass
            clus
vv           RIMS2 MUTATED RIMS2 WILD-TYPE
  STAGE I                3              61
  STAGE IA               1               0
  STAGE II               2              23
  STAGE IIA             12              97
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             0              10
  STAGE IIIB             6              35
  STAGE IIIC             1              30
  STAGE IV               3              32
  STAGE IVA              2              11
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  65 226  32
D1545V4, multiclass
    clus
vv   RIMS2 MUTATED RIMS2 WILD-TYPE
  T1             1               8
  T2             3              65
  T3            22             226
  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  71  61
D1545V5, multiclass
    clus
vv   RIMS2 MUTATED RIMS2 WILD-TYPE
  N0            22             198
  N1             9              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"
D1545V6, binary
                 cls
clus                0   1
  RIMS2 MUTATED    27   4
  RIMS2 WILD-TYPE 256  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RIMS2 MUTATED     27    4
  RIMS2 WILD-TYPE  256   44
   clus
vv  RIMS2 MUTATED RIMS2 WILD-TYPE
  0            27             256
  1             4              44
[1] 2 2
[1] FALSE
D1545V7, 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
D1545V8, binary
                 cls
clus                0   1
  RIMS2 MUTATED    28   8
  RIMS2 WILD-TYPE 289  40
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RIMS2 MUTATED     28    8
  RIMS2 WILD-TYPE  289   40
                               clus
vv                              RIMS2 MUTATED RIMS2 WILD-TYPE
  COLON ADENOCARCINOMA                     28             289
  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 237   2  20  15
D1545V9, multiclass
    clus
vv   RIMS2 MUTATED RIMS2 WILD-TYPE
  R0            20             237
  R1             0               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"
D1545V10, 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
D1545V11, 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(1546) Variable = CEP164 MUTATION ANALYSIS
D1546V1, survival
                  sevent
clus2                0   1
  CEP164 MUTATED    20   2
  CEP164 WILD-TYPE 262  71
  CEP164 MUTATED CEP164 WILD-TYPE 
              22              333 
  CEP164 MUTATED CEP164 WILD-TYPE 
               2               71 
$`CEP164 MUTATED`
TCGA-A6-4105 TCGA-A6-5665 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3518 
       14.53        22.06        23.87        20.12        19.66         1.02 
TCGA-AA-3555 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3833 TCGA-AA-3966 TCGA-AA-3994 
       29.95        26.99        19.04        15.95         2.01        27.02 
TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-6889 TCGA-AD-6895 TCGA-AU-3779 TCGA-AU-6004 
       34.98        35.01        56.55         0.72        14.50        27.09 
TCGA-AZ-6598 TCGA-CA-6717 TCGA-D5-6535 TCGA-G4-6588 
       49.41         0.33        15.12        26.17 

$`CEP164 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6782 TCGA-AA-3489 
       24.16        21.76        24.69        24.39        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        3.02         1.02        35.01        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       13.02        38.99         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        17.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       36.00         5.03        85.05        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 
       33.04         0.99        25.02         1.02        17.98        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 
       11.51        20.19        18.25         1.32        43.27        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  CEP164 MUTATED CEP164 WILD-TYPE 
            0.33             0.00 
  CEP164 MUTATED CEP164 WILD-TYPE 
           56.55           140.38 
  CEP164 MUTATED CEP164 WILD-TYPE 
           21.09            20.19 
[1] "0.3 - 56.5 (21.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2"  
D1546V2, 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       24        97         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CEP164 MUTATED           1          0          3          1        1
  CEP164 WILD-TYPE        18         10         38         30       34
                  vv
clus               STAGE IVA STAGE IVB
  CEP164 MUTATED           0         0
  CEP164 WILD-TYPE        13         1
D1546V3, multiclass
            clus
vv           CEP164 MUTATED CEP164 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA              12               97
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              3               38
  STAGE IIIC              1               30
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CEP164 MUTATED     0   1  19   3
  CEP164 WILD-TYPE   9  67 229  38
D1546V4, multiclass
    clus
vv   CEP164 MUTATED CEP164 WILD-TYPE
  T1              0                9
  T2              1               67
  T3             19              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
  CEP164 MUTATED    17   5   1
  CEP164 WILD-TYPE 203  75  65
D1546V5, multiclass
    clus
vv   CEP164 MUTATED CEP164 WILD-TYPE
  N0             17              203
  N1              5               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"
D1546V6, binary
                  cls
clus                 0   1
  CEP164 MUTATED    16   1
  CEP164 WILD-TYPE 267  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP164 MUTATED     16    1
  CEP164 WILD-TYPE  267   47
   clus
vv  CEP164 MUTATED CEP164 WILD-TYPE
  0             16              267
  1              1               47
[1] 2 2
[1] FALSE
D1546V7, 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
D1546V8, binary
                  cls
clus                 0   1
  CEP164 MUTATED    16   7
  CEP164 WILD-TYPE 301  41
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP164 MUTATED     16    7
  CEP164 WILD-TYPE  301   41
                               clus
vv                              CEP164 MUTATED CEP164 WILD-TYPE
  COLON ADENOCARCINOMA                      16              301
  COLON MUCINOUS ADENOCARCINOMA              7               41
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CEP164 MUTATED    12   0   1   3
  CEP164 WILD-TYPE 245   2  21  18
D1546V9, multiclass
    clus
vv   CEP164 MUTATED CEP164 WILD-TYPE
  R0             12              245
  R1              0                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"
D1546V10, 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
D1546V11, 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(1547) Variable = PON1 MUTATION ANALYSIS
D1547V1, survival
                sevent
clus2              0   1
  PON1 MUTATED     8   0
  PON1 WILD-TYPE 274  73
  PON1 MUTATED PON1 WILD-TYPE 
             8            347 
  PON1 MUTATED PON1 WILD-TYPE 
             0             73 
$`PON1 MUTATED`
TCGA-AA-3510 TCGA-AA-3672 TCGA-AA-3939 TCGA-AA-A010 TCGA-AZ-4315 TCGA-CA-6717 
       63.98         0.92        12.99        34.98        58.39         0.33 
TCGA-CM-6162 TCGA-D5-6930 
       12.00         1.51 

$`PON1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  PON1 MUTATED PON1 WILD-TYPE 
          0.33           0.00 
  PON1 MUTATED PON1 WILD-TYPE 
         63.98         140.38 
  PON1 MUTATED PON1 WILD-TYPE 
        12.495         20.280 
[1] "0.3 - 64.0 (12.5)"  "0.0 - 140.4 (20.3)"
[1] "hr="     "9300000"
D1547V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PON1 MUTATED         0        0        1         5         1         0
  PON1 WILD-TYPE      64        1       24       104         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PON1 MUTATED           1          0          1          0        0         0
  PON1 WILD-TYPE        18         10         40         31       35        13
                vv
clus             STAGE IVB
  PON1 MUTATED           0
  PON1 WILD-TYPE         1
D1547V3, multiclass
            clus
vv           PON1 MUTATED PON1 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             5            104
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PON1 MUTATED     0   0   8   1
  PON1 WILD-TYPE   9  68 240  40
D1547V4, multiclass
    clus
vv   PON1 MUTATED PON1 WILD-TYPE
  T1            0              9
  T2            0             68
  T3            8            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
  PON1 MUTATED     7   2   0
  PON1 WILD-TYPE 213  78  66
D1547V5, multiclass
    clus
vv   PON1 MUTATED PON1 WILD-TYPE
  N0            7            213
  N1            2             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"
D1547V6, binary
                cls
clus               0   1
  PON1 MUTATED     9   0
  PON1 WILD-TYPE 274  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  PON1 MUTATED      9    0
  PON1 WILD-TYPE  274   48
   clus
vv  PON1 MUTATED PON1 WILD-TYPE
  0            9            274
  1            0             48
[1] 2 2
[1] FALSE
D1547V7, binary
                cls
clus               0   1
  PON1 MUTATED     4   5
  PON1 WILD-TYPE 166 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  PON1 MUTATED      4    5
  PON1 WILD-TYPE  166  192
        clus
vv       PON1 MUTATED PON1 WILD-TYPE
  FEMALE            4            166
  MALE              5            192
[1] 2 2
[1] FALSE
D1547V8, binary
                cls
clus               0   1
  PON1 MUTATED     6   3
  PON1 WILD-TYPE 311  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  PON1 MUTATED      6    3
  PON1 WILD-TYPE  311   45
                               clus
vv                              PON1 MUTATED PON1 WILD-TYPE
  COLON ADENOCARCINOMA                     6            311
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PON1 MUTATED     8   0   0   1
  PON1 WILD-TYPE 249   2  22  20
D1547V9, multiclass
    clus
vv   PON1 MUTATED PON1 WILD-TYPE
  R0            8            249
  R1            0              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"
D1547V10, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PON1 MUTATED                                  0     1
  PON1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PON1 MUTATED                           0     3
  PON1 WILD-TYPE                        19   173
D1547V11, multiclass
                                  clus
vv                                 PON1 MUTATED PON1 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(1548) Variable = CORO1C MUTATION ANALYSIS
D1548V1, survival
                  sevent
clus2                0   1
  CORO1C MUTATED     6   0
  CORO1C WILD-TYPE 276  73
  CORO1C MUTATED CORO1C WILD-TYPE 
               6              349 
  CORO1C MUTATED CORO1C WILD-TYPE 
               0               73 
$`CORO1C MUTATED`
TCGA-AU-3779 TCGA-CA-6717 TCGA-CK-5913 TCGA-CM-5860 TCGA-D5-6540 TCGA-G4-6309 
       14.50         0.33        51.32        16.01        16.14        51.75 

$`CORO1C WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 
      102.44        40.34        15.62        49.08        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  CORO1C MUTATED CORO1C WILD-TYPE 
            0.33             0.00 
  CORO1C MUTATED CORO1C WILD-TYPE 
           51.75           140.38 
  CORO1C MUTATED CORO1C WILD-TYPE 
          16.075           20.280 
[1] "0.3 - 51.8 (16.1)"  "0.0 - 140.4 (20.3)"
[1] "hr="     "9300000"
D1548V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CORO1C MUTATED         1        0        0         4         0         0
  CORO1C WILD-TYPE      63        1       25       105         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CORO1C MUTATED           0          0          1          0        0
  CORO1C WILD-TYPE        19         10         40         31       35
                  vv
clus               STAGE IVA STAGE IVB
  CORO1C MUTATED           0         0
  CORO1C WILD-TYPE        13         1
D1548V3, multiclass
            clus
vv           CORO1C MUTATED CORO1C WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               4              105
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CORO1C MUTATED     0   1   5   0
  CORO1C WILD-TYPE   9  67 243  41
D1548V4, multiclass
    clus
vv   CORO1C MUTATED CORO1C WILD-TYPE
  T1              0                9
  T2              1               67
  T3              5              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
  CORO1C MUTATED     5   1   0
  CORO1C WILD-TYPE 215  79  66
D1548V5, multiclass
    clus
vv   CORO1C MUTATED CORO1C WILD-TYPE
  N0              5              215
  N1              1               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"
D1548V6, binary
                  cls
clus                 0   1
  CORO1C MUTATED     5   0
  CORO1C WILD-TYPE 278  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CORO1C MUTATED      5    0
  CORO1C WILD-TYPE  278   48
   clus
vv  CORO1C MUTATED CORO1C WILD-TYPE
  0              5              278
  1              0               48
[1] 2 2
[1] FALSE
D1548V7, binary
                  cls
clus                 0   1
  CORO1C MUTATED     3   3
  CORO1C WILD-TYPE 167 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CORO1C MUTATED      3    3
  CORO1C WILD-TYPE  167  194
        clus
vv       CORO1C MUTATED CORO1C WILD-TYPE
  FEMALE              3              167
  MALE                3              194
[1] 2 2
[1] FALSE
D1548V8, binary
                  cls
clus                 0   1
  CORO1C MUTATED     4   2
  CORO1C WILD-TYPE 313  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CORO1C MUTATED      4    2
  CORO1C WILD-TYPE  313   46
                               clus
vv                              CORO1C MUTATED CORO1C WILD-TYPE
  COLON ADENOCARCINOMA                       4              313
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CORO1C MUTATED     4   0   0   2
  CORO1C WILD-TYPE 253   2  22  19
D1548V9, multiclass
    clus
vv   CORO1C MUTATED CORO1C WILD-TYPE
  R0              4              253
  R1              0                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"
D1548V10, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CORO1C MUTATED                                  0     1
  CORO1C WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CORO1C MUTATED                           1     4
  CORO1C WILD-TYPE                        18   172
D1548V11, multiclass
                                  clus
vv                                 CORO1C MUTATED CORO1C 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(1549) Variable = KIFC2 MUTATION ANALYSIS
D1549V1, survival
                 sevent
clus2               0   1
  KIFC2 MUTATED     6   0
  KIFC2 WILD-TYPE 276  73
  KIFC2 MUTATED KIFC2 WILD-TYPE 
              6             349 
  KIFC2 MUTATED KIFC2 WILD-TYPE 
              0              73 
$`KIFC2 MUTATED`
TCGA-A6-5665 TCGA-AA-3697 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-6386 TCGA-DM-A1HB 
       22.06        85.05        14.50        27.09        17.82       135.65 

$`KIFC2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       10.88         0.20        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  KIFC2 MUTATED KIFC2 WILD-TYPE 
           14.5             0.0 
  KIFC2 MUTATED KIFC2 WILD-TYPE 
         135.65          140.38 
  KIFC2 MUTATED KIFC2 WILD-TYPE 
         24.575          20.120 
[1] "14.5 - 135.7 (24.6)" "0.0 - 140.4 (20.1)" 
[1] "hr="     "2.6e+07"
D1549V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIFC2 MUTATED         1        0        0         2         0         0
  KIFC2 WILD-TYPE      63        1       25       107         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KIFC2 MUTATED           1          0          2          0        0         0
  KIFC2 WILD-TYPE        18         10         39         31       35        13
                 vv
clus              STAGE IVB
  KIFC2 MUTATED           0
  KIFC2 WILD-TYPE         1
D1549V3, multiclass
            clus
vv           KIFC2 MUTATED KIFC2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              2             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KIFC2 MUTATED     0   1   5   0
  KIFC2 WILD-TYPE   9  67 243  41
D1549V4, multiclass
    clus
vv   KIFC2 MUTATED KIFC2 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             5             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
  KIFC2 MUTATED     4   2   0
  KIFC2 WILD-TYPE 216  78  66
D1549V5, multiclass
    clus
vv   KIFC2 MUTATED KIFC2 WILD-TYPE
  N0             4             216
  N1             2              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"
D1549V6, binary
                 cls
clus                0   1
  KIFC2 MUTATED     6   0
  KIFC2 WILD-TYPE 277  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIFC2 MUTATED      6    0
  KIFC2 WILD-TYPE  277   48
   clus
vv  KIFC2 MUTATED KIFC2 WILD-TYPE
  0             6             277
  1             0              48
[1] 2 2
[1] FALSE
D1549V7, 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
D1549V8, binary
                 cls
clus                0   1
  KIFC2 MUTATED     6   0
  KIFC2 WILD-TYPE 311  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIFC2 MUTATED      6    0
  KIFC2 WILD-TYPE  311   48
                               clus
vv                              KIFC2 MUTATED KIFC2 WILD-TYPE
  COLON ADENOCARCINOMA                      6             311
  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 252   2  22  21
D1549V9, multiclass
    clus
vv   KIFC2 MUTATED KIFC2 WILD-TYPE
  R0             5             252
  R1             0               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"
D1549V10, 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
D1549V11, 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(1550) Variable = NOD2 MUTATION ANALYSIS
D1550V1, survival
                sevent
clus2              0   1
  NOD2 MUTATED    14   2
  NOD2 WILD-TYPE 268  71
  NOD2 MUTATED NOD2 WILD-TYPE 
            16            339 
  NOD2 MUTATED NOD2 WILD-TYPE 
             2             71 
$`NOD2 MUTATED`
TCGA-A6-5665 TCGA-AA-3977 TCGA-AA-A01R TCGA-AD-6901 TCGA-AD-6964 TCGA-CM-4743 
       22.06        25.02        35.01        22.42        10.88        23.05 
TCGA-CM-4744 TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6165 TCGA-D5-6538 TCGA-F4-6855 
       20.02        15.02        12.00        16.04        17.13        35.41 
TCGA-F4-6856 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       19.43        22.09        35.80        26.17 

$`NOD2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
        0.79         0.72         5.79        27.42         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         2.01 
TCGA-CK-6751 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
      124.27        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        16.01         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 
       17.03        15.02        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
        0.53       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       55.04        51.75        45.11        36.72        36.00        13.78 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  NOD2 MUTATED NOD2 WILD-TYPE 
         10.88           0.00 
  NOD2 MUTATED NOD2 WILD-TYPE 
         35.80         140.38 
  NOD2 MUTATED NOD2 WILD-TYPE 
        22.075         20.120 
[1] "10.9 - 35.8 (22.1)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.4"
D1550V2, 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       25       102         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        17         10         39         31       35        13
                vv
clus             STAGE IVB
  NOD2 MUTATED           0
  NOD2 WILD-TYPE         1
D1550V3, multiclass
            clus
vv           NOD2 MUTATED NOD2 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             7            102
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             2             17
  STAGE IIIA            0             10
  STAGE IIIB            2             39
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NOD2 MUTATED     0   4  11   1
  NOD2 WILD-TYPE   9  64 237  40
D1550V4, multiclass
    clus
vv   NOD2 MUTATED NOD2 WILD-TYPE
  T1            0              9
  T2            4             64
  T3           11            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
  NOD2 MUTATED    11   2   3
  NOD2 WILD-TYPE 209  78  63
D1550V5, multiclass
    clus
vv   NOD2 MUTATED NOD2 WILD-TYPE
  N0           11            209
  N1            2             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"
D1550V6, binary
                cls
clus               0   1
  NOD2 MUTATED    12   0
  NOD2 WILD-TYPE 271  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOD2 MUTATED     12    0
  NOD2 WILD-TYPE  271   48
   clus
vv  NOD2 MUTATED NOD2 WILD-TYPE
  0           12            271
  1            0             48
[1] 2 2
[1] FALSE
D1550V7, 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
D1550V8, binary
                cls
clus               0   1
  NOD2 MUTATED    13   3
  NOD2 WILD-TYPE 304  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOD2 MUTATED     13    3
  NOD2 WILD-TYPE  304   45
                               clus
vv                              NOD2 MUTATED NOD2 WILD-TYPE
  COLON ADENOCARCINOMA                    13            304
  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 244   2  22  21
D1550V9, multiclass
    clus
vv   NOD2 MUTATED NOD2 WILD-TYPE
  R0           13            244
  R1            0              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"
D1550V10, 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
D1550V11, 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(1551) Variable = KIAA0196 MUTATION ANALYSIS
D1551V1, survival
                    sevent
clus2                  0   1
  KIAA0196 MUTATED     7   3
  KIAA0196 WILD-TYPE 275  70
  KIAA0196 MUTATED KIAA0196 WILD-TYPE 
                10                345 
  KIAA0196 MUTATED KIAA0196 WILD-TYPE 
                 3                 70 
$`KIAA0196 MUTATED`
TCGA-AA-3518 TCGA-AA-3525 TCGA-AA-A010 TCGA-AY-6197 TCGA-AZ-6608 TCGA-CA-6716 
        1.02         8.05        34.98        21.44         1.94         0.26 
TCGA-CM-6162 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-F4-6856 
       12.00        92.75        13.32        19.43 

$`KIAA0196 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 
       38.99         9.07        24.03        37.05        36.03        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
      100.01        29.56         5.23        11.74         3.19         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 
       33.67        13.25         0.53        35.41       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  KIAA0196 MUTATED KIAA0196 WILD-TYPE 
              0.26               0.00 
  KIAA0196 MUTATED KIAA0196 WILD-TYPE 
             92.75             140.38 
  KIAA0196 MUTATED KIAA0196 WILD-TYPE 
             12.66              20.98 
[1] "0.3 - 92.8 (12.7)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.8"
D1551V2, 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       25       104         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0196 MUTATED           0          1          2          0        0
  KIAA0196 WILD-TYPE        19          9         39         31       35
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA0196 MUTATED           0         0
  KIAA0196 WILD-TYPE        13         1
D1551V3, multiclass
            clus
vv           KIAA0196 MUTATED KIAA0196 WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  0                 25
  STAGE IIA                 5                104
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                1                  9
  STAGE IIIB                2                 39
  STAGE IIIC                0                 31
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA0196 MUTATED     0   2   7   1
  KIAA0196 WILD-TYPE   9  66 241  40
D1551V4, multiclass
    clus
vv   KIAA0196 MUTATED KIAA0196 WILD-TYPE
  T1                0                  9
  T2                2                 66
  T3                7                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
  KIAA0196 MUTATED     7   3   0
  KIAA0196 WILD-TYPE 213  77  66
D1551V5, multiclass
    clus
vv   KIAA0196 MUTATED KIAA0196 WILD-TYPE
  N0                7                213
  N1                3                 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"
D1551V6, binary
                    cls
clus                   0   1
  KIAA0196 MUTATED     9   0
  KIAA0196 WILD-TYPE 274  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0196 MUTATED      9    0
  KIAA0196 WILD-TYPE  274   48
   clus
vv  KIAA0196 MUTATED KIAA0196 WILD-TYPE
  0                9                274
  1                0                 48
[1] 2 2
[1] FALSE
D1551V7, 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
D1551V8, binary
                    cls
clus                   0   1
  KIAA0196 MUTATED     8   2
  KIAA0196 WILD-TYPE 309  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0196 MUTATED      8    2
  KIAA0196 WILD-TYPE  309   46
                               clus
vv                              KIAA0196 MUTATED KIAA0196 WILD-TYPE
  COLON ADENOCARCINOMA                         8                309
  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 251   2  22  20
D1551V9, multiclass
    clus
vv   KIAA0196 MUTATED KIAA0196 WILD-TYPE
  R0                6                251
  R1                0                  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"
D1551V10, 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
D1551V11, 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(1552) Variable = LRMP MUTATION ANALYSIS
D1552V1, survival
                sevent
clus2              0   1
  LRMP MUTATED     3   3
  LRMP WILD-TYPE 279  70
  LRMP MUTATED LRMP WILD-TYPE 
             6            349 
  LRMP MUTATED LRMP WILD-TYPE 
             3             70 
$`LRMP MUTATED`
TCGA-AA-3877 TCGA-AA-A00N TCGA-AY-6196 TCGA-CA-6717 TCGA-DM-A0XF TCGA-DM-A1D7 
       31.00         4.01         0.20         0.33        38.20        13.32 

$`LRMP WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       15.75        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 
       24.43       130.65        92.75        49.91        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  LRMP MUTATED LRMP WILD-TYPE 
           0.2            0.0 
  LRMP MUTATED LRMP WILD-TYPE 
         38.20         140.38 
  LRMP MUTATED LRMP WILD-TYPE 
         8.665         20.280 
[1] "0.2 - 38.2 (8.7)"   "0.0 - 140.4 (20.3)"
[1] "hr=" "4.5"
D1552V2, 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       25       107         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LRMP MUTATED           0          0          0          2        0         0
  LRMP WILD-TYPE        19         10         41         29       35        13
                vv
clus             STAGE IVB
  LRMP MUTATED           0
  LRMP WILD-TYPE         1
D1552V3, multiclass
            clus
vv           LRMP MUTATED LRMP WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             2            107
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            2             29
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  LRMP MUTATED     1   0   4   1
  LRMP WILD-TYPE   8  68 244  40
D1552V4, multiclass
    clus
vv   LRMP MUTATED LRMP WILD-TYPE
  T1            1              8
  T2            0             68
  T3            4            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
  LRMP MUTATED     4   0   2
  LRMP WILD-TYPE 216  80  64
D1552V5, multiclass
    clus
vv   LRMP MUTATED LRMP WILD-TYPE
  N0            4            216
  N1            0             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"
D1552V6, binary
                cls
clus               0   1
  LRMP MUTATED     5   0
  LRMP WILD-TYPE 278  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  LRMP MUTATED      5    0
  LRMP WILD-TYPE  278   48
   clus
vv  LRMP MUTATED LRMP WILD-TYPE
  0            5            278
  1            0             48
[1] 2 2
[1] FALSE
D1552V7, binary
                cls
clus               0   1
  LRMP MUTATED     2   4
  LRMP WILD-TYPE 168 193
[1] "tbl2"
                cls
clus             [,1] [,2]
  LRMP MUTATED      2    4
  LRMP WILD-TYPE  168  193
        clus
vv       LRMP MUTATED LRMP WILD-TYPE
  FEMALE            2            168
  MALE              4            193
[1] 2 2
[1] FALSE
D1552V8, binary
                cls
clus               0   1
  LRMP MUTATED     1   5
  LRMP WILD-TYPE 316  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  LRMP MUTATED      1    5
  LRMP WILD-TYPE  316   43
                               clus
vv                              LRMP MUTATED LRMP WILD-TYPE
  COLON ADENOCARCINOMA                     1            316
  COLON MUCINOUS ADENOCARCINOMA            5             43
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  LRMP MUTATED     3   0   0   1
  LRMP WILD-TYPE 254   2  22  20
D1552V9, multiclass
    clus
vv   LRMP MUTATED LRMP WILD-TYPE
  R0            3            254
  R1            0              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"
D1552V10, 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     3
  LRMP WILD-TYPE                        19   173
D1552V11, 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                                       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(1553) Variable = GSG2 MUTATION ANALYSIS
D1553V1, survival
                sevent
clus2              0   1
  GSG2 MUTATED     4   1
  GSG2 WILD-TYPE 278  72
  GSG2 MUTATED GSG2 WILD-TYPE 
             5            350 
  GSG2 MUTATED GSG2 WILD-TYPE 
             1             72 
$`GSG2 MUTATED`
TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-3856 TCGA-CM-5861 TCGA-F4-6570 
       22.06        20.12         0.99        15.02         6.18 

$`GSG2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       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        13.38        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  GSG2 MUTATED GSG2 WILD-TYPE 
          0.99           0.00 
  GSG2 MUTATED GSG2 WILD-TYPE 
         22.06         140.38 
  GSG2 MUTATED GSG2 WILD-TYPE 
         15.02          20.63 
[1] "1.0 - 22.1 (15.0)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "1.7"
D1553V2, 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       25       103         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        19         10         41         31       35        13
                vv
clus             STAGE IVB
  GSG2 MUTATED           0
  GSG2 WILD-TYPE         1
D1553V3, multiclass
            clus
vv           GSG2 MUTATED GSG2 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             6            103
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GSG2 MUTATED     0   0   6   0
  GSG2 WILD-TYPE   9  68 242  41
D1553V4, multiclass
    clus
vv   GSG2 MUTATED GSG2 WILD-TYPE
  T1            0              9
  T2            0             68
  T3            6            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
  GSG2 MUTATED     6   0   0
  GSG2 WILD-TYPE 214  80  66
D1553V5, multiclass
    clus
vv   GSG2 MUTATED GSG2 WILD-TYPE
  N0            6            214
  N1            0             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"
D1553V6, binary
                cls
clus               0   1
  GSG2 MUTATED     5   0
  GSG2 WILD-TYPE 278  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  GSG2 MUTATED      5    0
  GSG2 WILD-TYPE  278   48
   clus
vv  GSG2 MUTATED GSG2 WILD-TYPE
  0            5            278
  1            0             48
[1] 2 2
[1] FALSE
D1553V7, 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
D1553V8, binary
                cls
clus               0   1
  GSG2 MUTATED     5   1
  GSG2 WILD-TYPE 312  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  GSG2 MUTATED      5    1
  GSG2 WILD-TYPE  312   47
                               clus
vv                              GSG2 MUTATED GSG2 WILD-TYPE
  COLON ADENOCARCINOMA                     5            312
  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 252   2  22  21
D1553V9, multiclass
    clus
vv   GSG2 MUTATED GSG2 WILD-TYPE
  R0            5            252
  R1            0              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"
D1553V10, 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
D1553V11, 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(1554) Variable = GCNT4 MUTATION ANALYSIS
D1554V1, survival
                 sevent
clus2               0   1
  GCNT4 MUTATED     4   4
  GCNT4 WILD-TYPE 278  69
  GCNT4 MUTATED GCNT4 WILD-TYPE 
              8             347 
  GCNT4 MUTATED GCNT4 WILD-TYPE 
              4              69 
$`GCNT4 MUTATED`
TCGA-AA-3715 TCGA-AA-A00N TCGA-AZ-5407 TCGA-AZ-6598 TCGA-CA-6717 TCGA-D5-6540 
       19.04         4.01        61.41        49.41         0.33        16.14 
TCGA-F4-6570 TCGA-F4-6856 
        6.18        19.43 

$`GCNT4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6599 TCGA-AZ-6600 
        5.13        83.80        22.36        62.79         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-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        13.38        13.45        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  GCNT4 MUTATED GCNT4 WILD-TYPE 
           0.33            0.00 
  GCNT4 MUTATED GCNT4 WILD-TYPE 
          61.41          140.38 
  GCNT4 MUTATED GCNT4 WILD-TYPE 
          17.59           20.98 
[1] "0.3 - 61.4 (17.6)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "2.7"
D1554V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GCNT4 MUTATED         3        0        2         3         2         0
  GCNT4 WILD-TYPE      61        1       23       106         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GCNT4 MUTATED           0          0          0          0        0         0
  GCNT4 WILD-TYPE        19         10         41         31       35        13
                 vv
clus              STAGE IVB
  GCNT4 MUTATED           0
  GCNT4 WILD-TYPE         1
D1554V3, multiclass
            clus
vv           GCNT4 MUTATED GCNT4 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              3             106
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GCNT4 MUTATED     1   2   5   2
  GCNT4 WILD-TYPE   8  66 243  39
D1554V4, multiclass
    clus
vv   GCNT4 MUTATED GCNT4 WILD-TYPE
  T1             1               8
  T2             2              66
  T3             5             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
  GCNT4 MUTATED    10   0   0
  GCNT4 WILD-TYPE 210  80  66
D1554V5, multiclass
    clus
vv   GCNT4 MUTATED GCNT4 WILD-TYPE
  N0            10             210
  N1             0              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
  GCNT4 MUTATED     8   0
  GCNT4 WILD-TYPE 275  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GCNT4 MUTATED      8    0
  GCNT4 WILD-TYPE  275   48
   clus
vv  GCNT4 MUTATED GCNT4 WILD-TYPE
  0             8             275
  1             0              48
[1] 2 2
[1] FALSE
D1554V7, binary
                 cls
clus                0   1
  GCNT4 MUTATED     5   5
  GCNT4 WILD-TYPE 165 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GCNT4 MUTATED      5    5
  GCNT4 WILD-TYPE  165  192
        clus
vv       GCNT4 MUTATED GCNT4 WILD-TYPE
  FEMALE             5             165
  MALE               5             192
[1] 2 2
[1] FALSE
D1554V8, binary
                 cls
clus                0   1
  GCNT4 MUTATED     6   4
  GCNT4 WILD-TYPE 311  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GCNT4 MUTATED      6    4
  GCNT4 WILD-TYPE  311   44
                               clus
vv                              GCNT4 MUTATED GCNT4 WILD-TYPE
  COLON ADENOCARCINOMA                      6             311
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  GCNT4 MUTATED     6   0   0   2
  GCNT4 WILD-TYPE 251   2  22  19
D1554V9, multiclass
    clus
vv   GCNT4 MUTATED GCNT4 WILD-TYPE
  R0             6             251
  R1             0               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"
D1554V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GCNT4 MUTATED                                  0     1
  GCNT4 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GCNT4 MUTATED                           0     6
  GCNT4 WILD-TYPE                        19   170
D1554V11, multiclass
                                  clus
vv                                 GCNT4 MUTATED GCNT4 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(1555) Variable = ZSCAN20 MUTATION ANALYSIS
D1555V1, survival
                   sevent
clus2                 0   1
  ZSCAN20 MUTATED    10   3
  ZSCAN20 WILD-TYPE 272  70
  ZSCAN20 MUTATED ZSCAN20 WILD-TYPE 
               13               342 
  ZSCAN20 MUTATED ZSCAN20 WILD-TYPE 
                3                70 
$`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        15.75        58.39         0.10        23.05         1.51 
TCGA-DM-A1D4 
       92.75 

$`ZSCAN20 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6648 
       22.06        32.71        27.09        22.52         8.38        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 
       24.16        21.76        24.69        24.39        23.87        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 
       38.99        37.02        14.93         0.00        17.03         0.00 
TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
       33.07        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.33         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  ZSCAN20 MUTATED ZSCAN20 WILD-TYPE 
                0                 0 
  ZSCAN20 MUTATED ZSCAN20 WILD-TYPE 
            92.75            140.38 
  ZSCAN20 MUTATED ZSCAN20 WILD-TYPE 
           21.990            20.105 
[1] "0.0 - 92.8 (22.0)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.2"
D1555V2, 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       25       101         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZSCAN20 MUTATED           0          0          0          1        0
  ZSCAN20 WILD-TYPE        19         10         41         30       35
                   vv
clus                STAGE IVA STAGE IVB
  ZSCAN20 MUTATED           2         0
  ZSCAN20 WILD-TYPE        11         1
D1555V3, multiclass
            clus
vv           ZSCAN20 MUTATED ZSCAN20 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                8               101
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               1                30
  STAGE IV                 0                35
  STAGE IVA                2                11
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 237  41
D1555V4, multiclass
    clus
vv   ZSCAN20 MUTATED ZSCAN20 WILD-TYPE
  T1               0                 9
  T2               2                66
  T3              11               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
  ZSCAN20 MUTATED    10   2   1
  ZSCAN20 WILD-TYPE 210  78  65
D1555V5, multiclass
    clus
vv   ZSCAN20 MUTATED ZSCAN20 WILD-TYPE
  N0              10               210
  N1               2                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"
D1555V6, binary
                   cls
clus                  0   1
  ZSCAN20 MUTATED     9   2
  ZSCAN20 WILD-TYPE 274  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZSCAN20 MUTATED      9    2
  ZSCAN20 WILD-TYPE  274   46
   clus
vv  ZSCAN20 MUTATED ZSCAN20 WILD-TYPE
  0               9               274
  1               2                46
[1] 2 2
[1] FALSE
D1555V7, 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
D1555V8, binary
                   cls
clus                  0   1
  ZSCAN20 MUTATED    10   3
  ZSCAN20 WILD-TYPE 307  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZSCAN20 MUTATED     10    3
  ZSCAN20 WILD-TYPE  307   45
                               clus
vv                              ZSCAN20 MUTATED ZSCAN20 WILD-TYPE
  COLON ADENOCARCINOMA                       10               307
  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 249   2  22  20
D1555V9, multiclass
    clus
vv   ZSCAN20 MUTATED ZSCAN20 WILD-TYPE
  R0               8               249
  R1               0                 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"
D1555V10, 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
D1555V11, 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(1556) Variable = NUDT16L1 MUTATION ANALYSIS
D1556V1, survival
                    sevent
clus2                  0   1
  NUDT16L1 MUTATED     3   0
  NUDT16L1 WILD-TYPE 279  73
  NUDT16L1 MUTATED NUDT16L1 WILD-TYPE 
                 3                352 
  NUDT16L1 MUTATED NUDT16L1 WILD-TYPE 
                 0                 73 
$`NUDT16L1 MUTATED`
TCGA-AA-A01R TCGA-CK-6747 TCGA-CM-6674 
       35.01         2.93        12.95 

$`NUDT16L1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  NUDT16L1 MUTATED NUDT16L1 WILD-TYPE 
              2.93               0.00 
  NUDT16L1 MUTATED NUDT16L1 WILD-TYPE 
             35.01             140.38 
  NUDT16L1 MUTATED NUDT16L1 WILD-TYPE 
            12.950             20.235 
[1] "2.9 - 35.0 (12.9)"  "0.0 - 140.4 (20.2)"
[1] "hr="     "3300000"
D1556V2, 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       25       107         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NUDT16L1 MUTATED           1          0          0          0        0
  NUDT16L1 WILD-TYPE        18         10         41         31       35
                    vv
clus                 STAGE IVA STAGE IVB
  NUDT16L1 MUTATED           0         0
  NUDT16L1 WILD-TYPE        13         1
D1556V3, multiclass
            clus
vv           NUDT16L1 MUTATED NUDT16L1 WILD-TYPE
  STAGE I                   0                 64
  STAGE IA                  0                  1
  STAGE II                  0                 25
  STAGE IIA                 2                107
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 1                 18
  STAGE IIIA                0                 10
  STAGE IIIB                0                 41
  STAGE IIIC                0                 31
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  NUDT16L1 MUTATED     0   0   3   0
  NUDT16L1 WILD-TYPE   9  68 245  41
D1556V4, multiclass
    clus
vv   NUDT16L1 MUTATED NUDT16L1 WILD-TYPE
  T1                0                  9
  T2                0                 68
  T3                3                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
  NUDT16L1 MUTATED     2   0   1
  NUDT16L1 WILD-TYPE 218  80  65
D1556V5, multiclass
    clus
vv   NUDT16L1 MUTATED NUDT16L1 WILD-TYPE
  N0                2                218
  N1                0                 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"
D1556V6, binary
                    cls
clus                   0   1
  NUDT16L1 MUTATED     2   0
  NUDT16L1 WILD-TYPE 281  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  NUDT16L1 MUTATED      2    0
  NUDT16L1 WILD-TYPE  281   48
   clus
vv  NUDT16L1 MUTATED NUDT16L1 WILD-TYPE
  0                2                281
  1                0                 48
[1] 2 2
[1] FALSE
D1556V7, 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
D1556V8, binary
                    cls
clus                   0   1
  NUDT16L1 MUTATED     2   1
  NUDT16L1 WILD-TYPE 315  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  NUDT16L1 MUTATED      2    1
  NUDT16L1 WILD-TYPE  315   47
                               clus
vv                              NUDT16L1 MUTATED NUDT16L1 WILD-TYPE
  COLON ADENOCARCINOMA                         2                315
  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 255   2  22  20
D1556V9, multiclass
    clus
vv   NUDT16L1 MUTATED NUDT16L1 WILD-TYPE
  R0                2                255
  R1                0                  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"
D1556V10, continuous
[1] "Remove cluster labels:" "NUDT16L1 MUTATED"      
clus
  NUDT16L1 MUTATED NUDT16L1 WILD-TYPE 
                 2                343 
        TCGA-A6-2671         TCGA-A6-2672         TCGA-A6-2674 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-2676         TCGA-A6-2677         TCGA-A6-2678 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-2683         TCGA-A6-3807         TCGA-A6-3808 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-3809         TCGA-A6-3810         TCGA-A6-4105 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-5656         TCGA-A6-5657         TCGA-A6-5659 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-5660         TCGA-A6-5661         TCGA-A6-5662 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-5664         TCGA-A6-5665         TCGA-A6-5666 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-6137         TCGA-A6-6138         TCGA-A6-6141 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-6142         TCGA-A6-6648         TCGA-A6-6649 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-6651         TCGA-A6-6652         TCGA-A6-6653 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-6654         TCGA-A6-6780         TCGA-A6-6781 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-6782         TCGA-AA-3489         TCGA-AA-3492 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3496         TCGA-AA-3502         TCGA-AA-3510 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3511         TCGA-AA-3514         TCGA-AA-3516 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3517         TCGA-AA-3518         TCGA-AA-3519 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3520         TCGA-AA-3521         TCGA-AA-3522 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3524         TCGA-AA-3525         TCGA-AA-3526 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3527         TCGA-AA-3529         TCGA-AA-3530 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3531         TCGA-AA-3532         TCGA-AA-3534 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3538         TCGA-AA-3542         TCGA-AA-3543 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3544         TCGA-AA-3548         TCGA-AA-3549 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3552         TCGA-AA-3553         TCGA-AA-3554 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3555         TCGA-AA-3556         TCGA-AA-3558 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3560         TCGA-AA-3562         TCGA-AA-3655 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3660         TCGA-AA-3662         TCGA-AA-3663 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3664         TCGA-AA-3666         TCGA-AA-3667 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3672         TCGA-AA-3673         TCGA-AA-3678 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3679         TCGA-AA-3680         TCGA-AA-3681 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3684         TCGA-AA-3685         TCGA-AA-3688 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3692         TCGA-AA-3693         TCGA-AA-3695 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3696         TCGA-AA-3697         TCGA-AA-3710 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3712         TCGA-AA-3713         TCGA-AA-3715 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3811         TCGA-AA-3812         TCGA-AA-3814 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3815         TCGA-AA-3818         TCGA-AA-3819 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3821         TCGA-AA-3831         TCGA-AA-3833 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3837         TCGA-AA-3842         TCGA-AA-3844 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3845         TCGA-AA-3846         TCGA-AA-3848 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3850         TCGA-AA-3851         TCGA-AA-3852 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3854         TCGA-AA-3855         TCGA-AA-3856 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3858         TCGA-AA-3860         TCGA-AA-3861 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3864         TCGA-AA-3866         TCGA-AA-3867 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3869         TCGA-AA-3870         TCGA-AA-3872 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3875         TCGA-AA-3877         TCGA-AA-3930 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3939         TCGA-AA-3941         TCGA-AA-3947 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3949         TCGA-AA-3950         TCGA-AA-3952 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3955         TCGA-AA-3956         TCGA-AA-3966 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3968         TCGA-AA-3971         TCGA-AA-3972 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3973         TCGA-AA-3975         TCGA-AA-3976 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3977         TCGA-AA-3979         TCGA-AA-3980 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3982         TCGA-AA-3984         TCGA-AA-3986 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3989         TCGA-AA-3994         TCGA-AA-A004 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-A00A         TCGA-AA-A00D         TCGA-AA-A00E 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-A00F         TCGA-AA-A00J         TCGA-AA-A00K 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-A00L         TCGA-AA-A00N         TCGA-AA-A00O 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-A00Q         TCGA-AA-A00R         TCGA-AA-A00U 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-A00W         TCGA-AA-A00Z         TCGA-AA-A010 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-A017         TCGA-AA-A01D         TCGA-AA-A01F 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-A01G         TCGA-AA-A01I         TCGA-AA-A01K 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-A01P         TCGA-AA-A01Q         TCGA-AA-A01S 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-A01T         TCGA-AA-A01V         TCGA-AA-A01X 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-A01Z         TCGA-AA-A022         TCGA-AA-A024 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-A029         TCGA-AA-A02F         TCGA-AA-A02H 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-A02J         TCGA-AA-A02K         TCGA-AA-A02O 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-A02W         TCGA-AA-A02Y         TCGA-AA-A03F 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-A03J         TCGA-AD-5900         TCGA-AD-6548 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AD-6888         TCGA-AD-6889         TCGA-AD-6890 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AD-6895         TCGA-AD-6899         TCGA-AD-6901 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AD-6963         TCGA-AD-6964         TCGA-AD-6965 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AU-3779         TCGA-AU-6004         TCGA-AY-4070 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AY-4071         TCGA-AY-5543         TCGA-AY-6196 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AY-6197         TCGA-AY-6386         TCGA-AZ-4323 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AZ-4616         TCGA-AZ-4682         TCGA-AZ-5403 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AZ-5407         TCGA-AZ-6598         TCGA-AZ-6599 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AZ-6600         TCGA-AZ-6601         TCGA-AZ-6603 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AZ-6605         TCGA-AZ-6606         TCGA-AZ-6607 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AZ-6608         TCGA-CK-4947         TCGA-CK-4948 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CK-4950         TCGA-CK-4952         TCGA-CM-4743 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-4744         TCGA-CM-4746         TCGA-CM-4747 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-4752         TCGA-CM-5341         TCGA-CM-5344 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-5348         TCGA-CM-5349         TCGA-CM-5860 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-5861         TCGA-CM-5862         TCGA-CM-5863 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-5864         TCGA-CM-5868         TCGA-CM-6161 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-6162         TCGA-CM-6163         TCGA-CM-6164 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-6165         TCGA-CM-6166         TCGA-CM-6167 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-6168         TCGA-CM-6169         TCGA-CM-6170 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-6171         TCGA-CM-6172         TCGA-CM-6675 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-6676         TCGA-CM-6677         TCGA-CM-6678 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-6679         TCGA-CM-6680         TCGA-D5-5537 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-5538         TCGA-D5-5539         TCGA-D5-5540 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-5541         TCGA-D5-6529         TCGA-D5-6532 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-6533         TCGA-D5-6534         TCGA-D5-6535 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-6536         TCGA-D5-6537         TCGA-D5-6538 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-6539         TCGA-D5-6540         TCGA-D5-6541 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-6898         TCGA-D5-6920         TCGA-D5-6922 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-6923         TCGA-D5-6924         TCGA-D5-6926 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-6927         TCGA-D5-6928         TCGA-D5-6929 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-6930         TCGA-D5-6931         TCGA-D5-6932 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-7000         TCGA-DM-A0X9         TCGA-DM-A0XD 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-DM-A0XF         TCGA-DM-A1D0         TCGA-DM-A1D4 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-DM-A1D6         TCGA-DM-A1D7         TCGA-DM-A1D8 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-DM-A1D9         TCGA-DM-A1DA         TCGA-DM-A1DB 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-DM-A1HA         TCGA-DM-A1HB         TCGA-DM-A282 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-DM-A285         TCGA-DM-A28C         TCGA-DM-A28E 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-DM-A28F         TCGA-DM-A28G         TCGA-DM-A28H 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-DM-A28K         TCGA-F4-6459         TCGA-F4-6460 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-F4-6569         TCGA-F4-6570         TCGA-F4-6703 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-F4-6704         TCGA-F4-6806         TCGA-F4-6807 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-F4-6808         TCGA-F4-6809         TCGA-F4-6854 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-F4-6855         TCGA-F4-6856         TCGA-G4-6293 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-G4-6299         TCGA-G4-6303         TCGA-G4-6304 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-G4-6306         TCGA-G4-6307         TCGA-G4-6309 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-G4-6310         TCGA-G4-6315         TCGA-G4-6317 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-G4-6321         TCGA-G4-6323         TCGA-G4-6586 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-G4-6588         TCGA-G4-6625         TCGA-G4-6626 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-G4-6628 
"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
D1556V11, multiclass
[1] "Remove cluster labels:" "NUDT16L1 MUTATED"      
clus
  NUDT16L1 MUTATED NUDT16L1 WILD-TYPE 
                 2                204 
        TCGA-A6-2671         TCGA-A6-2672         TCGA-A6-2674 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-2676         TCGA-A6-2677         TCGA-A6-2678 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-2683         TCGA-A6-3807         TCGA-A6-3808 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-3809         TCGA-A6-3810         TCGA-A6-4105 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-5656         TCGA-A6-5657         TCGA-A6-5659 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-5660         TCGA-A6-5661         TCGA-A6-5662 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-5664         TCGA-A6-5665         TCGA-A6-5666 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-6137         TCGA-A6-6138         TCGA-A6-6141 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-6142         TCGA-A6-6648         TCGA-A6-6649 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-6651         TCGA-A6-6652         TCGA-A6-6653 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-6654         TCGA-A6-6780         TCGA-A6-6781 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-6782         TCGA-AD-5900         TCGA-AD-6548 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AD-6888         TCGA-AD-6889         TCGA-AD-6890 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AD-6895         TCGA-AD-6899         TCGA-AD-6901 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AD-6963         TCGA-AD-6964         TCGA-AD-6965 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AU-3779         TCGA-AU-6004         TCGA-AY-4070 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AY-4071         TCGA-AY-5543         TCGA-AY-6196 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AY-6197         TCGA-AY-6386         TCGA-AZ-4315 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AZ-4323         TCGA-AZ-4616         TCGA-AZ-4681 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AZ-4682         TCGA-AZ-5403         TCGA-AZ-5407 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AZ-6598         TCGA-AZ-6599         TCGA-AZ-6600 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AZ-6601         TCGA-AZ-6603         TCGA-AZ-6605 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AZ-6606         TCGA-AZ-6607         TCGA-AZ-6608 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CA-5254         TCGA-CA-5255         TCGA-CA-5796 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CA-5797         TCGA-CA-6715         TCGA-CA-6716 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CA-6717         TCGA-CA-6718         TCGA-CA-6719 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CK-4947         TCGA-CK-4948         TCGA-CK-4950 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CK-4952         TCGA-CK-5912         TCGA-CK-5913 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CK-5914         TCGA-CK-5915         TCGA-CK-5916 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CK-6746         TCGA-CK-6748         TCGA-CK-6751 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-4743         TCGA-CM-4744         TCGA-CM-4746 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-4747         TCGA-CM-4752         TCGA-CM-5341 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-5344         TCGA-CM-5348         TCGA-CM-5349 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-5860         TCGA-CM-5861         TCGA-CM-5862 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-5863         TCGA-CM-5864         TCGA-CM-5868 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-6161         TCGA-CM-6162         TCGA-CM-6163 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-6164         TCGA-CM-6165         TCGA-CM-6166 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-6167         TCGA-CM-6168         TCGA-CM-6169 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-6170         TCGA-CM-6171         TCGA-CM-6172 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-6675         TCGA-CM-6676         TCGA-CM-6677 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-6678         TCGA-CM-6679         TCGA-CM-6680 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-5537         TCGA-D5-5538         TCGA-D5-5539 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-5540         TCGA-D5-5541         TCGA-D5-6529 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-6532         TCGA-D5-6533         TCGA-D5-6534 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-6535         TCGA-D5-6536         TCGA-D5-6537 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-6538         TCGA-D5-6539         TCGA-D5-6540 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-6541         TCGA-D5-6898         TCGA-D5-6920 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-6922         TCGA-D5-6923         TCGA-D5-6924 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-6926         TCGA-D5-6927         TCGA-D5-6928 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-6929         TCGA-D5-6930         TCGA-D5-6931 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-6932         TCGA-D5-7000         TCGA-DM-A0X9 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-DM-A0XD         TCGA-DM-A0XF         TCGA-DM-A1D0 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-DM-A1D4         TCGA-DM-A1D6         TCGA-DM-A1D7 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-DM-A1D8         TCGA-DM-A1D9         TCGA-DM-A1DA 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-DM-A1DB         TCGA-DM-A1HA         TCGA-DM-A1HB 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-DM-A282         TCGA-DM-A285         TCGA-DM-A28C 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-DM-A28E         TCGA-DM-A28F         TCGA-DM-A28G 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-DM-A28H         TCGA-DM-A28K         TCGA-F4-6459 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-F4-6460         TCGA-F4-6569         TCGA-F4-6570 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-F4-6703         TCGA-F4-6704         TCGA-F4-6805 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-F4-6806         TCGA-F4-6807         TCGA-F4-6808 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-F4-6809         TCGA-F4-6854         TCGA-F4-6855 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-F4-6856         TCGA-G4-6293         TCGA-G4-6299 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-G4-6303         TCGA-G4-6304         TCGA-G4-6306 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-G4-6307         TCGA-G4-6309         TCGA-G4-6310 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-G4-6315         TCGA-G4-6317         TCGA-G4-6321 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-G4-6323         TCGA-G4-6586         TCGA-G4-6588 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-G4-6625         TCGA-G4-6626         TCGA-G4-6628 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 

Clustering(1557) Variable = APLP1 MUTATION ANALYSIS
D1557V1, survival
                 sevent
clus2               0   1
  APLP1 MUTATED    11   5
  APLP1 WILD-TYPE 271  68
  APLP1 MUTATED APLP1 WILD-TYPE 
             16             339 
  APLP1 MUTATED APLP1 WILD-TYPE 
              5              68 
$`APLP1 MUTATED`
TCGA-A6-2672 TCGA-A6-2677 TCGA-AA-3492 TCGA-AA-3525 TCGA-AA-3542 TCGA-AA-3821 
       46.65        24.33         3.02         8.05        12.99         1.02 
TCGA-AA-3831 TCGA-AA-3877 TCGA-AA-3977 TCGA-AA-A00N TCGA-AD-6965 TCGA-AZ-4315 
       17.98        31.00        25.02         4.01         0.20        58.39 
TCGA-AZ-6606 TCGA-CK-5913 TCGA-F4-6459 TCGA-F4-6856 
       11.74        51.32         8.61        19.43 

$`APLP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       43.76        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       33.34        32.75        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       24.03        37.05        36.03        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 
       34.03        29.00        29.00        26.01         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       25.02        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AU-3779 
        0.72         5.79        22.42        27.42        10.88        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
       17.56       102.44        40.34        15.62        49.08        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 
       35.97        60.79       117.07        98.24        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 
       33.67        13.25         0.53        35.41       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  APLP1 MUTATED APLP1 WILD-TYPE 
            0.2             0.0 
  APLP1 MUTATED APLP1 WILD-TYPE 
          58.39          140.38 
  APLP1 MUTATED APLP1 WILD-TYPE 
         15.485          20.980 
[1] "0.2 - 58.4 (15.5)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.9"
D1557V2, 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       24       106         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  APLP1 MUTATED           0          0          3          2        1         0
  APLP1 WILD-TYPE        19         10         38         29       34        13
                 vv
clus              STAGE IVB
  APLP1 MUTATED           0
  APLP1 WILD-TYPE         1
D1557V3, multiclass
            clus
vv           APLP1 MUTATED APLP1 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              3             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             3              38
  STAGE IIIC             2              29
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  APLP1 MUTATED     1   3   9   3
  APLP1 WILD-TYPE   8  65 239  38
D1557V4, multiclass
    clus
vv   APLP1 MUTATED APLP1 WILD-TYPE
  T1             1               8
  T2             3              65
  T3             9             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
  APLP1 MUTATED     9   2   5
  APLP1 WILD-TYPE 211  78  61
D1557V5, multiclass
    clus
vv   APLP1 MUTATED APLP1 WILD-TYPE
  N0             9             211
  N1             2              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"
D1557V6, binary
                 cls
clus                0   1
  APLP1 MUTATED    12   1
  APLP1 WILD-TYPE 271  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  APLP1 MUTATED     12    1
  APLP1 WILD-TYPE  271   47
   clus
vv  APLP1 MUTATED APLP1 WILD-TYPE
  0            12             271
  1             1              47
[1] 2 2
[1] FALSE
D1557V7, 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
D1557V8, binary
                 cls
clus                0   1
  APLP1 MUTATED    12   4
  APLP1 WILD-TYPE 305  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  APLP1 MUTATED     12    4
  APLP1 WILD-TYPE  305   44
                               clus
vv                              APLP1 MUTATED APLP1 WILD-TYPE
  COLON ADENOCARCINOMA                     12             305
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  APLP1 MUTATED    12   0   0   1
  APLP1 WILD-TYPE 245   2  22  20
D1557V9, multiclass
    clus
vv   APLP1 MUTATED APLP1 WILD-TYPE
  R0            12             245
  R1             0               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"
D1557V10, 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
D1557V11, 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(1558) Variable = OR9G4 MUTATION ANALYSIS
D1558V1, survival
                 sevent
clus2               0   1
  OR9G4 MUTATED     7   1
  OR9G4 WILD-TYPE 275  72
  OR9G4 MUTATED OR9G4 WILD-TYPE 
              8             347 
  OR9G4 MUTATED OR9G4 WILD-TYPE 
              1              72 
$`OR9G4 MUTATED`
TCGA-AA-3502 TCGA-AA-A00N TCGA-AA-A010 TCGA-CA-5796 TCGA-CA-6717 TCGA-D5-6535 
       35.01         4.01        34.98         3.25         0.33        15.12 
TCGA-F4-6807 TCGA-F4-6808 
       16.24        33.67 

$`OR9G4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        1.94         2.24         3.06         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.31        29.59        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  OR9G4 MUTATED OR9G4 WILD-TYPE 
           0.33            0.00 
  OR9G4 MUTATED OR9G4 WILD-TYPE 
          35.01          140.38 
  OR9G4 MUTATED OR9G4 WILD-TYPE 
          15.68           20.28 
[1] "0.3 - 35.0 (15.7)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1"  
D1558V2, 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       25       107         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        19         10         40         30       35        13
                 vv
clus              STAGE IVB
  OR9G4 MUTATED           0
  OR9G4 WILD-TYPE         1
D1558V3, multiclass
            clus
vv           OR9G4 MUTATED OR9G4 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              2             107
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR9G4 MUTATED     1   1   4   2
  OR9G4 WILD-TYPE   8  67 244  39
D1558V4, multiclass
    clus
vv   OR9G4 MUTATED OR9G4 WILD-TYPE
  T1             1               8
  T2             1              67
  T3             4             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
  OR9G4 MUTATED     6   1   1
  OR9G4 WILD-TYPE 214  79  65
D1558V5, multiclass
    clus
vv   OR9G4 MUTATED OR9G4 WILD-TYPE
  N0             6             214
  N1             1              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
  OR9G4 MUTATED     7   0
  OR9G4 WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR9G4 MUTATED      7    0
  OR9G4 WILD-TYPE  276   48
   clus
vv  OR9G4 MUTATED OR9G4 WILD-TYPE
  0             7             276
  1             0              48
[1] 2 2
[1] FALSE
D1558V7, 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
D1558V8, binary
                 cls
clus                0   1
  OR9G4 MUTATED     5   3
  OR9G4 WILD-TYPE 312  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR9G4 MUTATED      5    3
  OR9G4 WILD-TYPE  312   45
                               clus
vv                              OR9G4 MUTATED OR9G4 WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  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 251   2  22  19
D1558V9, multiclass
    clus
vv   OR9G4 MUTATED OR9G4 WILD-TYPE
  R0             6             251
  R1             0               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"
D1558V10, 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
D1558V11, 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(1559) Variable = LAMA3 MUTATION ANALYSIS
D1559V1, survival
                 sevent
clus2               0   1
  LAMA3 MUTATED    25   7
  LAMA3 WILD-TYPE 257  66
  LAMA3 MUTATED LAMA3 WILD-TYPE 
             32             323 
  LAMA3 MUTATED LAMA3 WILD-TYPE 
              7              66 
$`LAMA3 MUTATED`
TCGA-A6-2671 TCGA-A6-3807 TCGA-A6-5660 TCGA-A6-5665 TCGA-AA-3529 TCGA-AA-3662 
       43.76        34.65        29.19        22.06         0.00         6.05 
TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3685 TCGA-AA-3821 TCGA-AA-3861 TCGA-AA-3956 
        6.97         0.92        37.05         1.02        30.05        34.03 
TCGA-AA-3977 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-6598 
       25.02        18.05         4.01        34.98        58.39        49.41 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CM-4746 TCGA-CM-5349 TCGA-CM-6171 
       12.10       100.01         0.33        37.02        30.08        14.04 
TCGA-D5-6535 TCGA-D5-6540 TCGA-DM-A0X9 TCGA-F4-6570 TCGA-F4-6806 TCGA-G4-6323 
       15.12        16.14       119.70         6.18        29.59        13.78 
TCGA-G4-6588 TCGA-G4-6628 
       26.17        52.80 

$`LAMA3 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       33.34        32.75        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 
       30.44        33.53        23.61        22.09        32.71        27.09 
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 
       22.52         8.38        25.08        25.18        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        7.04         3.02         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 
       37.05        36.03         8.05        19.07        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-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-3688 TCGA-AA-3692 TCGA-AA-3696 
       15.02        11.01         5.98        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       33.04         0.99        25.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 
       26.01        24.00         2.01        20.98         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       62.79        61.41         6.77        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 
        2.93         2.01       124.27        23.05        20.02        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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       43.27        17.85         4.80        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       10.26        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       35.87         1.55        16.31        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        35.80        91.79        46.75 

  LAMA3 MUTATED LAMA3 WILD-TYPE 
              0               0 
  LAMA3 MUTATED LAMA3 WILD-TYPE 
         119.70          140.38 
  LAMA3 MUTATED LAMA3 WILD-TYPE 
         25.595          20.020 
[1] "0.0 - 119.7 (25.6)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1"  
D1559V2, 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       20        99         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        18         10         39         28       32        13
                 vv
clus              STAGE IVB
  LAMA3 MUTATED           0
  LAMA3 WILD-TYPE         1
D1559V3, multiclass
            clus
vv           LAMA3 MUTATED LAMA3 WILD-TYPE
  STAGE I                6              58
  STAGE IA               1               0
  STAGE II               5              20
  STAGE IIA             10              99
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             3              28
  STAGE IV               3              32
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LAMA3 MUTATED     0   7  20   6
  LAMA3 WILD-TYPE   9  61 228  35
D1559V4, multiclass
    clus
vv   LAMA3 MUTATED LAMA3 WILD-TYPE
  T1             0               9
  T2             7              61
  T3            20             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
  LAMA3 MUTATED    25   4   5
  LAMA3 WILD-TYPE 195  76  61
D1559V5, multiclass
    clus
vv   LAMA3 MUTATED LAMA3 WILD-TYPE
  N0            25             195
  N1             4              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"
D1559V6, binary
                 cls
clus                0   1
  LAMA3 MUTATED    27   3
  LAMA3 WILD-TYPE 256  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LAMA3 MUTATED     27    3
  LAMA3 WILD-TYPE  256   45
   clus
vv  LAMA3 MUTATED LAMA3 WILD-TYPE
  0            27             256
  1             3              45
[1] 2 2
[1] FALSE
D1559V7, 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
D1559V8, binary
                 cls
clus                0   1
  LAMA3 MUTATED    29   5
  LAMA3 WILD-TYPE 288  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LAMA3 MUTATED     29    5
  LAMA3 WILD-TYPE  288   43
                               clus
vv                              LAMA3 MUTATED LAMA3 WILD-TYPE
  COLON ADENOCARCINOMA                     29             288
  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 232   2  21  19
D1559V9, multiclass
    clus
vv   LAMA3 MUTATED LAMA3 WILD-TYPE
  R0            25             232
  R1             0               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"
D1559V10, 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
D1559V11, 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(1560) Variable = TRAF3IP3 MUTATION ANALYSIS
D1560V1, survival
                    sevent
clus2                  0   1
  TRAF3IP3 MUTATED     9   2
  TRAF3IP3 WILD-TYPE 273  71
  TRAF3IP3 MUTATED TRAF3IP3 WILD-TYPE 
                11                344 
  TRAF3IP3 MUTATED TRAF3IP3 WILD-TYPE 
                 2                 71 
$`TRAF3IP3 MUTATED`
TCGA-A6-2676 TCGA-AA-3525 TCGA-AA-3672 TCGA-AA-3811 TCGA-CA-6717 TCGA-CA-6718 
       42.90         8.05         0.92        10.06         0.33         0.10 
TCGA-CM-5860 TCGA-CM-5864 TCGA-D5-6533 TCGA-D5-6930 TCGA-DM-A1HB 
       16.01        15.02         1.32         1.51       135.65 

$`TRAF3IP3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 
        1.02         9.07        24.03        37.05        36.03        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        19.04        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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-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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       11.51        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-D5-6931 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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  TRAF3IP3 MUTATED TRAF3IP3 WILD-TYPE 
               0.1                0.0 
  TRAF3IP3 MUTATED TRAF3IP3 WILD-TYPE 
            135.65             140.38 
  TRAF3IP3 MUTATED TRAF3IP3 WILD-TYPE 
             8.050             20.995 
[1] "0.1 - 135.7 (8.1)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.2"
D1560V2, 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       25       104         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRAF3IP3 MUTATED           2          0          3          0        0
  TRAF3IP3 WILD-TYPE        17         10         38         31       35
                    vv
clus                 STAGE IVA STAGE IVB
  TRAF3IP3 MUTATED           0         0
  TRAF3IP3 WILD-TYPE        13         1
D1560V3, multiclass
            clus
vv           TRAF3IP3 MUTATED TRAF3IP3 WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  0                 25
  STAGE IIA                 5                104
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 2                 17
  STAGE IIIA                0                 10
  STAGE IIIB                3                 38
  STAGE IIIC                0                 31
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  TRAF3IP3 MUTATED     0   1   9   2
  TRAF3IP3 WILD-TYPE   9  67 239  39
D1560V4, multiclass
    clus
vv   TRAF3IP3 MUTATED TRAF3IP3 WILD-TYPE
  T1                0                  9
  T2                1                 67
  T3                9                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
  TRAF3IP3 MUTATED     8   3   1
  TRAF3IP3 WILD-TYPE 212  77  65
D1560V5, multiclass
    clus
vv   TRAF3IP3 MUTATED TRAF3IP3 WILD-TYPE
  N0                8                212
  N1                3                 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"
D1560V6, binary
                    cls
clus                   0   1
  TRAF3IP3 MUTATED    12   0
  TRAF3IP3 WILD-TYPE 271  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TRAF3IP3 MUTATED     12    0
  TRAF3IP3 WILD-TYPE  271   48
   clus
vv  TRAF3IP3 MUTATED TRAF3IP3 WILD-TYPE
  0               12                271
  1                0                 48
[1] 2 2
[1] FALSE
D1560V7, 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
D1560V8, binary
                    cls
clus                   0   1
  TRAF3IP3 MUTATED    10   2
  TRAF3IP3 WILD-TYPE 307  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TRAF3IP3 MUTATED     10    2
  TRAF3IP3 WILD-TYPE  307   46
                               clus
vv                              TRAF3IP3 MUTATED TRAF3IP3 WILD-TYPE
  COLON ADENOCARCINOMA                        10                307
  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 248   2  22  19
D1560V9, multiclass
    clus
vv   TRAF3IP3 MUTATED TRAF3IP3 WILD-TYPE
  R0                9                248
  R1                0                  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"
D1560V10, 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
D1560V11, 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(1561) Variable = CTNNA3 MUTATION ANALYSIS
D1561V1, survival
                  sevent
clus2                0   1
  CTNNA3 MUTATED    20   6
  CTNNA3 WILD-TYPE 262  67
  CTNNA3 MUTATED CTNNA3 WILD-TYPE 
              26              329 
  CTNNA3 MUTATED CTNNA3 WILD-TYPE 
               6               67 
$`CTNNA3 MUTATED`
TCGA-A6-2678 TCGA-A6-6653 TCGA-AA-3496 TCGA-AA-3511 TCGA-AA-3715 TCGA-AA-3850 
       42.28        24.39         1.02         6.97        19.04         0.00 
TCGA-AA-3864 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A02Y 
       53.00         2.01        25.02         4.01        34.98        39.98 
TCGA-AD-6964 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-5407 TCGA-AZ-6601 TCGA-CM-6171 
       10.88        21.44        17.82        61.41       100.01        14.04 
TCGA-D5-6540 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-7000 TCGA-F4-6570 TCGA-F4-6855 
       16.14        13.41         1.51        10.26         6.18        35.41 
TCGA-G4-6586 TCGA-G4-6588 
       35.80        26.17 

$`CTNNA3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2683 
       43.76        46.65        43.76        42.90        24.33        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         3.02        35.01        63.98 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3852 
       14.93         0.00        17.03        10.06        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
       14.01         0.92        41.00        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        15.75         0.20        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 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-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 
        9.04         9.44        11.64        12.00        11.38       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      117.07        98.24         8.61        13.38        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        91.79        46.75        52.80 

  CTNNA3 MUTATED CTNNA3 WILD-TYPE 
               0                0 
  CTNNA3 MUTATED CTNNA3 WILD-TYPE 
          100.01           140.38 
  CTNNA3 MUTATED CTNNA3 WILD-TYPE 
           18.43            20.28 
[1] "0.0 - 100.0 (18.4)" "0.0 - 140.4 (20.3)"
[1] "hr=" "1.2"
D1561V2, 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       20       102         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CTNNA3 MUTATED           0          0          2          0        1
  CTNNA3 WILD-TYPE        19         10         39         31       34
                  vv
clus               STAGE IVA STAGE IVB
  CTNNA3 MUTATED           0         0
  CTNNA3 WILD-TYPE        13         1
D1561V3, multiclass
            clus
vv           CTNNA3 MUTATED CTNNA3 WILD-TYPE
  STAGE I                 7               57
  STAGE IA                0                1
  STAGE II                5               20
  STAGE IIA               7              102
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CTNNA3 MUTATED     1   7  14   4
  CTNNA3 WILD-TYPE   8  61 234  37
D1561V4, multiclass
    clus
vv   CTNNA3 MUTATED CTNNA3 WILD-TYPE
  T1              1                8
  T2              7               61
  T3             14              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
  CTNNA3 MUTATED    22   3   1
  CTNNA3 WILD-TYPE 198  77  65
D1561V5, multiclass
    clus
vv   CTNNA3 MUTATED CTNNA3 WILD-TYPE
  N0             22              198
  N1              3               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"
D1561V6, binary
                  cls
clus                 0   1
  CTNNA3 MUTATED    22   1
  CTNNA3 WILD-TYPE 261  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNA3 MUTATED     22    1
  CTNNA3 WILD-TYPE  261   47
   clus
vv  CTNNA3 MUTATED CTNNA3 WILD-TYPE
  0             22              261
  1              1               47
[1] 2 2
[1] FALSE
D1561V7, 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
D1561V8, binary
                  cls
clus                 0   1
  CTNNA3 MUTATED    21   5
  CTNNA3 WILD-TYPE 296  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNA3 MUTATED     21    5
  CTNNA3 WILD-TYPE  296   43
                               clus
vv                              CTNNA3 MUTATED CTNNA3 WILD-TYPE
  COLON ADENOCARCINOMA                      21              296
  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 237   2  22  21
D1561V9, multiclass
    clus
vv   CTNNA3 MUTATED CTNNA3 WILD-TYPE
  R0             20              237
  R1              0                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"
D1561V10, 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
D1561V11, 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(1562) Variable = KIAA0319 MUTATION ANALYSIS
D1562V1, survival
                    sevent
clus2                  0   1
  KIAA0319 MUTATED    13   1
  KIAA0319 WILD-TYPE 269  72
  KIAA0319 MUTATED KIAA0319 WILD-TYPE 
                14                341 
  KIAA0319 MUTATED KIAA0319 WILD-TYPE 
                 1                 72 
$`KIAA0319 MUTATED`
TCGA-A6-3807 TCGA-A6-6780 TCGA-AA-3715 TCGA-AA-3941 TCGA-AA-A00J TCGA-AA-A01F 
       34.65        20.12        19.04        24.00        18.05        32.02 
TCGA-AD-6889 TCGA-AY-6197 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CK-5913 TCGA-D5-6535 
       56.55        21.44        58.39         0.33        51.32        15.12 
TCGA-DM-A1HB TCGA-G4-6304 
      135.65        53.62 

$`KIAA0319 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        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        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        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        15.75         0.20        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 
       19.43       107.67        74.56        65.85        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  KIAA0319 MUTATED KIAA0319 WILD-TYPE 
              0.33               0.00 
  KIAA0319 MUTATED KIAA0319 WILD-TYPE 
            135.65             140.38 
  KIAA0319 MUTATED KIAA0319 WILD-TYPE 
             28.01              19.99 
[1] "0.3 - 135.7 (28.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "4.3"
D1562V2, 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       24       102         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0319 MUTATED           0          0          4          1        0
  KIAA0319 WILD-TYPE        19         10         37         30       35
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA0319 MUTATED           1         0
  KIAA0319 WILD-TYPE        12         1
D1562V3, multiclass
            clus
vv           KIAA0319 MUTATED KIAA0319 WILD-TYPE
  STAGE I                   0                 64
  STAGE IA                  0                  1
  STAGE II                  1                 24
  STAGE IIA                 7                102
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                0                 10
  STAGE IIIB                4                 37
  STAGE IIIC                1                 30
  STAGE IV                  0                 35
  STAGE IVA                 1                 12
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of 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  68 236  38
D1562V4, multiclass
    clus
vv   KIAA0319 MUTATED KIAA0319 WILD-TYPE
  T1                0                  9
  T2                0                 68
  T3               12                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
  KIAA0319 MUTATED     9   5   1
  KIAA0319 WILD-TYPE 211  75  65
D1562V5, multiclass
    clus
vv   KIAA0319 MUTATED KIAA0319 WILD-TYPE
  N0                9                211
  N1                5                 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"
D1562V6, binary
                    cls
clus                   0   1
  KIAA0319 MUTATED    10   1
  KIAA0319 WILD-TYPE 273  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0319 MUTATED     10    1
  KIAA0319 WILD-TYPE  273   47
   clus
vv  KIAA0319 MUTATED KIAA0319 WILD-TYPE
  0               10                273
  1                1                 47
[1] 2 2
[1] FALSE
D1562V7, 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
D1562V8, binary
                    cls
clus                   0   1
  KIAA0319 MUTATED    12   3
  KIAA0319 WILD-TYPE 305  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0319 MUTATED     12    3
  KIAA0319 WILD-TYPE  305   45
                               clus
vv                              KIAA0319 MUTATED KIAA0319 WILD-TYPE
  COLON ADENOCARCINOMA                        12                305
  COLON MUCINOUS ADENOCARCINOMA                3                 45
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  KIAA0319 MUTATED     9   0   0   3
  KIAA0319 WILD-TYPE 248   2  22  18
D1562V9, multiclass
    clus
vv   KIAA0319 MUTATED KIAA0319 WILD-TYPE
  R0                9                248
  R1                0                  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"
D1562V10, 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
D1562V11, 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(1563) Variable = GLTSCR1 MUTATION ANALYSIS
D1563V1, survival
                   sevent
clus2                 0   1
  GLTSCR1 MUTATED    10   1
  GLTSCR1 WILD-TYPE 272  72
  GLTSCR1 MUTATED GLTSCR1 WILD-TYPE 
               11               344 
  GLTSCR1 MUTATED GLTSCR1 WILD-TYPE 
                1                72 
$`GLTSCR1 MUTATED`
TCGA-AA-3663 TCGA-AA-3870 TCGA-AA-3950 TCGA-AD-6548 TCGA-AD-6889 TCGA-AZ-6601 
        6.97        29.98        24.00        21.37        56.55       100.01 
TCGA-CK-6751 TCGA-D5-5538 TCGA-D5-6540 TCGA-D5-6930 TCGA-DM-A1HA 
      124.27        12.26        16.14         1.51       131.51 

$`GLTSCR1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       17.03        24.03        27.02        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       18.05        40.96         0.07         4.21         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        61.41        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  GLTSCR1 MUTATED GLTSCR1 WILD-TYPE 
             1.51              0.00 
  GLTSCR1 MUTATED GLTSCR1 WILD-TYPE 
           131.51            140.38 
  GLTSCR1 MUTATED GLTSCR1 WILD-TYPE 
            24.00             20.07 
[1] "1.5 - 131.5 (24.0)" "0.0 - 140.4 (20.1)"
[1] "hr=" "4.1"
D1563V2, 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       23       106         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GLTSCR1 MUTATED           0          0          1          1        1
  GLTSCR1 WILD-TYPE        19         10         40         30       34
                   vv
clus                STAGE IVA STAGE IVB
  GLTSCR1 MUTATED           0         0
  GLTSCR1 WILD-TYPE        13         1
D1563V3, multiclass
            clus
vv           GLTSCR1 MUTATED GLTSCR1 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 2                23
  STAGE IIA                3               106
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               1                30
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  GLTSCR1 MUTATED     0   3   8   0
  GLTSCR1 WILD-TYPE   9  65 240  41
D1563V4, multiclass
    clus
vv   GLTSCR1 MUTATED GLTSCR1 WILD-TYPE
  T1               0                 9
  T2               3                65
  T3               8               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
  GLTSCR1 MUTATED     8   1   2
  GLTSCR1 WILD-TYPE 212  79  64
D1563V5, multiclass
    clus
vv   GLTSCR1 MUTATED GLTSCR1 WILD-TYPE
  N0               8               212
  N1               1                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"
D1563V6, binary
                   cls
clus                  0   1
  GLTSCR1 MUTATED     9   1
  GLTSCR1 WILD-TYPE 274  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GLTSCR1 MUTATED      9    1
  GLTSCR1 WILD-TYPE  274   47
   clus
vv  GLTSCR1 MUTATED GLTSCR1 WILD-TYPE
  0               9               274
  1               1                47
[1] 2 2
[1] FALSE
D1563V7, 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
D1563V8, binary
                   cls
clus                  0   1
  GLTSCR1 MUTATED     7   4
  GLTSCR1 WILD-TYPE 310  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GLTSCR1 MUTATED      7    4
  GLTSCR1 WILD-TYPE  310   44
                               clus
vv                              GLTSCR1 MUTATED GLTSCR1 WILD-TYPE
  COLON ADENOCARCINOMA                        7               310
  COLON MUCINOUS ADENOCARCINOMA               4                44
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  GLTSCR1 MUTATED     7   0   0   1
  GLTSCR1 WILD-TYPE 250   2  22  20
D1563V9, multiclass
    clus
vv   GLTSCR1 MUTATED GLTSCR1 WILD-TYPE
  R0               7               250
  R1               0                 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"
D1563V10, 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
D1563V11, 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(1564) Variable = ZNF518A MUTATION ANALYSIS
D1564V1, survival
                   sevent
clus2                 0   1
  ZNF518A MUTATED    10   6
  ZNF518A WILD-TYPE 272  67
  ZNF518A MUTATED ZNF518A WILD-TYPE 
               16               339 
  ZNF518A MUTATED ZNF518A WILD-TYPE 
                6                67 
$`ZNF518A MUTATED`
TCGA-A6-6780 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3710 TCGA-AA-3846 TCGA-AA-3950 
       20.12         3.02         1.02        26.99        17.03        24.00 
TCGA-AA-A010 TCGA-AA-A01P TCGA-AD-6964 TCGA-AY-6197 TCGA-AZ-6598 TCGA-CA-6717 
       34.98        38.07        10.88        21.44        49.41         0.33 
TCGA-F4-6570 TCGA-F4-6856 TCGA-G4-6303 TCGA-G4-6588 
        6.18        19.43        65.85        26.17 

$`ZNF518A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3510 
       23.87        19.66        20.28         7.04        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02        14.93         0.00        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-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        13.38        13.45        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      107.67        74.56        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  ZNF518A MUTATED ZNF518A WILD-TYPE 
             0.33              0.00 
  ZNF518A MUTATED ZNF518A WILD-TYPE 
            65.85            140.38 
  ZNF518A MUTATED ZNF518A WILD-TYPE 
            20.78             20.19 
[1] "0.3 - 65.8 (20.8)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2.1"
D1564V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF518A MUTATED         1        0        3         9         2         0
  ZNF518A WILD-TYPE      63        1       22       100         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF518A MUTATED           1          0          0          0        1
  ZNF518A WILD-TYPE        18         10         41         31       34
                   vv
clus                STAGE IVA STAGE IVB
  ZNF518A MUTATED           0         0
  ZNF518A WILD-TYPE        13         1
D1564V3, multiclass
            clus
vv           ZNF518A MUTATED ZNF518A WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 3                22
  STAGE IIA                9               100
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               0                31
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ZNF518A MUTATED     0   1  14   3
  ZNF518A WILD-TYPE   9  67 234  38
D1564V4, multiclass
    clus
vv   ZNF518A MUTATED ZNF518A WILD-TYPE
  T1               0                 9
  T2               1                67
  T3              14               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
  ZNF518A MUTATED    15   2   1
  ZNF518A WILD-TYPE 205  78  65
D1564V5, multiclass
    clus
vv   ZNF518A MUTATED ZNF518A WILD-TYPE
  N0              15               205
  N1               2                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"
D1564V6, binary
                   cls
clus                  0   1
  ZNF518A MUTATED    12   1
  ZNF518A WILD-TYPE 271  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF518A MUTATED     12    1
  ZNF518A WILD-TYPE  271   47
   clus
vv  ZNF518A MUTATED ZNF518A WILD-TYPE
  0              12               271
  1               1                47
[1] 2 2
[1] FALSE
D1564V7, binary
                   cls
clus                  0   1
  ZNF518A MUTATED    13   5
  ZNF518A WILD-TYPE 157 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF518A MUTATED     13    5
  ZNF518A WILD-TYPE  157  192
        clus
vv       ZNF518A MUTATED ZNF518A WILD-TYPE
  FEMALE              13               157
  MALE                 5               192
[1] 2 2
[1] FALSE
D1564V8, binary
                   cls
clus                  0   1
  ZNF518A MUTATED    14   4
  ZNF518A WILD-TYPE 303  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF518A MUTATED     14    4
  ZNF518A WILD-TYPE  303   44
                               clus
vv                              ZNF518A MUTATED ZNF518A WILD-TYPE
  COLON ADENOCARCINOMA                       14               303
  COLON MUCINOUS ADENOCARCINOMA               4                44
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ZNF518A MUTATED    13   0   0   2
  ZNF518A WILD-TYPE 244   2  22  19
D1564V9, multiclass
    clus
vv   ZNF518A MUTATED ZNF518A WILD-TYPE
  R0              13               244
  R1               0                 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"
D1564V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF518A MUTATED                                  0     1
  ZNF518A WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ZNF518A MUTATED                           0     9
  ZNF518A WILD-TYPE                        19   167
D1564V11, multiclass
                                  clus
vv                                 ZNF518A MUTATED ZNF518A 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(1565) Variable = RCOR3 MUTATION ANALYSIS
D1565V1, survival
                 sevent
clus2               0   1
  RCOR3 MUTATED     8   2
  RCOR3 WILD-TYPE 274  71
  RCOR3 MUTATED RCOR3 WILD-TYPE 
             10             345 
  RCOR3 MUTATED RCOR3 WILD-TYPE 
              2              71 
$`RCOR3 MUTATED`
TCGA-A6-4105 TCGA-AA-3663 TCGA-AA-3877 TCGA-AA-A01Q TCGA-AD-6895 TCGA-AZ-6598 
       14.53         6.97        31.00         1.02         0.72        49.41 
TCGA-CM-5861 TCGA-D5-6927 TCGA-G4-6299 TCGA-G4-6304 
       15.02         9.44        74.56        53.62 

$`RCOR3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        18.05         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
      107.67        65.85        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  RCOR3 MUTATED RCOR3 WILD-TYPE 
           0.72            0.00 
  RCOR3 MUTATED RCOR3 WILD-TYPE 
          74.56          140.38 
  RCOR3 MUTATED RCOR3 WILD-TYPE 
         14.775          20.280 
[1] "0.7 - 74.6 (14.8)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.1"
D1565V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RCOR3 MUTATED         1        0        3         4         1         0
  RCOR3 WILD-TYPE      63        1       22       105         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RCOR3 MUTATED           0          0          0          1        1         0
  RCOR3 WILD-TYPE        19         10         41         30       34        13
                 vv
clus              STAGE IVB
  RCOR3 MUTATED           0
  RCOR3 WILD-TYPE         1
D1565V3, multiclass
            clus
vv           RCOR3 MUTATED RCOR3 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              4             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RCOR3 MUTATED     1   0   9   2
  RCOR3 WILD-TYPE   8  68 239  39
D1565V4, multiclass
    clus
vv   RCOR3 MUTATED RCOR3 WILD-TYPE
  T1             1               8
  T2             0              68
  T3             9             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
  RCOR3 MUTATED     9   1   2
  RCOR3 WILD-TYPE 211  79  64
D1565V5, multiclass
    clus
vv   RCOR3 MUTATED RCOR3 WILD-TYPE
  N0             9             211
  N1             1              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"
D1565V6, binary
                 cls
clus                0   1
  RCOR3 MUTATED     9   1
  RCOR3 WILD-TYPE 274  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RCOR3 MUTATED      9    1
  RCOR3 WILD-TYPE  274   47
   clus
vv  RCOR3 MUTATED RCOR3 WILD-TYPE
  0             9             274
  1             1              47
[1] 2 2
[1] FALSE
D1565V7, binary
                 cls
clus                0   1
  RCOR3 MUTATED     7   5
  RCOR3 WILD-TYPE 163 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RCOR3 MUTATED      7    5
  RCOR3 WILD-TYPE  163  192
        clus
vv       RCOR3 MUTATED RCOR3 WILD-TYPE
  FEMALE             7             163
  MALE               5             192
[1] 2 2
[1] FALSE
D1565V8, binary
                 cls
clus                0   1
  RCOR3 MUTATED    10   2
  RCOR3 WILD-TYPE 307  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RCOR3 MUTATED     10    2
  RCOR3 WILD-TYPE  307   46
                               clus
vv                              RCOR3 MUTATED RCOR3 WILD-TYPE
  COLON ADENOCARCINOMA                     10             307
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RCOR3 MUTATED     8   0   1   0
  RCOR3 WILD-TYPE 249   2  21  21
D1565V9, multiclass
    clus
vv   RCOR3 MUTATED RCOR3 WILD-TYPE
  R0             8             249
  R1             0               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"
D1565V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RCOR3 MUTATED                                  0     0
  RCOR3 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RCOR3 MUTATED                           0     7
  RCOR3 WILD-TYPE                        19   169
D1565V11, multiclass
                                  clus
vv                                 RCOR3 MUTATED RCOR3 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(1566) Variable = UVRAG MUTATION ANALYSIS
D1566V1, survival
                 sevent
clus2               0   1
  UVRAG MUTATED     6   0
  UVRAG WILD-TYPE 276  73
  UVRAG MUTATED UVRAG WILD-TYPE 
              6             349 
  UVRAG MUTATED UVRAG WILD-TYPE 
              0              73 
$`UVRAG MUTATED`
TCGA-AA-3510 TCGA-AA-3697 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-D5-6929 
       63.98        85.05         0.33         0.10         1.35        13.41 

$`UVRAG WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.07         0.26        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  UVRAG MUTATED UVRAG WILD-TYPE 
            0.1             0.0 
  UVRAG MUTATED UVRAG WILD-TYPE 
          85.05          140.38 
  UVRAG MUTATED UVRAG WILD-TYPE 
           7.38           20.28 
[1] "0.1 - 85.0 (7.4)"   "0.0 - 140.4 (20.3)"
[1] "hr="     "9400000"
D1566V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  UVRAG MUTATED         0        0        1         4         0         0
  UVRAG WILD-TYPE      64        1       24       105         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  UVRAG MUTATED           1          0          0          0        1         0
  UVRAG WILD-TYPE        18         10         41         31       34        13
                 vv
clus              STAGE IVB
  UVRAG MUTATED           0
  UVRAG WILD-TYPE         1
D1566V3, multiclass
            clus
vv           UVRAG MUTATED UVRAG WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              4             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  UVRAG MUTATED     0   0   7   0
  UVRAG WILD-TYPE   9  68 241  41
D1566V4, multiclass
    clus
vv   UVRAG MUTATED UVRAG WILD-TYPE
  T1             0               9
  T2             0              68
  T3             7             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
  UVRAG MUTATED     6   1   0
  UVRAG WILD-TYPE 214  79  66
D1566V5, multiclass
    clus
vv   UVRAG MUTATED UVRAG WILD-TYPE
  N0             6             214
  N1             1              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"
D1566V6, binary
                 cls
clus                0   1
  UVRAG MUTATED     6   1
  UVRAG WILD-TYPE 277  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UVRAG MUTATED      6    1
  UVRAG WILD-TYPE  277   47
   clus
vv  UVRAG MUTATED UVRAG WILD-TYPE
  0             6             277
  1             1              47
[1] 2 2
[1] FALSE
D1566V7, 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
D1566V8, binary
                 cls
clus                0   1
  UVRAG MUTATED     6   1
  UVRAG WILD-TYPE 311  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UVRAG MUTATED      6    1
  UVRAG WILD-TYPE  311   47
                               clus
vv                              UVRAG MUTATED UVRAG WILD-TYPE
  COLON ADENOCARCINOMA                      6             311
  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 253   2  22  18
D1566V9, multiclass
    clus
vv   UVRAG MUTATED UVRAG WILD-TYPE
  R0             4             253
  R1             0               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"
D1566V10, 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
D1566V11, 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(1567) Variable = IPPK MUTATION ANALYSIS
D1567V1, survival
                sevent
clus2              0   1
  IPPK MUTATED     8   1
  IPPK WILD-TYPE 274  72
  IPPK MUTATED IPPK WILD-TYPE 
             9            346 
  IPPK MUTATED IPPK WILD-TYPE 
             1             72 
$`IPPK MUTATED`
TCGA-A6-6780 TCGA-AA-3542 TCGA-AA-3864 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CM-5349 
       20.12        12.99        53.00       100.01         0.33        30.08 
TCGA-CM-6674 TCGA-D5-6533 TCGA-G4-6304 
       12.95         1.32        53.62 

$`IPPK WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       26.01         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 
       13.51        11.51        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      107.67        74.56        65.85        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  IPPK MUTATED IPPK WILD-TYPE 
          0.33           0.00 
  IPPK MUTATED IPPK WILD-TYPE 
        100.01         140.38 
  IPPK MUTATED IPPK WILD-TYPE 
        20.120         20.235 
[1] "0.3 - 100.0 (20.1)" "0.0 - 140.4 (20.2)"
[1] "hr=" "2.5"
D1567V2, 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       23       105         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IPPK MUTATED           0          0          1          1        0         0
  IPPK WILD-TYPE        19         10         40         30       35        13
                vv
clus             STAGE IVB
  IPPK MUTATED           0
  IPPK WILD-TYPE         1
D1567V3, multiclass
            clus
vv           IPPK MUTATED IPPK WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             4            105
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            1             30
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  IPPK MUTATED     0   0   7   2
  IPPK WILD-TYPE   9  68 241  39
D1567V4, multiclass
    clus
vv   IPPK MUTATED IPPK WILD-TYPE
  T1            0              9
  T2            0             68
  T3            7            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
  IPPK MUTATED     8   0   1
  IPPK WILD-TYPE 212  80  65
D1567V5, multiclass
    clus
vv   IPPK MUTATED IPPK WILD-TYPE
  N0            8            212
  N1            0             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"
D1567V6, binary
                cls
clus               0   1
  IPPK MUTATED     8   0
  IPPK WILD-TYPE 275  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  IPPK MUTATED      8    0
  IPPK WILD-TYPE  275   48
   clus
vv  IPPK MUTATED IPPK WILD-TYPE
  0            8            275
  1            0             48
[1] 2 2
[1] FALSE
D1567V7, 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
D1567V8, binary
                cls
clus               0   1
  IPPK MUTATED     7   2
  IPPK WILD-TYPE 310  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  IPPK MUTATED      7    2
  IPPK WILD-TYPE  310   46
                               clus
vv                              IPPK MUTATED IPPK WILD-TYPE
  COLON ADENOCARCINOMA                     7            310
  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 251   2  22  20
D1567V9, multiclass
    clus
vv   IPPK MUTATED IPPK WILD-TYPE
  R0            6            251
  R1            0              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"
D1567V10, 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
D1567V11, 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(1568) Variable = SLC38A9 MUTATION ANALYSIS
D1568V1, survival
                   sevent
clus2                 0   1
  SLC38A9 MUTATED    10   0
  SLC38A9 WILD-TYPE 272  73
  SLC38A9 MUTATED SLC38A9 WILD-TYPE 
               10               345 
  SLC38A9 MUTATED SLC38A9 WILD-TYPE 
                0                73 
$`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 
        0.10        23.05        37.02        11.64 

$`SLC38A9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.33         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
       21.99        21.14         2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  SLC38A9 MUTATED SLC38A9 WILD-TYPE 
              0.1               0.0 
  SLC38A9 MUTATED SLC38A9 WILD-TYPE 
            58.39            140.38 
  SLC38A9 MUTATED SLC38A9 WILD-TYPE 
            25.07             20.02 
[1] "0.1 - 58.4 (25.1)"  "0.0 - 140.4 (20.0)"
[1] "hr="     "2.5e+07"
D1568V2, 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       23       102         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC38A9 MUTATED           0          0          0          0        0
  SLC38A9 WILD-TYPE        19         10         41         31       35
                   vv
clus                STAGE IVA STAGE IVB
  SLC38A9 MUTATED           0         0
  SLC38A9 WILD-TYPE        13         1
D1568V3, multiclass
            clus
vv           SLC38A9 MUTATED SLC38A9 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 2                23
  STAGE IIA                7               102
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC38A9 MUTATED     0   2   9   0
  SLC38A9 WILD-TYPE   9  66 239  41
D1568V4, multiclass
    clus
vv   SLC38A9 MUTATED SLC38A9 WILD-TYPE
  T1               0                 9
  T2               2                66
  T3               9               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
  SLC38A9 MUTATED    11   0   0
  SLC38A9 WILD-TYPE 209  80  66
D1568V5, multiclass
    clus
vv   SLC38A9 MUTATED SLC38A9 WILD-TYPE
  N0              11               209
  N1               0                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"
D1568V6, binary
                   cls
clus                  0   1
  SLC38A9 MUTATED    11   0
  SLC38A9 WILD-TYPE 272  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC38A9 MUTATED     11    0
  SLC38A9 WILD-TYPE  272   48
   clus
vv  SLC38A9 MUTATED SLC38A9 WILD-TYPE
  0              11               272
  1               0                48
[1] 2 2
[1] FALSE
D1568V7, 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
D1568V8, binary
                   cls
clus                  0   1
  SLC38A9 MUTATED    10   1
  SLC38A9 WILD-TYPE 307  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC38A9 MUTATED     10    1
  SLC38A9 WILD-TYPE  307   47
                               clus
vv                              SLC38A9 MUTATED SLC38A9 WILD-TYPE
  COLON ADENOCARCINOMA                       10               307
  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 247   2  22  20
D1568V9, multiclass
    clus
vv   SLC38A9 MUTATED SLC38A9 WILD-TYPE
  R0              10               247
  R1               0                 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"
D1568V10, 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
D1568V11, 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(1569) Variable = HIST1H3B MUTATION ANALYSIS
D1569V1, survival
                    sevent
clus2                  0   1
  HIST1H3B MUTATED     1   3
  HIST1H3B WILD-TYPE 281  70
  HIST1H3B MUTATED HIST1H3B WILD-TYPE 
                 4                351 
  HIST1H3B MUTATED HIST1H3B WILD-TYPE 
                 3                 70 
$`HIST1H3B MUTATED`
TCGA-AA-3492 TCGA-AA-A00J TCGA-CK-5916 TCGA-DM-A1DB 
        3.02        18.05        21.14        44.32 

$`HIST1H3B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32        12.59       140.38         7.50       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  HIST1H3B MUTATED HIST1H3B WILD-TYPE 
              3.02               0.00 
  HIST1H3B MUTATED HIST1H3B WILD-TYPE 
             44.32             140.38 
  HIST1H3B MUTATED HIST1H3B WILD-TYPE 
            19.595             20.190 
[1] "3.0 - 44.3 (19.6)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "4.3"
D1569V2, 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       24       108         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HIST1H3B MUTATED           0          0          1          0        0
  HIST1H3B WILD-TYPE        19         10         40         31       35
                    vv
clus                 STAGE IVA STAGE IVB
  HIST1H3B MUTATED           0         0
  HIST1H3B WILD-TYPE        13         1
D1569V3, multiclass
            clus
vv           HIST1H3B MUTATED HIST1H3B WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  1                 24
  STAGE IIA                 1                108
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                0                 10
  STAGE IIIB                1                 40
  STAGE IIIC                0                 31
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  HIST1H3B MUTATED     1   0   2   1
  HIST1H3B WILD-TYPE   8  68 246  40
D1569V4, multiclass
    clus
vv   HIST1H3B MUTATED HIST1H3B WILD-TYPE
  T1                1                  8
  T2                0                 68
  T3                2                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
  HIST1H3B MUTATED     3   1   0
  HIST1H3B WILD-TYPE 217  79  66
D1569V5, multiclass
    clus
vv   HIST1H3B MUTATED HIST1H3B WILD-TYPE
  N0                3                217
  N1                1                 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"
D1569V6, binary
                    cls
clus                   0   1
  HIST1H3B MUTATED     4   0
  HIST1H3B WILD-TYPE 279  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H3B MUTATED      4    0
  HIST1H3B WILD-TYPE  279   48
   clus
vv  HIST1H3B MUTATED HIST1H3B WILD-TYPE
  0                4                279
  1                0                 48
[1] 2 2
[1] FALSE
D1569V7, 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
D1569V8, binary
                    cls
clus                   0   1
  HIST1H3B MUTATED     3   1
  HIST1H3B WILD-TYPE 314  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H3B MUTATED      3    1
  HIST1H3B WILD-TYPE  314   47
                               clus
vv                              HIST1H3B MUTATED HIST1H3B WILD-TYPE
  COLON ADENOCARCINOMA                         3                314
  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 255   2  22  20
D1569V9, multiclass
    clus
vv   HIST1H3B MUTATED HIST1H3B WILD-TYPE
  R0                2                255
  R1                0                  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"
D1569V10, 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
D1569V11, multiclass
[1] "Remove cluster labels:" "HIST1H3B MUTATED"      
clus
  HIST1H3B MUTATED HIST1H3B WILD-TYPE 
                 2                204 
        TCGA-A6-2671         TCGA-A6-2672         TCGA-A6-2674 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-A6-2676         TCGA-A6-2677         TCGA-A6-2678 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-A6-2683         TCGA-A6-3807         TCGA-A6-3808 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-A6-3809         TCGA-A6-3810         TCGA-A6-4105 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-A6-5656         TCGA-A6-5657         TCGA-A6-5659 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-A6-5660         TCGA-A6-5661         TCGA-A6-5662 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-A6-5664         TCGA-A6-5665         TCGA-A6-5666 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-A6-6137         TCGA-A6-6138         TCGA-A6-6141 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-A6-6142         TCGA-A6-6648         TCGA-A6-6649 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-A6-6651         TCGA-A6-6652         TCGA-A6-6653 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-A6-6654         TCGA-A6-6780         TCGA-A6-6781 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-A6-6782         TCGA-AD-5900         TCGA-AD-6548 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-AD-6888         TCGA-AD-6889         TCGA-AD-6890 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-AD-6895         TCGA-AD-6899         TCGA-AD-6901 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-AD-6963         TCGA-AD-6964         TCGA-AD-6965 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-AU-3779         TCGA-AU-6004         TCGA-AY-4070 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-AY-4071         TCGA-AY-5543         TCGA-AY-6196 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-AY-6197         TCGA-AY-6386         TCGA-AZ-4315 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-AZ-4323         TCGA-AZ-4616         TCGA-AZ-4681 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-AZ-4682         TCGA-AZ-5403         TCGA-AZ-5407 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-AZ-6598         TCGA-AZ-6599         TCGA-AZ-6600 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-AZ-6601         TCGA-AZ-6603         TCGA-AZ-6605 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-AZ-6606         TCGA-AZ-6607         TCGA-AZ-6608 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CA-5254         TCGA-CA-5255         TCGA-CA-5796 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CA-5797         TCGA-CA-6715         TCGA-CA-6716 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CA-6717         TCGA-CA-6718         TCGA-CA-6719 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CK-4947         TCGA-CK-4948         TCGA-CK-4950 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CK-4952         TCGA-CK-5912         TCGA-CK-5913 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CK-5914         TCGA-CK-5915         TCGA-CK-6746 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CK-6747         TCGA-CK-6748         TCGA-CK-6751 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CM-4743         TCGA-CM-4744         TCGA-CM-4746 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CM-4747         TCGA-CM-4752         TCGA-CM-5341 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CM-5344         TCGA-CM-5348         TCGA-CM-5349 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CM-5860         TCGA-CM-5861         TCGA-CM-5862 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CM-5863         TCGA-CM-5864         TCGA-CM-5868 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CM-6161         TCGA-CM-6162         TCGA-CM-6163 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CM-6164         TCGA-CM-6165         TCGA-CM-6166 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CM-6167         TCGA-CM-6168         TCGA-CM-6169 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CM-6170         TCGA-CM-6171         TCGA-CM-6172 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CM-6674         TCGA-CM-6675         TCGA-CM-6676 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CM-6677         TCGA-CM-6678         TCGA-CM-6679 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CM-6680         TCGA-D5-5537         TCGA-D5-5538 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-D5-5539         TCGA-D5-5540         TCGA-D5-5541 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-D5-6529         TCGA-D5-6532         TCGA-D5-6533 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-D5-6534         TCGA-D5-6535         TCGA-D5-6536 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-D5-6537         TCGA-D5-6538         TCGA-D5-6539 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-D5-6540         TCGA-D5-6541         TCGA-D5-6898 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-D5-6920         TCGA-D5-6922         TCGA-D5-6923 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-D5-6924         TCGA-D5-6926         TCGA-D5-6927 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-D5-6928         TCGA-D5-6929         TCGA-D5-6930 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-D5-6931         TCGA-D5-6932         TCGA-D5-7000 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-DM-A0X9         TCGA-DM-A0XD         TCGA-DM-A0XF 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-DM-A1D0         TCGA-DM-A1D4         TCGA-DM-A1D6 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-DM-A1D7         TCGA-DM-A1D8         TCGA-DM-A1D9 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-DM-A1DA         TCGA-DM-A1HA         TCGA-DM-A1HB 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-DM-A282         TCGA-DM-A285         TCGA-DM-A28C 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-DM-A28E         TCGA-DM-A28F         TCGA-DM-A28G 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-DM-A28H         TCGA-DM-A28K         TCGA-F4-6459 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-F4-6460         TCGA-F4-6569         TCGA-F4-6570 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-F4-6703         TCGA-F4-6704         TCGA-F4-6805 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-F4-6806         TCGA-F4-6807         TCGA-F4-6808 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-F4-6809         TCGA-F4-6854         TCGA-F4-6855 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-F4-6856         TCGA-G4-6293         TCGA-G4-6299 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-G4-6303         TCGA-G4-6304         TCGA-G4-6306 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-G4-6307         TCGA-G4-6309         TCGA-G4-6310 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-G4-6315         TCGA-G4-6317         TCGA-G4-6321 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-G4-6323         TCGA-G4-6586         TCGA-G4-6588 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-G4-6625         TCGA-G4-6626         TCGA-G4-6628 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 

Clustering(1570) Variable = PRKD1 MUTATION ANALYSIS
D1570V1, survival
                 sevent
clus2               0   1
  PRKD1 MUTATED    19   4
  PRKD1 WILD-TYPE 263  69
  PRKD1 MUTATED PRKD1 WILD-TYPE 
             23             332 
  PRKD1 MUTATED PRKD1 WILD-TYPE 
              4              69 
$`PRKD1 MUTATED`
TCGA-AA-3510 TCGA-AA-3655 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3821 TCGA-AA-3845 
       63.98        61.02        26.99        19.04         1.02         0.00 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-A010 TCGA-AA-A02J TCGA-AD-5900 TCGA-AZ-4315 
       34.06        25.02        34.98         5.03         0.07        58.39 
TCGA-AZ-6599 TCGA-AZ-6605 TCGA-CA-6717 TCGA-CM-5861 TCGA-CM-5864 TCGA-D5-6533 
        6.77         5.23         0.33        15.02        15.02         1.32 
TCGA-D5-6534 TCGA-D5-6538 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6628 
       43.27        17.13        35.41       107.67        52.80 

$`PRKD1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.03        85.05        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
        0.99        25.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       14.93        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       16.08        50.99        13.05        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        2.01        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 
       61.41        49.41        12.10       100.01        29.56        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01         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 
       12.26        19.59        13.51        11.51        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6299 
       16.24        33.67        13.25         0.53        19.43        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 
       91.79        46.75 

  PRKD1 MUTATED PRKD1 WILD-TYPE 
              0               0 
  PRKD1 MUTATED PRKD1 WILD-TYPE 
         107.67          140.38 
  PRKD1 MUTATED PRKD1 WILD-TYPE 
         19.040          20.235 
[1] "0.0 - 107.7 (19.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.3"
D1570V2, 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       23       101         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PRKD1 MUTATED           1          0          3          0        2         0
  PRKD1 WILD-TYPE        18         10         38         31       33        13
                 vv
clus              STAGE IVB
  PRKD1 MUTATED           0
  PRKD1 WILD-TYPE         1
D1570V3, multiclass
            clus
vv           PRKD1 MUTATED PRKD1 WILD-TYPE
  STAGE I                6              58
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              8             101
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             3              38
  STAGE IIIC             0              31
  STAGE IV               2              33
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PRKD1 MUTATED     0   7  14   3
  PRKD1 WILD-TYPE   9  61 234  38
D1570V4, multiclass
    clus
vv   PRKD1 MUTATED PRKD1 WILD-TYPE
  T1             0               9
  T2             7              61
  T3            14             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
  PRKD1 MUTATED    21   2   1
  PRKD1 WILD-TYPE 199  78  65
D1570V5, multiclass
    clus
vv   PRKD1 MUTATED PRKD1 WILD-TYPE
  N0            21             199
  N1             2              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"
D1570V6, binary
                 cls
clus                0   1
  PRKD1 MUTATED    19   2
  PRKD1 WILD-TYPE 264  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKD1 MUTATED     19    2
  PRKD1 WILD-TYPE  264   46
   clus
vv  PRKD1 MUTATED PRKD1 WILD-TYPE
  0            19             264
  1             2              46
[1] 2 2
[1] FALSE
D1570V7, 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
D1570V8, binary
                 cls
clus                0   1
  PRKD1 MUTATED    20   4
  PRKD1 WILD-TYPE 297  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKD1 MUTATED     20    4
  PRKD1 WILD-TYPE  297   44
                               clus
vv                              PRKD1 MUTATED PRKD1 WILD-TYPE
  COLON ADENOCARCINOMA                     20             297
  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 239   2  20  20
D1570V9, multiclass
    clus
vv   PRKD1 MUTATED PRKD1 WILD-TYPE
  R0            18             239
  R1             0               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"
D1570V10, 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
D1570V11, 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(1571) Variable = IL34 MUTATION ANALYSIS
D1571V1, survival
                sevent
clus2              0   1
  IL34 MUTATED     2   1
  IL34 WILD-TYPE 280  72
  IL34 MUTATED IL34 WILD-TYPE 
             3            352 
  IL34 MUTATED IL34 WILD-TYPE 
             1             72 
$`IL34 MUTATED`
TCGA-AA-3710 TCGA-AZ-6601 TCGA-CM-4743 
       26.99       100.01        23.05 

$`IL34 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14         2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  IL34 MUTATED IL34 WILD-TYPE 
         23.05           0.00 
  IL34 MUTATED IL34 WILD-TYPE 
        100.01         140.38 
  IL34 MUTATED IL34 WILD-TYPE 
         26.99          20.07 
[1] "23.1 - 100.0 (27.0)" "0.0 - 140.4 (20.1)" 
[1] "hr=" "1.2"
D1571V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IL34 MUTATED         0        0        1         2         0         0
  IL34 WILD-TYPE      64        1       24       107         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IL34 MUTATED           0          0          0          0        0         0
  IL34 WILD-TYPE        19         10         41         31       35        13
                vv
clus             STAGE IVB
  IL34 MUTATED           0
  IL34 WILD-TYPE         1
D1571V3, multiclass
            clus
vv           IL34 MUTATED IL34 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             2            107
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  IL34 MUTATED     0   0   3   0
  IL34 WILD-TYPE   9  68 245  41
D1571V4, multiclass
    clus
vv   IL34 MUTATED IL34 WILD-TYPE
  T1            0              9
  T2            0             68
  T3            3            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
  IL34 MUTATED     3   0   0
  IL34 WILD-TYPE 217  80  66
D1571V5, multiclass
    clus
vv   IL34 MUTATED IL34 WILD-TYPE
  N0            3            217
  N1            0             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"
D1571V6, binary
                cls
clus               0   1
  IL34 MUTATED     3   0
  IL34 WILD-TYPE 280  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  IL34 MUTATED      3    0
  IL34 WILD-TYPE  280   48
   clus
vv  IL34 MUTATED IL34 WILD-TYPE
  0            3            280
  1            0             48
[1] 2 2
[1] FALSE
D1571V7, binary
                cls
clus               0   1
  IL34 MUTATED     1   2
  IL34 WILD-TYPE 169 195
[1] "tbl2"
                cls
clus             [,1] [,2]
  IL34 MUTATED      1    2
  IL34 WILD-TYPE  169  195
        clus
vv       IL34 MUTATED IL34 WILD-TYPE
  FEMALE            1            169
  MALE              2            195
[1] 2 2
[1] FALSE
D1571V8, binary
                cls
clus               0   1
  IL34 MUTATED     3   0
  IL34 WILD-TYPE 314  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  IL34 MUTATED      3    0
  IL34 WILD-TYPE  314   48
                               clus
vv                              IL34 MUTATED IL34 WILD-TYPE
  COLON ADENOCARCINOMA                     3            314
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  IL34 MUTATED     2   0   0   0
  IL34 WILD-TYPE 255   2  22  21
D1571V9, multiclass
[1] "Remove cluster labels:" "IL34 MUTATED"          
clus
  IL34 MUTATED IL34 WILD-TYPE 
             2            300 
    TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810     TCGA-A6-5657 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-A6-5659     TCGA-A6-5661     TCGA-A6-5665     TCGA-A6-6781 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-AA-3489     TCGA-AA-3492     TCGA-AA-3496     TCGA-AA-3502 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-AA-3510     TCGA-AA-3511     TCGA-AA-3514     TCGA-AA-3517 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-AA-3518     TCGA-AA-3519     TCGA-AA-3520     TCGA-AA-3521 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-AA-3522     TCGA-AA-3524     TCGA-AA-3525     TCGA-AA-3526 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-AA-3527     TCGA-AA-3529     TCGA-AA-3530     TCGA-AA-3531 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-AA-3532     TCGA-AA-3534     TCGA-AA-3538     TCGA-AA-3542 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-AA-3543     TCGA-AA-3544     TCGA-AA-3548     TCGA-AA-3549 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-AA-3552     TCGA-AA-3553     TCGA-AA-3554     TCGA-AA-3555 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-AA-3556     TCGA-AA-3558     TCGA-AA-3560     TCGA-AA-3561 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-AA-3562     TCGA-AA-3655     TCGA-AA-3660     TCGA-AA-3662 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-AA-3663     TCGA-AA-3664     TCGA-AA-3666     TCGA-AA-3667 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-AA-3672     TCGA-AA-3673     TCGA-AA-3678     TCGA-AA-3679 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-AA-3680     TCGA-AA-3681     TCGA-AA-3684     TCGA-AA-3685 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-AA-3688     TCGA-AA-3692     TCGA-AA-3693     TCGA-AA-3695 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-AA-3696     TCGA-AA-3697     TCGA-AA-3712     TCGA-AA-3713 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-AA-3715     TCGA-AA-3811     TCGA-AA-3812     TCGA-AA-3814 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-AA-3815     TCGA-AA-3818     TCGA-AA-3819     TCGA-AA-3821 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-AA-3831     TCGA-AA-3833     TCGA-AA-3837     TCGA-AA-3842 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-AA-3844     TCGA-AA-3845     TCGA-AA-3846     TCGA-AA-3848 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-AA-3850     TCGA-AA-3851     TCGA-AA-3852     TCGA-AA-3854 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-AA-3855     TCGA-AA-3856     TCGA-AA-3858     TCGA-AA-3860 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-AA-3861     TCGA-AA-3864     TCGA-AA-3866     TCGA-AA-3867 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-AA-3869     TCGA-AA-3870     TCGA-AA-3872     TCGA-AA-3875 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-AA-3877     TCGA-AA-3930     TCGA-AA-3939     TCGA-AA-3941 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-AA-3947     TCGA-AA-3949     TCGA-AA-3950     TCGA-AA-3952 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-AA-3955     TCGA-AA-3956     TCGA-AA-3968     TCGA-AA-3971 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-AA-3972     TCGA-AA-3973     TCGA-AA-3975     TCGA-AA-3976 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-AA-3979     TCGA-AA-3984     TCGA-AA-3986     TCGA-AA-3989 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-AA-3994     TCGA-AA-A004     TCGA-AA-A00A     TCGA-AA-A00D 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-AA-A00E     TCGA-AA-A00F     TCGA-AA-A00J     TCGA-AA-A00K 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-AA-A00L     TCGA-AA-A00N     TCGA-AA-A00O     TCGA-AA-A00Q 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-AA-A00R     TCGA-AA-A00U     TCGA-AA-A00W     TCGA-AA-A00Z 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-AA-A010     TCGA-AA-A017     TCGA-AA-A01D     TCGA-AA-A01F 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-AA-A01G     TCGA-AA-A01I     TCGA-AA-A01K     TCGA-AA-A01P 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-AA-A01Q     TCGA-AA-A01R     TCGA-AA-A01S     TCGA-AA-A01T 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-AA-A01V     TCGA-AA-A01X     TCGA-AA-A01Z     TCGA-AA-A022 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-AA-A024     TCGA-AA-A029     TCGA-AA-A02F     TCGA-AA-A02H 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-AA-A02J     TCGA-AA-A02K     TCGA-AA-A02O     TCGA-AA-A02W 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-AA-A02Y     TCGA-AA-A03F     TCGA-AA-A03J     TCGA-AD-5900 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-AD-6548     TCGA-AD-6888     TCGA-AU-3779     TCGA-AU-6004 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-AY-4070     TCGA-AY-4071     TCGA-AY-5543     TCGA-AY-6196 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-AY-6197     TCGA-AY-6386     TCGA-AZ-4315     TCGA-AZ-4681 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-AZ-4682     TCGA-CA-5254     TCGA-CA-5255     TCGA-CA-5796 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-CA-5797     TCGA-CA-6715     TCGA-CA-6716     TCGA-CA-6717 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-CA-6718     TCGA-CA-6719     TCGA-CK-4947     TCGA-CK-4948 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-CK-4950     TCGA-CK-4952     TCGA-CK-5912     TCGA-CK-5913 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-CK-5914     TCGA-CK-5915     TCGA-CK-5916     TCGA-CK-6746 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-CK-6747     TCGA-CK-6748     TCGA-CK-6751     TCGA-CM-4744 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-CM-4746     TCGA-CM-4747     TCGA-CM-4752     TCGA-CM-5341 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-CM-5344     TCGA-CM-5348     TCGA-CM-5349     TCGA-CM-5860 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-CM-5861     TCGA-CM-5862     TCGA-CM-5863     TCGA-CM-5864 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-CM-5868     TCGA-CM-6161     TCGA-CM-6162     TCGA-CM-6163 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-CM-6164     TCGA-CM-6165     TCGA-CM-6166     TCGA-CM-6167 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-CM-6168     TCGA-CM-6169     TCGA-CM-6170     TCGA-CM-6171 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-CM-6172     TCGA-CM-6674     TCGA-CM-6675     TCGA-CM-6676 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-CM-6677     TCGA-CM-6678     TCGA-CM-6679     TCGA-CM-6680 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-D5-5537     TCGA-D5-5538     TCGA-D5-5539     TCGA-D5-5540 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-D5-5541     TCGA-D5-6529     TCGA-D5-6532     TCGA-D5-6533 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-D5-6534     TCGA-D5-6535     TCGA-D5-6536     TCGA-D5-6537 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-D5-6538     TCGA-D5-6539     TCGA-D5-6540     TCGA-D5-6541 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-D5-6898     TCGA-D5-6920     TCGA-D5-6922     TCGA-D5-6923 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-D5-6924     TCGA-D5-6926     TCGA-D5-6927     TCGA-D5-6928 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-D5-6929     TCGA-D5-6930     TCGA-D5-6931     TCGA-D5-6932 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-D5-7000     TCGA-F4-6459     TCGA-F4-6460     TCGA-F4-6569 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-F4-6570     TCGA-F4-6703     TCGA-F4-6704     TCGA-F4-6805 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-F4-6806     TCGA-F4-6807     TCGA-F4-6808     TCGA-F4-6809 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-F4-6854     TCGA-F4-6855     TCGA-F4-6856     TCGA-G4-6293 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-G4-6299     TCGA-G4-6303     TCGA-G4-6304     TCGA-G4-6306 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-G4-6307     TCGA-G4-6309     TCGA-G4-6310     TCGA-G4-6315 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-G4-6317     TCGA-G4-6321     TCGA-G4-6323     TCGA-G4-6586 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-G4-6588     TCGA-G4-6625     TCGA-G4-6626     TCGA-G4-6628 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
D1571V10, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IL34 MUTATED                                  0     0
  IL34 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  IL34 MUTATED                           0     2
  IL34 WILD-TYPE                        19   174
D1571V11, multiclass
[1] "Remove cluster labels:" "IL34 MUTATED"          
clus
  IL34 MUTATED IL34 WILD-TYPE 
             2            204 
    TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810     TCGA-A6-4105 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-A6-5656     TCGA-A6-5657     TCGA-A6-5659     TCGA-A6-5660 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-A6-5661     TCGA-A6-5662     TCGA-A6-5664     TCGA-A6-5665 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-A6-5666     TCGA-A6-6137     TCGA-A6-6138     TCGA-A6-6141 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-A6-6142     TCGA-A6-6648     TCGA-A6-6649     TCGA-A6-6651 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-A6-6652     TCGA-A6-6653     TCGA-A6-6654     TCGA-A6-6780 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-A6-6781     TCGA-A6-6782     TCGA-AD-5900     TCGA-AD-6548 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-AD-6888     TCGA-AD-6889     TCGA-AD-6890     TCGA-AD-6895 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-AD-6899     TCGA-AD-6901     TCGA-AD-6963     TCGA-AD-6964 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-AD-6965     TCGA-AU-3779     TCGA-AU-6004     TCGA-AY-4070 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-AY-4071     TCGA-AY-5543     TCGA-AY-6196     TCGA-AY-6197 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-AY-6386     TCGA-AZ-4315     TCGA-AZ-4323     TCGA-AZ-4616 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-AZ-4681     TCGA-AZ-4682     TCGA-AZ-5403     TCGA-AZ-5407 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-AZ-6598     TCGA-AZ-6599     TCGA-AZ-6600     TCGA-AZ-6603 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-AZ-6605     TCGA-AZ-6606     TCGA-AZ-6607     TCGA-AZ-6608 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-CA-5254     TCGA-CA-5255     TCGA-CA-5796     TCGA-CA-5797 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-CA-6715     TCGA-CA-6716     TCGA-CA-6717     TCGA-CA-6718 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-CA-6719     TCGA-CK-4947     TCGA-CK-4948     TCGA-CK-4950 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-CK-4952     TCGA-CK-5912     TCGA-CK-5913     TCGA-CK-5914 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-CK-5915     TCGA-CK-5916     TCGA-CK-6746     TCGA-CK-6747 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-CK-6748     TCGA-CK-6751     TCGA-CM-4744     TCGA-CM-4746 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-CM-4747     TCGA-CM-4752     TCGA-CM-5341     TCGA-CM-5344 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-CM-5348     TCGA-CM-5349     TCGA-CM-5860     TCGA-CM-5861 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-CM-5862     TCGA-CM-5863     TCGA-CM-5864     TCGA-CM-5868 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-CM-6161     TCGA-CM-6162     TCGA-CM-6163     TCGA-CM-6164 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-CM-6165     TCGA-CM-6166     TCGA-CM-6167     TCGA-CM-6168 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-CM-6169     TCGA-CM-6170     TCGA-CM-6171     TCGA-CM-6172 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-CM-6674     TCGA-CM-6675     TCGA-CM-6676     TCGA-CM-6677 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-CM-6678     TCGA-CM-6679     TCGA-CM-6680     TCGA-D5-5537 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-D5-5538     TCGA-D5-5539     TCGA-D5-5540     TCGA-D5-5541 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-D5-6529     TCGA-D5-6532     TCGA-D5-6533     TCGA-D5-6534 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-D5-6535     TCGA-D5-6536     TCGA-D5-6537     TCGA-D5-6538 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-D5-6539     TCGA-D5-6540     TCGA-D5-6541     TCGA-D5-6898 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-D5-6920     TCGA-D5-6922     TCGA-D5-6923     TCGA-D5-6924 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-D5-6926     TCGA-D5-6927     TCGA-D5-6928     TCGA-D5-6929 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-D5-6930     TCGA-D5-6931     TCGA-D5-6932     TCGA-D5-7000 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-DM-A0X9     TCGA-DM-A0XD     TCGA-DM-A0XF     TCGA-DM-A1D0 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-DM-A1D4     TCGA-DM-A1D6     TCGA-DM-A1D7     TCGA-DM-A1D8 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-DM-A1D9     TCGA-DM-A1DA     TCGA-DM-A1DB     TCGA-DM-A1HA 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-DM-A1HB     TCGA-DM-A282     TCGA-DM-A285     TCGA-DM-A28C 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-DM-A28E     TCGA-DM-A28F     TCGA-DM-A28G     TCGA-DM-A28H 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-DM-A28K     TCGA-F4-6459     TCGA-F4-6460     TCGA-F4-6569 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-F4-6570     TCGA-F4-6703     TCGA-F4-6704     TCGA-F4-6805 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-F4-6806     TCGA-F4-6807     TCGA-F4-6808     TCGA-F4-6809 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-F4-6854     TCGA-F4-6855     TCGA-F4-6856     TCGA-G4-6293 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-G4-6299     TCGA-G4-6303     TCGA-G4-6304     TCGA-G4-6306 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-G4-6307     TCGA-G4-6309     TCGA-G4-6310     TCGA-G4-6315 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-G4-6317     TCGA-G4-6321     TCGA-G4-6323     TCGA-G4-6586 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 
    TCGA-G4-6588     TCGA-G4-6625     TCGA-G4-6626     TCGA-G4-6628 
"IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" "IL34 WILD-TYPE" 

Clustering(1572) Variable = YIF1A MUTATION ANALYSIS
D1572V1, survival
                 sevent
clus2               0   1
  YIF1A MUTATED     4   3
  YIF1A WILD-TYPE 278  70
  YIF1A MUTATED YIF1A WILD-TYPE 
              7             348 
  YIF1A MUTATED YIF1A WILD-TYPE 
              3              70 
$`YIF1A MUTATED`
TCGA-A6-5665 TCGA-A6-6653 TCGA-AA-3492 TCGA-AA-3663 TCGA-AZ-6601 TCGA-F4-6570 
       22.06        24.39         3.02         6.97       100.01         6.18 
TCGA-G4-6588 
       26.17 

$`YIF1A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        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        13.38        13.45        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        52.80 

  YIF1A MUTATED YIF1A WILD-TYPE 
           3.02            0.00 
  YIF1A MUTATED YIF1A WILD-TYPE 
         100.01          140.38 
  YIF1A MUTATED YIF1A WILD-TYPE 
         22.060          20.155 
[1] "3.0 - 100.0 (22.1)" "0.0 - 140.4 (20.2)"
[1] "hr=" "2"  
D1572V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  YIF1A MUTATED         1        0        3         3         0         0
  YIF1A WILD-TYPE      63        1       22       106         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  YIF1A MUTATED           0          0          0          0        0         0
  YIF1A WILD-TYPE        19         10         41         31       35        13
                 vv
clus              STAGE IVB
  YIF1A MUTATED           0
  YIF1A WILD-TYPE         1
D1572V3, multiclass
            clus
vv           YIF1A MUTATED YIF1A WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              3             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  YIF1A MUTATED     0   1   6   0
  YIF1A WILD-TYPE   9  67 242  41
D1572V4, multiclass
    clus
vv   YIF1A MUTATED YIF1A WILD-TYPE
  T1             0               9
  T2             1              67
  T3             6             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
  YIF1A MUTATED     7   0   0
  YIF1A WILD-TYPE 213  80  66
D1572V5, multiclass
    clus
vv   YIF1A MUTATED YIF1A WILD-TYPE
  N0             7             213
  N1             0              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"
D1572V6, binary
                 cls
clus                0   1
  YIF1A MUTATED     7   0
  YIF1A WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YIF1A MUTATED      7    0
  YIF1A WILD-TYPE  276   48
   clus
vv  YIF1A MUTATED YIF1A WILD-TYPE
  0             7             276
  1             0              48
[1] 2 2
[1] FALSE
D1572V7, binary
                 cls
clus                0   1
  YIF1A MUTATED     4   3
  YIF1A WILD-TYPE 166 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YIF1A MUTATED      4    3
  YIF1A WILD-TYPE  166  194
        clus
vv       YIF1A MUTATED YIF1A WILD-TYPE
  FEMALE             4             166
  MALE               3             194
[1] 2 2
[1] FALSE
D1572V8, binary
                 cls
clus                0   1
  YIF1A MUTATED     7   0
  YIF1A WILD-TYPE 310  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YIF1A MUTATED      7    0
  YIF1A WILD-TYPE  310   48
                               clus
vv                              YIF1A MUTATED YIF1A WILD-TYPE
  COLON ADENOCARCINOMA                      7             310
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  YIF1A MUTATED     5   0   0   0
  YIF1A WILD-TYPE 252   2  22  21
D1572V9, multiclass
    clus
vv   YIF1A MUTATED YIF1A WILD-TYPE
  R0             5             252
  R1             0               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"
D1572V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  YIF1A MUTATED                                  0     0
  YIF1A WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  YIF1A MUTATED                           0     5
  YIF1A WILD-TYPE                        19   171
D1572V11, multiclass
                                  clus
vv                                 YIF1A MUTATED YIF1A 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(1573) Variable = LCK MUTATION ANALYSIS
D1573V1, survival
               sevent
clus2             0   1
  LCK MUTATED     6   1
  LCK WILD-TYPE 276  72
  LCK MUTATED LCK WILD-TYPE 
            7           348 
  LCK MUTATED LCK WILD-TYPE 
            1            72 
$`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 
       35.87 

$`LCK WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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-D5-5537 
       12.95        13.05        11.08        11.08        10.06        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 
        8.61        13.38        13.45         6.18         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  LCK MUTATED LCK WILD-TYPE 
        11.01          0.00 
  LCK MUTATED LCK WILD-TYPE 
       140.38        139.17 
  LCK MUTATED LCK WILD-TYPE 
       21.440        20.155 
[1] "11.0 - 140.4 (21.4)" "0.0 - 139.2 (20.2)" 
[1] "hr=" "1.9"
D1573V2, 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       25       105         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        19         10         40         30       35        12
               vv
clus            STAGE IVB
  LCK MUTATED           0
  LCK WILD-TYPE         1
D1573V3, multiclass
            clus
vv           LCK MUTATED LCK WILD-TYPE
  STAGE I              0            64
  STAGE IA             0             1
  STAGE II             0            25
  STAGE IIA            4           105
  STAGE IIB            1             7
  STAGE IIC            0             1
  STAGE III            0            19
  STAGE IIIA           0            10
  STAGE IIIB           1            40
  STAGE IIIC           1            30
  STAGE IV             0            35
  STAGE IVA            1            12
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of 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  68 243  38
D1573V4, multiclass
    clus
vv   LCK MUTATED LCK WILD-TYPE
  T1           0             9
  T2           0            68
  T3           5           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
  LCK MUTATED     5   2   1
  LCK WILD-TYPE 215  78  65
D1573V5, multiclass
    clus
vv   LCK MUTATED LCK WILD-TYPE
  N0           5           215
  N1           2            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"
D1573V6, binary
               cls
clus              0   1
  LCK MUTATED     5   1
  LCK WILD-TYPE 278  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  LCK MUTATED      5    1
  LCK WILD-TYPE  278   47
   clus
vv  LCK MUTATED LCK WILD-TYPE
  0           5           278
  1           1            47
[1] 2 2
[1] FALSE
D1573V7, 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
D1573V8, binary
               cls
clus              0   1
  LCK MUTATED     7   1
  LCK WILD-TYPE 310  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  LCK MUTATED      7    1
  LCK WILD-TYPE  310   47
                               clus
vv                              LCK MUTATED LCK WILD-TYPE
  COLON ADENOCARCINOMA                    7           310
  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 250   2  22  21
D1573V9, multiclass
    clus
vv   LCK MUTATED LCK WILD-TYPE
  R0           7           250
  R1           0             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"
D1573V10, 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
D1573V11, 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(1574) Variable = ANK3 MUTATION ANALYSIS
D1574V1, survival
                sevent
clus2              0   1
  ANK3 MUTATED    37   9
  ANK3 WILD-TYPE 245  64
  ANK3 MUTATED ANK3 WILD-TYPE 
            46            309 
  ANK3 MUTATED ANK3 WILD-TYPE 
             9             64 
$`ANK3 MUTATED`
TCGA-A6-2677 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6141 TCGA-AA-3492 TCGA-AA-3496 
       24.33        33.53        22.06         8.38         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3525 TCGA-AA-3554 TCGA-AA-3663 
       35.01        63.98        13.02         8.05        17.95         6.97 
TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3950 TCGA-AA-3977 
        0.92        19.04        19.04        10.06        24.00        25.02 
TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A00U TCGA-AA-A010 TCGA-AA-A01P TCGA-AA-A01Q 
       18.05         4.01        17.03        34.98        38.07         1.02 
TCGA-AA-A01R TCGA-AD-5900 TCGA-AD-6889 TCGA-AU-3779 TCGA-AU-6004 TCGA-AZ-4315 
       35.01         0.07        56.55        14.50        27.09        58.39 
TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CK-6747 TCGA-CM-6168 TCGA-CM-6171 
       49.41       100.01         0.33         2.93        12.99        14.04 
TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6928 TCGA-DM-A1HB TCGA-F4-6703 TCGA-F4-6808 
       16.14        12.39        11.64       135.65        35.87        33.67 
TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6586 TCGA-G4-6628 
       53.62        51.75        35.80        52.80 

$`ANK3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        42.90        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       31.63        30.44        29.19        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 
       27.09        22.52        25.08        25.18        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        7.04         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       24.03        37.05        36.03        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3555 
       14.01        33.99        21.01        13.02        24.00        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       78.08         6.05        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3815 
       36.00         5.03        85.05        26.99        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A00Z 
       38.04        27.02        42.02         0.99        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37         4.21 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
        0.20        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       61.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 
        1.55        16.31        29.59        16.24        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 
       35.41        19.43       107.67        74.56        65.85        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       26.17        91.79        46.75 

  ANK3 MUTATED ANK3 WILD-TYPE 
          0.07           0.00 
  ANK3 MUTATED ANK3 WILD-TYPE 
        135.65         140.38 
  ANK3 MUTATED ANK3 WILD-TYPE 
         19.04          20.28 
[1] "0.1 - 135.7 (19.0)" "0.0 - 140.4 (20.3)"
[1] "hr=" "1.1"
D1574V2, 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       17        92         5         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ANK3 MUTATED           6          0          5          1        1         0
  ANK3 WILD-TYPE        13         10         36         30       34        13
                vv
clus             STAGE IVB
  ANK3 MUTATED           0
  ANK3 WILD-TYPE         1
D1574V3, multiclass
            clus
vv           ANK3 MUTATED ANK3 WILD-TYPE
  STAGE I               7             57
  STAGE IA              0              1
  STAGE II              8             17
  STAGE IIA            17             92
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             6             13
  STAGE IIIA            0             10
  STAGE IIIB            5             36
  STAGE IIIC            1             30
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ANK3 MUTATED     1   7  37   4
  ANK3 WILD-TYPE   8  61 211  37
D1574V4, multiclass
    clus
vv   ANK3 MUTATED ANK3 WILD-TYPE
  T1            1              8
  T2            7             61
  T3           37            211
  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   7   5
  ANK3 WILD-TYPE 183  73  61
D1574V5, multiclass
    clus
vv   ANK3 MUTATED ANK3 WILD-TYPE
  N0           37            183
  N1            7             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"
D1574V6, binary
                cls
clus               0   1
  ANK3 MUTATED    44   1
  ANK3 WILD-TYPE 239  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  ANK3 MUTATED     44    1
  ANK3 WILD-TYPE  239   47
   clus
vv  ANK3 MUTATED ANK3 WILD-TYPE
  0           44            239
  1            1             47
[1] 2 2
[1] FALSE
D1574V7, binary
                cls
clus               0   1
  ANK3 MUTATED    26  23
  ANK3 WILD-TYPE 144 174
[1] "tbl2"
                cls
clus             [,1] [,2]
  ANK3 MUTATED     26   23
  ANK3 WILD-TYPE  144  174
        clus
vv       ANK3 MUTATED ANK3 WILD-TYPE
  FEMALE           26            144
  MALE             23            174
[1] 2 2
[1] FALSE
D1574V8, binary
                cls
clus               0   1
  ANK3 MUTATED    40   9
  ANK3 WILD-TYPE 277  39
[1] "tbl2"
                cls
clus             [,1] [,2]
  ANK3 MUTATED     40    9
  ANK3 WILD-TYPE  277   39
                               clus
vv                              ANK3 MUTATED ANK3 WILD-TYPE
  COLON ADENOCARCINOMA                    40            277
  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 218   2  21  19
D1574V9, multiclass
    clus
vv   ANK3 MUTATED ANK3 WILD-TYPE
  R0           39            218
  R1            0              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"
D1574V10, 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
D1574V11, 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(1575) Variable = CTNND1 MUTATION ANALYSIS
D1575V1, survival
                  sevent
clus2                0   1
  CTNND1 MUTATED    15   3
  CTNND1 WILD-TYPE 267  70
  CTNND1 MUTATED CTNND1 WILD-TYPE 
              18              337 
  CTNND1 MUTATED CTNND1 WILD-TYPE 
               3               70 
$`CTNND1 MUTATED`
TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3713 
       33.53        22.06        19.66        61.02         6.97        19.04 
TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-6895 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6601 
       34.98        35.01         0.72        58.39        49.41       100.01 
TCGA-CA-6717 TCGA-CM-4743 TCGA-CM-5864 TCGA-D5-6930 TCGA-DM-A1D7 TCGA-F4-6856 
        0.33        23.05        15.02         1.51        13.32        19.43 

$`CTNND1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       19.99        78.08         6.05        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       22.36        62.79        61.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
       21.99        21.14         2.93         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        16.01        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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-A1D8 
       24.43        38.20       130.65        92.75        49.91        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        35.41       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  CTNND1 MUTATED CTNND1 WILD-TYPE 
            0.33             0.00 
  CTNND1 MUTATED CTNND1 WILD-TYPE 
          100.01           140.38 
  CTNND1 MUTATED CTNND1 WILD-TYPE 
           20.86            20.19 
[1] "0.3 - 100.0 (20.9)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.4"
D1575V2, 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       21       101         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CTNND1 MUTATED           1          0          0          1        1
  CTNND1 WILD-TYPE        18         10         41         30       34
                  vv
clus               STAGE IVA STAGE IVB
  CTNND1 MUTATED           0         0
  CTNND1 WILD-TYPE        13         1
D1575V3, multiclass
            clus
vv           CTNND1 MUTATED CTNND1 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                4               21
  STAGE IIA               8              101
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              1               30
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CTNND1 MUTATED     0   2  15   2
  CTNND1 WILD-TYPE   9  66 233  39
D1575V4, multiclass
    clus
vv   CTNND1 MUTATED CTNND1 WILD-TYPE
  T1              0                9
  T2              2               66
  T3             15              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
  CTNND1 MUTATED    16   2   1
  CTNND1 WILD-TYPE 204  78  65
D1575V5, multiclass
    clus
vv   CTNND1 MUTATED CTNND1 WILD-TYPE
  N0             16              204
  N1              2               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"
D1575V6, binary
                  cls
clus                 0   1
  CTNND1 MUTATED    15   1
  CTNND1 WILD-TYPE 268  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNND1 MUTATED     15    1
  CTNND1 WILD-TYPE  268   47
   clus
vv  CTNND1 MUTATED CTNND1 WILD-TYPE
  0             15              268
  1              1               47
[1] 2 2
[1] FALSE
D1575V7, binary
                  cls
clus                 0   1
  CTNND1 MUTATED     5  14
  CTNND1 WILD-TYPE 165 183
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNND1 MUTATED      5   14
  CTNND1 WILD-TYPE  165  183
        clus
vv       CTNND1 MUTATED CTNND1 WILD-TYPE
  FEMALE              5              165
  MALE               14              183
[1] 2 2
[1] FALSE
D1575V8, binary
                  cls
clus                 0   1
  CTNND1 MUTATED    14   5
  CTNND1 WILD-TYPE 303  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNND1 MUTATED     14    5
  CTNND1 WILD-TYPE  303   43
                               clus
vv                              CTNND1 MUTATED CTNND1 WILD-TYPE
  COLON ADENOCARCINOMA                      14              303
  COLON MUCINOUS ADENOCARCINOMA              5               43
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CTNND1 MUTATED    13   0   1   1
  CTNND1 WILD-TYPE 244   2  21  20
D1575V9, multiclass
    clus
vv   CTNND1 MUTATED CTNND1 WILD-TYPE
  R0             13              244
  R1              0                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"
D1575V10, 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
D1575V11, 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(1576) Variable = MR1 MUTATION ANALYSIS
D1576V1, survival
               sevent
clus2             0   1
  MR1 MUTATED     5   0
  MR1 WILD-TYPE 277  73
  MR1 MUTATED MR1 WILD-TYPE 
            5           350 
  MR1 MUTATED MR1 WILD-TYPE 
            0            73 
$`MR1 MUTATED`
TCGA-A6-6782 TCGA-AA-3510 TCGA-AA-3977 TCGA-CA-6717 TCGA-CA-6718 
       20.28        63.98        25.02         0.33         0.10 

$`MR1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        19.66         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.26         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  MR1 MUTATED MR1 WILD-TYPE 
          0.1           0.0 
  MR1 MUTATED MR1 WILD-TYPE 
        63.98        140.38 
  MR1 MUTATED MR1 WILD-TYPE 
       20.280        20.155 
[1] "0.1 - 64.0 (20.3)"  "0.0 - 140.4 (20.2)"
[1] "hr="     "9100000"
D1576V2, 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       24       107         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        19         10         41         31       35        13
               vv
clus            STAGE IVB
  MR1 MUTATED           0
  MR1 WILD-TYPE         1
D1576V3, multiclass
            clus
vv           MR1 MUTATED MR1 WILD-TYPE
  STAGE I              0            64
  STAGE IA             0             1
  STAGE II             1            24
  STAGE IIA            2           107
  STAGE IIB            1             7
  STAGE IIC            0             1
  STAGE III            0            19
  STAGE IIIA           0            10
  STAGE IIIB           0            41
  STAGE IIIC           0            31
  STAGE IV             0            35
  STAGE IVA            0            13
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  MR1 MUTATED     0   1   3   1
  MR1 WILD-TYPE   9  67 245  40
D1576V4, multiclass
    clus
vv   MR1 MUTATED MR1 WILD-TYPE
  T1           0             9
  T2           1            67
  T3           3           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
  MR1 MUTATED     5   0   0
  MR1 WILD-TYPE 215  80  66
D1576V5, multiclass
    clus
vv   MR1 MUTATED MR1 WILD-TYPE
  N0           5           215
  N1           0            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
  MR1 MUTATED     3   0
  MR1 WILD-TYPE 280  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  MR1 MUTATED      3    0
  MR1 WILD-TYPE  280   48
   clus
vv  MR1 MUTATED MR1 WILD-TYPE
  0           3           280
  1           0            48
[1] 2 2
[1] FALSE
D1576V7, 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
D1576V8, binary
               cls
clus              0   1
  MR1 MUTATED     4   1
  MR1 WILD-TYPE 313  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  MR1 MUTATED      4    1
  MR1 WILD-TYPE  313   47
                               clus
vv                              MR1 MUTATED MR1 WILD-TYPE
  COLON ADENOCARCINOMA                    4           313
  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 256   2  22  19
D1576V9, multiclass
    clus
vv   MR1 MUTATED MR1 WILD-TYPE
  R0           1           256
  R1           0             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"
D1576V10, 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
D1576V11, 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(1577) Variable = ARID4B MUTATION ANALYSIS
D1577V1, survival
                  sevent
clus2                0   1
  ARID4B MUTATED     9   1
  ARID4B WILD-TYPE 273  72
  ARID4B MUTATED ARID4B WILD-TYPE 
              10              345 
  ARID4B MUTATED ARID4B WILD-TYPE 
               1               72 
$`ARID4B MUTATED`
TCGA-AA-3713 TCGA-AA-A00N TCGA-AD-6895 TCGA-AU-6004 TCGA-AY-6196 TCGA-CA-6716 
       19.04         4.01         0.72        27.09         0.20         0.26 
TCGA-CM-5349 TCGA-D5-6536 TCGA-DM-A1HA TCGA-G4-6588 
       30.08        17.85       131.51        26.17 

$`ARID4B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        14.50        16.31         0.95        15.75        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  ARID4B MUTATED ARID4B WILD-TYPE 
             0.2              0.0 
  ARID4B MUTATED ARID4B WILD-TYPE 
          131.51           140.38 
  ARID4B MUTATED ARID4B WILD-TYPE 
          18.445           20.280 
[1] "0.2 - 131.5 (18.4)" "0.0 - 140.4 (20.3)"
[1] "hr=" "1.9"
D1577V2, 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       25       104         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARID4B MUTATED           0          0          0          2        1
  ARID4B WILD-TYPE        19         10         41         29       34
                  vv
clus               STAGE IVA STAGE IVB
  ARID4B MUTATED           0         0
  ARID4B WILD-TYPE        13         1
D1577V3, multiclass
            clus
vv           ARID4B MUTATED ARID4B WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               5              104
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              2               29
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ARID4B MUTATED     0   1   9   1
  ARID4B WILD-TYPE   9  67 239  40
D1577V4, multiclass
    clus
vv   ARID4B MUTATED ARID4B WILD-TYPE
  T1              0                9
  T2              1               67
  T3              9              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
  ARID4B MUTATED     8   1   2
  ARID4B WILD-TYPE 212  79  64
D1577V5, multiclass
    clus
vv   ARID4B MUTATED ARID4B WILD-TYPE
  N0              8              212
  N1              1               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"
D1577V6, binary
                  cls
clus                 0   1
  ARID4B MUTATED     8   1
  ARID4B WILD-TYPE 275  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID4B MUTATED      8    1
  ARID4B WILD-TYPE  275   47
   clus
vv  ARID4B MUTATED ARID4B WILD-TYPE
  0              8              275
  1              1               47
[1] 2 2
[1] FALSE
D1577V7, 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
D1577V8, binary
                  cls
clus                 0   1
  ARID4B MUTATED     9   2
  ARID4B WILD-TYPE 308  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID4B MUTATED      9    2
  ARID4B WILD-TYPE  308   46
                               clus
vv                              ARID4B MUTATED ARID4B WILD-TYPE
  COLON ADENOCARCINOMA                       9              308
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ARID4B MUTATED     7   0   1   1
  ARID4B WILD-TYPE 250   2  21  20
D1577V9, multiclass
    clus
vv   ARID4B MUTATED ARID4B WILD-TYPE
  R0              7              250
  R1              0                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"
D1577V10, 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
D1577V11, 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(1578) Variable = G2E3 MUTATION ANALYSIS
D1578V1, survival
                sevent
clus2              0   1
  G2E3 MUTATED    10   2
  G2E3 WILD-TYPE 272  71
  G2E3 MUTATED G2E3 WILD-TYPE 
            12            343 
  G2E3 MUTATED G2E3 WILD-TYPE 
             2             71 
$`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         0.33 
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-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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-6677 TCGA-CM-6679 
       15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43        38.20       130.65        92.75        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  G2E3 MUTATED G2E3 WILD-TYPE 
          0.33           0.00 
  G2E3 MUTATED G2E3 WILD-TYPE 
         63.98         140.38 
  G2E3 MUTATED G2E3 WILD-TYPE 
         12.84          20.28 
[1] "0.3 - 64.0 (12.8)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.5"
D1578V2, 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       23       105         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        19         10         40         31       35        12
                vv
clus             STAGE IVB
  G2E3 MUTATED           0
  G2E3 WILD-TYPE         1
D1578V3, multiclass
            clus
vv           G2E3 MUTATED G2E3 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             4            105
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 241  38
D1578V4, multiclass
    clus
vv   G2E3 MUTATED G2E3 WILD-TYPE
  T1            0              9
  T2            2             66
  T3            7            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
  G2E3 MUTATED    10   2   0
  G2E3 WILD-TYPE 210  78  66
D1578V5, multiclass
    clus
vv   G2E3 MUTATED G2E3 WILD-TYPE
  N0           10            210
  N1            2             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"
D1578V6, binary
                cls
clus               0   1
  G2E3 MUTATED    11   1
  G2E3 WILD-TYPE 272  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  G2E3 MUTATED     11    1
  G2E3 WILD-TYPE  272   47
   clus
vv  G2E3 MUTATED G2E3 WILD-TYPE
  0           11            272
  1            1             47
[1] 2 2
[1] FALSE
D1578V7, 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
D1578V8, binary
                cls
clus               0   1
  G2E3 MUTATED     8   4
  G2E3 WILD-TYPE 309  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  G2E3 MUTATED      8    4
  G2E3 WILD-TYPE  309   44
                               clus
vv                              G2E3 MUTATED G2E3 WILD-TYPE
  COLON ADENOCARCINOMA                     8            309
  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 247   2  22  20
D1578V9, multiclass
    clus
vv   G2E3 MUTATED G2E3 WILD-TYPE
  R0           10            247
  R1            0              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"
D1578V10, 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
D1578V11, 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(1579) Variable = KCNC3 MUTATION ANALYSIS
D1579V1, survival
                 sevent
clus2               0   1
  KCNC3 MUTATED     6   4
  KCNC3 WILD-TYPE 276  69
  KCNC3 MUTATED KCNC3 WILD-TYPE 
             10             345 
  KCNC3 MUTATED KCNC3 WILD-TYPE 
              4              69 
$`KCNC3 MUTATED`
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3989 TCGA-CM-4743 
       26.99        19.04        19.04        10.06         7.96        23.05 
TCGA-D5-6540 TCGA-D5-6928 TCGA-DM-A1D8 TCGA-G4-6588 
       16.14        11.64        12.59        26.17 

$`KCNC3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3812 TCGA-AA-3815 
       19.00        36.00         5.03        85.05        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  KCNC3 MUTATED KCNC3 WILD-TYPE 
           7.96            0.00 
  KCNC3 MUTATED KCNC3 WILD-TYPE 
          26.99          140.38 
  KCNC3 MUTATED KCNC3 WILD-TYPE 
          17.59           20.98 
[1] "8.0 - 27.0 (17.6)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "2.9"
D1579V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KCNC3 MUTATED         1        0        1         4         1         0
  KCNC3 WILD-TYPE      63        1       24       105         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KCNC3 MUTATED           1          0          0          0        2         0
  KCNC3 WILD-TYPE        18         10         41         31       33        13
                 vv
clus              STAGE IVB
  KCNC3 MUTATED           0
  KCNC3 WILD-TYPE         1
D1579V3, multiclass
            clus
vv           KCNC3 MUTATED KCNC3 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              4             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               2              33
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KCNC3 MUTATED     0   1   9   1
  KCNC3 WILD-TYPE   9  67 239  40
D1579V4, multiclass
    clus
vv   KCNC3 MUTATED KCNC3 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             9             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
  KCNC3 MUTATED     8   1   2
  KCNC3 WILD-TYPE 212  79  64
D1579V5, multiclass
    clus
vv   KCNC3 MUTATED KCNC3 WILD-TYPE
  N0             8             212
  N1             1              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"
D1579V6, binary
                 cls
clus                0   1
  KCNC3 MUTATED     7   2
  KCNC3 WILD-TYPE 276  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNC3 MUTATED      7    2
  KCNC3 WILD-TYPE  276   46
   clus
vv  KCNC3 MUTATED KCNC3 WILD-TYPE
  0             7             276
  1             2              46
[1] 2 2
[1] FALSE
D1579V7, binary
                 cls
clus                0   1
  KCNC3 MUTATED     5   6
  KCNC3 WILD-TYPE 165 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNC3 MUTATED      5    6
  KCNC3 WILD-TYPE  165  191
        clus
vv       KCNC3 MUTATED KCNC3 WILD-TYPE
  FEMALE             5             165
  MALE               6             191
[1] 2 2
[1] FALSE
D1579V8, binary
                 cls
clus                0   1
  KCNC3 MUTATED     9   2
  KCNC3 WILD-TYPE 308  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNC3 MUTATED      9    2
  KCNC3 WILD-TYPE  308   46
                               clus
vv                              KCNC3 MUTATED KCNC3 WILD-TYPE
  COLON ADENOCARCINOMA                      9             308
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  KCNC3 MUTATED     7   0   2   1
  KCNC3 WILD-TYPE 250   2  20  20
D1579V9, multiclass
    clus
vv   KCNC3 MUTATED KCNC3 WILD-TYPE
  R0             7             250
  R1             0               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"
D1579V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KCNC3 MUTATED                                  0     0
  KCNC3 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KCNC3 MUTATED                           0     6
  KCNC3 WILD-TYPE                        19   170
D1579V11, multiclass
                                  clus
vv                                 KCNC3 MUTATED KCNC3 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(1580) Variable = PUS7 MUTATION ANALYSIS
D1580V1, survival
                sevent
clus2              0   1
  PUS7 MUTATED    13   0
  PUS7 WILD-TYPE 269  73
  PUS7 MUTATED PUS7 WILD-TYPE 
            13            342 
  PUS7 MUTATED PUS7 WILD-TYPE 
             0             73 
$`PUS7 MUTATED`
TCGA-A6-3809 TCGA-AA-3815 TCGA-AA-3855 TCGA-AA-3977 TCGA-AA-A00E TCGA-AA-A00R 
       32.75        33.04        32.05        25.02        30.02         0.99 
TCGA-AA-A010 TCGA-AD-6889 TCGA-CA-6717 TCGA-CA-6718 TCGA-D5-6928 TCGA-D5-6930 
       34.98        56.55         0.33         0.10        11.64         1.51 
TCGA-G4-6588 
       26.17 

$`PUS7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 
       10.06         0.00        33.07         0.00        36.03         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F 
        7.96        27.02        13.94        38.04        19.00        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        4.21         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07         0.26         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        52.80 

  PUS7 MUTATED PUS7 WILD-TYPE 
           0.1            0.0 
  PUS7 MUTATED PUS7 WILD-TYPE 
         56.55         140.38 
  PUS7 MUTATED PUS7 WILD-TYPE 
         26.17          20.07 
[1] "0.1 - 56.5 (26.2)"  "0.0 - 140.4 (20.1)"
[1] "hr="     "2.6e+07"
D1580V2, 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       25       101         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        19         10         41         31       35        13
                vv
clus             STAGE IVB
  PUS7 MUTATED           0
  PUS7 WILD-TYPE         1
D1580V3, multiclass
            clus
vv           PUS7 MUTATED PUS7 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             8            101
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PUS7 MUTATED     0   3   8   2
  PUS7 WILD-TYPE   9  65 240  39
D1580V4, multiclass
    clus
vv   PUS7 MUTATED PUS7 WILD-TYPE
  T1            0              9
  T2            3             65
  T3            8            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
  PUS7 MUTATED    13   0   0
  PUS7 WILD-TYPE 207  80  66
D1580V5, multiclass
    clus
vv   PUS7 MUTATED PUS7 WILD-TYPE
  N0           13            207
  N1            0             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"
D1580V6, binary
                cls
clus               0   1
  PUS7 MUTATED    12   0
  PUS7 WILD-TYPE 271  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  PUS7 MUTATED     12    0
  PUS7 WILD-TYPE  271   48
   clus
vv  PUS7 MUTATED PUS7 WILD-TYPE
  0           12            271
  1            0             48
[1] 2 2
[1] FALSE
D1580V7, 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
D1580V8, binary
                cls
clus               0   1
  PUS7 MUTATED     9   4
  PUS7 WILD-TYPE 308  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  PUS7 MUTATED      9    4
  PUS7 WILD-TYPE  308   44
                               clus
vv                              PUS7 MUTATED PUS7 WILD-TYPE
  COLON ADENOCARCINOMA                     9            308
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PUS7 MUTATED     9   0   0   2
  PUS7 WILD-TYPE 248   2  22  19
D1580V9, multiclass
    clus
vv   PUS7 MUTATED PUS7 WILD-TYPE
  R0            9            248
  R1            0              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"
D1580V10, 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
D1580V11, 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(1581) Variable = RASGRF2 MUTATION ANALYSIS
D1581V1, survival
                   sevent
clus2                 0   1
  RASGRF2 MUTATED    15   2
  RASGRF2 WILD-TYPE 267  71
  RASGRF2 MUTATED RASGRF2 WILD-TYPE 
               17               338 
  RASGRF2 MUTATED RASGRF2 WILD-TYPE 
                2                71 
$`RASGRF2 MUTATED`
TCGA-A6-5662 TCGA-AA-3510 TCGA-AA-3877 TCGA-AA-3950 TCGA-AA-3977 TCGA-AA-A00N 
       23.61        63.98        31.00        24.00        25.02         4.01 
TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4743 
       34.98        58.39       100.01         0.33         0.10        23.05 
TCGA-CM-5349 TCGA-D5-6535 TCGA-DM-A28E TCGA-G4-6586 TCGA-G4-6588 
       30.08        15.12       119.93        35.80        26.17 

$`RASGRF2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        33.53        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        18.05         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.26         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28F 
      131.51       135.65       139.17         6.12        81.37        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 
       45.11        36.72        36.00        22.09        13.78        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  RASGRF2 MUTATED RASGRF2 WILD-TYPE 
              0.1               0.0 
  RASGRF2 MUTATED RASGRF2 WILD-TYPE 
           119.93            140.38 
  RASGRF2 MUTATED RASGRF2 WILD-TYPE 
           26.170            19.825 
[1] "0.1 - 119.9 (26.2)" "0.0 - 140.4 (19.8)"
[1] "hr=" "2.4"
D1581V2, 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       23       100         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RASGRF2 MUTATED           0          0          1          0        0
  RASGRF2 WILD-TYPE        19         10         40         31       35
                   vv
clus                STAGE IVA STAGE IVB
  RASGRF2 MUTATED           1         0
  RASGRF2 WILD-TYPE        12         1
D1581V3, multiclass
            clus
vv           RASGRF2 MUTATED RASGRF2 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 2                23
  STAGE IIA                9               100
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                1                12
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 235  39
D1581V4, multiclass
    clus
vv   RASGRF2 MUTATED RASGRF2 WILD-TYPE
  T1               1                 8
  T2               1                67
  T3              13               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
  RASGRF2 MUTATED    15   1   1
  RASGRF2 WILD-TYPE 205  79  65
D1581V5, multiclass
    clus
vv   RASGRF2 MUTATED RASGRF2 WILD-TYPE
  N0              15               205
  N1               1                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"
D1581V6, binary
                   cls
clus                  0   1
  RASGRF2 MUTATED    14   1
  RASGRF2 WILD-TYPE 269  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RASGRF2 MUTATED     14    1
  RASGRF2 WILD-TYPE  269   47
   clus
vv  RASGRF2 MUTATED RASGRF2 WILD-TYPE
  0              14               269
  1               1                47
[1] 2 2
[1] FALSE
D1581V7, 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
D1581V8, binary
                   cls
clus                  0   1
  RASGRF2 MUTATED    13   4
  RASGRF2 WILD-TYPE 304  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RASGRF2 MUTATED     13    4
  RASGRF2 WILD-TYPE  304   44
                               clus
vv                              RASGRF2 MUTATED RASGRF2 WILD-TYPE
  COLON ADENOCARCINOMA                       13               304
  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 247   2  22  18
D1581V9, multiclass
    clus
vv   RASGRF2 MUTATED RASGRF2 WILD-TYPE
  R0              10               247
  R1               0                 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"
D1581V10, 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
D1581V11, 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(1582) Variable = TET1 MUTATION ANALYSIS
D1582V1, survival
                sevent
clus2              0   1
  TET1 MUTATED    18   4
  TET1 WILD-TYPE 264  69
  TET1 MUTATED TET1 WILD-TYPE 
            22            333 
  TET1 MUTATED TET1 WILD-TYPE 
             4             69 
$`TET1 MUTATED`
TCGA-A6-3809 TCGA-A6-5665 TCGA-AA-3696 TCGA-AA-3715 TCGA-AA-3837 TCGA-AA-3864 
       32.75        22.06         5.03        19.04        38.99        53.00 
TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A01K 
       24.00         2.01        25.02        18.05        38.04        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         0.10        14.04 
TCGA-CM-6678 TCGA-D5-6928 TCGA-F4-6570 TCGA-F4-6807 
       11.01        11.64         6.18        16.24 

$`TET1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3842 
        0.99        25.02         1.02        17.98        15.95        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-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-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       15.75        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.33         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 
       13.45        35.87         1.55        16.31        29.59        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  TET1 MUTATED TET1 WILD-TYPE 
           0.1            0.0 
  TET1 MUTATED TET1 WILD-TYPE 
         53.00         140.38 
  TET1 MUTATED TET1 WILD-TYPE 
        18.545         20.280 
[1] "0.1 - 53.0 (18.5)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.1"
D1582V2, 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       20       101         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        19         10         40         28       34        12
                vv
clus             STAGE IVB
  TET1 MUTATED           0
  TET1 WILD-TYPE         1
D1582V3, multiclass
            clus
vv           TET1 MUTATED TET1 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              5             20
  STAGE IIA             8            101
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            3             28
  STAGE IV              1             34
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  65 232  37
D1582V4, multiclass
    clus
vv   TET1 MUTATED TET1 WILD-TYPE
  T1            0              9
  T2            3             65
  T3           16            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
  TET1 MUTATED    17   3   3
  TET1 WILD-TYPE 203  77  63
D1582V5, multiclass
    clus
vv   TET1 MUTATED TET1 WILD-TYPE
  N0           17            203
  N1            3             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"
D1582V6, binary
                cls
clus               0   1
  TET1 MUTATED    18   2
  TET1 WILD-TYPE 265  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  TET1 MUTATED     18    2
  TET1 WILD-TYPE  265   46
   clus
vv  TET1 MUTATED TET1 WILD-TYPE
  0           18            265
  1            2             46
[1] 2 2
[1] FALSE
D1582V7, 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
D1582V8, binary
                cls
clus               0   1
  TET1 MUTATED    16   7
  TET1 WILD-TYPE 301  41
[1] "tbl2"
                cls
clus             [,1] [,2]
  TET1 MUTATED     16    7
  TET1 WILD-TYPE  301   41
                               clus
vv                              TET1 MUTATED TET1 WILD-TYPE
  COLON ADENOCARCINOMA                    16            301
  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 239   2  21  20
D1582V9, multiclass
    clus
vv   TET1 MUTATED TET1 WILD-TYPE
  R0           18            239
  R1            0              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"
D1582V10, 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
D1582V11, 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(1583) Variable = BRCA1 MUTATION ANALYSIS
D1583V1, survival
                 sevent
clus2               0   1
  BRCA1 MUTATED    17   8
  BRCA1 WILD-TYPE 265  65
  BRCA1 MUTATED BRCA1 WILD-TYPE 
             25             330 
  BRCA1 MUTATED BRCA1 WILD-TYPE 
              8              65 
$`BRCA1 MUTATED`
TCGA-A6-3809 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3715 
       32.75        20.28         3.02         1.02        63.98        19.04 
TCGA-AA-3977 TCGA-AA-A00E TCGA-AA-A010 TCGA-AD-6889 TCGA-AZ-6598 TCGA-AZ-6599 
       25.02        30.02        34.98        56.55        49.41         6.77 
TCGA-CA-5797 TCGA-CA-6717 TCGA-CK-4948 TCGA-CK-4952 TCGA-CM-5862 TCGA-CM-5864 
        3.29         0.33       102.44        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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 
       20.12        19.66         7.04        35.01         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37         4.21         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       22.36        62.79        61.41        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.25         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       40.34        49.08        51.32        21.99        21.14         2.93 
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        16.01 
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-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-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       11.01        10.06        12.03        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 
      119.70        24.43        38.20       130.65        92.75        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        13.38        13.45        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 
       44.68        55.04        51.75        45.11        36.72        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  BRCA1 MUTATED BRCA1 WILD-TYPE 
           0.33            0.00 
  BRCA1 MUTATED BRCA1 WILD-TYPE 
         135.65          140.38 
  BRCA1 MUTATED BRCA1 WILD-TYPE 
         20.280          20.155 
[1] "0.3 - 135.7 (20.3)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.3"
D1583V2, 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       20       100         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BRCA1 MUTATED           1          1          1          1        0         1
  BRCA1 WILD-TYPE        18          9         40         30       35        12
                 vv
clus              STAGE IVB
  BRCA1 MUTATED           0
  BRCA1 WILD-TYPE         1
D1583V3, multiclass
            clus
vv           BRCA1 MUTATED BRCA1 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               5              20
  STAGE IIA              9             100
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             1               9
  STAGE IIIB             1              40
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  64 230  37
D1583V4, multiclass
    clus
vv   BRCA1 MUTATED BRCA1 WILD-TYPE
  T1             0               9
  T2             4              64
  T3            18             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
  BRCA1 MUTATED    20   3   3
  BRCA1 WILD-TYPE 200  77  63
D1583V5, multiclass
    clus
vv   BRCA1 MUTATED BRCA1 WILD-TYPE
  N0            20             200
  N1             3              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"
D1583V6, binary
                 cls
clus                0   1
  BRCA1 MUTATED    19   1
  BRCA1 WILD-TYPE 264  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRCA1 MUTATED     19    1
  BRCA1 WILD-TYPE  264   47
   clus
vv  BRCA1 MUTATED BRCA1 WILD-TYPE
  0            19             264
  1             1              47
[1] 2 2
[1] FALSE
D1583V7, 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
D1583V8, binary
                 cls
clus                0   1
  BRCA1 MUTATED    21   5
  BRCA1 WILD-TYPE 296  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRCA1 MUTATED     21    5
  BRCA1 WILD-TYPE  296   43
                               clus
vv                              BRCA1 MUTATED BRCA1 WILD-TYPE
  COLON ADENOCARCINOMA                     21             296
  COLON MUCINOUS ADENOCARCINOMA             5              43
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  BRCA1 MUTATED    16   0   0   3
  BRCA1 WILD-TYPE 241   2  22  18
D1583V9, multiclass
    clus
vv   BRCA1 MUTATED BRCA1 WILD-TYPE
  R0            16             241
  R1             0               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"
D1583V10, 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
D1583V11, 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(1584) Variable = ACOX1 MUTATION ANALYSIS
D1584V1, survival
                 sevent
clus2               0   1
  ACOX1 MUTATED     7   3
  ACOX1 WILD-TYPE 275  70
  ACOX1 MUTATED ACOX1 WILD-TYPE 
             10             345 
  ACOX1 MUTATED ACOX1 WILD-TYPE 
              3              70 
$`ACOX1 MUTATED`
TCGA-A6-5661 TCGA-A6-6651 TCGA-AA-3975 TCGA-AA-A01K TCGA-AD-6889 TCGA-AZ-6598 
       33.53        21.76        34.06        31.00        56.55        49.41 
TCGA-AZ-6607 TCGA-CA-6718 TCGA-CM-6171 TCGA-F4-6570 
        3.19         0.10        14.04         6.18 

$`ACOX1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37         4.21         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.33         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  ACOX1 MUTATED ACOX1 WILD-TYPE 
            0.1             0.0 
  ACOX1 MUTATED ACOX1 WILD-TYPE 
          56.55          140.38 
  ACOX1 MUTATED ACOX1 WILD-TYPE 
          26.38           20.12 
[1] "0.1 - 56.5 (26.4)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.5"
D1584V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ACOX1 MUTATED         2        0        1         5         0         0
  ACOX1 WILD-TYPE      62        1       24       104         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ACOX1 MUTATED           0          0          1          1        1         0
  ACOX1 WILD-TYPE        19         10         40         30       34        13
                 vv
clus              STAGE IVB
  ACOX1 MUTATED           0
  ACOX1 WILD-TYPE         1
D1584V3, multiclass
            clus
vv           ACOX1 MUTATED ACOX1 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              5             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ACOX1 MUTATED     0   2   8   1
  ACOX1 WILD-TYPE   9  66 240  40
D1584V4, multiclass
    clus
vv   ACOX1 MUTATED ACOX1 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             8             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
  ACOX1 MUTATED     8   1   2
  ACOX1 WILD-TYPE 212  79  64
D1584V5, multiclass
    clus
vv   ACOX1 MUTATED ACOX1 WILD-TYPE
  N0             8             212
  N1             1              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"
D1584V6, binary
                 cls
clus                0   1
  ACOX1 MUTATED     8   1
  ACOX1 WILD-TYPE 275  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACOX1 MUTATED      8    1
  ACOX1 WILD-TYPE  275   47
   clus
vv  ACOX1 MUTATED ACOX1 WILD-TYPE
  0             8             275
  1             1              47
[1] 2 2
[1] FALSE
D1584V7, binary
                 cls
clus                0   1
  ACOX1 MUTATED     7   4
  ACOX1 WILD-TYPE 163 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACOX1 MUTATED      7    4
  ACOX1 WILD-TYPE  163  193
        clus
vv       ACOX1 MUTATED ACOX1 WILD-TYPE
  FEMALE             7             163
  MALE               4             193
[1] 2 2
[1] FALSE
D1584V8, binary
                 cls
clus                0   1
  ACOX1 MUTATED    11   0
  ACOX1 WILD-TYPE 306  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACOX1 MUTATED     11    0
  ACOX1 WILD-TYPE  306   48
                               clus
vv                              ACOX1 MUTATED ACOX1 WILD-TYPE
  COLON ADENOCARCINOMA                     11             306
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ACOX1 MUTATED     6   0   0   1
  ACOX1 WILD-TYPE 251   2  22  20
D1584V9, multiclass
    clus
vv   ACOX1 MUTATED ACOX1 WILD-TYPE
  R0             6             251
  R1             0               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"
D1584V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ACOX1 MUTATED                                  0     2
  ACOX1 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ACOX1 MUTATED                           1     5
  ACOX1 WILD-TYPE                        18   171
D1584V11, multiclass
                                  clus
vv                                 ACOX1 MUTATED ACOX1 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(1585) Variable = PIAS2 MUTATION ANALYSIS
D1585V1, survival
                 sevent
clus2               0   1
  PIAS2 MUTATED     3   0
  PIAS2 WILD-TYPE 279  73
  PIAS2 MUTATED PIAS2 WILD-TYPE 
              3             352 
  PIAS2 MUTATED PIAS2 WILD-TYPE 
              0              73 
$`PIAS2 MUTATED`
TCGA-AA-3555 TCGA-CA-6718 TCGA-CM-5860 
       29.95         0.10        16.01 

$`PIAS2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        17.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.33         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  PIAS2 MUTATED PIAS2 WILD-TYPE 
            0.1             0.0 
  PIAS2 MUTATED PIAS2 WILD-TYPE 
          29.95          140.38 
  PIAS2 MUTATED PIAS2 WILD-TYPE 
         16.010          20.235 
[1] "0.1 - 29.9 (16.0)"  "0.0 - 140.4 (20.2)"
[1] "hr="     "3300000"
D1585V2, 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       25       105         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        19         10         41         31       35        13
                 vv
clus              STAGE IVB
  PIAS2 MUTATED           0
  PIAS2 WILD-TYPE         1
D1585V3, multiclass
            clus
vv           PIAS2 MUTATED PIAS2 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              4             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PIAS2 MUTATED     0   0   4   0
  PIAS2 WILD-TYPE   9  68 244  41
D1585V4, multiclass
    clus
vv   PIAS2 MUTATED PIAS2 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             4             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
  PIAS2 MUTATED     4   0   0
  PIAS2 WILD-TYPE 216  80  66
D1585V5, multiclass
    clus
vv   PIAS2 MUTATED PIAS2 WILD-TYPE
  N0             4             216
  N1             0              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"
D1585V6, binary
                 cls
clus                0   1
  PIAS2 MUTATED     4   0
  PIAS2 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PIAS2 MUTATED      4    0
  PIAS2 WILD-TYPE  279   48
   clus
vv  PIAS2 MUTATED PIAS2 WILD-TYPE
  0             4             279
  1             0              48
[1] 2 2
[1] FALSE
D1585V7, 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
D1585V8, binary
                 cls
clus                0   1
  PIAS2 MUTATED     3   1
  PIAS2 WILD-TYPE 314  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PIAS2 MUTATED      3    1
  PIAS2 WILD-TYPE  314   47
                               clus
vv                              PIAS2 MUTATED PIAS2 WILD-TYPE
  COLON ADENOCARCINOMA                      3             314
  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 254   2  22  20
D1585V9, multiclass
    clus
vv   PIAS2 MUTATED PIAS2 WILD-TYPE
  R0             3             254
  R1             0               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"
D1585V10, 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
D1585V11, multiclass
[1] "Remove cluster labels:" "PIAS2 MUTATED"         
clus
  PIAS2 MUTATED PIAS2 WILD-TYPE 
              2             204 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-4105 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-A6-5656      TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5660 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-A6-5661      TCGA-A6-5662      TCGA-A6-5664      TCGA-A6-5665 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-A6-5666      TCGA-A6-6137      TCGA-A6-6138      TCGA-A6-6141 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-A6-6142      TCGA-A6-6648      TCGA-A6-6649      TCGA-A6-6651 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-A6-6652      TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-A6-6781      TCGA-A6-6782      TCGA-AD-5900      TCGA-AD-6548 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-AD-6888      TCGA-AD-6889      TCGA-AD-6890      TCGA-AD-6895 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-AD-6899      TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6964 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-AD-6965      TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-AY-4071      TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-AY-6386      TCGA-AZ-4315      TCGA-AZ-4323      TCGA-AZ-4616 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-AZ-4681      TCGA-AZ-4682      TCGA-AZ-5403      TCGA-AZ-5407 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-AZ-6598      TCGA-AZ-6599      TCGA-AZ-6600      TCGA-AZ-6601 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-AZ-6603      TCGA-AZ-6605      TCGA-AZ-6606      TCGA-AZ-6607 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-AZ-6608      TCGA-CA-5254      TCGA-CA-5255      TCGA-CA-5796 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-CA-5797      TCGA-CA-6715      TCGA-CA-6716      TCGA-CA-6717 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-CA-6719      TCGA-CK-4947      TCGA-CK-4948      TCGA-CK-4950 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-CK-4952      TCGA-CK-5912      TCGA-CK-5913      TCGA-CK-5914 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-CK-5915      TCGA-CK-5916      TCGA-CK-6746      TCGA-CK-6747 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-CK-6748      TCGA-CK-6751      TCGA-CM-4743      TCGA-CM-4744 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-CM-4746      TCGA-CM-4747      TCGA-CM-4752      TCGA-CM-5341 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-CM-5344      TCGA-CM-5348      TCGA-CM-5349      TCGA-CM-5861 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-CM-5862      TCGA-CM-5863      TCGA-CM-5864      TCGA-CM-5868 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-CM-6161      TCGA-CM-6162      TCGA-CM-6163      TCGA-CM-6164 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-CM-6165      TCGA-CM-6166      TCGA-CM-6167      TCGA-CM-6168 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-CM-6169      TCGA-CM-6170      TCGA-CM-6171      TCGA-CM-6172 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-CM-6674      TCGA-CM-6675      TCGA-CM-6676      TCGA-CM-6677 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-CM-6678      TCGA-CM-6679      TCGA-CM-6680      TCGA-D5-5537 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-D5-5538      TCGA-D5-5539      TCGA-D5-5540      TCGA-D5-5541 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-D5-6529      TCGA-D5-6532      TCGA-D5-6533      TCGA-D5-6534 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-D5-6535      TCGA-D5-6536      TCGA-D5-6537      TCGA-D5-6538 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-D5-6539      TCGA-D5-6540      TCGA-D5-6541      TCGA-D5-6898 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923      TCGA-D5-6924 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-D5-6926      TCGA-D5-6927      TCGA-D5-6928      TCGA-D5-6929 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-D5-6930      TCGA-D5-6931      TCGA-D5-6932      TCGA-D5-7000 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-DM-A0X9      TCGA-DM-A0XD      TCGA-DM-A0XF      TCGA-DM-A1D0 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-DM-A1D4      TCGA-DM-A1D6      TCGA-DM-A1D7      TCGA-DM-A1D8 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-DM-A1D9      TCGA-DM-A1DA      TCGA-DM-A1DB      TCGA-DM-A1HA 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-DM-A1HB      TCGA-DM-A282      TCGA-DM-A285      TCGA-DM-A28C 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-DM-A28E      TCGA-DM-A28F      TCGA-DM-A28G      TCGA-DM-A28H 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-DM-A28K      TCGA-F4-6459      TCGA-F4-6460      TCGA-F4-6569 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704      TCGA-F4-6805 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808      TCGA-F4-6809 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856      TCGA-G4-6293 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304      TCGA-G4-6306 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310      TCGA-G4-6315 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323      TCGA-G4-6586 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-G4-6588      TCGA-G4-6625      TCGA-G4-6626      TCGA-G4-6628 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 

Clustering(1586) Variable = GATAD2A MUTATION ANALYSIS
D1586V1, survival
                   sevent
clus2                 0   1
  GATAD2A MUTATED     8   1
  GATAD2A WILD-TYPE 274  72
  GATAD2A MUTATED GATAD2A WILD-TYPE 
                9               346 
  GATAD2A MUTATED GATAD2A WILD-TYPE 
                1                72 
$`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         0.07        58.39        14.04 
TCGA-F4-6569 TCGA-F4-6570 TCGA-G4-6304 
       13.45         6.18        53.62 

$`GATAD2A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 TCGA-AA-A02F 
       33.04        35.01        26.01        37.02        39.06        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-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        13.38        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      107.67        74.56        65.85        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  GATAD2A MUTATED GATAD2A WILD-TYPE 
             0.07              0.00 
  GATAD2A MUTATED GATAD2A WILD-TYPE 
            58.39            140.38 
  GATAD2A MUTATED GATAD2A WILD-TYPE 
           19.040            20.235 
[1] "0.1 - 58.4 (19.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2.2"
D1586V2, 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       24       107         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GATAD2A MUTATED           1          0          0          0        1
  GATAD2A WILD-TYPE        18         10         41         31       34
                   vv
clus                STAGE IVA STAGE IVB
  GATAD2A MUTATED           0         0
  GATAD2A WILD-TYPE        13         1
D1586V3, multiclass
            clus
vv           GATAD2A MUTATED GATAD2A WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                2               107
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               0                31
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  GATAD2A MUTATED     0   3   5   1
  GATAD2A WILD-TYPE   9  65 243  40
D1586V4, multiclass
    clus
vv   GATAD2A MUTATED GATAD2A WILD-TYPE
  T1               0                 9
  T2               3                65
  T3               5               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
  GATAD2A MUTATED     8   0   1
  GATAD2A WILD-TYPE 212  80  65
D1586V5, multiclass
    clus
vv   GATAD2A MUTATED GATAD2A WILD-TYPE
  N0               8               212
  N1               0                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"
D1586V6, binary
                   cls
clus                  0   1
  GATAD2A MUTATED     7   1
  GATAD2A WILD-TYPE 276  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GATAD2A MUTATED      7    1
  GATAD2A WILD-TYPE  276   47
   clus
vv  GATAD2A MUTATED GATAD2A WILD-TYPE
  0               7               276
  1               1                47
[1] 2 2
[1] FALSE
D1586V7, 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
D1586V8, binary
                   cls
clus                  0   1
  GATAD2A MUTATED     7   2
  GATAD2A WILD-TYPE 310  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GATAD2A MUTATED      7    2
  GATAD2A WILD-TYPE  310   46
                               clus
vv                              GATAD2A MUTATED GATAD2A WILD-TYPE
  COLON ADENOCARCINOMA                        7               310
  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 249   2  21  21
D1586V9, multiclass
    clus
vv   GATAD2A MUTATED GATAD2A WILD-TYPE
  R0               8               249
  R1               0                 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"
D1586V10, 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
D1586V11, 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(1587) Variable = SECISBP2 MUTATION ANALYSIS
D1587V1, survival
                    sevent
clus2                  0   1
  SECISBP2 MUTATED     7   1
  SECISBP2 WILD-TYPE 275  72
  SECISBP2 MUTATED SECISBP2 WILD-TYPE 
                 8                347 
  SECISBP2 MUTATED SECISBP2 WILD-TYPE 
                 1                 72 
$`SECISBP2 MUTATED`
TCGA-A6-2678 TCGA-A6-6648 TCGA-AA-3877 TCGA-AA-A01R TCGA-AZ-6605 TCGA-CA-6717 
       42.28        25.18        31.00        35.01         5.23         0.33 
TCGA-DM-A28H TCGA-G4-6588 
      117.07        26.17 

$`SECISBP2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2683 
       43.76        46.65        43.76        42.90        24.33        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        18.05         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
      100.01        29.56        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 
       81.37       119.93        35.97        60.79        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        91.79        46.75        52.80 

  SECISBP2 MUTATED SECISBP2 WILD-TYPE 
              0.33               0.00 
  SECISBP2 MUTATED SECISBP2 WILD-TYPE 
            117.07             140.38 
  SECISBP2 MUTATED SECISBP2 WILD-TYPE 
            28.585             20.020 
[1] "0.3 - 117.1 (28.6)" "0.0 - 140.4 (20.0)"
[1] "hr=" "2"  
D1587V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SECISBP2 MUTATED         1        0        0         2         0         0
  SECISBP2 WILD-TYPE      63        1       25       107         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SECISBP2 MUTATED           1          0          2          1        0
  SECISBP2 WILD-TYPE        18         10         39         30       35
                    vv
clus                 STAGE IVA STAGE IVB
  SECISBP2 MUTATED           1         0
  SECISBP2 WILD-TYPE        12         1
D1587V3, multiclass
            clus
vv           SECISBP2 MUTATED SECISBP2 WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  0                 25
  STAGE IIA                 2                107
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 1                 18
  STAGE IIIA                0                 10
  STAGE IIIB                2                 39
  STAGE IIIC                1                 30
  STAGE IV                  0                 35
  STAGE IVA                 1                 12
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of 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     1   0   6   1
  SECISBP2 WILD-TYPE   8  68 242  40
D1587V4, multiclass
    clus
vv   SECISBP2 MUTATED SECISBP2 WILD-TYPE
  T1                1                  8
  T2                0                 68
  T3                6                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
  SECISBP2 MUTATED     4   2   2
  SECISBP2 WILD-TYPE 216  78  64
D1587V5, multiclass
    clus
vv   SECISBP2 MUTATED SECISBP2 WILD-TYPE
  N0                4                216
  N1                2                 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"
D1587V6, binary
                    cls
clus                   0   1
  SECISBP2 MUTATED     7   1
  SECISBP2 WILD-TYPE 276  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SECISBP2 MUTATED      7    1
  SECISBP2 WILD-TYPE  276   47
   clus
vv  SECISBP2 MUTATED SECISBP2 WILD-TYPE
  0                7                276
  1                1                 47
[1] 2 2
[1] FALSE
D1587V7, binary
                    cls
clus                   0   1
  SECISBP2 MUTATED     3   5
  SECISBP2 WILD-TYPE 167 192
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SECISBP2 MUTATED      3    5
  SECISBP2 WILD-TYPE  167  192
        clus
vv       SECISBP2 MUTATED SECISBP2 WILD-TYPE
  FEMALE                3                167
  MALE                  5                192
[1] 2 2
[1] FALSE
D1587V8, binary
                    cls
clus                   0   1
  SECISBP2 MUTATED     5   3
  SECISBP2 WILD-TYPE 312  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SECISBP2 MUTATED      5    3
  SECISBP2 WILD-TYPE  312   45
                               clus
vv                              SECISBP2 MUTATED SECISBP2 WILD-TYPE
  COLON ADENOCARCINOMA                         5                312
  COLON MUCINOUS ADENOCARCINOMA                3                 45
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  SECISBP2 MUTATED     4   0   0   1
  SECISBP2 WILD-TYPE 253   2  22  20
D1587V9, multiclass
    clus
vv   SECISBP2 MUTATED SECISBP2 WILD-TYPE
  R0                4                253
  R1                0                  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"
D1587V10, 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
D1587V11, 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(1588) Variable = IL6R MUTATION ANALYSIS
D1588V1, survival
                sevent
clus2              0   1
  IL6R MUTATED     6   1
  IL6R WILD-TYPE 276  72
  IL6R MUTATED IL6R WILD-TYPE 
             7            348 
  IL6R MUTATED IL6R WILD-TYPE 
             1             72 
$`IL6R MUTATED`
TCGA-AA-3510 TCGA-AA-3715 TCGA-AA-3864 TCGA-AD-6895 TCGA-D5-6928 TCGA-DM-A1HB 
       63.98        19.04        53.00         0.72        11.64       135.65 
TCGA-DM-A282 
      139.17 

$`IL6R WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A285 TCGA-DM-A28C 
      140.38         7.50        44.32       131.51         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  IL6R MUTATED IL6R WILD-TYPE 
          0.72           0.00 
  IL6R MUTATED IL6R WILD-TYPE 
        139.17         140.38 
  IL6R MUTATED IL6R WILD-TYPE 
        53.000         20.155 
[1] "0.7 - 139.2 (53.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "3.1"
D1588V2, 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       22       107         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IL6R MUTATED           0          0          1          0        0         0
  IL6R WILD-TYPE        19         10         40         31       35        13
                vv
clus             STAGE IVB
  IL6R MUTATED           0
  IL6R WILD-TYPE         1
D1588V3, multiclass
            clus
vv           IL6R MUTATED IL6R WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              3             22
  STAGE IIA             2            107
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  IL6R MUTATED     0   0   7   0
  IL6R WILD-TYPE   9  68 241  41
D1588V4, multiclass
    clus
vv   IL6R MUTATED IL6R WILD-TYPE
  T1            0              9
  T2            0             68
  T3            7            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
  IL6R MUTATED     5   2   0
  IL6R WILD-TYPE 215  78  66
D1588V5, multiclass
    clus
vv   IL6R MUTATED IL6R WILD-TYPE
  N0            5            215
  N1            2             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"
D1588V6, binary
                cls
clus               0   1
  IL6R MUTATED     6   0
  IL6R WILD-TYPE 277  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  IL6R MUTATED      6    0
  IL6R WILD-TYPE  277   48
   clus
vv  IL6R MUTATED IL6R WILD-TYPE
  0            6            277
  1            0             48
[1] 2 2
[1] FALSE
D1588V7, 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
D1588V8, binary
                cls
clus               0   1
  IL6R MUTATED     6   1
  IL6R WILD-TYPE 311  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  IL6R MUTATED      6    1
  IL6R WILD-TYPE  311   47
                               clus
vv                              IL6R MUTATED IL6R WILD-TYPE
  COLON ADENOCARCINOMA                     6            311
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  IL6R MUTATED     4   0   0   0
  IL6R WILD-TYPE 253   2  22  21
D1588V9, multiclass
    clus
vv   IL6R MUTATED IL6R WILD-TYPE
  R0            4            253
  R1            0              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"
D1588V10, 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
D1588V11, 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(1589) Variable = AGBL5 MUTATION ANALYSIS
D1589V1, survival
                 sevent
clus2               0   1
  AGBL5 MUTATED    10   2
  AGBL5 WILD-TYPE 272  71
  AGBL5 MUTATED AGBL5 WILD-TYPE 
             12             343 
  AGBL5 MUTATED AGBL5 WILD-TYPE 
              2              71 
$`AGBL5 MUTATED`
TCGA-A6-5661 TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-A00J TCGA-AA-A00N TCGA-AD-5900 
       33.53        24.39        19.66        18.05         4.01         0.07 
TCGA-AD-6895 TCGA-AY-6197 TCGA-AZ-6608 TCGA-CM-4746 TCGA-DM-A1HB TCGA-G4-6309 
        0.72        21.44         1.94        37.02       135.65        51.75 

$`AGBL5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21        56.55         0.79         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        15.75         0.20        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  AGBL5 MUTATED AGBL5 WILD-TYPE 
           0.07            0.00 
  AGBL5 MUTATED AGBL5 WILD-TYPE 
         135.65          140.38 
  AGBL5 MUTATED AGBL5 WILD-TYPE 
          20.55           20.19 
[1] "0.1 - 135.7 (20.6)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.3"
D1589V2, 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       25       107         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AGBL5 MUTATED           0          1          3          1        0         0
  AGBL5 WILD-TYPE        19          9         38         30       35        13
                 vv
clus              STAGE IVB
  AGBL5 MUTATED           0
  AGBL5 WILD-TYPE         1
D1589V3, multiclass
            clus
vv           AGBL5 MUTATED AGBL5 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              2             107
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             3              38
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  AGBL5 MUTATED     0   4   5   3
  AGBL5 WILD-TYPE   9  64 243  38
D1589V4, multiclass
    clus
vv   AGBL5 MUTATED AGBL5 WILD-TYPE
  T1             0               9
  T2             4              64
  T3             5             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
  AGBL5 MUTATED     6   6   0
  AGBL5 WILD-TYPE 214  74  66
D1589V5, multiclass
    clus
vv   AGBL5 MUTATED AGBL5 WILD-TYPE
  N0             6             214
  N1             6              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"
D1589V6, binary
                 cls
clus                0   1
  AGBL5 MUTATED     8   0
  AGBL5 WILD-TYPE 275  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGBL5 MUTATED      8    0
  AGBL5 WILD-TYPE  275   48
   clus
vv  AGBL5 MUTATED AGBL5 WILD-TYPE
  0             8             275
  1             0              48
[1] 2 2
[1] FALSE
D1589V7, 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
D1589V8, binary
                 cls
clus                0   1
  AGBL5 MUTATED     8   4
  AGBL5 WILD-TYPE 309  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGBL5 MUTATED      8    4
  AGBL5 WILD-TYPE  309   44
                               clus
vv                              AGBL5 MUTATED AGBL5 WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  AGBL5 MUTATED     8   0   0   0
  AGBL5 WILD-TYPE 249   2  22  21
D1589V9, multiclass
    clus
vv   AGBL5 MUTATED AGBL5 WILD-TYPE
  R0             8             249
  R1             0               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"
D1589V10, 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
D1589V11, 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(1590) Variable = DEFB129 MUTATION ANALYSIS
D1590V1, survival
                   sevent
clus2                 0   1
  DEFB129 MUTATED     4   1
  DEFB129 WILD-TYPE 278  72
  DEFB129 MUTATED DEFB129 WILD-TYPE 
                5               350 
  DEFB129 MUTATED DEFB129 WILD-TYPE 
                1                72 
$`DEFB129 MUTATED`
TCGA-AA-3516 TCGA-AA-3710 TCGA-AA-3968 TCGA-D5-6536 TCGA-G4-6628 
       13.02        26.99        21.99        17.85        52.80 

$`DEFB129 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        1.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03         2.01        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 
       20.19        18.25         1.32        43.27        15.12         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 
       91.79        46.75 

  DEFB129 MUTATED DEFB129 WILD-TYPE 
            13.02              0.00 
  DEFB129 MUTATED DEFB129 WILD-TYPE 
            52.80            140.38 
  DEFB129 MUTATED DEFB129 WILD-TYPE 
           21.990            20.155 
[1] "13.0 - 52.8 (22.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D1590V2, 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       25       107         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DEFB129 MUTATED           1          0          0          0        0
  DEFB129 WILD-TYPE        18         10         41         31       35
                   vv
clus                STAGE IVA STAGE IVB
  DEFB129 MUTATED           0         0
  DEFB129 WILD-TYPE        13         1
D1590V3, multiclass
            clus
vv           DEFB129 MUTATED DEFB129 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                2               107
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  DEFB129 MUTATED     0   2   3   0
  DEFB129 WILD-TYPE   9  66 245  41
D1590V4, multiclass
    clus
vv   DEFB129 MUTATED DEFB129 WILD-TYPE
  T1               0                 9
  T2               2                66
  T3               3               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
  DEFB129 MUTATED     4   0   1
  DEFB129 WILD-TYPE 216  80  65
D1590V5, multiclass
    clus
vv   DEFB129 MUTATED DEFB129 WILD-TYPE
  N0               4               216
  N1               0                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"
D1590V6, binary
                   cls
clus                  0   1
  DEFB129 MUTATED     5   0
  DEFB129 WILD-TYPE 278  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DEFB129 MUTATED      5    0
  DEFB129 WILD-TYPE  278   48
   clus
vv  DEFB129 MUTATED DEFB129 WILD-TYPE
  0               5               278
  1               0                48
[1] 2 2
[1] FALSE
D1590V7, 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
D1590V8, binary
                   cls
clus                  0   1
  DEFB129 MUTATED     4   1
  DEFB129 WILD-TYPE 313  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DEFB129 MUTATED      4    1
  DEFB129 WILD-TYPE  313   47
                               clus
vv                              DEFB129 MUTATED DEFB129 WILD-TYPE
  COLON ADENOCARCINOMA                        4               313
  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 253   2  22  21
D1590V9, multiclass
    clus
vv   DEFB129 MUTATED DEFB129 WILD-TYPE
  R0               4               253
  R1               0                 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"
D1590V10, 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
D1590V11, multiclass
[1] "Remove cluster labels:" "DEFB129 MUTATED"       
clus
  DEFB129 MUTATED DEFB129 WILD-TYPE 
                2               204 
       TCGA-A6-2671        TCGA-A6-2672        TCGA-A6-2674        TCGA-A6-2676 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-A6-2677        TCGA-A6-2678        TCGA-A6-2683        TCGA-A6-3807 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-A6-3808        TCGA-A6-3809        TCGA-A6-3810        TCGA-A6-4105 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-A6-5656        TCGA-A6-5657        TCGA-A6-5659        TCGA-A6-5660 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-A6-5661        TCGA-A6-5662        TCGA-A6-5664        TCGA-A6-5665 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-A6-5666        TCGA-A6-6137        TCGA-A6-6138        TCGA-A6-6141 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-A6-6142        TCGA-A6-6648        TCGA-A6-6649        TCGA-A6-6651 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-A6-6652        TCGA-A6-6653        TCGA-A6-6654        TCGA-A6-6780 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-A6-6781        TCGA-A6-6782        TCGA-AD-5900        TCGA-AD-6548 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-AD-6888        TCGA-AD-6889        TCGA-AD-6890        TCGA-AD-6895 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-AD-6899        TCGA-AD-6901        TCGA-AD-6963        TCGA-AD-6964 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-AD-6965        TCGA-AU-3779        TCGA-AU-6004        TCGA-AY-4070 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-AY-4071        TCGA-AY-5543        TCGA-AY-6196        TCGA-AY-6197 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-AY-6386        TCGA-AZ-4315        TCGA-AZ-4323        TCGA-AZ-4616 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-AZ-4681        TCGA-AZ-4682        TCGA-AZ-5403        TCGA-AZ-5407 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-AZ-6598        TCGA-AZ-6599        TCGA-AZ-6600        TCGA-AZ-6601 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-AZ-6603        TCGA-AZ-6605        TCGA-AZ-6606        TCGA-AZ-6607 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-AZ-6608        TCGA-CA-5254        TCGA-CA-5255        TCGA-CA-5796 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-CA-5797        TCGA-CA-6715        TCGA-CA-6716        TCGA-CA-6717 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-CA-6718        TCGA-CA-6719        TCGA-CK-4947        TCGA-CK-4948 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-CK-4950        TCGA-CK-4952        TCGA-CK-5912        TCGA-CK-5913 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-CK-5914        TCGA-CK-5915        TCGA-CK-5916        TCGA-CK-6746 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-CK-6747        TCGA-CK-6748        TCGA-CK-6751        TCGA-CM-4743 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-CM-4744        TCGA-CM-4746        TCGA-CM-4747        TCGA-CM-4752 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-CM-5341        TCGA-CM-5344        TCGA-CM-5348        TCGA-CM-5349 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-CM-5860        TCGA-CM-5861        TCGA-CM-5862        TCGA-CM-5863 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-CM-5864        TCGA-CM-5868        TCGA-CM-6161        TCGA-CM-6162 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-CM-6163        TCGA-CM-6164        TCGA-CM-6165        TCGA-CM-6166 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-CM-6167        TCGA-CM-6168        TCGA-CM-6169        TCGA-CM-6170 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-CM-6171        TCGA-CM-6172        TCGA-CM-6674        TCGA-CM-6675 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-CM-6676        TCGA-CM-6677        TCGA-CM-6678        TCGA-CM-6679 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-CM-6680        TCGA-D5-5537        TCGA-D5-5538        TCGA-D5-5539 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-D5-5540        TCGA-D5-5541        TCGA-D5-6529        TCGA-D5-6532 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-D5-6533        TCGA-D5-6534        TCGA-D5-6535        TCGA-D5-6537 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-D5-6538        TCGA-D5-6539        TCGA-D5-6540        TCGA-D5-6541 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-D5-6898        TCGA-D5-6920        TCGA-D5-6922        TCGA-D5-6923 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-D5-6924        TCGA-D5-6926        TCGA-D5-6927        TCGA-D5-6928 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-D5-6929        TCGA-D5-6930        TCGA-D5-6931        TCGA-D5-6932 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-D5-7000        TCGA-DM-A0X9        TCGA-DM-A0XD        TCGA-DM-A0XF 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-DM-A1D0        TCGA-DM-A1D4        TCGA-DM-A1D6        TCGA-DM-A1D7 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-DM-A1D8        TCGA-DM-A1D9        TCGA-DM-A1DA        TCGA-DM-A1DB 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-DM-A1HA        TCGA-DM-A1HB        TCGA-DM-A282        TCGA-DM-A285 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-DM-A28C        TCGA-DM-A28E        TCGA-DM-A28F        TCGA-DM-A28G 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-DM-A28H        TCGA-DM-A28K        TCGA-F4-6459        TCGA-F4-6460 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-F4-6569        TCGA-F4-6570        TCGA-F4-6703        TCGA-F4-6704 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-F4-6805        TCGA-F4-6806        TCGA-F4-6807        TCGA-F4-6808 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-F4-6809        TCGA-F4-6854        TCGA-F4-6855        TCGA-F4-6856 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-G4-6293        TCGA-G4-6299        TCGA-G4-6303        TCGA-G4-6304 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-G4-6306        TCGA-G4-6307        TCGA-G4-6309        TCGA-G4-6310 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-G4-6315        TCGA-G4-6317        TCGA-G4-6321        TCGA-G4-6323 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-G4-6586        TCGA-G4-6588        TCGA-G4-6625        TCGA-G4-6626 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 

Clustering(1591) Variable = SIX5 MUTATION ANALYSIS
D1591V1, survival
                sevent
clus2              0   1
  SIX5 MUTATED     4   1
  SIX5 WILD-TYPE 278  72
  SIX5 MUTATED SIX5 WILD-TYPE 
             5            350 
  SIX5 MUTATED SIX5 WILD-TYPE 
             1             72 
$`SIX5 MUTATED`
TCGA-AA-3947 TCGA-AA-3966 TCGA-AD-5900 TCGA-F4-6570 TCGA-G4-6586 
       33.01         2.01         0.07         6.18        35.80 

$`SIX5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  SIX5 MUTATED SIX5 WILD-TYPE 
          0.07           0.00 
  SIX5 MUTATED SIX5 WILD-TYPE 
         35.80         140.38 
  SIX5 MUTATED SIX5 WILD-TYPE 
         6.180         20.235 
[1] "0.1 - 35.8 (6.2)"   "0.0 - 140.4 (20.2)"
[1] "hr=" "1.8"
D1591V2, 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       25       106         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        19         10         41         31       35        13
                vv
clus             STAGE IVB
  SIX5 MUTATED           0
  SIX5 WILD-TYPE         1
D1591V3, multiclass
            clus
vv           SIX5 MUTATED SIX5 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             3            106
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SIX5 MUTATED     0   1   3   1
  SIX5 WILD-TYPE   9  67 245  40
D1591V4, multiclass
    clus
vv   SIX5 MUTATED SIX5 WILD-TYPE
  T1            0              9
  T2            1             67
  T3            3            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
  SIX5 MUTATED     5   0   0
  SIX5 WILD-TYPE 215  80  66
D1591V5, multiclass
    clus
vv   SIX5 MUTATED SIX5 WILD-TYPE
  N0            5            215
  N1            0             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"
D1591V6, binary
                cls
clus               0   1
  SIX5 MUTATED     4   0
  SIX5 WILD-TYPE 279  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  SIX5 MUTATED      4    0
  SIX5 WILD-TYPE  279   48
   clus
vv  SIX5 MUTATED SIX5 WILD-TYPE
  0            4            279
  1            0             48
[1] 2 2
[1] FALSE
D1591V7, 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
D1591V8, binary
                cls
clus               0   1
  SIX5 MUTATED     2   3
  SIX5 WILD-TYPE 315  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  SIX5 MUTATED      2    3
  SIX5 WILD-TYPE  315   45
                               clus
vv                              SIX5 MUTATED SIX5 WILD-TYPE
  COLON ADENOCARCINOMA                     2            315
  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 253   2  22  21
D1591V9, multiclass
    clus
vv   SIX5 MUTATED SIX5 WILD-TYPE
  R0            4            253
  R1            0              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"
D1591V10, 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
D1591V11, 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(1592) Variable = ZNF577 MUTATION ANALYSIS
D1592V1, survival
                  sevent
clus2                0   1
  ZNF577 MUTATED    11   1
  ZNF577 WILD-TYPE 271  72
  ZNF577 MUTATED ZNF577 WILD-TYPE 
              12              343 
  ZNF577 MUTATED ZNF577 WILD-TYPE 
               1               72 
$`ZNF577 MUTATED`
TCGA-A6-2678 TCGA-A6-6649 TCGA-AA-3555 TCGA-AA-A00N TCGA-AA-A010 TCGA-CA-6717 
       42.28        24.16        29.95         4.01        34.98         0.33 
TCGA-CA-6718 TCGA-CM-5348 TCGA-CM-5864 TCGA-CM-6171 TCGA-D5-6931 TCGA-G4-6628 
        0.10        22.98        15.02        14.04        12.00        52.80 

$`ZNF577 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2683 
       43.76        46.65        43.76        42.90        24.33        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.18        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07         0.26         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 
       46.75 

  ZNF577 MUTATED ZNF577 WILD-TYPE 
             0.1              0.0 
  ZNF577 MUTATED ZNF577 WILD-TYPE 
           52.80           140.38 
  ZNF577 MUTATED ZNF577 WILD-TYPE 
           19.00            20.19 
[1] "0.1 - 52.8 (19.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2.1"
D1592V2, 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       25       106         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF577 MUTATED           0          0          3          1        0
  ZNF577 WILD-TYPE        19         10         38         30       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF577 MUTATED           0         0
  ZNF577 WILD-TYPE        13         1
D1592V3, multiclass
            clus
vv           ZNF577 MUTATED ZNF577 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               3              106
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              3               38
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF577 MUTATED     0   3   6   3
  ZNF577 WILD-TYPE   9  65 242  38
D1592V4, multiclass
    clus
vv   ZNF577 MUTATED ZNF577 WILD-TYPE
  T1              0                9
  T2              3               65
  T3              6              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
  ZNF577 MUTATED     8   3   1
  ZNF577 WILD-TYPE 212  77  65
D1592V5, multiclass
    clus
vv   ZNF577 MUTATED ZNF577 WILD-TYPE
  N0              8              212
  N1              3               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"
D1592V6, binary
                  cls
clus                 0   1
  ZNF577 MUTATED    12   0
  ZNF577 WILD-TYPE 271  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF577 MUTATED     12    0
  ZNF577 WILD-TYPE  271   48
   clus
vv  ZNF577 MUTATED ZNF577 WILD-TYPE
  0             12              271
  1              0               48
[1] 2 2
[1] FALSE
D1592V7, 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
D1592V8, binary
                  cls
clus                 0   1
  ZNF577 MUTATED     9   3
  ZNF577 WILD-TYPE 308  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF577 MUTATED      9    3
  ZNF577 WILD-TYPE  308   45
                               clus
vv                              ZNF577 MUTATED ZNF577 WILD-TYPE
  COLON ADENOCARCINOMA                       9              308
  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 248   2  22  19
D1592V9, multiclass
    clus
vv   ZNF577 MUTATED ZNF577 WILD-TYPE
  R0              9              248
  R1              0                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"
D1592V10, 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
D1592V11, 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(1593) Variable = GPBP1 MUTATION ANALYSIS
D1593V1, survival
                 sevent
clus2               0   1
  GPBP1 MUTATED     8   3
  GPBP1 WILD-TYPE 274  70
  GPBP1 MUTATED GPBP1 WILD-TYPE 
             11             344 
  GPBP1 MUTATED GPBP1 WILD-TYPE 
              3              70 
$`GPBP1 MUTATED`
TCGA-A6-6653 TCGA-AA-3489 TCGA-AA-3947 TCGA-AY-6386 TCGA-AZ-4315 TCGA-CM-4746 
       24.39         7.04        33.01        17.82        58.39        37.02 
TCGA-CM-6678 TCGA-D5-6929 TCGA-DM-A1D4 TCGA-DM-A1DA TCGA-G4-6588 
       11.01        13.41        92.75         7.50        26.17 

$`GPBP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
        0.20        21.44         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 
       10.26       119.70        24.43        38.20       130.65        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32        12.59       140.38        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  GPBP1 MUTATED GPBP1 WILD-TYPE 
           7.04            0.00 
  GPBP1 MUTATED GPBP1 WILD-TYPE 
          92.75          140.38 
  GPBP1 MUTATED GPBP1 WILD-TYPE 
         24.390          20.155 
[1] "7.0 - 92.8 (24.4)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D1593V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GPBP1 MUTATED         2        0        2         3         1         0
  GPBP1 WILD-TYPE      62        1       23       106         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GPBP1 MUTATED           0          0          1          1        1         1
  GPBP1 WILD-TYPE        19         10         40         30       34        12
                 vv
clus              STAGE IVB
  GPBP1 MUTATED           0
  GPBP1 WILD-TYPE         1
D1593V3, multiclass
            clus
vv           GPBP1 MUTATED GPBP1 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              3             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GPBP1 MUTATED     0   2   7   3
  GPBP1 WILD-TYPE   9  66 241  38
D1593V4, multiclass
    clus
vv   GPBP1 MUTATED GPBP1 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             7             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
  GPBP1 MUTATED     8   3   1
  GPBP1 WILD-TYPE 212  77  65
D1593V5, multiclass
    clus
vv   GPBP1 MUTATED GPBP1 WILD-TYPE
  N0             8             212
  N1             3              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"
D1593V6, binary
                 cls
clus                0   1
  GPBP1 MUTATED    10   2
  GPBP1 WILD-TYPE 273  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPBP1 MUTATED     10    2
  GPBP1 WILD-TYPE  273   46
   clus
vv  GPBP1 MUTATED GPBP1 WILD-TYPE
  0            10             273
  1             2              46
[1] 2 2
[1] FALSE
D1593V7, binary
                 cls
clus                0   1
  GPBP1 MUTATED     7   5
  GPBP1 WILD-TYPE 163 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPBP1 MUTATED      7    5
  GPBP1 WILD-TYPE  163  192
        clus
vv       GPBP1 MUTATED GPBP1 WILD-TYPE
  FEMALE             7             163
  MALE               5             192
[1] 2 2
[1] FALSE
D1593V8, binary
                 cls
clus                0   1
  GPBP1 MUTATED    11   1
  GPBP1 WILD-TYPE 306  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPBP1 MUTATED     11    1
  GPBP1 WILD-TYPE  306   47
                               clus
vv                              GPBP1 MUTATED GPBP1 WILD-TYPE
  COLON ADENOCARCINOMA                     11             306
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  GPBP1 MUTATED     9   0   0   0
  GPBP1 WILD-TYPE 248   2  22  21
D1593V9, multiclass
    clus
vv   GPBP1 MUTATED GPBP1 WILD-TYPE
  R0             9             248
  R1             0               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"
D1593V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GPBP1 MUTATED                                  0     0
  GPBP1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GPBP1 MUTATED                           2     7
  GPBP1 WILD-TYPE                        17   169
D1593V11, multiclass
                                  clus
vv                                 GPBP1 MUTATED GPBP1 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(1594) Variable = DOCK8 MUTATION ANALYSIS
D1594V1, survival
                 sevent
clus2               0   1
  DOCK8 MUTATED    16   3
  DOCK8 WILD-TYPE 266  70
  DOCK8 MUTATED DOCK8 WILD-TYPE 
             19             336 
  DOCK8 MUTATED DOCK8 WILD-TYPE 
              3              70 
$`DOCK8 MUTATED`
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3815 TCGA-AA-3842 TCGA-AA-3979 TCGA-AA-A010 
       78.08         6.97        33.04        37.02        24.00        34.98 
TCGA-AD-6890 TCGA-AU-6004 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-6598 TCGA-CA-6717 
        0.79        27.09         0.20        21.44        49.41         0.33 
TCGA-CA-6718 TCGA-CM-6167 TCGA-CM-6171 TCGA-D5-5537 TCGA-F4-6570 TCGA-G4-6309 
        0.10        14.99        14.04        45.40         6.18        51.75 
TCGA-G4-6628 
       52.80 

$`DOCK8 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        61.02         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       38.99        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        25.02        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21        56.55         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       15.75        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07         0.26         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       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        13.38        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 

  DOCK8 MUTATED DOCK8 WILD-TYPE 
            0.1             0.0 
  DOCK8 MUTATED DOCK8 WILD-TYPE 
          78.08          140.38 
  DOCK8 MUTATED DOCK8 WILD-TYPE 
          24.00           20.07 
[1] "0.1 - 78.1 (24.0)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.4"
D1594V2, 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       22       101         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        19          9         40         29       35        13
                 vv
clus              STAGE IVB
  DOCK8 MUTATED           0
  DOCK8 WILD-TYPE         1
D1594V3, multiclass
            clus
vv           DOCK8 MUTATED DOCK8 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              8             101
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             1              40
  STAGE IIIC             2              29
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DOCK8 MUTATED     1   4  14   1
  DOCK8 WILD-TYPE   8  64 234  40
D1594V4, multiclass
    clus
vv   DOCK8 MUTATED DOCK8 WILD-TYPE
  T1             1               8
  T2             4              64
  T3            14             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
  DOCK8 MUTATED    15   2   3
  DOCK8 WILD-TYPE 205  78  63
D1594V5, multiclass
    clus
vv   DOCK8 MUTATED DOCK8 WILD-TYPE
  N0            15             205
  N1             2              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"
D1594V6, binary
                 cls
clus                0   1
  DOCK8 MUTATED    15   0
  DOCK8 WILD-TYPE 268  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK8 MUTATED     15    0
  DOCK8 WILD-TYPE  268   48
   clus
vv  DOCK8 MUTATED DOCK8 WILD-TYPE
  0            15             268
  1             0              48
[1] 2 2
[1] FALSE
D1594V7, 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
D1594V8, binary
                 cls
clus                0   1
  DOCK8 MUTATED    18   2
  DOCK8 WILD-TYPE 299  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK8 MUTATED     18    2
  DOCK8 WILD-TYPE  299   46
                               clus
vv                              DOCK8 MUTATED DOCK8 WILD-TYPE
  COLON ADENOCARCINOMA                     18             299
  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 242   2  22  18
D1594V9, multiclass
    clus
vv   DOCK8 MUTATED DOCK8 WILD-TYPE
  R0            15             242
  R1             0               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"
D1594V10, 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
D1594V11, 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(1595) Variable = AKT1 MUTATION ANALYSIS
D1595V1, survival
                sevent
clus2              0   1
  AKT1 MUTATED     6   5
  AKT1 WILD-TYPE 276  68
  AKT1 MUTATED AKT1 WILD-TYPE 
            11            344 
  AKT1 MUTATED AKT1 WILD-TYPE 
             5             68 
$`AKT1 MUTATED`
TCGA-A6-5661 TCGA-A6-6141 TCGA-AA-3492 TCGA-AA-3516 TCGA-AA-3715 TCGA-AD-6889 
       33.53         8.38         3.02        13.02        19.04        56.55 
TCGA-AZ-6605 TCGA-CM-5864 TCGA-CM-6166 TCGA-D5-5537 TCGA-G4-6586 
        5.23        15.02        21.99        45.40        35.80 

$`AKT1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        6.97         1.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37         4.21         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        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-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       12.03        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  AKT1 MUTATED AKT1 WILD-TYPE 
          3.02           0.00 
  AKT1 MUTATED AKT1 WILD-TYPE 
         56.55         140.38 
  AKT1 MUTATED AKT1 WILD-TYPE 
        19.040         20.235 
[1] "3.0 - 56.5 (19.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2.5"
D1595V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AKT1 MUTATED         2        0        2         5         0         0
  AKT1 WILD-TYPE      62        1       23       104         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AKT1 MUTATED           1          0          1          0        0         0
  AKT1 WILD-TYPE        18         10         40         31       35        13
                vv
clus             STAGE IVB
  AKT1 MUTATED           0
  AKT1 WILD-TYPE         1
D1595V3, multiclass
            clus
vv           AKT1 MUTATED AKT1 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             5            104
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  AKT1 MUTATED     0   2   8   1
  AKT1 WILD-TYPE   9  66 240  40
D1595V4, multiclass
    clus
vv   AKT1 MUTATED AKT1 WILD-TYPE
  T1            0              9
  T2            2             66
  T3            8            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
  AKT1 MUTATED     8   1   2
  AKT1 WILD-TYPE 212  79  64
D1595V5, multiclass
    clus
vv   AKT1 MUTATED AKT1 WILD-TYPE
  N0            8            212
  N1            1             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"
D1595V6, binary
                cls
clus               0   1
  AKT1 MUTATED    10   0
  AKT1 WILD-TYPE 273  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  AKT1 MUTATED     10    0
  AKT1 WILD-TYPE  273   48
   clus
vv  AKT1 MUTATED AKT1 WILD-TYPE
  0           10            273
  1            0             48
[1] 2 2
[1] FALSE
D1595V7, binary
                cls
clus               0   1
  AKT1 MUTATED     5   6
  AKT1 WILD-TYPE 165 191
[1] "tbl2"
                cls
clus             [,1] [,2]
  AKT1 MUTATED      5    6
  AKT1 WILD-TYPE  165  191
        clus
vv       AKT1 MUTATED AKT1 WILD-TYPE
  FEMALE            5            165
  MALE              6            191
[1] 2 2
[1] FALSE
D1595V8, binary
                cls
clus               0   1
  AKT1 MUTATED    10   1
  AKT1 WILD-TYPE 307  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  AKT1 MUTATED     10    1
  AKT1 WILD-TYPE  307   47
                               clus
vv                              AKT1 MUTATED AKT1 WILD-TYPE
  COLON ADENOCARCINOMA                    10            307
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  AKT1 MUTATED     6   0   0   1
  AKT1 WILD-TYPE 251   2  22  20
D1595V9, multiclass
    clus
vv   AKT1 MUTATED AKT1 WILD-TYPE
  R0            6            251
  R1            0              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"
D1595V10, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AKT1 MUTATED                                  0     1
  AKT1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  AKT1 MUTATED                           2     5
  AKT1 WILD-TYPE                        17   171
D1595V11, multiclass
                                  clus
vv                                 AKT1 MUTATED AKT1 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(1596) Variable = GOLGA1 MUTATION ANALYSIS
D1596V1, survival
                  sevent
clus2                0   1
  GOLGA1 MUTATED     4   2
  GOLGA1 WILD-TYPE 278  71
  GOLGA1 MUTATED GOLGA1 WILD-TYPE 
               6              349 
  GOLGA1 MUTATED GOLGA1 WILD-TYPE 
               2               71 
$`GOLGA1 MUTATED`
TCGA-AA-3663 TCGA-AA-3877 TCGA-AA-A00N TCGA-AZ-6600 TCGA-CM-6675 TCGA-D5-5538 
        6.97        31.00         4.01        12.10        13.05        12.26 

$`GOLGA1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  GOLGA1 MUTATED GOLGA1 WILD-TYPE 
            4.01             0.00 
  GOLGA1 MUTATED GOLGA1 WILD-TYPE 
           31.00           140.38 
  GOLGA1 MUTATED GOLGA1 WILD-TYPE 
           12.18            20.98 
[1] "4.0 - 31.0 (12.2)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "2.9"
D1596V2, 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       24       108         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GOLGA1 MUTATED           0          0          1          0        1
  GOLGA1 WILD-TYPE        19         10         40         31       34
                  vv
clus               STAGE IVA STAGE IVB
  GOLGA1 MUTATED           0         1
  GOLGA1 WILD-TYPE        13         0
D1596V3, multiclass
            clus
vv           GOLGA1 MUTATED GOLGA1 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               1              108
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  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  68 244  39
D1596V4, multiclass
    clus
vv   GOLGA1 MUTATED GOLGA1 WILD-TYPE
  T1              1                8
  T2              0               68
  T3              4              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
  GOLGA1 MUTATED     4   2   1
  GOLGA1 WILD-TYPE 216  78  65
D1596V5, multiclass
    clus
vv   GOLGA1 MUTATED GOLGA1 WILD-TYPE
  N0              4              216
  N1              2               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"
D1596V6, binary
                  cls
clus                 0   1
  GOLGA1 MUTATED     5   2
  GOLGA1 WILD-TYPE 278  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GOLGA1 MUTATED      5    2
  GOLGA1 WILD-TYPE  278   46
   clus
vv  GOLGA1 MUTATED GOLGA1 WILD-TYPE
  0              5              278
  1              2               46
[1] 2 2
[1] FALSE
D1596V7, 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
D1596V8, binary
                  cls
clus                 0   1
  GOLGA1 MUTATED     5   2
  GOLGA1 WILD-TYPE 312  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GOLGA1 MUTATED      5    2
  GOLGA1 WILD-TYPE  312   46
                               clus
vv                              GOLGA1 MUTATED GOLGA1 WILD-TYPE
  COLON ADENOCARCINOMA                       5              312
  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 251   2  22  21
D1596V9, multiclass
    clus
vv   GOLGA1 MUTATED GOLGA1 WILD-TYPE
  R0              6              251
  R1              0                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"
D1596V10, 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
D1596V11, 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(1597) Variable = PDK1 MUTATION ANALYSIS
D1597V1, survival
                sevent
clus2              0   1
  PDK1 MUTATED     4   0
  PDK1 WILD-TYPE 278  73
  PDK1 MUTATED PDK1 WILD-TYPE 
             4            351 
  PDK1 MUTATED PDK1 WILD-TYPE 
             0             73 
$`PDK1 MUTATED`
TCGA-AA-3713 TCGA-AZ-4315 TCGA-CM-6166 TCGA-G4-6293 
       19.04        58.39        21.99       107.67 

$`PDK1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 
       33.67        13.25         0.53        35.41        19.43        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  PDK1 MUTATED PDK1 WILD-TYPE 
         19.04           0.00 
  PDK1 MUTATED PDK1 WILD-TYPE 
        107.67         140.38 
  PDK1 MUTATED PDK1 WILD-TYPE 
         40.19          20.12 
[1] "19.0 - 107.7 (40.2)" "0.0 - 140.4 (20.1)" 
[1] "hr="     "9400000"
D1597V2, 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       25       108         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        18         10         41         31       34        13
                vv
clus             STAGE IVB
  PDK1 MUTATED           0
  PDK1 WILD-TYPE         1
D1597V3, multiclass
            clus
vv           PDK1 MUTATED PDK1 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             1            108
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PDK1 MUTATED     0   1   3   1
  PDK1 WILD-TYPE   9  67 245  40
D1597V4, multiclass
    clus
vv   PDK1 MUTATED PDK1 WILD-TYPE
  T1            0              9
  T2            1             67
  T3            3            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
  PDK1 MUTATED     4   1   0
  PDK1 WILD-TYPE 216  79  66
D1597V5, multiclass
    clus
vv   PDK1 MUTATED PDK1 WILD-TYPE
  N0            4            216
  N1            1             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"
D1597V6, binary
                cls
clus               0   1
  PDK1 MUTATED     3   1
  PDK1 WILD-TYPE 280  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  PDK1 MUTATED      3    1
  PDK1 WILD-TYPE  280   47
   clus
vv  PDK1 MUTATED PDK1 WILD-TYPE
  0            3            280
  1            1             47
[1] 2 2
[1] FALSE
D1597V7, 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
D1597V8, binary
                cls
clus               0   1
  PDK1 MUTATED     5   0
  PDK1 WILD-TYPE 312  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  PDK1 MUTATED      5    0
  PDK1 WILD-TYPE  312   48
                               clus
vv                              PDK1 MUTATED PDK1 WILD-TYPE
  COLON ADENOCARCINOMA                     5            312
  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 254   2  21  20
D1597V9, multiclass
    clus
vv   PDK1 MUTATED PDK1 WILD-TYPE
  R0            3            254
  R1            0              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"
D1597V10, 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
D1597V11, 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(1598) Variable = NAE1 MUTATION ANALYSIS
D1598V1, survival
                sevent
clus2              0   1
  NAE1 MUTATED     4   1
  NAE1 WILD-TYPE 278  72
  NAE1 MUTATED NAE1 WILD-TYPE 
             5            350 
  NAE1 MUTATED NAE1 WILD-TYPE 
             1             72 
$`NAE1 MUTATED`
TCGA-A6-2676 TCGA-AA-3994 TCGA-AU-6004 TCGA-CM-5868 TCGA-CM-6164 
       42.90        27.02        27.09        17.03        29.03 

$`NAE1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        27.02        19.07         7.96        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       12.00        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  NAE1 MUTATED NAE1 WILD-TYPE 
         17.03           0.00 
  NAE1 MUTATED NAE1 WILD-TYPE 
         42.90         140.38 
  NAE1 MUTATED NAE1 WILD-TYPE 
         27.09          20.07 
[1] "17.0 - 42.9 (27.1)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.1"
D1598V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NAE1 MUTATED         1        0        0         1         1         0
  NAE1 WILD-TYPE      63        1       25       108         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NAE1 MUTATED           0          0          1          0        0         1
  NAE1 WILD-TYPE        19         10         40         31       35        12
                vv
clus             STAGE IVB
  NAE1 MUTATED           0
  NAE1 WILD-TYPE         1
D1598V3, multiclass
            clus
vv           NAE1 MUTATED NAE1 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             1            108
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NAE1 MUTATED     0   1   2   2
  NAE1 WILD-TYPE   9  67 246  39
D1598V4, multiclass
    clus
vv   NAE1 MUTATED NAE1 WILD-TYPE
  T1            0              9
  T2            1             67
  T3            2            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
  NAE1 MUTATED     3   2   0
  NAE1 WILD-TYPE 217  78  66
D1598V5, multiclass
    clus
vv   NAE1 MUTATED NAE1 WILD-TYPE
  N0            3            217
  N1            2             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"
D1598V6, binary
                cls
clus               0   1
  NAE1 MUTATED     4   1
  NAE1 WILD-TYPE 279  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  NAE1 MUTATED      4    1
  NAE1 WILD-TYPE  279   47
   clus
vv  NAE1 MUTATED NAE1 WILD-TYPE
  0            4            279
  1            1             47
[1] 2 2
[1] FALSE
D1598V7, binary
                cls
clus               0   1
  NAE1 MUTATED     4   1
  NAE1 WILD-TYPE 166 196
[1] "tbl2"
                cls
clus             [,1] [,2]
  NAE1 MUTATED      4    1
  NAE1 WILD-TYPE  166  196
        clus
vv       NAE1 MUTATED NAE1 WILD-TYPE
  FEMALE            4            166
  MALE              1            196
[1] 2 2
[1] FALSE
D1598V8, binary
                cls
clus               0   1
  NAE1 MUTATED     4   1
  NAE1 WILD-TYPE 313  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  NAE1 MUTATED      4    1
  NAE1 WILD-TYPE  313   47
                               clus
vv                              NAE1 MUTATED NAE1 WILD-TYPE
  COLON ADENOCARCINOMA                     4            313
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  NAE1 MUTATED     5   0   0   0
  NAE1 WILD-TYPE 252   2  22  21
D1598V9, multiclass
    clus
vv   NAE1 MUTATED NAE1 WILD-TYPE
  R0            5            252
  R1            0              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"
D1598V10, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NAE1 MUTATED                                  0     0
  NAE1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NAE1 MUTATED                           0     4
  NAE1 WILD-TYPE                        19   172
D1598V11, multiclass
                                  clus
vv                                 NAE1 MUTATED NAE1 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(1599) Variable = PLEKHA4 MUTATION ANALYSIS
D1599V1, survival
                   sevent
clus2                 0   1
  PLEKHA4 MUTATED     8   1
  PLEKHA4 WILD-TYPE 274  72
  PLEKHA4 MUTATED PLEKHA4 WILD-TYPE 
                9               346 
  PLEKHA4 MUTATED PLEKHA4 WILD-TYPE 
                1                72 
$`PLEKHA4 MUTATED`
TCGA-AA-3950 TCGA-AA-3980 TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-6599 TCGA-CM-5349 
       24.00        27.02        27.09        58.39         6.77        30.08 
TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-G4-6628 
      140.38       131.51        52.80 

$`PLEKHA4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41        49.41        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       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-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       35.80        26.17        91.79        46.75 

  PLEKHA4 MUTATED PLEKHA4 WILD-TYPE 
             6.77              0.00 
  PLEKHA4 MUTATED PLEKHA4 WILD-TYPE 
           140.38            139.17 
  PLEKHA4 MUTATED PLEKHA4 WILD-TYPE 
            30.08             19.99 
[1] "6.8 - 140.4 (30.1)" "0.0 - 139.2 (20.0)"
[1] "hr=" "3.6"
D1599V2, 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       25       105         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLEKHA4 MUTATED           1          0          0          1        0
  PLEKHA4 WILD-TYPE        18         10         41         30       35
                   vv
clus                STAGE IVA STAGE IVB
  PLEKHA4 MUTATED           0         0
  PLEKHA4 WILD-TYPE        13         1
D1599V3, multiclass
            clus
vv           PLEKHA4 MUTATED PLEKHA4 WILD-TYPE
  STAGE I                  4                60
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                4               105
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               1                30
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PLEKHA4 MUTATED     0   4   6   0
  PLEKHA4 WILD-TYPE   9  64 242  41
D1599V4, multiclass
    clus
vv   PLEKHA4 MUTATED PLEKHA4 WILD-TYPE
  T1               0                 9
  T2               4                64
  T3               6               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
  PLEKHA4 MUTATED     8   0   2
  PLEKHA4 WILD-TYPE 212  80  64
D1599V5, multiclass
    clus
vv   PLEKHA4 MUTATED PLEKHA4 WILD-TYPE
  N0               8               212
  N1               0                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"
D1599V6, binary
                   cls
clus                  0   1
  PLEKHA4 MUTATED     9   0
  PLEKHA4 WILD-TYPE 274  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHA4 MUTATED      9    0
  PLEKHA4 WILD-TYPE  274   48
   clus
vv  PLEKHA4 MUTATED PLEKHA4 WILD-TYPE
  0               9               274
  1               0                48
[1] 2 2
[1] FALSE
D1599V7, 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
D1599V8, binary
                   cls
clus                  0   1
  PLEKHA4 MUTATED     9   1
  PLEKHA4 WILD-TYPE 308  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHA4 MUTATED      9    1
  PLEKHA4 WILD-TYPE  308   47
                               clus
vv                              PLEKHA4 MUTATED PLEKHA4 WILD-TYPE
  COLON ADENOCARCINOMA                        9               308
  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 251   2  22  21
D1599V9, multiclass
    clus
vv   PLEKHA4 MUTATED PLEKHA4 WILD-TYPE
  R0               6               251
  R1               0                 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"
D1599V10, 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
D1599V11, 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(1600) Variable = ARAF MUTATION ANALYSIS
D1600V1, survival
                sevent
clus2              0   1
  ARAF MUTATED     6   4
  ARAF WILD-TYPE 276  69
  ARAF MUTATED ARAF WILD-TYPE 
            10            345 
  ARAF MUTATED ARAF WILD-TYPE 
             4             69 
$`ARAF MUTATED`
TCGA-A6-6651 TCGA-AA-3492 TCGA-AA-3518 TCGA-AA-3663 TCGA-AA-3715 TCGA-AA-3864 
       21.76         3.02         1.02         6.97        19.04        53.00 
TCGA-AZ-6601 TCGA-CK-5916 TCGA-CM-6674 TCGA-CM-6678 
      100.01        21.14        12.95        11.01 

$`ARAF WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        24.16        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 
       63.98         6.97         1.02        13.02        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99         2.93         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        16.01        15.02         5.03        15.02        15.02 
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-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  ARAF MUTATED ARAF WILD-TYPE 
          1.02           0.00 
  ARAF MUTATED ARAF WILD-TYPE 
        100.01         140.38 
  ARAF MUTATED ARAF WILD-TYPE 
        15.995         20.280 
[1] "1.0 - 100.0 (16.0)" "0.0 - 140.4 (20.3)"
[1] "hr=" "1.9"
D1600V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ARAF MUTATED         1        0        5         2         0         0
  ARAF WILD-TYPE      63        1       20       107         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ARAF MUTATED           0          0          1          0        0         1
  ARAF WILD-TYPE        19         10         40         31       35        12
                vv
clus             STAGE IVB
  ARAF MUTATED           0
  ARAF WILD-TYPE         1
D1600V3, multiclass
            clus
vv           ARAF MUTATED ARAF WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              5             20
  STAGE IIA             2            107
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ARAF MUTATED     1   0   8   1
  ARAF WILD-TYPE   8  68 240  40
D1600V4, multiclass
    clus
vv   ARAF MUTATED ARAF WILD-TYPE
  T1            1              8
  T2            0             68
  T3            8            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
  ARAF MUTATED     8   2   0
  ARAF WILD-TYPE 212  78  66
D1600V5, multiclass
    clus
vv   ARAF MUTATED ARAF WILD-TYPE
  N0            8            212
  N1            2             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"
D1600V6, binary
                cls
clus               0   1
  ARAF MUTATED     8   1
  ARAF WILD-TYPE 275  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  ARAF MUTATED      8    1
  ARAF WILD-TYPE  275   47
   clus
vv  ARAF MUTATED ARAF WILD-TYPE
  0            8            275
  1            1             47
[1] 2 2
[1] FALSE
D1600V7, binary
                cls
clus               0   1
  ARAF MUTATED     5   5
  ARAF WILD-TYPE 165 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  ARAF MUTATED      5    5
  ARAF WILD-TYPE  165  192
        clus
vv       ARAF MUTATED ARAF WILD-TYPE
  FEMALE            5            165
  MALE              5            192
[1] 2 2
[1] FALSE
D1600V8, binary
                cls
clus               0   1
  ARAF MUTATED    10   0
  ARAF WILD-TYPE 307  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  ARAF MUTATED     10    0
  ARAF WILD-TYPE  307   48
                               clus
vv                              ARAF MUTATED ARAF WILD-TYPE
  COLON ADENOCARCINOMA                    10            307
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ARAF MUTATED     7   0   0   1
  ARAF WILD-TYPE 250   2  22  20
D1600V9, multiclass
    clus
vv   ARAF MUTATED ARAF WILD-TYPE
  R0            7            250
  R1            0              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"
D1600V10, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARAF MUTATED                                  0     0
  ARAF WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ARAF MUTATED                           0     5
  ARAF WILD-TYPE                        19   171
D1600V11, multiclass
                                  clus
vv                                 ARAF MUTATED ARAF 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(1601) Variable = ZNF418 MUTATION ANALYSIS
D1601V1, survival
                  sevent
clus2                0   1
  ZNF418 MUTATED    11   2
  ZNF418 WILD-TYPE 271  71
  ZNF418 MUTATED ZNF418 WILD-TYPE 
              13              342 
  ZNF418 MUTATED ZNF418 WILD-TYPE 
               2               71 
$`ZNF418 MUTATED`
TCGA-A6-6653 TCGA-AA-3510 TCGA-AA-3715 TCGA-AA-3966 TCGA-AA-3977 TCGA-AZ-4315 
       24.39        63.98        19.04         2.01        25.02        58.39 
TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-6747 TCGA-CM-5868 TCGA-CM-6675 TCGA-D5-6535 
       49.41         0.33         2.93        17.03        13.05        15.12 
TCGA-D5-6931 
       12.00 

$`ZNF418 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        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-6161 
       16.01        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-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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         1.51 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  ZNF418 MUTATED ZNF418 WILD-TYPE 
            0.33             0.00 
  ZNF418 MUTATED ZNF418 WILD-TYPE 
           63.98           140.38 
  ZNF418 MUTATED ZNF418 WILD-TYPE 
           17.03            20.63 
[1] "0.3 - 64.0 (17.0)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "1.3"
D1601V2, 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       22       104         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF418 MUTATED           0          0          1          1        0
  ZNF418 WILD-TYPE        19         10         40         30       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF418 MUTATED           1         1
  ZNF418 WILD-TYPE        12         0
D1601V3, multiclass
            clus
vv           ZNF418 MUTATED ZNF418 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                3               22
  STAGE IIA               5              104
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               1               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
  ZNF418 MUTATED     0   2  10   2
  ZNF418 WILD-TYPE   9  66 238  39
D1601V4, multiclass
    clus
vv   ZNF418 MUTATED ZNF418 WILD-TYPE
  T1              0                9
  T2              2               66
  T3             10              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
  ZNF418 MUTATED    10   2   2
  ZNF418 WILD-TYPE 210  78  64
D1601V5, multiclass
    clus
vv   ZNF418 MUTATED ZNF418 WILD-TYPE
  N0             10              210
  N1              2               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"
D1601V6, binary
                  cls
clus                 0   1
  ZNF418 MUTATED     8   2
  ZNF418 WILD-TYPE 275  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF418 MUTATED      8    2
  ZNF418 WILD-TYPE  275   46
   clus
vv  ZNF418 MUTATED ZNF418 WILD-TYPE
  0              8              275
  1              2               46
[1] 2 2
[1] FALSE
D1601V7, 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
D1601V8, binary
                  cls
clus                 0   1
  ZNF418 MUTATED    12   2
  ZNF418 WILD-TYPE 305  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF418 MUTATED     12    2
  ZNF418 WILD-TYPE  305   46
                               clus
vv                              ZNF418 MUTATED ZNF418 WILD-TYPE
  COLON ADENOCARCINOMA                      12              305
  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 250   2  22  18
D1601V9, multiclass
    clus
vv   ZNF418 MUTATED ZNF418 WILD-TYPE
  R0              7              250
  R1              0                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"
D1601V10, 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
D1601V11, 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(1602) Variable = MGAT5 MUTATION ANALYSIS
D1602V1, survival
                 sevent
clus2               0   1
  MGAT5 MUTATED    10   3
  MGAT5 WILD-TYPE 272  70
  MGAT5 MUTATED MGAT5 WILD-TYPE 
             13             342 
  MGAT5 MUTATED MGAT5 WILD-TYPE 
              3              70 
$`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         0.33        16.01        12.00        51.75        36.72 
TCGA-G4-6586 
       35.80 

$`MGAT5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
        0.99        31.07        31.07        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6317 
       65.85        53.62        44.68        55.04        45.11        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        26.17        91.79        46.75        52.80 

  MGAT5 MUTATED MGAT5 WILD-TYPE 
           0.33            0.00 
  MGAT5 MUTATED MGAT5 WILD-TYPE 
          62.79          140.38 
  MGAT5 MUTATED MGAT5 WILD-TYPE 
         30.050          20.155 
[1] "0.3 - 62.8 (30.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1"  
D1602V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MGAT5 MUTATED         0        0        3         4         1         0
  MGAT5 WILD-TYPE      64        1       22       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        19         10         36         31       34        13
                 vv
clus              STAGE IVB
  MGAT5 MUTATED           0
  MGAT5 WILD-TYPE         1
D1602V3, multiclass
            clus
vv           MGAT5 MUTATED MGAT5 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              4             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             5              36
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MGAT5 MUTATED     0   0  12   2
  MGAT5 WILD-TYPE   9  68 236  39
D1602V4, multiclass
    clus
vv   MGAT5 MUTATED MGAT5 WILD-TYPE
  T1             0               9
  T2             0              68
  T3            12             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
  MGAT5 MUTATED     8   6   0
  MGAT5 WILD-TYPE 212  74  66
D1602V5, multiclass
    clus
vv   MGAT5 MUTATED MGAT5 WILD-TYPE
  N0             8             212
  N1             6              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"
D1602V6, binary
                 cls
clus                0   1
  MGAT5 MUTATED    11   1
  MGAT5 WILD-TYPE 272  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MGAT5 MUTATED     11    1
  MGAT5 WILD-TYPE  272   47
   clus
vv  MGAT5 MUTATED MGAT5 WILD-TYPE
  0            11             272
  1             1              47
[1] 2 2
[1] FALSE
D1602V7, binary
                 cls
clus                0   1
  MGAT5 MUTATED     6   8
  MGAT5 WILD-TYPE 164 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MGAT5 MUTATED      6    8
  MGAT5 WILD-TYPE  164  189
        clus
vv       MGAT5 MUTATED MGAT5 WILD-TYPE
  FEMALE             6             164
  MALE               8             189
[1] 2 2
[1] FALSE
D1602V8, binary
                 cls
clus                0   1
  MGAT5 MUTATED    12   2
  MGAT5 WILD-TYPE 305  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MGAT5 MUTATED     12    2
  MGAT5 WILD-TYPE  305   46
                               clus
vv                              MGAT5 MUTATED MGAT5 WILD-TYPE
  COLON ADENOCARCINOMA                     12             305
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MGAT5 MUTATED    10   0   0   2
  MGAT5 WILD-TYPE 247   2  22  19
D1602V9, multiclass
    clus
vv   MGAT5 MUTATED MGAT5 WILD-TYPE
  R0            10             247
  R1             0               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"
D1602V10, 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     8
  MGAT5 WILD-TYPE                        18   168
D1602V11, 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                                        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(1603) Variable = DCTN4 MUTATION ANALYSIS
D1603V1, survival
                 sevent
clus2               0   1
  DCTN4 MUTATED     3   3
  DCTN4 WILD-TYPE 279  70
  DCTN4 MUTATED DCTN4 WILD-TYPE 
              6             349 
  DCTN4 MUTATED DCTN4 WILD-TYPE 
              3              70 
$`DCTN4 MUTATED`
TCGA-A6-5657 TCGA-AA-3811 TCGA-AZ-5403 TCGA-CM-4743 TCGA-D5-6928 TCGA-G4-6626 
       31.63        10.06        62.79        23.05        11.64        46.75 

$`DCTN4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13        83.80        22.36        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6628 
       52.80 

  DCTN4 MUTATED DCTN4 WILD-TYPE 
          10.06            0.00 
  DCTN4 MUTATED DCTN4 WILD-TYPE 
          62.79          140.38 
  DCTN4 MUTATED DCTN4 WILD-TYPE 
          27.34           20.12 
[1] "10.1 - 62.8 (27.3)" "0.0 - 140.4 (20.1)"
[1] "hr=" "2"  
D1603V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DCTN4 MUTATED         0        0        1         3         0         0
  DCTN4 WILD-TYPE      64        1       24       106         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DCTN4 MUTATED           1          0          1          0        0         0
  DCTN4 WILD-TYPE        18         10         40         31       35        13
                 vv
clus              STAGE IVB
  DCTN4 MUTATED           0
  DCTN4 WILD-TYPE         1
D1603V3, multiclass
            clus
vv           DCTN4 MUTATED DCTN4 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              3             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DCTN4 MUTATED     0   0   6   0
  DCTN4 WILD-TYPE   9  68 242  41
D1603V4, multiclass
    clus
vv   DCTN4 MUTATED DCTN4 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             6             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
  DCTN4 MUTATED     4   1   1
  DCTN4 WILD-TYPE 216  79  65
D1603V5, multiclass
    clus
vv   DCTN4 MUTATED DCTN4 WILD-TYPE
  N0             4             216
  N1             1              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
  DCTN4 MUTATED     5   0
  DCTN4 WILD-TYPE 278  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DCTN4 MUTATED      5    0
  DCTN4 WILD-TYPE  278   48
   clus
vv  DCTN4 MUTATED DCTN4 WILD-TYPE
  0             5             278
  1             0              48
[1] 2 2
[1] FALSE
D1603V7, binary
                 cls
clus                0   1
  DCTN4 MUTATED     1   5
  DCTN4 WILD-TYPE 169 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DCTN4 MUTATED      1    5
  DCTN4 WILD-TYPE  169  192
        clus
vv       DCTN4 MUTATED DCTN4 WILD-TYPE
  FEMALE             1             169
  MALE               5             192
[1] 2 2
[1] FALSE
D1603V8, binary
                 cls
clus                0   1
  DCTN4 MUTATED     5   1
  DCTN4 WILD-TYPE 312  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DCTN4 MUTATED      5    1
  DCTN4 WILD-TYPE  312   47
                               clus
vv                              DCTN4 MUTATED DCTN4 WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DCTN4 MUTATED     5   0   0   0
  DCTN4 WILD-TYPE 252   2  22  21
D1603V9, multiclass
    clus
vv   DCTN4 MUTATED DCTN4 WILD-TYPE
  R0             5             252
  R1             0               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"
D1603V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DCTN4 MUTATED                                  0     0
  DCTN4 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DCTN4 MUTATED                           1     4
  DCTN4 WILD-TYPE                        18   172
D1603V11, multiclass
                                  clus
vv                                 DCTN4 MUTATED DCTN4 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(1604) Variable = IRS4 MUTATION ANALYSIS
D1604V1, survival
                sevent
clus2              0   1
  IRS4 MUTATED    19   6
  IRS4 WILD-TYPE 263  67
  IRS4 MUTATED IRS4 WILD-TYPE 
            25            330 
  IRS4 MUTATED IRS4 WILD-TYPE 
             6             67 
$`IRS4 MUTATED`
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5665 TCGA-AA-3510 
       46.65        42.90        31.63        33.53        22.06        63.98 
TCGA-AA-3663 TCGA-AA-3696 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3977 TCGA-AA-3979 
        6.97         5.03        19.04        10.06        25.02        24.00 
TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A01Q TCGA-AD-6889 TCGA-AD-6965 TCGA-AZ-4315 
        4.01         0.99         1.02        56.55         0.20        58.39 
TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6170 TCGA-CM-6171 
       49.41       100.01        15.02        15.02        15.02        14.04 
TCGA-G4-6315 
       36.72 

$`IRS4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       43.76        43.76        24.33        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5659 
       33.34        32.75        36.53        14.53        32.91        30.44 
TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       29.19        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 
        8.38        25.08        25.18        24.16        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 
       24.39        23.87        20.12        19.66        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        3.02         1.02        35.01         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 
       36.00        85.05        26.99        19.04        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       26.01        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W 
       18.05        38.04        27.02        42.02        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37         4.21         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AU-3779 
        0.72         5.79        22.42        27.42        10.88        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       61.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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-5864 TCGA-CM-5868 TCGA-CM-6161 
       30.08        16.01         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-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        51.75        45.11        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  IRS4 MUTATED IRS4 WILD-TYPE 
           0.2            0.0 
  IRS4 MUTATED IRS4 WILD-TYPE 
        100.01         140.38 
  IRS4 MUTATED IRS4 WILD-TYPE 
        22.060         20.155 
[1] "0.2 - 100.0 (22.1)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D1604V2, 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       19       103         5         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IRS4 MUTATED           1          0          3          0        3         0
  IRS4 WILD-TYPE        18         10         38         31       32        13
                vv
clus             STAGE IVB
  IRS4 MUTATED           0
  IRS4 WILD-TYPE         1
D1604V3, multiclass
            clus
vv           IRS4 MUTATED IRS4 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              6             19
  STAGE IIA             6            103
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            3             38
  STAGE IIIC            0             31
  STAGE IV              3             32
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  IRS4 MUTATED     0   4  18   5
  IRS4 WILD-TYPE   9  64 230  36
D1604V4, multiclass
    clus
vv   IRS4 MUTATED IRS4 WILD-TYPE
  T1            0              9
  T2            4             64
  T3           18            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
  IRS4 MUTATED    20   5   2
  IRS4 WILD-TYPE 200  75  64
D1604V5, multiclass
    clus
vv   IRS4 MUTATED IRS4 WILD-TYPE
  N0           20            200
  N1            5             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"
D1604V6, binary
                cls
clus               0   1
  IRS4 MUTATED    20   3
  IRS4 WILD-TYPE 263  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS4 MUTATED     20    3
  IRS4 WILD-TYPE  263   45
   clus
vv  IRS4 MUTATED IRS4 WILD-TYPE
  0           20            263
  1            3             45
[1] 2 2
[1] FALSE
D1604V7, 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
D1604V8, binary
                cls
clus               0   1
  IRS4 MUTATED    25   2
  IRS4 WILD-TYPE 292  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS4 MUTATED     25    2
  IRS4 WILD-TYPE  292   46
                               clus
vv                              IRS4 MUTATED IRS4 WILD-TYPE
  COLON ADENOCARCINOMA                    25            292
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  IRS4 MUTATED    19   0   2   1
  IRS4 WILD-TYPE 238   2  20  20
D1604V9, multiclass
    clus
vv   IRS4 MUTATED IRS4 WILD-TYPE
  R0           19            238
  R1            0              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"
D1604V10, 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
D1604V11, 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(1605) Variable = HAUS3 MUTATION ANALYSIS
D1605V1, survival
                 sevent
clus2               0   1
  HAUS3 MUTATED     6   3
  HAUS3 WILD-TYPE 276  70
  HAUS3 MUTATED HAUS3 WILD-TYPE 
              9             346 
  HAUS3 MUTATED HAUS3 WILD-TYPE 
              3              70 
$`HAUS3 MUTATED`
TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-A00N TCGA-AA-A010 TCGA-CK-5912 TCGA-D5-6932 
       22.06        63.98         4.01        34.98        49.08        11.38 
TCGA-DM-A1D0 TCGA-DM-A1HB TCGA-F4-6570 
      130.65       135.65         6.18 

$`HAUS3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
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         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        10.26       119.70        24.43        38.20 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  HAUS3 MUTATED HAUS3 WILD-TYPE 
           4.01            0.00 
  HAUS3 MUTATED HAUS3 WILD-TYPE 
         135.65          140.38 
  HAUS3 MUTATED HAUS3 WILD-TYPE 
          34.98           20.07 
[1] "4.0 - 135.7 (35.0)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.1"
D1605V2, 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       24       105         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        19         10         40         31       35        13
                 vv
clus              STAGE IVB
  HAUS3 MUTATED           0
  HAUS3 WILD-TYPE         1
D1605V3, multiclass
            clus
vv           HAUS3 MUTATED HAUS3 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              4             105
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HAUS3 MUTATED     0   1   6   2
  HAUS3 WILD-TYPE   9  67 242  39
D1605V4, multiclass
    clus
vv   HAUS3 MUTATED HAUS3 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             6             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
  HAUS3 MUTATED     8   1   0
  HAUS3 WILD-TYPE 212  79  66
D1605V5, multiclass
    clus
vv   HAUS3 MUTATED HAUS3 WILD-TYPE
  N0             8             212
  N1             1              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"
D1605V6, binary
                 cls
clus                0   1
  HAUS3 MUTATED     8   0
  HAUS3 WILD-TYPE 275  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAUS3 MUTATED      8    0
  HAUS3 WILD-TYPE  275   48
   clus
vv  HAUS3 MUTATED HAUS3 WILD-TYPE
  0             8             275
  1             0              48
[1] 2 2
[1] FALSE
D1605V7, 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
D1605V8, binary
                 cls
clus                0   1
  HAUS3 MUTATED     8   1
  HAUS3 WILD-TYPE 309  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAUS3 MUTATED      8    1
  HAUS3 WILD-TYPE  309   47
                               clus
vv                              HAUS3 MUTATED HAUS3 WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  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 251   2  22  20
D1605V9, multiclass
    clus
vv   HAUS3 MUTATED HAUS3 WILD-TYPE
  R0             6             251
  R1             0               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"
D1605V10, 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
D1605V11, 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(1606) Variable = ZNF451 MUTATION ANALYSIS
D1606V1, survival
                  sevent
clus2                0   1
  ZNF451 MUTATED    12   4
  ZNF451 WILD-TYPE 270  69
  ZNF451 MUTATED ZNF451 WILD-TYPE 
              16              339 
  ZNF451 MUTATED ZNF451 WILD-TYPE 
               4               69 
$`ZNF451 MUTATED`
TCGA-A6-6141 TCGA-AA-3526 TCGA-AA-3845 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 
        8.38        19.07         0.00        25.02         4.01        34.98 
TCGA-AZ-4315 TCGA-AZ-4616 TCGA-CA-6718 TCGA-CK-4950 TCGA-CK-5913 TCGA-CM-4743 
       58.39         5.13         0.10        40.34        51.32        23.05 
TCGA-CM-5348 TCGA-D5-6922 TCGA-F4-6570 TCGA-G4-6317 
       22.98        10.13         6.18        36.00 

$`ZNF451 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02        14.93        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        1.41        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.33         1.35        17.56       102.44 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58         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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       45.11        36.72        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  ZNF451 MUTATED ZNF451 WILD-TYPE 
               0                0 
  ZNF451 MUTATED ZNF451 WILD-TYPE 
           58.39           140.38 
  ZNF451 MUTATED ZNF451 WILD-TYPE 
          21.025           20.190 
[1] "0.0 - 58.4 (21.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.5"
D1606V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF451 MUTATED         2        0        0         8         2         0
  ZNF451 WILD-TYPE      62        1       25       101         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF451 MUTATED           0          2          1          1        1
  ZNF451 WILD-TYPE        19          8         40         30       34
                  vv
clus               STAGE IVA STAGE IVB
  ZNF451 MUTATED           0         0
  ZNF451 WILD-TYPE        13         1
D1606V3, multiclass
            clus
vv           ZNF451 MUTATED ZNF451 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               8              101
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              2                8
  STAGE IIIB              1               40
  STAGE IIIC              1               30
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF451 MUTATED     0   3  13   2
  ZNF451 WILD-TYPE   9  65 235  39
D1606V4, multiclass
    clus
vv   ZNF451 MUTATED ZNF451 WILD-TYPE
  T1              0                9
  T2              3               65
  T3             13              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
  ZNF451 MUTATED    13   3   2
  ZNF451 WILD-TYPE 207  77  64
D1606V5, multiclass
    clus
vv   ZNF451 MUTATED ZNF451 WILD-TYPE
  N0             13              207
  N1              3               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"
D1606V6, binary
                  cls
clus                 0   1
  ZNF451 MUTATED    13   1
  ZNF451 WILD-TYPE 270  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF451 MUTATED     13    1
  ZNF451 WILD-TYPE  270   47
   clus
vv  ZNF451 MUTATED ZNF451 WILD-TYPE
  0             13              270
  1              1               47
[1] 2 2
[1] FALSE
D1606V7, binary
                  cls
clus                 0   1
  ZNF451 MUTATED     8  10
  ZNF451 WILD-TYPE 162 187
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF451 MUTATED      8   10
  ZNF451 WILD-TYPE  162  187
        clus
vv       ZNF451 MUTATED ZNF451 WILD-TYPE
  FEMALE              8              162
  MALE               10              187
[1] 2 2
[1] FALSE
D1606V8, binary
                  cls
clus                 0   1
  ZNF451 MUTATED    17   1
  ZNF451 WILD-TYPE 300  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF451 MUTATED     17    1
  ZNF451 WILD-TYPE  300   47
                               clus
vv                              ZNF451 MUTATED ZNF451 WILD-TYPE
  COLON ADENOCARCINOMA                      17              300
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF451 MUTATED    11   1   0   3
  ZNF451 WILD-TYPE 246   1  22  18
D1606V9, multiclass
    clus
vv   ZNF451 MUTATED ZNF451 WILD-TYPE
  R0             11              246
  R1              1                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"
D1606V10, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF451 MUTATED                                  0     1
  ZNF451 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF451 MUTATED                           2     9
  ZNF451 WILD-TYPE                        17   167
D1606V11, multiclass
                                  clus
vv                                 ZNF451 MUTATED ZNF451 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(1607) Variable = CHST15 MUTATION ANALYSIS
D1607V1, survival
                  sevent
clus2                0   1
  CHST15 MUTATED    14   2
  CHST15 WILD-TYPE 268  71
  CHST15 MUTATED CHST15 WILD-TYPE 
              16              339 
  CHST15 MUTATED CHST15 WILD-TYPE 
               2               71 
$`CHST15 MUTATED`
TCGA-A6-3809 TCGA-A6-5656 TCGA-A6-5666 TCGA-A6-6780 TCGA-AA-3510 TCGA-AA-3663 
       32.75        32.91        32.71        20.12        63.98         6.97 
TCGA-AA-3833 TCGA-AA-3950 TCGA-AA-3977 TCGA-AA-A010 TCGA-AZ-5407 TCGA-AZ-6601 
       15.95        24.00        25.02        34.98        61.41       100.01 
TCGA-CK-4952 TCGA-D5-6540 TCGA-F4-6459 TCGA-G4-6309 
       15.62        16.14         8.61        51.75 

$`CHST15 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5657 
       16.57        34.65        33.34        36.53        14.53        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 
       21.76        24.69        24.39        23.87        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 
        7.04         3.02         1.02        35.01         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       78.08         6.05        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
        1.02        17.98        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       22.36        62.79        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 
        1.35        17.56       102.44        40.34        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 
       35.97        60.79       117.07        98.24        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       74.56        65.85        53.62        44.68        55.04        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  CHST15 MUTATED CHST15 WILD-TYPE 
            6.97             0.00 
  CHST15 MUTATED CHST15 WILD-TYPE 
          100.01           140.38 
  CHST15 MUTATED CHST15 WILD-TYPE 
          28.865           19.990 
[1] "7.0 - 100.0 (28.9)" "0.0 - 140.4 (20.0)"
[1] "hr=" "2.3"
D1607V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CHST15 MUTATED         3        0        3         4         3         1
  CHST15 WILD-TYPE      61        1       22       105         5         0
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CHST15 MUTATED           1          0          2          0        1
  CHST15 WILD-TYPE        18         10         39         31       34
                  vv
clus               STAGE IVA STAGE IVB
  CHST15 MUTATED           0         0
  CHST15 WILD-TYPE        13         1
D1607V3, multiclass
            clus
vv           CHST15 MUTATED CHST15 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                3               22
  STAGE IIA               4              105
  STAGE IIB               3                5
  STAGE IIC               1                0
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CHST15 MUTATED     1   3  10   5
  CHST15 WILD-TYPE   8  65 238  36
D1607V4, multiclass
    clus
vv   CHST15 MUTATED CHST15 WILD-TYPE
  T1              1                8
  T2              3               65
  T3             10              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
  CHST15 MUTATED    15   1   3
  CHST15 WILD-TYPE 205  79  63
D1607V5, multiclass
    clus
vv   CHST15 MUTATED CHST15 WILD-TYPE
  N0             15              205
  N1              1               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"
D1607V6, binary
                  cls
clus                 0   1
  CHST15 MUTATED    15   1
  CHST15 WILD-TYPE 268  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHST15 MUTATED     15    1
  CHST15 WILD-TYPE  268   47
   clus
vv  CHST15 MUTATED CHST15 WILD-TYPE
  0             15              268
  1              1               47
[1] 2 2
[1] FALSE
D1607V7, binary
                  cls
clus                 0   1
  CHST15 MUTATED    11   8
  CHST15 WILD-TYPE 159 189
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHST15 MUTATED     11    8
  CHST15 WILD-TYPE  159  189
        clus
vv       CHST15 MUTATED CHST15 WILD-TYPE
  FEMALE             11              159
  MALE                8              189
[1] 2 2
[1] FALSE
D1607V8, binary
                  cls
clus                 0   1
  CHST15 MUTATED    14   5
  CHST15 WILD-TYPE 303  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHST15 MUTATED     14    5
  CHST15 WILD-TYPE  303   43
                               clus
vv                              CHST15 MUTATED CHST15 WILD-TYPE
  COLON ADENOCARCINOMA                      14              303
  COLON MUCINOUS ADENOCARCINOMA              5               43
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CHST15 MUTATED    10   0   1   2
  CHST15 WILD-TYPE 247   2  21  19
D1607V9, multiclass
    clus
vv   CHST15 MUTATED CHST15 WILD-TYPE
  R0             10              247
  R1              0                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"
D1607V10, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CHST15 MUTATED                                  0     0
  CHST15 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CHST15 MUTATED                           1    10
  CHST15 WILD-TYPE                        18   166
D1607V11, multiclass
                                  clus
vv                                 CHST15 MUTATED CHST15 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(1608) Variable = CCDC62 MUTATION ANALYSIS
D1608V1, survival
                  sevent
clus2                0   1
  CCDC62 MUTATED     8   2
  CCDC62 WILD-TYPE 274  71
  CCDC62 MUTATED CCDC62 WILD-TYPE 
              10              345 
  CCDC62 MUTATED CCDC62 WILD-TYPE 
               2               71 
$`CCDC62 MUTATED`
TCGA-AA-3510 TCGA-AA-3715 TCGA-AD-6889 TCGA-CA-6717 TCGA-CK-5916 TCGA-CM-6166 
       63.98        19.04        56.55         0.33        21.14        21.99 
TCGA-CM-6168 TCGA-D5-6534 TCGA-D5-6932 TCGA-G4-6588 
       12.99        43.27        11.38        26.17 

$`CCDC62 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        51.32        21.99         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-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-6169 TCGA-CM-6170 
       14.04        29.03        16.04        14.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 
       13.51        11.51        20.19        18.25         1.32        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  CCDC62 MUTATED CCDC62 WILD-TYPE 
            0.33             0.00 
  CCDC62 MUTATED CCDC62 WILD-TYPE 
           63.98           140.38 
  CCDC62 MUTATED CCDC62 WILD-TYPE 
          21.565           20.120 
[1] "0.3 - 64.0 (21.6)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.1"
D1608V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CCDC62 MUTATED         2        0        2         6         0         0
  CCDC62 WILD-TYPE      62        1       23       103         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC62 MUTATED           1          0          0          0        0
  CCDC62 WILD-TYPE        18         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  CCDC62 MUTATED           0         0
  CCDC62 WILD-TYPE        13         1
D1608V3, multiclass
            clus
vv           CCDC62 MUTATED CCDC62 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               6              103
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CCDC62 MUTATED     1   1   9   0
  CCDC62 WILD-TYPE   8  67 239  41
D1608V4, multiclass
    clus
vv   CCDC62 MUTATED CCDC62 WILD-TYPE
  T1              1                8
  T2              1               67
  T3              9              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
  CCDC62 MUTATED    10   0   1
  CCDC62 WILD-TYPE 210  80  65
D1608V5, multiclass
    clus
vv   CCDC62 MUTATED CCDC62 WILD-TYPE
  N0             10              210
  N1              0               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"
D1608V6, binary
                  cls
clus                 0   1
  CCDC62 MUTATED    11   0
  CCDC62 WILD-TYPE 272  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC62 MUTATED     11    0
  CCDC62 WILD-TYPE  272   48
   clus
vv  CCDC62 MUTATED CCDC62 WILD-TYPE
  0             11              272
  1              0               48
[1] 2 2
[1] FALSE
D1608V7, binary
                  cls
clus                 0   1
  CCDC62 MUTATED     5   6
  CCDC62 WILD-TYPE 165 191
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC62 MUTATED      5    6
  CCDC62 WILD-TYPE  165  191
        clus
vv       CCDC62 MUTATED CCDC62 WILD-TYPE
  FEMALE              5              165
  MALE                6              191
[1] 2 2
[1] FALSE
D1608V8, binary
                  cls
clus                 0   1
  CCDC62 MUTATED     9   2
  CCDC62 WILD-TYPE 308  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC62 MUTATED      9    2
  CCDC62 WILD-TYPE  308   46
                               clus
vv                              CCDC62 MUTATED CCDC62 WILD-TYPE
  COLON ADENOCARCINOMA                       9              308
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CCDC62 MUTATED     8   0   0   2
  CCDC62 WILD-TYPE 249   2  22  19
D1608V9, multiclass
    clus
vv   CCDC62 MUTATED CCDC62 WILD-TYPE
  R0              8              249
  R1              0                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"
D1608V10, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCDC62 MUTATED                                  0     2
  CCDC62 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CCDC62 MUTATED                           1     5
  CCDC62 WILD-TYPE                        18   171
D1608V11, multiclass
                                  clus
vv                                 CCDC62 MUTATED CCDC62 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(1609) Variable = ERCC6L MUTATION ANALYSIS
D1609V1, survival
                  sevent
clus2                0   1
  ERCC6L MUTATED     9   2
  ERCC6L WILD-TYPE 273  71
  ERCC6L MUTATED ERCC6L WILD-TYPE 
              11              344 
  ERCC6L MUTATED ERCC6L WILD-TYPE 
               2               71 
$`ERCC6L MUTATED`
TCGA-A6-2672 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6141 TCGA-AA-3660 TCGA-AA-3860 
       46.65        33.53        22.06         8.38        78.08        31.07 
TCGA-AA-3950 TCGA-AA-A01D TCGA-AD-6895 TCGA-AZ-6601 TCGA-G4-6586 
       24.00        10.98         0.72       100.01        35.80 

$`ERCC6L WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       31.63        30.44        29.19        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 
       27.09        22.52        25.08        25.18        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        7.04         3.02         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 
        0.00        36.03        32.05         0.99        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  ERCC6L MUTATED ERCC6L WILD-TYPE 
            0.72             0.00 
  ERCC6L MUTATED ERCC6L WILD-TYPE 
          100.01           140.38 
  ERCC6L MUTATED ERCC6L WILD-TYPE 
          31.070           20.005 
[1] "0.7 - 100.0 (31.1)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.5"
D1609V2, 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       23       103         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ERCC6L MUTATED           0          0          2          1        0
  ERCC6L WILD-TYPE        19         10         39         30       35
                  vv
clus               STAGE IVA STAGE IVB
  ERCC6L MUTATED           0         0
  ERCC6L WILD-TYPE        13         1
D1609V3, multiclass
            clus
vv           ERCC6L MUTATED ERCC6L WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               6              103
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ERCC6L MUTATED     0   0  12   0
  ERCC6L WILD-TYPE   9  68 236  41
D1609V4, multiclass
    clus
vv   ERCC6L MUTATED ERCC6L WILD-TYPE
  T1              0                9
  T2              0               68
  T3             12              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
  ERCC6L MUTATED     8   3   1
  ERCC6L WILD-TYPE 212  77  65
D1609V5, multiclass
    clus
vv   ERCC6L MUTATED ERCC6L WILD-TYPE
  N0              8              212
  N1              3               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"
D1609V6, binary
                  cls
clus                 0   1
  ERCC6L MUTATED    11   0
  ERCC6L WILD-TYPE 272  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ERCC6L MUTATED     11    0
  ERCC6L WILD-TYPE  272   48
   clus
vv  ERCC6L MUTATED ERCC6L WILD-TYPE
  0             11              272
  1              0               48
[1] 2 2
[1] FALSE
D1609V7, 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
D1609V8, binary
                  cls
clus                 0   1
  ERCC6L MUTATED    10   2
  ERCC6L WILD-TYPE 307  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ERCC6L MUTATED     10    2
  ERCC6L WILD-TYPE  307   46
                               clus
vv                              ERCC6L MUTATED ERCC6L WILD-TYPE
  COLON ADENOCARCINOMA                      10              307
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ERCC6L MUTATED     9   0   0   0
  ERCC6L WILD-TYPE 248   2  22  21
D1609V9, multiclass
    clus
vv   ERCC6L MUTATED ERCC6L WILD-TYPE
  R0              9              248
  R1              0                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"
D1609V10, 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
D1609V11, 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(1610) Variable = MCF2L2 MUTATION ANALYSIS
D1610V1, survival
                  sevent
clus2                0   1
  MCF2L2 MUTATED    14   3
  MCF2L2 WILD-TYPE 268  70
  MCF2L2 MUTATED MCF2L2 WILD-TYPE 
              17              338 
  MCF2L2 MUTATED MCF2L2 WILD-TYPE 
               3               70 
$`MCF2L2 MUTATED`
TCGA-AA-3510 TCGA-AA-3952 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A01R TCGA-AA-A02Y 
       63.98         2.01        25.02         4.01        35.01        39.98 
TCGA-AD-6964 TCGA-AU-6004 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-6164 TCGA-D5-6535 
       10.88        27.09         0.33         0.10        29.03        15.12 
TCGA-D5-6536 TCGA-D5-6540 TCGA-D5-6929 TCGA-G4-6309 TCGA-G4-6588 
       17.85        16.14        13.41        51.75        26.17 

$`MCF2L2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       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        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
       14.01         0.92        41.00        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07         0.26         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
        1.32        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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       74.56        65.85        53.62        44.68        55.04        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  MCF2L2 MUTATED MCF2L2 WILD-TYPE 
             0.1              0.0 
  MCF2L2 MUTATED MCF2L2 WILD-TYPE 
           63.98           140.38 
  MCF2L2 MUTATED MCF2L2 WILD-TYPE 
          17.850           20.235 
[1] "0.1 - 64.0 (17.9)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1"  
D1610V2, 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       24       103         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MCF2L2 MUTATED           1          0          2          1        1
  MCF2L2 WILD-TYPE        18         10         39         30       34
                  vv
clus               STAGE IVA STAGE IVB
  MCF2L2 MUTATED           0         0
  MCF2L2 WILD-TYPE        13         1
D1610V3, multiclass
            clus
vv           MCF2L2 MUTATED MCF2L2 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               6              103
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              1               30
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MCF2L2 MUTATED     0   4  12   3
  MCF2L2 WILD-TYPE   9  64 236  38
D1610V4, multiclass
    clus
vv   MCF2L2 MUTATED MCF2L2 WILD-TYPE
  T1              0                9
  T2              4               64
  T3             12              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
  MCF2L2 MUTATED    13   3   3
  MCF2L2 WILD-TYPE 207  77  63
D1610V5, multiclass
    clus
vv   MCF2L2 MUTATED MCF2L2 WILD-TYPE
  N0             13              207
  N1              3               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"
D1610V6, binary
                  cls
clus                 0   1
  MCF2L2 MUTATED    14   1
  MCF2L2 WILD-TYPE 269  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MCF2L2 MUTATED     14    1
  MCF2L2 WILD-TYPE  269   47
   clus
vv  MCF2L2 MUTATED MCF2L2 WILD-TYPE
  0             14              269
  1              1               47
[1] 2 2
[1] FALSE
D1610V7, 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
D1610V8, binary
                  cls
clus                 0   1
  MCF2L2 MUTATED    15   4
  MCF2L2 WILD-TYPE 302  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MCF2L2 MUTATED     15    4
  MCF2L2 WILD-TYPE  302   44
                               clus
vv                              MCF2L2 MUTATED MCF2L2 WILD-TYPE
  COLON ADENOCARCINOMA                      15              302
  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 244   2  22  17
D1610V9, multiclass
    clus
vv   MCF2L2 MUTATED MCF2L2 WILD-TYPE
  R0             13              244
  R1              0                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"
D1610V10, 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
D1610V11, 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(1611) Variable = KIF5B MUTATION ANALYSIS
D1611V1, survival
                 sevent
clus2               0   1
  KIF5B MUTATED    11   2
  KIF5B WILD-TYPE 271  71
  KIF5B MUTATED KIF5B WILD-TYPE 
             13             342 
  KIF5B MUTATED KIF5B WILD-TYPE 
              2              71 
$`KIF5B MUTATED`
TCGA-A6-6781 TCGA-AA-3663 TCGA-AA-3864 TCGA-AA-3977 TCGA-AA-A00N TCGA-AD-6889 
       19.66         6.97        53.00        25.02         4.01        56.55 
TCGA-CA-6718 TCGA-CM-6161 TCGA-CM-6171 TCGA-CM-6674 TCGA-D5-6537 TCGA-G4-6310 
        0.10        15.02        14.04        12.95         4.80        45.11 
TCGA-G4-6317 
       36.00 

$`KIF5B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37         4.21         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.33         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 
       18.25         1.32        43.27        15.12        17.85        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6321 
       53.62        44.68        55.04        51.75        36.72        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  KIF5B MUTATED KIF5B WILD-TYPE 
            0.1             0.0 
  KIF5B MUTATED KIF5B WILD-TYPE 
          56.55          140.38 
  KIF5B MUTATED KIF5B WILD-TYPE 
          15.02           20.63 
[1] "0.1 - 56.5 (15.0)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "1.3"
D1611V2, 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       22       106         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        19         10         39         29       35        13
                 vv
clus              STAGE IVB
  KIF5B MUTATED           0
  KIF5B WILD-TYPE         1
D1611V3, multiclass
            clus
vv           KIF5B MUTATED KIF5B WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              3             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             2              29
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KIF5B MUTATED     0   3   8   3
  KIF5B WILD-TYPE   9  65 240  38
D1611V4, multiclass
    clus
vv   KIF5B MUTATED KIF5B WILD-TYPE
  T1             0               9
  T2             3              65
  T3             8             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
  KIF5B MUTATED    10   3   1
  KIF5B WILD-TYPE 210  77  65
D1611V5, multiclass
    clus
vv   KIF5B MUTATED KIF5B WILD-TYPE
  N0            10             210
  N1             3              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"
D1611V6, binary
                 cls
clus                0   1
  KIF5B MUTATED    10   0
  KIF5B WILD-TYPE 273  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF5B MUTATED     10    0
  KIF5B WILD-TYPE  273   48
   clus
vv  KIF5B MUTATED KIF5B WILD-TYPE
  0            10             273
  1             0              48
[1] 2 2
[1] FALSE
D1611V7, 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
D1611V8, binary
                 cls
clus                0   1
  KIF5B MUTATED    12   2
  KIF5B WILD-TYPE 305  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF5B MUTATED     12    2
  KIF5B WILD-TYPE  305   46
                               clus
vv                              KIF5B MUTATED KIF5B WILD-TYPE
  COLON ADENOCARCINOMA                     12             305
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  KIF5B MUTATED    11   0   0   1
  KIF5B WILD-TYPE 246   2  22  20
D1611V9, multiclass
    clus
vv   KIF5B MUTATED KIF5B WILD-TYPE
  R0            11             246
  R1             0               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"
D1611V10, 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
D1611V11, 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(1612) Variable = CDC14A MUTATION ANALYSIS
D1612V1, survival
                  sevent
clus2                0   1
  CDC14A MUTATED     8   1
  CDC14A WILD-TYPE 274  72
  CDC14A MUTATED CDC14A WILD-TYPE 
               9              346 
  CDC14A MUTATED CDC14A WILD-TYPE 
               1               72 
$`CDC14A MUTATED`
TCGA-AD-5900 TCGA-AU-3779 TCGA-AZ-4315 TCGA-CK-5916 TCGA-CM-6162 TCGA-D5-6928 
        0.07        14.50        58.39        21.14        12.00        11.64 
TCGA-DM-A1HB TCGA-F4-6856 TCGA-G4-6588 
      135.65        19.43        26.17 

$`CDC14A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
       40.34        15.62        49.08        51.32        21.99         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        91.79        46.75        52.80 

  CDC14A MUTATED CDC14A WILD-TYPE 
            0.07             0.00 
  CDC14A MUTATED CDC14A WILD-TYPE 
          135.65           140.38 
  CDC14A MUTATED CDC14A WILD-TYPE 
          19.430           20.235 
[1] "0.1 - 135.7 (19.4)" "0.0 - 140.4 (20.2)"
[1] "hr=" "2.2"
D1612V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CDC14A MUTATED         3        0        0         5         0         0
  CDC14A WILD-TYPE      61        1       25       104         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CDC14A MUTATED           0          0          2          0        0
  CDC14A WILD-TYPE        19         10         39         31       35
                  vv
clus               STAGE IVA STAGE IVB
  CDC14A MUTATED           0         0
  CDC14A WILD-TYPE        13         1
D1612V3, multiclass
            clus
vv           CDC14A MUTATED CDC14A WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               5              104
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CDC14A MUTATED     1   2   7   0
  CDC14A WILD-TYPE   8  66 241  41
D1612V4, multiclass
    clus
vv   CDC14A MUTATED CDC14A WILD-TYPE
  T1              1                8
  T2              2               66
  T3              7              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
  CDC14A MUTATED     8   2   0
  CDC14A WILD-TYPE 212  78  66
D1612V5, multiclass
    clus
vv   CDC14A MUTATED CDC14A WILD-TYPE
  N0              8              212
  N1              2               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"
D1612V6, binary
                  cls
clus                 0   1
  CDC14A MUTATED     9   0
  CDC14A WILD-TYPE 274  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDC14A MUTATED      9    0
  CDC14A WILD-TYPE  274   48
   clus
vv  CDC14A MUTATED CDC14A WILD-TYPE
  0              9              274
  1              0               48
[1] 2 2
[1] FALSE
D1612V7, binary
                  cls
clus                 0   1
  CDC14A MUTATED     5   5
  CDC14A WILD-TYPE 165 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDC14A MUTATED      5    5
  CDC14A WILD-TYPE  165  192
        clus
vv       CDC14A MUTATED CDC14A WILD-TYPE
  FEMALE              5              165
  MALE                5              192
[1] 2 2
[1] FALSE
D1612V8, binary
                  cls
clus                 0   1
  CDC14A MUTATED     6   4
  CDC14A WILD-TYPE 311  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDC14A MUTATED      6    4
  CDC14A WILD-TYPE  311   44
                               clus
vv                              CDC14A MUTATED CDC14A WILD-TYPE
  COLON ADENOCARCINOMA                       6              311
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CDC14A MUTATED     8   0   0   1
  CDC14A WILD-TYPE 249   2  22  20
D1612V9, multiclass
    clus
vv   CDC14A MUTATED CDC14A WILD-TYPE
  R0              8              249
  R1              0                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"
D1612V10, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDC14A MUTATED                                  0     0
  CDC14A WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CDC14A MUTATED                           0     9
  CDC14A WILD-TYPE                        19   167
D1612V11, multiclass
                                  clus
vv                                 CDC14A MUTATED CDC14A 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(1613) Variable = ARHGAP11A MUTATION ANALYSIS
D1613V1, survival
                     sevent
clus2                   0   1
  ARHGAP11A MUTATED    11   2
  ARHGAP11A WILD-TYPE 271  71
  ARHGAP11A MUTATED ARHGAP11A WILD-TYPE 
                 13                 342 
  ARHGAP11A MUTATED ARHGAP11A WILD-TYPE 
                  2                  71 
$`ARHGAP11A MUTATED`
TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3662 TCGA-AA-3977 TCGA-AA-A01X TCGA-AD-6889 
       20.12        19.66         6.05        25.02        26.01        56.55 
TCGA-AD-6964 TCGA-AU-6004 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CM-5348 TCGA-CM-6166 
       10.88        27.09       100.01         0.33        22.98        21.99 
TCGA-D5-5541 
       11.51 

$`ARHGAP11A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       23.87        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37         4.21         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       19.59        13.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  ARHGAP11A MUTATED ARHGAP11A WILD-TYPE 
               0.33                0.00 
  ARHGAP11A MUTATED ARHGAP11A WILD-TYPE 
             100.01              140.38 
  ARHGAP11A MUTATED ARHGAP11A WILD-TYPE 
             21.990              20.105 
[1] "0.3 - 100.0 (22.0)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.4"
D1613V2, 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       24       105         8         1
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARHGAP11A MUTATED           1          0          2          1        1
  ARHGAP11A WILD-TYPE        18         10         39         30       34
                     vv
clus                  STAGE IVA STAGE IVB
  ARHGAP11A MUTATED           0         0
  ARHGAP11A WILD-TYPE        13         1
D1613V3, multiclass
            clus
vv           ARHGAP11A MUTATED ARHGAP11A WILD-TYPE
  STAGE I                    2                  62
  STAGE IA                   0                   1
  STAGE II                   1                  24
  STAGE IIA                  4                 105
  STAGE IIB                  0                   8
  STAGE IIC                  0                   1
  STAGE III                  1                  18
  STAGE IIIA                 0                  10
  STAGE IIIB                 2                  39
  STAGE IIIC                 1                  30
  STAGE IV                   1                  34
  STAGE IVA                  0                  13
  STAGE IVB                  0                   1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2  T3  T4
  ARHGAP11A MUTATED     0   4   7   3
  ARHGAP11A WILD-TYPE   9  64 241  38
D1613V4, multiclass
    clus
vv   ARHGAP11A MUTATED ARHGAP11A WILD-TYPE
  T1                 0                   9
  T2                 4                  64
  T3                 7                 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
  ARHGAP11A MUTATED     8   4   2
  ARHGAP11A WILD-TYPE 212  76  64
D1613V5, multiclass
    clus
vv   ARHGAP11A MUTATED ARHGAP11A WILD-TYPE
  N0                 8                 212
  N1                 4                  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"
D1613V6, binary
                     cls
clus                    0   1
  ARHGAP11A MUTATED     9   1
  ARHGAP11A WILD-TYPE 274  47
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  ARHGAP11A MUTATED      9    1
  ARHGAP11A WILD-TYPE  274   47
   clus
vv  ARHGAP11A MUTATED ARHGAP11A WILD-TYPE
  0                 9                 274
  1                 1                  47
[1] 2 2
[1] FALSE
D1613V7, 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
D1613V8, binary
                     cls
clus                    0   1
  ARHGAP11A MUTATED    11   3
  ARHGAP11A WILD-TYPE 306  45
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  ARHGAP11A MUTATED     11    3
  ARHGAP11A WILD-TYPE  306   45
                               clus
vv                              ARHGAP11A MUTATED ARHGAP11A WILD-TYPE
  COLON ADENOCARCINOMA                         11                 306
  COLON MUCINOUS ADENOCARCINOMA                 3                  45
[1] 2 2
[1] FALSE
                     vv
clus                   R0  R1  R2  RX
  ARHGAP11A MUTATED     6   0   1   2
  ARHGAP11A WILD-TYPE 251   2  21  19
D1613V9, multiclass
    clus
vv   ARHGAP11A MUTATED ARHGAP11A WILD-TYPE
  R0                 6                 251
  R1                 0                   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"
D1613V10, 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
D1613V11, 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(1614) Variable = PRDM14 MUTATION ANALYSIS
D1614V1, survival
                  sevent
clus2                0   1
  PRDM14 MUTATED    11   1
  PRDM14 WILD-TYPE 271  72
  PRDM14 MUTATED PRDM14 WILD-TYPE 
              12              343 
  PRDM14 MUTATED PRDM14 WILD-TYPE 
               1               72 
$`PRDM14 MUTATED`
TCGA-A6-3809 TCGA-A6-5657 TCGA-A6-5661 TCGA-AA-3663 TCGA-AA-3697 TCGA-AA-3710 
       32.75        31.63        33.53         6.97        85.05        26.99 
TCGA-AA-3845 TCGA-AA-3949 TCGA-AU-3779 TCGA-AZ-4315 TCGA-CA-6719 TCGA-CM-6167 
        0.00        26.01        14.50        58.39         1.35        14.99 

$`PRDM14 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       30.44        29.19        23.61        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3713 
        5.98        37.05        19.00        36.00         5.03        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.33         0.10        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  PRDM14 MUTATED PRDM14 WILD-TYPE 
               0                0 
  PRDM14 MUTATED PRDM14 WILD-TYPE 
           85.05           140.38 
  PRDM14 MUTATED PRDM14 WILD-TYPE 
           26.50            20.12 
[1] "0.0 - 85.0 (26.5)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "2.6"
D1614V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PRDM14 MUTATED         0        0        1         6         1         0
  PRDM14 WILD-TYPE      64        1       24       103         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PRDM14 MUTATED           1          0          2          1        0
  PRDM14 WILD-TYPE        18         10         39         30       35
                  vv
clus               STAGE IVA STAGE IVB
  PRDM14 MUTATED           0         0
  PRDM14 WILD-TYPE        13         1
D1614V3, multiclass
            clus
vv           PRDM14 MUTATED PRDM14 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               6              103
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PRDM14 MUTATED     0   0  11   1
  PRDM14 WILD-TYPE   9  68 237  40
D1614V4, multiclass
    clus
vv   PRDM14 MUTATED PRDM14 WILD-TYPE
  T1              0                9
  T2              0               68
  T3             11              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
  PRDM14 MUTATED     9   2   1
  PRDM14 WILD-TYPE 211  78  65
D1614V5, multiclass
    clus
vv   PRDM14 MUTATED PRDM14 WILD-TYPE
  N0              9              211
  N1              2               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"
D1614V6, binary
                  cls
clus                 0   1
  PRDM14 MUTATED    12   0
  PRDM14 WILD-TYPE 271  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRDM14 MUTATED     12    0
  PRDM14 WILD-TYPE  271   48
   clus
vv  PRDM14 MUTATED PRDM14 WILD-TYPE
  0             12              271
  1              0               48
[1] 2 2
[1] FALSE
D1614V7, binary
                  cls
clus                 0   1
  PRDM14 MUTATED     7   5
  PRDM14 WILD-TYPE 163 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRDM14 MUTATED      7    5
  PRDM14 WILD-TYPE  163  192
        clus
vv       PRDM14 MUTATED PRDM14 WILD-TYPE
  FEMALE              7              163
  MALE                5              192
[1] 2 2
[1] FALSE
D1614V8, binary
                  cls
clus                 0   1
  PRDM14 MUTATED    10   2
  PRDM14 WILD-TYPE 307  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRDM14 MUTATED     10    2
  PRDM14 WILD-TYPE  307   46
                               clus
vv                              PRDM14 MUTATED PRDM14 WILD-TYPE
  COLON ADENOCARCINOMA                      10              307
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PRDM14 MUTATED    11   0   0   1
  PRDM14 WILD-TYPE 246   2  22  20
D1614V9, multiclass
    clus
vv   PRDM14 MUTATED PRDM14 WILD-TYPE
  R0             11              246
  R1              0                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"
D1614V10, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PRDM14 MUTATED                                  0     1
  PRDM14 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PRDM14 MUTATED                           3     3
  PRDM14 WILD-TYPE                        16   173
D1614V11, multiclass
                                  clus
vv                                 PRDM14 MUTATED PRDM14 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(1615) Variable = LRRTM2 MUTATION ANALYSIS
D1615V1, survival
                  sevent
clus2                0   1
  LRRTM2 MUTATED     5   0
  LRRTM2 WILD-TYPE 277  73
  LRRTM2 MUTATED LRRTM2 WILD-TYPE 
               5              350 
  LRRTM2 MUTATED LRRTM2 WILD-TYPE 
               0               73 
$`LRRTM2 MUTATED`
TCGA-AA-3833 TCGA-AU-3779 TCGA-D5-6529 TCGA-F4-6856 TCGA-G4-6304 
       15.95        14.50        20.19        19.43        53.62 

$`LRRTM2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
        1.02        17.98        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       11.51        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 
       33.67        13.25         0.53        35.41       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  LRRTM2 MUTATED LRRTM2 WILD-TYPE 
            14.5              0.0 
  LRRTM2 MUTATED LRRTM2 WILD-TYPE 
           53.62           140.38 
  LRRTM2 MUTATED LRRTM2 WILD-TYPE 
           19.43            20.63 
[1] "14.5 - 53.6 (19.4)" "0.0 - 140.4 (20.6)"
[1] "hr="     "9100000"
D1615V2, 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       25       106         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LRRTM2 MUTATED           0          0          0          0        0
  LRRTM2 WILD-TYPE        19         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  LRRTM2 MUTATED           0         0
  LRRTM2 WILD-TYPE        13         1
D1615V3, multiclass
            clus
vv           LRRTM2 MUTATED LRRTM2 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               3              106
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  LRRTM2 MUTATED     0   1   3   1
  LRRTM2 WILD-TYPE   9  67 245  40
D1615V4, multiclass
    clus
vv   LRRTM2 MUTATED LRRTM2 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              3              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
  LRRTM2 MUTATED     5   0   0
  LRRTM2 WILD-TYPE 215  80  66
D1615V5, multiclass
    clus
vv   LRRTM2 MUTATED LRRTM2 WILD-TYPE
  N0              5              215
  N1              0               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"
D1615V6, binary
                  cls
clus                 0   1
  LRRTM2 MUTATED     5   0
  LRRTM2 WILD-TYPE 278  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRTM2 MUTATED      5    0
  LRRTM2 WILD-TYPE  278   48
   clus
vv  LRRTM2 MUTATED LRRTM2 WILD-TYPE
  0              5              278
  1              0               48
[1] 2 2
[1] FALSE
D1615V7, 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
D1615V8, binary
                  cls
clus                 0   1
  LRRTM2 MUTATED     4   1
  LRRTM2 WILD-TYPE 313  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRTM2 MUTATED      4    1
  LRRTM2 WILD-TYPE  313   47
                               clus
vv                              LRRTM2 MUTATED LRRTM2 WILD-TYPE
  COLON ADENOCARCINOMA                       4              313
  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 252   2  22  21
D1615V9, multiclass
    clus
vv   LRRTM2 MUTATED LRRTM2 WILD-TYPE
  R0              5              252
  R1              0                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"
D1615V10, 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
D1615V11, 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(1616) Variable = RAPGEF2 MUTATION ANALYSIS
D1616V1, survival
                   sevent
clus2                 0   1
  RAPGEF2 MUTATED    16   4
  RAPGEF2 WILD-TYPE 266  69
  RAPGEF2 MUTATED RAPGEF2 WILD-TYPE 
               20               335 
  RAPGEF2 MUTATED RAPGEF2 WILD-TYPE 
                4                69 
$`RAPGEF2 MUTATED`
TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6781 TCGA-AA-3655 TCGA-AA-3821 TCGA-AA-3833 
       22.06         8.38        19.66        61.02         1.02        15.95 
TCGA-AA-3864 TCGA-AA-3977 TCGA-AA-A010 TCGA-AA-A01P TCGA-AD-5900 TCGA-AD-6895 
       53.00        25.02        34.98        38.07         0.07         0.72 
TCGA-AZ-4315 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CK-5916 TCGA-DM-A0XD TCGA-DM-A1HB 
       58.39       100.01         0.33        21.14        24.43       135.65 
TCGA-G4-6586 TCGA-G4-6588 
       35.80        26.17 

$`RAPGEF2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.09        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        0.99        25.02        17.98        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
       40.96        21.37         4.21        56.55         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
       40.34        15.62        49.08        51.32        21.99         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        91.79        46.75        52.80 

  RAPGEF2 MUTATED RAPGEF2 WILD-TYPE 
             0.07              0.00 
  RAPGEF2 MUTATED RAPGEF2 WILD-TYPE 
           135.65            140.38 
  RAPGEF2 MUTATED RAPGEF2 WILD-TYPE 
           24.725            19.990 
[1] "0.1 - 135.7 (24.7)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.3"
D1616V2, 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       22       100         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RAPGEF2 MUTATED           1          0          1          1        0
  RAPGEF2 WILD-TYPE        18         10         40         30       35
                   vv
clus                STAGE IVA STAGE IVB
  RAPGEF2 MUTATED           0         0
  RAPGEF2 WILD-TYPE        13         1
D1616V3, multiclass
            clus
vv           RAPGEF2 MUTATED RAPGEF2 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 3                22
  STAGE IIA                9               100
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               1                30
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  RAPGEF2 MUTATED     1   3  15   2
  RAPGEF2 WILD-TYPE   8  65 233  39
D1616V4, multiclass
    clus
vv   RAPGEF2 MUTATED RAPGEF2 WILD-TYPE
  T1               1                 8
  T2               3                65
  T3              15               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
  RAPGEF2 MUTATED    17   4   0
  RAPGEF2 WILD-TYPE 203  76  66
D1616V5, multiclass
    clus
vv   RAPGEF2 MUTATED RAPGEF2 WILD-TYPE
  N0              17               203
  N1               4                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"
D1616V6, binary
                   cls
clus                  0   1
  RAPGEF2 MUTATED    17   0
  RAPGEF2 WILD-TYPE 266  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RAPGEF2 MUTATED     17    0
  RAPGEF2 WILD-TYPE  266   48
   clus
vv  RAPGEF2 MUTATED RAPGEF2 WILD-TYPE
  0              17               266
  1               0                48
[1] 2 2
[1] FALSE
D1616V7, 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
D1616V8, binary
                   cls
clus                  0   1
  RAPGEF2 MUTATED    17   4
  RAPGEF2 WILD-TYPE 300  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RAPGEF2 MUTATED     17    4
  RAPGEF2 WILD-TYPE  300   44
                               clus
vv                              RAPGEF2 MUTATED RAPGEF2 WILD-TYPE
  COLON ADENOCARCINOMA                       17               300
  COLON MUCINOUS ADENOCARCINOMA               4                44
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  RAPGEF2 MUTATED    13   0   0   2
  RAPGEF2 WILD-TYPE 244   2  22  19
D1616V9, multiclass
    clus
vv   RAPGEF2 MUTATED RAPGEF2 WILD-TYPE
  R0              13               244
  R1               0                 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"
D1616V10, 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
D1616V11, 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(1617) Variable = DDX11 MUTATION ANALYSIS
D1617V1, survival
                 sevent
clus2               0   1
  DDX11 MUTATED     5   2
  DDX11 WILD-TYPE 277  71
  DDX11 MUTATED DDX11 WILD-TYPE 
              7             348 
  DDX11 MUTATED DDX11 WILD-TYPE 
              2              71 
$`DDX11 MUTATED`
TCGA-A6-5665 TCGA-AA-3655 TCGA-AA-3715 TCGA-AZ-6599 TCGA-CM-6674 TCGA-G4-6586 
       22.06        61.02        19.04         6.77        12.95        35.80 
TCGA-G4-6588 
       26.17 

$`DDX11 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41        49.41        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       36.00        22.09        13.78        91.79        46.75        52.80 

  DDX11 MUTATED DDX11 WILD-TYPE 
           6.77            0.00 
  DDX11 MUTATED DDX11 WILD-TYPE 
          61.02          140.38 
  DDX11 MUTATED DDX11 WILD-TYPE 
         22.060          20.155 
[1] "6.8 - 61.0 (22.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.4"
D1617V2, 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       23       105         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        19         10         41         31       35        13
                 vv
clus              STAGE IVB
  DDX11 MUTATED           0
  DDX11 WILD-TYPE         1
D1617V3, multiclass
            clus
vv           DDX11 MUTATED DDX11 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              4             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DDX11 MUTATED     0   1   6   0
  DDX11 WILD-TYPE   9  67 242  41
D1617V4, multiclass
    clus
vv   DDX11 MUTATED DDX11 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             6             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
  DDX11 MUTATED     7   0   0
  DDX11 WILD-TYPE 213  80  66
D1617V5, multiclass
    clus
vv   DDX11 MUTATED DDX11 WILD-TYPE
  N0             7             213
  N1             0              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"
D1617V6, binary
                 cls
clus                0   1
  DDX11 MUTATED     6   0
  DDX11 WILD-TYPE 277  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX11 MUTATED      6    0
  DDX11 WILD-TYPE  277   48
   clus
vv  DDX11 MUTATED DDX11 WILD-TYPE
  0             6             277
  1             0              48
[1] 2 2
[1] FALSE
D1617V7, 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
D1617V8, binary
                 cls
clus                0   1
  DDX11 MUTATED     7   0
  DDX11 WILD-TYPE 310  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX11 MUTATED      7    0
  DDX11 WILD-TYPE  310   48
                               clus
vv                              DDX11 MUTATED DDX11 WILD-TYPE
  COLON ADENOCARCINOMA                      7             310
  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 251   2  22  21
D1617V9, multiclass
    clus
vv   DDX11 MUTATED DDX11 WILD-TYPE
  R0             6             251
  R1             0               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"
D1617V10, 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
D1617V11, 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(1618) Variable = CDHR3 MUTATION ANALYSIS
D1618V1, survival
                 sevent
clus2               0   1
  CDHR3 MUTATED    12   1
  CDHR3 WILD-TYPE 270  72
  CDHR3 MUTATED CDHR3 WILD-TYPE 
             13             342 
  CDHR3 MUTATED CDHR3 WILD-TYPE 
              1              72 
$`CDHR3 MUTATED`
TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6141 TCGA-AA-3510 TCGA-AD-5900 TCGA-AD-6964 
       33.53        22.06         8.38        63.98         0.07        10.88 
TCGA-AZ-4315 TCGA-CA-6717 TCGA-CM-4743 TCGA-CM-6674 TCGA-D5-6927 TCGA-D5-6930 
       58.39         0.33        23.05        12.95         9.44         1.51 
TCGA-DM-A1HB 
      135.65 

$`CDHR3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       32.71        27.09        22.52        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14         2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  CDHR3 MUTATED CDHR3 WILD-TYPE 
           0.07            0.00 
  CDHR3 MUTATED CDHR3 WILD-TYPE 
         135.65          140.38 
  CDHR3 MUTATED CDHR3 WILD-TYPE 
         12.950          20.235 
[1] "0.1 - 135.7 (12.9)" "0.0 - 140.4 (20.2)"
[1] "hr=" "2.9"
D1618V2, 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       24       100         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        19         10         40         31       35        13
                 vv
clus              STAGE IVB
  CDHR3 MUTATED           0
  CDHR3 WILD-TYPE         1
D1618V3, multiclass
            clus
vv           CDHR3 MUTATED CDHR3 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              9             100
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CDHR3 MUTATED     0   1  11   1
  CDHR3 WILD-TYPE   9  67 237  40
D1618V4, multiclass
    clus
vv   CDHR3 MUTATED CDHR3 WILD-TYPE
  T1             0               9
  T2             1              67
  T3            11             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
  CDHR3 MUTATED    11   1   1
  CDHR3 WILD-TYPE 209  79  65
D1618V5, multiclass
    clus
vv   CDHR3 MUTATED CDHR3 WILD-TYPE
  N0            11             209
  N1             1              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"
D1618V6, binary
                 cls
clus                0   1
  CDHR3 MUTATED    11   0
  CDHR3 WILD-TYPE 272  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDHR3 MUTATED     11    0
  CDHR3 WILD-TYPE  272   48
   clus
vv  CDHR3 MUTATED CDHR3 WILD-TYPE
  0            11             272
  1             0              48
[1] 2 2
[1] FALSE
D1618V7, 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
D1618V8, binary
                 cls
clus                0   1
  CDHR3 MUTATED    10   3
  CDHR3 WILD-TYPE 307  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDHR3 MUTATED     10    3
  CDHR3 WILD-TYPE  307   45
                               clus
vv                              CDHR3 MUTATED CDHR3 WILD-TYPE
  COLON ADENOCARCINOMA                     10             307
  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 248   2  22  20
D1618V9, multiclass
    clus
vv   CDHR3 MUTATED CDHR3 WILD-TYPE
  R0             9             248
  R1             0               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"
D1618V10, 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
D1618V11, 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(1619) Variable = P2RY11 MUTATION ANALYSIS
D1619V1, survival
                  sevent
clus2                0   1
  P2RY11 MUTATED     3   1
  P2RY11 WILD-TYPE 279  72
  P2RY11 MUTATED P2RY11 WILD-TYPE 
               4              351 
  P2RY11 MUTATED P2RY11 WILD-TYPE 
               1               72 
$`P2RY11 MUTATED`
TCGA-AA-3663 TCGA-AZ-6601 TCGA-D5-6540 TCGA-G4-6628 
        6.97       100.01        16.14        52.80 

$`P2RY11 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       26.17        91.79        46.75 

  P2RY11 MUTATED P2RY11 WILD-TYPE 
            6.97             0.00 
  P2RY11 MUTATED P2RY11 WILD-TYPE 
          100.01           140.38 
  P2RY11 MUTATED P2RY11 WILD-TYPE 
           34.47            20.19 
[1] "7.0 - 100.0 (34.5)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.5"
D1619V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  P2RY11 MUTATED         2        0        2         0         1         0
  P2RY11 WILD-TYPE      62        1       23       109         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  P2RY11 MUTATED           0          0          0          0        0
  P2RY11 WILD-TYPE        19         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  P2RY11 MUTATED           0         0
  P2RY11 WILD-TYPE        13         1
D1619V3, multiclass
            clus
vv           P2RY11 MUTATED P2RY11 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               0              109
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  P2RY11 MUTATED     0   2   2   1
  P2RY11 WILD-TYPE   9  66 246  40
D1619V4, multiclass
    clus
vv   P2RY11 MUTATED P2RY11 WILD-TYPE
  T1              0                9
  T2              2               66
  T3              2              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
  P2RY11 MUTATED     5   0   0
  P2RY11 WILD-TYPE 215  80  66
D1619V5, multiclass
    clus
vv   P2RY11 MUTATED P2RY11 WILD-TYPE
  N0              5              215
  N1              0               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"
D1619V6, binary
                  cls
clus                 0   1
  P2RY11 MUTATED     4   0
  P2RY11 WILD-TYPE 279  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  P2RY11 MUTATED      4    0
  P2RY11 WILD-TYPE  279   48
   clus
vv  P2RY11 MUTATED P2RY11 WILD-TYPE
  0              4              279
  1              0               48
[1] 2 2
[1] FALSE
D1619V7, binary
                  cls
clus                 0   1
  P2RY11 MUTATED     1   4
  P2RY11 WILD-TYPE 169 193
[1] "tbl2"
                  cls
clus               [,1] [,2]
  P2RY11 MUTATED      1    4
  P2RY11 WILD-TYPE  169  193
        clus
vv       P2RY11 MUTATED P2RY11 WILD-TYPE
  FEMALE              1              169
  MALE                4              193
[1] 2 2
[1] FALSE
D1619V8, binary
                  cls
clus                 0   1
  P2RY11 MUTATED     4   1
  P2RY11 WILD-TYPE 313  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  P2RY11 MUTATED      4    1
  P2RY11 WILD-TYPE  313   47
                               clus
vv                              P2RY11 MUTATED P2RY11 WILD-TYPE
  COLON ADENOCARCINOMA                       4              313
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  P2RY11 MUTATED     3   0   0   1
  P2RY11 WILD-TYPE 254   2  22  20
D1619V9, multiclass
    clus
vv   P2RY11 MUTATED P2RY11 WILD-TYPE
  R0              3              254
  R1              0                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"
D1619V10, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  P2RY11 MUTATED                                  0     0
  P2RY11 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  P2RY11 MUTATED                           0     4
  P2RY11 WILD-TYPE                        19   172
D1619V11, multiclass
                                  clus
vv                                 P2RY11 MUTATED P2RY11 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 = TGIF1 MUTATION ANALYSIS
D1620V1, survival
                 sevent
clus2               0   1
  TGIF1 MUTATED     6   2
  TGIF1 WILD-TYPE 276  71
  TGIF1 MUTATED TGIF1 WILD-TYPE 
              8             347 
  TGIF1 MUTATED TGIF1 WILD-TYPE 
              2              71 
$`TGIF1 MUTATED`
TCGA-AA-3510 TCGA-AA-3848 TCGA-CA-6716 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6927 
       63.98        10.06         0.26        15.58        12.39         9.44 
TCGA-D5-6932 TCGA-DM-A28C 
       11.38        81.37 

$`TGIF1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       17.03         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6922 
        4.80        17.13        12.49        16.14         7.53        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         1.51 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28E 
       44.32       131.51       135.65       139.17         6.12       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  TGIF1 MUTATED TGIF1 WILD-TYPE 
           0.26            0.00 
  TGIF1 MUTATED TGIF1 WILD-TYPE 
          81.37          140.38 
  TGIF1 MUTATED TGIF1 WILD-TYPE 
         11.885          20.980 
[1] "0.3 - 81.4 (11.9)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.1"
D1620V2, 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       24       103         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        19         10         41         30       35        13
                 vv
clus              STAGE IVB
  TGIF1 MUTATED           0
  TGIF1 WILD-TYPE         1
D1620V3, multiclass
            clus
vv           TGIF1 MUTATED TGIF1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              6             103
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TGIF1 MUTATED     0   1   8   0
  TGIF1 WILD-TYPE   9  67 240  41
D1620V4, multiclass
    clus
vv   TGIF1 MUTATED TGIF1 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             8             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
  TGIF1 MUTATED     8   0   1
  TGIF1 WILD-TYPE 212  80  65
D1620V5, multiclass
    clus
vv   TGIF1 MUTATED TGIF1 WILD-TYPE
  N0             8             212
  N1             0              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
  TGIF1 MUTATED     8   0
  TGIF1 WILD-TYPE 275  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TGIF1 MUTATED      8    0
  TGIF1 WILD-TYPE  275   48
   clus
vv  TGIF1 MUTATED TGIF1 WILD-TYPE
  0             8             275
  1             0              48
[1] 2 2
[1] FALSE
D1620V7, 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
D1620V8, binary
                 cls
clus                0   1
  TGIF1 MUTATED     9   0
  TGIF1 WILD-TYPE 308  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TGIF1 MUTATED      9    0
  TGIF1 WILD-TYPE  308   48
                               clus
vv                              TGIF1 MUTATED TGIF1 WILD-TYPE
  COLON ADENOCARCINOMA                      9             308
  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 251   2  22  19
D1620V9, multiclass
    clus
vv   TGIF1 MUTATED TGIF1 WILD-TYPE
  R0             6             251
  R1             0               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"
D1620V10, 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
D1620V11, 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(1621) Variable = HECTD2 MUTATION ANALYSIS
D1621V1, survival
                  sevent
clus2                0   1
  HECTD2 MUTATED     7   2
  HECTD2 WILD-TYPE 275  71
  HECTD2 MUTATED HECTD2 WILD-TYPE 
               9              346 
  HECTD2 MUTATED HECTD2 WILD-TYPE 
               2               71 
$`HECTD2 MUTATED`
TCGA-AA-3950 TCGA-AA-A00E TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-6606 TCGA-CA-5796 
       24.00        30.02         4.01        34.98        11.74         3.25 
TCGA-CA-6717 TCGA-CA-6718 TCGA-D5-6927 
        0.33         0.10         9.44 

$`HECTD2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
      100.01        29.56         5.23         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.06         3.29         0.07         0.26         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  HECTD2 MUTATED HECTD2 WILD-TYPE 
             0.1              0.0 
  HECTD2 MUTATED HECTD2 WILD-TYPE 
           34.98           140.38 
  HECTD2 MUTATED HECTD2 WILD-TYPE 
            9.44            20.63 
[1] "0.1 - 35.0 (9.4)"   "0.0 - 140.4 (20.6)"
[1] "hr=" "2.2"
D1621V2, 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       25       102         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HECTD2 MUTATED           0          0          0          0        1
  HECTD2 WILD-TYPE        19         10         41         31       34
                  vv
clus               STAGE IVA STAGE IVB
  HECTD2 MUTATED           0         0
  HECTD2 WILD-TYPE        13         1
D1621V3, multiclass
            clus
vv           HECTD2 MUTATED HECTD2 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               7              102
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  HECTD2 MUTATED     0   0   7   3
  HECTD2 WILD-TYPE   9  68 241  38
D1621V4, multiclass
    clus
vv   HECTD2 MUTATED HECTD2 WILD-TYPE
  T1              0                9
  T2              0               68
  T3              7              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
  HECTD2 MUTATED     9   0   1
  HECTD2 WILD-TYPE 211  80  65
D1621V5, multiclass
    clus
vv   HECTD2 MUTATED HECTD2 WILD-TYPE
  N0              9              211
  N1              0               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"
D1621V6, binary
                  cls
clus                 0   1
  HECTD2 MUTATED     9   1
  HECTD2 WILD-TYPE 274  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HECTD2 MUTATED      9    1
  HECTD2 WILD-TYPE  274   47
   clus
vv  HECTD2 MUTATED HECTD2 WILD-TYPE
  0              9              274
  1              1               47
[1] 2 2
[1] FALSE
D1621V7, 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
D1621V8, binary
                  cls
clus                 0   1
  HECTD2 MUTATED     6   4
  HECTD2 WILD-TYPE 311  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HECTD2 MUTATED      6    4
  HECTD2 WILD-TYPE  311   44
                               clus
vv                              HECTD2 MUTATED HECTD2 WILD-TYPE
  COLON ADENOCARCINOMA                       6              311
  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 250   2  22  19
D1621V9, multiclass
    clus
vv   HECTD2 MUTATED HECTD2 WILD-TYPE
  R0              7              250
  R1              0                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"
D1621V10, 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
D1621V11, 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(1622) Variable = VPRBP MUTATION ANALYSIS
D1622V1, survival
                 sevent
clus2               0   1
  VPRBP MUTATED    11   1
  VPRBP WILD-TYPE 271  72
  VPRBP MUTATED VPRBP WILD-TYPE 
             12             343 
  VPRBP MUTATED VPRBP WILD-TYPE 
              1              72 
$`VPRBP MUTATED`
TCGA-A6-5661 TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3844 TCGA-AA-A010 TCGA-AD-6895 
       33.53        24.39        19.66        14.93        34.98         0.72 
TCGA-AY-6386 TCGA-CA-6718 TCGA-CK-5916 TCGA-CM-5868 TCGA-CM-6171 TCGA-G4-6309 
       17.82         0.10        21.14        17.03        14.04        51.75 

$`VPRBP WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       38.99        37.02         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
        0.07        21.37         4.21        56.55         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 
       16.31         0.95        15.75         0.20        21.44        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.33         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        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-6172 TCGA-CM-6674 TCGA-CM-6675 
       12.99        13.02        15.02        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  VPRBP MUTATED VPRBP WILD-TYPE 
            0.1             0.0 
  VPRBP MUTATED VPRBP WILD-TYPE 
          51.75          140.38 
  VPRBP MUTATED VPRBP WILD-TYPE 
          18.74           20.28 
[1] "0.1 - 51.8 (18.7)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "2.1"
D1622V2, 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       25       106         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  VPRBP MUTATED           0          0          2          2        0         1
  VPRBP WILD-TYPE        19         10         39         29       35        12
                 vv
clus              STAGE IVB
  VPRBP MUTATED           0
  VPRBP WILD-TYPE         1
D1622V3, multiclass
            clus
vv           VPRBP MUTATED VPRBP WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              3             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             2              29
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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   3
  VPRBP WILD-TYPE   8  66 241  38
D1622V4, multiclass
    clus
vv   VPRBP MUTATED VPRBP WILD-TYPE
  T1             1               8
  T2             2              66
  T3             7             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
  VPRBP MUTATED     7   5   1
  VPRBP WILD-TYPE 213  75  65
D1622V5, multiclass
    clus
vv   VPRBP MUTATED VPRBP WILD-TYPE
  N0             7             213
  N1             5              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"
D1622V6, binary
                 cls
clus                0   1
  VPRBP MUTATED    10   1
  VPRBP WILD-TYPE 273  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VPRBP MUTATED     10    1
  VPRBP WILD-TYPE  273   47
   clus
vv  VPRBP MUTATED VPRBP WILD-TYPE
  0            10             273
  1             1              47
[1] 2 2
[1] FALSE
D1622V7, binary
                 cls
clus                0   1
  VPRBP MUTATED     9   4
  VPRBP WILD-TYPE 161 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VPRBP MUTATED      9    4
  VPRBP WILD-TYPE  161  193
        clus
vv       VPRBP MUTATED VPRBP WILD-TYPE
  FEMALE             9             161
  MALE               4             193
[1] 2 2
[1] FALSE
D1622V8, binary
                 cls
clus                0   1
  VPRBP MUTATED    12   1
  VPRBP WILD-TYPE 305  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VPRBP MUTATED     12    1
  VPRBP WILD-TYPE  305   47
                               clus
vv                              VPRBP MUTATED VPRBP WILD-TYPE
  COLON ADENOCARCINOMA                     12             305
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  VPRBP MUTATED     9   0   0   2
  VPRBP WILD-TYPE 248   2  22  19
D1622V9, multiclass
    clus
vv   VPRBP MUTATED VPRBP WILD-TYPE
  R0             9             248
  R1             0               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"
D1622V10, 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     6
  VPRBP WILD-TYPE                        16   170
D1622V11, 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                                        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(1623) Variable = KPNA3 MUTATION ANALYSIS
D1623V1, survival
                 sevent
clus2               0   1
  KPNA3 MUTATED     3   1
  KPNA3 WILD-TYPE 279  72
  KPNA3 MUTATED KPNA3 WILD-TYPE 
              4             351 
  KPNA3 MUTATED KPNA3 WILD-TYPE 
              1              72 
$`KPNA3 MUTATED`
TCGA-AA-3663 TCGA-AA-A00A TCGA-AZ-6598 TCGA-CM-5348 
        6.97        38.04        49.41        22.98 

$`KPNA3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13        83.80        22.36        62.79        61.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  KPNA3 MUTATED KPNA3 WILD-TYPE 
           6.97            0.00 
  KPNA3 MUTATED KPNA3 WILD-TYPE 
          49.41          140.38 
  KPNA3 MUTATED KPNA3 WILD-TYPE 
          30.51           20.12 
[1] "7.0 - 49.4 (30.5)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.1"
D1623V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KPNA3 MUTATED         0        0        2         2         0         0
  KPNA3 WILD-TYPE      64        1       23       107         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KPNA3 MUTATED           0          0          1          0        0         0
  KPNA3 WILD-TYPE        19         10         40         31       35        13
                 vv
clus              STAGE IVB
  KPNA3 MUTATED           0
  KPNA3 WILD-TYPE         1
D1623V3, multiclass
            clus
vv           KPNA3 MUTATED KPNA3 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              2             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KPNA3 MUTATED     0   0   5   0
  KPNA3 WILD-TYPE   9  68 243  41
D1623V4, multiclass
    clus
vv   KPNA3 MUTATED KPNA3 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             5             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
  KPNA3 MUTATED     4   1   0
  KPNA3 WILD-TYPE 216  79  66
D1623V5, multiclass
    clus
vv   KPNA3 MUTATED KPNA3 WILD-TYPE
  N0             4             216
  N1             1              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"
D1623V6, binary
                 cls
clus                0   1
  KPNA3 MUTATED     4   0
  KPNA3 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KPNA3 MUTATED      4    0
  KPNA3 WILD-TYPE  279   48
   clus
vv  KPNA3 MUTATED KPNA3 WILD-TYPE
  0             4             279
  1             0              48
[1] 2 2
[1] FALSE
D1623V7, binary
                 cls
clus                0   1
  KPNA3 MUTATED     2   3
  KPNA3 WILD-TYPE 168 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KPNA3 MUTATED      2    3
  KPNA3 WILD-TYPE  168  194
        clus
vv       KPNA3 MUTATED KPNA3 WILD-TYPE
  FEMALE             2             168
  MALE               3             194
[1] 2 2
[1] FALSE
D1623V8, binary
                 cls
clus                0   1
  KPNA3 MUTATED     5   0
  KPNA3 WILD-TYPE 312  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KPNA3 MUTATED      5    0
  KPNA3 WILD-TYPE  312   48
                               clus
vv                              KPNA3 MUTATED KPNA3 WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  KPNA3 MUTATED     4   0   0   0
  KPNA3 WILD-TYPE 253   2  22  21
D1623V9, multiclass
    clus
vv   KPNA3 MUTATED KPNA3 WILD-TYPE
  R0             4             253
  R1             0               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"
D1623V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KPNA3 MUTATED                                  0     0
  KPNA3 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KPNA3 MUTATED                           0     2
  KPNA3 WILD-TYPE                        19   174
D1623V11, multiclass
[1] "Remove cluster labels:" "KPNA3 MUTATED"         
clus
  KPNA3 MUTATED KPNA3 WILD-TYPE 
              2             204 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-4105 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-A6-5656      TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5660 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-A6-5661      TCGA-A6-5662      TCGA-A6-5664      TCGA-A6-5665 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-A6-5666      TCGA-A6-6137      TCGA-A6-6138      TCGA-A6-6141 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-A6-6142      TCGA-A6-6648      TCGA-A6-6649      TCGA-A6-6651 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-A6-6652      TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-A6-6781      TCGA-A6-6782      TCGA-AD-5900      TCGA-AD-6548 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-AD-6888      TCGA-AD-6889      TCGA-AD-6890      TCGA-AD-6895 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-AD-6899      TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6964 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-AD-6965      TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-AY-4071      TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-AY-6386      TCGA-AZ-4315      TCGA-AZ-4323      TCGA-AZ-4616 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-AZ-4681      TCGA-AZ-4682      TCGA-AZ-5403      TCGA-AZ-5407 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-AZ-6599      TCGA-AZ-6600      TCGA-AZ-6601      TCGA-AZ-6603 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-AZ-6605      TCGA-AZ-6606      TCGA-AZ-6607      TCGA-AZ-6608 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-CA-5254      TCGA-CA-5255      TCGA-CA-5796      TCGA-CA-5797 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-CA-6715      TCGA-CA-6716      TCGA-CA-6717      TCGA-CA-6718 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-CA-6719      TCGA-CK-4947      TCGA-CK-4948      TCGA-CK-4950 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-CK-4952      TCGA-CK-5912      TCGA-CK-5913      TCGA-CK-5914 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-CK-5915      TCGA-CK-5916      TCGA-CK-6746      TCGA-CK-6747 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-CK-6748      TCGA-CK-6751      TCGA-CM-4743      TCGA-CM-4744 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-CM-4746      TCGA-CM-4747      TCGA-CM-4752      TCGA-CM-5341 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-CM-5344      TCGA-CM-5349      TCGA-CM-5860      TCGA-CM-5861 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-CM-5862      TCGA-CM-5863      TCGA-CM-5864      TCGA-CM-5868 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-CM-6161      TCGA-CM-6162      TCGA-CM-6163      TCGA-CM-6164 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-CM-6165      TCGA-CM-6166      TCGA-CM-6167      TCGA-CM-6168 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-CM-6169      TCGA-CM-6170      TCGA-CM-6171      TCGA-CM-6172 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-CM-6674      TCGA-CM-6675      TCGA-CM-6676      TCGA-CM-6677 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-CM-6678      TCGA-CM-6679      TCGA-CM-6680      TCGA-D5-5537 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-D5-5538      TCGA-D5-5539      TCGA-D5-5540      TCGA-D5-5541 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-D5-6529      TCGA-D5-6532      TCGA-D5-6533      TCGA-D5-6534 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-D5-6535      TCGA-D5-6536      TCGA-D5-6537      TCGA-D5-6538 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-D5-6539      TCGA-D5-6540      TCGA-D5-6541      TCGA-D5-6898 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923      TCGA-D5-6924 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-D5-6926      TCGA-D5-6927      TCGA-D5-6928      TCGA-D5-6929 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-D5-6930      TCGA-D5-6931      TCGA-D5-6932      TCGA-D5-7000 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-DM-A0X9      TCGA-DM-A0XD      TCGA-DM-A0XF      TCGA-DM-A1D0 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-DM-A1D4      TCGA-DM-A1D6      TCGA-DM-A1D7      TCGA-DM-A1D8 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-DM-A1D9      TCGA-DM-A1DA      TCGA-DM-A1DB      TCGA-DM-A1HA 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-DM-A1HB      TCGA-DM-A282      TCGA-DM-A285      TCGA-DM-A28C 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-DM-A28E      TCGA-DM-A28F      TCGA-DM-A28G      TCGA-DM-A28H 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-DM-A28K      TCGA-F4-6459      TCGA-F4-6460      TCGA-F4-6569 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704      TCGA-F4-6805 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808      TCGA-F4-6809 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856      TCGA-G4-6293 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304      TCGA-G4-6306 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310      TCGA-G4-6315 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323      TCGA-G4-6586 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-G4-6588      TCGA-G4-6625      TCGA-G4-6626      TCGA-G4-6628 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 

Clustering(1624) Variable = XRCC6 MUTATION ANALYSIS
D1624V1, survival
                 sevent
clus2               0   1
  XRCC6 MUTATED     5   2
  XRCC6 WILD-TYPE 277  71
  XRCC6 MUTATED XRCC6 WILD-TYPE 
              7             348 
  XRCC6 MUTATED XRCC6 WILD-TYPE 
              2              71 
$`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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20       130.65        92.75        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  XRCC6 MUTATED XRCC6 WILD-TYPE 
          11.64            0.00 
  XRCC6 MUTATED XRCC6 WILD-TYPE 
         135.65          140.38 
  XRCC6 MUTATED XRCC6 WILD-TYPE 
         19.040          20.235 
[1] "11.6 - 135.7 (19.0)" "0.0 - 140.4 (20.2)" 
[1] "hr=" "1"  
D1624V2, 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       24       106         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        19         10         40         31       35        13
                 vv
clus              STAGE IVB
  XRCC6 MUTATED           0
  XRCC6 WILD-TYPE         1
D1624V3, multiclass
            clus
vv           XRCC6 MUTATED XRCC6 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              3             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  XRCC6 MUTATED     0   1   5   1
  XRCC6 WILD-TYPE   9  67 243  40
D1624V4, multiclass
    clus
vv   XRCC6 MUTATED XRCC6 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             5             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
  XRCC6 MUTATED     6   1   0
  XRCC6 WILD-TYPE 214  79  66
D1624V5, multiclass
    clus
vv   XRCC6 MUTATED XRCC6 WILD-TYPE
  N0             6             214
  N1             1              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"
D1624V6, binary
                 cls
clus                0   1
  XRCC6 MUTATED     7   0
  XRCC6 WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XRCC6 MUTATED      7    0
  XRCC6 WILD-TYPE  276   48
   clus
vv  XRCC6 MUTATED XRCC6 WILD-TYPE
  0             7             276
  1             0              48
[1] 2 2
[1] FALSE
D1624V7, 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
D1624V8, binary
                 cls
clus                0   1
  XRCC6 MUTATED     5   2
  XRCC6 WILD-TYPE 312  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XRCC6 MUTATED      5    2
  XRCC6 WILD-TYPE  312   46
                               clus
vv                              XRCC6 MUTATED XRCC6 WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  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 252   2  22  21
D1624V9, multiclass
    clus
vv   XRCC6 MUTATED XRCC6 WILD-TYPE
  R0             5             252
  R1             0               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"
D1624V10, 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
D1624V11, 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(1625) Variable = ZNF594 MUTATION ANALYSIS
D1625V1, survival
                  sevent
clus2                0   1
  ZNF594 MUTATED    11   2
  ZNF594 WILD-TYPE 271  71
  ZNF594 MUTATED ZNF594 WILD-TYPE 
              13              342 
  ZNF594 MUTATED ZNF594 WILD-TYPE 
               2               71 
$`ZNF594 MUTATED`
TCGA-A6-6141 TCGA-AA-3950 TCGA-AA-3977 TCGA-AZ-4315 TCGA-AZ-5403 TCGA-CA-6717 
        8.38        24.00        25.02        58.39        62.79         0.33 
TCGA-CA-6718 TCGA-CM-4752 TCGA-CM-6171 TCGA-CM-6677 TCGA-D5-6898 TCGA-F4-6570 
        0.10        13.02        14.04        11.08         7.53         6.18 
TCGA-G4-6309 
       51.75 

$`ZNF594 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07         0.26         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        16.14        15.58        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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        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        13.38        13.45        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  ZNF594 MUTATED ZNF594 WILD-TYPE 
             0.1              0.0 
  ZNF594 MUTATED ZNF594 WILD-TYPE 
           62.79           140.38 
  ZNF594 MUTATED ZNF594 WILD-TYPE 
           13.02            20.63 
[1] "0.1 - 62.8 (13.0)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "1.3"
D1625V2, 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       24       100         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF594 MUTATED           0          0          1          0        0
  ZNF594 WILD-TYPE        19         10         40         31       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF594 MUTATED           0         0
  ZNF594 WILD-TYPE        13         1
D1625V3, multiclass
            clus
vv           ZNF594 MUTATED ZNF594 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               9              100
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF594 MUTATED     0   3  11   0
  ZNF594 WILD-TYPE   9  65 237  41
D1625V4, multiclass
    clus
vv   ZNF594 MUTATED ZNF594 WILD-TYPE
  T1              0                9
  T2              3               65
  T3             11              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
  ZNF594 MUTATED    13   1   0
  ZNF594 WILD-TYPE 207  79  66
D1625V5, multiclass
    clus
vv   ZNF594 MUTATED ZNF594 WILD-TYPE
  N0             13              207
  N1              1               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"
D1625V6, binary
                  cls
clus                 0   1
  ZNF594 MUTATED    12   0
  ZNF594 WILD-TYPE 271  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF594 MUTATED     12    0
  ZNF594 WILD-TYPE  271   48
   clus
vv  ZNF594 MUTATED ZNF594 WILD-TYPE
  0             12              271
  1              0               48
[1] 2 2
[1] FALSE
D1625V7, 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
D1625V8, binary
                  cls
clus                 0   1
  ZNF594 MUTATED    12   2
  ZNF594 WILD-TYPE 305  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF594 MUTATED     12    2
  ZNF594 WILD-TYPE  305   46
                               clus
vv                              ZNF594 MUTATED ZNF594 WILD-TYPE
  COLON ADENOCARCINOMA                      12              305
  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 248   2  22  19
D1625V9, multiclass
    clus
vv   ZNF594 MUTATED ZNF594 WILD-TYPE
  R0              9              248
  R1              0                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"
D1625V10, 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
D1625V11, 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(1626) Variable = PPIL5 MUTATION ANALYSIS
D1626V1, survival
                 sevent
clus2               0   1
  PPIL5 MUTATED     2   2
  PPIL5 WILD-TYPE 280  71
  PPIL5 MUTATED PPIL5 WILD-TYPE 
              4             351 
  PPIL5 MUTATED PPIL5 WILD-TYPE 
              2              71 
$`PPIL5 MUTATED`
TCGA-A6-2671 TCGA-AA-A01P TCGA-D5-6927 TCGA-G4-6588 
       43.76        38.07         9.44        26.17 

$`PPIL5 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  PPIL5 MUTATED PPIL5 WILD-TYPE 
           9.44            0.00 
  PPIL5 MUTATED PPIL5 WILD-TYPE 
          43.76          140.38 
  PPIL5 MUTATED PPIL5 WILD-TYPE 
          32.12           20.12 
[1] "9.4 - 43.8 (32.1)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "2.3"
D1626V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PPIL5 MUTATED         0        0        0         2         0         0
  PPIL5 WILD-TYPE      64        1       25       107         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PPIL5 MUTATED           2          0          0          0        1         0
  PPIL5 WILD-TYPE        17         10         41         31       34        13
                 vv
clus              STAGE IVB
  PPIL5 MUTATED           0
  PPIL5 WILD-TYPE         1
D1626V3, multiclass
            clus
vv           PPIL5 MUTATED PPIL5 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              2             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PPIL5 MUTATED     0   0   5   0
  PPIL5 WILD-TYPE   9  68 243  41
D1626V4, multiclass
    clus
vv   PPIL5 MUTATED PPIL5 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             5             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
  PPIL5 MUTATED     2   1   2
  PPIL5 WILD-TYPE 218  79  64
D1626V5, multiclass
    clus
vv   PPIL5 MUTATED PPIL5 WILD-TYPE
  N0             2             218
  N1             1              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"
D1626V6, binary
                 cls
clus                0   1
  PPIL5 MUTATED     4   1
  PPIL5 WILD-TYPE 279  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPIL5 MUTATED      4    1
  PPIL5 WILD-TYPE  279   47
   clus
vv  PPIL5 MUTATED PPIL5 WILD-TYPE
  0             4             279
  1             1              47
[1] 2 2
[1] FALSE
D1626V7, binary
                 cls
clus                0   1
  PPIL5 MUTATED     2   3
  PPIL5 WILD-TYPE 168 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPIL5 MUTATED      2    3
  PPIL5 WILD-TYPE  168  194
        clus
vv       PPIL5 MUTATED PPIL5 WILD-TYPE
  FEMALE             2             168
  MALE               3             194
[1] 2 2
[1] FALSE
D1626V8, binary
                 cls
clus                0   1
  PPIL5 MUTATED     5   0
  PPIL5 WILD-TYPE 312  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPIL5 MUTATED      5    0
  PPIL5 WILD-TYPE  312   48
                               clus
vv                              PPIL5 MUTATED PPIL5 WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PPIL5 MUTATED     5   0   0   0
  PPIL5 WILD-TYPE 252   2  22  21
D1626V9, multiclass
    clus
vv   PPIL5 MUTATED PPIL5 WILD-TYPE
  R0             5             252
  R1             0               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"
D1626V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PPIL5 MUTATED                                  0     0
  PPIL5 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PPIL5 MUTATED                           0     3
  PPIL5 WILD-TYPE                        19   173
D1626V11, multiclass
                                  clus
vv                                 PPIL5 MUTATED PPIL5 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(1627) Variable = SESTD1 MUTATION ANALYSIS
D1627V1, survival
                  sevent
clus2                0   1
  SESTD1 MUTATED    11   5
  SESTD1 WILD-TYPE 271  68
  SESTD1 MUTATED SESTD1 WILD-TYPE 
              16              339 
  SESTD1 MUTATED SESTD1 WILD-TYPE 
               5               68 
$`SESTD1 MUTATED`
TCGA-A6-2678 TCGA-A6-6653 TCGA-A6-6780 TCGA-AA-3492 TCGA-AA-3529 TCGA-AA-3554 
       42.28        24.39        20.12         3.02         0.00        17.95 
TCGA-AA-3952 TCGA-AA-A00J TCGA-AA-A01Q TCGA-AU-6004 TCGA-AZ-6598 TCGA-CA-6717 
        2.01        18.05         1.02        27.09        49.41         0.33 
TCGA-D5-6930 TCGA-F4-6855 TCGA-G4-6303 TCGA-G4-6628 
        1.51        35.41        65.85        52.80 

$`SESTD1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2683 
       43.76        46.65        43.76        42.90        24.33        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6781 
       25.18        24.16        21.76        24.69        23.87        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 
       37.05        36.03         8.05        19.07        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3556 
       33.99        21.01        13.02        24.00        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-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-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.20        14.50        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 
       29.59        16.24        33.67        13.25         0.53        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      107.67        74.56        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       26.17        91.79        46.75 

  SESTD1 MUTATED SESTD1 WILD-TYPE 
               0                0 
  SESTD1 MUTATED SESTD1 WILD-TYPE 
           65.85           140.38 
  SESTD1 MUTATED SESTD1 WILD-TYPE 
          19.085           20.280 
[1] "0.0 - 65.8 (19.1)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.7"
D1627V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SESTD1 MUTATED         3        0        3         5         0         0
  SESTD1 WILD-TYPE      61        1       22       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        19         10         39         29       34
                  vv
clus               STAGE IVA STAGE IVB
  SESTD1 MUTATED           0         0
  SESTD1 WILD-TYPE        13         1
D1627V3, multiclass
            clus
vv           SESTD1 MUTATED SESTD1 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                3               22
  STAGE IIA               5              104
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              2               29
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SESTD1 MUTATED     0   3  12   1
  SESTD1 WILD-TYPE   9  65 236  40
D1627V4, multiclass
    clus
vv   SESTD1 MUTATED SESTD1 WILD-TYPE
  T1              0                9
  T2              3               65
  T3             12              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
  SESTD1 MUTATED    11   3   2
  SESTD1 WILD-TYPE 209  77  64
D1627V5, multiclass
    clus
vv   SESTD1 MUTATED SESTD1 WILD-TYPE
  N0             11              209
  N1              3               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"
D1627V6, binary
                  cls
clus                 0   1
  SESTD1 MUTATED    13   1
  SESTD1 WILD-TYPE 270  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SESTD1 MUTATED     13    1
  SESTD1 WILD-TYPE  270   47
   clus
vv  SESTD1 MUTATED SESTD1 WILD-TYPE
  0             13              270
  1              1               47
[1] 2 2
[1] FALSE
D1627V7, binary
                  cls
clus                 0   1
  SESTD1 MUTATED     9   7
  SESTD1 WILD-TYPE 161 190
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SESTD1 MUTATED      9    7
  SESTD1 WILD-TYPE  161  190
        clus
vv       SESTD1 MUTATED SESTD1 WILD-TYPE
  FEMALE              9              161
  MALE                7              190
[1] 2 2
[1] FALSE
D1627V8, binary
                  cls
clus                 0   1
  SESTD1 MUTATED    12   4
  SESTD1 WILD-TYPE 305  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SESTD1 MUTATED     12    4
  SESTD1 WILD-TYPE  305   44
                               clus
vv                              SESTD1 MUTATED SESTD1 WILD-TYPE
  COLON ADENOCARCINOMA                      12              305
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SESTD1 MUTATED    12   0   0   1
  SESTD1 WILD-TYPE 245   2  22  20
D1627V9, multiclass
    clus
vv   SESTD1 MUTATED SESTD1 WILD-TYPE
  R0             12              245
  R1              0                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"
D1627V10, 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     9
  SESTD1 WILD-TYPE                        19   167
D1627V11, 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                                         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(1628) Variable = AGTPBP1 MUTATION ANALYSIS
D1628V1, survival
                   sevent
clus2                 0   1
  AGTPBP1 MUTATED    13   3
  AGTPBP1 WILD-TYPE 269  70
  AGTPBP1 MUTATED AGTPBP1 WILD-TYPE 
               16               339 
  AGTPBP1 MUTATED AGTPBP1 WILD-TYPE 
                3                70 
$`AGTPBP1 MUTATED`
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-6649 TCGA-A6-6780 TCGA-AA-3510 
       33.53        23.61        32.71        24.16        20.12        63.98 
TCGA-AA-A00J TCGA-AA-A02J TCGA-AD-6964 TCGA-AY-6197 TCGA-AZ-4315 TCGA-CA-6717 
       18.05         5.03        10.88        21.44        58.39         0.33 
TCGA-CM-5349 TCGA-D5-6534 TCGA-DM-A1HA TCGA-F4-6570 
       30.08        43.27       131.51         6.18 

$`AGTPBP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5664 TCGA-A6-5665 
       32.91        31.63        30.44        29.19        22.09        22.06 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 
       27.09        22.52         8.38        25.08        25.18        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 
       24.69        24.39        23.87        19.66        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        3.02         1.02        35.01         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       51.98        39.98         2.01        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
        0.20        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 
       13.51        11.51        20.19        18.25         1.32        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  AGTPBP1 MUTATED AGTPBP1 WILD-TYPE 
             0.33              0.00 
  AGTPBP1 MUTATED AGTPBP1 WILD-TYPE 
           131.51            140.38 
  AGTPBP1 MUTATED AGTPBP1 WILD-TYPE 
           23.885            19.990 
[1] "0.3 - 131.5 (23.9)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.3"
D1628V2, 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       23       101         8         0
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AGTPBP1 MUTATED           0          0          2          1        1
  AGTPBP1 WILD-TYPE        19         10         39         30       34
                   vv
clus                STAGE IVA STAGE IVB
  AGTPBP1 MUTATED           1         0
  AGTPBP1 WILD-TYPE        12         1
D1628V3, multiclass
            clus
vv           AGTPBP1 MUTATED AGTPBP1 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 2                23
  STAGE IIA                8               101
  STAGE IIB                0                 8
  STAGE IIC                1                 0
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               2                39
  STAGE IIIC               1                30
  STAGE IV                 1                34
  STAGE IVA                1                12
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of 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  68 235  37
D1628V4, multiclass
    clus
vv   AGTPBP1 MUTATED AGTPBP1 WILD-TYPE
  T1               0                 9
  T2               0                68
  T3              13               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
  AGTPBP1 MUTATED    12   2   3
  AGTPBP1 WILD-TYPE 208  78  63
D1628V5, multiclass
    clus
vv   AGTPBP1 MUTATED AGTPBP1 WILD-TYPE
  N0              12               208
  N1               2                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"
D1628V6, binary
                   cls
clus                  0   1
  AGTPBP1 MUTATED    12   2
  AGTPBP1 WILD-TYPE 271  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  AGTPBP1 MUTATED     12    2
  AGTPBP1 WILD-TYPE  271   46
   clus
vv  AGTPBP1 MUTATED AGTPBP1 WILD-TYPE
  0              12               271
  1               2                46
[1] 2 2
[1] FALSE
D1628V7, 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
D1628V8, binary
                   cls
clus                  0   1
  AGTPBP1 MUTATED    13   4
  AGTPBP1 WILD-TYPE 304  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  AGTPBP1 MUTATED     13    4
  AGTPBP1 WILD-TYPE  304   44
                               clus
vv                              AGTPBP1 MUTATED AGTPBP1 WILD-TYPE
  COLON ADENOCARCINOMA                       13               304
  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 248   2  21  20
D1628V9, multiclass
    clus
vv   AGTPBP1 MUTATED AGTPBP1 WILD-TYPE
  R0               9               248
  R1               0                 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"
D1628V10, 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
D1628V11, 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(1629) Variable = ATL2 MUTATION ANALYSIS
D1629V1, survival
                sevent
clus2              0   1
  ATL2 MUTATED     3   3
  ATL2 WILD-TYPE 279  70
  ATL2 MUTATED ATL2 WILD-TYPE 
             6            349 
  ATL2 MUTATED ATL2 WILD-TYPE 
             3             70 
$`ATL2 MUTATED`
TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-6600 TCGA-AZ-6608 TCGA-CM-6168 TCGA-G4-6303 
       34.98        58.39        12.10         1.94        12.99        65.85 

$`ATL2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77       100.01        29.56         5.23        11.74         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 
        0.53        35.41        19.43       107.67        74.56        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  ATL2 MUTATED ATL2 WILD-TYPE 
          1.94           0.00 
  ATL2 MUTATED ATL2 WILD-TYPE 
         65.85         140.38 
  ATL2 MUTATED ATL2 WILD-TYPE 
        23.985         20.190 
[1] "1.9 - 65.8 (24.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2"  
D1629V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATL2 MUTATED         0        0        0         2         1         0
  ATL2 WILD-TYPE      64        1       25       107         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ATL2 MUTATED           0          1          0          0        2         0
  ATL2 WILD-TYPE        19          9         41         31       33        13
                vv
clus             STAGE IVB
  ATL2 MUTATED           0
  ATL2 WILD-TYPE         1
D1629V3, multiclass
            clus
vv           ATL2 MUTATED ATL2 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             2            107
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            1              9
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              2             33
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ATL2 MUTATED     0   1   3   2
  ATL2 WILD-TYPE   9  67 245  39
D1629V4, multiclass
    clus
vv   ATL2 MUTATED ATL2 WILD-TYPE
  T1            0              9
  T2            1             67
  T3            3            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
  ATL2 MUTATED     3   3   0
  ATL2 WILD-TYPE 217  77  66
D1629V5, multiclass
    clus
vv   ATL2 MUTATED ATL2 WILD-TYPE
  N0            3            217
  N1            3             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"
D1629V6, binary
                cls
clus               0   1
  ATL2 MUTATED     4   2
  ATL2 WILD-TYPE 279  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATL2 MUTATED      4    2
  ATL2 WILD-TYPE  279   46
   clus
vv  ATL2 MUTATED ATL2 WILD-TYPE
  0            4            279
  1            2             46
[1] 2 2
[1] FALSE
D1629V7, binary
                cls
clus               0   1
  ATL2 MUTATED     4   2
  ATL2 WILD-TYPE 166 195
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATL2 MUTATED      4    2
  ATL2 WILD-TYPE  166  195
        clus
vv       ATL2 MUTATED ATL2 WILD-TYPE
  FEMALE            4            166
  MALE              2            195
[1] 2 2
[1] FALSE
D1629V8, binary
                cls
clus               0   1
  ATL2 MUTATED     6   0
  ATL2 WILD-TYPE 311  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATL2 MUTATED      6    0
  ATL2 WILD-TYPE  311   48
                               clus
vv                              ATL2 MUTATED ATL2 WILD-TYPE
  COLON ADENOCARCINOMA                     6            311
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ATL2 MUTATED     4   0   0   0
  ATL2 WILD-TYPE 253   2  22  21
D1629V9, multiclass
    clus
vv   ATL2 MUTATED ATL2 WILD-TYPE
  R0            4            253
  R1            0              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"
D1629V10, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATL2 MUTATED                                  0     0
  ATL2 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ATL2 MUTATED                           2     3
  ATL2 WILD-TYPE                        17   173
D1629V11, multiclass
                                  clus
vv                                 ATL2 MUTATED ATL2 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(1630) Variable = SIGLEC14 MUTATION ANALYSIS
D1630V1, survival
                    sevent
clus2                  0   1
  SIGLEC14 MUTATED     5   2
  SIGLEC14 WILD-TYPE 277  71
  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
                 7                348 
  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
                 2                 71 
$`SIGLEC14 MUTATED`
TCGA-AA-3977 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CM-4752 TCGA-D5-6927 TCGA-DM-A282 
       25.02        49.41       100.01        13.02         9.44       139.17 
TCGA-G4-6588 
       26.17 

$`SIGLEC14 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A285 
      140.38         7.50        44.32       131.51       135.65         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        52.80 

  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
              9.44               0.00 
  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
            139.17             140.38 
  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
             26.17              20.07 
[1] "9.4 - 139.2 (26.2)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.4"
D1630V2, 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       23       104         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SIGLEC14 MUTATED           0          0          0          0        0
  SIGLEC14 WILD-TYPE        19         10         41         31       35
                    vv
clus                 STAGE IVA STAGE IVB
  SIGLEC14 MUTATED           0         0
  SIGLEC14 WILD-TYPE        13         1
D1630V3, multiclass
            clus
vv           SIGLEC14 MUTATED SIGLEC14 WILD-TYPE
  STAGE I                   0                 64
  STAGE IA                  0                  1
  STAGE II                  2                 23
  STAGE IIA                 5                104
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                0                 10
  STAGE IIIB                0                 41
  STAGE IIIC                0                 31
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  SIGLEC14 MUTATED     0   1   7   0
  SIGLEC14 WILD-TYPE   9  67 241  41
D1630V4, multiclass
    clus
vv   SIGLEC14 MUTATED SIGLEC14 WILD-TYPE
  T1                0                  9
  T2                1                 67
  T3                7                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
  SIGLEC14 MUTATED     8   0   0
  SIGLEC14 WILD-TYPE 212  80  66
D1630V5, multiclass
    clus
vv   SIGLEC14 MUTATED SIGLEC14 WILD-TYPE
  N0                8                212
  N1                0                 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"
D1630V6, binary
                    cls
clus                   0   1
  SIGLEC14 MUTATED     6   0
  SIGLEC14 WILD-TYPE 277  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SIGLEC14 MUTATED      6    0
  SIGLEC14 WILD-TYPE  277   48
   clus
vv  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE
  0                6                277
  1                0                 48
[1] 2 2
[1] FALSE
D1630V7, 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
D1630V8, binary
                    cls
clus                   0   1
  SIGLEC14 MUTATED     8   0
  SIGLEC14 WILD-TYPE 309  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SIGLEC14 MUTATED      8    0
  SIGLEC14 WILD-TYPE  309   48
                               clus
vv                              SIGLEC14 MUTATED SIGLEC14 WILD-TYPE
  COLON ADENOCARCINOMA                         8                309
  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 253   2  22  21
D1630V9, multiclass
    clus
vv   SIGLEC14 MUTATED SIGLEC14 WILD-TYPE
  R0                4                253
  R1                0                  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"
D1630V10, 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
D1630V11, 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(1631) Variable = OR5R1 MUTATION ANALYSIS
D1631V1, survival
                 sevent
clus2               0   1
  OR5R1 MUTATED     9   4
  OR5R1 WILD-TYPE 273  69
  OR5R1 MUTATED OR5R1 WILD-TYPE 
             13             342 
  OR5R1 MUTATED OR5R1 WILD-TYPE 
              4              69 
$`OR5R1 MUTATED`
TCGA-AA-3510 TCGA-AA-3845 TCGA-AA-3950 TCGA-AA-3955 TCGA-AZ-4681 TCGA-AZ-6598 
       63.98         0.00        24.00        20.98        83.80        49.41 
TCGA-AZ-6599 TCGA-CA-6717 TCGA-CK-4947 TCGA-D5-6533 TCGA-D5-6929 TCGA-F4-6854 
        6.77         0.33        17.56         1.32        13.41         0.53 
TCGA-G4-6626 
       46.75 

$`OR5R1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
       17.98        15.95        38.99        37.02        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3956 
       12.99        24.00        33.01        26.01         2.01        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         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-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       62.79        61.41        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 
        3.29         0.07         0.26         0.10         1.35       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
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-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       22.09        13.78        35.80        26.17        91.79        52.80 

  OR5R1 MUTATED OR5R1 WILD-TYPE 
              0               0 
  OR5R1 MUTATED OR5R1 WILD-TYPE 
          83.80          140.38 
  OR5R1 MUTATED OR5R1 WILD-TYPE 
         17.560          20.235 
[1] "0.0 - 83.8 (17.6)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.5"
D1631V2, 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       23       102         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR5R1 MUTATED           0          0          2          0        1         1
  OR5R1 WILD-TYPE        19         10         39         31       34        12
                 vv
clus              STAGE IVB
  OR5R1 MUTATED           0
  OR5R1 WILD-TYPE         1
D1631V3, multiclass
            clus
vv           OR5R1 MUTATED OR5R1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              7             102
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 238  39
D1631V4, multiclass
    clus
vv   OR5R1 MUTATED OR5R1 WILD-TYPE
  T1             0               9
  T2             2              66
  T3            10             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
  OR5R1 MUTATED    11   2   1
  OR5R1 WILD-TYPE 209  78  65
D1631V5, multiclass
    clus
vv   OR5R1 MUTATED OR5R1 WILD-TYPE
  N0            11             209
  N1             2              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"
D1631V6, binary
                 cls
clus                0   1
  OR5R1 MUTATED    11   1
  OR5R1 WILD-TYPE 272  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5R1 MUTATED     11    1
  OR5R1 WILD-TYPE  272   47
   clus
vv  OR5R1 MUTATED OR5R1 WILD-TYPE
  0            11             272
  1             1              47
[1] 2 2
[1] FALSE
D1631V7, 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
D1631V8, binary
                 cls
clus                0   1
  OR5R1 MUTATED    12   2
  OR5R1 WILD-TYPE 305  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5R1 MUTATED     12    2
  OR5R1 WILD-TYPE  305   46
                               clus
vv                              OR5R1 MUTATED OR5R1 WILD-TYPE
  COLON ADENOCARCINOMA                     12             305
  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 247   2  22  19
D1631V9, multiclass
    clus
vv   OR5R1 MUTATED OR5R1 WILD-TYPE
  R0            10             247
  R1             0               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"
D1631V10, 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
D1631V11, 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(1632) Variable = ITGA5 MUTATION ANALYSIS
D1632V1, survival
                 sevent
clus2               0   1
  ITGA5 MUTATED    14   1
  ITGA5 WILD-TYPE 268  72
  ITGA5 MUTATED ITGA5 WILD-TYPE 
             15             340 
  ITGA5 MUTATED ITGA5 WILD-TYPE 
              1              72 
$`ITGA5 MUTATED`
TCGA-AA-3511 TCGA-AA-3877 TCGA-AA-A00E TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A02J 
        6.97        31.00        30.02         0.99        34.98         5.03 
TCGA-AZ-4315 TCGA-CA-6715 TCGA-CM-4746 TCGA-CM-5861 TCGA-CM-5863 TCGA-D5-6928 
       58.39         0.07        37.02        15.02        15.02        11.64 
TCGA-D5-6930 TCGA-G4-6293 TCGA-G4-6586 
        1.51       107.67        35.80 

$`ITGA5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01        63.98         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       27.02        42.02        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02K 
       37.02        39.06        51.98        39.98         2.01        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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 
       16.01         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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       19.43        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  ITGA5 MUTATED ITGA5 WILD-TYPE 
           0.07            0.00 
  ITGA5 MUTATED ITGA5 WILD-TYPE 
         107.67          140.38 
  ITGA5 MUTATED ITGA5 WILD-TYPE 
         15.020          20.235 
[1] "0.1 - 107.7 (15.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "3"  
D1632V2, 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       24       103         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        18         10         39         31       33        13
                 vv
clus              STAGE IVB
  ITGA5 MUTATED           0
  ITGA5 WILD-TYPE         1
D1632V3, multiclass
            clus
vv           ITGA5 MUTATED ITGA5 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              6             103
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               2              33
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ITGA5 MUTATED     1   2  10   3
  ITGA5 WILD-TYPE   8  66 238  38
D1632V4, multiclass
    clus
vv   ITGA5 MUTATED ITGA5 WILD-TYPE
  T1             1               8
  T2             2              66
  T3            10             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
  ITGA5 MUTATED    12   3   1
  ITGA5 WILD-TYPE 208  77  65
D1632V5, multiclass
    clus
vv   ITGA5 MUTATED ITGA5 WILD-TYPE
  N0            12             208
  N1             3              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"
D1632V6, binary
                 cls
clus                0   1
  ITGA5 MUTATED    14   2
  ITGA5 WILD-TYPE 269  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGA5 MUTATED     14    2
  ITGA5 WILD-TYPE  269   46
   clus
vv  ITGA5 MUTATED ITGA5 WILD-TYPE
  0            14             269
  1             2              46
[1] 2 2
[1] FALSE
D1632V7, 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
D1632V8, binary
                 cls
clus                0   1
  ITGA5 MUTATED    12   4
  ITGA5 WILD-TYPE 305  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGA5 MUTATED     12    4
  ITGA5 WILD-TYPE  305   44
                               clus
vv                              ITGA5 MUTATED ITGA5 WILD-TYPE
  COLON ADENOCARCINOMA                     12             305
  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 244   2  20  20
D1632V9, multiclass
    clus
vv   ITGA5 MUTATED ITGA5 WILD-TYPE
  R0            13             244
  R1             0               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"
D1632V10, 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
D1632V11, 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(1633) Variable = VPS72 MUTATION ANALYSIS
D1633V1, survival
                 sevent
clus2               0   1
  VPS72 MUTATED     8   0
  VPS72 WILD-TYPE 274  73
  VPS72 MUTATED VPS72 WILD-TYPE 
              8             347 
  VPS72 MUTATED VPS72 WILD-TYPE 
              0              73 
$`VPS72 MUTATED`
TCGA-A6-5665 TCGA-AA-3864 TCGA-AD-5900 TCGA-CM-5348 TCGA-CM-6171 TCGA-D5-6927 
       22.06        53.00         0.07        22.98        14.04         9.44 
TCGA-D5-6931 TCGA-G4-6309 
       12.00        51.75 

$`VPS72 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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         1.51 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  VPS72 MUTATED VPS72 WILD-TYPE 
           0.07            0.00 
  VPS72 MUTATED VPS72 WILD-TYPE 
          53.00          140.38 
  VPS72 MUTATED VPS72 WILD-TYPE 
          18.05           20.19 
[1] "0.1 - 53.0 (18.0)"  "0.0 - 140.4 (20.2)"
[1] "hr="     "9300000"
D1633V2, 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       24       107         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        19         10         39         30       35        13
                 vv
clus              STAGE IVB
  VPS72 MUTATED           0
  VPS72 WILD-TYPE         1
D1633V3, multiclass
            clus
vv           VPS72 MUTATED VPS72 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              2             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  VPS72 MUTATED     0   2   5   1
  VPS72 WILD-TYPE   9  66 243  40
D1633V4, multiclass
    clus
vv   VPS72 MUTATED VPS72 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             5             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
  VPS72 MUTATED     5   2   1
  VPS72 WILD-TYPE 215  78  65
D1633V5, multiclass
    clus
vv   VPS72 MUTATED VPS72 WILD-TYPE
  N0             5             215
  N1             2              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"
D1633V6, binary
                 cls
clus                0   1
  VPS72 MUTATED     7   0
  VPS72 WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VPS72 MUTATED      7    0
  VPS72 WILD-TYPE  276   48
   clus
vv  VPS72 MUTATED VPS72 WILD-TYPE
  0             7             276
  1             0              48
[1] 2 2
[1] FALSE
D1633V7, 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
D1633V8, binary
                 cls
clus                0   1
  VPS72 MUTATED     7   1
  VPS72 WILD-TYPE 310  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VPS72 MUTATED      7    1
  VPS72 WILD-TYPE  310   47
                               clus
vv                              VPS72 MUTATED VPS72 WILD-TYPE
  COLON ADENOCARCINOMA                      7             310
  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 249   2  22  21
D1633V9, multiclass
    clus
vv   VPS72 MUTATED VPS72 WILD-TYPE
  R0             8             249
  R1             0               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"
D1633V10, 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
D1633V11, 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(1634) Variable = PKDREJ MUTATION ANALYSIS
D1634V1, survival
                  sevent
clus2                0   1
  PKDREJ MUTATED    26   3
  PKDREJ WILD-TYPE 256  70
  PKDREJ MUTATED PKDREJ WILD-TYPE 
              29              326 
  PKDREJ MUTATED PKDREJ WILD-TYPE 
               3               70 
$`PKDREJ MUTATED`
TCGA-A6-5666 TCGA-A6-6781 TCGA-AA-3663 TCGA-AA-3688 TCGA-AA-3950 TCGA-AA-3977 
       32.71        19.66         6.97        19.00        24.00        25.02 
TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A017 TCGA-AD-6889 TCGA-AU-6004 
       18.05         4.01        34.98        15.02        56.55        27.09 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4952 TCGA-CK-5913 
       21.44        58.39         0.33         0.10        15.62        51.32 
TCGA-CM-5349 TCGA-CM-5868 TCGA-CM-6162 TCGA-D5-6535 TCGA-D5-6540 TCGA-D5-6898 
       30.08        17.03        12.00        15.12        16.14         7.53 
TCGA-DM-A0XD TCGA-F4-6570 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6628 
       24.43         6.18        74.56        53.62        52.80 

$`PKDREJ WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
       11.01         5.98        37.05        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       21.99        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37         4.21         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        15.75         0.20        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07         0.26         1.35        17.56       102.44        40.34 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        21.99        21.14         2.93         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        16.01        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-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 
       20.19        18.25         1.32        43.27        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       17.13        12.49        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        11.38        10.26       119.70        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.38        13.45        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
      107.67        65.85        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 
       91.79        46.75 

  PKDREJ MUTATED PKDREJ WILD-TYPE 
             0.1              0.0 
  PKDREJ MUTATED PKDREJ WILD-TYPE 
           74.56           140.38 
  PKDREJ MUTATED PKDREJ WILD-TYPE 
          19.660           20.235 
[1] "0.1 - 74.6 (19.7)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2.2"
D1634V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PKDREJ MUTATED         4        0        1        12         3         1
  PKDREJ WILD-TYPE      60        1       24        97         5         0
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PKDREJ MUTATED           2          0          3          2        1
  PKDREJ WILD-TYPE        17         10         38         29       34
                  vv
clus               STAGE IVA STAGE IVB
  PKDREJ MUTATED           1         0
  PKDREJ WILD-TYPE        12         1
D1634V3, multiclass
            clus
vv           PKDREJ MUTATED PKDREJ WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA              12               97
  STAGE IIB               3                5
  STAGE IIC               1                0
  STAGE III               2               17
  STAGE IIIA              0               10
  STAGE IIIB              3               38
  STAGE IIIC              2               29
  STAGE IV                1               34
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PKDREJ MUTATED     0   5  18   8
  PKDREJ WILD-TYPE   9  63 230  33
D1634V4, multiclass
    clus
vv   PKDREJ MUTATED PKDREJ WILD-TYPE
  T1              0                9
  T2              5               63
  T3             18              230
  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
  PKDREJ MUTATED    22   6   3
  PKDREJ WILD-TYPE 198  74  63
D1634V5, multiclass
    clus
vv   PKDREJ MUTATED PKDREJ WILD-TYPE
  N0             22              198
  N1              6               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"
D1634V6, binary
                  cls
clus                 0   1
  PKDREJ MUTATED    24   2
  PKDREJ WILD-TYPE 259  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PKDREJ MUTATED     24    2
  PKDREJ WILD-TYPE  259   46
   clus
vv  PKDREJ MUTATED PKDREJ WILD-TYPE
  0             24              259
  1              2               46
[1] 2 2
[1] FALSE
D1634V7, binary
                  cls
clus                 0   1
  PKDREJ MUTATED    14  17
  PKDREJ WILD-TYPE 156 180
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PKDREJ MUTATED     14   17
  PKDREJ WILD-TYPE  156  180
        clus
vv       PKDREJ MUTATED PKDREJ WILD-TYPE
  FEMALE             14              156
  MALE               17              180
[1] 2 2
[1] FALSE
D1634V8, binary
                  cls
clus                 0   1
  PKDREJ MUTATED    23   8
  PKDREJ WILD-TYPE 294  40
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PKDREJ MUTATED     23    8
  PKDREJ WILD-TYPE  294   40
                               clus
vv                              PKDREJ MUTATED PKDREJ WILD-TYPE
  COLON ADENOCARCINOMA                      23              294
  COLON MUCINOUS ADENOCARCINOMA              8               40
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PKDREJ MUTATED    21   0   1   5
  PKDREJ WILD-TYPE 236   2  21  16
D1634V9, multiclass
    clus
vv   PKDREJ MUTATED PKDREJ WILD-TYPE
  R0             21              236
  R1              0                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"
D1634V10, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PKDREJ MUTATED                                  0     3
  PKDREJ WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PKDREJ MUTATED                           0    18
  PKDREJ WILD-TYPE                        19   158
D1634V11, multiclass
                                  clus
vv                                 PKDREJ MUTATED PKDREJ WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         3                7
  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(1635) Variable = CUTC MUTATION ANALYSIS
D1635V1, survival
                sevent
clus2              0   1
  CUTC MUTATED     3   1
  CUTC WILD-TYPE 279  72
  CUTC MUTATED CUTC WILD-TYPE 
             4            351 
  CUTC MUTATED CUTC WILD-TYPE 
             1             72 
$`CUTC MUTATED`
TCGA-A6-5665 TCGA-A6-5666 TCGA-AZ-6608 TCGA-G4-6628 
       22.06        32.71         1.94        52.80 

$`CUTC WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.09        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       26.17        91.79        46.75 

  CUTC MUTATED CUTC WILD-TYPE 
          1.94           0.00 
  CUTC MUTATED CUTC WILD-TYPE 
         52.80         140.38 
  CUTC MUTATED CUTC WILD-TYPE 
        27.385         20.120 
[1] "1.9 - 52.8 (27.4)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.1"
D1635V2, 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       25       107         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        19          9         41         31       35        13
                vv
clus             STAGE IVB
  CUTC MUTATED           0
  CUTC WILD-TYPE         1
D1635V3, multiclass
            clus
vv           CUTC MUTATED CUTC WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             2            107
  STAGE IIB             0              8
  STAGE IIC             1              0
  STAGE III             0             19
  STAGE IIIA            1              9
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CUTC MUTATED     0   2   2   1
  CUTC WILD-TYPE   9  66 246  40
D1635V4, multiclass
    clus
vv   CUTC MUTATED CUTC WILD-TYPE
  T1            0              9
  T2            2             66
  T3            2            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
  CUTC MUTATED     4   1   0
  CUTC WILD-TYPE 216  79  66
D1635V5, multiclass
    clus
vv   CUTC MUTATED CUTC WILD-TYPE
  N0            4            216
  N1            1             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"
D1635V6, binary
                cls
clus               0   1
  CUTC MUTATED     5   0
  CUTC WILD-TYPE 278  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUTC MUTATED      5    0
  CUTC WILD-TYPE  278   48
   clus
vv  CUTC MUTATED CUTC WILD-TYPE
  0            5            278
  1            0             48
[1] 2 2
[1] FALSE
D1635V7, 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
D1635V8, binary
                cls
clus               0   1
  CUTC MUTATED     5   0
  CUTC WILD-TYPE 312  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUTC MUTATED      5    0
  CUTC WILD-TYPE  312   48
                               clus
vv                              CUTC MUTATED CUTC WILD-TYPE
  COLON ADENOCARCINOMA                     5            312
  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 254   2  22  21
D1635V9, multiclass
    clus
vv   CUTC MUTATED CUTC WILD-TYPE
  R0            3            254
  R1            0              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"
D1635V10, 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
D1635V11, 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(1636) Variable = PYHIN1 MUTATION ANALYSIS
D1636V1, survival
                  sevent
clus2                0   1
  PYHIN1 MUTATED    12   5
  PYHIN1 WILD-TYPE 270  68
  PYHIN1 MUTATED PYHIN1 WILD-TYPE 
              17              338 
  PYHIN1 MUTATED PYHIN1 WILD-TYPE 
               5               68 
$`PYHIN1 MUTATED`
TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3818 TCGA-AA-3842 
       63.98         6.97        19.04        19.04         0.99        37.02 
TCGA-AA-3930 TCGA-AA-A010 TCGA-AZ-6598 TCGA-CA-5254 TCGA-CM-4744 TCGA-CM-5861 
        2.01        34.98        49.41         2.24        20.02        15.02 
TCGA-CM-6169 TCGA-CM-6172 TCGA-D5-5541 TCGA-DM-A1D0 TCGA-DM-A1DA 
       13.02        11.01        11.51       130.65         7.50 

$`PYHIN1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.03        85.05        26.99        10.06        35.05        33.04 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3844 
       25.02         1.02        17.98        15.95        38.99        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       31.00        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13        83.80        22.36        62.79        61.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        1.94         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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-5862 
       29.06        22.03        22.98        30.08        16.01         5.03 
TCGA-CM-5863 TCGA-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-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       14.04        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        13.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        24.43        38.20        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       12.59       140.38        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  PYHIN1 MUTATED PYHIN1 WILD-TYPE 
            0.99             0.00 
  PYHIN1 MUTATED PYHIN1 WILD-TYPE 
          130.65           140.38 
  PYHIN1 MUTATED PYHIN1 WILD-TYPE 
          15.020           20.995 
[1] "1.0 - 130.7 (15.0)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.5"
D1636V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PYHIN1 MUTATED         1        0        4         5         2         0
  PYHIN1 WILD-TYPE      63        1       21       104         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PYHIN1 MUTATED           0          1          2          1        2
  PYHIN1 WILD-TYPE        19          9         39         30       33
                  vv
clus               STAGE IVA STAGE IVB
  PYHIN1 MUTATED           0         0
  PYHIN1 WILD-TYPE        13         1
D1636V3, multiclass
            clus
vv           PYHIN1 MUTATED PYHIN1 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                4               21
  STAGE IIA               5              104
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              1                9
  STAGE IIIB              2               39
  STAGE IIIC              1               30
  STAGE IV                2               33
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PYHIN1 MUTATED     0   2  14   2
  PYHIN1 WILD-TYPE   9  66 234  39
D1636V4, multiclass
    clus
vv   PYHIN1 MUTATED PYHIN1 WILD-TYPE
  T1              0                9
  T2              2               66
  T3             14              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
  PYHIN1 MUTATED    13   3   2
  PYHIN1 WILD-TYPE 207  77  64
D1636V5, multiclass
    clus
vv   PYHIN1 MUTATED PYHIN1 WILD-TYPE
  N0             13              207
  N1              3               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"
D1636V6, binary
                  cls
clus                 0   1
  PYHIN1 MUTATED    14   2
  PYHIN1 WILD-TYPE 269  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PYHIN1 MUTATED     14    2
  PYHIN1 WILD-TYPE  269   46
   clus
vv  PYHIN1 MUTATED PYHIN1 WILD-TYPE
  0             14              269
  1              2               46
[1] 2 2
[1] FALSE
D1636V7, binary
                  cls
clus                 0   1
  PYHIN1 MUTATED     9   9
  PYHIN1 WILD-TYPE 161 188
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PYHIN1 MUTATED      9    9
  PYHIN1 WILD-TYPE  161  188
        clus
vv       PYHIN1 MUTATED PYHIN1 WILD-TYPE
  FEMALE              9              161
  MALE                9              188
[1] 2 2
[1] FALSE
D1636V8, binary
                  cls
clus                 0   1
  PYHIN1 MUTATED    18   0
  PYHIN1 WILD-TYPE 299  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PYHIN1 MUTATED     18    0
  PYHIN1 WILD-TYPE  299   48
                               clus
vv                              PYHIN1 MUTATED PYHIN1 WILD-TYPE
  COLON ADENOCARCINOMA                      18              299
  COLON MUCINOUS ADENOCARCINOMA              0               48
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PYHIN1 MUTATED    11   0   2   2
  PYHIN1 WILD-TYPE 246   2  20  19
D1636V9, multiclass
    clus
vv   PYHIN1 MUTATED PYHIN1 WILD-TYPE
  R0             11              246
  R1              0                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"
D1636V10, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PYHIN1 MUTATED                                  0     1
  PYHIN1 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PYHIN1 MUTATED                           1     8
  PYHIN1 WILD-TYPE                        18   168
D1636V11, multiclass
                                  clus
vv                                 PYHIN1 MUTATED PYHIN1 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(1637) Variable = SRL MUTATION ANALYSIS
D1637V1, survival
               sevent
clus2             0   1
  SRL MUTATED     8   4
  SRL WILD-TYPE 274  69
  SRL MUTATED SRL WILD-TYPE 
           12           343 
  SRL MUTATED SRL WILD-TYPE 
            4            69 
$`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 
        0.33        13.02        11.08        24.43        44.32       135.65 

$`SRL WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41        49.41        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
       12.59       140.38         7.50       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  SRL MUTATED SRL WILD-TYPE 
         0.33          0.00 
  SRL MUTATED SRL WILD-TYPE 
       135.65        140.38 
  SRL MUTATED SRL WILD-TYPE 
        16.57         20.28 
[1] "0.3 - 135.7 (16.6)" "0.0 - 140.4 (20.3)"
[1] "hr=" "1.7"
D1637V2, 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       24       103         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        19         10         39         31       35        13
               vv
clus            STAGE IVB
  SRL MUTATED           0
  SRL WILD-TYPE         1
D1637V3, multiclass
            clus
vv           SRL MUTATED SRL WILD-TYPE
  STAGE I              2            62
  STAGE IA             0             1
  STAGE II             1            24
  STAGE IIA            6           103
  STAGE IIB            1             7
  STAGE IIC            0             1
  STAGE III            0            19
  STAGE IIIA           0            10
  STAGE IIIB           2            39
  STAGE IIIC           0            31
  STAGE IV             0            35
  STAGE IVA            0            13
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  SRL MUTATED     0   2   9   1
  SRL WILD-TYPE   9  66 239  40
D1637V4, multiclass
    clus
vv   SRL MUTATED SRL WILD-TYPE
  T1           0             9
  T2           2            66
  T3           9           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
  SRL MUTATED    10   2   0
  SRL WILD-TYPE 210  78  66
D1637V5, multiclass
    clus
vv   SRL MUTATED SRL WILD-TYPE
  N0          10           210
  N1           2            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"
D1637V6, binary
               cls
clus              0   1
  SRL MUTATED     9   0
  SRL WILD-TYPE 274  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  SRL MUTATED      9    0
  SRL WILD-TYPE  274   48
   clus
vv  SRL MUTATED SRL WILD-TYPE
  0           9           274
  1           0            48
[1] 2 2
[1] FALSE
D1637V7, 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
D1637V8, binary
               cls
clus              0   1
  SRL MUTATED     9   3
  SRL WILD-TYPE 308  45
[1] "tbl2"
               cls
clus            [,1] [,2]
  SRL MUTATED      9    3
  SRL WILD-TYPE  308   45
                               clus
vv                              SRL MUTATED SRL WILD-TYPE
  COLON ADENOCARCINOMA                    9           308
  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 251   2  22  20
D1637V9, multiclass
    clus
vv   SRL MUTATED SRL WILD-TYPE
  R0           6           251
  R1           0             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"
D1637V10, 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
D1637V11, 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(1638) Variable = ATP13A3 MUTATION ANALYSIS
D1638V1, survival
                   sevent
clus2                 0   1
  ATP13A3 MUTATED    10   3
  ATP13A3 WILD-TYPE 272  70
  ATP13A3 MUTATED ATP13A3 WILD-TYPE 
               13               342 
  ATP13A3 MUTATED ATP13A3 WILD-TYPE 
                3                70 
$`ATP13A3 MUTATED`
TCGA-A6-5661 TCGA-A6-6141 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3715 TCGA-AA-3815 
       33.53         8.38        19.66         3.02        19.04        33.04 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6964 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4315 
       56.55         0.79        10.88         0.20        21.44        58.39 
TCGA-G4-6309 
       51.75 

$`ATP13A3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       26.99        19.04        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       21.37         4.21         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  ATP13A3 MUTATED ATP13A3 WILD-TYPE 
              0.2               0.0 
  ATP13A3 MUTATED ATP13A3 WILD-TYPE 
            58.39            140.38 
  ATP13A3 MUTATED ATP13A3 WILD-TYPE 
           19.660            20.235 
[1] "0.2 - 58.4 (19.7)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D1638V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATP13A3 MUTATED         0        0        2         6         0         0
  ATP13A3 WILD-TYPE      64        1       23       103         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP13A3 MUTATED           0          0          1          2        0
  ATP13A3 WILD-TYPE        19         10         40         29       35
                   vv
clus                STAGE IVA STAGE IVB
  ATP13A3 MUTATED           0         0
  ATP13A3 WILD-TYPE        13         1
D1638V3, multiclass
            clus
vv           ATP13A3 MUTATED ATP13A3 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 2                23
  STAGE IIA                6               103
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               2                29
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ATP13A3 MUTATED     1   0  10   2
  ATP13A3 WILD-TYPE   8  68 238  39
D1638V4, multiclass
    clus
vv   ATP13A3 MUTATED ATP13A3 WILD-TYPE
  T1               1                 8
  T2               0                68
  T3              10               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
  ATP13A3 MUTATED     9   2   2
  ATP13A3 WILD-TYPE 211  78  64
D1638V5, multiclass
    clus
vv   ATP13A3 MUTATED ATP13A3 WILD-TYPE
  N0               9               211
  N1               2                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"
D1638V6, binary
                   cls
clus                  0   1
  ATP13A3 MUTATED     8   0
  ATP13A3 WILD-TYPE 275  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ATP13A3 MUTATED      8    0
  ATP13A3 WILD-TYPE  275   48
   clus
vv  ATP13A3 MUTATED ATP13A3 WILD-TYPE
  0               8               275
  1               0                48
[1] 2 2
[1] FALSE
D1638V7, binary
                   cls
clus                  0   1
  ATP13A3 MUTATED     4   9
  ATP13A3 WILD-TYPE 166 188
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ATP13A3 MUTATED      4    9
  ATP13A3 WILD-TYPE  166  188
        clus
vv       ATP13A3 MUTATED ATP13A3 WILD-TYPE
  FEMALE               4               166
  MALE                 9               188
[1] 2 2
[1] FALSE
D1638V8, binary
                   cls
clus                  0   1
  ATP13A3 MUTATED    11   2
  ATP13A3 WILD-TYPE 306  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ATP13A3 MUTATED     11    2
  ATP13A3 WILD-TYPE  306   46
                               clus
vv                              ATP13A3 MUTATED ATP13A3 WILD-TYPE
  COLON ADENOCARCINOMA                       11               306
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ATP13A3 MUTATED     9   0   0   0
  ATP13A3 WILD-TYPE 248   2  22  21
D1638V9, multiclass
    clus
vv   ATP13A3 MUTATED ATP13A3 WILD-TYPE
  R0               9               248
  R1               0                 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"
D1638V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATP13A3 MUTATED                                  0     1
  ATP13A3 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ATP13A3 MUTATED                           3     6
  ATP13A3 WILD-TYPE                        16   170
D1638V11, multiclass
                                  clus
vv                                 ATP13A3 MUTATED ATP13A3 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(1639) Variable = CELSR1 MUTATION ANALYSIS
D1639V1, survival
                  sevent
clus2                0   1
  CELSR1 MUTATED    21   1
  CELSR1 WILD-TYPE 261  72
  CELSR1 MUTATED CELSR1 WILD-TYPE 
              22              333 
  CELSR1 MUTATED CELSR1 WILD-TYPE 
               1               72 
$`CELSR1 MUTATED`
TCGA-A6-6653 TCGA-AA-3663 TCGA-AA-3713 TCGA-AA-3819 TCGA-AA-3875 TCGA-AA-3877 
       24.39         6.97        19.04        25.02        18.05        31.00 
TCGA-AA-3947 TCGA-AA-A01Q TCGA-AA-A02O TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6895 
       33.01         1.02         0.92         0.07        56.55         0.72 
TCGA-AU-6004 TCGA-AZ-6598 TCGA-CM-4743 TCGA-CM-5341 TCGA-CM-5861 TCGA-CM-6674 
       27.09        49.41        23.05        29.06        15.02        12.95 
TCGA-DM-A1D9 TCGA-F4-6856 TCGA-G4-6306 TCGA-G4-6628 
      140.38        19.43        44.68        52.80 

$`CELSR1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       33.04         0.99         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       29.98         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02W TCGA-AA-A02Y 
       39.98         2.01         5.03        14.01        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        21.37         4.21         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14         2.93         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        16.01 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA 
      130.65        92.75        49.91        13.32        12.59         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 
      107.67        74.56        65.85        53.62        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       26.17        91.79        46.75 

  CELSR1 MUTATED CELSR1 WILD-TYPE 
            0.07             0.00 
  CELSR1 MUTATED CELSR1 WILD-TYPE 
          140.38           139.17 
  CELSR1 MUTATED CELSR1 WILD-TYPE 
           23.72            20.12 
[1] "0.1 - 140.4 (23.7)" "0.0 - 139.2 (20.1)"
[1] "hr=" "5.1"
D1639V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CELSR1 MUTATED         7        0        4         7         1         0
  CELSR1 WILD-TYPE      57        1       21       102         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CELSR1 MUTATED           0          1          0          0        1
  CELSR1 WILD-TYPE        19          9         41         31       34
                  vv
clus               STAGE IVA STAGE IVB
  CELSR1 MUTATED           0         0
  CELSR1 WILD-TYPE        13         1
D1639V3, multiclass
            clus
vv           CELSR1 MUTATED CELSR1 WILD-TYPE
  STAGE I                 7               57
  STAGE IA                0                1
  STAGE II                4               21
  STAGE IIA               7              102
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              1                9
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CELSR1 MUTATED     2   7  12   1
  CELSR1 WILD-TYPE   7  61 236  40
D1639V4, multiclass
    clus
vv   CELSR1 MUTATED CELSR1 WILD-TYPE
  T1              2                7
  T2              7               61
  T3             12              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
  CELSR1 MUTATED    20   2   0
  CELSR1 WILD-TYPE 200  78  66
D1639V5, multiclass
    clus
vv   CELSR1 MUTATED CELSR1 WILD-TYPE
  N0             20              200
  N1              2               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"
D1639V6, binary
                  cls
clus                 0   1
  CELSR1 MUTATED    18   1
  CELSR1 WILD-TYPE 265  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CELSR1 MUTATED     18    1
  CELSR1 WILD-TYPE  265   47
   clus
vv  CELSR1 MUTATED CELSR1 WILD-TYPE
  0             18              265
  1              1               47
[1] 2 2
[1] FALSE
D1639V7, 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
D1639V8, binary
                  cls
clus                 0   1
  CELSR1 MUTATED    18   4
  CELSR1 WILD-TYPE 299  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CELSR1 MUTATED     18    4
  CELSR1 WILD-TYPE  299   44
                               clus
vv                              CELSR1 MUTATED CELSR1 WILD-TYPE
  COLON ADENOCARCINOMA                      18              299
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CELSR1 MUTATED    16   0   1   0
  CELSR1 WILD-TYPE 241   2  21  21
D1639V9, multiclass
    clus
vv   CELSR1 MUTATED CELSR1 WILD-TYPE
  R0             16              241
  R1              0                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"
D1639V10, 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
D1639V11, 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(1640) Variable = OLFML1 MUTATION ANALYSIS
D1640V1, survival
                  sevent
clus2                0   1
  OLFML1 MUTATED     9   1
  OLFML1 WILD-TYPE 273  72
  OLFML1 MUTATED OLFML1 WILD-TYPE 
              10              345 
  OLFML1 MUTATED OLFML1 WILD-TYPE 
               1               72 
$`OLFML1 MUTATED`
TCGA-AA-3510 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3864 TCGA-AA-3875 TCGA-AA-3966 
       63.98        26.99        19.04        53.00        18.05         2.01 
TCGA-AA-A010 TCGA-CA-6717 TCGA-CM-6161 TCGA-D5-6931 
       34.98         0.33        15.02        12.00 

$`OLFML1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
       36.00         5.03        85.05        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       26.01        24.00         2.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  OLFML1 MUTATED OLFML1 WILD-TYPE 
            0.33             0.00 
  OLFML1 MUTATED OLFML1 WILD-TYPE 
           63.98           140.38 
  OLFML1 MUTATED OLFML1 WILD-TYPE 
          18.545           20.280 
[1] "0.3 - 64.0 (18.5)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "2.1"
D1640V2, 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       22       105         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OLFML1 MUTATED           0          0          0          1        0
  OLFML1 WILD-TYPE        19         10         41         30       35
                  vv
clus               STAGE IVA STAGE IVB
  OLFML1 MUTATED           0         0
  OLFML1 WILD-TYPE        13         1
D1640V3, multiclass
            clus
vv           OLFML1 MUTATED OLFML1 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                3               22
  STAGE IIA               4              105
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  OLFML1 MUTATED     1   1   7   2
  OLFML1 WILD-TYPE   8  67 241  39
D1640V4, multiclass
    clus
vv   OLFML1 MUTATED OLFML1 WILD-TYPE
  T1              1                8
  T2              1               67
  T3              7              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
  OLFML1 MUTATED    10   0   1
  OLFML1 WILD-TYPE 210  80  65
D1640V5, multiclass
    clus
vv   OLFML1 MUTATED OLFML1 WILD-TYPE
  N0             10              210
  N1              0               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"
D1640V6, binary
                  cls
clus                 0   1
  OLFML1 MUTATED    11   0
  OLFML1 WILD-TYPE 272  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OLFML1 MUTATED     11    0
  OLFML1 WILD-TYPE  272   48
   clus
vv  OLFML1 MUTATED OLFML1 WILD-TYPE
  0             11              272
  1              0               48
[1] 2 2
[1] FALSE
D1640V7, 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
D1640V8, binary
                  cls
clus                 0   1
  OLFML1 MUTATED     9   2
  OLFML1 WILD-TYPE 308  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OLFML1 MUTATED      9    2
  OLFML1 WILD-TYPE  308   46
                               clus
vv                              OLFML1 MUTATED OLFML1 WILD-TYPE
  COLON ADENOCARCINOMA                       9              308
  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 248   2  22  20
D1640V9, multiclass
    clus
vv   OLFML1 MUTATED OLFML1 WILD-TYPE
  R0              9              248
  R1              0                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"
D1640V10, 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
D1640V11, 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(1641) Variable = GSTA5 MUTATION ANALYSIS
D1641V1, survival
                 sevent
clus2               0   1
  GSTA5 MUTATED     5   1
  GSTA5 WILD-TYPE 277  72
  GSTA5 MUTATED GSTA5 WILD-TYPE 
              6             349 
  GSTA5 MUTATED GSTA5 WILD-TYPE 
              1              72 
$`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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 
        0.53        35.41        19.43       107.67        74.56        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  GSTA5 MUTATED GSTA5 WILD-TYPE 
          22.98            0.00 
  GSTA5 MUTATED GSTA5 WILD-TYPE 
          85.05          140.38 
  GSTA5 MUTATED GSTA5 WILD-TYPE 
          50.83           19.99 
[1] "23.0 - 85.0 (50.8)" "0.0 - 140.4 (20.0)"
[1] "hr=" "2.5"
D1641V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GSTA5 MUTATED         0        0        0         2         0         0
  GSTA5 WILD-TYPE      64        1       25       107         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GSTA5 MUTATED           1          0          1          0        1         0
  GSTA5 WILD-TYPE        18         10         40         31       34        13
                 vv
clus              STAGE IVB
  GSTA5 MUTATED           0
  GSTA5 WILD-TYPE         1
D1641V3, multiclass
            clus
vv           GSTA5 MUTATED GSTA5 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              2             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GSTA5 MUTATED     0   1   5   0
  GSTA5 WILD-TYPE   9  67 243  41
D1641V4, multiclass
    clus
vv   GSTA5 MUTATED GSTA5 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             5             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
  GSTA5 MUTATED     4   2   0
  GSTA5 WILD-TYPE 216  78  66
D1641V5, multiclass
    clus
vv   GSTA5 MUTATED GSTA5 WILD-TYPE
  N0             4             216
  N1             2              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"
D1641V6, binary
                 cls
clus                0   1
  GSTA5 MUTATED     4   1
  GSTA5 WILD-TYPE 279  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GSTA5 MUTATED      4    1
  GSTA5 WILD-TYPE  279   47
   clus
vv  GSTA5 MUTATED GSTA5 WILD-TYPE
  0             4             279
  1             1              47
[1] 2 2
[1] FALSE
D1641V7, 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
D1641V8, binary
                 cls
clus                0   1
  GSTA5 MUTATED     5   1
  GSTA5 WILD-TYPE 312  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GSTA5 MUTATED      5    1
  GSTA5 WILD-TYPE  312   47
                               clus
vv                              GSTA5 MUTATED GSTA5 WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  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 252   2  22  21
D1641V9, multiclass
    clus
vv   GSTA5 MUTATED GSTA5 WILD-TYPE
  R0             5             252
  R1             0               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"
D1641V10, 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
D1641V11, 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(1642) Variable = TM7SF4 MUTATION ANALYSIS
D1642V1, survival
                  sevent
clus2                0   1
  TM7SF4 MUTATED     6   1
  TM7SF4 WILD-TYPE 276  72
  TM7SF4 MUTATED TM7SF4 WILD-TYPE 
               7              348 
  TM7SF4 MUTATED TM7SF4 WILD-TYPE 
               1               72 
$`TM7SF4 MUTATED`
TCGA-A6-3809 TCGA-A6-6648 TCGA-AA-A010 TCGA-AD-5900 TCGA-CM-4746 TCGA-D5-6537 
       32.75        25.18        34.98         0.07        37.02         4.80 
TCGA-D5-6928 
       11.64 

$`TM7SF4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        15.12        17.85        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  TM7SF4 MUTATED TM7SF4 WILD-TYPE 
            0.07             0.00 
  TM7SF4 MUTATED TM7SF4 WILD-TYPE 
           37.02           140.38 
  TM7SF4 MUTATED TM7SF4 WILD-TYPE 
          25.180           20.155 
[1] "0.1 - 37.0 (25.2)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1"  
D1642V2, 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       25       108         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TM7SF4 MUTATED           0          0          1          0        0
  TM7SF4 WILD-TYPE        19         10         40         31       35
                  vv
clus               STAGE IVA STAGE IVB
  TM7SF4 MUTATED           1         0
  TM7SF4 WILD-TYPE        12         1
D1642V3, multiclass
            clus
vv           TM7SF4 MUTATED TM7SF4 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               1              108
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 245  39
D1642V4, multiclass
    clus
vv   TM7SF4 MUTATED TM7SF4 WILD-TYPE
  T1              0                9
  T2              2               66
  T3              3              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
  TM7SF4 MUTATED     6   1   0
  TM7SF4 WILD-TYPE 214  79  66
D1642V5, multiclass
    clus
vv   TM7SF4 MUTATED TM7SF4 WILD-TYPE
  N0              6              214
  N1              1               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"
D1642V6, binary
                  cls
clus                 0   1
  TM7SF4 MUTATED     4   1
  TM7SF4 WILD-TYPE 279  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TM7SF4 MUTATED      4    1
  TM7SF4 WILD-TYPE  279   47
   clus
vv  TM7SF4 MUTATED TM7SF4 WILD-TYPE
  0              4              279
  1              1               47
[1] 2 2
[1] FALSE
D1642V7, 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
D1642V8, binary
                  cls
clus                 0   1
  TM7SF4 MUTATED     4   3
  TM7SF4 WILD-TYPE 313  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TM7SF4 MUTATED      4    3
  TM7SF4 WILD-TYPE  313   45
                               clus
vv                              TM7SF4 MUTATED TM7SF4 WILD-TYPE
  COLON ADENOCARCINOMA                       4              313
  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 251   2  22  21
D1642V9, multiclass
    clus
vv   TM7SF4 MUTATED TM7SF4 WILD-TYPE
  R0              6              251
  R1              0                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"
D1642V10, 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
D1642V11, 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(1643) Variable = PLCB2 MUTATION ANALYSIS
D1643V1, survival
                 sevent
clus2               0   1
  PLCB2 MUTATED     6   3
  PLCB2 WILD-TYPE 276  70
  PLCB2 MUTATED PLCB2 WILD-TYPE 
              9             346 
  PLCB2 MUTATED PLCB2 WILD-TYPE 
              3              70 
$`PLCB2 MUTATED`
TCGA-AA-3672 TCGA-AA-3949 TCGA-AA-3977 TCGA-AZ-4315 TCGA-AZ-6608 TCGA-CK-5914 
        0.92        26.01        25.02        58.39         1.94        21.99 
TCGA-D5-6536 TCGA-DM-A1D6 TCGA-DM-A1DB 
       17.85        49.91        44.32 

$`PLCB2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
        6.05         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
      100.01        29.56         5.23        11.74         3.19         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-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-A1HA 
       92.75        13.32        12.59       140.38         7.50       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  PLCB2 MUTATED PLCB2 WILD-TYPE 
           0.92            0.00 
  PLCB2 MUTATED PLCB2 WILD-TYPE 
          58.39          140.38 
  PLCB2 MUTATED PLCB2 WILD-TYPE 
          25.02           20.07 
[1] "0.9 - 58.4 (25.0)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.5"
D1643V2, 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       25       105         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        18          9         39         31       35        13
                 vv
clus              STAGE IVB
  PLCB2 MUTATED           0
  PLCB2 WILD-TYPE         1
D1643V3, multiclass
            clus
vv           PLCB2 MUTATED PLCB2 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              4             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             1               9
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PLCB2 MUTATED     0   2   7   0
  PLCB2 WILD-TYPE   9  66 241  41
D1643V4, multiclass
    clus
vv   PLCB2 MUTATED PLCB2 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             7             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
  PLCB2 MUTATED     5   4   0
  PLCB2 WILD-TYPE 215  76  66
D1643V5, multiclass
    clus
vv   PLCB2 MUTATED PLCB2 WILD-TYPE
  N0             5             215
  N1             4              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"
D1643V6, binary
                 cls
clus                0   1
  PLCB2 MUTATED     7   0
  PLCB2 WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLCB2 MUTATED      7    0
  PLCB2 WILD-TYPE  276   48
   clus
vv  PLCB2 MUTATED PLCB2 WILD-TYPE
  0             7             276
  1             0              48
[1] 2 2
[1] FALSE
D1643V7, 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
D1643V8, binary
                 cls
clus                0   1
  PLCB2 MUTATED     7   2
  PLCB2 WILD-TYPE 310  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLCB2 MUTATED      7    2
  PLCB2 WILD-TYPE  310   46
                               clus
vv                              PLCB2 MUTATED PLCB2 WILD-TYPE
  COLON ADENOCARCINOMA                      7             310
  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 253   2  22  20
D1643V9, multiclass
    clus
vv   PLCB2 MUTATED PLCB2 WILD-TYPE
  R0             4             253
  R1             0               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"
D1643V10, 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
D1643V11, 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(1644) Variable = LRBA MUTATION ANALYSIS
D1644V1, survival
                sevent
clus2              0   1
  LRBA MUTATED    21   5
  LRBA WILD-TYPE 261  68
  LRBA MUTATED LRBA WILD-TYPE 
            26            329 
  LRBA MUTATED LRBA WILD-TYPE 
             5             68 
$`LRBA MUTATED`
TCGA-A6-2671 TCGA-A6-4105 TCGA-A6-6653 TCGA-AA-3510 TCGA-AA-3660 TCGA-AA-3662 
       43.76        14.53        24.39        63.98        78.08         6.05 
TCGA-AA-3821 TCGA-AA-3977 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A02O 
        1.02        25.02        18.05         4.01        34.98         0.92 
TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CA-6718 
       27.09        58.39        61.41        49.41         0.33         0.10 
TCGA-CK-5914 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-6674 TCGA-F4-6809 TCGA-F4-6854 
       21.99        30.08        15.02        12.95        13.25         0.53 
TCGA-G4-6293 TCGA-G4-6628 
      107.67        52.80 

$`LRBA WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 
       34.65        33.34        32.75        36.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       24.16        21.76        24.69        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       61.02         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       19.00        30.02        34.03        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
       14.01        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6599 TCGA-AZ-6600 
        5.13        83.80        22.36        62.79         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.14         2.93         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        16.01         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.41        19.43        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       13.78        35.80        26.17        91.79        46.75 

  LRBA MUTATED LRBA WILD-TYPE 
           0.1            0.0 
  LRBA MUTATED LRBA WILD-TYPE 
        107.67         140.38 
  LRBA MUTATED LRBA WILD-TYPE 
         23.19          20.12 
[1] "0.1 - 107.7 (23.2)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.3"
D1644V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LRBA MUTATED         5        0        4         8         2         0
  LRBA WILD-TYPE      59        1       21       101         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LRBA MUTATED           1          0          2          0        2         1
  LRBA WILD-TYPE        18         10         39         31       33        12
                vv
clus             STAGE IVB
  LRBA MUTATED           0
  LRBA WILD-TYPE         1
D1644V3, multiclass
            clus
vv           LRBA MUTATED LRBA WILD-TYPE
  STAGE I               5             59
  STAGE IA              0              1
  STAGE II              4             21
  STAGE IIA             8            101
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            2             39
  STAGE IIIC            0             31
  STAGE IV              2             33
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  LRBA MUTATED     1   5  16   4
  LRBA WILD-TYPE   8  63 232  37
D1644V4, multiclass
    clus
vv   LRBA MUTATED LRBA WILD-TYPE
  T1            1              8
  T2            5             63
  T3           16            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
  LRBA MUTATED    20   4   2
  LRBA WILD-TYPE 200  76  64
D1644V5, multiclass
    clus
vv   LRBA MUTATED LRBA WILD-TYPE
  N0           20            200
  N1            4             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"
D1644V6, binary
                cls
clus               0   1
  LRBA MUTATED    20   3
  LRBA WILD-TYPE 263  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  LRBA MUTATED     20    3
  LRBA WILD-TYPE  263   45
   clus
vv  LRBA MUTATED LRBA WILD-TYPE
  0           20            263
  1            3             45
[1] 2 2
[1] FALSE
D1644V7, binary
                cls
clus               0   1
  LRBA MUTATED    12  14
  LRBA WILD-TYPE 158 183
[1] "tbl2"
                cls
clus             [,1] [,2]
  LRBA MUTATED     12   14
  LRBA WILD-TYPE  158  183
        clus
vv       LRBA MUTATED LRBA WILD-TYPE
  FEMALE           12            158
  MALE             14            183
[1] 2 2
[1] FALSE
D1644V8, binary
                cls
clus               0   1
  LRBA MUTATED    22   4
  LRBA WILD-TYPE 295  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  LRBA MUTATED     22    4
  LRBA WILD-TYPE  295   44
                               clus
vv                              LRBA MUTATED LRBA WILD-TYPE
  COLON ADENOCARCINOMA                    22            295
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  LRBA MUTATED    17   0   1   3
  LRBA WILD-TYPE 240   2  21  18
D1644V9, multiclass
    clus
vv   LRBA MUTATED LRBA WILD-TYPE
  R0           17            240
  R1            0              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"
D1644V10, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LRBA MUTATED                                  0     2
  LRBA WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  LRBA MUTATED                           0    15
  LRBA WILD-TYPE                        19   161
D1644V11, multiclass
                                  clus
vv                                 LRBA MUTATED LRBA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              8
  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(1645) Variable = MED24 MUTATION ANALYSIS
D1645V1, survival
                 sevent
clus2               0   1
  MED24 MUTATED     8   1
  MED24 WILD-TYPE 274  72
  MED24 MUTATED MED24 WILD-TYPE 
              9             346 
  MED24 MUTATED MED24 WILD-TYPE 
              1              72 
$`MED24 MUTATED`
TCGA-A6-6780 TCGA-AA-3520 TCGA-AA-3555 TCGA-AA-3663 TCGA-AA-A01K TCGA-AA-A01R 
       20.12        24.03        29.95         6.97        31.00        35.01 
TCGA-CA-6719 TCGA-D5-6930 TCGA-F4-6570 
        1.35         1.51         6.18 

$`MED24 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        1.02         9.07        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P 
       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        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  MED24 MUTATED MED24 WILD-TYPE 
           1.35            0.00 
  MED24 MUTATED MED24 WILD-TYPE 
          35.01          140.38 
  MED24 MUTATED MED24 WILD-TYPE 
         20.120          20.235 
[1] "1.4 - 35.0 (20.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D1645V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MED24 MUTATED         0        0        2         5         0         0
  MED24 WILD-TYPE      64        1       23       104         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MED24 MUTATED           1          0          0          1        0         0
  MED24 WILD-TYPE        18         10         41         30       35        13
                 vv
clus              STAGE IVB
  MED24 MUTATED           0
  MED24 WILD-TYPE         1
D1645V3, multiclass
            clus
vv           MED24 MUTATED MED24 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              5             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MED24 MUTATED     0   0   9   0
  MED24 WILD-TYPE   9  68 239  41
D1645V4, multiclass
    clus
vv   MED24 MUTATED MED24 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             9             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
  MED24 MUTATED     7   0   2
  MED24 WILD-TYPE 213  80  64
D1645V5, multiclass
    clus
vv   MED24 MUTATED MED24 WILD-TYPE
  N0             7             213
  N1             0              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"
D1645V6, binary
                 cls
clus                0   1
  MED24 MUTATED     8   0
  MED24 WILD-TYPE 275  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED24 MUTATED      8    0
  MED24 WILD-TYPE  275   48
   clus
vv  MED24 MUTATED MED24 WILD-TYPE
  0             8             275
  1             0              48
[1] 2 2
[1] FALSE
D1645V7, binary
                 cls
clus                0   1
  MED24 MUTATED     4   5
  MED24 WILD-TYPE 166 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED24 MUTATED      4    5
  MED24 WILD-TYPE  166  192
        clus
vv       MED24 MUTATED MED24 WILD-TYPE
  FEMALE             4             166
  MALE               5             192
[1] 2 2
[1] FALSE
D1645V8, binary
                 cls
clus                0   1
  MED24 MUTATED     5   4
  MED24 WILD-TYPE 312  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED24 MUTATED      5    4
  MED24 WILD-TYPE  312   44
                               clus
vv                              MED24 MUTATED MED24 WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MED24 MUTATED     7   0   0   1
  MED24 WILD-TYPE 250   2  22  20
D1645V9, multiclass
    clus
vv   MED24 MUTATED MED24 WILD-TYPE
  R0             7             250
  R1             0               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"
D1645V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MED24 MUTATED                                  0     1
  MED24 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MED24 MUTATED                           0     3
  MED24 WILD-TYPE                        19   173
D1645V11, multiclass
                                  clus
vv                                 MED24 MUTATED MED24 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(1646) Variable = SRGAP3 MUTATION ANALYSIS
D1646V1, survival
                  sevent
clus2                0   1
  SRGAP3 MUTATED    13   3
  SRGAP3 WILD-TYPE 269  70
  SRGAP3 MUTATED SRGAP3 WILD-TYPE 
              16              339 
  SRGAP3 MUTATED SRGAP3 WILD-TYPE 
               3               70 
$`SRGAP3 MUTATED`
TCGA-A6-6653 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3715 TCGA-AA-3815 TCGA-AA-3950 
       24.39         6.05         2.01        19.04        33.04        24.00 
TCGA-AA-A029 TCGA-AD-5900 TCGA-AD-6895 TCGA-CA-6717 TCGA-CM-6674 TCGA-D5-6535 
       51.98         0.07         0.72         0.33        12.95        15.12 
TCGA-D5-6927 TCGA-D5-6930 TCGA-DM-A285 TCGA-G4-6310 
        9.44         1.51         6.12        45.11 

$`SRGAP3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       19.99        13.94        19.99        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       85.05        26.99        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       39.06        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  SRGAP3 MUTATED SRGAP3 WILD-TYPE 
            0.07             0.00 
  SRGAP3 MUTATED SRGAP3 WILD-TYPE 
           51.98           140.38 
  SRGAP3 MUTATED SRGAP3 WILD-TYPE 
          11.195           20.980 
[1] "0.1 - 52.0 (11.2)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.4"
D1646V2, 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       23       103         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SRGAP3 MUTATED           1          0          2          0        2
  SRGAP3 WILD-TYPE        18         10         39         31       33
                  vv
clus               STAGE IVA STAGE IVB
  SRGAP3 MUTATED           0         0
  SRGAP3 WILD-TYPE        13         1
D1646V3, multiclass
            clus
vv           SRGAP3 MUTATED SRGAP3 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               6              103
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              0               31
  STAGE IV                2               33
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SRGAP3 MUTATED     0   2  13   2
  SRGAP3 WILD-TYPE   9  66 235  39
D1646V4, multiclass
    clus
vv   SRGAP3 MUTATED SRGAP3 WILD-TYPE
  T1              0                9
  T2              2               66
  T3             13              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
  SRGAP3 MUTATED    11   4   2
  SRGAP3 WILD-TYPE 209  76  64
D1646V5, multiclass
    clus
vv   SRGAP3 MUTATED SRGAP3 WILD-TYPE
  N0             11              209
  N1              4               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"
D1646V6, binary
                  cls
clus                 0   1
  SRGAP3 MUTATED    11   2
  SRGAP3 WILD-TYPE 272  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SRGAP3 MUTATED     11    2
  SRGAP3 WILD-TYPE  272   46
   clus
vv  SRGAP3 MUTATED SRGAP3 WILD-TYPE
  0             11              272
  1              2               46
[1] 2 2
[1] FALSE
D1646V7, 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
D1646V8, binary
                  cls
clus                 0   1
  SRGAP3 MUTATED    12   5
  SRGAP3 WILD-TYPE 305  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SRGAP3 MUTATED     12    5
  SRGAP3 WILD-TYPE  305   43
                               clus
vv                              SRGAP3 MUTATED SRGAP3 WILD-TYPE
  COLON ADENOCARCINOMA                      12              305
  COLON MUCINOUS ADENOCARCINOMA              5               43
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SRGAP3 MUTATED    10   0   1   3
  SRGAP3 WILD-TYPE 247   2  21  18
D1646V9, multiclass
    clus
vv   SRGAP3 MUTATED SRGAP3 WILD-TYPE
  R0             10              247
  R1              0                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"
D1646V10, 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
D1646V11, 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(1647) Variable = AAMP MUTATION ANALYSIS
D1647V1, survival
                sevent
clus2              0   1
  AAMP MUTATED     3   0
  AAMP WILD-TYPE 279  73
  AAMP MUTATED AAMP WILD-TYPE 
             3            352 
  AAMP MUTATED AAMP WILD-TYPE 
             0             73 
$`AAMP MUTATED`
TCGA-A6-6781 TCGA-G4-6309 TCGA-G4-6628 
       19.66        51.75        52.80 

$`AAMP WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       35.80        26.17        91.79        46.75 

  AAMP MUTATED AAMP WILD-TYPE 
         19.66           0.00 
  AAMP MUTATED AAMP WILD-TYPE 
         52.80         140.38 
  AAMP MUTATED AAMP WILD-TYPE 
        51.750         20.155 
[1] "19.7 - 52.8 (51.8)" "0.0 - 140.4 (20.2)"
[1] "hr="     "9300000"
D1647V2, 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       25       109         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        19         10         40         30       35        13
                vv
clus             STAGE IVB
  AAMP MUTATED           0
  AAMP WILD-TYPE         1
D1647V3, multiclass
            clus
vv           AAMP MUTATED AAMP WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             0            109
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            1             30
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  AAMP MUTATED     0   1   1   1
  AAMP WILD-TYPE   9  67 247  40
D1647V4, multiclass
    clus
vv   AAMP MUTATED AAMP WILD-TYPE
  T1            0              9
  T2            1             67
  T3            1            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
  AAMP MUTATED     1   2   0
  AAMP WILD-TYPE 219  78  66
D1647V5, multiclass
    clus
vv   AAMP MUTATED AAMP WILD-TYPE
  N0            1            219
  N1            2             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"
D1647V6, binary
                cls
clus               0   1
  AAMP MUTATED     2   0
  AAMP WILD-TYPE 281  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  AAMP MUTATED      2    0
  AAMP WILD-TYPE  281   48
   clus
vv  AAMP MUTATED AAMP WILD-TYPE
  0            2            281
  1            0             48
[1] 2 2
[1] FALSE
D1647V7, 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
D1647V8, binary
                cls
clus               0   1
  AAMP MUTATED     2   1
  AAMP WILD-TYPE 315  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  AAMP MUTATED      2    1
  AAMP WILD-TYPE  315   47
                               clus
vv                              AAMP MUTATED AAMP WILD-TYPE
  COLON ADENOCARCINOMA                     2            315
  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 254   2  22  21
D1647V9, multiclass
    clus
vv   AAMP MUTATED AAMP WILD-TYPE
  R0            3            254
  R1            0              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"
D1647V10, 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
D1647V11, 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(1648) Variable = TRAM1L1 MUTATION ANALYSIS
D1648V1, survival
                   sevent
clus2                 0   1
  TRAM1L1 MUTATED    10   2
  TRAM1L1 WILD-TYPE 272  71
  TRAM1L1 MUTATED TRAM1L1 WILD-TYPE 
               12               343 
  TRAM1L1 MUTATED TRAM1L1 WILD-TYPE 
                2                71 
$`TRAM1L1 MUTATED`
TCGA-AA-3713 TCGA-AA-3815 TCGA-AA-3950 TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-6598 
       19.04        33.04        24.00         4.01        34.98        49.41 
TCGA-CA-6719 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5861 TCGA-CM-6171 TCGA-CM-6674 
        1.35        29.06        22.03        15.02        14.04        12.95 

$`TRAM1L1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5348 TCGA-CM-5349 
       20.02        37.02        25.02        13.02        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       16.01         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  TRAM1L1 MUTATED TRAM1L1 WILD-TYPE 
             1.35              0.00 
  TRAM1L1 MUTATED TRAM1L1 WILD-TYPE 
            49.41            140.38 
  TRAM1L1 MUTATED TRAM1L1 WILD-TYPE 
           20.535            20.190 
[1] "1.4 - 49.4 (20.5)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1"  
D1648V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TRAM1L1 MUTATED         1        0        1         5         2         0
  TRAM1L1 WILD-TYPE      63        1       24       104         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRAM1L1 MUTATED           0          1          1          0        1
  TRAM1L1 WILD-TYPE        19          9         40         31       34
                   vv
clus                STAGE IVA STAGE IVB
  TRAM1L1 MUTATED           0         0
  TRAM1L1 WILD-TYPE        13         1
D1648V3, multiclass
            clus
vv           TRAM1L1 MUTATED TRAM1L1 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                5               104
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               1                 9
  STAGE IIIB               1                40
  STAGE IIIC               0                31
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TRAM1L1 MUTATED     0   2   8   2
  TRAM1L1 WILD-TYPE   9  66 240  39
D1648V4, multiclass
    clus
vv   TRAM1L1 MUTATED TRAM1L1 WILD-TYPE
  T1               0                 9
  T2               2                66
  T3               8               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
  TRAM1L1 MUTATED    10   2   0
  TRAM1L1 WILD-TYPE 210  78  66
D1648V5, multiclass
    clus
vv   TRAM1L1 MUTATED TRAM1L1 WILD-TYPE
  N0              10               210
  N1               2                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"
D1648V6, binary
                   cls
clus                  0   1
  TRAM1L1 MUTATED    10   1
  TRAM1L1 WILD-TYPE 273  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TRAM1L1 MUTATED     10    1
  TRAM1L1 WILD-TYPE  273   47
   clus
vv  TRAM1L1 MUTATED TRAM1L1 WILD-TYPE
  0              10               273
  1               1                47
[1] 2 2
[1] FALSE
D1648V7, binary
                   cls
clus                  0   1
  TRAM1L1 MUTATED     8   4
  TRAM1L1 WILD-TYPE 162 193
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TRAM1L1 MUTATED      8    4
  TRAM1L1 WILD-TYPE  162  193
        clus
vv       TRAM1L1 MUTATED TRAM1L1 WILD-TYPE
  FEMALE               8               162
  MALE                 4               193
[1] 2 2
[1] FALSE
D1648V8, binary
                   cls
clus                  0   1
  TRAM1L1 MUTATED    10   2
  TRAM1L1 WILD-TYPE 307  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TRAM1L1 MUTATED     10    2
  TRAM1L1 WILD-TYPE  307   46
                               clus
vv                              TRAM1L1 MUTATED TRAM1L1 WILD-TYPE
  COLON ADENOCARCINOMA                       10               307
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  TRAM1L1 MUTATED     9   0   1   1
  TRAM1L1 WILD-TYPE 248   2  21  20
D1648V9, multiclass
    clus
vv   TRAM1L1 MUTATED TRAM1L1 WILD-TYPE
  R0               9               248
  R1               0                 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"
D1648V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRAM1L1 MUTATED                                  0     1
  TRAM1L1 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  TRAM1L1 MUTATED                           0     6
  TRAM1L1 WILD-TYPE                        19   170
D1648V11, multiclass
                                  clus
vv                                 TRAM1L1 MUTATED TRAM1L1 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(1649) Variable = HYDIN MUTATION ANALYSIS
D1649V1, survival
                 sevent
clus2               0   1
  HYDIN MUTATED    62  14
  HYDIN WILD-TYPE 220  59
  HYDIN MUTATED HYDIN WILD-TYPE 
             76             279 
  HYDIN MUTATED HYDIN WILD-TYPE 
             14              59 
$`HYDIN MUTATED`
TCGA-A6-3809 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5665 
       32.75        32.91        30.44        29.19        33.53        22.06 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6653 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3510 
        8.38        25.08        24.39        20.28         3.02        63.98 
TCGA-AA-3518 TCGA-AA-3524 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3666 
        1.02        36.03        61.02         6.05         6.97         2.01 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3815 TCGA-AA-3833 TCGA-AA-3846 TCGA-AA-3854 
       26.99        19.04        33.04        15.95        17.03        36.03 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3972 
       30.05        53.00        31.00        33.01        24.00        50.99 
TCGA-AA-3977 TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A03F TCGA-AD-5900 
       25.02        18.05         4.01        34.98        18.05         0.07 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6965 TCGA-AU-6004 
        4.21        56.55         0.72         5.79         0.20        27.09 
TCGA-AY-6196 TCGA-AZ-4315 TCGA-AZ-4682 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-AZ-6606 
        0.20        58.39        22.36        49.41       100.01        11.74 
TCGA-AZ-6607 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-6747 TCGA-CM-4746 TCGA-CM-4747 
        3.19         0.33         0.10         2.93        37.02        25.02 
TCGA-CM-6162 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6680 TCGA-D5-5537 
       12.00        14.04        12.95        13.05        12.03        45.40 
TCGA-D5-5538 TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6541 TCGA-D5-6924 TCGA-D5-6927 
       12.26        15.12        17.13        15.58        14.30         9.44 
TCGA-D5-6932 TCGA-DM-A1D9 TCGA-DM-A282 TCGA-DM-A28G TCGA-F4-6570 TCGA-F4-6855 
       11.38       140.38       139.17        60.79         6.18        35.41 
TCGA-G4-6317 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 
       36.00        35.80        26.17        52.80 

$`HYDIN WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5657 
       16.57        34.65        33.34        36.53        14.53        31.63 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6648 
       23.61        22.09        32.71        27.09        22.52        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       24.16        21.76        24.69        23.87        20.12        19.66 
TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        7.04         1.02        35.01         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3526 
       38.99         9.07        24.03        37.05         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 
       13.94        19.99        78.08        54.02        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3811 
       19.00        36.00         5.03        85.05        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 
       35.05         0.99        25.02         1.02        17.98        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02        14.93         0.00        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 
        0.00        32.05         0.99        31.07        31.07        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        18.05         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        26.01         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       21.99        16.08        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J 
        5.03        14.01         0.92        41.00        39.98        40.96 
TCGA-AD-6548 TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AU-3779 
       21.37         0.79        22.42        27.42        10.88        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        15.75        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
        5.13        83.80        62.79        61.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       29.56         5.23         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07         0.26         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4752 TCGA-CM-5341 
        2.01       124.27        23.05        20.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        16.01        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-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5539 
       11.01        11.08        11.08        11.01        10.06        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 
       17.85         4.80        12.49        16.14         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         1.51 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        49.91        13.32        12.59         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       135.65         6.12        81.37       119.93        35.97 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      117.07        98.24         8.61        13.38        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 
       44.68        55.04        51.75        45.11        36.72        22.09 
TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 
       13.78        91.79        46.75 

  HYDIN MUTATED HYDIN WILD-TYPE 
           0.07            0.00 
  HYDIN MUTATED HYDIN WILD-TYPE 
         140.38          135.65 
  HYDIN MUTATED HYDIN WILD-TYPE 
          22.21           20.02 
[1] "0.1 - 140.4 (22.2)" "0.0 - 135.7 (20.0)"
[1] "hr=" "1.2"
D1649V2, 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       15        79         2         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HYDIN MUTATED           3          0          6          4        4         3
  HYDIN WILD-TYPE        16         10         35         27       31        10
                 vv
clus              STAGE IVB
  HYDIN MUTATED           1
  HYDIN WILD-TYPE         0
D1649V3, multiclass
            clus
vv           HYDIN MUTATED HYDIN WILD-TYPE
  STAGE I               10              54
  STAGE IA               0               1
  STAGE II              10              15
  STAGE IIA             30              79
  STAGE IIB              6               2
  STAGE IIC              0               1
  STAGE III              3              16
  STAGE IIIA             0              10
  STAGE IIIB             6              35
  STAGE IIIC             4              27
  STAGE IV               4              31
  STAGE IVA              3              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
  HYDIN MUTATED     1  11  55  13
  HYDIN WILD-TYPE   8  57 193  28
D1649V4, multiclass
    clus
vv   HYDIN MUTATED HYDIN WILD-TYPE
  T1             1               8
  T2            11              57
  T3            55             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   8  14
  HYDIN WILD-TYPE 163  72  52
D1649V5, multiclass
    clus
vv   HYDIN MUTATED HYDIN WILD-TYPE
  N0            57             163
  N1             8              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"
D1649V6, binary
                 cls
clus                0   1
  HYDIN MUTATED    59   8
  HYDIN WILD-TYPE 224  40
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HYDIN MUTATED     59    8
  HYDIN WILD-TYPE  224   40
   clus
vv  HYDIN MUTATED HYDIN WILD-TYPE
  0            59             224
  1             8              40
[1] 2 2
[1] FALSE
D1649V7, 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
D1649V8, binary
                 cls
clus                0   1
  HYDIN MUTATED    68  12
  HYDIN WILD-TYPE 249  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HYDIN MUTATED     68   12
  HYDIN WILD-TYPE  249   36
                               clus
vv                              HYDIN MUTATED HYDIN WILD-TYPE
  COLON ADENOCARCINOMA                     68             249
  COLON MUCINOUS ADENOCARCINOMA            12              36
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  HYDIN MUTATED    54   0   2   6
  HYDIN WILD-TYPE 203   2  20  15
D1649V9, multiclass
    clus
vv   HYDIN MUTATED HYDIN WILD-TYPE
  R0            54             203
  R1             0               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"
D1649V10, 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
D1649V11, 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(1650) Variable = CARD6 MUTATION ANALYSIS
D1650V1, survival
                 sevent
clus2               0   1
  CARD6 MUTATED    12   3
  CARD6 WILD-TYPE 270  70
  CARD6 MUTATED CARD6 WILD-TYPE 
             15             340 
  CARD6 MUTATED CARD6 WILD-TYPE 
              3              70 
$`CARD6 MUTATED`
TCGA-AA-3511 TCGA-AA-3518 TCGA-AA-3811 TCGA-AA-A010 TCGA-AA-A01P TCGA-AD-6889 
        6.97         1.02        10.06        34.98        38.07        56.55 
TCGA-AY-6196 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CM-5341 TCGA-D5-5540 
        0.20         0.33         0.10         1.35        29.06        13.51 
TCGA-D5-6928 TCGA-DM-A28F TCGA-G4-6588 
       11.64        35.97        26.17 

$`CARD6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01        63.98         1.02        13.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        19.04        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       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        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37         4.21         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        15.75        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        3.29         0.07         0.26        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       13.02        22.03        22.98        30.08        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
      119.93        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        91.79        46.75        52.80 

  CARD6 MUTATED CARD6 WILD-TYPE 
            0.1             0.0 
  CARD6 MUTATED CARD6 WILD-TYPE 
          56.55          140.38 
  CARD6 MUTATED CARD6 WILD-TYPE 
          11.64           20.63 
[1] "0.1 - 56.5 (11.6)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "1.5"
D1650V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CARD6 MUTATED         0        0        1         8         1         0
  CARD6 WILD-TYPE      64        1       24       101         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CARD6 MUTATED           2          1          1          1        0         0
  CARD6 WILD-TYPE        17          9         40         30       35        13
                 vv
clus              STAGE IVB
  CARD6 MUTATED           0
  CARD6 WILD-TYPE         1
D1650V3, multiclass
            clus
vv           CARD6 MUTATED CARD6 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              8             101
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             1               9
  STAGE IIIB             1              40
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CARD6 MUTATED     0   1  12   2
  CARD6 WILD-TYPE   9  67 236  39
D1650V4, multiclass
    clus
vv   CARD6 MUTATED CARD6 WILD-TYPE
  T1             0               9
  T2             1              67
  T3            12             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
  CARD6 MUTATED    10   3   2
  CARD6 WILD-TYPE 210  77  64
D1650V5, multiclass
    clus
vv   CARD6 MUTATED CARD6 WILD-TYPE
  N0            10             210
  N1             3              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"
D1650V6, binary
                 cls
clus                0   1
  CARD6 MUTATED    14   0
  CARD6 WILD-TYPE 269  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CARD6 MUTATED     14    0
  CARD6 WILD-TYPE  269   48
   clus
vv  CARD6 MUTATED CARD6 WILD-TYPE
  0            14             269
  1             0              48
[1] 2 2
[1] FALSE
D1650V7, binary
                 cls
clus                0   1
  CARD6 MUTATED     6   9
  CARD6 WILD-TYPE 164 188
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CARD6 MUTATED      6    9
  CARD6 WILD-TYPE  164  188
        clus
vv       CARD6 MUTATED CARD6 WILD-TYPE
  FEMALE             6             164
  MALE               9             188
[1] 2 2
[1] FALSE
D1650V8, binary
                 cls
clus                0   1
  CARD6 MUTATED    12   3
  CARD6 WILD-TYPE 305  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CARD6 MUTATED     12    3
  CARD6 WILD-TYPE  305   45
                               clus
vv                              CARD6 MUTATED CARD6 WILD-TYPE
  COLON ADENOCARCINOMA                     12             305
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CARD6 MUTATED    10   0   0   3
  CARD6 WILD-TYPE 247   2  22  18
D1650V9, multiclass
    clus
vv   CARD6 MUTATED CARD6 WILD-TYPE
  R0            10             247
  R1             0               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"
D1650V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CARD6 MUTATED                                  0     4
  CARD6 WILD-TYPE                                1     6
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CARD6 MUTATED                           0     6
  CARD6 WILD-TYPE                        19   170
D1650V11, multiclass
                                  clus
vv                                 CARD6 MUTATED CARD6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        4               6
  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(1651) Variable = C14ORF118 MUTATION ANALYSIS
D1651V1, survival
                     sevent
clus2                   0   1
  C14ORF118 MUTATED     7   1
  C14ORF118 WILD-TYPE 275  72
  C14ORF118 MUTATED C14ORF118 WILD-TYPE 
                  8                 347 
  C14ORF118 MUTATED C14ORF118 WILD-TYPE 
                  1                  72 
$`C14ORF118 MUTATED`
TCGA-AA-A010 TCGA-AA-A01K TCGA-CM-6163 TCGA-D5-6529 TCGA-D5-6535 TCGA-DM-A28F 
       34.98        31.00        14.04        20.19        15.12        35.97 
TCGA-G4-6310 TCGA-G4-6586 
       45.11        35.80 

$`C14ORF118 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02        12.00        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        13.51        11.51 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        43.27        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
        6.12        81.37       119.93        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        51.75        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        26.17        91.79        46.75        52.80 

  C14ORF118 MUTATED C14ORF118 WILD-TYPE 
              14.04                0.00 
  C14ORF118 MUTATED C14ORF118 WILD-TYPE 
              45.11              140.38 
  C14ORF118 MUTATED C14ORF118 WILD-TYPE 
              32.99               20.02 
[1] "14.0 - 45.1 (33.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.7"
D1651V2, 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       25       106         7         1
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C14ORF118 MUTATED           0          0          3          1        0
  C14ORF118 WILD-TYPE        19         10         38         30       35
                     vv
clus                  STAGE IVA STAGE IVB
  C14ORF118 MUTATED           0         0
  C14ORF118 WILD-TYPE        13         1
D1651V3, multiclass
            clus
vv           C14ORF118 MUTATED C14ORF118 WILD-TYPE
  STAGE I                    1                  63
  STAGE IA                   0                   1
  STAGE II                   0                  25
  STAGE IIA                  3                 106
  STAGE IIB                  1                   7
  STAGE IIC                  0                   1
  STAGE III                  0                  19
  STAGE IIIA                 0                  10
  STAGE IIIB                 3                  38
  STAGE IIIC                 1                  30
  STAGE IV                   0                  35
  STAGE IVA                  0                  13
  STAGE IVB                  0                   1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2  T3  T4
  C14ORF118 MUTATED     1   0   7   1
  C14ORF118 WILD-TYPE   8  68 241  40
D1651V4, multiclass
    clus
vv   C14ORF118 MUTATED C14ORF118 WILD-TYPE
  T1                 1                   8
  T2                 0                  68
  T3                 7                 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
  C14ORF118 MUTATED     5   3   1
  C14ORF118 WILD-TYPE 215  77  65
D1651V5, multiclass
    clus
vv   C14ORF118 MUTATED C14ORF118 WILD-TYPE
  N0                 5                 215
  N1                 3                  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"
D1651V6, binary
                     cls
clus                    0   1
  C14ORF118 MUTATED     8   0
  C14ORF118 WILD-TYPE 275  48
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF118 MUTATED      8    0
  C14ORF118 WILD-TYPE  275   48
   clus
vv  C14ORF118 MUTATED C14ORF118 WILD-TYPE
  0                 8                 275
  1                 0                  48
[1] 2 2
[1] FALSE
D1651V7, 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
D1651V8, binary
                     cls
clus                    0   1
  C14ORF118 MUTATED     9   0
  C14ORF118 WILD-TYPE 308  48
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF118 MUTATED      9    0
  C14ORF118 WILD-TYPE  308   48
                               clus
vv                              C14ORF118 MUTATED C14ORF118 WILD-TYPE
  COLON ADENOCARCINOMA                          9                 308
  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 250   2  22  20
D1651V9, multiclass
    clus
vv   C14ORF118 MUTATED C14ORF118 WILD-TYPE
  R0                 7                 250
  R1                 0                   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"
D1651V10, 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
D1651V11, 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(1652) Variable = FAM83D MUTATION ANALYSIS
D1652V1, survival
                  sevent
clus2                0   1
  FAM83D MUTATED    10   1
  FAM83D WILD-TYPE 272  72
  FAM83D MUTATED FAM83D WILD-TYPE 
              11              344 
  FAM83D MUTATED FAM83D WILD-TYPE 
               1               72 
$`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       107.67        36.00 

$`FAM83D WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 
       33.67        13.25         0.53        35.41        19.43        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.72        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  FAM83D MUTATED FAM83D WILD-TYPE 
            3.02             0.00 
  FAM83D MUTATED FAM83D WILD-TYPE 
          135.65           140.38 
  FAM83D MUTATED FAM83D WILD-TYPE 
           34.98            19.99 
[1] "3.0 - 135.7 (35.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "3.6"
D1652V2, 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       22       107         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM83D MUTATED           2          0          1          2        0
  FAM83D WILD-TYPE        17         10         40         29       35
                  vv
clus               STAGE IVA STAGE IVB
  FAM83D MUTATED           0         0
  FAM83D WILD-TYPE        13         1
D1652V3, multiclass
            clus
vv           FAM83D MUTATED FAM83D WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                3               22
  STAGE IIA               2              107
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               2               17
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              2               29
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FAM83D MUTATED     0   0  10   1
  FAM83D WILD-TYPE   9  68 238  40
D1652V4, multiclass
    clus
vv   FAM83D MUTATED FAM83D WILD-TYPE
  T1              0                9
  T2              0               68
  T3             10              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
  FAM83D MUTATED     6   2   3
  FAM83D WILD-TYPE 214  78  63
D1652V5, multiclass
    clus
vv   FAM83D MUTATED FAM83D WILD-TYPE
  N0              6              214
  N1              2               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"
D1652V6, binary
                  cls
clus                 0   1
  FAM83D MUTATED    10   0
  FAM83D WILD-TYPE 273  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM83D MUTATED     10    0
  FAM83D WILD-TYPE  273   48
   clus
vv  FAM83D MUTATED FAM83D WILD-TYPE
  0             10              273
  1              0               48
[1] 2 2
[1] FALSE
D1652V7, 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
D1652V8, binary
                  cls
clus                 0   1
  FAM83D MUTATED    10   1
  FAM83D WILD-TYPE 307  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM83D MUTATED     10    1
  FAM83D WILD-TYPE  307   47
                               clus
vv                              FAM83D MUTATED FAM83D WILD-TYPE
  COLON ADENOCARCINOMA                      10              307
  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 248   2  22  21
D1652V9, multiclass
    clus
vv   FAM83D MUTATED FAM83D WILD-TYPE
  R0              9              248
  R1              0                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"
D1652V10, 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
D1652V11, 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(1653) Variable = GATA1 MUTATION ANALYSIS
D1653V1, survival
                 sevent
clus2               0   1
  GATA1 MUTATED    12   3
  GATA1 WILD-TYPE 270  70
  GATA1 MUTATED GATA1 WILD-TYPE 
             15             340 
  GATA1 MUTATED GATA1 WILD-TYPE 
              3              70 
$`GATA1 MUTATED`
TCGA-AA-3492 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3966 
        3.02        78.08         6.97        33.01        24.00         2.01 
TCGA-AA-A01R TCGA-AD-5900 TCGA-AY-5543 TCGA-AY-6196 TCGA-CK-4952 TCGA-CK-5914 
       35.01         0.07        15.75         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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3664 
       19.99        13.94        19.99        61.02         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       24.00        26.01         2.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      107.67        74.56        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  GATA1 MUTATED GATA1 WILD-TYPE 
           0.07            0.00 
  GATA1 MUTATED GATA1 WILD-TYPE 
          78.08          140.38 
  GATA1 MUTATED GATA1 WILD-TYPE 
         15.750          20.235 
[1] "0.1 - 78.1 (15.8)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D1653V2, 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       22       105         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GATA1 MUTATED           2          0          2          1        1         1
  GATA1 WILD-TYPE        17         10         39         30       34        12
                 vv
clus              STAGE IVB
  GATA1 MUTATED           0
  GATA1 WILD-TYPE         1
D1653V3, multiclass
            clus
vv           GATA1 MUTATED GATA1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              4             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 235  39
D1653V4, multiclass
    clus
vv   GATA1 MUTATED GATA1 WILD-TYPE
  T1             0               9
  T2             1              67
  T3            13             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
  GATA1 MUTATED     9   4   3
  GATA1 WILD-TYPE 211  76  63
D1653V5, multiclass
    clus
vv   GATA1 MUTATED GATA1 WILD-TYPE
  N0             9             211
  N1             4              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"
D1653V6, binary
                 cls
clus                0   1
  GATA1 MUTATED    10   2
  GATA1 WILD-TYPE 273  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GATA1 MUTATED     10    2
  GATA1 WILD-TYPE  273   46
   clus
vv  GATA1 MUTATED GATA1 WILD-TYPE
  0            10             273
  1             2              46
[1] 2 2
[1] FALSE
D1653V7, 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
D1653V8, binary
                 cls
clus                0   1
  GATA1 MUTATED     9   7
  GATA1 WILD-TYPE 308  41
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GATA1 MUTATED      9    7
  GATA1 WILD-TYPE  308   41
                               clus
vv                              GATA1 MUTATED GATA1 WILD-TYPE
  COLON ADENOCARCINOMA                      9             308
  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 244   2  22  19
D1653V9, multiclass
    clus
vv   GATA1 MUTATED GATA1 WILD-TYPE
  R0            13             244
  R1             0               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"
D1653V10, 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
D1653V11, 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(1654) Variable = OR6C1 MUTATION ANALYSIS
D1654V1, survival
                 sevent
clus2               0   1
  OR6C1 MUTATED     6   1
  OR6C1 WILD-TYPE 276  72
  OR6C1 MUTATED OR6C1 WILD-TYPE 
              7             348 
  OR6C1 MUTATED OR6C1 WILD-TYPE 
              1              72 
$`OR6C1 MUTATED`
TCGA-A6-6651 TCGA-A6-6782 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-DM-A285 
       21.76        20.28        58.39         0.33         0.10         6.12 
TCGA-DM-A28E 
      119.93 

$`OR6C1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        24.16        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.26         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  OR6C1 MUTATED OR6C1 WILD-TYPE 
            0.1             0.0 
  OR6C1 MUTATED OR6C1 WILD-TYPE 
         119.93          140.38 
  OR6C1 MUTATED OR6C1 WILD-TYPE 
         20.280          20.155 
[1] "0.1 - 119.9 (20.3)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.7"
D1654V2, 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       25       105         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        19         10         40         31       34        13
                 vv
clus              STAGE IVB
  OR6C1 MUTATED           0
  OR6C1 WILD-TYPE         1
D1654V3, multiclass
            clus
vv           OR6C1 MUTATED OR6C1 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              4             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR6C1 MUTATED     0   0   6   1
  OR6C1 WILD-TYPE   9  68 242  40
D1654V4, multiclass
    clus
vv   OR6C1 MUTATED OR6C1 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             6             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
  OR6C1 MUTATED     5   1   1
  OR6C1 WILD-TYPE 215  79  65
D1654V5, multiclass
    clus
vv   OR6C1 MUTATED OR6C1 WILD-TYPE
  N0             5             215
  N1             1              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"
D1654V6, binary
                 cls
clus                0   1
  OR6C1 MUTATED     4   1
  OR6C1 WILD-TYPE 279  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR6C1 MUTATED      4    1
  OR6C1 WILD-TYPE  279   47
   clus
vv  OR6C1 MUTATED OR6C1 WILD-TYPE
  0             4             279
  1             1              47
[1] 2 2
[1] FALSE
D1654V7, 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
D1654V8, binary
                 cls
clus                0   1
  OR6C1 MUTATED     5   2
  OR6C1 WILD-TYPE 312  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR6C1 MUTATED      5    2
  OR6C1 WILD-TYPE  312   46
                               clus
vv                              OR6C1 MUTATED OR6C1 WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  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 256   2  22  19
D1654V9, multiclass
    clus
vv   OR6C1 MUTATED OR6C1 WILD-TYPE
  R0             1             256
  R1             0               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"
D1654V10, 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
D1654V11, 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(1655) Variable = SEC31A MUTATION ANALYSIS
D1655V1, survival
                  sevent
clus2                0   1
  SEC31A MUTATED    10   2
  SEC31A WILD-TYPE 272  71
  SEC31A MUTATED SEC31A WILD-TYPE 
              12              343 
  SEC31A MUTATED SEC31A WILD-TYPE 
               2               71 
$`SEC31A MUTATED`
TCGA-A6-5665 TCGA-AA-3543 TCGA-AA-3662 TCGA-AA-3819 TCGA-AD-6889 TCGA-AD-6895 
       22.06         0.99         6.05        25.02        56.55         0.72 
TCGA-CA-6717 TCGA-CM-6167 TCGA-F4-6570 TCGA-F4-6856 TCGA-G4-6309 TCGA-G4-6626 
        0.33        14.99         6.18        19.43        51.75        46.75 

$`SEC31A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       26.01        12.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       33.04         0.99         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 
       40.96         0.07        21.37         4.21         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 
       33.67        13.25         0.53        35.41       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6628 
       52.80 

  SEC31A MUTATED SEC31A WILD-TYPE 
            0.33             0.00 
  SEC31A MUTATED SEC31A WILD-TYPE 
           56.55           140.38 
  SEC31A MUTATED SEC31A WILD-TYPE 
           17.21            20.28 
[1] "0.3 - 56.5 (17.2)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.1"
D1655V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SEC31A MUTATED         2        0        0         6         0         0
  SEC31A WILD-TYPE      62        1       25       103         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SEC31A MUTATED           0          0          1          1        1
  SEC31A WILD-TYPE        19         10         40         30       34
                  vv
clus               STAGE IVA STAGE IVB
  SEC31A MUTATED           0         0
  SEC31A WILD-TYPE        13         1
D1655V3, multiclass
            clus
vv           SEC31A MUTATED SEC31A WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               6              103
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              1               30
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SEC31A MUTATED     0   2   9   1
  SEC31A WILD-TYPE   9  66 239  40
D1655V4, multiclass
    clus
vv   SEC31A MUTATED SEC31A WILD-TYPE
  T1              0                9
  T2              2               66
  T3              9              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     8   2   2
  SEC31A WILD-TYPE 212  78  64
D1655V5, multiclass
    clus
vv   SEC31A MUTATED SEC31A WILD-TYPE
  N0              8              212
  N1              2               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"
D1655V6, binary
                  cls
clus                 0   1
  SEC31A MUTATED    10   1
  SEC31A WILD-TYPE 273  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEC31A MUTATED     10    1
  SEC31A WILD-TYPE  273   47
   clus
vv  SEC31A MUTATED SEC31A WILD-TYPE
  0             10              273
  1              1               47
[1] 2 2
[1] FALSE
D1655V7, binary
                  cls
clus                 0   1
  SEC31A MUTATED     6   6
  SEC31A WILD-TYPE 164 191
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEC31A MUTATED      6    6
  SEC31A WILD-TYPE  164  191
        clus
vv       SEC31A MUTATED SEC31A WILD-TYPE
  FEMALE              6              164
  MALE                6              191
[1] 2 2
[1] FALSE
D1655V8, binary
                  cls
clus                 0   1
  SEC31A MUTATED     9   3
  SEC31A WILD-TYPE 308  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEC31A MUTATED      9    3
  SEC31A WILD-TYPE  308   45
                               clus
vv                              SEC31A MUTATED SEC31A WILD-TYPE
  COLON ADENOCARCINOMA                       9              308
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SEC31A MUTATED     8   0   1   1
  SEC31A WILD-TYPE 249   2  21  20
D1655V9, multiclass
    clus
vv   SEC31A MUTATED SEC31A WILD-TYPE
  R0              8              249
  R1              0                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"
D1655V10, 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
D1655V11, 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(1656) Variable = SULF2 MUTATION ANALYSIS
D1656V1, survival
                 sevent
clus2               0   1
  SULF2 MUTATED    20   1
  SULF2 WILD-TYPE 262  72
  SULF2 MUTATED SULF2 WILD-TYPE 
             21             334 
  SULF2 MUTATED SULF2 WILD-TYPE 
              1              72 
$`SULF2 MUTATED`
TCGA-AA-3518 TCGA-AA-3525 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-A00E TCGA-AD-6895 
        1.02         8.05        30.05        53.00        30.02         0.72 
TCGA-CA-6718 TCGA-CM-5860 TCGA-CM-5861 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6536 
        0.10        16.01        15.02        19.59        11.51        17.85 
TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6928 TCGA-D5-6929 TCGA-DM-A1D9 
        4.80        16.14        15.58        11.64        13.41       140.38 
TCGA-G4-6309 TCGA-G4-6317 TCGA-G4-6321 
       51.75        36.00        22.09 

$`SULF2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 
       38.99         9.07        24.03        37.05        36.03        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
        0.99        31.07        31.07        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F 
        7.96        27.02        13.94        38.04        19.00        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
        0.07        21.37         4.21        56.55         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.33         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        12.26        13.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 
        1.32        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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6323 TCGA-G4-6586 
       44.68        55.04        45.11        36.72        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  SULF2 MUTATED SULF2 WILD-TYPE 
            0.1             0.0 
  SULF2 MUTATED SULF2 WILD-TYPE 
         140.38          139.17 
  SULF2 MUTATED SULF2 WILD-TYPE 
         16.010          20.995 
[1] "0.1 - 140.4 (16.0)" "0.0 - 139.2 (21.0)"
[1] "hr=" "4.2"
D1656V2, 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       23        99         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SULF2 MUTATED           1          1          4          1        1         0
  SULF2 WILD-TYPE        18          9         37         30       34        13
                 vv
clus              STAGE IVB
  SULF2 MUTATED           0
  SULF2 WILD-TYPE         1
D1656V3, multiclass
            clus
vv           SULF2 MUTATED SULF2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA             10              99
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             1               9
  STAGE IIIB             4              37
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SULF2 MUTATED     0   2  20   0
  SULF2 WILD-TYPE   9  66 228  41
D1656V4, multiclass
    clus
vv   SULF2 MUTATED SULF2 WILD-TYPE
  T1             0               9
  T2             2              66
  T3            20             228
  T4             0              41
[1] 4 2
[1] TRUE
[1] "dimension 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  72  65
D1656V5, multiclass
    clus
vv   SULF2 MUTATED SULF2 WILD-TYPE
  N0            13             207
  N1             8              72
  N2             1              65
[1] 3 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
  SULF2 MUTATED    17   1
  SULF2 WILD-TYPE 266  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SULF2 MUTATED     17    1
  SULF2 WILD-TYPE  266   47
   clus
vv  SULF2 MUTATED SULF2 WILD-TYPE
  0            17             266
  1             1              47
[1] 2 2
[1] FALSE
D1656V7, 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
D1656V8, binary
                 cls
clus                0   1
  SULF2 MUTATED    19   3
  SULF2 WILD-TYPE 298  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SULF2 MUTATED     19    3
  SULF2 WILD-TYPE  298   45
                               clus
vv                              SULF2 MUTATED SULF2 WILD-TYPE
  COLON ADENOCARCINOMA                     19             298
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SULF2 MUTATED    19   0   0   1
  SULF2 WILD-TYPE 238   2  22  20
D1656V9, multiclass
    clus
vv   SULF2 MUTATED SULF2 WILD-TYPE
  R0            19             238
  R1             0               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"
D1656V10, 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
D1656V11, 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(1657) Variable = SLC8A2 MUTATION ANALYSIS
D1657V1, survival
                  sevent
clus2                0   1
  SLC8A2 MUTATED    12   1
  SLC8A2 WILD-TYPE 270  72
  SLC8A2 MUTATED SLC8A2 WILD-TYPE 
              13              342 
  SLC8A2 MUTATED SLC8A2 WILD-TYPE 
               1               72 
$`SLC8A2 MUTATED`
TCGA-A6-6780 TCGA-AA-3555 TCGA-AA-A01R TCGA-AD-6889 TCGA-AU-6004 TCGA-AZ-4315 
       20.12        29.95        35.01        56.55        27.09        58.39 
TCGA-AZ-6598 TCGA-CM-4744 TCGA-CM-5861 TCGA-CM-6162 TCGA-D5-6535 TCGA-D5-6930 
       49.41        20.02        15.02        12.00        15.12         1.51 
TCGA-G4-6586 
       35.80 

$`SLC8A2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        17.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37         4.21         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        16.01         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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        43.27        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        26.17        91.79        46.75        52.80 

  SLC8A2 MUTATED SLC8A2 WILD-TYPE 
            1.51             0.00 
  SLC8A2 MUTATED SLC8A2 WILD-TYPE 
           58.39           140.38 
  SLC8A2 MUTATED SLC8A2 WILD-TYPE 
           27.09            20.09 
[1] "1.5 - 58.4 (27.1)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "3.1"
D1657V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC8A2 MUTATED         2        0        1         8         0         0
  SLC8A2 WILD-TYPE      62        1       24       101         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC8A2 MUTATED           1          0          2          0        0
  SLC8A2 WILD-TYPE        18         10         39         31       35
                  vv
clus               STAGE IVA STAGE IVB
  SLC8A2 MUTATED           0         0
  SLC8A2 WILD-TYPE        13         1
D1657V3, multiclass
            clus
vv           SLC8A2 MUTATED SLC8A2 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               8              101
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SLC8A2 MUTATED     0   2  12   0
  SLC8A2 WILD-TYPE   9  66 236  41
D1657V4, multiclass
    clus
vv   SLC8A2 MUTATED SLC8A2 WILD-TYPE
  T1              0                9
  T2              2               66
  T3             12              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
  SLC8A2 MUTATED    11   2   1
  SLC8A2 WILD-TYPE 209  78  65
D1657V5, multiclass
    clus
vv   SLC8A2 MUTATED SLC8A2 WILD-TYPE
  N0             11              209
  N1              2               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"
D1657V6, binary
                  cls
clus                 0   1
  SLC8A2 MUTATED    11   0
  SLC8A2 WILD-TYPE 272  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC8A2 MUTATED     11    0
  SLC8A2 WILD-TYPE  272   48
   clus
vv  SLC8A2 MUTATED SLC8A2 WILD-TYPE
  0             11              272
  1              0               48
[1] 2 2
[1] FALSE
D1657V7, binary
                  cls
clus                 0   1
  SLC8A2 MUTATED     8   6
  SLC8A2 WILD-TYPE 162 191
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC8A2 MUTATED      8    6
  SLC8A2 WILD-TYPE  162  191
        clus
vv       SLC8A2 MUTATED SLC8A2 WILD-TYPE
  FEMALE              8              162
  MALE                6              191
[1] 2 2
[1] FALSE
D1657V8, binary
                  cls
clus                 0   1
  SLC8A2 MUTATED     9   5
  SLC8A2 WILD-TYPE 308  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC8A2 MUTATED      9    5
  SLC8A2 WILD-TYPE  308   43
                               clus
vv                              SLC8A2 MUTATED SLC8A2 WILD-TYPE
  COLON ADENOCARCINOMA                       9              308
  COLON MUCINOUS ADENOCARCINOMA              5               43
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SLC8A2 MUTATED    10   0   0   1
  SLC8A2 WILD-TYPE 247   2  22  20
D1657V9, multiclass
    clus
vv   SLC8A2 MUTATED SLC8A2 WILD-TYPE
  R0             10              247
  R1              0                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"
D1657V10, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC8A2 MUTATED                                  0     1
  SLC8A2 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SLC8A2 MUTATED                           0    10
  SLC8A2 WILD-TYPE                        19   166
D1657V11, multiclass
                                  clus
vv                                 SLC8A2 MUTATED SLC8A2 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(1658) Variable = C14ORF180 MUTATION ANALYSIS
D1658V1, survival
                     sevent
clus2                   0   1
  C14ORF180 MUTATED     2   2
  C14ORF180 WILD-TYPE 280  71
  C14ORF180 MUTATED C14ORF180 WILD-TYPE 
                  4                 351 
  C14ORF180 MUTATED C14ORF180 WILD-TYPE 
                  2                  71 
$`C14ORF180 MUTATED`
TCGA-AU-6004 TCGA-AZ-6598 TCGA-DM-A1D7 TCGA-G4-6628 
       27.09        49.41        13.32        52.80 

$`C14ORF180 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       26.17        91.79        46.75 

  C14ORF180 MUTATED C14ORF180 WILD-TYPE 
              13.32                0.00 
  C14ORF180 MUTATED C14ORF180 WILD-TYPE 
              52.80              140.38 
  C14ORF180 MUTATED C14ORF180 WILD-TYPE 
              38.25               20.12 
[1] "13.3 - 52.8 (38.2)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.6"
D1658V2, 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       24       108         8         1
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C14ORF180 MUTATED           0          0          0          0        0
  C14ORF180 WILD-TYPE        19         10         41         31       35
                     vv
clus                  STAGE IVA STAGE IVB
  C14ORF180 MUTATED           0         0
  C14ORF180 WILD-TYPE        13         1
D1658V3, multiclass
            clus
vv           C14ORF180 MUTATED C14ORF180 WILD-TYPE
  STAGE I                    2                  62
  STAGE IA                   0                   1
  STAGE II                   1                  24
  STAGE IIA                  1                 108
  STAGE IIB                  0                   8
  STAGE IIC                  0                   1
  STAGE III                  0                  19
  STAGE IIIA                 0                  10
  STAGE IIIB                 0                  41
  STAGE IIIC                 0                  31
  STAGE IV                   0                  35
  STAGE IVA                  0                  13
  STAGE IVB                  0                   1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2  T3  T4
  C14ORF180 MUTATED     0   2   2   0
  C14ORF180 WILD-TYPE   9  66 246  41
D1658V4, multiclass
    clus
vv   C14ORF180 MUTATED C14ORF180 WILD-TYPE
  T1                 0                   9
  T2                 2                  66
  T3                 2                 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
  C14ORF180 MUTATED     4   0   0
  C14ORF180 WILD-TYPE 216  80  66
D1658V5, multiclass
    clus
vv   C14ORF180 MUTATED C14ORF180 WILD-TYPE
  N0                 4                 216
  N1                 0                  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"
D1658V6, binary
                     cls
clus                    0   1
  C14ORF180 MUTATED     3   0
  C14ORF180 WILD-TYPE 280  48
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF180 MUTATED      3    0
  C14ORF180 WILD-TYPE  280   48
   clus
vv  C14ORF180 MUTATED C14ORF180 WILD-TYPE
  0                 3                 280
  1                 0                  48
[1] 2 2
[1] FALSE
D1658V7, 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
D1658V8, binary
                     cls
clus                    0   1
  C14ORF180 MUTATED     4   0
  C14ORF180 WILD-TYPE 313  48
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF180 MUTATED      4    0
  C14ORF180 WILD-TYPE  313   48
                               clus
vv                              C14ORF180 MUTATED C14ORF180 WILD-TYPE
  COLON ADENOCARCINOMA                          4                 313
  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 255   2  22  21
D1658V9, multiclass
[1] "Remove cluster labels:" "C14ORF180 MUTATED"     
clus
  C14ORF180 MUTATED C14ORF180 WILD-TYPE 
                  2                 300 
         TCGA-A6-2671          TCGA-A6-2672          TCGA-A6-2674 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-A6-2676          TCGA-A6-2677          TCGA-A6-2678 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-A6-2683          TCGA-A6-3807          TCGA-A6-3808 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-A6-3809          TCGA-A6-3810          TCGA-A6-5657 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-A6-5659          TCGA-A6-5661          TCGA-A6-5665 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-A6-6781          TCGA-AA-3489          TCGA-AA-3492 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3496          TCGA-AA-3502          TCGA-AA-3510 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3511          TCGA-AA-3514          TCGA-AA-3517 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3518          TCGA-AA-3519          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-3526          TCGA-AA-3527 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3529          TCGA-AA-3530          TCGA-AA-3531 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3532          TCGA-AA-3534          TCGA-AA-3538 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3542          TCGA-AA-3543          TCGA-AA-3544 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3548          TCGA-AA-3549          TCGA-AA-3552 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3553          TCGA-AA-3554          TCGA-AA-3555 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3556          TCGA-AA-3558          TCGA-AA-3560 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3561          TCGA-AA-3562          TCGA-AA-3655 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3660          TCGA-AA-3662          TCGA-AA-3663 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3664          TCGA-AA-3666          TCGA-AA-3667 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3672          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-3688 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3692          TCGA-AA-3693          TCGA-AA-3695 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3696          TCGA-AA-3697          TCGA-AA-3710 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3712          TCGA-AA-3713          TCGA-AA-3715 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3811          TCGA-AA-3812          TCGA-AA-3814 
"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-3844 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3845          TCGA-AA-3846          TCGA-AA-3848 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3850          TCGA-AA-3851          TCGA-AA-3852 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3854          TCGA-AA-3855          TCGA-AA-3856 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3858          TCGA-AA-3860          TCGA-AA-3861 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3864          TCGA-AA-3866          TCGA-AA-3867 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3869          TCGA-AA-3870          TCGA-AA-3872 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3875          TCGA-AA-3877          TCGA-AA-3930 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3939          TCGA-AA-3941          TCGA-AA-3947 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3949          TCGA-AA-3950          TCGA-AA-3952 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3955          TCGA-AA-3956          TCGA-AA-3968 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3971          TCGA-AA-3972          TCGA-AA-3973 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3975          TCGA-AA-3976          TCGA-AA-3979 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3984          TCGA-AA-3986          TCGA-AA-3989 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3994          TCGA-AA-A004          TCGA-AA-A00A 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-A00D          TCGA-AA-A00E          TCGA-AA-A00F 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-A00J          TCGA-AA-A00K          TCGA-AA-A00L 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-A00N          TCGA-AA-A00O          TCGA-AA-A00Q 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-A00R          TCGA-AA-A00U          TCGA-AA-A00W 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-A00Z          TCGA-AA-A010          TCGA-AA-A017 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-A01D          TCGA-AA-A01F          TCGA-AA-A01G 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-A01I          TCGA-AA-A01K          TCGA-AA-A01P 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-A01Q          TCGA-AA-A01R          TCGA-AA-A01S 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-A01T          TCGA-AA-A01V          TCGA-AA-A01X 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-A01Z          TCGA-AA-A022          TCGA-AA-A024 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-A029          TCGA-AA-A02F          TCGA-AA-A02H 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-A02J          TCGA-AA-A02K          TCGA-AA-A02O 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-A02W          TCGA-AA-A02Y          TCGA-AA-A03F 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-A03J          TCGA-AD-5900          TCGA-AD-6548 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AD-6888          TCGA-AU-3779          TCGA-AY-4070 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AY-4071          TCGA-AY-5543          TCGA-AY-6196 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AY-6197          TCGA-AY-6386          TCGA-AZ-4315 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AZ-4681          TCGA-AZ-4682          TCGA-CA-5254 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-CA-5255          TCGA-CA-5796          TCGA-CA-5797 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-CA-6715          TCGA-CA-6716          TCGA-CA-6717 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-CA-6718          TCGA-CA-6719          TCGA-CK-4947 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-CK-4948          TCGA-CK-4950          TCGA-CK-4952 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-CK-5912          TCGA-CK-5913          TCGA-CK-5914 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-CK-5915          TCGA-CK-5916          TCGA-CK-6746 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-CK-6747          TCGA-CK-6748          TCGA-CK-6751 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-CM-4743          TCGA-CM-4744          TCGA-CM-4746 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-CM-4747          TCGA-CM-4752          TCGA-CM-5341 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-CM-5344          TCGA-CM-5348          TCGA-CM-5349 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-CM-5860          TCGA-CM-5861          TCGA-CM-5862 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-CM-5863          TCGA-CM-5864          TCGA-CM-5868 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-CM-6161          TCGA-CM-6162          TCGA-CM-6163 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-CM-6164          TCGA-CM-6165          TCGA-CM-6166 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-CM-6167          TCGA-CM-6168          TCGA-CM-6169 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-CM-6170          TCGA-CM-6171          TCGA-CM-6172 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-CM-6674          TCGA-CM-6675          TCGA-CM-6676 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-CM-6677          TCGA-CM-6678          TCGA-CM-6679 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-CM-6680          TCGA-D5-5537          TCGA-D5-5538 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-D5-5539          TCGA-D5-5540          TCGA-D5-5541 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-D5-6529          TCGA-D5-6532          TCGA-D5-6533 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-D5-6534          TCGA-D5-6535          TCGA-D5-6536 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-D5-6537          TCGA-D5-6538          TCGA-D5-6539 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-D5-6540          TCGA-D5-6541          TCGA-D5-6898 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-D5-6920          TCGA-D5-6922          TCGA-D5-6923 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-D5-6924          TCGA-D5-6926          TCGA-D5-6927 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-D5-6928          TCGA-D5-6929          TCGA-D5-6930 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-D5-6931          TCGA-D5-6932          TCGA-D5-7000 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-F4-6459          TCGA-F4-6460          TCGA-F4-6569 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-F4-6570          TCGA-F4-6703          TCGA-F4-6704 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-F4-6805          TCGA-F4-6806          TCGA-F4-6807 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-F4-6808          TCGA-F4-6809          TCGA-F4-6854 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-F4-6855          TCGA-F4-6856          TCGA-G4-6293 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-G4-6299          TCGA-G4-6303          TCGA-G4-6304 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-G4-6306          TCGA-G4-6307          TCGA-G4-6309 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-G4-6310          TCGA-G4-6315          TCGA-G4-6317 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-G4-6321          TCGA-G4-6323          TCGA-G4-6586 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-G4-6588          TCGA-G4-6625          TCGA-G4-6626 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
D1658V10, 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
D1658V11, 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(1659) Variable = C3ORF63 MUTATION ANALYSIS
D1659V1, survival
                   sevent
clus2                 0   1
  C3ORF63 MUTATED    16   5
  C3ORF63 WILD-TYPE 266  68
  C3ORF63 MUTATED C3ORF63 WILD-TYPE 
               21               334 
  C3ORF63 MUTATED C3ORF63 WILD-TYPE 
                5                68 
$`C3ORF63 MUTATED`
TCGA-A6-3809 TCGA-A6-5661 TCGA-AA-3555 TCGA-AA-3845 TCGA-AA-A00N TCGA-AA-A010 
       32.75        33.53        29.95         0.00         4.01        34.98 
TCGA-AD-6895 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6608 TCGA-CA-6717 TCGA-CK-5912 
        0.72        58.39        49.41         1.94         0.33        49.08 
TCGA-CM-4743 TCGA-CM-5348 TCGA-CM-6169 TCGA-D5-5540 TCGA-D5-6532 TCGA-G4-6307 
       23.05        22.98        13.02        13.51        18.25        55.04 
TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6588 
       51.75        36.72        26.17 

$`C3ORF63 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       38.99        37.02        14.93        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        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        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21        56.55         0.79         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13        83.80        22.36        62.79        61.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        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         2.93         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-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        16.01        15.02         5.03        15.02        15.02 
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-D5-5541 TCGA-D5-6529 
       12.03        45.40        12.26        19.59        11.51        20.19 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       53.62        44.68        45.11        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        91.79        46.75        52.80 

  C3ORF63 MUTATED C3ORF63 WILD-TYPE 
                0                 0 
  C3ORF63 MUTATED C3ORF63 WILD-TYPE 
            58.39            140.38 
  C3ORF63 MUTATED C3ORF63 WILD-TYPE 
           26.170            20.005 
[1] "0.0 - 58.4 (26.2)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1.1"
D1659V2, 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       24        98         5         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C3ORF63 MUTATED           0          1          3          0        1
  C3ORF63 WILD-TYPE        19          9         38         31       34
                   vv
clus                STAGE IVA STAGE IVB
  C3ORF63 MUTATED           0         0
  C3ORF63 WILD-TYPE        13         1
D1659V3, multiclass
            clus
vv           C3ORF63 MUTATED C3ORF63 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA               11                98
  STAGE IIB                3                 5
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               1                 9
  STAGE IIIB               3                38
  STAGE IIIC               0                31
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C3ORF63 MUTATED     0   2  17   3
  C3ORF63 WILD-TYPE   9  66 231  38
D1659V4, multiclass
    clus
vv   C3ORF63 MUTATED C3ORF63 WILD-TYPE
  T1               0                 9
  T2               2                66
  T3              17               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
  C3ORF63 MUTATED    16   6   0
  C3ORF63 WILD-TYPE 204  74  66
D1659V5, multiclass
    clus
vv   C3ORF63 MUTATED C3ORF63 WILD-TYPE
  N0              16               204
  N1               6                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"
D1659V6, binary
                   cls
clus                  0   1
  C3ORF63 MUTATED    18   1
  C3ORF63 WILD-TYPE 265  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF63 MUTATED     18    1
  C3ORF63 WILD-TYPE  265   47
   clus
vv  C3ORF63 MUTATED C3ORF63 WILD-TYPE
  0              18               265
  1               1                47
[1] 2 2
[1] FALSE
D1659V7, binary
                   cls
clus                  0   1
  C3ORF63 MUTATED    11  11
  C3ORF63 WILD-TYPE 159 186
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF63 MUTATED     11   11
  C3ORF63 WILD-TYPE  159  186
        clus
vv       C3ORF63 MUTATED C3ORF63 WILD-TYPE
  FEMALE              11               159
  MALE                11               186
[1] 2 2
[1] FALSE
D1659V8, binary
                   cls
clus                  0   1
  C3ORF63 MUTATED    18   4
  C3ORF63 WILD-TYPE 299  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF63 MUTATED     18    4
  C3ORF63 WILD-TYPE  299   44
                               clus
vv                              C3ORF63 MUTATED C3ORF63 WILD-TYPE
  COLON ADENOCARCINOMA                       18               299
  COLON MUCINOUS ADENOCARCINOMA               4                44
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  C3ORF63 MUTATED    17   0   0   2
  C3ORF63 WILD-TYPE 240   2  22  19
D1659V9, multiclass
    clus
vv   C3ORF63 MUTATED C3ORF63 WILD-TYPE
  R0              17               240
  R1               0                 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"
D1659V10, 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    13
  C3ORF63 WILD-TYPE                        16   163
D1659V11, 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                                         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(1660) Variable = XKR3 MUTATION ANALYSIS
D1660V1, survival
                sevent
clus2              0   1
  XKR3 MUTATED    10   1
  XKR3 WILD-TYPE 272  72
  XKR3 MUTATED XKR3 WILD-TYPE 
            11            344 
  XKR3 MUTATED XKR3 WILD-TYPE 
             1             72 
$`XKR3 MUTATED`
TCGA-A6-6780 TCGA-AA-3660 TCGA-AA-3710 TCGA-AA-3821 TCGA-AZ-4315 TCGA-AZ-6601 
       20.12        78.08        26.99         1.02        58.39       100.01 
TCGA-CA-6717 TCGA-CM-5861 TCGA-D5-5541 TCGA-G4-6307 TCGA-G4-6628 
        0.33        15.02        11.51        55.04        52.80 

$`XKR3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        61.02         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       33.04         0.99        25.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        61.41        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        53.62        44.68        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 
       91.79        46.75 

  XKR3 MUTATED XKR3 WILD-TYPE 
          0.33           0.00 
  XKR3 MUTATED XKR3 WILD-TYPE 
        100.01         140.38 
  XKR3 MUTATED XKR3 WILD-TYPE 
        26.990         20.105 
[1] "0.3 - 100.0 (27.0)" "0.0 - 140.4 (20.1)"
[1] "hr=" "3.6"
D1660V2, 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       23       103         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        19         10         39         31       35        13
                vv
clus             STAGE IVB
  XKR3 MUTATED           0
  XKR3 WILD-TYPE         1
D1660V3, multiclass
            clus
vv           XKR3 MUTATED XKR3 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             6            103
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            2             39
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  XKR3 MUTATED     0   2  10   0
  XKR3 WILD-TYPE   9  66 238  41
D1660V4, multiclass
    clus
vv   XKR3 MUTATED XKR3 WILD-TYPE
  T1            0              9
  T2            2             66
  T3           10            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
  XKR3 MUTATED    10   2   0
  XKR3 WILD-TYPE 210  78  66
D1660V5, multiclass
    clus
vv   XKR3 MUTATED XKR3 WILD-TYPE
  N0           10            210
  N1            2             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"
D1660V6, binary
                cls
clus               0   1
  XKR3 MUTATED    11   0
  XKR3 WILD-TYPE 272  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  XKR3 MUTATED     11    0
  XKR3 WILD-TYPE  272   48
   clus
vv  XKR3 MUTATED XKR3 WILD-TYPE
  0           11            272
  1            0             48
[1] 2 2
[1] FALSE
D1660V7, 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
D1660V8, binary
                cls
clus               0   1
  XKR3 MUTATED     9   3
  XKR3 WILD-TYPE 308  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  XKR3 MUTATED      9    3
  XKR3 WILD-TYPE  308   45
                               clus
vv                              XKR3 MUTATED XKR3 WILD-TYPE
  COLON ADENOCARCINOMA                     9            308
  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 248   2  22  20
D1660V9, multiclass
    clus
vv   XKR3 MUTATED XKR3 WILD-TYPE
  R0            9            248
  R1            0              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"
D1660V10, 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
D1660V11, 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(1661) Variable = RBP3 MUTATION ANALYSIS
D1661V1, survival
                sevent
clus2              0   1
  RBP3 MUTATED    10   3
  RBP3 WILD-TYPE 272  70
  RBP3 MUTATED RBP3 WILD-TYPE 
            13            342 
  RBP3 MUTATED RBP3 WILD-TYPE 
             3             70 
$`RBP3 MUTATED`
TCGA-A6-6651 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3947 TCGA-AA-A010 
       21.76        63.98         6.97         2.01        33.01        34.98 
TCGA-AU-6004 TCGA-AZ-6598 TCGA-AZ-6603 TCGA-CM-4743 TCGA-D5-6540 TCGA-DM-A1HB 
       27.09        49.41        29.56        23.05        16.14       135.65 
TCGA-G4-6304 
       53.62 

$`RBP3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        24.16        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10       100.01         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 
       35.41        19.43       107.67        74.56        65.85        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  RBP3 MUTATED RBP3 WILD-TYPE 
          2.01           0.00 
  RBP3 MUTATED RBP3 WILD-TYPE 
        135.65         140.38 
  RBP3 MUTATED RBP3 WILD-TYPE 
         29.56          19.99 
[1] "2.0 - 135.7 (29.6)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.3"
D1661V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RBP3 MUTATED         2        0        3         1         3         0
  RBP3 WILD-TYPE      62        1       22       108         5         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RBP3 MUTATED           1          0          2          0        0         0
  RBP3 WILD-TYPE        18         10         39         31       35        13
                vv
clus             STAGE IVB
  RBP3 MUTATED           0
  RBP3 WILD-TYPE         1
D1661V3, multiclass
            clus
vv           RBP3 MUTATED RBP3 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              3             22
  STAGE IIA             1            108
  STAGE IIB             3              5
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            2             39
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RBP3 MUTATED     0   3   7   3
  RBP3 WILD-TYPE   9  65 241  38
D1661V4, multiclass
    clus
vv   RBP3 MUTATED RBP3 WILD-TYPE
  T1            0              9
  T2            3             65
  T3            7            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
  RBP3 MUTATED     9   4   0
  RBP3 WILD-TYPE 211  76  66
D1661V5, multiclass
    clus
vv   RBP3 MUTATED RBP3 WILD-TYPE
  N0            9            211
  N1            4             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"
D1661V6, binary
                cls
clus               0   1
  RBP3 MUTATED    10   0
  RBP3 WILD-TYPE 273  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBP3 MUTATED     10    0
  RBP3 WILD-TYPE  273   48
   clus
vv  RBP3 MUTATED RBP3 WILD-TYPE
  0           10            273
  1            0             48
[1] 2 2
[1] FALSE
D1661V7, binary
                cls
clus               0   1
  RBP3 MUTATED     7   6
  RBP3 WILD-TYPE 163 191
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBP3 MUTATED      7    6
  RBP3 WILD-TYPE  163  191
        clus
vv       RBP3 MUTATED RBP3 WILD-TYPE
  FEMALE            7            163
  MALE              6            191
[1] 2 2
[1] FALSE
D1661V8, binary
                cls
clus               0   1
  RBP3 MUTATED    11   2
  RBP3 WILD-TYPE 306  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBP3 MUTATED     11    2
  RBP3 WILD-TYPE  306   46
                               clus
vv                              RBP3 MUTATED RBP3 WILD-TYPE
  COLON ADENOCARCINOMA                    11            306
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RBP3 MUTATED     9   0   0   0
  RBP3 WILD-TYPE 248   2  22  21
D1661V9, multiclass
    clus
vv   RBP3 MUTATED RBP3 WILD-TYPE
  R0            9            248
  R1            0              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"
D1661V10, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RBP3 MUTATED                                  0     0
  RBP3 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RBP3 MUTATED                           0     8
  RBP3 WILD-TYPE                        19   168
D1661V11, multiclass
                                  clus
vv                                 RBP3 MUTATED RBP3 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(1662) Variable = ACADVL MUTATION ANALYSIS
D1662V1, survival
                  sevent
clus2                0   1
  ACADVL MUTATED     4   1
  ACADVL WILD-TYPE 278  72
  ACADVL MUTATED ACADVL WILD-TYPE 
               5              350 
  ACADVL MUTATED ACADVL WILD-TYPE 
               1               72 
$`ACADVL MUTATED`
TCGA-AA-3544 TCGA-DM-A1D8 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 
       14.01        12.59        35.80        26.17        52.80 

$`ACADVL WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01        12.99         0.99        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        49.91        13.32       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6625 TCGA-G4-6626 
       91.79        46.75 

  ACADVL MUTATED ACADVL WILD-TYPE 
           12.59             0.00 
  ACADVL MUTATED ACADVL WILD-TYPE 
           52.80           140.38 
  ACADVL MUTATED ACADVL WILD-TYPE 
          26.170           20.155 
[1] "12.6 - 52.8 (26.2)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D1662V2, 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       25       107         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ACADVL MUTATED           1          0          0          0        0
  ACADVL WILD-TYPE        18         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  ACADVL MUTATED           0         0
  ACADVL WILD-TYPE        13         1
D1662V3, multiclass
            clus
vv           ACADVL MUTATED ACADVL WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               2              107
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ACADVL MUTATED     0   2   4   0
  ACADVL WILD-TYPE   9  66 244  41
D1662V4, multiclass
    clus
vv   ACADVL MUTATED ACADVL WILD-TYPE
  T1              0                9
  T2              2               66
  T3              4              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
  ACADVL MUTATED     4   1   1
  ACADVL WILD-TYPE 216  79  65
D1662V5, multiclass
    clus
vv   ACADVL MUTATED ACADVL WILD-TYPE
  N0              4              216
  N1              1               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"
D1662V6, binary
                  cls
clus                 0   1
  ACADVL MUTATED     5   0
  ACADVL WILD-TYPE 278  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACADVL MUTATED      5    0
  ACADVL WILD-TYPE  278   48
   clus
vv  ACADVL MUTATED ACADVL WILD-TYPE
  0              5              278
  1              0               48
[1] 2 2
[1] FALSE
D1662V7, 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
D1662V8, binary
                  cls
clus                 0   1
  ACADVL MUTATED     6   0
  ACADVL WILD-TYPE 311  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACADVL MUTATED      6    0
  ACADVL WILD-TYPE  311   48
                               clus
vv                              ACADVL MUTATED ACADVL WILD-TYPE
  COLON ADENOCARCINOMA                       6              311
  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 252   2  22  21
D1662V9, multiclass
    clus
vv   ACADVL MUTATED ACADVL WILD-TYPE
  R0              5              252
  R1              0                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"
D1662V10, 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
D1662V11, 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(1663) Variable = VCAN MUTATION ANALYSIS
D1663V1, survival
                sevent
clus2              0   1
  VCAN MUTATED    28   6
  VCAN WILD-TYPE 254  67
  VCAN MUTATED VCAN WILD-TYPE 
            34            321 
  VCAN MUTATED VCAN WILD-TYPE 
             6             67 
$`VCAN MUTATED`
TCGA-A6-5660 TCGA-A6-6653 TCGA-AA-3510 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3534 
       29.19        24.39        63.98         1.02         9.07        29.00 
TCGA-AA-3555 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3811 TCGA-AA-3831 TCGA-AA-3977 
       29.95         6.05         2.01        10.06        17.98        25.02 
TCGA-AA-A00E TCGA-AA-A00N TCGA-AA-A010 TCGA-AU-3779 TCGA-AY-6196 TCGA-AZ-4315 
       30.02         4.01        34.98        14.50         0.20        58.39 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5914 TCGA-CK-5916 TCGA-CM-5349 TCGA-D5-6539 
        0.33         0.10        21.99        21.14        30.08        12.49 
TCGA-D5-6927 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A1D9 TCGA-DM-A1DA 
        9.44        12.00        11.38       119.70       140.38         7.50 
TCGA-DM-A28E TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6628 
      119.93        74.56        65.85        52.80 

$`VCAN WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3520 TCGA-AA-3522 
        6.97         1.02        13.02        38.99        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        17.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       19.99        13.94        19.99        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        19.04        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
        0.99        25.02         1.02        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        19.00        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        27.09        16.31         0.95        15.75        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07         0.26         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-6747 
      102.44        40.34        15.62        49.08        51.32         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-7000 
       14.30         9.04        11.64        13.41         1.51        10.26 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
       12.59        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
       81.37        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       19.43       107.67        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       26.17        91.79        46.75 

  VCAN MUTATED VCAN WILD-TYPE 
           0.1            0.0 
  VCAN MUTATED VCAN WILD-TYPE 
        140.38         139.17 
  VCAN MUTATED VCAN WILD-TYPE 
        21.565         20.120 
[1] "0.1 - 140.4 (21.6)" "0.0 - 139.2 (20.1)"
[1] "hr=" "1.4"
D1663V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  VCAN MUTATED         3        0        1        16         2         0
  VCAN WILD-TYPE      61        1       24        93         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  VCAN MUTATED           4          1          1          5        3         0
  VCAN WILD-TYPE        15          9         40         26       32        13
                vv
clus             STAGE IVB
  VCAN MUTATED           0
  VCAN WILD-TYPE         1
D1663V3, multiclass
            clus
vv           VCAN MUTATED VCAN WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA            16             93
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             4             15
  STAGE IIIA            1              9
  STAGE IIIB            1             40
  STAGE IIIC            5             26
  STAGE IV              3             32
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  VCAN MUTATED     1   3  29   4
  VCAN WILD-TYPE   8  65 219  37
D1663V4, multiclass
    clus
vv   VCAN MUTATED VCAN WILD-TYPE
  T1            1              8
  T2            3             65
  T3           29            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
  VCAN MUTATED    24   4   9
  VCAN WILD-TYPE 196  76  57
D1663V5, multiclass
    clus
vv   VCAN MUTATED VCAN WILD-TYPE
  N0           24            196
  N1            4             76
  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"
D1663V6, binary
                cls
clus               0   1
  VCAN MUTATED    31   3
  VCAN WILD-TYPE 252  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  VCAN MUTATED     31    3
  VCAN WILD-TYPE  252   45
   clus
vv  VCAN MUTATED VCAN WILD-TYPE
  0           31            252
  1            3             45
[1] 2 2
[1] FALSE
D1663V7, binary
                cls
clus               0   1
  VCAN MUTATED    17  20
  VCAN WILD-TYPE 153 177
[1] "tbl2"
                cls
clus             [,1] [,2]
  VCAN MUTATED     17   20
  VCAN WILD-TYPE  153  177
        clus
vv       VCAN MUTATED VCAN WILD-TYPE
  FEMALE           17            153
  MALE             20            177
[1] 2 2
[1] FALSE
D1663V8, binary
                cls
clus               0   1
  VCAN MUTATED    33   4
  VCAN WILD-TYPE 284  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  VCAN MUTATED     33    4
  VCAN WILD-TYPE  284   44
                               clus
vv                              VCAN MUTATED VCAN WILD-TYPE
  COLON ADENOCARCINOMA                    33            284
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  VCAN MUTATED    24   0   2   4
  VCAN WILD-TYPE 233   2  20  17
D1663V9, multiclass
    clus
vv   VCAN MUTATED VCAN WILD-TYPE
  R0           24            233
  R1            0              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"
D1663V10, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  VCAN MUTATED                                  0     2
  VCAN WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  VCAN MUTATED                           1    18
  VCAN WILD-TYPE                        18   158
D1663V11, multiclass
                                  clus
vv                                 VCAN MUTATED VCAN 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(1664) Variable = RIC8B MUTATION ANALYSIS
D1664V1, survival
                 sevent
clus2               0   1
  RIC8B MUTATED     7   2
  RIC8B WILD-TYPE 275  71
  RIC8B MUTATED RIC8B WILD-TYPE 
              9             346 
  RIC8B MUTATED RIC8B WILD-TYPE 
              2              71 
$`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         0.33        15.62 
TCGA-CM-5349 TCGA-CM-5860 TCGA-G4-6626 
       30.08        16.01        46.75 

$`RIC8B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 
        0.10         1.35        17.56       102.44        40.34        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.03        22.98        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       35.80        26.17        91.79        52.80 

  RIC8B MUTATED RIC8B WILD-TYPE 
           0.33            0.00 
  RIC8B MUTATED RIC8B WILD-TYPE 
          63.98          140.38 
  RIC8B MUTATED RIC8B WILD-TYPE 
         18.050          20.235 
[1] "0.3 - 64.0 (18.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1"  
D1664V2, 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       23       104         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RIC8B MUTATED           1          0          1          0        0         0
  RIC8B WILD-TYPE        18         10         40         31       35        13
                 vv
clus              STAGE IVB
  RIC8B MUTATED           0
  RIC8B WILD-TYPE         1
D1664V3, multiclass
            clus
vv           RIC8B MUTATED RIC8B WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              5             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RIC8B MUTATED     0   0   7   2
  RIC8B WILD-TYPE   9  68 241  39
D1664V4, multiclass
    clus
vv   RIC8B MUTATED RIC8B WILD-TYPE
  T1             0               9
  T2             0              68
  T3             7             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
  RIC8B MUTATED     7   1   1
  RIC8B WILD-TYPE 213  79  65
D1664V5, multiclass
    clus
vv   RIC8B MUTATED RIC8B WILD-TYPE
  N0             7             213
  N1             1              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"
D1664V6, binary
                 cls
clus                0   1
  RIC8B MUTATED     8   0
  RIC8B WILD-TYPE 275  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RIC8B MUTATED      8    0
  RIC8B WILD-TYPE  275   48
   clus
vv  RIC8B MUTATED RIC8B WILD-TYPE
  0             8             275
  1             0              48
[1] 2 2
[1] FALSE
D1664V7, 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
D1664V8, binary
                 cls
clus                0   1
  RIC8B MUTATED     6   3
  RIC8B WILD-TYPE 311  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RIC8B MUTATED      6    3
  RIC8B WILD-TYPE  311   45
                               clus
vv                              RIC8B MUTATED RIC8B WILD-TYPE
  COLON ADENOCARCINOMA                      6             311
  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 251   2  22  19
D1664V9, multiclass
    clus
vv   RIC8B MUTATED RIC8B WILD-TYPE
  R0             6             251
  R1             0               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"
D1664V10, 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
D1664V11, 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(1665) Variable = FAM163A MUTATION ANALYSIS
D1665V1, survival
                   sevent
clus2                 0   1
  FAM163A MUTATED     5   0
  FAM163A WILD-TYPE 277  73
  FAM163A MUTATED FAM163A WILD-TYPE 
                5               350 
  FAM163A MUTATED FAM163A WILD-TYPE 
                0                73 
$`FAM163A MUTATED`
TCGA-A6-5665 TCGA-AA-3710 TCGA-AA-3821 TCGA-AA-3877 TCGA-G4-6628 
       22.06        26.99         1.02        31.00        52.80 

$`FAM163A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 
       35.05        33.04         0.99        25.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       27.02        29.98        18.05         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 
       91.79        46.75 

  FAM163A MUTATED FAM163A WILD-TYPE 
             1.02              0.00 
  FAM163A MUTATED FAM163A WILD-TYPE 
            52.80            140.38 
  FAM163A MUTATED FAM163A WILD-TYPE 
            26.99             20.07 
[1] "1.0 - 52.8 (27.0)"  "0.0 - 140.4 (20.1)"
[1] "hr="     "9100000"
D1665V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FAM163A MUTATED         3        0        0         2         0         0
  FAM163A WILD-TYPE      61        1       25       107         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM163A MUTATED           0          0          0          0        0
  FAM163A WILD-TYPE        19         10         41         31       35
                   vv
clus                STAGE IVA STAGE IVB
  FAM163A MUTATED           0         0
  FAM163A WILD-TYPE        13         1
D1665V3, multiclass
            clus
vv           FAM163A MUTATED FAM163A WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                2               107
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  FAM163A MUTATED     1   2   2   0
  FAM163A WILD-TYPE   8  66 246  41
D1665V4, multiclass
    clus
vv   FAM163A MUTATED FAM163A WILD-TYPE
  T1               1                 8
  T2               2                66
  T3               2               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
  FAM163A MUTATED     5   0   0
  FAM163A WILD-TYPE 215  80  66
D1665V5, multiclass
    clus
vv   FAM163A MUTATED FAM163A WILD-TYPE
  N0               5               215
  N1               0                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"
D1665V6, binary
                   cls
clus                  0   1
  FAM163A MUTATED     5   0
  FAM163A WILD-TYPE 278  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM163A MUTATED      5    0
  FAM163A WILD-TYPE  278   48
   clus
vv  FAM163A MUTATED FAM163A WILD-TYPE
  0               5               278
  1               0                48
[1] 2 2
[1] FALSE
D1665V7, binary
                   cls
clus                  0   1
  FAM163A MUTATED     4   1
  FAM163A WILD-TYPE 166 196
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM163A MUTATED      4    1
  FAM163A WILD-TYPE  166  196
        clus
vv       FAM163A MUTATED FAM163A WILD-TYPE
  FEMALE               4               166
  MALE                 1               196
[1] 2 2
[1] FALSE
D1665V8, binary
                   cls
clus                  0   1
  FAM163A MUTATED     3   2
  FAM163A WILD-TYPE 314  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM163A MUTATED      3    2
  FAM163A WILD-TYPE  314   46
                               clus
vv                              FAM163A MUTATED FAM163A WILD-TYPE
  COLON ADENOCARCINOMA                        3               314
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  FAM163A MUTATED     5   0   0   0
  FAM163A WILD-TYPE 252   2  22  21
D1665V9, multiclass
    clus
vv   FAM163A MUTATED FAM163A WILD-TYPE
  R0               5               252
  R1               0                 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"
D1665V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM163A MUTATED                                  0     0
  FAM163A WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  FAM163A MUTATED                           0     2
  FAM163A WILD-TYPE                        19   174
D1665V11, multiclass
[1] "Remove cluster labels:" "FAM163A MUTATED"       
clus
  FAM163A MUTATED FAM163A WILD-TYPE 
                2               204 
       TCGA-A6-2671        TCGA-A6-2672        TCGA-A6-2674        TCGA-A6-2676 
"FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" 
       TCGA-A6-2677        TCGA-A6-2678        TCGA-A6-2683        TCGA-A6-3807 
"FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" 
       TCGA-A6-3808        TCGA-A6-3809        TCGA-A6-3810        TCGA-A6-4105 
"FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" 
       TCGA-A6-5656        TCGA-A6-5657        TCGA-A6-5659        TCGA-A6-5660 
"FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" 
       TCGA-A6-5661        TCGA-A6-5662        TCGA-A6-5664        TCGA-A6-5666 
"FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" 
       TCGA-A6-6137        TCGA-A6-6138        TCGA-A6-6141        TCGA-A6-6142 
"FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" 
       TCGA-A6-6648        TCGA-A6-6649        TCGA-A6-6651        TCGA-A6-6652 
"FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" 
       TCGA-A6-6653        TCGA-A6-6654        TCGA-A6-6780        TCGA-A6-6781 
"FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" 
       TCGA-A6-6782        TCGA-AD-5900        TCGA-AD-6548        TCGA-AD-6888 
"FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" 
       TCGA-AD-6889        TCGA-AD-6890        TCGA-AD-6895        TCGA-AD-6899 
"FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" 
       TCGA-AD-6901        TCGA-AD-6963        TCGA-AD-6964        TCGA-AD-6965 
"FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" 
       TCGA-AU-3779        TCGA-AU-6004        TCGA-AY-4070        TCGA-AY-4071 
"FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" 
       TCGA-AY-5543        TCGA-AY-6196        TCGA-AY-6197        TCGA-AY-6386 
"FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" 
       TCGA-AZ-4315        TCGA-AZ-4323        TCGA-AZ-4616        TCGA-AZ-4681 
"FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" 
       TCGA-AZ-4682        TCGA-AZ-5403        TCGA-AZ-5407        TCGA-AZ-6598 
"FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" 
       TCGA-AZ-6599        TCGA-AZ-6600        TCGA-AZ-6601        TCGA-AZ-6603 
"FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" 
       TCGA-AZ-6605        TCGA-AZ-6606        TCGA-AZ-6607        TCGA-AZ-6608 
"FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" 
       TCGA-CA-5254        TCGA-CA-5255        TCGA-CA-5796        TCGA-CA-5797 
"FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" 
       TCGA-CA-6715        TCGA-CA-6716        TCGA-CA-6717        TCGA-CA-6718 
"FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" 
       TCGA-CA-6719        TCGA-CK-4947        TCGA-CK-4948        TCGA-CK-4950 
"FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" 
       TCGA-CK-4952        TCGA-CK-5912        TCGA-CK-5913        TCGA-CK-5914 
"FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" 
       TCGA-CK-5915        TCGA-CK-5916        TCGA-CK-6746        TCGA-CK-6747 
"FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" 
       TCGA-CK-6748        TCGA-CK-6751        TCGA-CM-4743        TCGA-CM-4744 
"FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" 
       TCGA-CM-4746        TCGA-CM-4747        TCGA-CM-4752        TCGA-CM-5341 
"FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" 
       TCGA-CM-5344        TCGA-CM-5348        TCGA-CM-5349        TCGA-CM-5860 
"FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" 
       TCGA-CM-5861        TCGA-CM-5862        TCGA-CM-5863        TCGA-CM-5864 
"FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" 
       TCGA-CM-5868        TCGA-CM-6161        TCGA-CM-6162        TCGA-CM-6163 
"FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" 
       TCGA-CM-6164        TCGA-CM-6165        TCGA-CM-6166        TCGA-CM-6167 
"FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" 
       TCGA-CM-6168        TCGA-CM-6169        TCGA-CM-6170        TCGA-CM-6171 
"FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" 
       TCGA-CM-6172        TCGA-CM-6674        TCGA-CM-6675        TCGA-CM-6676 
"FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" 
       TCGA-CM-6677        TCGA-CM-6678        TCGA-CM-6679        TCGA-CM-6680 
"FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" 
       TCGA-D5-5537        TCGA-D5-5538        TCGA-D5-5539        TCGA-D5-5540 
"FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" 
       TCGA-D5-5541        TCGA-D5-6529        TCGA-D5-6532        TCGA-D5-6533 
"FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" 
       TCGA-D5-6534        TCGA-D5-6535        TCGA-D5-6536        TCGA-D5-6537 
"FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" 
       TCGA-D5-6538        TCGA-D5-6539        TCGA-D5-6540        TCGA-D5-6541 
"FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" 
       TCGA-D5-6898        TCGA-D5-6920        TCGA-D5-6922        TCGA-D5-6923 
"FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" 
       TCGA-D5-6924        TCGA-D5-6926        TCGA-D5-6927        TCGA-D5-6928 
"FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" 
       TCGA-D5-6929        TCGA-D5-6930        TCGA-D5-6931        TCGA-D5-6932 
"FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" 
       TCGA-D5-7000        TCGA-DM-A0X9        TCGA-DM-A0XD        TCGA-DM-A0XF 
"FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" 
       TCGA-DM-A1D0        TCGA-DM-A1D4        TCGA-DM-A1D6        TCGA-DM-A1D7 
"FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" 
       TCGA-DM-A1D8        TCGA-DM-A1D9        TCGA-DM-A1DA        TCGA-DM-A1DB 
"FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" 
       TCGA-DM-A1HA        TCGA-DM-A1HB        TCGA-DM-A282        TCGA-DM-A285 
"FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" 
       TCGA-DM-A28C        TCGA-DM-A28E        TCGA-DM-A28F        TCGA-DM-A28G 
"FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" 
       TCGA-DM-A28H        TCGA-DM-A28K        TCGA-F4-6459        TCGA-F4-6460 
"FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" 
       TCGA-F4-6569        TCGA-F4-6570        TCGA-F4-6703        TCGA-F4-6704 
"FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" 
       TCGA-F4-6805        TCGA-F4-6806        TCGA-F4-6807        TCGA-F4-6808 
"FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" 
       TCGA-F4-6809        TCGA-F4-6854        TCGA-F4-6855        TCGA-F4-6856 
"FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" 
       TCGA-G4-6293        TCGA-G4-6299        TCGA-G4-6303        TCGA-G4-6304 
"FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" 
       TCGA-G4-6306        TCGA-G4-6307        TCGA-G4-6309        TCGA-G4-6310 
"FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" 
       TCGA-G4-6315        TCGA-G4-6317        TCGA-G4-6321        TCGA-G4-6323 
"FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" 
       TCGA-G4-6586        TCGA-G4-6588        TCGA-G4-6625        TCGA-G4-6626 
"FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" "FAM163A WILD-TYPE" 

Clustering(1666) Variable = WNK4 MUTATION ANALYSIS
D1666V1, survival
                sevent
clus2              0   1
  WNK4 MUTATED    10   1
  WNK4 WILD-TYPE 272  72
  WNK4 MUTATED WNK4 WILD-TYPE 
            11            344 
  WNK4 MUTATED WNK4 WILD-TYPE 
             1             72 
$`WNK4 MUTATED`
TCGA-A6-6653 TCGA-AA-3492 TCGA-AA-3663 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3950 
       24.39         3.02         6.97        53.00        31.00        24.00 
TCGA-AU-6004 TCGA-AZ-4315 TCGA-CK-6747 TCGA-D5-6928 TCGA-D5-6930 
       27.09        58.39         2.93        11.64         1.51 

$`WNK4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  WNK4 MUTATED WNK4 WILD-TYPE 
          1.51           0.00 
  WNK4 MUTATED WNK4 WILD-TYPE 
         58.39         140.38 
  WNK4 MUTATED WNK4 WILD-TYPE 
        24.000         20.155 
[1] "1.5 - 58.4 (24.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2.1"
D1666V2, 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       22       104         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        19         10         41         31       35        13
                vv
clus             STAGE IVB
  WNK4 MUTATED           0
  WNK4 WILD-TYPE         1
D1666V3, multiclass
            clus
vv           WNK4 MUTATED WNK4 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              3             22
  STAGE IIA             5            104
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  WNK4 MUTATED     1   2   8   0
  WNK4 WILD-TYPE   8  66 240  41
D1666V4, multiclass
    clus
vv   WNK4 MUTATED WNK4 WILD-TYPE
  T1            1              8
  T2            2             66
  T3            8            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
  WNK4 MUTATED    11   0   0
  WNK4 WILD-TYPE 209  80  66
D1666V5, multiclass
    clus
vv   WNK4 MUTATED WNK4 WILD-TYPE
  N0           11            209
  N1            0             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
  WNK4 MUTATED    10   0
  WNK4 WILD-TYPE 273  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNK4 MUTATED     10    0
  WNK4 WILD-TYPE  273   48
   clus
vv  WNK4 MUTATED WNK4 WILD-TYPE
  0           10            273
  1            0             48
[1] 2 2
[1] FALSE
D1666V7, 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
D1666V8, binary
                cls
clus               0   1
  WNK4 MUTATED     7   4
  WNK4 WILD-TYPE 310  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNK4 MUTATED      7    4
  WNK4 WILD-TYPE  310   44
                               clus
vv                              WNK4 MUTATED WNK4 WILD-TYPE
  COLON ADENOCARCINOMA                     7            310
  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 248   2  22  20
D1666V9, multiclass
    clus
vv   WNK4 MUTATED WNK4 WILD-TYPE
  R0            9            248
  R1            0              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"
D1666V10, 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
D1666V11, 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(1667) Variable = S100A2 MUTATION ANALYSIS
D1667V1, survival
                  sevent
clus2                0   1
  S100A2 MUTATED     5   1
  S100A2 WILD-TYPE 277  72
  S100A2 MUTATED S100A2 WILD-TYPE 
               6              349 
  S100A2 MUTATED S100A2 WILD-TYPE 
               1               72 
$`S100A2 MUTATED`
TCGA-A6-5657 TCGA-AA-3966 TCGA-AA-A010 TCGA-CA-6719 TCGA-DM-A1D4 TCGA-DM-A28K 
       31.63         2.01        34.98         1.35        92.75        98.24 

$`S100A2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.33         0.10        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43        38.20       130.65        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  S100A2 MUTATED S100A2 WILD-TYPE 
            1.35             0.00 
  S100A2 MUTATED S100A2 WILD-TYPE 
           98.24           140.38 
  S100A2 MUTATED S100A2 WILD-TYPE 
          33.305           20.120 
[1] "1.4 - 98.2 (33.3)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "2"  
D1667V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  S100A2 MUTATED         1        0        0         4         1         0
  S100A2 WILD-TYPE      63        1       25       105         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  S100A2 MUTATED           0          0          1          0        0
  S100A2 WILD-TYPE        19         10         40         31       35
                  vv
clus               STAGE IVA STAGE IVB
  S100A2 MUTATED           0         0
  S100A2 WILD-TYPE        13         1
D1667V3, multiclass
            clus
vv           S100A2 MUTATED S100A2 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               4              105
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  S100A2 MUTATED     0   1   5   1
  S100A2 WILD-TYPE   9  67 243  40
D1667V4, multiclass
    clus
vv   S100A2 MUTATED S100A2 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              5              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
  S100A2 MUTATED     6   1   0
  S100A2 WILD-TYPE 214  79  66
D1667V5, multiclass
    clus
vv   S100A2 MUTATED S100A2 WILD-TYPE
  N0              6              214
  N1              1               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"
D1667V6, binary
                  cls
clus                 0   1
  S100A2 MUTATED     6   0
  S100A2 WILD-TYPE 277  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  S100A2 MUTATED      6    0
  S100A2 WILD-TYPE  277   48
   clus
vv  S100A2 MUTATED S100A2 WILD-TYPE
  0              6              277
  1              0               48
[1] 2 2
[1] FALSE
D1667V7, binary
                  cls
clus                 0   1
  S100A2 MUTATED     2   5
  S100A2 WILD-TYPE 168 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  S100A2 MUTATED      2    5
  S100A2 WILD-TYPE  168  192
        clus
vv       S100A2 MUTATED S100A2 WILD-TYPE
  FEMALE              2              168
  MALE                5              192
[1] 2 2
[1] FALSE
D1667V8, binary
                  cls
clus                 0   1
  S100A2 MUTATED     5   2
  S100A2 WILD-TYPE 312  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  S100A2 MUTATED      5    2
  S100A2 WILD-TYPE  312   46
                               clus
vv                              S100A2 MUTATED S100A2 WILD-TYPE
  COLON ADENOCARCINOMA                       5              312
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  S100A2 MUTATED     2   0   0   2
  S100A2 WILD-TYPE 255   2  22  19
D1667V9, multiclass
    clus
vv   S100A2 MUTATED S100A2 WILD-TYPE
  R0              2              255
  R1              0                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"
D1667V10, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  S100A2 MUTATED                                  0     1
  S100A2 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  S100A2 MUTATED                           1     3
  S100A2 WILD-TYPE                        18   173
D1667V11, multiclass
                                  clus
vv                                 S100A2 MUTATED S100A2 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(1668) Variable = SPARC MUTATION ANALYSIS
D1668V1, survival
                 sevent
clus2               0   1
  SPARC MUTATED     7   0
  SPARC WILD-TYPE 275  73
  SPARC MUTATED SPARC WILD-TYPE 
              7             348 
  SPARC MUTATED SPARC WILD-TYPE 
              0              73 
$`SPARC MUTATED`
TCGA-A6-6141 TCGA-AA-3510 TCGA-AA-3977 TCGA-AA-A00E TCGA-AD-5900 TCGA-AD-6889 
        8.38        63.98        25.02        30.02         0.07        56.55 
TCGA-DM-A1HB 
      135.65 

$`SPARC WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       40.96        21.37         4.21         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  SPARC MUTATED SPARC WILD-TYPE 
           0.07            0.00 
  SPARC MUTATED SPARC WILD-TYPE 
         135.65          140.38 
  SPARC MUTATED SPARC WILD-TYPE 
          30.02           20.07 
[1] "0.1 - 135.7 (30.0)" "0.0 - 140.4 (20.1)"
[1] "hr="     "2.6e+07"
D1668V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SPARC MUTATED         1        0        1         4         0         0
  SPARC WILD-TYPE      63        1       24       105         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SPARC MUTATED           0          0          1          0        0         0
  SPARC WILD-TYPE        19         10         40         31       35        13
                 vv
clus              STAGE IVB
  SPARC MUTATED           0
  SPARC WILD-TYPE         1
D1668V3, multiclass
            clus
vv           SPARC MUTATED SPARC WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              4             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SPARC MUTATED     0   2   6   0
  SPARC WILD-TYPE   9  66 242  41
D1668V4, multiclass
    clus
vv   SPARC MUTATED SPARC WILD-TYPE
  T1             0               9
  T2             2              66
  T3             6             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
  SPARC MUTATED     7   1   0
  SPARC WILD-TYPE 213  79  66
D1668V5, multiclass
    clus
vv   SPARC MUTATED SPARC WILD-TYPE
  N0             7             213
  N1             1              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"
D1668V6, binary
                 cls
clus                0   1
  SPARC MUTATED     6   0
  SPARC WILD-TYPE 277  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPARC MUTATED      6    0
  SPARC WILD-TYPE  277   48
   clus
vv  SPARC MUTATED SPARC WILD-TYPE
  0             6             277
  1             0              48
[1] 2 2
[1] FALSE
D1668V7, binary
                 cls
clus                0   1
  SPARC MUTATED     1   7
  SPARC WILD-TYPE 169 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPARC MUTATED      1    7
  SPARC WILD-TYPE  169  190
        clus
vv       SPARC MUTATED SPARC WILD-TYPE
  FEMALE             1             169
  MALE               7             190
[1] 2 2
[1] FALSE
D1668V8, binary
                 cls
clus                0   1
  SPARC MUTATED     7   1
  SPARC WILD-TYPE 310  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPARC MUTATED      7    1
  SPARC WILD-TYPE  310   47
                               clus
vv                              SPARC MUTATED SPARC WILD-TYPE
  COLON ADENOCARCINOMA                      7             310
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SPARC MUTATED     4   0   0   0
  SPARC WILD-TYPE 253   2  22  21
D1668V9, multiclass
    clus
vv   SPARC MUTATED SPARC WILD-TYPE
  R0             4             253
  R1             0               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"
D1668V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SPARC MUTATED                                  0     1
  SPARC WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SPARC MUTATED                           1     2
  SPARC WILD-TYPE                        18   174
D1668V11, multiclass
                                  clus
vv                                 SPARC MUTATED SPARC 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(1669) Variable = PKD2L1 MUTATION ANALYSIS
D1669V1, survival
                  sevent
clus2                0   1
  PKD2L1 MUTATED    17   3
  PKD2L1 WILD-TYPE 265  70
  PKD2L1 MUTATED PKD2L1 WILD-TYPE 
              20              335 
  PKD2L1 MUTATED PKD2L1 WILD-TYPE 
               3               70 
$`PKD2L1 MUTATED`
TCGA-A6-5659 TCGA-A6-6141 TCGA-A6-6781 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3555 
       30.44         8.38        19.66        33.99        13.02        29.95 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-5900 TCGA-AD-6889 
       19.04        19.04        34.98        35.01         0.07        56.55 
TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6716 TCGA-CK-4952 TCGA-CM-4743 TCGA-D5-6535 
       58.39        49.41         0.26        15.62        23.05        15.12 
TCGA-D5-6540 TCGA-G4-6293 
       16.14       107.67 

$`PKD2L1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 
        0.99        14.01        21.01        24.00        17.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3811 
       19.00        36.00         5.03        85.05        26.99        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       40.96        21.37         4.21         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       40.34        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        17.85         4.80        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       19.43        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  PKD2L1 MUTATED PKD2L1 WILD-TYPE 
            0.07             0.00 
  PKD2L1 MUTATED PKD2L1 WILD-TYPE 
          107.67           140.38 
  PKD2L1 MUTATED PKD2L1 WILD-TYPE 
          21.355           20.190 
[1] "0.1 - 107.7 (21.4)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.6"
D1669V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PKD2L1 MUTATED         3        0        2         7         1         0
  PKD2L1 WILD-TYPE      61        1       23       102         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PKD2L1 MUTATED           3          0          1          3        1
  PKD2L1 WILD-TYPE        16         10         40         28       34
                  vv
clus               STAGE IVA STAGE IVB
  PKD2L1 MUTATED           0         0
  PKD2L1 WILD-TYPE        13         1
D1669V3, multiclass
            clus
vv           PKD2L1 MUTATED PKD2L1 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               7              102
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               3               16
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              3               28
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PKD2L1 MUTATED     0   3  15   3
  PKD2L1 WILD-TYPE   9  65 233  38
D1669V4, multiclass
    clus
vv   PKD2L1 MUTATED PKD2L1 WILD-TYPE
  T1              0                9
  T2              3               65
  T3             15              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    14   3   4
  PKD2L1 WILD-TYPE 206  77  62
D1669V5, multiclass
    clus
vv   PKD2L1 MUTATED PKD2L1 WILD-TYPE
  N0             14              206
  N1              3               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"
D1669V6, binary
                  cls
clus                 0   1
  PKD2L1 MUTATED    16   1
  PKD2L1 WILD-TYPE 267  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PKD2L1 MUTATED     16    1
  PKD2L1 WILD-TYPE  267   47
   clus
vv  PKD2L1 MUTATED PKD2L1 WILD-TYPE
  0             16              267
  1              1               47
[1] 2 2
[1] FALSE
D1669V7, binary
                  cls
clus                 0   1
  PKD2L1 MUTATED     8  13
  PKD2L1 WILD-TYPE 162 184
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PKD2L1 MUTATED      8   13
  PKD2L1 WILD-TYPE  162  184
        clus
vv       PKD2L1 MUTATED PKD2L1 WILD-TYPE
  FEMALE              8              162
  MALE               13              184
[1] 2 2
[1] FALSE
D1669V8, binary
                  cls
clus                 0   1
  PKD2L1 MUTATED    15   6
  PKD2L1 WILD-TYPE 302  42
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PKD2L1 MUTATED     15    6
  PKD2L1 WILD-TYPE  302   42
                               clus
vv                              PKD2L1 MUTATED PKD2L1 WILD-TYPE
  COLON ADENOCARCINOMA                      15              302
  COLON MUCINOUS ADENOCARCINOMA              6               42
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PKD2L1 MUTATED    14   0   1   3
  PKD2L1 WILD-TYPE 243   2  21  18
D1669V9, multiclass
    clus
vv   PKD2L1 MUTATED PKD2L1 WILD-TYPE
  R0             14              243
  R1              0                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"
D1669V10, 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    10
  PKD2L1 WILD-TYPE                        18   166
D1669V11, 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                                        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(1670) Variable = NME7 MUTATION ANALYSIS
D1670V1, survival
                sevent
clus2              0   1
  NME7 MUTATED     3   2
  NME7 WILD-TYPE 279  71
  NME7 MUTATED NME7 WILD-TYPE 
             5            350 
  NME7 MUTATED NME7 WILD-TYPE 
             2             71 
$`NME7 MUTATED`
TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-5403 TCGA-CM-4743 
        4.01        34.98        58.39        62.79        23.05 

$`NME7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  NME7 MUTATED NME7 WILD-TYPE 
          4.01           0.00 
  NME7 MUTATED NME7 WILD-TYPE 
         62.79         140.38 
  NME7 MUTATED NME7 WILD-TYPE 
         34.98          20.07 
[1] "4.0 - 62.8 (35.0)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.4"
D1670V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NME7 MUTATED         0        0        2         2         2         0
  NME7 WILD-TYPE      64        1       23       107         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NME7 MUTATED           0          0          0          0        0         0
  NME7 WILD-TYPE        19         10         41         31       35        13
                vv
clus             STAGE IVB
  NME7 MUTATED           0
  NME7 WILD-TYPE         1
D1670V3, multiclass
            clus
vv           NME7 MUTATED NME7 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             2            107
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NME7 MUTATED     0   0   3   3
  NME7 WILD-TYPE   9  68 245  38
D1670V4, multiclass
    clus
vv   NME7 MUTATED NME7 WILD-TYPE
  T1            0              9
  T2            0             68
  T3            3            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
  NME7 MUTATED     6   0   0
  NME7 WILD-TYPE 214  80  66
D1670V5, multiclass
    clus
vv   NME7 MUTATED NME7 WILD-TYPE
  N0            6            214
  N1            0             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
  NME7 MUTATED     5   0
  NME7 WILD-TYPE 278  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  NME7 MUTATED      5    0
  NME7 WILD-TYPE  278   48
   clus
vv  NME7 MUTATED NME7 WILD-TYPE
  0            5            278
  1            0             48
[1] 2 2
[1] FALSE
D1670V7, binary
                cls
clus               0   1
  NME7 MUTATED     2   4
  NME7 WILD-TYPE 168 193
[1] "tbl2"
                cls
clus             [,1] [,2]
  NME7 MUTATED      2    4
  NME7 WILD-TYPE  168  193
        clus
vv       NME7 MUTATED NME7 WILD-TYPE
  FEMALE            2            168
  MALE              4            193
[1] 2 2
[1] FALSE
D1670V8, binary
                cls
clus               0   1
  NME7 MUTATED     5   1
  NME7 WILD-TYPE 312  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  NME7 MUTATED      5    1
  NME7 WILD-TYPE  312   47
                               clus
vv                              NME7 MUTATED NME7 WILD-TYPE
  COLON ADENOCARCINOMA                     5            312
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  NME7 MUTATED     5   0   0   0
  NME7 WILD-TYPE 252   2  22  21
D1670V9, multiclass
    clus
vv   NME7 MUTATED NME7 WILD-TYPE
  R0            5            252
  R1            0              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"
D1670V10, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NME7 MUTATED                                  0     0
  NME7 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NME7 MUTATED                           0     3
  NME7 WILD-TYPE                        19   173
D1670V11, multiclass
                                  clus
vv                                 NME7 MUTATED NME7 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(1671) Variable = C17ORF71 MUTATION ANALYSIS
D1671V1, survival
                    sevent
clus2                  0   1
  C17ORF71 MUTATED     7   2
  C17ORF71 WILD-TYPE 275  71
  C17ORF71 MUTATED C17ORF71 WILD-TYPE 
                 9                346 
  C17ORF71 MUTATED C17ORF71 WILD-TYPE 
                 2                 71 
$`C17ORF71 MUTATED`
TCGA-A6-6654 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3815 TCGA-AA-A00N TCGA-AA-A010 
       23.87        19.04        19.04        33.04         4.01        34.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-6679 
       30.08        16.01        10.06 

$`C17ORF71 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
       36.00         5.03        85.05        26.99        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.03        22.98        15.02         5.03        15.02        15.02 
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-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  C17ORF71 MUTATED C17ORF71 WILD-TYPE 
              4.01               0.00 
  C17ORF71 MUTATED C17ORF71 WILD-TYPE 
             34.98             140.38 
  C17ORF71 MUTATED C17ORF71 WILD-TYPE 
            19.040             20.235 
[1] "4.0 - 35.0 (19.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.4"
D1671V2, 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       24       105         6         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C17ORF71 MUTATED           0          0          1          0        1
  C17ORF71 WILD-TYPE        19         10         40         31       34
                    vv
clus                 STAGE IVA STAGE IVB
  C17ORF71 MUTATED           0         0
  C17ORF71 WILD-TYPE        13         1
D1671V3, multiclass
            clus
vv           C17ORF71 MUTATED C17ORF71 WILD-TYPE
  STAGE I                   0                 64
  STAGE IA                  0                  1
  STAGE II                  1                 24
  STAGE IIA                 4                105
  STAGE IIB                 2                  6
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                0                 10
  STAGE IIIB                1                 40
  STAGE IIIC                0                 31
  STAGE IV                  1                 34
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C17ORF71 MUTATED     0   0   7   2
  C17ORF71 WILD-TYPE   9  68 241  39
D1671V4, multiclass
    clus
vv   C17ORF71 MUTATED C17ORF71 WILD-TYPE
  T1                0                  9
  T2                0                 68
  T3                7                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
  C17ORF71 MUTATED     8   1   0
  C17ORF71 WILD-TYPE 212  79  66
D1671V5, multiclass
    clus
vv   C17ORF71 MUTATED C17ORF71 WILD-TYPE
  N0                8                212
  N1                1                 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"
D1671V6, binary
                    cls
clus                   0   1
  C17ORF71 MUTATED     8   1
  C17ORF71 WILD-TYPE 275  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C17ORF71 MUTATED      8    1
  C17ORF71 WILD-TYPE  275   47
   clus
vv  C17ORF71 MUTATED C17ORF71 WILD-TYPE
  0                8                275
  1                1                 47
[1] 2 2
[1] FALSE
D1671V7, 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
D1671V8, binary
                    cls
clus                   0   1
  C17ORF71 MUTATED     8   1
  C17ORF71 WILD-TYPE 309  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C17ORF71 MUTATED      8    1
  C17ORF71 WILD-TYPE  309   47
                               clus
vv                              C17ORF71 MUTATED C17ORF71 WILD-TYPE
  COLON ADENOCARCINOMA                         8                309
  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 250   2  21  21
D1671V9, multiclass
    clus
vv   C17ORF71 MUTATED C17ORF71 WILD-TYPE
  R0                7                250
  R1                0                  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"
D1671V10, 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
D1671V11, 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(1672) Variable = CCDC64B MUTATION ANALYSIS
D1672V1, survival
                   sevent
clus2                 0   1
  CCDC64B MUTATED     3   2
  CCDC64B WILD-TYPE 279  71
  CCDC64B MUTATED CCDC64B WILD-TYPE 
                5               350 
  CCDC64B MUTATED CCDC64B WILD-TYPE 
                2                71 
$`CCDC64B MUTATED`
TCGA-A6-2671 TCGA-AA-3815 TCGA-AA-3821 TCGA-AZ-6601 TCGA-DM-A1HB 
       43.76        33.04         1.02       100.01       135.65 

$`CCDC64B WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 
       10.06        35.05         0.99        25.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  CCDC64B MUTATED CCDC64B WILD-TYPE 
             1.02              0.00 
  CCDC64B MUTATED CCDC64B WILD-TYPE 
           135.65            140.38 
  CCDC64B MUTATED CCDC64B WILD-TYPE 
            43.76             20.07 
[1] "1.0 - 135.7 (43.8)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.1"
D1672V2, 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       24       108         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC64B MUTATED           0          0          1          0        1
  CCDC64B WILD-TYPE        19         10         40         31       34
                   vv
clus                STAGE IVA STAGE IVB
  CCDC64B MUTATED           0         0
  CCDC64B WILD-TYPE        13         1
D1672V3, multiclass
            clus
vv           CCDC64B MUTATED CCDC64B WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                1               108
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               0                31
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CCDC64B MUTATED     0   1   4   0
  CCDC64B WILD-TYPE   9  67 244  41
D1672V4, multiclass
    clus
vv   CCDC64B MUTATED CCDC64B WILD-TYPE
  T1               0                 9
  T2               1                67
  T3               4               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
  CCDC64B MUTATED     3   1   1
  CCDC64B WILD-TYPE 217  79  65
D1672V5, multiclass
    clus
vv   CCDC64B MUTATED CCDC64B WILD-TYPE
  N0               3               217
  N1               1                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"
D1672V6, binary
                   cls
clus                  0   1
  CCDC64B MUTATED     4   1
  CCDC64B WILD-TYPE 279  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC64B MUTATED      4    1
  CCDC64B WILD-TYPE  279   47
   clus
vv  CCDC64B MUTATED CCDC64B WILD-TYPE
  0               4               279
  1               1                47
[1] 2 2
[1] FALSE
D1672V7, 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
D1672V8, binary
                   cls
clus                  0   1
  CCDC64B MUTATED     4   1
  CCDC64B WILD-TYPE 313  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC64B MUTATED      4    1
  CCDC64B WILD-TYPE  313   47
                               clus
vv                              CCDC64B MUTATED CCDC64B WILD-TYPE
  COLON ADENOCARCINOMA                        4               313
  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 254   2  22  21
D1672V9, multiclass
    clus
vv   CCDC64B MUTATED CCDC64B WILD-TYPE
  R0               3               254
  R1               0                 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"
D1672V10, 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
D1672V11, 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(1673) Variable = C12ORF24 MUTATION ANALYSIS
D1673V1, survival
                    sevent
clus2                  0   1
  C12ORF24 MUTATED     4   0
  C12ORF24 WILD-TYPE 278  73
  C12ORF24 MUTATED C12ORF24 WILD-TYPE 
                 4                351 
  C12ORF24 MUTATED C12ORF24 WILD-TYPE 
                 0                 73 
$`C12ORF24 MUTATED`
TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-A010 TCGA-CK-4952 
       22.06        63.98        34.98        15.62 

$`C12ORF24 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       40.34        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  C12ORF24 MUTATED C12ORF24 WILD-TYPE 
             15.62               0.00 
  C12ORF24 MUTATED C12ORF24 WILD-TYPE 
             63.98             140.38 
  C12ORF24 MUTATED C12ORF24 WILD-TYPE 
             28.52              20.12 
[1] "15.6 - 64.0 (28.5)" "0.0 - 140.4 (20.1)"
[1] "hr="     "9100000"
D1673V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C12ORF24 MUTATED         0        0        1         1         1         0
  C12ORF24 WILD-TYPE      64        1       24       108         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C12ORF24 MUTATED           1          0          0          0        0
  C12ORF24 WILD-TYPE        18         10         41         31       35
                    vv
clus                 STAGE IVA STAGE IVB
  C12ORF24 MUTATED           0         0
  C12ORF24 WILD-TYPE        13         1
D1673V3, multiclass
            clus
vv           C12ORF24 MUTATED C12ORF24 WILD-TYPE
  STAGE I                   0                 64
  STAGE IA                  0                  1
  STAGE II                  1                 24
  STAGE IIA                 1                108
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 1                 18
  STAGE IIIA                0                 10
  STAGE IIIB                0                 41
  STAGE IIIC                0                 31
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C12ORF24 MUTATED     0   0   2   2
  C12ORF24 WILD-TYPE   9  68 246  39
D1673V4, multiclass
    clus
vv   C12ORF24 MUTATED C12ORF24 WILD-TYPE
  T1                0                  9
  T2                0                 68
  T3                2                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
  C12ORF24 MUTATED     3   0   1
  C12ORF24 WILD-TYPE 217  80  65
D1673V5, multiclass
    clus
vv   C12ORF24 MUTATED C12ORF24 WILD-TYPE
  N0                3                217
  N1                0                 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"
D1673V6, binary
                    cls
clus                   0   1
  C12ORF24 MUTATED     4   0
  C12ORF24 WILD-TYPE 279  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF24 MUTATED      4    0
  C12ORF24 WILD-TYPE  279   48
   clus
vv  C12ORF24 MUTATED C12ORF24 WILD-TYPE
  0                4                279
  1                0                 48
[1] 2 2
[1] FALSE
D1673V7, binary
                    cls
clus                   0   1
  C12ORF24 MUTATED     3   1
  C12ORF24 WILD-TYPE 167 196
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF24 MUTATED      3    1
  C12ORF24 WILD-TYPE  167  196
        clus
vv       C12ORF24 MUTATED C12ORF24 WILD-TYPE
  FEMALE                3                167
  MALE                  1                196
[1] 2 2
[1] FALSE
D1673V8, binary
                    cls
clus                   0   1
  C12ORF24 MUTATED     3   1
  C12ORF24 WILD-TYPE 314  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF24 MUTATED      3    1
  C12ORF24 WILD-TYPE  314   47
                               clus
vv                              C12ORF24 MUTATED C12ORF24 WILD-TYPE
  COLON ADENOCARCINOMA                         3                314
  COLON MUCINOUS ADENOCARCINOMA                1                 47
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C12ORF24 MUTATED     3   0   0   1
  C12ORF24 WILD-TYPE 254   2  22  20
D1673V9, multiclass
    clus
vv   C12ORF24 MUTATED C12ORF24 WILD-TYPE
  R0                3                254
  R1                0                  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"
D1673V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C12ORF24 MUTATED                                  0     0
  C12ORF24 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C12ORF24 MUTATED                           0     2
  C12ORF24 WILD-TYPE                        19   174
D1673V11, multiclass
[1] "Remove cluster labels:" "C12ORF24 MUTATED"      
clus
  C12ORF24 MUTATED C12ORF24 WILD-TYPE 
                 2                204 
        TCGA-A6-2671         TCGA-A6-2672         TCGA-A6-2674 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-A6-2676         TCGA-A6-2677         TCGA-A6-2678 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-A6-2683         TCGA-A6-3807         TCGA-A6-3808 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-A6-3809         TCGA-A6-3810         TCGA-A6-4105 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-A6-5656         TCGA-A6-5657         TCGA-A6-5659 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-A6-5660         TCGA-A6-5661         TCGA-A6-5662 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-A6-5664         TCGA-A6-5666         TCGA-A6-6137 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-A6-6138         TCGA-A6-6141         TCGA-A6-6142 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-A6-6648         TCGA-A6-6649         TCGA-A6-6651 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-A6-6652         TCGA-A6-6653         TCGA-A6-6654 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-A6-6780         TCGA-A6-6781         TCGA-A6-6782 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-AD-5900         TCGA-AD-6548         TCGA-AD-6888 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-AD-6889         TCGA-AD-6890         TCGA-AD-6895 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-AD-6899         TCGA-AD-6901         TCGA-AD-6963 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-AD-6964         TCGA-AD-6965         TCGA-AU-3779 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-AU-6004         TCGA-AY-4070         TCGA-AY-4071 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-AY-5543         TCGA-AY-6196         TCGA-AY-6197 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-AY-6386         TCGA-AZ-4315         TCGA-AZ-4323 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-AZ-4616         TCGA-AZ-4681         TCGA-AZ-4682 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-AZ-5403         TCGA-AZ-5407         TCGA-AZ-6598 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-AZ-6599         TCGA-AZ-6600         TCGA-AZ-6601 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-AZ-6603         TCGA-AZ-6605         TCGA-AZ-6606 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-AZ-6607         TCGA-AZ-6608         TCGA-CA-5254 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-CA-5255         TCGA-CA-5796         TCGA-CA-5797 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-CA-6715         TCGA-CA-6716         TCGA-CA-6717 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-CA-6718         TCGA-CA-6719         TCGA-CK-4947 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-CK-4948         TCGA-CK-4950         TCGA-CK-5912 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-CK-5913         TCGA-CK-5914         TCGA-CK-5915 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-CK-5916         TCGA-CK-6746         TCGA-CK-6747 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-CK-6748         TCGA-CK-6751         TCGA-CM-4743 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-CM-4744         TCGA-CM-4746         TCGA-CM-4747 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-CM-4752         TCGA-CM-5341         TCGA-CM-5344 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-CM-5348         TCGA-CM-5349         TCGA-CM-5860 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-CM-5861         TCGA-CM-5862         TCGA-CM-5863 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-CM-5864         TCGA-CM-5868         TCGA-CM-6161 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-CM-6162         TCGA-CM-6163         TCGA-CM-6164 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-CM-6165         TCGA-CM-6166         TCGA-CM-6167 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-CM-6168         TCGA-CM-6169         TCGA-CM-6170 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-CM-6171         TCGA-CM-6172         TCGA-CM-6674 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-CM-6675         TCGA-CM-6676         TCGA-CM-6677 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-CM-6678         TCGA-CM-6679         TCGA-CM-6680 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-D5-5537         TCGA-D5-5538         TCGA-D5-5539 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-D5-5540         TCGA-D5-5541         TCGA-D5-6529 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-D5-6532         TCGA-D5-6533         TCGA-D5-6534 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-D5-6535         TCGA-D5-6536         TCGA-D5-6537 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-D5-6538         TCGA-D5-6539         TCGA-D5-6540 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-D5-6541         TCGA-D5-6898         TCGA-D5-6920 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-D5-6922         TCGA-D5-6923         TCGA-D5-6924 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-D5-6926         TCGA-D5-6927         TCGA-D5-6928 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-D5-6929         TCGA-D5-6930         TCGA-D5-6931 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-D5-6932         TCGA-D5-7000         TCGA-DM-A0X9 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-DM-A0XD         TCGA-DM-A0XF         TCGA-DM-A1D0 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-DM-A1D4         TCGA-DM-A1D6         TCGA-DM-A1D7 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-DM-A1D8         TCGA-DM-A1D9         TCGA-DM-A1DA 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-DM-A1DB         TCGA-DM-A1HA         TCGA-DM-A1HB 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-DM-A282         TCGA-DM-A285         TCGA-DM-A28C 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-DM-A28E         TCGA-DM-A28F         TCGA-DM-A28G 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-DM-A28H         TCGA-DM-A28K         TCGA-F4-6459 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-F4-6460         TCGA-F4-6569         TCGA-F4-6570 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-F4-6703         TCGA-F4-6704         TCGA-F4-6805 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-F4-6806         TCGA-F4-6807         TCGA-F4-6808 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-F4-6809         TCGA-F4-6854         TCGA-F4-6855 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-F4-6856         TCGA-G4-6293         TCGA-G4-6299 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-G4-6303         TCGA-G4-6304         TCGA-G4-6306 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-G4-6307         TCGA-G4-6309         TCGA-G4-6310 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-G4-6315         TCGA-G4-6317         TCGA-G4-6321 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-G4-6323         TCGA-G4-6586         TCGA-G4-6588 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 
        TCGA-G4-6625         TCGA-G4-6626         TCGA-G4-6628 
"C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" "C12ORF24 WILD-TYPE" 

Clustering(1674) Variable = GDF6 MUTATION ANALYSIS
D1674V1, survival
                sevent
clus2              0   1
  GDF6 MUTATED     3   2
  GDF6 WILD-TYPE 279  71
  GDF6 MUTATED GDF6 WILD-TYPE 
             5            350 
  GDF6 MUTATED GDF6 WILD-TYPE 
             2             71 
$`GDF6 MUTATED`
TCGA-A6-6653 TCGA-AA-3662 TCGA-AA-3715 TCGA-DM-A28F TCGA-G4-6304 
       24.39         6.05        19.04        35.97        53.62 

$`GDF6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       19.99        13.94        19.99        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G 
      135.65       139.17         6.12        81.37       119.93        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  GDF6 MUTATED GDF6 WILD-TYPE 
          6.05           0.00 
  GDF6 MUTATED GDF6 WILD-TYPE 
         53.62         140.38 
  GDF6 MUTATED GDF6 WILD-TYPE 
        24.390         20.155 
[1] "6.0 - 53.6 (24.4)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.8"
D1674V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GDF6 MUTATED         1        0        1         1         1         0
  GDF6 WILD-TYPE      63        1       24       108         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GDF6 MUTATED           0          0          1          0        1         0
  GDF6 WILD-TYPE        19         10         40         31       34        13
                vv
clus             STAGE IVB
  GDF6 MUTATED           0
  GDF6 WILD-TYPE         1
D1674V3, multiclass
            clus
vv           GDF6 MUTATED GDF6 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             1            108
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GDF6 MUTATED     0   1   3   2
  GDF6 WILD-TYPE   9  67 245  39
D1674V4, multiclass
    clus
vv   GDF6 MUTATED GDF6 WILD-TYPE
  T1            0              9
  T2            1             67
  T3            3            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
  GDF6 MUTATED     4   1   1
  GDF6 WILD-TYPE 216  79  65
D1674V5, multiclass
    clus
vv   GDF6 MUTATED GDF6 WILD-TYPE
  N0            4            216
  N1            1             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"
D1674V6, binary
                cls
clus               0   1
  GDF6 MUTATED     5   1
  GDF6 WILD-TYPE 278  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  GDF6 MUTATED      5    1
  GDF6 WILD-TYPE  278   47
   clus
vv  GDF6 MUTATED GDF6 WILD-TYPE
  0            5            278
  1            1             47
[1] 2 2
[1] FALSE
D1674V7, binary
                cls
clus               0   1
  GDF6 MUTATED     3   3
  GDF6 WILD-TYPE 167 194
[1] "tbl2"
                cls
clus             [,1] [,2]
  GDF6 MUTATED      3    3
  GDF6 WILD-TYPE  167  194
        clus
vv       GDF6 MUTATED GDF6 WILD-TYPE
  FEMALE            3            167
  MALE              3            194
[1] 2 2
[1] FALSE
D1674V8, binary
                cls
clus               0   1
  GDF6 MUTATED     6   0
  GDF6 WILD-TYPE 311  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  GDF6 MUTATED      6    0
  GDF6 WILD-TYPE  311   48
                               clus
vv                              GDF6 MUTATED GDF6 WILD-TYPE
  COLON ADENOCARCINOMA                     6            311
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  GDF6 MUTATED     3   0   1   0
  GDF6 WILD-TYPE 254   2  21  21
D1674V9, multiclass
    clus
vv   GDF6 MUTATED GDF6 WILD-TYPE
  R0            3            254
  R1            0              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"
D1674V10, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GDF6 MUTATED                                  0     0
  GDF6 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GDF6 MUTATED                           0     3
  GDF6 WILD-TYPE                        19   173
D1674V11, multiclass
                                  clus
vv                                 GDF6 MUTATED GDF6 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 = TARBP2 MUTATION ANALYSIS
D1675V1, survival
                  sevent
clus2                0   1
  TARBP2 MUTATED     6   2
  TARBP2 WILD-TYPE 276  71
  TARBP2 MUTATED TARBP2 WILD-TYPE 
               8              347 
  TARBP2 MUTATED TARBP2 WILD-TYPE 
               2               71 
$`TARBP2 MUTATED`
TCGA-AA-3510 TCGA-AA-A01R TCGA-AZ-6598 TCGA-AZ-6599 TCGA-CA-6717 TCGA-CK-5913 
       63.98        35.01        49.41         6.77         0.33        51.32 
TCGA-CM-4752 TCGA-CM-6674 
       13.02        12.95 

$`TARBP2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 
        5.13        83.80        22.36        62.79        61.41        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  TARBP2 MUTATED TARBP2 WILD-TYPE 
            0.33             0.00 
  TARBP2 MUTATED TARBP2 WILD-TYPE 
           63.98           140.38 
  TARBP2 MUTATED TARBP2 WILD-TYPE 
          24.015           20.190 
[1] "0.3 - 64.0 (24.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1"  
D1675V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TARBP2 MUTATED         1        0        3         4         0         0
  TARBP2 WILD-TYPE      63        1       22       105         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TARBP2 MUTATED           1          0          0          0        0
  TARBP2 WILD-TYPE        18         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  TARBP2 MUTATED           0         0
  TARBP2 WILD-TYPE        13         1
D1675V3, multiclass
            clus
vv           TARBP2 MUTATED TARBP2 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                3               22
  STAGE IIA               4              105
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TARBP2 MUTATED     0   1   7   1
  TARBP2 WILD-TYPE   9  67 241  40
D1675V4, multiclass
    clus
vv   TARBP2 MUTATED TARBP2 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              7              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
  TARBP2 MUTATED     8   0   1
  TARBP2 WILD-TYPE 212  80  65
D1675V5, multiclass
    clus
vv   TARBP2 MUTATED TARBP2 WILD-TYPE
  N0              8              212
  N1              0               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"
D1675V6, binary
                  cls
clus                 0   1
  TARBP2 MUTATED     6   0
  TARBP2 WILD-TYPE 277  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TARBP2 MUTATED      6    0
  TARBP2 WILD-TYPE  277   48
   clus
vv  TARBP2 MUTATED TARBP2 WILD-TYPE
  0              6              277
  1              0               48
[1] 2 2
[1] FALSE
D1675V7, binary
                  cls
clus                 0   1
  TARBP2 MUTATED     3   6
  TARBP2 WILD-TYPE 167 191
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TARBP2 MUTATED      3    6
  TARBP2 WILD-TYPE  167  191
        clus
vv       TARBP2 MUTATED TARBP2 WILD-TYPE
  FEMALE              3              167
  MALE                6              191
[1] 2 2
[1] FALSE
D1675V8, binary
                  cls
clus                 0   1
  TARBP2 MUTATED     7   2
  TARBP2 WILD-TYPE 310  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TARBP2 MUTATED      7    2
  TARBP2 WILD-TYPE  310   46
                               clus
vv                              TARBP2 MUTATED TARBP2 WILD-TYPE
  COLON ADENOCARCINOMA                       7              310
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TARBP2 MUTATED     5   0   0   2
  TARBP2 WILD-TYPE 252   2  22  19
D1675V9, multiclass
    clus
vv   TARBP2 MUTATED TARBP2 WILD-TYPE
  R0              5              252
  R1              0                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"
D1675V10, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TARBP2 MUTATED                                  0     1
  TARBP2 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TARBP2 MUTATED                           1     4
  TARBP2 WILD-TYPE                        18   172
D1675V11, multiclass
                                  clus
vv                                 TARBP2 MUTATED TARBP2 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(1676) Variable = VWA5A MUTATION ANALYSIS
D1676V1, survival
                 sevent
clus2               0   1
  VWA5A MUTATED     8   3
  VWA5A WILD-TYPE 274  70
  VWA5A MUTATED VWA5A WILD-TYPE 
             11             344 
  VWA5A MUTATED VWA5A WILD-TYPE 
              3              70 
$`VWA5A MUTATED`
TCGA-A6-2683 TCGA-A6-6653 TCGA-AA-3522 TCGA-AA-3672 TCGA-AA-3821 TCGA-AA-3966 
       16.57        24.39        37.05         0.92         1.02         2.01 
TCGA-AA-A010 TCGA-AZ-6598 TCGA-CM-6168 TCGA-G4-6303 TCGA-G4-6307 
       34.98        49.41        12.99        65.85        55.04 

$`VWA5A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
        9.07        24.03        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
        0.99        25.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       26.01        24.00         2.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       74.56        53.62        44.68        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  VWA5A MUTATED VWA5A WILD-TYPE 
           0.92            0.00 
  VWA5A MUTATED VWA5A WILD-TYPE 
          65.85          140.38 
  VWA5A MUTATED VWA5A WILD-TYPE 
         24.390          20.155 
[1] "0.9 - 65.8 (24.4)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D1676V2, 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       24       106         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        18         10         40         31       33        13
                 vv
clus              STAGE IVB
  VWA5A MUTATED           0
  VWA5A WILD-TYPE         1
D1676V3, multiclass
            clus
vv           VWA5A MUTATED VWA5A WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              3             106
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               2              33
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  VWA5A MUTATED     0   2   7   3
  VWA5A WILD-TYPE   9  66 241  38
D1676V4, multiclass
    clus
vv   VWA5A MUTATED VWA5A WILD-TYPE
  T1             0               9
  T2             2              66
  T3             7             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
  VWA5A MUTATED     9   3   0
  VWA5A WILD-TYPE 211  77  66
D1676V5, multiclass
    clus
vv   VWA5A MUTATED VWA5A WILD-TYPE
  N0             9             211
  N1             3              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"
D1676V6, binary
                 cls
clus                0   1
  VWA5A MUTATED     8   2
  VWA5A WILD-TYPE 275  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VWA5A MUTATED      8    2
  VWA5A WILD-TYPE  275   46
   clus
vv  VWA5A MUTATED VWA5A WILD-TYPE
  0             8             275
  1             2              46
[1] 2 2
[1] FALSE
D1676V7, 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
D1676V8, binary
                 cls
clus                0   1
  VWA5A MUTATED    10   2
  VWA5A WILD-TYPE 307  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VWA5A MUTATED     10    2
  VWA5A WILD-TYPE  307   46
                               clus
vv                              VWA5A MUTATED VWA5A WILD-TYPE
  COLON ADENOCARCINOMA                     10             307
  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 249   2  22  20
D1676V9, multiclass
    clus
vv   VWA5A MUTATED VWA5A WILD-TYPE
  R0             8             249
  R1             0               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"
D1676V10, 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
D1676V11, 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(1677) Variable = BFAR MUTATION ANALYSIS
D1677V1, survival
                sevent
clus2              0   1
  BFAR MUTATED     8   0
  BFAR WILD-TYPE 274  73
  BFAR MUTATED BFAR WILD-TYPE 
             8            347 
  BFAR MUTATED BFAR WILD-TYPE 
             0             73 
$`BFAR MUTATED`
TCGA-AA-3672 TCGA-AD-6963 TCGA-AU-6004 TCGA-AZ-4681 TCGA-CA-6717 TCGA-CA-6718 
        0.92        27.42        27.09        83.80         0.33         0.10 
TCGA-CK-4947 TCGA-G4-6321 
       17.56        22.09 

$`BFAR WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
        6.05         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        15.75 
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        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
        1.35       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       55.04        51.75        45.11        36.72        36.00        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  BFAR MUTATED BFAR WILD-TYPE 
           0.1            0.0 
  BFAR MUTATED BFAR WILD-TYPE 
         83.80         140.38 
  BFAR MUTATED BFAR WILD-TYPE 
        19.825         20.190 
[1] "0.1 - 83.8 (19.8)"  "0.0 - 140.4 (20.2)"
[1] "hr="     "9200000"
D1677V2, 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       25       106         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BFAR MUTATED           2          0          0          0        0         1
  BFAR WILD-TYPE        17         10         41         31       35        12
                vv
clus             STAGE IVB
  BFAR MUTATED           0
  BFAR WILD-TYPE         1
D1677V3, multiclass
            clus
vv           BFAR MUTATED BFAR WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             3            106
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             2             17
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 243  40
D1677V4, multiclass
    clus
vv   BFAR MUTATED BFAR WILD-TYPE
  T1            0              9
  T2            2             66
  T3            5            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
  BFAR MUTATED     5   3   0
  BFAR WILD-TYPE 215  77  66
D1677V5, multiclass
    clus
vv   BFAR MUTATED BFAR WILD-TYPE
  N0            5            215
  N1            3             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"
D1677V6, binary
                cls
clus               0   1
  BFAR MUTATED     6   0
  BFAR WILD-TYPE 277  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  BFAR MUTATED      6    0
  BFAR WILD-TYPE  277   48
   clus
vv  BFAR MUTATED BFAR WILD-TYPE
  0            6            277
  1            0             48
[1] 2 2
[1] FALSE
D1677V7, 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
D1677V8, binary
                cls
clus               0   1
  BFAR MUTATED     7   1
  BFAR WILD-TYPE 310  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  BFAR MUTATED      7    1
  BFAR WILD-TYPE  310   47
                               clus
vv                              BFAR MUTATED BFAR WILD-TYPE
  COLON ADENOCARCINOMA                     7            310
  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 253   2  22  18
D1677V9, multiclass
    clus
vv   BFAR MUTATED BFAR WILD-TYPE
  R0            4            253
  R1            0              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"
D1677V10, 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
D1677V11, 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(1678) Variable = ARSF MUTATION ANALYSIS
D1678V1, survival
                sevent
clus2              0   1
  ARSF MUTATED     8   3
  ARSF WILD-TYPE 274  70
  ARSF MUTATED ARSF WILD-TYPE 
            11            344 
  ARSF MUTATED ARSF WILD-TYPE 
             3             70 
$`ARSF MUTATED`
TCGA-A6-6654 TCGA-AA-3516 TCGA-AA-3864 TCGA-AY-5543 TCGA-CM-4752 TCGA-CM-6162 
       23.87        13.02        53.00        15.75        13.02        12.00 
TCGA-D5-5537 TCGA-D5-6922 TCGA-DM-A0XD TCGA-F4-6856 TCGA-G4-6315 
       45.40        10.13        24.43        19.43        36.72 

$`ARSF WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 
        0.20        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-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        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-D5-5538 TCGA-D5-5539 
       11.08        11.01        10.06        12.03        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58         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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       10.26       119.70        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 
       33.67        13.25         0.53        35.41       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  ARSF MUTATED ARSF WILD-TYPE 
         10.13           0.00 
  ARSF MUTATED ARSF WILD-TYPE 
         53.00         140.38 
  ARSF MUTATED ARSF WILD-TYPE 
        19.430         20.235 
[1] "10.1 - 53.0 (19.4)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.4"
D1678V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ARSF MUTATED         1        0        1         3         0         0
  ARSF WILD-TYPE      63        1       24       106         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ARSF MUTATED           1          1          2          0        1         1
  ARSF WILD-TYPE        18          9         39         31       34        12
                vv
clus             STAGE IVB
  ARSF MUTATED           0
  ARSF WILD-TYPE         1
D1678V3, multiclass
            clus
vv           ARSF MUTATED ARSF WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             3            106
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            1              9
  STAGE IIIB            2             39
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ARSF MUTATED     0   1  10   0
  ARSF WILD-TYPE   9  67 238  41
D1678V4, multiclass
    clus
vv   ARSF MUTATED ARSF WILD-TYPE
  T1            0              9
  T2            1             67
  T3           10            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
  ARSF MUTATED     4   5   2
  ARSF WILD-TYPE 216  75  64
D1678V5, multiclass
    clus
vv   ARSF MUTATED ARSF WILD-TYPE
  N0            4            216
  N1            5             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"
D1678V6, binary
                cls
clus               0   1
  ARSF MUTATED     8   2
  ARSF WILD-TYPE 275  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  ARSF MUTATED      8    2
  ARSF WILD-TYPE  275   46
   clus
vv  ARSF MUTATED ARSF WILD-TYPE
  0            8            275
  1            2             46
[1] 2 2
[1] FALSE
D1678V7, binary
                cls
clus               0   1
  ARSF MUTATED     4   7
  ARSF WILD-TYPE 166 190
[1] "tbl2"
                cls
clus             [,1] [,2]
  ARSF MUTATED      4    7
  ARSF WILD-TYPE  166  190
        clus
vv       ARSF MUTATED ARSF WILD-TYPE
  FEMALE            4            166
  MALE              7            190
[1] 2 2
[1] FALSE
D1678V8, binary
                cls
clus               0   1
  ARSF MUTATED     8   3
  ARSF WILD-TYPE 309  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  ARSF MUTATED      8    3
  ARSF WILD-TYPE  309   45
                               clus
vv                              ARSF MUTATED ARSF WILD-TYPE
  COLON ADENOCARCINOMA                     8            309
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ARSF MUTATED     7   0   0   1
  ARSF WILD-TYPE 250   2  22  20
D1678V9, multiclass
    clus
vv   ARSF MUTATED ARSF WILD-TYPE
  R0            7            250
  R1            0              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"
D1678V10, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARSF MUTATED                                  0     0
  ARSF WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ARSF MUTATED                           2     7
  ARSF WILD-TYPE                        17   169
D1678V11, multiclass
                                  clus
vv                                 ARSF MUTATED ARSF 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(1679) Variable = OSBPL5 MUTATION ANALYSIS
D1679V1, survival
                  sevent
clus2                0   1
  OSBPL5 MUTATED    10   4
  OSBPL5 WILD-TYPE 272  69
  OSBPL5 MUTATED OSBPL5 WILD-TYPE 
              14              341 
  OSBPL5 MUTATED OSBPL5 WILD-TYPE 
               4               69 
$`OSBPL5 MUTATED`
TCGA-A6-6781 TCGA-AA-3518 TCGA-AA-3821 TCGA-AA-3930 TCGA-AA-A01R TCGA-AD-6964 
       19.66         1.02         1.02         2.01        35.01        10.88 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-D5-6533 TCGA-D5-6538 TCGA-D5-6898 TCGA-D5-6928 
        6.77       100.01         1.32        17.13         7.53        11.64 
TCGA-G4-6299 TCGA-G4-6586 
       74.56        35.80 

$`OSBPL5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 
       35.05        33.04         0.99        25.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3941 
       27.02        29.98        18.05        31.00        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       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        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       61.41        49.41        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       11.51        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.41        19.43       107.67        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        26.17        91.79        46.75        52.80 

  OSBPL5 MUTATED OSBPL5 WILD-TYPE 
            1.02             0.00 
  OSBPL5 MUTATED OSBPL5 WILD-TYPE 
          100.01           140.38 
  OSBPL5 MUTATED OSBPL5 WILD-TYPE 
           11.26            20.98 
[1] "1.0 - 100.0 (11.3)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.6"
D1679V2, 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       24       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OSBPL5 MUTATED           1          0          2          2        1
  OSBPL5 WILD-TYPE        18         10         39         29       34
                  vv
clus               STAGE IVA STAGE IVB
  OSBPL5 MUTATED           0         0
  OSBPL5 WILD-TYPE        13         1
D1679V3, multiclass
            clus
vv           OSBPL5 MUTATED OSBPL5 WILD-TYPE
  STAGE I                 3               61
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               3              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              2               29
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  OSBPL5 MUTATED     0   3   8   3
  OSBPL5 WILD-TYPE   9  65 240  38
D1679V4, multiclass
    clus
vv   OSBPL5 MUTATED OSBPL5 WILD-TYPE
  T1              0                9
  T2              3               65
  T3              8              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
  OSBPL5 MUTATED     8   1   5
  OSBPL5 WILD-TYPE 212  79  61
D1679V5, multiclass
    clus
vv   OSBPL5 MUTATED OSBPL5 WILD-TYPE
  N0              8              212
  N1              1               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"
D1679V6, binary
                  cls
clus                 0   1
  OSBPL5 MUTATED    10   1
  OSBPL5 WILD-TYPE 273  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OSBPL5 MUTATED     10    1
  OSBPL5 WILD-TYPE  273   47
   clus
vv  OSBPL5 MUTATED OSBPL5 WILD-TYPE
  0             10              273
  1              1               47
[1] 2 2
[1] FALSE
D1679V7, 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
D1679V8, binary
                  cls
clus                 0   1
  OSBPL5 MUTATED    10   4
  OSBPL5 WILD-TYPE 307  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OSBPL5 MUTATED     10    4
  OSBPL5 WILD-TYPE  307   44
                               clus
vv                              OSBPL5 MUTATED OSBPL5 WILD-TYPE
  COLON ADENOCARCINOMA                      10              307
  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 247   2  21  21
D1679V9, multiclass
    clus
vv   OSBPL5 MUTATED OSBPL5 WILD-TYPE
  R0             10              247
  R1              0                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"
D1679V10, 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
D1679V11, 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(1680) Variable = FMO1 MUTATION ANALYSIS
D1680V1, survival
                sevent
clus2              0   1
  FMO1 MUTATED     5   2
  FMO1 WILD-TYPE 277  71
  FMO1 MUTATED FMO1 WILD-TYPE 
             7            348 
  FMO1 MUTATED FMO1 WILD-TYPE 
             2             71 
$`FMO1 MUTATED`
TCGA-AA-3667 TCGA-AA-3837 TCGA-AZ-4315 TCGA-CK-5913 TCGA-CK-5916 TCGA-D5-6928 
       14.01        38.99        58.39        51.32        21.14        11.64 
TCGA-G4-6626 
       46.75 

$`FMO1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3672 TCGA-AA-3673 
        6.05         6.97        54.02         2.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       17.98        15.95        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       40.34        15.62        49.08        21.99         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       22.09        13.78        35.80        26.17        91.79        52.80 

  FMO1 MUTATED FMO1 WILD-TYPE 
         11.64           0.00 
  FMO1 MUTATED FMO1 WILD-TYPE 
         58.39         140.38 
  FMO1 MUTATED FMO1 WILD-TYPE 
         38.99          20.07 
[1] "11.6 - 58.4 (39.0)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1"  
D1680V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FMO1 MUTATED         2        0        0         5         0         0
  FMO1 WILD-TYPE      62        1       25       104         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FMO1 MUTATED           0          0          0          0        0         0
  FMO1 WILD-TYPE        19         10         41         31       35        13
                vv
clus             STAGE IVB
  FMO1 MUTATED           0
  FMO1 WILD-TYPE         1
D1680V3, multiclass
            clus
vv           FMO1 MUTATED FMO1 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             5            104
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  FMO1 MUTATED     1   1   5   0
  FMO1 WILD-TYPE   8  67 243  41
D1680V4, multiclass
    clus
vv   FMO1 MUTATED FMO1 WILD-TYPE
  T1            1              8
  T2            1             67
  T3            5            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
  FMO1 MUTATED     7   0   0
  FMO1 WILD-TYPE 213  80  66
D1680V5, multiclass
    clus
vv   FMO1 MUTATED FMO1 WILD-TYPE
  N0            7            213
  N1            0             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"
D1680V6, binary
                cls
clus               0   1
  FMO1 MUTATED     6   0
  FMO1 WILD-TYPE 277  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  FMO1 MUTATED      6    0
  FMO1 WILD-TYPE  277   48
   clus
vv  FMO1 MUTATED FMO1 WILD-TYPE
  0            6            277
  1            0             48
[1] 2 2
[1] FALSE
D1680V7, binary
                cls
clus               0   1
  FMO1 MUTATED     3   4
  FMO1 WILD-TYPE 167 193
[1] "tbl2"
                cls
clus             [,1] [,2]
  FMO1 MUTATED      3    4
  FMO1 WILD-TYPE  167  193
        clus
vv       FMO1 MUTATED FMO1 WILD-TYPE
  FEMALE            3            167
  MALE              4            193
[1] 2 2
[1] FALSE
D1680V8, binary
                cls
clus               0   1
  FMO1 MUTATED     5   2
  FMO1 WILD-TYPE 312  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  FMO1 MUTATED      5    2
  FMO1 WILD-TYPE  312   46
                               clus
vv                              FMO1 MUTATED FMO1 WILD-TYPE
  COLON ADENOCARCINOMA                     5            312
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  FMO1 MUTATED     5   0   0   2
  FMO1 WILD-TYPE 252   2  22  19
D1680V9, multiclass
    clus
vv   FMO1 MUTATED FMO1 WILD-TYPE
  R0            5            252
  R1            0              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"
D1680V10, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FMO1 MUTATED                                  0     0
  FMO1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  FMO1 MUTATED                           0     5
  FMO1 WILD-TYPE                        19   171
D1680V11, multiclass
                                  clus
vv                                 FMO1 MUTATED FMO1 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(1681) Variable = ZNF286A MUTATION ANALYSIS
D1681V1, survival
                   sevent
clus2                 0   1
  ZNF286A MUTATED     5   1
  ZNF286A WILD-TYPE 277  72
  ZNF286A MUTATED ZNF286A WILD-TYPE 
                6               349 
  ZNF286A MUTATED ZNF286A WILD-TYPE 
                1                72 
$`ZNF286A MUTATED`
TCGA-A6-6141 TCGA-AA-A010 TCGA-AD-5900 TCGA-AZ-4315 TCGA-AZ-6601 TCGA-CA-6717 
        8.38        34.98         0.07        58.39       100.01         0.33 

$`ZNF286A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  ZNF286A MUTATED ZNF286A WILD-TYPE 
             0.07              0.00 
  ZNF286A MUTATED ZNF286A WILD-TYPE 
           100.01            140.38 
  ZNF286A MUTATED ZNF286A WILD-TYPE 
            21.68             20.19 
[1] "0.1 - 100.0 (21.7)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.6"
D1681V2, 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       24       105         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF286A MUTATED           0          0          0          0        0
  ZNF286A WILD-TYPE        19         10         41         31       35
                   vv
clus                STAGE IVA STAGE IVB
  ZNF286A MUTATED           0         0
  ZNF286A WILD-TYPE        13         1
D1681V3, multiclass
            clus
vv           ZNF286A MUTATED ZNF286A WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                4               105
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ZNF286A MUTATED     0   1   5   1
  ZNF286A WILD-TYPE   9  67 243  40
D1681V4, multiclass
    clus
vv   ZNF286A MUTATED ZNF286A WILD-TYPE
  T1               0                 9
  T2               1                67
  T3               5               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
  ZNF286A MUTATED     7   0   0
  ZNF286A WILD-TYPE 213  80  66
D1681V5, multiclass
    clus
vv   ZNF286A MUTATED ZNF286A WILD-TYPE
  N0               7               213
  N1               0                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
  ZNF286A MUTATED     6   0
  ZNF286A WILD-TYPE 277  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF286A MUTATED      6    0
  ZNF286A WILD-TYPE  277   48
   clus
vv  ZNF286A MUTATED ZNF286A WILD-TYPE
  0               6               277
  1               0                48
[1] 2 2
[1] FALSE
D1681V7, 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
D1681V8, binary
                   cls
clus                  0   1
  ZNF286A MUTATED     5   2
  ZNF286A WILD-TYPE 312  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF286A MUTATED      5    2
  ZNF286A WILD-TYPE  312   46
                               clus
vv                              ZNF286A MUTATED ZNF286A WILD-TYPE
  COLON ADENOCARCINOMA                        5               312
  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 253   2  22  20
D1681V9, multiclass
    clus
vv   ZNF286A MUTATED ZNF286A WILD-TYPE
  R0               4               253
  R1               0                 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"
D1681V10, 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
D1681V11, 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(1682) Variable = CCDC66 MUTATION ANALYSIS
D1682V1, survival
                  sevent
clus2                0   1
  CCDC66 MUTATED     6   3
  CCDC66 WILD-TYPE 276  70
  CCDC66 MUTATED CCDC66 WILD-TYPE 
               9              346 
  CCDC66 MUTATED CCDC66 WILD-TYPE 
               3               70 
$`CCDC66 MUTATED`
TCGA-A6-5665 TCGA-AA-3877 TCGA-AA-A02K TCGA-AD-6964 TCGA-CA-6717 TCGA-CA-6718 
       22.06        31.00        14.01        10.88         0.33         0.10 
TCGA-CK-5913 TCGA-D5-6540 TCGA-F4-6570 
       51.32        16.14         6.18 

$`CCDC66 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
       39.98         2.01         5.03         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  CCDC66 MUTATED CCDC66 WILD-TYPE 
             0.1              0.0 
  CCDC66 MUTATED CCDC66 WILD-TYPE 
           51.32           140.38 
  CCDC66 MUTATED CCDC66 WILD-TYPE 
           14.01            20.63 
[1] "0.1 - 51.3 (14.0)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "2.3"
D1682V2, 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       25       104         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC66 MUTATED           0          0          0          0        1
  CCDC66 WILD-TYPE        19         10         41         31       34
                  vv
clus               STAGE IVA STAGE IVB
  CCDC66 MUTATED           0         0
  CCDC66 WILD-TYPE        13         1
D1682V3, multiclass
            clus
vv           CCDC66 MUTATED CCDC66 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               5              104
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CCDC66 MUTATED     1   1   5   2
  CCDC66 WILD-TYPE   8  67 243  39
D1682V4, multiclass
    clus
vv   CCDC66 MUTATED CCDC66 WILD-TYPE
  T1              1                8
  T2              1               67
  T3              5              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
  CCDC66 MUTATED     7   0   2
  CCDC66 WILD-TYPE 213  80  64
D1682V5, multiclass
    clus
vv   CCDC66 MUTATED CCDC66 WILD-TYPE
  N0              7              213
  N1              0               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"
D1682V6, binary
                  cls
clus                 0   1
  CCDC66 MUTATED     6   1
  CCDC66 WILD-TYPE 277  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC66 MUTATED      6    1
  CCDC66 WILD-TYPE  277   47
   clus
vv  CCDC66 MUTATED CCDC66 WILD-TYPE
  0              6              277
  1              1               47
[1] 2 2
[1] FALSE
D1682V7, 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
D1682V8, binary
                  cls
clus                 0   1
  CCDC66 MUTATED     6   3
  CCDC66 WILD-TYPE 311  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC66 MUTATED      6    3
  CCDC66 WILD-TYPE  311   45
                               clus
vv                              CCDC66 MUTATED CCDC66 WILD-TYPE
  COLON ADENOCARCINOMA                       6              311
  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 253   2  21  18
D1682V9, multiclass
    clus
vv   CCDC66 MUTATED CCDC66 WILD-TYPE
  R0              4              253
  R1              0                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"
D1682V10, 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
D1682V11, 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(1683) Variable = NTSR2 MUTATION ANALYSIS
D1683V1, survival
                 sevent
clus2               0   1
  NTSR2 MUTATED     5   3
  NTSR2 WILD-TYPE 277  70
  NTSR2 MUTATED NTSR2 WILD-TYPE 
              8             347 
  NTSR2 MUTATED NTSR2 WILD-TYPE 
              3              70 
$`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         0.33 
TCGA-DM-A1D6 TCGA-G4-6309 
       49.91        51.75 

$`NTSR2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
       17.98        15.95        38.99        37.02        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       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        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        92.75        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  NTSR2 MUTATED NTSR2 WILD-TYPE 
              0               0 
  NTSR2 MUTATED NTSR2 WILD-TYPE 
          53.00          140.38 
  NTSR2 MUTATED NTSR2 WILD-TYPE 
         18.015          20.190 
[1] "0.0 - 53.0 (18.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.8"
D1683V2, 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       22       106         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        19         10         40         31       35        13
                 vv
clus              STAGE IVB
  NTSR2 MUTATED           0
  NTSR2 WILD-TYPE         1
D1683V3, multiclass
            clus
vv           NTSR2 MUTATED NTSR2 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              3             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NTSR2 MUTATED     0   0   7   1
  NTSR2 WILD-TYPE   9  68 241  40
D1683V4, multiclass
    clus
vv   NTSR2 MUTATED NTSR2 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             7             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
  NTSR2 MUTATED     7   1   0
  NTSR2 WILD-TYPE 213  79  66
D1683V5, multiclass
    clus
vv   NTSR2 MUTATED NTSR2 WILD-TYPE
  N0             7             213
  N1             1              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"
D1683V6, binary
                 cls
clus                0   1
  NTSR2 MUTATED     8   0
  NTSR2 WILD-TYPE 275  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTSR2 MUTATED      8    0
  NTSR2 WILD-TYPE  275   48
   clus
vv  NTSR2 MUTATED NTSR2 WILD-TYPE
  0             8             275
  1             0              48
[1] 2 2
[1] FALSE
D1683V7, 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
D1683V8, binary
                 cls
clus                0   1
  NTSR2 MUTATED     5   3
  NTSR2 WILD-TYPE 312  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTSR2 MUTATED      5    3
  NTSR2 WILD-TYPE  312   45
                               clus
vv                              NTSR2 MUTATED NTSR2 WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  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 251   2  22  20
D1683V9, multiclass
    clus
vv   NTSR2 MUTATED NTSR2 WILD-TYPE
  R0             6             251
  R1             0               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"
D1683V10, 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
D1683V11, 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(1684) Variable = XPOT MUTATION ANALYSIS
D1684V1, survival
                sevent
clus2              0   1
  XPOT MUTATED     5   2
  XPOT WILD-TYPE 277  71
  XPOT MUTATED XPOT WILD-TYPE 
             7            348 
  XPOT MUTATED XPOT WILD-TYPE 
             2             71 
$`XPOT MUTATED`
TCGA-AA-A00N TCGA-AA-A00R TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-4947 TCGA-G4-6586 
        4.01         0.99        49.41         0.33        17.56        35.80 
TCGA-G4-6588 
       26.17 

$`XPOT WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W 
       18.05        38.04        27.02        42.02        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13        83.80        22.36        62.79        61.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.26         0.10         1.35       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       36.00        22.09        13.78        91.79        46.75        52.80 

  XPOT MUTATED XPOT WILD-TYPE 
          0.33           0.00 
  XPOT MUTATED XPOT WILD-TYPE 
         49.41         140.38 
  XPOT MUTATED XPOT WILD-TYPE 
        17.560         20.235 
[1] "0.3 - 49.4 (17.6)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.9"
D1684V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  XPOT MUTATED         1        0        1         4         1         0
  XPOT WILD-TYPE      63        1       24       105         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  XPOT MUTATED           0          0          0          0        0         1
  XPOT WILD-TYPE        19         10         41         31       35        12
                vv
clus             STAGE IVB
  XPOT MUTATED           0
  XPOT WILD-TYPE         1
D1684V3, multiclass
            clus
vv           XPOT MUTATED XPOT WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             4            105
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  XPOT MUTATED     0   1   5   2
  XPOT WILD-TYPE   9  67 243  39
D1684V4, multiclass
    clus
vv   XPOT MUTATED XPOT WILD-TYPE
  T1            0              9
  T2            1             67
  T3            5            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
  XPOT MUTATED     7   1   0
  XPOT WILD-TYPE 213  79  66
D1684V5, multiclass
    clus
vv   XPOT MUTATED XPOT WILD-TYPE
  N0            7            213
  N1            1             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"
D1684V6, binary
                cls
clus               0   1
  XPOT MUTATED     7   0
  XPOT WILD-TYPE 276  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  XPOT MUTATED      7    0
  XPOT WILD-TYPE  276   48
   clus
vv  XPOT MUTATED XPOT WILD-TYPE
  0            7            276
  1            0             48
[1] 2 2
[1] FALSE
D1684V7, binary
                cls
clus               0   1
  XPOT MUTATED     6   2
  XPOT WILD-TYPE 164 195
[1] "tbl2"
                cls
clus             [,1] [,2]
  XPOT MUTATED      6    2
  XPOT WILD-TYPE  164  195
        clus
vv       XPOT MUTATED XPOT WILD-TYPE
  FEMALE            6            164
  MALE              2            195
[1] 2 2
[1] FALSE
D1684V8, binary
                cls
clus               0   1
  XPOT MUTATED     6   2
  XPOT WILD-TYPE 311  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  XPOT MUTATED      6    2
  XPOT WILD-TYPE  311   46
                               clus
vv                              XPOT MUTATED XPOT WILD-TYPE
  COLON ADENOCARCINOMA                     6            311
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  XPOT MUTATED     5   0   0   2
  XPOT WILD-TYPE 252   2  22  19
D1684V9, multiclass
    clus
vv   XPOT MUTATED XPOT WILD-TYPE
  R0            5            252
  R1            0              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"
D1684V10, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XPOT MUTATED                                  0     1
  XPOT WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  XPOT MUTATED                           0     4
  XPOT WILD-TYPE                        19   172
D1684V11, multiclass
                                  clus
vv                                 XPOT MUTATED XPOT 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(1685) Variable = SORBS1 MUTATION ANALYSIS
D1685V1, survival
                  sevent
clus2                0   1
  SORBS1 MUTATED     8   1
  SORBS1 WILD-TYPE 274  72
  SORBS1 MUTATED SORBS1 WILD-TYPE 
               9              346 
  SORBS1 MUTATED SORBS1 WILD-TYPE 
               1               72 
$`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 
       56.55        21.44        58.39 

$`SORBS1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       43.76        43.76        24.33        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       33.34        32.75        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03         2.01        21.99        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        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        15.75         0.20        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  SORBS1 MUTATED SORBS1 WILD-TYPE 
           16.08             0.00 
  SORBS1 MUTATED SORBS1 WILD-TYPE 
           58.39           140.38 
  SORBS1 MUTATED SORBS1 WILD-TYPE 
          34.980           20.005 
[1] "16.1 - 58.4 (35.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "2.6"
D1685V2, 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       25       106         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SORBS1 MUTATED           1          0          2          0        0
  SORBS1 WILD-TYPE        18         10         39         31       35
                  vv
clus               STAGE IVA STAGE IVB
  SORBS1 MUTATED           0         0
  SORBS1 WILD-TYPE        13         1
D1685V3, multiclass
            clus
vv           SORBS1 MUTATED SORBS1 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               3              106
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SORBS1 MUTATED     0   2   5   3
  SORBS1 WILD-TYPE   9  66 243  38
D1685V4, multiclass
    clus
vv   SORBS1 MUTATED SORBS1 WILD-TYPE
  T1              0                9
  T2              2               66
  T3              5              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
  SORBS1 MUTATED     7   3   0
  SORBS1 WILD-TYPE 213  77  66
D1685V5, multiclass
    clus
vv   SORBS1 MUTATED SORBS1 WILD-TYPE
  N0              7              213
  N1              3               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"
D1685V6, binary
                  cls
clus                 0   1
  SORBS1 MUTATED     7   0
  SORBS1 WILD-TYPE 276  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SORBS1 MUTATED      7    0
  SORBS1 WILD-TYPE  276   48
   clus
vv  SORBS1 MUTATED SORBS1 WILD-TYPE
  0              7              276
  1              0               48
[1] 2 2
[1] FALSE
D1685V7, 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
D1685V8, binary
                  cls
clus                 0   1
  SORBS1 MUTATED     9   1
  SORBS1 WILD-TYPE 308  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SORBS1 MUTATED      9    1
  SORBS1 WILD-TYPE  308   47
                               clus
vv                              SORBS1 MUTATED SORBS1 WILD-TYPE
  COLON ADENOCARCINOMA                       9              308
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SORBS1 MUTATED     7   0   0   1
  SORBS1 WILD-TYPE 250   2  22  20
D1685V9, multiclass
    clus
vv   SORBS1 MUTATED SORBS1 WILD-TYPE
  R0              7              250
  R1              0                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"
D1685V10, 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
D1685V11, 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(1686) Variable = MACROD1 MUTATION ANALYSIS
D1686V1, survival
                   sevent
clus2                 0   1
  MACROD1 MUTATED     2   1
  MACROD1 WILD-TYPE 280  72
  MACROD1 MUTATED MACROD1 WILD-TYPE 
                3               352 
  MACROD1 MUTATED MACROD1 WILD-TYPE 
                1                72 
$`MACROD1 MUTATED`
TCGA-AA-3492 TCGA-F4-6460 TCGA-G4-6586 
        3.02        13.38        35.80 

$`MACROD1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  MACROD1 MUTATED MACROD1 WILD-TYPE 
             3.02              0.00 
  MACROD1 MUTATED MACROD1 WILD-TYPE 
            35.80            140.38 
  MACROD1 MUTATED MACROD1 WILD-TYPE 
           13.380            20.235 
[1] "3.0 - 35.8 (13.4)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2.6"
D1686V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MACROD1 MUTATED         0        0        1         1         0         0
  MACROD1 WILD-TYPE      64        1       24       108         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MACROD1 MUTATED           0          0          1          0        0
  MACROD1 WILD-TYPE        19         10         40         31       35
                   vv
clus                STAGE IVA STAGE IVB
  MACROD1 MUTATED           0         0
  MACROD1 WILD-TYPE        13         1
D1686V3, multiclass
            clus
vv           MACROD1 MUTATED MACROD1 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                1               108
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  MACROD1 MUTATED     0   0   3   0
  MACROD1 WILD-TYPE   9  68 245  41
D1686V4, multiclass
    clus
vv   MACROD1 MUTATED MACROD1 WILD-TYPE
  T1               0                 9
  T2               0                68
  T3               3               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
  MACROD1 MUTATED     2   1   0
  MACROD1 WILD-TYPE 218  79  66
D1686V5, multiclass
    clus
vv   MACROD1 MUTATED MACROD1 WILD-TYPE
  N0               2               218
  N1               1                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"
D1686V6, binary
                   cls
clus                  0   1
  MACROD1 MUTATED     3   0
  MACROD1 WILD-TYPE 280  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MACROD1 MUTATED      3    0
  MACROD1 WILD-TYPE  280   48
   clus
vv  MACROD1 MUTATED MACROD1 WILD-TYPE
  0               3               280
  1               0                48
[1] 2 2
[1] FALSE
D1686V7, binary
                   cls
clus                  0   1
  MACROD1 MUTATED     3   0
  MACROD1 WILD-TYPE 167 197
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MACROD1 MUTATED      3    0
  MACROD1 WILD-TYPE  167  197
        clus
vv       MACROD1 MUTATED MACROD1 WILD-TYPE
  FEMALE               3               167
  MALE                 0               197
[1] 2 2
[1] FALSE
D1686V8, binary
                   cls
clus                  0   1
  MACROD1 MUTATED     3   0
  MACROD1 WILD-TYPE 314  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MACROD1 MUTATED      3    0
  MACROD1 WILD-TYPE  314   48
                               clus
vv                              MACROD1 MUTATED MACROD1 WILD-TYPE
  COLON ADENOCARCINOMA                        3               314
  COLON MUCINOUS ADENOCARCINOMA               0                48
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  MACROD1 MUTATED     3   0   0   0
  MACROD1 WILD-TYPE 254   2  22  21
D1686V9, multiclass
    clus
vv   MACROD1 MUTATED MACROD1 WILD-TYPE
  R0               3               254
  R1               0                 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"
D1686V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MACROD1 MUTATED                                  0     0
  MACROD1 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  MACROD1 MUTATED                           0     2
  MACROD1 WILD-TYPE                        19   174
D1686V11, multiclass
[1] "Remove cluster labels:" "MACROD1 MUTATED"       
clus
  MACROD1 MUTATED MACROD1 WILD-TYPE 
                2               204 
       TCGA-A6-2671        TCGA-A6-2672        TCGA-A6-2674        TCGA-A6-2676 
"MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" 
       TCGA-A6-2677        TCGA-A6-2678        TCGA-A6-2683        TCGA-A6-3807 
"MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" 
       TCGA-A6-3808        TCGA-A6-3809        TCGA-A6-3810        TCGA-A6-4105 
"MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" 
       TCGA-A6-5656        TCGA-A6-5657        TCGA-A6-5659        TCGA-A6-5660 
"MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" 
       TCGA-A6-5661        TCGA-A6-5662        TCGA-A6-5664        TCGA-A6-5665 
"MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" 
       TCGA-A6-5666        TCGA-A6-6137        TCGA-A6-6138        TCGA-A6-6141 
"MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" 
       TCGA-A6-6142        TCGA-A6-6648        TCGA-A6-6649        TCGA-A6-6651 
"MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" 
       TCGA-A6-6652        TCGA-A6-6653        TCGA-A6-6654        TCGA-A6-6780 
"MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" 
       TCGA-A6-6781        TCGA-A6-6782        TCGA-AD-5900        TCGA-AD-6548 
"MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" 
       TCGA-AD-6888        TCGA-AD-6889        TCGA-AD-6890        TCGA-AD-6895 
"MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" 
       TCGA-AD-6899        TCGA-AD-6901        TCGA-AD-6963        TCGA-AD-6964 
"MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" 
       TCGA-AD-6965        TCGA-AU-3779        TCGA-AU-6004        TCGA-AY-4070 
"MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" 
       TCGA-AY-4071        TCGA-AY-5543        TCGA-AY-6196        TCGA-AY-6197 
"MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" 
       TCGA-AY-6386        TCGA-AZ-4315        TCGA-AZ-4323        TCGA-AZ-4616 
"MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" 
       TCGA-AZ-4681        TCGA-AZ-4682        TCGA-AZ-5403        TCGA-AZ-5407 
"MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" 
       TCGA-AZ-6598        TCGA-AZ-6599        TCGA-AZ-6600        TCGA-AZ-6601 
"MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" 
       TCGA-AZ-6603        TCGA-AZ-6605        TCGA-AZ-6606        TCGA-AZ-6607 
"MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" 
       TCGA-AZ-6608        TCGA-CA-5254        TCGA-CA-5255        TCGA-CA-5796 
"MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" 
       TCGA-CA-5797        TCGA-CA-6715        TCGA-CA-6716        TCGA-CA-6717 
"MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" 
       TCGA-CA-6718        TCGA-CA-6719        TCGA-CK-4947        TCGA-CK-4948 
"MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" 
       TCGA-CK-4950        TCGA-CK-4952        TCGA-CK-5912        TCGA-CK-5913 
"MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" 
       TCGA-CK-5914        TCGA-CK-5915        TCGA-CK-5916        TCGA-CK-6746 
"MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" 
       TCGA-CK-6747        TCGA-CK-6748        TCGA-CK-6751        TCGA-CM-4743 
"MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" 
       TCGA-CM-4744        TCGA-CM-4746        TCGA-CM-4747        TCGA-CM-4752 
"MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" 
       TCGA-CM-5341        TCGA-CM-5344        TCGA-CM-5348        TCGA-CM-5349 
"MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" 
       TCGA-CM-5860        TCGA-CM-5861        TCGA-CM-5862        TCGA-CM-5863 
"MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" 
       TCGA-CM-5864        TCGA-CM-5868        TCGA-CM-6161        TCGA-CM-6162 
"MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" 
       TCGA-CM-6163        TCGA-CM-6164        TCGA-CM-6165        TCGA-CM-6166 
"MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" 
       TCGA-CM-6167        TCGA-CM-6168        TCGA-CM-6169        TCGA-CM-6170 
"MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" 
       TCGA-CM-6171        TCGA-CM-6172        TCGA-CM-6674        TCGA-CM-6675 
"MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" 
       TCGA-CM-6676        TCGA-CM-6677        TCGA-CM-6678        TCGA-CM-6679 
"MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" 
       TCGA-CM-6680        TCGA-D5-5537        TCGA-D5-5538        TCGA-D5-5539 
"MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" 
       TCGA-D5-5540        TCGA-D5-5541        TCGA-D5-6529        TCGA-D5-6532 
"MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" 
       TCGA-D5-6533        TCGA-D5-6534        TCGA-D5-6535        TCGA-D5-6536 
"MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" 
       TCGA-D5-6537        TCGA-D5-6538        TCGA-D5-6539        TCGA-D5-6540 
"MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" 
       TCGA-D5-6541        TCGA-D5-6898        TCGA-D5-6920        TCGA-D5-6922 
"MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" 
       TCGA-D5-6923        TCGA-D5-6924        TCGA-D5-6926        TCGA-D5-6927 
"MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" 
       TCGA-D5-6928        TCGA-D5-6929        TCGA-D5-6930        TCGA-D5-6931 
"MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" 
       TCGA-D5-6932        TCGA-D5-7000        TCGA-DM-A0X9        TCGA-DM-A0XD 
"MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" 
       TCGA-DM-A0XF        TCGA-DM-A1D0        TCGA-DM-A1D4        TCGA-DM-A1D6 
"MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" 
       TCGA-DM-A1D7        TCGA-DM-A1D8        TCGA-DM-A1D9        TCGA-DM-A1DA 
"MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" 
       TCGA-DM-A1DB        TCGA-DM-A1HA        TCGA-DM-A1HB        TCGA-DM-A282 
"MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" 
       TCGA-DM-A285        TCGA-DM-A28C        TCGA-DM-A28E        TCGA-DM-A28F 
"MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" 
       TCGA-DM-A28G        TCGA-DM-A28H        TCGA-DM-A28K        TCGA-F4-6459 
"MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" 
       TCGA-F4-6569        TCGA-F4-6570        TCGA-F4-6703        TCGA-F4-6704 
"MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" 
       TCGA-F4-6805        TCGA-F4-6806        TCGA-F4-6807        TCGA-F4-6808 
"MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" 
       TCGA-F4-6809        TCGA-F4-6854        TCGA-F4-6855        TCGA-F4-6856 
"MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" 
       TCGA-G4-6293        TCGA-G4-6299        TCGA-G4-6303        TCGA-G4-6304 
"MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" 
       TCGA-G4-6306        TCGA-G4-6307        TCGA-G4-6309        TCGA-G4-6310 
"MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" 
       TCGA-G4-6315        TCGA-G4-6317        TCGA-G4-6321        TCGA-G4-6323 
"MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" 
       TCGA-G4-6588        TCGA-G4-6625        TCGA-G4-6626        TCGA-G4-6628 
"MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" "MACROD1 WILD-TYPE" 

Clustering(1687) Variable = CAPSL MUTATION ANALYSIS
D1687V1, survival
                 sevent
clus2               0   1
  CAPSL MUTATED     5   2
  CAPSL WILD-TYPE 277  71
  CAPSL MUTATED CAPSL WILD-TYPE 
              7             348 
  CAPSL MUTATED CAPSL WILD-TYPE 
              2              71 
$`CAPSL MUTATED`
TCGA-AA-3510 TCGA-AA-3672 TCGA-AA-3697 TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-6606 
       63.98         0.92        85.05         4.01        34.98        11.74 
TCGA-CA-6717 
        0.33 

$`CAPSL WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  CAPSL MUTATED CAPSL WILD-TYPE 
           0.33            0.00 
  CAPSL MUTATED CAPSL WILD-TYPE 
          85.05          140.38 
  CAPSL MUTATED CAPSL WILD-TYPE 
         11.740          20.235 
[1] "0.3 - 85.0 (11.7)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.3"
D1687V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CAPSL MUTATED         0        0        1         1         2         0
  CAPSL WILD-TYPE      64        1       24       108         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CAPSL MUTATED           2          0          0          0        1         0
  CAPSL WILD-TYPE        17         10         41         31       34        13
                 vv
clus              STAGE IVB
  CAPSL MUTATED           0
  CAPSL WILD-TYPE         1
D1687V3, multiclass
            clus
vv           CAPSL MUTATED CAPSL WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              1             108
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CAPSL MUTATED     0   0   4   3
  CAPSL WILD-TYPE   9  68 244  38
D1687V4, multiclass
    clus
vv   CAPSL MUTATED CAPSL WILD-TYPE
  T1             0               9
  T2             0              68
  T3             4             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
  CAPSL MUTATED     5   1   1
  CAPSL WILD-TYPE 215  79  65
D1687V5, multiclass
    clus
vv   CAPSL MUTATED CAPSL WILD-TYPE
  N0             5             215
  N1             1              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"
D1687V6, binary
                 cls
clus                0   1
  CAPSL MUTATED     6   1
  CAPSL WILD-TYPE 277  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CAPSL MUTATED      6    1
  CAPSL WILD-TYPE  277   47
   clus
vv  CAPSL MUTATED CAPSL WILD-TYPE
  0             6             277
  1             1              47
[1] 2 2
[1] FALSE
D1687V7, binary
                 cls
clus                0   1
  CAPSL MUTATED     2   5
  CAPSL WILD-TYPE 168 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CAPSL MUTATED      2    5
  CAPSL WILD-TYPE  168  192
        clus
vv       CAPSL MUTATED CAPSL WILD-TYPE
  FEMALE             2             168
  MALE               5             192
[1] 2 2
[1] FALSE
D1687V8, binary
                 cls
clus                0   1
  CAPSL MUTATED     5   2
  CAPSL WILD-TYPE 312  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CAPSL MUTATED      5    2
  CAPSL WILD-TYPE  312   46
                               clus
vv                              CAPSL MUTATED CAPSL WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CAPSL MUTATED     5   0   0   1
  CAPSL WILD-TYPE 252   2  22  20
D1687V9, multiclass
    clus
vv   CAPSL MUTATED CAPSL WILD-TYPE
  R0             5             252
  R1             0               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"
D1687V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CAPSL MUTATED                                  0     1
  CAPSL WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CAPSL MUTATED                           0     1
  CAPSL WILD-TYPE                        19   175
D1687V11, multiclass
[1] "Remove cluster labels:" "CAPSL MUTATED"         
clus
  CAPSL MUTATED CAPSL WILD-TYPE 
              2             204 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-4105 
"CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" 
     TCGA-A6-5656      TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5660 
"CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" 
     TCGA-A6-5661      TCGA-A6-5662      TCGA-A6-5664      TCGA-A6-5665 
"CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" 
     TCGA-A6-5666      TCGA-A6-6137      TCGA-A6-6138      TCGA-A6-6141 
"CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" 
     TCGA-A6-6142      TCGA-A6-6648      TCGA-A6-6649      TCGA-A6-6651 
"CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" 
     TCGA-A6-6652      TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780 
"CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" 
     TCGA-A6-6781      TCGA-A6-6782      TCGA-AD-5900      TCGA-AD-6548 
"CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" 
     TCGA-AD-6888      TCGA-AD-6889      TCGA-AD-6890      TCGA-AD-6895 
"CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" 
     TCGA-AD-6899      TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6964 
"CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" 
     TCGA-AD-6965      TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070 
"CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" 
     TCGA-AY-4071      TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197 
"CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" 
     TCGA-AY-6386      TCGA-AZ-4315      TCGA-AZ-4323      TCGA-AZ-4616 
"CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" 
     TCGA-AZ-4681      TCGA-AZ-4682      TCGA-AZ-5403      TCGA-AZ-5407 
"CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" 
     TCGA-AZ-6598      TCGA-AZ-6599      TCGA-AZ-6600      TCGA-AZ-6601 
"CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" 
     TCGA-AZ-6603      TCGA-AZ-6605      TCGA-AZ-6607      TCGA-AZ-6608 
"CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" 
     TCGA-CA-5254      TCGA-CA-5255      TCGA-CA-5796      TCGA-CA-5797 
"CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" 
     TCGA-CA-6715      TCGA-CA-6716      TCGA-CA-6718      TCGA-CA-6719 
"CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" 
     TCGA-CK-4947      TCGA-CK-4948      TCGA-CK-4950      TCGA-CK-4952 
"CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" 
     TCGA-CK-5912      TCGA-CK-5913      TCGA-CK-5914      TCGA-CK-5915 
"CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" 
     TCGA-CK-5916      TCGA-CK-6746      TCGA-CK-6747      TCGA-CK-6748 
"CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" 
     TCGA-CK-6751      TCGA-CM-4743      TCGA-CM-4744      TCGA-CM-4746 
"CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" 
     TCGA-CM-4747      TCGA-CM-4752      TCGA-CM-5341      TCGA-CM-5344 
"CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" 
     TCGA-CM-5348      TCGA-CM-5349      TCGA-CM-5860      TCGA-CM-5861 
"CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" 
     TCGA-CM-5862      TCGA-CM-5863      TCGA-CM-5864      TCGA-CM-5868 
"CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" 
     TCGA-CM-6161      TCGA-CM-6162      TCGA-CM-6163      TCGA-CM-6164 
"CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" 
     TCGA-CM-6165      TCGA-CM-6166      TCGA-CM-6167      TCGA-CM-6168 
"CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" 
     TCGA-CM-6169      TCGA-CM-6170      TCGA-CM-6171      TCGA-CM-6172 
"CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" 
     TCGA-CM-6674      TCGA-CM-6675      TCGA-CM-6676      TCGA-CM-6677 
"CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" 
     TCGA-CM-6678      TCGA-CM-6679      TCGA-CM-6680      TCGA-D5-5537 
"CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" 
     TCGA-D5-5538      TCGA-D5-5539      TCGA-D5-5540      TCGA-D5-5541 
"CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" 
     TCGA-D5-6529      TCGA-D5-6532      TCGA-D5-6533      TCGA-D5-6534 
"CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" 
     TCGA-D5-6535      TCGA-D5-6536      TCGA-D5-6537      TCGA-D5-6538 
"CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" 
     TCGA-D5-6539      TCGA-D5-6540      TCGA-D5-6541      TCGA-D5-6898 
"CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" 
     TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923      TCGA-D5-6924 
"CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" 
     TCGA-D5-6926      TCGA-D5-6927      TCGA-D5-6928      TCGA-D5-6929 
"CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" 
     TCGA-D5-6930      TCGA-D5-6931      TCGA-D5-6932      TCGA-D5-7000 
"CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" 
     TCGA-DM-A0X9      TCGA-DM-A0XD      TCGA-DM-A0XF      TCGA-DM-A1D0 
"CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" 
     TCGA-DM-A1D4      TCGA-DM-A1D6      TCGA-DM-A1D7      TCGA-DM-A1D8 
"CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" 
     TCGA-DM-A1D9      TCGA-DM-A1DA      TCGA-DM-A1DB      TCGA-DM-A1HA 
"CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" 
     TCGA-DM-A1HB      TCGA-DM-A282      TCGA-DM-A285      TCGA-DM-A28C 
"CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" 
     TCGA-DM-A28E      TCGA-DM-A28F      TCGA-DM-A28G      TCGA-DM-A28H 
"CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" 
     TCGA-DM-A28K      TCGA-F4-6459      TCGA-F4-6460      TCGA-F4-6569 
"CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" 
     TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704      TCGA-F4-6805 
"CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" 
     TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808      TCGA-F4-6809 
"CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" 
     TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856      TCGA-G4-6293 
"CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" 
     TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304      TCGA-G4-6306 
"CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" 
     TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310      TCGA-G4-6315 
"CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" 
     TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323      TCGA-G4-6586 
"CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" 
     TCGA-G4-6588      TCGA-G4-6625      TCGA-G4-6626      TCGA-G4-6628 
"CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" "CAPSL WILD-TYPE" 

Clustering(1688) Variable = FAM55C MUTATION ANALYSIS
D1688V1, survival
                  sevent
clus2                0   1
  FAM55C MUTATED     5   1
  FAM55C WILD-TYPE 277  72
  FAM55C MUTATED FAM55C WILD-TYPE 
               6              349 
  FAM55C MUTATED FAM55C WILD-TYPE 
               1               72 
$`FAM55C MUTATED`
TCGA-A6-5661 TCGA-AA-3710 TCGA-AA-3715 TCGA-CM-5348 TCGA-D5-5541 TCGA-D5-6930 
       33.53        26.99        19.04        22.98        11.51         1.51 

$`FAM55C WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
       36.00         5.03        85.05        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  FAM55C MUTATED FAM55C WILD-TYPE 
            1.51             0.00 
  FAM55C MUTATED FAM55C WILD-TYPE 
           33.53           140.38 
  FAM55C MUTATED FAM55C WILD-TYPE 
           21.01            20.19 
[1] "1.5 - 33.5 (21.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D1688V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FAM55C MUTATED         0        0        1         3         0         0
  FAM55C WILD-TYPE      64        1       24       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM55C MUTATED           0          0          2          0        0
  FAM55C WILD-TYPE        19         10         39         31       35
                  vv
clus               STAGE IVA STAGE IVB
  FAM55C MUTATED           0         0
  FAM55C WILD-TYPE        13         1
D1688V3, multiclass
            clus
vv           FAM55C MUTATED FAM55C WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               3              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FAM55C MUTATED     0   0   6   0
  FAM55C WILD-TYPE   9  68 242  41
D1688V4, multiclass
    clus
vv   FAM55C MUTATED FAM55C WILD-TYPE
  T1              0                9
  T2              0               68
  T3              6              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
  FAM55C MUTATED     4   2   0
  FAM55C WILD-TYPE 216  78  66
D1688V5, multiclass
    clus
vv   FAM55C MUTATED FAM55C WILD-TYPE
  N0              4              216
  N1              2               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"
D1688V6, binary
                  cls
clus                 0   1
  FAM55C MUTATED     6   0
  FAM55C WILD-TYPE 277  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM55C MUTATED      6    0
  FAM55C WILD-TYPE  277   48
   clus
vv  FAM55C MUTATED FAM55C WILD-TYPE
  0              6              277
  1              0               48
[1] 2 2
[1] FALSE
D1688V7, binary
                  cls
clus                 0   1
  FAM55C MUTATED     2   4
  FAM55C WILD-TYPE 168 193
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM55C MUTATED      2    4
  FAM55C WILD-TYPE  168  193
        clus
vv       FAM55C MUTATED FAM55C WILD-TYPE
  FEMALE              2              168
  MALE                4              193
[1] 2 2
[1] FALSE
D1688V8, binary
                  cls
clus                 0   1
  FAM55C MUTATED     5   1
  FAM55C WILD-TYPE 312  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM55C MUTATED      5    1
  FAM55C WILD-TYPE  312   47
                               clus
vv                              FAM55C MUTATED FAM55C WILD-TYPE
  COLON ADENOCARCINOMA                       5              312
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  FAM55C MUTATED     6   0   0   0
  FAM55C WILD-TYPE 251   2  22  21
D1688V9, multiclass
    clus
vv   FAM55C MUTATED FAM55C WILD-TYPE
  R0              6              251
  R1              0                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"
D1688V10, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM55C MUTATED                                  0     0
  FAM55C WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  FAM55C MUTATED                           1     3
  FAM55C WILD-TYPE                        18   173
D1688V11, multiclass
                                  clus
vv                                 FAM55C MUTATED FAM55C 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(1689) Variable = TXNRD1 MUTATION ANALYSIS
D1689V1, survival
                  sevent
clus2                0   1
  TXNRD1 MUTATED     5   3
  TXNRD1 WILD-TYPE 277  70
  TXNRD1 MUTATED TXNRD1 WILD-TYPE 
               8              347 
  TXNRD1 MUTATED TXNRD1 WILD-TYPE 
               3               70 
$`TXNRD1 MUTATED`
TCGA-AA-3977 TCGA-AA-A00N TCGA-AD-5900 TCGA-AD-6964 TCGA-CA-6717 TCGA-CA-6718 
       25.02         4.01         0.07        10.88         0.33         0.10 
TCGA-DM-A0XF TCGA-G4-6628 
       38.20        52.80 

$`TXNRD1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 
       12.00        11.38        10.26       119.70        24.43       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       13.78        35.80        26.17        91.79        46.75 

  TXNRD1 MUTATED TXNRD1 WILD-TYPE 
            0.07             0.00 
  TXNRD1 MUTATED TXNRD1 WILD-TYPE 
           52.80           140.38 
  TXNRD1 MUTATED TXNRD1 WILD-TYPE 
           7.445           20.280 
[1] "0.1 - 52.8 (7.4)"   "0.0 - 140.4 (20.3)"
[1] "hr=" "2.8"
D1689V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TXNRD1 MUTATED         2        0        0         2         1         0
  TXNRD1 WILD-TYPE      62        1       25       107         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TXNRD1 MUTATED           0          0          0          1        0
  TXNRD1 WILD-TYPE        19         10         41         30       35
                  vv
clus               STAGE IVA STAGE IVB
  TXNRD1 MUTATED           0         0
  TXNRD1 WILD-TYPE        13         1
D1689V3, multiclass
            clus
vv           TXNRD1 MUTATED TXNRD1 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               2              107
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TXNRD1 MUTATED     0   3   3   2
  TXNRD1 WILD-TYPE   9  65 245  39
D1689V4, multiclass
    clus
vv   TXNRD1 MUTATED TXNRD1 WILD-TYPE
  T1              0                9
  T2              3               65
  T3              3              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
  TXNRD1 MUTATED     6   0   2
  TXNRD1 WILD-TYPE 214  80  64
D1689V5, multiclass
    clus
vv   TXNRD1 MUTATED TXNRD1 WILD-TYPE
  N0              6              214
  N1              0               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"
D1689V6, binary
                  cls
clus                 0   1
  TXNRD1 MUTATED     5   0
  TXNRD1 WILD-TYPE 278  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TXNRD1 MUTATED      5    0
  TXNRD1 WILD-TYPE  278   48
   clus
vv  TXNRD1 MUTATED TXNRD1 WILD-TYPE
  0              5              278
  1              0               48
[1] 2 2
[1] FALSE
D1689V7, binary
                  cls
clus                 0   1
  TXNRD1 MUTATED     1   7
  TXNRD1 WILD-TYPE 169 190
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TXNRD1 MUTATED      1    7
  TXNRD1 WILD-TYPE  169  190
        clus
vv       TXNRD1 MUTATED TXNRD1 WILD-TYPE
  FEMALE              1              169
  MALE                7              190
[1] 2 2
[1] FALSE
D1689V8, binary
                  cls
clus                 0   1
  TXNRD1 MUTATED     4   4
  TXNRD1 WILD-TYPE 313  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TXNRD1 MUTATED      4    4
  TXNRD1 WILD-TYPE  313   44
                               clus
vv                              TXNRD1 MUTATED TXNRD1 WILD-TYPE
  COLON ADENOCARCINOMA                       4              313
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TXNRD1 MUTATED     3   0   0   2
  TXNRD1 WILD-TYPE 254   2  22  19
D1689V9, multiclass
    clus
vv   TXNRD1 MUTATED TXNRD1 WILD-TYPE
  R0              3              254
  R1              0                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"
D1689V10, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TXNRD1 MUTATED                                  0     2
  TXNRD1 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TXNRD1 MUTATED                           0     4
  TXNRD1 WILD-TYPE                        19   172
D1689V11, multiclass
                                  clus
vv                                 TXNRD1 MUTATED TXNRD1 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(1690) Variable = UST MUTATION ANALYSIS
D1690V1, survival
               sevent
clus2             0   1
  UST MUTATED     8   1
  UST WILD-TYPE 274  72
  UST MUTATED UST WILD-TYPE 
            9           346 
  UST MUTATED UST WILD-TYPE 
            1            72 
$`UST MUTATED`
TCGA-A6-6141 TCGA-AA-3510 TCGA-AA-3955 TCGA-AD-5900 TCGA-AZ-6600 TCGA-D5-5539 
        8.38        63.98        20.98         0.07        12.10        19.59 
TCGA-D5-6535 TCGA-DM-A1HB TCGA-G4-6317 
       15.12       135.65        36.00 

$`UST WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 
       22.36        62.79        61.41        49.41         6.77       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       51.75        45.11        36.72        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  UST MUTATED UST WILD-TYPE 
         0.07          0.00 
  UST MUTATED UST WILD-TYPE 
       135.65        140.38 
  UST MUTATED UST WILD-TYPE 
       19.590        20.235 
[1] "0.1 - 135.7 (19.6)" "0.0 - 140.4 (20.2)"
[1] "hr=" "2.3"
D1690V2, 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       24       108         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        19          9         38         30       34        13
               vv
clus            STAGE IVB
  UST MUTATED           0
  UST WILD-TYPE         1
D1690V3, multiclass
            clus
vv           UST MUTATED UST WILD-TYPE
  STAGE I              1            63
  STAGE IA             0             1
  STAGE II             1            24
  STAGE IIA            1           108
  STAGE IIB            0             8
  STAGE IIC            0             1
  STAGE III            0            19
  STAGE IIIA           1             9
  STAGE IIIB           3            38
  STAGE IIIC           1            30
  STAGE IV             1            34
  STAGE IVA            0            13
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  UST MUTATED     0   2   6   1
  UST WILD-TYPE   9  66 242  40
D1690V4, multiclass
    clus
vv   UST MUTATED UST WILD-TYPE
  T1           0             9
  T2           2            66
  T3           6           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
  UST MUTATED     3   4   2
  UST WILD-TYPE 217  76  64
D1690V5, multiclass
    clus
vv   UST MUTATED UST WILD-TYPE
  N0           3           217
  N1           4            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"
D1690V6, binary
               cls
clus              0   1
  UST MUTATED     5   1
  UST WILD-TYPE 278  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  UST MUTATED      5    1
  UST WILD-TYPE  278   47
   clus
vv  UST MUTATED UST WILD-TYPE
  0           5           278
  1           1            47
[1] 2 2
[1] FALSE
D1690V7, 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
D1690V8, binary
               cls
clus              0   1
  UST MUTATED     7   2
  UST WILD-TYPE 310  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  UST MUTATED      7    2
  UST WILD-TYPE  310   46
                               clus
vv                              UST MUTATED UST WILD-TYPE
  COLON ADENOCARCINOMA                    7           310
  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 252   2  22  20
D1690V9, multiclass
    clus
vv   UST MUTATED UST WILD-TYPE
  R0           5           252
  R1           0             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"
D1690V10, 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
D1690V11, 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(1691) Variable = KCNJ16 MUTATION ANALYSIS
D1691V1, survival
                  sevent
clus2                0   1
  KCNJ16 MUTATED     5   1
  KCNJ16 WILD-TYPE 277  72
  KCNJ16 MUTATED KCNJ16 WILD-TYPE 
               6              349 
  KCNJ16 MUTATED KCNJ16 WILD-TYPE 
               1               72 
$`KCNJ16 MUTATED`
TCGA-AA-3510 TCGA-AA-3525 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6895 TCGA-CA-6717 
       63.98         8.05         4.01        34.98         0.72         0.33 

$`KCNJ16 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 
        1.02         9.07        24.03        37.05        36.03        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  KCNJ16 MUTATED KCNJ16 WILD-TYPE 
            0.33             0.00 
  KCNJ16 MUTATED KCNJ16 WILD-TYPE 
           63.98           140.38 
  KCNJ16 MUTATED KCNJ16 WILD-TYPE 
            6.03            20.28 
[1] "0.3 - 64.0 (6.0)"   "0.0 - 140.4 (20.3)"
[1] "hr=" "1.1"
D1691V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KCNJ16 MUTATED         0        0        1         2         2         0
  KCNJ16 WILD-TYPE      64        1       24       107         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KCNJ16 MUTATED           0          0          1          0        0
  KCNJ16 WILD-TYPE        19         10         40         31       35
                  vv
clus               STAGE IVA STAGE IVB
  KCNJ16 MUTATED           0         0
  KCNJ16 WILD-TYPE        13         1
D1691V3, multiclass
            clus
vv           KCNJ16 MUTATED KCNJ16 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               2              107
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  KCNJ16 MUTATED     0   0   5   2
  KCNJ16 WILD-TYPE   9  68 243  39
D1691V4, multiclass
    clus
vv   KCNJ16 MUTATED KCNJ16 WILD-TYPE
  T1              0                9
  T2              0               68
  T3              5              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
  KCNJ16 MUTATED     5   2   0
  KCNJ16 WILD-TYPE 215  78  66
D1691V5, multiclass
    clus
vv   KCNJ16 MUTATED KCNJ16 WILD-TYPE
  N0              5              215
  N1              2               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"
D1691V6, binary
                  cls
clus                 0   1
  KCNJ16 MUTATED     6   0
  KCNJ16 WILD-TYPE 277  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCNJ16 MUTATED      6    0
  KCNJ16 WILD-TYPE  277   48
   clus
vv  KCNJ16 MUTATED KCNJ16 WILD-TYPE
  0              6              277
  1              0               48
[1] 2 2
[1] FALSE
D1691V7, binary
                  cls
clus                 0   1
  KCNJ16 MUTATED     2   5
  KCNJ16 WILD-TYPE 168 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCNJ16 MUTATED      2    5
  KCNJ16 WILD-TYPE  168  192
        clus
vv       KCNJ16 MUTATED KCNJ16 WILD-TYPE
  FEMALE              2              168
  MALE                5              192
[1] 2 2
[1] FALSE
D1691V8, binary
                  cls
clus                 0   1
  KCNJ16 MUTATED     5   2
  KCNJ16 WILD-TYPE 312  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCNJ16 MUTATED      5    2
  KCNJ16 WILD-TYPE  312   46
                               clus
vv                              KCNJ16 MUTATED KCNJ16 WILD-TYPE
  COLON ADENOCARCINOMA                       5              312
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  KCNJ16 MUTATED     5   0   0   1
  KCNJ16 WILD-TYPE 252   2  22  20
D1691V9, multiclass
    clus
vv   KCNJ16 MUTATED KCNJ16 WILD-TYPE
  R0              5              252
  R1              0                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"
D1691V10, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KCNJ16 MUTATED                                  0     1
  KCNJ16 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  KCNJ16 MUTATED                           0     1
  KCNJ16 WILD-TYPE                        19   175
D1691V11, multiclass
[1] "Remove cluster labels:" "KCNJ16 MUTATED"        
clus
  KCNJ16 MUTATED KCNJ16 WILD-TYPE 
               2              204 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-4105 
"KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" 
      TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660 
"KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" 
      TCGA-A6-5661       TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5665 
"KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" 
      TCGA-A6-5666       TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141 
"KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" 
      TCGA-A6-6142       TCGA-A6-6648       TCGA-A6-6649       TCGA-A6-6651 
"KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" 
      TCGA-A6-6652       TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780 
"KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" 
      TCGA-A6-6781       TCGA-A6-6782       TCGA-AD-5900       TCGA-AD-6548 
"KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" 
      TCGA-AD-6888       TCGA-AD-6889       TCGA-AD-6890       TCGA-AD-6899 
"KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" 
      TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6964       TCGA-AD-6965 
"KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" 
      TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070       TCGA-AY-4071 
"KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" 
      TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386 
"KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" 
      TCGA-AZ-4315       TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4681 
"KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" 
      TCGA-AZ-4682       TCGA-AZ-5403       TCGA-AZ-5407       TCGA-AZ-6598 
"KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" 
      TCGA-AZ-6599       TCGA-AZ-6600       TCGA-AZ-6601       TCGA-AZ-6603 
"KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" 
      TCGA-AZ-6605       TCGA-AZ-6606       TCGA-AZ-6607       TCGA-AZ-6608 
"KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" 
      TCGA-CA-5254       TCGA-CA-5255       TCGA-CA-5796       TCGA-CA-5797 
"KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" 
      TCGA-CA-6715       TCGA-CA-6716       TCGA-CA-6718       TCGA-CA-6719 
"KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" 
      TCGA-CK-4947       TCGA-CK-4948       TCGA-CK-4950       TCGA-CK-4952 
"KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" 
      TCGA-CK-5912       TCGA-CK-5913       TCGA-CK-5914       TCGA-CK-5915 
"KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" 
      TCGA-CK-5916       TCGA-CK-6746       TCGA-CK-6747       TCGA-CK-6748 
"KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" 
      TCGA-CK-6751       TCGA-CM-4743       TCGA-CM-4744       TCGA-CM-4746 
"KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" 
      TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341       TCGA-CM-5344 
"KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" 
      TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860       TCGA-CM-5861 
"KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" 
      TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864       TCGA-CM-5868 
"KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" 
      TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163       TCGA-CM-6164 
"KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" 
      TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167       TCGA-CM-6168 
"KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" 
      TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171       TCGA-CM-6172 
"KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" 
      TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676       TCGA-CM-6677 
"KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" 
      TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680       TCGA-D5-5537 
"KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" 
      TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540       TCGA-D5-5541 
"KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" 
      TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533       TCGA-D5-6534 
"KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" 
      TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537       TCGA-D5-6538 
"KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" 
      TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541       TCGA-D5-6898 
"KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" 
      TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923       TCGA-D5-6924 
"KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" 
      TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928       TCGA-D5-6929 
"KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" 
      TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932       TCGA-D5-7000 
"KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" 
      TCGA-DM-A0X9       TCGA-DM-A0XD       TCGA-DM-A0XF       TCGA-DM-A1D0 
"KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" 
      TCGA-DM-A1D4       TCGA-DM-A1D6       TCGA-DM-A1D7       TCGA-DM-A1D8 
"KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" 
      TCGA-DM-A1D9       TCGA-DM-A1DA       TCGA-DM-A1DB       TCGA-DM-A1HA 
"KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" 
      TCGA-DM-A1HB       TCGA-DM-A282       TCGA-DM-A285       TCGA-DM-A28C 
"KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" 
      TCGA-DM-A28E       TCGA-DM-A28F       TCGA-DM-A28G       TCGA-DM-A28H 
"KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" 
      TCGA-DM-A28K       TCGA-F4-6459       TCGA-F4-6460       TCGA-F4-6569 
"KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" 
      TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704       TCGA-F4-6805 
"KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" 
      TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808       TCGA-F4-6809 
"KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" 
      TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856       TCGA-G4-6293 
"KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" 
      TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304       TCGA-G4-6306 
"KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" 
      TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310       TCGA-G4-6315 
"KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323       TCGA-G4-6586 
"KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" 
      TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628 
"KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" "KCNJ16 WILD-TYPE" 

Clustering(1692) Variable = REM1 MUTATION ANALYSIS
D1692V1, survival
                sevent
clus2              0   1
  REM1 MUTATED     3   1
  REM1 WILD-TYPE 279  72
  REM1 MUTATED REM1 WILD-TYPE 
             4            351 
  REM1 MUTATED REM1 WILD-TYPE 
             1             72 
$`REM1 MUTATED`
TCGA-AA-A00R TCGA-AZ-5407 TCGA-F4-6570 TCGA-G4-6586 
        0.99        61.41         6.18        35.80 

$`REM1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U 
       18.05        38.04         4.01        27.02        42.02        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 
        1.41         5.13        83.80        22.36        62.79        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 
       45.11        36.72        36.00        22.09        13.78        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  REM1 MUTATED REM1 WILD-TYPE 
          0.99           0.00 
  REM1 MUTATED REM1 WILD-TYPE 
         61.41         140.38 
  REM1 MUTATED REM1 WILD-TYPE 
         20.99          20.19 
[1] "1.0 - 61.4 (21.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D1692V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  REM1 MUTATED         2        0        0         2         0         0
  REM1 WILD-TYPE      62        1       25       107         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  REM1 MUTATED           0          0          0          0        0         0
  REM1 WILD-TYPE        19         10         41         31       35        13
                vv
clus             STAGE IVB
  REM1 MUTATED           0
  REM1 WILD-TYPE         1
D1692V3, multiclass
            clus
vv           REM1 MUTATED REM1 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             2            107
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  REM1 MUTATED     1   1   2   0
  REM1 WILD-TYPE   8  67 246  41
D1692V4, multiclass
    clus
vv   REM1 MUTATED REM1 WILD-TYPE
  T1            1              8
  T2            1             67
  T3            2            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
  REM1 MUTATED     4   0   0
  REM1 WILD-TYPE 216  80  66
D1692V5, multiclass
    clus
vv   REM1 MUTATED REM1 WILD-TYPE
  N0            4            216
  N1            0             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"
D1692V6, binary
                cls
clus               0   1
  REM1 MUTATED     4   0
  REM1 WILD-TYPE 279  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  REM1 MUTATED      4    0
  REM1 WILD-TYPE  279   48
   clus
vv  REM1 MUTATED REM1 WILD-TYPE
  0            4            279
  1            0             48
[1] 2 2
[1] FALSE
D1692V7, binary
                cls
clus               0   1
  REM1 MUTATED     4   0
  REM1 WILD-TYPE 166 197
[1] "tbl2"
                cls
clus             [,1] [,2]
  REM1 MUTATED      4    0
  REM1 WILD-TYPE  166  197
        clus
vv       REM1 MUTATED REM1 WILD-TYPE
  FEMALE            4            166
  MALE              0            197
[1] 2 2
[1] FALSE
D1692V8, binary
                cls
clus               0   1
  REM1 MUTATED     4   0
  REM1 WILD-TYPE 313  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  REM1 MUTATED      4    0
  REM1 WILD-TYPE  313   48
                               clus
vv                              REM1 MUTATED REM1 WILD-TYPE
  COLON ADENOCARCINOMA                     4            313
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  REM1 MUTATED     3   0   0   0
  REM1 WILD-TYPE 254   2  22  21
D1692V9, multiclass
    clus
vv   REM1 MUTATED REM1 WILD-TYPE
  R0            3            254
  R1            0              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"
D1692V10, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  REM1 MUTATED                                  0     0
  REM1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  REM1 MUTATED                           0     3
  REM1 WILD-TYPE                        19   173
D1692V11, multiclass
                                  clus
vv                                 REM1 MUTATED REM1 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(1693) Variable = TMEM171 MUTATION ANALYSIS
D1693V1, survival
                   sevent
clus2                 0   1
  TMEM171 MUTATED     5   0
  TMEM171 WILD-TYPE 277  73
  TMEM171 MUTATED TMEM171 WILD-TYPE 
                5               350 
  TMEM171 MUTATED TMEM171 WILD-TYPE 
                0                73 
$`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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
        6.05         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 
       10.06         0.00        33.07         0.00        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  TMEM171 MUTATED TMEM171 WILD-TYPE 
             0.92              0.00 
  TMEM171 MUTATED TMEM171 WILD-TYPE 
            58.39            140.38 
  TMEM171 MUTATED TMEM171 WILD-TYPE 
           19.040            20.235 
[1] "0.9 - 58.4 (19.0)"  "0.0 - 140.4 (20.2)"
[1] "hr="     "9100000"
D1693V2, 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       25       108         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM171 MUTATED           1          0          1          0        1
  TMEM171 WILD-TYPE        18         10         40         31       34
                   vv
clus                STAGE IVA STAGE IVB
  TMEM171 MUTATED           0         0
  TMEM171 WILD-TYPE        13         1
D1693V3, multiclass
            clus
vv           TMEM171 MUTATED TMEM171 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                1               108
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               0                31
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TMEM171 MUTATED     0   1   4   0
  TMEM171 WILD-TYPE   9  67 244  41
D1693V4, multiclass
    clus
vv   TMEM171 MUTATED TMEM171 WILD-TYPE
  T1               0                 9
  T2               1                67
  T3               4               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
  TMEM171 MUTATED     3   2   0
  TMEM171 WILD-TYPE 217  78  66
D1693V5, multiclass
    clus
vv   TMEM171 MUTATED TMEM171 WILD-TYPE
  N0               3               217
  N1               2                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"
D1693V6, binary
                   cls
clus                  0   1
  TMEM171 MUTATED     4   1
  TMEM171 WILD-TYPE 279  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM171 MUTATED      4    1
  TMEM171 WILD-TYPE  279   47
   clus
vv  TMEM171 MUTATED TMEM171 WILD-TYPE
  0               4               279
  1               1                47
[1] 2 2
[1] FALSE
D1693V7, 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
D1693V8, binary
                   cls
clus                  0   1
  TMEM171 MUTATED     3   2
  TMEM171 WILD-TYPE 314  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM171 MUTATED      3    2
  TMEM171 WILD-TYPE  314   46
                               clus
vv                              TMEM171 MUTATED TMEM171 WILD-TYPE
  COLON ADENOCARCINOMA                        3               314
  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 253   2  21  21
D1693V9, multiclass
    clus
vv   TMEM171 MUTATED TMEM171 WILD-TYPE
  R0               4               253
  R1               0                 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"
D1693V10, 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
D1693V11, multiclass
[1] "Remove cluster labels:" "TMEM171 MUTATED"       
clus
  TMEM171 MUTATED TMEM171 WILD-TYPE 
                2               204 
       TCGA-A6-2671        TCGA-A6-2672        TCGA-A6-2674        TCGA-A6-2676 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-A6-2677        TCGA-A6-2678        TCGA-A6-2683        TCGA-A6-3807 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-A6-3808        TCGA-A6-3809        TCGA-A6-3810        TCGA-A6-4105 
"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-A6-6649        TCGA-A6-6651 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-A6-6652        TCGA-A6-6653        TCGA-A6-6654        TCGA-A6-6780 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-A6-6781        TCGA-A6-6782        TCGA-AD-5900        TCGA-AD-6548 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-AD-6888        TCGA-AD-6889        TCGA-AD-6890        TCGA-AD-6895 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-AD-6899        TCGA-AD-6901        TCGA-AD-6963        TCGA-AD-6964 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-AD-6965        TCGA-AU-3779        TCGA-AU-6004        TCGA-AY-4070 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-AY-4071        TCGA-AY-5543        TCGA-AY-6196        TCGA-AY-6197 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-AY-6386        TCGA-AZ-4323        TCGA-AZ-4616        TCGA-AZ-4681 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-AZ-4682        TCGA-AZ-5403        TCGA-AZ-5407        TCGA-AZ-6598 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-AZ-6599        TCGA-AZ-6600        TCGA-AZ-6601        TCGA-AZ-6603 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-AZ-6605        TCGA-AZ-6606        TCGA-AZ-6607        TCGA-AZ-6608 
"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-5912        TCGA-CK-5913        TCGA-CK-5914 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-CK-5915        TCGA-CK-5916        TCGA-CK-6746        TCGA-CK-6747 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-CK-6748        TCGA-CK-6751        TCGA-CM-4743        TCGA-CM-4744 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-CM-4746        TCGA-CM-4747        TCGA-CM-4752        TCGA-CM-5341 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-CM-5344        TCGA-CM-5348        TCGA-CM-5349        TCGA-CM-5860 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-CM-5861        TCGA-CM-5862        TCGA-CM-5863        TCGA-CM-5864 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-CM-5868        TCGA-CM-6161        TCGA-CM-6163        TCGA-CM-6164 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-CM-6165        TCGA-CM-6166        TCGA-CM-6167        TCGA-CM-6168 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-CM-6169        TCGA-CM-6170        TCGA-CM-6171        TCGA-CM-6172 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-CM-6674        TCGA-CM-6675        TCGA-CM-6676        TCGA-CM-6677 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-CM-6678        TCGA-CM-6679        TCGA-CM-6680        TCGA-D5-5537 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-D5-5538        TCGA-D5-5539        TCGA-D5-5540        TCGA-D5-5541 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-D5-6529        TCGA-D5-6532        TCGA-D5-6533        TCGA-D5-6534 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-D5-6535        TCGA-D5-6536        TCGA-D5-6537        TCGA-D5-6538 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-D5-6539        TCGA-D5-6540        TCGA-D5-6541        TCGA-D5-6898 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-D5-6920        TCGA-D5-6922        TCGA-D5-6923        TCGA-D5-6924 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-D5-6926        TCGA-D5-6927        TCGA-D5-6928        TCGA-D5-6929 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-D5-6930        TCGA-D5-6931        TCGA-D5-6932        TCGA-D5-7000 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-DM-A0X9        TCGA-DM-A0XD        TCGA-DM-A0XF        TCGA-DM-A1D0 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-DM-A1D4        TCGA-DM-A1D6        TCGA-DM-A1D7        TCGA-DM-A1D8 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-DM-A1D9        TCGA-DM-A1DA        TCGA-DM-A1DB        TCGA-DM-A1HA 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-DM-A1HB        TCGA-DM-A282        TCGA-DM-A285        TCGA-DM-A28C 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-DM-A28E        TCGA-DM-A28F        TCGA-DM-A28G        TCGA-DM-A28H 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-DM-A28K        TCGA-F4-6459        TCGA-F4-6460        TCGA-F4-6569 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-F4-6570        TCGA-F4-6703        TCGA-F4-6704        TCGA-F4-6805 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-F4-6806        TCGA-F4-6807        TCGA-F4-6808        TCGA-F4-6809 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-F4-6854        TCGA-F4-6855        TCGA-F4-6856        TCGA-G4-6293 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-G4-6299        TCGA-G4-6303        TCGA-G4-6304        TCGA-G4-6306 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-G4-6307        TCGA-G4-6309        TCGA-G4-6310        TCGA-G4-6315 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-G4-6317        TCGA-G4-6321        TCGA-G4-6323        TCGA-G4-6586 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 
       TCGA-G4-6588        TCGA-G4-6625        TCGA-G4-6626        TCGA-G4-6628 
"TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" "TMEM171 WILD-TYPE" 

Clustering(1694) Variable = TMEM229B MUTATION ANALYSIS
D1694V1, survival
                    sevent
clus2                  0   1
  TMEM229B MUTATED     4   0
  TMEM229B WILD-TYPE 278  73
  TMEM229B MUTATED TMEM229B WILD-TYPE 
                 4                351 
  TMEM229B MUTATED TMEM229B WILD-TYPE 
                 0                 73 
$`TMEM229B MUTATED`
TCGA-AD-6890 TCGA-AD-6895 TCGA-CM-4746 TCGA-CM-5344 
        0.79         0.72        37.02        22.03 

$`TMEM229B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       21.37         4.21        56.55         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         2.01       124.27        23.05        20.02 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  TMEM229B MUTATED TMEM229B WILD-TYPE 
              0.72               0.00 
  TMEM229B MUTATED TMEM229B WILD-TYPE 
             37.02             140.38 
  TMEM229B MUTATED TMEM229B WILD-TYPE 
             11.41              20.19 
[1] "0.7 - 37.0 (11.4)"  "0.0 - 140.4 (20.2)"
[1] "hr="     "3300000"
D1694V2, 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       25       109         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM229B MUTATED           0          0          1          0        0
  TMEM229B WILD-TYPE        19         10         40         31       35
                    vv
clus                 STAGE IVA STAGE IVB
  TMEM229B MUTATED           0         0
  TMEM229B WILD-TYPE        13         1
D1694V3, multiclass
[1] "Remove cluster labels:" "TMEM229B MUTATED"      
clus
  TMEM229B MUTATED TMEM229B WILD-TYPE 
                 2                356 
        TCGA-A6-2671         TCGA-A6-2672         TCGA-A6-2674 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-A6-2676         TCGA-A6-2677         TCGA-A6-2678 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-A6-2683         TCGA-A6-3807         TCGA-A6-3808 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-A6-3809         TCGA-A6-3810         TCGA-A6-4105 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-A6-5656         TCGA-A6-5657         TCGA-A6-5659 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-A6-5660         TCGA-A6-5661         TCGA-A6-5662 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-A6-5664         TCGA-A6-5665         TCGA-A6-5666 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-A6-6137         TCGA-A6-6138         TCGA-A6-6141 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-A6-6142         TCGA-A6-6648         TCGA-A6-6649 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-A6-6651         TCGA-A6-6652         TCGA-A6-6653 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-A6-6654         TCGA-A6-6780         TCGA-A6-6781 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-A6-6782         TCGA-AA-3489         TCGA-AA-3492 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3496         TCGA-AA-3502         TCGA-AA-3510 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3511         TCGA-AA-3514         TCGA-AA-3516 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3517         TCGA-AA-3518         TCGA-AA-3519 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3520         TCGA-AA-3521         TCGA-AA-3522 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3524         TCGA-AA-3525         TCGA-AA-3526 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3527         TCGA-AA-3529         TCGA-AA-3530 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3531         TCGA-AA-3532         TCGA-AA-3534 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3538         TCGA-AA-3542         TCGA-AA-3543 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3544         TCGA-AA-3548         TCGA-AA-3549 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3552         TCGA-AA-3553         TCGA-AA-3554 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3555         TCGA-AA-3556         TCGA-AA-3558 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3560         TCGA-AA-3561         TCGA-AA-3562 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3655         TCGA-AA-3660         TCGA-AA-3662 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3663         TCGA-AA-3664         TCGA-AA-3666 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3667         TCGA-AA-3672         TCGA-AA-3673 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3678         TCGA-AA-3679         TCGA-AA-3680 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3681         TCGA-AA-3684         TCGA-AA-3685 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3688         TCGA-AA-3692         TCGA-AA-3693 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3695         TCGA-AA-3696         TCGA-AA-3697 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3710         TCGA-AA-3712         TCGA-AA-3713 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3715         TCGA-AA-3811         TCGA-AA-3812 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3814         TCGA-AA-3815         TCGA-AA-3818 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3819         TCGA-AA-3821         TCGA-AA-3831 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3833         TCGA-AA-3837         TCGA-AA-3842 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3844         TCGA-AA-3845         TCGA-AA-3846 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3848         TCGA-AA-3850         TCGA-AA-3851 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3852         TCGA-AA-3854         TCGA-AA-3855 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3856         TCGA-AA-3858         TCGA-AA-3860 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3861         TCGA-AA-3864         TCGA-AA-3866 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3867         TCGA-AA-3869         TCGA-AA-3870 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3872         TCGA-AA-3875         TCGA-AA-3877 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3930         TCGA-AA-3939         TCGA-AA-3941 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3947         TCGA-AA-3949         TCGA-AA-3950 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3952         TCGA-AA-3955         TCGA-AA-3956 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3966         TCGA-AA-3968         TCGA-AA-3971 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3972         TCGA-AA-3973         TCGA-AA-3975 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3976         TCGA-AA-3979         TCGA-AA-3980 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3982         TCGA-AA-3984         TCGA-AA-3986 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3989         TCGA-AA-3994         TCGA-AA-A004 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-A00A         TCGA-AA-A00D         TCGA-AA-A00E 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-A00F         TCGA-AA-A00J         TCGA-AA-A00K 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-A00L         TCGA-AA-A00N         TCGA-AA-A00O 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-A00Q         TCGA-AA-A00R         TCGA-AA-A00U 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-A00W         TCGA-AA-A00Z         TCGA-AA-A010 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-A017         TCGA-AA-A01D         TCGA-AA-A01F 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-A01G         TCGA-AA-A01I         TCGA-AA-A01K 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-A01P         TCGA-AA-A01Q         TCGA-AA-A01R 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-A01S         TCGA-AA-A01T         TCGA-AA-A01V 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-A01X         TCGA-AA-A01Z         TCGA-AA-A022 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-A024         TCGA-AA-A029         TCGA-AA-A02F 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-A02H         TCGA-AA-A02J         TCGA-AA-A02K 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-A02O         TCGA-AA-A02W         TCGA-AA-A02Y 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-A03F         TCGA-AA-A03J         TCGA-AD-5900 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AD-6548         TCGA-AD-6888         TCGA-AD-6889 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AD-6899         TCGA-AU-3779         TCGA-AU-6004 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AY-4070         TCGA-AY-4071         TCGA-AY-5543 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AY-6196         TCGA-AY-6197         TCGA-AY-6386 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AZ-4315         TCGA-AZ-4323         TCGA-AZ-4616 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AZ-4681         TCGA-AZ-4682         TCGA-AZ-5403 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AZ-5407         TCGA-AZ-6598         TCGA-AZ-6599 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AZ-6600         TCGA-AZ-6601         TCGA-AZ-6605 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AZ-6606         TCGA-AZ-6607         TCGA-AZ-6608 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CA-5254         TCGA-CA-5255         TCGA-CA-5796 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CA-5797         TCGA-CA-6715         TCGA-CA-6716 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CA-6717         TCGA-CA-6718         TCGA-CA-6719 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CK-4947         TCGA-CK-4948         TCGA-CK-4950 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CK-4952         TCGA-CK-5912         TCGA-CK-5913 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CK-5914         TCGA-CK-5915         TCGA-CK-5916 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CK-6746         TCGA-CK-6747         TCGA-CK-6748 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CK-6751         TCGA-CM-4743         TCGA-CM-4744 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CM-4747         TCGA-CM-4752         TCGA-CM-5341 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CM-5348         TCGA-CM-5349         TCGA-CM-5860 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CM-5861         TCGA-CM-5862         TCGA-CM-5863 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CM-5864         TCGA-CM-5868         TCGA-CM-6161 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CM-6162         TCGA-CM-6163         TCGA-CM-6164 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CM-6165         TCGA-CM-6166         TCGA-CM-6167 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CM-6168         TCGA-CM-6169         TCGA-CM-6170 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CM-6171         TCGA-CM-6172         TCGA-CM-6674 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CM-6675         TCGA-CM-6676         TCGA-CM-6677 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CM-6678         TCGA-CM-6679         TCGA-CM-6680 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-D5-5537         TCGA-D5-5538         TCGA-D5-5539 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-D5-5540         TCGA-D5-5541         TCGA-D5-6529 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-D5-6532         TCGA-D5-6533         TCGA-D5-6534 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-D5-6535         TCGA-D5-6536         TCGA-D5-6537 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-D5-6538         TCGA-D5-6539         TCGA-D5-6540 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-D5-6541         TCGA-D5-6898         TCGA-D5-6920 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-D5-6922         TCGA-D5-6923         TCGA-D5-6924 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-D5-6926         TCGA-D5-6927         TCGA-D5-6928 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-D5-6929         TCGA-D5-6930         TCGA-D5-6931 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-D5-6932         TCGA-D5-7000         TCGA-DM-A0X9 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-DM-A0XD         TCGA-DM-A0XF         TCGA-DM-A1D0 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-DM-A1D4         TCGA-DM-A1D6         TCGA-DM-A1D7 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-DM-A1D9         TCGA-DM-A1DA         TCGA-DM-A1DB 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-DM-A1HA         TCGA-DM-A1HB         TCGA-DM-A282 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-DM-A285         TCGA-DM-A28C         TCGA-DM-A28E 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-DM-A28F         TCGA-DM-A28G         TCGA-DM-A28H 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-DM-A28K         TCGA-F4-6459         TCGA-F4-6460 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-F4-6569         TCGA-F4-6570         TCGA-F4-6703 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-F4-6704         TCGA-F4-6805         TCGA-F4-6806 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-F4-6807         TCGA-F4-6808         TCGA-F4-6809 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-F4-6854         TCGA-F4-6855         TCGA-F4-6856 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-G4-6293         TCGA-G4-6299         TCGA-G4-6303 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-G4-6304         TCGA-G4-6306         TCGA-G4-6307 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-G4-6309         TCGA-G4-6310         TCGA-G4-6315 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-G4-6317         TCGA-G4-6321         TCGA-G4-6323 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-G4-6586         TCGA-G4-6588         TCGA-G4-6625 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-G4-6626         TCGA-G4-6628 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
                    vv
clus                  T1  T2  T3  T4
  TMEM229B MUTATED     1   1   2   0
  TMEM229B WILD-TYPE   8  67 246  41
D1694V4, multiclass
    clus
vv   TMEM229B MUTATED TMEM229B WILD-TYPE
  T1                1                  8
  T2                1                 67
  T3                2                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
  TMEM229B MUTATED     2   2   0
  TMEM229B WILD-TYPE 218  78  66
D1694V5, multiclass
    clus
vv   TMEM229B MUTATED TMEM229B WILD-TYPE
  N0                2                218
  N1                2                 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"
D1694V6, binary
                    cls
clus                   0   1
  TMEM229B MUTATED     2   0
  TMEM229B WILD-TYPE 281  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMEM229B MUTATED      2    0
  TMEM229B WILD-TYPE  281   48
   clus
vv  TMEM229B MUTATED TMEM229B WILD-TYPE
  0                2                281
  1                0                 48
[1] 2 2
[1] FALSE
D1694V7, 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
D1694V8, binary
                    cls
clus                   0   1
  TMEM229B MUTATED     4   0
  TMEM229B WILD-TYPE 313  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMEM229B MUTATED      4    0
  TMEM229B WILD-TYPE  313   48
                               clus
vv                              TMEM229B MUTATED TMEM229B WILD-TYPE
  COLON ADENOCARCINOMA                         4                313
  COLON MUCINOUS ADENOCARCINOMA                0                 48
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  TMEM229B MUTATED     2   0   0   0
  TMEM229B WILD-TYPE 255   2  22  21
D1694V9, multiclass
[1] "Remove cluster labels:" "TMEM229B MUTATED"      
clus
  TMEM229B MUTATED TMEM229B WILD-TYPE 
                 2                300 
        TCGA-A6-2671         TCGA-A6-2672         TCGA-A6-2674 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-A6-2676         TCGA-A6-2677         TCGA-A6-2678 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-A6-2683         TCGA-A6-3807         TCGA-A6-3808 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-A6-3809         TCGA-A6-3810         TCGA-A6-5657 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-A6-5659         TCGA-A6-5661         TCGA-A6-5665 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-A6-6781         TCGA-AA-3489         TCGA-AA-3492 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3496         TCGA-AA-3502         TCGA-AA-3510 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3511         TCGA-AA-3514         TCGA-AA-3517 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3518         TCGA-AA-3519         TCGA-AA-3520 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3521         TCGA-AA-3522         TCGA-AA-3524 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3525         TCGA-AA-3526         TCGA-AA-3527 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3529         TCGA-AA-3530         TCGA-AA-3531 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3532         TCGA-AA-3534         TCGA-AA-3538 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3542         TCGA-AA-3543         TCGA-AA-3544 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3548         TCGA-AA-3549         TCGA-AA-3552 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3553         TCGA-AA-3554         TCGA-AA-3555 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3556         TCGA-AA-3558         TCGA-AA-3560 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3561         TCGA-AA-3562         TCGA-AA-3655 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3660         TCGA-AA-3662         TCGA-AA-3663 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3664         TCGA-AA-3666         TCGA-AA-3667 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3672         TCGA-AA-3673         TCGA-AA-3678 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3679         TCGA-AA-3680         TCGA-AA-3681 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3684         TCGA-AA-3685         TCGA-AA-3688 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3692         TCGA-AA-3693         TCGA-AA-3695 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3696         TCGA-AA-3697         TCGA-AA-3710 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3712         TCGA-AA-3713         TCGA-AA-3715 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3811         TCGA-AA-3812         TCGA-AA-3814 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3815         TCGA-AA-3818         TCGA-AA-3819 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3821         TCGA-AA-3831         TCGA-AA-3833 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3837         TCGA-AA-3842         TCGA-AA-3844 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3845         TCGA-AA-3846         TCGA-AA-3848 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3850         TCGA-AA-3851         TCGA-AA-3852 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3854         TCGA-AA-3855         TCGA-AA-3856 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3858         TCGA-AA-3860         TCGA-AA-3861 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3864         TCGA-AA-3866         TCGA-AA-3867 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3869         TCGA-AA-3870         TCGA-AA-3872 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3875         TCGA-AA-3877         TCGA-AA-3930 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3939         TCGA-AA-3941         TCGA-AA-3947 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3949         TCGA-AA-3950         TCGA-AA-3952 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3955         TCGA-AA-3956         TCGA-AA-3968 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3971         TCGA-AA-3972         TCGA-AA-3973 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3975         TCGA-AA-3976         TCGA-AA-3979 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3984         TCGA-AA-3986         TCGA-AA-3989 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3994         TCGA-AA-A004         TCGA-AA-A00A 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-A00D         TCGA-AA-A00E         TCGA-AA-A00F 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-A00J         TCGA-AA-A00K         TCGA-AA-A00L 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-A00N         TCGA-AA-A00O         TCGA-AA-A00Q 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-A00R         TCGA-AA-A00U         TCGA-AA-A00W 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-A00Z         TCGA-AA-A010         TCGA-AA-A017 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-A01D         TCGA-AA-A01F         TCGA-AA-A01G 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-A01I         TCGA-AA-A01K         TCGA-AA-A01P 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-A01Q         TCGA-AA-A01R         TCGA-AA-A01S 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-A01T         TCGA-AA-A01V         TCGA-AA-A01X 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-A01Z         TCGA-AA-A022         TCGA-AA-A024 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-A029         TCGA-AA-A02F         TCGA-AA-A02H 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-A02J         TCGA-AA-A02K         TCGA-AA-A02O 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-A02W         TCGA-AA-A02Y         TCGA-AA-A03F 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-A03J         TCGA-AD-5900         TCGA-AD-6548 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AD-6888         TCGA-AU-3779         TCGA-AU-6004 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AY-4070         TCGA-AY-4071         TCGA-AY-5543 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AY-6196         TCGA-AY-6197         TCGA-AY-6386 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AZ-4315         TCGA-AZ-4681         TCGA-AZ-4682 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CA-5254         TCGA-CA-5255         TCGA-CA-5796 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CA-5797         TCGA-CA-6715         TCGA-CA-6716 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CA-6717         TCGA-CA-6718         TCGA-CA-6719 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CK-4947         TCGA-CK-4948         TCGA-CK-4950 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CK-4952         TCGA-CK-5912         TCGA-CK-5913 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CK-5914         TCGA-CK-5915         TCGA-CK-5916 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CK-6746         TCGA-CK-6747         TCGA-CK-6748 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CK-6751         TCGA-CM-4743         TCGA-CM-4744 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CM-4747         TCGA-CM-4752         TCGA-CM-5341 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CM-5348         TCGA-CM-5349         TCGA-CM-5860 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CM-5861         TCGA-CM-5862         TCGA-CM-5863 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CM-5864         TCGA-CM-5868         TCGA-CM-6161 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CM-6162         TCGA-CM-6163         TCGA-CM-6164 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CM-6165         TCGA-CM-6166         TCGA-CM-6167 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CM-6168         TCGA-CM-6169         TCGA-CM-6170 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CM-6171         TCGA-CM-6172         TCGA-CM-6674 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CM-6675         TCGA-CM-6676         TCGA-CM-6677 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CM-6678         TCGA-CM-6679         TCGA-CM-6680 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-D5-5537         TCGA-D5-5538         TCGA-D5-5539 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-D5-5540         TCGA-D5-5541         TCGA-D5-6529 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-D5-6532         TCGA-D5-6533         TCGA-D5-6534 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-D5-6535         TCGA-D5-6536         TCGA-D5-6537 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-D5-6538         TCGA-D5-6539         TCGA-D5-6540 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-D5-6541         TCGA-D5-6898         TCGA-D5-6920 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-D5-6922         TCGA-D5-6923         TCGA-D5-6924 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-D5-6926         TCGA-D5-6927         TCGA-D5-6928 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-D5-6929         TCGA-D5-6930         TCGA-D5-6931 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-D5-6932         TCGA-D5-7000         TCGA-F4-6459 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-F4-6460         TCGA-F4-6569         TCGA-F4-6570 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-F4-6703         TCGA-F4-6704         TCGA-F4-6805 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-F4-6806         TCGA-F4-6807         TCGA-F4-6808 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-F4-6809         TCGA-F4-6854         TCGA-F4-6855 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-F4-6856         TCGA-G4-6293         TCGA-G4-6299 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-G4-6303         TCGA-G4-6304         TCGA-G4-6306 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-G4-6307         TCGA-G4-6309         TCGA-G4-6310 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-G4-6315         TCGA-G4-6317         TCGA-G4-6321 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-G4-6323         TCGA-G4-6586         TCGA-G4-6588 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-G4-6625         TCGA-G4-6626         TCGA-G4-6628 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
D1694V10, 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
D1694V11, 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(1695) Variable = IL8 MUTATION ANALYSIS
D1695V1, survival
               sevent
clus2             0   1
  IL8 MUTATED     2   2
  IL8 WILD-TYPE 280  71
  IL8 MUTATED IL8 WILD-TYPE 
            4           351 
  IL8 MUTATED IL8 WILD-TYPE 
            2            71 
$`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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 
       12.39        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-A0X9 
       13.41         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  IL8 MUTATED IL8 WILD-TYPE 
         3.19          0.00 
  IL8 MUTATED IL8 WILD-TYPE 
        21.14        140.38 
  IL8 MUTATED IL8 WILD-TYPE 
        14.35         20.28 
[1] "3.2 - 21.1 (14.3)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "4.4"
D1695V2, 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       25       109         7         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IL8 MUTATED           0          1          0          1        1         0
  IL8 WILD-TYPE        19          9         41         30       34        13
               vv
clus            STAGE IVB
  IL8 MUTATED           0
  IL8 WILD-TYPE         1
D1695V3, multiclass
            clus
vv           IL8 MUTATED IL8 WILD-TYPE
  STAGE I              1            63
  STAGE IA             0             1
  STAGE II             0            25
  STAGE IIA            0           109
  STAGE IIB            1             7
  STAGE IIC            0             1
  STAGE III            0            19
  STAGE IIIA           1             9
  STAGE IIIB           0            41
  STAGE IIIC           1            30
  STAGE IV             1            34
  STAGE IVA            0            13
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  IL8 MUTATED     1   0   0   4
  IL8 WILD-TYPE   8  68 248  37
D1695V4, multiclass
    clus
vv   IL8 MUTATED IL8 WILD-TYPE
  T1           1             8
  T2           0            68
  T3           0           248
  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  78  65
D1695V5, multiclass
    clus
vv   IL8 MUTATED IL8 WILD-TYPE
  N0           2           218
  N1           2            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"
D1695V6, binary
               cls
clus              0   1
  IL8 MUTATED     2   1
  IL8 WILD-TYPE 281  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  IL8 MUTATED      2    1
  IL8 WILD-TYPE  281   47
   clus
vv  IL8 MUTATED IL8 WILD-TYPE
  0           2           281
  1           1            47
[1] 2 2
[1] FALSE
D1695V7, 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
D1695V8, binary
               cls
clus              0   1
  IL8 MUTATED     4   1
  IL8 WILD-TYPE 313  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  IL8 MUTATED      4    1
  IL8 WILD-TYPE  313   47
                               clus
vv                              IL8 MUTATED IL8 WILD-TYPE
  COLON ADENOCARCINOMA                    4           313
  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 255   2  22  19
D1695V9, multiclass
    clus
vv   IL8 MUTATED IL8 WILD-TYPE
  R0           2           255
  R1           0             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"
D1695V10, 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
D1695V11, 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(1696) Variable = KIF14 MUTATION ANALYSIS
D1696V1, survival
                 sevent
clus2               0   1
  KIF14 MUTATED     9   2
  KIF14 WILD-TYPE 273  71
  KIF14 MUTATED KIF14 WILD-TYPE 
             11             344 
  KIF14 MUTATED KIF14 WILD-TYPE 
              2              71 
$`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         0.33       131.51        98.24        35.41 

$`KIF14 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79       117.07         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  KIF14 MUTATED KIF14 WILD-TYPE 
           0.33            0.00 
  KIF14 MUTATED KIF14 WILD-TYPE 
         131.51          140.38 
  KIF14 MUTATED KIF14 WILD-TYPE 
         25.020          20.155 
[1] "0.3 - 131.5 (25.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.5"
D1696V2, 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       23       104         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        19         10         41         30       35        13
                 vv
clus              STAGE IVB
  KIF14 MUTATED           0
  KIF14 WILD-TYPE         1
D1696V3, multiclass
            clus
vv           KIF14 MUTATED KIF14 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              5             104
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KIF14 MUTATED     0   1   8   2
  KIF14 WILD-TYPE   9  67 240  39
D1696V4, multiclass
    clus
vv   KIF14 MUTATED KIF14 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             8             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
  KIF14 MUTATED    10   0   1
  KIF14 WILD-TYPE 210  80  65
D1696V5, multiclass
    clus
vv   KIF14 MUTATED KIF14 WILD-TYPE
  N0            10             210
  N1             0              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"
D1696V6, binary
                 cls
clus                0   1
  KIF14 MUTATED    10   0
  KIF14 WILD-TYPE 273  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF14 MUTATED     10    0
  KIF14 WILD-TYPE  273   48
   clus
vv  KIF14 MUTATED KIF14 WILD-TYPE
  0            10             273
  1             0              48
[1] 2 2
[1] FALSE
D1696V7, 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
D1696V8, binary
                 cls
clus                0   1
  KIF14 MUTATED     7   4
  KIF14 WILD-TYPE 310  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF14 MUTATED      7    4
  KIF14 WILD-TYPE  310   44
                               clus
vv                              KIF14 MUTATED KIF14 WILD-TYPE
  COLON ADENOCARCINOMA                      7             310
  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 252   2  22  20
D1696V9, multiclass
    clus
vv   KIF14 MUTATED KIF14 WILD-TYPE
  R0             5             252
  R1             0               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"
D1696V10, 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
D1696V11, 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(1697) Variable = ZNF660 MUTATION ANALYSIS
D1697V1, survival
                  sevent
clus2                0   1
  ZNF660 MUTATED     6   1
  ZNF660 WILD-TYPE 276  72
  ZNF660 MUTATED ZNF660 WILD-TYPE 
               7              348 
  ZNF660 MUTATED ZNF660 WILD-TYPE 
               1               72 
$`ZNF660 MUTATED`
TCGA-AA-3510 TCGA-AA-3555 TCGA-CA-6718 TCGA-CK-5916 TCGA-CM-5861 TCGA-G4-6299 
       63.98        29.95         0.10        21.14        15.02        74.56 
TCGA-G4-6588 
       26.17 

$`ZNF660 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        17.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.33         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
       40.34        15.62        49.08        51.32        21.99         2.93 
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        16.01 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 
        0.53        35.41        19.43       107.67        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        52.80 

  ZNF660 MUTATED ZNF660 WILD-TYPE 
             0.1              0.0 
  ZNF660 MUTATED ZNF660 WILD-TYPE 
           74.56           140.38 
  ZNF660 MUTATED ZNF660 WILD-TYPE 
           26.17            20.07 
[1] "0.1 - 74.6 (26.2)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.9"
D1697V2, 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       24       105         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF660 MUTATED           0          0          0          1        0
  ZNF660 WILD-TYPE        19         10         41         30       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF660 MUTATED           0         0
  ZNF660 WILD-TYPE        13         1
D1697V3, multiclass
            clus
vv           ZNF660 MUTATED ZNF660 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               4              105
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF660 MUTATED     1   0   6   0
  ZNF660 WILD-TYPE   8  68 242  41
D1697V4, multiclass
    clus
vv   ZNF660 MUTATED ZNF660 WILD-TYPE
  T1              1                8
  T2              0               68
  T3              6              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
  ZNF660 MUTATED     6   0   1
  ZNF660 WILD-TYPE 214  80  65
D1697V5, multiclass
    clus
vv   ZNF660 MUTATED ZNF660 WILD-TYPE
  N0              6              214
  N1              0               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"
D1697V6, binary
                  cls
clus                 0   1
  ZNF660 MUTATED     7   0
  ZNF660 WILD-TYPE 276  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF660 MUTATED      7    0
  ZNF660 WILD-TYPE  276   48
   clus
vv  ZNF660 MUTATED ZNF660 WILD-TYPE
  0              7              276
  1              0               48
[1] 2 2
[1] FALSE
D1697V7, 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
D1697V8, binary
                  cls
clus                 0   1
  ZNF660 MUTATED     6   1
  ZNF660 WILD-TYPE 311  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF660 MUTATED      6    1
  ZNF660 WILD-TYPE  311   47
                               clus
vv                              ZNF660 MUTATED ZNF660 WILD-TYPE
  COLON ADENOCARCINOMA                       6              311
  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 252   2  22  19
D1697V9, multiclass
    clus
vv   ZNF660 MUTATED ZNF660 WILD-TYPE
  R0              5              252
  R1              0                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"
D1697V10, 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
D1697V11, 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(1698) Variable = TRPC6 MUTATION ANALYSIS
D1698V1, survival
                 sevent
clus2               0   1
  TRPC6 MUTATED    18   3
  TRPC6 WILD-TYPE 264  70
  TRPC6 MUTATED TRPC6 WILD-TYPE 
             21             334 
  TRPC6 MUTATED TRPC6 WILD-TYPE 
              3              70 
$`TRPC6 MUTATED`
TCGA-A6-6781 TCGA-AA-3516 TCGA-AA-3846 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00L 
       19.66        13.02        17.03        38.04        30.02        38.04 
TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-5900 TCGA-AD-6963 TCGA-AZ-4315 TCGA-AZ-6598 
       34.98        35.01         0.07        27.42        58.39        49.41 
TCGA-AZ-6600 TCGA-CA-6717 TCGA-CK-4952 TCGA-CM-5860 TCGA-CM-6676 TCGA-D5-6927 
       12.10         0.33        15.62        16.01        11.08         9.44 
TCGA-F4-6807 TCGA-G4-6586 TCGA-G4-6628 
       16.24        35.80        52.80 

$`TRPC6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3848 
       15.95        38.99        37.02        14.93         0.00        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F 
       19.07         7.96        27.02        13.94        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-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       62.79        61.41         6.77       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      102.44        40.34        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       16.31        29.59        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       13.78        26.17        91.79        46.75 

  TRPC6 MUTATED TRPC6 WILD-TYPE 
           0.07            0.00 
  TRPC6 MUTATED TRPC6 WILD-TYPE 
          58.39          140.38 
  TRPC6 MUTATED TRPC6 WILD-TYPE 
         19.660          20.235 
[1] "0.1 - 58.4 (19.7)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.4"
D1698V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TRPC6 MUTATED         3        0        1        10         1         0
  TRPC6 WILD-TYPE      61        1       24        99         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TRPC6 MUTATED           3          0          0          2        1         0
  TRPC6 WILD-TYPE        16         10         41         29       34        13
                 vv
clus              STAGE IVB
  TRPC6 MUTATED           0
  TRPC6 WILD-TYPE         1
D1698V3, multiclass
            clus
vv           TRPC6 MUTATED TRPC6 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA             10              99
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              3              16
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             2              29
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TRPC6 MUTATED     0   3  15   4
  TRPC6 WILD-TYPE   9  65 233  37
D1698V4, multiclass
    clus
vv   TRPC6 MUTATED TRPC6 WILD-TYPE
  T1             0               9
  T2             3              65
  T3            15             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
  TRPC6 MUTATED    16   2   4
  TRPC6 WILD-TYPE 204  78  62
D1698V5, multiclass
    clus
vv   TRPC6 MUTATED TRPC6 WILD-TYPE
  N0            16             204
  N1             2              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"
D1698V6, binary
                 cls
clus                0   1
  TRPC6 MUTATED    17   1
  TRPC6 WILD-TYPE 266  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPC6 MUTATED     17    1
  TRPC6 WILD-TYPE  266   47
   clus
vv  TRPC6 MUTATED TRPC6 WILD-TYPE
  0            17             266
  1             1              47
[1] 2 2
[1] FALSE
D1698V7, binary
                 cls
clus                0   1
  TRPC6 MUTATED     8  14
  TRPC6 WILD-TYPE 162 183
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPC6 MUTATED      8   14
  TRPC6 WILD-TYPE  162  183
        clus
vv       TRPC6 MUTATED TRPC6 WILD-TYPE
  FEMALE             8             162
  MALE              14             183
[1] 2 2
[1] FALSE
D1698V8, binary
                 cls
clus                0   1
  TRPC6 MUTATED    16   6
  TRPC6 WILD-TYPE 301  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPC6 MUTATED     16    6
  TRPC6 WILD-TYPE  301   42
                               clus
vv                              TRPC6 MUTATED TRPC6 WILD-TYPE
  COLON ADENOCARCINOMA                     16             301
  COLON MUCINOUS ADENOCARCINOMA             6              42
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TRPC6 MUTATED    16   0   0   2
  TRPC6 WILD-TYPE 241   2  22  19
D1698V9, multiclass
    clus
vv   TRPC6 MUTATED TRPC6 WILD-TYPE
  R0            16             241
  R1             0               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"
D1698V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRPC6 MUTATED                                  0     1
  TRPC6 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TRPC6 MUTATED                           1    12
  TRPC6 WILD-TYPE                        18   164
D1698V11, multiclass
                                  clus
vv                                 TRPC6 MUTATED TRPC6 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(1699) Variable = RXRA MUTATION ANALYSIS
D1699V1, survival
                sevent
clus2              0   1
  RXRA MUTATED     6   2
  RXRA WILD-TYPE 276  71
  RXRA MUTATED RXRA WILD-TYPE 
             8            347 
  RXRA MUTATED RXRA WILD-TYPE 
             2             71 
$`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        19.43 

$`RXRA WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  RXRA MUTATED RXRA WILD-TYPE 
          3.02           0.00 
  RXRA MUTATED RXRA WILD-TYPE 
        135.65         140.38 
  RXRA MUTATED RXRA WILD-TYPE 
        24.035         20.120 
[1] "3.0 - 135.7 (24.0)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.2"
D1699V2, 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       23       106         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        19         10         40         31       35        13
                vv
clus             STAGE IVB
  RXRA MUTATED           0
  RXRA WILD-TYPE         1
D1699V3, multiclass
            clus
vv           RXRA MUTATED RXRA WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             3            106
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RXRA MUTATED     0   2   6   0
  RXRA WILD-TYPE   9  66 242  41
D1699V4, multiclass
    clus
vv   RXRA MUTATED RXRA WILD-TYPE
  T1            0              9
  T2            2             66
  T3            6            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
  RXRA MUTATED     7   1   0
  RXRA WILD-TYPE 213  79  66
D1699V5, multiclass
    clus
vv   RXRA MUTATED RXRA WILD-TYPE
  N0            7            213
  N1            1             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"
D1699V6, binary
                cls
clus               0   1
  RXRA MUTATED     6   0
  RXRA WILD-TYPE 277  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  RXRA MUTATED      6    0
  RXRA WILD-TYPE  277   48
   clus
vv  RXRA MUTATED RXRA WILD-TYPE
  0            6            277
  1            0             48
[1] 2 2
[1] FALSE
D1699V7, 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
D1699V8, binary
                cls
clus               0   1
  RXRA MUTATED     6   2
  RXRA WILD-TYPE 311  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  RXRA MUTATED      6    2
  RXRA WILD-TYPE  311   46
                               clus
vv                              RXRA MUTATED RXRA WILD-TYPE
  COLON ADENOCARCINOMA                     6            311
  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 252   2  22  21
D1699V9, multiclass
    clus
vv   RXRA MUTATED RXRA WILD-TYPE
  R0            5            252
  R1            0              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"
D1699V10, 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
D1699V11, 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(1700) Variable = TMEM20 MUTATION ANALYSIS
D1700V1, survival
                  sevent
clus2                0   1
  TMEM20 MUTATED     1   1
  TMEM20 WILD-TYPE 281  72
  TMEM20 MUTATED TMEM20 WILD-TYPE 
               2              353 
  TMEM20 MUTATED TMEM20 WILD-TYPE 
               1               72 
$`TMEM20 MUTATED`
TCGA-A6-2676 TCGA-A6-6781 
       42.90        19.66 

$`TMEM20 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  TMEM20 MUTATED TMEM20 WILD-TYPE 
           19.66             0.00 
  TMEM20 MUTATED TMEM20 WILD-TYPE 
           42.90           140.38 
  TMEM20 MUTATED TMEM20 WILD-TYPE 
           31.28            20.19 
[1] "19.7 - 42.9 (31.3)" "0.0 - 140.4 (20.2)"
[1] "Remove cluster labels:" "TMEM20 MUTATED"        
D1700V2, 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       24       109         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM20 MUTATED           0          0          0          1        0
  TMEM20 WILD-TYPE        19         10         41         30       35
                  vv
clus               STAGE IVA STAGE IVB
  TMEM20 MUTATED           0         0
  TMEM20 WILD-TYPE        13         1
D1700V3, multiclass
            clus
vv           TMEM20 MUTATED TMEM20 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               0              109
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TMEM20 MUTATED     0   0   0   3
  TMEM20 WILD-TYPE   9  68 248  38
D1700V4, multiclass
    clus
vv   TMEM20 MUTATED TMEM20 WILD-TYPE
  T1              0                9
  T2              0               68
  T3              0              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
  TMEM20 MUTATED     2   1   0
  TMEM20 WILD-TYPE 218  79  66
D1700V5, multiclass
    clus
vv   TMEM20 MUTATED TMEM20 WILD-TYPE
  N0              2              218
  N1              1               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"
D1700V6, binary
                  cls
clus                 0   1
  TMEM20 MUTATED     2   0
  TMEM20 WILD-TYPE 281  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM20 MUTATED      2    0
  TMEM20 WILD-TYPE  281   48
   clus
vv  TMEM20 MUTATED TMEM20 WILD-TYPE
  0              2              281
  1              0               48
[1] 2 2
[1] FALSE
D1700V7, 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
D1700V8, binary
                  cls
clus                 0   1
  TMEM20 MUTATED     2   1
  TMEM20 WILD-TYPE 315  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM20 MUTATED      2    1
  TMEM20 WILD-TYPE  315   47
                               clus
vv                              TMEM20 MUTATED TMEM20 WILD-TYPE
  COLON ADENOCARCINOMA                       2              315
  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 254   2  22  21
D1700V9, multiclass
    clus
vv   TMEM20 MUTATED TMEM20 WILD-TYPE
  R0              3              254
  R1              0                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"
D1700V10, 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
D1700V11, multiclass
[1] "Remove cluster labels:" "TMEM20 MUTATED"        
clus
  TMEM20 MUTATED TMEM20 WILD-TYPE 
               2              204 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2677 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807       TCGA-A6-3808 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-4105       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-A6-6649       TCGA-A6-6651       TCGA-A6-6652 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780       TCGA-A6-6782 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-AD-5900       TCGA-AD-6548       TCGA-AD-6888       TCGA-AD-6889 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-AD-6890       TCGA-AD-6895       TCGA-AD-6899       TCGA-AD-6901 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-AD-6963       TCGA-AD-6964       TCGA-AD-6965       TCGA-AU-3779 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-AU-6004       TCGA-AY-4070       TCGA-AY-4071       TCGA-AY-5543 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386       TCGA-AZ-4315 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4681       TCGA-AZ-4682 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-AZ-5403       TCGA-AZ-5407       TCGA-AZ-6598       TCGA-AZ-6599 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-AZ-6600       TCGA-AZ-6601       TCGA-AZ-6603       TCGA-AZ-6605 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-AZ-6606       TCGA-AZ-6607       TCGA-AZ-6608       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-5912       TCGA-CK-5913       TCGA-CK-5914       TCGA-CK-5915 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-CK-5916       TCGA-CK-6746       TCGA-CK-6747       TCGA-CK-6748 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-CK-6751       TCGA-CM-4743       TCGA-CM-4744       TCGA-CM-4746 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341       TCGA-CM-5344 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860       TCGA-CM-5861 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864       TCGA-CM-5868 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163       TCGA-CM-6164 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167       TCGA-CM-6168 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171       TCGA-CM-6172 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676       TCGA-CM-6677 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680       TCGA-D5-5537 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540       TCGA-D5-5541 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533       TCGA-D5-6534 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537       TCGA-D5-6538 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541       TCGA-D5-6898 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923       TCGA-D5-6924 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928       TCGA-D5-6929 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932       TCGA-D5-7000 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-DM-A0X9       TCGA-DM-A0XD       TCGA-DM-A0XF       TCGA-DM-A1D0 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-DM-A1D4       TCGA-DM-A1D6       TCGA-DM-A1D7       TCGA-DM-A1D8 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-DM-A1D9       TCGA-DM-A1DA       TCGA-DM-A1DB       TCGA-DM-A1HA 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-DM-A1HB       TCGA-DM-A282       TCGA-DM-A285       TCGA-DM-A28C 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-DM-A28E       TCGA-DM-A28F       TCGA-DM-A28G       TCGA-DM-A28H 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-DM-A28K       TCGA-F4-6459       TCGA-F4-6460       TCGA-F4-6569 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704       TCGA-F4-6805 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808       TCGA-F4-6809 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856       TCGA-G4-6293 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304       TCGA-G4-6306 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310       TCGA-G4-6315 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323       TCGA-G4-6586 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 
      TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628 
"TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" "TMEM20 WILD-TYPE" 

Clustering(1701) Variable = SLC16A1 MUTATION ANALYSIS
D1701V1, survival
                   sevent
clus2                 0   1
  SLC16A1 MUTATED     5   2
  SLC16A1 WILD-TYPE 277  71
  SLC16A1 MUTATED SLC16A1 WILD-TYPE 
                7               348 
  SLC16A1 MUTATED SLC16A1 WILD-TYPE 
                2                71 
$`SLC16A1 MUTATED`
TCGA-A6-5665 TCGA-AA-3663 TCGA-AA-3715 TCGA-AA-3966 TCGA-CA-6717 TCGA-CK-5916 
       22.06         6.97        19.04         2.01         0.33        21.14 
TCGA-G4-6293 
      107.67 

$`SLC16A1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32        21.99         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.41        19.43        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  SLC16A1 MUTATED SLC16A1 WILD-TYPE 
             0.33              0.00 
  SLC16A1 MUTATED SLC16A1 WILD-TYPE 
           107.67            140.38 
  SLC16A1 MUTATED SLC16A1 WILD-TYPE 
           19.040            20.235 
[1] "0.3 - 107.7 (19.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.4"
D1701V2, 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       23       106         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC16A1 MUTATED           1          0          0          0        0
  SLC16A1 WILD-TYPE        18         10         41         31       35
                   vv
clus                STAGE IVA STAGE IVB
  SLC16A1 MUTATED           0         0
  SLC16A1 WILD-TYPE        13         1
D1701V3, multiclass
            clus
vv           SLC16A1 MUTATED SLC16A1 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 2                23
  STAGE IIA                3               106
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC16A1 MUTATED     1   0   6   0
  SLC16A1 WILD-TYPE   8  68 242  41
D1701V4, multiclass
    clus
vv   SLC16A1 MUTATED SLC16A1 WILD-TYPE
  T1               1                 8
  T2               0                68
  T3               6               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
  SLC16A1 MUTATED     6   1   0
  SLC16A1 WILD-TYPE 214  79  66
D1701V5, multiclass
    clus
vv   SLC16A1 MUTATED SLC16A1 WILD-TYPE
  N0               6               214
  N1               1                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
  SLC16A1 MUTATED     7   0
  SLC16A1 WILD-TYPE 276  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC16A1 MUTATED      7    0
  SLC16A1 WILD-TYPE  276   48
   clus
vv  SLC16A1 MUTATED SLC16A1 WILD-TYPE
  0               7               276
  1               0                48
[1] 2 2
[1] FALSE
D1701V7, 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
D1701V8, binary
                   cls
clus                  0   1
  SLC16A1 MUTATED     5   2
  SLC16A1 WILD-TYPE 312  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC16A1 MUTATED      5    2
  SLC16A1 WILD-TYPE  312   46
                               clus
vv                              SLC16A1 MUTATED SLC16A1 WILD-TYPE
  COLON ADENOCARCINOMA                        5               312
  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 253   2  22  19
D1701V9, multiclass
    clus
vv   SLC16A1 MUTATED SLC16A1 WILD-TYPE
  R0               4               253
  R1               0                 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"
D1701V10, 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
D1701V11, 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(1702) Variable = MFSD9 MUTATION ANALYSIS
D1702V1, survival
                 sevent
clus2               0   1
  MFSD9 MUTATED     6   3
  MFSD9 WILD-TYPE 276  70
  MFSD9 MUTATED MFSD9 WILD-TYPE 
              9             346 
  MFSD9 MUTATED MFSD9 WILD-TYPE 
              3              70 
$`MFSD9 MUTATED`
TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3518 TCGA-AA-A024 TCGA-AU-6004 TCGA-CM-4743 
       19.66         3.02         1.02        39.06        27.09        23.05 
TCGA-DM-A28F TCGA-DM-A28H TCGA-G4-6588 
       35.97       117.07        26.17 

$`MFSD9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       23.87        20.12        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 
       63.98         6.97         1.02        13.02        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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 
       35.01        26.01        37.02        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       81.37       119.93        60.79        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        91.79        46.75        52.80 

  MFSD9 MUTATED MFSD9 WILD-TYPE 
           1.02            0.00 
  MFSD9 MUTATED MFSD9 WILD-TYPE 
         117.07          140.38 
  MFSD9 MUTATED MFSD9 WILD-TYPE 
          26.17           20.07 
[1] "1.0 - 117.1 (26.2)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.4"
D1702V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MFSD9 MUTATED         1        0        2         4         0         0
  MFSD9 WILD-TYPE      63        1       23       105         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MFSD9 MUTATED           0          0          1          2        0         0
  MFSD9 WILD-TYPE        19         10         40         29       35        13
                 vv
clus              STAGE IVB
  MFSD9 MUTATED           0
  MFSD9 WILD-TYPE         1
D1702V3, multiclass
            clus
vv           MFSD9 MUTATED MFSD9 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              4             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             2              29
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MFSD9 MUTATED     0   1   8   1
  MFSD9 WILD-TYPE   9  67 240  40
D1702V4, multiclass
    clus
vv   MFSD9 MUTATED MFSD9 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             8             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
  MFSD9 MUTATED     7   2   1
  MFSD9 WILD-TYPE 213  78  65
D1702V5, multiclass
    clus
vv   MFSD9 MUTATED MFSD9 WILD-TYPE
  N0             7             213
  N1             2              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"
D1702V6, binary
                 cls
clus                0   1
  MFSD9 MUTATED     9   0
  MFSD9 WILD-TYPE 274  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MFSD9 MUTATED      9    0
  MFSD9 WILD-TYPE  274   48
   clus
vv  MFSD9 MUTATED MFSD9 WILD-TYPE
  0             9             274
  1             0              48
[1] 2 2
[1] FALSE
D1702V7, binary
                 cls
clus                0   1
  MFSD9 MUTATED     5   5
  MFSD9 WILD-TYPE 165 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MFSD9 MUTATED      5    5
  MFSD9 WILD-TYPE  165  192
        clus
vv       MFSD9 MUTATED MFSD9 WILD-TYPE
  FEMALE             5             165
  MALE               5             192
[1] 2 2
[1] FALSE
D1702V8, binary
                 cls
clus                0   1
  MFSD9 MUTATED     8   2
  MFSD9 WILD-TYPE 309  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MFSD9 MUTATED      8    2
  MFSD9 WILD-TYPE  309   46
                               clus
vv                              MFSD9 MUTATED MFSD9 WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MFSD9 MUTATED     8   0   0   0
  MFSD9 WILD-TYPE 249   2  22  21
D1702V9, multiclass
    clus
vv   MFSD9 MUTATED MFSD9 WILD-TYPE
  R0             8             249
  R1             0               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"
D1702V10, 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     6
  MFSD9 WILD-TYPE                        19   170
D1702V11, 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                                        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 = LYST MUTATION ANALYSIS
D1703V1, survival
                sevent
clus2              0   1
  LYST MUTATED    28   5
  LYST WILD-TYPE 254  68
  LYST MUTATED LYST WILD-TYPE 
            33            322 
  LYST MUTATED LYST WILD-TYPE 
             5             68 
$`LYST MUTATED`
TCGA-A6-2676 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-6141 TCGA-A6-6652 
       42.90        33.53        23.61        32.71         8.38        24.69 
TCGA-A6-6781 TCGA-AA-3514 TCGA-AA-3525 TCGA-AA-3555 TCGA-AA-3663 TCGA-AA-3715 
       19.66         1.02         8.05        29.95         6.97        19.04 
TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3977 TCGA-AA-A00A TCGA-AA-A00N 
       31.00        33.01        24.00        25.02        38.04         4.01 
TCGA-AA-A010 TCGA-AA-A02W TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AU-6004 
       34.98        41.00         4.21         0.72        10.88        27.09 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-4952 TCGA-CM-6167 
       21.44        58.39        49.41         0.33        15.62        14.99 
TCGA-CM-6171 TCGA-D5-6928 TCGA-G4-6586 
       14.04        11.64        35.80 

$`LYST WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 
       31.63        30.44        29.19        22.09        22.06        27.09 
TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6653 
       22.52        25.08        25.18        24.16        21.76        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         6.97        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 
        9.07        24.03        37.05        36.03        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.05        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
        2.01        12.99        24.00        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
        7.96        27.02        13.94        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 
       39.98        18.05        40.96         0.07        21.37        56.55 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
        0.79         5.79        22.42        27.42         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        15.75         0.20        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13        83.80        22.36        62.79        61.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  LYST MUTATED LYST WILD-TYPE 
          0.33           0.00 
  LYST MUTATED LYST WILD-TYPE 
         58.39         140.38 
  LYST MUTATED LYST WILD-TYPE 
         23.61          20.07 
[1] "0.3 - 58.4 (23.6)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.2"
D1703V2, 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       22        98         4         0
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LYST MUTATED           1          0          2          2        0         2
  LYST WILD-TYPE        18         10         39         29       35        11
                vv
clus             STAGE IVB
  LYST MUTATED           0
  LYST WILD-TYPE         1
D1703V3, multiclass
            clus
vv           LYST MUTATED LYST WILD-TYPE
  STAGE I               5             59
  STAGE IA              0              1
  STAGE II              3             22
  STAGE IIA            11             98
  STAGE IIB             4              4
  STAGE IIC             1              0
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            2             39
  STAGE IIIC            2             29
  STAGE IV              0             35
  STAGE IVA             2             11
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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   6  19   8
  LYST WILD-TYPE   8  62 229  33
D1703V4, multiclass
    clus
vv   LYST MUTATED LYST WILD-TYPE
  T1            1              8
  T2            6             62
  T3           19            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   3   4
  LYST WILD-TYPE 194  77  62
D1703V5, multiclass
    clus
vv   LYST MUTATED LYST WILD-TYPE
  N0           26            194
  N1            3             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"
D1703V6, binary
                cls
clus               0   1
  LYST MUTATED    26   2
  LYST WILD-TYPE 257  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  LYST MUTATED     26    2
  LYST WILD-TYPE  257   46
   clus
vv  LYST MUTATED LYST WILD-TYPE
  0           26            257
  1            2             46
[1] 2 2
[1] FALSE
D1703V7, 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
D1703V8, binary
                cls
clus               0   1
  LYST MUTATED    25   9
  LYST WILD-TYPE 292  39
[1] "tbl2"
                cls
clus             [,1] [,2]
  LYST MUTATED     25    9
  LYST WILD-TYPE  292   39
                               clus
vv                              LYST MUTATED LYST WILD-TYPE
  COLON ADENOCARCINOMA                    25            292
  COLON MUCINOUS ADENOCARCINOMA            9             39
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  LYST MUTATED    24   0   0   2
  LYST WILD-TYPE 233   2  22  19
D1703V9, multiclass
    clus
vv   LYST MUTATED LYST WILD-TYPE
  R0           24            233
  R1            0              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"
D1703V10, 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
D1703V11, 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(1704) Variable = GLT8D1 MUTATION ANALYSIS
D1704V1, survival
                  sevent
clus2                0   1
  GLT8D1 MUTATED     7   0
  GLT8D1 WILD-TYPE 275  73
  GLT8D1 MUTATED GLT8D1 WILD-TYPE 
               7              348 
  GLT8D1 MUTATED GLT8D1 WILD-TYPE 
               0               73 
$`GLT8D1 MUTATED`
TCGA-A6-6780 TCGA-AA-A010 TCGA-AD-5900 TCGA-AD-6895 TCGA-AZ-4315 TCGA-CK-4952 
       20.12        34.98         0.07         0.72        58.39        15.62 
TCGA-D5-6930 
        1.51 

$`GLT8D1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 
        0.10         1.35        17.56       102.44        40.34        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  GLT8D1 MUTATED GLT8D1 WILD-TYPE 
            0.07             0.00 
  GLT8D1 MUTATED GLT8D1 WILD-TYPE 
           58.39           140.38 
  GLT8D1 MUTATED GLT8D1 WILD-TYPE 
           15.62            20.63 
[1] "0.1 - 58.4 (15.6)"  "0.0 - 140.4 (20.6)"
[1] "hr="     "9100000"
D1704V2, 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       25       105         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GLT8D1 MUTATED           1          0          0          0        0
  GLT8D1 WILD-TYPE        18         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  GLT8D1 MUTATED           0         0
  GLT8D1 WILD-TYPE        13         1
D1704V3, multiclass
            clus
vv           GLT8D1 MUTATED GLT8D1 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               4              105
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GLT8D1 MUTATED     0   1   5   2
  GLT8D1 WILD-TYPE   9  67 243  39
D1704V4, multiclass
    clus
vv   GLT8D1 MUTATED GLT8D1 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              5              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
  GLT8D1 MUTATED     6   1   1
  GLT8D1 WILD-TYPE 214  79  65
D1704V5, multiclass
    clus
vv   GLT8D1 MUTATED GLT8D1 WILD-TYPE
  N0              6              214
  N1              1               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"
D1704V6, binary
                  cls
clus                 0   1
  GLT8D1 MUTATED     5   0
  GLT8D1 WILD-TYPE 278  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLT8D1 MUTATED      5    0
  GLT8D1 WILD-TYPE  278   48
   clus
vv  GLT8D1 MUTATED GLT8D1 WILD-TYPE
  0              5              278
  1              0               48
[1] 2 2
[1] FALSE
D1704V7, 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
D1704V8, binary
                  cls
clus                 0   1
  GLT8D1 MUTATED     4   4
  GLT8D1 WILD-TYPE 313  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLT8D1 MUTATED      4    4
  GLT8D1 WILD-TYPE  313   44
                               clus
vv                              GLT8D1 MUTATED GLT8D1 WILD-TYPE
  COLON ADENOCARCINOMA                       4              313
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  GLT8D1 MUTATED     5   0   0   1
  GLT8D1 WILD-TYPE 252   2  22  20
D1704V9, multiclass
    clus
vv   GLT8D1 MUTATED GLT8D1 WILD-TYPE
  R0              5              252
  R1              0                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"
D1704V10, 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
D1704V11, 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(1705) Variable = RRP9 MUTATION ANALYSIS
D1705V1, survival
                sevent
clus2              0   1
  RRP9 MUTATED    10   2
  RRP9 WILD-TYPE 272  71
  RRP9 MUTATED RRP9 WILD-TYPE 
            12            343 
  RRP9 MUTATED RRP9 WILD-TYPE 
             2             71 
$`RRP9 MUTATED`
TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3833 TCGA-AA-3864 TCGA-AA-3979 TCGA-AA-A01R 
        6.97         0.92        15.95        53.00        24.00        35.01 
TCGA-CK-4952 TCGA-CK-5916 TCGA-CM-6163 TCGA-D5-6538 TCGA-D5-6927 TCGA-DM-A0XF 
       15.62        21.14        14.04        17.13         9.44        38.20 

$`RRP9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.05        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        25.02        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 
        1.35        17.56       102.44        40.34        49.08        51.32 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99         2.93         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        16.01        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02        12.00        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  RRP9 MUTATED RRP9 WILD-TYPE 
          0.92           0.00 
  RRP9 MUTATED RRP9 WILD-TYPE 
         53.00         140.38 
  RRP9 MUTATED RRP9 WILD-TYPE 
         16.54          20.28 
[1] "0.9 - 53.0 (16.5)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1"  
D1705V2, 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       23       106         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RRP9 MUTATED           3          0          1          1        0         0
  RRP9 WILD-TYPE        16         10         40         30       35        13
                vv
clus             STAGE IVB
  RRP9 MUTATED           0
  RRP9 WILD-TYPE         1
D1705V3, multiclass
            clus
vv           RRP9 MUTATED RRP9 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             3            106
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             3             16
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            1             30
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RRP9 MUTATED     2   0   9   1
  RRP9 WILD-TYPE   7  68 239  40
D1705V4, multiclass
    clus
vv   RRP9 MUTATED RRP9 WILD-TYPE
  T1            2              7
  T2            0             68
  T3            9            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
  RRP9 MUTATED     7   1   4
  RRP9 WILD-TYPE 213  79  62
D1705V5, multiclass
    clus
vv   RRP9 MUTATED RRP9 WILD-TYPE
  N0            7            213
  N1            1             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"
D1705V6, binary
                cls
clus               0   1
  RRP9 MUTATED    12   0
  RRP9 WILD-TYPE 271  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  RRP9 MUTATED     12    0
  RRP9 WILD-TYPE  271   48
   clus
vv  RRP9 MUTATED RRP9 WILD-TYPE
  0           12            271
  1            0             48
[1] 2 2
[1] FALSE
D1705V7, 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
D1705V8, binary
                cls
clus               0   1
  RRP9 MUTATED     9   3
  RRP9 WILD-TYPE 308  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  RRP9 MUTATED      9    3
  RRP9 WILD-TYPE  308   45
                               clus
vv                              RRP9 MUTATED RRP9 WILD-TYPE
  COLON ADENOCARCINOMA                     9            308
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RRP9 MUTATED     9   0   0   2
  RRP9 WILD-TYPE 248   2  22  19
D1705V9, multiclass
    clus
vv   RRP9 MUTATED RRP9 WILD-TYPE
  R0            9            248
  R1            0              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"
D1705V10, 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
D1705V11, 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(1706) Variable = HSPA4L MUTATION ANALYSIS
D1706V1, survival
                  sevent
clus2                0   1
  HSPA4L MUTATED     7   1
  HSPA4L WILD-TYPE 275  72
  HSPA4L MUTATED HSPA4L WILD-TYPE 
               8              347 
  HSPA4L MUTATED HSPA4L WILD-TYPE 
               1               72 
$`HSPA4L MUTATED`
TCGA-AA-3555 TCGA-AA-3663 TCGA-AA-3715 TCGA-AA-3950 TCGA-AZ-4315 TCGA-CA-6717 
       29.95         6.97        19.04        24.00        58.39         0.33 
TCGA-DM-A28H TCGA-G4-6310 
      117.07        45.11 

$`HSPA4L WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        17.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 
       81.37       119.93        35.97        60.79        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        51.75        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  HSPA4L MUTATED HSPA4L WILD-TYPE 
            0.33             0.00 
  HSPA4L MUTATED HSPA4L WILD-TYPE 
          117.07           140.38 
  HSPA4L MUTATED HSPA4L WILD-TYPE 
          26.975           20.120 
[1] "0.3 - 117.1 (27.0)" "0.0 - 140.4 (20.1)"
[1] "hr=" "2.3"
D1706V2, 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       23       105         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HSPA4L MUTATED           0          0          1          1        0
  HSPA4L WILD-TYPE        19         10         40         30       35
                  vv
clus               STAGE IVA STAGE IVB
  HSPA4L MUTATED           0         0
  HSPA4L WILD-TYPE        13         1
D1706V3, multiclass
            clus
vv           HSPA4L MUTATED HSPA4L WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               4              105
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  HSPA4L MUTATED     0   0   8   0
  HSPA4L WILD-TYPE   9  68 240  41
D1706V4, multiclass
    clus
vv   HSPA4L MUTATED HSPA4L WILD-TYPE
  T1              0                9
  T2              0               68
  T3              8              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
  HSPA4L MUTATED     6   1   1
  HSPA4L WILD-TYPE 214  79  65
D1706V5, multiclass
    clus
vv   HSPA4L MUTATED HSPA4L WILD-TYPE
  N0              6              214
  N1              1               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"
D1706V6, binary
                  cls
clus                 0   1
  HSPA4L MUTATED     8   0
  HSPA4L WILD-TYPE 275  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HSPA4L MUTATED      8    0
  HSPA4L WILD-TYPE  275   48
   clus
vv  HSPA4L MUTATED HSPA4L WILD-TYPE
  0              8              275
  1              0               48
[1] 2 2
[1] FALSE
D1706V7, 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
D1706V8, binary
                  cls
clus                 0   1
  HSPA4L MUTATED     5   3
  HSPA4L WILD-TYPE 312  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HSPA4L MUTATED      5    3
  HSPA4L WILD-TYPE  312   45
                               clus
vv                              HSPA4L MUTATED HSPA4L WILD-TYPE
  COLON ADENOCARCINOMA                       5              312
  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 251   2  22  20
D1706V9, multiclass
    clus
vv   HSPA4L MUTATED HSPA4L WILD-TYPE
  R0              6              251
  R1              0                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"
D1706V10, 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
D1706V11, 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(1707) Variable = CASC4 MUTATION ANALYSIS
D1707V1, survival
                 sevent
clus2               0   1
  CASC4 MUTATED     5   0
  CASC4 WILD-TYPE 277  73
  CASC4 MUTATED CASC4 WILD-TYPE 
              5             350 
  CASC4 MUTATED CASC4 WILD-TYPE 
              0              73 
$`CASC4 MUTATED`
TCGA-A6-6651 TCGA-AA-3554 TCGA-AA-A010 TCGA-CM-4746 TCGA-D5-6533 
       21.76        17.95        34.98        37.02         1.32 

$`CASC4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        24.16        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  CASC4 MUTATED CASC4 WILD-TYPE 
           1.32            0.00 
  CASC4 MUTATED CASC4 WILD-TYPE 
          37.02          140.38 
  CASC4 MUTATED CASC4 WILD-TYPE 
         21.760          20.155 
[1] "1.3 - 37.0 (21.8)"  "0.0 - 140.4 (20.2)"
[1] "hr="     "9100000"
D1707V2, 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       25       108         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CASC4 MUTATED           0          0          2          0        0         0
  CASC4 WILD-TYPE        19         10         39         31       35        13
                 vv
clus              STAGE IVB
  CASC4 MUTATED           0
  CASC4 WILD-TYPE         1
D1707V3, multiclass
            clus
vv           CASC4 MUTATED CASC4 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              1             108
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CASC4 MUTATED     0   1   2   2
  CASC4 WILD-TYPE   9  67 246  39
D1707V4, multiclass
    clus
vv   CASC4 MUTATED CASC4 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             2             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
  CASC4 MUTATED     4   1   0
  CASC4 WILD-TYPE 216  79  66
D1707V5, multiclass
    clus
vv   CASC4 MUTATED CASC4 WILD-TYPE
  N0             4             216
  N1             1              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"
D1707V6, binary
                 cls
clus                0   1
  CASC4 MUTATED     4   0
  CASC4 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASC4 MUTATED      4    0
  CASC4 WILD-TYPE  279   48
   clus
vv  CASC4 MUTATED CASC4 WILD-TYPE
  0             4             279
  1             0              48
[1] 2 2
[1] FALSE
D1707V7, 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
D1707V8, binary
                 cls
clus                0   1
  CASC4 MUTATED     5   0
  CASC4 WILD-TYPE 312  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASC4 MUTATED      5    0
  CASC4 WILD-TYPE  312   48
                               clus
vv                              CASC4 MUTATED CASC4 WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  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 253   2  22  21
D1707V9, multiclass
    clus
vv   CASC4 MUTATED CASC4 WILD-TYPE
  R0             4             253
  R1             0               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"
D1707V10, 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
D1707V11, 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(1708) Variable = RAG1 MUTATION ANALYSIS
D1708V1, survival
                sevent
clus2              0   1
  RAG1 MUTATED    12   1
  RAG1 WILD-TYPE 270  72
  RAG1 MUTATED RAG1 WILD-TYPE 
            13            342 
  RAG1 MUTATED RAG1 WILD-TYPE 
             1             72 
$`RAG1 MUTATED`
TCGA-A6-5661 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3877 TCGA-AA-3976 TCGA-AA-3977 
       33.53        19.66        63.98        31.00        26.01        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6889 TCGA-AZ-4315 TCGA-CM-6161 TCGA-D5-6536 
        4.01        34.98        56.55        58.39        15.02        17.85 
TCGA-D5-6540 
       16.14 

$`RAG1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       27.02        29.98        18.05         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        15.12         4.80        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  RAG1 MUTATED RAG1 WILD-TYPE 
          4.01           0.00 
  RAG1 MUTATED RAG1 WILD-TYPE 
         63.98         140.38 
  RAG1 MUTATED RAG1 WILD-TYPE 
         26.01          20.07 
[1] "4.0 - 64.0 (26.0)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "3.3"
D1708V2, 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       24       104         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        19          9         41         30       35        13
                vv
clus             STAGE IVB
  RAG1 MUTATED           0
  RAG1 WILD-TYPE         1
D1708V3, multiclass
            clus
vv           RAG1 MUTATED RAG1 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             5            104
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            1              9
  STAGE IIIB            0             41
  STAGE IIIC            1             30
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RAG1 MUTATED     1   4   6   3
  RAG1 WILD-TYPE   8  64 242  38
D1708V4, multiclass
    clus
vv   RAG1 MUTATED RAG1 WILD-TYPE
  T1            1              8
  T2            4             64
  T3            6            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
  RAG1 MUTATED    12   2   0
  RAG1 WILD-TYPE 208  78  66
D1708V5, multiclass
    clus
vv   RAG1 MUTATED RAG1 WILD-TYPE
  N0           12            208
  N1            2             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"
D1708V6, binary
                cls
clus               0   1
  RAG1 MUTATED    12   0
  RAG1 WILD-TYPE 271  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAG1 MUTATED     12    0
  RAG1 WILD-TYPE  271   48
   clus
vv  RAG1 MUTATED RAG1 WILD-TYPE
  0           12            271
  1            0             48
[1] 2 2
[1] FALSE
D1708V7, 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
D1708V8, binary
                cls
clus               0   1
  RAG1 MUTATED    10   4
  RAG1 WILD-TYPE 307  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAG1 MUTATED     10    4
  RAG1 WILD-TYPE  307   44
                               clus
vv                              RAG1 MUTATED RAG1 WILD-TYPE
  COLON ADENOCARCINOMA                    10            307
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RAG1 MUTATED    12   0   0   0
  RAG1 WILD-TYPE 245   2  22  21
D1708V9, multiclass
    clus
vv   RAG1 MUTATED RAG1 WILD-TYPE
  R0           12            245
  R1            0              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"
D1708V10, 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
D1708V11, 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(1709) Variable = ZNF416 MUTATION ANALYSIS
D1709V1, survival
                  sevent
clus2                0   1
  ZNF416 MUTATED     5   2
  ZNF416 WILD-TYPE 277  71
  ZNF416 MUTATED ZNF416 WILD-TYPE 
               7              348 
  ZNF416 MUTATED ZNF416 WILD-TYPE 
               2               71 
$`ZNF416 MUTATED`
TCGA-AA-A010 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CA-6718 
       34.98        21.44        58.39       100.01         0.33         0.10 
TCGA-F4-6570 
        6.18 

$`ZNF416 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        15.75         0.20        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-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        13.38        13.45        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  ZNF416 MUTATED ZNF416 WILD-TYPE 
             0.1              0.0 
  ZNF416 MUTATED ZNF416 WILD-TYPE 
          100.01           140.38 
  ZNF416 MUTATED ZNF416 WILD-TYPE 
          21.440           20.155 
[1] "0.1 - 100.0 (21.4)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D1709V2, 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       23       104         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF416 MUTATED           0          0          0          0        0
  ZNF416 WILD-TYPE        19         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF416 MUTATED           0         0
  ZNF416 WILD-TYPE        13         1
D1709V3, multiclass
            clus
vv           ZNF416 MUTATED ZNF416 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               5              104
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF416 MUTATED     0   0   6   2
  ZNF416 WILD-TYPE   9  68 242  39
D1709V4, multiclass
    clus
vv   ZNF416 MUTATED ZNF416 WILD-TYPE
  T1              0                9
  T2              0               68
  T3              6              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
  ZNF416 MUTATED     8   0   0
  ZNF416 WILD-TYPE 212  80  66
D1709V5, multiclass
    clus
vv   ZNF416 MUTATED ZNF416 WILD-TYPE
  N0              8              212
  N1              0               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"
D1709V6, binary
                  cls
clus                 0   1
  ZNF416 MUTATED     7   0
  ZNF416 WILD-TYPE 276  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF416 MUTATED      7    0
  ZNF416 WILD-TYPE  276   48
   clus
vv  ZNF416 MUTATED ZNF416 WILD-TYPE
  0              7              276
  1              0               48
[1] 2 2
[1] FALSE
D1709V7, 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
D1709V8, binary
                  cls
clus                 0   1
  ZNF416 MUTATED     7   1
  ZNF416 WILD-TYPE 310  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF416 MUTATED      7    1
  ZNF416 WILD-TYPE  310   47
                               clus
vv                              ZNF416 MUTATED ZNF416 WILD-TYPE
  COLON ADENOCARCINOMA                       7              310
  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 252   2  22  19
D1709V9, multiclass
    clus
vv   ZNF416 MUTATED ZNF416 WILD-TYPE
  R0              5              252
  R1              0                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"
D1709V10, 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
D1709V11, 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(1710) Variable = GRM1 MUTATION ANALYSIS
D1710V1, survival
                sevent
clus2              0   1
  GRM1 MUTATED    22   2
  GRM1 WILD-TYPE 260  71
  GRM1 MUTATED GRM1 WILD-TYPE 
            24            331 
  GRM1 MUTATED GRM1 WILD-TYPE 
             2             71 
$`GRM1 MUTATED`
TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3672 TCGA-AA-3812 TCGA-AA-3949 
       20.28         3.02        63.98         0.92        35.05        26.01 
TCGA-AA-3966 TCGA-AA-A00E TCGA-AA-A00J TCGA-AD-6963 TCGA-AY-6196 TCGA-AZ-6598 
        2.01        30.02        18.05        27.42         0.20        49.41 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5913 TCGA-CK-6751 TCGA-CM-6165 TCGA-CM-6168 
        0.33         0.10        51.32       124.27        16.04        12.99 
TCGA-CM-6674 TCGA-D5-5538 TCGA-D5-6529 TCGA-D5-6540 TCGA-D5-6541 TCGA-G4-6588 
       12.95        12.26        20.19        16.14        15.58        26.17 

$`GRM1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       23.87        20.12        19.66         7.04         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        19.04        10.06        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       38.04        19.00        34.03        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        15.75        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07         0.26         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 
      102.44        40.34        15.62        49.08        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 
       12.00        14.04        29.03        21.99        14.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        14.04        11.01        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 
       11.01        10.06        12.03        45.40        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       11.51        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
        4.80        17.13        12.49         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 
       52.80 

  GRM1 MUTATED GRM1 WILD-TYPE 
           0.1            0.0 
  GRM1 MUTATED GRM1 WILD-TYPE 
        124.27         140.38 
  GRM1 MUTATED GRM1 WILD-TYPE 
        17.095         20.980 
[1] "0.1 - 124.3 (17.1)" "0.0 - 140.4 (21.0)"
[1] "hr=" "2.5"
D1710V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GRM1 MUTATED         2        0        4        12         1         0
  GRM1 WILD-TYPE      62        1       21        97         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GRM1 MUTATED           1          0          3          1        2         0
  GRM1 WILD-TYPE        18         10         38         30       33        13
                vv
clus             STAGE IVB
  GRM1 MUTATED           0
  GRM1 WILD-TYPE         1
D1710V3, multiclass
            clus
vv           GRM1 MUTATED GRM1 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              4             21
  STAGE IIA            12             97
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            3             38
  STAGE IIIC            1             30
  STAGE IV              2             33
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GRM1 MUTATED     0   2  21   4
  GRM1 WILD-TYPE   9  66 227  37
D1710V4, multiclass
    clus
vv   GRM1 MUTATED GRM1 WILD-TYPE
  T1            0              9
  T2            2             66
  T3           21            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
  GRM1 MUTATED    20   4   3
  GRM1 WILD-TYPE 200  76  63
D1710V5, multiclass
    clus
vv   GRM1 MUTATED GRM1 WILD-TYPE
  N0           20            200
  N1            4             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"
D1710V6, binary
                cls
clus               0   1
  GRM1 MUTATED    19   2
  GRM1 WILD-TYPE 264  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRM1 MUTATED     19    2
  GRM1 WILD-TYPE  264   46
   clus
vv  GRM1 MUTATED GRM1 WILD-TYPE
  0           19            264
  1            2             46
[1] 2 2
[1] FALSE
D1710V7, binary
                cls
clus               0   1
  GRM1 MUTATED    13  14
  GRM1 WILD-TYPE 157 183
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRM1 MUTATED     13   14
  GRM1 WILD-TYPE  157  183
        clus
vv       GRM1 MUTATED GRM1 WILD-TYPE
  FEMALE           13            157
  MALE             14            183
[1] 2 2
[1] FALSE
D1710V8, binary
                cls
clus               0   1
  GRM1 MUTATED    20   7
  GRM1 WILD-TYPE 297  41
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRM1 MUTATED     20    7
  GRM1 WILD-TYPE  297   41
                               clus
vv                              GRM1 MUTATED GRM1 WILD-TYPE
  COLON ADENOCARCINOMA                    20            297
  COLON MUCINOUS ADENOCARCINOMA            7             41
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  GRM1 MUTATED    17   0   2   4
  GRM1 WILD-TYPE 240   2  20  17
D1710V9, multiclass
    clus
vv   GRM1 MUTATED GRM1 WILD-TYPE
  R0           17            240
  R1            0              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"
D1710V10, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GRM1 MUTATED                                  0     2
  GRM1 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GRM1 MUTATED                           1    13
  GRM1 WILD-TYPE                        18   163
D1710V11, multiclass
                                  clus
vv                                 GRM1 MUTATED GRM1 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(1711) Variable = CHMP4B MUTATION ANALYSIS
D1711V1, survival
                  sevent
clus2                0   1
  CHMP4B MUTATED     2   1
  CHMP4B WILD-TYPE 280  72
  CHMP4B MUTATED CHMP4B WILD-TYPE 
               3              352 
  CHMP4B MUTATED CHMP4B WILD-TYPE 
               1               72 
$`CHMP4B MUTATED`
TCGA-A6-6780 TCGA-AA-3811 TCGA-D5-6540 
       20.12        10.06        16.14 

$`CHMP4B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  CHMP4B MUTATED CHMP4B WILD-TYPE 
           10.06             0.00 
  CHMP4B MUTATED CHMP4B WILD-TYPE 
           20.12           140.38 
  CHMP4B MUTATED CHMP4B WILD-TYPE 
           16.14            20.63 
[1] "10.1 - 20.1 (16.1)" "0.0 - 140.4 (20.6)"
[1] "hr=" "2.5"
D1711V2, 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       25       108         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CHMP4B MUTATED           1          0          0          0        0
  CHMP4B WILD-TYPE        18         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  CHMP4B MUTATED           0         0
  CHMP4B WILD-TYPE        13         1
D1711V3, multiclass
            clus
vv           CHMP4B MUTATED CHMP4B WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               1              108
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CHMP4B MUTATED     0   1   2   0
  CHMP4B WILD-TYPE   9  67 246  41
D1711V4, multiclass
    clus
vv   CHMP4B MUTATED CHMP4B WILD-TYPE
  T1              0                9
  T2              1               67
  T3              2              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
  CHMP4B MUTATED     2   0   1
  CHMP4B WILD-TYPE 218  80  65
D1711V5, multiclass
    clus
vv   CHMP4B MUTATED CHMP4B WILD-TYPE
  N0              2              218
  N1              0               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"
D1711V6, binary
                  cls
clus                 0   1
  CHMP4B MUTATED     2   0
  CHMP4B WILD-TYPE 281  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHMP4B MUTATED      2    0
  CHMP4B WILD-TYPE  281   48
   clus
vv  CHMP4B MUTATED CHMP4B WILD-TYPE
  0              2              281
  1              0               48
[1] 2 2
[1] FALSE
D1711V7, 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
D1711V8, binary
                  cls
clus                 0   1
  CHMP4B MUTATED     1   2
  CHMP4B WILD-TYPE 316  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHMP4B MUTATED      1    2
  CHMP4B WILD-TYPE  316   46
                               clus
vv                              CHMP4B MUTATED CHMP4B WILD-TYPE
  COLON ADENOCARCINOMA                       1              316
  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 255   2  22  21
D1711V9, multiclass
[1] "Remove cluster labels:" "CHMP4B MUTATED"        
clus
  CHMP4B MUTATED CHMP4B WILD-TYPE 
               2              300 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-5657 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-A6-5659       TCGA-A6-5661       TCGA-A6-5665       TCGA-A6-6781 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3489       TCGA-AA-3492       TCGA-AA-3496       TCGA-AA-3502 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3510       TCGA-AA-3511       TCGA-AA-3514       TCGA-AA-3517 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3518       TCGA-AA-3519       TCGA-AA-3520       TCGA-AA-3521 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3522       TCGA-AA-3524       TCGA-AA-3525       TCGA-AA-3526 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3527       TCGA-AA-3529       TCGA-AA-3530       TCGA-AA-3531 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3532       TCGA-AA-3534       TCGA-AA-3538       TCGA-AA-3542 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3543       TCGA-AA-3544       TCGA-AA-3548       TCGA-AA-3549 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3552       TCGA-AA-3553       TCGA-AA-3554       TCGA-AA-3555 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3556       TCGA-AA-3558       TCGA-AA-3560       TCGA-AA-3561 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3562       TCGA-AA-3655       TCGA-AA-3660       TCGA-AA-3662 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3663       TCGA-AA-3664       TCGA-AA-3666       TCGA-AA-3667 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3672       TCGA-AA-3673       TCGA-AA-3678       TCGA-AA-3679 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3680       TCGA-AA-3681       TCGA-AA-3684       TCGA-AA-3685 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3688       TCGA-AA-3692       TCGA-AA-3693       TCGA-AA-3695 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3696       TCGA-AA-3697       TCGA-AA-3710       TCGA-AA-3712 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3713       TCGA-AA-3715       TCGA-AA-3812       TCGA-AA-3814 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3815       TCGA-AA-3818       TCGA-AA-3819       TCGA-AA-3821 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3831       TCGA-AA-3833       TCGA-AA-3837       TCGA-AA-3842 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3844       TCGA-AA-3845       TCGA-AA-3846       TCGA-AA-3848 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3850       TCGA-AA-3851       TCGA-AA-3852       TCGA-AA-3854 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3855       TCGA-AA-3856       TCGA-AA-3858       TCGA-AA-3860 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3861       TCGA-AA-3864       TCGA-AA-3866       TCGA-AA-3867 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3869       TCGA-AA-3870       TCGA-AA-3872       TCGA-AA-3875 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3877       TCGA-AA-3930       TCGA-AA-3939       TCGA-AA-3941 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3947       TCGA-AA-3949       TCGA-AA-3950       TCGA-AA-3952 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3955       TCGA-AA-3956       TCGA-AA-3968       TCGA-AA-3971 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3972       TCGA-AA-3973       TCGA-AA-3975       TCGA-AA-3976 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3979       TCGA-AA-3984       TCGA-AA-3986       TCGA-AA-3989 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3994       TCGA-AA-A004       TCGA-AA-A00A       TCGA-AA-A00D 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-A00E       TCGA-AA-A00F       TCGA-AA-A00J       TCGA-AA-A00K 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-A00L       TCGA-AA-A00N       TCGA-AA-A00O       TCGA-AA-A00Q 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-A00R       TCGA-AA-A00U       TCGA-AA-A00W       TCGA-AA-A00Z 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-A010       TCGA-AA-A017       TCGA-AA-A01D       TCGA-AA-A01F 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-A01G       TCGA-AA-A01I       TCGA-AA-A01K       TCGA-AA-A01P 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-A01Q       TCGA-AA-A01R       TCGA-AA-A01S       TCGA-AA-A01T 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-A01V       TCGA-AA-A01X       TCGA-AA-A01Z       TCGA-AA-A022 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-A024       TCGA-AA-A029       TCGA-AA-A02F       TCGA-AA-A02H 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-A02J       TCGA-AA-A02K       TCGA-AA-A02O       TCGA-AA-A02W 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-A02Y       TCGA-AA-A03F       TCGA-AA-A03J       TCGA-AD-5900 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AD-6548       TCGA-AD-6888       TCGA-AU-3779       TCGA-AU-6004 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AY-4070       TCGA-AY-4071       TCGA-AY-5543       TCGA-AY-6196 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AY-6197       TCGA-AY-6386       TCGA-AZ-4315       TCGA-AZ-4681 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AZ-4682       TCGA-CA-5254       TCGA-CA-5255       TCGA-CA-5796 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CA-5797       TCGA-CA-6715       TCGA-CA-6716       TCGA-CA-6717 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CA-6718       TCGA-CA-6719       TCGA-CK-4947       TCGA-CK-4948 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CK-4950       TCGA-CK-4952       TCGA-CK-5912       TCGA-CK-5913 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CK-5914       TCGA-CK-5915       TCGA-CK-5916       TCGA-CK-6746 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CK-6747       TCGA-CK-6748       TCGA-CK-6751       TCGA-CM-4743 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CM-4744       TCGA-CM-4746       TCGA-CM-4747       TCGA-CM-4752 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CM-5341       TCGA-CM-5344       TCGA-CM-5348       TCGA-CM-5349 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CM-5860       TCGA-CM-5861       TCGA-CM-5862       TCGA-CM-5863 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CM-5864       TCGA-CM-5868       TCGA-CM-6161       TCGA-CM-6162 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CM-6163       TCGA-CM-6164       TCGA-CM-6165       TCGA-CM-6166 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CM-6167       TCGA-CM-6168       TCGA-CM-6169       TCGA-CM-6170 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CM-6171       TCGA-CM-6172       TCGA-CM-6674       TCGA-CM-6675 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CM-6676       TCGA-CM-6677       TCGA-CM-6678       TCGA-CM-6679 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CM-6680       TCGA-D5-5537       TCGA-D5-5538       TCGA-D5-5539 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-D5-5540       TCGA-D5-5541       TCGA-D5-6529       TCGA-D5-6532 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-D5-6533       TCGA-D5-6534       TCGA-D5-6535       TCGA-D5-6536 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-D5-6537       TCGA-D5-6538       TCGA-D5-6539       TCGA-D5-6541 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-D5-6898       TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-D5-6924       TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-D5-6929       TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-D5-7000       TCGA-F4-6459       TCGA-F4-6460       TCGA-F4-6569 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704       TCGA-F4-6805 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808       TCGA-F4-6809 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856       TCGA-G4-6293 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304       TCGA-G4-6306 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310       TCGA-G4-6315 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323       TCGA-G4-6586 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
D1711V10, 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
D1711V11, multiclass
[1] "Remove cluster labels:" "CHMP4B MUTATED"        
clus
  CHMP4B MUTATED CHMP4B WILD-TYPE 
               2              204 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-4105 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-A6-5661       TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5665 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-A6-5666       TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-A6-6142       TCGA-A6-6648       TCGA-A6-6649       TCGA-A6-6651 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-A6-6652       TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6781 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-A6-6782       TCGA-AD-5900       TCGA-AD-6548       TCGA-AD-6888 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AD-6889       TCGA-AD-6890       TCGA-AD-6895       TCGA-AD-6899 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6964       TCGA-AD-6965 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070       TCGA-AY-4071 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AZ-4315       TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4681 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AZ-4682       TCGA-AZ-5403       TCGA-AZ-5407       TCGA-AZ-6598 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AZ-6599       TCGA-AZ-6600       TCGA-AZ-6601       TCGA-AZ-6603 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AZ-6605       TCGA-AZ-6606       TCGA-AZ-6607       TCGA-AZ-6608 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CA-5254       TCGA-CA-5255       TCGA-CA-5796       TCGA-CA-5797 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CA-6715       TCGA-CA-6716       TCGA-CA-6717       TCGA-CA-6718 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CA-6719       TCGA-CK-4947       TCGA-CK-4948       TCGA-CK-4950 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CK-4952       TCGA-CK-5912       TCGA-CK-5913       TCGA-CK-5914 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CK-5915       TCGA-CK-5916       TCGA-CK-6746       TCGA-CK-6747 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CK-6748       TCGA-CK-6751       TCGA-CM-4743       TCGA-CM-4744 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CM-4746       TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CM-5344       TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CM-5861       TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CM-5868       TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CM-6164       TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CM-6168       TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CM-6172       TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CM-6677       TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-D5-5537       TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-D5-5541       TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-D5-6534       TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-D5-6538       TCGA-D5-6539       TCGA-D5-6541       TCGA-D5-6898 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923       TCGA-D5-6924 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928       TCGA-D5-6929 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932       TCGA-D5-7000 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-DM-A0X9       TCGA-DM-A0XD       TCGA-DM-A0XF       TCGA-DM-A1D0 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-DM-A1D4       TCGA-DM-A1D6       TCGA-DM-A1D7       TCGA-DM-A1D8 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-DM-A1D9       TCGA-DM-A1DA       TCGA-DM-A1DB       TCGA-DM-A1HA 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-DM-A1HB       TCGA-DM-A282       TCGA-DM-A285       TCGA-DM-A28C 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-DM-A28E       TCGA-DM-A28F       TCGA-DM-A28G       TCGA-DM-A28H 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-DM-A28K       TCGA-F4-6459       TCGA-F4-6460       TCGA-F4-6569 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704       TCGA-F4-6805 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808       TCGA-F4-6809 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856       TCGA-G4-6293 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304       TCGA-G4-6306 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310       TCGA-G4-6315 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323       TCGA-G4-6586 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 

Clustering(1712) Variable = CYP20A1 MUTATION ANALYSIS
D1712V1, survival
                   sevent
clus2                 0   1
  CYP20A1 MUTATED     6   2
  CYP20A1 WILD-TYPE 276  71
  CYP20A1 MUTATED CYP20A1 WILD-TYPE 
                8               347 
  CYP20A1 MUTATED CYP20A1 WILD-TYPE 
                2                71 
$`CYP20A1 MUTATED`
TCGA-A6-6781 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3856 TCGA-AD-6964 TCGA-AY-6197 
       19.66         6.97         0.92         0.99        10.88        21.44 
TCGA-AZ-4315 TCGA-D5-6537 
       58.39         4.80 

$`CYP20A1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 
        0.00        33.07         0.00        36.03        32.05        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
        0.72         5.79        22.42        27.42         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       27.09        16.31         0.95        15.75         0.20        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  CYP20A1 MUTATED CYP20A1 WILD-TYPE 
             0.92              0.00 
  CYP20A1 MUTATED CYP20A1 WILD-TYPE 
            58.39            140.38 
  CYP20A1 MUTATED CYP20A1 WILD-TYPE 
            8.925            20.980 
[1] "0.9 - 58.4 (8.9)"   "0.0 - 140.4 (21.0)"
[1] "hr=" "1.9"
D1712V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CYP20A1 MUTATED         0        0        1         3         0         0
  CYP20A1 WILD-TYPE      64        1       24       106         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CYP20A1 MUTATED           1          0          1          1        0
  CYP20A1 WILD-TYPE        18         10         40         30       35
                   vv
clus                STAGE IVA STAGE IVB
  CYP20A1 MUTATED           0         0
  CYP20A1 WILD-TYPE        13         1
D1712V3, multiclass
            clus
vv           CYP20A1 MUTATED CYP20A1 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                3               106
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               1                30
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CYP20A1 MUTATED     0   0   6   2
  CYP20A1 WILD-TYPE   9  68 242  39
D1712V4, multiclass
    clus
vv   CYP20A1 MUTATED CYP20A1 WILD-TYPE
  T1               0                 9
  T2               0                68
  T3               6               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
  CYP20A1 MUTATED     4   3   1
  CYP20A1 WILD-TYPE 216  77  65
D1712V5, multiclass
    clus
vv   CYP20A1 MUTATED CYP20A1 WILD-TYPE
  N0               4               216
  N1               3                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"
D1712V6, binary
                   cls
clus                  0   1
  CYP20A1 MUTATED     4   0
  CYP20A1 WILD-TYPE 279  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP20A1 MUTATED      4    0
  CYP20A1 WILD-TYPE  279   48
   clus
vv  CYP20A1 MUTATED CYP20A1 WILD-TYPE
  0               4               279
  1               0                48
[1] 2 2
[1] FALSE
D1712V7, binary
                   cls
clus                  0   1
  CYP20A1 MUTATED     1   7
  CYP20A1 WILD-TYPE 169 190
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP20A1 MUTATED      1    7
  CYP20A1 WILD-TYPE  169  190
        clus
vv       CYP20A1 MUTATED CYP20A1 WILD-TYPE
  FEMALE               1               169
  MALE                 7               190
[1] 2 2
[1] FALSE
D1712V8, binary
                   cls
clus                  0   1
  CYP20A1 MUTATED     7   1
  CYP20A1 WILD-TYPE 310  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP20A1 MUTATED      7    1
  CYP20A1 WILD-TYPE  310   47
                               clus
vv                              CYP20A1 MUTATED CYP20A1 WILD-TYPE
  COLON ADENOCARCINOMA                        7               310
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  CYP20A1 MUTATED     7   0   0   0
  CYP20A1 WILD-TYPE 250   2  22  21
D1712V9, multiclass
    clus
vv   CYP20A1 MUTATED CYP20A1 WILD-TYPE
  R0               7               250
  R1               0                 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"
D1712V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CYP20A1 MUTATED                                  0     0
  CYP20A1 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CYP20A1 MUTATED                           0     5
  CYP20A1 WILD-TYPE                        19   171
D1712V11, multiclass
                                  clus
vv                                 CYP20A1 MUTATED CYP20A1 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(1713) Variable = ZNF630 MUTATION ANALYSIS
D1713V1, survival
                  sevent
clus2                0   1
  ZNF630 MUTATED     6   0
  ZNF630 WILD-TYPE 276  73
  ZNF630 MUTATED ZNF630 WILD-TYPE 
               6              349 
  ZNF630 MUTATED ZNF630 WILD-TYPE 
               0               73 
$`ZNF630 MUTATED`
TCGA-AA-3555 TCGA-AZ-4315 TCGA-AZ-4681 TCGA-CM-6164 TCGA-D5-5540 TCGA-G4-6588 
       29.95        58.39        83.80        29.03        13.51        26.17 

$`ZNF630 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        17.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         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        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        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        12.26        19.59        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 
       52.80 

  ZNF630 MUTATED ZNF630 WILD-TYPE 
           13.51             0.00 
  ZNF630 MUTATED ZNF630 WILD-TYPE 
           83.80           140.38 
  ZNF630 MUTATED ZNF630 WILD-TYPE 
           29.49            20.02 
[1] "13.5 - 83.8 (29.5)" "0.0 - 140.4 (20.0)"
[1] "hr="     "9300000"
D1713V2, 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       25       102         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF630 MUTATED           0          0          0          0        0
  ZNF630 WILD-TYPE        19         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF630 MUTATED           0         0
  ZNF630 WILD-TYPE        13         1
D1713V3, multiclass
            clus
vv           ZNF630 MUTATED ZNF630 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               7              102
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF630 MUTATED     0   0   7   0
  ZNF630 WILD-TYPE   9  68 241  41
D1713V4, multiclass
    clus
vv   ZNF630 MUTATED ZNF630 WILD-TYPE
  T1              0                9
  T2              0               68
  T3              7              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
  ZNF630 MUTATED     7   0   0
  ZNF630 WILD-TYPE 213  80  66
D1713V5, multiclass
    clus
vv   ZNF630 MUTATED ZNF630 WILD-TYPE
  N0              7              213
  N1              0               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
  ZNF630 MUTATED     7   0
  ZNF630 WILD-TYPE 276  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF630 MUTATED      7    0
  ZNF630 WILD-TYPE  276   48
   clus
vv  ZNF630 MUTATED ZNF630 WILD-TYPE
  0              7              276
  1              0               48
[1] 2 2
[1] FALSE
D1713V7, 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
D1713V8, binary
                  cls
clus                 0   1
  ZNF630 MUTATED     6   1
  ZNF630 WILD-TYPE 311  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF630 MUTATED      6    1
  ZNF630 WILD-TYPE  311   47
                               clus
vv                              ZNF630 MUTATED ZNF630 WILD-TYPE
  COLON ADENOCARCINOMA                       6              311
  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 250   2  22  21
D1713V9, multiclass
    clus
vv   ZNF630 MUTATED ZNF630 WILD-TYPE
  R0              7              250
  R1              0                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"
D1713V10, 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
D1713V11, 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(1714) Variable = VEZF1 MUTATION ANALYSIS
D1714V1, survival
                 sevent
clus2               0   1
  VEZF1 MUTATED     6   0
  VEZF1 WILD-TYPE 276  73
  VEZF1 MUTATED VEZF1 WILD-TYPE 
              6             349 
  VEZF1 MUTATED VEZF1 WILD-TYPE 
              0              73 
$`VEZF1 MUTATED`
TCGA-AD-6895 TCGA-CM-6171 TCGA-D5-6928 TCGA-D5-6930 TCGA-F4-6856 TCGA-G4-6588 
        0.72        14.04        11.64         1.51        19.43        26.17 

$`VEZF1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21        56.55         0.79         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        35.41       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 
       52.80 

  VEZF1 MUTATED VEZF1 WILD-TYPE 
           0.72            0.00 
  VEZF1 MUTATED VEZF1 WILD-TYPE 
          26.17          140.38 
  VEZF1 MUTATED VEZF1 WILD-TYPE 
          12.84           20.98 
[1] "0.7 - 26.2 (12.8)"  "0.0 - 140.4 (21.0)"
[1] "hr="     "3300000"
D1714V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  VEZF1 MUTATED         2        0        0         3         0         0
  VEZF1 WILD-TYPE      62        1       25       106         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  VEZF1 MUTATED           0          0          0          0        0         0
  VEZF1 WILD-TYPE        19         10         41         31       35        13
                 vv
clus              STAGE IVB
  VEZF1 MUTATED           0
  VEZF1 WILD-TYPE         1
D1714V3, multiclass
            clus
vv           VEZF1 MUTATED VEZF1 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              3             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  VEZF1 MUTATED     0   2   4   0
  VEZF1 WILD-TYPE   9  66 244  41
D1714V4, multiclass
    clus
vv   VEZF1 MUTATED VEZF1 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             4             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
  VEZF1 MUTATED     5   1   0
  VEZF1 WILD-TYPE 215  79  66
D1714V5, multiclass
    clus
vv   VEZF1 MUTATED VEZF1 WILD-TYPE
  N0             5             215
  N1             1              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"
D1714V6, binary
                 cls
clus                0   1
  VEZF1 MUTATED     5   0
  VEZF1 WILD-TYPE 278  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VEZF1 MUTATED      5    0
  VEZF1 WILD-TYPE  278   48
   clus
vv  VEZF1 MUTATED VEZF1 WILD-TYPE
  0             5             278
  1             0              48
[1] 2 2
[1] FALSE
D1714V7, binary
                 cls
clus                0   1
  VEZF1 MUTATED     2   4
  VEZF1 WILD-TYPE 168 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VEZF1 MUTATED      2    4
  VEZF1 WILD-TYPE  168  193
        clus
vv       VEZF1 MUTATED VEZF1 WILD-TYPE
  FEMALE             2             168
  MALE               4             193
[1] 2 2
[1] FALSE
D1714V8, binary
                 cls
clus                0   1
  VEZF1 MUTATED     3   3
  VEZF1 WILD-TYPE 314  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VEZF1 MUTATED      3    3
  VEZF1 WILD-TYPE  314   45
                               clus
vv                              VEZF1 MUTATED VEZF1 WILD-TYPE
  COLON ADENOCARCINOMA                      3             314
  COLON MUCINOUS ADENOCARCINOMA             3              45
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  VEZF1 MUTATED     5   0   0   0
  VEZF1 WILD-TYPE 252   2  22  21
D1714V9, multiclass
    clus
vv   VEZF1 MUTATED VEZF1 WILD-TYPE
  R0             5             252
  R1             0               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"
D1714V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  VEZF1 MUTATED                                  0     0
  VEZF1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  VEZF1 MUTATED                           0     6
  VEZF1 WILD-TYPE                        19   170
D1714V11, multiclass
                                  clus
vv                                 VEZF1 MUTATED VEZF1 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(1715) Variable = C16ORF88 MUTATION ANALYSIS
D1715V1, survival
                    sevent
clus2                  0   1
  C16ORF88 MUTATED     7   0
  C16ORF88 WILD-TYPE 275  73
  C16ORF88 MUTATED C16ORF88 WILD-TYPE 
                 7                348 
  C16ORF88 MUTATED C16ORF88 WILD-TYPE 
                 0                 73 
$`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 
       19.43 

$`C16ORF88 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01         0.92        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.41       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  C16ORF88 MUTATED C16ORF88 WILD-TYPE 
             15.02               0.00 
  C16ORF88 MUTATED C16ORF88 WILD-TYPE 
             50.04             140.38 
  C16ORF88 MUTATED C16ORF88 WILD-TYPE 
            22.060             20.105 
[1] "15.0 - 50.0 (22.1)" "0.0 - 140.4 (20.1)"
[1] "hr="     "9200000"
D1715V2, 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       24       105         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C16ORF88 MUTATED           1          0          0          0        0
  C16ORF88 WILD-TYPE        18         10         41         31       35
                    vv
clus                 STAGE IVA STAGE IVB
  C16ORF88 MUTATED           0         0
  C16ORF88 WILD-TYPE        13         1
D1715V3, multiclass
            clus
vv           C16ORF88 MUTATED C16ORF88 WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  1                 24
  STAGE IIA                 4                105
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 1                 18
  STAGE IIIA                0                 10
  STAGE IIIB                0                 41
  STAGE IIIC                0                 31
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C16ORF88 MUTATED     0   1   6   0
  C16ORF88 WILD-TYPE   9  67 242  41
D1715V4, multiclass
    clus
vv   C16ORF88 MUTATED C16ORF88 WILD-TYPE
  T1                0                  9
  T2                1                 67
  T3                6                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
  C16ORF88 MUTATED     6   0   1
  C16ORF88 WILD-TYPE 214  80  65
D1715V5, multiclass
    clus
vv   C16ORF88 MUTATED C16ORF88 WILD-TYPE
  N0                6                214
  N1                0                 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"
D1715V6, binary
                    cls
clus                   0   1
  C16ORF88 MUTATED     6   0
  C16ORF88 WILD-TYPE 277  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF88 MUTATED      6    0
  C16ORF88 WILD-TYPE  277   48
   clus
vv  C16ORF88 MUTATED C16ORF88 WILD-TYPE
  0                6                277
  1                0                 48
[1] 2 2
[1] FALSE
D1715V7, 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
D1715V8, binary
                    cls
clus                   0   1
  C16ORF88 MUTATED     4   3
  C16ORF88 WILD-TYPE 313  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF88 MUTATED      4    3
  C16ORF88 WILD-TYPE  313   45
                               clus
vv                              C16ORF88 MUTATED C16ORF88 WILD-TYPE
  COLON ADENOCARCINOMA                         4                313
  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 251   2  22  21
D1715V9, multiclass
    clus
vv   C16ORF88 MUTATED C16ORF88 WILD-TYPE
  R0                6                251
  R1                0                  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"
D1715V10, 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
D1715V11, 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(1716) Variable = CLGN MUTATION ANALYSIS
D1716V1, survival
                sevent
clus2              0   1
  CLGN MUTATED     9   1
  CLGN WILD-TYPE 273  72
  CLGN MUTATED CLGN WILD-TYPE 
            10            345 
  CLGN MUTATED CLGN WILD-TYPE 
             1             72 
$`CLGN MUTATED`
TCGA-A6-4105 TCGA-A6-5660 TCGA-A6-5661 TCGA-AA-3510 TCGA-AA-3710 TCGA-AD-5900 
       14.53        29.19        33.53        63.98        26.99         0.07 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CM-4746 
       17.82        58.39         0.33        37.02 

$`CLGN WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       31.63        30.44        23.61        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4323 
       16.31         0.95        15.75         0.20        21.44         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  CLGN MUTATED CLGN WILD-TYPE 
          0.07           0.00 
  CLGN MUTATED CLGN WILD-TYPE 
         63.98         140.38 
  CLGN MUTATED CLGN WILD-TYPE 
         28.09          20.12 
[1] "0.1 - 64.0 (28.1)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "2.2"
D1716V2, 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       24       104         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        19         10         40         30       35        13
                vv
clus             STAGE IVB
  CLGN MUTATED           0
  CLGN WILD-TYPE         1
D1716V3, multiclass
            clus
vv           CLGN MUTATED CLGN WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             5            104
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            1             30
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CLGN MUTATED     0   2   8   1
  CLGN WILD-TYPE   9  66 240  40
D1716V4, multiclass
    clus
vv   CLGN MUTATED CLGN WILD-TYPE
  T1            0              9
  T2            2             66
  T3            8            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
  CLGN MUTATED     9   1   1
  CLGN WILD-TYPE 211  79  65
D1716V5, multiclass
    clus
vv   CLGN MUTATED CLGN WILD-TYPE
  N0            9            211
  N1            1             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"
D1716V6, binary
                cls
clus               0   1
  CLGN MUTATED     9   0
  CLGN WILD-TYPE 274  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  CLGN MUTATED      9    0
  CLGN WILD-TYPE  274   48
   clus
vv  CLGN MUTATED CLGN WILD-TYPE
  0            9            274
  1            0             48
[1] 2 2
[1] FALSE
D1716V7, 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
D1716V8, binary
                cls
clus               0   1
  CLGN MUTATED     9   2
  CLGN WILD-TYPE 308  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  CLGN MUTATED      9    2
  CLGN WILD-TYPE  308   46
                               clus
vv                              CLGN MUTATED CLGN WILD-TYPE
  COLON ADENOCARCINOMA                     9            308
  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 250   2  22  19
D1716V9, multiclass
    clus
vv   CLGN MUTATED CLGN WILD-TYPE
  R0            7            250
  R1            0              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"
D1716V10, 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
D1716V11, 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(1717) Variable = MCM4 MUTATION ANALYSIS
D1717V1, survival
                sevent
clus2              0   1
  MCM4 MUTATED    10   2
  MCM4 WILD-TYPE 272  71
  MCM4 MUTATED MCM4 WILD-TYPE 
            12            343 
  MCM4 MUTATED MCM4 WILD-TYPE 
             2             71 
$`MCM4 MUTATED`
TCGA-A6-6781 TCGA-AA-3821 TCGA-AA-3845 TCGA-AA-A00J TCGA-AA-A010 TCGA-AZ-6598 
       19.66         1.02         0.00        18.05        34.98        49.41 
TCGA-CA-6717 TCGA-CK-4950 TCGA-CK-5913 TCGA-CM-5348 TCGA-CM-6165 TCGA-D5-6929 
        0.33        40.34        51.32        22.98        16.04        13.41 

$`MCM4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 
       10.06        35.05        33.04         0.99        25.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02        14.93        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 
       17.56       102.44        15.62        49.08        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  MCM4 MUTATED MCM4 WILD-TYPE 
             0              0 
  MCM4 MUTATED MCM4 WILD-TYPE 
         51.32         140.38 
  MCM4 MUTATED MCM4 WILD-TYPE 
        18.855         20.280 
[1] "0.0 - 51.3 (18.9)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.1"
D1717V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MCM4 MUTATED         1        0        1         4         1         0
  MCM4 WILD-TYPE      63        1       24       105         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MCM4 MUTATED           0          1          2          1        1         0
  MCM4 WILD-TYPE        19          9         39         30       34        13
                vv
clus             STAGE IVB
  MCM4 MUTATED           0
  MCM4 WILD-TYPE         1
D1717V3, multiclass
            clus
vv           MCM4 MUTATED MCM4 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             4            105
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            1              9
  STAGE IIIB            2             39
  STAGE IIIC            1             30
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MCM4 MUTATED     0   1   8   3
  MCM4 WILD-TYPE   9  67 240  38
D1717V4, multiclass
    clus
vv   MCM4 MUTATED MCM4 WILD-TYPE
  T1            0              9
  T2            1             67
  T3            8            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
  MCM4 MUTATED     7   5   0
  MCM4 WILD-TYPE 213  75  66
D1717V5, multiclass
    clus
vv   MCM4 MUTATED MCM4 WILD-TYPE
  N0            7            213
  N1            5             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"
D1717V6, binary
                cls
clus               0   1
  MCM4 MUTATED     8   1
  MCM4 WILD-TYPE 275  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCM4 MUTATED      8    1
  MCM4 WILD-TYPE  275   47
   clus
vv  MCM4 MUTATED MCM4 WILD-TYPE
  0            8            275
  1            1             47
[1] 2 2
[1] FALSE
D1717V7, binary
                cls
clus               0   1
  MCM4 MUTATED     7   5
  MCM4 WILD-TYPE 163 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCM4 MUTATED      7    5
  MCM4 WILD-TYPE  163  192
        clus
vv       MCM4 MUTATED MCM4 WILD-TYPE
  FEMALE            7            163
  MALE              5            192
[1] 2 2
[1] FALSE
D1717V8, binary
                cls
clus               0   1
  MCM4 MUTATED     8   4
  MCM4 WILD-TYPE 309  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCM4 MUTATED      8    4
  MCM4 WILD-TYPE  309   44
                               clus
vv                              MCM4 MUTATED MCM4 WILD-TYPE
  COLON ADENOCARCINOMA                     8            309
  COLON MUCINOUS ADENOCARCINOMA            4             44
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MCM4 MUTATED     8   1   0   2
  MCM4 WILD-TYPE 249   1  22  19
D1717V9, multiclass
    clus
vv   MCM4 MUTATED MCM4 WILD-TYPE
  R0            8            249
  R1            1              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"
D1717V10, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MCM4 MUTATED                                  0     1
  MCM4 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MCM4 MUTATED                           1     6
  MCM4 WILD-TYPE                        18   170
D1717V11, multiclass
                                  clus
vv                                 MCM4 MUTATED MCM4 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(1718) Variable = CLTCL1 MUTATION ANALYSIS
D1718V1, survival
                  sevent
clus2                0   1
  CLTCL1 MUTATED    15   2
  CLTCL1 WILD-TYPE 267  71
  CLTCL1 MUTATED CLTCL1 WILD-TYPE 
              17              338 
  CLTCL1 MUTATED CLTCL1 WILD-TYPE 
               2               71 
$`CLTCL1 MUTATED`
TCGA-AA-3660 TCGA-AA-3713 TCGA-AA-3818 TCGA-AA-3877 TCGA-AA-3972 TCGA-AA-3977 
       78.08        19.04         0.99        31.00        50.99        25.02 
TCGA-AA-A010 TCGA-AD-5900 TCGA-AZ-6599 TCGA-CA-6717 TCGA-CK-4950 TCGA-CM-5348 
       34.98         0.07         6.77         0.33        40.34        22.98 
TCGA-D5-6928 TCGA-F4-6808 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6588 
       11.64        33.67        55.04        36.72        26.17 

$`CLTCL1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        61.02         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05        33.04        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       27.02        29.98        18.05         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
        2.01        21.99        16.08        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 
        0.26         0.10         1.35        17.56       102.44        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       29.59        16.24        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 
      107.67        74.56        65.85        53.62        44.68        51.75 
TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       45.11        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  CLTCL1 MUTATED CLTCL1 WILD-TYPE 
            0.07             0.00 
  CLTCL1 MUTATED CLTCL1 WILD-TYPE 
           78.08           140.38 
  CLTCL1 MUTATED CLTCL1 WILD-TYPE 
          26.170           20.005 
[1] "0.1 - 78.1 (26.2)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1.9"
D1718V2, 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       24       104         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CLTCL1 MUTATED           0          1          2          0        3
  CLTCL1 WILD-TYPE        19          9         39         31       32
                  vv
clus               STAGE IVA STAGE IVB
  CLTCL1 MUTATED           0         0
  CLTCL1 WILD-TYPE        13         1
D1718V3, multiclass
            clus
vv           CLTCL1 MUTATED CLTCL1 WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               5              104
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              1                9
  STAGE IIIB              2               39
  STAGE IIIC              0               31
  STAGE IV                3               32
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CLTCL1 MUTATED     2   3  12   1
  CLTCL1 WILD-TYPE   7  65 236  40
D1718V4, multiclass
    clus
vv   CLTCL1 MUTATED CLTCL1 WILD-TYPE
  T1              2                7
  T2              3               65
  T3             12              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
  CLTCL1 MUTATED    13   5   0
  CLTCL1 WILD-TYPE 207  75  66
D1718V5, multiclass
    clus
vv   CLTCL1 MUTATED CLTCL1 WILD-TYPE
  N0             13              207
  N1              5               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"
D1718V6, binary
                  cls
clus                 0   1
  CLTCL1 MUTATED    12   3
  CLTCL1 WILD-TYPE 271  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLTCL1 MUTATED     12    3
  CLTCL1 WILD-TYPE  271   45
   clus
vv  CLTCL1 MUTATED CLTCL1 WILD-TYPE
  0             12              271
  1              3               45
[1] 2 2
[1] FALSE
D1718V7, 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
D1718V8, binary
                  cls
clus                 0   1
  CLTCL1 MUTATED    14   4
  CLTCL1 WILD-TYPE 303  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLTCL1 MUTATED     14    4
  CLTCL1 WILD-TYPE  303   44
                               clus
vv                              CLTCL1 MUTATED CLTCL1 WILD-TYPE
  COLON ADENOCARCINOMA                      14              303
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CLTCL1 MUTATED    12   1   2   1
  CLTCL1 WILD-TYPE 245   1  20  20
D1718V9, multiclass
    clus
vv   CLTCL1 MUTATED CLTCL1 WILD-TYPE
  R0             12              245
  R1              1                1
  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"
D1718V10, 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
D1718V11, 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(1719) Variable = MPZL1 MUTATION ANALYSIS
D1719V1, survival
                 sevent
clus2               0   1
  MPZL1 MUTATED     5   2
  MPZL1 WILD-TYPE 277  71
  MPZL1 MUTATED MPZL1 WILD-TYPE 
              7             348 
  MPZL1 MUTATED MPZL1 WILD-TYPE 
              2              71 
$`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         0.10         7.50       135.65 
TCGA-G4-6626 
       46.75 

$`MPZL1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 
       56.55         0.79         0.72         5.79        22.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.33         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-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-A282 TCGA-DM-A285 
       12.59       140.38        44.32       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       22.09        13.78        35.80        26.17        91.79        52.80 

  MPZL1 MUTATED MPZL1 WILD-TYPE 
            0.1             0.0 
  MPZL1 MUTATED MPZL1 WILD-TYPE 
         135.65          140.38 
  MPZL1 MUTATED MPZL1 WILD-TYPE 
          32.75           20.07 
[1] "0.1 - 135.7 (32.8)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1"  
D1719V2, 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       25       107         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        18         10         40         30       35        13
                 vv
clus              STAGE IVB
  MPZL1 MUTATED           0
  MPZL1 WILD-TYPE         1
D1719V3, multiclass
            clus
vv           MPZL1 MUTATED MPZL1 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              2             107
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MPZL1 MUTATED     0   0   6   1
  MPZL1 WILD-TYPE   9  68 242  40
D1719V4, multiclass
    clus
vv   MPZL1 MUTATED MPZL1 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             6             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
  MPZL1 MUTATED     4   1   2
  MPZL1 WILD-TYPE 216  79  64
D1719V5, multiclass
    clus
vv   MPZL1 MUTATED MPZL1 WILD-TYPE
  N0             4             216
  N1             1              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"
D1719V6, binary
                 cls
clus                0   1
  MPZL1 MUTATED     6   0
  MPZL1 WILD-TYPE 277  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MPZL1 MUTATED      6    0
  MPZL1 WILD-TYPE  277   48
   clus
vv  MPZL1 MUTATED MPZL1 WILD-TYPE
  0             6             277
  1             0              48
[1] 2 2
[1] FALSE
D1719V7, 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
D1719V8, binary
                 cls
clus                0   1
  MPZL1 MUTATED     5   2
  MPZL1 WILD-TYPE 312  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MPZL1 MUTATED      5    2
  MPZL1 WILD-TYPE  312   46
                               clus
vv                              MPZL1 MUTATED MPZL1 WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  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 254   2  22  20
D1719V9, multiclass
    clus
vv   MPZL1 MUTATED MPZL1 WILD-TYPE
  R0             3             254
  R1             0               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"
D1719V10, 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
D1719V11, 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(1720) Variable = PSMC3 MUTATION ANALYSIS
D1720V1, survival
                 sevent
clus2               0   1
  PSMC3 MUTATED     8   1
  PSMC3 WILD-TYPE 274  72
  PSMC3 MUTATED PSMC3 WILD-TYPE 
              9             346 
  PSMC3 MUTATED PSMC3 WILD-TYPE 
              1              72 
$`PSMC3 MUTATED`
TCGA-A6-3810 TCGA-AA-3655 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-A01D TCGA-AU-6004 
       36.53        61.02        85.05        19.04        10.98        27.09 
TCGA-CA-5255 TCGA-CM-5860 TCGA-G4-6588 
        3.06        16.01        26.17 

$`PSMC3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.03        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       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        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5796 
        5.23        11.74         3.19         1.94         2.24         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        91.79        46.75        52.80 

  PSMC3 MUTATED PSMC3 WILD-TYPE 
           3.06            0.00 
  PSMC3 MUTATED PSMC3 WILD-TYPE 
          85.05          140.38 
  PSMC3 MUTATED PSMC3 WILD-TYPE 
         26.170          20.155 
[1] "3.1 - 85.0 (26.2)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2.3"
D1720V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PSMC3 MUTATED         1        0        1         5         0         0
  PSMC3 WILD-TYPE      63        1       24       104         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PSMC3 MUTATED           1          0          0          1        1         0
  PSMC3 WILD-TYPE        18         10         41         30       34        13
                 vv
clus              STAGE IVB
  PSMC3 MUTATED           0
  PSMC3 WILD-TYPE         1
D1720V3, multiclass
            clus
vv           PSMC3 MUTATED PSMC3 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              5             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PSMC3 MUTATED     0   1   9   0
  PSMC3 WILD-TYPE   9  67 239  41
D1720V4, multiclass
    clus
vv   PSMC3 MUTATED PSMC3 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             9             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
  PSMC3 MUTATED     9   0   1
  PSMC3 WILD-TYPE 211  80  65
D1720V5, multiclass
    clus
vv   PSMC3 MUTATED PSMC3 WILD-TYPE
  N0             9             211
  N1             0              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"
D1720V6, binary
                 cls
clus                0   1
  PSMC3 MUTATED     9   1
  PSMC3 WILD-TYPE 274  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSMC3 MUTATED      9    1
  PSMC3 WILD-TYPE  274   47
   clus
vv  PSMC3 MUTATED PSMC3 WILD-TYPE
  0             9             274
  1             1              47
[1] 2 2
[1] FALSE
D1720V7, binary
                 cls
clus                0   1
  PSMC3 MUTATED     4   6
  PSMC3 WILD-TYPE 166 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSMC3 MUTATED      4    6
  PSMC3 WILD-TYPE  166  191
        clus
vv       PSMC3 MUTATED PSMC3 WILD-TYPE
  FEMALE             4             166
  MALE               6             191
[1] 2 2
[1] FALSE
D1720V8, binary
                 cls
clus                0   1
  PSMC3 MUTATED     9   1
  PSMC3 WILD-TYPE 308  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSMC3 MUTATED      9    1
  PSMC3 WILD-TYPE  308   47
                               clus
vv                              PSMC3 MUTATED PSMC3 WILD-TYPE
  COLON ADENOCARCINOMA                      9             308
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PSMC3 MUTATED     8   0   1   1
  PSMC3 WILD-TYPE 249   2  21  20
D1720V9, multiclass
    clus
vv   PSMC3 MUTATED PSMC3 WILD-TYPE
  R0             8             249
  R1             0               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"
D1720V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PSMC3 MUTATED                                  0     1
  PSMC3 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PSMC3 MUTATED                           0     4
  PSMC3 WILD-TYPE                        19   172
D1720V11, multiclass
                                  clus
vv                                 PSMC3 MUTATED PSMC3 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(1721) Variable = HIST1H1B MUTATION ANALYSIS
D1721V1, survival
                    sevent
clus2                  0   1
  HIST1H1B MUTATED     7   0
  HIST1H1B WILD-TYPE 275  73
  HIST1H1B MUTATED HIST1H1B WILD-TYPE 
                 7                348 
  HIST1H1B MUTATED HIST1H1B WILD-TYPE 
                 0                 73 
$`HIST1H1B MUTATED`
TCGA-A6-2672 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3662 TCGA-CM-6165 TCGA-D5-6928 
       46.65        22.06        19.66         6.05        16.04        11.64 
TCGA-D5-6930 
        1.51 

$`HIST1H1B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  HIST1H1B MUTATED HIST1H1B WILD-TYPE 
              1.51               0.00 
  HIST1H1B MUTATED HIST1H1B WILD-TYPE 
             46.65             140.38 
  HIST1H1B MUTATED HIST1H1B WILD-TYPE 
             16.04              20.63 
[1] "1.5 - 46.6 (16.0)"  "0.0 - 140.4 (20.6)"
[1] "hr="     "9100000"
D1721V2, 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       25       105         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HIST1H1B MUTATED           0          0          1          1        1
  HIST1H1B WILD-TYPE        19         10         40         30       34
                    vv
clus                 STAGE IVA STAGE IVB
  HIST1H1B MUTATED           0         0
  HIST1H1B WILD-TYPE        13         1
D1721V3, multiclass
            clus
vv           HIST1H1B MUTATED HIST1H1B WILD-TYPE
  STAGE I                   0                 64
  STAGE IA                  0                  1
  STAGE II                  0                 25
  STAGE IIA                 4                105
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                0                 10
  STAGE IIIB                1                 40
  STAGE IIIC                1                 30
  STAGE IV                  1                 34
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  HIST1H1B MUTATED     0   0   5   2
  HIST1H1B WILD-TYPE   9  68 243  39
D1721V4, multiclass
    clus
vv   HIST1H1B MUTATED HIST1H1B WILD-TYPE
  T1                0                  9
  T2                0                 68
  T3                5                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
  HIST1H1B MUTATED     4   2   1
  HIST1H1B WILD-TYPE 216  78  65
D1721V5, multiclass
    clus
vv   HIST1H1B MUTATED HIST1H1B WILD-TYPE
  N0                4                216
  N1                2                 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
  HIST1H1B MUTATED     5   1
  HIST1H1B WILD-TYPE 278  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1B MUTATED      5    1
  HIST1H1B WILD-TYPE  278   47
   clus
vv  HIST1H1B MUTATED HIST1H1B WILD-TYPE
  0                5                278
  1                1                 47
[1] 2 2
[1] FALSE
D1721V7, 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
D1721V8, binary
                    cls
clus                   0   1
  HIST1H1B MUTATED     4   3
  HIST1H1B WILD-TYPE 313  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1B MUTATED      4    3
  HIST1H1B WILD-TYPE  313   45
                               clus
vv                              HIST1H1B MUTATED HIST1H1B WILD-TYPE
  COLON ADENOCARCINOMA                         4                313
  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 251   2  21  21
D1721V9, multiclass
    clus
vv   HIST1H1B MUTATED HIST1H1B WILD-TYPE
  R0                6                251
  R1                0                  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"
D1721V10, 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
D1721V11, 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(1722) Variable = WNT8A MUTATION ANALYSIS
D1722V1, survival
                 sevent
clus2               0   1
  WNT8A MUTATED     5   0
  WNT8A WILD-TYPE 277  73
  WNT8A MUTATED WNT8A WILD-TYPE 
              5             350 
  WNT8A MUTATED WNT8A WILD-TYPE 
              0              73 
$`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        36.72 

$`WNT8A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  WNT8A MUTATED WNT8A WILD-TYPE 
          19.66            0.00 
  WNT8A MUTATED WNT8A WILD-TYPE 
         124.27          140.38 
  WNT8A MUTATED WNT8A WILD-TYPE 
          34.98           20.07 
[1] "19.7 - 124.3 (35.0)" "0.0 - 140.4 (20.1)" 
[1] "hr="     "9300000"
D1722V2, 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       25       109         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        19         10         41         30       34        13
                 vv
clus              STAGE IVB
  WNT8A MUTATED           0
  WNT8A WILD-TYPE         1
D1722V3, multiclass
            clus
vv           WNT8A MUTATED WNT8A WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              0             109
  STAGE IIB              1               7
  STAGE IIC              1               0
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  WNT8A MUTATED     0   1   1   3
  WNT8A WILD-TYPE   9  67 247  38
D1722V4, multiclass
    clus
vv   WNT8A MUTATED WNT8A WILD-TYPE
  T1             0               9
  T2             1              67
  T3             1             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
  WNT8A MUTATED     3   2   0
  WNT8A WILD-TYPE 217  78  66
D1722V5, multiclass
    clus
vv   WNT8A MUTATED WNT8A WILD-TYPE
  N0             3             217
  N1             2              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"
D1722V6, binary
                 cls
clus                0   1
  WNT8A MUTATED     2   1
  WNT8A WILD-TYPE 281  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WNT8A MUTATED      2    1
  WNT8A WILD-TYPE  281   47
   clus
vv  WNT8A MUTATED WNT8A WILD-TYPE
  0             2             281
  1             1              47
[1] 2 2
[1] FALSE
D1722V7, 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
D1722V8, binary
                 cls
clus                0   1
  WNT8A MUTATED     3   2
  WNT8A WILD-TYPE 314  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WNT8A MUTATED      3    2
  WNT8A WILD-TYPE  314   46
                               clus
vv                              WNT8A MUTATED WNT8A WILD-TYPE
  COLON ADENOCARCINOMA                      3             314
  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 254   2  22  20
D1722V9, multiclass
    clus
vv   WNT8A MUTATED WNT8A WILD-TYPE
  R0             3             254
  R1             0               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"
D1722V10, 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
D1722V11, 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(1723) Variable = RARS2 MUTATION ANALYSIS
D1723V1, survival
                 sevent
clus2               0   1
  RARS2 MUTATED     4   2
  RARS2 WILD-TYPE 278  71
  RARS2 MUTATED RARS2 WILD-TYPE 
              6             349 
  RARS2 MUTATED RARS2 WILD-TYPE 
              2              71 
$`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         0.33       102.44        40.34 

$`RARS2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4952 TCGA-CK-5912 
        0.26         0.10         1.35        17.56        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  RARS2 MUTATED RARS2 WILD-TYPE 
           0.33            0.00 
  RARS2 MUTATED RARS2 WILD-TYPE 
         102.44          140.38 
  RARS2 MUTATED RARS2 WILD-TYPE 
          29.69           20.19 
[1] "0.3 - 102.4 (29.7)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D1723V2, 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       24       106         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RARS2 MUTATED           0          2          0          0        0         0
  RARS2 WILD-TYPE        19          8         41         31       35        13
                 vv
clus              STAGE IVB
  RARS2 MUTATED           0
  RARS2 WILD-TYPE         1
D1723V3, multiclass
            clus
vv           RARS2 MUTATED RARS2 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              3             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             2               8
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RARS2 MUTATED     0   0   6   1
  RARS2 WILD-TYPE   9  68 242  40
D1723V4, multiclass
    clus
vv   RARS2 MUTATED RARS2 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             6             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
  RARS2 MUTATED     5   2   0
  RARS2 WILD-TYPE 215  78  66
D1723V5, multiclass
    clus
vv   RARS2 MUTATED RARS2 WILD-TYPE
  N0             5             215
  N1             2              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"
D1723V6, binary
                 cls
clus                0   1
  RARS2 MUTATED     7   0
  RARS2 WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RARS2 MUTATED      7    0
  RARS2 WILD-TYPE  276   48
   clus
vv  RARS2 MUTATED RARS2 WILD-TYPE
  0             7             276
  1             0              48
[1] 2 2
[1] FALSE
D1723V7, 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
D1723V8, binary
                 cls
clus                0   1
  RARS2 MUTATED     5   2
  RARS2 WILD-TYPE 312  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RARS2 MUTATED      5    2
  RARS2 WILD-TYPE  312   46
                               clus
vv                              RARS2 MUTATED RARS2 WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RARS2 MUTATED     5   1   0   1
  RARS2 WILD-TYPE 252   1  22  20
D1723V9, multiclass
    clus
vv   RARS2 MUTATED RARS2 WILD-TYPE
  R0             5             252
  R1             1               1
  R2             0              22
  RX             1              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1723V10, 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
D1723V11, 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(1724) Variable = TEX11 MUTATION ANALYSIS
D1724V1, survival
                 sevent
clus2               0   1
  TEX11 MUTATED    12   4
  TEX11 WILD-TYPE 270  69
  TEX11 MUTATED TEX11 WILD-TYPE 
             16             339 
  TEX11 MUTATED TEX11 WILD-TYPE 
              4              69 
$`TEX11 MUTATED`
TCGA-A6-2678 TCGA-A6-5666 TCGA-AA-3516 TCGA-AA-3672 TCGA-AA-A00N TCGA-AY-6197 
       42.28        32.71        13.02         0.92         4.01        21.44 
TCGA-AZ-6598 TCGA-CA-6719 TCGA-CK-5913 TCGA-CM-4743 TCGA-CM-6163 TCGA-CM-6171 
       49.41         1.35        51.32        23.05        14.04        14.04 
TCGA-D5-5540 TCGA-D5-6540 TCGA-DM-A285 TCGA-G4-6321 
       13.51        16.14         6.12        22.09 

$`TEX11 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2683 
       43.76        46.65        43.76        42.90        24.33        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       27.09        16.31         0.95        15.75         0.20        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 
        3.29         0.07         0.26         0.33         0.10        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 
      102.44        40.34        15.62        49.08        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-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-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       19.59        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       45.11        36.72        36.00        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  TEX11 MUTATED TEX11 WILD-TYPE 
           0.92            0.00 
  TEX11 MUTATED TEX11 WILD-TYPE 
          51.32          140.38 
  TEX11 MUTATED TEX11 WILD-TYPE 
          15.09           20.28 
[1] "0.9 - 51.3 (15.1)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.5"
D1724V2, 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       24       104         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        15         10         40         31       34        13
                 vv
clus              STAGE IVB
  TEX11 MUTATED           0
  TEX11 WILD-TYPE         1
D1724V3, multiclass
            clus
vv           TEX11 MUTATED TEX11 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              5             104
  STAGE IIB              1               7
  STAGE IIC              1               0
  STAGE III              4              15
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TEX11 MUTATED     1   3  11   2
  TEX11 WILD-TYPE   8  65 237  39
D1724V4, multiclass
    clus
vv   TEX11 MUTATED TEX11 WILD-TYPE
  T1             1               8
  T2             3              65
  T3            11             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
  TEX11 MUTATED    11   3   3
  TEX11 WILD-TYPE 209  77  63
D1724V5, multiclass
    clus
vv   TEX11 MUTATED TEX11 WILD-TYPE
  N0            11             209
  N1             3              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"
D1724V6, binary
                 cls
clus                0   1
  TEX11 MUTATED    12   1
  TEX11 WILD-TYPE 271  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TEX11 MUTATED     12    1
  TEX11 WILD-TYPE  271   47
   clus
vv  TEX11 MUTATED TEX11 WILD-TYPE
  0            12             271
  1             1              47
[1] 2 2
[1] FALSE
D1724V7, 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
D1724V8, binary
                 cls
clus                0   1
  TEX11 MUTATED    13   4
  TEX11 WILD-TYPE 304  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TEX11 MUTATED     13    4
  TEX11 WILD-TYPE  304   44
                               clus
vv                              TEX11 MUTATED TEX11 WILD-TYPE
  COLON ADENOCARCINOMA                     13             304
  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 246   2  22  19
D1724V9, multiclass
    clus
vv   TEX11 MUTATED TEX11 WILD-TYPE
  R0            11             246
  R1             0               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"
D1724V10, 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
D1724V11, 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(1725) Variable = VPS13C MUTATION ANALYSIS
D1725V1, survival
                  sevent
clus2                0   1
  VPS13C MUTATED    21   2
  VPS13C WILD-TYPE 261  71
  VPS13C MUTATED VPS13C WILD-TYPE 
              23              332 
  VPS13C MUTATED VPS13C WILD-TYPE 
               2               71 
$`VPS13C MUTATED`
TCGA-A6-5665 TCGA-A6-6142 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3525 TCGA-AA-3552 
       22.06        25.08        19.66        63.98         8.05        13.02 
TCGA-AA-3555 TCGA-AA-3663 TCGA-AA-3713 TCGA-AA-3864 TCGA-AA-3950 TCGA-AA-3955 
       29.95         6.97        19.04        53.00        24.00        20.98 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R TCGA-AA-A03J TCGA-AD-6895 TCGA-AZ-4315 
        4.01        34.98        35.01        40.96         0.72        58.39 
TCGA-CA-6717 TCGA-CK-6747 TCGA-D5-6922 TCGA-DM-A1HB TCGA-DM-A28H 
        0.33         2.93        10.13       135.65       117.07 

$`VPS13C WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6648 
       22.09        32.71        27.09        22.52         8.38        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       37.05        36.03        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 
       33.99        21.01        24.00        17.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01         2.01        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  VPS13C MUTATED VPS13C WILD-TYPE 
            0.33             0.00 
  VPS13C MUTATED VPS13C WILD-TYPE 
          135.65           140.38 
  VPS13C MUTATED VPS13C WILD-TYPE 
           22.06            20.07 
[1] "0.3 - 135.7 (22.1)" "0.0 - 140.4 (20.1)"
[1] "hr=" "3"  
D1725V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  VPS13C MUTATED         1        0        3         7         2         0
  VPS13C WILD-TYPE      63        1       22       102         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  VPS13C MUTATED           1          1          3          3        1
  VPS13C WILD-TYPE        18          9         38         28       34
                  vv
clus               STAGE IVA STAGE IVB
  VPS13C MUTATED           1         0
  VPS13C WILD-TYPE        12         1
D1725V3, multiclass
            clus
vv           VPS13C MUTATED VPS13C WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                3               22
  STAGE IIA               7              102
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              1                9
  STAGE IIIB              3               38
  STAGE IIIC              3               28
  STAGE IV                1               34
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  VPS13C MUTATED     0   2  19   3
  VPS13C WILD-TYPE   9  66 229  38
D1725V4, multiclass
    clus
vv   VPS13C MUTATED VPS13C WILD-TYPE
  T1              0                9
  T2              2               66
  T3             19              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
  VPS13C MUTATED    14   6   4
  VPS13C WILD-TYPE 206  74  62
D1725V5, multiclass
    clus
vv   VPS13C MUTATED VPS13C WILD-TYPE
  N0             14              206
  N1              6               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"
D1725V6, binary
                  cls
clus                 0   1
  VPS13C MUTATED    19   2
  VPS13C WILD-TYPE 264  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VPS13C MUTATED     19    2
  VPS13C WILD-TYPE  264   46
   clus
vv  VPS13C MUTATED VPS13C WILD-TYPE
  0             19              264
  1              2               46
[1] 2 2
[1] FALSE
D1725V7, binary
                  cls
clus                 0   1
  VPS13C MUTATED     8  16
  VPS13C WILD-TYPE 162 181
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VPS13C MUTATED      8   16
  VPS13C WILD-TYPE  162  181
        clus
vv       VPS13C MUTATED VPS13C WILD-TYPE
  FEMALE              8              162
  MALE               16              181
[1] 2 2
[1] FALSE
D1725V8, binary
                  cls
clus                 0   1
  VPS13C MUTATED    18   6
  VPS13C WILD-TYPE 299  42
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VPS13C MUTATED     18    6
  VPS13C WILD-TYPE  299   42
                               clus
vv                              VPS13C MUTATED VPS13C WILD-TYPE
  COLON ADENOCARCINOMA                      18              299
  COLON MUCINOUS ADENOCARCINOMA              6               42
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  VPS13C MUTATED    17   0   1   2
  VPS13C WILD-TYPE 240   2  21  19
D1725V9, multiclass
    clus
vv   VPS13C MUTATED VPS13C WILD-TYPE
  R0             17              240
  R1              0                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"
D1725V10, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  VPS13C MUTATED                                  0     1
  VPS13C WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  VPS13C MUTATED                           0     9
  VPS13C WILD-TYPE                        19   167
D1725V11, multiclass
                                  clus
vv                                 VPS13C MUTATED VPS13C 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(1726) Variable = IGFBP3 MUTATION ANALYSIS
D1726V1, survival
                  sevent
clus2                0   1
  IGFBP3 MUTATED     4   2
  IGFBP3 WILD-TYPE 278  71
  IGFBP3 MUTATED IGFBP3 WILD-TYPE 
               6              349 
  IGFBP3 MUTATED IGFBP3 WILD-TYPE 
               2               71 
$`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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        42.90        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
       40.34        15.62        49.08        51.32        21.99         2.93 
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        16.01 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  IGFBP3 MUTATED IGFBP3 WILD-TYPE 
            2.01             0.00 
  IGFBP3 MUTATED IGFBP3 WILD-TYPE 
           58.39           140.38 
  IGFBP3 MUTATED IGFBP3 WILD-TYPE 
           18.08            20.19 
[1] "2.0 - 58.4 (18.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.8"
D1726V2, 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       25       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IGFBP3 MUTATED           0          0          0          1        0
  IGFBP3 WILD-TYPE        19         10         41         30       35
                  vv
clus               STAGE IVA STAGE IVB
  IGFBP3 MUTATED           1         0
  IGFBP3 WILD-TYPE        12         1
D1726V3, multiclass
            clus
vv           IGFBP3 MUTATED IGFBP3 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               3              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  68 244  40
D1726V4, multiclass
    clus
vv   IGFBP3 MUTATED IGFBP3 WILD-TYPE
  T1              1                8
  T2              0               68
  T3              4              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
  IGFBP3 MUTATED     4   1   1
  IGFBP3 WILD-TYPE 216  79  65
D1726V5, multiclass
    clus
vv   IGFBP3 MUTATED IGFBP3 WILD-TYPE
  N0              4              216
  N1              1               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"
D1726V6, binary
                  cls
clus                 0   1
  IGFBP3 MUTATED     5   1
  IGFBP3 WILD-TYPE 278  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGFBP3 MUTATED      5    1
  IGFBP3 WILD-TYPE  278   47
   clus
vv  IGFBP3 MUTATED IGFBP3 WILD-TYPE
  0              5              278
  1              1               47
[1] 2 2
[1] FALSE
D1726V7, 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
D1726V8, binary
                  cls
clus                 0   1
  IGFBP3 MUTATED     5   1
  IGFBP3 WILD-TYPE 312  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGFBP3 MUTATED      5    1
  IGFBP3 WILD-TYPE  312   47
                               clus
vv                              IGFBP3 MUTATED IGFBP3 WILD-TYPE
  COLON ADENOCARCINOMA                       5              312
  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 253   2  22  20
D1726V9, multiclass
    clus
vv   IGFBP3 MUTATED IGFBP3 WILD-TYPE
  R0              4              253
  R1              0                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"
D1726V10, 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
D1726V11, 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(1727) Variable = HLA-DRA MUTATION ANALYSIS
D1727V1, survival
                   sevent
clus2                 0   1
  HLA-DRA MUTATED    10   1
  HLA-DRA WILD-TYPE 272  72
  HLA-DRA MUTATED HLA-DRA WILD-TYPE 
               11               344 
  HLA-DRA MUTATED HLA-DRA WILD-TYPE 
                1                72 
$`HLA-DRA MUTATED`
TCGA-A6-2676 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6142 TCGA-AA-3511 TCGA-AA-3660 
       42.90        22.06         8.38        25.08         6.97        78.08 
TCGA-AA-3864 TCGA-AA-3977 TCGA-AA-A00J TCGA-CM-6171 TCGA-D5-6927 
       53.00        25.02        18.05        14.04         9.44 

$`HLA-DRA WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 
       32.71        27.09        22.52        25.18        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 
        7.04         3.02         1.02        35.01        63.98         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  HLA-DRA MUTATED HLA-DRA WILD-TYPE 
             6.97              0.00 
  HLA-DRA MUTATED HLA-DRA WILD-TYPE 
            78.08            140.38 
  HLA-DRA MUTATED HLA-DRA WILD-TYPE 
           22.060            20.155 
[1] "7.0 - 78.1 (22.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2.6"
D1727V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HLA-DRA MUTATED         1        0        3         3         1         0
  HLA-DRA WILD-TYPE      63        1       22       106         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HLA-DRA MUTATED           0          0          1          0        0
  HLA-DRA WILD-TYPE        19         10         40         31       35
                   vv
clus                STAGE IVA STAGE IVB
  HLA-DRA MUTATED           1         0
  HLA-DRA WILD-TYPE        12         1
D1727V3, multiclass
            clus
vv           HLA-DRA MUTATED HLA-DRA WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 3                22
  STAGE IIA                3               106
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                1                12
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of 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-DRA MUTATED     0   2   6   3
  HLA-DRA WILD-TYPE   9  66 242  38
D1727V4, multiclass
    clus
vv   HLA-DRA MUTATED HLA-DRA WILD-TYPE
  T1               0                 9
  T2               2                66
  T3               6               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
  HLA-DRA MUTATED     9   2   0
  HLA-DRA WILD-TYPE 211  78  66
D1727V5, multiclass
    clus
vv   HLA-DRA MUTATED HLA-DRA WILD-TYPE
  N0               9               211
  N1               2                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"
D1727V6, binary
                   cls
clus                  0   1
  HLA-DRA MUTATED     9   1
  HLA-DRA WILD-TYPE 274  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HLA-DRA MUTATED      9    1
  HLA-DRA WILD-TYPE  274   47
   clus
vv  HLA-DRA MUTATED HLA-DRA WILD-TYPE
  0               9               274
  1               1                47
[1] 2 2
[1] FALSE
D1727V7, binary
                   cls
clus                  0   1
  HLA-DRA MUTATED     5   6
  HLA-DRA WILD-TYPE 165 191
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HLA-DRA MUTATED      5    6
  HLA-DRA WILD-TYPE  165  191
        clus
vv       HLA-DRA MUTATED HLA-DRA WILD-TYPE
  FEMALE               5               165
  MALE                 6               191
[1] 2 2
[1] FALSE
D1727V8, binary
                   cls
clus                  0   1
  HLA-DRA MUTATED    10   1
  HLA-DRA WILD-TYPE 307  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HLA-DRA MUTATED     10    1
  HLA-DRA WILD-TYPE  307   47
                               clus
vv                              HLA-DRA MUTATED HLA-DRA WILD-TYPE
  COLON ADENOCARCINOMA                       10               307
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  HLA-DRA MUTATED     8   0   0   0
  HLA-DRA WILD-TYPE 249   2  22  21
D1727V9, multiclass
    clus
vv   HLA-DRA MUTATED HLA-DRA WILD-TYPE
  R0               8               249
  R1               0                 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"
D1727V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HLA-DRA MUTATED                                  0     0
  HLA-DRA WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  HLA-DRA MUTATED                           1     5
  HLA-DRA WILD-TYPE                        18   171
D1727V11, multiclass
                                  clus
vv                                 HLA-DRA MUTATED HLA-DRA 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(1728) Variable = MUS81 MUTATION ANALYSIS
D1728V1, survival
                 sevent
clus2               0   1
  MUS81 MUTATED     7   0
  MUS81 WILD-TYPE 275  73
  MUS81 MUTATED MUS81 WILD-TYPE 
              7             348 
  MUS81 MUTATED MUS81 WILD-TYPE 
              0              73 
$`MUS81 MUTATED`
TCGA-A6-5665 TCGA-AA-3877 TCGA-AD-6889 TCGA-AY-6197 TCGA-CK-4947 TCGA-CM-5861 
       22.06        31.00        56.55        21.44        17.56        15.02 
TCGA-CM-5864 
       15.02 

$`MUS81 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.33         0.10         1.35       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01         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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  MUS81 MUTATED MUS81 WILD-TYPE 
          15.02            0.00 
  MUS81 MUTATED MUS81 WILD-TYPE 
          56.55          140.38 
  MUS81 MUTATED MUS81 WILD-TYPE 
         21.440          20.155 
[1] "15.0 - 56.5 (21.4)" "0.0 - 140.4 (20.2)"
[1] "hr="     "9200000"
D1728V2, 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       25       105         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MUS81 MUTATED           0          0          0          0        0         1
  MUS81 WILD-TYPE        19         10         41         31       35        12
                 vv
clus              STAGE IVB
  MUS81 MUTATED           0
  MUS81 WILD-TYPE         1
D1728V3, multiclass
            clus
vv           MUS81 MUTATED MUS81 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              4             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 244  40
D1728V4, multiclass
    clus
vv   MUS81 MUTATED MUS81 WILD-TYPE
  T1             1               8
  T2             1              67
  T3             4             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
  MUS81 MUTATED     6   1   0
  MUS81 WILD-TYPE 214  79  66
D1728V5, multiclass
    clus
vv   MUS81 MUTATED MUS81 WILD-TYPE
  N0             6             214
  N1             1              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"
D1728V6, binary
                 cls
clus                0   1
  MUS81 MUTATED     6   0
  MUS81 WILD-TYPE 277  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUS81 MUTATED      6    0
  MUS81 WILD-TYPE  277   48
   clus
vv  MUS81 MUTATED MUS81 WILD-TYPE
  0             6             277
  1             0              48
[1] 2 2
[1] FALSE
D1728V7, 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
D1728V8, binary
                 cls
clus                0   1
  MUS81 MUTATED     6   1
  MUS81 WILD-TYPE 311  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUS81 MUTATED      6    1
  MUS81 WILD-TYPE  311   47
                               clus
vv                              MUS81 MUTATED MUS81 WILD-TYPE
  COLON ADENOCARCINOMA                      6             311
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MUS81 MUTATED     5   0   0   1
  MUS81 WILD-TYPE 252   2  22  20
D1728V9, multiclass
    clus
vv   MUS81 MUTATED MUS81 WILD-TYPE
  R0             5             252
  R1             0               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"
D1728V10, 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
D1728V11, 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(1729) Variable = PIGN MUTATION ANALYSIS
D1729V1, survival
                sevent
clus2              0   1
  PIGN MUTATED     6   1
  PIGN WILD-TYPE 276  72
  PIGN MUTATED PIGN WILD-TYPE 
             7            348 
  PIGN MUTATED PIGN WILD-TYPE 
             1             72 
$`PIGN MUTATED`
TCGA-AA-3950 TCGA-AA-3966 TCGA-AD-6964 TCGA-CM-5348 TCGA-CM-5861 TCGA-D5-6928 
       24.00         2.01        10.88        22.98        15.02        11.64 
TCGA-F4-6703 
       35.87 

$`PIGN WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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        16.01 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       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        13.38        13.45         6.18         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  PIGN MUTATED PIGN WILD-TYPE 
          2.01           0.00 
  PIGN MUTATED PIGN WILD-TYPE 
         35.87         140.38 
  PIGN MUTATED PIGN WILD-TYPE 
        15.020         20.235 
[1] "2.0 - 35.9 (15.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1"  
D1729V2, 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       25       104         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        19         10         40         31       35        13
                vv
clus             STAGE IVB
  PIGN MUTATED           0
  PIGN WILD-TYPE         1
D1729V3, multiclass
            clus
vv           PIGN MUTATED PIGN WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             5            104
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PIGN MUTATED     0   0   6   1
  PIGN WILD-TYPE   9  68 242  40
D1729V4, multiclass
    clus
vv   PIGN MUTATED PIGN WILD-TYPE
  T1            0              9
  T2            0             68
  T3            6            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
  PIGN MUTATED     5   1   1
  PIGN WILD-TYPE 215  79  65
D1729V5, multiclass
    clus
vv   PIGN MUTATED PIGN WILD-TYPE
  N0            5            215
  N1            1             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"
D1729V6, binary
                cls
clus               0   1
  PIGN MUTATED     6   0
  PIGN WILD-TYPE 277  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGN MUTATED      6    0
  PIGN WILD-TYPE  277   48
   clus
vv  PIGN MUTATED PIGN WILD-TYPE
  0            6            277
  1            0             48
[1] 2 2
[1] FALSE
D1729V7, 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
D1729V8, binary
                cls
clus               0   1
  PIGN MUTATED     4   3
  PIGN WILD-TYPE 313  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGN MUTATED      4    3
  PIGN WILD-TYPE  313   45
                               clus
vv                              PIGN MUTATED PIGN WILD-TYPE
  COLON ADENOCARCINOMA                     4            313
  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 252   2  22  21
D1729V9, multiclass
    clus
vv   PIGN MUTATED PIGN WILD-TYPE
  R0            5            252
  R1            0              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"
D1729V10, 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
D1729V11, 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(1730) Variable = ELANE MUTATION ANALYSIS
D1730V1, survival
                 sevent
clus2               0   1
  ELANE MUTATED     6   1
  ELANE WILD-TYPE 276  72
  ELANE MUTATED ELANE WILD-TYPE 
              7             348 
  ELANE MUTATED ELANE WILD-TYPE 
              1              72 
$`ELANE MUTATED`
TCGA-A6-6654 TCGA-AA-3663 TCGA-AA-A010 TCGA-AZ-4315 TCGA-CK-5916 TCGA-CM-5861 
       23.87         6.97        34.98        58.39        21.14        15.02 
TCGA-G4-6304 
       53.62 

$`ELANE WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        51.32        21.99         2.93         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        16.01         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 
       35.41        19.43       107.67        74.56        65.85        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  ELANE MUTATED ELANE WILD-TYPE 
           6.97            0.00 
  ELANE MUTATED ELANE WILD-TYPE 
          58.39          140.38 
  ELANE MUTATED ELANE WILD-TYPE 
          23.87           20.07 
[1] "7.0 - 58.4 (23.9)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.8"
D1730V2, 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       24       107         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        19         10         40         31       35        13
                 vv
clus              STAGE IVB
  ELANE MUTATED           0
  ELANE WILD-TYPE         1
D1730V3, multiclass
            clus
vv           ELANE MUTATED ELANE WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              2             107
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ELANE MUTATED     1   0   4   2
  ELANE WILD-TYPE   8  68 244  39
D1730V4, multiclass
    clus
vv   ELANE MUTATED ELANE WILD-TYPE
  T1             1               8
  T2             0              68
  T3             4             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
  ELANE MUTATED     6   1   0
  ELANE WILD-TYPE 214  79  66
D1730V5, multiclass
    clus
vv   ELANE MUTATED ELANE WILD-TYPE
  N0             6             214
  N1             1              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"
D1730V6, binary
                 cls
clus                0   1
  ELANE MUTATED     7   0
  ELANE WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ELANE MUTATED      7    0
  ELANE WILD-TYPE  276   48
   clus
vv  ELANE MUTATED ELANE WILD-TYPE
  0             7             276
  1             0              48
[1] 2 2
[1] FALSE
D1730V7, 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
D1730V8, binary
                 cls
clus                0   1
  ELANE MUTATED     7   0
  ELANE WILD-TYPE 310  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ELANE MUTATED      7    0
  ELANE WILD-TYPE  310   48
                               clus
vv                              ELANE MUTATED ELANE WILD-TYPE
  COLON ADENOCARCINOMA                      7             310
  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 252   2  22  20
D1730V9, multiclass
    clus
vv   ELANE MUTATED ELANE WILD-TYPE
  R0             5             252
  R1             0               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"
D1730V10, 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
D1730V11, 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(1731) Variable = C1ORF116 MUTATION ANALYSIS
D1731V1, survival
                    sevent
clus2                  0   1
  C1ORF116 MUTATED     6   0
  C1ORF116 WILD-TYPE 276  73
  C1ORF116 MUTATED C1ORF116 WILD-TYPE 
                 6                349 
  C1ORF116 MUTATED C1ORF116 WILD-TYPE 
                 0                 73 
$`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        56.55        58.39         0.33 

$`C1ORF116 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37         4.21         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  C1ORF116 MUTATED C1ORF116 WILD-TYPE 
              0.33               0.00 
  C1ORF116 MUTATED C1ORF116 WILD-TYPE 
             85.05             140.38 
  C1ORF116 MUTATED C1ORF116 WILD-TYPE 
             45.29              20.02 
[1] "0.3 - 85.0 (45.3)"  "0.0 - 140.4 (20.0)"
[1] "hr="     "2.6e+07"
D1731V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C1ORF116 MUTATED         0        0        0         4         0         0
  C1ORF116 WILD-TYPE      64        1       25       105         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C1ORF116 MUTATED           1          0          0          1        0
  C1ORF116 WILD-TYPE        18         10         41         30       35
                    vv
clus                 STAGE IVA STAGE IVB
  C1ORF116 MUTATED           0         0
  C1ORF116 WILD-TYPE        13         1
D1731V3, multiclass
            clus
vv           C1ORF116 MUTATED C1ORF116 WILD-TYPE
  STAGE I                   0                 64
  STAGE IA                  0                  1
  STAGE II                  0                 25
  STAGE IIA                 4                105
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 1                 18
  STAGE IIIA                0                 10
  STAGE IIIB                0                 41
  STAGE IIIC                1                 30
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C1ORF116 MUTATED     0   0   6   0
  C1ORF116 WILD-TYPE   9  68 242  41
D1731V4, multiclass
    clus
vv   C1ORF116 MUTATED C1ORF116 WILD-TYPE
  T1                0                  9
  T2                0                 68
  T3                6                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
  C1ORF116 MUTATED     5   0   1
  C1ORF116 WILD-TYPE 215  80  65
D1731V5, multiclass
    clus
vv   C1ORF116 MUTATED C1ORF116 WILD-TYPE
  N0                5                215
  N1                0                 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"
D1731V6, binary
                    cls
clus                   0   1
  C1ORF116 MUTATED     6   0
  C1ORF116 WILD-TYPE 277  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF116 MUTATED      6    0
  C1ORF116 WILD-TYPE  277   48
   clus
vv  C1ORF116 MUTATED C1ORF116 WILD-TYPE
  0                6                277
  1                0                 48
[1] 2 2
[1] FALSE
D1731V7, 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
D1731V8, binary
                    cls
clus                   0   1
  C1ORF116 MUTATED     4   2
  C1ORF116 WILD-TYPE 313  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF116 MUTATED      4    2
  C1ORF116 WILD-TYPE  313   46
                               clus
vv                              C1ORF116 MUTATED C1ORF116 WILD-TYPE
  COLON ADENOCARCINOMA                         4                313
  COLON MUCINOUS ADENOCARCINOMA                2                 46
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C1ORF116 MUTATED     4   0   0   1
  C1ORF116 WILD-TYPE 253   2  22  20
D1731V9, multiclass
    clus
vv   C1ORF116 MUTATED C1ORF116 WILD-TYPE
  R0                4                253
  R1                0                  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"
D1731V10, 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
D1731V11, 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(1732) Variable = DEPDC5 MUTATION ANALYSIS
D1732V1, survival
                  sevent
clus2                0   1
  DEPDC5 MUTATED    15   3
  DEPDC5 WILD-TYPE 267  70
  DEPDC5 MUTATED DEPDC5 WILD-TYPE 
              18              337 
  DEPDC5 MUTATED DEPDC5 WILD-TYPE 
               3               70 
$`DEPDC5 MUTATED`
TCGA-A6-5661 TCGA-A6-6141 TCGA-A6-6781 TCGA-AA-3715 TCGA-AA-3819 TCGA-AA-A00N 
       33.53         8.38        19.66        19.04        25.02         4.01 
TCGA-AA-A01R TCGA-AD-6895 TCGA-AU-6004 TCGA-AY-6196 TCGA-AY-6197 TCGA-CM-4744 
       35.01         0.72        27.09         0.20        21.44        20.02 
TCGA-CM-4746 TCGA-CM-6171 TCGA-D5-6927 TCGA-DM-A28F TCGA-G4-6586 TCGA-G4-6625 
       37.02        14.04         9.44        35.97        35.80        91.79 

$`DEPDC5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
        0.99         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        4.21        56.55         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        15.75 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
      124.27        23.05        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G 
      135.65       139.17         6.12        81.37       119.93        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6626 
       36.72        36.00        22.09        13.78        26.17        46.75 
TCGA-G4-6628 
       52.80 

  DEPDC5 MUTATED DEPDC5 WILD-TYPE 
             0.2              0.0 
  DEPDC5 MUTATED DEPDC5 WILD-TYPE 
           91.79           140.38 
  DEPDC5 MUTATED DEPDC5 WILD-TYPE 
           20.73            20.19 
[1] "0.2 - 91.8 (20.7)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D1732V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEPDC5 MUTATED         5        0        1         7         1         0
  DEPDC5 WILD-TYPE      59        1       24       102         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DEPDC5 MUTATED           1          0          1          2        0
  DEPDC5 WILD-TYPE        18         10         40         29       35
                  vv
clus               STAGE IVA STAGE IVB
  DEPDC5 MUTATED           0         0
  DEPDC5 WILD-TYPE        13         1
D1732V3, multiclass
            clus
vv           DEPDC5 MUTATED DEPDC5 WILD-TYPE
  STAGE I                 5               59
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               7              102
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              2               29
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  DEPDC5 MUTATED     0   5  12   2
  DEPDC5 WILD-TYPE   9  63 236  39
D1732V4, multiclass
    clus
vv   DEPDC5 MUTATED DEPDC5 WILD-TYPE
  T1              0                9
  T2              5               63
  T3             12              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
  DEPDC5 MUTATED    14   3   2
  DEPDC5 WILD-TYPE 206  77  64
D1732V5, multiclass
    clus
vv   DEPDC5 MUTATED DEPDC5 WILD-TYPE
  N0             14              206
  N1              3               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"
D1732V6, binary
                  cls
clus                 0   1
  DEPDC5 MUTATED    14   0
  DEPDC5 WILD-TYPE 269  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DEPDC5 MUTATED     14    0
  DEPDC5 WILD-TYPE  269   48
   clus
vv  DEPDC5 MUTATED DEPDC5 WILD-TYPE
  0             14              269
  1              0               48
[1] 2 2
[1] FALSE
D1732V7, binary
                  cls
clus                 0   1
  DEPDC5 MUTATED     6  13
  DEPDC5 WILD-TYPE 164 184
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DEPDC5 MUTATED      6   13
  DEPDC5 WILD-TYPE  164  184
        clus
vv       DEPDC5 MUTATED DEPDC5 WILD-TYPE
  FEMALE              6              164
  MALE               13              184
[1] 2 2
[1] FALSE
D1732V8, binary
                  cls
clus                 0   1
  DEPDC5 MUTATED    15   4
  DEPDC5 WILD-TYPE 302  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DEPDC5 MUTATED     15    4
  DEPDC5 WILD-TYPE  302   44
                               clus
vv                              DEPDC5 MUTATED DEPDC5 WILD-TYPE
  COLON ADENOCARCINOMA                      15              302
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  DEPDC5 MUTATED    15   0   0   1
  DEPDC5 WILD-TYPE 242   2  22  20
D1732V9, multiclass
    clus
vv   DEPDC5 MUTATED DEPDC5 WILD-TYPE
  R0             15              242
  R1              0                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"
D1732V10, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEPDC5 MUTATED                                  0     0
  DEPDC5 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  DEPDC5 MUTATED                           3    12
  DEPDC5 WILD-TYPE                        16   164
D1732V11, multiclass
                                  clus
vv                                 DEPDC5 MUTATED DEPDC5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               10
  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(1733) Variable = SON MUTATION ANALYSIS
D1733V1, survival
               sevent
clus2             0   1
  SON MUTATED    16   4
  SON WILD-TYPE 266  69
  SON MUTATED SON WILD-TYPE 
           20           335 
  SON MUTATED SON WILD-TYPE 
            4            69 
$`SON MUTATED`
TCGA-A6-3809 TCGA-A6-5660 TCGA-A6-5666 TCGA-AA-3492 TCGA-AA-3672 TCGA-AA-3854 
       32.75        29.19        32.71         3.02         0.92        36.03 
TCGA-AA-3864 TCGA-AA-3875 TCGA-AA-3966 TCGA-AA-A02W TCGA-AZ-4315 TCGA-AZ-5407 
       53.00        18.05         2.01        41.00        58.39        61.41 
TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CM-4746 TCGA-CM-5349 TCGA-D5-6541 
       49.41       100.01         0.33        37.02        30.08        15.58 
TCGA-F4-6570 TCGA-G4-6586 
        6.18        35.80 

$`SON WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        33.53        23.61        22.09        22.06 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
        0.00        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03        14.01         0.92        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       62.79         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 
        2.93         2.01       124.27        23.05        20.02        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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        16.14         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-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        13.38        13.45        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        26.17        91.79        46.75        52.80 

  SON MUTATED SON WILD-TYPE 
         0.33          0.00 
  SON MUTATED SON WILD-TYPE 
       100.01        140.38 
  SON MUTATED SON WILD-TYPE 
        32.73         19.99 
[1] "0.3 - 100.0 (32.7)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.3"
D1733V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SON MUTATED         5        0        4         7         1         1
  SON WILD-TYPE      59        1       21       102         7         0
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SON MUTATED           1          0          0          1        0         0
  SON WILD-TYPE        18         10         41         30       35        13
               vv
clus            STAGE IVB
  SON MUTATED           0
  SON WILD-TYPE         1
D1733V3, multiclass
            clus
vv           SON MUTATED SON WILD-TYPE
  STAGE I              5            59
  STAGE IA             0             1
  STAGE II             4            21
  STAGE IIA            7           102
  STAGE IIB            1             7
  STAGE IIC            1             0
  STAGE III            1            18
  STAGE IIIA           0            10
  STAGE IIIB           0            41
  STAGE IIIC           1            30
  STAGE IV             0            35
  STAGE IVA            0            13
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  SON MUTATED     2   3  13   2
  SON WILD-TYPE   7  65 235  39
D1733V4, multiclass
    clus
vv   SON MUTATED SON WILD-TYPE
  T1           2             7
  T2           3            65
  T3          13           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
  SON MUTATED    18   1   1
  SON WILD-TYPE 202  79  65
D1733V5, multiclass
    clus
vv   SON MUTATED SON WILD-TYPE
  N0          18           202
  N1           1            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"
D1733V6, binary
               cls
clus              0   1
  SON MUTATED    19   0
  SON WILD-TYPE 264  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  SON MUTATED     19    0
  SON WILD-TYPE  264   48
   clus
vv  SON MUTATED SON WILD-TYPE
  0          19           264
  1           0            48
[1] 2 2
[1] FALSE
D1733V7, binary
               cls
clus              0   1
  SON MUTATED    12   8
  SON WILD-TYPE 158 189
[1] "tbl2"
               cls
clus            [,1] [,2]
  SON MUTATED     12    8
  SON WILD-TYPE  158  189
        clus
vv       SON MUTATED SON WILD-TYPE
  FEMALE          12           158
  MALE             8           189
[1] 2 2
[1] FALSE
D1733V8, binary
               cls
clus              0   1
  SON MUTATED    16   4
  SON WILD-TYPE 301  44
[1] "tbl2"
               cls
clus            [,1] [,2]
  SON MUTATED     16    4
  SON WILD-TYPE  301   44
                               clus
vv                              SON MUTATED SON WILD-TYPE
  COLON ADENOCARCINOMA                   16           301
  COLON MUCINOUS ADENOCARCINOMA           4            44
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  SON MUTATED    13   0   0   1
  SON WILD-TYPE 244   2  22  20
D1733V9, multiclass
    clus
vv   SON MUTATED SON WILD-TYPE
  R0          13           244
  R1           0             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"
D1733V10, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SON MUTATED                                  0     1
  SON WILD-TYPE                                1     9
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  SON MUTATED                           2    10
  SON WILD-TYPE                        17   166
D1733V11, multiclass
                                  clus
vv                                 SON MUTATED SON 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(1734) Variable = LRRC15 MUTATION ANALYSIS
D1734V1, survival
                  sevent
clus2                0   1
  LRRC15 MUTATED     7   1
  LRRC15 WILD-TYPE 275  72
  LRRC15 MUTATED LRRC15 WILD-TYPE 
               8              347 
  LRRC15 MUTATED LRRC15 WILD-TYPE 
               1               72 
$`LRRC15 MUTATED`
TCGA-A6-5664 TCGA-A6-6781 TCGA-AA-3977 TCGA-AD-6889 TCGA-D5-6540 TCGA-DM-A1DB 
       22.09        19.66        25.02        56.55        16.14        44.32 
TCGA-F4-6460 TCGA-G4-6586 
       13.38        35.80 

$`LRRC15 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37         4.21         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        26.17        91.79        46.75        52.80 

  LRRC15 MUTATED LRRC15 WILD-TYPE 
           13.38             0.00 
  LRRC15 MUTATED LRRC15 WILD-TYPE 
           56.55           140.38 
  LRRC15 MUTATED LRRC15 WILD-TYPE 
          23.555           20.120 
[1] "13.4 - 56.5 (23.6)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.9"
D1734V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LRRC15 MUTATED         1        0        0         4         0         0
  LRRC15 WILD-TYPE      63        1       25       105         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LRRC15 MUTATED           0          0          1          2        0
  LRRC15 WILD-TYPE        19         10         40         29       35
                  vv
clus               STAGE IVA STAGE IVB
  LRRC15 MUTATED           0         0
  LRRC15 WILD-TYPE        13         1
D1734V3, multiclass
            clus
vv           LRRC15 MUTATED LRRC15 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               4              105
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              2               29
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  LRRC15 MUTATED     0   2   5   2
  LRRC15 WILD-TYPE   9  66 243  39
D1734V4, multiclass
    clus
vv   LRRC15 MUTATED LRRC15 WILD-TYPE
  T1              0                9
  T2              2               66
  T3              5              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
  LRRC15 MUTATED     6   2   1
  LRRC15 WILD-TYPE 214  78  65
D1734V5, multiclass
    clus
vv   LRRC15 MUTATED LRRC15 WILD-TYPE
  N0              6              214
  N1              2               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"
D1734V6, binary
                  cls
clus                 0   1
  LRRC15 MUTATED     6   0
  LRRC15 WILD-TYPE 277  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRC15 MUTATED      6    0
  LRRC15 WILD-TYPE  277   48
   clus
vv  LRRC15 MUTATED LRRC15 WILD-TYPE
  0              6              277
  1              0               48
[1] 2 2
[1] FALSE
D1734V7, binary
                  cls
clus                 0   1
  LRRC15 MUTATED     3   6
  LRRC15 WILD-TYPE 167 191
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRC15 MUTATED      3    6
  LRRC15 WILD-TYPE  167  191
        clus
vv       LRRC15 MUTATED LRRC15 WILD-TYPE
  FEMALE              3              167
  MALE                6              191
[1] 2 2
[1] FALSE
D1734V8, binary
                  cls
clus                 0   1
  LRRC15 MUTATED     7   2
  LRRC15 WILD-TYPE 310  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRC15 MUTATED      7    2
  LRRC15 WILD-TYPE  310   46
                               clus
vv                              LRRC15 MUTATED LRRC15 WILD-TYPE
  COLON ADENOCARCINOMA                       7              310
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  LRRC15 MUTATED     5   0   0   0
  LRRC15 WILD-TYPE 252   2  22  21
D1734V9, multiclass
    clus
vv   LRRC15 MUTATED LRRC15 WILD-TYPE
  R0              5              252
  R1              0                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"
D1734V10, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LRRC15 MUTATED                                  0     1
  LRRC15 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  LRRC15 MUTATED                           1     5
  LRRC15 WILD-TYPE                        18   171
D1734V11, multiclass
                                  clus
vv                                 LRRC15 MUTATED LRRC15 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(1735) Variable = POLA1 MUTATION ANALYSIS
D1735V1, survival
                 sevent
clus2               0   1
  POLA1 MUTATED     6   1
  POLA1 WILD-TYPE 276  72
  POLA1 MUTATED POLA1 WILD-TYPE 
              7             348 
  POLA1 MUTATED POLA1 WILD-TYPE 
              1              72 
$`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        15.75        15.02        18.25 
TCGA-D5-6540 
       16.14 

$`POLA1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
        0.00        17.03         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 
        0.20        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-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
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-D5-6533 
       12.26        19.59        13.51        11.51        20.19         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  POLA1 MUTATED POLA1 WILD-TYPE 
          10.06            0.00 
  POLA1 MUTATED POLA1 WILD-TYPE 
          34.98          140.38 
  POLA1 MUTATED POLA1 WILD-TYPE 
          16.14           20.63 
[1] "10.1 - 35.0 (16.1)" "0.0 - 140.4 (20.6)"
[1] "hr=" "1.1"
D1735V2, 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       25       107         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        19         10         41         30       35        12
                 vv
clus              STAGE IVB
  POLA1 MUTATED           0
  POLA1 WILD-TYPE         1
D1735V3, multiclass
            clus
vv           POLA1 MUTATED POLA1 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              2             107
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 244  38
D1735V4, multiclass
    clus
vv   POLA1 MUTATED POLA1 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             4             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
  POLA1 MUTATED     7   1   1
  POLA1 WILD-TYPE 213  79  65
D1735V5, multiclass
    clus
vv   POLA1 MUTATED POLA1 WILD-TYPE
  N0             7             213
  N1             1              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"
D1735V6, binary
                 cls
clus                0   1
  POLA1 MUTATED     7   1
  POLA1 WILD-TYPE 276  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POLA1 MUTATED      7    1
  POLA1 WILD-TYPE  276   47
   clus
vv  POLA1 MUTATED POLA1 WILD-TYPE
  0             7             276
  1             1              47
[1] 2 2
[1] FALSE
D1735V7, 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
D1735V8, binary
                 cls
clus                0   1
  POLA1 MUTATED     7   2
  POLA1 WILD-TYPE 310  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POLA1 MUTATED      7    2
  POLA1 WILD-TYPE  310   46
                               clus
vv                              POLA1 MUTATED POLA1 WILD-TYPE
  COLON ADENOCARCINOMA                      7             310
  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 249   2  22  20
D1735V9, multiclass
    clus
vv   POLA1 MUTATED POLA1 WILD-TYPE
  R0             8             249
  R1             0               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"
D1735V10, 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
D1735V11, 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(1736) Variable = C3ORF27 MUTATION ANALYSIS
D1736V1, survival
                   sevent
clus2                 0   1
  C3ORF27 MUTATED     2   1
  C3ORF27 WILD-TYPE 280  72
  C3ORF27 MUTATED C3ORF27 WILD-TYPE 
                3               352 
  C3ORF27 MUTATED C3ORF27 WILD-TYPE 
                1                72 
$`C3ORF27 MUTATED`
TCGA-AA-3850 TCGA-AA-A010 TCGA-D5-6923 
        0.00        34.98        12.43 

$`C3ORF27 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
        0.00        17.03        10.06        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  C3ORF27 MUTATED C3ORF27 WILD-TYPE 
                0                 0 
  C3ORF27 MUTATED C3ORF27 WILD-TYPE 
            34.98            140.38 
  C3ORF27 MUTATED C3ORF27 WILD-TYPE 
           12.430            20.235 
[1] "0.0 - 35.0 (12.4)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "3"  
D1736V2, 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       25       109         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C3ORF27 MUTATED           0          0          0          0        0
  C3ORF27 WILD-TYPE        19         10         41         31       35
                   vv
clus                STAGE IVA STAGE IVB
  C3ORF27 MUTATED           0         0
  C3ORF27 WILD-TYPE        13         1
D1736V3, multiclass
            clus
vv           C3ORF27 MUTATED C3ORF27 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                0               109
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C3ORF27 MUTATED     0   2   0   1
  C3ORF27 WILD-TYPE   9  66 248  40
D1736V4, multiclass
    clus
vv   C3ORF27 MUTATED C3ORF27 WILD-TYPE
  T1               0                 9
  T2               2                66
  T3               0               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
  C3ORF27 MUTATED     3   0   0
  C3ORF27 WILD-TYPE 217  80  66
D1736V5, multiclass
    clus
vv   C3ORF27 MUTATED C3ORF27 WILD-TYPE
  N0               3               217
  N1               0                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"
D1736V6, binary
                   cls
clus                  0   1
  C3ORF27 MUTATED     3   0
  C3ORF27 WILD-TYPE 280  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF27 MUTATED      3    0
  C3ORF27 WILD-TYPE  280   48
   clus
vv  C3ORF27 MUTATED C3ORF27 WILD-TYPE
  0               3               280
  1               0                48
[1] 2 2
[1] FALSE
D1736V7, 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
D1736V8, binary
                   cls
clus                  0   1
  C3ORF27 MUTATED     3   0
  C3ORF27 WILD-TYPE 314  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF27 MUTATED      3    0
  C3ORF27 WILD-TYPE  314   48
                               clus
vv                              C3ORF27 MUTATED C3ORF27 WILD-TYPE
  COLON ADENOCARCINOMA                        3               314
  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 254   2  22  21
D1736V9, multiclass
    clus
vv   C3ORF27 MUTATED C3ORF27 WILD-TYPE
  R0               3               254
  R1               0                 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"
D1736V10, 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
D1736V11, multiclass
[1] "Remove cluster labels:" "C3ORF27 MUTATED"       
clus
  C3ORF27 MUTATED C3ORF27 WILD-TYPE 
                1               205 
       TCGA-A6-2671        TCGA-A6-2672        TCGA-A6-2674        TCGA-A6-2676 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-A6-2677        TCGA-A6-2678        TCGA-A6-2683        TCGA-A6-3807 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-A6-3808        TCGA-A6-3809        TCGA-A6-3810        TCGA-A6-4105 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-A6-5656        TCGA-A6-5657        TCGA-A6-5659        TCGA-A6-5660 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-A6-5661        TCGA-A6-5662        TCGA-A6-5664        TCGA-A6-5665 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-A6-5666        TCGA-A6-6137        TCGA-A6-6138        TCGA-A6-6141 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-A6-6142        TCGA-A6-6648        TCGA-A6-6649        TCGA-A6-6651 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-A6-6652        TCGA-A6-6653        TCGA-A6-6654        TCGA-A6-6780 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-A6-6781        TCGA-A6-6782        TCGA-AD-5900        TCGA-AD-6548 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-AD-6888        TCGA-AD-6889        TCGA-AD-6890        TCGA-AD-6895 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-AD-6899        TCGA-AD-6901        TCGA-AD-6963        TCGA-AD-6964 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-AD-6965        TCGA-AU-3779        TCGA-AU-6004        TCGA-AY-4070 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-AY-4071        TCGA-AY-5543        TCGA-AY-6196        TCGA-AY-6197 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-AY-6386        TCGA-AZ-4315        TCGA-AZ-4323        TCGA-AZ-4616 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-AZ-4681        TCGA-AZ-4682        TCGA-AZ-5403        TCGA-AZ-5407 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-AZ-6598        TCGA-AZ-6599        TCGA-AZ-6600        TCGA-AZ-6601 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-AZ-6603        TCGA-AZ-6605        TCGA-AZ-6606        TCGA-AZ-6607 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-AZ-6608        TCGA-CA-5254        TCGA-CA-5255        TCGA-CA-5796 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-CA-5797        TCGA-CA-6715        TCGA-CA-6716        TCGA-CA-6717 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-CA-6718        TCGA-CA-6719        TCGA-CK-4947        TCGA-CK-4948 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-CK-4950        TCGA-CK-4952        TCGA-CK-5912        TCGA-CK-5913 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-CK-5914        TCGA-CK-5915        TCGA-CK-5916        TCGA-CK-6746 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-CK-6747        TCGA-CK-6748        TCGA-CK-6751        TCGA-CM-4743 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-CM-4744        TCGA-CM-4746        TCGA-CM-4747        TCGA-CM-4752 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-CM-5341        TCGA-CM-5344        TCGA-CM-5348        TCGA-CM-5349 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-CM-5860        TCGA-CM-5861        TCGA-CM-5862        TCGA-CM-5863 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-CM-5864        TCGA-CM-5868        TCGA-CM-6161        TCGA-CM-6162 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-CM-6163        TCGA-CM-6164        TCGA-CM-6165        TCGA-CM-6166 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-CM-6167        TCGA-CM-6168        TCGA-CM-6169        TCGA-CM-6170 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-CM-6171        TCGA-CM-6172        TCGA-CM-6674        TCGA-CM-6675 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-CM-6676        TCGA-CM-6677        TCGA-CM-6678        TCGA-CM-6679 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-CM-6680        TCGA-D5-5537        TCGA-D5-5538        TCGA-D5-5539 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-D5-5540        TCGA-D5-5541        TCGA-D5-6529        TCGA-D5-6532 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-D5-6533        TCGA-D5-6534        TCGA-D5-6535        TCGA-D5-6536 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-D5-6537        TCGA-D5-6538        TCGA-D5-6539        TCGA-D5-6540 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-D5-6541        TCGA-D5-6898        TCGA-D5-6920        TCGA-D5-6922 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-D5-6924        TCGA-D5-6926        TCGA-D5-6927        TCGA-D5-6928 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-D5-6929        TCGA-D5-6930        TCGA-D5-6931        TCGA-D5-6932 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-D5-7000        TCGA-DM-A0X9        TCGA-DM-A0XD        TCGA-DM-A0XF 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-DM-A1D0        TCGA-DM-A1D4        TCGA-DM-A1D6        TCGA-DM-A1D7 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-DM-A1D8        TCGA-DM-A1D9        TCGA-DM-A1DA        TCGA-DM-A1DB 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-DM-A1HA        TCGA-DM-A1HB        TCGA-DM-A282        TCGA-DM-A285 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-DM-A28C        TCGA-DM-A28E        TCGA-DM-A28F        TCGA-DM-A28G 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-DM-A28H        TCGA-DM-A28K        TCGA-F4-6459        TCGA-F4-6460 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-F4-6569        TCGA-F4-6570        TCGA-F4-6703        TCGA-F4-6704 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-F4-6805        TCGA-F4-6806        TCGA-F4-6807        TCGA-F4-6808 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-F4-6809        TCGA-F4-6854        TCGA-F4-6855        TCGA-F4-6856 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-G4-6293        TCGA-G4-6299        TCGA-G4-6303        TCGA-G4-6304 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-G4-6306        TCGA-G4-6307        TCGA-G4-6309        TCGA-G4-6310 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-G4-6315        TCGA-G4-6317        TCGA-G4-6321        TCGA-G4-6323 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-G4-6586        TCGA-G4-6588        TCGA-G4-6625        TCGA-G4-6626 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-G4-6628 
"C3ORF27 WILD-TYPE" 

Clustering(1737) Variable = ZNF821 MUTATION ANALYSIS
D1737V1, survival
                  sevent
clus2                0   1
  ZNF821 MUTATED     4   1
  ZNF821 WILD-TYPE 278  72
  ZNF821 MUTATED ZNF821 WILD-TYPE 
               5              350 
  ZNF821 MUTATED ZNF821 WILD-TYPE 
               1               72 
$`ZNF821 MUTATED`
TCGA-AA-3518 TCGA-AA-3710 TCGA-AA-A01R TCGA-AD-6964 TCGA-G4-6306 
        1.02        26.99        35.01        10.88        44.68 

$`ZNF821 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       38.99         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  ZNF821 MUTATED ZNF821 WILD-TYPE 
            1.02             0.00 
  ZNF821 MUTATED ZNF821 WILD-TYPE 
           44.68           140.38 
  ZNF821 MUTATED ZNF821 WILD-TYPE 
          26.990           20.155 
[1] "1.0 - 44.7 (27.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D1737V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF821 MUTATED         0        0        0         3         0         0
  ZNF821 WILD-TYPE      64        1       25       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF821 MUTATED           1          0          0          0        0
  ZNF821 WILD-TYPE        18         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF821 MUTATED           0         0
  ZNF821 WILD-TYPE        13         1
D1737V3, multiclass
            clus
vv           ZNF821 MUTATED ZNF821 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               3              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF821 MUTATED     0   1   3   1
  ZNF821 WILD-TYPE   9  67 245  40
D1737V4, multiclass
    clus
vv   ZNF821 MUTATED ZNF821 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              3              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
  ZNF821 MUTATED     3   0   2
  ZNF821 WILD-TYPE 217  80  64
D1737V5, multiclass
    clus
vv   ZNF821 MUTATED ZNF821 WILD-TYPE
  N0              3              217
  N1              0               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"
D1737V6, binary
                  cls
clus                 0   1
  ZNF821 MUTATED     4   0
  ZNF821 WILD-TYPE 279  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF821 MUTATED      4    0
  ZNF821 WILD-TYPE  279   48
   clus
vv  ZNF821 MUTATED ZNF821 WILD-TYPE
  0              4              279
  1              0               48
[1] 2 2
[1] FALSE
D1737V7, binary
                  cls
clus                 0   1
  ZNF821 MUTATED     2   3
  ZNF821 WILD-TYPE 168 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF821 MUTATED      2    3
  ZNF821 WILD-TYPE  168  194
        clus
vv       ZNF821 MUTATED ZNF821 WILD-TYPE
  FEMALE              2              168
  MALE                3              194
[1] 2 2
[1] FALSE
D1737V8, binary
                  cls
clus                 0   1
  ZNF821 MUTATED     4   1
  ZNF821 WILD-TYPE 313  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF821 MUTATED      4    1
  ZNF821 WILD-TYPE  313   47
                               clus
vv                              ZNF821 MUTATED ZNF821 WILD-TYPE
  COLON ADENOCARCINOMA                       4              313
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF821 MUTATED     4   0   0   0
  ZNF821 WILD-TYPE 253   2  22  21
D1737V9, multiclass
    clus
vv   ZNF821 MUTATED ZNF821 WILD-TYPE
  R0              4              253
  R1              0                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"
D1737V10, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF821 MUTATED                                  0     0
  ZNF821 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF821 MUTATED                           0     2
  ZNF821 WILD-TYPE                        19   174
D1737V11, multiclass
[1] "Remove cluster labels:" "ZNF821 MUTATED"        
clus
  ZNF821 MUTATED ZNF821 WILD-TYPE 
               2              204 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-4105 
"ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" 
      TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660 
"ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" 
      TCGA-A6-5661       TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5665 
"ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" 
      TCGA-A6-5666       TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141 
"ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" 
      TCGA-A6-6142       TCGA-A6-6648       TCGA-A6-6649       TCGA-A6-6651 
"ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" 
      TCGA-A6-6652       TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780 
"ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" 
      TCGA-A6-6781       TCGA-A6-6782       TCGA-AD-5900       TCGA-AD-6548 
"ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" 
      TCGA-AD-6888       TCGA-AD-6889       TCGA-AD-6890       TCGA-AD-6895 
"ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" 
      TCGA-AD-6899       TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6965 
"ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" 
      TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070       TCGA-AY-4071 
"ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" 
      TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386 
"ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" 
      TCGA-AZ-4315       TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4681 
"ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" 
      TCGA-AZ-4682       TCGA-AZ-5403       TCGA-AZ-5407       TCGA-AZ-6598 
"ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" 
      TCGA-AZ-6599       TCGA-AZ-6600       TCGA-AZ-6601       TCGA-AZ-6603 
"ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" 
      TCGA-AZ-6605       TCGA-AZ-6606       TCGA-AZ-6607       TCGA-AZ-6608 
"ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" 
      TCGA-CA-5254       TCGA-CA-5255       TCGA-CA-5796       TCGA-CA-5797 
"ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" 
      TCGA-CA-6715       TCGA-CA-6716       TCGA-CA-6717       TCGA-CA-6718 
"ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" 
      TCGA-CA-6719       TCGA-CK-4947       TCGA-CK-4948       TCGA-CK-4950 
"ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" 
      TCGA-CK-4952       TCGA-CK-5912       TCGA-CK-5913       TCGA-CK-5914 
"ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" 
      TCGA-CK-5915       TCGA-CK-5916       TCGA-CK-6746       TCGA-CK-6747 
"ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" 
      TCGA-CK-6748       TCGA-CK-6751       TCGA-CM-4743       TCGA-CM-4744 
"ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" 
      TCGA-CM-4746       TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341 
"ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" 
      TCGA-CM-5344       TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860 
"ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" 
      TCGA-CM-5861       TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864 
"ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" 
      TCGA-CM-5868       TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163 
"ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" 
      TCGA-CM-6164       TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167 
"ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" 
      TCGA-CM-6168       TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171 
"ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" 
      TCGA-CM-6172       TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676 
"ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" 
      TCGA-CM-6677       TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680 
"ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" 
      TCGA-D5-5537       TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540 
"ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" 
      TCGA-D5-5541       TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533 
"ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" 
      TCGA-D5-6534       TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537 
"ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" 
      TCGA-D5-6538       TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541 
"ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" 
      TCGA-D5-6898       TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923 
"ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" 
      TCGA-D5-6924       TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928 
"ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" 
      TCGA-D5-6929       TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932 
"ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" 
      TCGA-D5-7000       TCGA-DM-A0X9       TCGA-DM-A0XD       TCGA-DM-A0XF 
"ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" 
      TCGA-DM-A1D0       TCGA-DM-A1D4       TCGA-DM-A1D6       TCGA-DM-A1D7 
"ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" 
      TCGA-DM-A1D8       TCGA-DM-A1D9       TCGA-DM-A1DA       TCGA-DM-A1DB 
"ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" 
      TCGA-DM-A1HA       TCGA-DM-A1HB       TCGA-DM-A282       TCGA-DM-A285 
"ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" 
      TCGA-DM-A28C       TCGA-DM-A28E       TCGA-DM-A28F       TCGA-DM-A28G 
"ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" 
      TCGA-DM-A28H       TCGA-DM-A28K       TCGA-F4-6459       TCGA-F4-6460 
"ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" 
      TCGA-F4-6569       TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704 
"ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" 
      TCGA-F4-6805       TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808 
"ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" 
      TCGA-F4-6809       TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856 
"ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" 
      TCGA-G4-6293       TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304 
"ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" 
      TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310       TCGA-G4-6315 
"ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323       TCGA-G4-6586 
"ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" 
      TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628 
"ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" "ZNF821 WILD-TYPE" 

Clustering(1738) Variable = TRHDE MUTATION ANALYSIS
D1738V1, survival
                 sevent
clus2               0   1
  TRHDE MUTATED    22   5
  TRHDE WILD-TYPE 260  68
  TRHDE MUTATED TRHDE WILD-TYPE 
             27             328 
  TRHDE MUTATED TRHDE WILD-TYPE 
              5              68 
$`TRHDE MUTATED`
TCGA-A6-5661 TCGA-A6-6138 TCGA-AA-3492 TCGA-AA-3518 TCGA-AA-3663 TCGA-AA-3672 
       33.53        22.52         3.02         1.02         6.97         0.92 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 TCGA-AY-4071 
       25.02        24.00        18.05         4.01        34.98         0.95 
TCGA-AZ-4315 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-5349 
       58.39         1.94         3.06         0.33         0.10        30.08 
TCGA-CM-6678 TCGA-D5-6535 TCGA-DM-A1HB TCGA-DM-A285 TCGA-F4-6569 TCGA-G4-6299 
       11.01        15.12       135.65         6.12        13.45        74.56 
TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6628 
       13.78        91.79        52.80 

$`TRHDE WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 
        6.97         1.02        13.02        38.99         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.05        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3980 
       16.08        50.99        13.05        34.06        26.01        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       19.00        30.02        34.03        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
       11.74         3.19         2.24         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.26         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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-F4-6570 TCGA-F4-6703 
      117.07        98.24         8.61        13.38         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 
        0.53        35.41        19.43       107.67        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 
       22.09        35.80        26.17        46.75 

  TRHDE MUTATED TRHDE WILD-TYPE 
            0.1             0.0 
  TRHDE MUTATED TRHDE WILD-TYPE 
         135.65          140.38 
  TRHDE MUTATED TRHDE WILD-TYPE 
          13.78           20.98 
[1] "0.1 - 135.7 (13.8)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.1"
D1738V2, 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       23       100         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        18          9         38         30       34        12
                 vv
clus              STAGE IVB
  TRHDE MUTATED           0
  TRHDE WILD-TYPE         1
D1738V3, multiclass
            clus
vv           TRHDE MUTATED TRHDE WILD-TYPE
  STAGE I                4              60
  STAGE IA               1               0
  STAGE II               2              23
  STAGE IIA              9             100
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             1               9
  STAGE IIIB             3              38
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  63 232  37
D1738V4, multiclass
    clus
vv   TRHDE MUTATED TRHDE WILD-TYPE
  T1             1               8
  T2             5              63
  T3            16             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
  TRHDE MUTATED    19   6   2
  TRHDE WILD-TYPE 201  74  64
D1738V5, multiclass
    clus
vv   TRHDE MUTATED TRHDE WILD-TYPE
  N0            19             201
  N1             6              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"
D1738V6, binary
                 cls
clus                0   1
  TRHDE MUTATED    21   2
  TRHDE WILD-TYPE 262  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRHDE MUTATED     21    2
  TRHDE WILD-TYPE  262   46
   clus
vv  TRHDE MUTATED TRHDE WILD-TYPE
  0            21             262
  1             2              46
[1] 2 2
[1] FALSE
D1738V7, 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
D1738V8, binary
                 cls
clus                0   1
  TRHDE MUTATED    22   4
  TRHDE WILD-TYPE 295  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRHDE MUTATED     22    4
  TRHDE WILD-TYPE  295   44
                               clus
vv                              TRHDE MUTATED TRHDE WILD-TYPE
  COLON ADENOCARCINOMA                     22             295
  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 239   2  22  17
D1738V9, multiclass
    clus
vv   TRHDE MUTATED TRHDE WILD-TYPE
  R0            18             239
  R1             0               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"
D1738V10, 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
D1738V11, 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(1739) Variable = NT5C3L MUTATION ANALYSIS
D1739V1, survival
                  sevent
clus2                0   1
  NT5C3L MUTATED     5   0
  NT5C3L WILD-TYPE 277  73
  NT5C3L MUTATED NT5C3L WILD-TYPE 
               5              350 
  NT5C3L MUTATED NT5C3L WILD-TYPE 
               0               73 
$`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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  NT5C3L MUTATED NT5C3L WILD-TYPE 
           13.02             0.00 
  NT5C3L MUTATED NT5C3L WILD-TYPE 
           35.01           140.38 
  NT5C3L MUTATED NT5C3L WILD-TYPE 
          25.020           20.105 
[1] "13.0 - 35.0 (25.0)" "0.0 - 140.4 (20.1)"
[1] "hr="     "9100000"
D1739V2, 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       25       107         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NT5C3L MUTATED           1          0          1          0        0
  NT5C3L WILD-TYPE        18         10         40         31       35
                  vv
clus               STAGE IVA STAGE IVB
  NT5C3L MUTATED           0         0
  NT5C3L WILD-TYPE        13         1
D1739V3, multiclass
            clus
vv           NT5C3L MUTATED NT5C3L WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               2              107
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  NT5C3L MUTATED     0   1   4   0
  NT5C3L WILD-TYPE   9  67 244  41
D1739V4, multiclass
    clus
vv   NT5C3L MUTATED NT5C3L WILD-TYPE
  T1              0                9
  T2              1               67
  T3              4              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
  NT5C3L MUTATED     3   1   1
  NT5C3L WILD-TYPE 217  79  65
D1739V5, multiclass
    clus
vv   NT5C3L MUTATED NT5C3L WILD-TYPE
  N0              3              217
  N1              1               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"
D1739V6, binary
                  cls
clus                 0   1
  NT5C3L MUTATED     3   0
  NT5C3L WILD-TYPE 280  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NT5C3L MUTATED      3    0
  NT5C3L WILD-TYPE  280   48
   clus
vv  NT5C3L MUTATED NT5C3L WILD-TYPE
  0              3              280
  1              0               48
[1] 2 2
[1] FALSE
D1739V7, 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
D1739V8, binary
                  cls
clus                 0   1
  NT5C3L MUTATED     2   3
  NT5C3L WILD-TYPE 315  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NT5C3L MUTATED      2    3
  NT5C3L WILD-TYPE  315   45
                               clus
vv                              NT5C3L MUTATED NT5C3L WILD-TYPE
  COLON ADENOCARCINOMA                       2              315
  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 254   2  22  21
D1739V9, multiclass
    clus
vv   NT5C3L MUTATED NT5C3L WILD-TYPE
  R0              3              254
  R1              0                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"
D1739V10, 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
D1739V11, multiclass
[1] "Remove cluster labels:" "NT5C3L MUTATED"        
clus
  NT5C3L MUTATED NT5C3L WILD-TYPE 
               2              204 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-4105 
"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-A6-6649       TCGA-A6-6651 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-A6-6652       TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6781 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-A6-6782       TCGA-AD-5900       TCGA-AD-6548       TCGA-AD-6888 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-AD-6889       TCGA-AD-6890       TCGA-AD-6895       TCGA-AD-6899 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6964       TCGA-AD-6965 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070       TCGA-AY-4071 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-AZ-4315       TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4681 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-AZ-4682       TCGA-AZ-5403       TCGA-AZ-5407       TCGA-AZ-6598 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-AZ-6599       TCGA-AZ-6600       TCGA-AZ-6601       TCGA-AZ-6603 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-AZ-6605       TCGA-AZ-6606       TCGA-AZ-6607       TCGA-AZ-6608 
"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-5912       TCGA-CK-5913       TCGA-CK-5914 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-CK-5915       TCGA-CK-5916       TCGA-CK-6746       TCGA-CK-6747 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-CK-6748       TCGA-CK-6751       TCGA-CM-4743       TCGA-CM-4744 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-CM-4746       TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-CM-5344       TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-CM-5861       TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-CM-5868       TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-CM-6164       TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-CM-6168       TCGA-CM-6170       TCGA-CM-6171       TCGA-CM-6172 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676       TCGA-CM-6677 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680       TCGA-D5-5537 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540       TCGA-D5-5541 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533       TCGA-D5-6534 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537       TCGA-D5-6538 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541       TCGA-D5-6898 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923       TCGA-D5-6924 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928       TCGA-D5-6929 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932       TCGA-D5-7000 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-DM-A0X9       TCGA-DM-A0XD       TCGA-DM-A0XF       TCGA-DM-A1D0 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-DM-A1D4       TCGA-DM-A1D6       TCGA-DM-A1D7       TCGA-DM-A1D8 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-DM-A1D9       TCGA-DM-A1DA       TCGA-DM-A1DB       TCGA-DM-A1HA 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-DM-A1HB       TCGA-DM-A282       TCGA-DM-A285       TCGA-DM-A28C 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-DM-A28E       TCGA-DM-A28F       TCGA-DM-A28G       TCGA-DM-A28H 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-DM-A28K       TCGA-F4-6459       TCGA-F4-6460       TCGA-F4-6569 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704       TCGA-F4-6805 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808       TCGA-F4-6809 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856       TCGA-G4-6293 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304       TCGA-G4-6306 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310       TCGA-G4-6315 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323       TCGA-G4-6586 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 
      TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628 
"NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" "NT5C3L WILD-TYPE" 

Clustering(1740) Variable = FAM133A MUTATION ANALYSIS
D1740V1, survival
                   sevent
clus2                 0   1
  FAM133A MUTATED     9   0
  FAM133A WILD-TYPE 273  73
  FAM133A MUTATED FAM133A WILD-TYPE 
                9               346 
  FAM133A MUTATED FAM133A WILD-TYPE 
                0                73 
$`FAM133A MUTATED`
TCGA-A6-5659 TCGA-A6-6141 TCGA-AA-3672 TCGA-AA-3977 TCGA-AA-A010 TCGA-CA-6717 
       30.44         8.38         0.92        25.02        34.98         0.33 
TCGA-CM-6677 TCGA-D5-6930 TCGA-DM-A1HB 
       11.08         1.51       135.65 

$`FAM133A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  FAM133A MUTATED FAM133A WILD-TYPE 
             0.33              0.00 
  FAM133A MUTATED FAM133A WILD-TYPE 
           135.65            140.38 
  FAM133A MUTATED FAM133A WILD-TYPE 
           11.080            20.235 
[1] "0.3 - 135.7 (11.1)" "0.0 - 140.4 (20.2)"
[1] "hr="     "9300000"
D1740V2, 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       25       103         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM133A MUTATED           1          0          1          0        0
  FAM133A WILD-TYPE        18         10         40         31       35
                   vv
clus                STAGE IVA STAGE IVB
  FAM133A MUTATED           0         0
  FAM133A WILD-TYPE        13         1
D1740V3, multiclass
            clus
vv           FAM133A MUTATED FAM133A WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                6               103
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  FAM133A MUTATED     0   2   8   1
  FAM133A WILD-TYPE   9  66 240  40
D1740V4, multiclass
    clus
vv   FAM133A MUTATED FAM133A WILD-TYPE
  T1               0                 9
  T2               2                66
  T3               8               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
  FAM133A MUTATED     9   2   0
  FAM133A WILD-TYPE 211  78  66
D1740V5, multiclass
    clus
vv   FAM133A MUTATED FAM133A WILD-TYPE
  N0               9               211
  N1               2                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"
D1740V6, binary
                   cls
clus                  0   1
  FAM133A MUTATED    10   0
  FAM133A WILD-TYPE 273  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM133A MUTATED     10    0
  FAM133A WILD-TYPE  273   48
   clus
vv  FAM133A MUTATED FAM133A WILD-TYPE
  0              10               273
  1               0                48
[1] 2 2
[1] FALSE
D1740V7, 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
D1740V8, binary
                   cls
clus                  0   1
  FAM133A MUTATED     9   2
  FAM133A WILD-TYPE 308  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM133A MUTATED      9    2
  FAM133A WILD-TYPE  308   46
                               clus
vv                              FAM133A MUTATED FAM133A WILD-TYPE
  COLON ADENOCARCINOMA                        9               308
  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 250   2  22  20
D1740V9, multiclass
    clus
vv   FAM133A MUTATED FAM133A WILD-TYPE
  R0               7               250
  R1               0                 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"
D1740V10, 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
D1740V11, 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(1741) Variable = SYT16 MUTATION ANALYSIS
D1741V1, survival
                 sevent
clus2               0   1
  SYT16 MUTATED     9   3
  SYT16 WILD-TYPE 273  70
  SYT16 MUTATED SYT16 WILD-TYPE 
             12             343 
  SYT16 MUTATED SYT16 WILD-TYPE 
              3              70 
$`SYT16 MUTATED`
TCGA-A6-3808 TCGA-A6-6653 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3858 
       33.34        24.39        85.05        26.99        19.04        31.07 
TCGA-AA-A01R TCGA-CA-6718 TCGA-CK-5912 TCGA-CM-6165 TCGA-F4-6570 TCGA-G4-6321 
       35.01         0.10        49.08        16.04         6.18        22.09 

$`SYT16 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
        5.03        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3861 
        0.00        36.03        32.05         0.99        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.33         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      102.44        40.34        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 
        2.93         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 
       16.01        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       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        13.38        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  SYT16 MUTATED SYT16 WILD-TYPE 
            0.1             0.0 
  SYT16 MUTATED SYT16 WILD-TYPE 
          85.05          140.38 
  SYT16 MUTATED SYT16 WILD-TYPE 
          25.69           20.02 
[1] "0.1 - 85.0 (25.7)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1.1"
D1741V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SYT16 MUTATED         3        0        1         6         0         0
  SYT16 WILD-TYPE      61        1       24       103         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SYT16 MUTATED           3          0          0          0        0         0
  SYT16 WILD-TYPE        16         10         41         31       35        13
                 vv
clus              STAGE IVB
  SYT16 MUTATED           0
  SYT16 WILD-TYPE         1
D1741V3, multiclass
            clus
vv           SYT16 MUTATED SYT16 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              6             103
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              3              16
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SYT16 MUTATED     0   4   9   0
  SYT16 WILD-TYPE   9  64 239  41
D1741V4, multiclass
    clus
vv   SYT16 MUTATED SYT16 WILD-TYPE
  T1             0               9
  T2             4              64
  T3             9             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
  SYT16 MUTATED    11   1   1
  SYT16 WILD-TYPE 209  79  65
D1741V5, multiclass
    clus
vv   SYT16 MUTATED SYT16 WILD-TYPE
  N0            11             209
  N1             1              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"
D1741V6, binary
                 cls
clus                0   1
  SYT16 MUTATED    11   0
  SYT16 WILD-TYPE 272  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYT16 MUTATED     11    0
  SYT16 WILD-TYPE  272   48
   clus
vv  SYT16 MUTATED SYT16 WILD-TYPE
  0            11             272
  1             0              48
[1] 2 2
[1] FALSE
D1741V7, binary
                 cls
clus                0   1
  SYT16 MUTATED     4   9
  SYT16 WILD-TYPE 166 188
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYT16 MUTATED      4    9
  SYT16 WILD-TYPE  166  188
        clus
vv       SYT16 MUTATED SYT16 WILD-TYPE
  FEMALE             4             166
  MALE               9             188
[1] 2 2
[1] FALSE
D1741V8, binary
                 cls
clus                0   1
  SYT16 MUTATED    12   1
  SYT16 WILD-TYPE 305  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYT16 MUTATED     12    1
  SYT16 WILD-TYPE  305   47
                               clus
vv                              SYT16 MUTATED SYT16 WILD-TYPE
  COLON ADENOCARCINOMA                     12             305
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SYT16 MUTATED    10   0   0   2
  SYT16 WILD-TYPE 247   2  22  19
D1741V9, multiclass
    clus
vv   SYT16 MUTATED SYT16 WILD-TYPE
  R0            10             247
  R1             0               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"
D1741V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SYT16 MUTATED                                  0     1
  SYT16 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SYT16 MUTATED                           0     6
  SYT16 WILD-TYPE                        19   170
D1741V11, multiclass
                                  clus
vv                                 SYT16 MUTATED SYT16 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(1742) Variable = ZNF546 MUTATION ANALYSIS
D1742V1, survival
                  sevent
clus2                0   1
  ZNF546 MUTATED    11   3
  ZNF546 WILD-TYPE 271  70
  ZNF546 MUTATED ZNF546 WILD-TYPE 
              14              341 
  ZNF546 MUTATED ZNF546 WILD-TYPE 
               3               70 
$`ZNF546 MUTATED`
TCGA-A6-3809 TCGA-A6-5666 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3977 TCGA-AA-A00N 
       32.75        32.71         3.02        63.98        25.02         4.01 
TCGA-AA-A010 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CM-6678 
       34.98        21.44        17.82        58.39         0.33        11.01 
TCGA-F4-6570 TCGA-G4-6310 
        6.18        45.11 

$`ZNF546 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       19.66        20.28         7.04         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.95        15.75         0.20         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-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        13.38        13.45        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        51.75        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  ZNF546 MUTATED ZNF546 WILD-TYPE 
            0.33             0.00 
  ZNF546 MUTATED ZNF546 WILD-TYPE 
           63.98           140.38 
  ZNF546 MUTATED ZNF546 WILD-TYPE 
           23.23            20.12 
[1] "0.3 - 64.0 (23.2)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.1"
D1742V2, 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       23       104         5         0
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF546 MUTATED           0          0          2          0        0
  ZNF546 WILD-TYPE        19         10         39         31       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF546 MUTATED           1         0
  ZNF546 WILD-TYPE        12         1
D1742V3, multiclass
            clus
vv           ZNF546 MUTATED ZNF546 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               5              104
  STAGE IIB               3                5
  STAGE IIC               1                0
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 239  36
D1742V4, multiclass
    clus
vv   ZNF546 MUTATED ZNF546 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              9              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
  ZNF546 MUTATED    12   3   0
  ZNF546 WILD-TYPE 208  77  66
D1742V5, multiclass
    clus
vv   ZNF546 MUTATED ZNF546 WILD-TYPE
  N0             12              208
  N1              3               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"
D1742V6, binary
                  cls
clus                 0   1
  ZNF546 MUTATED    12   1
  ZNF546 WILD-TYPE 271  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF546 MUTATED     12    1
  ZNF546 WILD-TYPE  271   47
   clus
vv  ZNF546 MUTATED ZNF546 WILD-TYPE
  0             12              271
  1              1               47
[1] 2 2
[1] FALSE
D1742V7, 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
D1742V8, binary
                  cls
clus                 0   1
  ZNF546 MUTATED    12   3
  ZNF546 WILD-TYPE 305  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF546 MUTATED     12    3
  ZNF546 WILD-TYPE  305   45
                               clus
vv                              ZNF546 MUTATED ZNF546 WILD-TYPE
  COLON ADENOCARCINOMA                      12              305
  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 245   2  22  20
D1742V9, multiclass
    clus
vv   ZNF546 MUTATED ZNF546 WILD-TYPE
  R0             12              245
  R1              0                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"
D1742V10, 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
D1742V11, 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(1743) Variable = TTLL5 MUTATION ANALYSIS
D1743V1, survival
                 sevent
clus2               0   1
  TTLL5 MUTATED     9   2
  TTLL5 WILD-TYPE 273  71
  TTLL5 MUTATED TTLL5 WILD-TYPE 
             11             344 
  TTLL5 MUTATED TTLL5 WILD-TYPE 
              2              71 
$`TTLL5 MUTATED`
TCGA-AA-3492 TCGA-AA-3864 TCGA-AA-3966 TCGA-AD-6964 TCGA-AU-6004 TCGA-AZ-4315 
        3.02        53.00         2.01        10.88        27.09        58.39 
TCGA-CA-5254 TCGA-CA-6717 TCGA-DM-A1HB TCGA-DM-A28H TCGA-G4-6306 
        2.24         0.33       135.65       117.07        44.68 

$`TTLL5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19         1.94         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  TTLL5 MUTATED TTLL5 WILD-TYPE 
           0.33            0.00 
  TTLL5 MUTATED TTLL5 WILD-TYPE 
         135.65          140.38 
  TTLL5 MUTATED TTLL5 WILD-TYPE 
         27.090          20.155 
[1] "0.3 - 135.7 (27.1)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.7"
D1743V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TTLL5 MUTATED         1        0        2         5         0         0
  TTLL5 WILD-TYPE      63        1       23       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        19         10         40         30       35        13
                 vv
clus              STAGE IVB
  TTLL5 MUTATED           0
  TTLL5 WILD-TYPE         1
D1743V3, multiclass
            clus
vv           TTLL5 MUTATED TTLL5 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              5             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TTLL5 MUTATED     0   2   8   1
  TTLL5 WILD-TYPE   9  66 240  40
D1743V4, multiclass
    clus
vv   TTLL5 MUTATED TTLL5 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             8             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
  TTLL5 MUTATED     8   1   2
  TTLL5 WILD-TYPE 212  79  64
D1743V5, multiclass
    clus
vv   TTLL5 MUTATED TTLL5 WILD-TYPE
  N0             8             212
  N1             1              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"
D1743V6, binary
                 cls
clus                0   1
  TTLL5 MUTATED    10   0
  TTLL5 WILD-TYPE 273  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TTLL5 MUTATED     10    0
  TTLL5 WILD-TYPE  273   48
   clus
vv  TTLL5 MUTATED TTLL5 WILD-TYPE
  0            10             273
  1             0              48
[1] 2 2
[1] FALSE
D1743V7, 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
D1743V8, binary
                 cls
clus                0   1
  TTLL5 MUTATED     9   2
  TTLL5 WILD-TYPE 308  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TTLL5 MUTATED      9    2
  TTLL5 WILD-TYPE  308   46
                               clus
vv                              TTLL5 MUTATED TTLL5 WILD-TYPE
  COLON ADENOCARCINOMA                      9             308
  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 252   2  22  19
D1743V9, multiclass
    clus
vv   TTLL5 MUTATED TTLL5 WILD-TYPE
  R0             5             252
  R1             0               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"
D1743V10, 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
D1743V11, 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(1744) Variable = FOXF2 MUTATION ANALYSIS
D1744V1, survival
                 sevent
clus2               0   1
  FOXF2 MUTATED     1   2
  FOXF2 WILD-TYPE 281  71
  FOXF2 MUTATED FOXF2 WILD-TYPE 
              3             352 
  FOXF2 MUTATED FOXF2 WILD-TYPE 
              2              71 
$`FOXF2 MUTATED`
TCGA-AA-3492 TCGA-AZ-6598 TCGA-CA-6718 
        3.02        49.41         0.10 

$`FOXF2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.33         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  FOXF2 MUTATED FOXF2 WILD-TYPE 
            0.1             0.0 
  FOXF2 MUTATED FOXF2 WILD-TYPE 
          49.41          140.38 
  FOXF2 MUTATED FOXF2 WILD-TYPE 
          3.020          20.235 
[1] "0.1 - 49.4 (3.0)"   "0.0 - 140.4 (20.2)"
[1] "hr=" "4.2"
D1744V2, 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       23       107         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        19         10         41         31       35        13
                 vv
clus              STAGE IVB
  FOXF2 MUTATED           0
  FOXF2 WILD-TYPE         1
D1744V3, multiclass
            clus
vv           FOXF2 MUTATED FOXF2 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              2             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FOXF2 MUTATED     0   0   4   0
  FOXF2 WILD-TYPE   9  68 244  41
D1744V4, multiclass
    clus
vv   FOXF2 MUTATED FOXF2 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             4             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
  FOXF2 MUTATED     4   0   0
  FOXF2 WILD-TYPE 216  80  66
D1744V5, multiclass
    clus
vv   FOXF2 MUTATED FOXF2 WILD-TYPE
  N0             4             216
  N1             0              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"
D1744V6, binary
                 cls
clus                0   1
  FOXF2 MUTATED     3   0
  FOXF2 WILD-TYPE 280  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXF2 MUTATED      3    0
  FOXF2 WILD-TYPE  280   48
   clus
vv  FOXF2 MUTATED FOXF2 WILD-TYPE
  0             3             280
  1             0              48
[1] 2 2
[1] FALSE
D1744V7, 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
D1744V8, binary
                 cls
clus                0   1
  FOXF2 MUTATED     4   0
  FOXF2 WILD-TYPE 313  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXF2 MUTATED      4    0
  FOXF2 WILD-TYPE  313   48
                               clus
vv                              FOXF2 MUTATED FOXF2 WILD-TYPE
  COLON ADENOCARCINOMA                      4             313
  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 255   2  22  20
D1744V9, multiclass
    clus
vv   FOXF2 MUTATED FOXF2 WILD-TYPE
  R0             2             255
  R1             0               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"
D1744V10, 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
D1744V11, multiclass
[1] "Remove cluster labels:" "FOXF2 MUTATED"         
clus
  FOXF2 MUTATED FOXF2 WILD-TYPE 
              2             204 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-4105 
"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-A6-6649      TCGA-A6-6651 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-A6-6652      TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-A6-6781      TCGA-A6-6782      TCGA-AD-5900      TCGA-AD-6548 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-AD-6888      TCGA-AD-6889      TCGA-AD-6890      TCGA-AD-6895 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-AD-6899      TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6964 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-AD-6965      TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-AY-4071      TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-AY-6386      TCGA-AZ-4315      TCGA-AZ-4323      TCGA-AZ-4616 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-AZ-4681      TCGA-AZ-4682      TCGA-AZ-5403      TCGA-AZ-5407 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-AZ-6599      TCGA-AZ-6600      TCGA-AZ-6601      TCGA-AZ-6603 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-AZ-6605      TCGA-AZ-6606      TCGA-AZ-6607      TCGA-AZ-6608 
"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-5912      TCGA-CK-5913      TCGA-CK-5914      TCGA-CK-5915 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-CK-5916      TCGA-CK-6746      TCGA-CK-6747      TCGA-CK-6748 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-CK-6751      TCGA-CM-4743      TCGA-CM-4744      TCGA-CM-4746 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-CM-4747      TCGA-CM-4752      TCGA-CM-5341      TCGA-CM-5344 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-CM-5348      TCGA-CM-5349      TCGA-CM-5860      TCGA-CM-5861 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-CM-5862      TCGA-CM-5863      TCGA-CM-5864      TCGA-CM-5868 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-CM-6161      TCGA-CM-6162      TCGA-CM-6163      TCGA-CM-6164 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-CM-6165      TCGA-CM-6166      TCGA-CM-6167      TCGA-CM-6168 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-CM-6169      TCGA-CM-6170      TCGA-CM-6171      TCGA-CM-6172 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-CM-6674      TCGA-CM-6675      TCGA-CM-6676      TCGA-CM-6677 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-CM-6678      TCGA-CM-6679      TCGA-CM-6680      TCGA-D5-5537 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-D5-5538      TCGA-D5-5539      TCGA-D5-5540      TCGA-D5-5541 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-D5-6529      TCGA-D5-6532      TCGA-D5-6533      TCGA-D5-6534 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-D5-6535      TCGA-D5-6536      TCGA-D5-6537      TCGA-D5-6538 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-D5-6539      TCGA-D5-6540      TCGA-D5-6541      TCGA-D5-6898 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923      TCGA-D5-6924 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-D5-6926      TCGA-D5-6927      TCGA-D5-6928      TCGA-D5-6929 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-D5-6930      TCGA-D5-6931      TCGA-D5-6932      TCGA-D5-7000 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-DM-A0X9      TCGA-DM-A0XD      TCGA-DM-A0XF      TCGA-DM-A1D0 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-DM-A1D4      TCGA-DM-A1D6      TCGA-DM-A1D7      TCGA-DM-A1D8 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-DM-A1D9      TCGA-DM-A1DA      TCGA-DM-A1DB      TCGA-DM-A1HA 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-DM-A1HB      TCGA-DM-A282      TCGA-DM-A285      TCGA-DM-A28C 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-DM-A28E      TCGA-DM-A28F      TCGA-DM-A28G      TCGA-DM-A28H 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-DM-A28K      TCGA-F4-6459      TCGA-F4-6460      TCGA-F4-6569 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704      TCGA-F4-6805 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808      TCGA-F4-6809 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856      TCGA-G4-6293 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304      TCGA-G4-6306 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310      TCGA-G4-6315 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323      TCGA-G4-6586 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 
     TCGA-G4-6588      TCGA-G4-6625      TCGA-G4-6626      TCGA-G4-6628 
"FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" "FOXF2 WILD-TYPE" 

Clustering(1745) Variable = PKHD1 MUTATION ANALYSIS
D1745V1, survival
                 sevent
clus2               0   1
  PKHD1 MUTATED    37  18
  PKHD1 WILD-TYPE 245  55
  PKHD1 MUTATED PKHD1 WILD-TYPE 
             55             300 
  PKHD1 MUTATED PKHD1 WILD-TYPE 
             18              55 
$`PKHD1 MUTATED`
TCGA-A6-2677 TCGA-A6-3809 TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3516 
       24.33        32.75        22.06         3.02        63.98        13.02 
TCGA-AA-3542 TCGA-AA-3553 TCGA-AA-3663 TCGA-AA-3680 TCGA-AA-3697 TCGA-AA-3710 
       12.99        24.00         6.97        11.01        85.05        26.99 
TCGA-AA-3833 TCGA-AA-3845 TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       15.95         0.00        53.00        33.01        26.01        24.00 
TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-3989 TCGA-AA-A00A TCGA-AA-A00N TCGA-AA-A010 
        2.01        25.02         7.96        38.04         4.01        34.98 
TCGA-AA-A01R TCGA-AA-A029 TCGA-AZ-4315 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 
       35.01        51.98        58.39        62.79        49.41        12.10 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4948 TCGA-CK-5916 
        1.94         2.24         0.33         0.10       102.44        21.14 
TCGA-CK-6748 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5864 
        2.01        22.03        30.08        16.01         5.03        15.02 
TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6540 TCGA-D5-6923 
       12.26        13.51        18.25        43.27        16.14        12.43 
TCGA-D5-6928 TCGA-DM-A1D8 TCGA-DM-A1DB TCGA-DM-A28F TCGA-F4-6570 TCGA-G4-6321 
       11.64        12.59        44.32        35.97         6.18        22.09 
TCGA-G4-6626 
       46.75 

$`PKHD1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        42.90        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       34.65        33.34        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       30.44        29.19        33.53        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 
       20.28         7.04         1.02        35.01         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3713 
        5.98        37.05        19.00        36.00         5.03        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
        1.02        17.98        38.99        37.02        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E 
       27.02        19.07        27.02        13.94        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 
       83.80        22.36        61.41         6.77       100.01        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         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 
        0.07         0.26         1.35        17.56        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       49.08        51.32        21.99         2.93       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 
       11.51        20.19         1.32        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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G 
      135.65       139.17         6.12        81.37       119.93        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      117.07        98.24         8.61        13.38        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       36.00        13.78        35.80        26.17        91.79        52.80 

  PKHD1 MUTATED PKHD1 WILD-TYPE 
              0               0 
  PKHD1 MUTATED PKHD1 WILD-TYPE 
         102.44          140.38 
  PKHD1 MUTATED PKHD1 WILD-TYPE 
         21.140          20.155 
[1] "0.0 - 102.4 (21.1)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.8"
D1745V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PKHD1 MUTATED         5        0        7        22         4         0
  PKHD1 WILD-TYPE      59        1       18        87         4         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PKHD1 MUTATED           4          2          4          2        4         1
  PKHD1 WILD-TYPE        15          8         37         29       31        12
                 vv
clus              STAGE IVB
  PKHD1 MUTATED           0
  PKHD1 WILD-TYPE         1
D1745V3, multiclass
            clus
vv           PKHD1 MUTATED PKHD1 WILD-TYPE
  STAGE I                5              59
  STAGE IA               0               1
  STAGE II               7              18
  STAGE IIA             22              87
  STAGE IIB              4               4
  STAGE IIC              0               1
  STAGE III              4              15
  STAGE IIIA             2               8
  STAGE IIIB             4              37
  STAGE IIIC             2              29
  STAGE IV               4              31
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  61 205  35
D1745V4, multiclass
    clus
vv   PKHD1 MUTATED PKHD1 WILD-TYPE
  T1             1               8
  T2             7              61
  T3            43             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
  PKHD1 MUTATED    40  11   6
  PKHD1 WILD-TYPE 180  69  60
D1745V5, multiclass
    clus
vv   PKHD1 MUTATED PKHD1 WILD-TYPE
  N0            40             180
  N1            11              69
  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"
D1745V6, binary
                 cls
clus                0   1
  PKHD1 MUTATED    47   5
  PKHD1 WILD-TYPE 236  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PKHD1 MUTATED     47    5
  PKHD1 WILD-TYPE  236   43
   clus
vv  PKHD1 MUTATED PKHD1 WILD-TYPE
  0            47             236
  1             5              43
[1] 2 2
[1] FALSE
D1745V7, 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
D1745V8, binary
                 cls
clus                0   1
  PKHD1 MUTATED    44  13
  PKHD1 WILD-TYPE 273  35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PKHD1 MUTATED     44   13
  PKHD1 WILD-TYPE  273   35
                               clus
vv                              PKHD1 MUTATED PKHD1 WILD-TYPE
  COLON ADENOCARCINOMA                     44             273
  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 217   2  20  16
D1745V9, multiclass
    clus
vv   PKHD1 MUTATED PKHD1 WILD-TYPE
  R0            40             217
  R1             0               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"
D1745V10, 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
D1745V11, 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(1746) Variable = OR8K1 MUTATION ANALYSIS
D1746V1, survival
                 sevent
clus2               0   1
  OR8K1 MUTATED     8   0
  OR8K1 WILD-TYPE 274  73
  OR8K1 MUTATED OR8K1 WILD-TYPE 
              8             347 
  OR8K1 MUTATED OR8K1 WILD-TYPE 
              0              73 
$`OR8K1 MUTATED`
TCGA-AA-3530 TCGA-AA-3660 TCGA-AA-3977 TCGA-AA-A010 TCGA-AU-6004 TCGA-CA-6717 
       19.07        78.08        25.02        34.98        27.09         0.33 
TCGA-CM-5861 TCGA-G4-6586 
       15.02        35.80 

$`OR8K1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
        8.05        19.07         0.00        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        61.02         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        26.17        91.79        46.75        52.80 

  OR8K1 MUTATED OR8K1 WILD-TYPE 
           0.33            0.00 
  OR8K1 MUTATED OR8K1 WILD-TYPE 
          78.08          140.38 
  OR8K1 MUTATED OR8K1 WILD-TYPE 
         26.055          20.120 
[1] "0.3 - 78.1 (26.1)"  "0.0 - 140.4 (20.1)"
[1] "hr="     "9300000"
D1746V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR8K1 MUTATED         2        0        2         3         1         0
  OR8K1 WILD-TYPE      62        1       23       106         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR8K1 MUTATED           1          0          0          0        0         0
  OR8K1 WILD-TYPE        18         10         41         31       35        13
                 vv
clus              STAGE IVB
  OR8K1 MUTATED           0
  OR8K1 WILD-TYPE         1
D1746V3, multiclass
            clus
vv           OR8K1 MUTATED OR8K1 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              3             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR8K1 MUTATED     0   3   5   2
  OR8K1 WILD-TYPE   9  65 243  39
D1746V4, multiclass
    clus
vv   OR8K1 MUTATED OR8K1 WILD-TYPE
  T1             0               9
  T2             3              65
  T3             5             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
  OR8K1 MUTATED     9   0   1
  OR8K1 WILD-TYPE 211  80  65
D1746V5, multiclass
    clus
vv   OR8K1 MUTATED OR8K1 WILD-TYPE
  N0             9             211
  N1             0              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"
D1746V6, binary
                 cls
clus                0   1
  OR8K1 MUTATED     9   0
  OR8K1 WILD-TYPE 274  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR8K1 MUTATED      9    0
  OR8K1 WILD-TYPE  274   48
   clus
vv  OR8K1 MUTATED OR8K1 WILD-TYPE
  0             9             274
  1             0              48
[1] 2 2
[1] FALSE
D1746V7, binary
                 cls
clus                0   1
  OR8K1 MUTATED     6   4
  OR8K1 WILD-TYPE 164 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR8K1 MUTATED      6    4
  OR8K1 WILD-TYPE  164  193
        clus
vv       OR8K1 MUTATED OR8K1 WILD-TYPE
  FEMALE             6             164
  MALE               4             193
[1] 2 2
[1] FALSE
D1746V8, binary
                 cls
clus                0   1
  OR8K1 MUTATED     9   1
  OR8K1 WILD-TYPE 308  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR8K1 MUTATED      9    1
  OR8K1 WILD-TYPE  308   47
                               clus
vv                              OR8K1 MUTATED OR8K1 WILD-TYPE
  COLON ADENOCARCINOMA                      9             308
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  OR8K1 MUTATED     8   0   0   1
  OR8K1 WILD-TYPE 249   2  22  20
D1746V9, multiclass
    clus
vv   OR8K1 MUTATED OR8K1 WILD-TYPE
  R0             8             249
  R1             0               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"
D1746V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR8K1 MUTATED                                  0     1
  OR8K1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR8K1 MUTATED                           0     3
  OR8K1 WILD-TYPE                        19   173
D1746V11, multiclass
                                  clus
vv                                 OR8K1 MUTATED OR8K1 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(1747) Variable = ITPRIPL1 MUTATION ANALYSIS
D1747V1, survival
                    sevent
clus2                  0   1
  ITPRIPL1 MUTATED     7   0
  ITPRIPL1 WILD-TYPE 275  73
  ITPRIPL1 MUTATED ITPRIPL1 WILD-TYPE 
                 7                348 
  ITPRIPL1 MUTATED ITPRIPL1 WILD-TYPE 
                 0                 73 
$`ITPRIPL1 MUTATED`
TCGA-A6-6781 TCGA-AA-3502 TCGA-AA-3949 TCGA-AZ-4315 TCGA-D5-6927 TCGA-D5-6930 
       19.66        35.01        26.01        58.39         9.44         1.51 
TCGA-G4-6625 
       91.79 

$`ITPRIPL1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        26.17        46.75        52.80 

  ITPRIPL1 MUTATED ITPRIPL1 WILD-TYPE 
              1.51               0.00 
  ITPRIPL1 MUTATED ITPRIPL1 WILD-TYPE 
             91.79             140.38 
  ITPRIPL1 MUTATED ITPRIPL1 WILD-TYPE 
            26.010             20.155 
[1] "1.5 - 91.8 (26.0)"  "0.0 - 140.4 (20.2)"
[1] "hr="     "9300000"
D1747V2, 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       25       105         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ITPRIPL1 MUTATED           0          0          1          1        0
  ITPRIPL1 WILD-TYPE        19         10         40         30       35
                    vv
clus                 STAGE IVA STAGE IVB
  ITPRIPL1 MUTATED           0         0
  ITPRIPL1 WILD-TYPE        13         1
D1747V3, multiclass
            clus
vv           ITPRIPL1 MUTATED ITPRIPL1 WILD-TYPE
  STAGE I                   1                 63
  STAGE IA                  0                  1
  STAGE II                  0                 25
  STAGE IIA                 4                105
  STAGE IIB                 0                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                0                 10
  STAGE IIIB                1                 40
  STAGE IIIC                1                 30
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  ITPRIPL1 MUTATED     0   1   5   1
  ITPRIPL1 WILD-TYPE   9  67 243  40
D1747V4, multiclass
    clus
vv   ITPRIPL1 MUTATED ITPRIPL1 WILD-TYPE
  T1                0                  9
  T2                1                 67
  T3                5                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
  ITPRIPL1 MUTATED     5   2   0
  ITPRIPL1 WILD-TYPE 215  78  66
D1747V5, multiclass
    clus
vv   ITPRIPL1 MUTATED ITPRIPL1 WILD-TYPE
  N0                5                215
  N1                2                 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"
D1747V6, binary
                    cls
clus                   0   1
  ITPRIPL1 MUTATED     6   0
  ITPRIPL1 WILD-TYPE 277  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ITPRIPL1 MUTATED      6    0
  ITPRIPL1 WILD-TYPE  277   48
   clus
vv  ITPRIPL1 MUTATED ITPRIPL1 WILD-TYPE
  0                6                277
  1                0                 48
[1] 2 2
[1] FALSE
D1747V7, 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
D1747V8, binary
                    cls
clus                   0   1
  ITPRIPL1 MUTATED     4   3
  ITPRIPL1 WILD-TYPE 313  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ITPRIPL1 MUTATED      4    3
  ITPRIPL1 WILD-TYPE  313   45
                               clus
vv                              ITPRIPL1 MUTATED ITPRIPL1 WILD-TYPE
  COLON ADENOCARCINOMA                         4                313
  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 250   2  22  21
D1747V9, multiclass
    clus
vv   ITPRIPL1 MUTATED ITPRIPL1 WILD-TYPE
  R0                7                250
  R1                0                  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"
D1747V10, 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
D1747V11, 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(1748) Variable = LIPH MUTATION ANALYSIS
D1748V1, survival
                sevent
clus2              0   1
  LIPH MUTATED     8   1
  LIPH WILD-TYPE 274  72
  LIPH MUTATED LIPH WILD-TYPE 
             9            346 
  LIPH MUTATED LIPH WILD-TYPE 
             1             72 
$`LIPH MUTATED`
TCGA-A6-6141 TCGA-AA-3947 TCGA-AA-A010 TCGA-CA-6717 TCGA-CK-5913 TCGA-D5-6532 
        8.38        33.01        34.98         0.33        51.32        18.25 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6626 
       22.09        26.17        46.75 

$`LIPH WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 
       13.78        35.80        91.79        52.80 

  LIPH MUTATED LIPH WILD-TYPE 
          0.33           0.00 
  LIPH MUTATED LIPH WILD-TYPE 
         51.32         140.38 
  LIPH MUTATED LIPH WILD-TYPE 
         26.17          20.07 
[1] "0.3 - 51.3 (26.2)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "2"  
D1748V2, 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       25       103         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        18         10         41         31       35        13
                vv
clus             STAGE IVB
  LIPH MUTATED           0
  LIPH WILD-TYPE         1
D1748V3, multiclass
            clus
vv           LIPH MUTATED LIPH WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             6            103
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  LIPH MUTATED     0   1   6   2
  LIPH WILD-TYPE   9  67 242  39
D1748V4, multiclass
    clus
vv   LIPH MUTATED LIPH WILD-TYPE
  T1            0              9
  T2            1             67
  T3            6            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
  LIPH MUTATED     8   1   0
  LIPH WILD-TYPE 212  79  66
D1748V5, multiclass
    clus
vv   LIPH MUTATED LIPH WILD-TYPE
  N0            8            212
  N1            1             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"
D1748V6, binary
                cls
clus               0   1
  LIPH MUTATED     7   0
  LIPH WILD-TYPE 276  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIPH MUTATED      7    0
  LIPH WILD-TYPE  276   48
   clus
vv  LIPH MUTATED LIPH WILD-TYPE
  0            7            276
  1            0             48
[1] 2 2
[1] FALSE
D1748V7, 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
D1748V8, binary
                cls
clus               0   1
  LIPH MUTATED     7   2
  LIPH WILD-TYPE 310  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIPH MUTATED      7    2
  LIPH WILD-TYPE  310   46
                               clus
vv                              LIPH MUTATED LIPH WILD-TYPE
  COLON ADENOCARCINOMA                     7            310
  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 251   2  22  19
D1748V9, multiclass
    clus
vv   LIPH MUTATED LIPH WILD-TYPE
  R0            6            251
  R1            0              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"
D1748V10, 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
D1748V11, 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(1749) Variable = MORC2 MUTATION ANALYSIS
D1749V1, survival
                 sevent
clus2               0   1
  MORC2 MUTATED     8   3
  MORC2 WILD-TYPE 274  70
  MORC2 MUTATED MORC2 WILD-TYPE 
             11             344 
  MORC2 MUTATED MORC2 WILD-TYPE 
              3              70 
$`MORC2 MUTATED`
TCGA-A6-6137 TCGA-AA-3510 TCGA-AA-3542 TCGA-AA-3811 TCGA-AA-A00R TCGA-AY-6196 
       27.09        63.98        12.99        10.06         0.99         0.20 
TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-D5-6532 TCGA-D5-6927 
       58.39        49.41       100.01        18.25         9.44 

$`MORC2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        32.71        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        19.04        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
       42.02        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        15.75        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  MORC2 MUTATED MORC2 WILD-TYPE 
            0.2             0.0 
  MORC2 MUTATED MORC2 WILD-TYPE 
         100.01          140.38 
  MORC2 MUTATED MORC2 WILD-TYPE 
         18.250          20.235 
[1] "0.2 - 100.0 (18.2)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1"  
D1749V2, 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       22       106         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        18         10         40         29       35        13
                 vv
clus              STAGE IVB
  MORC2 MUTATED           0
  MORC2 WILD-TYPE         1
D1749V3, multiclass
            clus
vv           MORC2 MUTATED MORC2 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              3             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             2              29
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MORC2 MUTATED     0   1  10   1
  MORC2 WILD-TYPE   9  67 238  40
D1749V4, multiclass
    clus
vv   MORC2 MUTATED MORC2 WILD-TYPE
  T1             0               9
  T2             1              67
  T3            10             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
  MORC2 MUTATED     8   1   3
  MORC2 WILD-TYPE 212  79  63
D1749V5, multiclass
    clus
vv   MORC2 MUTATED MORC2 WILD-TYPE
  N0             8             212
  N1             1              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"
D1749V6, binary
                 cls
clus                0   1
  MORC2 MUTATED     9   0
  MORC2 WILD-TYPE 274  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MORC2 MUTATED      9    0
  MORC2 WILD-TYPE  274   48
   clus
vv  MORC2 MUTATED MORC2 WILD-TYPE
  0             9             274
  1             0              48
[1] 2 2
[1] FALSE
D1749V7, 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
D1749V8, binary
                 cls
clus                0   1
  MORC2 MUTATED    11   1
  MORC2 WILD-TYPE 306  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MORC2 MUTATED     11    1
  MORC2 WILD-TYPE  306   47
                               clus
vv                              MORC2 MUTATED MORC2 WILD-TYPE
  COLON ADENOCARCINOMA                     11             306
  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 249   2  22  20
D1749V9, multiclass
    clus
vv   MORC2 MUTATED MORC2 WILD-TYPE
  R0             8             249
  R1             0               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"
D1749V10, 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
D1749V11, 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(1750) Variable = OR51E2 MUTATION ANALYSIS
D1750V1, survival
                  sevent
clus2                0   1
  OR51E2 MUTATED     5   0
  OR51E2 WILD-TYPE 277  73
  OR51E2 MUTATED OR51E2 WILD-TYPE 
               5              350 
  OR51E2 MUTATED OR51E2 WILD-TYPE 
               0               73 
$`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        13.45 

$`OR51E2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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-6679 TCGA-CM-6680 
       11.01        12.95        13.05        11.08        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6703 
      117.07        98.24         8.61        13.38         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  OR51E2 MUTATED OR51E2 WILD-TYPE 
           11.01             0.00 
  OR51E2 MUTATED OR51E2 WILD-TYPE 
           63.98           140.38 
  OR51E2 MUTATED OR51E2 WILD-TYPE 
          13.450           20.235 
[1] "11.0 - 64.0 (13.4)" "0.0 - 140.4 (20.2)"
[1] "hr="     "9100000"
D1750V2, 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       24       108         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR51E2 MUTATED           1          0          0          0        0
  OR51E2 WILD-TYPE        18         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  OR51E2 MUTATED           1         0
  OR51E2 WILD-TYPE        12         1
D1750V3, multiclass
            clus
vv           OR51E2 MUTATED OR51E2 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               1              108
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 245  40
D1750V4, multiclass
    clus
vv   OR51E2 MUTATED OR51E2 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              3              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
  OR51E2 MUTATED     3   1   1
  OR51E2 WILD-TYPE 217  79  65
D1750V5, multiclass
    clus
vv   OR51E2 MUTATED OR51E2 WILD-TYPE
  N0              3              217
  N1              1               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"
D1750V6, binary
                  cls
clus                 0   1
  OR51E2 MUTATED     4   1
  OR51E2 WILD-TYPE 279  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51E2 MUTATED      4    1
  OR51E2 WILD-TYPE  279   47
   clus
vv  OR51E2 MUTATED OR51E2 WILD-TYPE
  0              4              279
  1              1               47
[1] 2 2
[1] FALSE
D1750V7, 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
D1750V8, binary
                  cls
clus                 0   1
  OR51E2 MUTATED     4   1
  OR51E2 WILD-TYPE 313  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51E2 MUTATED      4    1
  OR51E2 WILD-TYPE  313   47
                               clus
vv                              OR51E2 MUTATED OR51E2 WILD-TYPE
  COLON ADENOCARCINOMA                       4              313
  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 252   2  22  21
D1750V9, multiclass
    clus
vv   OR51E2 MUTATED OR51E2 WILD-TYPE
  R0              5              252
  R1              0                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"
D1750V10, 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
D1750V11, 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(1751) Variable = APAF1 MUTATION ANALYSIS
D1751V1, survival
                 sevent
clus2               0   1
  APAF1 MUTATED    16   2
  APAF1 WILD-TYPE 266  71
  APAF1 MUTATED APAF1 WILD-TYPE 
             18             337 
  APAF1 MUTATED APAF1 WILD-TYPE 
              2              71 
$`APAF1 MUTATED`
TCGA-A6-5665 TCGA-A6-5666 TCGA-AA-3502 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3833 
       22.06        32.71        35.01        19.04        19.04        15.95 
TCGA-AA-3950 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-CA-6718 TCGA-CK-4947 
       24.00        25.02         4.01        34.98         0.10        17.56 
TCGA-CM-5341 TCGA-CM-6170 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6540 TCGA-G4-6299 
       29.06        15.02        12.26        13.51        16.14        74.56 

$`APAF1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.09        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3510 
       19.66        20.28         7.04         3.02         1.02        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       85.05        26.99        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
       25.02         1.02        17.98        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        0.33         1.35       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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-D5-5539 TCGA-D5-5541 TCGA-D5-6529 
       10.06        12.03        45.40        19.59        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 
        0.53        35.41        19.43       107.67        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  APAF1 MUTATED APAF1 WILD-TYPE 
            0.1             0.0 
  APAF1 MUTATED APAF1 WILD-TYPE 
          74.56          140.38 
  APAF1 MUTATED APAF1 WILD-TYPE 
          19.04           20.28 
[1] "0.1 - 74.6 (19.0)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.7"
D1751V2, 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       24       104         6         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  APAF1 MUTATED           0          1          1          1        1         1
  APAF1 WILD-TYPE        19          9         40         30       34        12
                 vv
clus              STAGE IVB
  APAF1 MUTATED           0
  APAF1 WILD-TYPE         1
D1751V3, multiclass
            clus
vv           APAF1 MUTATED APAF1 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              5             104
  STAGE IIB              2               6
  STAGE IIC              1               0
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             1              40
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  63 239  37
D1751V4, multiclass
    clus
vv   APAF1 MUTATED APAF1 WILD-TYPE
  T1             0               9
  T2             5              63
  T3             9             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
  APAF1 MUTATED    14   3   1
  APAF1 WILD-TYPE 206  77  65
D1751V5, multiclass
    clus
vv   APAF1 MUTATED APAF1 WILD-TYPE
  N0            14             206
  N1             3              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"
D1751V6, binary
                 cls
clus                0   1
  APAF1 MUTATED    16   1
  APAF1 WILD-TYPE 267  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  APAF1 MUTATED     16    1
  APAF1 WILD-TYPE  267   47
   clus
vv  APAF1 MUTATED APAF1 WILD-TYPE
  0            16             267
  1             1              47
[1] 2 2
[1] FALSE
D1751V7, 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
D1751V8, binary
                 cls
clus                0   1
  APAF1 MUTATED    15   3
  APAF1 WILD-TYPE 302  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  APAF1 MUTATED     15    3
  APAF1 WILD-TYPE  302   45
                               clus
vv                              APAF1 MUTATED APAF1 WILD-TYPE
  COLON ADENOCARCINOMA                     15             302
  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 244   2  21  19
D1751V9, multiclass
    clus
vv   APAF1 MUTATED APAF1 WILD-TYPE
  R0            13             244
  R1             0               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"
D1751V10, 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
D1751V11, 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(1752) Variable = TRIM34 MUTATION ANALYSIS
D1752V1, survival
                  sevent
clus2                0   1
  TRIM34 MUTATED     6   0
  TRIM34 WILD-TYPE 276  73
  TRIM34 MUTATED TRIM34 WILD-TYPE 
               6              349 
  TRIM34 MUTATED TRIM34 WILD-TYPE 
               0               73 
$`TRIM34 MUTATED`
TCGA-AY-6196 TCGA-CM-6674 TCGA-D5-6533 TCGA-DM-A0X9 TCGA-DM-A1HB TCGA-G4-6293 
        0.20        12.95         1.32       119.70       135.65       107.67 

$`TRIM34 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        15.75        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       11.51        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         1.51        12.00        11.38        10.26 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        35.41        19.43        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  TRIM34 MUTATED TRIM34 WILD-TYPE 
             0.2              0.0 
  TRIM34 MUTATED TRIM34 WILD-TYPE 
          135.65           140.38 
  TRIM34 MUTATED TRIM34 WILD-TYPE 
           60.31            20.19 
[1] "0.2 - 135.7 (60.3)" "0.0 - 140.4 (20.2)"
[1] "hr="     "2.9e+07"
D1752V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TRIM34 MUTATED         0        0        0         2         0         0
  TRIM34 WILD-TYPE      64        1       25       107         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRIM34 MUTATED           1          0          2          1        0
  TRIM34 WILD-TYPE        18         10         39         30       35
                  vv
clus               STAGE IVA STAGE IVB
  TRIM34 MUTATED           0         0
  TRIM34 WILD-TYPE        13         1
D1752V3, multiclass
            clus
vv           TRIM34 MUTATED TRIM34 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               2              107
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TRIM34 MUTATED     0   0   5   1
  TRIM34 WILD-TYPE   9  68 243  40
D1752V4, multiclass
    clus
vv   TRIM34 MUTATED TRIM34 WILD-TYPE
  T1              0                9
  T2              0               68
  T3              5              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
  TRIM34 MUTATED     3   2   1
  TRIM34 WILD-TYPE 217  78  65
D1752V5, multiclass
    clus
vv   TRIM34 MUTATED TRIM34 WILD-TYPE
  N0              3              217
  N1              2               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"
D1752V6, binary
                  cls
clus                 0   1
  TRIM34 MUTATED     5   0
  TRIM34 WILD-TYPE 278  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM34 MUTATED      5    0
  TRIM34 WILD-TYPE  278   48
   clus
vv  TRIM34 MUTATED TRIM34 WILD-TYPE
  0              5              278
  1              0               48
[1] 2 2
[1] FALSE
D1752V7, binary
                  cls
clus                 0   1
  TRIM34 MUTATED     3   3
  TRIM34 WILD-TYPE 167 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM34 MUTATED      3    3
  TRIM34 WILD-TYPE  167  194
        clus
vv       TRIM34 MUTATED TRIM34 WILD-TYPE
  FEMALE              3              167
  MALE                3              194
[1] 2 2
[1] FALSE
D1752V8, binary
                  cls
clus                 0   1
  TRIM34 MUTATED     5   1
  TRIM34 WILD-TYPE 312  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM34 MUTATED      5    1
  TRIM34 WILD-TYPE  312   47
                               clus
vv                              TRIM34 MUTATED TRIM34 WILD-TYPE
  COLON ADENOCARCINOMA                       5              312
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TRIM34 MUTATED     4   0   0   0
  TRIM34 WILD-TYPE 253   2  22  21
D1752V9, multiclass
    clus
vv   TRIM34 MUTATED TRIM34 WILD-TYPE
  R0              4              253
  R1              0                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"
D1752V10, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRIM34 MUTATED                                  0     0
  TRIM34 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TRIM34 MUTATED                           0     6
  TRIM34 WILD-TYPE                        19   170
D1752V11, multiclass
                                  clus
vv                                 TRIM34 MUTATED TRIM34 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(1753) Variable = PCDHGA4 MUTATION ANALYSIS
D1753V1, survival
                   sevent
clus2                 0   1
  PCDHGA4 MUTATED    13   4
  PCDHGA4 WILD-TYPE 269  69
  PCDHGA4 MUTATED PCDHGA4 WILD-TYPE 
               17               338 
  PCDHGA4 MUTATED PCDHGA4 WILD-TYPE 
                4                69 
$`PCDHGA4 MUTATED`
TCGA-A6-5659 TCGA-A6-6141 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3710 TCGA-AA-3713 
       30.44         8.38        19.66         3.02        26.99        19.04 
TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-A00N TCGA-AD-6899 TCGA-AZ-4315 TCGA-AZ-6601 
       53.00        33.01         4.01         5.79        58.39       100.01 
TCGA-CA-6717 TCGA-CM-6171 TCGA-CM-6676 TCGA-G4-6309 TCGA-G4-6588 
        0.33        14.04        11.08        51.75        26.17 

$`PCDHGA4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         0.72        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        61.41        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       74.56        65.85        53.62        44.68        55.04        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       36.72        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  PCDHGA4 MUTATED PCDHGA4 WILD-TYPE 
             0.33              0.00 
  PCDHGA4 MUTATED PCDHGA4 WILD-TYPE 
           100.01            140.38 
  PCDHGA4 MUTATED PCDHGA4 WILD-TYPE 
           19.660            20.235 
[1] "0.3 - 100.0 (19.7)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1"  
D1753V2, 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       21       104         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PCDHGA4 MUTATED           0          0          1          2        1
  PCDHGA4 WILD-TYPE        19         10         40         29       34
                   vv
clus                STAGE IVA STAGE IVB
  PCDHGA4 MUTATED           0         0
  PCDHGA4 WILD-TYPE        13         1
D1753V3, multiclass
            clus
vv           PCDHGA4 MUTATED PCDHGA4 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 4                21
  STAGE IIA                5               104
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               2                29
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PCDHGA4 MUTATED     0   3  10   5
  PCDHGA4 WILD-TYPE   9  65 238  36
D1753V4, multiclass
    clus
vv   PCDHGA4 MUTATED PCDHGA4 WILD-TYPE
  T1               0                 9
  T2               3                65
  T3              10               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
  PCDHGA4 MUTATED    15   2   1
  PCDHGA4 WILD-TYPE 205  78  65
D1753V5, multiclass
    clus
vv   PCDHGA4 MUTATED PCDHGA4 WILD-TYPE
  N0              15               205
  N1               2                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"
D1753V6, binary
                   cls
clus                  0   1
  PCDHGA4 MUTATED    15   1
  PCDHGA4 WILD-TYPE 268  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHGA4 MUTATED     15    1
  PCDHGA4 WILD-TYPE  268   47
   clus
vv  PCDHGA4 MUTATED PCDHGA4 WILD-TYPE
  0              15               268
  1               1                47
[1] 2 2
[1] FALSE
D1753V7, 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
D1753V8, binary
                   cls
clus                  0   1
  PCDHGA4 MUTATED    13   5
  PCDHGA4 WILD-TYPE 304  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHGA4 MUTATED     13    5
  PCDHGA4 WILD-TYPE  304   43
                               clus
vv                              PCDHGA4 MUTATED PCDHGA4 WILD-TYPE
  COLON ADENOCARCINOMA                       13               304
  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 244   2  21  20
D1753V9, multiclass
    clus
vv   PCDHGA4 MUTATED PCDHGA4 WILD-TYPE
  R0              13               244
  R1               0                 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"
D1753V10, 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
D1753V11, 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(1754) Variable = DBF4 MUTATION ANALYSIS
D1754V1, survival
                sevent
clus2              0   1
  DBF4 MUTATED     6   0
  DBF4 WILD-TYPE 276  73
  DBF4 MUTATED DBF4 WILD-TYPE 
             6            349 
  DBF4 MUTATED DBF4 WILD-TYPE 
             0             73 
$`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         0.33         0.10        10.26 

$`DBF4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.26         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  DBF4 MUTATED DBF4 WILD-TYPE 
           0.1            0.0 
  DBF4 MUTATED DBF4 WILD-TYPE 
         32.75         140.38 
  DBF4 MUTATED DBF4 WILD-TYPE 
         8.615         20.980 
[1] "0.1 - 32.8 (8.6)"   "0.0 - 140.4 (21.0)"
[1] "hr="     "3300000"
D1754V2, 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       24       106         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        19         10         40         31       35        13
                vv
clus             STAGE IVB
  DBF4 MUTATED           0
  DBF4 WILD-TYPE         1
D1754V3, multiclass
            clus
vv           DBF4 MUTATED DBF4 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             3            106
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  DBF4 MUTATED     0   1   4   2
  DBF4 WILD-TYPE   9  67 244  39
D1754V4, multiclass
    clus
vv   DBF4 MUTATED DBF4 WILD-TYPE
  T1            0              9
  T2            1             67
  T3            4            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
  DBF4 MUTATED     6   1   0
  DBF4 WILD-TYPE 214  79  66
D1754V5, multiclass
    clus
vv   DBF4 MUTATED DBF4 WILD-TYPE
  N0            6            214
  N1            1             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"
D1754V6, binary
                cls
clus               0   1
  DBF4 MUTATED     7   0
  DBF4 WILD-TYPE 276  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  DBF4 MUTATED      7    0
  DBF4 WILD-TYPE  276   48
   clus
vv  DBF4 MUTATED DBF4 WILD-TYPE
  0            7            276
  1            0             48
[1] 2 2
[1] FALSE
D1754V7, 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
D1754V8, binary
                cls
clus               0   1
  DBF4 MUTATED     3   4
  DBF4 WILD-TYPE 314  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  DBF4 MUTATED      3    4
  DBF4 WILD-TYPE  314   44
                               clus
vv                              DBF4 MUTATED DBF4 WILD-TYPE
  COLON ADENOCARCINOMA                     3            314
  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 252   2  22  19
D1754V9, multiclass
    clus
vv   DBF4 MUTATED DBF4 WILD-TYPE
  R0            5            252
  R1            0              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"
D1754V10, 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
D1754V11, 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(1755) Variable = VIM MUTATION ANALYSIS
D1755V1, survival
               sevent
clus2             0   1
  VIM MUTATED     5   2
  VIM WILD-TYPE 277  71
  VIM MUTATED VIM WILD-TYPE 
            7           348 
  VIM MUTATED VIM WILD-TYPE 
            2            71 
$`VIM MUTATED`
TCGA-AA-3510 TCGA-AA-3713 TCGA-AA-A00K TCGA-AA-A00R TCGA-AA-A02K TCGA-CK-4950 
       63.98        19.04        18.05         0.99        14.01        40.34 
TCGA-D5-5537 
       45.40 

$`VIM WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       27.02        42.02        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 
        0.10         1.35        17.56       102.44        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  VIM MUTATED VIM WILD-TYPE 
         0.99          0.00 
  VIM MUTATED VIM WILD-TYPE 
        63.98        140.38 
  VIM MUTATED VIM WILD-TYPE 
       19.040        20.235 
[1] "1.0 - 64.0 (19.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D1755V2, 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       24       107         8         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  VIM MUTATED           0          1          0          0        2         0
  VIM WILD-TYPE        19          9         41         31       33        13
               vv
clus            STAGE IVB
  VIM MUTATED           0
  VIM WILD-TYPE         1
D1755V3, multiclass
            clus
vv           VIM MUTATED VIM WILD-TYPE
  STAGE I              1            63
  STAGE IA             0             1
  STAGE II             1            24
  STAGE IIA            2           107
  STAGE IIB            0             8
  STAGE IIC            0             1
  STAGE III            0            19
  STAGE IIIA           1             9
  STAGE IIIB           0            41
  STAGE IIIC           0            31
  STAGE IV             2            33
  STAGE IVA            0            13
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  VIM MUTATED     0   1   5   1
  VIM WILD-TYPE   9  67 243  40
D1755V4, multiclass
    clus
vv   VIM MUTATED VIM WILD-TYPE
  T1           0             9
  T2           1            67
  T3           5           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
  VIM MUTATED     4   1   2
  VIM WILD-TYPE 216  79  64
D1755V5, multiclass
    clus
vv   VIM MUTATED VIM WILD-TYPE
  N0           4           216
  N1           1            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"
D1755V6, binary
               cls
clus              0   1
  VIM MUTATED     4   2
  VIM WILD-TYPE 279  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  VIM MUTATED      4    2
  VIM WILD-TYPE  279   46
   clus
vv  VIM MUTATED VIM WILD-TYPE
  0           4           279
  1           2            46
[1] 2 2
[1] FALSE
D1755V7, 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
D1755V8, binary
               cls
clus              0   1
  VIM MUTATED     7   0
  VIM WILD-TYPE 310  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  VIM MUTATED      7    0
  VIM WILD-TYPE  310   48
                               clus
vv                              VIM MUTATED VIM WILD-TYPE
  COLON ADENOCARCINOMA                    7           310
  COLON MUCINOUS ADENOCARCINOMA           0            48
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  VIM MUTATED     3   1   2   1
  VIM WILD-TYPE 254   1  20  20
D1755V9, multiclass
    clus
vv   VIM MUTATED VIM WILD-TYPE
  R0           3           254
  R1           1             1
  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"
D1755V10, 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
D1755V11, multiclass
[1] "Remove cluster labels:" "VIM MUTATED"           
clus
  VIM MUTATED VIM WILD-TYPE 
            2           204 
   TCGA-A6-2671    TCGA-A6-2672    TCGA-A6-2674    TCGA-A6-2676    TCGA-A6-2677 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-A6-2678    TCGA-A6-2683    TCGA-A6-3807    TCGA-A6-3808    TCGA-A6-3809 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-A6-3810    TCGA-A6-4105    TCGA-A6-5656    TCGA-A6-5657    TCGA-A6-5659 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-A6-5660    TCGA-A6-5661    TCGA-A6-5662    TCGA-A6-5664    TCGA-A6-5665 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-A6-5666    TCGA-A6-6137    TCGA-A6-6138    TCGA-A6-6141    TCGA-A6-6142 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-A6-6648    TCGA-A6-6649    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-6548    TCGA-AD-6888    TCGA-AD-6889    TCGA-AD-6890    TCGA-AD-6895 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-AD-6899    TCGA-AD-6901    TCGA-AD-6963    TCGA-AD-6964    TCGA-AD-6965 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-AU-3779    TCGA-AU-6004    TCGA-AY-4070    TCGA-AY-4071    TCGA-AY-5543 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-AY-6196    TCGA-AY-6197    TCGA-AY-6386    TCGA-AZ-4315    TCGA-AZ-4323 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-AZ-4616    TCGA-AZ-4681    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-6601    TCGA-AZ-6603 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-AZ-6605    TCGA-AZ-6606    TCGA-AZ-6607    TCGA-AZ-6608    TCGA-CA-5254 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-CA-5255    TCGA-CA-5796    TCGA-CA-5797    TCGA-CA-6715    TCGA-CA-6716 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-CA-6717    TCGA-CA-6718    TCGA-CA-6719    TCGA-CK-4947    TCGA-CK-4948 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-CK-4952    TCGA-CK-5912    TCGA-CK-5913    TCGA-CK-5914    TCGA-CK-5915 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-CK-5916    TCGA-CK-6746    TCGA-CK-6747    TCGA-CK-6748    TCGA-CK-6751 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-CM-4743    TCGA-CM-4744    TCGA-CM-4746    TCGA-CM-4747    TCGA-CM-4752 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-CM-5341    TCGA-CM-5344    TCGA-CM-5348    TCGA-CM-5349    TCGA-CM-5860 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-CM-5861    TCGA-CM-5862    TCGA-CM-5863    TCGA-CM-5864    TCGA-CM-5868 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-CM-6161    TCGA-CM-6162    TCGA-CM-6163    TCGA-CM-6164    TCGA-CM-6165 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-CM-6166    TCGA-CM-6167    TCGA-CM-6168    TCGA-CM-6169    TCGA-CM-6170 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-CM-6171    TCGA-CM-6172    TCGA-CM-6674    TCGA-CM-6675    TCGA-CM-6676 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-CM-6677    TCGA-CM-6678    TCGA-CM-6679    TCGA-CM-6680    TCGA-D5-5538 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-D5-5539    TCGA-D5-5540    TCGA-D5-5541    TCGA-D5-6529    TCGA-D5-6532 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-D5-6533    TCGA-D5-6534    TCGA-D5-6535    TCGA-D5-6536    TCGA-D5-6537 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-D5-6538    TCGA-D5-6539    TCGA-D5-6540    TCGA-D5-6541    TCGA-D5-6898 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-D5-6920    TCGA-D5-6922    TCGA-D5-6923    TCGA-D5-6924    TCGA-D5-6926 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-D5-6927    TCGA-D5-6928    TCGA-D5-6929    TCGA-D5-6930    TCGA-D5-6931 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-D5-6932    TCGA-D5-7000    TCGA-DM-A0X9    TCGA-DM-A0XD    TCGA-DM-A0XF 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-DM-A1D0    TCGA-DM-A1D4    TCGA-DM-A1D6    TCGA-DM-A1D7    TCGA-DM-A1D8 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-DM-A1D9    TCGA-DM-A1DA    TCGA-DM-A1DB    TCGA-DM-A1HA    TCGA-DM-A1HB 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-DM-A282    TCGA-DM-A285    TCGA-DM-A28C    TCGA-DM-A28E    TCGA-DM-A28F 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-DM-A28G    TCGA-DM-A28H    TCGA-DM-A28K    TCGA-F4-6459    TCGA-F4-6460 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-F4-6569    TCGA-F4-6570    TCGA-F4-6703    TCGA-F4-6704    TCGA-F4-6805 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-F4-6806    TCGA-F4-6807    TCGA-F4-6808    TCGA-F4-6809    TCGA-F4-6854 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-F4-6855    TCGA-F4-6856    TCGA-G4-6293    TCGA-G4-6299    TCGA-G4-6303 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-G4-6304    TCGA-G4-6306    TCGA-G4-6307    TCGA-G4-6309    TCGA-G4-6310 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 
   TCGA-G4-6315    TCGA-G4-6317    TCGA-G4-6321    TCGA-G4-6323    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-G4-6626    TCGA-G4-6628 
"VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" "VIM WILD-TYPE" 

Clustering(1756) Variable = SLIT1 MUTATION ANALYSIS
D1756V1, survival
                 sevent
clus2               0   1
  SLIT1 MUTATED    18   5
  SLIT1 WILD-TYPE 264  68
  SLIT1 MUTATED SLIT1 WILD-TYPE 
             23             332 
  SLIT1 MUTATED SLIT1 WILD-TYPE 
              5              68 
$`SLIT1 MUTATED`
TCGA-A6-5666 TCGA-AA-3492 TCGA-AA-3542 TCGA-AA-3660 TCGA-AA-3672 TCGA-AA-3710 
       32.71         3.02        12.99        78.08         0.92        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3819 TCGA-AA-3877 TCGA-AA-A00N TCGA-AA-A03F 
       19.04        19.04        25.02        31.00         4.01        18.05 
TCGA-AY-6196 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CK-5916 TCGA-CM-5860 TCGA-CM-5868 
        0.20        58.39         0.33        21.14        16.01        17.03 
TCGA-CM-6168 TCGA-CM-6171 TCGA-D5-6930 TCGA-DM-A1HB TCGA-F4-6460 
       12.99        14.04         1.51       135.65        13.38 

$`SLIT1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3811 
       37.05        19.00        36.00         5.03        85.05        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05        33.04         0.99         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       27.02        29.98        18.05         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 
       14.01         0.92        41.00        39.98        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        15.75        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
       40.34        15.62        49.08        51.32        21.99         2.93 
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-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-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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
      117.07        98.24         8.61        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  SLIT1 MUTATED SLIT1 WILD-TYPE 
            0.2             0.0 
  SLIT1 MUTATED SLIT1 WILD-TYPE 
         135.65          140.38 
  SLIT1 MUTATED SLIT1 WILD-TYPE 
         17.030          20.995 
[1] "0.2 - 135.7 (17.0)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.2"
D1756V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLIT1 MUTATED         3        0        3         7         2         1
  SLIT1 WILD-TYPE      61        1       22       102         6         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SLIT1 MUTATED           2          0          2          2        1         1
  SLIT1 WILD-TYPE        17         10         39         29       34        12
                 vv
clus              STAGE IVB
  SLIT1 MUTATED           0
  SLIT1 WILD-TYPE         1
D1756V3, multiclass
            clus
vv           SLIT1 MUTATED SLIT1 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              7             102
  STAGE IIB              2               6
  STAGE IIC              1               0
  STAGE III              2              17
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             2              29
  STAGE IV               1              34
  STAGE IVA              1              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SLIT1 MUTATED     2   1  17   4
  SLIT1 WILD-TYPE   7  67 231  37
D1756V4, multiclass
    clus
vv   SLIT1 MUTATED SLIT1 WILD-TYPE
  T1             2               7
  T2             1              67
  T3            17             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
  SLIT1 MUTATED    17   4   3
  SLIT1 WILD-TYPE 203  76  63
D1756V5, multiclass
    clus
vv   SLIT1 MUTATED SLIT1 WILD-TYPE
  N0            17             203
  N1             4              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"
D1756V6, binary
                 cls
clus                0   1
  SLIT1 MUTATED    20   2
  SLIT1 WILD-TYPE 263  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SLIT1 MUTATED     20    2
  SLIT1 WILD-TYPE  263   46
   clus
vv  SLIT1 MUTATED SLIT1 WILD-TYPE
  0            20             263
  1             2              46
[1] 2 2
[1] FALSE
D1756V7, binary
                 cls
clus                0   1
  SLIT1 MUTATED    13  11
  SLIT1 WILD-TYPE 157 186
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SLIT1 MUTATED     13   11
  SLIT1 WILD-TYPE  157  186
        clus
vv       SLIT1 MUTATED SLIT1 WILD-TYPE
  FEMALE            13             157
  MALE              11             186
[1] 2 2
[1] FALSE
D1756V8, binary
                 cls
clus                0   1
  SLIT1 MUTATED    18   6
  SLIT1 WILD-TYPE 299  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SLIT1 MUTATED     18    6
  SLIT1 WILD-TYPE  299   42
                               clus
vv                              SLIT1 MUTATED SLIT1 WILD-TYPE
  COLON ADENOCARCINOMA                     18             299
  COLON MUCINOUS ADENOCARCINOMA             6              42
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SLIT1 MUTATED    18   0   1   3
  SLIT1 WILD-TYPE 239   2  21  18
D1756V9, multiclass
    clus
vv   SLIT1 MUTATED SLIT1 WILD-TYPE
  R0            18             239
  R1             0               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"
D1756V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLIT1 MUTATED                                  0     1
  SLIT1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SLIT1 MUTATED                           1    11
  SLIT1 WILD-TYPE                        18   165
D1756V11, multiclass
                                  clus
vv                                 SLIT1 MUTATED SLIT1 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(1757) Variable = PLEKHO2 MUTATION ANALYSIS
D1757V1, survival
                   sevent
clus2                 0   1
  PLEKHO2 MUTATED     4   3
  PLEKHO2 WILD-TYPE 278  70
  PLEKHO2 MUTATED PLEKHO2 WILD-TYPE 
                7               348 
  PLEKHO2 MUTATED PLEKHO2 WILD-TYPE 
                3                70 
$`PLEKHO2 MUTATED`
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3837 TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-A00N 
       26.99        19.04        38.99         0.00         0.00         4.01 
TCGA-G4-6628 
       52.80 

$`PLEKHO2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3811 
       19.00        36.00         5.03        85.05        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 
       15.95        37.02        14.93        17.03        10.06        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 

  PLEKHO2 MUTATED PLEKHO2 WILD-TYPE 
                0                 0 
  PLEKHO2 MUTATED PLEKHO2 WILD-TYPE 
            52.80            140.38 
  PLEKHO2 MUTATED PLEKHO2 WILD-TYPE 
           19.040            20.235 
[1] "0.0 - 52.8 (19.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2.7"
D1757V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PLEKHO2 MUTATED         2        0        0         3         1         0
  PLEKHO2 WILD-TYPE      62        1       25       106         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLEKHO2 MUTATED           0          0          0          0        1
  PLEKHO2 WILD-TYPE        19         10         41         31       34
                   vv
clus                STAGE IVA STAGE IVB
  PLEKHO2 MUTATED           0         0
  PLEKHO2 WILD-TYPE        13         1
D1757V3, multiclass
            clus
vv           PLEKHO2 MUTATED PLEKHO2 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                3               106
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               0                31
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PLEKHO2 MUTATED     0   2   4   1
  PLEKHO2 WILD-TYPE   9  66 244  40
D1757V4, multiclass
    clus
vv   PLEKHO2 MUTATED PLEKHO2 WILD-TYPE
  T1               0                 9
  T2               2                66
  T3               4               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
  PLEKHO2 MUTATED     7   0   0
  PLEKHO2 WILD-TYPE 213  80  66
D1757V5, multiclass
    clus
vv   PLEKHO2 MUTATED PLEKHO2 WILD-TYPE
  N0               7               213
  N1               0                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"
D1757V6, binary
                   cls
clus                  0   1
  PLEKHO2 MUTATED     6   1
  PLEKHO2 WILD-TYPE 277  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHO2 MUTATED      6    1
  PLEKHO2 WILD-TYPE  277   47
   clus
vv  PLEKHO2 MUTATED PLEKHO2 WILD-TYPE
  0               6               277
  1               1                47
[1] 2 2
[1] FALSE
D1757V7, binary
                   cls
clus                  0   1
  PLEKHO2 MUTATED     2   5
  PLEKHO2 WILD-TYPE 168 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHO2 MUTATED      2    5
  PLEKHO2 WILD-TYPE  168  192
        clus
vv       PLEKHO2 MUTATED PLEKHO2 WILD-TYPE
  FEMALE               2               168
  MALE                 5               192
[1] 2 2
[1] FALSE
D1757V8, binary
                   cls
clus                  0   1
  PLEKHO2 MUTATED     5   2
  PLEKHO2 WILD-TYPE 312  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHO2 MUTATED      5    2
  PLEKHO2 WILD-TYPE  312   46
                               clus
vv                              PLEKHO2 MUTATED PLEKHO2 WILD-TYPE
  COLON ADENOCARCINOMA                        5               312
  COLON MUCINOUS ADENOCARCINOMA               2                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  PLEKHO2 MUTATED     6   0   1   0
  PLEKHO2 WILD-TYPE 251   2  21  21
D1757V9, multiclass
    clus
vv   PLEKHO2 MUTATED PLEKHO2 WILD-TYPE
  R0               6               251
  R1               0                 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"
D1757V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PLEKHO2 MUTATED                                  0     0
  PLEKHO2 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  PLEKHO2 MUTATED                           0     1
  PLEKHO2 WILD-TYPE                        19   175
D1757V11, multiclass
[1] "Remove cluster labels:" "PLEKHO2 MUTATED"       
clus
  PLEKHO2 MUTATED PLEKHO2 WILD-TYPE 
                1               205 
       TCGA-A6-2671        TCGA-A6-2672        TCGA-A6-2674        TCGA-A6-2676 
"PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" 
       TCGA-A6-2677        TCGA-A6-2678        TCGA-A6-2683        TCGA-A6-3807 
"PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" 
       TCGA-A6-3808        TCGA-A6-3809        TCGA-A6-3810        TCGA-A6-4105 
"PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" 
       TCGA-A6-5656        TCGA-A6-5657        TCGA-A6-5659        TCGA-A6-5660 
"PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" 
       TCGA-A6-5661        TCGA-A6-5662        TCGA-A6-5664        TCGA-A6-5665 
"PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" 
       TCGA-A6-5666        TCGA-A6-6137        TCGA-A6-6138        TCGA-A6-6141 
"PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" 
       TCGA-A6-6142        TCGA-A6-6648        TCGA-A6-6649        TCGA-A6-6651 
"PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" 
       TCGA-A6-6652        TCGA-A6-6653        TCGA-A6-6654        TCGA-A6-6780 
"PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" 
       TCGA-A6-6781        TCGA-A6-6782        TCGA-AD-5900        TCGA-AD-6548 
"PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" 
       TCGA-AD-6888        TCGA-AD-6889        TCGA-AD-6890        TCGA-AD-6895 
"PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" 
       TCGA-AD-6899        TCGA-AD-6901        TCGA-AD-6963        TCGA-AD-6964 
"PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" 
       TCGA-AD-6965        TCGA-AU-3779        TCGA-AU-6004        TCGA-AY-4070 
"PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" 
       TCGA-AY-4071        TCGA-AY-5543        TCGA-AY-6196        TCGA-AY-6197 
"PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" 
       TCGA-AY-6386        TCGA-AZ-4315        TCGA-AZ-4323        TCGA-AZ-4616 
"PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" 
       TCGA-AZ-4681        TCGA-AZ-4682        TCGA-AZ-5403        TCGA-AZ-5407 
"PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" 
       TCGA-AZ-6598        TCGA-AZ-6599        TCGA-AZ-6600        TCGA-AZ-6601 
"PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" 
       TCGA-AZ-6603        TCGA-AZ-6605        TCGA-AZ-6606        TCGA-AZ-6607 
"PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" 
       TCGA-AZ-6608        TCGA-CA-5254        TCGA-CA-5255        TCGA-CA-5796 
"PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" 
       TCGA-CA-5797        TCGA-CA-6715        TCGA-CA-6716        TCGA-CA-6717 
"PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" 
       TCGA-CA-6718        TCGA-CA-6719        TCGA-CK-4947        TCGA-CK-4948 
"PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" 
       TCGA-CK-4950        TCGA-CK-4952        TCGA-CK-5912        TCGA-CK-5913 
"PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" 
       TCGA-CK-5914        TCGA-CK-5915        TCGA-CK-5916        TCGA-CK-6746 
"PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" 
       TCGA-CK-6747        TCGA-CK-6748        TCGA-CK-6751        TCGA-CM-4743 
"PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" 
       TCGA-CM-4744        TCGA-CM-4746        TCGA-CM-4747        TCGA-CM-4752 
"PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" 
       TCGA-CM-5341        TCGA-CM-5344        TCGA-CM-5348        TCGA-CM-5349 
"PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" 
       TCGA-CM-5860        TCGA-CM-5861        TCGA-CM-5862        TCGA-CM-5863 
"PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" 
       TCGA-CM-5864        TCGA-CM-5868        TCGA-CM-6161        TCGA-CM-6162 
"PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" 
       TCGA-CM-6163        TCGA-CM-6164        TCGA-CM-6165        TCGA-CM-6166 
"PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" 
       TCGA-CM-6167        TCGA-CM-6168        TCGA-CM-6169        TCGA-CM-6170 
"PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" 
       TCGA-CM-6171        TCGA-CM-6172        TCGA-CM-6674        TCGA-CM-6675 
"PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" 
       TCGA-CM-6676        TCGA-CM-6677        TCGA-CM-6678        TCGA-CM-6679 
"PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" 
       TCGA-CM-6680        TCGA-D5-5537        TCGA-D5-5538        TCGA-D5-5539 
"PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" 
       TCGA-D5-5540        TCGA-D5-5541        TCGA-D5-6529        TCGA-D5-6532 
"PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" 
       TCGA-D5-6533        TCGA-D5-6534        TCGA-D5-6535        TCGA-D5-6536 
"PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" 
       TCGA-D5-6537        TCGA-D5-6538        TCGA-D5-6539        TCGA-D5-6540 
"PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" 
       TCGA-D5-6541        TCGA-D5-6898        TCGA-D5-6920        TCGA-D5-6922 
"PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" 
       TCGA-D5-6923        TCGA-D5-6924        TCGA-D5-6926        TCGA-D5-6927 
"PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" 
       TCGA-D5-6928        TCGA-D5-6929        TCGA-D5-6930        TCGA-D5-6931 
"PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" 
       TCGA-D5-6932        TCGA-D5-7000        TCGA-DM-A0X9        TCGA-DM-A0XD 
"PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" 
       TCGA-DM-A0XF        TCGA-DM-A1D0        TCGA-DM-A1D4        TCGA-DM-A1D6 
"PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" 
       TCGA-DM-A1D7        TCGA-DM-A1D8        TCGA-DM-A1D9        TCGA-DM-A1DA 
"PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" 
       TCGA-DM-A1DB        TCGA-DM-A1HA        TCGA-DM-A1HB        TCGA-DM-A282 
"PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" 
       TCGA-DM-A285        TCGA-DM-A28C        TCGA-DM-A28E        TCGA-DM-A28F 
"PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" 
       TCGA-DM-A28G        TCGA-DM-A28H        TCGA-DM-A28K        TCGA-F4-6459 
"PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" 
       TCGA-F4-6460        TCGA-F4-6569        TCGA-F4-6570        TCGA-F4-6703 
"PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" 
       TCGA-F4-6704        TCGA-F4-6805        TCGA-F4-6806        TCGA-F4-6807 
"PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" 
       TCGA-F4-6808        TCGA-F4-6809        TCGA-F4-6854        TCGA-F4-6855 
"PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" 
       TCGA-F4-6856        TCGA-G4-6293        TCGA-G4-6299        TCGA-G4-6303 
"PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" 
       TCGA-G4-6304        TCGA-G4-6306        TCGA-G4-6307        TCGA-G4-6309 
"PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" 
       TCGA-G4-6310        TCGA-G4-6315        TCGA-G4-6317        TCGA-G4-6321 
"PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" 
       TCGA-G4-6323        TCGA-G4-6586        TCGA-G4-6588        TCGA-G4-6625 
"PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" "PLEKHO2 WILD-TYPE" 
       TCGA-G4-6626 
"PLEKHO2 WILD-TYPE" 

Clustering(1758) Variable = C13ORF23 MUTATION ANALYSIS
D1758V1, survival
                    sevent
clus2                  0   1
  C13ORF23 MUTATED    10   2
  C13ORF23 WILD-TYPE 272  71
  C13ORF23 MUTATED C13ORF23 WILD-TYPE 
                12                343 
  C13ORF23 MUTATED C13ORF23 WILD-TYPE 
                 2                 71 
$`C13ORF23 MUTATED`
TCGA-AA-3543 TCGA-AA-A00J TCGA-AA-A010 TCGA-AD-6889 TCGA-AD-6963 TCGA-AZ-6598 
        0.99        18.05        34.98        56.55        27.42        49.41 
TCGA-CA-6717 TCGA-D5-6928 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-G4-6293 TCGA-G4-6628 
        0.33        11.64       140.38        44.32       107.67        52.80 

$`C13ORF23 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01        12.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37         4.21         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        0.72         5.79        22.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        35.41        19.43        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 
       46.75 

  C13ORF23 MUTATED C13ORF23 WILD-TYPE 
              0.33               0.00 
  C13ORF23 MUTATED C13ORF23 WILD-TYPE 
            140.38             139.17 
  C13ORF23 MUTATED C13ORF23 WILD-TYPE 
             39.65              20.02 
[1] "0.3 - 140.4 (39.6)" "0.0 - 139.2 (20.0)"
[1] "hr=" "2.1"
D1758V2, 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       24       104         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C13ORF23 MUTATED           1          0          1          0        0
  C13ORF23 WILD-TYPE        18         10         40         31       35
                    vv
clus                 STAGE IVA STAGE IVB
  C13ORF23 MUTATED           0         0
  C13ORF23 WILD-TYPE        13         1
D1758V3, multiclass
            clus
vv           C13ORF23 MUTATED C13ORF23 WILD-TYPE
  STAGE I                   2                 62
  STAGE IA                  0                  1
  STAGE II                  1                 24
  STAGE IIA                 5                104
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 1                 18
  STAGE IIIA                0                 10
  STAGE IIIB                1                 40
  STAGE IIIC                0                 31
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C13ORF23 MUTATED     0   2   8   2
  C13ORF23 WILD-TYPE   9  66 240  39
D1758V4, multiclass
    clus
vv   C13ORF23 MUTATED C13ORF23 WILD-TYPE
  T1                0                  9
  T2                2                 66
  T3                8                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
  C13ORF23 MUTATED    10   2   0
  C13ORF23 WILD-TYPE 210  78  66
D1758V5, multiclass
    clus
vv   C13ORF23 MUTATED C13ORF23 WILD-TYPE
  N0               10                210
  N1                2                 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"
D1758V6, binary
                    cls
clus                   0   1
  C13ORF23 MUTATED    10   0
  C13ORF23 WILD-TYPE 273  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C13ORF23 MUTATED     10    0
  C13ORF23 WILD-TYPE  273   48
   clus
vv  C13ORF23 MUTATED C13ORF23 WILD-TYPE
  0               10                273
  1                0                 48
[1] 2 2
[1] FALSE
D1758V7, 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
D1758V8, binary
                    cls
clus                   0   1
  C13ORF23 MUTATED     8   4
  C13ORF23 WILD-TYPE 309  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C13ORF23 MUTATED      8    4
  C13ORF23 WILD-TYPE  309   44
                               clus
vv                              C13ORF23 MUTATED C13ORF23 WILD-TYPE
  COLON ADENOCARCINOMA                         8                309
  COLON MUCINOUS ADENOCARCINOMA                4                 44
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C13ORF23 MUTATED     6   0   0   1
  C13ORF23 WILD-TYPE 251   2  22  20
D1758V9, multiclass
    clus
vv   C13ORF23 MUTATED C13ORF23 WILD-TYPE
  R0                6                251
  R1                0                  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"
D1758V10, 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
D1758V11, 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(1759) Variable = DNAJC6 MUTATION ANALYSIS
D1759V1, survival
                  sevent
clus2                0   1
  DNAJC6 MUTATED     8   1
  DNAJC6 WILD-TYPE 274  72
  DNAJC6 MUTATED DNAJC6 WILD-TYPE 
               9              346 
  DNAJC6 MUTATED DNAJC6 WILD-TYPE 
               1               72 
$`DNAJC6 MUTATED`
TCGA-AA-3514 TCGA-AA-A010 TCGA-AD-5900 TCGA-AZ-4315 TCGA-CM-5860 TCGA-CM-5862 
        1.02        34.98         0.07        58.39        16.01         5.03 
TCGA-CM-6171 TCGA-F4-6569 TCGA-G4-6304 
       14.04        13.45        53.62 

$`DNAJC6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01        63.98         6.97        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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-5863 TCGA-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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.38         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      107.67        74.56        65.85        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  DNAJC6 MUTATED DNAJC6 WILD-TYPE 
            0.07             0.00 
  DNAJC6 MUTATED DNAJC6 WILD-TYPE 
           58.39           140.38 
  DNAJC6 MUTATED DNAJC6 WILD-TYPE 
           14.04            20.63 
[1] "0.1 - 58.4 (14.0)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "1.7"
D1759V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DNAJC6 MUTATED         4        0        0         2         2         0
  DNAJC6 WILD-TYPE      60        1       25       107         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DNAJC6 MUTATED           0          0          0          0        0
  DNAJC6 WILD-TYPE        19         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  DNAJC6 MUTATED           1         0
  DNAJC6 WILD-TYPE        12         1
D1759V3, multiclass
            clus
vv           DNAJC6 MUTATED DNAJC6 WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               2              107
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  DNAJC6 MUTATED     0   4   3   2
  DNAJC6 WILD-TYPE   9  64 245  39
D1759V4, multiclass
    clus
vv   DNAJC6 MUTATED DNAJC6 WILD-TYPE
  T1              0                9
  T2              4               64
  T3              3              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
  DNAJC6 MUTATED     8   1   0
  DNAJC6 WILD-TYPE 212  79  66
D1759V5, multiclass
    clus
vv   DNAJC6 MUTATED DNAJC6 WILD-TYPE
  N0              8              212
  N1              1               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"
D1759V6, binary
                  cls
clus                 0   1
  DNAJC6 MUTATED     7   1
  DNAJC6 WILD-TYPE 276  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAJC6 MUTATED      7    1
  DNAJC6 WILD-TYPE  276   47
   clus
vv  DNAJC6 MUTATED DNAJC6 WILD-TYPE
  0              7              276
  1              1               47
[1] 2 2
[1] FALSE
D1759V7, binary
                  cls
clus                 0   1
  DNAJC6 MUTATED     4   5
  DNAJC6 WILD-TYPE 166 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAJC6 MUTATED      4    5
  DNAJC6 WILD-TYPE  166  192
        clus
vv       DNAJC6 MUTATED DNAJC6 WILD-TYPE
  FEMALE              4              166
  MALE                5              192
[1] 2 2
[1] FALSE
D1759V8, binary
                  cls
clus                 0   1
  DNAJC6 MUTATED     8   1
  DNAJC6 WILD-TYPE 309  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAJC6 MUTATED      8    1
  DNAJC6 WILD-TYPE  309   47
                               clus
vv                              DNAJC6 MUTATED DNAJC6 WILD-TYPE
  COLON ADENOCARCINOMA                       8              309
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  DNAJC6 MUTATED     9   0   0   0
  DNAJC6 WILD-TYPE 248   2  22  21
D1759V9, multiclass
    clus
vv   DNAJC6 MUTATED DNAJC6 WILD-TYPE
  R0              9              248
  R1              0                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"
D1759V10, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DNAJC6 MUTATED                                  0     0
  DNAJC6 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  DNAJC6 MUTATED                           0     7
  DNAJC6 WILD-TYPE                        19   169
D1759V11, multiclass
                                  clus
vv                                 DNAJC6 MUTATED DNAJC6 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(1760) Variable = SLC46A3 MUTATION ANALYSIS
D1760V1, survival
                   sevent
clus2                 0   1
  SLC46A3 MUTATED     7   1
  SLC46A3 WILD-TYPE 275  72
  SLC46A3 MUTATED SLC46A3 WILD-TYPE 
                8               347 
  SLC46A3 MUTATED SLC46A3 WILD-TYPE 
                1                72 
$`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         0.33 

$`SLC46A3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
       12.99         0.99        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       27.02        29.98        18.05         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41        49.41        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  SLC46A3 MUTATED SLC46A3 WILD-TYPE 
             0.33              0.00 
  SLC46A3 MUTATED SLC46A3 WILD-TYPE 
            63.98            140.38 
  SLC46A3 MUTATED SLC46A3 WILD-TYPE 
           23.375            20.190 
[1] "0.3 - 64.0 (23.4)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.6"
D1760V2, 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       24       108         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC46A3 MUTATED           0          0          0          1        0
  SLC46A3 WILD-TYPE        19         10         41         30       35
                   vv
clus                STAGE IVA STAGE IVB
  SLC46A3 MUTATED           0         0
  SLC46A3 WILD-TYPE        13         1
D1760V3, multiclass
            clus
vv           SLC46A3 MUTATED SLC46A3 WILD-TYPE
  STAGE I                  4                60
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                1               108
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               1                30
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC46A3 MUTATED     1   3   2   2
  SLC46A3 WILD-TYPE   8  65 246  39
D1760V4, multiclass
    clus
vv   SLC46A3 MUTATED SLC46A3 WILD-TYPE
  T1               1                 8
  T2               3                65
  T3               2               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
  SLC46A3 MUTATED     7   1   0
  SLC46A3 WILD-TYPE 213  79  66
D1760V5, multiclass
    clus
vv   SLC46A3 MUTATED SLC46A3 WILD-TYPE
  N0               7               213
  N1               1                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"
D1760V6, binary
                   cls
clus                  0   1
  SLC46A3 MUTATED     6   0
  SLC46A3 WILD-TYPE 277  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC46A3 MUTATED      6    0
  SLC46A3 WILD-TYPE  277   48
   clus
vv  SLC46A3 MUTATED SLC46A3 WILD-TYPE
  0               6               277
  1               0                48
[1] 2 2
[1] FALSE
D1760V7, 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
D1760V8, binary
                   cls
clus                  0   1
  SLC46A3 MUTATED     5   3
  SLC46A3 WILD-TYPE 312  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC46A3 MUTATED      5    3
  SLC46A3 WILD-TYPE  312   45
                               clus
vv                              SLC46A3 MUTATED SLC46A3 WILD-TYPE
  COLON ADENOCARCINOMA                        5               312
  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 251   2  22  20
D1760V9, multiclass
    clus
vv   SLC46A3 MUTATED SLC46A3 WILD-TYPE
  R0               6               251
  R1               0                 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"
D1760V10, 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
D1760V11, 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(1761) Variable = HBS1L MUTATION ANALYSIS
D1761V1, survival
                 sevent
clus2               0   1
  HBS1L MUTATED     7   4
  HBS1L WILD-TYPE 275  69
  HBS1L MUTATED HBS1L WILD-TYPE 
             11             344 
  HBS1L MUTATED HBS1L WILD-TYPE 
              4              69 
$`HBS1L MUTATED`
TCGA-A6-5665 TCGA-A6-6653 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3715 TCGA-AA-A00N 
       22.06        24.39        63.98         6.97        19.04         4.01 
TCGA-AD-6964 TCGA-AU-6004 TCGA-AZ-6607 TCGA-CA-6718 TCGA-G4-6304 
       10.88        27.09         3.19         0.10        53.62 

$`HBS1L WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.33         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  HBS1L MUTATED HBS1L WILD-TYPE 
            0.1             0.0 
  HBS1L MUTATED HBS1L WILD-TYPE 
          63.98          140.38 
  HBS1L MUTATED HBS1L WILD-TYPE 
         19.040          20.235 
[1] "0.1 - 64.0 (19.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2"  
D1761V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HBS1L MUTATED         2        0        3         2         3         0
  HBS1L WILD-TYPE      62        1       22       107         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HBS1L MUTATED           0          0          0          0        1         0
  HBS1L WILD-TYPE        19         10         41         31       34        13
                 vv
clus              STAGE IVB
  HBS1L MUTATED           0
  HBS1L WILD-TYPE         1
D1761V3, multiclass
            clus
vv           HBS1L MUTATED HBS1L WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              2             107
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HBS1L MUTATED     0   2   5   5
  HBS1L WILD-TYPE   9  66 243  36
D1761V4, multiclass
    clus
vv   HBS1L MUTATED HBS1L WILD-TYPE
  T1             0               9
  T2             2              66
  T3             5             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
  HBS1L MUTATED    10   0   2
  HBS1L WILD-TYPE 210  80  64
D1761V5, multiclass
    clus
vv   HBS1L MUTATED HBS1L WILD-TYPE
  N0            10             210
  N1             0              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"
D1761V6, binary
                 cls
clus                0   1
  HBS1L MUTATED     9   1
  HBS1L WILD-TYPE 274  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HBS1L MUTATED      9    1
  HBS1L WILD-TYPE  274   47
   clus
vv  HBS1L MUTATED HBS1L WILD-TYPE
  0             9             274
  1             1              47
[1] 2 2
[1] FALSE
D1761V7, binary
                 cls
clus                0   1
  HBS1L MUTATED     4   8
  HBS1L WILD-TYPE 166 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HBS1L MUTATED      4    8
  HBS1L WILD-TYPE  166  189
        clus
vv       HBS1L MUTATED HBS1L WILD-TYPE
  FEMALE             4             166
  MALE               8             189
[1] 2 2
[1] FALSE
D1761V8, binary
                 cls
clus                0   1
  HBS1L MUTATED    11   1
  HBS1L WILD-TYPE 306  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HBS1L MUTATED     11    1
  HBS1L WILD-TYPE  306   47
                               clus
vv                              HBS1L MUTATED HBS1L WILD-TYPE
  COLON ADENOCARCINOMA                     11             306
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  HBS1L MUTATED     7   0   0   2
  HBS1L WILD-TYPE 250   2  22  19
D1761V9, multiclass
    clus
vv   HBS1L MUTATED HBS1L WILD-TYPE
  R0             7             250
  R1             0               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"
D1761V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HBS1L MUTATED                                  0     1
  HBS1L WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HBS1L MUTATED                           0     7
  HBS1L WILD-TYPE                        19   169
D1761V11, multiclass
                                  clus
vv                                 HBS1L MUTATED HBS1L 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(1762) Variable = TSC2 MUTATION ANALYSIS
D1762V1, survival
                sevent
clus2              0   1
  TSC2 MUTATED    10   3
  TSC2 WILD-TYPE 272  70
  TSC2 MUTATED TSC2 WILD-TYPE 
            13            342 
  TSC2 MUTATED TSC2 WILD-TYPE 
             3             70 
$`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        56.55         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 
       35.41 

$`TSC2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        32.71        27.09         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37         4.21         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 
       14.50        27.09        16.31         0.95        15.75        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41        49.41         6.77       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99        21.14         2.93       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 
       20.19        18.25         1.32        43.27        15.12         4.80 
TCGA-D5-6538 TCGA-D5-6540 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-D5-6924 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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  TSC2 MUTATED TSC2 WILD-TYPE 
           0.2            0.0 
  TSC2 MUTATED TSC2 WILD-TYPE 
         56.55         140.38 
  TSC2 MUTATED TSC2 WILD-TYPE 
         12.49          20.63 
[1] "0.2 - 56.5 (12.5)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "1.6"
D1762V2, 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       24       104         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TSC2 MUTATED           1          1          0          1        3         0
  TSC2 WILD-TYPE        18          9         41         30       32        13
                vv
clus             STAGE IVB
  TSC2 MUTATED           0
  TSC2 WILD-TYPE         1
D1762V3, multiclass
            clus
vv           TSC2 MUTATED TSC2 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             5            104
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            1              9
  STAGE IIIB            0             41
  STAGE IIIC            1             30
  STAGE IV              3             32
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TSC2 MUTATED     0   2  11   2
  TSC2 WILD-TYPE   9  66 237  39
D1762V4, multiclass
    clus
vv   TSC2 MUTATED TSC2 WILD-TYPE
  T1            0              9
  T2            2             66
  T3           11            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
  TSC2 MUTATED    10   3   2
  TSC2 WILD-TYPE 210  77  64
D1762V5, multiclass
    clus
vv   TSC2 MUTATED TSC2 WILD-TYPE
  N0           10            210
  N1            3             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"
D1762V6, binary
                cls
clus               0   1
  TSC2 MUTATED     9   3
  TSC2 WILD-TYPE 274  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  TSC2 MUTATED      9    3
  TSC2 WILD-TYPE  274   45
   clus
vv  TSC2 MUTATED TSC2 WILD-TYPE
  0            9            274
  1            3             45
[1] 2 2
[1] FALSE
D1762V7, 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
D1762V8, binary
                cls
clus               0   1
  TSC2 MUTATED    13   2
  TSC2 WILD-TYPE 304  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  TSC2 MUTATED     13    2
  TSC2 WILD-TYPE  304   46
                               clus
vv                              TSC2 MUTATED TSC2 WILD-TYPE
  COLON ADENOCARCINOMA                    13            304
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TSC2 MUTATED     9   0   1   2
  TSC2 WILD-TYPE 248   2  21  19
D1762V9, multiclass
    clus
vv   TSC2 MUTATED TSC2 WILD-TYPE
  R0            9            248
  R1            0              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"
D1762V10, 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
D1762V11, 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(1763) Variable = ABCG2 MUTATION ANALYSIS
D1763V1, survival
                 sevent
clus2               0   1
  ABCG2 MUTATED    11   0
  ABCG2 WILD-TYPE 271  73
  ABCG2 MUTATED ABCG2 WILD-TYPE 
             11             344 
  ABCG2 MUTATED ABCG2 WILD-TYPE 
              0              73 
$`ABCG2 MUTATED`
TCGA-AA-3672 TCGA-AA-3977 TCGA-AA-A00A TCGA-AA-A010 TCGA-AD-6965 TCGA-CA-6717 
        0.92        25.02        38.04        34.98         0.20         0.33 
TCGA-D5-6540 TCGA-D5-6922 TCGA-G4-6306 TCGA-G4-6317 TCGA-G4-6628 
       16.14        10.13        44.68        36.00        52.80 

$`ABCG2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
        6.05         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D 
       27.02        19.07         7.96        27.02        13.94        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AU-3779 
        0.72         5.79        22.42        27.42        10.88        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58         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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 
      107.67        74.56        65.85        53.62        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       45.11        36.72        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 
       91.79        46.75 

  ABCG2 MUTATED ABCG2 WILD-TYPE 
            0.2             0.0 
  ABCG2 MUTATED ABCG2 WILD-TYPE 
          52.80          140.38 
  ABCG2 MUTATED ABCG2 WILD-TYPE 
         25.020          20.155 
[1] "0.2 - 52.8 (25.0)"  "0.0 - 140.4 (20.2)"
[1] "hr="     "2.5e+07"
D1763V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ABCG2 MUTATED         2        0        0         3         1         0
  ABCG2 WILD-TYPE      62        1       25       106         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ABCG2 MUTATED           1          1          0          1        0         0
  ABCG2 WILD-TYPE        18          9         41         30       35        13
                 vv
clus              STAGE IVB
  ABCG2 MUTATED           0
  ABCG2 WILD-TYPE         1
D1763V3, multiclass
            clus
vv           ABCG2 MUTATED ABCG2 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              3             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             1               9
  STAGE IIIB             0              41
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ABCG2 MUTATED     0   4   5   2
  ABCG2 WILD-TYPE   9  64 243  39
D1763V4, multiclass
    clus
vv   ABCG2 MUTATED ABCG2 WILD-TYPE
  T1             0               9
  T2             4              64
  T3             5             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     7   2   2
  ABCG2 WILD-TYPE 213  78  64
D1763V5, multiclass
    clus
vv   ABCG2 MUTATED ABCG2 WILD-TYPE
  N0             7             213
  N1             2              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"
D1763V6, binary
                 cls
clus                0   1
  ABCG2 MUTATED     8   0
  ABCG2 WILD-TYPE 275  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCG2 MUTATED      8    0
  ABCG2 WILD-TYPE  275   48
   clus
vv  ABCG2 MUTATED ABCG2 WILD-TYPE
  0             8             275
  1             0              48
[1] 2 2
[1] FALSE
D1763V7, binary
                 cls
clus                0   1
  ABCG2 MUTATED     3   8
  ABCG2 WILD-TYPE 167 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCG2 MUTATED      3    8
  ABCG2 WILD-TYPE  167  189
        clus
vv       ABCG2 MUTATED ABCG2 WILD-TYPE
  FEMALE             3             167
  MALE               8             189
[1] 2 2
[1] FALSE
D1763V8, binary
                 cls
clus                0   1
  ABCG2 MUTATED     9   2
  ABCG2 WILD-TYPE 308  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCG2 MUTATED      9    2
  ABCG2 WILD-TYPE  308   46
                               clus
vv                              ABCG2 MUTATED ABCG2 WILD-TYPE
  COLON ADENOCARCINOMA                      9             308
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ABCG2 MUTATED     8   0   0   1
  ABCG2 WILD-TYPE 249   2  22  20
D1763V9, multiclass
    clus
vv   ABCG2 MUTATED ABCG2 WILD-TYPE
  R0             8             249
  R1             0               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"
D1763V10, 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
D1763V11, 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(1764) Variable = EFHD1 MUTATION ANALYSIS
D1764V1, survival
                 sevent
clus2               0   1
  EFHD1 MUTATED     4   1
  EFHD1 WILD-TYPE 278  72
  EFHD1 MUTATED EFHD1 WILD-TYPE 
              5             350 
  EFHD1 MUTATED EFHD1 WILD-TYPE 
              1              72 
$`EFHD1 MUTATED`
TCGA-AA-3968 TCGA-AA-A00R TCGA-AY-6197 TCGA-AZ-6601 TCGA-G4-6628 
       21.99         0.99        21.44       100.01        52.80 

$`EFHD1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 
       24.00         2.01        20.98        34.03         2.01        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W 
       38.04         4.01        27.02        42.02        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 
       91.79        46.75 

  EFHD1 MUTATED EFHD1 WILD-TYPE 
           0.99            0.00 
  EFHD1 MUTATED EFHD1 WILD-TYPE 
         100.01          140.38 
  EFHD1 MUTATED EFHD1 WILD-TYPE 
          21.99           20.07 
[1] "1.0 - 100.0 (22.0)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.7"
D1764V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EFHD1 MUTATED         3        0        1         1         0         0
  EFHD1 WILD-TYPE      61        1       24       108         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EFHD1 MUTATED           0          0          0          0        0         0
  EFHD1 WILD-TYPE        19         10         41         31       35        13
                 vv
clus              STAGE IVB
  EFHD1 MUTATED           0
  EFHD1 WILD-TYPE         1
D1764V3, multiclass
            clus
vv           EFHD1 MUTATED EFHD1 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              1             108
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EFHD1 MUTATED     0   3   2   0
  EFHD1 WILD-TYPE   9  65 246  41
D1764V4, multiclass
    clus
vv   EFHD1 MUTATED EFHD1 WILD-TYPE
  T1             0               9
  T2             3              65
  T3             2             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
  EFHD1 MUTATED     5   0   0
  EFHD1 WILD-TYPE 215  80  66
D1764V5, multiclass
    clus
vv   EFHD1 MUTATED EFHD1 WILD-TYPE
  N0             5             215
  N1             0              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"
D1764V6, binary
                 cls
clus                0   1
  EFHD1 MUTATED     4   0
  EFHD1 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHD1 MUTATED      4    0
  EFHD1 WILD-TYPE  279   48
   clus
vv  EFHD1 MUTATED EFHD1 WILD-TYPE
  0             4             279
  1             0              48
[1] 2 2
[1] FALSE
D1764V7, binary
                 cls
clus                0   1
  EFHD1 MUTATED     2   3
  EFHD1 WILD-TYPE 168 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHD1 MUTATED      2    3
  EFHD1 WILD-TYPE  168  194
        clus
vv       EFHD1 MUTATED EFHD1 WILD-TYPE
  FEMALE             2             168
  MALE               3             194
[1] 2 2
[1] FALSE
D1764V8, binary
                 cls
clus                0   1
  EFHD1 MUTATED     5   0
  EFHD1 WILD-TYPE 312  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHD1 MUTATED      5    0
  EFHD1 WILD-TYPE  312   48
                               clus
vv                              EFHD1 MUTATED EFHD1 WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  EFHD1 MUTATED     4   0   0   0
  EFHD1 WILD-TYPE 253   2  22  21
D1764V9, multiclass
    clus
vv   EFHD1 MUTATED EFHD1 WILD-TYPE
  R0             4             253
  R1             0               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"
D1764V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EFHD1 MUTATED                                  0     0
  EFHD1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  EFHD1 MUTATED                           0     3
  EFHD1 WILD-TYPE                        19   173
D1764V11, multiclass
                                  clus
vv                                 EFHD1 MUTATED EFHD1 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(1765) Variable = IFI35 MUTATION ANALYSIS
D1765V1, survival
                 sevent
clus2               0   1
  IFI35 MUTATED     4   4
  IFI35 WILD-TYPE 278  69
  IFI35 MUTATED IFI35 WILD-TYPE 
              8             347 
  IFI35 MUTATED IFI35 WILD-TYPE 
              4              69 
$`IFI35 MUTATED`
TCGA-A6-2677 TCGA-AA-3715 TCGA-AA-A00N TCGA-CM-5861 TCGA-DM-A1D0 TCGA-DM-A1DB 
       24.33        19.04         4.01        15.02       130.65        44.32 
TCGA-G4-6317 TCGA-G4-6323 
       36.00        13.78 

$`IFI35 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        42.90        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43        38.20        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 
       44.68        55.04        51.75        45.11        36.72        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  IFI35 MUTATED IFI35 WILD-TYPE 
           4.01            0.00 
  IFI35 MUTATED IFI35 WILD-TYPE 
         130.65          140.38 
  IFI35 MUTATED IFI35 WILD-TYPE 
         21.685          20.190 
[1] "4.0 - 130.7 (21.7)" "0.0 - 140.4 (20.2)"
[1] "hr=" "2"  
D1765V2, 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       24       106         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        19         10         41         29       35        13
                 vv
clus              STAGE IVB
  IFI35 MUTATED           0
  IFI35 WILD-TYPE         1
D1765V3, multiclass
            clus
vv           IFI35 MUTATED IFI35 WILD-TYPE
  STAGE I                0              64
  STAGE IA               1               0
  STAGE II               1              24
  STAGE IIA              3             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             0              41
  STAGE IIIC             2              29
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  IFI35 MUTATED     0   0   6   1
  IFI35 WILD-TYPE   9  68 242  40
D1765V4, multiclass
    clus
vv   IFI35 MUTATED IFI35 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             6             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
  IFI35 MUTATED     6   0   2
  IFI35 WILD-TYPE 214  80  64
D1765V5, multiclass
    clus
vv   IFI35 MUTATED IFI35 WILD-TYPE
  N0             6             214
  N1             0              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"
D1765V6, binary
                 cls
clus                0   1
  IFI35 MUTATED     6   0
  IFI35 WILD-TYPE 277  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFI35 MUTATED      6    0
  IFI35 WILD-TYPE  277   48
   clus
vv  IFI35 MUTATED IFI35 WILD-TYPE
  0             6             277
  1             0              48
[1] 2 2
[1] FALSE
D1765V7, 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
D1765V8, binary
                 cls
clus                0   1
  IFI35 MUTATED     7   1
  IFI35 WILD-TYPE 310  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFI35 MUTATED      7    1
  IFI35 WILD-TYPE  310   47
                               clus
vv                              IFI35 MUTATED IFI35 WILD-TYPE
  COLON ADENOCARCINOMA                      7             310
  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 251   2  22  21
D1765V9, multiclass
    clus
vv   IFI35 MUTATED IFI35 WILD-TYPE
  R0             6             251
  R1             0               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"
D1765V10, 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
D1765V11, 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(1766) Variable = RABGAP1 MUTATION ANALYSIS
D1766V1, survival
                   sevent
clus2                 0   1
  RABGAP1 MUTATED    11   1
  RABGAP1 WILD-TYPE 271  72
  RABGAP1 MUTATED RABGAP1 WILD-TYPE 
               12               343 
  RABGAP1 MUTATED RABGAP1 WILD-TYPE 
                1                72 
$`RABGAP1 MUTATED`
TCGA-AA-3672 TCGA-AA-3844 TCGA-AA-A004 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-5900 
        0.92        14.93        13.94         4.01        34.98         0.07 
TCGA-AD-6889 TCGA-AD-6895 TCGA-CM-6162 TCGA-D5-6532 TCGA-F4-6807 TCGA-F4-6856 
       56.55         0.72        12.00        18.25        16.24        19.43 

$`RABGAP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
        6.05         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 
       17.98        15.95        38.99        37.02         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D 
       27.02        19.07         7.96        27.02        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       21.37         4.21         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 
       35.87         1.55        16.31        29.59        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        35.41       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  RABGAP1 MUTATED RABGAP1 WILD-TYPE 
             0.07              0.00 
  RABGAP1 MUTATED RABGAP1 WILD-TYPE 
            56.55            140.38 
  RABGAP1 MUTATED RABGAP1 WILD-TYPE 
           14.435            21.010 
[1] "0.1 - 56.5 (14.4)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.7"
D1766V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RABGAP1 MUTATED         2        0        0         3         2         0
  RABGAP1 WILD-TYPE      62        1       25       106         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RABGAP1 MUTATED           1          0          1          2        0
  RABGAP1 WILD-TYPE        18         10         40         29       35
                   vv
clus                STAGE IVA STAGE IVB
  RABGAP1 MUTATED           0         0
  RABGAP1 WILD-TYPE        13         1
D1766V3, multiclass
            clus
vv           RABGAP1 MUTATED RABGAP1 WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                3               106
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               0                10
  STAGE IIIB               1                40
  STAGE IIIC               2                29
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  RABGAP1 MUTATED     0   2   8   2
  RABGAP1 WILD-TYPE   9  66 240  39
D1766V4, multiclass
    clus
vv   RABGAP1 MUTATED RABGAP1 WILD-TYPE
  T1               0                 9
  T2               2                66
  T3               8               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
  RABGAP1 MUTATED     7   3   2
  RABGAP1 WILD-TYPE 213  77  64
D1766V5, multiclass
    clus
vv   RABGAP1 MUTATED RABGAP1 WILD-TYPE
  N0               7               213
  N1               3                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"
D1766V6, binary
                   cls
clus                  0   1
  RABGAP1 MUTATED    10   0
  RABGAP1 WILD-TYPE 273  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RABGAP1 MUTATED     10    0
  RABGAP1 WILD-TYPE  273   48
   clus
vv  RABGAP1 MUTATED RABGAP1 WILD-TYPE
  0              10               273
  1               0                48
[1] 2 2
[1] FALSE
D1766V7, binary
                   cls
clus                  0   1
  RABGAP1 MUTATED     5   7
  RABGAP1 WILD-TYPE 165 190
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RABGAP1 MUTATED      5    7
  RABGAP1 WILD-TYPE  165  190
        clus
vv       RABGAP1 MUTATED RABGAP1 WILD-TYPE
  FEMALE               5               165
  MALE                 7               190
[1] 2 2
[1] FALSE
D1766V8, binary
                   cls
clus                  0   1
  RABGAP1 MUTATED     8   4
  RABGAP1 WILD-TYPE 309  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RABGAP1 MUTATED      8    4
  RABGAP1 WILD-TYPE  309   44
                               clus
vv                              RABGAP1 MUTATED RABGAP1 WILD-TYPE
  COLON ADENOCARCINOMA                        8               309
  COLON MUCINOUS ADENOCARCINOMA               4                44
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  RABGAP1 MUTATED    10   0   0   0
  RABGAP1 WILD-TYPE 247   2  22  21
D1766V9, multiclass
    clus
vv   RABGAP1 MUTATED RABGAP1 WILD-TYPE
  R0              10               247
  R1               0                 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"
D1766V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RABGAP1 MUTATED                                  0     1
  RABGAP1 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  RABGAP1 MUTATED                           0     6
  RABGAP1 WILD-TYPE                        19   170
D1766V11, multiclass
                                  clus
vv                                 RABGAP1 MUTATED RABGAP1 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(1767) Variable = PHLDB2 MUTATION ANALYSIS
D1767V1, survival
                  sevent
clus2                0   1
  PHLDB2 MUTATED    15   2
  PHLDB2 WILD-TYPE 267  71
  PHLDB2 MUTATED PHLDB2 WILD-TYPE 
              17              338 
  PHLDB2 MUTATED PHLDB2 WILD-TYPE 
               2               71 
$`PHLDB2 MUTATED`
TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3525 TCGA-AA-3697 TCGA-AA-3819 
       22.06        63.98        13.02         8.05        85.05        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AU-6004 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CK-4952 
        4.01        34.98        27.09        58.39         0.33        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        51.75 

$`PHLDB2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       35.01         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       24.03        37.05        36.03        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 
        5.98        37.05        19.00        36.00         5.03        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        21.44        17.82         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 
        0.10         1.35        17.56       102.44        40.34        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       35.97        60.79        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       74.56        65.85        44.68        55.04        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  PHLDB2 MUTATED PHLDB2 WILD-TYPE 
            0.33             0.00 
  PHLDB2 MUTATED PHLDB2 WILD-TYPE 
          117.07           140.38 
  PHLDB2 MUTATED PHLDB2 WILD-TYPE 
           25.02            20.07 
[1] "0.3 - 117.1 (25.0)" "0.0 - 140.4 (20.1)"
[1] "hr=" "2.6"
D1767V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PHLDB2 MUTATED         1        0        1         6         3         0
  PHLDB2 WILD-TYPE      63        1       24       103         5         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PHLDB2 MUTATED           3          0          3          1        0
  PHLDB2 WILD-TYPE        16         10         38         30       35
                  vv
clus               STAGE IVA STAGE IVB
  PHLDB2 MUTATED           0         0
  PHLDB2 WILD-TYPE        13         1
D1767V3, multiclass
            clus
vv           PHLDB2 MUTATED PHLDB2 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               6              103
  STAGE IIB               3                5
  STAGE IIC               0                1
  STAGE III               3               16
  STAGE IIIA              0               10
  STAGE IIIB              3               38
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PHLDB2 MUTATED     0   1  13   4
  PHLDB2 WILD-TYPE   9  67 235  37
D1767V4, multiclass
    clus
vv   PHLDB2 MUTATED PHLDB2 WILD-TYPE
  T1              0                9
  T2              1               67
  T3             13              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
  PHLDB2 MUTATED    12   3   3
  PHLDB2 WILD-TYPE 208  77  63
D1767V5, multiclass
    clus
vv   PHLDB2 MUTATED PHLDB2 WILD-TYPE
  N0             12              208
  N1              3               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"
D1767V6, binary
                  cls
clus                 0   1
  PHLDB2 MUTATED    17   0
  PHLDB2 WILD-TYPE 266  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PHLDB2 MUTATED     17    0
  PHLDB2 WILD-TYPE  266   48
   clus
vv  PHLDB2 MUTATED PHLDB2 WILD-TYPE
  0             17              266
  1              0               48
[1] 2 2
[1] FALSE
D1767V7, 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
D1767V8, binary
                  cls
clus                 0   1
  PHLDB2 MUTATED    14   4
  PHLDB2 WILD-TYPE 303  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PHLDB2 MUTATED     14    4
  PHLDB2 WILD-TYPE  303   44
                               clus
vv                              PHLDB2 MUTATED PHLDB2 WILD-TYPE
  COLON ADENOCARCINOMA                      14              303
  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 244   2  22  18
D1767V9, multiclass
    clus
vv   PHLDB2 MUTATED PHLDB2 WILD-TYPE
  R0             13              244
  R1              0                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"
D1767V10, 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
D1767V11, 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(1768) Variable = RPS6KC1 MUTATION ANALYSIS
D1768V1, survival
                   sevent
clus2                 0   1
  RPS6KC1 MUTATED    11   2
  RPS6KC1 WILD-TYPE 271  71
  RPS6KC1 MUTATED RPS6KC1 WILD-TYPE 
               13               342 
  RPS6KC1 MUTATED RPS6KC1 WILD-TYPE 
                2                71 
$`RPS6KC1 MUTATED`
TCGA-A6-6780 TCGA-AA-3713 TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-3977 TCGA-AA-A010 
       20.12        19.04        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        56.55        21.44         0.33        15.02        45.40 
TCGA-D5-6532 
       18.25 

$`RPS6KC1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       39.06        51.98        39.98         2.01         5.03         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        4.21         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 
       19.59        13.51        11.51        20.19         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  RPS6KC1 MUTATED RPS6KC1 WILD-TYPE 
             0.33              0.00 
  RPS6KC1 MUTATED RPS6KC1 WILD-TYPE 
            56.55            140.38 
  RPS6KC1 MUTATED RPS6KC1 WILD-TYPE 
           21.440            20.105 
[1] "0.3 - 56.5 (21.4)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.5"
D1768V2, 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       24       102         5         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RPS6KC1 MUTATED           1          0          0          0        2
  RPS6KC1 WILD-TYPE        18         10         41         31       33
                   vv
clus                STAGE IVA STAGE IVB
  RPS6KC1 MUTATED           0         0
  RPS6KC1 WILD-TYPE        13         1
D1768V3, multiclass
            clus
vv           RPS6KC1 MUTATED RPS6KC1 WILD-TYPE
  STAGE I                  0                64
  STAGE IA                 0                 1
  STAGE II                 1                24
  STAGE IIA                7               102
  STAGE IIB                3                 5
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               0                31
  STAGE IV                 2                33
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  RPS6KC1 MUTATED     0   1  10   4
  RPS6KC1 WILD-TYPE   9  67 238  37
D1768V4, multiclass
    clus
vv   RPS6KC1 MUTATED RPS6KC1 WILD-TYPE
  T1               0                 9
  T2               1                67
  T3              10               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
  RPS6KC1 MUTATED    12   0   3
  RPS6KC1 WILD-TYPE 208  80  63
D1768V5, multiclass
    clus
vv   RPS6KC1 MUTATED RPS6KC1 WILD-TYPE
  N0              12               208
  N1               0                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"
D1768V6, binary
                   cls
clus                  0   1
  RPS6KC1 MUTATED     8   2
  RPS6KC1 WILD-TYPE 275  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPS6KC1 MUTATED      8    2
  RPS6KC1 WILD-TYPE  275   46
   clus
vv  RPS6KC1 MUTATED RPS6KC1 WILD-TYPE
  0               8               275
  1               2                46
[1] 2 2
[1] FALSE
D1768V7, 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
D1768V8, binary
                   cls
clus                  0   1
  RPS6KC1 MUTATED    12   3
  RPS6KC1 WILD-TYPE 305  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPS6KC1 MUTATED     12    3
  RPS6KC1 WILD-TYPE  305   45
                               clus
vv                              RPS6KC1 MUTATED RPS6KC1 WILD-TYPE
  COLON ADENOCARCINOMA                       12               305
  COLON MUCINOUS ADENOCARCINOMA               3                45
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  RPS6KC1 MUTATED     7   0   2   3
  RPS6KC1 WILD-TYPE 250   2  20  18
D1768V9, multiclass
    clus
vv   RPS6KC1 MUTATED RPS6KC1 WILD-TYPE
  R0               7               250
  R1               0                 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"
D1768V10, 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
D1768V11, 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(1769) Variable = AOX1 MUTATION ANALYSIS
D1769V1, survival
                sevent
clus2              0   1
  AOX1 MUTATED     9   2
  AOX1 WILD-TYPE 273  71
  AOX1 MUTATED AOX1 WILD-TYPE 
            11            344 
  AOX1 MUTATED AOX1 WILD-TYPE 
             2             71 
$`AOX1 MUTATED`
TCGA-A6-5665 TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-3966 TCGA-AA-3977 TCGA-AD-6889 
       22.06        53.00        33.01         2.01        25.02        56.55 
TCGA-AU-6004 TCGA-CA-6717 TCGA-CK-5916 TCGA-CM-6170 TCGA-DM-A28F 
       27.09         0.33        21.14        15.02        35.97 

$`AOX1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37         4.21         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
      139.17         6.12        81.37       119.93        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  AOX1 MUTATED AOX1 WILD-TYPE 
          0.33           0.00 
  AOX1 MUTATED AOX1 WILD-TYPE 
         56.55         140.38 
  AOX1 MUTATED AOX1 WILD-TYPE 
        25.020         20.005 
[1] "0.3 - 56.5 (25.0)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1.2"
D1769V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AOX1 MUTATED         3        0        1         4         1         0
  AOX1 WILD-TYPE      61        1       24       105         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        19         10         40         31       35        13
                vv
clus             STAGE IVB
  AOX1 MUTATED           0
  AOX1 WILD-TYPE         1
D1769V3, multiclass
            clus
vv           AOX1 MUTATED AOX1 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             4            105
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  AOX1 MUTATED     1   3   6   1
  AOX1 WILD-TYPE   8  65 242  40
D1769V4, multiclass
    clus
vv   AOX1 MUTATED AOX1 WILD-TYPE
  T1            1              8
  T2            3             65
  T3            6            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
  AOX1 MUTATED    10   1   0
  AOX1 WILD-TYPE 210  79  66
D1769V5, multiclass
    clus
vv   AOX1 MUTATED AOX1 WILD-TYPE
  N0           10            210
  N1            1             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"
D1769V6, binary
                cls
clus               0   1
  AOX1 MUTATED    10   0
  AOX1 WILD-TYPE 273  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  AOX1 MUTATED     10    0
  AOX1 WILD-TYPE  273   48
   clus
vv  AOX1 MUTATED AOX1 WILD-TYPE
  0           10            273
  1            0             48
[1] 2 2
[1] FALSE
D1769V7, binary
                cls
clus               0   1
  AOX1 MUTATED     6   5
  AOX1 WILD-TYPE 164 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  AOX1 MUTATED      6    5
  AOX1 WILD-TYPE  164  192
        clus
vv       AOX1 MUTATED AOX1 WILD-TYPE
  FEMALE            6            164
  MALE              5            192
[1] 2 2
[1] FALSE
D1769V8, binary
                cls
clus               0   1
  AOX1 MUTATED     8   3
  AOX1 WILD-TYPE 309  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  AOX1 MUTATED      8    3
  AOX1 WILD-TYPE  309   45
                               clus
vv                              AOX1 MUTATED AOX1 WILD-TYPE
  COLON ADENOCARCINOMA                     8            309
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  AOX1 MUTATED     5   0   0   2
  AOX1 WILD-TYPE 252   2  22  19
D1769V9, multiclass
    clus
vv   AOX1 MUTATED AOX1 WILD-TYPE
  R0            5            252
  R1            0              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"
D1769V10, 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
D1769V11, 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(1770) Variable = MTMR12 MUTATION ANALYSIS
D1770V1, survival
                  sevent
clus2                0   1
  MTMR12 MUTATED    10   1
  MTMR12 WILD-TYPE 272  72
  MTMR12 MUTATED MTMR12 WILD-TYPE 
              11              344 
  MTMR12 MUTATED MTMR12 WILD-TYPE 
               1               72 
$`MTMR12 MUTATED`
TCGA-A6-5657 TCGA-AA-3510 TCGA-AA-3844 TCGA-AA-3982 TCGA-AA-A010 TCGA-AZ-4315 
       31.63        63.98        14.93        27.02        34.98        58.39 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-6171 TCGA-D5-6928 TCGA-DM-A1DA 
        0.33         0.10        14.04        11.64         7.50 

$`MTMR12 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3986 
       34.06        26.01        25.02        24.00        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07         0.26         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       12.59       140.38        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  MTMR12 MUTATED MTMR12 WILD-TYPE 
             0.1              0.0 
  MTMR12 MUTATED MTMR12 WILD-TYPE 
           63.98           140.38 
  MTMR12 MUTATED MTMR12 WILD-TYPE 
          14.930           20.235 
[1] "0.1 - 64.0 (14.9)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2.2"
D1770V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MTMR12 MUTATED         1        0        1         5         1         0
  MTMR12 WILD-TYPE      63        1       24       104         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MTMR12 MUTATED           0          0          2          2        0
  MTMR12 WILD-TYPE        19         10         39         29       35
                  vv
clus               STAGE IVA STAGE IVB
  MTMR12 MUTATED           0         0
  MTMR12 WILD-TYPE        13         1
D1770V3, multiclass
            clus
vv           MTMR12 MUTATED MTMR12 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               5              104
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              2               29
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MTMR12 MUTATED     0   1  10   1
  MTMR12 WILD-TYPE   9  67 238  40
D1770V4, multiclass
    clus
vv   MTMR12 MUTATED MTMR12 WILD-TYPE
  T1              0                9
  T2              1               67
  T3             10              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
  MTMR12 MUTATED     8   2   2
  MTMR12 WILD-TYPE 212  78  64
D1770V5, multiclass
    clus
vv   MTMR12 MUTATED MTMR12 WILD-TYPE
  N0              8              212
  N1              2               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"
D1770V6, binary
                  cls
clus                 0   1
  MTMR12 MUTATED    12   0
  MTMR12 WILD-TYPE 271  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MTMR12 MUTATED     12    0
  MTMR12 WILD-TYPE  271   48
   clus
vv  MTMR12 MUTATED MTMR12 WILD-TYPE
  0             12              271
  1              0               48
[1] 2 2
[1] FALSE
D1770V7, binary
                  cls
clus                 0   1
  MTMR12 MUTATED     5   7
  MTMR12 WILD-TYPE 165 190
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MTMR12 MUTATED      5    7
  MTMR12 WILD-TYPE  165  190
        clus
vv       MTMR12 MUTATED MTMR12 WILD-TYPE
  FEMALE              5              165
  MALE                7              190
[1] 2 2
[1] FALSE
D1770V8, binary
                  cls
clus                 0   1
  MTMR12 MUTATED    10   2
  MTMR12 WILD-TYPE 307  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MTMR12 MUTATED     10    2
  MTMR12 WILD-TYPE  307   46
                               clus
vv                              MTMR12 MUTATED MTMR12 WILD-TYPE
  COLON ADENOCARCINOMA                      10              307
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  MTMR12 MUTATED     8   0   0   2
  MTMR12 WILD-TYPE 249   2  22  19
D1770V9, multiclass
    clus
vv   MTMR12 MUTATED MTMR12 WILD-TYPE
  R0              8              249
  R1              0                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"
D1770V10, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MTMR12 MUTATED                                  0     2
  MTMR12 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MTMR12 MUTATED                           1     4
  MTMR12 WILD-TYPE                        18   172
D1770V11, multiclass
                                  clus
vv                                 MTMR12 MUTATED MTMR12 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(1771) Variable = ADCY9 MUTATION ANALYSIS
D1771V1, survival
                 sevent
clus2               0   1
  ADCY9 MUTATED    16   0
  ADCY9 WILD-TYPE 266  73
  ADCY9 MUTATED ADCY9 WILD-TYPE 
             16             339 
  ADCY9 MUTATED ADCY9 WILD-TYPE 
              0              73 
$`ADCY9 MUTATED`
TCGA-A6-6653 TCGA-AA-3511 TCGA-AA-3713 TCGA-AA-3867 TCGA-AA-3972 TCGA-AA-3977 
       24.39         6.97        19.04        24.03        50.99        25.02 
TCGA-AA-A01R TCGA-AZ-4315 TCGA-AZ-5407 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4952 
       35.01        58.39        61.41         0.33         0.10        15.62 
TCGA-CM-6162 TCGA-D5-6533 TCGA-D5-6540 TCGA-F4-6703 
       12.00         1.32        16.14        35.87 

$`ADCY9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
       31.07        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
        2.01        21.99        16.08        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13        83.80        22.36        62.79        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 
        0.26         1.35        17.56       102.44        40.34        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 
       13.51        11.51        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-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  ADCY9 MUTATED ADCY9 WILD-TYPE 
            0.1             0.0 
  ADCY9 MUTATED ADCY9 WILD-TYPE 
          61.41          140.38 
  ADCY9 MUTATED ADCY9 WILD-TYPE 
         21.535          20.190 
[1] "0.1 - 61.4 (21.5)"  "0.0 - 140.4 (20.2)"
[1] "hr="     "2.6e+07"
D1771V2, 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       24       105         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ADCY9 MUTATED           3          0          2          0        3         0
  ADCY9 WILD-TYPE        16         10         39         31       32        13
                 vv
clus              STAGE IVB
  ADCY9 MUTATED           0
  ADCY9 WILD-TYPE         1
D1771V3, multiclass
            clus
vv           ADCY9 MUTATED ADCY9 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              4             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              3              16
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               3              32
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ADCY9 MUTATED     1   3  10   4
  ADCY9 WILD-TYPE   8  65 238  37
D1771V4, multiclass
    clus
vv   ADCY9 MUTATED ADCY9 WILD-TYPE
  T1             1               8
  T2             3              65
  T3            10             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
  ADCY9 MUTATED    12   2   4
  ADCY9 WILD-TYPE 208  78  62
D1771V5, multiclass
    clus
vv   ADCY9 MUTATED ADCY9 WILD-TYPE
  N0            12             208
  N1             2              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"
D1771V6, binary
                 cls
clus                0   1
  ADCY9 MUTATED    13   3
  ADCY9 WILD-TYPE 270  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADCY9 MUTATED     13    3
  ADCY9 WILD-TYPE  270   45
   clus
vv  ADCY9 MUTATED ADCY9 WILD-TYPE
  0            13             270
  1             3              45
[1] 2 2
[1] FALSE
D1771V7, 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
D1771V8, binary
                 cls
clus                0   1
  ADCY9 MUTATED    13   5
  ADCY9 WILD-TYPE 304  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADCY9 MUTATED     13    5
  ADCY9 WILD-TYPE  304   43
                               clus
vv                              ADCY9 MUTATED ADCY9 WILD-TYPE
  COLON ADENOCARCINOMA                     13             304
  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 249   2  19  17
D1771V9, multiclass
    clus
vv   ADCY9 MUTATED ADCY9 WILD-TYPE
  R0             8             249
  R1             0               2
  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"
D1771V10, 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
D1771V11, 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(1772) Variable = CLK4 MUTATION ANALYSIS
D1772V1, survival
                sevent
clus2              0   1
  CLK4 MUTATED     8   1
  CLK4 WILD-TYPE 274  72
  CLK4 MUTATED CLK4 WILD-TYPE 
             9            346 
  CLK4 MUTATED CLK4 WILD-TYPE 
             1             72 
$`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         0.10        16.14 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-F4-6460 
       12.59       140.38        13.38 

$`CLK4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        33.53        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.33         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1DA TCGA-DM-A1DB 
      130.65        92.75        49.91        13.32         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 
       35.97        60.79       117.07        98.24         8.61        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  CLK4 MUTATED CLK4 WILD-TYPE 
           0.1            0.0 
  CLK4 MUTATED CLK4 WILD-TYPE 
        140.38         139.17 
  CLK4 MUTATED CLK4 WILD-TYPE 
         13.38          20.63 
[1] "0.1 - 140.4 (13.4)" "0.0 - 139.2 (20.6)"
[1] "hr=" "1.7"
D1772V2, 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       25       105         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        19         10         40         30       35        12
                vv
clus             STAGE IVB
  CLK4 MUTATED           0
  CLK4 WILD-TYPE         1
D1772V3, multiclass
            clus
vv           CLK4 MUTATED CLK4 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             4            105
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            1             30
  STAGE IV              0             35
  STAGE IVA             1             12
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 240  41
D1772V4, multiclass
    clus
vv   CLK4 MUTATED CLK4 WILD-TYPE
  T1            0              9
  T2            1             67
  T3            8            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
  CLK4 MUTATED     5   2   2
  CLK4 WILD-TYPE 215  78  64
D1772V5, multiclass
    clus
vv   CLK4 MUTATED CLK4 WILD-TYPE
  N0            5            215
  N1            2             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"
D1772V6, binary
                cls
clus               0   1
  CLK4 MUTATED     6   1
  CLK4 WILD-TYPE 277  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  CLK4 MUTATED      6    1
  CLK4 WILD-TYPE  277   47
   clus
vv  CLK4 MUTATED CLK4 WILD-TYPE
  0            6            277
  1            1             47
[1] 2 2
[1] FALSE
D1772V7, 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
D1772V8, binary
                cls
clus               0   1
  CLK4 MUTATED     6   3
  CLK4 WILD-TYPE 311  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  CLK4 MUTATED      6    3
  CLK4 WILD-TYPE  311   45
                               clus
vv                              CLK4 MUTATED CLK4 WILD-TYPE
  COLON ADENOCARCINOMA                     6            311
  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 252   2  22  20
D1772V9, multiclass
    clus
vv   CLK4 MUTATED CLK4 WILD-TYPE
  R0            5            252
  R1            0              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"
D1772V10, 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
D1772V11, 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(1773) Variable = PTPN14 MUTATION ANALYSIS
D1773V1, survival
                  sevent
clus2                0   1
  PTPN14 MUTATED    16   1
  PTPN14 WILD-TYPE 266  72
  PTPN14 MUTATED PTPN14 WILD-TYPE 
              17              338 
  PTPN14 MUTATED PTPN14 WILD-TYPE 
               1               72 
$`PTPN14 MUTATED`
TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3710 
       22.06        22.52        24.39        20.12        19.66        26.99 
TCGA-AA-3864 TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-A01R TCGA-AY-6197 TCGA-AZ-4315 
       53.00        24.00         2.01        35.01        21.44        58.39 
TCGA-AZ-6598 TCGA-CA-6717 TCGA-CA-6718 TCGA-D5-6533 TCGA-D5-6928 
       49.41         0.33         0.10         1.32        11.64 

$`PTPN14 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.09        32.71        27.09         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 
       24.16        21.76        24.69        23.87        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        3.02         1.02        35.01        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 
       37.05        19.00        36.00         5.03        85.05        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07         0.26         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
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-D5-6929 
       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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  PTPN14 MUTATED PTPN14 WILD-TYPE 
             0.1              0.0 
  PTPN14 MUTATED PTPN14 WILD-TYPE 
           58.39           140.38 
  PTPN14 MUTATED PTPN14 WILD-TYPE 
          22.060           20.005 
[1] "0.1 - 58.4 (22.1)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "3.3"
D1773V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PTPN14 MUTATED         2        0        2        11         0         0
  PTPN14 WILD-TYPE      62        1       23        98         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PTPN14 MUTATED           1          0          1          1        0
  PTPN14 WILD-TYPE        18         10         40         30       35
                  vv
clus               STAGE IVA STAGE IVB
  PTPN14 MUTATED           0         0
  PTPN14 WILD-TYPE        13         1
D1773V3, multiclass
            clus
vv           PTPN14 MUTATED PTPN14 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA              11               98
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PTPN14 MUTATED     0   2  14   2
  PTPN14 WILD-TYPE   9  66 234  39
D1773V4, multiclass
    clus
vv   PTPN14 MUTATED PTPN14 WILD-TYPE
  T1              0                9
  T2              2               66
  T3             14              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
  PTPN14 MUTATED    16   1   1
  PTPN14 WILD-TYPE 204  79  65
D1773V5, multiclass
    clus
vv   PTPN14 MUTATED PTPN14 WILD-TYPE
  N0             16              204
  N1              1               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"
D1773V6, binary
                  cls
clus                 0   1
  PTPN14 MUTATED    14   0
  PTPN14 WILD-TYPE 269  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN14 MUTATED     14    0
  PTPN14 WILD-TYPE  269   48
   clus
vv  PTPN14 MUTATED PTPN14 WILD-TYPE
  0             14              269
  1              0               48
[1] 2 2
[1] FALSE
D1773V7, binary
                  cls
clus                 0   1
  PTPN14 MUTATED     7  11
  PTPN14 WILD-TYPE 163 186
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN14 MUTATED      7   11
  PTPN14 WILD-TYPE  163  186
        clus
vv       PTPN14 MUTATED PTPN14 WILD-TYPE
  FEMALE              7              163
  MALE               11              186
[1] 2 2
[1] FALSE
D1773V8, binary
                  cls
clus                 0   1
  PTPN14 MUTATED    11   7
  PTPN14 WILD-TYPE 306  41
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN14 MUTATED     11    7
  PTPN14 WILD-TYPE  306   41
                               clus
vv                              PTPN14 MUTATED PTPN14 WILD-TYPE
  COLON ADENOCARCINOMA                      11              306
  COLON MUCINOUS ADENOCARCINOMA              7               41
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PTPN14 MUTATED    11   0   0   2
  PTPN14 WILD-TYPE 246   2  22  19
D1773V9, multiclass
    clus
vv   PTPN14 MUTATED PTPN14 WILD-TYPE
  R0             11              246
  R1              0                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"
D1773V10, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTPN14 MUTATED                                  0     2
  PTPN14 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PTPN14 MUTATED                           0    10
  PTPN14 WILD-TYPE                        19   166
D1773V11, multiclass
                                  clus
vv                                 PTPN14 MUTATED PTPN14 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(1774) Variable = PRSS48 MUTATION ANALYSIS
D1774V1, survival
                  sevent
clus2                0   1
  PRSS48 MUTATED     5   1
  PRSS48 WILD-TYPE 277  72
  PRSS48 MUTATED PRSS48 WILD-TYPE 
               6              349 
  PRSS48 MUTATED PRSS48 WILD-TYPE 
               1               72 
$`PRSS48 MUTATED`
TCGA-AD-6889 TCGA-CM-5348 TCGA-D5-6536 TCGA-D5-6541 TCGA-F4-6570 TCGA-G4-6323 
       56.55        22.98        17.85        15.58         6.18        13.78 

$`PRSS48 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        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        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       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        13.38        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  PRSS48 MUTATED PRSS48 WILD-TYPE 
            6.18             0.00 
  PRSS48 MUTATED PRSS48 WILD-TYPE 
           56.55           140.38 
  PRSS48 MUTATED PRSS48 WILD-TYPE 
          16.715           20.280 
[1] "6.2 - 56.5 (16.7)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.2"
D1774V2, 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       25       104         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PRSS48 MUTATED           0          0          1          0        0
  PRSS48 WILD-TYPE        19         10         40         31       35
                  vv
clus               STAGE IVA STAGE IVB
  PRSS48 MUTATED           0         0
  PRSS48 WILD-TYPE        13         1
D1774V3, multiclass
            clus
vv           PRSS48 MUTATED PRSS48 WILD-TYPE
  STAGE I                 0               64
  STAGE IA                1                0
  STAGE II                0               25
  STAGE IIA               5              104
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PRSS48 MUTATED     0   0   6   0
  PRSS48 WILD-TYPE   9  68 242  41
D1774V4, multiclass
    clus
vv   PRSS48 MUTATED PRSS48 WILD-TYPE
  T1              0                9
  T2              0               68
  T3              6              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
  PRSS48 MUTATED     6   1   0
  PRSS48 WILD-TYPE 214  79  66
D1774V5, multiclass
    clus
vv   PRSS48 MUTATED PRSS48 WILD-TYPE
  N0              6              214
  N1              1               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"
D1774V6, binary
                  cls
clus                 0   1
  PRSS48 MUTATED     6   0
  PRSS48 WILD-TYPE 277  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRSS48 MUTATED      6    0
  PRSS48 WILD-TYPE  277   48
   clus
vv  PRSS48 MUTATED PRSS48 WILD-TYPE
  0              6              277
  1              0               48
[1] 2 2
[1] FALSE
D1774V7, 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
D1774V8, binary
                  cls
clus                 0   1
  PRSS48 MUTATED     7   0
  PRSS48 WILD-TYPE 310  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRSS48 MUTATED      7    0
  PRSS48 WILD-TYPE  310   48
                               clus
vv                              PRSS48 MUTATED PRSS48 WILD-TYPE
  COLON ADENOCARCINOMA                       7              310
  COLON MUCINOUS ADENOCARCINOMA              0               48
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PRSS48 MUTATED     6   0   0   0
  PRSS48 WILD-TYPE 251   2  22  21
D1774V9, multiclass
    clus
vv   PRSS48 MUTATED PRSS48 WILD-TYPE
  R0              6              251
  R1              0                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"
D1774V10, 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
D1774V11, 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(1775) Variable = TOX MUTATION ANALYSIS
D1775V1, survival
               sevent
clus2             0   1
  TOX MUTATED    12   3
  TOX WILD-TYPE 270  70
  TOX MUTATED TOX WILD-TYPE 
           15           340 
  TOX MUTATED TOX WILD-TYPE 
            3            70 
$`TOX MUTATED`
TCGA-A6-6780 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3710 TCGA-AA-3950 
       20.12        63.98         6.97        54.02        26.99        24.00 
TCGA-AA-3968 TCGA-AA-3977 TCGA-AA-A00A TCGA-AA-A00J TCGA-AA-A010 TCGA-AZ-4315 
       21.99        25.02        38.04        18.05        34.98        58.39 
TCGA-AZ-6601 TCGA-DM-A28F TCGA-G4-6626 
      100.01        35.97        46.75 

$`TOX WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3666 
       13.94        19.99        61.02        78.08         6.05         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 
       26.01         2.01        20.98        34.03         2.01        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D 
       27.02        19.07         7.96        27.02        13.94        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
      119.93        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       35.80        26.17        91.79        52.80 

  TOX MUTATED TOX WILD-TYPE 
         6.97          0.00 
  TOX MUTATED TOX WILD-TYPE 
       100.01        140.38 
  TOX MUTATED TOX WILD-TYPE 
       34.980        19.625 
[1] "7.0 - 100.0 (35.0)" "0.0 - 140.4 (19.6)"
[1] "hr=" "1.5"
D1775V2, 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       21       103         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        19         10         39         31       35        13
               vv
clus            STAGE IVB
  TOX MUTATED           0
  TOX WILD-TYPE         1
D1775V3, multiclass
            clus
vv           TOX MUTATED TOX WILD-TYPE
  STAGE I              1            63
  STAGE IA             0             1
  STAGE II             4            21
  STAGE IIA            6           103
  STAGE IIB            1             7
  STAGE IIC            0             1
  STAGE III            0            19
  STAGE IIIA           0            10
  STAGE IIIB           2            39
  STAGE IIIC           0            31
  STAGE IV             0            35
  STAGE IVA            0            13
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  TOX MUTATED     0   2  11   2
  TOX WILD-TYPE   9  66 237  39
D1775V4, multiclass
    clus
vv   TOX MUTATED TOX WILD-TYPE
  T1           0             9
  T2           2            66
  T3          11           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
  TOX MUTATED    13   2   0
  TOX WILD-TYPE 207  78  66
D1775V5, multiclass
    clus
vv   TOX MUTATED TOX WILD-TYPE
  N0          13           207
  N1           2            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"
D1775V6, binary
               cls
clus              0   1
  TOX MUTATED    13   0
  TOX WILD-TYPE 270  48
[1] "tbl2"
               cls
clus            [,1] [,2]
  TOX MUTATED     13    0
  TOX WILD-TYPE  270   48
   clus
vv  TOX MUTATED TOX WILD-TYPE
  0          13           270
  1           0            48
[1] 2 2
[1] FALSE
D1775V7, 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
D1775V8, binary
               cls
clus              0   1
  TOX MUTATED    12   3
  TOX WILD-TYPE 305  45
[1] "tbl2"
               cls
clus            [,1] [,2]
  TOX MUTATED     12    3
  TOX WILD-TYPE  305   45
                               clus
vv                              TOX MUTATED TOX WILD-TYPE
  COLON ADENOCARCINOMA                   12           305
  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 246   2  22  21
D1775V9, multiclass
    clus
vv   TOX MUTATED TOX WILD-TYPE
  R0          11           246
  R1           0             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"
D1775V10, 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
D1775V11, 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(1776) Variable = C6ORF203 MUTATION ANALYSIS
D1776V1, survival
                    sevent
clus2                  0   1
  C6ORF203 MUTATED     4   0
  C6ORF203 WILD-TYPE 278  73
  C6ORF203 MUTATED C6ORF203 WILD-TYPE 
                 4                351 
  C6ORF203 MUTATED C6ORF203 WILD-TYPE 
                 0                 73 
$`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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93         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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  C6ORF203 MUTATED C6ORF203 WILD-TYPE 
              6.97               0.00 
  C6ORF203 MUTATED C6ORF203 WILD-TYPE 
             53.00             140.38 
  C6ORF203 MUTATED C6ORF203 WILD-TYPE 
            29.015             20.120 
[1] "7.0 - 53.0 (29.0)"  "0.0 - 140.4 (20.1)"
[1] "hr="     "9100000"
D1776V2, 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       23       108         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C6ORF203 MUTATED           0          0          0          0        0
  C6ORF203 WILD-TYPE        19         10         41         31       35
                    vv
clus                 STAGE IVA STAGE IVB
  C6ORF203 MUTATED           0         0
  C6ORF203 WILD-TYPE        13         1
D1776V3, multiclass
            clus
vv           C6ORF203 MUTATED C6ORF203 WILD-TYPE
  STAGE I                   0                 64
  STAGE IA                  0                  1
  STAGE II                  2                 23
  STAGE IIA                 1                108
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 0                 19
  STAGE IIIA                0                 10
  STAGE IIIB                0                 41
  STAGE IIIC                0                 31
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C6ORF203 MUTATED     0   0   3   1
  C6ORF203 WILD-TYPE   9  68 245  40
D1776V4, multiclass
    clus
vv   C6ORF203 MUTATED C6ORF203 WILD-TYPE
  T1                0                  9
  T2                0                 68
  T3                3                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
  C6ORF203 MUTATED     4   0   0
  C6ORF203 WILD-TYPE 216  80  66
D1776V5, multiclass
    clus
vv   C6ORF203 MUTATED C6ORF203 WILD-TYPE
  N0                4                216
  N1                0                 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
  C6ORF203 MUTATED     4   0
  C6ORF203 WILD-TYPE 279  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF203 MUTATED      4    0
  C6ORF203 WILD-TYPE  279   48
   clus
vv  C6ORF203 MUTATED C6ORF203 WILD-TYPE
  0                4                279
  1                0                 48
[1] 2 2
[1] FALSE
D1776V7, 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
D1776V8, binary
                    cls
clus                   0   1
  C6ORF203 MUTATED     4   0
  C6ORF203 WILD-TYPE 313  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF203 MUTATED      4    0
  C6ORF203 WILD-TYPE  313   48
                               clus
vv                              C6ORF203 MUTATED C6ORF203 WILD-TYPE
  COLON ADENOCARCINOMA                         4                313
  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 253   2  22  21
D1776V9, multiclass
    clus
vv   C6ORF203 MUTATED C6ORF203 WILD-TYPE
  R0                4                253
  R1                0                  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"
D1776V10, 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
D1776V11, multiclass
[1] "Remove cluster labels:" "C6ORF203 MUTATED"      
clus
  C6ORF203 MUTATED C6ORF203 WILD-TYPE 
                 1                205 
        TCGA-A6-2671         TCGA-A6-2672         TCGA-A6-2674 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-A6-2676         TCGA-A6-2677         TCGA-A6-2678 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-A6-2683         TCGA-A6-3807         TCGA-A6-3808 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-A6-3809         TCGA-A6-3810         TCGA-A6-4105 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-A6-5656         TCGA-A6-5657         TCGA-A6-5659 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-A6-5660         TCGA-A6-5661         TCGA-A6-5662 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-A6-5664         TCGA-A6-5665         TCGA-A6-5666 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-A6-6137         TCGA-A6-6138         TCGA-A6-6141 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-A6-6142         TCGA-A6-6648         TCGA-A6-6649 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-A6-6651         TCGA-A6-6652         TCGA-A6-6653 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-A6-6654         TCGA-A6-6780         TCGA-A6-6781 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-A6-6782         TCGA-AD-5900         TCGA-AD-6548 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-AD-6888         TCGA-AD-6889         TCGA-AD-6890 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-AD-6895         TCGA-AD-6899         TCGA-AD-6901 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-AD-6963         TCGA-AD-6964         TCGA-AD-6965 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-AU-3779         TCGA-AU-6004         TCGA-AY-4070 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-AY-4071         TCGA-AY-5543         TCGA-AY-6196 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-AY-6197         TCGA-AY-6386         TCGA-AZ-4315 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-AZ-4323         TCGA-AZ-4616         TCGA-AZ-4681 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-AZ-4682         TCGA-AZ-5403         TCGA-AZ-5407 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-AZ-6598         TCGA-AZ-6599         TCGA-AZ-6600 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-AZ-6601         TCGA-AZ-6603         TCGA-AZ-6605 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-AZ-6606         TCGA-AZ-6607         TCGA-AZ-6608 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CA-5254         TCGA-CA-5255         TCGA-CA-5796 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CA-5797         TCGA-CA-6715         TCGA-CA-6716 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CA-6717         TCGA-CA-6718         TCGA-CA-6719 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CK-4947         TCGA-CK-4948         TCGA-CK-4950 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CK-4952         TCGA-CK-5912         TCGA-CK-5913 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CK-5914         TCGA-CK-5915         TCGA-CK-5916 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CK-6746         TCGA-CK-6747         TCGA-CK-6748 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CK-6751         TCGA-CM-4744         TCGA-CM-4746 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CM-4747         TCGA-CM-4752         TCGA-CM-5341 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CM-5344         TCGA-CM-5348         TCGA-CM-5349 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CM-5860         TCGA-CM-5861         TCGA-CM-5862 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CM-5863         TCGA-CM-5864         TCGA-CM-5868 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CM-6161         TCGA-CM-6162         TCGA-CM-6163 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CM-6164         TCGA-CM-6165         TCGA-CM-6166 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CM-6167         TCGA-CM-6168         TCGA-CM-6169 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CM-6170         TCGA-CM-6171         TCGA-CM-6172 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CM-6674         TCGA-CM-6675         TCGA-CM-6676 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CM-6677         TCGA-CM-6678         TCGA-CM-6679 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CM-6680         TCGA-D5-5537         TCGA-D5-5538 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-D5-5539         TCGA-D5-5540         TCGA-D5-5541 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-D5-6529         TCGA-D5-6532         TCGA-D5-6533 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-D5-6534         TCGA-D5-6535         TCGA-D5-6536 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-D5-6537         TCGA-D5-6538         TCGA-D5-6539 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-D5-6540         TCGA-D5-6541         TCGA-D5-6898 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-D5-6920         TCGA-D5-6922         TCGA-D5-6923 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-D5-6924         TCGA-D5-6926         TCGA-D5-6927 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-D5-6928         TCGA-D5-6929         TCGA-D5-6930 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-D5-6931         TCGA-D5-6932         TCGA-D5-7000 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-DM-A0X9         TCGA-DM-A0XD         TCGA-DM-A0XF 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-DM-A1D0         TCGA-DM-A1D4         TCGA-DM-A1D6 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-DM-A1D7         TCGA-DM-A1D8         TCGA-DM-A1D9 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-DM-A1DA         TCGA-DM-A1DB         TCGA-DM-A1HA 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-DM-A1HB         TCGA-DM-A282         TCGA-DM-A285 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-DM-A28C         TCGA-DM-A28E         TCGA-DM-A28F 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-DM-A28G         TCGA-DM-A28H         TCGA-DM-A28K 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-F4-6459         TCGA-F4-6460         TCGA-F4-6569 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-F4-6570         TCGA-F4-6703         TCGA-F4-6704 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-F4-6805         TCGA-F4-6806         TCGA-F4-6807 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-F4-6808         TCGA-F4-6809         TCGA-F4-6854 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-F4-6855         TCGA-F4-6856         TCGA-G4-6293 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-G4-6299         TCGA-G4-6303         TCGA-G4-6304 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-G4-6306         TCGA-G4-6307         TCGA-G4-6309 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-G4-6310         TCGA-G4-6315         TCGA-G4-6317 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-G4-6321         TCGA-G4-6323         TCGA-G4-6586 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-G4-6588         TCGA-G4-6625         TCGA-G4-6626 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-G4-6628 
"C6ORF203 WILD-TYPE" 

Clustering(1777) Variable = TAP2 MUTATION ANALYSIS
D1777V1, survival
                sevent
clus2              0   1
  TAP2 MUTATED    13   0
  TAP2 WILD-TYPE 269  73
  TAP2 MUTATED TAP2 WILD-TYPE 
            13            342 
  TAP2 MUTATED TAP2 WILD-TYPE 
             0             73 
$`TAP2 MUTATED`
TCGA-AA-3510 TCGA-AA-3672 TCGA-AA-3877 TCGA-AA-A00L TCGA-AA-A010 TCGA-AD-6889 
       63.98         0.92        31.00        38.04        34.98        56.55 
TCGA-AZ-5407 TCGA-CA-6717 TCGA-CM-4743 TCGA-CM-6674 TCGA-F4-6856 TCGA-G4-6309 
       61.41         0.33        23.05        12.95        19.43        51.75 
TCGA-G4-6588 
       26.17 

$`TAP2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        18.05         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-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-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        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        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37         4.21         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14         2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        35.41       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        52.80 

  TAP2 MUTATED TAP2 WILD-TYPE 
          0.33           0.00 
  TAP2 MUTATED TAP2 WILD-TYPE 
         63.98         140.38 
  TAP2 MUTATED TAP2 WILD-TYPE 
        31.000         20.005 
[1] "0.3 - 64.0 (31.0)"  "0.0 - 140.4 (20.0)"
[1] "hr="     "2.6e+07"
D1777V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TAP2 MUTATED         3        0        1         6         2         0
  TAP2 WILD-TYPE      61        1       24       103         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TAP2 MUTATED           1          0          1          0        0         0
  TAP2 WILD-TYPE        18         10         40         31       35        13
                vv
clus             STAGE IVB
  TAP2 MUTATED           0
  TAP2 WILD-TYPE         1
D1777V3, multiclass
            clus
vv           TAP2 MUTATED TAP2 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             6            103
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TAP2 MUTATED     2   1   9   2
  TAP2 WILD-TYPE   7  67 239  39
D1777V4, multiclass
    clus
vv   TAP2 MUTATED TAP2 WILD-TYPE
  T1            2              7
  T2            1             67
  T3            9            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
  TAP2 MUTATED    12   2   0
  TAP2 WILD-TYPE 208  78  66
D1777V5, multiclass
    clus
vv   TAP2 MUTATED TAP2 WILD-TYPE
  N0           12            208
  N1            2             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"
D1777V6, binary
                cls
clus               0   1
  TAP2 MUTATED    13   0
  TAP2 WILD-TYPE 270  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAP2 MUTATED     13    0
  TAP2 WILD-TYPE  270   48
   clus
vv  TAP2 MUTATED TAP2 WILD-TYPE
  0           13            270
  1            0             48
[1] 2 2
[1] FALSE
D1777V7, binary
                cls
clus               0   1
  TAP2 MUTATED     7   7
  TAP2 WILD-TYPE 163 190
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAP2 MUTATED      7    7
  TAP2 WILD-TYPE  163  190
        clus
vv       TAP2 MUTATED TAP2 WILD-TYPE
  FEMALE            7            163
  MALE              7            190
[1] 2 2
[1] FALSE
D1777V8, binary
                cls
clus               0   1
  TAP2 MUTATED    11   3
  TAP2 WILD-TYPE 306  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAP2 MUTATED     11    3
  TAP2 WILD-TYPE  306   45
                               clus
vv                              TAP2 MUTATED TAP2 WILD-TYPE
  COLON ADENOCARCINOMA                    11            306
  COLON MUCINOUS ADENOCARCINOMA            3             45
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TAP2 MUTATED    10   0   0   2
  TAP2 WILD-TYPE 247   2  22  19
D1777V9, multiclass
    clus
vv   TAP2 MUTATED TAP2 WILD-TYPE
  R0           10            247
  R1            0              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"
D1777V10, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TAP2 MUTATED                                  0     2
  TAP2 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TAP2 MUTATED                           1     6
  TAP2 WILD-TYPE                        18   170
D1777V11, multiclass
                                  clus
vv                                 TAP2 MUTATED TAP2 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(1778) Variable = SCARA5 MUTATION ANALYSIS
D1778V1, survival
                  sevent
clus2                0   1
  SCARA5 MUTATED     6   6
  SCARA5 WILD-TYPE 276  67
  SCARA5 MUTATED SCARA5 WILD-TYPE 
              12              343 
  SCARA5 MUTATED SCARA5 WILD-TYPE 
               6               67 
$`SCARA5 MUTATED`
TCGA-AA-3715 TCGA-AA-3864 TCGA-AA-A00O TCGA-AA-A02H TCGA-AZ-4315 TCGA-AZ-6598 
       19.04        53.00        27.02         2.01        58.39        49.41 
TCGA-AZ-6601 TCGA-CK-4952 TCGA-D5-6540 TCGA-DM-A1D4 TCGA-DM-A1HB TCGA-F4-6570 
      100.01        15.62        16.14        92.75       135.65         6.18 

$`SCARA5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
        4.01        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       62.79        61.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       102.44        40.34        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        24.43        38.20       130.65        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        13.38        13.45        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  SCARA5 MUTATED SCARA5 WILD-TYPE 
            2.01             0.00 
  SCARA5 MUTATED SCARA5 WILD-TYPE 
          135.65           140.38 
  SCARA5 MUTATED SCARA5 WILD-TYPE 
          38.215           20.120 
[1] "2.0 - 135.7 (38.2)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.4"
D1778V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SCARA5 MUTATED         1        0        4         3         0         0
  SCARA5 WILD-TYPE      63        1       21       106         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SCARA5 MUTATED           1          0          1          1        1
  SCARA5 WILD-TYPE        18         10         40         30       34
                  vv
clus               STAGE IVA STAGE IVB
  SCARA5 MUTATED           0         0
  SCARA5 WILD-TYPE        13         1
D1778V3, multiclass
            clus
vv           SCARA5 MUTATED SCARA5 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                4               21
  STAGE IIA               3              106
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              1               30
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SCARA5 MUTATED     0   1  10   1
  SCARA5 WILD-TYPE   9  67 238  40
D1778V4, multiclass
    clus
vv   SCARA5 MUTATED SCARA5 WILD-TYPE
  T1              0                9
  T2              1               67
  T3             10              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
  SCARA5 MUTATED     8   1   3
  SCARA5 WILD-TYPE 212  79  63
D1778V5, multiclass
    clus
vv   SCARA5 MUTATED SCARA5 WILD-TYPE
  N0              8              212
  N1              1               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"
D1778V6, binary
                  cls
clus                 0   1
  SCARA5 MUTATED    10   1
  SCARA5 WILD-TYPE 273  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SCARA5 MUTATED     10    1
  SCARA5 WILD-TYPE  273   47
   clus
vv  SCARA5 MUTATED SCARA5 WILD-TYPE
  0             10              273
  1              1               47
[1] 2 2
[1] FALSE
D1778V7, binary
                  cls
clus                 0   1
  SCARA5 MUTATED     5   7
  SCARA5 WILD-TYPE 165 190
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SCARA5 MUTATED      5    7
  SCARA5 WILD-TYPE  165  190
        clus
vv       SCARA5 MUTATED SCARA5 WILD-TYPE
  FEMALE              5              165
  MALE                7              190
[1] 2 2
[1] FALSE
D1778V8, binary
                  cls
clus                 0   1
  SCARA5 MUTATED    10   2
  SCARA5 WILD-TYPE 307  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SCARA5 MUTATED     10    2
  SCARA5 WILD-TYPE  307   46
                               clus
vv                              SCARA5 MUTATED SCARA5 WILD-TYPE
  COLON ADENOCARCINOMA                      10              307
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SCARA5 MUTATED     6   0   1   1
  SCARA5 WILD-TYPE 251   2  21  20
D1778V9, multiclass
    clus
vv   SCARA5 MUTATED SCARA5 WILD-TYPE
  R0              6              251
  R1              0                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"
D1778V10, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SCARA5 MUTATED                                  0     0
  SCARA5 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SCARA5 MUTATED                           0     8
  SCARA5 WILD-TYPE                        19   168
D1778V11, multiclass
                                  clus
vv                                 SCARA5 MUTATED SCARA5 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(1779) Variable = LARP7 MUTATION ANALYSIS
D1779V1, survival
                 sevent
clus2               0   1
  LARP7 MUTATED     6   2
  LARP7 WILD-TYPE 276  71
  LARP7 MUTATED LARP7 WILD-TYPE 
              8             347 
  LARP7 MUTATED LARP7 WILD-TYPE 
              2              71 
$`LARP7 MUTATED`
TCGA-AA-3492 TCGA-AD-6895 TCGA-AZ-6603 TCGA-CA-6717 TCGA-D5-6535 TCGA-DM-A28K 
        3.02         0.72        29.56         0.33        15.12        98.24 
TCGA-F4-6703 TCGA-G4-6628 
       35.87        52.80 

$`LARP7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        4.21        56.55         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10       100.01         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        43.27        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 
        8.61        13.38        13.45         6.18         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       13.78        35.80        26.17        91.79        46.75 

  LARP7 MUTATED LARP7 WILD-TYPE 
           0.33            0.00 
  LARP7 MUTATED LARP7 WILD-TYPE 
          98.24          140.38 
  LARP7 MUTATED LARP7 WILD-TYPE 
          22.34           20.19 
[1] "0.3 - 98.2 (22.3)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D1779V2, 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       24       106         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LARP7 MUTATED           0          0          1          0        0         0
  LARP7 WILD-TYPE        19         10         40         31       35        13
                 vv
clus              STAGE IVB
  LARP7 MUTATED           0
  LARP7 WILD-TYPE         1
D1779V3, multiclass
            clus
vv           LARP7 MUTATED LARP7 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              3             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LARP7 MUTATED     0   2   6   0
  LARP7 WILD-TYPE   9  66 242  41
D1779V4, multiclass
    clus
vv   LARP7 MUTATED LARP7 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             6             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
  LARP7 MUTATED     5   3   0
  LARP7 WILD-TYPE 215  77  66
D1779V5, multiclass
    clus
vv   LARP7 MUTATED LARP7 WILD-TYPE
  N0             5             215
  N1             3              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"
D1779V6, binary
                 cls
clus                0   1
  LARP7 MUTATED     5   0
  LARP7 WILD-TYPE 278  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LARP7 MUTATED      5    0
  LARP7 WILD-TYPE  278   48
   clus
vv  LARP7 MUTATED LARP7 WILD-TYPE
  0             5             278
  1             0              48
[1] 2 2
[1] FALSE
D1779V7, 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
D1779V8, binary
                 cls
clus                0   1
  LARP7 MUTATED     6   2
  LARP7 WILD-TYPE 311  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LARP7 MUTATED      6    2
  LARP7 WILD-TYPE  311   46
                               clus
vv                              LARP7 MUTATED LARP7 WILD-TYPE
  COLON ADENOCARCINOMA                      6             311
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  LARP7 MUTATED     3   0   0   2
  LARP7 WILD-TYPE 254   2  22  19
D1779V9, multiclass
    clus
vv   LARP7 MUTATED LARP7 WILD-TYPE
  R0             3             254
  R1             0               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"
D1779V10, 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
D1779V11, 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(1780) Variable = CCPG1 MUTATION ANALYSIS
D1780V1, survival
                 sevent
clus2               0   1
  CCPG1 MUTATED     8   3
  CCPG1 WILD-TYPE 274  70
  CCPG1 MUTATED CCPG1 WILD-TYPE 
             11             344 
  CCPG1 MUTATED CCPG1 WILD-TYPE 
              3              70 
$`CCPG1 MUTATED`
TCGA-A6-6781 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 
       19.66         6.97         0.92        25.02         4.01        34.98 
TCGA-AD-6964 TCGA-AY-4071 TCGA-AZ-4315 TCGA-CA-6718 TCGA-DM-A1HB 
       10.88         0.95        58.39         0.10       135.65 

$`CCPG1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42         0.20        14.50        27.09        16.31 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.33         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  CCPG1 MUTATED CCPG1 WILD-TYPE 
            0.1             0.0 
  CCPG1 MUTATED CCPG1 WILD-TYPE 
         135.65          140.38 
  CCPG1 MUTATED CCPG1 WILD-TYPE 
          10.88           20.63 
[1] "0.1 - 135.7 (10.9)" "0.0 - 140.4 (20.6)"
[1] "hr=" "1.4"
D1780V2, 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       24       107         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        18         10         40         30       35        13
                 vv
clus              STAGE IVB
  CCPG1 MUTATED           0
  CCPG1 WILD-TYPE         1
D1780V3, multiclass
            clus
vv           CCPG1 MUTATED CCPG1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              2             107
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CCPG1 MUTATED     1   1   5   4
  CCPG1 WILD-TYPE   8  67 243  37
D1780V4, multiclass
    clus
vv   CCPG1 MUTATED CCPG1 WILD-TYPE
  T1             1               8
  T2             1              67
  T3             5             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
  CCPG1 MUTATED     7   3   1
  CCPG1 WILD-TYPE 213  77  65
D1780V5, multiclass
    clus
vv   CCPG1 MUTATED CCPG1 WILD-TYPE
  N0             7             213
  N1             3              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"
D1780V6, binary
                 cls
clus                0   1
  CCPG1 MUTATED     7   0
  CCPG1 WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCPG1 MUTATED      7    0
  CCPG1 WILD-TYPE  276   48
   clus
vv  CCPG1 MUTATED CCPG1 WILD-TYPE
  0             7             276
  1             0              48
[1] 2 2
[1] FALSE
D1780V7, 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
D1780V8, binary
                 cls
clus                0   1
  CCPG1 MUTATED     8   2
  CCPG1 WILD-TYPE 309  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCPG1 MUTATED      8    2
  CCPG1 WILD-TYPE  309   46
                               clus
vv                              CCPG1 MUTATED CCPG1 WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  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 250   2  22  20
D1780V9, multiclass
    clus
vv   CCPG1 MUTATED CCPG1 WILD-TYPE
  R0             7             250
  R1             0               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"
D1780V10, 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
D1780V11, 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(1781) Variable = YTHDF2 MUTATION ANALYSIS
D1781V1, survival
                  sevent
clus2                0   1
  YTHDF2 MUTATED     9   1
  YTHDF2 WILD-TYPE 273  72
  YTHDF2 MUTATED YTHDF2 WILD-TYPE 
              10              345 
  YTHDF2 MUTATED YTHDF2 WILD-TYPE 
               1               72 
$`YTHDF2 MUTATED`
TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-A010 TCGA-AD-5900 TCGA-AZ-6601 TCGA-CA-6718 
       22.06        19.66        34.98         0.07       100.01         0.10 
TCGA-CK-5913 TCGA-CM-5344 TCGA-CM-6162 TCGA-D5-6930 
       51.32        22.03        12.00         1.51 

$`YTHDF2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  YTHDF2 MUTATED YTHDF2 WILD-TYPE 
            0.07             0.00 
  YTHDF2 MUTATED YTHDF2 WILD-TYPE 
          100.01           140.38 
  YTHDF2 MUTATED YTHDF2 WILD-TYPE 
          20.845           20.190 
[1] "0.1 - 100.0 (20.8)" "0.0 - 140.4 (20.2)"
[1] "hr=" "2.2"
D1781V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  YTHDF2 MUTATED         1        0        1         4         1         0
  YTHDF2 WILD-TYPE      63        1       24       105         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  YTHDF2 MUTATED           0          0          2          1        0
  YTHDF2 WILD-TYPE        19         10         39         30       35
                  vv
clus               STAGE IVA STAGE IVB
  YTHDF2 MUTATED           0         0
  YTHDF2 WILD-TYPE        13         1
D1781V3, multiclass
            clus
vv           YTHDF2 MUTATED YTHDF2 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               4              105
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  YTHDF2 MUTATED     0   1   7   2
  YTHDF2 WILD-TYPE   9  67 241  39
D1781V4, multiclass
    clus
vv   YTHDF2 MUTATED YTHDF2 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              7              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
  YTHDF2 MUTATED     7   3   0
  YTHDF2 WILD-TYPE 213  77  66
D1781V5, multiclass
    clus
vv   YTHDF2 MUTATED YTHDF2 WILD-TYPE
  N0              7              213
  N1              3               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"
D1781V6, binary
                  cls
clus                 0   1
  YTHDF2 MUTATED     7   0
  YTHDF2 WILD-TYPE 276  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  YTHDF2 MUTATED      7    0
  YTHDF2 WILD-TYPE  276   48
   clus
vv  YTHDF2 MUTATED YTHDF2 WILD-TYPE
  0              7              276
  1              0               48
[1] 2 2
[1] FALSE
D1781V7, binary
                  cls
clus                 0   1
  YTHDF2 MUTATED     5   5
  YTHDF2 WILD-TYPE 165 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  YTHDF2 MUTATED      5    5
  YTHDF2 WILD-TYPE  165  192
        clus
vv       YTHDF2 MUTATED YTHDF2 WILD-TYPE
  FEMALE              5              165
  MALE                5              192
[1] 2 2
[1] FALSE
D1781V8, binary
                  cls
clus                 0   1
  YTHDF2 MUTATED     6   4
  YTHDF2 WILD-TYPE 311  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  YTHDF2 MUTATED      6    4
  YTHDF2 WILD-TYPE  311   44
                               clus
vv                              YTHDF2 MUTATED YTHDF2 WILD-TYPE
  COLON ADENOCARCINOMA                       6              311
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  YTHDF2 MUTATED     7   0   0   2
  YTHDF2 WILD-TYPE 250   2  22  19
D1781V9, multiclass
    clus
vv   YTHDF2 MUTATED YTHDF2 WILD-TYPE
  R0              7              250
  R1              0                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"
D1781V10, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  YTHDF2 MUTATED                                  0     1
  YTHDF2 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  YTHDF2 MUTATED                           0     8
  YTHDF2 WILD-TYPE                        19   168
D1781V11, multiclass
                                  clus
vv                                 YTHDF2 MUTATED YTHDF2 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(1782) Variable = DNAH3 MUTATION ANALYSIS
D1782V1, survival
                 sevent
clus2               0   1
  DNAH3 MUTATED    37   7
  DNAH3 WILD-TYPE 245  66
  DNAH3 MUTATED DNAH3 WILD-TYPE 
             44             311 
  DNAH3 MUTATED DNAH3 WILD-TYPE 
              7              66 
$`DNAH3 MUTATED`
TCGA-A6-5661 TCGA-A6-6653 TCGA-A6-6780 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3558 
       33.53        24.39        20.12        63.98        29.95        20.98 
TCGA-AA-3715 TCGA-AA-3821 TCGA-AA-3845 TCGA-AA-3861 TCGA-AA-3877 TCGA-AA-3947 
       19.04         1.02         0.00        30.05        31.00        33.01 
TCGA-AA-3950 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-A00F TCGA-AA-A00N TCGA-AA-A00Q 
       24.00        25.02        24.00        34.03         4.01        42.02 
TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6963 TCGA-AD-6964 
       34.98        35.01         0.07        56.55        27.42        10.88 
TCGA-AZ-4315 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-6715 TCGA-CA-6716 
       58.39        61.41        49.41       100.01         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CM-4743 
        0.33         0.10       102.44        40.34        49.08        23.05 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-6171 TCGA-D5-6923 TCGA-D5-6924 TCGA-F4-6703 
       16.01        15.02        14.04        12.43        14.30        35.87 
TCGA-G4-6586 TCGA-G4-6588 
       35.80        26.17 

$`DNAH3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6781 
       25.18        24.16        21.76        24.69        23.87        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       23.01        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 
       10.06        35.05        33.04         0.99        25.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02        14.93        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 
       29.98        18.05         2.01        12.99        24.00        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3980 TCGA-AA-3982 
       50.99        13.05        34.06        26.01        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00R 
       30.02        18.05        18.05        38.04        27.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       39.98        18.05        40.96        21.37         4.21         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        0.72         5.79        22.42         0.20        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        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6599 
        1.41         5.13        83.80        22.36        62.79         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6719 TCGA-CK-4947 
        2.24         3.06         3.25         3.29         1.35        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         2.93         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-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-6172 
       21.99        14.99        12.99        13.02        15.02        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.39        10.13         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        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        13.38        13.45         6.18         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        91.79        46.75        52.80 

  DNAH3 MUTATED DNAH3 WILD-TYPE 
              0               0 
  DNAH3 MUTATED DNAH3 WILD-TYPE 
         102.44          140.38 
  DNAH3 MUTATED DNAH3 WILD-TYPE 
         25.595          19.430 
[1] "0.0 - 102.4 (25.6)" "0.0 - 140.4 (19.4)"
[1] "hr=" "1.5"
D1782V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DNAH3 MUTATED         9        0        4        19         4         0
  DNAH3 WILD-TYPE      55        1       21        90         4         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DNAH3 MUTATED           1          2          2          1        0         0
  DNAH3 WILD-TYPE        18          8         39         30       35        13
                 vv
clus              STAGE IVB
  DNAH3 MUTATED           0
  DNAH3 WILD-TYPE         1
D1782V3, multiclass
            clus
vv           DNAH3 MUTATED DNAH3 WILD-TYPE
  STAGE I                9              55
  STAGE IA               0               1
  STAGE II               4              21
  STAGE IIA             19              90
  STAGE IIB              4               4
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             2               8
  STAGE IIIB             2              39
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DNAH3 MUTATED     2   8  29   6
  DNAH3 WILD-TYPE   7  60 219  35
D1782V4, multiclass
    clus
vv   DNAH3 MUTATED DNAH3 WILD-TYPE
  T1             2               7
  T2             8              60
  T3            29             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
  DNAH3 MUTATED    38   4   3
  DNAH3 WILD-TYPE 182  76  63
D1782V5, multiclass
    clus
vv   DNAH3 MUTATED DNAH3 WILD-TYPE
  N0            38             182
  N1             4              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"
D1782V6, binary
                 cls
clus                0   1
  DNAH3 MUTATED    37   0
  DNAH3 WILD-TYPE 246  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH3 MUTATED     37    0
  DNAH3 WILD-TYPE  246   48
   clus
vv  DNAH3 MUTATED DNAH3 WILD-TYPE
  0            37             246
  1             0              48
[1] 2 2
[1] FALSE
D1782V7, binary
                 cls
clus                0   1
  DNAH3 MUTATED    18  27
  DNAH3 WILD-TYPE 152 170
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH3 MUTATED     18   27
  DNAH3 WILD-TYPE  152  170
        clus
vv       DNAH3 MUTATED DNAH3 WILD-TYPE
  FEMALE            18             152
  MALE              27             170
[1] 2 2
[1] FALSE
D1782V8, binary
                 cls
clus                0   1
  DNAH3 MUTATED    35  10
  DNAH3 WILD-TYPE 282  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH3 MUTATED     35   10
  DNAH3 WILD-TYPE  282   38
                               clus
vv                              DNAH3 MUTATED DNAH3 WILD-TYPE
  COLON ADENOCARCINOMA                     35             282
  COLON MUCINOUS ADENOCARCINOMA            10              38
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DNAH3 MUTATED    28   1   1   6
  DNAH3 WILD-TYPE 229   1  21  15
D1782V9, multiclass
    clus
vv   DNAH3 MUTATED DNAH3 WILD-TYPE
  R0            28             229
  R1             1               1
  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"
D1782V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DNAH3 MUTATED                                  0     5
  DNAH3 WILD-TYPE                                1     5
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DNAH3 MUTATED                           2    21
  DNAH3 WILD-TYPE                        17   155
D1782V11, multiclass
                                  clus
vv                                 DNAH3 MUTATED DNAH3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        5               5
  BLACK OR AFRICAN AMERICAN                    2              17
  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(1783) Variable = UGGT1 MUTATION ANALYSIS
D1783V1, survival
                 sevent
clus2               0   1
  UGGT1 MUTATED    12   4
  UGGT1 WILD-TYPE 270  69
  UGGT1 MUTATED UGGT1 WILD-TYPE 
             16             339 
  UGGT1 MUTATED UGGT1 WILD-TYPE 
              4              69 
$`UGGT1 MUTATED`
TCGA-A6-3809 TCGA-A6-6141 TCGA-AA-3492 TCGA-AA-3672 TCGA-AA-3968 TCGA-AA-A00N 
       32.75         8.38         3.02         0.92        21.99         4.01 
TCGA-AA-A010 TCGA-AZ-6606 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-6748 TCGA-CK-6751 
       34.98        11.74         0.33         0.10         2.01       124.27 
TCGA-D5-6540 TCGA-D5-6928 TCGA-DM-A1HB TCGA-F4-6459 
       16.14        11.64       135.65         8.61 

$`UGGT1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
        2.01        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07         0.26         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79       117.07        98.24        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  UGGT1 MUTATED UGGT1 WILD-TYPE 
            0.1             0.0 
  UGGT1 MUTATED UGGT1 WILD-TYPE 
         135.65          140.38 
  UGGT1 MUTATED UGGT1 WILD-TYPE 
         10.125          20.980 
[1] "0.1 - 135.7 (10.1)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.4"
D1783V2, 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       23       105         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  UGGT1 MUTATED           1          0          2          0        2         0
  UGGT1 WILD-TYPE        18         10         39         31       33        13
                 vv
clus              STAGE IVB
  UGGT1 MUTATED           0
  UGGT1 WILD-TYPE         1
D1783V3, multiclass
            clus
vv           UGGT1 MUTATED UGGT1 WILD-TYPE
  STAGE I                3              61
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              4             105
  STAGE IIB              3               5
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               2              33
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  UGGT1 MUTATED     0   3   9   5
  UGGT1 WILD-TYPE   9  65 239  36
D1783V4, multiclass
    clus
vv   UGGT1 MUTATED UGGT1 WILD-TYPE
  T1             0               9
  T2             3              65
  T3             9             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   2
  UGGT1 WILD-TYPE 208  77  64
D1783V5, multiclass
    clus
vv   UGGT1 MUTATED UGGT1 WILD-TYPE
  N0            12             208
  N1             3              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"
D1783V6, binary
                 cls
clus                0   1
  UGGT1 MUTATED    14   2
  UGGT1 WILD-TYPE 269  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UGGT1 MUTATED     14    2
  UGGT1 WILD-TYPE  269   46
   clus
vv  UGGT1 MUTATED UGGT1 WILD-TYPE
  0            14             269
  1             2              46
[1] 2 2
[1] FALSE
D1783V7, binary
                 cls
clus                0   1
  UGGT1 MUTATED     9   8
  UGGT1 WILD-TYPE 161 189
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UGGT1 MUTATED      9    8
  UGGT1 WILD-TYPE  161  189
        clus
vv       UGGT1 MUTATED UGGT1 WILD-TYPE
  FEMALE             9             161
  MALE               8             189
[1] 2 2
[1] FALSE
D1783V8, binary
                 cls
clus                0   1
  UGGT1 MUTATED    10   7
  UGGT1 WILD-TYPE 307  41
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UGGT1 MUTATED     10    7
  UGGT1 WILD-TYPE  307   41
                               clus
vv                              UGGT1 MUTATED UGGT1 WILD-TYPE
  COLON ADENOCARCINOMA                     10             307
  COLON MUCINOUS ADENOCARCINOMA             7              41
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  UGGT1 MUTATED    10   0   0   4
  UGGT1 WILD-TYPE 247   2  22  17
D1783V9, multiclass
    clus
vv   UGGT1 MUTATED UGGT1 WILD-TYPE
  R0            10             247
  R1             0               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"
D1783V10, 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
D1783V11, 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(1784) Variable = TEX13A MUTATION ANALYSIS
D1784V1, survival
                  sevent
clus2                0   1
  TEX13A MUTATED     7   1
  TEX13A WILD-TYPE 275  72
  TEX13A MUTATED TEX13A WILD-TYPE 
               8              347 
  TEX13A MUTATED TEX13A WILD-TYPE 
               1               72 
$`TEX13A MUTATED`
TCGA-AA-3672 TCGA-AA-3815 TCGA-AA-3950 TCGA-AA-3979 TCGA-AA-3989 TCGA-CM-6167 
        0.92        33.04        24.00        24.00         7.96        14.99 
TCGA-D5-6930 TCGA-G4-6586 
        1.51        35.80 

$`TEX13A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
        6.05         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        25.02        27.02        27.02        19.07 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        26.17        91.79        46.75        52.80 

  TEX13A MUTATED TEX13A WILD-TYPE 
            0.92             0.00 
  TEX13A MUTATED TEX13A WILD-TYPE 
           35.80           140.38 
  TEX13A MUTATED TEX13A WILD-TYPE 
          19.495           20.190 
[1] "0.9 - 35.8 (19.5)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D1784V2, 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       25       103         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TEX13A MUTATED           1          0          0          1        1
  TEX13A WILD-TYPE        18         10         41         30       34
                  vv
clus               STAGE IVA STAGE IVB
  TEX13A MUTATED           0         0
  TEX13A WILD-TYPE        13         1
D1784V3, multiclass
            clus
vv           TEX13A MUTATED TEX13A WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               6              103
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              1               30
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TEX13A MUTATED     0   0   9   0
  TEX13A WILD-TYPE   9  68 239  41
D1784V4, multiclass
    clus
vv   TEX13A MUTATED TEX13A WILD-TYPE
  T1              0                9
  T2              0               68
  T3              9              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   1   2
  TEX13A WILD-TYPE 214  79  64
D1784V5, multiclass
    clus
vv   TEX13A MUTATED TEX13A WILD-TYPE
  N0              6              214
  N1              1               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"
D1784V6, binary
                  cls
clus                 0   1
  TEX13A MUTATED     8   1
  TEX13A WILD-TYPE 275  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TEX13A MUTATED      8    1
  TEX13A WILD-TYPE  275   47
   clus
vv  TEX13A MUTATED TEX13A WILD-TYPE
  0              8              275
  1              1               47
[1] 2 2
[1] FALSE
D1784V7, binary
                  cls
clus                 0   1
  TEX13A MUTATED     6   3
  TEX13A WILD-TYPE 164 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TEX13A MUTATED      6    3
  TEX13A WILD-TYPE  164  194
        clus
vv       TEX13A MUTATED TEX13A WILD-TYPE
  FEMALE              6              164
  MALE                3              194
[1] 2 2
[1] FALSE
D1784V8, binary
                  cls
clus                 0   1
  TEX13A MUTATED     7   2
  TEX13A WILD-TYPE 310  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TEX13A MUTATED      7    2
  TEX13A WILD-TYPE  310   46
                               clus
vv                              TEX13A MUTATED TEX13A WILD-TYPE
  COLON ADENOCARCINOMA                       7              310
  COLON MUCINOUS ADENOCARCINOMA              2               46
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TEX13A MUTATED     8   0   1   0
  TEX13A WILD-TYPE 249   2  21  21
D1784V9, multiclass
    clus
vv   TEX13A MUTATED TEX13A WILD-TYPE
  R0              8              249
  R1              0                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"
D1784V10, 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                           1     2
  TEX13A WILD-TYPE                        18   174
D1784V11, multiclass
                                  clus
vv                                 TEX13A MUTATED TEX13A 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(1785) Variable = CSNK1E MUTATION ANALYSIS
D1785V1, survival
                  sevent
clus2                0   1
  CSNK1E MUTATED     6   2
  CSNK1E WILD-TYPE 276  71
  CSNK1E MUTATED CSNK1E WILD-TYPE 
               8              347 
  CSNK1E MUTATED CSNK1E WILD-TYPE 
               2               71 
$`CSNK1E MUTATED`
TCGA-A6-3809 TCGA-A6-5657 TCGA-AA-3492 TCGA-AY-6197 TCGA-AZ-6601 TCGA-CA-6716 
       32.75        31.63         3.02        21.44       100.01         0.26 
TCGA-CM-6674 TCGA-D5-6931 
       12.95        12.00 

$`CSNK1E WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  CSNK1E MUTATED CSNK1E WILD-TYPE 
            0.26             0.00 
  CSNK1E MUTATED CSNK1E WILD-TYPE 
          100.01           140.38 
  CSNK1E MUTATED CSNK1E WILD-TYPE 
          17.195           20.190 
[1] "0.3 - 100.0 (17.2)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D1785V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CSNK1E MUTATED         0        0        2         3         1         0
  CSNK1E WILD-TYPE      64        1       23       106         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CSNK1E MUTATED           0          0          1          1        0
  CSNK1E WILD-TYPE        19         10         40         30       35
                  vv
clus               STAGE IVA STAGE IVB
  CSNK1E MUTATED           0         0
  CSNK1E WILD-TYPE        13         1
D1785V3, multiclass
            clus
vv           CSNK1E MUTATED CSNK1E WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               3              106
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CSNK1E MUTATED     0   0   6   2
  CSNK1E WILD-TYPE   9  68 242  39
D1785V4, multiclass
    clus
vv   CSNK1E MUTATED CSNK1E WILD-TYPE
  T1              0                9
  T2              0               68
  T3              6              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
  CSNK1E MUTATED     6   1   1
  CSNK1E WILD-TYPE 214  79  65
D1785V5, multiclass
    clus
vv   CSNK1E MUTATED CSNK1E WILD-TYPE
  N0              6              214
  N1              1               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"
D1785V6, binary
                  cls
clus                 0   1
  CSNK1E MUTATED     7   0
  CSNK1E WILD-TYPE 276  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CSNK1E MUTATED      7    0
  CSNK1E WILD-TYPE  276   48
   clus
vv  CSNK1E MUTATED CSNK1E WILD-TYPE
  0              7              276
  1              0               48
[1] 2 2
[1] FALSE
D1785V7, binary
                  cls
clus                 0   1
  CSNK1E MUTATED     2   6
  CSNK1E WILD-TYPE 168 191
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CSNK1E MUTATED      2    6
  CSNK1E WILD-TYPE  168  191
        clus
vv       CSNK1E MUTATED CSNK1E WILD-TYPE
  FEMALE              2              168
  MALE                6              191
[1] 2 2
[1] FALSE
D1785V8, binary
                  cls
clus                 0   1
  CSNK1E MUTATED     7   1
  CSNK1E WILD-TYPE 310  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CSNK1E MUTATED      7    1
  CSNK1E WILD-TYPE  310   47
                               clus
vv                              CSNK1E MUTATED CSNK1E WILD-TYPE
  COLON ADENOCARCINOMA                       7              310
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CSNK1E MUTATED     6   0   0   1
  CSNK1E WILD-TYPE 251   2  22  20
D1785V9, multiclass
    clus
vv   CSNK1E MUTATED CSNK1E WILD-TYPE
  R0              6              251
  R1              0                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"
D1785V10, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CSNK1E MUTATED                                  0     1
  CSNK1E WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CSNK1E MUTATED                           1     5
  CSNK1E WILD-TYPE                        18   171
D1785V11, multiclass
                                  clus
vv                                 CSNK1E MUTATED CSNK1E 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(1786) Variable = MRPL10 MUTATION ANALYSIS
D1786V1, survival
                  sevent
clus2                0   1
  MRPL10 MUTATED     3   1
  MRPL10 WILD-TYPE 279  72
  MRPL10 MUTATED MRPL10 WILD-TYPE 
               4              351 
  MRPL10 MUTATED MRPL10 WILD-TYPE 
               1               72 
$`MRPL10 MUTATED`
TCGA-AA-A00N TCGA-AD-5900 TCGA-CM-4752 TCGA-CM-5344 
        4.01         0.07        13.02        22.03 

$`MRPL10 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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-5860 
       37.02        25.02        29.06        22.98        30.08        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  MRPL10 MUTATED MRPL10 WILD-TYPE 
            0.07             0.00 
  MRPL10 MUTATED MRPL10 WILD-TYPE 
           22.03           140.38 
  MRPL10 MUTATED MRPL10 WILD-TYPE 
           8.515           20.280 
[1] "0.1 - 22.0 (8.5)"   "0.0 - 140.4 (20.3)"
[1] "hr=" "2.8"
D1786V2, 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       25       108         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MRPL10 MUTATED           0          0          1          0        0
  MRPL10 WILD-TYPE        19         10         40         31       35
                  vv
clus               STAGE IVA STAGE IVB
  MRPL10 MUTATED           0         0
  MRPL10 WILD-TYPE        13         1
D1786V3, multiclass
            clus
vv           MRPL10 MUTATED MRPL10 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               1              108
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MRPL10 MUTATED     0   1   2   1
  MRPL10 WILD-TYPE   9  67 246  40
D1786V4, multiclass
    clus
vv   MRPL10 MUTATED MRPL10 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              2              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
  MRPL10 MUTATED     3   1   0
  MRPL10 WILD-TYPE 217  79  66
D1786V5, multiclass
    clus
vv   MRPL10 MUTATED MRPL10 WILD-TYPE
  N0              3              217
  N1              1               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"
D1786V6, binary
                  cls
clus                 0   1
  MRPL10 MUTATED     3   0
  MRPL10 WILD-TYPE 280  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPL10 MUTATED      3    0
  MRPL10 WILD-TYPE  280   48
   clus
vv  MRPL10 MUTATED MRPL10 WILD-TYPE
  0              3              280
  1              0               48
[1] 2 2
[1] FALSE
D1786V7, 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
D1786V8, binary
                  cls
clus                 0   1
  MRPL10 MUTATED     2   2
  MRPL10 WILD-TYPE 315  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPL10 MUTATED      2    2
  MRPL10 WILD-TYPE  315   46
                               clus
vv                              MRPL10 MUTATED MRPL10 WILD-TYPE
  COLON ADENOCARCINOMA                       2              315
  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 253   2  22  21
D1786V9, multiclass
    clus
vv   MRPL10 MUTATED MRPL10 WILD-TYPE
  R0              4              253
  R1              0                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"
D1786V10, 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
D1786V11, 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(1787) Variable = C8ORF80 MUTATION ANALYSIS
D1787V1, survival
                   sevent
clus2                 0   1
  C8ORF80 MUTATED    10   3
  C8ORF80 WILD-TYPE 272  70
  C8ORF80 MUTATED C8ORF80 WILD-TYPE 
               13               342 
  C8ORF80 MUTATED C8ORF80 WILD-TYPE 
                3                70 
$`C8ORF80 MUTATED`
TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3713 TCGA-AA-3821 TCGA-AA-3947 TCGA-AA-3966 
       61.02         6.97        19.04         1.02        33.01         2.01 
TCGA-AA-3977 TCGA-AD-6899 TCGA-AD-6965 TCGA-AZ-6601 TCGA-CA-6717 TCGA-F4-6570 
       25.02         5.79         0.20       100.01         0.33         6.18 
TCGA-G4-6304 
       53.62 

$`C8ORF80 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       33.04         0.99        25.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       26.01        24.00         2.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 
        4.21        56.55         0.79         0.72        22.42        27.42 
TCGA-AD-6964 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        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        13.38        13.45        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 
       35.41        19.43       107.67        74.56        65.85        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  C8ORF80 MUTATED C8ORF80 WILD-TYPE 
              0.2               0.0 
  C8ORF80 MUTATED C8ORF80 WILD-TYPE 
           100.01            140.38 
  C8ORF80 MUTATED C8ORF80 WILD-TYPE 
             6.97             20.63 
[1] "0.2 - 100.0 (7.0)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "1.1"
D1787V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C8ORF80 MUTATED         1        0        3         4         2         0
  C8ORF80 WILD-TYPE      63        1       22       105         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C8ORF80 MUTATED           0          0          0          1        1
  C8ORF80 WILD-TYPE        19         10         41         30       34
                   vv
clus                STAGE IVA STAGE IVB
  C8ORF80 MUTATED           0         0
  C8ORF80 WILD-TYPE        13         1
D1787V3, multiclass
            clus
vv           C8ORF80 MUTATED C8ORF80 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 3                22
  STAGE IIA                4               105
  STAGE IIB                2                 6
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               1                30
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C8ORF80 MUTATED     0   2   8   4
  C8ORF80 WILD-TYPE   9  66 240  37
D1787V4, multiclass
    clus
vv   C8ORF80 MUTATED C8ORF80 WILD-TYPE
  T1               0                 9
  T2               2                66
  T3               8               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
  C8ORF80 MUTATED    12   0   2
  C8ORF80 WILD-TYPE 208  80  64
D1787V5, multiclass
    clus
vv   C8ORF80 MUTATED C8ORF80 WILD-TYPE
  N0              12               208
  N1               0                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"
D1787V6, binary
                   cls
clus                  0   1
  C8ORF80 MUTATED    10   1
  C8ORF80 WILD-TYPE 273  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C8ORF80 MUTATED     10    1
  C8ORF80 WILD-TYPE  273   47
   clus
vv  C8ORF80 MUTATED C8ORF80 WILD-TYPE
  0              10               273
  1               1                47
[1] 2 2
[1] FALSE
D1787V7, binary
                   cls
clus                  0   1
  C8ORF80 MUTATED     6   8
  C8ORF80 WILD-TYPE 164 189
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C8ORF80 MUTATED      6    8
  C8ORF80 WILD-TYPE  164  189
        clus
vv       C8ORF80 MUTATED C8ORF80 WILD-TYPE
  FEMALE               6               164
  MALE                 8               189
[1] 2 2
[1] FALSE
D1787V8, binary
                   cls
clus                  0   1
  C8ORF80 MUTATED     9   5
  C8ORF80 WILD-TYPE 308  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C8ORF80 MUTATED      9    5
  C8ORF80 WILD-TYPE  308   43
                               clus
vv                              C8ORF80 MUTATED C8ORF80 WILD-TYPE
  COLON ADENOCARCINOMA                        9               308
  COLON MUCINOUS ADENOCARCINOMA               5                43
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  C8ORF80 MUTATED     7   0   1   1
  C8ORF80 WILD-TYPE 250   2  21  20
D1787V9, multiclass
    clus
vv   C8ORF80 MUTATED C8ORF80 WILD-TYPE
  R0               7               250
  R1               0                 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"
D1787V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C8ORF80 MUTATED                                  0     1
  C8ORF80 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C8ORF80 MUTATED                           0     5
  C8ORF80 WILD-TYPE                        19   171
D1787V11, multiclass
                                  clus
vv                                 C8ORF80 MUTATED C8ORF80 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(1788) Variable = CPB2 MUTATION ANALYSIS
D1788V1, survival
                sevent
clus2              0   1
  CPB2 MUTATED     7   2
  CPB2 WILD-TYPE 275  71
  CPB2 MUTATED CPB2 WILD-TYPE 
             9            346 
  CPB2 MUTATED CPB2 WILD-TYPE 
             2             71 
$`CPB2 MUTATED`
TCGA-AA-3510 TCGA-AA-3950 TCGA-AA-A010 TCGA-AD-6889 TCGA-AZ-6598 TCGA-CA-6717 
       63.98        24.00        34.98        56.55        49.41         0.33 
TCGA-CM-5864 TCGA-F4-6570 TCGA-G4-6625 
       15.02         6.18        91.79 

$`CPB2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37         4.21         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.38        13.45        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        46.75        52.80 

  CPB2 MUTATED CPB2 WILD-TYPE 
          0.33           0.00 
  CPB2 MUTATED CPB2 WILD-TYPE 
         91.79         140.38 
  CPB2 MUTATED CPB2 WILD-TYPE 
         34.98          20.07 
[1] "0.3 - 91.8 (35.0)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.4"
D1788V2, 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       23       104         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        19         10         41         31       35        13
                vv
clus             STAGE IVB
  CPB2 MUTATED           0
  CPB2 WILD-TYPE         1
D1788V3, multiclass
            clus
vv           CPB2 MUTATED CPB2 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             5            104
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CPB2 MUTATED     0   1   7   1
  CPB2 WILD-TYPE   9  67 241  40
D1788V4, multiclass
    clus
vv   CPB2 MUTATED CPB2 WILD-TYPE
  T1            0              9
  T2            1             67
  T3            7            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
  CPB2 MUTATED     9   0   0
  CPB2 WILD-TYPE 211  80  66
D1788V5, multiclass
    clus
vv   CPB2 MUTATED CPB2 WILD-TYPE
  N0            9            211
  N1            0             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"
D1788V6, binary
                cls
clus               0   1
  CPB2 MUTATED     8   0
  CPB2 WILD-TYPE 275  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  CPB2 MUTATED      8    0
  CPB2 WILD-TYPE  275   48
   clus
vv  CPB2 MUTATED CPB2 WILD-TYPE
  0            8            275
  1            0             48
[1] 2 2
[1] FALSE
D1788V7, 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
D1788V8, binary
                cls
clus               0   1
  CPB2 MUTATED     7   2
  CPB2 WILD-TYPE 310  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  CPB2 MUTATED      7    2
  CPB2 WILD-TYPE  310   46
                               clus
vv                              CPB2 MUTATED CPB2 WILD-TYPE
  COLON ADENOCARCINOMA                     7            310
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CPB2 MUTATED     6   0   0   1
  CPB2 WILD-TYPE 251   2  22  20
D1788V9, multiclass
    clus
vv   CPB2 MUTATED CPB2 WILD-TYPE
  R0            6            251
  R1            0              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"
D1788V10, 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
D1788V11, 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(1789) Variable = GRAMD1C MUTATION ANALYSIS
D1789V1, survival
                   sevent
clus2                 0   1
  GRAMD1C MUTATED     8   1
  GRAMD1C WILD-TYPE 274  72
  GRAMD1C MUTATED GRAMD1C WILD-TYPE 
                9               346 
  GRAMD1C MUTATED GRAMD1C WILD-TYPE 
                1                72 
$`GRAMD1C MUTATED`
TCGA-AA-A010 TCGA-AZ-4315 TCGA-CK-6747 TCGA-CM-6167 TCGA-CM-6680 TCGA-DM-A1D0 
       34.98        58.39         2.93        14.99        12.03       130.65 
TCGA-F4-6460 TCGA-G4-6303 TCGA-G4-6628 
       13.38        65.85        52.80 

$`GRAMD1C WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        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 
       16.01        15.02         5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-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        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       19.43       107.67        74.56        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       35.80        26.17        91.79        46.75 

  GRAMD1C MUTATED GRAMD1C WILD-TYPE 
             2.93              0.00 
  GRAMD1C MUTATED GRAMD1C WILD-TYPE 
           130.65            140.38 
  GRAMD1C MUTATED GRAMD1C WILD-TYPE 
           34.980            20.155 
[1] "2.9 - 130.7 (35.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "3.1"
D1789V2, 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       25       104         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GRAMD1C MUTATED           0          0          2          1        1
  GRAMD1C WILD-TYPE        19         10         39         30       34
                   vv
clus                STAGE IVA STAGE IVB
  GRAMD1C MUTATED           0         0
  GRAMD1C WILD-TYPE        13         1
D1789V3, multiclass
            clus
vv           GRAMD1C MUTATED GRAMD1C WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                5               104
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               2                39
  STAGE IIIC               1                30
  STAGE IV                 1                34
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  GRAMD1C MUTATED     0   1   9   1
  GRAMD1C WILD-TYPE   9  67 239  40
D1789V4, multiclass
    clus
vv   GRAMD1C MUTATED GRAMD1C WILD-TYPE
  T1               0                 9
  T2               1                67
  T3               9               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
  GRAMD1C MUTATED     7   2   2
  GRAMD1C WILD-TYPE 213  78  64
D1789V5, multiclass
    clus
vv   GRAMD1C MUTATED GRAMD1C WILD-TYPE
  N0               7               213
  N1               2                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"
D1789V6, binary
                   cls
clus                  0   1
  GRAMD1C MUTATED     9   1
  GRAMD1C WILD-TYPE 274  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GRAMD1C MUTATED      9    1
  GRAMD1C WILD-TYPE  274   47
   clus
vv  GRAMD1C MUTATED GRAMD1C WILD-TYPE
  0               9               274
  1               1                47
[1] 2 2
[1] FALSE
D1789V7, 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
D1789V8, binary
                   cls
clus                  0   1
  GRAMD1C MUTATED    11   0
  GRAMD1C WILD-TYPE 306  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GRAMD1C MUTATED     11    0
  GRAMD1C WILD-TYPE  306   48
                               clus
vv                              GRAMD1C MUTATED GRAMD1C WILD-TYPE
  COLON ADENOCARCINOMA                       11               306
  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 248   2  22  20
D1789V9, multiclass
    clus
vv   GRAMD1C MUTATED GRAMD1C WILD-TYPE
  R0               9               248
  R1               0                 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"
D1789V10, 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
D1789V11, 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(1790) Variable = TSC1 MUTATION ANALYSIS
D1790V1, survival
                sevent
clus2              0   1
  TSC1 MUTATED     9   2
  TSC1 WILD-TYPE 273  71
  TSC1 MUTATED TSC1 WILD-TYPE 
            11            344 
  TSC1 MUTATED TSC1 WILD-TYPE 
             2             71 
$`TSC1 MUTATED`
TCGA-AA-3950 TCGA-AA-A00J TCGA-AA-A00N TCGA-AD-5900 TCGA-AD-6548 TCGA-AY-6197 
       24.00        18.05         4.01         0.07        21.37        21.44 
TCGA-CK-4952 TCGA-CM-6162 TCGA-D5-5541 TCGA-D5-6537 TCGA-G4-6628 
       15.62        12.00        11.51         4.80        52.80 

$`TSC1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       18.05        40.96         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       27.09        16.31         0.95        15.75         0.20        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 
        1.35        17.56       102.44        40.34        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        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        12.26        19.59        13.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 
       91.79        46.75 

  TSC1 MUTATED TSC1 WILD-TYPE 
          0.07           0.00 
  TSC1 MUTATED TSC1 WILD-TYPE 
         52.80         140.38 
  TSC1 MUTATED TSC1 WILD-TYPE 
         15.62          20.63 
[1] "0.1 - 52.8 (15.6)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "1.2"
D1790V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TSC1 MUTATED         3        0        0         3         2         0
  TSC1 WILD-TYPE      61        1       25       106         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TSC1 MUTATED           1          0          4          0        0         0
  TSC1 WILD-TYPE        18         10         37         31       35        13
                vv
clus             STAGE IVB
  TSC1 MUTATED           0
  TSC1 WILD-TYPE         1
D1790V3, multiclass
            clus
vv           TSC1 MUTATED TSC1 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             3            106
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            4             37
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TSC1 MUTATED     0   3   6   4
  TSC1 WILD-TYPE   9  65 242  37
D1790V4, multiclass
    clus
vv   TSC1 MUTATED TSC1 WILD-TYPE
  T1            0              9
  T2            3             65
  T3            6            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
  TSC1 MUTATED     8   4   1
  TSC1 WILD-TYPE 212  76  65
D1790V5, multiclass
    clus
vv   TSC1 MUTATED TSC1 WILD-TYPE
  N0            8            212
  N1            4             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"
D1790V6, binary
                cls
clus               0   1
  TSC1 MUTATED     9   0
  TSC1 WILD-TYPE 274  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  TSC1 MUTATED      9    0
  TSC1 WILD-TYPE  274   48
   clus
vv  TSC1 MUTATED TSC1 WILD-TYPE
  0            9            274
  1            0             48
[1] 2 2
[1] FALSE
D1790V7, binary
                cls
clus               0   1
  TSC1 MUTATED     6   7
  TSC1 WILD-TYPE 164 190
[1] "tbl2"
                cls
clus             [,1] [,2]
  TSC1 MUTATED      6    7
  TSC1 WILD-TYPE  164  190
        clus
vv       TSC1 MUTATED TSC1 WILD-TYPE
  FEMALE            6            164
  MALE              7            190
[1] 2 2
[1] FALSE
D1790V8, binary
                cls
clus               0   1
  TSC1 MUTATED     7   6
  TSC1 WILD-TYPE 310  42
[1] "tbl2"
                cls
clus             [,1] [,2]
  TSC1 MUTATED      7    6
  TSC1 WILD-TYPE  310   42
                               clus
vv                              TSC1 MUTATED TSC1 WILD-TYPE
  COLON ADENOCARCINOMA                     7            310
  COLON MUCINOUS ADENOCARCINOMA            6             42
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TSC1 MUTATED    11   0   0   2
  TSC1 WILD-TYPE 246   2  22  19
D1790V9, multiclass
    clus
vv   TSC1 MUTATED TSC1 WILD-TYPE
  R0           11            246
  R1            0              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"
D1790V10, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TSC1 MUTATED                                  0     0
  TSC1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TSC1 MUTATED                           0     9
  TSC1 WILD-TYPE                        19   167
D1790V11, multiclass
                                  clus
vv                                 TSC1 MUTATED TSC1 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(1791) Variable = FAM91A1 MUTATION ANALYSIS
D1791V1, survival
                   sevent
clus2                 0   1
  FAM91A1 MUTATED     6   4
  FAM91A1 WILD-TYPE 276  69
  FAM91A1 MUTATED FAM91A1 WILD-TYPE 
               10               345 
  FAM91A1 MUTATED FAM91A1 WILD-TYPE 
                4                69 
$`FAM91A1 MUTATED`
TCGA-A6-4105 TCGA-AA-3815 TCGA-AA-A010 TCGA-AD-6889 TCGA-AD-6964 TCGA-AZ-4315 
       14.53        33.04        34.98        56.55        10.88        58.39 
TCGA-AZ-6599 TCGA-CA-6717 TCGA-D5-6532 TCGA-DM-A1D4 
        6.77         0.33        18.25        92.75 

$`FAM91A1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37         4.21         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
        0.72         5.79        22.42        27.42         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41        49.41        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       11.51        20.19         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        24.43        38.20       130.65        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  FAM91A1 MUTATED FAM91A1 WILD-TYPE 
             0.33              0.00 
  FAM91A1 MUTATED FAM91A1 WILD-TYPE 
            92.75            140.38 
  FAM91A1 MUTATED FAM91A1 WILD-TYPE 
           25.645            20.190 
[1] "0.3 - 92.8 (25.6)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.6"
D1791V2, 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       25       102         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM91A1 MUTATED           0          0          0          0        0
  FAM91A1 WILD-TYPE        19         10         41         31       35
                   vv
clus                STAGE IVA STAGE IVB
  FAM91A1 MUTATED           0         0
  FAM91A1 WILD-TYPE        13         1
D1791V3, multiclass
            clus
vv           FAM91A1 MUTATED FAM91A1 WILD-TYPE
  STAGE I                  1                63
  STAGE IA                 0                 1
  STAGE II                 0                25
  STAGE IIA                7               102
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               0                31
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  FAM91A1 MUTATED     0   1   7   2
  FAM91A1 WILD-TYPE   9  67 241  39
D1791V4, multiclass
    clus
vv   FAM91A1 MUTATED FAM91A1 WILD-TYPE
  T1               0                 9
  T2               1                67
  T3               7               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
  FAM91A1 MUTATED     9   0   1
  FAM91A1 WILD-TYPE 211  80  65
D1791V5, multiclass
    clus
vv   FAM91A1 MUTATED FAM91A1 WILD-TYPE
  N0               9               211
  N1               0                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"
D1791V6, binary
                   cls
clus                  0   1
  FAM91A1 MUTATED     8   0
  FAM91A1 WILD-TYPE 275  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM91A1 MUTATED      8    0
  FAM91A1 WILD-TYPE  275   48
   clus
vv  FAM91A1 MUTATED FAM91A1 WILD-TYPE
  0               8               275
  1               0                48
[1] 2 2
[1] FALSE
D1791V7, 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
D1791V8, binary
                   cls
clus                  0   1
  FAM91A1 MUTATED     9   1
  FAM91A1 WILD-TYPE 308  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM91A1 MUTATED      9    1
  FAM91A1 WILD-TYPE  308   47
                               clus
vv                              FAM91A1 MUTATED FAM91A1 WILD-TYPE
  COLON ADENOCARCINOMA                        9               308
  COLON MUCINOUS ADENOCARCINOMA               1                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  FAM91A1 MUTATED     4   0   0   1
  FAM91A1 WILD-TYPE 253   2  22  20
D1791V9, multiclass
    clus
vv   FAM91A1 MUTATED FAM91A1 WILD-TYPE
  R0               4               253
  R1               0                 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"
D1791V10, 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
D1791V11, 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(1792) Variable = HDAC11 MUTATION ANALYSIS
D1792V1, survival
                  sevent
clus2                0   1
  HDAC11 MUTATED     4   3
  HDAC11 WILD-TYPE 278  70
  HDAC11 MUTATED HDAC11 WILD-TYPE 
               7              348 
  HDAC11 MUTATED HDAC11 WILD-TYPE 
               3               70 
$`HDAC11 MUTATED`
TCGA-A6-5661 TCGA-AA-3516 TCGA-AY-6197 TCGA-AZ-6601 TCGA-CM-5861 TCGA-CM-5862 
       33.53        13.02        21.44       100.01        15.02         5.03 
TCGA-G4-6628 
       52.80 

$`HDAC11 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 

  HDAC11 MUTATED HDAC11 WILD-TYPE 
            5.03             0.00 
  HDAC11 MUTATED HDAC11 WILD-TYPE 
          100.01           140.38 
  HDAC11 MUTATED HDAC11 WILD-TYPE 
          21.440           20.155 
[1] "5.0 - 100.0 (21.4)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.5"
D1792V2, 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       24       106         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HDAC11 MUTATED           1          0          0          0        0
  HDAC11 WILD-TYPE        18         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  HDAC11 MUTATED           1         0
  HDAC11 WILD-TYPE        12         1
D1792V3, multiclass
            clus
vv           HDAC11 MUTATED HDAC11 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               3              106
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 242  40
D1792V4, multiclass
    clus
vv   HDAC11 MUTATED HDAC11 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              6              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
  HDAC11 MUTATED     6   1   1
  HDAC11 WILD-TYPE 214  79  65
D1792V5, multiclass
    clus
vv   HDAC11 MUTATED HDAC11 WILD-TYPE
  N0              6              214
  N1              1               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"
D1792V6, binary
                  cls
clus                 0   1
  HDAC11 MUTATED     5   1
  HDAC11 WILD-TYPE 278  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HDAC11 MUTATED      5    1
  HDAC11 WILD-TYPE  278   47
   clus
vv  HDAC11 MUTATED HDAC11 WILD-TYPE
  0              5              278
  1              1               47
[1] 2 2
[1] FALSE
D1792V7, 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
D1792V8, binary
                  cls
clus                 0   1
  HDAC11 MUTATED     7   1
  HDAC11 WILD-TYPE 310  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HDAC11 MUTATED      7    1
  HDAC11 WILD-TYPE  310   47
                               clus
vv                              HDAC11 MUTATED HDAC11 WILD-TYPE
  COLON ADENOCARCINOMA                       7              310
  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 252   2  22  20
D1792V9, multiclass
    clus
vv   HDAC11 MUTATED HDAC11 WILD-TYPE
  R0              5              252
  R1              0                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"
D1792V10, 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
D1792V11, 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(1793) Variable = GANAB MUTATION ANALYSIS
D1793V1, survival
                 sevent
clus2               0   1
  GANAB MUTATED     8   5
  GANAB WILD-TYPE 274  68
  GANAB MUTATED GANAB WILD-TYPE 
             13             342 
  GANAB MUTATED GANAB WILD-TYPE 
              5              68 
$`GANAB MUTATED`
TCGA-A6-3809 TCGA-A6-6781 TCGA-AA-3516 TCGA-AA-3846 TCGA-AA-A01P TCGA-AY-4071 
       32.75        19.66        13.02        17.03        38.07         0.95 
TCGA-AZ-4315 TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-6717 TCGA-CA-6719 TCGA-CM-4743 
       58.39         5.23         1.94         0.33         1.35        23.05 
TCGA-CM-5349 
       30.08 

$`GANAB WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 
       38.99        37.02        14.93         0.00        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       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        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 
       49.41         6.77        12.10       100.01        29.56        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.26         0.10        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  GANAB MUTATED GANAB WILD-TYPE 
           0.33            0.00 
  GANAB MUTATED GANAB WILD-TYPE 
          58.39          140.38 
  GANAB MUTATED GANAB WILD-TYPE 
          17.03           20.63 
[1] "0.3 - 58.4 (17.0)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "2.7"
D1793V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GANAB MUTATED         1        0        0         6         1         0
  GANAB WILD-TYPE      63        1       25       103         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GANAB MUTATED           2          1          1          1        0         0
  GANAB WILD-TYPE        17          9         40         30       35        13
                 vv
clus              STAGE IVB
  GANAB MUTATED           0
  GANAB WILD-TYPE         1
D1793V3, multiclass
            clus
vv           GANAB MUTATED GANAB WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              6             103
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             1               9
  STAGE IIIB             1              40
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GANAB MUTATED     1   1   8   3
  GANAB WILD-TYPE   8  67 240  38
D1793V4, multiclass
    clus
vv   GANAB MUTATED GANAB WILD-TYPE
  T1             1               8
  T2             1              67
  T3             8             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
  GANAB MUTATED     8   4   1
  GANAB WILD-TYPE 212  76  65
D1793V5, multiclass
    clus
vv   GANAB MUTATED GANAB WILD-TYPE
  N0             8             212
  N1             4              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"
D1793V6, binary
                 cls
clus                0   1
  GANAB MUTATED    11   0
  GANAB WILD-TYPE 272  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GANAB MUTATED     11    0
  GANAB WILD-TYPE  272   48
   clus
vv  GANAB MUTATED GANAB WILD-TYPE
  0            11             272
  1             0              48
[1] 2 2
[1] FALSE
D1793V7, binary
                 cls
clus                0   1
  GANAB MUTATED     7   6
  GANAB WILD-TYPE 163 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GANAB MUTATED      7    6
  GANAB WILD-TYPE  163  191
        clus
vv       GANAB MUTATED GANAB WILD-TYPE
  FEMALE             7             163
  MALE               6             191
[1] 2 2
[1] FALSE
D1793V8, binary
                 cls
clus                0   1
  GANAB MUTATED     8   4
  GANAB WILD-TYPE 309  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GANAB MUTATED      8    4
  GANAB WILD-TYPE  309   44
                               clus
vv                              GANAB MUTATED GANAB WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  COLON MUCINOUS ADENOCARCINOMA             4              44
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  GANAB MUTATED     8   0   0   2
  GANAB WILD-TYPE 249   2  22  19
D1793V9, multiclass
    clus
vv   GANAB MUTATED GANAB WILD-TYPE
  R0             8             249
  R1             0               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"
D1793V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GANAB MUTATED                                  0     2
  GANAB WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GANAB MUTATED                           0     8
  GANAB WILD-TYPE                        19   168
D1793V11, multiclass
                                  clus
vv                                 GANAB MUTATED GANAB 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(1794) Variable = DDX55 MUTATION ANALYSIS
D1794V1, survival
                 sevent
clus2               0   1
  DDX55 MUTATED     9   1
  DDX55 WILD-TYPE 273  72
  DDX55 MUTATED DDX55 WILD-TYPE 
             10             345 
  DDX55 MUTATED DDX55 WILD-TYPE 
              1              72 
$`DDX55 MUTATED`
TCGA-A6-5665 TCGA-AA-3531 TCGA-AA-3864 TCGA-AA-3950 TCGA-AD-6895 TCGA-AZ-6598 
       22.06        34.03        53.00        24.00         0.72        49.41 
TCGA-CA-6717 TCGA-CM-6169 TCGA-D5-6929 TCGA-DM-A1HB 
        0.33        13.02        13.41       135.65 

$`DDX55 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
       19.07         0.00        19.07        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.26         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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-D5-5540 
       10.06        12.03        45.40        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  DDX55 MUTATED DDX55 WILD-TYPE 
           0.33            0.00 
  DDX55 MUTATED DDX55 WILD-TYPE 
         135.65          140.38 
  DDX55 MUTATED DDX55 WILD-TYPE 
          23.03           20.12 
[1] "0.3 - 135.7 (23.0)" "0.0 - 140.4 (20.1)"
[1] "hr=" "2.7"
D1794V2, 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       23       104         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DDX55 MUTATED           0          0          1          0        1         0
  DDX55 WILD-TYPE        19         10         40         31       34        13
                 vv
clus              STAGE IVB
  DDX55 MUTATED           0
  DDX55 WILD-TYPE         1
D1794V3, multiclass
            clus
vv           DDX55 MUTATED DDX55 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              5             104
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DDX55 MUTATED     0   0  10   0
  DDX55 WILD-TYPE   9  68 238  41
D1794V4, multiclass
    clus
vv   DDX55 MUTATED DDX55 WILD-TYPE
  T1             0               9
  T2             0              68
  T3            10             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
  DDX55 MUTATED     7   3   0
  DDX55 WILD-TYPE 213  77  66
D1794V5, multiclass
    clus
vv   DDX55 MUTATED DDX55 WILD-TYPE
  N0             7             213
  N1             3              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"
D1794V6, binary
                 cls
clus                0   1
  DDX55 MUTATED     7   1
  DDX55 WILD-TYPE 276  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX55 MUTATED      7    1
  DDX55 WILD-TYPE  276   47
   clus
vv  DDX55 MUTATED DDX55 WILD-TYPE
  0             7             276
  1             1              47
[1] 2 2
[1] FALSE
D1794V7, 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
D1794V8, binary
                 cls
clus                0   1
  DDX55 MUTATED     8   2
  DDX55 WILD-TYPE 309  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX55 MUTATED      8    2
  DDX55 WILD-TYPE  309   46
                               clus
vv                              DDX55 MUTATED DDX55 WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DDX55 MUTATED     6   0   0   1
  DDX55 WILD-TYPE 251   2  22  20
D1794V9, multiclass
    clus
vv   DDX55 MUTATED DDX55 WILD-TYPE
  R0             6             251
  R1             0               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"
D1794V10, 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
D1794V11, 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(1795) Variable = EVI2A MUTATION ANALYSIS
D1795V1, survival
                 sevent
clus2               0   1
  EVI2A MUTATED     7   0
  EVI2A WILD-TYPE 275  73
  EVI2A MUTATED EVI2A WILD-TYPE 
              7             348 
  EVI2A MUTATED EVI2A WILD-TYPE 
              0              73 
$`EVI2A MUTATED`
TCGA-A6-5659 TCGA-A6-6653 TCGA-AA-3525 TCGA-AA-A00A TCGA-DM-A1D9 TCGA-DM-A282 
       30.44        24.39         8.05        38.04       140.38       139.17 
TCGA-G4-6304 
       53.62 

$`EVI2A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 
        9.07        24.03        37.05        36.03        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E 
       19.07         7.96        27.02        13.94        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-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-A285 
       12.59         7.50        44.32       131.51       135.65         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 
       35.41        19.43       107.67        74.56        65.85        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  EVI2A MUTATED EVI2A WILD-TYPE 
           8.05            0.00 
  EVI2A MUTATED EVI2A WILD-TYPE 
         140.38          135.65 
  EVI2A MUTATED EVI2A WILD-TYPE 
         38.040          20.005 
[1] "8.1 - 140.4 (38.0)" "0.0 - 135.7 (20.0)"
[1] "hr="     "2.7e+07"
D1795V2, 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       25       106         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EVI2A MUTATED           1          0          1          0        0         0
  EVI2A WILD-TYPE        18         10         40         31       35        13
                 vv
clus              STAGE IVB
  EVI2A MUTATED           0
  EVI2A WILD-TYPE         1
D1795V3, multiclass
            clus
vv           EVI2A MUTATED EVI2A WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              3             106
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EVI2A MUTATED     0   2   5   1
  EVI2A WILD-TYPE   9  66 243  40
D1795V4, multiclass
    clus
vv   EVI2A MUTATED EVI2A WILD-TYPE
  T1             0               9
  T2             2              66
  T3             5             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
  EVI2A MUTATED     6   1   1
  EVI2A WILD-TYPE 214  79  65
D1795V5, multiclass
    clus
vv   EVI2A MUTATED EVI2A WILD-TYPE
  N0             6             214
  N1             1              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"
D1795V6, binary
                 cls
clus                0   1
  EVI2A MUTATED     8   0
  EVI2A WILD-TYPE 275  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EVI2A MUTATED      8    0
  EVI2A WILD-TYPE  275   48
   clus
vv  EVI2A MUTATED EVI2A WILD-TYPE
  0             8             275
  1             0              48
[1] 2 2
[1] FALSE
D1795V7, binary
                 cls
clus                0   1
  EVI2A MUTATED     3   5
  EVI2A WILD-TYPE 167 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EVI2A MUTATED      3    5
  EVI2A WILD-TYPE  167  192
        clus
vv       EVI2A MUTATED EVI2A WILD-TYPE
  FEMALE             3             167
  MALE               5             192
[1] 2 2
[1] FALSE
D1795V8, binary
                 cls
clus                0   1
  EVI2A MUTATED     8   0
  EVI2A WILD-TYPE 309  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EVI2A MUTATED      8    0
  EVI2A WILD-TYPE  309   48
                               clus
vv                              EVI2A MUTATED EVI2A WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  EVI2A MUTATED     5   0   0   0
  EVI2A WILD-TYPE 252   2  22  21
D1795V9, multiclass
    clus
vv   EVI2A MUTATED EVI2A WILD-TYPE
  R0             5             252
  R1             0               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"
D1795V10, 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
D1795V11, 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(1796) Variable = OR51B6 MUTATION ANALYSIS
D1796V1, survival
                  sevent
clus2                0   1
  OR51B6 MUTATED     3   0
  OR51B6 WILD-TYPE 279  73
  OR51B6 MUTATED OR51B6 WILD-TYPE 
               3              352 
  OR51B6 MUTATED OR51B6 WILD-TYPE 
               0               73 
$`OR51B6 MUTATED`
TCGA-A6-6653 TCGA-AZ-4315 TCGA-CM-5348 
       24.39        58.39        22.98 

$`OR51B6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
        0.95        15.75         0.20        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  OR51B6 MUTATED OR51B6 WILD-TYPE 
           22.98             0.00 
  OR51B6 MUTATED OR51B6 WILD-TYPE 
           58.39           140.38 
  OR51B6 MUTATED OR51B6 WILD-TYPE 
           24.39            20.07 
[1] "23.0 - 58.4 (24.4)" "0.0 - 140.4 (20.1)"
[1] "hr="     "9100000"
D1796V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR51B6 MUTATED         1        0        0         1         0         0
  OR51B6 WILD-TYPE      63        1       25       108         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR51B6 MUTATED           0          0          1          0        0
  OR51B6 WILD-TYPE        19         10         40         31       35
                  vv
clus               STAGE IVA STAGE IVB
  OR51B6 MUTATED           0         0
  OR51B6 WILD-TYPE        13         1
D1796V3, multiclass
            clus
vv           OR51B6 MUTATED OR51B6 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               1              108
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  OR51B6 MUTATED     0   1   2   0
  OR51B6 WILD-TYPE   9  67 246  41
D1796V4, multiclass
    clus
vv   OR51B6 MUTATED OR51B6 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              2              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
  OR51B6 MUTATED     2   1   0
  OR51B6 WILD-TYPE 218  79  66
D1796V5, multiclass
    clus
vv   OR51B6 MUTATED OR51B6 WILD-TYPE
  N0              2              218
  N1              1               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"
D1796V6, binary
                  cls
clus                 0   1
  OR51B6 MUTATED     3   0
  OR51B6 WILD-TYPE 280  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51B6 MUTATED      3    0
  OR51B6 WILD-TYPE  280   48
   clus
vv  OR51B6 MUTATED OR51B6 WILD-TYPE
  0              3              280
  1              0               48
[1] 2 2
[1] FALSE
D1796V7, binary
                  cls
clus                 0   1
  OR51B6 MUTATED     0   3
  OR51B6 WILD-TYPE 170 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51B6 MUTATED      0    3
  OR51B6 WILD-TYPE  170  194
        clus
vv       OR51B6 MUTATED OR51B6 WILD-TYPE
  FEMALE              0              170
  MALE                3              194
[1] 2 2
[1] FALSE
D1796V8, binary
                  cls
clus                 0   1
  OR51B6 MUTATED     3   0
  OR51B6 WILD-TYPE 314  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51B6 MUTATED      3    0
  OR51B6 WILD-TYPE  314   48
                               clus
vv                              OR51B6 MUTATED OR51B6 WILD-TYPE
  COLON ADENOCARCINOMA                       3              314
  COLON MUCINOUS ADENOCARCINOMA              0               48
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  OR51B6 MUTATED     2   0   0   0
  OR51B6 WILD-TYPE 255   2  22  21
D1796V9, multiclass
[1] "Remove cluster labels:" "OR51B6 MUTATED"        
clus
  OR51B6 MUTATED OR51B6 WILD-TYPE 
               2              300 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-5657 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-A6-5659       TCGA-A6-5661       TCGA-A6-5665       TCGA-A6-6781 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3489       TCGA-AA-3492       TCGA-AA-3496       TCGA-AA-3502 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3510       TCGA-AA-3511       TCGA-AA-3514       TCGA-AA-3517 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3518       TCGA-AA-3519       TCGA-AA-3520       TCGA-AA-3521 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3522       TCGA-AA-3524       TCGA-AA-3525       TCGA-AA-3526 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3527       TCGA-AA-3529       TCGA-AA-3530       TCGA-AA-3531 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3532       TCGA-AA-3534       TCGA-AA-3538       TCGA-AA-3542 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3543       TCGA-AA-3544       TCGA-AA-3548       TCGA-AA-3549 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3552       TCGA-AA-3553       TCGA-AA-3554       TCGA-AA-3555 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3556       TCGA-AA-3558       TCGA-AA-3560       TCGA-AA-3561 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3562       TCGA-AA-3655       TCGA-AA-3660       TCGA-AA-3662 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3663       TCGA-AA-3664       TCGA-AA-3666       TCGA-AA-3667 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3672       TCGA-AA-3673       TCGA-AA-3678       TCGA-AA-3679 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3680       TCGA-AA-3681       TCGA-AA-3684       TCGA-AA-3685 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3688       TCGA-AA-3692       TCGA-AA-3693       TCGA-AA-3695 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3696       TCGA-AA-3697       TCGA-AA-3710       TCGA-AA-3712 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3713       TCGA-AA-3715       TCGA-AA-3811       TCGA-AA-3812 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3814       TCGA-AA-3815       TCGA-AA-3818       TCGA-AA-3819 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3821       TCGA-AA-3831       TCGA-AA-3833       TCGA-AA-3837 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3842       TCGA-AA-3844       TCGA-AA-3845       TCGA-AA-3846 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3848       TCGA-AA-3850       TCGA-AA-3851       TCGA-AA-3852 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3854       TCGA-AA-3855       TCGA-AA-3856       TCGA-AA-3858 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3860       TCGA-AA-3861       TCGA-AA-3864       TCGA-AA-3866 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3867       TCGA-AA-3869       TCGA-AA-3870       TCGA-AA-3872 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3875       TCGA-AA-3877       TCGA-AA-3930       TCGA-AA-3939 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3941       TCGA-AA-3947       TCGA-AA-3949       TCGA-AA-3950 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3952       TCGA-AA-3955       TCGA-AA-3956       TCGA-AA-3968 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3971       TCGA-AA-3972       TCGA-AA-3973       TCGA-AA-3975 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3976       TCGA-AA-3979       TCGA-AA-3984       TCGA-AA-3986 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3989       TCGA-AA-3994       TCGA-AA-A004       TCGA-AA-A00A 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-A00D       TCGA-AA-A00E       TCGA-AA-A00F       TCGA-AA-A00J 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-A00K       TCGA-AA-A00L       TCGA-AA-A00N       TCGA-AA-A00O 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-A00Q       TCGA-AA-A00R       TCGA-AA-A00U       TCGA-AA-A00W 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-A00Z       TCGA-AA-A010       TCGA-AA-A017       TCGA-AA-A01D 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-A01F       TCGA-AA-A01G       TCGA-AA-A01I       TCGA-AA-A01K 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-A01P       TCGA-AA-A01Q       TCGA-AA-A01R       TCGA-AA-A01S 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-A01T       TCGA-AA-A01V       TCGA-AA-A01X       TCGA-AA-A01Z 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-A022       TCGA-AA-A024       TCGA-AA-A029       TCGA-AA-A02F 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-A02H       TCGA-AA-A02J       TCGA-AA-A02K       TCGA-AA-A02O 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-A02W       TCGA-AA-A02Y       TCGA-AA-A03F       TCGA-AA-A03J 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AD-5900       TCGA-AD-6548       TCGA-AD-6888       TCGA-AU-3779 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AU-6004       TCGA-AY-4070       TCGA-AY-4071       TCGA-AY-5543 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386       TCGA-AZ-4681 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AZ-4682       TCGA-CA-5254       TCGA-CA-5255       TCGA-CA-5796 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-CA-5797       TCGA-CA-6715       TCGA-CA-6716       TCGA-CA-6717 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-CA-6718       TCGA-CA-6719       TCGA-CK-4947       TCGA-CK-4948 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-CK-4950       TCGA-CK-4952       TCGA-CK-5912       TCGA-CK-5913 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-CK-5914       TCGA-CK-5915       TCGA-CK-5916       TCGA-CK-6746 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-CK-6747       TCGA-CK-6748       TCGA-CK-6751       TCGA-CM-4743 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-CM-4744       TCGA-CM-4746       TCGA-CM-4747       TCGA-CM-4752 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-CM-5341       TCGA-CM-5344       TCGA-CM-5349       TCGA-CM-5860 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-CM-5861       TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-CM-5868       TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-CM-6164       TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-CM-6168       TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-CM-6172       TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-CM-6677       TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-D5-5537       TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-D5-5541       TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-D5-6534       TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-D5-6538       TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-D5-6898       TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-D5-6924       TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-D5-6929       TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-D5-7000       TCGA-F4-6459       TCGA-F4-6460       TCGA-F4-6569 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704       TCGA-F4-6805 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808       TCGA-F4-6809 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856       TCGA-G4-6293 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304       TCGA-G4-6306 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310       TCGA-G4-6315 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323       TCGA-G4-6586 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
D1796V10, continuous
[1] "Remove cluster labels:" "OR51B6 MUTATED"        
clus
  OR51B6 MUTATED OR51B6 WILD-TYPE 
               2              343 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-4105 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-A6-5661       TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5665 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-A6-5666       TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-A6-6142       TCGA-A6-6648       TCGA-A6-6649       TCGA-A6-6651 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-A6-6652       TCGA-A6-6654       TCGA-A6-6780       TCGA-A6-6781 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-A6-6782       TCGA-AA-3489       TCGA-AA-3492       TCGA-AA-3496 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3502       TCGA-AA-3510       TCGA-AA-3511       TCGA-AA-3514 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3516       TCGA-AA-3517       TCGA-AA-3518       TCGA-AA-3519 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3520       TCGA-AA-3521       TCGA-AA-3522       TCGA-AA-3524 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3525       TCGA-AA-3526       TCGA-AA-3527       TCGA-AA-3529 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3530       TCGA-AA-3531       TCGA-AA-3532       TCGA-AA-3534 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3538       TCGA-AA-3542       TCGA-AA-3543       TCGA-AA-3544 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3548       TCGA-AA-3549       TCGA-AA-3552       TCGA-AA-3553 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3554       TCGA-AA-3555       TCGA-AA-3556       TCGA-AA-3558 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3560       TCGA-AA-3562       TCGA-AA-3655       TCGA-AA-3660 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3662       TCGA-AA-3663       TCGA-AA-3664       TCGA-AA-3666 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3667       TCGA-AA-3672       TCGA-AA-3673       TCGA-AA-3678 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3679       TCGA-AA-3680       TCGA-AA-3681       TCGA-AA-3684 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3685       TCGA-AA-3688       TCGA-AA-3692       TCGA-AA-3693 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3695       TCGA-AA-3696       TCGA-AA-3697       TCGA-AA-3710 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3712       TCGA-AA-3713       TCGA-AA-3715       TCGA-AA-3811 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3812       TCGA-AA-3814       TCGA-AA-3815       TCGA-AA-3818 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3819       TCGA-AA-3821       TCGA-AA-3831       TCGA-AA-3833 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3837       TCGA-AA-3842       TCGA-AA-3844       TCGA-AA-3845 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3846       TCGA-AA-3848       TCGA-AA-3850       TCGA-AA-3851 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3852       TCGA-AA-3854       TCGA-AA-3855       TCGA-AA-3856 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3858       TCGA-AA-3860       TCGA-AA-3861       TCGA-AA-3864 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3866       TCGA-AA-3867       TCGA-AA-3869       TCGA-AA-3870 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3872       TCGA-AA-3875       TCGA-AA-3877       TCGA-AA-3930 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3939       TCGA-AA-3941       TCGA-AA-3947       TCGA-AA-3949 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3950       TCGA-AA-3952       TCGA-AA-3955       TCGA-AA-3956 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3966       TCGA-AA-3968       TCGA-AA-3971       TCGA-AA-3972 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3973       TCGA-AA-3975       TCGA-AA-3976       TCGA-AA-3977 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3979       TCGA-AA-3980       TCGA-AA-3982       TCGA-AA-3984 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-3986       TCGA-AA-3989       TCGA-AA-3994       TCGA-AA-A004 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-A00A       TCGA-AA-A00D       TCGA-AA-A00E       TCGA-AA-A00F 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-A00J       TCGA-AA-A00K       TCGA-AA-A00L       TCGA-AA-A00N 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-A00O       TCGA-AA-A00Q       TCGA-AA-A00R       TCGA-AA-A00U 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-A00W       TCGA-AA-A00Z       TCGA-AA-A010       TCGA-AA-A017 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-A01D       TCGA-AA-A01F       TCGA-AA-A01G       TCGA-AA-A01I 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-A01K       TCGA-AA-A01P       TCGA-AA-A01Q       TCGA-AA-A01R 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-A01S       TCGA-AA-A01T       TCGA-AA-A01V       TCGA-AA-A01X 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-A01Z       TCGA-AA-A022       TCGA-AA-A024       TCGA-AA-A029 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-A02F       TCGA-AA-A02H       TCGA-AA-A02J       TCGA-AA-A02K 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-A02O       TCGA-AA-A02W       TCGA-AA-A02Y       TCGA-AA-A03F 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AA-A03J       TCGA-AD-5900       TCGA-AD-6548       TCGA-AD-6888 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AD-6889       TCGA-AD-6890       TCGA-AD-6895       TCGA-AD-6899 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6964       TCGA-AD-6965 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070       TCGA-AY-4071 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4682       TCGA-AZ-5403 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AZ-5407       TCGA-AZ-6598       TCGA-AZ-6599       TCGA-AZ-6600 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AZ-6601       TCGA-AZ-6603       TCGA-AZ-6605       TCGA-AZ-6606 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-AZ-6607       TCGA-AZ-6608       TCGA-CK-4947       TCGA-CK-4948 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-CK-4950       TCGA-CK-4952       TCGA-CM-4743       TCGA-CM-4744 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-CM-4746       TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-CM-5344       TCGA-CM-5349       TCGA-CM-5860       TCGA-CM-5861 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864       TCGA-CM-5868 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163       TCGA-CM-6164 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167       TCGA-CM-6168 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171       TCGA-CM-6172 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676       TCGA-CM-6677 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680       TCGA-D5-5537 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540       TCGA-D5-5541 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533       TCGA-D5-6534 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537       TCGA-D5-6538 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541       TCGA-D5-6898 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923       TCGA-D5-6924 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928       TCGA-D5-6929 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932       TCGA-D5-7000 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-DM-A0X9       TCGA-DM-A0XD       TCGA-DM-A0XF       TCGA-DM-A1D0 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-DM-A1D4       TCGA-DM-A1D6       TCGA-DM-A1D7       TCGA-DM-A1D8 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-DM-A1D9       TCGA-DM-A1DA       TCGA-DM-A1DB       TCGA-DM-A1HA 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-DM-A1HB       TCGA-DM-A282       TCGA-DM-A285       TCGA-DM-A28C 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-DM-A28E       TCGA-DM-A28F       TCGA-DM-A28G       TCGA-DM-A28H 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-DM-A28K       TCGA-F4-6459       TCGA-F4-6460       TCGA-F4-6569 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704       TCGA-F4-6806 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-F4-6807       TCGA-F4-6808       TCGA-F4-6809       TCGA-F4-6854 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-F4-6855       TCGA-F4-6856       TCGA-G4-6293       TCGA-G4-6299 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-G4-6303       TCGA-G4-6304       TCGA-G4-6306       TCGA-G4-6307 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-G4-6309       TCGA-G4-6310       TCGA-G4-6315       TCGA-G4-6317 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-G4-6321       TCGA-G4-6323       TCGA-G4-6586       TCGA-G4-6588 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
      TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628 
"OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" "OR51B6 WILD-TYPE" 
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR51B6 MUTATED                                  0     0
  OR51B6 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  OR51B6 MUTATED                           0     3
  OR51B6 WILD-TYPE                        19   173
D1796V11, multiclass
                                  clus
vv                                 OR51B6 MUTATED OR51B6 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(1797) Variable = KIAA0020 MUTATION ANALYSIS
D1797V1, survival
                    sevent
clus2                  0   1
  KIAA0020 MUTATED     7   3
  KIAA0020 WILD-TYPE 275  70
  KIAA0020 MUTATED KIAA0020 WILD-TYPE 
                10                345 
  KIAA0020 MUTATED KIAA0020 WILD-TYPE 
                 3                 70 
$`KIAA0020 MUTATED`
TCGA-A6-5661 TCGA-A6-6781 TCGA-AA-A00A TCGA-AA-A00N TCGA-AA-A01R TCGA-AD-6899 
       33.53        19.66        38.04         4.01        35.01         5.79 
TCGA-AD-6964 TCGA-CA-5796 TCGA-CM-6674 TCGA-G4-6588 
       10.88         3.25        12.95        26.17 

$`KIAA0020 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D 
       27.02        19.07         7.96        27.02        13.94        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       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        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        0.95        15.75         0.20        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5797 
       11.74         3.19         1.94         2.24         3.06         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  KIAA0020 MUTATED KIAA0020 WILD-TYPE 
              3.25               0.00 
  KIAA0020 MUTATED KIAA0020 WILD-TYPE 
             38.04             140.38 
  KIAA0020 MUTATED KIAA0020 WILD-TYPE 
            16.305             20.280 
[1] "3.2 - 38.0 (16.3)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "2.2"
D1797V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIAA0020 MUTATED         0        0        0         5         1         0
  KIAA0020 WILD-TYPE      64        1       25       104         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0020 MUTATED           1          0          0          2        0
  KIAA0020 WILD-TYPE        18         10         41         29       35
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA0020 MUTATED           0         0
  KIAA0020 WILD-TYPE        13         1
D1797V3, multiclass
            clus
vv           KIAA0020 MUTATED KIAA0020 WILD-TYPE
  STAGE I                   0                 64
  STAGE IA                  0                  1
  STAGE II                  0                 25
  STAGE IIA                 5                104
  STAGE IIB                 1                  7
  STAGE IIC                 0                  1
  STAGE III                 1                 18
  STAGE IIIA                0                 10
  STAGE IIIB                0                 41
  STAGE IIIC                2                 29
  STAGE IV                  0                 35
  STAGE IVA                 0                 13
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA0020 MUTATED     0   0   6   4
  KIAA0020 WILD-TYPE   9  68 242  37
D1797V4, multiclass
    clus
vv   KIAA0020 MUTATED KIAA0020 WILD-TYPE
  T1                0                  9
  T2                0                 68
  T3                6                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
  KIAA0020 MUTATED     6   1   3
  KIAA0020 WILD-TYPE 214  79  63
D1797V5, multiclass
    clus
vv   KIAA0020 MUTATED KIAA0020 WILD-TYPE
  N0                6                214
  N1                1                 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"
D1797V6, binary
                    cls
clus                   0   1
  KIAA0020 MUTATED     7   0
  KIAA0020 WILD-TYPE 276  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0020 MUTATED      7    0
  KIAA0020 WILD-TYPE  276   48
   clus
vv  KIAA0020 MUTATED KIAA0020 WILD-TYPE
  0                7                276
  1                0                 48
[1] 2 2
[1] FALSE
D1797V7, binary
                    cls
clus                   0   1
  KIAA0020 MUTATED     3   7
  KIAA0020 WILD-TYPE 167 190
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0020 MUTATED      3    7
  KIAA0020 WILD-TYPE  167  190
        clus
vv       KIAA0020 MUTATED KIAA0020 WILD-TYPE
  FEMALE                3                167
  MALE                  7                190
[1] 2 2
[1] FALSE
D1797V8, binary
                    cls
clus                   0   1
  KIAA0020 MUTATED     5   5
  KIAA0020 WILD-TYPE 312  43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0020 MUTATED      5    5
  KIAA0020 WILD-TYPE  312   43
                               clus
vv                              KIAA0020 MUTATED KIAA0020 WILD-TYPE
  COLON ADENOCARCINOMA                         5                312
  COLON MUCINOUS ADENOCARCINOMA                5                 43
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  KIAA0020 MUTATED     8   0   0   0
  KIAA0020 WILD-TYPE 249   2  22  21
D1797V9, multiclass
    clus
vv   KIAA0020 MUTATED KIAA0020 WILD-TYPE
  R0                8                249
  R1                0                  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"
D1797V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIAA0020 MUTATED                                  0     1
  KIAA0020 WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  KIAA0020 MUTATED                           1     5
  KIAA0020 WILD-TYPE                        18   171
D1797V11, multiclass
                                  clus
vv                                 KIAA0020 MUTATED KIAA0020 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(1798) Variable = ENC1 MUTATION ANALYSIS
D1798V1, survival
                sevent
clus2              0   1
  ENC1 MUTATED    10   2
  ENC1 WILD-TYPE 272  71
  ENC1 MUTATED ENC1 WILD-TYPE 
            12            343 
  ENC1 MUTATED ENC1 WILD-TYPE 
             2             71 
$`ENC1 MUTATED`
TCGA-AA-3510 TCGA-AA-3851 TCGA-AA-3949 TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-6598 
       63.98        33.07        26.01        34.98        58.39        49.41 
TCGA-CM-6171 TCGA-D5-5540 TCGA-D5-6541 TCGA-F4-6808 TCGA-G4-6303 TCGA-G4-6586 
       14.04        13.51        15.58        33.67        65.85        35.80 

$`ENC1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       17.03        10.06         0.00         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        16.14         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  ENC1 MUTATED ENC1 WILD-TYPE 
         13.51           0.00 
  ENC1 MUTATED ENC1 WILD-TYPE 
         65.85         140.38 
  ENC1 MUTATED ENC1 WILD-TYPE 
        34.325         19.990 
[1] "13.5 - 65.8 (34.3)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.8"
D1798V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ENC1 MUTATED         2        0        2         5         1         0
  ENC1 WILD-TYPE      62        1       23       104         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ENC1 MUTATED           0          0          1          0        1         0
  ENC1 WILD-TYPE        19         10         40         31       34        13
                vv
clus             STAGE IVB
  ENC1 MUTATED           0
  ENC1 WILD-TYPE         1
D1798V3, multiclass
            clus
vv           ENC1 MUTATED ENC1 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             5            104
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              1             34
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ENC1 MUTATED     1   1   9   1
  ENC1 WILD-TYPE   8  67 239  40
D1798V4, multiclass
    clus
vv   ENC1 MUTATED ENC1 WILD-TYPE
  T1            1              8
  T2            1             67
  T3            9            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
  ENC1 MUTATED    10   2   0
  ENC1 WILD-TYPE 210  78  66
D1798V5, multiclass
    clus
vv   ENC1 MUTATED ENC1 WILD-TYPE
  N0           10            210
  N1            2             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"
D1798V6, binary
                cls
clus               0   1
  ENC1 MUTATED    10   1
  ENC1 WILD-TYPE 273  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  ENC1 MUTATED     10    1
  ENC1 WILD-TYPE  273   47
   clus
vv  ENC1 MUTATED ENC1 WILD-TYPE
  0           10            273
  1            1             47
[1] 2 2
[1] FALSE
D1798V7, binary
                cls
clus               0   1
  ENC1 MUTATED     7   5
  ENC1 WILD-TYPE 163 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  ENC1 MUTATED      7    5
  ENC1 WILD-TYPE  163  192
        clus
vv       ENC1 MUTATED ENC1 WILD-TYPE
  FEMALE            7            163
  MALE              5            192
[1] 2 2
[1] FALSE
D1798V8, binary
                cls
clus               0   1
  ENC1 MUTATED    11   1
  ENC1 WILD-TYPE 306  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  ENC1 MUTATED     11    1
  ENC1 WILD-TYPE  306   47
                               clus
vv                              ENC1 MUTATED ENC1 WILD-TYPE
  COLON ADENOCARCINOMA                    11            306
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ENC1 MUTATED    11   0   0   0
  ENC1 WILD-TYPE 246   2  22  21
D1798V9, multiclass
    clus
vv   ENC1 MUTATED ENC1 WILD-TYPE
  R0           11            246
  R1            0              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"
D1798V10, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ENC1 MUTATED                                  0     0
  ENC1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ENC1 MUTATED                           0     8
  ENC1 WILD-TYPE                        19   168
D1798V11, multiclass
                                  clus
vv                                 ENC1 MUTATED ENC1 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(1799) Variable = OR14J1 MUTATION ANALYSIS
D1799V1, survival
                  sevent
clus2                0   1
  OR14J1 MUTATED     7   1
  OR14J1 WILD-TYPE 275  72
  OR14J1 MUTATED OR14J1 WILD-TYPE 
               8              347 
  OR14J1 MUTATED OR14J1 WILD-TYPE 
               1               72 
$`OR14J1 MUTATED`
TCGA-A6-6652 TCGA-AA-3815 TCGA-AA-A010 TCGA-AZ-6599 TCGA-D5-6535 TCGA-D5-6538 
       24.69        33.04        34.98         6.77        15.12        17.13 
TCGA-G4-6307 TCGA-G4-6628 
       55.04        52.80 

$`OR14J1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41        49.41        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 
       18.25         1.32        43.27        17.85         4.80        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       13.78        35.80        26.17        91.79        46.75 

  OR14J1 MUTATED OR14J1 WILD-TYPE 
            6.77             0.00 
  OR14J1 MUTATED OR14J1 WILD-TYPE 
           55.04           140.38 
  OR14J1 MUTATED OR14J1 WILD-TYPE 
          28.865           20.120 
[1] "6.8 - 55.0 (28.9)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "2"  
D1799V2, 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       25       108         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR14J1 MUTATED           0          0          3          0        0
  OR14J1 WILD-TYPE        19         10         38         31       35
                  vv
clus               STAGE IVA STAGE IVB
  OR14J1 MUTATED           1         0
  OR14J1 WILD-TYPE        12         1
D1799V3, multiclass
            clus
vv           OR14J1 MUTATED OR14J1 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               1              108
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              3               38
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 243  40
D1799V4, multiclass
    clus
vv   OR14J1 MUTATED OR14J1 WILD-TYPE
  T1              0                9
  T2              2               66
  T3              5              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
  OR14J1 MUTATED     5   2   1
  OR14J1 WILD-TYPE 215  78  65
D1799V5, multiclass
    clus
vv   OR14J1 MUTATED OR14J1 WILD-TYPE
  N0              5              215
  N1              2               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"
D1799V6, binary
                  cls
clus                 0   1
  OR14J1 MUTATED     5   1
  OR14J1 WILD-TYPE 278  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR14J1 MUTATED      5    1
  OR14J1 WILD-TYPE  278   47
   clus
vv  OR14J1 MUTATED OR14J1 WILD-TYPE
  0              5              278
  1              1               47
[1] 2 2
[1] FALSE
D1799V7, 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
D1799V8, binary
                  cls
clus                 0   1
  OR14J1 MUTATED     8   0
  OR14J1 WILD-TYPE 309  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR14J1 MUTATED      8    0
  OR14J1 WILD-TYPE  309   48
                               clus
vv                              OR14J1 MUTATED OR14J1 WILD-TYPE
  COLON ADENOCARCINOMA                       8              309
  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 252   2  22  20
D1799V9, multiclass
    clus
vv   OR14J1 MUTATED OR14J1 WILD-TYPE
  R0              5              252
  R1              0                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"
D1799V10, 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
D1799V11, 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(1800) Variable = ZFP3 MUTATION ANALYSIS
D1800V1, survival
                sevent
clus2              0   1
  ZFP3 MUTATED     9   1
  ZFP3 WILD-TYPE 273  72
  ZFP3 MUTATED ZFP3 WILD-TYPE 
            10            345 
  ZFP3 MUTATED ZFP3 WILD-TYPE 
             1             72 
$`ZFP3 MUTATED`
TCGA-A6-2672 TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3525 TCGA-AA-3555 TCGA-AA-3833 
       46.65        22.06        63.98         8.05        29.95        15.95 
TCGA-AA-3977 TCGA-AA-A010 TCGA-CA-6717 TCGA-DM-A1D4 
       25.02        34.98         0.33        92.75 

$`ZFP3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       24.03        37.05        36.03        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
       25.02         1.02        17.98        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        24.43        38.20       130.65        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  ZFP3 MUTATED ZFP3 WILD-TYPE 
          0.33           0.00 
  ZFP3 MUTATED ZFP3 WILD-TYPE 
         92.75         140.38 
  ZFP3 MUTATED ZFP3 WILD-TYPE 
        27.485         20.020 
[1] "0.3 - 92.8 (27.5)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "2.8"
D1800V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZFP3 MUTATED         0        0        1         5         1         0
  ZFP3 WILD-TYPE      64        1       24       104         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ZFP3 MUTATED           0          0          2          0        0         0
  ZFP3 WILD-TYPE        19         10         39         31       35        13
                vv
clus             STAGE IVB
  ZFP3 MUTATED           0
  ZFP3 WILD-TYPE         1
D1800V3, multiclass
            clus
vv           ZFP3 MUTATED ZFP3 WILD-TYPE
  STAGE I               0             64
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             5            104
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            2             39
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ZFP3 MUTATED     0   1   8   1
  ZFP3 WILD-TYPE   9  67 240  40
D1800V4, multiclass
    clus
vv   ZFP3 MUTATED ZFP3 WILD-TYPE
  T1            0              9
  T2            1             67
  T3            8            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
  ZFP3 MUTATED     8   2   0
  ZFP3 WILD-TYPE 212  78  66
D1800V5, multiclass
    clus
vv   ZFP3 MUTATED ZFP3 WILD-TYPE
  N0            8            212
  N1            2             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"
D1800V6, binary
                cls
clus               0   1
  ZFP3 MUTATED     9   0
  ZFP3 WILD-TYPE 274  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZFP3 MUTATED      9    0
  ZFP3 WILD-TYPE  274   48
   clus
vv  ZFP3 MUTATED ZFP3 WILD-TYPE
  0            9            274
  1            0             48
[1] 2 2
[1] FALSE
D1800V7, binary
                cls
clus               0   1
  ZFP3 MUTATED     5   5
  ZFP3 WILD-TYPE 165 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZFP3 MUTATED      5    5
  ZFP3 WILD-TYPE  165  192
        clus
vv       ZFP3 MUTATED ZFP3 WILD-TYPE
  FEMALE            5            165
  MALE              5            192
[1] 2 2
[1] FALSE
D1800V8, binary
                cls
clus               0   1
  ZFP3 MUTATED     8   2
  ZFP3 WILD-TYPE 309  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZFP3 MUTATED      8    2
  ZFP3 WILD-TYPE  309   46
                               clus
vv                              ZFP3 MUTATED ZFP3 WILD-TYPE
  COLON ADENOCARCINOMA                     8            309
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ZFP3 MUTATED     7   0   0   1
  ZFP3 WILD-TYPE 250   2  22  20
D1800V9, multiclass
    clus
vv   ZFP3 MUTATED ZFP3 WILD-TYPE
  R0            7            250
  R1            0              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"
D1800V10, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZFP3 MUTATED                                  0     1
  ZFP3 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ZFP3 MUTATED                           0     3
  ZFP3 WILD-TYPE                        19   173
D1800V11, multiclass
                                  clus
vv                                 ZFP3 MUTATED ZFP3 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(1801) Variable = S1PR1 MUTATION ANALYSIS
D1801V1, survival
                 sevent
clus2               0   1
  S1PR1 MUTATED     8   3
  S1PR1 WILD-TYPE 274  70
  S1PR1 MUTATED S1PR1 WILD-TYPE 
             11             344 
  S1PR1 MUTATED S1PR1 WILD-TYPE 
              3              70 
$`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         1.51        24.43       117.07        36.00 

$`S1PR1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        19.04        19.04 
TCGA-AA-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-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       10.26       119.70        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.72        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  S1PR1 MUTATED S1PR1 WILD-TYPE 
           1.02            0.00 
  S1PR1 MUTATED S1PR1 WILD-TYPE 
         117.07          140.38 
  S1PR1 MUTATED S1PR1 WILD-TYPE 
          24.43           20.07 
[1] "1.0 - 117.1 (24.4)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.3"
D1801V2, 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       25       105         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        18         10         40         29       35        11
                 vv
clus              STAGE IVB
  S1PR1 MUTATED           0
  S1PR1 WILD-TYPE         1
D1801V3, multiclass
            clus
vv           S1PR1 MUTATED S1PR1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              4             105
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             2              29
  STAGE IV               0              35
  STAGE IVA              2              11
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  67 239  40
D1801V4, multiclass
    clus
vv   S1PR1 MUTATED S1PR1 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             9             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
  S1PR1 MUTATED     6   2   3
  S1PR1 WILD-TYPE 214  78  63
D1801V5, multiclass
    clus
vv   S1PR1 MUTATED S1PR1 WILD-TYPE
  N0             6             214
  N1             2              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"
D1801V6, binary
                 cls
clus                0   1
  S1PR1 MUTATED     8   2
  S1PR1 WILD-TYPE 275  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  S1PR1 MUTATED      8    2
  S1PR1 WILD-TYPE  275   46
   clus
vv  S1PR1 MUTATED S1PR1 WILD-TYPE
  0             8             275
  1             2              46
[1] 2 2
[1] FALSE
D1801V7, 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
D1801V8, binary
                 cls
clus                0   1
  S1PR1 MUTATED     8   3
  S1PR1 WILD-TYPE 309  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  S1PR1 MUTATED      8    3
  S1PR1 WILD-TYPE  309   45
                               clus
vv                              S1PR1 MUTATED S1PR1 WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  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 248   2  22  21
D1801V9, multiclass
    clus
vv   S1PR1 MUTATED S1PR1 WILD-TYPE
  R0             9             248
  R1             0               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"
D1801V10, 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
D1801V11, 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(1802) Variable = UAP1 MUTATION ANALYSIS
D1802V1, survival
                sevent
clus2              0   1
  UAP1 MUTATED     4   2
  UAP1 WILD-TYPE 278  71
  UAP1 MUTATED UAP1 WILD-TYPE 
             6            349 
  UAP1 MUTATED UAP1 WILD-TYPE 
             2             71 
$`UAP1 MUTATED`
TCGA-AA-3492 TCGA-AU-6004 TCGA-AY-6196 TCGA-CA-6718 TCGA-CK-5912 TCGA-D5-6931 
        3.02        27.09         0.20         0.10        49.08        12.00 

$`UAP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       15.75        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.33         1.35        17.56       102.44        40.34 
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         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  UAP1 MUTATED UAP1 WILD-TYPE 
           0.1            0.0 
  UAP1 MUTATED UAP1 WILD-TYPE 
         49.08         140.38 
  UAP1 MUTATED UAP1 WILD-TYPE 
          7.51          20.28 
[1] "0.1 - 49.1 (7.5)"   "0.0 - 140.4 (20.3)"
[1] "hr=" "2.6"
D1802V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  UAP1 MUTATED         2        0        1         1         0         0
  UAP1 WILD-TYPE      62        1       24       108         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  UAP1 MUTATED           0          0          0          2        0         0
  UAP1 WILD-TYPE        19         10         41         29       35        13
                vv
clus             STAGE IVB
  UAP1 MUTATED           0
  UAP1 WILD-TYPE         1
D1802V3, multiclass
            clus
vv           UAP1 MUTATED UAP1 WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              1             24
  STAGE IIA             1            108
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            2             29
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  UAP1 MUTATED     0   2   3   1
  UAP1 WILD-TYPE   9  66 245  40
D1802V4, multiclass
    clus
vv   UAP1 MUTATED UAP1 WILD-TYPE
  T1            0              9
  T2            2             66
  T3            3            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
  UAP1 MUTATED     4   0   2
  UAP1 WILD-TYPE 216  80  64
D1802V5, multiclass
    clus
vv   UAP1 MUTATED UAP1 WILD-TYPE
  N0            4            216
  N1            0             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"
D1802V6, binary
                cls
clus               0   1
  UAP1 MUTATED     4   0
  UAP1 WILD-TYPE 279  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  UAP1 MUTATED      4    0
  UAP1 WILD-TYPE  279   48
   clus
vv  UAP1 MUTATED UAP1 WILD-TYPE
  0            4            279
  1            0             48
[1] 2 2
[1] FALSE
D1802V7, binary
                cls
clus               0   1
  UAP1 MUTATED     2   4
  UAP1 WILD-TYPE 168 193
[1] "tbl2"
                cls
clus             [,1] [,2]
  UAP1 MUTATED      2    4
  UAP1 WILD-TYPE  168  193
        clus
vv       UAP1 MUTATED UAP1 WILD-TYPE
  FEMALE            2            168
  MALE              4            193
[1] 2 2
[1] FALSE
D1802V8, binary
                cls
clus               0   1
  UAP1 MUTATED     5   1
  UAP1 WILD-TYPE 312  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  UAP1 MUTATED      5    1
  UAP1 WILD-TYPE  312   47
                               clus
vv                              UAP1 MUTATED UAP1 WILD-TYPE
  COLON ADENOCARCINOMA                     5            312
  COLON MUCINOUS ADENOCARCINOMA            1             47
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  UAP1 MUTATED     4   0   0   2
  UAP1 WILD-TYPE 253   2  22  19
D1802V9, multiclass
    clus
vv   UAP1 MUTATED UAP1 WILD-TYPE
  R0            4            253
  R1            0              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"
D1802V10, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UAP1 MUTATED                                  0     1
  UAP1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  UAP1 MUTATED                           0     4
  UAP1 WILD-TYPE                        19   172
D1802V11, multiclass
                                  clus
vv                                 UAP1 MUTATED UAP1 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(1803) Variable = TACC2 MUTATION ANALYSIS
D1803V1, survival
                 sevent
clus2               0   1
  TACC2 MUTATED    21   3
  TACC2 WILD-TYPE 261  70
  TACC2 MUTATED TACC2 WILD-TYPE 
             24             331 
  TACC2 MUTATED TACC2 WILD-TYPE 
              3              70 
$`TACC2 MUTATED`
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3543 TCGA-AA-3555 TCGA-AA-3663 TCGA-AA-3713 
        3.02        35.01         0.99        29.95         6.97        19.04 
TCGA-AA-3850 TCGA-AA-3950 TCGA-AA-A00A TCGA-AA-A00J TCGA-AA-A010 TCGA-AA-A01Q 
        0.00        24.00        38.04        18.05        34.98         1.02 
TCGA-AD-6895 TCGA-AU-6004 TCGA-AY-6197 TCGA-CA-6717 TCGA-CK-4950 TCGA-CK-5914 
        0.72        27.09        21.44         0.33        40.34        21.99 
TCGA-CM-6162 TCGA-D5-6928 TCGA-D5-6930 TCGA-F4-6570 TCGA-G4-6586 TCGA-G4-6588 
       12.00        11.64         1.51         6.18        35.80        26.17 

$`TACC2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
       12.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.05        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
        0.00        17.03        10.06        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D 
       27.02        19.07         7.96        27.02        13.94        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21        56.55         0.79         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       15.75         0.20        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 
        0.26         0.10         1.35        17.56       102.44        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32        21.14         2.93         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        16.01        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 
       36.72        36.00        22.09        13.78        91.79        46.75 
TCGA-G4-6628 
       52.80 

  TACC2 MUTATED TACC2 WILD-TYPE 
              0               0 
  TACC2 MUTATED TACC2 WILD-TYPE 
          40.34          140.38 
  TACC2 MUTATED TACC2 WILD-TYPE 
         18.545          20.280 
[1] "0.0 - 40.3 (18.5)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.1"
D1803V2, 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       22        99         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TACC2 MUTATED           0          1          3          0        1         0
  TACC2 WILD-TYPE        19          9         38         31       34        13
                 vv
clus              STAGE IVB
  TACC2 MUTATED           0
  TACC2 WILD-TYPE         1
D1803V3, multiclass
            clus
vv           TACC2 MUTATED TACC2 WILD-TYPE
  STAGE I                4              60
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA             10              99
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             3              38
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TACC2 MUTATED     0   4  18   3
  TACC2 WILD-TYPE   9  64 230  38
D1803V4, multiclass
    clus
vv   TACC2 MUTATED TACC2 WILD-TYPE
  T1             0               9
  T2             4              64
  T3            18             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
  TACC2 MUTATED    20   5   0
  TACC2 WILD-TYPE 200  75  66
D1803V5, multiclass
    clus
vv   TACC2 MUTATED TACC2 WILD-TYPE
  N0            20             200
  N1             5              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"
D1803V6, binary
                 cls
clus                0   1
  TACC2 MUTATED    20   1
  TACC2 WILD-TYPE 263  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TACC2 MUTATED     20    1
  TACC2 WILD-TYPE  263   47
   clus
vv  TACC2 MUTATED TACC2 WILD-TYPE
  0            20             263
  1             1              47
[1] 2 2
[1] FALSE
D1803V7, 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
D1803V8, binary
                 cls
clus                0   1
  TACC2 MUTATED    17   8
  TACC2 WILD-TYPE 300  40
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TACC2 MUTATED     17    8
  TACC2 WILD-TYPE  300   40
                               clus
vv                              TACC2 MUTATED TACC2 WILD-TYPE
  COLON ADENOCARCINOMA                     17             300
  COLON MUCINOUS ADENOCARCINOMA             8              40
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TACC2 MUTATED    19   1   1   3
  TACC2 WILD-TYPE 238   1  21  18
D1803V9, multiclass
    clus
vv   TACC2 MUTATED TACC2 WILD-TYPE
  R0            19             238
  R1             1               1
  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"
D1803V10, 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
D1803V11, 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(1804) Variable = GLRA1 MUTATION ANALYSIS
D1804V1, survival
                 sevent
clus2               0   1
  GLRA1 MUTATED     8   2
  GLRA1 WILD-TYPE 274  71
  GLRA1 MUTATED GLRA1 WILD-TYPE 
             10             345 
  GLRA1 MUTATED GLRA1 WILD-TYPE 
              2              71 
$`GLRA1 MUTATED`
TCGA-A6-2676 TCGA-A6-6137 TCGA-AA-A010 TCGA-AU-3779 TCGA-AU-6004 TCGA-CA-6717 
       42.90        27.09        34.98        14.50        27.09         0.33 
TCGA-CM-4746 TCGA-D5-6535 TCGA-D5-6538 TCGA-F4-6570 
       37.02        15.12        17.13         6.18 

$`GLRA1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
        0.20        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  GLRA1 MUTATED GLRA1 WILD-TYPE 
           0.33            0.00 
  GLRA1 MUTATED GLRA1 WILD-TYPE 
          42.90          140.38 
  GLRA1 MUTATED GLRA1 WILD-TYPE 
          22.11           20.19 
[1] "0.3 - 42.9 (22.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D1804V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GLRA1 MUTATED         2        0        0         3         2         0
  GLRA1 WILD-TYPE      62        1       25       106         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GLRA1 MUTATED           0          0          3          0        0         0
  GLRA1 WILD-TYPE        19         10         38         31       35        13
                 vv
clus              STAGE IVB
  GLRA1 MUTATED           0
  GLRA1 WILD-TYPE         1
D1804V3, multiclass
            clus
vv           GLRA1 MUTATED GLRA1 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              3             106
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             3              38
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GLRA1 MUTATED     0   2   6   2
  GLRA1 WILD-TYPE   9  66 242  39
D1804V4, multiclass
    clus
vv   GLRA1 MUTATED GLRA1 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             6             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
  GLRA1 MUTATED     7   2   1
  GLRA1 WILD-TYPE 213  78  65
D1804V5, multiclass
    clus
vv   GLRA1 MUTATED GLRA1 WILD-TYPE
  N0             7             213
  N1             2              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"
D1804V6, binary
                 cls
clus                0   1
  GLRA1 MUTATED     9   0
  GLRA1 WILD-TYPE 274  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GLRA1 MUTATED      9    0
  GLRA1 WILD-TYPE  274   48
   clus
vv  GLRA1 MUTATED GLRA1 WILD-TYPE
  0             9             274
  1             0              48
[1] 2 2
[1] FALSE
D1804V7, binary
                 cls
clus                0   1
  GLRA1 MUTATED     7   3
  GLRA1 WILD-TYPE 163 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GLRA1 MUTATED      7    3
  GLRA1 WILD-TYPE  163  194
        clus
vv       GLRA1 MUTATED GLRA1 WILD-TYPE
  FEMALE             7             163
  MALE               3             194
[1] 2 2
[1] FALSE
D1804V8, binary
                 cls
clus                0   1
  GLRA1 MUTATED     9   1
  GLRA1 WILD-TYPE 308  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GLRA1 MUTATED      9    1
  GLRA1 WILD-TYPE  308   47
                               clus
vv                              GLRA1 MUTATED GLRA1 WILD-TYPE
  COLON ADENOCARCINOMA                      9             308
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  GLRA1 MUTATED     7   0   0   2
  GLRA1 WILD-TYPE 250   2  22  19
D1804V9, multiclass
    clus
vv   GLRA1 MUTATED GLRA1 WILD-TYPE
  R0             7             250
  R1             0               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"
D1804V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GLRA1 MUTATED                                  0     1
  GLRA1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GLRA1 MUTATED                           1     7
  GLRA1 WILD-TYPE                        18   169
D1804V11, multiclass
                                  clus
vv                                 GLRA1 MUTATED GLRA1 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(1805) Variable = CFP MUTATION ANALYSIS
D1805V1, survival
               sevent
clus2             0   1
  CFP MUTATED     7   0
  CFP WILD-TYPE 275  73
  CFP MUTATED CFP WILD-TYPE 
            7           348 
  CFP MUTATED CFP WILD-TYPE 
            0            73 
$`CFP MUTATED`
TCGA-AA-3662 TCGA-AA-3877 TCGA-AA-3939 TCGA-CA-6717 TCGA-CK-5913 TCGA-CM-6162 
        6.05        31.00        12.99         0.33        51.32        12.00 
TCGA-G4-6588 
       26.17 

$`CFP WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        21.99        21.14         2.93         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        16.01        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        52.80 

  CFP MUTATED CFP WILD-TYPE 
         0.33          0.00 
  CFP MUTATED CFP WILD-TYPE 
        51.32        140.38 
  CFP MUTATED CFP WILD-TYPE 
       12.990        20.235 
[1] "0.3 - 51.3 (13.0)"  "0.0 - 140.4 (20.2)"
[1] "hr="     "9200000"
D1805V2, continuous
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CFP MUTATED         1        0        0         4         0         0
  CFP WILD-TYPE      63        1       25       105         8         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CFP MUTATED           0          0          1          0        1         0
  CFP WILD-TYPE        19         10         40         31       34        13
               vv
clus            STAGE IVB
  CFP MUTATED           0
  CFP WILD-TYPE         1
D1805V3, multiclass
            clus
vv           CFP MUTATED CFP WILD-TYPE
  STAGE I              1            63
  STAGE IA             0             1
  STAGE II             0            25
  STAGE IIA            4           105
  STAGE IIB            0             8
  STAGE IIC            0             1
  STAGE III            0            19
  STAGE IIIA           0            10
  STAGE IIIB           1            40
  STAGE IIIC           0            31
  STAGE IV             1            34
  STAGE IVA            0            13
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  CFP MUTATED     1   0   5   1
  CFP WILD-TYPE   8  68 243  40
D1805V4, multiclass
    clus
vv   CFP MUTATED CFP WILD-TYPE
  T1           1             8
  T2           0            68
  T3           5           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
  CFP MUTATED     5   1   1
  CFP WILD-TYPE 215  79  65
D1805V5, multiclass
    clus
vv   CFP MUTATED CFP WILD-TYPE
  N0           5           215
  N1           1            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"
D1805V6, binary
               cls
clus              0   1
  CFP MUTATED     5   1
  CFP WILD-TYPE 278  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  CFP MUTATED      5    1
  CFP WILD-TYPE  278   47
   clus
vv  CFP MUTATED CFP WILD-TYPE
  0           5           278
  1           1            47
[1] 2 2
[1] FALSE
D1805V7, binary
               cls
clus              0   1
  CFP MUTATED     5   2
  CFP WILD-TYPE 165 195
[1] "tbl2"
               cls
clus            [,1] [,2]
  CFP MUTATED      5    2
  CFP WILD-TYPE  165  195
        clus
vv       CFP MUTATED CFP WILD-TYPE
  FEMALE           5           165
  MALE             2           195
[1] 2 2
[1] FALSE
D1805V8, binary
               cls
clus              0   1
  CFP MUTATED     4   3
  CFP WILD-TYPE 313  45
[1] "tbl2"
               cls
clus            [,1] [,2]
  CFP MUTATED      4    3
  CFP WILD-TYPE  313   45
                               clus
vv                              CFP MUTATED CFP WILD-TYPE
  COLON ADENOCARCINOMA                    4           313
  COLON MUCINOUS ADENOCARCINOMA           3            45
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  CFP MUTATED     4   0   1   2
  CFP WILD-TYPE 253   2  21  19
D1805V9, multiclass
    clus
vv   CFP MUTATED CFP WILD-TYPE
  R0           4           253
  R1           0             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"
D1805V10, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CFP MUTATED                                  0     1
  CFP WILD-TYPE                                1     9
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  CFP MUTATED                           0     3
  CFP WILD-TYPE                        19   173
D1805V11, multiclass
                                  clus
vv                                 CFP MUTATED CFP 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(1806) Variable = GNG12 MUTATION ANALYSIS
D1806V1, survival
                 sevent
clus2               0   1
  GNG12 MUTATED     7   1
  GNG12 WILD-TYPE 275  72
  GNG12 MUTATED GNG12 WILD-TYPE 
              8             347 
  GNG12 MUTATED GNG12 WILD-TYPE 
              1              72 
$`GNG12 MUTATED`
TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3663 TCGA-AD-6889 TCGA-AZ-6598 TCGA-DM-A1HB 
       22.06        19.66         6.97        56.55        49.41       135.65 
TCGA-G4-6586 TCGA-G4-6628 
       35.80        52.80 

$`GNG12 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37         4.21         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        26.17        91.79        46.75 

  GNG12 MUTATED GNG12 WILD-TYPE 
           6.97            0.00 
  GNG12 MUTATED GNG12 WILD-TYPE 
         135.65          140.38 
  GNG12 MUTATED GNG12 WILD-TYPE 
         42.605          20.020 
[1] "7.0 - 135.7 (42.6)" "0.0 - 140.4 (20.0)"
[1] "hr=" "2.9"
D1806V2, 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       23       106         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        19         10         40         30       35        13
                 vv
clus              STAGE IVB
  GNG12 MUTATED           0
  GNG12 WILD-TYPE         1
D1806V3, multiclass
            clus
vv           GNG12 MUTATED GNG12 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              3             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GNG12 MUTATED     0   1   6   1
  GNG12 WILD-TYPE   9  67 242  40
D1806V4, multiclass
    clus
vv   GNG12 MUTATED GNG12 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             6             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
  GNG12 MUTATED     6   2   0
  GNG12 WILD-TYPE 214  78  66
D1806V5, multiclass
    clus
vv   GNG12 MUTATED GNG12 WILD-TYPE
  N0             6             214
  N1             2              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"
D1806V6, binary
                 cls
clus                0   1
  GNG12 MUTATED     6   0
  GNG12 WILD-TYPE 277  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNG12 MUTATED      6    0
  GNG12 WILD-TYPE  277   48
   clus
vv  GNG12 MUTATED GNG12 WILD-TYPE
  0             6             277
  1             0              48
[1] 2 2
[1] FALSE
D1806V7, 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
D1806V8, binary
                 cls
clus                0   1
  GNG12 MUTATED     7   1
  GNG12 WILD-TYPE 310  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNG12 MUTATED      7    1
  GNG12 WILD-TYPE  310   47
                               clus
vv                              GNG12 MUTATED GNG12 WILD-TYPE
  COLON ADENOCARCINOMA                      7             310
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  GNG12 MUTATED     5   0   0   0
  GNG12 WILD-TYPE 252   2  22  21
D1806V9, multiclass
    clus
vv   GNG12 MUTATED GNG12 WILD-TYPE
  R0             5             252
  R1             0               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"
D1806V10, 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
D1806V11, 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(1807) Variable = SPATA6 MUTATION ANALYSIS
D1807V1, survival
                  sevent
clus2                0   1
  SPATA6 MUTATED     4   2
  SPATA6 WILD-TYPE 278  71
  SPATA6 MUTATED SPATA6 WILD-TYPE 
               6              349 
  SPATA6 MUTATED SPATA6 WILD-TYPE 
               2               71 
$`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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14         2.93         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-5864 TCGA-CM-5868 TCGA-CM-6161 
       16.01        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 
       18.25         1.32        43.27        15.12        17.85        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 
        0.53        35.41        19.43       107.67        74.56        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  SPATA6 MUTATED SPATA6 WILD-TYPE 
            1.02             0.00 
  SPATA6 MUTATED SPATA6 WILD-TYPE 
          124.27           140.38 
  SPATA6 MUTATED SPATA6 WILD-TYPE 
          20.515           20.190 
[1] "1.0 - 124.3 (20.5)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D1807V2, 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       24       109         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SPATA6 MUTATED           0          0          3          0        1
  SPATA6 WILD-TYPE        19         10         38         31       34
                  vv
clus               STAGE IVA STAGE IVB
  SPATA6 MUTATED           0         0
  SPATA6 WILD-TYPE        13         1
D1807V3, multiclass
            clus
vv           SPATA6 MUTATED SPATA6 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               0              109
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              3               38
  STAGE IIIC              0               31
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SPATA6 MUTATED     0   1   5   0
  SPATA6 WILD-TYPE   9  67 243  41
D1807V4, multiclass
    clus
vv   SPATA6 MUTATED SPATA6 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              5              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
  SPATA6 MUTATED     2   4   0
  SPATA6 WILD-TYPE 218  76  66
D1807V5, multiclass
    clus
vv   SPATA6 MUTATED SPATA6 WILD-TYPE
  N0              2              218
  N1              4               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
  SPATA6 MUTATED     3   1
  SPATA6 WILD-TYPE 280  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPATA6 MUTATED      3    1
  SPATA6 WILD-TYPE  280   47
   clus
vv  SPATA6 MUTATED SPATA6 WILD-TYPE
  0              3              280
  1              1               47
[1] 2 2
[1] FALSE
D1807V7, 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
D1807V8, binary
                  cls
clus                 0   1
  SPATA6 MUTATED     3   3
  SPATA6 WILD-TYPE 314  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPATA6 MUTATED      3    3
  SPATA6 WILD-TYPE  314   45
                               clus
vv                              SPATA6 MUTATED SPATA6 WILD-TYPE
  COLON ADENOCARCINOMA                       3              314
  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 252   2  22  20
D1807V9, multiclass
    clus
vv   SPATA6 MUTATED SPATA6 WILD-TYPE
  R0              5              252
  R1              0                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"
D1807V10, 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
D1807V11, 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(1808) Variable = BRD2 MUTATION ANALYSIS
D1808V1, survival
                sevent
clus2              0   1
  BRD2 MUTATED     7   2
  BRD2 WILD-TYPE 275  71
  BRD2 MUTATED BRD2 WILD-TYPE 
             9            346 
  BRD2 MUTATED BRD2 WILD-TYPE 
             2             71 
$`BRD2 MUTATED`
TCGA-A6-3809 TCGA-AA-3821 TCGA-AZ-6599 TCGA-CM-4743 TCGA-CM-4746 TCGA-D5-6924 
       32.75         1.02         6.77        23.05        37.02        14.30 
TCGA-DM-A0X9 TCGA-G4-6588 TCGA-G4-6626 
      119.70        26.17        46.75 

$`BRD2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 
       10.06        35.05        33.04         0.99        25.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 
        2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        11.38        10.26        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 
       13.78        35.80        91.79        52.80 

  BRD2 MUTATED BRD2 WILD-TYPE 
          1.02           0.00 
  BRD2 MUTATED BRD2 WILD-TYPE 
        119.70         140.38 
  BRD2 MUTATED BRD2 WILD-TYPE 
         26.17          20.07 
[1] "1.0 - 119.7 (26.2)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.1"
D1808V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BRD2 MUTATED         3        0        0         5         2         0
  BRD2 WILD-TYPE      61        1       25       104         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        19         10         41         31       35        13
                vv
clus             STAGE IVB
  BRD2 MUTATED           0
  BRD2 WILD-TYPE         1
D1808V3, multiclass
            clus
vv           BRD2 MUTATED BRD2 WILD-TYPE
  STAGE I               3             61
  STAGE IA              0              1
  STAGE II              0             25
  STAGE IIA             5            104
  STAGE IIB             2              6
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  BRD2 MUTATED     0   3   5   2
  BRD2 WILD-TYPE   9  65 243  39
D1808V4, multiclass
    clus
vv   BRD2 MUTATED BRD2 WILD-TYPE
  T1            0              9
  T2            3             65
  T3            5            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    10   0   0
  BRD2 WILD-TYPE 210  80  66
D1808V5, multiclass
    clus
vv   BRD2 MUTATED BRD2 WILD-TYPE
  N0           10            210
  N1            0             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
  BRD2 MUTATED     8   0
  BRD2 WILD-TYPE 275  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD2 MUTATED      8    0
  BRD2 WILD-TYPE  275   48
   clus
vv  BRD2 MUTATED BRD2 WILD-TYPE
  0            8            275
  1            0             48
[1] 2 2
[1] FALSE
D1808V7, binary
                cls
clus               0   1
  BRD2 MUTATED     5   5
  BRD2 WILD-TYPE 165 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD2 MUTATED      5    5
  BRD2 WILD-TYPE  165  192
        clus
vv       BRD2 MUTATED BRD2 WILD-TYPE
  FEMALE            5            165
  MALE              5            192
[1] 2 2
[1] FALSE
D1808V8, binary
                cls
clus               0   1
  BRD2 MUTATED     8   2
  BRD2 WILD-TYPE 309  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD2 MUTATED      8    2
  BRD2 WILD-TYPE  309   46
                               clus
vv                              BRD2 MUTATED BRD2 WILD-TYPE
  COLON ADENOCARCINOMA                     8            309
  COLON MUCINOUS ADENOCARCINOMA            2             46
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  BRD2 MUTATED     7   0   0   1
  BRD2 WILD-TYPE 250   2  22  20
D1808V9, multiclass
    clus
vv   BRD2 MUTATED BRD2 WILD-TYPE
  R0            7            250
  R1            0              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"
D1808V10, 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
D1808V11, 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(1809) Variable = DSCAM MUTATION ANALYSIS
D1809V1, survival
                 sevent
clus2               0   1
  DSCAM MUTATED    22  10
  DSCAM WILD-TYPE 260  63
  DSCAM MUTATED DSCAM WILD-TYPE 
             32             323 
  DSCAM MUTATED DSCAM WILD-TYPE 
             10              63 
$`DSCAM MUTATED`
TCGA-A6-5666 TCGA-A6-6780 TCGA-AA-3510 TCGA-AA-3678 TCGA-AA-3815 TCGA-AA-3867 
       32.71        20.12        63.98        47.01        33.04        24.03 
TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3977 TCGA-AA-A010 TCGA-AA-A01R 
        2.01        33.01        24.00        25.02        34.98        35.01 
TCGA-AD-6899 TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-4682 TCGA-AZ-6598 TCGA-AZ-6601 
        5.79        27.09        58.39        22.36        49.41       100.01 
TCGA-AZ-6603 TCGA-CA-6717 TCGA-CM-6171 TCGA-D5-5538 TCGA-D5-6537 TCGA-D5-6541 
       29.56         0.33        14.04        12.26         4.80        15.58 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-DM-A28F TCGA-F4-6459 TCGA-F4-6809 
        9.44        11.64         1.51        35.97         8.61        13.25 
TCGA-F4-6854 TCGA-G4-6309 
        0.53        51.75 

$`DSCAM WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01         0.92        50.04        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        53.00        17.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       31.00        12.99        24.00        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 
       21.37         4.21        56.55         0.79         0.72        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       15.75         0.20        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6605 
       83.80        62.79        61.41         6.77        12.10         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.26         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       12.03        45.40        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 
       18.25         1.32        43.27        15.12        17.85        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 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-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       14.30         9.04        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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G 
      135.65       139.17         6.12        81.37       119.93        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
      117.07        98.24        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6855 
        1.55        16.31        29.59        16.24        33.67        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  DSCAM MUTATED DSCAM WILD-TYPE 
           0.33            0.00 
  DSCAM MUTATED DSCAM WILD-TYPE 
         100.01          140.38 
  DSCAM MUTATED DSCAM WILD-TYPE 
         24.015          19.990 
[1] "0.3 - 100.0 (24.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.5"
D1809V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DSCAM MUTATED         2        0        3        11         2         1
  DSCAM WILD-TYPE      62        1       22        98         6         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DSCAM MUTATED           3          0          5          1        2         2
  DSCAM WILD-TYPE        16         10         36         30       33        11
                 vv
clus              STAGE IVB
  DSCAM MUTATED           0
  DSCAM WILD-TYPE         1
D1809V3, multiclass
            clus
vv           DSCAM MUTATED DSCAM WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA             11              98
  STAGE IIB              2               6
  STAGE IIC              1               0
  STAGE III              3              16
  STAGE IIIA             0              10
  STAGE IIIB             5              36
  STAGE IIIC             1              30
  STAGE IV               2              33
  STAGE IVA              2              11
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DSCAM MUTATED     0   5  25   4
  DSCAM WILD-TYPE   9  63 223  37
D1809V4, multiclass
    clus
vv   DSCAM MUTATED DSCAM WILD-TYPE
  T1             0               9
  T2             5              63
  T3            25             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
  DSCAM MUTATED    21   7   6
  DSCAM WILD-TYPE 199  73  60
D1809V5, multiclass
    clus
vv   DSCAM MUTATED DSCAM WILD-TYPE
  N0            21             199
  N1             7              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"
D1809V6, binary
                 cls
clus                0   1
  DSCAM MUTATED    24   4
  DSCAM WILD-TYPE 259  44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DSCAM MUTATED     24    4
  DSCAM WILD-TYPE  259   44
   clus
vv  DSCAM MUTATED DSCAM WILD-TYPE
  0            24             259
  1             4              44
[1] 2 2
[1] FALSE
D1809V7, binary
                 cls
clus                0   1
  DSCAM MUTATED    15  19
  DSCAM WILD-TYPE 155 178
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DSCAM MUTATED     15   19
  DSCAM WILD-TYPE  155  178
        clus
vv       DSCAM MUTATED DSCAM WILD-TYPE
  FEMALE            15             155
  MALE              19             178
[1] 2 2
[1] FALSE
D1809V8, binary
                 cls
clus                0   1
  DSCAM MUTATED    26   8
  DSCAM WILD-TYPE 291  40
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DSCAM MUTATED     26    8
  DSCAM WILD-TYPE  291   40
                               clus
vv                              DSCAM MUTATED DSCAM WILD-TYPE
  COLON ADENOCARCINOMA                     26             291
  COLON MUCINOUS ADENOCARCINOMA             8              40
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DSCAM MUTATED    23   0   2   1
  DSCAM WILD-TYPE 234   2  20  20
D1809V9, multiclass
    clus
vv   DSCAM MUTATED DSCAM WILD-TYPE
  R0            23             234
  R1             0               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"
D1809V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DSCAM MUTATED                                  0     1
  DSCAM WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DSCAM MUTATED                           1    20
  DSCAM WILD-TYPE                        18   156
D1809V11, multiclass
                                  clus
vv                                 DSCAM MUTATED DSCAM WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               9
  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(1810) Variable = SMPDL3B MUTATION ANALYSIS
D1810V1, survival
                   sevent
clus2                 0   1
  SMPDL3B MUTATED     6   3
  SMPDL3B WILD-TYPE 276  70
  SMPDL3B MUTATED SMPDL3B WILD-TYPE 
                9               346 
  SMPDL3B MUTATED SMPDL3B WILD-TYPE 
                3                70 
$`SMPDL3B MUTATED`
TCGA-AA-3662 TCGA-AA-3864 TCGA-AA-3975 TCGA-AY-5543 TCGA-AZ-6598 TCGA-CK-5916 
        6.05        53.00        34.06        15.75        49.41        21.14 
TCGA-CM-5860 TCGA-F4-6570 TCGA-G4-6321 
       16.01         6.18        22.09 

$`SMPDL3B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 
        0.20        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-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        61.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32        21.99         2.93         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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.38        13.45        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 
       51.75        45.11        36.72        36.00        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  SMPDL3B MUTATED SMPDL3B WILD-TYPE 
             6.05              0.00 
  SMPDL3B MUTATED SMPDL3B WILD-TYPE 
            53.00            140.38 
  SMPDL3B MUTATED SMPDL3B WILD-TYPE 
           21.140            20.155 
[1] "6.0 - 53.0 (21.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.6"
D1810V2, 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       23       107         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SMPDL3B MUTATED           1          0          0          0        1
  SMPDL3B WILD-TYPE        18         10         41         31       34
                   vv
clus                STAGE IVA STAGE IVB
  SMPDL3B MUTATED           1         0
  SMPDL3B WILD-TYPE        12         1
D1810V3, multiclass
            clus
vv           SMPDL3B MUTATED SMPDL3B WILD-TYPE
  STAGE I                  2                62
  STAGE IA                 0                 1
  STAGE II                 2                23
  STAGE IIA                2               107
  STAGE IIB                0                 8
  STAGE IIC                0                 1
  STAGE III                1                18
  STAGE IIIA               0                10
  STAGE IIIB               0                41
  STAGE IIIC               0                31
  STAGE IV                 1                34
  STAGE IVA                1                12
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 243  40
D1810V4, multiclass
    clus
vv   SMPDL3B MUTATED SMPDL3B WILD-TYPE
  T1               1                 8
  T2               2                66
  T3               5               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
  SMPDL3B MUTATED     6   2   1
  SMPDL3B WILD-TYPE 214  78  65
D1810V5, multiclass
    clus
vv   SMPDL3B MUTATED SMPDL3B WILD-TYPE
  N0               6               214
  N1               2                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"
D1810V6, binary
                   cls
clus                  0   1
  SMPDL3B MUTATED     5   2
  SMPDL3B WILD-TYPE 278  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMPDL3B MUTATED      5    2
  SMPDL3B WILD-TYPE  278   46
   clus
vv  SMPDL3B MUTATED SMPDL3B WILD-TYPE
  0               5               278
  1               2                46
[1] 2 2
[1] FALSE
D1810V7, 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
D1810V8, binary
                   cls
clus                  0   1
  SMPDL3B MUTATED     9   0
  SMPDL3B WILD-TYPE 308  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMPDL3B MUTATED      9    0
  SMPDL3B WILD-TYPE  308   48
                               clus
vv                              SMPDL3B MUTATED SMPDL3B WILD-TYPE
  COLON ADENOCARCINOMA                        9               308
  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 251   2  21  20
D1810V9, multiclass
    clus
vv   SMPDL3B MUTATED SMPDL3B WILD-TYPE
  R0               6               251
  R1               0                 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"
D1810V10, 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
D1810V11, 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(1811) Variable = RNF20 MUTATION ANALYSIS
D1811V1, survival
                 sevent
clus2               0   1
  RNF20 MUTATED    15   3
  RNF20 WILD-TYPE 267  70
  RNF20 MUTATED RNF20 WILD-TYPE 
             18             337 
  RNF20 MUTATED RNF20 WILD-TYPE 
              3              70 
$`RNF20 MUTATED`
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3543 TCGA-AA-3680 TCGA-AA-3685 
       23.87        20.12        19.66         0.99        11.01        37.05 
TCGA-AA-3947 TCGA-AA-A01I TCGA-AD-6964 TCGA-AU-6004 TCGA-AY-6197 TCGA-AZ-6598 
       33.01        31.00        10.88        27.09        21.44        49.41 
TCGA-CM-4746 TCGA-CM-6162 TCGA-CM-6677 TCGA-D5-6928 TCGA-DM-A28H TCGA-G4-6628 
       37.02        12.00        11.08        11.64       117.07        52.80 

$`RNF20 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 
       14.01         0.92        50.04        47.01        15.02         5.98 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.20        14.50        16.31         0.95        15.75         0.20 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 
       46.75 

  RNF20 MUTATED RNF20 WILD-TYPE 
           0.99            0.00 
  RNF20 MUTATED RNF20 WILD-TYPE 
         117.07          140.38 
  RNF20 MUTATED RNF20 WILD-TYPE 
         22.655          20.020 
[1] "1.0 - 117.1 (22.7)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.4"
D1811V2, 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       23       105         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        19         10         39         29       34        13
                 vv
clus              STAGE IVB
  RNF20 MUTATED           0
  RNF20 WILD-TYPE         1
D1811V3, multiclass
            clus
vv           RNF20 MUTATED RNF20 WILD-TYPE
  STAGE I                5              59
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              4             105
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             2              29
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RNF20 MUTATED     0   5   9   4
  RNF20 WILD-TYPE   9  63 239  37
D1811V4, multiclass
    clus
vv   RNF20 MUTATED RNF20 WILD-TYPE
  T1             0               9
  T2             5              63
  T3             9             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
  RNF20 MUTATED    12   3   3
  RNF20 WILD-TYPE 208  77  63
D1811V5, multiclass
    clus
vv   RNF20 MUTATED RNF20 WILD-TYPE
  N0            12             208
  N1             3              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"
D1811V6, binary
                 cls
clus                0   1
  RNF20 MUTATED    12   1
  RNF20 WILD-TYPE 271  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF20 MUTATED     12    1
  RNF20 WILD-TYPE  271   47
   clus
vv  RNF20 MUTATED RNF20 WILD-TYPE
  0            12             271
  1             1              47
[1] 2 2
[1] FALSE
D1811V7, 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
D1811V8, binary
                 cls
clus                0   1
  RNF20 MUTATED    12   6
  RNF20 WILD-TYPE 305  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF20 MUTATED     12    6
  RNF20 WILD-TYPE  305   42
                               clus
vv                              RNF20 MUTATED RNF20 WILD-TYPE
  COLON ADENOCARCINOMA                     12             305
  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 245   2  21  21
D1811V9, multiclass
    clus
vv   RNF20 MUTATED RNF20 WILD-TYPE
  R0            12             245
  R1             0               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"
D1811V10, 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
D1811V11, 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(1812) Variable = ATP2B4 MUTATION ANALYSIS
D1812V1, survival
                  sevent
clus2                0   1
  ATP2B4 MUTATED    11   5
  ATP2B4 WILD-TYPE 271  68
  ATP2B4 MUTATED ATP2B4 WILD-TYPE 
              16              339 
  ATP2B4 MUTATED ATP2B4 WILD-TYPE 
               5               68 
$`ATP2B4 MUTATED`
TCGA-A6-5665 TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-A010 TCGA-AA-A024 TCGA-AD-6889 
       22.06        24.00         2.01        34.98        39.06        56.55 
TCGA-AZ-5403 TCGA-AZ-6601 TCGA-CK-5914 TCGA-CM-5862 TCGA-CM-6161 TCGA-CM-6165 
       62.79       100.01        21.99         5.03        15.02        16.04 
TCGA-CM-6676 TCGA-DM-A28G TCGA-F4-6856 TCGA-G4-6588 
       11.08        60.79        19.43        26.17 

$`ATP2B4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       26.01        37.02        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37         4.21         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 
       58.39         1.41         5.13        83.80        22.36        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 
      102.44        40.34        15.62        49.08        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
      119.93        35.97       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 
       16.24        33.67        13.25         0.53        35.41       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  ATP2B4 MUTATED ATP2B4 WILD-TYPE 
            2.01             0.00 
  ATP2B4 MUTATED ATP2B4 WILD-TYPE 
          100.01           140.38 
  ATP2B4 MUTATED ATP2B4 WILD-TYPE 
           23.03            20.02 
[1] "2.0 - 100.0 (23.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.2"
D1812V2, 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       22       101         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP2B4 MUTATED           0          0          1          0        0
  ATP2B4 WILD-TYPE        19         10         40         31       35
                  vv
clus               STAGE IVA STAGE IVB
  ATP2B4 MUTATED           1         0
  ATP2B4 WILD-TYPE        12         1
D1812V3, multiclass
            clus
vv           ATP2B4 MUTATED ATP2B4 WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                3               22
  STAGE IIA               8              101
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of 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  64 235  40
D1812V4, multiclass
    clus
vv   ATP2B4 MUTATED ATP2B4 WILD-TYPE
  T1              0                9
  T2              4               64
  T3             13              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
  ATP2B4 MUTATED    16   2   0
  ATP2B4 WILD-TYPE 204  78  66
D1812V5, multiclass
    clus
vv   ATP2B4 MUTATED ATP2B4 WILD-TYPE
  N0             16              204
  N1              2               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"
D1812V6, binary
                  cls
clus                 0   1
  ATP2B4 MUTATED    14   1
  ATP2B4 WILD-TYPE 269  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2B4 MUTATED     14    1
  ATP2B4 WILD-TYPE  269   47
   clus
vv  ATP2B4 MUTATED ATP2B4 WILD-TYPE
  0             14              269
  1              1               47
[1] 2 2
[1] FALSE
D1812V7, 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
D1812V8, binary
                  cls
clus                 0   1
  ATP2B4 MUTATED    14   4
  ATP2B4 WILD-TYPE 303  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2B4 MUTATED     14    4
  ATP2B4 WILD-TYPE  303   44
                               clus
vv                              ATP2B4 MUTATED ATP2B4 WILD-TYPE
  COLON ADENOCARCINOMA                      14              303
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ATP2B4 MUTATED    11   0   0   2
  ATP2B4 WILD-TYPE 246   2  22  19
D1812V9, multiclass
    clus
vv   ATP2B4 MUTATED ATP2B4 WILD-TYPE
  R0             11              246
  R1              0                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"
D1812V10, 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
D1812V11, 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(1813) Variable = ULK2 MUTATION ANALYSIS
D1813V1, survival
                sevent
clus2              0   1
  ULK2 MUTATED     8   4
  ULK2 WILD-TYPE 274  69
  ULK2 MUTATED ULK2 WILD-TYPE 
            12            343 
  ULK2 MUTATED ULK2 WILD-TYPE 
             4             69 
$`ULK2 MUTATED`
TCGA-AA-3492 TCGA-AA-3833 TCGA-AA-A00N TCGA-AA-A01R TCGA-AU-6004 TCGA-AZ-4315 
        3.02        15.95         4.01        35.01        27.09        58.39 
TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CK-5913 TCGA-CM-5861 TCGA-DM-A1HB TCGA-F4-6703 
       49.41       100.01        51.32        15.02       135.65        35.87 

$`ULK2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       17.98        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
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        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       61.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 
      102.44        40.34        15.62        49.08        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 
       98.24         8.61        13.38        13.45         6.18         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  ULK2 MUTATED ULK2 WILD-TYPE 
          3.02           0.00 
  ULK2 MUTATED ULK2 WILD-TYPE 
        135.65         140.38 
  ULK2 MUTATED ULK2 WILD-TYPE 
         35.44          20.02 
[1] "3.0 - 135.7 (35.4)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1"  
D1813V2, 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       22       104         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        18         10         40         31       35        13
                vv
clus             STAGE IVB
  ULK2 MUTATED           0
  ULK2 WILD-TYPE         1
D1813V3, multiclass
            clus
vv           ULK2 MUTATED ULK2 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              3             22
  STAGE IIA             5            104
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            0             31
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ULK2 MUTATED     0   1  10   1
  ULK2 WILD-TYPE   9  67 238  40
D1813V4, multiclass
    clus
vv   ULK2 MUTATED ULK2 WILD-TYPE
  T1            0              9
  T2            1             67
  T3           10            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
  ULK2 MUTATED    10   1   1
  ULK2 WILD-TYPE 210  79  65
D1813V5, multiclass
    clus
vv   ULK2 MUTATED ULK2 WILD-TYPE
  N0           10            210
  N1            1             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"
D1813V6, binary
                cls
clus               0   1
  ULK2 MUTATED    10   0
  ULK2 WILD-TYPE 273  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  ULK2 MUTATED     10    0
  ULK2 WILD-TYPE  273   48
   clus
vv  ULK2 MUTATED ULK2 WILD-TYPE
  0           10            273
  1            0             48
[1] 2 2
[1] FALSE
D1813V7, 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
D1813V8, binary
                cls
clus               0   1
  ULK2 MUTATED    10   2
  ULK2 WILD-TYPE 307  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  ULK2 MUTATED     10    2
  ULK2 WILD-TYPE  307   46
                               clus
vv                              ULK2 MUTATED ULK2 WILD-TYPE
  COLON ADENOCARCINOMA                    10            307
  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 249   2  22  20
D1813V9, multiclass
    clus
vv   ULK2 MUTATED ULK2 WILD-TYPE
  R0            8            249
  R1            0              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"
D1813V10, 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
D1813V11, 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(1814) Variable = TAS1R3 MUTATION ANALYSIS
D1814V1, survival
                  sevent
clus2                0   1
  TAS1R3 MUTATED     6   1
  TAS1R3 WILD-TYPE 276  72
  TAS1R3 MUTATED TAS1R3 WILD-TYPE 
               7              348 
  TAS1R3 MUTATED TAS1R3 WILD-TYPE 
               1               72 
$`TAS1R3 MUTATED`
TCGA-A6-6781 TCGA-AY-6197 TCGA-CK-5916 TCGA-CM-4743 TCGA-CM-5868 TCGA-CM-6679 
       19.66        21.44        21.14        23.05        17.03        10.06 
TCGA-G4-6588 
       26.17 

$`TAS1R3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        15.75         0.20        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93         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        16.01 
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-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.08        11.01        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        52.80 

  TAS1R3 MUTATED TAS1R3 WILD-TYPE 
           10.06             0.00 
  TAS1R3 MUTATED TAS1R3 WILD-TYPE 
           26.17           140.38 
  TAS1R3 MUTATED TAS1R3 WILD-TYPE 
          21.140           20.155 
[1] "10.1 - 26.2 (21.1)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D1814V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TAS1R3 MUTATED         1        0        0         4         0         0
  TAS1R3 WILD-TYPE      63        1       25       105         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TAS1R3 MUTATED           0          0          0          1        0
  TAS1R3 WILD-TYPE        19         10         41         30       35
                  vv
clus               STAGE IVA STAGE IVB
  TAS1R3 MUTATED           1         0
  TAS1R3 WILD-TYPE        12         1
D1814V3, multiclass
            clus
vv           TAS1R3 MUTATED TAS1R3 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               4              105
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               1               12
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TAS1R3 MUTATED     1   0   4   2
  TAS1R3 WILD-TYPE   8  68 244  39
D1814V4, multiclass
    clus
vv   TAS1R3 MUTATED TAS1R3 WILD-TYPE
  T1              1                8
  T2              0               68
  T3              4              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
  TAS1R3 MUTATED     5   2   0
  TAS1R3 WILD-TYPE 215  78  66
D1814V5, multiclass
    clus
vv   TAS1R3 MUTATED TAS1R3 WILD-TYPE
  N0              5              215
  N1              2               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"
D1814V6, binary
                  cls
clus                 0   1
  TAS1R3 MUTATED     4   1
  TAS1R3 WILD-TYPE 279  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TAS1R3 MUTATED      4    1
  TAS1R3 WILD-TYPE  279   47
   clus
vv  TAS1R3 MUTATED TAS1R3 WILD-TYPE
  0              4              279
  1              1               47
[1] 2 2
[1] FALSE
D1814V7, binary
                  cls
clus                 0   1
  TAS1R3 MUTATED     3   4
  TAS1R3 WILD-TYPE 167 193
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TAS1R3 MUTATED      3    4
  TAS1R3 WILD-TYPE  167  193
        clus
vv       TAS1R3 MUTATED TAS1R3 WILD-TYPE
  FEMALE              3              167
  MALE                4              193
[1] 2 2
[1] FALSE
D1814V8, binary
                  cls
clus                 0   1
  TAS1R3 MUTATED     6   1
  TAS1R3 WILD-TYPE 311  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TAS1R3 MUTATED      6    1
  TAS1R3 WILD-TYPE  311   47
                               clus
vv                              TAS1R3 MUTATED TAS1R3 WILD-TYPE
  COLON ADENOCARCINOMA                       6              311
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TAS1R3 MUTATED     6   0   0   1
  TAS1R3 WILD-TYPE 251   2  22  20
D1814V9, multiclass
    clus
vv   TAS1R3 MUTATED TAS1R3 WILD-TYPE
  R0              6              251
  R1              0                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"
D1814V10, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TAS1R3 MUTATED                                  0     0
  TAS1R3 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TAS1R3 MUTATED                           0     7
  TAS1R3 WILD-TYPE                        19   169
D1814V11, multiclass
                                  clus
vv                                 TAS1R3 MUTATED TAS1R3 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(1815) Variable = ZNF185 MUTATION ANALYSIS
D1815V1, survival
                  sevent
clus2                0   1
  ZNF185 MUTATED     9   0
  ZNF185 WILD-TYPE 273  73
  ZNF185 MUTATED ZNF185 WILD-TYPE 
               9              346 
  ZNF185 MUTATED ZNF185 WILD-TYPE 
               0               73 
$`ZNF185 MUTATED`
TCGA-A6-5665 TCGA-A6-6138 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3947 TCGA-AD-5900 
       22.06        22.52        85.05        26.99        33.01         0.07 
TCGA-CM-6675 TCGA-D5-6920 TCGA-G4-6299 
       13.05        12.39        74.56 

$`ZNF185 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.09        32.71        27.09         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.03        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        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        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58         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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      107.67        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  ZNF185 MUTATED ZNF185 WILD-TYPE 
            0.07             0.00 
  ZNF185 MUTATED ZNF185 WILD-TYPE 
           85.05           140.38 
  ZNF185 MUTATED ZNF185 WILD-TYPE 
           22.52            20.07 
[1] "0.1 - 85.0 (22.5)"  "0.0 - 140.4 (20.1)"
[1] "hr="     "2.6e+07"
D1815V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF185 MUTATED         2        0        0         4         1         0
  ZNF185 WILD-TYPE      62        1       25       105         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF185 MUTATED           1          0          0          1        0
  ZNF185 WILD-TYPE        18         10         41         30       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF185 MUTATED           0         1
  ZNF185 WILD-TYPE        13         0
D1815V3, multiclass
            clus
vv           ZNF185 MUTATED ZNF185 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               4              105
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  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  66 241  40
D1815V4, multiclass
    clus
vv   ZNF185 MUTATED ZNF185 WILD-TYPE
  T1              0                9
  T2              2               66
  T3              7              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
  ZNF185 MUTATED     8   0   2
  ZNF185 WILD-TYPE 212  80  64
D1815V5, multiclass
    clus
vv   ZNF185 MUTATED ZNF185 WILD-TYPE
  N0              8              212
  N1              0               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"
D1815V6, binary
                  cls
clus                 0   1
  ZNF185 MUTATED     8   1
  ZNF185 WILD-TYPE 275  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF185 MUTATED      8    1
  ZNF185 WILD-TYPE  275   47
   clus
vv  ZNF185 MUTATED ZNF185 WILD-TYPE
  0              8              275
  1              1               47
[1] 2 2
[1] FALSE
D1815V7, 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
D1815V8, binary
                  cls
clus                 0   1
  ZNF185 MUTATED     8   2
  ZNF185 WILD-TYPE 309  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF185 MUTATED      8    2
  ZNF185 WILD-TYPE  309   46
                               clus
vv                              ZNF185 MUTATED ZNF185 WILD-TYPE
  COLON ADENOCARCINOMA                       8              309
  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 248   2  22  21
D1815V9, multiclass
    clus
vv   ZNF185 MUTATED ZNF185 WILD-TYPE
  R0              9              248
  R1              0                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"
D1815V10, 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
D1815V11, 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(1816) Variable = ZNF142 MUTATION ANALYSIS
D1816V1, survival
                  sevent
clus2                0   1
  ZNF142 MUTATED    10   4
  ZNF142 WILD-TYPE 272  69
  ZNF142 MUTATED ZNF142 WILD-TYPE 
              14              341 
  ZNF142 MUTATED ZNF142 WILD-TYPE 
               4               69 
$`ZNF142 MUTATED`
TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3663 TCGA-AA-3821 TCGA-AA-3864 TCGA-AA-A00N 
       22.06         3.02         6.97         1.02        53.00         4.01 
TCGA-AA-A010 TCGA-AA-A02W TCGA-AD-5900 TCGA-AZ-6598 TCGA-CM-4743 TCGA-D5-6540 
       34.98        41.00         0.07        49.41        23.05        16.14 
TCGA-F4-6570 TCGA-G4-6586 
        6.18        35.80 

$`ZNF142 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       33.04         0.99        25.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-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        13.38        13.45        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        26.17        91.79        46.75        52.80 

  ZNF142 MUTATED ZNF142 WILD-TYPE 
            0.07             0.00 
  ZNF142 MUTATED ZNF142 WILD-TYPE 
           53.00           140.38 
  ZNF142 MUTATED ZNF142 WILD-TYPE 
           19.10            20.19 
[1] "0.1 - 53.0 (19.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.7"
D1816V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF142 MUTATED         4        0        4         4         2         0
  ZNF142 WILD-TYPE      60        1       21       105         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF142 MUTATED           0          0          0          0        0
  ZNF142 WILD-TYPE        19         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF142 MUTATED           0         0
  ZNF142 WILD-TYPE        13         1
D1816V3, multiclass
            clus
vv           ZNF142 MUTATED ZNF142 WILD-TYPE
  STAGE I                 4               60
  STAGE IA                0                1
  STAGE II                4               21
  STAGE IIA               4              105
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF142 MUTATED     0   4   8   2
  ZNF142 WILD-TYPE   9  64 240  39
D1816V4, multiclass
    clus
vv   ZNF142 MUTATED ZNF142 WILD-TYPE
  T1              0                9
  T2              4               64
  T3              8              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
  ZNF142 MUTATED    14   0   0
  ZNF142 WILD-TYPE 206  80  66
D1816V5, multiclass
    clus
vv   ZNF142 MUTATED ZNF142 WILD-TYPE
  N0             14              206
  N1              0               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"
D1816V6, binary
                  cls
clus                 0   1
  ZNF142 MUTATED    12   0
  ZNF142 WILD-TYPE 271  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF142 MUTATED     12    0
  ZNF142 WILD-TYPE  271   48
   clus
vv  ZNF142 MUTATED ZNF142 WILD-TYPE
  0             12              271
  1              0               48
[1] 2 2
[1] FALSE
D1816V7, binary
                  cls
clus                 0   1
  ZNF142 MUTATED     8   6
  ZNF142 WILD-TYPE 162 191
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF142 MUTATED      8    6
  ZNF142 WILD-TYPE  162  191
        clus
vv       ZNF142 MUTATED ZNF142 WILD-TYPE
  FEMALE              8              162
  MALE                6              191
[1] 2 2
[1] FALSE
D1816V8, binary
                  cls
clus                 0   1
  ZNF142 MUTATED    10   4
  ZNF142 WILD-TYPE 307  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF142 MUTATED     10    4
  ZNF142 WILD-TYPE  307   44
                               clus
vv                              ZNF142 MUTATED ZNF142 WILD-TYPE
  COLON ADENOCARCINOMA                      10              307
  COLON MUCINOUS ADENOCARCINOMA              4               44
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF142 MUTATED    13   0   0   0
  ZNF142 WILD-TYPE 244   2  22  21
D1816V9, multiclass
    clus
vv   ZNF142 MUTATED ZNF142 WILD-TYPE
  R0             13              244
  R1              0                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"
D1816V10, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF142 MUTATED                                  0     0
  ZNF142 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF142 MUTATED                           0     7
  ZNF142 WILD-TYPE                        19   169
D1816V11, multiclass
                                  clus
vv                                 ZNF142 MUTATED ZNF142 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(1817) Variable = TBCE MUTATION ANALYSIS
D1817V1, survival
                sevent
clus2              0   1
  TBCE MUTATED     2   0
  TBCE WILD-TYPE 280  73
  TBCE MUTATED TBCE WILD-TYPE 
             2            353 
  TBCE MUTATED TBCE WILD-TYPE 
             0             73 
$`TBCE MUTATED`
TCGA-AA-3977 TCGA-AA-A029 
       25.02        51.98 

$`TBCE WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  TBCE MUTATED TBCE WILD-TYPE 
         25.02           0.00 
  TBCE MUTATED TBCE WILD-TYPE 
         51.98         140.38 
  TBCE MUTATED TBCE WILD-TYPE 
         38.50          20.12 
[1] "25.0 - 52.0 (38.5)" "0.0 - 140.4 (20.1)"
[1] "Remove cluster labels:" "TBCE MUTATED"          
D1817V2, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TBCE MUTATED         0        0        1         1         0         0
  TBCE WILD-TYPE      64        1       24       108         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TBCE MUTATED           0          0          0          0        0         0
  TBCE WILD-TYPE        19         10         41         31       35        13
                vv
clus             STAGE IVB
  TBCE MUTATED           0
  TBCE WILD-TYPE         1
D1817V3, multiclass
[1] "Remove cluster labels:" "TBCE MUTATED"          
clus
  TBCE MUTATED TBCE WILD-TYPE 
             2            356 
    TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810     TCGA-A6-4105 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-A6-5656     TCGA-A6-5657     TCGA-A6-5659     TCGA-A6-5660 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-A6-5661     TCGA-A6-5662     TCGA-A6-5664     TCGA-A6-5665 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-A6-5666     TCGA-A6-6137     TCGA-A6-6138     TCGA-A6-6141 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-A6-6142     TCGA-A6-6648     TCGA-A6-6649     TCGA-A6-6651 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-A6-6652     TCGA-A6-6653     TCGA-A6-6654     TCGA-A6-6780 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-A6-6781     TCGA-A6-6782     TCGA-AA-3489     TCGA-AA-3492 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3496     TCGA-AA-3502     TCGA-AA-3510     TCGA-AA-3511 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3514     TCGA-AA-3516     TCGA-AA-3517     TCGA-AA-3518 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3519     TCGA-AA-3520     TCGA-AA-3521     TCGA-AA-3522 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3524     TCGA-AA-3525     TCGA-AA-3526     TCGA-AA-3527 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3529     TCGA-AA-3530     TCGA-AA-3531     TCGA-AA-3532 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3534     TCGA-AA-3538     TCGA-AA-3542     TCGA-AA-3543 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3544     TCGA-AA-3548     TCGA-AA-3549     TCGA-AA-3552 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3553     TCGA-AA-3554     TCGA-AA-3555     TCGA-AA-3556 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3558     TCGA-AA-3560     TCGA-AA-3561     TCGA-AA-3562 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3655     TCGA-AA-3660     TCGA-AA-3662     TCGA-AA-3663 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3664     TCGA-AA-3666     TCGA-AA-3667     TCGA-AA-3672 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3673     TCGA-AA-3678     TCGA-AA-3679     TCGA-AA-3680 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3681     TCGA-AA-3684     TCGA-AA-3685     TCGA-AA-3688 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3692     TCGA-AA-3693     TCGA-AA-3695     TCGA-AA-3696 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3697     TCGA-AA-3710     TCGA-AA-3712     TCGA-AA-3713 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3715     TCGA-AA-3811     TCGA-AA-3812     TCGA-AA-3814 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3815     TCGA-AA-3818     TCGA-AA-3819     TCGA-AA-3821 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3831     TCGA-AA-3833     TCGA-AA-3837     TCGA-AA-3842 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3844     TCGA-AA-3845     TCGA-AA-3846     TCGA-AA-3848 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3850     TCGA-AA-3851     TCGA-AA-3852     TCGA-AA-3854 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3855     TCGA-AA-3856     TCGA-AA-3858     TCGA-AA-3860 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3861     TCGA-AA-3864     TCGA-AA-3866     TCGA-AA-3867 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3869     TCGA-AA-3870     TCGA-AA-3872     TCGA-AA-3875 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3877     TCGA-AA-3930     TCGA-AA-3939     TCGA-AA-3941 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3947     TCGA-AA-3949     TCGA-AA-3950     TCGA-AA-3952 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3955     TCGA-AA-3956     TCGA-AA-3966     TCGA-AA-3968 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3971     TCGA-AA-3972     TCGA-AA-3973     TCGA-AA-3975 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3976     TCGA-AA-3979     TCGA-AA-3980     TCGA-AA-3982 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3986     TCGA-AA-3989     TCGA-AA-3994     TCGA-AA-A004 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-A00A     TCGA-AA-A00D     TCGA-AA-A00E     TCGA-AA-A00F 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-A00J     TCGA-AA-A00K     TCGA-AA-A00L     TCGA-AA-A00N 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-A00O     TCGA-AA-A00Q     TCGA-AA-A00R     TCGA-AA-A00U 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-A00W     TCGA-AA-A00Z     TCGA-AA-A010     TCGA-AA-A017 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-A01D     TCGA-AA-A01F     TCGA-AA-A01G     TCGA-AA-A01I 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-A01K     TCGA-AA-A01P     TCGA-AA-A01Q     TCGA-AA-A01R 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-A01S     TCGA-AA-A01T     TCGA-AA-A01V     TCGA-AA-A01X 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-A01Z     TCGA-AA-A022     TCGA-AA-A024     TCGA-AA-A02F 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-A02H     TCGA-AA-A02J     TCGA-AA-A02K     TCGA-AA-A02O 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-A02W     TCGA-AA-A02Y     TCGA-AA-A03F     TCGA-AA-A03J 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AD-5900     TCGA-AD-6548     TCGA-AD-6888     TCGA-AD-6889 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AD-6899     TCGA-AU-3779     TCGA-AU-6004     TCGA-AY-4070 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AY-4071     TCGA-AY-5543     TCGA-AY-6196     TCGA-AY-6197 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AY-6386     TCGA-AZ-4315     TCGA-AZ-4323     TCGA-AZ-4616 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AZ-4681     TCGA-AZ-4682     TCGA-AZ-5403     TCGA-AZ-5407 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AZ-6598     TCGA-AZ-6599     TCGA-AZ-6600     TCGA-AZ-6601 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AZ-6605     TCGA-AZ-6606     TCGA-AZ-6607     TCGA-AZ-6608 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CA-5254     TCGA-CA-5255     TCGA-CA-5796     TCGA-CA-5797 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CA-6715     TCGA-CA-6716     TCGA-CA-6717     TCGA-CA-6718 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CA-6719     TCGA-CK-4947     TCGA-CK-4948     TCGA-CK-4950 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CK-4952     TCGA-CK-5912     TCGA-CK-5913     TCGA-CK-5914 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CK-5915     TCGA-CK-5916     TCGA-CK-6746     TCGA-CK-6747 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CK-6748     TCGA-CK-6751     TCGA-CM-4743     TCGA-CM-4744 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CM-4746     TCGA-CM-4747     TCGA-CM-4752     TCGA-CM-5341 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CM-5344     TCGA-CM-5348     TCGA-CM-5349     TCGA-CM-5860 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CM-5861     TCGA-CM-5862     TCGA-CM-5863     TCGA-CM-5864 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CM-5868     TCGA-CM-6161     TCGA-CM-6162     TCGA-CM-6163 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CM-6164     TCGA-CM-6165     TCGA-CM-6166     TCGA-CM-6167 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CM-6168     TCGA-CM-6169     TCGA-CM-6170     TCGA-CM-6171 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CM-6172     TCGA-CM-6674     TCGA-CM-6675     TCGA-CM-6676 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CM-6677     TCGA-CM-6678     TCGA-CM-6679     TCGA-CM-6680 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-D5-5537     TCGA-D5-5538     TCGA-D5-5539     TCGA-D5-5540 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-D5-5541     TCGA-D5-6529     TCGA-D5-6532     TCGA-D5-6533 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-D5-6534     TCGA-D5-6535     TCGA-D5-6536     TCGA-D5-6537 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-D5-6538     TCGA-D5-6539     TCGA-D5-6540     TCGA-D5-6541 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-D5-6898     TCGA-D5-6920     TCGA-D5-6922     TCGA-D5-6923 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-D5-6924     TCGA-D5-6926     TCGA-D5-6927     TCGA-D5-6928 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-D5-6929     TCGA-D5-6930     TCGA-D5-6931     TCGA-D5-6932 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-D5-7000     TCGA-DM-A0X9     TCGA-DM-A0XD     TCGA-DM-A0XF 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-DM-A1D0     TCGA-DM-A1D4     TCGA-DM-A1D6     TCGA-DM-A1D7 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-DM-A1D9     TCGA-DM-A1DA     TCGA-DM-A1DB     TCGA-DM-A1HA 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-DM-A1HB     TCGA-DM-A282     TCGA-DM-A285     TCGA-DM-A28C 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-DM-A28E     TCGA-DM-A28F     TCGA-DM-A28G     TCGA-DM-A28H 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-DM-A28K     TCGA-F4-6459     TCGA-F4-6460     TCGA-F4-6569 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-F4-6570     TCGA-F4-6703     TCGA-F4-6704     TCGA-F4-6805 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-F4-6806     TCGA-F4-6807     TCGA-F4-6808     TCGA-F4-6809 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-F4-6854     TCGA-F4-6855     TCGA-F4-6856     TCGA-G4-6293 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-G4-6299     TCGA-G4-6303     TCGA-G4-6304     TCGA-G4-6306 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-G4-6307     TCGA-G4-6309     TCGA-G4-6310     TCGA-G4-6315 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-G4-6317     TCGA-G4-6321     TCGA-G4-6323     TCGA-G4-6586 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-G4-6588     TCGA-G4-6625     TCGA-G4-6626     TCGA-G4-6628 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
                vv
clus              T1  T2  T3  T4
  TBCE MUTATED     0   1   2   0
  TBCE WILD-TYPE   9  67 246  41
D1817V4, multiclass
    clus
vv   TBCE MUTATED TBCE WILD-TYPE
  T1            0              9
  T2            1             67
  T3            2            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
  TBCE MUTATED     3   0   0
  TBCE WILD-TYPE 217  80  66
D1817V5, multiclass
    clus
vv   TBCE MUTATED TBCE WILD-TYPE
  N0            3            217
  N1            0             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"
D1817V6, binary
                cls
clus               0   1
  TBCE MUTATED     2   0
  TBCE WILD-TYPE 281  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  TBCE MUTATED      2    0
  TBCE WILD-TYPE  281   48
   clus
vv  TBCE MUTATED TBCE WILD-TYPE
  0            2            281
  1            0             48
[1] 2 2
[1] FALSE
D1817V7, binary
                cls
clus               0   1
  TBCE MUTATED     1   2
  TBCE WILD-TYPE 169 195
[1] "tbl2"
                cls
clus             [,1] [,2]
  TBCE MUTATED      1    2
  TBCE WILD-TYPE  169  195
        clus
vv       TBCE MUTATED TBCE WILD-TYPE
  FEMALE            1            169
  MALE              2            195
[1] 2 2
[1] FALSE
D1817V8, binary
                cls
clus               0   1
  TBCE MUTATED     3   0
  TBCE WILD-TYPE 314  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  TBCE MUTATED      3    0
  TBCE WILD-TYPE  314   48
                               clus
vv                              TBCE MUTATED TBCE WILD-TYPE
  COLON ADENOCARCINOMA                     3            314
  COLON MUCINOUS ADENOCARCINOMA            0             48
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TBCE MUTATED     2   0   0   0
  TBCE WILD-TYPE 255   2  22  21
D1817V9, multiclass
[1] "Remove cluster labels:" "TBCE MUTATED"          
clus
  TBCE MUTATED TBCE WILD-TYPE 
             2            300 
    TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810     TCGA-A6-5657 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-A6-5659     TCGA-A6-5661     TCGA-A6-5665     TCGA-A6-6781 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3489     TCGA-AA-3492     TCGA-AA-3496     TCGA-AA-3502 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3510     TCGA-AA-3511     TCGA-AA-3514     TCGA-AA-3517 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3518     TCGA-AA-3519     TCGA-AA-3520     TCGA-AA-3521 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3522     TCGA-AA-3524     TCGA-AA-3525     TCGA-AA-3526 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3527     TCGA-AA-3529     TCGA-AA-3530     TCGA-AA-3531 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3532     TCGA-AA-3534     TCGA-AA-3538     TCGA-AA-3542 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3543     TCGA-AA-3544     TCGA-AA-3548     TCGA-AA-3549 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3552     TCGA-AA-3553     TCGA-AA-3554     TCGA-AA-3555 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3556     TCGA-AA-3558     TCGA-AA-3560     TCGA-AA-3561 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3562     TCGA-AA-3655     TCGA-AA-3660     TCGA-AA-3662 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3663     TCGA-AA-3664     TCGA-AA-3666     TCGA-AA-3667 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3672     TCGA-AA-3673     TCGA-AA-3678     TCGA-AA-3679 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3680     TCGA-AA-3681     TCGA-AA-3684     TCGA-AA-3685 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3688     TCGA-AA-3692     TCGA-AA-3693     TCGA-AA-3695 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3696     TCGA-AA-3697     TCGA-AA-3710     TCGA-AA-3712 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3713     TCGA-AA-3715     TCGA-AA-3811     TCGA-AA-3812 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3814     TCGA-AA-3815     TCGA-AA-3818     TCGA-AA-3819 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3821     TCGA-AA-3831     TCGA-AA-3833     TCGA-AA-3837 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3842     TCGA-AA-3844     TCGA-AA-3845     TCGA-AA-3846 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3848     TCGA-AA-3850     TCGA-AA-3851     TCGA-AA-3852 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3854     TCGA-AA-3855     TCGA-AA-3856     TCGA-AA-3858 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3860     TCGA-AA-3861     TCGA-AA-3864     TCGA-AA-3866 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3867     TCGA-AA-3869     TCGA-AA-3870     TCGA-AA-3872 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3875     TCGA-AA-3877     TCGA-AA-3930     TCGA-AA-3939 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3941     TCGA-AA-3947     TCGA-AA-3949     TCGA-AA-3950 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3952     TCGA-AA-3955     TCGA-AA-3956     TCGA-AA-3968 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3971     TCGA-AA-3972     TCGA-AA-3973     TCGA-AA-3975 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3976     TCGA-AA-3979     TCGA-AA-3986     TCGA-AA-3989 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3994     TCGA-AA-A004     TCGA-AA-A00A     TCGA-AA-A00D 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-A00E     TCGA-AA-A00F     TCGA-AA-A00J     TCGA-AA-A00K 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-A00L     TCGA-AA-A00N     TCGA-AA-A00O     TCGA-AA-A00Q 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-A00R     TCGA-AA-A00U     TCGA-AA-A00W     TCGA-AA-A00Z 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-A010     TCGA-AA-A017     TCGA-AA-A01D     TCGA-AA-A01F 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-A01G     TCGA-AA-A01I     TCGA-AA-A01K     TCGA-AA-A01P 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-A01Q     TCGA-AA-A01R     TCGA-AA-A01S     TCGA-AA-A01T 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-A01V     TCGA-AA-A01X     TCGA-AA-A01Z     TCGA-AA-A022 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-A024     TCGA-AA-A02F     TCGA-AA-A02H     TCGA-AA-A02J 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-A02K     TCGA-AA-A02O     TCGA-AA-A02W     TCGA-AA-A02Y 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-A03F     TCGA-AA-A03J     TCGA-AD-5900     TCGA-AD-6548 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AD-6888     TCGA-AU-3779     TCGA-AU-6004     TCGA-AY-4070 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AY-4071     TCGA-AY-5543     TCGA-AY-6196     TCGA-AY-6197 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AY-6386     TCGA-AZ-4315     TCGA-AZ-4681     TCGA-AZ-4682 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CA-5254     TCGA-CA-5255     TCGA-CA-5796     TCGA-CA-5797 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CA-6715     TCGA-CA-6716     TCGA-CA-6717     TCGA-CA-6718 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CA-6719     TCGA-CK-4947     TCGA-CK-4948     TCGA-CK-4950 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CK-4952     TCGA-CK-5912     TCGA-CK-5913     TCGA-CK-5914 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CK-5915     TCGA-CK-5916     TCGA-CK-6746     TCGA-CK-6747 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CK-6748     TCGA-CK-6751     TCGA-CM-4743     TCGA-CM-4744 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CM-4746     TCGA-CM-4747     TCGA-CM-4752     TCGA-CM-5341 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CM-5344     TCGA-CM-5348     TCGA-CM-5349     TCGA-CM-5860 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CM-5861     TCGA-CM-5862     TCGA-CM-5863     TCGA-CM-5864 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CM-5868     TCGA-CM-6161     TCGA-CM-6162     TCGA-CM-6163 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CM-6164     TCGA-CM-6165     TCGA-CM-6166     TCGA-CM-6167 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CM-6168     TCGA-CM-6169     TCGA-CM-6170     TCGA-CM-6171 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CM-6172     TCGA-CM-6674     TCGA-CM-6675     TCGA-CM-6676 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CM-6677     TCGA-CM-6678     TCGA-CM-6679     TCGA-CM-6680 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-D5-5537     TCGA-D5-5538     TCGA-D5-5539     TCGA-D5-5540 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-D5-5541     TCGA-D5-6529     TCGA-D5-6532     TCGA-D5-6533 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-D5-6534     TCGA-D5-6535     TCGA-D5-6536     TCGA-D5-6537 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-D5-6538     TCGA-D5-6539     TCGA-D5-6540     TCGA-D5-6541 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-D5-6898     TCGA-D5-6920     TCGA-D5-6922     TCGA-D5-6923 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-D5-6924     TCGA-D5-6926     TCGA-D5-6927     TCGA-D5-6928 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-D5-6929     TCGA-D5-6930     TCGA-D5-6931     TCGA-D5-6932 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-D5-7000     TCGA-F4-6459     TCGA-F4-6460     TCGA-F4-6569 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-F4-6570     TCGA-F4-6703     TCGA-F4-6704     TCGA-F4-6805 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-F4-6806     TCGA-F4-6807     TCGA-F4-6808     TCGA-F4-6809 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-F4-6854     TCGA-F4-6855     TCGA-F4-6856     TCGA-G4-6293 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-G4-6299     TCGA-G4-6303     TCGA-G4-6304     TCGA-G4-6306 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-G4-6307     TCGA-G4-6309     TCGA-G4-6310     TCGA-G4-6315 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-G4-6317     TCGA-G4-6321     TCGA-G4-6323     TCGA-G4-6586 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-G4-6588     TCGA-G4-6625     TCGA-G4-6626     TCGA-G4-6628 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
D1817V10, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TBCE MUTATED                                  0     0
  TBCE WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TBCE MUTATED                           0     0
  TBCE WILD-TYPE                        19   176
D1817V11, multiclass

Clustering(1818) Variable = TIPARP MUTATION ANALYSIS
D1818V1, survival
                  sevent
clus2                0   1
  TIPARP MUTATED     4   1
  TIPARP WILD-TYPE 278  72
  TIPARP MUTATED TIPARP WILD-TYPE 
               5              350 
  TIPARP MUTATED TIPARP WILD-TYPE 
               1               72 
$`TIPARP MUTATED`
TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-CA-6717 TCGA-CM-6675 
       25.02         4.01        34.98         0.33        13.05 

$`TIPARP WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        35.41        19.43       107.67        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  TIPARP MUTATED TIPARP WILD-TYPE 
            0.33             0.00 
  TIPARP MUTATED TIPARP WILD-TYPE 
           34.98           140.38 
  TIPARP MUTATED TIPARP WILD-TYPE 
          13.050           20.235 
[1] "0.3 - 35.0 (13.1)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.7"
D1818V2, 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       25       108         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TIPARP MUTATED           0          0          0          0        0
  TIPARP WILD-TYPE        19         10         41         31       35
                  vv
clus               STAGE IVA STAGE IVB
  TIPARP MUTATED           0         1
  TIPARP WILD-TYPE        13         0
D1818V3, multiclass
            clus
vv           TIPARP MUTATED TIPARP WILD-TYPE
  STAGE I                 0               64
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               1              108
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              0               41
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  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  67 246  39
D1818V4, multiclass
    clus
vv   TIPARP MUTATED TIPARP WILD-TYPE
  T1              0                9
  T2              1               67
  T3              2              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
  TIPARP MUTATED     4   0   1
  TIPARP WILD-TYPE 216  80  65
D1818V5, multiclass
    clus
vv   TIPARP MUTATED TIPARP WILD-TYPE
  N0              4              216
  N1              0               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"
D1818V6, binary
                  cls
clus                 0   1
  TIPARP MUTATED     3   1
  TIPARP WILD-TYPE 280  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TIPARP MUTATED      3    1
  TIPARP WILD-TYPE  280   47
   clus
vv  TIPARP MUTATED TIPARP WILD-TYPE
  0              3              280
  1              1               47
[1] 2 2
[1] FALSE
D1818V7, 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
D1818V8, binary
                  cls
clus                 0   1
  TIPARP MUTATED     3   2
  TIPARP WILD-TYPE 314  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TIPARP MUTATED      3    2
  TIPARP WILD-TYPE  314   46
                               clus
vv                              TIPARP MUTATED TIPARP WILD-TYPE
  COLON ADENOCARCINOMA                       3              314
  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 254   2  22  20
D1818V9, multiclass
    clus
vv   TIPARP MUTATED TIPARP WILD-TYPE
  R0              3              254
  R1              0                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"
D1818V10, 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
D1818V11, multiclass
[1] "Remove cluster labels:" "TIPARP MUTATED"        
clus
  TIPARP MUTATED TIPARP WILD-TYPE 
               2              204 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-4105 
"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-A6-6649       TCGA-A6-6651 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-A6-6652       TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-A6-6781       TCGA-A6-6782       TCGA-AD-5900       TCGA-AD-6548 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-AD-6888       TCGA-AD-6889       TCGA-AD-6890       TCGA-AD-6895 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-AD-6899       TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6964 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-AD-6965       TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-AY-4071       TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-AY-6386       TCGA-AZ-4315       TCGA-AZ-4323       TCGA-AZ-4616 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-AZ-4681       TCGA-AZ-4682       TCGA-AZ-5403       TCGA-AZ-5407 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-AZ-6598       TCGA-AZ-6599       TCGA-AZ-6600       TCGA-AZ-6601 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-AZ-6603       TCGA-AZ-6605       TCGA-AZ-6606       TCGA-AZ-6607 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-AZ-6608       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-5912       TCGA-CK-5913       TCGA-CK-5914 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-CK-5915       TCGA-CK-5916       TCGA-CK-6746       TCGA-CK-6747 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-CK-6748       TCGA-CK-6751       TCGA-CM-4743       TCGA-CM-4744 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-CM-4746       TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-CM-5344       TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-CM-5861       TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-CM-5868       TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-CM-6164       TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-CM-6168       TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-CM-6172       TCGA-CM-6674       TCGA-CM-6676       TCGA-CM-6677 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680       TCGA-D5-5537 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540       TCGA-D5-5541 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533       TCGA-D5-6534 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537       TCGA-D5-6538 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541       TCGA-D5-6898 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923       TCGA-D5-6924 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928       TCGA-D5-6929 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932       TCGA-D5-7000 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-DM-A0X9       TCGA-DM-A0XD       TCGA-DM-A0XF       TCGA-DM-A1D0 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-DM-A1D4       TCGA-DM-A1D6       TCGA-DM-A1D7       TCGA-DM-A1D8 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-DM-A1D9       TCGA-DM-A1DA       TCGA-DM-A1DB       TCGA-DM-A1HA 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-DM-A1HB       TCGA-DM-A282       TCGA-DM-A285       TCGA-DM-A28C 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-DM-A28E       TCGA-DM-A28F       TCGA-DM-A28G       TCGA-DM-A28H 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-DM-A28K       TCGA-F4-6459       TCGA-F4-6460       TCGA-F4-6569 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704       TCGA-F4-6805 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808       TCGA-F4-6809 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856       TCGA-G4-6293 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304       TCGA-G4-6306 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310       TCGA-G4-6315 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323       TCGA-G4-6586 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 
      TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628 
"TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" "TIPARP WILD-TYPE" 

Clustering(1819) Variable = LIMA1 MUTATION ANALYSIS
D1819V1, survival
                 sevent
clus2               0   1
  LIMA1 MUTATED     9   3
  LIMA1 WILD-TYPE 273  70
  LIMA1 MUTATED LIMA1 WILD-TYPE 
             12             343 
  LIMA1 MUTATED LIMA1 WILD-TYPE 
              3              70 
$`LIMA1 MUTATED`
TCGA-AA-3672 TCGA-AA-3811 TCGA-AA-3821 TCGA-AA-A00N TCGA-AZ-4315 TCGA-AZ-6598 
        0.92        10.06         1.02         4.01        58.39        49.41 
TCGA-D5-6926 TCGA-DM-A1HB TCGA-F4-6808 TCGA-G4-6304 TCGA-G4-6323 TCGA-G4-6628 
        9.04       135.65        33.67        53.62        13.78        52.80 

$`LIMA1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
        6.05         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 
       35.05        33.04         0.99        25.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       16.24        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        44.68        55.04        51.75        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.72        36.00        22.09        35.80        26.17        91.79 
TCGA-G4-6626 
       46.75 

  LIMA1 MUTATED LIMA1 WILD-TYPE 
           0.92            0.00 
  LIMA1 MUTATED LIMA1 WILD-TYPE 
         135.65          140.38 
  LIMA1 MUTATED LIMA1 WILD-TYPE 
         23.725          20.190 
[1] "0.9 - 135.7 (23.7)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D1819V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LIMA1 MUTATED         3        1        1         2         2         0
  LIMA1 WILD-TYPE      61        0       24       107         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LIMA1 MUTATED           2          1          1          0        0         0
  LIMA1 WILD-TYPE        17          9         40         31       35        13
                 vv
clus              STAGE IVB
  LIMA1 MUTATED           0
  LIMA1 WILD-TYPE         1
D1819V3, multiclass
            clus
vv           LIMA1 MUTATED LIMA1 WILD-TYPE
  STAGE I                3              61
  STAGE IA               1               0
  STAGE II               1              24
  STAGE IIA              2             107
  STAGE IIB              2               6
  STAGE IIC              0               1
  STAGE III              2              17
  STAGE IIIA             1               9
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LIMA1 MUTATED     1   2   6   3
  LIMA1 WILD-TYPE   8  66 242  38
D1819V4, multiclass
    clus
vv   LIMA1 MUTATED LIMA1 WILD-TYPE
  T1             1               8
  T2             2              66
  T3             6             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
  LIMA1 MUTATED     9   3   1
  LIMA1 WILD-TYPE 211  77  65
D1819V5, multiclass
    clus
vv   LIMA1 MUTATED LIMA1 WILD-TYPE
  N0             9             211
  N1             3              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"
D1819V6, binary
                 cls
clus                0   1
  LIMA1 MUTATED    11   0
  LIMA1 WILD-TYPE 272  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LIMA1 MUTATED     11    0
  LIMA1 WILD-TYPE  272   48
   clus
vv  LIMA1 MUTATED LIMA1 WILD-TYPE
  0            11             272
  1             0              48
[1] 2 2
[1] FALSE
D1819V7, binary
                 cls
clus                0   1
  LIMA1 MUTATED     7   6
  LIMA1 WILD-TYPE 163 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LIMA1 MUTATED      7    6
  LIMA1 WILD-TYPE  163  191
        clus
vv       LIMA1 MUTATED LIMA1 WILD-TYPE
  FEMALE             7             163
  MALE               6             191
[1] 2 2
[1] FALSE
D1819V8, binary
                 cls
clus                0   1
  LIMA1 MUTATED    11   2
  LIMA1 WILD-TYPE 306  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LIMA1 MUTATED     11    2
  LIMA1 WILD-TYPE  306   46
                               clus
vv                              LIMA1 MUTATED LIMA1 WILD-TYPE
  COLON ADENOCARCINOMA                     11             306
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  LIMA1 MUTATED    11   0   0   0
  LIMA1 WILD-TYPE 246   2  22  21
D1819V9, multiclass
    clus
vv   LIMA1 MUTATED LIMA1 WILD-TYPE
  R0            11             246
  R1             0               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"
D1819V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LIMA1 MUTATED                                  0     0
  LIMA1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  LIMA1 MUTATED                           1     7
  LIMA1 WILD-TYPE                        18   169
D1819V11, multiclass
                                  clus
vv                                 LIMA1 MUTATED LIMA1 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(1820) Variable = SFTPB MUTATION ANALYSIS
D1820V1, survival
                 sevent
clus2               0   1
  SFTPB MUTATED     8   1
  SFTPB WILD-TYPE 274  72
  SFTPB MUTATED SFTPB WILD-TYPE 
              9             346 
  SFTPB MUTATED SFTPB WILD-TYPE 
              1              72 
$`SFTPB MUTATED`
TCGA-A6-5661 TCGA-AA-3681 TCGA-AA-3833 TCGA-AZ-6605 TCGA-CM-5344 TCGA-D5-6535 
       33.53         5.98        15.95         5.23        22.03        15.12 
TCGA-G4-6299 TCGA-G4-6317 TCGA-G4-6628 
       74.56        36.00        52.80 

$`SFTPB WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       47.01        15.02        11.01        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10       100.01        29.56        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.41        19.43       107.67        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 
       55.04        51.75        45.11        36.72        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       35.80        26.17        91.79        46.75 

  SFTPB MUTATED SFTPB WILD-TYPE 
           5.23            0.00 
  SFTPB MUTATED SFTPB WILD-TYPE 
          74.56          140.38 
  SFTPB MUTATED SFTPB WILD-TYPE 
         22.030          20.155 
[1] "5.2 - 74.6 (22.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "2.2"
D1820V2, 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       25       107         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        18         10         38         29       35        13
                 vv
clus              STAGE IVB
  SFTPB MUTATED           0
  SFTPB WILD-TYPE         1
D1820V3, multiclass
            clus
vv           SFTPB MUTATED SFTPB WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              2             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             3              38
  STAGE IIIC             2              29
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SFTPB MUTATED     0   1   7   1
  SFTPB WILD-TYPE   9  67 241  40
D1820V4, multiclass
    clus
vv   SFTPB MUTATED SFTPB WILD-TYPE
  T1             0               9
  T2             1              67
  T3             7             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
  SFTPB MUTATED     3   4   2
  SFTPB WILD-TYPE 217  76  64
D1820V5, multiclass
    clus
vv   SFTPB MUTATED SFTPB WILD-TYPE
  N0             3             217
  N1             4              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"
D1820V6, binary
                 cls
clus                0   1
  SFTPB MUTATED     7   0
  SFTPB WILD-TYPE 276  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SFTPB MUTATED      7    0
  SFTPB WILD-TYPE  276   48
   clus
vv  SFTPB MUTATED SFTPB WILD-TYPE
  0             7             276
  1             0              48
[1] 2 2
[1] FALSE
D1820V7, 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
D1820V8, binary
                 cls
clus                0   1
  SFTPB MUTATED     9   0
  SFTPB WILD-TYPE 308  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SFTPB MUTATED      9    0
  SFTPB WILD-TYPE  308   48
                               clus
vv                              SFTPB MUTATED SFTPB WILD-TYPE
  COLON ADENOCARCINOMA                      9             308
  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 250   2  22  20
D1820V9, multiclass
    clus
vv   SFTPB MUTATED SFTPB WILD-TYPE
  R0             7             250
  R1             0               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"
D1820V10, 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
D1820V11, 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(1821) Variable = IL7R MUTATION ANALYSIS
D1821V1, survival
                sevent
clus2              0   1
  IL7R MUTATED     8   2
  IL7R WILD-TYPE 274  71
  IL7R MUTATED IL7R WILD-TYPE 
            10            345 
  IL7R MUTATED IL7R WILD-TYPE 
             2             71 
$`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         0.10 
TCGA-CM-6168 TCGA-D5-6920 TCGA-F4-6703 TCGA-G4-6317 
       12.99        12.39        35.87        36.00 

$`IL7R WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       34.98        15.02        10.98        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58         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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45         6.18         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       45.11        36.72        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       91.79        46.75        52.80 

  IL7R MUTATED IL7R WILD-TYPE 
           0.1            0.0 
  IL7R MUTATED IL7R WILD-TYPE 
         63.98         140.38 
  IL7R MUTATED IL7R WILD-TYPE 
         31.23          20.12 
[1] "0.1 - 64.0 (31.2)"  "0.0 - 140.4 (20.1)"
[1] "hr=" "1.1"
D1821V2, 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       23       105         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        19         10         40         30       35        13
                vv
clus             STAGE IVB
  IL7R MUTATED           0
  IL7R WILD-TYPE         1
D1821V3, multiclass
            clus
vv           IL7R MUTATED IL7R WILD-TYPE
  STAGE I               2             62
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             4            105
  STAGE IIB             1              7
  STAGE IIC             0              1
  STAGE III             0             19
  STAGE IIIA            0             10
  STAGE IIIB            1             40
  STAGE IIIC            1             30
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  IL7R MUTATED     0   2   8   1
  IL7R WILD-TYPE   9  66 240  40
D1821V4, multiclass
    clus
vv   IL7R MUTATED IL7R WILD-TYPE
  T1            0              9
  T2            2             66
  T3            8            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
  IL7R MUTATED     9   1   1
  IL7R WILD-TYPE 211  79  65
D1821V5, multiclass
    clus
vv   IL7R MUTATED IL7R WILD-TYPE
  N0            9            211
  N1            1             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"
D1821V6, binary
                cls
clus               0   1
  IL7R MUTATED     8   0
  IL7R WILD-TYPE 275  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  IL7R MUTATED      8    0
  IL7R WILD-TYPE  275   48
   clus
vv  IL7R MUTATED IL7R WILD-TYPE
  0            8            275
  1            0             48
[1] 2 2
[1] FALSE
D1821V7, 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
D1821V8, binary
                cls
clus               0   1
  IL7R MUTATED    10   1
  IL7R WILD-TYPE 307  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  IL7R MUTATED     10    1
  IL7R WILD-TYPE  307   47
                               clus
vv                              IL7R MUTATED IL7R WILD-TYPE
  COLON ADENOCARCINOMA                    10            307
  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 249   2  22  19
D1821V9, multiclass
    clus
vv   IL7R MUTATED IL7R WILD-TYPE
  R0            8            249
  R1            0              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"
D1821V10, 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
D1821V11, 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(1822) Variable = FAAH2 MUTATION ANALYSIS
D1822V1, survival
                 sevent
clus2               0   1
  FAAH2 MUTATED     9   2
  FAAH2 WILD-TYPE 273  71
  FAAH2 MUTATED FAAH2 WILD-TYPE 
             11             344 
  FAAH2 MUTATED FAAH2 WILD-TYPE 
              2              71 
$`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        15.75 
TCGA-AZ-6599 TCGA-CK-4947 TCGA-CM-6676 TCGA-D5-6535 TCGA-G4-6315 
        6.77        17.56        11.08        15.12        36.72 

$`FAAH2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        1.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 
        1.02         9.07        24.03        37.05        36.03        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       30.02        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-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-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41        49.41        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         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        16.01        15.02         5.03        15.02        15.02 
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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 
       20.19        18.25         1.32        43.27        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        13.38        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        35.41        19.43       107.67        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

  FAAH2 MUTATED FAAH2 WILD-TYPE 
           6.77            0.00 
  FAAH2 MUTATED FAAH2 WILD-TYPE 
          36.72          140.38 
  FAAH2 MUTATED FAAH2 WILD-TYPE 
          15.12           20.98 
[1] "6.8 - 36.7 (15.1)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1.2"
D1822V2, 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       25       107         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FAAH2 MUTATED           1          0          2          1        1         2
  FAAH2 WILD-TYPE        18         10         39         30       34        11
                 vv
clus              STAGE IVB
  FAAH2 MUTATED           0
  FAAH2 WILD-TYPE         1
D1822V3, multiclass
            clus
vv           FAAH2 MUTATED FAAH2 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               0              25
  STAGE IIA              2             107
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             1              30
  STAGE IV               1              34
  STAGE IVA              2              11
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of 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  66 240  40
D1822V4, multiclass
    clus
vv   FAAH2 MUTATED FAAH2 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             8             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
  FAAH2 MUTATED     4   5   2
  FAAH2 WILD-TYPE 216  75  64
D1822V5, multiclass
    clus
vv   FAAH2 MUTATED FAAH2 WILD-TYPE
  N0             4             216
  N1             5              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"
D1822V6, binary
                 cls
clus                0   1
  FAAH2 MUTATED     7   2
  FAAH2 WILD-TYPE 276  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FAAH2 MUTATED      7    2
  FAAH2 WILD-TYPE  276   46
   clus
vv  FAAH2 MUTATED FAAH2 WILD-TYPE
  0             7             276
  1             2              46
[1] 2 2
[1] FALSE
D1822V7, 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
D1822V8, binary
                 cls
clus                0   1
  FAAH2 MUTATED    10   1
  FAAH2 WILD-TYPE 307  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FAAH2 MUTATED     10    1
  FAAH2 WILD-TYPE  307   47
                               clus
vv                              FAAH2 MUTATED FAAH2 WILD-TYPE
  COLON ADENOCARCINOMA                     10             307
  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 250   2  22  19
D1822V9, multiclass
    clus
vv   FAAH2 MUTATED FAAH2 WILD-TYPE
  R0             7             250
  R1             0               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"
D1822V10, 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
D1822V11, 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(1823) Variable = CNKSR3 MUTATION ANALYSIS
D1823V1, survival
                  sevent
clus2                0   1
  CNKSR3 MUTATED     5   4
  CNKSR3 WILD-TYPE 277  69
  CNKSR3 MUTATED CNKSR3 WILD-TYPE 
               9              346 
  CNKSR3 MUTATED CNKSR3 WILD-TYPE 
               4               69 
$`CNKSR3 MUTATED`
TCGA-A6-6780 TCGA-AA-A029 TCGA-AD-6895 TCGA-AD-6901 TCGA-AY-4071 TCGA-AZ-6598 
       20.12        51.98         0.72        22.42         0.95        49.41 
TCGA-CM-6680 TCGA-D5-6533 TCGA-DM-A1DA 
       12.03         1.32         7.50 

$`CNKSR3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
       56.55         0.79         5.79        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        27.09        16.31        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 
       13.51        11.51        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  CNKSR3 MUTATED CNKSR3 WILD-TYPE 
            0.72             0.00 
  CNKSR3 MUTATED CNKSR3 WILD-TYPE 
           51.98           140.38 
  CNKSR3 MUTATED CNKSR3 WILD-TYPE 
           12.03            20.63 
[1] "0.7 - 52.0 (12.0)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "2.8"
D1823V2, 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       23       108         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CNKSR3 MUTATED           0          0          2          1        0
  CNKSR3 WILD-TYPE        19         10         39         30       35
                  vv
clus               STAGE IVA STAGE IVB
  CNKSR3 MUTATED           0         0
  CNKSR3 WILD-TYPE        13         1
D1823V3, multiclass
            clus
vv           CNKSR3 MUTATED CNKSR3 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               1              108
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               0               19
  STAGE IIIA              0               10
  STAGE IIIB              2               39
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CNKSR3 MUTATED     1   0   7   1
  CNKSR3 WILD-TYPE   8  68 241  40
D1823V4, multiclass
    clus
vv   CNKSR3 MUTATED CNKSR3 WILD-TYPE
  T1              1                8
  T2              0               68
  T3              7              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
  CNKSR3 MUTATED     6   1   2
  CNKSR3 WILD-TYPE 214  79  64
D1823V5, multiclass
    clus
vv   CNKSR3 MUTATED CNKSR3 WILD-TYPE
  N0              6              214
  N1              1               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"
D1823V6, binary
                  cls
clus                 0   1
  CNKSR3 MUTATED     4   0
  CNKSR3 WILD-TYPE 279  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CNKSR3 MUTATED      4    0
  CNKSR3 WILD-TYPE  279   48
   clus
vv  CNKSR3 MUTATED CNKSR3 WILD-TYPE
  0              4              279
  1              0               48
[1] 2 2
[1] FALSE
D1823V7, 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
D1823V8, binary
                  cls
clus                 0   1
  CNKSR3 MUTATED     7   1
  CNKSR3 WILD-TYPE 310  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CNKSR3 MUTATED      7    1
  CNKSR3 WILD-TYPE  310   47
                               clus
vv                              CNKSR3 MUTATED CNKSR3 WILD-TYPE
  COLON ADENOCARCINOMA                       7              310
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CNKSR3 MUTATED     4   0   0   0
  CNKSR3 WILD-TYPE 253   2  22  21
D1823V9, multiclass
    clus
vv   CNKSR3 MUTATED CNKSR3 WILD-TYPE
  R0              4              253
  R1              0                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"
D1823V10, 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
D1823V11, 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(1824) Variable = KLF11 MUTATION ANALYSIS
D1824V1, survival
                 sevent
clus2               0   1
  KLF11 MUTATED     5   1
  KLF11 WILD-TYPE 277  72
  KLF11 MUTATED KLF11 WILD-TYPE 
              6             349 
  KLF11 MUTATED KLF11 WILD-TYPE 
              1              72 
$`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         0.33        15.02        19.59 

$`KLF11 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        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 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13        83.80        22.36        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32        21.99        21.14         2.93 
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        16.01 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

  KLF11 MUTATED KLF11 WILD-TYPE 
           0.33            0.00 
  KLF11 MUTATED KLF11 WILD-TYPE 
          62.79          140.38 
  KLF11 MUTATED KLF11 WILD-TYPE 
         17.305          20.280 
[1] "0.3 - 62.8 (17.3)"  "0.0 - 140.4 (20.3)"
[1] "hr=" "1.2"
D1824V2, 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       24       107         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        19          9         41         31       34        13
                 vv
clus              STAGE IVB
  KLF11 MUTATED           0
  KLF11 WILD-TYPE         1
D1824V3, multiclass
            clus
vv           KLF11 MUTATED KLF11 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              2             107
  STAGE IIB              1               7
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             1               9
  STAGE IIIB             0              41
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KLF11 MUTATED     1   0   4   2
  KLF11 WILD-TYPE   8  68 244  39
D1824V4, multiclass
    clus
vv   KLF11 MUTATED KLF11 WILD-TYPE
  T1             1               8
  T2             0              68
  T3             4             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
  KLF11 MUTATED     5   1   1
  KLF11 WILD-TYPE 215  79  65
D1824V5, multiclass
    clus
vv   KLF11 MUTATED KLF11 WILD-TYPE
  N0             5             215
  N1             1              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
  KLF11 MUTATED     4   1
  KLF11 WILD-TYPE 279  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLF11 MUTATED      4    1
  KLF11 WILD-TYPE  279   47
   clus
vv  KLF11 MUTATED KLF11 WILD-TYPE
  0             4             279
  1             1              47
[1] 2 2
[1] FALSE
D1824V7, 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
D1824V8, binary
                 cls
clus                0   1
  KLF11 MUTATED     4   3
  KLF11 WILD-TYPE 313  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLF11 MUTATED      4    3
  KLF11 WILD-TYPE  313   45
                               clus
vv                              KLF11 MUTATED KLF11 WILD-TYPE
  COLON ADENOCARCINOMA                      4             313
  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 254   2  21  19
D1824V9, multiclass
    clus
vv   KLF11 MUTATED KLF11 WILD-TYPE
  R0             3             254
  R1             0               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"
D1824V10, 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
D1824V11, 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(1825) Variable = TRIB1 MUTATION ANALYSIS
D1825V1, survival
                 sevent
clus2               0   1
  TRIB1 MUTATED     5   2
  TRIB1 WILD-TYPE 277  71
  TRIB1 MUTATED TRIB1 WILD-TYPE 
              7             348 
  TRIB1 MUTATED TRIB1 WILD-TYPE 
              2              71 
$`TRIB1 MUTATED`
TCGA-A6-6781 TCGA-AA-3715 TCGA-AD-6964 TCGA-AY-6197 TCGA-CK-4950 TCGA-CK-4952 
       19.66        19.04        10.88        21.44        40.34        15.62 
TCGA-D5-6533 
        1.32 

$`TRIB1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        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-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.20        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-5912 
        0.33         0.10         1.35        17.56       102.44        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 
       19.59        13.51        11.51        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         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  TRIB1 MUTATED TRIB1 WILD-TYPE 
           1.32            0.00 
  TRIB1 MUTATED TRIB1 WILD-TYPE 
          40.34          140.38 
  TRIB1 MUTATED TRIB1 WILD-TYPE 
          19.04           20.63 
[1] "1.3 - 40.3 (19.0)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "1.9"
D1825V2, 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       24       108         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TRIB1 MUTATED           1          1          1          1        0         0
  TRIB1 WILD-TYPE        18          9         40         30       35        13
                 vv
clus              STAGE IVB
  TRIB1 MUTATED           0
  TRIB1 WILD-TYPE         1
D1825V3, multiclass
            clus
vv           TRIB1 MUTATED TRIB1 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              1             108
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              1              18
  STAGE IIIA             1               9
  STAGE IIIB             1              40
  STAGE IIIC             1              30
  STAGE IV               0              35
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TRIB1 MUTATED     0   0   3   4
  TRIB1 WILD-TYPE   9  68 245  37
D1825V4, multiclass
    clus
vv   TRIB1 MUTATED TRIB1 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             3             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
  TRIB1 MUTATED     3   2   2
  TRIB1 WILD-TYPE 217  78  64
D1825V5, multiclass
    clus
vv   TRIB1 MUTATED TRIB1 WILD-TYPE
  N0             3             217
  N1             2              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"
D1825V6, binary
                 cls
clus                0   1
  TRIB1 MUTATED     4   0
  TRIB1 WILD-TYPE 279  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRIB1 MUTATED      4    0
  TRIB1 WILD-TYPE  279   48
   clus
vv  TRIB1 MUTATED TRIB1 WILD-TYPE
  0             4             279
  1             0              48
[1] 2 2
[1] FALSE
D1825V7, 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
D1825V8, binary
                 cls
clus                0   1
  TRIB1 MUTATED     5   2
  TRIB1 WILD-TYPE 312  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRIB1 MUTATED      5    2
  TRIB1 WILD-TYPE  312   46
                               clus
vv                              TRIB1 MUTATED TRIB1 WILD-TYPE
  COLON ADENOCARCINOMA                      5             312
  COLON MUCINOUS ADENOCARCINOMA             2              46
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TRIB1 MUTATED     4   1   0   1
  TRIB1 WILD-TYPE 253   1  22  20
D1825V9, multiclass
    clus
vv   TRIB1 MUTATED TRIB1 WILD-TYPE
  R0             4             253
  R1             1               1
  R2             0              22
  RX             1              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1825V10, 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
D1825V11, 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(1826) Variable = DAB2 MUTATION ANALYSIS
D1826V1, survival
                sevent
clus2              0   1
  DAB2 MUTATED    12   1
  DAB2 WILD-TYPE 270  72
  DAB2 MUTATED DAB2 WILD-TYPE 
            13            342 
  DAB2 MUTATED DAB2 WILD-TYPE 
             1             72 
$`DAB2 MUTATED`
TCGA-A6-6141 TCGA-AA-3510 TCGA-AA-3678 TCGA-AA-3685 TCGA-AA-A01G TCGA-AZ-4315 
        8.38        63.98        47.01        37.05        12.00        58.39 
TCGA-CK-6751 TCGA-CM-6165 TCGA-CM-6167 TCGA-D5-6927 TCGA-DM-A28H TCGA-F4-6570 
      124.27        16.04        14.99         9.44       117.07         6.18 
TCGA-G4-6586 
       35.80 

$`DAB2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3679 
       54.02         2.01        14.01         0.92        50.04        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
       11.01         5.98        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-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        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        13.38        13.45        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       35.41        19.43       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        45.11        36.72        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        26.17        91.79        46.75        52.80 

  DAB2 MUTATED DAB2 WILD-TYPE 
          6.18           0.00 
  DAB2 MUTATED DAB2 WILD-TYPE 
        124.27         140.38 
  DAB2 MUTATED DAB2 WILD-TYPE 
        35.800         20.155 
[1] "6.2 - 124.3 (35.8)" "0.0 - 140.4 (20.2)"
[1] "hr=" "4.4"
D1826V2, 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       23       102         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        18         10         41         29       35        13
                vv
clus             STAGE IVB
  DAB2 MUTATED           0
  DAB2 WILD-TYPE         1
D1826V3, multiclass
            clus
vv           DAB2 MUTATED DAB2 WILD-TYPE
  STAGE I               1             63
  STAGE IA              0              1
  STAGE II              2             23
  STAGE IIA             7            102
  STAGE IIB             0              8
  STAGE IIC             0              1
  STAGE III             1             18
  STAGE IIIA            0             10
  STAGE IIIB            0             41
  STAGE IIIC            2             29
  STAGE IV              0             35
  STAGE IVA             0             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  DAB2 MUTATED     0   2  11   0
  DAB2 WILD-TYPE   9  66 237  41
D1826V4, multiclass
    clus
vv   DAB2 MUTATED DAB2 WILD-TYPE
  T1            0              9
  T2            2             66
  T3           11            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
  DAB2 MUTATED    10   1   2
  DAB2 WILD-TYPE 210  79  64
D1826V5, multiclass
    clus
vv   DAB2 MUTATED DAB2 WILD-TYPE
  N0           10            210
  N1            1             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"
D1826V6, binary
                cls
clus               0   1
  DAB2 MUTATED    12   0
  DAB2 WILD-TYPE 271  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  DAB2 MUTATED     12    0
  DAB2 WILD-TYPE  271   48
   clus
vv  DAB2 MUTATED DAB2 WILD-TYPE
  0           12            271
  1            0             48
[1] 2 2
[1] FALSE
D1826V7, 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
D1826V8, binary
                cls
clus               0   1
  DAB2 MUTATED    11   2
  DAB2 WILD-TYPE 306  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  DAB2 MUTATED     11    2
  DAB2 WILD-TYPE  306   46
                               clus
vv                              DAB2 MUTATED DAB2 WILD-TYPE
  COLON ADENOCARCINOMA                    11            306
  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 247   2  22  20
D1826V9, multiclass
    clus
vv   DAB2 MUTATED DAB2 WILD-TYPE
  R0           10            247
  R1            0              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"
D1826V10, 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
D1826V11, 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(1827) Variable = ZNF557 MUTATION ANALYSIS
D1827V1, survival
                  sevent
clus2                0   1
  ZNF557 MUTATED     8   0
  ZNF557 WILD-TYPE 274  73
  ZNF557 MUTATED ZNF557 WILD-TYPE 
               8              347 
  ZNF557 MUTATED ZNF557 WILD-TYPE 
               0               73 
$`ZNF557 MUTATED`
TCGA-A6-5661 TCGA-AA-3510 TCGA-AA-3949 TCGA-AD-6895 TCGA-AZ-4315 TCGA-CM-6171 
       33.53        63.98        26.01         0.72        58.39        14.04 
TCGA-G4-6304 TCGA-G4-6586 
       53.62        35.80 

$`ZNF557 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 
       35.41        19.43       107.67        74.56        65.85        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        26.17        91.79        46.75        52.80 

  ZNF557 MUTATED ZNF557 WILD-TYPE 
            0.72             0.00 
  ZNF557 MUTATED ZNF557 WILD-TYPE 
           63.98           140.38 
  ZNF557 MUTATED ZNF557 WILD-TYPE 
          34.665           20.020 
[1] "0.7 - 64.0 (34.7)"  "0.0 - 140.4 (20.0)"
[1] "hr="     "2.6e+07"
D1827V2, 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       24       106         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF557 MUTATED           1          0          1          0        0
  ZNF557 WILD-TYPE        18         10         40         31       35
                  vv
clus               STAGE IVA STAGE IVB
  ZNF557 MUTATED           0         0
  ZNF557 WILD-TYPE        13         1
D1827V3, multiclass
            clus
vv           ZNF557 MUTATED ZNF557 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                1               24
  STAGE IIA               3              106
  STAGE IIB               1                7
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              0               31
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF557 MUTATED     0   1   7   1
  ZNF557 WILD-TYPE   9  67 241  40
D1827V4, multiclass
    clus
vv   ZNF557 MUTATED ZNF557 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              7              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
  ZNF557 MUTATED     6   2   1
  ZNF557 WILD-TYPE 214  78  65
D1827V5, multiclass
    clus
vv   ZNF557 MUTATED ZNF557 WILD-TYPE
  N0              6              214
  N1              2               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"
D1827V6, binary
                  cls
clus                 0   1
  ZNF557 MUTATED     8   0
  ZNF557 WILD-TYPE 275  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF557 MUTATED      8    0
  ZNF557 WILD-TYPE  275   48
   clus
vv  ZNF557 MUTATED ZNF557 WILD-TYPE
  0              8              275
  1              0               48
[1] 2 2
[1] FALSE
D1827V7, 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
D1827V8, binary
                  cls
clus                 0   1
  ZNF557 MUTATED     8   1
  ZNF557 WILD-TYPE 309  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF557 MUTATED      8    1
  ZNF557 WILD-TYPE  309   47
                               clus
vv                              ZNF557 MUTATED ZNF557 WILD-TYPE
  COLON ADENOCARCINOMA                       8              309
  COLON MUCINOUS ADENOCARCINOMA              1               47
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF557 MUTATED     8   0   0   0
  ZNF557 WILD-TYPE 249   2  22  21
D1827V9, multiclass
    clus
vv   ZNF557 MUTATED ZNF557 WILD-TYPE
  R0              8              249
  R1              0                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"
D1827V10, 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
D1827V11, 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(1828) Variable = OR5K2 MUTATION ANALYSIS
D1828V1, survival
                 sevent
clus2               0   1
  OR5K2 MUTATED     9   0
  OR5K2 WILD-TYPE 273  73
  OR5K2 MUTATED OR5K2 WILD-TYPE 
              9             346 
  OR5K2 MUTATED OR5K2 WILD-TYPE 
              0              73 
$`OR5K2 MUTATED`
TCGA-A6-5665 TCGA-A6-6649 TCGA-AA-3510 TCGA-AA-3713 TCGA-AD-5900 TCGA-AD-6889 
       22.06        24.16        63.98        19.04         0.07        56.55 
TCGA-AU-6004 TCGA-AY-6386 TCGA-AZ-4315 
       27.09        17.82        58.39 

$`OR5K2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.18        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       40.96        21.37         4.21         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        15.75         0.20        21.44         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 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         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  OR5K2 MUTATED OR5K2 WILD-TYPE 
           0.07            0.00 
  OR5K2 MUTATED OR5K2 WILD-TYPE 
          63.98          140.38 
  OR5K2 MUTATED OR5K2 WILD-TYPE 
          24.16           20.07 
[1] "0.1 - 64.0 (24.2)"  "0.0 - 140.4 (20.1)"
[1] "hr="     "2.6e+07"
D1828V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR5K2 MUTATED         2        0        1         3         0         0
  OR5K2 WILD-TYPE      62        1       24       106         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR5K2 MUTATED           0          0          2          0        1         0
  OR5K2 WILD-TYPE        19         10         39         31       34        13
                 vv
clus              STAGE IVB
  OR5K2 MUTATED           0
  OR5K2 WILD-TYPE         1
D1828V3, multiclass
            clus
vv           OR5K2 MUTATED OR5K2 WILD-TYPE
  STAGE I                2              62
  STAGE IA               0               1
  STAGE II               1              24
  STAGE IIA              3             106
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR5K2 MUTATED     0   2   7   0
  OR5K2 WILD-TYPE   9  66 241  41
D1828V4, multiclass
    clus
vv   OR5K2 MUTATED OR5K2 WILD-TYPE
  T1             0               9
  T2             2              66
  T3             7             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
  OR5K2 MUTATED     7   2   0
  OR5K2 WILD-TYPE 213  78  66
D1828V5, multiclass
    clus
vv   OR5K2 MUTATED OR5K2 WILD-TYPE
  N0             7             213
  N1             2              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"
D1828V6, binary
                 cls
clus                0   1
  OR5K2 MUTATED     7   1
  OR5K2 WILD-TYPE 276  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5K2 MUTATED      7    1
  OR5K2 WILD-TYPE  276   47
   clus
vv  OR5K2 MUTATED OR5K2 WILD-TYPE
  0             7             276
  1             1              47
[1] 2 2
[1] FALSE
D1828V7, binary
                 cls
clus                0   1
  OR5K2 MUTATED     3   6
  OR5K2 WILD-TYPE 167 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5K2 MUTATED      3    6
  OR5K2 WILD-TYPE  167  191
        clus
vv       OR5K2 MUTATED OR5K2 WILD-TYPE
  FEMALE             3             167
  MALE               6             191
[1] 2 2
[1] FALSE
D1828V8, binary
                 cls
clus                0   1
  OR5K2 MUTATED     8   1
  OR5K2 WILD-TYPE 309  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5K2 MUTATED      8    1
  OR5K2 WILD-TYPE  309   47
                               clus
vv                              OR5K2 MUTATED OR5K2 WILD-TYPE
  COLON ADENOCARCINOMA                      8             309
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  OR5K2 MUTATED     6   0   1   0
  OR5K2 WILD-TYPE 251   2  21  21
D1828V9, multiclass
    clus
vv   OR5K2 MUTATED OR5K2 WILD-TYPE
  R0             6             251
  R1             0               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"
D1828V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR5K2 MUTATED                                  0     1
  OR5K2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR5K2 MUTATED                           1     5
  OR5K2 WILD-TYPE                        18   171
D1828V11, multiclass
                                  clus
vv                                 OR5K2 MUTATED OR5K2 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(1829) Variable = PGAP3 MUTATION ANALYSIS
D1829V1, survival
                 sevent
clus2               0   1
  PGAP3 MUTATED     4   3
  PGAP3 WILD-TYPE 278  70
  PGAP3 MUTATED PGAP3 WILD-TYPE 
              7             348 
  PGAP3 MUTATED PGAP3 WILD-TYPE 
              3              70 
$`PGAP3 MUTATED`
TCGA-AA-3525 TCGA-AA-3710 TCGA-AA-3972 TCGA-AD-6895 TCGA-AZ-6598 TCGA-AZ-6601 
        8.05        26.99        50.99         0.72        49.41       100.01 
TCGA-F4-6459 
        8.61 

$`PGAP3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       20.98        34.03         2.01        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       22.36        62.79        61.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-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 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 

  PGAP3 MUTATED PGAP3 WILD-TYPE 
           0.72            0.00 
  PGAP3 MUTATED PGAP3 WILD-TYPE 
         100.01          140.38 
  PGAP3 MUTATED PGAP3 WILD-TYPE 
         26.990          20.155 
[1] "0.7 - 100.0 (27.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.4"
D1829V2, 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       23       108         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PGAP3 MUTATED           0          0          2          0        1         0
  PGAP3 WILD-TYPE        19         10         39         31       34        13
                 vv
clus              STAGE IVB
  PGAP3 MUTATED           0
  PGAP3 WILD-TYPE         1
D1829V3, multiclass
            clus
vv           PGAP3 MUTATED PGAP3 WILD-TYPE
  STAGE I                0              64
  STAGE IA               0               1
  STAGE II               2              23
  STAGE IIA              1             108
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             2              39
  STAGE IIIC             0              31
  STAGE IV               1              34
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PGAP3 MUTATED     0   0   7   0
  PGAP3 WILD-TYPE   9  68 241  41
D1829V4, multiclass
    clus
vv   PGAP3 MUTATED PGAP3 WILD-TYPE
  T1             0               9
  T2             0              68
  T3             7             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
  PGAP3 MUTATED     3   3   1
  PGAP3 WILD-TYPE 217  77  65
D1829V5, multiclass
    clus
vv   PGAP3 MUTATED PGAP3 WILD-TYPE
  N0             3             217
  N1             3              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"
D1829V6, binary
                 cls
clus                0   1
  PGAP3 MUTATED     4   1
  PGAP3 WILD-TYPE 279  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PGAP3 MUTATED      4    1
  PGAP3 WILD-TYPE  279   47
   clus
vv  PGAP3 MUTATED PGAP3 WILD-TYPE
  0             4             279
  1             1              47
[1] 2 2
[1] FALSE
D1829V7, 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
D1829V8, binary
                 cls
clus                0   1
  PGAP3 MUTATED     7   0
  PGAP3 WILD-TYPE 310  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PGAP3 MUTATED      7    0
  PGAP3 WILD-TYPE  310   48
                               clus
vv                              PGAP3 MUTATED PGAP3 WILD-TYPE
  COLON ADENOCARCINOMA                      7             310
  COLON MUCINOUS ADENOCARCINOMA             0              48
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PGAP3 MUTATED     3   0   1   0
  PGAP3 WILD-TYPE 254   2  21  21
D1829V9, multiclass
    clus
vv   PGAP3 MUTATED PGAP3 WILD-TYPE
  R0             3             254
  R1             0               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"
D1829V10, 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
D1829V11, 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(1830) Variable = TEK MUTATION ANALYSIS
D1830V1, survival
               sevent
clus2             0   1
  TEK MUTATED    17  10
  TEK WILD-TYPE 265  63
  TEK MUTATED TEK WILD-TYPE 
           27           328 
  TEK MUTATED TEK WILD-TYPE 
           10            63 
$`TEK MUTATED`
TCGA-A6-2676 TCGA-A6-5657 TCGA-A6-5661 TCGA-AA-3660 TCGA-AA-3713 TCGA-AA-3845 
       42.90        31.63        33.53        78.08        19.04         0.00 
TCGA-AA-3947 TCGA-AA-3989 TCGA-AA-A00N TCGA-AA-A00Q TCGA-AA-A010 TCGA-AD-5900 
       33.01         7.96         4.01        42.02        34.98         0.07 
TCGA-AY-6196 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-6718 TCGA-CK-4948 
        0.20        58.39        49.41       100.01         0.10       102.44 
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        36.72 

$`TEK WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       30.44        29.19        23.61        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       14.93        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        27.02        19.07        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       27.02         0.99        17.03        14.99        21.99        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        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        15.75        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13        83.80        22.36        62.79        61.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        0.33         1.35        17.56        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       13.51        11.51        18.25         1.32        43.27        15.12 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43        38.20       130.65        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-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 
       13.38        13.45        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      107.67        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       51.75        45.11        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  TEK MUTATED TEK WILD-TYPE 
            0             0 
  TEK MUTATED TEK WILD-TYPE 
       135.65        140.38 
  TEK MUTATED TEK WILD-TYPE 
       33.010        20.005 
[1] "0.0 - 135.7 (33.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.4"
D1830V2, 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       22       100         4         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TEK MUTATED           0          1          5          1        3         0
  TEK WILD-TYPE        19          9         36         30       32        13
               vv
clus            STAGE IVB
  TEK MUTATED           0
  TEK WILD-TYPE         1
D1830V3, multiclass
            clus
vv           TEK MUTATED TEK WILD-TYPE
  STAGE I              2            62
  STAGE IA             0             1
  STAGE II             3            22
  STAGE IIA            9           100
  STAGE IIB            4             4
  STAGE IIC            0             1
  STAGE III            0            19
  STAGE IIIA           1             9
  STAGE IIIB           5            36
  STAGE IIIC           1            30
  STAGE IV             3            32
  STAGE IVA            0            13
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  TEK MUTATED     0   2  21   5
  TEK WILD-TYPE   9  66 227  36
D1830V4, multiclass
    clus
vv   TEK MUTATED TEK WILD-TYPE
  T1           0             9
  T2           2            66
  T3          21           227
  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  73  64
D1830V5, multiclass
    clus
vv   TEK MUTATED TEK WILD-TYPE
  N0          19           201
  N1           7            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"
D1830V6, binary
               cls
clus              0   1
  TEK MUTATED    21   3
  TEK WILD-TYPE 262  45
[1] "tbl2"
               cls
clus            [,1] [,2]
  TEK MUTATED     21    3
  TEK WILD-TYPE  262   45
   clus
vv  TEK MUTATED TEK WILD-TYPE
  0          21           262
  1           3            45
[1] 2 2
[1] FALSE
D1830V7, 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
D1830V8, binary
               cls
clus              0   1
  TEK MUTATED    24   4
  TEK WILD-TYPE 293  44
[1] "tbl2"
               cls
clus            [,1] [,2]
  TEK MUTATED     24    4
  TEK WILD-TYPE  293   44
                               clus
vv                              TEK MUTATED TEK WILD-TYPE
  COLON ADENOCARCINOMA                   24           293
  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 237   2  20  20
D1830V9, multiclass
    clus
vv   TEK MUTATED TEK WILD-TYPE
  R0          20           237
  R1           0             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"
D1830V10, 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
D1830V11, 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(1831) Variable = C5ORF36 MUTATION ANALYSIS
D1831V1, survival
                   sevent
clus2                 0   1
  C5ORF36 MUTATED    12   4
  C5ORF36 WILD-TYPE 270  69
  C5ORF36 MUTATED C5ORF36 WILD-TYPE 
               16               339 
  C5ORF36 MUTATED C5ORF36 WILD-TYPE 
                4                69 
$`C5ORF36 MUTATED`
TCGA-A6-2678 TCGA-A6-6780 TCGA-AA-3663 TCGA-AA-3977 TCGA-AA-A00N TCGA-AD-5900 
       42.28        20.12         6.97        25.02         4.01         0.07 
TCGA-AD-6889 TCGA-AD-6964 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CA-6718 
       56.55        10.88        49.41       100.01         0.33         0.10 
TCGA-CM-5348 TCGA-D5-7000 TCGA-G4-6299 TCGA-G4-6628 
       22.98        10.26        74.56        52.80 

$`C5ORF36 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2683 
       43.76        46.65        43.76        42.90        24.33        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       15.75         0.20        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13        83.80        22.36        62.79        61.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        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        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         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         1.51        12.00 
TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      107.67        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       26.17        91.79        46.75 

  C5ORF36 MUTATED C5ORF36 WILD-TYPE 
             0.07              0.00 
  C5ORF36 MUTATED C5ORF36 WILD-TYPE 
           100.01            140.38 
  C5ORF36 MUTATED C5ORF36 WILD-TYPE 
            21.55             20.19 
[1] "0.1 - 100.0 (21.6)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1"  
D1831V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C5ORF36 MUTATED         3        0        3         5         1         0
  C5ORF36 WILD-TYPE      61        1       22       104         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C5ORF36 MUTATED           0          0          2          1        0
  C5ORF36 WILD-TYPE        19         10         39         30       35
                   vv
clus                STAGE IVA STAGE IVB
  C5ORF36 MUTATED           0         0
  C5ORF36 WILD-TYPE        13         1
D1831V3, multiclass
            clus
vv           C5ORF36 MUTATED C5ORF36 WILD-TYPE
  STAGE I                  3                61
  STAGE IA                 0                 1
  STAGE II                 3                22
  STAGE IIA                5               104
  STAGE IIB                1                 7
  STAGE IIC                0                 1
  STAGE III                0                19
  STAGE IIIA               0                10
  STAGE IIIB               2                39
  STAGE IIIC               1                30
  STAGE IV                 0                35
  STAGE IVA                0                13
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C5ORF36 MUTATED     0   4  11   2
  C5ORF36 WILD-TYPE   9  64 237  39
D1831V4, multiclass
    clus
vv   C5ORF36 MUTATED C5ORF36 WILD-TYPE
  T1               0                 9
  T2               4                64
  T3              11               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
  C5ORF36 MUTATED    13   2   2
  C5ORF36 WILD-TYPE 207  78  64
D1831V5, multiclass
    clus
vv   C5ORF36 MUTATED C5ORF36 WILD-TYPE
  N0              13               207
  N1               2                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"
D1831V6, binary
                   cls
clus                  0   1
  C5ORF36 MUTATED    12   0
  C5ORF36 WILD-TYPE 271  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF36 MUTATED     12    0
  C5ORF36 WILD-TYPE  271   48
   clus
vv  C5ORF36 MUTATED C5ORF36 WILD-TYPE
  0              12               271
  1               0                48
[1] 2 2
[1] FALSE
D1831V7, binary
                   cls
clus                  0   1
  C5ORF36 MUTATED     4  13
  C5ORF36 WILD-TYPE 166 184
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF36 MUTATED      4   13
  C5ORF36 WILD-TYPE  166  184
        clus
vv       C5ORF36 MUTATED C5ORF36 WILD-TYPE
  FEMALE               4               166
  MALE                13               184
[1] 2 2
[1] FALSE
D1831V8, binary
                   cls
clus                  0   1
  C5ORF36 MUTATED    12   5
  C5ORF36 WILD-TYPE 305  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF36 MUTATED     12    5
  C5ORF36 WILD-TYPE  305   43
                               clus
vv                              C5ORF36 MUTATED C5ORF36 WILD-TYPE
  COLON ADENOCARCINOMA                       12               305
  COLON MUCINOUS ADENOCARCINOMA               5                43
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  C5ORF36 MUTATED     9   0   0   2
  C5ORF36 WILD-TYPE 248   2  22  19
D1831V9, multiclass
    clus
vv   C5ORF36 MUTATED C5ORF36 WILD-TYPE
  R0               9               248
  R1               0                 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"
D1831V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C5ORF36 MUTATED                                  0     3
  C5ORF36 WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C5ORF36 MUTATED                           0    10
  C5ORF36 WILD-TYPE                        19   166
D1831V11, multiclass
                                  clus
vv                                 C5ORF36 MUTATED C5ORF36 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          3                 7
  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(1832) Variable = CHRNA1 MUTATION ANALYSIS
D1832V1, survival
                  sevent
clus2                0   1
  CHRNA1 MUTATED     7   2
  CHRNA1 WILD-TYPE 275  71
  CHRNA1 MUTATED CHRNA1 WILD-TYPE 
               9              346 
  CHRNA1 MUTATED CHRNA1 WILD-TYPE 
               2               71 
$`CHRNA1 MUTATED`
TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3697 TCGA-CA-6717 
       22.06        19.66        21.01        17.95        85.05         0.33 
TCGA-D5-6532 TCGA-D5-6537 TCGA-DM-A285 
       18.25         4.80         6.12 

$`CHRNA1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 
       12.99         0.99        14.01        33.99        13.02        24.00 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 
        5.98        37.05        19.00        36.00         5.03        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.26         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        40.34        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         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        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 
       19.59        13.51        11.51        20.19         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        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         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-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        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       45.11        36.72        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.17        91.79        46.75        52.80 

  CHRNA1 MUTATED CHRNA1 WILD-TYPE 
            0.33             0.00 
  CHRNA1 MUTATED CHRNA1 WILD-TYPE 
           85.05           140.38 
  CHRNA1 MUTATED CHRNA1 WILD-TYPE 
           18.25            20.63 
[1] "0.3 - 85.0 (18.2)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "1.3"
D1832V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CHRNA1 MUTATED         1        0        0         4         0         0
  CHRNA1 WILD-TYPE      63        1       25       105         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CHRNA1 MUTATED           1          0          1          1        1
  CHRNA1 WILD-TYPE        18         10         40         30       34
                  vv
clus               STAGE IVA STAGE IVB
  CHRNA1 MUTATED           0         0
  CHRNA1 WILD-TYPE        13         1
D1832V3, multiclass
            clus
vv           CHRNA1 MUTATED CHRNA1 WILD-TYPE
  STAGE I                 1               63
  STAGE IA                0                1
  STAGE II                0               25
  STAGE IIA               4              105
  STAGE IIB               0                8
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              1               40
  STAGE IIIC              1               30
  STAGE IV                1               34
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CHRNA1 MUTATED     0   1   7   1
  CHRNA1 WILD-TYPE   9  67 241  40
D1832V4, multiclass
    clus
vv   CHRNA1 MUTATED CHRNA1 WILD-TYPE
  T1              0                9
  T2              1               67
  T3              7              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
  CHRNA1 MUTATED     6   2   1
  CHRNA1 WILD-TYPE 214  78  65
D1832V5, multiclass
    clus
vv   CHRNA1 MUTATED CHRNA1 WILD-TYPE
  N0              6              214
  N1              2               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"
D1832V6, binary
                  cls
clus                 0   1
  CHRNA1 MUTATED     6   1
  CHRNA1 WILD-TYPE 277  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHRNA1 MUTATED      6    1
  CHRNA1 WILD-TYPE  277   47
   clus
vv  CHRNA1 MUTATED CHRNA1 WILD-TYPE
  0              6              277
  1              1               47
[1] 2 2
[1] FALSE
D1832V7, binary
                  cls
clus                 0   1
  CHRNA1 MUTATED     3   6
  CHRNA1 WILD-TYPE 167 191
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHRNA1 MUTATED      3    6
  CHRNA1 WILD-TYPE  167  191
        clus
vv       CHRNA1 MUTATED CHRNA1 WILD-TYPE
  FEMALE              3              167
  MALE                6              191
[1] 2 2
[1] FALSE
D1832V8, binary
                  cls
clus                 0   1
  CHRNA1 MUTATED     6   3
  CHRNA1 WILD-TYPE 311  45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHRNA1 MUTATED      6    3
  CHRNA1 WILD-TYPE  311   45
                               clus
vv                              CHRNA1 MUTATED CHRNA1 WILD-TYPE
  COLON ADENOCARCINOMA                       6              311
  COLON MUCINOUS ADENOCARCINOMA              3               45
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CHRNA1 MUTATED     7   0   0   1
  CHRNA1 WILD-TYPE 250   2  22  20
D1832V9, multiclass
    clus
vv   CHRNA1 MUTATED CHRNA1 WILD-TYPE
  R0              7              250
  R1              0                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"
D1832V10, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CHRNA1 MUTATED                                  0     1
  CHRNA1 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CHRNA1 MUTATED                           0     5
  CHRNA1 WILD-TYPE                        19   171
D1832V11, multiclass
                                  clus
vv                                 CHRNA1 MUTATED CHRNA1 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(1833) Variable = TRIM33 MUTATION ANALYSIS
D1833V1, survival
                  sevent
clus2                0   1
  TRIM33 MUTATED    12   2
  TRIM33 WILD-TYPE 270  71
  TRIM33 MUTATED TRIM33 WILD-TYPE 
              14              341 
  TRIM33 MUTATED TRIM33 WILD-TYPE 
               2               71 
$`TRIM33 MUTATED`
TCGA-A6-5660 TCGA-A6-5661 TCGA-AA-3525 TCGA-AA-3811 TCGA-AA-3864 TCGA-AA-A010 
       29.19        33.53         8.05        10.06        53.00        34.98 
TCGA-AY-6197 TCGA-AZ-6598 TCGA-CK-5914 TCGA-CM-6171 TCGA-D5-6930 TCGA-F4-6856 
       21.44        49.41        21.99        14.04         1.51        19.43 
TCGA-G4-6307 TCGA-G4-6588 
       55.04        26.17 

$`TRIM33 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       32.91        31.63        30.44        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 
        9.07        24.03        37.05        36.03        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        19.04        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        15.75         0.20        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 
      102.44        40.34        15.62        49.08        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         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 
       16.01        15.02         5.03        15.02        15.02        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        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 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-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        13.38        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        35.41       107.67        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        51.75        45.11        36.72        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        91.79        46.75        52.80 

  TRIM33 MUTATED TRIM33 WILD-TYPE 
            1.51             0.00 
  TRIM33 MUTATED TRIM33 WILD-TYPE 
           55.04           140.38 
  TRIM33 MUTATED TRIM33 WILD-TYPE 
           24.08            20.02 
[1] "1.5 - 55.0 (24.1)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1.6"
D1833V2, 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       23       105         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRIM33 MUTATED           1          0          3          1        0
  TRIM33 WILD-TYPE        18         10         38         30       35
                  vv
clus               STAGE IVA STAGE IVB
  TRIM33 MUTATED           0         0
  TRIM33 WILD-TYPE        13         1
D1833V3, multiclass
            clus
vv           TRIM33 MUTATED TRIM33 WILD-TYPE
  STAGE I                 2               62
  STAGE IA                0                1
  STAGE II                2               23
  STAGE IIA               4              105
  STAGE IIB               2                6
  STAGE IIC               0                1
  STAGE III               1               18
  STAGE IIIA              0               10
  STAGE IIIB              3               38
  STAGE IIIC              1               30
  STAGE IV                0               35
  STAGE IVA               0               13
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TRIM33 MUTATED     0   2  11   2
  TRIM33 WILD-TYPE   9  66 237  39
D1833V4, multiclass
    clus
vv   TRIM33 MUTATED TRIM33 WILD-TYPE
  T1              0                9
  T2              2               66
  T3             11              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
  TRIM33 MUTATED    10   3   2
  TRIM33 WILD-TYPE 210  77  64
D1833V5, multiclass
    clus
vv   TRIM33 MUTATED TRIM33 WILD-TYPE
  N0             10              210
  N1              3               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"
D1833V6, binary
                  cls
clus                 0   1
  TRIM33 MUTATED    11   0
  TRIM33 WILD-TYPE 272  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM33 MUTATED     11    0
  TRIM33 WILD-TYPE  272   48
   clus
vv  TRIM33 MUTATED TRIM33 WILD-TYPE
  0             11              272
  1              0               48
[1] 2 2
[1] FALSE
D1833V7, 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
D1833V8, binary
                  cls
clus                 0   1
  TRIM33 MUTATED    13   2
  TRIM33 WILD-TYPE 304  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM33 MUTATED     13    2
  TRIM33 WILD-TYPE  304   46
                               clus
vv                              TRIM33 MUTATED TRIM33 WILD-TYPE
  COLON ADENOCARCINOMA                      13              304
  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 246   2  22  19
D1833V9, multiclass
    clus
vv   TRIM33 MUTATED TRIM33 WILD-TYPE
  R0             11              246
  R1              0                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"
D1833V10, 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
D1833V11, 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(1834) Variable = XRCC1 MUTATION ANALYSIS
D1834V1, survival
                 sevent
clus2               0   1
  XRCC1 MUTATED     5   3
  XRCC1 WILD-TYPE 277  70
  XRCC1 MUTATED XRCC1 WILD-TYPE 
              8             347 
  XRCC1 MUTATED XRCC1 WILD-TYPE 
              3              70 
$`XRCC1 MUTATED`
TCGA-AA-3663 TCGA-AA-A01Z TCGA-AA-A02K TCGA-AZ-6601 TCGA-CK-5914 TCGA-D5-6927 
        6.97        37.02        14.01       100.01        21.99         9.44 
TCGA-D5-7000 TCGA-G4-6303 
       10.26        65.85 

$`XRCC1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        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-A024 TCGA-AA-A029 
        1.02        33.04        35.01        26.01        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
       39.98         2.01         5.03         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        15.75 
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-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        51.32        21.14         2.93         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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        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 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         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         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        11.38       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       19.43       107.67        74.56        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       51.75        45.11        36.72        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

  XRCC1 MUTATED XRCC1 WILD-TYPE 
           6.97            0.00 
  XRCC1 MUTATED XRCC1 WILD-TYPE 
         100.01          140.38 
  XRCC1 MUTATED XRCC1 WILD-TYPE 
          18.00           20.19 
[1] "7.0 - 100.0 (18.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.4"
D1834V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  XRCC1 MUTATED         1        0        3         1         0         0
  XRCC1 WILD-TYPE      63        1       22       108         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  XRCC1 MUTATED           0          0          1          0        2         0
  XRCC1 WILD-TYPE        19         10         40         31       33        13
                 vv
clus              STAGE IVB
  XRCC1 MUTATED           0
  XRCC1 WILD-TYPE         1
D1834V3, multiclass
            clus
vv           XRCC1 MUTATED XRCC1 WILD-TYPE
  STAGE I                1              63
  STAGE IA               0               1
  STAGE II               3              22
  STAGE IIA              1             108
  STAGE IIB              0               8
  STAGE IIC              0               1
  STAGE III              0              19
  STAGE IIIA             0              10
  STAGE IIIB             1              40
  STAGE IIIC             0              31
  STAGE IV               2              33
  STAGE IVA              0              13
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  XRCC1 MUTATED     0   1   6   1
  XRCC1 WILD-TYPE   9  67 242  40
D1834V4, multiclass
    clus
vv   XRCC1 MUTATED XRCC1 WILD-TYPE
  T1             0               9
  T2             1              67
  T3             6             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
  XRCC1 MUTATED     5   2   1
  XRCC1 WILD-TYPE 215  78  65
D1834V5, multiclass
    clus
vv   XRCC1 MUTATED XRCC1 WILD-TYPE
  N0             5             215
  N1             2              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"
D1834V6, binary
                 cls
clus                0   1
  XRCC1 MUTATED     5   2
  XRCC1 WILD-TYPE 278  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XRCC1 MUTATED      5    2
  XRCC1 WILD-TYPE  278   46
   clus
vv  XRCC1 MUTATED XRCC1 WILD-TYPE
  0             5             278
  1             2              46
[1] 2 2
[1] FALSE
D1834V7, binary
                 cls
clus                0   1
  XRCC1 MUTATED     2   6
  XRCC1 WILD-TYPE 168 191
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XRCC1 MUTATED      2    6
  XRCC1 WILD-TYPE  168  191
        clus
vv       XRCC1 MUTATED XRCC1 WILD-TYPE
  FEMALE             2             168
  MALE               6             191
[1] 2 2
[1] FALSE
D1834V8, binary
                 cls
clus                0   1
  XRCC1 MUTATED     7   1
  XRCC1 WILD-TYPE 310  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XRCC1 MUTATED      7    1
  XRCC1 WILD-TYPE  310   47
                               clus
vv                              XRCC1 MUTATED XRCC1 WILD-TYPE
  COLON ADENOCARCINOMA                      7             310
  COLON MUCINOUS ADENOCARCINOMA             1              47
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  XRCC1 MUTATED     5   0   1   1
  XRCC1 WILD-TYPE 252   2  21  20
D1834V9, multiclass
    clus
vv   XRCC1 MUTATED XRCC1 WILD-TYPE
  R0             5             252
  R1             0               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"
D1834V10, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XRCC1 MUTATED                                  0     0
  XRCC1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  XRCC1 MUTATED                           0     5
  XRCC1 WILD-TYPE                        19   171
D1834V11, multiclass
                                  clus
vv                                 XRCC1 MUTATED XRCC1 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"
